******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.3.3 (Release date: Sun Feb 7 15:39:52 2021 -0800) For further information on how to interpret these results please access https://meme-suite.org/meme. To get a copy of the MEME Suite software please access https://meme-suite.org. ******************************************************************************** ******************************************************************************** REFERENCE ******************************************************************************** If you use this program in your research, please cite: Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. ******************************************************************************** ******************************************************************************** TRAINING SET ******************************************************************************** PRIMARY SEQUENCES= ../result/final_prediction/GM12878/fasta/RankLinear0.6_10/HDGF.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr19:56110422-56110442 1.0000 20 chr19:7099138-7099158 1.0000 20 chr11:67573340-67573360 1.0000 20 chr10:121485404-12148542 1.0000 20 chr7:123175135-123175155 1.0000 20 chr17:74497823-74497843 1.0000 20 chr19:46000487-46000507 1.0000 20 chr11:3444301-3444321 1.0000 20 chr3:128840967-128840987 1.0000 20 chr8:11314153-11314173 1.0000 20 chr19:18747401-18747421 1.0000 20 chr17:76136646-76136666 1.0000 20 chr1:117368934-117368954 1.0000 20 chr2:8716385-8716405 1.0000 20 chr19:51870995-51871015 1.0000 20 chr16:5148176-5148196 1.0000 20 chr14:106154200-10615422 1.0000 20 chr20:62485189-62485209 1.0000 20 chr12:113497084-11349710 1.0000 20 chr12:125348768-12534878 1.0000 20 chr19:1812794-1812814 1.0000 20 chr19:46379736-46379756 1.0000 20 chr19:42386715-42386735 1.0000 20 chr3:50336922-50336942 1.0000 20 chr10:3215357-3215377 1.0000 20 chr5:133892640-133892660 1.0000 20 chr21:37528817-37528837 1.0000 20 chrX:148620990-148621010 1.0000 20 chr19:41110061-41110081 1.0000 20 chr15:78178061-78178081 1.0000 20 chr3:125634981-125635001 1.0000 20 chr12:109125840-10912586 1.0000 20 chr9:136890184-136890204 1.0000 20 chr4:3957606-3957626 1.0000 20 chr17:42853174-42853194 1.0000 20 chr14:105131693-10513171 1.0000 20 chr17:40374120-40374140 1.0000 20 chr14:91821598-91821618 1.0000 20 chr1:27963228-27963248 1.0000 20 chr8:12448780-12448800 1.0000 20 chr14:93144371-93144391 1.0000 20 chr8:8085564-8085584 1.0000 20 chr18:77794046-77794066 1.0000 20 chr19:39897016-39897036 1.0000 20 chr21:46340156-46340176 1.0000 20 chr7:100765523-100765543 1.0000 20 chr8:143407501-143407521 1.0000 20 chr1:25362714-25362734 1.0000 20 chr2:97438593-97438613 1.0000 20 chr7:36192582-36192602 1.0000 20 chr12:7046038-7046058 1.0000 20 chr1:181105812-181105832 1.0000 20 chr20:4804282-4804302 1.0000 20 chr17:57906373-57906393 1.0000 20 chr12:8396067-8396087 1.0000 20 chr12:50561304-50561324 1.0000 20 chr3:38178733-38178753 1.0000 20 chr16:85857260-85857280 1.0000 20 chrX:15756266-15756286 1.0000 20 chr1:11863634-11863654 1.0000 20 chr18:60865591-60865611 1.0000 20 chr14:95725201-95725221 1.0000 20 chr19:48996120-48996140 1.0000 20 chr10:45464468-45464488 1.0000 20 chr19:6517469-6517489 1.0000 20 chr3:122870844-122870864 1.0000 20 chr19:39368760-39368780 1.0000 20 chr9:92113254-92113274 1.0000 20 chr7:74203069-74203089 1.0000 20 chr6:159274242-159274262 1.0000 20 chr16:89259006-89259026 1.0000 20 chr19:45579182-45579202 1.0000 20 chr19:18282554-18282574 1.0000 20 chr11:67139253-67139273 1.0000 20 chr10:79221805-79221825 1.0000 20 chr16:2186210-2186230 1.0000 20 chr9:130533740-130533760 1.0000 20 chr1:9970673-9970693 1.0000 20 chr2:99089608-99089628 1.0000 20 chr6:30654028-30654048 1.0000 20 chr19:9929891-9929911 1.0000 20 chr12:58148575-58148595 1.0000 20 chr6:31764020-31764040 1.0000 20 chr14:106155275-10615529 1.0000 20 chr10:103874930-10387495 1.0000 20 chr19:36135389-36135409 1.0000 20 chr10:105451534-10545155 1.0000 20 chr19:50143575-50143595 1.0000 20 chr11:60719386-60719406 1.0000 20 chr3:120315131-120315151 1.0000 20 chr21:43374735-43374755 1.0000 20 chr17:7210810-7210830 1.0000 20 chrX:135992415-135992435 1.0000 20 chr5:34929480-34929500 1.0000 20 chr6:53224454-53224474 1.0000 20 chr2:10573542-10573562 1.0000 20 chr2:25518097-25518117 1.0000 20 chr14:106029249-10602926 1.0000 20 chr10:115720886-11572090 1.0000 20 chr10:134408106-13440812 1.0000 20 chr5:139041008-139041028 1.0000 20 chr6:149353617-149353637 1.0000 20 chr2:220159260-220159280 1.0000 20 chr14:106149517-10614953 1.0000 20 chr1:1851094-1851114 1.0000 20 chr8:123511947-123511967 1.0000 20 chr10:125803497-12580351 1.0000 20 chr20:61603547-61603567 1.0000 20 chr8:11389390-11389410 1.0000 20 chrX:155238714-155238734 1.0000 20 chr14:106051851-10605187 1.0000 20 chr6:160402303-160402323 1.0000 20 chr5:176881165-176881185 1.0000 20 chr7:74001968-74001988 1.0000 20 chr3:194871553-194871573 1.0000 20 chr9:92099591-92099611 1.0000 20 chr11:6256171-6256191 1.0000 20 chr17:7232891-7232911 1.0000 20 chr16:11265874-11265894 1.0000 20 chr16:23859427-23859447 1.0000 20 chr16:56985290-56985310 1.0000 20 chr18:12377455-12377475 1.0000 20 chr19:41120037-41120057 1.0000 20 chr19:37340791-37340811 1.0000 20 chr19:42391196-42391216 1.0000 20 chr11:64008927-64008947 1.0000 20 chr16:53086927-53086947 1.0000 20 chr19:6767657-6767677 1.0000 20 chr1:27995644-27995664 1.0000 20 chr11:73096123-73096143 1.0000 20 chrX:2438731-2438751 1.0000 20 chr19:3154657-3154677 1.0000 20 chr22:24187047-24187067 1.0000 20 chr14:106034500-10603452 1.0000 20 chr14:106151449-10615146 1.0000 20 chr6:119635984-119636004 1.0000 20 chr16:29819245-29819265 1.0000 20 chr18:60830021-60830041 1.0000 20 chr19:7757151-7757171 1.0000 20 chr7:143083136-143083156 1.0000 20 chr20:36013445-36013465 1.0000 20 chr17:44264323-44264343 1.0000 20 chr17:79227673-79227693 1.0000 20 chr19:10216100-10216120 1.0000 20 chr11:82611632-82611652 1.0000 20 chr19:42704058-42704078 1.0000 20 chr7:44078903-44078923 1.0000 20 chr5:176018859-176018879 1.0000 20 chr7:44621963-44621983 1.0000 20 chr22:18359891-18359911 1.0000 20 chr4:37688255-37688275 1.0000 20 chrX:149108387-149108407 1.0000 20 chr19:680925-680945 1.0000 20 chr1:27951238-27951258 1.0000 20 chr12:111107096-11110711 1.0000 20 chr10:103454553-10345457 1.0000 20 chr16:57048935-57048955 1.0000 20 chr5:177547952-177547972 1.0000 20 chr8:125208766-125208786 1.0000 20 chr16:1393178-1393198 1.0000 20 chr10:12084299-12084319 1.0000 20 chr17:79227474-79227494 1.0000 20 chr12:57487618-57487638 1.0000 20 chr1:169013654-169013674 1.0000 20 chr10:125152862-12515288 1.0000 20 chr19:6516305-6516325 1.0000 20 chr2:43446411-43446431 1.0000 20 chrX:148621193-148621213 1.0000 20 chr3:127542475-127542495 1.0000 20 chr22:29138541-29138561 1.0000 20 chr14:24901219-24901239 1.0000 20 chr16:81130124-81130144 1.0000 20 chr3:196189681-196189701 1.0000 20 chr12:1714425-1714445 1.0000 20 chr11:64072678-64072698 1.0000 20 chr11:72449852-72449872 1.0000 20 chr6:39346149-39346169 1.0000 20 chr9:114790746-114790766 1.0000 20 chr20:32581180-32581200 1.0000 20 chr8:58162257-58162277 1.0000 20 chr16:75599906-75599926 1.0000 20 chr12:16985575-16985595 1.0000 20 chr16:58232405-58232425 1.0000 20 chrX:20160089-20160109 1.0000 20 chr1:236313436-236313456 1.0000 20 chr17:4812265-4812285 1.0000 20 chr7:98593740-98593760 1.0000 20 chr20:42142904-42142924 1.0000 20 chr19:47128401-47128421 1.0000 20 chr21:45395166-45395186 1.0000 20 chr1:168993601-168993621 1.0000 20 chr22:50752994-50753014 1.0000 20 chr12:56366880-56366900 1.0000 20 chr7:99964377-99964397 1.0000 20 chr1:155940781-155940801 1.0000 20 chr10:76587077-76587097 1.0000 20 chr11:117680643-11768066 1.0000 20 chr2:112811981-112812001 1.0000 20 chr2:242806579-242806599 1.0000 20 chr14:106035734-10603575 1.0000 20 chr2:97467887-97467907 1.0000 20 chr7:65564944-65564964 1.0000 20 chr14:100061649-10006166 1.0000 20 chr20:25291350-25291370 1.0000 20 chr20:4794437-4794457 1.0000 20 chr22:42466924-42466944 1.0000 20 chr9:37369733-37369753 1.0000 20 chr1:1840890-1840910 1.0000 20 chr12:121952015-12195203 1.0000 20 chr17:26904062-26904082 1.0000 20 chr9:139962561-139962581 1.0000 20 chr19:6663348-6663368 1.0000 20 chr7:2934026-2934046 1.0000 20 chr5:102594339-102594359 1.0000 20 chr1:206287970-206287990 1.0000 20 chr10:75910966-75910986 1.0000 20 chr19:38997739-38997759 1.0000 20 chr1:966515-966535 1.0000 20 chrX:1572027-1572047 1.0000 20 chr1:32403196-32403216 1.0000 20 chr14:73714270-73714290 1.0000 20 chr6:34191612-34191632 1.0000 20 chr22:38577268-38577288 1.0000 20 chr19:49217420-49217440 1.0000 20 chr19:42634258-42634278 1.0000 20 chr16:31153748-31153768 1.0000 20 chr3:53197280-53197300 1.0000 20 chr6:36091633-36091653 1.0000 20 chr2:231523685-231523705 1.0000 20 chr10:16478943-16478963 1.0000 20 chr19:7396426-7396446 1.0000 20 chr4:154408958-154408978 1.0000 20 chr14:77444363-77444383 1.0000 20 chr6:33045930-33045950 1.0000 20 chr1:12107067-12107087 1.0000 20 chr8:145026708-145026728 1.0000 20 chr6:157542814-157542834 1.0000 20 chr4:185213838-185213858 1.0000 20 chr17:76130316-76130336 1.0000 20 chr19:48828693-48828713 1.0000 20 chr1:23961373-23961393 1.0000 20 chr11:64655652-64655672 1.0000 20 chr19:38827642-38827662 1.0000 20 chr14:106157240-10615726 1.0000 20 chr10:121072823-12107284 1.0000 20 chr22:37704530-37704550 1.0000 20 chr1:6408316-6408336 1.0000 20 chr1:117100295-117100315 1.0000 20 chr16:21528793-21528813 1.0000 20 chr22:42323059-42323079 1.0000 20 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme -oc ../result/final_prediction/GM12878/inference_raw/MEME/RankLinear0.6_10_HDGF/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/GM12878/fasta/RankLinear0.6_10/HDGF.fasta model: mod= zoops nmotifs= 5 evt= inf objective function: em= E-value of product of p-values starts= E-value of product of p-values strands: + width: minw= 8 maxw= 8 nsites: minsites= 2 maxsites= 250 wnsites= 0.8 theta: spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 trim: wg= 11 ws= 1 endgaps= yes data: n= 5000 N= 250 sample: seed= 0 hsfrac= 0 searchsize= 5000 norand= no csites= 1000 Letter frequencies in dataset: A 0.215 C 0.292 G 0.291 T 0.202 Background letter frequencies (from file dataset with add-one prior applied): A 0.215 C 0.292 G 0.291 T 0.202 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TGTGTGTG MEME-1 width = 8 sites = 40 llr = 326 E-value = 3.6e-034 ******************************************************************************** -------------------------------------------------------------------------------- Motif TGTGTGTG MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::::11:1 pos.-specific C :1:::1:: probability G 182917:a matrix T 919191a: bits 2.3 * 2.1 * 1.8 * * 1.6 * * * ** Relative 1.4 * *** ** Entropy 1.2 * *** ** (11.8 bits) 0.9 ***** ** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel TGTGTGTG consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTGTGTG MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr4:185213838-185213858 12 1.19e-05 tgtgtgtgag tgtgtgtg t chr20:4794437-4794457 1 1.19e-05 . tgtgtgtg tggagggtat chr2:242806579-242806599 13 1.19e-05 ctgtgtgtac tgtgtgtg chr12:16985575-16985595 1 1.19e-05 . tgtgtgtg tgtgtgtgtg chr8:125208766-125208786 1 1.19e-05 . tgtgtgtg agtgtgtgta chr7:143083136-143083156 9 1.19e-05 gtggtgta tgtgtgtg gtct chr14:106151449-10615146 9 1.19e-05 cgtgtgtg tgtgtgtg aggt chr14:106034500-10603452 2 1.19e-05 c tgtgtgtg tatgtgtttg chr9:92099591-92099611 11 1.19e-05 gtggtggctg tgtgtgtg gt chrX:155238714-155238734 13 1.19e-05 tgtgtgtgtt tgtgtgtg chr1:27963228-27963248 3 1.19e-05 Ag tgtgtgtg tgtgtgtgtg chr19:6663348-6663368 8 2.02e-05 gtaatgt tgtgtttg tcatt chr20:61603547-61603567 5 2.02e-05 accc tgtgtttg aatgtgtg chr21:43374735-43374755 8 2.90e-05 gtgtgag tgtgtatg tgtgg chr10:45464468-45464488 9 2.90e-05 tgagcatg tgtgtatg tgtt chr14:95725201-95725221 2 2.90e-05 a tgtgtatg tatctgtggt chr1:236313436-236313456 10 3.73e-05 gtgtgcctc tgtttgtg tct chr17:40374120-40374140 6 4.93e-05 gtgtc tctgtgtg ctgtggg chr14:106154200-10615422 13 4.93e-05 tctgtgcgtt tctgtgtg chr10:76587077-76587097 7 6.65e-05 TGGGTT TGGGTGTG GTGGAT chr14:106029249-10602926 13 6.65e-05 tgagggtgtg tgggtgtg chr8:11314153-11314173 5 6.65e-05 CTAT TGGGTGTG TGCTCTGG chr6:160402303-160402323 13 7.92e-05 tgcacgagtg tgtgagtg chr10:134408106-13440812 10 8.75e-05 tggggtgcg tttgtgtg cct chr2:10573542-10573562 10 8.75e-05 tggtgtgac tttgtgtg atg chr22:37704530-37704550 2 1.08e-04 a tgtgtgta catgtatgtg chr1:27951238-27951258 13 1.08e-04 tgggtgtctc tgtgtctg chr2:99089608-99089628 11 1.31e-04 tggagggcag tgtgggtg ca chr21:45395166-45395186 7 1.57e-04 tgtttt ggtgtgtg ctggca chr14:106149517-10614953 4 1.57e-04 gac ggtgtgtg agggtgtgt chr3:53197280-53197300 4 1.93e-04 GAC TGTGATTG TGGGGAACC chr8:58162257-58162277 8 1.93e-04 ATGTACG TGTGATTG TGTGT chr19:39897016-39897036 6 1.93e-04 ctctc tctgtatg tctcttg chr5:176018859-176018879 9 2.41e-04 gatggtga tggttgtg atgg chr19:6517469-6517489 13 2.84e-04 taaccgtgta cgtgtgtg chr17:76130316-76130336 7 3.09e-04 tgtgaa tctgagtg tctatg chr11:64655652-64655672 5 3.66e-04 GACC TGTTTCTG GGGTTCAC chr19:680925-680945 1 4.49e-04 . TGGGTGTA ACCAGAGGGG chr1:117100295-117100315 11 5.58e-04 ccttcctttt tctttttg ga chr6:30654028-30654048 5 6.09e-04 GTGG TGGGGGTG ATGTGAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTGTGTG MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr4:185213838-185213858 1.2e-05 11_[+1]_1 chr20:4794437-4794457 1.2e-05 [+1]_12 chr2:242806579-242806599 1.2e-05 12_[+1] chr12:16985575-16985595 1.2e-05 [+1]_12 chr8:125208766-125208786 1.2e-05 [+1]_12 chr7:143083136-143083156 1.2e-05 8_[+1]_4 chr14:106151449-10615146 1.2e-05 8_[+1]_4 chr14:106034500-10603452 1.2e-05 1_[+1]_11 chr9:92099591-92099611 1.2e-05 10_[+1]_2 chrX:155238714-155238734 1.2e-05 12_[+1] chr1:27963228-27963248 1.2e-05 2_[+1]_10 chr19:6663348-6663368 2e-05 7_[+1]_5 chr20:61603547-61603567 2e-05 4_[+1]_8 chr21:43374735-43374755 2.9e-05 7_[+1]_5 chr10:45464468-45464488 2.9e-05 8_[+1]_4 chr14:95725201-95725221 2.9e-05 1_[+1]_11 chr1:236313436-236313456 3.7e-05 9_[+1]_3 chr17:40374120-40374140 4.9e-05 5_[+1]_7 chr14:106154200-10615422 4.9e-05 12_[+1] chr10:76587077-76587097 6.7e-05 6_[+1]_6 chr14:106029249-10602926 6.7e-05 12_[+1] chr8:11314153-11314173 6.7e-05 4_[+1]_8 chr6:160402303-160402323 7.9e-05 12_[+1] chr10:134408106-13440812 8.8e-05 9_[+1]_3 chr2:10573542-10573562 8.8e-05 9_[+1]_3 chr22:37704530-37704550 0.00011 1_[+1]_11 chr1:27951238-27951258 0.00011 12_[+1] chr2:99089608-99089628 0.00013 10_[+1]_2 chr21:45395166-45395186 0.00016 6_[+1]_6 chr14:106149517-10614953 0.00016 3_[+1]_9 chr3:53197280-53197300 0.00019 3_[+1]_9 chr8:58162257-58162277 0.00019 7_[+1]_5 chr19:39897016-39897036 0.00019 5_[+1]_7 chr5:176018859-176018879 0.00024 8_[+1]_4 chr19:6517469-6517489 0.00028 12_[+1] chr17:76130316-76130336 0.00031 6_[+1]_6 chr11:64655652-64655672 0.00037 4_[+1]_8 chr19:680925-680945 0.00045 [+1]_12 chr1:117100295-117100315 0.00056 10_[+1]_2 chr6:30654028-30654048 0.00061 4_[+1]_8 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTGTGTG MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TGTGTGTG width=8 seqs=40 chr4:185213838-185213858 ( 12) TGTGTGTG 1 chr20:4794437-4794457 ( 1) TGTGTGTG 1 chr2:242806579-242806599 ( 13) TGTGTGTG 1 chr12:16985575-16985595 ( 1) TGTGTGTG 1 chr8:125208766-125208786 ( 1) TGTGTGTG 1 chr7:143083136-143083156 ( 9) TGTGTGTG 1 chr14:106151449-10615146 ( 9) TGTGTGTG 1 chr14:106034500-10603452 ( 2) TGTGTGTG 1 chr9:92099591-92099611 ( 11) TGTGTGTG 1 chrX:155238714-155238734 ( 13) TGTGTGTG 1 chr1:27963228-27963248 ( 3) TGTGTGTG 1 chr19:6663348-6663368 ( 8) TGTGTTTG 1 chr20:61603547-61603567 ( 5) TGTGTTTG 1 chr21:43374735-43374755 ( 8) TGTGTATG 1 chr10:45464468-45464488 ( 9) TGTGTATG 1 chr14:95725201-95725221 ( 2) TGTGTATG 1 chr1:236313436-236313456 ( 10) TGTTTGTG 1 chr17:40374120-40374140 ( 6) TCTGTGTG 1 chr14:106154200-10615422 ( 13) TCTGTGTG 1 chr10:76587077-76587097 ( 7) TGGGTGTG 1 chr14:106029249-10602926 ( 13) TGGGTGTG 1 chr8:11314153-11314173 ( 5) TGGGTGTG 1 chr6:160402303-160402323 ( 13) TGTGAGTG 1 chr10:134408106-13440812 ( 10) TTTGTGTG 1 chr2:10573542-10573562 ( 10) TTTGTGTG 1 chr22:37704530-37704550 ( 2) TGTGTGTA 1 chr1:27951238-27951258 ( 13) TGTGTCTG 1 chr2:99089608-99089628 ( 11) TGTGGGTG 1 chr21:45395166-45395186 ( 7) GGTGTGTG 1 chr14:106149517-10614953 ( 4) GGTGTGTG 1 chr3:53197280-53197300 ( 4) TGTGATTG 1 chr8:58162257-58162277 ( 8) TGTGATTG 1 chr19:39897016-39897036 ( 6) TCTGTATG 1 chr5:176018859-176018879 ( 9) TGGTTGTG 1 chr19:6517469-6517489 ( 13) CGTGTGTG 1 chr17:76130316-76130336 ( 7) TCTGAGTG 1 chr11:64655652-64655672 ( 5) TGTTTCTG 1 chr19:680925-680945 ( 1) TGGGTGTA 1 chr1:117100295-117100315 ( 11) TCTTTTTG 1 chr6:30654028-30654048 ( 5) TGGGGGTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTGTGTG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 7.81182 E= 3.6e-034 -1197 -354 -254 220 -1197 -123 151 -201 -1197 -1197 -95 207 -1197 -1197 163 -101 -111 -1197 -254 207 -111 -255 132 -69 -1197 -1197 -1197 231 -210 -1197 171 -1197 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTGTGTG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 40 E= 3.6e-034 0.000000 0.025000 0.050000 0.925000 0.000000 0.125000 0.825000 0.050000 0.000000 0.000000 0.150000 0.850000 0.000000 0.000000 0.900000 0.100000 0.100000 0.000000 0.050000 0.850000 0.100000 0.050000 0.725000 0.125000 0.000000 0.000000 0.000000 1.000000 0.050000 0.000000 0.950000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTGTGTG MEME-1 regular expression -------------------------------------------------------------------------------- TGTGTGTG -------------------------------------------------------------------------------- Time 4.73 secs. ******************************************************************************** ******************************************************************************** MOTIF CACACACA MEME-2 width = 8 sites = 34 llr = 269 E-value = 1.9e-020 ******************************************************************************** -------------------------------------------------------------------------------- Motif CACACACA MEME-2 Description -------------------------------------------------------------------------------- Simplified A :9:a:7:a pos.-specific C 919:719: probability G ::::11:: matrix T 1:1:211: bits 2.3 * * 2.1 * * 1.8 * * 1.6 * * Relative 1.4 **** * Entropy 1.2 **** ** (11.4 bits) 0.9 **** *** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel CACACACA consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACACACA MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr6:157542814-157542834 8 1.55e-05 gtgcgtg cacacaca tatac chr2:97467887-97467907 1 1.55e-05 . cacacaca gatacaccca chr17:4812265-4812285 3 1.55e-05 ca cacacaca cacccagaca chr9:114790746-114790766 11 1.55e-05 cacacatacg cacacaca TG chr6:159274242-159274262 3 1.55e-05 tg cacacaca cggtacacca chr1:181105812-181105832 7 1.55e-05 acacac cacacaca cagaca chr21:46340156-46340176 2 1.55e-05 a cacacaca ccacactacg chr5:133892640-133892660 3 1.55e-05 ac cacacaca cacctcacac chr11:117680643-11768066 12 2.63e-05 cacgcatatt cacataca c chr8:123511947-123511967 4 2.63e-05 cat cacataca cacatatca chr2:8716385-8716405 5 2.63e-05 cctg cacataca ccatacac chr14:106157240-10615726 13 3.70e-05 atacaccacc cacacata chr12:56366880-56366900 7 3.70e-05 catata cacacata taccac chr3:194871553-194871573 1 3.70e-05 . cacacata cgcacactct chr20:36013445-36013465 10 5.25e-05 AGGCAGGGT CACAGACA CCC chr14:105131693-10513171 4 5.25e-05 aca cacagaca cacagacac chr15:78178061-78178081 12 5.25e-05 cacacgtgca cacagaca c chr10:125152862-12515288 6 6.33e-05 actta catacaca CCCCCAT chrX:2438731-2438751 8 6.33e-05 tcatcct catacaca tcatc chr19:18282554-18282574 6 8.44e-05 CCCAT CACACCCA GAATCCA chr2:97438593-97438613 4 9.89e-05 acc cacactca tactcccca chr2:25518097-25518117 1 1.20e-04 . CCCACACA CGGGCTCAGC chr1:6408316-6408336 3 1.81e-04 CC CACATCCA CGTCCAACCA chr14:106035734-10603575 1 2.49e-04 . cacaccta tacaccacac chr18:60865591-60865611 13 2.49e-04 cacacactga catagaca chr7:44621963-44621983 6 2.74e-04 GCCCC CTCACACA GCCCGGC chr6:39346149-39346169 7 3.03e-04 atacaa tacataca acatac chr14:106155275-10615529 3 3.32e-04 ca cacagtca cacaccaacc chr3:127542475-127542495 8 3.71e-04 gagatac cacatgca tacag chr1:117368934-117368954 12 4.14e-04 CACCCAGGTC CCTACACA C chr19:42634258-42634278 1 4.80e-04 . cacacgta aaaagtatac chr11:72449852-72449872 9 4.80e-04 CCTACCAC CCCACCCA ATGG chr14:106051851-10605187 8 4.80e-04 ccattta cccaccca tccat chr3:196189681-196189701 2 5.88e-04 A TACACTCA ACTCTCCCAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACACACA MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr6:157542814-157542834 1.6e-05 7_[+2]_5 chr2:97467887-97467907 1.6e-05 [+2]_12 chr17:4812265-4812285 1.6e-05 2_[+2]_10 chr9:114790746-114790766 1.6e-05 10_[+2]_2 chr6:159274242-159274262 1.6e-05 2_[+2]_10 chr1:181105812-181105832 1.6e-05 6_[+2]_6 chr21:46340156-46340176 1.6e-05 1_[+2]_11 chr5:133892640-133892660 1.6e-05 2_[+2]_10 chr11:117680643-11768066 2.6e-05 11_[+2]_1 chr8:123511947-123511967 2.6e-05 3_[+2]_9 chr2:8716385-8716405 2.6e-05 4_[+2]_8 chr14:106157240-10615726 3.7e-05 12_[+2] chr12:56366880-56366900 3.7e-05 6_[+2]_6 chr3:194871553-194871573 3.7e-05 [+2]_12 chr20:36013445-36013465 5.3e-05 9_[+2]_3 chr14:105131693-10513171 5.3e-05 3_[+2]_9 chr15:78178061-78178081 5.3e-05 11_[+2]_1 chr10:125152862-12515288 6.3e-05 5_[+2]_7 chrX:2438731-2438751 6.3e-05 7_[+2]_5 chr19:18282554-18282574 8.4e-05 5_[+2]_7 chr2:97438593-97438613 9.9e-05 3_[+2]_9 chr2:25518097-25518117 0.00012 [+2]_12 chr1:6408316-6408336 0.00018 2_[+2]_10 chr14:106035734-10603575 0.00025 [+2]_12 chr18:60865591-60865611 0.00025 12_[+2] chr7:44621963-44621983 0.00027 5_[+2]_7 chr6:39346149-39346169 0.0003 6_[+2]_6 chr14:106155275-10615529 0.00033 2_[+2]_10 chr3:127542475-127542495 0.00037 7_[+2]_5 chr1:117368934-117368954 0.00041 11_[+2]_1 chr19:42634258-42634278 0.00048 [+2]_12 chr11:72449852-72449872 0.00048 8_[+2]_4 chr14:106051851-10605187 0.00048 7_[+2]_5 chr3:196189681-196189701 0.00059 1_[+2]_11 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACACACA MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CACACACA width=8 seqs=34 chr6:157542814-157542834 ( 8) CACACACA 1 chr2:97467887-97467907 ( 1) CACACACA 1 chr17:4812265-4812285 ( 3) CACACACA 1 chr9:114790746-114790766 ( 11) CACACACA 1 chr6:159274242-159274262 ( 3) CACACACA 1 chr1:181105812-181105832 ( 7) CACACACA 1 chr21:46340156-46340176 ( 2) CACACACA 1 chr5:133892640-133892660 ( 3) CACACACA 1 chr11:117680643-11768066 ( 12) CACATACA 1 chr8:123511947-123511967 ( 4) CACATACA 1 chr2:8716385-8716405 ( 5) CACATACA 1 chr14:106157240-10615726 ( 13) CACACATA 1 chr12:56366880-56366900 ( 7) CACACATA 1 chr3:194871553-194871573 ( 1) CACACATA 1 chr20:36013445-36013465 ( 10) CACAGACA 1 chr14:105131693-10513171 ( 4) CACAGACA 1 chr15:78178061-78178081 ( 12) CACAGACA 1 chr10:125152862-12515288 ( 6) CATACACA 1 chrX:2438731-2438751 ( 8) CATACACA 1 chr19:18282554-18282574 ( 6) CACACCCA 1 chr2:97438593-97438613 ( 4) CACACTCA 1 chr2:25518097-25518117 ( 1) CCCACACA 1 chr1:6408316-6408336 ( 3) CACATCCA 1 chr14:106035734-10603575 ( 1) CACACCTA 1 chr18:60865591-60865611 ( 13) CATAGACA 1 chr7:44621963-44621983 ( 6) CTCACACA 1 chr6:39346149-39346169 ( 7) TACATACA 1 chr14:106155275-10615529 ( 3) CACAGTCA 1 chr3:127542475-127542495 ( 8) CACATGCA 1 chr1:117368934-117368954 ( 12) CCTACACA 1 chr19:42634258-42634278 ( 1) CACACGTA 1 chr11:72449852-72449872 ( 9) CCCACCCA 1 chr14:106051851-10605187 ( 8) CCCACCCA 1 chr3:196189681-196189701 ( 2) TACACTCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACACACA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 7.93789 E= 1.9e-020 -1173 169 -1173 -178 199 -131 -1173 -278 -1173 159 -1173 -78 222 -1173 -1173 -1173 -1173 121 -98 -19 171 -99 -230 -119 -1173 154 -1173 -46 222 -1173 -1173 -1173 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACACACA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 1.9e-020 0.000000 0.941176 0.000000 0.058824 0.852941 0.117647 0.000000 0.029412 0.000000 0.882353 0.000000 0.117647 1.000000 0.000000 0.000000 0.000000 0.000000 0.676471 0.147059 0.176471 0.705882 0.147059 0.058824 0.088235 0.000000 0.852941 0.000000 0.147059 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACACACA MEME-2 regular expression -------------------------------------------------------------------------------- CACACACA -------------------------------------------------------------------------------- Time 7.87 secs. ******************************************************************************** ******************************************************************************** MOTIF TGTGTGTG MEME-3 width = 8 sites = 10 llr = 96 E-value = 3.8e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif TGTGTGTG MEME-3 Description -------------------------------------------------------------------------------- Simplified A :::1:::2 pos.-specific C 1::1:::: probability G :a:8:9:8 matrix T 9:a:a1a: bits 2.3 * * * 2.1 * * * 1.8 *** * * 1.6 *** * * Relative 1.4 *** *** Entropy 1.2 *** **** (13.9 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel TGTGTGTG consensus A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTGTGTG MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr4:185213838-185213858 2 1.19e-05 g tgtgtgtg agtgtgtgtg chr12:16985575-16985595 11 1.19e-05 tgtgtgtgtg tgtgtgtg tg chrX:155238714-155238734 3 1.19e-05 tc tgtgtgtg tttgtgtgtg chr1:27963228-27963248 13 1.19e-05 tgtgtgtgtg tgtgtgtg chr2:242806579-242806599 4 2.08e-05 tgc tgtgtgta ctgtgtgtg chr8:125208766-125208786 11 2.08e-05 tgtgtgtgag tgtgtgta tg chr22:37704530-37704550 12 3.79e-05 tgtgtgtaca tgtatgtg t chr14:106034500-10603452 12 3.79e-05 tgtgtgtgta tgtgtttg c chr14:106154200-10615422 1 4.98e-05 . tgtctgtg cgtttctgtg chr14:106151449-10615146 1 6.71e-05 . cgtgtgtg tgtgtgtgag -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTGTGTG MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr4:185213838-185213858 1.2e-05 1_[+3]_11 chr12:16985575-16985595 1.2e-05 10_[+3]_2 chrX:155238714-155238734 1.2e-05 2_[+3]_10 chr1:27963228-27963248 1.2e-05 12_[+3] chr2:242806579-242806599 2.1e-05 3_[+3]_9 chr8:125208766-125208786 2.1e-05 10_[+3]_2 chr22:37704530-37704550 3.8e-05 11_[+3]_1 chr14:106034500-10603452 3.8e-05 11_[+3]_1 chr14:106154200-10615422 5e-05 [+3]_12 chr14:106151449-10615146 6.7e-05 [+3]_12 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTGTGTG MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TGTGTGTG width=8 seqs=10 chr4:185213838-185213858 ( 2) TGTGTGTG 1 chr12:16985575-16985595 ( 11) TGTGTGTG 1 chrX:155238714-155238734 ( 3) TGTGTGTG 1 chr1:27963228-27963248 ( 13) TGTGTGTG 1 chr2:242806579-242806599 ( 4) TGTGTGTA 1 chr8:125208766-125208786 ( 11) TGTGTGTA 1 chr22:37704530-37704550 ( 12) TGTATGTG 1 chr14:106034500-10603452 ( 12) TGTGTTTG 1 chr14:106154200-10615422 ( 1) TGTCTGTG 1 chr14:106151449-10615146 ( 1) CGTGTGTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTGTGTG MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 9.81663 E= 3.8e-002 -997 -155 -997 216 -997 -997 178 -997 -997 -997 -997 231 -110 -155 146 -997 -997 -997 -997 231 -997 -997 163 -101 -997 -997 -997 231 -11 -997 146 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTGTGTG MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 10 E= 3.8e-002 0.000000 0.100000 0.000000 0.900000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.100000 0.100000 0.800000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.900000 0.100000 0.000000 0.000000 0.000000 1.000000 0.200000 0.000000 0.800000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTGTGTG MEME-3 regular expression -------------------------------------------------------------------------------- TGTGTGT[GA] -------------------------------------------------------------------------------- Time 10.79 secs. ******************************************************************************** ******************************************************************************** MOTIF RGAGRVRG MEME-4 width = 8 sites = 29 llr = 210 E-value = 8.4e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif RGAGRVRG MEME-4 Description -------------------------------------------------------------------------------- Simplified A 42a:636: pos.-specific C :::::4:: probability G 68:a424a matrix T :::::::: bits 2.3 * 2.1 * 1.8 ** * 1.6 ** * Relative 1.4 ** * Entropy 1.2 *** ** (10.4 bits) 0.9 ***** ** 0.7 ***** ** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel GGAGACAG consensus A GAG sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RGAGRVRG MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr17:7232891-7232911 12 3.61e-05 TGCGACAGTG GGAGAAAG A chr16:5148176-5148196 11 3.61e-05 GCAGAGCCCA GGAGACAG GT chr19:48828693-48828713 11 6.28e-05 agcgagcgag agagaaag gg chr20:25291350-25291370 1 6.28e-05 . agagacag gcaagaagac chr12:1714425-1714445 1 6.28e-05 . AGAGACAG AGGGTGGTGT chr19:10216100-10216120 3 6.28e-05 gg agagacag agagagATGG chr19:42391196-42391216 4 6.28e-05 CAC AGAGACAG GGACAGGAC chr7:123175135-123175155 5 6.28e-05 gcga agagacag gaagaggg chr4:154408958-154408978 6 1.81e-04 GACAA GGAGAGAG ACCCTTG chr6:36091633-36091653 3 1.81e-04 AG GGAGGCAG GCCTTAGGGG chr14:24901219-24901239 13 1.81e-04 CTTACGCTGT GGAGAAGG chr10:121485404-12148542 11 1.81e-04 gagacacccg ggagaagg cg chr22:24187047-24187067 8 2.69e-04 CTGGGGG AGAGGAAG GGAGC chr11:64008927-64008947 1 3.91e-04 . GGAGGAGG TGAAAGGCGG chr17:7210810-7210830 6 3.91e-04 CGGTG GGAGGGAG GGTGGAG chr19:45579182-45579202 2 3.91e-04 A GGAGAGGG GAAACCGAAG chr7:100765523-100765543 12 3.91e-04 CTGCAGCGGA ggagaggg g chr4:3957606-3957626 10 3.91e-04 AAGGGCTCA GGAGGCGG GGC chr11:3444301-3444321 1 3.91e-04 . GGAGGCGG AGCTTAGGAC chr19:7099138-7099158 8 3.91e-04 CCAGGAC GGAGGGAG GGGAA chr19:38827642-38827662 11 5.08e-04 gaacaagagc agaggcgg gg chr19:38997739-38997759 13 5.08e-04 GCCTGGACAC AGAGGCGG chr1:168993601-168993621 12 5.08e-04 gggaaggaag gaagaaag g chr19:39368760-39368780 1 5.08e-04 . AGAGGAGG CTGTGGGCAG chr17:42853174-42853194 2 5.08e-04 C GAAGACAG CGCCAATGGG chr10:75910966-75910986 1 6.82e-04 . AGAGGGGG CGGGACCAGA chr7:99964377-99964397 6 6.82e-04 GGAGG GAAGGAAG AGATGGG chr19:1812794-1812814 12 6.82e-04 gtccaggaca gaaggcag g chr16:23859427-23859447 5 8.37e-04 GGAA GAAGAGGG TGTGAGGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RGAGRVRG MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr17:7232891-7232911 3.6e-05 11_[+4]_1 chr16:5148176-5148196 3.6e-05 10_[+4]_2 chr19:48828693-48828713 6.3e-05 10_[+4]_2 chr20:25291350-25291370 6.3e-05 [+4]_12 chr12:1714425-1714445 6.3e-05 [+4]_12 chr19:10216100-10216120 6.3e-05 2_[+4]_10 chr19:42391196-42391216 6.3e-05 3_[+4]_9 chr7:123175135-123175155 6.3e-05 4_[+4]_8 chr4:154408958-154408978 0.00018 5_[+4]_7 chr6:36091633-36091653 0.00018 2_[+4]_10 chr14:24901219-24901239 0.00018 12_[+4] chr10:121485404-12148542 0.00018 10_[+4]_2 chr22:24187047-24187067 0.00027 7_[+4]_5 chr11:64008927-64008947 0.00039 [+4]_12 chr17:7210810-7210830 0.00039 5_[+4]_7 chr19:45579182-45579202 0.00039 1_[+4]_11 chr7:100765523-100765543 0.00039 11_[+4]_1 chr4:3957606-3957626 0.00039 9_[+4]_3 chr11:3444301-3444321 0.00039 [+4]_12 chr19:7099138-7099158 0.00039 7_[+4]_5 chr19:38827642-38827662 0.00051 10_[+4]_2 chr19:38997739-38997759 0.00051 12_[+4] chr1:168993601-168993621 0.00051 11_[+4]_1 chr19:39368760-39368780 0.00051 [+4]_12 chr17:42853174-42853194 0.00051 1_[+4]_11 chr10:75910966-75910986 0.00068 [+4]_12 chr7:99964377-99964397 0.00068 5_[+4]_7 chr19:1812794-1812814 0.00068 11_[+4]_1 chr16:23859427-23859447 0.00084 4_[+4]_8 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RGAGRVRG MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF RGAGRVRG width=8 seqs=29 chr17:7232891-7232911 ( 12) GGAGAAAG 1 chr16:5148176-5148196 ( 11) GGAGACAG 1 chr19:48828693-48828713 ( 11) AGAGAAAG 1 chr20:25291350-25291370 ( 1) AGAGACAG 1 chr12:1714425-1714445 ( 1) AGAGACAG 1 chr19:10216100-10216120 ( 3) AGAGACAG 1 chr19:42391196-42391216 ( 4) AGAGACAG 1 chr7:123175135-123175155 ( 5) AGAGACAG 1 chr4:154408958-154408978 ( 6) GGAGAGAG 1 chr6:36091633-36091653 ( 3) GGAGGCAG 1 chr14:24901219-24901239 ( 13) GGAGAAGG 1 chr10:121485404-12148542 ( 11) GGAGAAGG 1 chr22:24187047-24187067 ( 8) AGAGGAAG 1 chr11:64008927-64008947 ( 1) GGAGGAGG 1 chr17:7210810-7210830 ( 6) GGAGGGAG 1 chr19:45579182-45579202 ( 2) GGAGAGGG 1 chr7:100765523-100765543 ( 12) GGAGAGGG 1 chr4:3957606-3957626 ( 10) GGAGGCGG 1 chr11:3444301-3444321 ( 1) GGAGGCGG 1 chr19:7099138-7099158 ( 8) GGAGGGAG 1 chr19:38827642-38827662 ( 11) AGAGGCGG 1 chr19:38997739-38997759 ( 13) AGAGGCGG 1 chr1:168993601-168993621 ( 12) GAAGAAAG 1 chr19:39368760-39368780 ( 1) AGAGGAGG 1 chr17:42853174-42853194 ( 2) GAAGACAG 1 chr10:75910966-75910986 ( 1) AGAGGGGG 1 chr7:99964377-99964397 ( 6) GAAGGAAG 1 chr19:1812794-1812814 ( 12) GAAGGCAG 1 chr16:23859427-23859447 ( 5) GAAGAGGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RGAGRVRG MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 8.4923 E= 8.4e-005 82 -1150 109 -1150 -32 -1150 151 -1150 222 -1150 -1150 -1150 -1150 -1150 178 -1150 136 -1150 63 -1150 53 62 -27 -1150 145 -1150 51 -1150 -1150 -1150 178 -1150 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RGAGRVRG MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 8.4e-005 0.379310 0.000000 0.620690 0.000000 0.172414 0.000000 0.827586 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.551724 0.000000 0.448276 0.000000 0.310345 0.448276 0.241379 0.000000 0.586207 0.000000 0.413793 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RGAGRVRG MEME-4 regular expression -------------------------------------------------------------------------------- [GA]GAG[AG][CAG][AG]G -------------------------------------------------------------------------------- Time 13.21 secs. ******************************************************************************** ******************************************************************************** MOTIF CCCTCCTC MEME-5 width = 8 sites = 26 llr = 190 E-value = 6.6e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCCTCCTC MEME-5 Description -------------------------------------------------------------------------------- Simplified A :::2:::: pos.-specific C 7a8:aa37 probability G :::::::1 matrix T 3:28::72 bits 2.3 2.1 1.8 * 1.6 * *** Relative 1.4 * *** Entropy 1.2 ******* (10.5 bits) 0.9 ******* 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel CCCTCCTC consensus T C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCTCCTC MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr6:119635984-119636004 9 4.28e-05 CACAGCCT TCCTCCTC CTCC chr7:36192582-36192602 1 4.28e-05 . TCCTCCTC TCGCACGCCA chr8:12448780-12448800 9 4.28e-05 CTGCAACC TCCTCCTC ACTG chr9:136890184-136890204 12 4.28e-05 ctcctccatc tcctcctc c chr7:2934026-2934046 8 7.78e-05 cttcatc ccttcctc cgtcc chr18:60830021-60830041 11 7.78e-05 CCAAACTCTG ccctcctt cc chr5:34929480-34929500 8 7.78e-05 AGGCCTA CCTTCCTC CCACG chr19:41120037-41120057 1 1.14e-04 . ccctcccc ttacctcttt chr9:130533740-130533760 12 1.14e-04 TCGCTCCGCC CCCTCCCC A chr3:38178733-38178753 3 1.14e-04 GC CCCTCCCC GCCACCGCCT chr3:128840967-128840987 9 1.14e-04 cacctcag cccTCCCC GACT chr16:53086927-53086947 12 1.39e-04 ctcctcctgc tcttcctc c chr4:37688255-37688275 5 1.91e-04 TCCA CCCACCTC AGCTTGGC chr20:4804282-4804302 2 1.91e-04 t tcctcccc ttgtctcctg chr19:51870995-51871015 8 1.91e-04 AGCCCCG CCCACCTC TCTCG chr1:117100295-117100315 1 2.47e-04 . ccttcctt tttctttttg chr12:121952015-12195203 7 2.47e-04 aagcga ccctcctg cctcag chr16:58232405-58232425 5 2.47e-04 CTGA CCCTCCTG TCACCCAA chr9:92113254-92113274 5 2.47e-04 CTCT Tccacctc tctcccct chr3:122870844-122870864 7 2.47e-04 ttcctt ccttcctt ccttcc chr1:155940781-155940801 9 3.16e-04 cagggtct ccctccta ggct chr7:98593740-98593760 7 4.51e-04 TACTTA CCCTCATC CCATCA chr11:64072678-64072698 2 4.51e-04 C CACTCCTC TCGCGCGCAG chr16:89259006-89259026 7 4.51e-04 TCCGCC TCCTCCCT AAcccc chr19:42704058-42704078 11 4.78e-04 ccagccttct ccctccac cc chrX:148621193-148621213 3 5.30e-04 TG CCCACCCC AGCACCTTTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCTCCTC MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr6:119635984-119636004 4.3e-05 8_[+5]_4 chr7:36192582-36192602 4.3e-05 [+5]_12 chr8:12448780-12448800 4.3e-05 8_[+5]_4 chr9:136890184-136890204 4.3e-05 11_[+5]_1 chr7:2934026-2934046 7.8e-05 7_[+5]_5 chr18:60830021-60830041 7.8e-05 10_[+5]_2 chr5:34929480-34929500 7.8e-05 7_[+5]_5 chr19:41120037-41120057 0.00011 [+5]_12 chr9:130533740-130533760 0.00011 11_[+5]_1 chr3:38178733-38178753 0.00011 2_[+5]_10 chr3:128840967-128840987 0.00011 8_[+5]_4 chr16:53086927-53086947 0.00014 11_[+5]_1 chr4:37688255-37688275 0.00019 4_[+5]_8 chr20:4804282-4804302 0.00019 1_[+5]_11 chr19:51870995-51871015 0.00019 7_[+5]_5 chr1:117100295-117100315 0.00025 [+5]_12 chr12:121952015-12195203 0.00025 6_[+5]_6 chr16:58232405-58232425 0.00025 4_[+5]_8 chr9:92113254-92113274 0.00025 4_[+5]_8 chr3:122870844-122870864 0.00025 6_[+5]_6 chr1:155940781-155940801 0.00032 8_[+5]_4 chr7:98593740-98593760 0.00045 6_[+5]_6 chr11:64072678-64072698 0.00045 1_[+5]_11 chr16:89259006-89259026 0.00045 6_[+5]_6 chr19:42704058-42704078 0.00048 10_[+5]_2 chrX:148621193-148621213 0.00053 2_[+5]_10 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCTCCTC MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CCCTCCTC width=8 seqs=26 chr6:119635984-119636004 ( 9) TCCTCCTC 1 chr7:36192582-36192602 ( 1) TCCTCCTC 1 chr8:12448780-12448800 ( 9) TCCTCCTC 1 chr9:136890184-136890204 ( 12) TCCTCCTC 1 chr7:2934026-2934046 ( 8) CCTTCCTC 1 chr18:60830021-60830041 ( 11) CCCTCCTT 1 chr5:34929480-34929500 ( 8) CCTTCCTC 1 chr19:41120037-41120057 ( 1) CCCTCCCC 1 chr9:130533740-130533760 ( 12) CCCTCCCC 1 chr3:38178733-38178753 ( 3) CCCTCCCC 1 chr3:128840967-128840987 ( 9) CCCTCCCC 1 chr16:53086927-53086947 ( 12) TCTTCCTC 1 chr4:37688255-37688275 ( 5) CCCACCTC 1 chr20:4804282-4804302 ( 2) TCCTCCCC 1 chr19:51870995-51871015 ( 8) CCCACCTC 1 chr1:117100295-117100315 ( 1) CCTTCCTT 1 chr12:121952015-12195203 ( 7) CCCTCCTG 1 chr16:58232405-58232425 ( 5) CCCTCCTG 1 chr9:92113254-92113274 ( 5) TCCACCTC 1 chr3:122870844-122870864 ( 7) CCTTCCTT 1 chr1:155940781-155940801 ( 9) CCCTCCTA 1 chr7:98593740-98593760 ( 7) CCCTCATC 1 chr11:64072678-64072698 ( 2) CACTCCTC 1 chr16:89259006-89259026 ( 7) TCCTCCCT 1 chr19:42704058-42704078 ( 11) CCCTCCAC 1 chrX:148621193-148621213 ( 3) CCCACCCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCTCCTC MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 8.5921 E= 6.6e-003 -1134 124 -1134 61 -248 172 -1134 -1134 -1134 147 -1134 -7 -48 -1134 -1134 207 -1134 177 -1134 -1134 -248 172 -1134 -1134 -248 -12 -1134 178 -248 132 -192 -39 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCTCCTC MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 6.6e-003 0.000000 0.692308 0.000000 0.307692 0.038462 0.961538 0.000000 0.000000 0.000000 0.807692 0.000000 0.192308 0.153846 0.000000 0.000000 0.846154 0.000000 1.000000 0.000000 0.000000 0.038462 0.961538 0.000000 0.000000 0.038462 0.269231 0.000000 0.692308 0.038462 0.730769 0.076923 0.153846 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCTCCTC MEME-5 regular expression -------------------------------------------------------------------------------- [CT]CCTCC[TC]C -------------------------------------------------------------------------------- Time 13.91 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr19:56110422-56110442 4.61e-01 20 chr19:7099138-7099158 3.26e-01 20 chr11:67573340-67573360 8.28e-01 20 chr10:121485404-12148542 7.14e-02 20 chr7:123175135-123175155 9.51e-02 4_[+4(6.28e-05)]_8 chr17:74497823-74497843 5.51e-01 20 chr19:46000487-46000507 4.67e-01 20 chr11:3444301-3444321 2.66e-01 20 chr3:128840967-128840987 1.09e-01 20 chr8:11314153-11314173 4.72e-03 4_[+1(6.65e-05)]_8 chr19:18747401-18747421 8.53e-01 20 chr17:76136646-76136666 6.69e-01 20 chr1:117368934-117368954 6.47e-02 20 chr2:8716385-8716405 1.09e-02 4_[+2(2.63e-05)]_8 chr19:51870995-51871015 7.63e-02 20 chr16:5148176-5148196 7.44e-02 10_[+4(3.61e-05)]_2 chr14:106154200-10615422 7.50e-04 [+3(4.98e-05)]_4_[+1(4.93e-05)] chr20:62485189-62485209 2.51e-01 20 chr12:113497084-11349710 1.63e-01 20 chr12:125348768-12534878 3.88e-01 20 chr19:1812794-1812814 3.53e-01 20 chr19:46379736-46379756 2.54e-01 20 chr19:42386715-42386735 3.31e-01 20 chr3:50336922-50336942 2.82e-01 20 chr10:3215357-3215377 3.58e-01 20 chr5:133892640-133892660 4.16e-03 2_[+2(1.55e-05)]_10 chr21:37528817-37528837 3.04e-01 20 chrX:148620990-148621010 7.87e-01 20 chr19:41110061-41110081 6.01e-01 20 chr15:78178061-78178081 2.41e-02 11_[+2(5.25e-05)]_1 chr3:125634981-125635001 8.38e-01 20 chr12:109125840-10912586 4.65e-01 20 chr9:136890184-136890204 5.39e-02 11_[+5(4.28e-05)]_1 chr4:3957606-3957626 3.48e-01 20 chr17:42853174-42853194 2.56e-01 20 chr14:105131693-10513171 4.13e-02 3_[+2(5.25e-05)]_[+2(5.25e-05)]_1 chr17:40374120-40374140 3.76e-03 5_[+1(4.93e-05)]_7 chr14:91821598-91821618 1.89e-01 20 chr1:27963228-27963248 1.07e-04 2_[+1(1.19e-05)]_[+1(1.19e-05)]_2 chr8:12448780-12448800 3.21e-02 8_[+5(4.28e-05)]_4 chr14:93144371-93144391 1.37e-01 20 chr8:8085564-8085584 8.54e-01 20 chr18:77794046-77794066 6.64e-01 20 chr19:39897016-39897036 7.28e-03 20 chr21:46340156-46340176 8.05e-03 1_[+2(1.55e-05)]_11 chr7:100765523-100765543 2.62e-01 20 chr8:143407501-143407521 7.59e-01 20 chr1:25362714-25362734 7.98e-01 20 chr2:97438593-97438613 1.71e-02 3_[+2(9.89e-05)]_9 chr7:36192582-36192602 5.25e-02 [+5(4.28e-05)]_12 chr12:7046038-7046058 2.13e-01 20 chr1:181105812-181105832 3.40e-03 6_[+2(1.55e-05)]_6 chr20:4804282-4804302 1.15e-01 20 chr17:57906373-57906393 3.71e-01 20 chr12:8396067-8396087 3.18e-01 20 chr12:50561304-50561324 6.20e-01 20 chr3:38178733-38178753 9.32e-02 20 chr16:85857260-85857280 8.15e-01 20 chrX:15756266-15756286 1.88e-01 20 chr1:11863634-11863654 9.34e-01 20 chr18:60865591-60865611 5.13e-02 20 chr14:95725201-95725221 4.05e-04 1_[+1(2.90e-05)]_11 chr19:48996120-48996140 2.57e-01 20 chr10:45464468-45464488 2.34e-04 6_[+3(2.08e-05)]_6 chr19:6517469-6517489 3.72e-03 12_[+3(6.71e-05)] chr3:122870844-122870864 2.77e-01 20 chr19:39368760-39368780 5.52e-02 20 chr9:92113254-92113274 1.27e-01 20 chr7:74203069-74203089 9.61e-01 20 chr6:159274242-159274262 7.54e-03 2_[+2(1.55e-05)]_10 chr16:89259006-89259026 2.14e-01 20 chr19:45579182-45579202 3.41e-01 20 chr19:18282554-18282574 2.60e-02 5_[+2(8.44e-05)]_7 chr11:67139253-67139273 3.89e-01 20 chr10:79221805-79221825 6.19e-01 20 chr16:2186210-2186230 4.91e-01 20 chr9:130533740-130533760 8.73e-02 20 chr1:9970673-9970693 7.39e-01 20 chr2:99089608-99089628 2.68e-03 20 chr6:30654028-30654048 4.21e-02 20 chr19:9929891-9929911 4.02e-01 20 chr12:58148575-58148595 2.10e-01 20 chr6:31764020-31764040 9.91e-01 20 chr14:106155275-10615529 6.57e-02 20 chr10:103874930-10387495 1.74e-01 20 chr19:36135389-36135409 2.96e-01 20 chr10:105451534-10545155 3.20e-01 20 chr19:50143575-50143595 7.77e-01 20 chr11:60719386-60719406 8.33e-01 20 chr3:120315131-120315151 7.57e-01 20 chr21:43374735-43374755 4.15e-04 7_[+1(2.90e-05)]_5 chr17:7210810-7210830 1.06e-01 20 chrX:135992415-135992435 4.81e-01 20 chr5:34929480-34929500 8.39e-02 7_[+5(7.78e-05)]_5 chr6:53224454-53224474 5.29e-01 20 chr2:10573542-10573562 5.50e-03 9_[+1(8.75e-05)]_3 chr2:25518097-25518117 1.81e-02 20 chr14:106029249-10602926 2.32e-03 12_[+1(6.65e-05)] chr10:115720886-11572090 2.56e-01 20 chr10:134408106-13440812 5.30e-03 9_[+1(8.75e-05)]_3 chr5:139041008-139041028 4.08e-01 20 chr6:149353617-149353637 8.09e-01 20 chr2:220159260-220159280 5.64e-02 20 chr14:106149517-10614953 4.30e-03 20 chr1:1851094-1851114 6.10e-01 20 chr8:123511947-123511967 1.61e-02 3_[+2(2.63e-05)]_9 chr10:125803497-12580351 6.53e-01 20 chr20:61603547-61603567 3.89e-04 4_[+1(2.02e-05)]_8 chr8:11389390-11389410 9.58e-01 20 chrX:155238714-155238734 1.15e-04 2_[+1(1.19e-05)]_2_[+1(1.19e-05)] chr14:106051851-10605187 6.09e-02 20 chr6:160402303-160402323 4.40e-03 12_[+1(7.92e-05)] chr5:176881165-176881185 3.93e-01 20 chr7:74001968-74001988 3.70e-01 20 chr3:194871553-194871573 1.98e-02 [+2(3.70e-05)]_12 chr9:92099591-92099611 5.24e-05 8_[+1(1.19e-05)]_4 chr11:6256171-6256191 8.11e-01 20 chr17:7232891-7232911 2.57e-02 11_[+4(3.61e-05)]_1 chr16:11265874-11265894 7.08e-02 20 chr16:23859427-23859447 4.26e-02 20 chr16:56985290-56985310 4.57e-01 20 chr18:12377455-12377475 6.23e-01 20 chr19:41120037-41120057 5.95e-02 20 chr19:37340791-37340811 6.27e-01 20 chr19:42391196-42391216 2.28e-02 3_[+4(6.28e-05)]_9 chr11:64008927-64008947 1.83e-01 20 chr16:53086927-53086947 1.97e-01 20 chr19:6767657-6767677 9.13e-01 20 chr1:27995644-27995664 1.84e-01 20 chr11:73096123-73096143 1.94e-01 20 chrX:2438731-2438751 1.38e-02 7_[+2(6.33e-05)]_5 chr19:3154657-3154677 6.68e-01 20 chr22:24187047-24187067 9.74e-02 20 chr14:106034500-10603452 1.11e-04 1_[+1(1.19e-05)]_2_[+1(2.02e-05)]_1 chr14:106151449-10615146 1.01e-04 2_[+1(1.19e-05)]_10 chr6:119635984-119636004 3.16e-02 8_[+5(4.28e-05)]_4 chr16:29819245-29819265 5.58e-01 20 chr18:60830021-60830041 1.02e-01 10_[+5(7.78e-05)]_2 chr19:7757151-7757171 5.89e-01 20 chr7:143083136-143083156 8.68e-05 8_[+1(1.19e-05)]_4 chr20:36013445-36013465 3.55e-02 9_[+2(5.25e-05)]_3 chr17:44264323-44264343 8.38e-01 20 chr17:79227673-79227693 8.22e-01 20 chr19:10216100-10216120 9.17e-02 2_[+4(6.28e-05)]_10 chr11:82611632-82611652 7.59e-01 20 chr19:42704058-42704078 2.38e-01 20 chr7:44078903-44078923 9.68e-01 20 chr5:176018859-176018879 2.90e-02 20 chr7:44621963-44621983 4.19e-02 20 chr22:18359891-18359911 7.52e-01 20 chr4:37688255-37688275 1.71e-02 20 chrX:149108387-149108407 4.26e-01 20 chr19:680925-680945 5.57e-03 20 chr1:27951238-27951258 3.84e-03 20 chr12:111107096-11110711 8.62e-01 20 chr10:103454553-10345457 8.31e-01 20 chr16:57048935-57048955 7.53e-01 20 chr5:177547952-177547972 5.25e-01 20 chr8:125208766-125208786 8.44e-05 [+1(1.19e-05)]_2_[+3(2.08e-05)]_2 chr16:1393178-1393198 7.42e-01 20 chr10:12084299-12084319 5.27e-01 20 chr17:79227474-79227494 5.05e-01 20 chr12:57487618-57487638 4.06e-01 20 chr1:169013654-169013674 8.35e-01 20 chr10:125152862-12515288 1.38e-02 5_[+2(6.33e-05)]_7 chr19:6516305-6516325 7.34e-01 20 chr2:43446411-43446431 1.29e-01 20 chrX:148621193-148621213 1.53e-01 20 chr3:127542475-127542495 7.43e-02 20 chr22:29138541-29138561 7.76e-01 20 chr14:24901219-24901239 3.36e-02 20 chr16:81130124-81130144 4.45e-01 20 chr3:196189681-196189701 1.10e-01 20 chr12:1714425-1714445 9.66e-03 [+4(6.28e-05)]_12 chr11:64072678-64072698 2.60e-01 20 chr11:72449852-72449872 6.12e-02 20 chr6:39346149-39346169 9.79e-02 20 chr9:114790746-114790766 9.29e-03 [+2(3.70e-05)]_2_[+2(1.55e-05)]_2 chr20:32581180-32581200 2.35e-01 20 chr8:58162257-58162277 1.95e-02 20 chr16:75599906-75599926 5.14e-01 20 chr12:16985575-16985595 1.20e-04 [+1(1.19e-05)]_[+1(1.19e-05)]_4 chr16:58232405-58232425 1.05e-01 20 chrX:20160089-20160109 6.20e-01 20 chr1:236313436-236313456 1.77e-03 9_[+1(3.73e-05)]_3 chr17:4812265-4812285 8.57e-03 [+2(1.55e-05)]_[+2(8.44e-05)]_4 chr7:98593740-98593760 1.61e-01 20 chr20:42142904-42142924 4.48e-01 20 chr19:47128401-47128421 4.26e-01 20 chr21:45395166-45395186 7.72e-03 20 chr1:168993601-168993621 4.11e-01 20 chr22:50752994-50753014 5.08e-01 20 chr12:56366880-56366900 1.59e-02 6_[+2(3.70e-05)]_6 chr7:99964377-99964397 4.48e-01 20 chr1:155940781-155940801 1.30e-01 20 chr10:76587077-76587097 5.88e-03 6_[+1(6.65e-05)]_6 chr11:117680643-11768066 9.81e-03 11_[+2(2.63e-05)]_1 chr2:112811981-112812001 5.77e-01 20 chr2:242806579-242806599 1.11e-04 3_[+3(2.08e-05)]_1_[+1(1.19e-05)] chr14:106035734-10603575 4.88e-02 20 chr2:97467887-97467907 4.10e-03 [+2(1.55e-05)]_12 chr7:65564944-65564964 8.67e-01 20 chr14:100061649-10006166 9.51e-01 20 chr20:25291350-25291370 4.32e-02 [+4(6.28e-05)]_12 chr20:4794437-4794457 5.96e-05 [+1(1.19e-05)]_12 chr22:42466924-42466944 6.00e-01 20 chr9:37369733-37369753 7.02e-02 20 chr1:1840890-1840910 6.77e-01 20 chr12:121952015-12195203 1.86e-01 20 chr17:26904062-26904082 3.51e-01 20 chr9:139962561-139962581 4.78e-01 20 chr19:6663348-6663368 3.27e-04 7_[+1(2.02e-05)]_5 chr7:2934026-2934046 8.67e-02 7_[+5(7.78e-05)]_5 chr5:102594339-102594359 7.31e-01 20 chr1:206287970-206287990 9.60e-01 20 chr10:75910966-75910986 2.99e-01 20 chr19:38997739-38997759 1.44e-01 20 chr1:966515-966535 5.92e-01 20 chrX:1572027-1572047 7.79e-01 20 chr1:32403196-32403216 3.10e-01 20 chr14:73714270-73714290 2.43e-01 20 chr6:34191612-34191632 4.97e-01 20 chr22:38577268-38577288 9.06e-01 20 chr19:49217420-49217440 8.98e-01 20 chr19:42634258-42634278 9.50e-02 20 chr16:31153748-31153768 8.09e-01 20 chr3:53197280-53197300 2.01e-02 20 chr6:36091633-36091653 1.45e-01 20 chr2:231523685-231523705 6.46e-01 20 chr10:16478943-16478963 7.15e-01 20 chr19:7396426-7396446 9.37e-01 20 chr4:154408958-154408978 2.23e-01 20 chr14:77444363-77444383 5.56e-01 20 chr6:33045930-33045950 6.09e-01 20 chr1:12107067-12107087 5.46e-01 20 chr8:145026708-145026728 8.71e-01 20 chr6:157542814-157542834 1.67e-03 7_[+2(1.55e-05)]_5 chr4:185213838-185213858 9.07e-05 1_[+1(1.19e-05)]_2_[+1(1.19e-05)]_1 chr17:76130316-76130336 2.66e-02 20 chr19:48828693-48828713 1.19e-01 10_[+4(6.28e-05)]_2 chr1:23961373-23961393 6.87e-01 20 chr11:64655652-64655672 6.54e-02 20 chr19:38827642-38827662 3.56e-01 20 chr14:106157240-10615726 1.49e-02 12_[+2(3.70e-05)] chr10:121072823-12107284 2.64e-01 20 chr22:37704530-37704550 2.87e-05 1_[+3(2.08e-05)]_2_[+3(3.79e-05)]_1 chr1:6408316-6408336 2.57e-02 20 chr1:117100295-117100315 3.24e-03 20 chr16:21528793-21528813 8.05e-01 20 chr22:42323059-42323079 5.85e-01 20 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c17n10.farnam.hpc.yale.internal ********************************************************************************