******************************************************************************** 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/worm/fasta/RankLinear2.0_40/hlh-12.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chrV:265725-265805 1.0000 80 chrM:8799-8879 1.0000 80 chrV:265394-265474 1.0000 80 chrX:7507253-7507333 1.0000 80 chrV:17687571-17687651 1.0000 80 chrIV:13549483-13549563 1.0000 80 chrX:8640813-8640893 1.0000 80 chrX:7681030-7681110 1.0000 80 chrX:5709413-5709493 1.0000 80 chrM:3262-3342 1.0000 80 chrII:2570712-2570792 1.0000 80 chrIII:4449502-4449582 1.0000 80 chrV:18712288-18712368 1.0000 80 chrIV:16775183-16775263 1.0000 80 chrM:8480-8560 1.0000 80 chrX:8838228-8838308 1.0000 80 chrX:10124493-10124573 1.0000 80 chrIV:4930953-4931033 1.0000 80 chrM:10112-10192 1.0000 80 chrII:14617092-14617172 1.0000 80 chrM:10819-10899 1.0000 80 chrX:9024354-9024434 1.0000 80 chrI:11803284-11803364 1.0000 80 chrV:9091517-9091597 1.0000 80 chrM:2992-3072 1.0000 80 chrIII:1600861-1600941 1.0000 80 chrV:5284759-5284839 1.0000 80 chrM:5965-6045 1.0000 80 chrX:3793525-3793605 1.0000 80 chrX:7773723-7773803 1.0000 80 chrII:12541734-12541814 1.0000 80 chrX:11993319-11993399 1.0000 80 chrV:18707260-18707340 1.0000 80 chrIV:12005511-12005591 1.0000 80 chrM:4911-4991 1.0000 80 chrII:11966354-11966434 1.0000 80 chrX:13653800-13653880 1.0000 80 chrIV:873347-873427 1.0000 80 chrV:13567063-13567143 1.0000 80 chrII:14409853-14409933 1.0000 80 chrIII:10746519-10746599 1.0000 80 chrIII:7494945-7495025 1.0000 80 chrV:20847742-20847822 1.0000 80 chrIII:931567-931647 1.0000 80 chrM:2109-2189 1.0000 80 chrM:7191-7271 1.0000 80 chrM:9106-9186 1.0000 80 chrX:16619379-16619459 1.0000 80 chrX:13655842-13655922 1.0000 80 chrX:16558882-16558962 1.0000 80 chrV:16593394-16593474 1.0000 80 chrX:8971622-8971702 1.0000 80 chrX:6286370-6286450 1.0000 80 chrII:8441656-8441736 1.0000 80 chrX:14478868-14478948 1.0000 80 chrIII:5853357-5853437 1.0000 80 chrM:4634-4714 1.0000 80 chrIV:5038870-5038950 1.0000 80 chrIV:14576601-14576681 1.0000 80 chrX:10018396-10018476 1.0000 80 chrM:1205-1285 1.0000 80 chrX:8638896-8638976 1.0000 80 chrX:4445040-4445120 1.0000 80 chrV:18412425-18412505 1.0000 80 chrIII:7642220-7642300 1.0000 80 chrM:12382-12462 1.0000 80 chrX:6867819-6867899 1.0000 80 chrX:8939665-8939745 1.0000 80 chrX:8638635-8638715 1.0000 80 chrX:16378032-16378112 1.0000 80 chrM:2313-2393 1.0000 80 chrII:11880671-11880751 1.0000 80 chrV:18710289-18710369 1.0000 80 chrX:13781712-13781792 1.0000 80 chrIII:1616687-1616767 1.0000 80 chrII:5353829-5353909 1.0000 80 chrIV:16776057-16776137 1.0000 80 chrI:7872166-7872246 1.0000 80 chrI:11978761-11978841 1.0000 80 chrX:4444233-4444313 1.0000 80 chrV:12510126-12510206 1.0000 80 chrIII:13188110-13188190 1.0000 80 chrX:8650685-8650765 1.0000 80 chrV:3686051-3686131 1.0000 80 chrIII:3869469-3869549 1.0000 80 chrI:852202-852282 1.0000 80 chrIII:12250662-12250742 1.0000 80 chrX:5713708-5713788 1.0000 80 chrX:16931396-16931476 1.0000 80 chrIII:5769874-5769954 1.0000 80 chrV:6335368-6335448 1.0000 80 chrX:10145176-10145256 1.0000 80 chrIV:6481144-6481224 1.0000 80 chrV:9318174-9318254 1.0000 80 chrIV:12417890-12417970 1.0000 80 chrX:10821379-10821459 1.0000 80 chrIV:16399237-16399317 1.0000 80 chrX:9078307-9078387 1.0000 80 chrII:5293482-5293562 1.0000 80 chrX:12458134-12458214 1.0000 80 chrIII:12614807-12614887 1.0000 80 chrIV:9477702-9477782 1.0000 80 chrII:8547123-8547203 1.0000 80 chrX:14804849-14804929 1.0000 80 chrI:11584716-11584796 1.0000 80 chrX:16928290-16928370 1.0000 80 chrIV:9191299-9191379 1.0000 80 chrIV:14225090-14225170 1.0000 80 chrIV:991314-991394 1.0000 80 chrI:6136591-6136671 1.0000 80 chrX:6593565-6593645 1.0000 80 chrII:11157765-11157845 1.0000 80 chrX:1880823-1880903 1.0000 80 chrV:19126020-19126100 1.0000 80 chrIII:1601602-1601682 1.0000 80 chrIV:11026162-11026242 1.0000 80 chrX:11757827-11757907 1.0000 80 chrI:11374409-11374489 1.0000 80 chrIII:5305869-5305949 1.0000 80 chrX:9637822-9637902 1.0000 80 chrX:14115706-14115786 1.0000 80 chrX:6292271-6292351 1.0000 80 ******************************************************************************** ******************************************************************************** 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/worm/inference_raw/MEME/RankLinear2.0_40_hlh-12/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/worm/fasta/RankLinear2.0_40/hlh-12.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= 122 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= 9760 N= 122 sample: seed= 0 hsfrac= 0 searchsize= 9760 norand= no csites= 1000 Letter frequencies in dataset: A 0.274 C 0.207 G 0.228 T 0.291 Background letter frequencies (from file dataset with add-one prior applied): A 0.274 C 0.207 G 0.228 T 0.291 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TCGAAYCC MEME-1 width = 8 sites = 28 llr = 246 E-value = 4.5e-012 ******************************************************************************** -------------------------------------------------------------------------------- Motif TCGAAYCC MEME-1 Description -------------------------------------------------------------------------------- Simplified A :::a7::: pos.-specific C :9:::6a8 probability G ::a:1::: matrix T a1::24:2 bits 2.3 * 2.0 * * 1.8 **** * 1.6 **** * Relative 1.4 **** * Entropy 1.1 **** *** (12.7 bits) 0.9 **** *** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel TCGAACCC consensus TT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCGAAYCC MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:6292271-6292351 22 9.15e-06 GTATGGGGAA TCGAACCC CAGACTTCTC chrX:11757827-11757907 19 9.15e-06 CGAGTGGGGT TCGAACCC ACGAGGTGTT chrX:1880823-1880903 9 9.15e-06 ACCGGGAA TCGAACCC GGGACCTCTC chrII:11157765-11157845 52 9.15e-06 AATGCGGGGC TCGAACCC GCGACAACCA chrIV:6481144-6481224 71 9.15e-06 GGTCGCCGGT TCGAACCC GG chrIV:14576601-14576681 36 9.15e-06 TCGGGGGGAA TCGAACCC CCGTCGAATG chrX:14478868-14478948 24 9.15e-06 AATGCGGGGC TCGAACCC GCGACAACCA chrX:10145176-10145256 34 2.20e-05 GATTGTAGGT TCGAATCC TGCCGTGGTC chrX:8971622-8971702 41 2.20e-05 CCGCGTAGGT TCGAATCC TGCTGACTGC chrI:6136591-6136671 60 3.93e-05 TGTCGCGGGT TCGAGCCC CGCATTGGGC chrX:7773723-7773803 49 3.93e-05 GGTTGGTGGT TCGAGCCC ACCCGGGAGC chrIV:12417890-12417970 51 5.22e-05 ACGGCAGGAT TCGAACCT GCAATCTTCT chrX:10018396-10018476 44 5.22e-05 acggtaggat tcgaacct acaatcttct chrI:11803284-11803364 47 5.22e-05 TCAGCAGGAT TCGAACCT ACGCGGGCAG chrIII:4449502-4449582 46 5.22e-05 ACGGCAGGAT TCGAACCT GCAATCTTCT chrII:5293482-5293562 23 6.58e-05 AGGCCGGGGT TCGATTCC CCGCAACGGA chrI:11978761-11978841 56 6.58e-05 AGGCCGGGGT TCGATTCC CCGCAACGGA chrX:4445040-4445120 27 6.58e-05 GGTCGCTGGT TCGATTCC AGCATGAGGC chrX:6286370-6286450 4 6.58e-05 GGT TCGATTCC CCATACCTCC chrIV:16775183-16775263 52 6.58e-05 CGACGGGGGT TCGATTCC CCCCGAACGC chrX:7681030-7681110 63 6.58e-05 AGGCCGGGGT TCGATTCC CCGCAACGGA chrX:14115706-14115786 39 8.94e-05 GACTGCAGGT TCGAGTCC TGCCTCGGTC chrX:9637822-9637902 45 8.94e-05 GTATGGGGAA TTGAACCC CAGCCCTCTC chrX:12458134-12458214 57 8.94e-05 GTATGGGGAA TTGAACCC CAGCCCTCTC chrX:7507253-7507333 52 8.94e-05 GTATGGGGAA TTGAACCC CAGCCCTCTC chrX:5709413-5709493 41 1.07e-04 CTCATCCTGA TCGAATCT TTTTTGTTTC chrX:3793525-3793605 54 1.31e-04 CTGGCCGGGA TCGAACCG GCGATCTTCT chrX:8650685-8650765 39 1.61e-04 TCGGGCGGGC TCGAACCA CCGACCTTCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCGAAYCC MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:6292271-6292351 9.1e-06 21_[+1]_51 chrX:11757827-11757907 9.1e-06 18_[+1]_54 chrX:1880823-1880903 9.1e-06 8_[+1]_64 chrII:11157765-11157845 9.1e-06 51_[+1]_21 chrIV:6481144-6481224 9.1e-06 70_[+1]_2 chrIV:14576601-14576681 9.1e-06 35_[+1]_37 chrX:14478868-14478948 9.1e-06 23_[+1]_49 chrX:10145176-10145256 2.2e-05 33_[+1]_39 chrX:8971622-8971702 2.2e-05 40_[+1]_32 chrI:6136591-6136671 3.9e-05 59_[+1]_13 chrX:7773723-7773803 3.9e-05 48_[+1]_24 chrIV:12417890-12417970 5.2e-05 50_[+1]_22 chrX:10018396-10018476 5.2e-05 43_[+1]_29 chrI:11803284-11803364 5.2e-05 46_[+1]_26 chrIII:4449502-4449582 5.2e-05 45_[+1]_27 chrII:5293482-5293562 6.6e-05 22_[+1]_50 chrI:11978761-11978841 6.6e-05 55_[+1]_17 chrX:4445040-4445120 6.6e-05 26_[+1]_46 chrX:6286370-6286450 6.6e-05 3_[+1]_69 chrIV:16775183-16775263 6.6e-05 51_[+1]_21 chrX:7681030-7681110 6.6e-05 62_[+1]_10 chrX:14115706-14115786 8.9e-05 38_[+1]_34 chrX:9637822-9637902 8.9e-05 44_[+1]_28 chrX:12458134-12458214 8.9e-05 56_[+1]_16 chrX:7507253-7507333 8.9e-05 51_[+1]_21 chrX:5709413-5709493 0.00011 40_[+1]_32 chrX:3793525-3793605 0.00013 53_[+1]_19 chrX:8650685-8650765 0.00016 38_[+1]_34 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCGAAYCC MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TCGAAYCC width=8 seqs=28 chrX:6292271-6292351 ( 22) TCGAACCC 1 chrX:11757827-11757907 ( 19) TCGAACCC 1 chrX:1880823-1880903 ( 9) TCGAACCC 1 chrII:11157765-11157845 ( 52) TCGAACCC 1 chrIV:6481144-6481224 ( 71) TCGAACCC 1 chrIV:14576601-14576681 ( 36) TCGAACCC 1 chrX:14478868-14478948 ( 24) TCGAACCC 1 chrX:10145176-10145256 ( 34) TCGAATCC 1 chrX:8971622-8971702 ( 41) TCGAATCC 1 chrI:6136591-6136671 ( 60) TCGAGCCC 1 chrX:7773723-7773803 ( 49) TCGAGCCC 1 chrIV:12417890-12417970 ( 51) TCGAACCT 1 chrX:10018396-10018476 ( 44) TCGAACCT 1 chrI:11803284-11803364 ( 47) TCGAACCT 1 chrIII:4449502-4449582 ( 46) TCGAACCT 1 chrII:5293482-5293562 ( 23) TCGATTCC 1 chrI:11978761-11978841 ( 56) TCGATTCC 1 chrX:4445040-4445120 ( 27) TCGATTCC 1 chrX:6286370-6286450 ( 4) TCGATTCC 1 chrIV:16775183-16775263 ( 52) TCGATTCC 1 chrX:7681030-7681110 ( 63) TCGATTCC 1 chrX:14115706-14115786 ( 39) TCGAGTCC 1 chrX:9637822-9637902 ( 45) TTGAACCC 1 chrX:12458134-12458214 ( 57) TTGAACCC 1 chrX:7507253-7507333 ( 52) TTGAACCC 1 chrX:5709413-5709493 ( 41) TCGAATCT 1 chrX:3793525-3793605 ( 54) TCGAACCG 1 chrX:8650685-8650765 ( 39) TCGAACCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCGAAYCC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 8906 bayes= 9.53365 E= 4.5e-012 -1145 -1145 -1145 178 -1145 211 -1145 -144 -1145 -1145 213 -1145 187 -1145 -1145 -1145 131 -1145 -109 -44 -1145 163 -1145 30 -1145 227 -1145 -1145 -293 185 -267 -70 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCGAAYCC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 4.5e-012 0.000000 0.000000 0.000000 1.000000 0.000000 0.892857 0.000000 0.107143 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.678571 0.000000 0.107143 0.214286 0.000000 0.642857 0.000000 0.357143 0.000000 1.000000 0.000000 0.000000 0.035714 0.750000 0.035714 0.178571 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCGAAYCC MEME-1 regular expression -------------------------------------------------------------------------------- TCGA[AT][CT]CC -------------------------------------------------------------------------------- Time 1.72 secs. ******************************************************************************** ******************************************************************************** MOTIF GGYAGAGC MEME-2 width = 8 sites = 18 llr = 169 E-value = 1.4e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGYAGAGC MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::8:8:: pos.-specific C ::52:21a probability G aa2:a:9: matrix T ::3::::: bits 2.3 * 2.0 ** * * 1.8 ** * ** 1.6 ** * ** Relative 1.4 ** ** ** Entropy 1.1 ** ***** (13.6 bits) 0.9 ** ***** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel GGCAGAGC consensus T C sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGYAGAGC MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:14804849-14804929 44 8.69e-06 ATAGCTCAGT GGCAGAGC ATTCGACTGC chrV:6335368-6335448 46 8.69e-06 ATAGCTCAGT GGCAGAGC ATTCGATTGC chrX:8638896-8638976 42 8.69e-06 ATAGCTCAGT GGCAGAGC ATTCGACTGC chrI:11803284-11803364 60 8.69e-06 AACCTACGCG GGCAGAGC CCATTTGATT chrIII:5305869-5305949 52 3.05e-05 ATAGCTCAGT GGTAGAGC GTTGGTCTTG chrV:19126020-19126100 41 3.05e-05 TAGCTCAGTT GGGAGAGC GCACGACTGA chrX:6593565-6593645 48 3.05e-05 TAGCTCAGTT GGGAGAGC GTACGACTGA chrI:6136591-6136671 23 3.05e-05 TAGCTCAGTC GGTAGAGC ACCAGACTCT chrIV:991314-991394 4 3.05e-05 CCC GGGAGAGC CCGAGAGAGG chrV:9318174-9318254 44 3.05e-05 ATAGCTCAGG GGTAGAGC GCTCGCTTCG chrIV:5038870-5038950 67 3.05e-05 TAGCTCAGTT GGTAGAGC GTGAGA chrX:7773723-7773803 12 3.71e-05 TGGCGCAATA GGCAGCGC GTTCGGCTGT chrI:11374409-11374489 46 4.36e-05 ACGCTGGCGT GGCCGAGC ACATCCTCGG chrIII:5769874-5769954 38 4.36e-05 GTGGAGAGAT GGCCGAGC GGTCCAAGGC chrX:9637822-9637902 72 6.01e-05 CCCATGCTAA GGGAGCGC T chrII:14617092-14617172 5 6.01e-05 AGGC GGTAGCGC ATTTCGCTGT chrIII:5853357-5853437 62 8.15e-05 GTATTTGTTA GGCCGCGC TCTCTTAGCG chrV:18712288-18712368 54 8.94e-05 AATGACAGAT GGCAGACC GCTGGTAGAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGYAGAGC MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:14804849-14804929 8.7e-06 43_[+2]_29 chrV:6335368-6335448 8.7e-06 45_[+2]_27 chrX:8638896-8638976 8.7e-06 41_[+2]_31 chrI:11803284-11803364 8.7e-06 59_[+2]_13 chrIII:5305869-5305949 3e-05 51_[+2]_21 chrV:19126020-19126100 3e-05 40_[+2]_32 chrX:6593565-6593645 3e-05 47_[+2]_25 chrI:6136591-6136671 3e-05 22_[+2]_50 chrIV:991314-991394 3e-05 3_[+2]_69 chrV:9318174-9318254 3e-05 43_[+2]_29 chrIV:5038870-5038950 3e-05 66_[+2]_6 chrX:7773723-7773803 3.7e-05 11_[+2]_61 chrI:11374409-11374489 4.4e-05 45_[+2]_27 chrIII:5769874-5769954 4.4e-05 37_[+2]_35 chrX:9637822-9637902 6e-05 71_[+2]_1 chrII:14617092-14617172 6e-05 4_[+2]_68 chrIII:5853357-5853437 8.2e-05 61_[+2]_11 chrV:18712288-18712368 8.9e-05 53_[+2]_19 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGYAGAGC MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGYAGAGC width=8 seqs=18 chrX:14804849-14804929 ( 44) GGCAGAGC 1 chrV:6335368-6335448 ( 46) GGCAGAGC 1 chrX:8638896-8638976 ( 42) GGCAGAGC 1 chrI:11803284-11803364 ( 60) GGCAGAGC 1 chrIII:5305869-5305949 ( 52) GGTAGAGC 1 chrV:19126020-19126100 ( 41) GGGAGAGC 1 chrX:6593565-6593645 ( 48) GGGAGAGC 1 chrI:6136591-6136671 ( 23) GGTAGAGC 1 chrIV:991314-991394 ( 4) GGGAGAGC 1 chrV:9318174-9318254 ( 44) GGTAGAGC 1 chrIV:5038870-5038950 ( 67) GGTAGAGC 1 chrX:7773723-7773803 ( 12) GGCAGCGC 1 chrI:11374409-11374489 ( 46) GGCCGAGC 1 chrIII:5769874-5769954 ( 38) GGCCGAGC 1 chrX:9637822-9637902 ( 72) GGGAGCGC 1 chrII:14617092-14617172 ( 5) GGTAGCGC 1 chrIII:5853357-5853437 ( 62) GGCCGCGC 1 chrV:18712288-18712368 ( 54) GGCAGACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGYAGAGC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 8906 bayes= 9.08228 E= 1.4e-005 -1081 -1081 213 -1081 -1081 -1081 213 -1081 -1081 127 -4 -6 161 -32 -1081 -1081 -1081 -1081 213 -1081 151 10 -1081 -1081 -1081 -190 205 -1081 -1081 227 -1081 -1081 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGYAGAGC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 18 E= 1.4e-005 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.222222 0.277778 0.833333 0.166667 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.777778 0.222222 0.000000 0.000000 0.000000 0.055556 0.944444 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGYAGAGC MEME-2 regular expression -------------------------------------------------------------------------------- GG[CTG]AG[AC]GC -------------------------------------------------------------------------------- Time 3.03 secs. ******************************************************************************** ******************************************************************************** MOTIF TAGCTCAG MEME-3 width = 8 sites = 10 llr = 108 E-value = 2.1e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif TAGCTCAG MEME-3 Description -------------------------------------------------------------------------------- Simplified A :9::::a: pos.-specific C :::a:a:: probability G ::a::::a matrix T a1::a::: bits 2.3 * * 2.0 ** * * 1.8 * ****** 1.6 * ****** Relative 1.4 ******** Entropy 1.1 ******** (15.6 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel TAGCTCAG consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAGCTCAG MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIII:5305869-5305949 43 1.42e-05 GGCGCCCTTA TAGCTCAG TGGTAGAGCG chrV:19126020-19126100 31 1.42e-05 TCTGCCTCGA TAGCTCAG TTGGGAGAGC chrX:6593565-6593645 38 1.42e-05 ACTGCCTCGA TAGCTCAG TTGGGAGAGC chrI:6136591-6136671 13 1.42e-05 GCCGCCCGGT TAGCTCAG TCGGTAGAGC chrX:14804849-14804929 35 1.42e-05 CACGGGGGTA TAGCTCAG TGGCAGAGCA chrV:9318174-9318254 35 1.42e-05 CGTGGGGGTA TAGCTCAG GGGTAGAGCG chrV:6335368-6335448 37 1.42e-05 TCGTGGGGTA TAGCTCAG TGGCAGAGCA chrX:8638896-8638976 33 1.42e-05 TGTGGGGGTA TAGCTCAG TGGCAGAGCA chrIV:5038870-5038950 57 1.42e-05 TGGGCCTCCT TAGCTCAG TTGGTAGAGC chrX:13655842-13655922 31 2.92e-05 GTAGTTTAAC TTGCTCAG TAGTCACAAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAGCTCAG MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIII:5305869-5305949 1.4e-05 42_[+3]_30 chrV:19126020-19126100 1.4e-05 30_[+3]_42 chrX:6593565-6593645 1.4e-05 37_[+3]_35 chrI:6136591-6136671 1.4e-05 12_[+3]_60 chrX:14804849-14804929 1.4e-05 34_[+3]_38 chrV:9318174-9318254 1.4e-05 34_[+3]_38 chrV:6335368-6335448 1.4e-05 36_[+3]_36 chrX:8638896-8638976 1.4e-05 32_[+3]_40 chrIV:5038870-5038950 1.4e-05 56_[+3]_16 chrX:13655842-13655922 2.9e-05 30_[+3]_42 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAGCTCAG MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TAGCTCAG width=8 seqs=10 chrIII:5305869-5305949 ( 43) TAGCTCAG 1 chrV:19126020-19126100 ( 31) TAGCTCAG 1 chrX:6593565-6593645 ( 38) TAGCTCAG 1 chrI:6136591-6136671 ( 13) TAGCTCAG 1 chrX:14804849-14804929 ( 35) TAGCTCAG 1 chrV:9318174-9318254 ( 35) TAGCTCAG 1 chrV:6335368-6335448 ( 37) TAGCTCAG 1 chrX:8638896-8638976 ( 33) TAGCTCAG 1 chrIV:5038870-5038950 ( 57) TAGCTCAG 1 chrX:13655842-13655922 ( 31) TTGCTCAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAGCTCAG MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 8906 bayes= 10.0488 E= 2.1e-003 -997 -997 -997 178 172 -997 -997 -154 -997 -997 213 -997 -997 227 -997 -997 -997 -997 -997 178 -997 227 -997 -997 187 -997 -997 -997 -997 -997 213 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAGCTCAG MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 10 E= 2.1e-003 0.000000 0.000000 0.000000 1.000000 0.900000 0.000000 0.000000 0.100000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAGCTCAG MEME-3 regular expression -------------------------------------------------------------------------------- TAGCTCAG -------------------------------------------------------------------------------- Time 4.19 secs. ******************************************************************************** ******************************************************************************** MOTIF YCTCTCCC MEME-4 width = 8 sites = 10 llr = 99 E-value = 2.6e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif YCTCTCCC MEME-4 Description -------------------------------------------------------------------------------- Simplified A ::::3::: pos.-specific C 5a:a:a8a probability G ::::::2: matrix T 5:a:7::: bits 2.3 * * * * 2.0 * * * * 1.8 *** * * 1.6 *** *** Relative 1.4 *** *** Entropy 1.1 **** *** (14.3 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel CCTCTCCC consensus T A G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCTCTCCC MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:9637822-9637902 57 6.66e-06 GAACCCCAGC CCTCTCCC ATGCTAAGGG chrX:12458134-12458214 69 6.66e-06 GAACCCCAGC CCTCTCCC ATGC chrIII:7494945-7495025 6 6.66e-06 TCCGA CCTCTCCC GTCACCGCAA chrX:7507253-7507333 64 6.66e-06 GAACCCCAGC CCTCTCCC ATGCTAAGG chrIV:5038870-5038950 3 1.60e-05 TG TCTCTCCC CCCGCTCTTC chrII:5293482-5293562 2 3.11e-05 C TCTCACCC ATAAGGCCGG chrI:11978761-11978841 35 3.11e-05 GATTTATGGC TCTCACCC ATAAGGCCGG chrX:7681030-7681110 42 3.11e-05 GATTTATGGC TCTCACCC ATAAGGCCGG chrX:1880823-1880903 21 3.85e-05 GAACCCGGGA CCTCTCGC ACCCGAAGCG chrIII:5305869-5305949 22 4.88e-05 TCTAATCACT TCTCTCGC CGCGGCGCCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCTCTCCC MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:9637822-9637902 6.7e-06 56_[+4]_16 chrX:12458134-12458214 6.7e-06 68_[+4]_4 chrIII:7494945-7495025 6.7e-06 5_[+4]_67 chrX:7507253-7507333 6.7e-06 63_[+4]_9 chrIV:5038870-5038950 1.6e-05 2_[+4]_70 chrII:5293482-5293562 3.1e-05 1_[+4]_71 chrI:11978761-11978841 3.1e-05 34_[+4]_38 chrX:7681030-7681110 3.1e-05 41_[+4]_31 chrX:1880823-1880903 3.8e-05 20_[+4]_52 chrIII:5305869-5305949 4.9e-05 21_[+4]_51 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCTCTCCC MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF YCTCTCCC width=8 seqs=10 chrX:9637822-9637902 ( 57) CCTCTCCC 1 chrX:12458134-12458214 ( 69) CCTCTCCC 1 chrIII:7494945-7495025 ( 6) CCTCTCCC 1 chrX:7507253-7507333 ( 64) CCTCTCCC 1 chrIV:5038870-5038950 ( 3) TCTCTCCC 1 chrII:5293482-5293562 ( 2) TCTCACCC 1 chrI:11978761-11978841 ( 35) TCTCACCC 1 chrX:7681030-7681110 ( 42) TCTCACCC 1 chrX:1880823-1880903 ( 21) CCTCTCGC 1 chrIII:5305869-5305949 ( 22) TCTCTCGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCTCTCCC MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 8906 bayes= 10.7412 E= 2.6e+001 -997 127 -997 78 -997 227 -997 -997 -997 -997 -997 178 -997 227 -997 -997 13 -997 -997 127 -997 227 -997 -997 -997 195 -19 -997 -997 227 -997 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCTCTCCC MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 10 E= 2.6e+001 0.000000 0.500000 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.300000 0.000000 0.000000 0.700000 0.000000 1.000000 0.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCTCTCCC MEME-4 regular expression -------------------------------------------------------------------------------- [CT]CTC[TA]C[CG]C -------------------------------------------------------------------------------- Time 5.41 secs. ******************************************************************************** ******************************************************************************** MOTIF CTCCGTWG MEME-5 width = 8 sites = 7 llr = 75 E-value = 1.0e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTCCGTWG MEME-5 Description -------------------------------------------------------------------------------- Simplified A ::::::6: pos.-specific C a:aa:::: probability G ::::a::a matrix T :a:::a4: bits 2.3 * ** 2.0 * *** * 1.8 ****** * 1.6 ****** * Relative 1.4 ****** * Entropy 1.1 ****** * (15.5 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel CTCCGTAG consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCCGTWG MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIV:12417890-12417970 70 1.07e-05 CAATCTTCTG CTCCGTAG GCA chrX:10018396-10018476 63 1.07e-05 caatcttctg ctccgtag gcagacgcgt chrIII:4449502-4449582 65 1.07e-05 CAATCTTCTG CTCCGTAG GCAGACGC chrX:8640813-8640893 15 1.07e-05 CAATCTTCTG CTCCGTAG GCAGACGCGT chrI:11978761-11978841 2 2.21e-05 G CTCCGTTG TGGTCTAGTG chrX:16558882-16558962 59 2.21e-05 ATTTTCTCGT CTCCGTTG TGGTCTAGTG chrX:7681030-7681110 9 2.21e-05 TCACCCAT CTCCGTTG TGGTCTAGTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCCGTWG MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIV:12417890-12417970 1.1e-05 69_[+5]_3 chrX:10018396-10018476 1.1e-05 62_[+5]_10 chrIII:4449502-4449582 1.1e-05 64_[+5]_8 chrX:8640813-8640893 1.1e-05 14_[+5]_58 chrI:11978761-11978841 2.2e-05 1_[+5]_71 chrX:16558882-16558962 2.2e-05 58_[+5]_14 chrX:7681030-7681110 2.2e-05 8_[+5]_64 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCCGTWG MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CTCCGTWG width=8 seqs=7 chrIV:12417890-12417970 ( 70) CTCCGTAG 1 chrX:10018396-10018476 ( 63) CTCCGTAG 1 chrIII:4449502-4449582 ( 65) CTCCGTAG 1 chrX:8640813-8640893 ( 15) CTCCGTAG 1 chrI:11978761-11978841 ( 2) CTCCGTTG 1 chrX:16558882-16558962 ( 59) CTCCGTTG 1 chrX:7681030-7681110 ( 9) CTCCGTTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCCGTWG MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 8906 bayes= 10.1558 E= 1.0e+002 -945 227 -945 -945 -945 -945 -945 178 -945 227 -945 -945 -945 227 -945 -945 -945 -945 213 -945 -945 -945 -945 178 106 -945 -945 56 -945 -945 213 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCCGTWG MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 7 E= 1.0e+002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.571429 0.000000 0.000000 0.428571 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCCGTWG MEME-5 regular expression -------------------------------------------------------------------------------- CTCCGT[AT]G -------------------------------------------------------------------------------- Time 8.05 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrV:265725-265805 9.57e-01 80 chrM:8799-8879 7.84e-01 80 chrV:265394-265474 7.35e-01 80 chrX:7507253-7507333 6.50e-04 51_[+1(8.94e-05)]_4_[+4(6.66e-06)]_\ 9 chrV:17687571-17687651 4.07e-01 80 chrIV:13549483-13549563 9.78e-01 80 chrX:8640813-8640893 9.53e-03 14_[+5(1.07e-05)]_58 chrX:7681030-7681110 3.71e-05 8_[+5(2.21e-05)]_25_[+4(3.11e-05)]_\ 13_[+1(6.58e-05)]_10 chrX:5709413-5709493 8.08e-02 80 chrM:3262-3342 7.64e-01 80 chrII:2570712-2570792 1.00e+00 80 chrIII:4449502-4449582 3.08e-04 45_[+1(5.22e-05)]_11_[+5(1.07e-05)]_\ 8 chrV:18712288-18712368 2.76e-01 53_[+2(8.94e-05)]_19 chrIV:16775183-16775263 1.17e-01 51_[+1(6.58e-05)]_21 chrM:8480-8560 4.84e-01 80 chrX:8838228-8838308 9.97e-01 80 chrX:10124493-10124573 2.27e-01 80 chrIV:4930953-4931033 9.80e-01 80 chrM:10112-10192 9.99e-01 80 chrII:14617092-14617172 1.18e-02 4_[+2(6.01e-05)]_68 chrM:10819-10899 9.57e-01 80 chrX:9024354-9024434 7.09e-01 80 chrI:11803284-11803364 5.74e-04 46_[+1(5.22e-05)]_5_[+2(8.69e-06)]_\ 13 chrV:9091517-9091597 1.41e-01 80 chrM:2992-3072 8.02e-01 80 chrIII:1600861-1600941 9.70e-01 80 chrV:5284759-5284839 9.71e-01 80 chrM:5965-6045 3.94e-01 80 chrX:3793525-3793605 1.90e-01 80 chrX:7773723-7773803 1.06e-03 11_[+2(3.71e-05)]_29_[+1(3.93e-05)]_\ 24 chrII:12541734-12541814 3.61e-01 80 chrX:11993319-11993399 7.07e-01 80 chrV:18707260-18707340 9.99e-01 80 chrIV:12005511-12005591 7.61e-01 80 chrM:4911-4991 8.63e-01 80 chrII:11966354-11966434 9.31e-01 80 chrX:13653800-13653880 8.83e-01 80 chrIV:873347-873427 6.80e-01 80 chrV:13567063-13567143 6.73e-01 80 chrII:14409853-14409933 3.57e-01 80 chrIII:10746519-10746599 1.92e-01 80 chrIII:7494945-7495025 1.89e-02 5_[+4(6.66e-06)]_67 chrV:20847742-20847822 1.86e-01 80 chrIII:931567-931647 9.92e-01 80 chrM:2109-2189 9.89e-01 80 chrM:7191-7271 9.68e-01 80 chrM:9106-9186 9.59e-01 80 chrX:16619379-16619459 9.19e-01 80 chrX:13655842-13655922 1.45e-02 30_[+3(2.92e-05)]_42 chrX:16558882-16558962 2.21e-02 58_[+5(2.21e-05)]_14 chrV:16593394-16593474 7.23e-01 80 chrX:8971622-8971702 1.00e-02 40_[+1(2.20e-05)]_32 chrX:6286370-6286450 1.17e-01 3_[+1(6.58e-05)]_69 chrII:8441656-8441736 9.21e-01 80 chrX:14478868-14478948 1.10e-02 23_[+1(9.15e-06)]_49 chrIII:5853357-5853437 1.71e-01 61_[+2(8.15e-05)]_11 chrM:4634-4714 9.96e-01 80 chrIV:5038870-5038950 3.83e-07 2_[+4(1.60e-05)]_46_[+3(1.42e-05)]_\ 2_[+2(3.05e-05)]_6 chrIV:14576601-14576681 9.17e-03 35_[+1(9.15e-06)]_37 chrX:10018396-10018476 3.28e-04 43_[+1(5.22e-05)]_11_[+5(1.07e-05)]_\ 10 chrM:1205-1285 4.41e-01 80 chrX:8638896-8638976 1.30e-04 32_[+3(1.42e-05)]_1_[+2(8.69e-06)]_\ 31 chrX:4445040-4445120 1.17e-01 26_[+1(6.58e-05)]_46 chrV:18412425-18412505 5.94e-01 80 chrIII:7642220-7642300 9.90e-01 80 chrM:12382-12462 2.83e-01 80 chrX:6867819-6867899 8.38e-01 80 chrX:8939665-8939745 9.06e-01 80 chrX:8638635-8638715 1.46e-01 80 chrX:16378032-16378112 1.00e+00 80 chrM:2313-2393 8.68e-01 80 chrII:11880671-11880751 1.68e-01 80 chrV:18710289-18710369 7.62e-01 80 chrX:13781712-13781792 9.81e-01 80 chrIII:1616687-1616767 5.79e-01 80 chrII:5353829-5353909 5.46e-01 80 chrIV:16776057-16776137 2.55e-01 80 chrI:7872166-7872246 6.35e-01 80 chrI:11978761-11978841 3.71e-05 1_[+5(2.21e-05)]_25_[+4(3.11e-05)]_\ 13_[+1(6.58e-05)]_17 chrX:4444233-4444313 5.83e-01 80 chrV:12510126-12510206 9.58e-01 80 chrIII:13188110-13188190 7.99e-01 80 chrX:8650685-8650765 5.37e-02 80 chrV:3686051-3686131 7.62e-01 80 chrIII:3869469-3869549 9.68e-01 80 chrI:852202-852282 4.09e-01 80 chrIII:12250662-12250742 4.69e-01 80 chrX:5713708-5713788 9.36e-01 80 chrX:16931396-16931476 9.19e-01 80 chrIII:5769874-5769954 9.22e-02 37_[+2(4.36e-05)]_35 chrV:6335368-6335448 2.45e-05 36_[+3(1.42e-05)]_1_[+2(8.69e-06)]_\ 27 chrX:10145176-10145256 2.25e-02 33_[+1(2.20e-05)]_39 chrIV:6481144-6481224 7.84e-03 70_[+1(9.15e-06)]_2 chrV:9318174-9318254 4.41e-04 34_[+3(1.42e-05)]_1_[+2(3.05e-05)]_\ 29 chrIV:12417890-12417970 1.35e-03 50_[+1(5.22e-05)]_11_[+5(1.07e-05)]_\ 3 chrX:10821379-10821459 6.58e-01 80 chrIV:16399237-16399317 8.41e-01 80 chrX:9078307-9078387 5.54e-01 80 chrII:5293482-5293562 2.21e-03 1_[+4(3.11e-05)]_13_[+1(6.58e-05)]_\ 50 chrX:12458134-12458214 8.53e-04 56_[+1(8.94e-05)]_4_[+4(6.66e-06)]_\ 4 chrIII:12614807-12614887 3.47e-01 80 chrIV:9477702-9477782 7.55e-01 80 chrII:8547123-8547203 3.77e-01 80 chrX:14804849-14804929 7.44e-05 34_[+3(1.42e-05)]_1_[+2(8.69e-06)]_\ 29 chrI:11584716-11584796 1.18e-01 80 chrX:16928290-16928370 6.11e-02 80 chrIV:9191299-9191379 6.91e-01 80 chrIV:14225090-14225170 4.06e-01 80 chrIV:991314-991394 8.05e-03 3_[+2(3.05e-05)]_69 chrI:6136591-6136671 3.43e-06 12_[+3(1.42e-05)]_2_[+2(3.05e-05)]_\ 29_[+1(3.93e-05)]_13 chrX:6593565-6593645 2.10e-04 37_[+3(1.42e-05)]_2_[+2(3.05e-05)]_\ 25 chrII:11157765-11157845 4.46e-02 51_[+1(9.15e-06)]_21 chrX:1880823-1880903 1.21e-03 8_[+1(9.15e-06)]_4_[+4(3.85e-05)]_\ 52 chrV:19126020-19126100 8.26e-05 30_[+3(1.42e-05)]_2_[+2(3.05e-05)]_\ 32 chrIII:1601602-1601682 3.80e-01 80 chrIV:11026162-11026242 7.59e-01 80 chrX:11757827-11757907 2.07e-02 18_[+1(9.15e-06)]_54 chrI:11374409-11374489 2.30e-02 45_[+2(4.36e-05)]_27 chrIII:5305869-5305949 2.12e-06 21_[+4(4.88e-05)]_13_[+3(1.42e-05)]_\ 1_[+2(3.05e-05)]_21 chrX:9637822-9637902 1.06e-05 44_[+1(8.94e-05)]_4_[+4(6.66e-06)]_\ 7_[+2(6.01e-05)]_1 chrX:14115706-14115786 3.98e-02 38_[+1(8.94e-05)]_34 chrX:6292271-6292351 2.21e-03 21_[+1(9.15e-06)]_51 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c27n05.farnam.hpc.yale.internal ********************************************************************************