******************************************************************************** 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/lin-11.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chrM:12014-12094 1.0000 80 chrM:3973-4053 1.0000 80 chrM:169-249 1.0000 80 chrM:7605-7685 1.0000 80 chrM:5537-5617 1.0000 80 chrM:12719-12799 1.0000 80 chrM:337-417 1.0000 80 chrM:5737-5817 1.0000 80 chrM:2771-2851 1.0000 80 chrX:5056376-5056456 1.0000 80 chrI:10252758-10252838 1.0000 80 chrX:8603144-8603224 1.0000 80 chrI:10260304-10260384 1.0000 80 chrI:933475-933555 1.0000 80 chrM:11380-11460 1.0000 80 chrX:8602900-8602980 1.0000 80 chrIII:931566-931646 1.0000 80 chrM:6393-6473 1.0000 80 chrM:9668-9748 1.0000 80 chrV:1821418-1821498 1.0000 80 chrM:9456-9536 1.0000 80 chrI:10248234-10248314 1.0000 80 chrM:10810-10890 1.0000 80 chrIV:15289703-15289783 1.0000 80 chrIV:14576643-14576723 1.0000 80 chrIV:1981159-1981239 1.0000 80 chrX:8156127-8156207 1.0000 80 chrIV:11071021-11071101 1.0000 80 chrI:9249362-9249442 1.0000 80 chrV:19343512-19343592 1.0000 80 chrV:16622049-16622129 1.0000 80 chrIII:3499991-3500071 1.0000 80 chrIV:14013870-14013950 1.0000 80 chrM:6950-7030 1.0000 80 chrV:16699889-16699969 1.0000 80 chrM:8330-8410 1.0000 80 chrI:11584749-11584829 1.0000 80 chrM:1304-1384 1.0000 80 chrII:2570631-2570711 1.0000 80 chrIII:1218389-1218469 1.0000 80 chrIII:3620866-3620946 1.0000 80 chrV:19637613-19637693 1.0000 80 chrI:12225470-12225550 1.0000 80 chrIII:445713-445793 1.0000 80 chrI:10235289-10235369 1.0000 80 chrV:3587780-3587860 1.0000 80 chrV:13869058-13869138 1.0000 80 chrII:5399335-5399415 1.0000 80 chrV:12510128-12510208 1.0000 80 chrII:4130280-4130360 1.0000 80 chrX:3994591-3994671 1.0000 80 chrII:13986222-13986302 1.0000 80 chrV:19722960-19723040 1.0000 80 chrV:14876368-14876448 1.0000 80 chrI:3567655-3567735 1.0000 80 chrI:10237374-10237454 1.0000 80 chrIII:3664400-3664480 1.0000 80 chrIII:8650372-8650452 1.0000 80 chrV:3098995-3099075 1.0000 80 chrX:9296773-9296853 1.0000 80 chrV:4499262-4499342 1.0000 80 chrX:8969823-8969903 1.0000 80 chrIII:4542535-4542615 1.0000 80 chrV:13176503-13176583 1.0000 80 chrX:13577895-13577975 1.0000 80 chrIII:1122395-1122475 1.0000 80 chrIII:12399839-12399919 1.0000 80 chrI:8530104-8530184 1.0000 80 chrII:6848475-6848555 1.0000 80 chrII:5293438-5293518 1.0000 80 chrV:7231039-7231119 1.0000 80 chrI:1575666-1575746 1.0000 80 chrII:7001611-7001691 1.0000 80 chrIV:11928541-11928621 1.0000 80 chrII:8128886-8128966 1.0000 80 chrI:6136571-6136651 1.0000 80 chrM:4688-4768 1.0000 80 chrV:8785767-8785847 1.0000 80 chrX:16040533-16040613 1.0000 80 chrX:14115655-14115735 1.0000 80 chrM:9248-9328 1.0000 80 chrIV:5334718-5334798 1.0000 80 chrII:10743797-10743877 1.0000 80 chrII:6565247-6565327 1.0000 80 chrI:2180138-2180218 1.0000 80 chrII:14249582-14249662 1.0000 80 chrI:14804998-14805078 1.0000 80 chrIII:11875994-11876074 1.0000 80 chrIII:8971827-8971907 1.0000 80 chrI:1836540-1836620 1.0000 80 chrI:11978735-11978815 1.0000 80 chrV:14855824-14855904 1.0000 80 chrIV:6576068-6576148 1.0000 80 chrII:7676310-7676390 1.0000 80 chrIV:2639825-2639905 1.0000 80 chrI:7474898-7474978 1.0000 80 chrX:12890259-12890339 1.0000 80 chrIII:1824652-1824732 1.0000 80 chrV:9583089-9583169 1.0000 80 chrIII:7444913-7444993 1.0000 80 chrX:16602569-16602649 1.0000 80 chrX:17611214-17611294 1.0000 80 chrM:12512-12592 1.0000 80 chrIII:10432296-10432376 1.0000 80 chrV:16553067-16553147 1.0000 80 chrV:14504925-14505005 1.0000 80 chrX:4962468-4962548 1.0000 80 chrI:6532077-6532157 1.0000 80 chrIII:3175121-3175201 1.0000 80 chrIV:16863611-16863691 1.0000 80 chrII:4238060-4238140 1.0000 80 chrX:14229616-14229696 1.0000 80 chrIII:3476338-3476418 1.0000 80 chrX:13415103-13415183 1.0000 80 chrV:15553967-15554047 1.0000 80 chrIII:7030555-7030635 1.0000 80 chrV:11933473-11933553 1.0000 80 chrI:14606042-14606122 1.0000 80 chrI:5300742-5300822 1.0000 80 chrIII:1601587-1601667 1.0000 80 chrX:3348019-3348099 1.0000 80 chrII:7708746-7708826 1.0000 80 chrI:9268983-9269063 1.0000 80 chrIV:16399158-16399238 1.0000 80 chrIII:5769839-5769919 1.0000 80 chrI:4132282-4132362 1.0000 80 chrIII:13105962-13106042 1.0000 80 chrX:13143385-13143465 1.0000 80 chrIII:8106632-8106712 1.0000 80 chrI:4633639-4633719 1.0000 80 chrIV:842804-842884 1.0000 80 chrX:13653801-13653881 1.0000 80 chrX:16928316-16928396 1.0000 80 chrI:13421184-13421264 1.0000 80 chrIV:1388241-1388321 1.0000 80 chrIV:16388457-16388537 1.0000 80 chrI:1175860-1175940 1.0000 80 chrI:11505491-11505571 1.0000 80 chrX:12367661-12367741 1.0000 80 chrIII:2576882-2576962 1.0000 80 chrX:16944158-16944238 1.0000 80 chrII:3521483-3521563 1.0000 80 chrII:6721709-6721789 1.0000 80 chrIV:16776061-16776141 1.0000 80 chrV:4648145-4648225 1.0000 80 chrX:8386142-8386222 1.0000 80 chrI:488392-488472 1.0000 80 chrIII:535358-535438 1.0000 80 chrX:7794506-7794586 1.0000 80 chrIII:6805540-6805620 1.0000 80 chrIII:11236931-11237011 1.0000 80 chrI:11609168-11609248 1.0000 80 chrII:3567733-3567813 1.0000 80 chrIV:9316181-9316261 1.0000 80 chrIII:9052654-9052734 1.0000 80 chrI:13310286-13310366 1.0000 80 chrX:8646469-8646549 1.0000 80 chrII:6898156-6898236 1.0000 80 chrIII:13225235-13225315 1.0000 80 chrIII:10624775-10624855 1.0000 80 chrII:5577157-5577237 1.0000 80 chrI:2292945-2293025 1.0000 80 chrIV:5038936-5039016 1.0000 80 chrII:6859053-6859133 1.0000 80 chrV:53439-53519 1.0000 80 chrII:6248633-6248713 1.0000 80 chrX:8971622-8971702 1.0000 80 chrI:12065861-12065941 1.0000 80 chrIV:620458-620538 1.0000 80 chrV:13962153-13962233 1.0000 80 chrV:4731526-4731606 1.0000 80 chrIV:11310762-11310842 1.0000 80 chrX:4444913-4444993 1.0000 80 chrIV:3233085-3233165 1.0000 80 chrI:7712655-7712735 1.0000 80 chrII:10303926-10304006 1.0000 80 chrIV:2993329-2993409 1.0000 80 chrX:10821310-10821390 1.0000 80 chrIII:9104202-9104282 1.0000 80 chrX:9078311-9078391 1.0000 80 chrV:12780415-12780495 1.0000 80 chrI:10807294-10807374 1.0000 80 chrIV:9191333-9191413 1.0000 80 chrV:15551825-15551905 1.0000 80 chrI:14721596-14721676 1.0000 80 chrX:14804879-14804959 1.0000 80 chrIII:8768031-8768111 1.0000 80 chrI:3873924-3874004 1.0000 80 chrX:6286255-6286335 1.0000 80 chrV:19126013-19126093 1.0000 80 chrII:4942479-4942559 1.0000 80 chrV:20694121-20694201 1.0000 80 chrI:1481590-1481670 1.0000 80 chrIII:8653055-8653135 1.0000 80 chrX:5707989-5708069 1.0000 80 chrI:10927459-10927539 1.0000 80 chrIV:16865685-16865765 1.0000 80 chrX:5319374-5319454 1.0000 80 chrIII:3916793-3916873 1.0000 80 chrV:2674028-2674108 1.0000 80 chrIV:9477711-9477791 1.0000 80 chrIII:7642180-7642260 1.0000 80 chrII:8547089-8547169 1.0000 80 chrX:8638898-8638978 1.0000 80 chrIII:4568695-4568775 1.0000 80 chrX:17610460-17610540 1.0000 80 chrX:6903184-6903264 1.0000 80 chrX:12843659-12843739 1.0000 80 chrII:14635389-14635469 1.0000 80 chrV:6709216-6709296 1.0000 80 chrIV:11026156-11026236 1.0000 80 chrM:2099-2179 1.0000 80 chrX:4444265-4444345 1.0000 80 chrI:9605743-9605823 1.0000 80 chrX:9622806-9622886 1.0000 80 chrX:6220130-6220210 1.0000 80 chrIV:7789613-7789693 1.0000 80 chrIII:5211266-5211346 1.0000 80 chrX:1858827-1858907 1.0000 80 chrIV:3552204-3552284 1.0000 80 chrIII:4171145-4171225 1.0000 80 chrX:1837870-1837950 1.0000 80 chrI:11323334-11323414 1.0000 80 chrI:1823115-1823195 1.0000 80 chrII:11959387-11959467 1.0000 80 chrI:13161030-13161110 1.0000 80 chrIII:5211468-5211548 1.0000 80 chrII:9566164-9566244 1.0000 80 chrIII:4369515-4369595 1.0000 80 chrX:9637833-9637913 1.0000 80 chrV:1474746-1474826 1.0000 80 chrI:1958525-1958605 1.0000 80 chrX:6371340-6371420 1.0000 80 chrIII:6133433-6133513 1.0000 80 chrI:9267093-9267173 1.0000 80 chrI:6091078-6091158 1.0000 80 chrIII:1604698-1604778 1.0000 80 chrIV:3524792-3524872 1.0000 80 chrIV:10374049-10374129 1.0000 80 chrX:11252643-11252723 1.0000 80 chrX:15297529-15297609 1.0000 80 chrX:10963761-10963841 1.0000 80 chrIII:6158747-6158827 1.0000 80 chrII:6047806-6047886 1.0000 80 chrIII:4426751-4426831 1.0000 80 chrI:2410114-2410194 1.0000 80 chrII:14063262-14063342 1.0000 80 chrIII:5555103-5555183 1.0000 80 chrIV:143950-144030 1.0000 80 chrIV:17087584-17087664 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_lin-11/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/worm/fasta/RankLinear2.0_40/lin-11.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= 20000 N= 250 sample: seed= 0 hsfrac= 0 searchsize= 20000 norand= no csites= 1000 Letter frequencies in dataset: A 0.25 C 0.233 G 0.24 T 0.277 Background letter frequencies (from file dataset with add-one prior applied): A 0.25 C 0.233 G 0.24 T 0.277 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF AGTGGTTA MEME-1 width = 8 sites = 19 llr = 201 E-value = 1.9e-010 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGTGGTTA MEME-1 Description -------------------------------------------------------------------------------- Simplified A a::::::a pos.-specific C ::::::1: probability G :a:aa::: matrix T ::a::a9: bits 2.1 * ** 1.9 ****** * 1.7 ****** * 1.5 ******** Relative 1.3 ******** Entropy 1.1 ******** (15.3 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel AGTGGTTA consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGTGGTTA MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIII:6158747-6158827 44 1.84e-05 GTCATGTCCG AGTGGTTA AGGAGATTGA chrI:13161030-13161110 44 1.84e-05 CTCGTGGTGT AGTGGTTA TCACATCTGT chrII:11959387-11959467 1 1.84e-05 . AGTGGTTA TCACGTCTGC chrX:1858827-1858907 5 1.84e-05 GTCT AGTGGTTA GGATTCGTGG chrI:9605743-9605823 26 1.84e-05 GCGATGTCCG AGTGGTTA AGGAGTTGGA chrX:4444265-4444345 10 1.84e-05 ATGTGGTCT AGTGGTTA GGATTCGTGG chrX:12843659-12843739 42 1.84e-05 CTCGTGGTGT AGTGGTTA TCACATCTGT chrX:5707989-5708069 52 1.84e-05 CAGGTGGCCG AGTGGTTA AGGCGATGGA chrIV:620458-620538 37 1.84e-05 CCTCTGGTGT AGTGGTTA TCACGTCTGC chrI:12065861-12065941 17 1.84e-05 CTCGTGGTGT AGTGGTTA TCACATCTGT chrV:53439-53519 50 1.84e-05 cgcatggccg agtggtta gtacgtatgc chrII:6898156-6898236 51 1.84e-05 CATGTGGTCT AGTGGTTA GGATTCGTGG chrX:8646469-8646549 24 1.84e-05 CATGTGGTCT AGTGGTTA GGATTCGTGG chrIV:16388457-16388537 12 1.84e-05 TGCGTAGTAT AGTGGTTA GTACTCCACG chrIV:842804-842884 18 1.84e-05 CATGTGGTCT AGTGGTTA GGATTCGTGG chrI:11978735-11978815 42 1.84e-05 GTTGTGGTCT AGTGGTTA GGATTTATGG chrII:5293438-5293518 27 1.84e-05 GTTGTGGTCT AGTGGTTA GGATTTATGG chrIII:11875994-11876074 60 3.38e-05 GAGGGCAACA AGTGGTCA AGTGAAACTG chrIV:15289703-15289783 64 3.38e-05 CGATCCGCTC AGTGGTCA AAGTTTTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGTGGTTA MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIII:6158747-6158827 1.8e-05 43_[+1]_29 chrI:13161030-13161110 1.8e-05 43_[+1]_29 chrII:11959387-11959467 1.8e-05 [+1]_72 chrX:1858827-1858907 1.8e-05 4_[+1]_68 chrI:9605743-9605823 1.8e-05 25_[+1]_47 chrX:4444265-4444345 1.8e-05 9_[+1]_63 chrX:12843659-12843739 1.8e-05 41_[+1]_31 chrX:5707989-5708069 1.8e-05 51_[+1]_21 chrIV:620458-620538 1.8e-05 36_[+1]_36 chrI:12065861-12065941 1.8e-05 16_[+1]_56 chrV:53439-53519 1.8e-05 49_[+1]_23 chrII:6898156-6898236 1.8e-05 50_[+1]_22 chrX:8646469-8646549 1.8e-05 23_[+1]_49 chrIV:16388457-16388537 1.8e-05 11_[+1]_61 chrIV:842804-842884 1.8e-05 17_[+1]_55 chrI:11978735-11978815 1.8e-05 41_[+1]_31 chrII:5293438-5293518 1.8e-05 26_[+1]_46 chrIII:11875994-11876074 3.4e-05 59_[+1]_13 chrIV:15289703-15289783 3.4e-05 63_[+1]_9 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGTGGTTA MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AGTGGTTA width=8 seqs=19 chrIII:6158747-6158827 ( 44) AGTGGTTA 1 chrI:13161030-13161110 ( 44) AGTGGTTA 1 chrII:11959387-11959467 ( 1) AGTGGTTA 1 chrX:1858827-1858907 ( 5) AGTGGTTA 1 chrI:9605743-9605823 ( 26) AGTGGTTA 1 chrX:4444265-4444345 ( 10) AGTGGTTA 1 chrX:12843659-12843739 ( 42) AGTGGTTA 1 chrX:5707989-5708069 ( 52) AGTGGTTA 1 chrIV:620458-620538 ( 37) AGTGGTTA 1 chrI:12065861-12065941 ( 17) AGTGGTTA 1 chrV:53439-53519 ( 50) AGTGGTTA 1 chrII:6898156-6898236 ( 51) AGTGGTTA 1 chrX:8646469-8646549 ( 24) AGTGGTTA 1 chrIV:16388457-16388537 ( 12) AGTGGTTA 1 chrIV:842804-842884 ( 18) AGTGGTTA 1 chrI:11978735-11978815 ( 42) AGTGGTTA 1 chrII:5293438-5293518 ( 27) AGTGGTTA 1 chrIII:11875994-11876074 ( 60) AGTGGTCA 1 chrIV:15289703-15289783 ( 64) AGTGGTCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGTGGTTA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 10.1012 E= 1.9e-010 200 -1089 -1089 -1089 -1089 -1089 206 -1089 -1089 -1089 -1089 185 -1089 -1089 206 -1089 -1089 -1089 206 -1089 -1089 -1089 -1089 185 -1089 -114 -1089 169 200 -1089 -1089 -1089 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGTGGTTA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 1.9e-010 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.105263 0.000000 0.894737 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGTGGTTA MEME-1 regular expression -------------------------------------------------------------------------------- AGTGGTTA -------------------------------------------------------------------------------- Time 7.96 secs. ******************************************************************************** ******************************************************************************** MOTIF CTCCGCCC MEME-2 width = 8 sites = 27 llr = 247 E-value = 1.9e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTCCGCCC MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C a2aa2aa8 probability G :1::7::2 matrix T :7::1::: bits 2.1 * ** ** 1.9 * ** ** 1.7 * ** ** 1.5 * ** ** Relative 1.3 * ** *** Entropy 1.1 * ** *** (13.2 bits) 0.8 * ****** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel CTCCGCCC consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCCGCCC MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrI:11323334-11323414 72 1.06e-05 AATTGAGCCA CTCCGCCC C chrIII:4171145-4171225 66 1.06e-05 GCAAAGAACG CTCCGCCC ACAAACA chrI:14721596-14721676 6 1.06e-05 CGAGT CTCCGCCC CTTTGCAATG chrIII:11236931-11237011 36 1.06e-05 CATTGCCTGC CTCCGCCC CGCCCACATT chrI:4132282-4132362 37 1.06e-05 CCGAGCAAGT CTCCGCCC ACTTTAACCG chrI:14606042-14606122 41 1.06e-05 CACCCCCTGG CTCCGCCC ATTTTTCTGC chrII:4238060-4238140 64 1.06e-05 TGCAACTTAG CTCCGCCC ACCCTTTGA chrI:9249362-9249442 53 1.06e-05 GGGGTTGAGA CTCCGCCC ACCGCAAGGC chrI:10248234-10248314 7 1.06e-05 CAATAA CTCCGCCC ATCAACCAGC chrV:1821418-1821498 20 1.06e-05 AAATACCCGA CTCCGCCC ACATGCAAGG chrIV:16865685-16865765 63 1.96e-05 ATTTACGAAG CCCCGCCC AAGAATTTTT chrIII:4542535-4542615 55 1.96e-05 GCCGTTTTAG CCCCGCCC CTTGAAATAT chrIV:2993329-2993409 51 4.09e-05 cccccccccc ctcccccc GTGTCGGGGT chrV:3587780-3587860 54 4.09e-05 GATTTCGCAA CTCCGCCG CACAGTTTTA chrIV:11310762-11310842 61 5.31e-05 GGGCGTGTAA CTCCTCCC CATAATTCGT chrI:14804998-14805078 47 5.31e-05 CCCCCTCCTC CTCCTCCC CACCATCATC chrX:14115655-14115735 20 5.31e-05 GGCAAACGAC CTCCTCCC ACTTTCGTGG chrI:6136571-6136651 22 6.24e-05 CATGTTGTGT CGCCGCCC GGTTAGCTCA chrI:11584749-11584829 34 6.24e-05 TAAGAGTTAA CGCCGCCC GGTTAGCTCA chrI:1836540-1836620 36 8.03e-05 GGCATATATC CCCCGCCG GCCCCCGAAA chrV:19722960-19723040 56 8.03e-05 GCCCTTCCCT CCCCGCCG ACCATCGGCT chrX:3994591-3994671 71 8.03e-05 GGTTCGATTC CCCCCCCC CC chrI:2180138-2180218 53 9.09e-05 TGGTGGGGAA CTCCCCCG CTTTTTCTCT chrI:10235289-10235369 43 9.09e-05 ACGCAGTACC CTCCCCCG GCGCTGCATT chrIII:5555103-5555183 64 1.23e-04 ACTCATTAAG CACCGCCC ATTTAGTTT chrV:4648145-4648225 25 1.23e-04 CATCCACCGC CTCCTCCG GATGGGAGGA chrV:14504925-14505005 56 1.42e-04 GGGAGGAGGG CGCCCCCC GAGTAATACC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCCGCCC MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrI:11323334-11323414 1.1e-05 71_[+2]_1 chrIII:4171145-4171225 1.1e-05 65_[+2]_7 chrI:14721596-14721676 1.1e-05 5_[+2]_67 chrIII:11236931-11237011 1.1e-05 35_[+2]_37 chrI:4132282-4132362 1.1e-05 36_[+2]_36 chrI:14606042-14606122 1.1e-05 40_[+2]_32 chrII:4238060-4238140 1.1e-05 63_[+2]_9 chrI:9249362-9249442 1.1e-05 52_[+2]_20 chrI:10248234-10248314 1.1e-05 6_[+2]_66 chrV:1821418-1821498 1.1e-05 19_[+2]_53 chrIV:16865685-16865765 2e-05 62_[+2]_10 chrIII:4542535-4542615 2e-05 54_[+2]_18 chrIV:2993329-2993409 4.1e-05 50_[+2]_22 chrV:3587780-3587860 4.1e-05 53_[+2]_19 chrIV:11310762-11310842 5.3e-05 60_[+2]_12 chrI:14804998-14805078 5.3e-05 46_[+2]_26 chrX:14115655-14115735 5.3e-05 19_[+2]_53 chrI:6136571-6136651 6.2e-05 21_[+2]_51 chrI:11584749-11584829 6.2e-05 33_[+2]_39 chrI:1836540-1836620 8e-05 35_[+2]_37 chrV:19722960-19723040 8e-05 55_[+2]_17 chrX:3994591-3994671 8e-05 70_[+2]_2 chrI:2180138-2180218 9.1e-05 52_[+2]_20 chrI:10235289-10235369 9.1e-05 42_[+2]_30 chrIII:5555103-5555183 0.00012 63_[+2]_9 chrV:4648145-4648225 0.00012 24_[+2]_48 chrV:14504925-14505005 0.00014 55_[+2]_17 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCCGCCC MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CTCCGCCC width=8 seqs=27 chrI:11323334-11323414 ( 72) CTCCGCCC 1 chrIII:4171145-4171225 ( 66) CTCCGCCC 1 chrI:14721596-14721676 ( 6) CTCCGCCC 1 chrIII:11236931-11237011 ( 36) CTCCGCCC 1 chrI:4132282-4132362 ( 37) CTCCGCCC 1 chrI:14606042-14606122 ( 41) CTCCGCCC 1 chrII:4238060-4238140 ( 64) CTCCGCCC 1 chrI:9249362-9249442 ( 53) CTCCGCCC 1 chrI:10248234-10248314 ( 7) CTCCGCCC 1 chrV:1821418-1821498 ( 20) CTCCGCCC 1 chrIV:16865685-16865765 ( 63) CCCCGCCC 1 chrIII:4542535-4542615 ( 55) CCCCGCCC 1 chrIV:2993329-2993409 ( 51) CTCCCCCC 1 chrV:3587780-3587860 ( 54) CTCCGCCG 1 chrIV:11310762-11310842 ( 61) CTCCTCCC 1 chrI:14804998-14805078 ( 47) CTCCTCCC 1 chrX:14115655-14115735 ( 20) CTCCTCCC 1 chrI:6136571-6136651 ( 22) CGCCGCCC 1 chrI:11584749-11584829 ( 34) CGCCGCCC 1 chrI:1836540-1836620 ( 36) CCCCGCCG 1 chrV:19722960-19723040 ( 56) CCCCGCCG 1 chrX:3994591-3994671 ( 71) CCCCCCCC 1 chrI:2180138-2180218 ( 53) CTCCCCCG 1 chrI:10235289-10235369 ( 43) CTCCCCCG 1 chrIII:5555103-5555183 ( 64) CACCGCCC 1 chrV:4648145-4648225 ( 25) CTCCTCCG 1 chrV:14504925-14505005 ( 56) CGCCCCCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCCGCCC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 11.3477 E= 1.9e-006 -1140 210 -1140 -1140 -275 -33 -111 127 -1140 210 -1140 -1140 -1140 210 -1140 -1140 -1140 -33 147 -90 -1140 210 -1140 -1140 -1140 210 -1140 -1140 -1140 174 -11 -1140 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCCGCCC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 1.9e-006 0.000000 1.000000 0.000000 0.000000 0.037037 0.185185 0.111111 0.666667 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.185185 0.666667 0.148148 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.777778 0.222222 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCCGCCC MEME-2 regular expression -------------------------------------------------------------------------------- CTCCGCC[CG] -------------------------------------------------------------------------------- Time 11.65 secs. ******************************************************************************** ******************************************************************************** MOTIF YGYGCGGC MEME-3 width = 8 sites = 33 llr = 291 E-value = 3.0e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif YGYGCGGC MEME-3 Description -------------------------------------------------------------------------------- Simplified A :2:::::: pos.-specific C 6:5:81:a probability G :8:a29a: matrix T 4:5::::: bits 2.1 * ** 1.9 * ** 1.7 * *** 1.5 ***** Relative 1.3 * ***** Entropy 1.1 ******** (12.7 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel CGTGCGGC consensus TAC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YGYGCGGC MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIII:4171145-4171225 20 9.78e-06 ATGTCATCTG CGCGCGGC ATATCTGCAA chrIII:4568695-4568775 28 9.78e-06 ATGAAAATGT CGCGCGGC GGAATTGCGA chrV:13962153-13962233 54 9.78e-06 GCATAAACTG CGCGCGGC AACTGCAAAA chrIV:16865685-16865765 31 2.14e-05 TGCAAAACCC CGTGCGGC ACAATTGCGT chrI:3873924-3874004 17 2.14e-05 CCATGACTTT Cgtgcggc gagattgcga chrIV:9316181-9316261 40 2.14e-05 TGAATAAAAC CGTGCGGC GGAATTGCGA chrI:4132282-4132362 53 2.14e-05 CCACTTTAAC CGTGCGGC GTGCAGCGTT chrII:4238060-4238140 42 2.14e-05 TGCGAAAATG CGTGCGGC GCGTTGCAAC chrIII:1824652-1824732 48 2.14e-05 AACTAAACCC CGTGCGGC GCTCTTGCAA chrIV:11310762-11310842 32 3.30e-05 AGAGGAAAAG TGCGCGGC GGGCTTGCAG chrI:14606042-14606122 16 3.30e-05 GCTGGAAAAG TGCGCGGC AGACTTGCAC chrIII:4542535-4542615 13 3.30e-05 ATAGAAAAAA TGCGCGGC GTGCTTGCAA chrI:1958525-1958605 43 4.68e-05 TGCGCAACGG TGTGCGGC GGCCTTGCAG chrI:11323334-11323414 25 4.68e-05 ATGTCAAGTG TGTGCGGC GGTTTGCAAA chrIII:3916793-3916873 16 4.68e-05 ACCTAAAGTG TGTGCGGC GACTTTGCAA chrIII:8768031-8768111 51 4.68e-05 CTGAGTAAAC TGTGCGGC GTGTTTGCGG chrIII:11236931-11237011 16 4.68e-05 TGGAAAAAAG TGTGCGGC GGCATTGCCT chrIII:3175121-3175201 39 4.68e-05 CTCTTAACTC TGTGCGGC ACCATTGCGG chrII:5399335-5399415 34 4.68e-05 AGCTGCACAC TGTGCGGC ACAATTGCGA chrX:11252643-11252723 11 5.70e-05 TCCATTGCGC CACGCGGC CACACAGACT chrX:1858827-1858907 31 5.70e-05 GGTTTTCACC CACGCGGC CCGGGTTCGA chrX:6220130-6220210 4 5.70e-05 CGC CACGCGGC CACATTTTCA chrX:4444265-4444345 36 5.70e-05 GGTTTTCACC CACGCGGC CCGGGTTCGA chrX:8646469-8646549 50 5.70e-05 GGTTTTCACC CACGCGGC CCGGGTTCGA chrIV:842804-842884 44 5.70e-05 GGTTTTCACC CACGCGGC CCGGGTTCGA chrIII:5555103-5555183 13 7.92e-05 CCAAACTGTG CGCGGGGC ACTTGCGCAA chrIII:10432296-10432376 41 1.03e-04 GGTTCAAACC TACGCGGC CCCCATTATC chrIII:3499991-3500071 20 1.03e-04 TTCCCGCTTT CGTGGGGC CTCAAACCCG chrII:3567733-3567813 38 1.30e-04 GTAAGCCCAA TGCGGGGC TCGAACCCGC chrIV:14013870-14013950 24 1.30e-04 TTTATTGGTT TGCGGGGC GGCTTCGAAT chrI:1836540-1836620 1 1.44e-04 . TGTGGGGC GCGTCGTCGT chrX:12367661-12367741 64 1.65e-04 GACGAGAGAC CGTGCCGC ATCGGAATA chrIV:1981159-1981239 10 1.65e-04 CCACTTTTC CGTGCCGC ATCGCAAATA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YGYGCGGC MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIII:4171145-4171225 9.8e-06 19_[+3]_53 chrIII:4568695-4568775 9.8e-06 27_[+3]_45 chrV:13962153-13962233 9.8e-06 53_[+3]_19 chrIV:16865685-16865765 2.1e-05 30_[+3]_42 chrI:3873924-3874004 2.1e-05 16_[+3]_56 chrIV:9316181-9316261 2.1e-05 39_[+3]_33 chrI:4132282-4132362 2.1e-05 52_[+3]_20 chrII:4238060-4238140 2.1e-05 41_[+3]_31 chrIII:1824652-1824732 2.1e-05 47_[+3]_25 chrIV:11310762-11310842 3.3e-05 31_[+3]_41 chrI:14606042-14606122 3.3e-05 15_[+3]_57 chrIII:4542535-4542615 3.3e-05 12_[+3]_60 chrI:1958525-1958605 4.7e-05 42_[+3]_30 chrI:11323334-11323414 4.7e-05 24_[+3]_48 chrIII:3916793-3916873 4.7e-05 15_[+3]_57 chrIII:8768031-8768111 4.7e-05 50_[+3]_22 chrIII:11236931-11237011 4.7e-05 15_[+3]_57 chrIII:3175121-3175201 4.7e-05 38_[+3]_34 chrII:5399335-5399415 4.7e-05 33_[+3]_39 chrX:11252643-11252723 5.7e-05 10_[+3]_62 chrX:1858827-1858907 5.7e-05 30_[+3]_42 chrX:6220130-6220210 5.7e-05 3_[+3]_69 chrX:4444265-4444345 5.7e-05 35_[+3]_37 chrX:8646469-8646549 5.7e-05 49_[+3]_23 chrIV:842804-842884 5.7e-05 43_[+3]_29 chrIII:5555103-5555183 7.9e-05 12_[+3]_60 chrIII:10432296-10432376 0.0001 40_[+3]_32 chrIII:3499991-3500071 0.0001 19_[+3]_53 chrII:3567733-3567813 0.00013 37_[+3]_35 chrIV:14013870-14013950 0.00013 23_[+3]_49 chrI:1836540-1836620 0.00014 [+3]_72 chrX:12367661-12367741 0.00016 63_[+3]_9 chrIV:1981159-1981239 0.00016 9_[+3]_63 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YGYGCGGC MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF YGYGCGGC width=8 seqs=33 chrIII:4171145-4171225 ( 20) CGCGCGGC 1 chrIII:4568695-4568775 ( 28) CGCGCGGC 1 chrV:13962153-13962233 ( 54) CGCGCGGC 1 chrIV:16865685-16865765 ( 31) CGTGCGGC 1 chrI:3873924-3874004 ( 17) CGTGCGGC 1 chrIV:9316181-9316261 ( 40) CGTGCGGC 1 chrI:4132282-4132362 ( 53) CGTGCGGC 1 chrII:4238060-4238140 ( 42) CGTGCGGC 1 chrIII:1824652-1824732 ( 48) CGTGCGGC 1 chrIV:11310762-11310842 ( 32) TGCGCGGC 1 chrI:14606042-14606122 ( 16) TGCGCGGC 1 chrIII:4542535-4542615 ( 13) TGCGCGGC 1 chrI:1958525-1958605 ( 43) TGTGCGGC 1 chrI:11323334-11323414 ( 25) TGTGCGGC 1 chrIII:3916793-3916873 ( 16) TGTGCGGC 1 chrIII:8768031-8768111 ( 51) TGTGCGGC 1 chrIII:11236931-11237011 ( 16) TGTGCGGC 1 chrIII:3175121-3175201 ( 39) TGTGCGGC 1 chrII:5399335-5399415 ( 34) TGTGCGGC 1 chrX:11252643-11252723 ( 11) CACGCGGC 1 chrX:1858827-1858907 ( 31) CACGCGGC 1 chrX:6220130-6220210 ( 4) CACGCGGC 1 chrX:4444265-4444345 ( 36) CACGCGGC 1 chrX:8646469-8646549 ( 50) CACGCGGC 1 chrIV:842804-842884 ( 44) CACGCGGC 1 chrIII:5555103-5555183 ( 13) CGCGGGGC 1 chrIII:10432296-10432376 ( 41) TACGCGGC 1 chrIII:3499991-3500071 ( 20) CGTGGGGC 1 chrII:3567733-3567813 ( 38) TGCGGGGC 1 chrIV:14013870-14013950 ( 24) TGCGGGGC 1 chrI:1836540-1836620 ( 1) TGTGGGGC 1 chrX:12367661-12367741 ( 64) CGTGCCGC 1 chrIV:1981159-1981239 ( 10) CGTGCCGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YGYGCGGC MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 10.8621 E= 3.0e-008 -1169 131 -1169 62 -24 -1169 171 -1169 -1169 106 -1169 90 -1169 -1169 206 -1169 -1169 187 -66 -1169 -1169 -194 197 -1169 -1169 -1169 206 -1169 -1169 210 -1169 -1169 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YGYGCGGC MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 33 E= 3.0e-008 0.000000 0.575758 0.000000 0.424242 0.212121 0.000000 0.787879 0.000000 0.000000 0.484848 0.000000 0.515152 0.000000 0.000000 1.000000 0.000000 0.000000 0.848485 0.151515 0.000000 0.000000 0.060606 0.939394 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YGYGCGGC MEME-3 regular expression -------------------------------------------------------------------------------- [CT][GA][TC]GCGGC -------------------------------------------------------------------------------- Time 15.34 secs. ******************************************************************************** ******************************************************************************** MOTIF GGGTTCGA MEME-4 width = 8 sites = 19 llr = 189 E-value = 2.2e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGGTTCGA MEME-4 Description -------------------------------------------------------------------------------- Simplified A 2::::::a pos.-specific C :1:::a:: probability G 69a:::a: matrix T 2::aa::: bits 2.1 * ** 1.9 ****** 1.7 ******* 1.5 ******* Relative 1.3 ******* Entropy 1.1 ******* (14.4 bits) 0.8 ******* 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel GGGTTCGA consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGTTCGA MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:1858827-1858907 41 1.48e-05 CACGCGGCCC GGGTTCGA TTCCCGGCAT chrX:4444265-4444345 46 1.48e-05 CACGCGGCCC GGGTTCGA TTCCCGGCAT chrIV:5038936-5039016 34 1.48e-05 TTAAGGTCAG GGGTTCGA GTCCCCTAGG chrII:5577157-5577237 54 1.48e-05 GGTCCTAGCC GGGTTCGA ACCGGCGATC chrX:8646469-8646549 60 1.48e-05 CACGCGGCCC GGGTTCGA TTCCCGGCAT chrIII:2576882-2576962 45 1.48e-05 ATTAACAGCA GGGTTCGA GCCTTTCTTG chrIV:842804-842884 54 1.48e-05 CACGCGGCCC GGGTTCGA TTCCCGGCAT chrII:6565247-6565327 51 1.48e-05 TTAAGGTCAG GGGTTCGA GTCCCCTAGG chrII:7001611-7001691 65 1.48e-05 GAGAAGTCTG GGGTTCGA TTCCCCAT chrII:5293438-5293518 63 1.48e-05 CATAAGGCCG GGGTTCGA TTCCCCGCAA chrX:3994591-3994671 60 1.48e-05 CATTCGACGG GGGTTCGA TTCCCCCCCC chrI:2410114-2410194 60 3.19e-05 TGTAGCGCGC TGGTTCGA TCCCCACCAA chrV:2674028-2674108 31 3.19e-05 AGAAGGTCGC TGGTTCGA TTCCAGCATG chrI:12065861-12065941 54 3.19e-05 AGAAGGTCGG TGGTTCGA GCCCGCCCGA chrIV:16388457-16388537 48 3.19e-05 GTGGCGACGC TGGTTCGA TTCCAGCCGC chrI:9605743-9605823 72 4.74e-05 TTGCCCGCGT AGGTTCGA A chrX:8971622-8971702 37 4.74e-05 CTGCCCGCGT AGGTTCGA ATCCTGCTGA chrII:6248633-6248713 65 4.74e-05 CACACAATGT AGGTTCGA CCCCCGCT chrX:6371340-6371420 60 6.18e-05 CAATGGTAGC GCGTTCGA CTCCAGATCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGTTCGA MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:1858827-1858907 1.5e-05 40_[+4]_32 chrX:4444265-4444345 1.5e-05 45_[+4]_27 chrIV:5038936-5039016 1.5e-05 33_[+4]_39 chrII:5577157-5577237 1.5e-05 53_[+4]_19 chrX:8646469-8646549 1.5e-05 59_[+4]_13 chrIII:2576882-2576962 1.5e-05 44_[+4]_28 chrIV:842804-842884 1.5e-05 53_[+4]_19 chrII:6565247-6565327 1.5e-05 50_[+4]_22 chrII:7001611-7001691 1.5e-05 64_[+4]_8 chrII:5293438-5293518 1.5e-05 62_[+4]_10 chrX:3994591-3994671 1.5e-05 59_[+4]_13 chrI:2410114-2410194 3.2e-05 59_[+4]_13 chrV:2674028-2674108 3.2e-05 30_[+4]_42 chrI:12065861-12065941 3.2e-05 53_[+4]_19 chrIV:16388457-16388537 3.2e-05 47_[+4]_25 chrI:9605743-9605823 4.7e-05 71_[+4]_1 chrX:8971622-8971702 4.7e-05 36_[+4]_36 chrII:6248633-6248713 4.7e-05 64_[+4]_8 chrX:6371340-6371420 6.2e-05 59_[+4]_13 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGTTCGA MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGGTTCGA width=8 seqs=19 chrX:1858827-1858907 ( 41) GGGTTCGA 1 chrX:4444265-4444345 ( 46) GGGTTCGA 1 chrIV:5038936-5039016 ( 34) GGGTTCGA 1 chrII:5577157-5577237 ( 54) GGGTTCGA 1 chrX:8646469-8646549 ( 60) GGGTTCGA 1 chrIII:2576882-2576962 ( 45) GGGTTCGA 1 chrIV:842804-842884 ( 54) GGGTTCGA 1 chrII:6565247-6565327 ( 51) GGGTTCGA 1 chrII:7001611-7001691 ( 65) GGGTTCGA 1 chrII:5293438-5293518 ( 63) GGGTTCGA 1 chrX:3994591-3994671 ( 60) GGGTTCGA 1 chrI:2410114-2410194 ( 60) TGGTTCGA 1 chrV:2674028-2674108 ( 31) TGGTTCGA 1 chrI:12065861-12065941 ( 54) TGGTTCGA 1 chrIV:16388457-16388537 ( 48) TGGTTCGA 1 chrI:9605743-9605823 ( 72) AGGTTCGA 1 chrX:8971622-8971702 ( 37) AGGTTCGA 1 chrII:6248633-6248713 ( 65) AGGTTCGA 1 chrX:6371340-6371420 ( 60) GCGTTCGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGTTCGA MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 9.27554 E= 2.2e-005 -66 -1089 139 -39 -1089 -214 198 -1089 -1089 -1089 206 -1089 -1089 -1089 -1089 185 -1089 -1089 -1089 185 -1089 210 -1089 -1089 -1089 -1089 206 -1089 200 -1089 -1089 -1089 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGTTCGA MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 2.2e-005 0.157895 0.000000 0.631579 0.210526 0.000000 0.052632 0.947368 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGTTCGA MEME-4 regular expression -------------------------------------------------------------------------------- [GT]GGTTCGA -------------------------------------------------------------------------------- Time 18.85 secs. ******************************************************************************** ******************************************************************************** MOTIF TAGCTCAG MEME-5 width = 8 sites = 14 llr = 150 E-value = 3.7e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif TAGCTCAG MEME-5 Description -------------------------------------------------------------------------------- Simplified A :a::::a: pos.-specific C :::a:a:: probability G ::a:1::a matrix T a:::9::: bits 2.1 ** * * 1.9 **** *** 1.7 **** *** 1.5 **** *** Relative 1.3 ******** Entropy 1.1 ******** (15.5 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel TAGCTCAG consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAGCTCAG MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:8638898-8638978 31 1.50e-05 TGTGGGGGTA TAGCTCAG TGGCAGAGCA chrIII:8653055-8653135 7 1.50e-05 CCTCGA TAGCTCAG TTGGGAGAGC chrV:19126013-19126093 38 1.50e-05 TCTGCCTCGA TAGCTCAG TTGGGAGAGC chrX:6286255-6286335 73 1.50e-05 TGCGGGGGTA TAGCTCAG chrX:14804879-14804959 5 1.50e-05 GGTA TAGCTCAG TGGCAGAGCA chrIII:535358-535438 31 1.50e-05 GTGCCGTCGA TAGCTCAG TTGGTAGAGC chrI:11505491-11505571 67 1.50e-05 ATCGGGGGTA TAGCTCAG TGGCAG chrIV:16399158-16399238 33 1.50e-05 TGCGGGGGTA TAGCTCAG TGGTAGAGCG chrII:6565247-6565327 8 1.50e-05 GCCTCCT TAGCTCAG TTGGTAGAGC chrI:6136571-6136651 33 1.50e-05 GCCGCCCGGT TAGCTCAG TCGGTAGAGC chrII:7001611-7001691 23 1.50e-05 GTTACCTGTG TAGCTCAG GGGTAGAGCG chrI:11584749-11584829 45 1.50e-05 GCCGCCCGGT TAGCTCAG TCGGTAGAGC chrIII:8106632-8106712 28 2.80e-05 GCCGCTTCCG TAGCGCAG TAGGCAGCGC chrIII:1122395-1122475 46 2.80e-05 TGTTGCCGTT TAGCGCAG GCGGGAGTGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAGCTCAG MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:8638898-8638978 1.5e-05 30_[+5]_42 chrIII:8653055-8653135 1.5e-05 6_[+5]_66 chrV:19126013-19126093 1.5e-05 37_[+5]_35 chrX:6286255-6286335 1.5e-05 72_[+5] chrX:14804879-14804959 1.5e-05 4_[+5]_68 chrIII:535358-535438 1.5e-05 30_[+5]_42 chrI:11505491-11505571 1.5e-05 66_[+5]_6 chrIV:16399158-16399238 1.5e-05 32_[+5]_40 chrII:6565247-6565327 1.5e-05 7_[+5]_65 chrI:6136571-6136651 1.5e-05 32_[+5]_40 chrII:7001611-7001691 1.5e-05 22_[+5]_50 chrI:11584749-11584829 1.5e-05 44_[+5]_28 chrIII:8106632-8106712 2.8e-05 27_[+5]_45 chrIII:1122395-1122475 2.8e-05 45_[+5]_27 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAGCTCAG MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TAGCTCAG width=8 seqs=14 chrX:8638898-8638978 ( 31) TAGCTCAG 1 chrIII:8653055-8653135 ( 7) TAGCTCAG 1 chrV:19126013-19126093 ( 38) TAGCTCAG 1 chrX:6286255-6286335 ( 73) TAGCTCAG 1 chrX:14804879-14804959 ( 5) TAGCTCAG 1 chrIII:535358-535438 ( 31) TAGCTCAG 1 chrI:11505491-11505571 ( 67) TAGCTCAG 1 chrIV:16399158-16399238 ( 33) TAGCTCAG 1 chrII:6565247-6565327 ( 8) TAGCTCAG 1 chrI:6136571-6136651 ( 33) TAGCTCAG 1 chrII:7001611-7001691 ( 23) TAGCTCAG 1 chrI:11584749-11584829 ( 45) TAGCTCAG 1 chrIII:8106632-8106712 ( 28) TAGCGCAG 1 chrIII:1122395-1122475 ( 46) TAGCGCAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAGCTCAG MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 10.1909 E= 3.7e-004 -1045 -1045 -1045 185 200 -1045 -1045 -1045 -1045 -1045 206 -1045 -1045 210 -1045 -1045 -1045 -1045 -75 163 -1045 210 -1045 -1045 200 -1045 -1045 -1045 -1045 -1045 206 -1045 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAGCTCAG MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 14 E= 3.7e-004 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.142857 0.857143 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-5 regular expression -------------------------------------------------------------------------------- TAGCTCAG -------------------------------------------------------------------------------- Time 22.32 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrM:12014-12094 9.01e-01 80 chrM:3973-4053 3.06e-01 80 chrM:169-249 9.99e-01 80 chrM:7605-7685 9.51e-01 80 chrM:5537-5617 8.70e-01 80 chrM:12719-12799 1.00e+00 80 chrM:337-417 8.21e-01 80 chrM:5737-5817 1.00e+00 80 chrM:2771-2851 6.93e-01 80 chrX:5056376-5056456 9.58e-01 80 chrI:10252758-10252838 9.98e-01 80 chrX:8603144-8603224 7.91e-01 80 chrI:10260304-10260384 7.66e-01 80 chrI:933475-933555 9.64e-01 80 chrM:11380-11460 1.00e+00 80 chrX:8602900-8602980 1.00e+00 80 chrIII:931566-931646 6.62e-01 80 chrM:6393-6473 8.32e-01 80 chrM:9668-9748 9.34e-01 80 chrV:1821418-1821498 1.48e-02 19_[+2(1.06e-05)]_53 chrM:9456-9536 9.41e-01 80 chrI:10248234-10248314 2.40e-02 6_[+2(1.06e-05)]_66 chrM:10810-10890 8.97e-01 80 chrIV:15289703-15289783 4.23e-04 21_[+4(6.18e-05)]_19_[+4(6.18e-05)]_\ 7_[+1(3.38e-05)]_9 chrIV:14576643-14576723 9.24e-01 80 chrIV:1981159-1981239 2.70e-01 80 chrX:8156127-8156207 7.97e-02 80 chrIV:11071021-11071101 1.00e+00 80 chrI:9249362-9249442 8.27e-03 52_[+2(1.06e-05)]_20 chrV:19343512-19343592 9.78e-01 80 chrV:16622049-16622129 5.42e-01 80 chrIII:3499991-3500071 9.65e-02 80 chrIV:14013870-14013950 1.84e-02 80 chrM:6950-7030 1.00e+00 80 chrV:16699889-16699969 6.11e-01 80 chrM:8330-8410 8.89e-01 80 chrI:11584749-11584829 5.20e-04 33_[+2(6.24e-05)]_3_[+5(1.50e-05)]_\ 28 chrM:1304-1384 1.00e+00 80 chrII:2570631-2570711 1.00e+00 80 chrIII:1218389-1218469 7.44e-01 80 chrIII:3620866-3620946 3.94e-01 80 chrV:19637613-19637693 9.23e-01 80 chrI:12225470-12225550 2.74e-01 80 chrIII:445713-445793 9.24e-01 80 chrI:10235289-10235369 1.34e-01 42_[+2(9.09e-05)]_30 chrV:3587780-3587860 6.74e-03 53_[+2(4.09e-05)]_19 chrV:13869058-13869138 7.96e-01 80 chrII:5399335-5399415 2.73e-01 33_[+3(4.68e-05)]_39 chrV:12510128-12510208 9.99e-01 80 chrII:4130280-4130360 1.00e+00 80 chrX:3994591-3994671 2.36e-03 59_[+4(1.48e-05)]_2_[+2(8.03e-05)]_\ 3 chrII:13986222-13986302 1.00e+00 80 chrV:19722960-19723040 3.10e-01 55_[+2(8.03e-05)]_17 chrV:14876368-14876448 2.73e-01 80 chrI:3567655-3567735 9.88e-01 80 chrI:10237374-10237454 3.60e-01 80 chrIII:3664400-3664480 1.39e-01 80 chrIII:8650372-8650452 3.38e-01 80 chrV:3098995-3099075 1.00e+00 80 chrX:9296773-9296853 2.49e-01 80 chrV:4499262-4499342 8.79e-01 80 chrX:8969823-8969903 9.96e-01 80 chrIII:4542535-4542615 5.67e-04 12_[+3(3.30e-05)]_34_[+2(1.96e-05)]_\ 18 chrV:13176503-13176583 1.30e-01 80 chrX:13577895-13577975 9.99e-01 80 chrIII:1122395-1122475 1.48e-03 45_[+5(2.80e-05)]_27 chrIII:12399839-12399919 5.34e-01 80 chrI:8530104-8530184 1.70e-01 80 chrII:6848475-6848555 9.75e-01 80 chrII:5293438-5293518 3.83e-04 26_[+1(1.84e-05)]_28_[+4(1.48e-05)]_\ 10 chrV:7231039-7231119 8.70e-01 80 chrI:1575666-1575746 4.59e-01 80 chrII:7001611-7001691 5.75e-04 22_[+5(1.50e-05)]_34_[+4(1.48e-05)]_\ 8 chrIV:11928541-11928621 5.28e-01 80 chrII:8128886-8128966 5.85e-01 80 chrI:6136571-6136651 4.82e-04 21_[+2(6.24e-05)]_3_[+5(1.50e-05)]_\ 40 chrM:4688-4768 7.71e-01 80 chrV:8785767-8785847 3.97e-02 80 chrX:16040533-16040613 5.60e-01 80 chrX:14115655-14115735 1.66e-02 19_[+2(5.31e-05)]_53 chrM:9248-9328 9.48e-01 80 chrIV:5334718-5334798 9.16e-02 80 chrII:10743797-10743877 9.96e-01 80 chrII:6565247-6565327 3.44e-04 7_[+5(1.50e-05)]_35_[+4(1.48e-05)]_\ 22 chrI:2180138-2180218 1.75e-01 52_[+2(9.09e-05)]_20 chrII:14249582-14249662 1.57e-01 80 chrI:14804998-14805078 9.49e-02 46_[+2(5.31e-05)]_26 chrIII:11875994-11876074 1.03e-01 59_[+1(3.38e-05)]_13 chrIII:8971827-8971907 9.53e-01 80 chrI:1836540-1836620 2.76e-02 35_[+2(8.03e-05)]_37 chrI:11978735-11978815 1.15e-02 41_[+1(1.84e-05)]_31 chrV:14855824-14855904 4.29e-01 80 chrIV:6576068-6576148 1.00e+00 80 chrII:7676310-7676390 9.85e-01 80 chrIV:2639825-2639905 4.91e-01 80 chrI:7474898-7474978 9.82e-01 80 chrX:12890259-12890339 7.98e-01 80 chrIII:1824652-1824732 5.11e-02 47_[+3(2.14e-05)]_25 chrV:9583089-9583169 8.01e-01 80 chrIII:7444913-7444993 8.34e-01 80 chrX:16602569-16602649 3.21e-01 80 chrX:17611214-17611294 7.49e-01 80 chrM:12512-12592 9.93e-01 80 chrIII:10432296-10432376 2.38e-02 80 chrV:16553067-16553147 9.54e-01 80 chrV:14504925-14505005 6.43e-02 80 chrX:4962468-4962548 3.95e-01 80 chrI:6532077-6532157 4.94e-01 80 chrIII:3175121-3175201 8.43e-02 38_[+3(4.68e-05)]_34 chrIV:16863611-16863691 3.95e-02 80 chrII:4238060-4238140 5.01e-05 18_[+3(2.14e-05)]_15_[+3(2.14e-05)]_\ 14_[+2(1.06e-05)]_9 chrX:14229616-14229696 9.95e-01 80 chrIII:3476338-3476418 7.97e-01 80 chrX:13415103-13415183 1.07e-01 80 chrV:15553967-15554047 7.26e-01 80 chrIII:7030555-7030635 6.31e-01 80 chrV:11933473-11933553 9.78e-01 80 chrI:14606042-14606122 6.21e-04 15_[+3(3.30e-05)]_17_[+2(1.06e-05)]_\ 32 chrI:5300742-5300822 5.09e-01 80 chrIII:1601587-1601667 9.93e-01 80 chrX:3348019-3348099 1.18e-01 80 chrII:7708746-7708826 3.85e-01 80 chrI:9268983-9269063 2.69e-01 80 chrIV:16399158-16399238 9.93e-03 32_[+5(1.50e-05)]_40 chrIII:5769839-5769919 4.59e-01 80 chrI:4132282-4132362 1.11e-04 11_[+3(3.30e-05)]_17_[+2(1.06e-05)]_\ 8_[+3(2.14e-05)]_20 chrIII:13105962-13106042 6.30e-01 80 chrX:13143385-13143465 8.70e-01 80 chrIII:8106632-8106712 2.31e-03 27_[+5(2.80e-05)]_45 chrI:4633639-4633719 3.09e-01 80 chrIV:842804-842884 5.92e-06 17_[+1(1.84e-05)]_18_[+3(5.70e-05)]_\ 2_[+4(1.48e-05)]_19 chrX:13653801-13653881 7.96e-01 80 chrX:16928316-16928396 3.05e-01 80 chrI:13421184-13421264 4.41e-02 80 chrIV:1388241-1388321 5.54e-01 80 chrIV:16388457-16388537 1.06e-03 11_[+1(1.84e-05)]_28_[+4(3.19e-05)]_\ 25 chrI:1175860-1175940 3.47e-01 80 chrI:11505491-11505571 3.89e-02 66_[+5(1.50e-05)]_6 chrX:12367661-12367741 2.64e-01 80 chrIII:2576882-2576962 1.34e-01 44_[+4(1.48e-05)]_28 chrX:16944158-16944238 7.45e-01 80 chrII:3521483-3521563 2.85e-01 80 chrII:6721709-6721789 7.86e-01 80 chrIV:16776061-16776141 1.10e-01 80 chrV:4648145-4648225 1.39e-01 80 chrX:8386142-8386222 2.21e-01 80 chrI:488392-488472 7.60e-01 80 chrIII:535358-535438 1.06e-02 30_[+5(1.50e-05)]_42 chrX:7794506-7794586 3.55e-01 80 chrIII:6805540-6805620 1.23e-01 80 chrIII:11236931-11237011 2.80e-03 15_[+3(4.68e-05)]_12_[+2(1.06e-05)]_\ 37 chrI:11609168-11609248 9.70e-01 80 chrII:3567733-3567813 2.30e-02 80 chrIV:9316181-9316261 3.38e-02 39_[+3(2.14e-05)]_33 chrIII:9052654-9052734 4.06e-01 80 chrI:13310286-13310366 3.76e-01 80 chrX:8646469-8646549 5.87e-06 23_[+1(1.84e-05)]_18_[+3(5.70e-05)]_\ 2_[+4(1.48e-05)]_13 chrII:6898156-6898236 1.37e-02 50_[+1(1.84e-05)]_22 chrIII:13225235-13225315 7.32e-01 80 chrIII:10624775-10624855 6.87e-01 80 chrII:5577157-5577237 9.05e-02 53_[+4(1.48e-05)]_19 chrI:2292945-2293025 5.15e-01 80 chrIV:5038936-5039016 1.25e-02 33_[+4(1.48e-05)]_39 chrII:6859053-6859133 9.83e-01 80 chrV:53439-53519 4.98e-02 49_[+1(1.84e-05)]_23 chrII:6248633-6248713 5.45e-03 64_[+4(4.74e-05)]_8 chrX:8971622-8971702 2.27e-02 36_[+4(4.74e-05)]_36 chrI:12065861-12065941 8.77e-05 16_[+1(1.84e-05)]_29_[+4(3.19e-05)]_\ 19 chrIV:620458-620538 1.23e-01 36_[+1(1.84e-05)]_36 chrV:13962153-13962233 6.23e-02 53_[+3(9.78e-06)]_19 chrV:4731526-4731606 5.66e-01 80 chrIV:11310762-11310842 3.21e-03 31_[+3(3.30e-05)]_21_[+2(5.31e-05)]_\ 12 chrX:4444913-4444993 6.60e-01 80 chrIV:3233085-3233165 7.81e-01 80 chrI:7712655-7712735 7.57e-01 80 chrII:10303926-10304006 7.67e-01 80 chrIV:2993329-2993409 1.20e-01 39_[+2(8.03e-05)]_3_[+2(4.09e-05)]_\ 22 chrX:10821310-10821390 5.77e-01 80 chrIII:9104202-9104282 4.51e-02 80 chrX:9078311-9078391 9.43e-01 80 chrV:12780415-12780495 9.20e-01 80 chrI:10807294-10807374 8.23e-01 80 chrIV:9191333-9191413 8.92e-01 80 chrV:15551825-15551905 8.28e-01 80 chrI:14721596-14721676 1.08e-02 5_[+2(1.06e-05)]_67 chrX:14804879-14804959 6.42e-03 4_[+5(1.50e-05)]_68 chrIII:8768031-8768111 2.59e-01 50_[+3(4.68e-05)]_22 chrI:3873924-3874004 4.13e-02 16_[+3(2.14e-05)]_56 chrX:6286255-6286335 1.47e-02 72_[+5(1.50e-05)] chrV:19126013-19126093 2.34e-02 37_[+5(1.50e-05)]_35 chrII:4942479-4942559 9.29e-01 80 chrV:20694121-20694201 7.51e-01 80 chrI:1481590-1481670 9.90e-01 80 chrIII:8653055-8653135 5.62e-03 6_[+5(1.50e-05)]_66 chrX:5707989-5708069 5.08e-02 51_[+1(1.84e-05)]_21 chrI:10927459-10927539 9.80e-01 80 chrIV:16865685-16865765 1.89e-03 30_[+3(2.14e-05)]_24_[+2(1.96e-05)]_\ 10 chrX:5319374-5319454 2.58e-01 80 chrIII:3916793-3916873 4.84e-02 15_[+3(4.68e-05)]_57 chrV:2674028-2674108 7.39e-02 30_[+4(3.19e-05)]_42 chrIV:9477711-9477791 7.18e-01 80 chrIII:7642180-7642260 8.72e-01 80 chrII:8547089-8547169 1.23e-01 80 chrX:8638898-8638978 5.99e-03 30_[+5(1.50e-05)]_42 chrIII:4568695-4568775 4.98e-02 27_[+3(9.78e-06)]_16_[+3(2.14e-05)]_\ 21 chrX:17610460-17610540 5.40e-01 80 chrX:6903184-6903264 4.59e-01 80 chrX:12843659-12843739 3.63e-02 41_[+1(1.84e-05)]_31 chrII:14635389-14635469 2.62e-01 80 chrV:6709216-6709296 2.17e-01 80 chrIV:11026156-11026236 9.92e-01 80 chrM:2099-2179 9.71e-01 80 chrX:4444265-4444345 5.92e-06 9_[+1(1.84e-05)]_18_[+3(5.70e-05)]_\ 2_[+4(1.48e-05)]_27 chrI:9605743-9605823 1.46e-04 25_[+1(1.84e-05)]_38_[+4(4.74e-05)]_\ 1 chrX:9622806-9622886 2.21e-01 80 chrX:6220130-6220210 2.08e-01 3_[+3(5.70e-05)]_69 chrIV:7789613-7789693 8.69e-01 80 chrIII:5211266-5211346 7.67e-01 80 chrX:1858827-1858907 5.92e-06 4_[+1(1.84e-05)]_18_[+3(5.70e-05)]_\ 2_[+4(1.48e-05)]_32 chrIV:3552204-3552284 5.87e-01 80 chrIII:4171145-4171225 3.19e-04 19_[+3(9.78e-06)]_38_[+2(1.06e-05)]_\ 7 chrX:1837870-1837950 1.24e-01 80 chrI:11323334-11323414 2.82e-03 24_[+3(4.68e-05)]_39_[+2(1.06e-05)]_\ 1 chrI:1823115-1823195 9.36e-01 80 chrII:11959387-11959467 1.19e-03 [+1(1.84e-05)]_72 chrI:13161030-13161110 2.47e-02 43_[+1(1.84e-05)]_29 chrIII:5211468-5211548 6.89e-01 80 chrII:9566164-9566244 4.06e-01 80 chrIII:4369515-4369595 5.28e-01 80 chrX:9637833-9637913 3.10e-01 80 chrV:1474746-1474826 4.85e-01 80 chrI:1958525-1958605 1.35e-01 19_[+3(4.68e-05)]_15_[+3(4.68e-05)]_\ 30 chrX:6371340-6371420 8.05e-02 59_[+4(6.18e-05)]_13 chrIII:6133433-6133513 9.22e-01 80 chrI:9267093-9267173 2.21e-01 80 chrI:6091078-6091158 4.91e-01 80 chrIII:1604698-1604778 1.40e-01 80 chrIV:3524792-3524872 1.39e-01 80 chrIV:10374049-10374129 5.74e-01 80 chrX:11252643-11252723 6.70e-04 10_[+3(5.70e-05)]_12_[+5(5.41e-05)]_\ 42 chrX:15297529-15297609 8.41e-01 80 chrX:10963761-10963841 5.36e-01 80 chrIII:6158747-6158827 1.02e-02 43_[+1(1.84e-05)]_29 chrII:6047806-6047886 9.80e-01 80 chrIII:4426751-4426831 5.97e-01 80 chrI:2410114-2410194 2.16e-03 59_[+4(3.19e-05)]_13 chrII:14063262-14063342 3.54e-01 80 chrIII:5555103-5555183 1.05e-02 12_[+3(7.92e-05)]_60 chrIV:143950-144030 3.93e-01 80 chrIV:17087584-17087664 4.46e-01 80 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c27n06.farnam.hpc.yale.internal ********************************************************************************