/test-data/meme/meme/meme_output_txt_1.txt

https://bitbucket.org/cistrome/cistrome-harvard/ · Plain Text · 325 lines · 288 code · 37 blank · 0 comment · 0 complexity · e10abfb51a2b5c00990e2dd4803152d0 MD5 · raw file

  1. ********************************************************************************
  2. MEME - Motif discovery tool
  3. ********************************************************************************
  4. MEME version 4.6.0 (Release date: Thu Jan 20 14:06:48 PST 2011)
  5. For further information on how to interpret these results or to get
  6. a copy of the MEME software please access http://meme.nbcr.net.
  7. This file may be used as input to the MAST algorithm for searching
  8. sequence databases for matches to groups of motifs. MAST is available
  9. for interactive use and downloading at http://meme.nbcr.net.
  10. ********************************************************************************
  11. ********************************************************************************
  12. REFERENCE
  13. ********************************************************************************
  14. If you use this program in your research, please cite:
  15. Timothy L. Bailey and Charles Elkan,
  16. "Fitting a mixture model by expectation maximization to discover
  17. motifs in biopolymers", Proceedings of the Second International
  18. Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
  19. AAAI Press, Menlo Park, California, 1994.
  20. ********************************************************************************
  21. ********************************************************************************
  22. TRAINING SET
  23. ********************************************************************************
  24. DATAFILE= dataset_3.dat
  25. ALPHABET= ACDEFGHIKLMNPQRSTVWY
  26. Sequence name Weight Length Sequence name Weight Length
  27. ------------- ------ ------ ------------- ------ ------
  28. chr21_19617074_19617124_ 1.0000 50 chr21_26934381_26934431_ 1.0000 50
  29. chr21_28217753_28217803_ 1.0000 50 chr21_31710037_31710087_ 1.0000 50
  30. chr21_31744582_31744632_ 1.0000 50 chr21_31768316_31768366_ 1.0000 50
  31. chr21_31914206_31914256_ 1.0000 50 chr21_31933633_31933683_ 1.0000 50
  32. chr21_31962741_31962791_ 1.0000 50 chr21_31964683_31964733_ 1.0000 50
  33. chr21_31973364_31973414_ 1.0000 50 chr21_31992870_31992920_ 1.0000 50
  34. chr21_32185595_32185645_ 1.0000 50 chr21_32202076_32202126_ 1.0000 50
  35. chr21_32253899_32253949_ 1.0000 50 chr21_32410820_32410870_ 1.0000 50
  36. chr21_36411748_36411798_ 1.0000 50 chr21_37838750_37838800_ 1.0000 50
  37. chr21_45705687_45705737_ 1.0000 50 chr21_45971413_45971463_ 1.0000 50
  38. chr21_45978668_45978718_ 1.0000 50 chr21_45993530_45993580_ 1.0000 50
  39. chr21_46020421_46020471_ 1.0000 50 chr21_46031920_46031970_ 1.0000 50
  40. chr21_46046964_46047014_ 1.0000 50 chr21_46057197_46057247_ 1.0000 50
  41. chr21_46086869_46086919_ 1.0000 50 chr21_46102103_46102153_ 1.0000 50
  42. chr21_47517957_47518007_ 1.0000 50 chr21_47575506_47575556_ 1.0000 50
  43. ********************************************************************************
  44. ********************************************************************************
  45. COMMAND LINE SUMMARY
  46. ********************************************************************************
  47. This information can also be useful in the event you wish to report a
  48. problem with the MEME software.
  49. command: meme dataset_3.dat -o dataset_4_files -nostatus
  50. model: mod= zoops nmotifs= 1 evt= inf
  51. object function= E-value of product of p-values
  52. width: minw= 8 maxw= 50 minic= 0.00
  53. width: wg= 11 ws= 1 endgaps= yes
  54. nsites: minsites= 2 maxsites= 30 wnsites= 0.8
  55. theta: prob= 1 spmap= pam spfuzz= 120
  56. global: substring= yes branching= no wbranch= no
  57. em: prior= megap b= 7500 maxiter= 50
  58. distance= 1e-05
  59. data: n= 1500 N= 30
  60. sample: seed= 0 seqfrac= 1
  61. Dirichlet mixture priors file: prior30.plib
  62. Letter frequencies in dataset:
  63. A 0.294 C 0.231 D 0.000 E 0.000 F 0.000 G 0.257 H 0.000 I 0.000 K 0.000
  64. L 0.000 M 0.000 N 0.000 P 0.000 Q 0.000 R 0.000 S 0.000 T 0.217 V 0.000
  65. W 0.000 Y 0.000
  66. Background letter frequencies (from dataset with add-one prior applied):
  67. A 0.291 C 0.229 D 0.001 E 0.001 F 0.001 G 0.255 H 0.001 I 0.001 K 0.001
  68. L 0.001 M 0.001 N 0.001 P 0.001 Q 0.001 R 0.001 S 0.001 T 0.215 V 0.001
  69. W 0.001 Y 0.001
  70. ********************************************************************************
  71. ********************************************************************************
  72. MOTIF 1 width = 11 sites = 25 llr = 239 E-value = 2.4e-011
  73. ********************************************************************************
  74. --------------------------------------------------------------------------------
  75. Motif 1 Description
  76. --------------------------------------------------------------------------------
  77. Simplified A 2323:a:a8a8
  78. pos.-specific C ::3::::::::
  79. probability D :::::::::::
  80. matrix E :::::::::::
  81. F :::::::::::
  82. G 7746::::::1
  83. H :::::::::::
  84. I :::::::::::
  85. K :::::::::::
  86. L :::::::::::
  87. M :::::::::::
  88. N :::::::::::
  89. P :::::::::::
  90. Q :::::::::::
  91. R :::::::::::
  92. S :::::::::::
  93. T 1:2:a:a:2::
  94. V :::::::::::
  95. W :::::::::::
  96. Y :::::::::::
  97. bits 10.6
  98. 9.5
  99. 8.5
  100. 7.4
  101. Relative 6.3
  102. Entropy 5.3
  103. (13.8 bits) 4.2
  104. 3.2
  105. 2.1 * **
  106. 1.1 ** ********
  107. 0.0 -----------
  108. Multilevel GGGGTATAAAA
  109. consensus AACA T
  110. sequence
  111. --------------------------------------------------------------------------------
  112. --------------------------------------------------------------------------------
  113. Motif 1 sites sorted by position p-value
  114. --------------------------------------------------------------------------------
  115. Sequence name Start P-value Site
  116. ------------- ----- --------- -----------
  117. chr21_46046964_46047014_ 13 1.06e-06 AAGGCCAGGA GGGGTATAAAA GCCTGAGAGC
  118. chr21_46057197_46057247_ 37 3.41e-06 ACAGGCCCTG GGCATATAAAA GCC
  119. chr21_45971413_45971463_ 10 3.41e-06 CAGGCCCTG GGCATATAAAA GCCCCAGCAG
  120. chr21_31964683_31964733_ 14 3.41e-06 GATTCACTGA GGCATATAAAA GGCCCTCTGC
  121. chr21_45993530_45993580_ 8 4.00e-06 CCAAGGA GGAGTATAAAA GCCCCACAAA
  122. chr21_32202076_32202126_ 14 5.01e-06 CCACCAGCTT GAGGTATAAAA AGCCCTGTAC
  123. chr21_46031920_46031970_ 16 6.06e-06 ATACCCAGGG AGGGTATAAAA CCTCAGCAGC
  124. chr21_32410820_32410870_ 22 8.67e-06 AATCACTGAG GATGTATAAAA GTCCCAGGGA
  125. chr21_32185595_32185645_ 19 8.67e-06 CACCAGAGCT GGGATATATAA AGAAGGTTCT
  126. chr21_31992870_31992920_ 17 8.67e-06 CACTATTGAA GATGTATAAAA TTTCATTTGC
  127. chr21_46020421_46020471_ 3 1.21e-05 GA GACATATAAAA GCCAACATCC
  128. chr21_47517957_47518007_ 33 1.59e-05 CCGGCGGGGC GGGGTATAAAG GGGGCGG
  129. chr21_45978668_45978718_ 5 1.59e-05 CAGA GGGGTATAAAG GTTCCGACCA
  130. chr21_31914206_31914256_ 16 1.68e-05 CCCACTACTT AGAGTATAAAA TCATTCTGAG
  131. chr21_32253899_32253949_ 20 2.03e-05 CACCAGCAAG GATATATAAAA GCTCAGGAGT
  132. chr21_31744582_31744632_ 13 3.06e-05 CAGGTCTAAG AGCATATATAA CTTGGAGTCC
  133. chr21_19617074_19617124_ 40 3.06e-05 CCTCGGGACG TGGGTATATAA
  134. chr21_45705687_45705737_ 38 3.82e-05 CGTGGTCGCG GGGGTATAACA GC
  135. chr21_31768316_31768366_ 1 3.82e-05 . AACGTATATAA ATGGTCCTGT
  136. chr21_47575506_47575556_ 31 4.02e-05 GCTGCCGGTG AGCGTATAAAG GCCCTGGCG
  137. chr21_26934381_26934431_ 28 5.52e-05 AGTCACAAGT GAGTTATAAAA GGGTCGCACG
  138. chr21_31710037_31710087_ 15 5.94e-05 CCCAGGTTTC TGAGTATATAA TCGCCGCACC
  139. chr21_36411748_36411798_ 23 6.78e-05 AGTTTCAGTT GGCATCTAAAA ATTATATAAC
  140. chr21_31933633_31933683_ 3 2.08e-04 TC AGAGTATATAT AAATGTTCCT
  141. chr21_31962741_31962791_ 14 4.05e-04 TATAACTCAG GTTGGATAAAA TAATTTGTAC
  142. --------------------------------------------------------------------------------
  143. --------------------------------------------------------------------------------
  144. Motif 1 block diagrams
  145. --------------------------------------------------------------------------------
  146. SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
  147. ------------- ---------------- -------------
  148. chr21_46046964_46047014_ 1.1e-06 12_[1]_27
  149. chr21_46057197_46057247_ 3.4e-06 36_[1]_3
  150. chr21_45971413_45971463_ 3.4e-06 9_[1]_30
  151. chr21_31964683_31964733_ 3.4e-06 13_[1]_26
  152. chr21_45993530_45993580_ 4e-06 7_[1]_32
  153. chr21_32202076_32202126_ 5e-06 13_[1]_26
  154. chr21_46031920_46031970_ 6.1e-06 15_[1]_24
  155. chr21_32410820_32410870_ 8.7e-06 21_[1]_18
  156. chr21_32185595_32185645_ 8.7e-06 18_[1]_21
  157. chr21_31992870_31992920_ 8.7e-06 16_[1]_23
  158. chr21_46020421_46020471_ 1.2e-05 2_[1]_37
  159. chr21_47517957_47518007_ 1.6e-05 32_[1]_7
  160. chr21_45978668_45978718_ 1.6e-05 4_[1]_35
  161. chr21_31914206_31914256_ 1.7e-05 15_[1]_24
  162. chr21_32253899_32253949_ 2e-05 19_[1]_20
  163. chr21_31744582_31744632_ 3.1e-05 12_[1]_27
  164. chr21_19617074_19617124_ 3.1e-05 39_[1]
  165. chr21_45705687_45705737_ 3.8e-05 37_[1]_2
  166. chr21_31768316_31768366_ 3.8e-05 [1]_39
  167. chr21_47575506_47575556_ 4e-05 30_[1]_9
  168. chr21_26934381_26934431_ 5.5e-05 27_[1]_12
  169. chr21_31710037_31710087_ 5.9e-05 14_[1]_25
  170. chr21_36411748_36411798_ 6.8e-05 22_[1]_17
  171. chr21_31933633_31933683_ 0.00021 2_[1]_37
  172. chr21_31962741_31962791_ 0.0004 13_[1]_26
  173. --------------------------------------------------------------------------------
  174. --------------------------------------------------------------------------------
  175. Motif 1 in BLOCKS format
  176. --------------------------------------------------------------------------------
  177. BL MOTIF 1 width=11 seqs=25
  178. chr21_46046964_46047014_ ( 13) GGGGTATAAAA 1
  179. chr21_46057197_46057247_ ( 37) GGCATATAAAA 1
  180. chr21_45971413_45971463_ ( 10) GGCATATAAAA 1
  181. chr21_31964683_31964733_ ( 14) GGCATATAAAA 1
  182. chr21_45993530_45993580_ ( 8) GGAGTATAAAA 1
  183. chr21_32202076_32202126_ ( 14) GAGGTATAAAA 1
  184. chr21_46031920_46031970_ ( 16) AGGGTATAAAA 1
  185. chr21_32410820_32410870_ ( 22) GATGTATAAAA 1
  186. chr21_32185595_32185645_ ( 19) GGGATATATAA 1
  187. chr21_31992870_31992920_ ( 17) GATGTATAAAA 1
  188. chr21_46020421_46020471_ ( 3) GACATATAAAA 1
  189. chr21_47517957_47518007_ ( 33) GGGGTATAAAG 1
  190. chr21_45978668_45978718_ ( 5) GGGGTATAAAG 1
  191. chr21_31914206_31914256_ ( 16) AGAGTATAAAA 1
  192. chr21_32253899_32253949_ ( 20) GATATATAAAA 1
  193. chr21_31744582_31744632_ ( 13) AGCATATATAA 1
  194. chr21_19617074_19617124_ ( 40) TGGGTATATAA 1
  195. chr21_45705687_45705737_ ( 38) GGGGTATAACA 1
  196. chr21_31768316_31768366_ ( 1) AACGTATATAA 1
  197. chr21_47575506_47575556_ ( 31) AGCGTATAAAG 1
  198. chr21_26934381_26934431_ ( 28) GAGTTATAAAA 1
  199. chr21_31710037_31710087_ ( 15) TGAGTATATAA 1
  200. chr21_36411748_36411798_ ( 23) GGCATCTAAAA 1
  201. chr21_31933633_31933683_ ( 3) AGAGTATATAT 1
  202. chr21_31962741_31962791_ ( 14) GTTGGATAAAA 1
  203. //
  204. --------------------------------------------------------------------------------
  205. --------------------------------------------------------------------------------
  206. Motif 1 position-specific scoring matrix
  207. --------------------------------------------------------------------------------
  208. log-odds matrix: alength= 20 w= 11 n= 1200 bayes= 5.33554 E= 2.4e-011
  209. -32 -680 91 77 7 138 -20 55 64 107 11 150 142 72 87 396 -148 221 -140 -36
  210. -11 -680 89 76 7 137 -21 55 63 107 10 149 141 71 87 396 -239 220 -140 -36
  211. -79 41 4 21 -7 44 -62 42 -5 99 0 99 138 52 42 399 -46 223 -173 -68
  212. 11 -677 48 47 -2 127 -43 46 27 101 3 124 138 60 62 397 -235 220 -160 -55
  213. -596 -820 12 -21 -53 -267 -74 37 16 44 -37 98 31 9 19 319 212 127 -193 -95
  214. 165 -261 70 110 77 -521 -4 147 95 201 90 121 124 91 107 425 -527 314 -95 8
  215. -838 -990 -89 -149 -151 -841 -161 -117 -113 -66 -209 -68 -69 -129 -91 111 221 -55 -255 -173
  216. 176 -858 -79 -103 -115 -717 -148 -95 -108 -17 -162 -61 -12 -95 -69 193 -737 52 -240 -153
  217. 134 -686 0 16 -12 -553 -68 44 -8 96 -9 88 124 41 36 384 11 216 -177 -71
  218. 165 -261 70 110 77 -521 -4 147 95 201 90 121 124 91 107 425 -527 314 -95 8
  219. 147 -614 89 129 93 -121 12 160 113 217 108 144 144 111 125 447 -241 332 -81 22
  220. --------------------------------------------------------------------------------
  221. --------------------------------------------------------------------------------
  222. Motif 1 position-specific probability matrix
  223. --------------------------------------------------------------------------------
  224. letter-probability matrix: alength= 20 w= 11 nsites= 25 E= 2.4e-011
  225. 0.240000 0.000000 0.000000 0.000000 0.000000 0.680000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.080000 0.000000 0.000000 0.000000
  226. 0.280000 0.000000 0.000000 0.000000 0.000000 0.680000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.040000 0.000000 0.000000 0.000000
  227. 0.160000 0.320000 0.000000 0.000000 0.000000 0.360000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.160000 0.000000 0.000000 0.000000
  228. 0.320000 0.000000 0.000000 0.000000 0.000000 0.640000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.040000 0.000000 0.000000 0.000000
  229. 0.000000 0.000000 0.000000 0.000000 0.000000 0.040000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.960000 0.000000 0.000000 0.000000
  230. 0.960000 0.040000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
  231. 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000
  232. 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
  233. 0.760000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.240000 0.000000 0.000000 0.000000
  234. 0.960000 0.040000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
  235. 0.840000 0.000000 0.000000 0.000000 0.000000 0.120000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.040000 0.000000 0.000000 0.000000
  236. --------------------------------------------------------------------------------
  237. --------------------------------------------------------------------------------
  238. Motif 1 regular expression
  239. --------------------------------------------------------------------------------
  240. [GA][GA][GC][GA]TATA[AT]AA
  241. --------------------------------------------------------------------------------
  242. Time 2.13 secs.
  243. ********************************************************************************
  244. ********************************************************************************
  245. SUMMARY OF MOTIFS
  246. ********************************************************************************
  247. --------------------------------------------------------------------------------
  248. Combined block diagrams: non-overlapping sites with p-value < 0.0001
  249. --------------------------------------------------------------------------------
  250. SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM
  251. ------------- ---------------- -------------
  252. chr21_19617074_19617124_ 1.22e-03 39_[1(3.06e-05)]
  253. chr21_26934381_26934431_ 2.21e-03 27_[1(5.52e-05)]_12
  254. chr21_28217753_28217803_ 7.29e-01 50
  255. chr21_31710037_31710087_ 2.37e-03 14_[1(5.94e-05)]_25
  256. chr21_31744582_31744632_ 1.22e-03 12_[1(3.06e-05)]_27
  257. chr21_31768316_31768366_ 1.53e-03 [1(3.82e-05)]_39
  258. chr21_31914206_31914256_ 6.70e-04 15_[1(1.68e-05)]_24
  259. chr21_31933633_31933683_ 1.81e-03 4_[1(4.54e-05)]_35
  260. chr21_31962741_31962791_ 1.61e-02 50
  261. chr21_31964683_31964733_ 1.36e-04 13_[1(3.41e-06)]_26
  262. chr21_31973364_31973414_ 1.99e-01 50
  263. chr21_31992870_31992920_ 3.47e-04 16_[1(8.67e-06)]_23
  264. chr21_32185595_32185645_ 3.47e-04 18_[1(8.67e-06)]_21
  265. chr21_32202076_32202126_ 2.01e-04 13_[1(5.01e-06)]_26
  266. chr21_32253899_32253949_ 8.11e-04 19_[1(2.03e-05)]_20
  267. chr21_32410820_32410870_ 3.47e-04 21_[1(8.67e-06)]_18
  268. chr21_36411748_36411798_ 2.71e-03 22_[1(6.78e-05)]_17
  269. chr21_37838750_37838800_ 8.23e-02 50
  270. chr21_45705687_45705737_ 1.53e-03 37_[1(3.82e-05)]_2
  271. chr21_45971413_45971463_ 1.36e-04 9_[1(3.41e-06)]_30
  272. chr21_45978668_45978718_ 6.37e-04 4_[1(1.59e-05)]_35
  273. chr21_45993530_45993580_ 1.60e-04 7_[1(4.00e-06)]_32
  274. chr21_46020421_46020471_ 4.83e-04 2_[1(1.21e-05)]_37
  275. chr21_46031920_46031970_ 2.43e-04 15_[1(6.06e-06)]_24
  276. chr21_46046964_46047014_ 4.26e-05 12_[1(1.06e-06)]_27
  277. chr21_46057197_46057247_ 1.36e-04 36_[1(3.41e-06)]_3
  278. chr21_46086869_46086919_ 4.30e-02 50
  279. chr21_46102103_46102153_ 4.30e-02 50
  280. chr21_47517957_47518007_ 6.37e-04 32_[1(1.59e-05)]_7
  281. chr21_47575506_47575556_ 1.61e-03 30_[1(4.02e-05)]_9
  282. --------------------------------------------------------------------------------
  283. ********************************************************************************
  284. ********************************************************************************
  285. Stopped because nmotifs = 1 reached.
  286. ********************************************************************************
  287. CPU: scofield
  288. ********************************************************************************