Mercurial > repos > iuc > meme_streme
view test-data/meme_output_test1.txt @ 0:7653ebd919bb draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
| author | iuc |
|---|---|
| date | Mon, 14 Jul 2025 21:33:08 +0000 |
| parents | |
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model: mod= zoops nmotifs= 1 evt= inf objective function: em= E-value of product of p-values starts= E-value of product of p-values width: minw= 8 maxw= 50 nsites: minsites= 2 maxsites= 30 wnsites= 0.8 theta: spmap= pam spfuzz= 120 em: prior= megap b= 7500 maxiter= 50 distance= 1e-05 trim: wg= 11 ws= 1 endgaps= yes data: n= 1500 N= 30 sample: seed= 0 hsfrac= 0 searchsize= 1500 norand= no csites= 1000 Dirichlet mixture priors file: prior30.plib Letter frequencies in dataset: A 0.294 C 0.231 D 0 E 0 F 0 G 0.257 H 0 I 0 K 0 L 0 M 0 N 0 P 0 Q 0 R 0 S 0 T 0.217 V 0 W 0 Y 0 Background letter frequencies (from file dataset with add-one prior applied): A 0.291 C 0.229 D 0.000658 E 0.000658 F 0.000658 G 0.255 H 0.000658 I 0.000658 K 0.000658 L 0.000658 M 0.000658 N 0.000658 P 0.000658 Q 0.000658 R 0.000658 S 0.000658 T 0.215 V 0.000658 W 0.000658 Y 0.000658 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF GGGGTATAAAA MEME-1 width = 11 sites = 25 llr = 239 E-value = 2.4e-011 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGGGTATAAAA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 2323:a:a8a8 pos.-specific C ::3:::::::: probability D ::::::::::: matrix E ::::::::::: F ::::::::::: G 7746::::::1 H ::::::::::: I ::::::::::: K ::::::::::: L ::::::::::: M ::::::::::: N ::::::::::: P ::::::::::: Q ::::::::::: R ::::::::::: S ::::::::::: T 1:2:a:a:2:: V ::::::::::: W ::::::::::: Y ::::::::::: bits 10.6 9.5 8.5 7.4 Relative 6.3 Entropy 5.3 (13.8 bits) 4.2 3.2 2.1 * ** 1.1 ** ******** 0.0 ----------- Multilevel GGGGTATAAAA consensus AACA T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGGTATAAAA MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------- chr21_46046964_46047014_ 13 1.06e-06 AAGGCCAGGA GGGGTATAAAA GCCTGAGAGC chr21_46057197_46057247_ 37 3.41e-06 ACAGGCCCTG GGCATATAAAA GCC chr21_45971413_45971463_ 10 3.41e-06 CAGGCCCTG GGCATATAAAA GCCCCAGCAG chr21_31964683_31964733_ 14 3.41e-06 GATTCACTGA GGCATATAAAA GGCCCTCTGC chr21_45993530_45993580_ 8 4.00e-06 CCAAGGA GGAGTATAAAA GCCCCACAAA chr21_32202076_32202126_ 14 5.01e-06 CCACCAGCTT GAGGTATAAAA AGCCCTGTAC chr21_46031920_46031970_ 16 6.06e-06 ATACCCAGGG AGGGTATAAAA CCTCAGCAGC chr21_32410820_32410870_ 22 8.67e-06 AATCACTGAG GATGTATAAAA GTCCCAGGGA chr21_32185595_32185645_ 19 8.67e-06 CACCAGAGCT GGGATATATAA AGAAGGTTCT chr21_31992870_31992920_ 17 8.67e-06 CACTATTGAA GATGTATAAAA TTTCATTTGC chr21_46020421_46020471_ 3 1.21e-05 GA GACATATAAAA GCCAACATCC chr21_47517957_47518007_ 33 1.59e-05 CCGGCGGGGC GGGGTATAAAG GGGGCGG chr21_45978668_45978718_ 5 1.59e-05 CAGA GGGGTATAAAG GTTCCGACCA chr21_31914206_31914256_ 16 1.68e-05 CCCACTACTT AGAGTATAAAA TCATTCTGAG chr21_32253899_32253949_ 20 2.03e-05 CACCAGCAAG GATATATAAAA GCTCAGGAGT chr21_31744582_31744632_ 13 3.06e-05 CAGGTCTAAG AGCATATATAA CTTGGAGTCC chr21_19617074_19617124_ 40 3.06e-05 CCTCGGGACG TGGGTATATAA chr21_45705687_45705737_ 38 3.82e-05 CGTGGTCGCG GGGGTATAACA GC chr21_31768316_31768366_ 1 3.82e-05 . AACGTATATAA ATGGTCCTGT chr21_47575506_47575556_ 31 4.02e-05 GCTGCCGGTG AGCGTATAAAG GCCCTGGCG chr21_26934381_26934431_ 28 5.52e-05 AGTCACAAGT GAGTTATAAAA GGGTCGCACG chr21_31710037_31710087_ 15 5.94e-05 CCCAGGTTTC TGAGTATATAA TCGCCGCACC chr21_36411748_36411798_ 23 6.78e-05 AGTTTCAGTT GGCATCtaaaa attatataac chr21_31933633_31933683_ 3 2.08e-04 TC AGAGTATATAT AAATGTTCCT chr21_31962741_31962791_ 14 4.05e-04 TATAACTCAG GTTGGATAAAA TAATTTGTAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGGTATAAAA MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr21_46046964_46047014_ 1.1e-06 12_[1]_27 chr21_46057197_46057247_ 3.4e-06 36_[1]_3 chr21_45971413_45971463_ 3.4e-06 9_[1]_30 chr21_31964683_31964733_ 3.4e-06 13_[1]_26 chr21_45993530_45993580_ 4e-06 7_[1]_32 chr21_32202076_32202126_ 5e-06 13_[1]_26 chr21_46031920_46031970_ 6.1e-06 15_[1]_24 chr21_32410820_32410870_ 8.7e-06 21_[1]_18 chr21_32185595_32185645_ 8.7e-06 18_[1]_21 chr21_31992870_31992920_ 8.7e-06 16_[1]_23 chr21_46020421_46020471_ 1.2e-05 2_[1]_37 chr21_47517957_47518007_ 1.6e-05 32_[1]_7 chr21_45978668_45978718_ 1.6e-05 4_[1]_35 chr21_31914206_31914256_ 1.7e-05 15_[1]_24 chr21_32253899_32253949_ 2e-05 19_[1]_20 chr21_31744582_31744632_ 3.1e-05 12_[1]_27 chr21_19617074_19617124_ 3.1e-05 39_[1] chr21_45705687_45705737_ 3.8e-05 37_[1]_2 chr21_31768316_31768366_ 3.8e-05 [1]_39 chr21_47575506_47575556_ 4e-05 30_[1]_9 chr21_26934381_26934431_ 5.5e-05 27_[1]_12 chr21_31710037_31710087_ 5.9e-05 14_[1]_25 chr21_36411748_36411798_ 6.8e-05 22_[1]_17 chr21_31933633_31933683_ 0.00021 2_[1]_37 chr21_31962741_31962791_ 0.0004 13_[1]_26 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGGTATAAAA MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGGGTATAAAA width=11 seqs=25 chr21_46046964_46047014_ ( 13) GGGGTATAAAA 1 chr21_46057197_46057247_ ( 37) GGCATATAAAA 1 chr21_45971413_45971463_ ( 10) GGCATATAAAA 1 chr21_31964683_31964733_ ( 14) GGCATATAAAA 1 chr21_45993530_45993580_ ( 8) GGAGTATAAAA 1 chr21_32202076_32202126_ ( 14) GAGGTATAAAA 1 chr21_46031920_46031970_ ( 16) AGGGTATAAAA 1 chr21_32410820_32410870_ ( 22) GATGTATAAAA 1 chr21_32185595_32185645_ ( 19) GGGATATATAA 1 chr21_31992870_31992920_ ( 17) GATGTATAAAA 1 chr21_46020421_46020471_ ( 3) GACATATAAAA 1 chr21_47517957_47518007_ ( 33) GGGGTATAAAG 1 chr21_45978668_45978718_ ( 5) GGGGTATAAAG 1 chr21_31914206_31914256_ ( 16) AGAGTATAAAA 1 chr21_32253899_32253949_ ( 20) GATATATAAAA 1 chr21_31744582_31744632_ ( 13) AGCATATATAA 1 chr21_19617074_19617124_ ( 40) TGGGTATATAA 1 chr21_45705687_45705737_ ( 38) GGGGTATAACA 1 chr21_31768316_31768366_ ( 1) AACGTATATAA 1 chr21_47575506_47575556_ ( 31) AGCGTATAAAG 1 chr21_26934381_26934431_ ( 28) GAGTTATAAAA 1 chr21_31710037_31710087_ ( 15) TGAGTATATAA 1 chr21_36411748_36411798_ ( 23) GGCATCTAAAA 1 chr21_31933633_31933683_ ( 3) AGAGTATATAT 1 chr21_31962741_31962791_ ( 14) GTTGGATAAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGGTATAAAA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 11 n= 1200 bayes= 5.33554 E= 2.4e-011 -32 -680 91 77 7 138 -20 55 64 107 11 150 142 72 87 396 -148 221 -140 -36 -11 -680 89 76 7 137 -21 55 63 107 10 149 141 71 87 396 -239 220 -140 -36 -79 41 4 21 -7 44 -62 42 -5 99 0 99 138 52 42 399 -46 223 -173 -68 11 -677 48 47 -2 127 -43 46 27 101 3 124 138 60 62 397 -235 220 -160 -55 -596 -820 12 -21 -53 -267 -74 37 16 44 -37 98 31 9 19 319 212 127 -193 -95 165 -261 70 110 77 -521 -4 147 95 201 90 121 124 91 107 425 -527 314 -95 8 -838 -990 -89 -149 -151 -841 -161 -117 -113 -66 -209 -68 -69 -129 -91 111 221 -55 -255 -173 176 -858 -79 -103 -115 -717 -148 -95 -108 -17 -162 -61 -12 -95 -69 193 -737 52 -240 -153 134 -686 0 16 -12 -553 -68 44 -8 96 -9 88 124 41 36 384 11 216 -177 -71 165 -261 70 110 77 -521 -4 147 95 201 90 121 124 91 107 425 -527 314 -95 8 147 -614 89 129 93 -121 12 160 113 217 108 144 144 111 125 447 -241 332 -81 22 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGGTATAAAA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 11 nsites= 25 E= 2.4e-011 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 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 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 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 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 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 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 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 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 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 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGGTATAAAA MEME-1 regular expression -------------------------------------------------------------------------------- [GA][GA][GC][GA]TATA[AT]AA --------------------------------------------------------------------------------