/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
- ********************************************************************************
- MEME - Motif discovery tool
- ********************************************************************************
- MEME version 4.6.0 (Release date: Thu Jan 20 14:06:48 PST 2011)
- For further information on how to interpret these results or to get
- a copy of the MEME software please access http://meme.nbcr.net.
- This file may be used as input to the MAST algorithm for searching
- sequence databases for matches to groups of motifs. MAST is available
- for interactive use and downloading at http://meme.nbcr.net.
- ********************************************************************************
- ********************************************************************************
- 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
- ********************************************************************************
- DATAFILE= dataset_3.dat
- ALPHABET= ACDEFGHIKLMNPQRSTVWY
- Sequence name Weight Length Sequence name Weight Length
- ------------- ------ ------ ------------- ------ ------
- chr21_19617074_19617124_ 1.0000 50 chr21_26934381_26934431_ 1.0000 50
- chr21_28217753_28217803_ 1.0000 50 chr21_31710037_31710087_ 1.0000 50
- chr21_31744582_31744632_ 1.0000 50 chr21_31768316_31768366_ 1.0000 50
- chr21_31914206_31914256_ 1.0000 50 chr21_31933633_31933683_ 1.0000 50
- chr21_31962741_31962791_ 1.0000 50 chr21_31964683_31964733_ 1.0000 50
- chr21_31973364_31973414_ 1.0000 50 chr21_31992870_31992920_ 1.0000 50
- chr21_32185595_32185645_ 1.0000 50 chr21_32202076_32202126_ 1.0000 50
- chr21_32253899_32253949_ 1.0000 50 chr21_32410820_32410870_ 1.0000 50
- chr21_36411748_36411798_ 1.0000 50 chr21_37838750_37838800_ 1.0000 50
- chr21_45705687_45705737_ 1.0000 50 chr21_45971413_45971463_ 1.0000 50
- chr21_45978668_45978718_ 1.0000 50 chr21_45993530_45993580_ 1.0000 50
- chr21_46020421_46020471_ 1.0000 50 chr21_46031920_46031970_ 1.0000 50
- chr21_46046964_46047014_ 1.0000 50 chr21_46057197_46057247_ 1.0000 50
- chr21_46086869_46086919_ 1.0000 50 chr21_46102103_46102153_ 1.0000 50
- chr21_47517957_47518007_ 1.0000 50 chr21_47575506_47575556_ 1.0000 50
- ********************************************************************************
- ********************************************************************************
- COMMAND LINE SUMMARY
- ********************************************************************************
- This information can also be useful in the event you wish to report a
- problem with the MEME software.
- command: meme dataset_3.dat -o dataset_4_files -nostatus
- model: mod= zoops nmotifs= 1 evt= inf
- object function= E-value of product of p-values
- width: minw= 8 maxw= 50 minic= 0.00
- width: wg= 11 ws= 1 endgaps= yes
- nsites: minsites= 2 maxsites= 30 wnsites= 0.8
- theta: prob= 1 spmap= pam spfuzz= 120
- global: substring= yes branching= no wbranch= no
- em: prior= megap b= 7500 maxiter= 50
- distance= 1e-05
- data: n= 1500 N= 30
- sample: seed= 0 seqfrac= 1
- Dirichlet mixture priors file: prior30.plib
- Letter frequencies in dataset:
- 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
- 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
- W 0.000 Y 0.000
- Background letter frequencies (from dataset with add-one prior applied):
- 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
- 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
- W 0.001 Y 0.001
- ********************************************************************************
- ********************************************************************************
- MOTIF 1 width = 11 sites = 25 llr = 239 E-value = 2.4e-011
- ********************************************************************************
- --------------------------------------------------------------------------------
- Motif 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 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 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 1 in BLOCKS format
- --------------------------------------------------------------------------------
- BL MOTIF 1 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 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 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 1 regular expression
- --------------------------------------------------------------------------------
- [GA][GA][GC][GA]TATA[AT]AA
- --------------------------------------------------------------------------------
- Time 2.13 secs.
- ********************************************************************************
- ********************************************************************************
- SUMMARY OF MOTIFS
- ********************************************************************************
- --------------------------------------------------------------------------------
- Combined block diagrams: non-overlapping sites with p-value < 0.0001
- --------------------------------------------------------------------------------
- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM
- ------------- ---------------- -------------
- chr21_19617074_19617124_ 1.22e-03 39_[1(3.06e-05)]
- chr21_26934381_26934431_ 2.21e-03 27_[1(5.52e-05)]_12
- chr21_28217753_28217803_ 7.29e-01 50
- chr21_31710037_31710087_ 2.37e-03 14_[1(5.94e-05)]_25
- chr21_31744582_31744632_ 1.22e-03 12_[1(3.06e-05)]_27
- chr21_31768316_31768366_ 1.53e-03 [1(3.82e-05)]_39
- chr21_31914206_31914256_ 6.70e-04 15_[1(1.68e-05)]_24
- chr21_31933633_31933683_ 1.81e-03 4_[1(4.54e-05)]_35
- chr21_31962741_31962791_ 1.61e-02 50
- chr21_31964683_31964733_ 1.36e-04 13_[1(3.41e-06)]_26
- chr21_31973364_31973414_ 1.99e-01 50
- chr21_31992870_31992920_ 3.47e-04 16_[1(8.67e-06)]_23
- chr21_32185595_32185645_ 3.47e-04 18_[1(8.67e-06)]_21
- chr21_32202076_32202126_ 2.01e-04 13_[1(5.01e-06)]_26
- chr21_32253899_32253949_ 8.11e-04 19_[1(2.03e-05)]_20
- chr21_32410820_32410870_ 3.47e-04 21_[1(8.67e-06)]_18
- chr21_36411748_36411798_ 2.71e-03 22_[1(6.78e-05)]_17
- chr21_37838750_37838800_ 8.23e-02 50
- chr21_45705687_45705737_ 1.53e-03 37_[1(3.82e-05)]_2
- chr21_45971413_45971463_ 1.36e-04 9_[1(3.41e-06)]_30
- chr21_45978668_45978718_ 6.37e-04 4_[1(1.59e-05)]_35
- chr21_45993530_45993580_ 1.60e-04 7_[1(4.00e-06)]_32
- chr21_46020421_46020471_ 4.83e-04 2_[1(1.21e-05)]_37
- chr21_46031920_46031970_ 2.43e-04 15_[1(6.06e-06)]_24
- chr21_46046964_46047014_ 4.26e-05 12_[1(1.06e-06)]_27
- chr21_46057197_46057247_ 1.36e-04 36_[1(3.41e-06)]_3
- chr21_46086869_46086919_ 4.30e-02 50
- chr21_46102103_46102153_ 4.30e-02 50
- chr21_47517957_47518007_ 6.37e-04 32_[1(1.59e-05)]_7
- chr21_47575506_47575556_ 1.61e-03 30_[1(4.02e-05)]_9
- --------------------------------------------------------------------------------
- ********************************************************************************
- ********************************************************************************
- Stopped because nmotifs = 1 reached.
- ********************************************************************************
- CPU: scofield
- ********************************************************************************