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comparison test-data/meme_output_test2.txt @ 7:0c97e5c18468 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
author iuc
date Mon, 14 Jul 2025 21:33:41 +0000
parents f33d77dcacce
children
comparison
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6:fd05b142b3a3 7:0c97e5c18468
1 ******************************************************************************** 1 ********************************************************************************
2 SUMMARY OF MOTIFS 2 MOTIF GGSRTATAAAA MEME-1 width = 11 sites = 30 llr = 254 E-value = 5.1e-040
3 ******************************************************************************** 3 ********************************************************************************
4 --------------------------------------------------------------------------------
5 Motif GGSRTATAAAA MEME-1 Description
6 --------------------------------------------------------------------------------
7 Simplified A 3313:9:a798
8 pos.-specific C 1:3::1:::1:
9 probability G 6756::::::2
10 matrix T 1:11a1a:3::
11
12 bits 2.2 *
13 2.0 * *
14 1.8 * *
15 1.5 * ** *
16 Relative 1.3 * ** *
17 Entropy 1.1 ******
18 (12.2 bits) 0.9 * *******
19 0.7 * *******
20 0.4 ** ********
21 0.2 ***********
22 0.0 -----------
23
24 Multilevel GGGGTATAAAA
25 consensus AACA T
26 sequence
27
28 --------------------------------------------------------------------------------
4 29
5 -------------------------------------------------------------------------------- 30 --------------------------------------------------------------------------------
6 Combined block diagrams: non-overlapping sites with p-value < 0.0001 31 Motif GGSRTATAAAA MEME-1 sites sorted by position p-value
7 -------------------------------------------------------------------------------- 32 --------------------------------------------------------------------------------
8 SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM 33 Sequence name Start P-value Site
34 ------------- ----- --------- -----------
35 chr21_46046964_46047014_ 13 4.51e-07 AAGGCCAGGA GGGGTATAAAA GCCTGAGAGC
36 chr21_46031920_46031970_ 16 2.22e-06 ATACCCAGGG AGGGTATAAAA CCTCAGCAGC
37 chr21_32202076_32202126_ 14 2.74e-06 CCACCAGCTT GAGGTATAAAA AGCCCTGTAC
38 chr21_46057197_46057247_ 37 4.86e-06 ACAGGCCCTG GGCATATAAAA GCC
39 chr21_45993530_45993580_ 8 4.86e-06 CCAAGGA GGAGTATAAAA GCCCCACAAA
40 chr21_45971413_45971463_ 10 4.86e-06 CAGGCCCTG GGCATATAAAA GCCCCAGCAG
41 chr21_31964683_31964733_ 14 4.86e-06 GATTCACTGA GGCATATAAAA GGCCCTCTGC
42 chr21_47517957_47518007_ 33 6.48e-06 CCGGCGGGGC GGGGTATAAAG GGGGCGG
43 chr21_45978668_45978718_ 5 6.48e-06 CAGA GGGGTATAAAG GTTCCGACCA
44 chr21_32185595_32185645_ 19 6.48e-06 CACCAGAGCT GGGATATATAA AGAAGGTTCT
45 chr21_32410820_32410870_ 22 1.38e-05 AATCACTGAG GATGTATAAAA GTCCCAGGGA
46 chr21_31992870_31992920_ 17 1.38e-05 CACTATTGAA GATGTATAAAA TTTCATTTGC
47 chr21_19617074_19617124_ 40 1.41e-05 CCTCGGGACG TGGGTATATAA
48 chr21_31914206_31914256_ 16 1.61e-05 CCCACTACTT AGAGTATAAAA TCATTCTGAG
49 chr21_46020421_46020471_ 3 1.95e-05 GA GACATATAAAA GCCAACATCC
50 chr21_32253899_32253949_ 18 1.95e-05 CCCACCAGCA AGGATATATAA AAGCTCAGGA
51 chr21_45705687_45705737_ 38 2.16e-05 CGTGGTCGCG GGGGTATAACA GC
52 chr21_47575506_47575556_ 31 3.04e-05 GCTGCCGGTG AGCGTATAAAG GCCCTGGCG
53 chr21_31744582_31744632_ 13 3.04e-05 CAGGTCTAAG AGCATATATAA CTTGGAGTCC
54 chr21_31768316_31768366_ 1 3.67e-05 . AACGTATATAA ATGGTCCTGT
55 chr21_26934381_26934431_ 28 3.93e-05 AGTCACAAGT GAGTTATAAAA GGGTCGCACG
56 chr21_31933633_31933683_ 5 5.65e-05 TCAG AGTATATATAA ATGTTCCTGT
57 chr21_31710037_31710087_ 15 6.24e-05 CCCAGGTTTC TGAGTATATAA TCGCCGCACC
58 chr21_36411748_36411798_ 23 7.15e-05 AGTTTCAGTT GGCATCtaaaa attatataac
59 chr21_46102103_46102153_ 37 1.39e-04 TGCCTGGGTC CAGGTATAAAG GCT
60 chr21_46086869_46086919_ 38 1.39e-04 TGCCTGGGCC CAGGTATAAAG GC
61 chr21_37838750_37838800_ 3 4.81e-04 ga tggttttataa ggggcctcac
62 chr21_31962741_31962791_ 14 8.57e-04 TATAACTCAG GTTGGATAAAA TAATTTGTAC
63 chr21_31973364_31973414_ 8 1.47e-03 aaactta aaactctataa acttaaaact
64 chr21_28217753_28217803_ 27 2.64e-03 GGTGGGGGTG GGGGTTTCACT GGTCCACTAT
65 --------------------------------------------------------------------------------
66
67 --------------------------------------------------------------------------------
68 Motif GGSRTATAAAA MEME-1 block diagrams
69 --------------------------------------------------------------------------------
70 SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
9 ------------- ---------------- ------------- 71 ------------- ---------------- -------------
10 chr21_19617074_19617124_ 5.63e-04 39_[+1(1.41e-05)] 72 chr21_46046964_46047014_ 4.5e-07 12_[+1]_27
11 chr21_26934381_26934431_ 1.57e-03 27_[+1(3.93e-05)]_12 73 chr21_46031920_46031970_ 2.2e-06 15_[+1]_24
12 chr21_28217753_28217803_ 1.00e-01 50 74 chr21_32202076_32202126_ 2.7e-06 13_[+1]_26
13 chr21_31710037_31710087_ 2.49e-03 14_[+1(6.24e-05)]_25 75 chr21_46057197_46057247_ 4.9e-06 36_[+1]_3
14 chr21_31744582_31744632_ 1.22e-03 12_[+1(3.04e-05)]_27 76 chr21_45993530_45993580_ 4.9e-06 7_[+1]_32
15 chr21_31768316_31768366_ 1.47e-03 [+1(3.67e-05)]_39 77 chr21_45971413_45971463_ 4.9e-06 9_[+1]_30
16 chr21_31914206_31914256_ 6.45e-04 15_[+1(1.61e-05)]_24 78 chr21_31964683_31964733_ 4.9e-06 13_[+1]_26
17 chr21_31933633_31933683_ 2.26e-03 4_[+1(5.65e-05)]_35 79 chr21_47517957_47518007_ 6.5e-06 32_[+1]_7
18 chr21_31962741_31962791_ 3.37e-02 50 80 chr21_45978668_45978718_ 6.5e-06 4_[+1]_35
19 chr21_31964683_31964733_ 1.95e-04 13_[+1(4.86e-06)]_26 81 chr21_32185595_32185645_ 6.5e-06 18_[+1]_21
20 chr21_31973364_31973414_ 5.73e-02 50 82 chr21_32410820_32410870_ 1.4e-05 21_[+1]_18
21 chr21_31992870_31992920_ 5.52e-04 16_[+1(1.38e-05)]_23 83 chr21_31992870_31992920_ 1.4e-05 16_[+1]_23
22 chr21_32185595_32185645_ 2.59e-04 18_[+1(6.48e-06)]_21 84 chr21_19617074_19617124_ 1.4e-05 39_[+1]
23 chr21_32202076_32202126_ 1.10e-04 13_[+1(2.74e-06)]_26 85 chr21_31914206_31914256_ 1.6e-05 15_[+1]_24
24 chr21_32253899_32253949_ 7.78e-04 17_[+1(1.95e-05)]_22 86 chr21_46020421_46020471_ 1.9e-05 2_[+1]_37
25 chr21_32410820_32410870_ 5.52e-04 21_[+1(1.38e-05)]_18 87 chr21_32253899_32253949_ 1.9e-05 17_[+1]_22
26 chr21_36411748_36411798_ 2.85e-03 22_[+1(7.15e-05)]_17 88 chr21_45705687_45705737_ 2.2e-05 37_[+1]_2
27 chr21_37838750_37838800_ 1.90e-02 50 89 chr21_47575506_47575556_ 3e-05 30_[+1]_9
28 chr21_45705687_45705737_ 8.63e-04 37_[+1(2.16e-05)]_2 90 chr21_31744582_31744632_ 3e-05 12_[+1]_27
29 chr21_45971413_45971463_ 1.95e-04 9_[+1(4.86e-06)]_30 91 chr21_31768316_31768366_ 3.7e-05 [+1]_39
30 chr21_45978668_45978718_ 2.59e-04 4_[+1(6.48e-06)]_35 92 chr21_26934381_26934431_ 3.9e-05 27_[+1]_12
31 chr21_45993530_45993580_ 1.95e-04 7_[+1(4.86e-06)]_32 93 chr21_31933633_31933683_ 5.6e-05 4_[+1]_35
32 chr21_46020421_46020471_ 7.78e-04 2_[+1(1.95e-05)]_37 94 chr21_31710037_31710087_ 6.2e-05 14_[+1]_25
33 chr21_46031920_46031970_ 8.89e-05 15_[+1(2.22e-06)]_24 95 chr21_36411748_36411798_ 7.1e-05 22_[+1]_17
34 chr21_46046964_46047014_ 1.80e-05 12_[+1(4.51e-07)]_27 96 chr21_46102103_46102153_ 0.00014 36_[+1]_3
35 chr21_46057197_46057247_ 1.95e-04 36_[+1(4.86e-06)]_3 97 chr21_46086869_46086919_ 0.00014 37_[+1]_2
36 chr21_46086869_46086919_ 5.54e-03 50 98 chr21_37838750_37838800_ 0.00048 2_[+1]_37
37 chr21_46102103_46102153_ 5.54e-03 50 99 chr21_31962741_31962791_ 0.00086 13_[+1]_26
38 chr21_47517957_47518007_ 2.59e-04 32_[+1(6.48e-06)]_7 100 chr21_31973364_31973414_ 0.0015 7_[+1]_32
39 chr21_47575506_47575556_ 1.22e-03 30_[+1(3.04e-05)]_9 101 chr21_28217753_28217803_ 0.0026 26_[+1]_13
40 -------------------------------------------------------------------------------- 102 --------------------------------------------------------------------------------
103
104 --------------------------------------------------------------------------------
105 Motif GGSRTATAAAA MEME-1 in BLOCKS format
106 --------------------------------------------------------------------------------
107 BL MOTIF GGSRTATAAAA width=11 seqs=30
108 chr21_46046964_46047014_ ( 13) GGGGTATAAAA 1
109 chr21_46031920_46031970_ ( 16) AGGGTATAAAA 1
110 chr21_32202076_32202126_ ( 14) GAGGTATAAAA 1
111 chr21_46057197_46057247_ ( 37) GGCATATAAAA 1
112 chr21_45993530_45993580_ ( 8) GGAGTATAAAA 1
113 chr21_45971413_45971463_ ( 10) GGCATATAAAA 1
114 chr21_31964683_31964733_ ( 14) GGCATATAAAA 1
115 chr21_47517957_47518007_ ( 33) GGGGTATAAAG 1
116 chr21_45978668_45978718_ ( 5) GGGGTATAAAG 1
117 chr21_32185595_32185645_ ( 19) GGGATATATAA 1
118 chr21_32410820_32410870_ ( 22) GATGTATAAAA 1
119 chr21_31992870_31992920_ ( 17) GATGTATAAAA 1
120 chr21_19617074_19617124_ ( 40) TGGGTATATAA 1
121 chr21_31914206_31914256_ ( 16) AGAGTATAAAA 1
122 chr21_46020421_46020471_ ( 3) GACATATAAAA 1
123 chr21_32253899_32253949_ ( 18) AGGATATATAA 1
124 chr21_45705687_45705737_ ( 38) GGGGTATAACA 1
125 chr21_47575506_47575556_ ( 31) AGCGTATAAAG 1
126 chr21_31744582_31744632_ ( 13) AGCATATATAA 1
127 chr21_31768316_31768366_ ( 1) AACGTATATAA 1
128 chr21_26934381_26934431_ ( 28) GAGTTATAAAA 1
129 chr21_31933633_31933683_ ( 5) AGTATATATAA 1
130 chr21_31710037_31710087_ ( 15) TGAGTATATAA 1
131 chr21_36411748_36411798_ ( 23) GGCATCTAAAA 1
132 chr21_46102103_46102153_ ( 37) CAGGTATAAAG 1
133 chr21_46086869_46086919_ ( 38) CAGGTATAAAG 1
134 chr21_37838750_37838800_ ( 3) TGGTTTTATAA 1
135 chr21_31962741_31962791_ ( 14) GTTGGATAAAA 1
136 chr21_31973364_31973414_ ( 8) AAACTCTATAA 1
137 chr21_28217753_28217803_ ( 27) GGGGTTTCACT 1
138 //
139
140 --------------------------------------------------------------------------------
141
142 --------------------------------------------------------------------------------
143 Motif GGSRTATAAAA MEME-1 position-specific scoring matrix
144 --------------------------------------------------------------------------------
145 log-odds matrix: alength= 4 w= 11 n= 1200 bayes= 5.2854 E= 5.1e-040
146 -14 -179 114 -112
147 3 -1155 137 -270
148 -114 20 86 -71
149 3 -279 122 -170
150 -1155 -1155 -295 215
151 156 -179 -1155 -170
152 -1155 -1155 -1155 220
153 172 -279 -1155 -1155
154 125 -1155 -1155 46
155 167 -179 -1155 -1155
156 144 -1155 -63 -270
157 --------------------------------------------------------------------------------
158
159 --------------------------------------------------------------------------------
160 Motif GGSRTATAAAA MEME-1 position-specific probability matrix
161 --------------------------------------------------------------------------------
162 letter-probability matrix: alength= 4 w= 11 nsites= 30 E= 5.1e-040
163 0.266667 0.066667 0.566667 0.100000
164 0.300000 0.000000 0.666667 0.033333
165 0.133333 0.266667 0.466667 0.133333
166 0.300000 0.033333 0.600000 0.066667
167 0.000000 0.000000 0.033333 0.966667
168 0.866667 0.066667 0.000000 0.066667
169 0.000000 0.000000 0.000000 1.000000
170 0.966667 0.033333 0.000000 0.000000
171 0.700000 0.000000 0.000000 0.300000
172 0.933333 0.066667 0.000000 0.000000
173 0.800000 0.000000 0.166667 0.033333
174 --------------------------------------------------------------------------------
175
176 --------------------------------------------------------------------------------
177 Motif GGSRTATAAAA MEME-1 regular expression
178 --------------------------------------------------------------------------------
179 [GA][GA][GC][GA]TATA[AT]AA
180 --------------------------------------------------------------------------------