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diff test-data/meme_output_test2.txt @ 0:7653ebd919bb 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 21:33:08 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/meme_output_test2.txt	Mon Jul 14 21:33:08 2025 +0000
@@ -0,0 +1,180 @@
+********************************************************************************
+MOTIF GGSRTATAAAA MEME-1	width =  11  sites =  30  llr = 254  E-value = 5.1e-040
+********************************************************************************
+--------------------------------------------------------------------------------
+	Motif GGSRTATAAAA MEME-1 Description
+--------------------------------------------------------------------------------
+Simplified        A  3313:9:a798
+pos.-specific     C  1:3::1:::1:
+probability       G  6756::::::2
+matrix            T  1:11a1a:3::
+
+         bits    2.2       *    
+                 2.0     * *    
+                 1.8     * *    
+                 1.5     * ** * 
+Relative         1.3     * ** * 
+Entropy          1.1     ****** 
+(12.2 bits)      0.9  *  *******
+                 0.7  *  *******
+                 0.4 ** ********
+                 0.2 ***********
+                 0.0 -----------
+
+Multilevel           GGGGTATAAAA
+consensus            AACA    T  
+sequence                        
+                                
+--------------------------------------------------------------------------------
+
+--------------------------------------------------------------------------------
+	Motif GGSRTATAAAA MEME-1 sites sorted by position p-value
+--------------------------------------------------------------------------------
+Sequence name             Start   P-value               Site  
+-------------             ----- ---------            -----------
+chr21_46046964_46047014_     13  4.51e-07 AAGGCCAGGA GGGGTATAAAA GCCTGAGAGC
+chr21_46031920_46031970_     16  2.22e-06 ATACCCAGGG AGGGTATAAAA CCTCAGCAGC
+chr21_32202076_32202126_     14  2.74e-06 CCACCAGCTT GAGGTATAAAA AGCCCTGTAC
+chr21_46057197_46057247_     37  4.86e-06 ACAGGCCCTG GGCATATAAAA GCC       
+chr21_45993530_45993580_      8  4.86e-06    CCAAGGA GGAGTATAAAA GCCCCACAAA
+chr21_45971413_45971463_     10  4.86e-06  CAGGCCCTG GGCATATAAAA GCCCCAGCAG
+chr21_31964683_31964733_     14  4.86e-06 GATTCACTGA GGCATATAAAA GGCCCTCTGC
+chr21_47517957_47518007_     33  6.48e-06 CCGGCGGGGC GGGGTATAAAG GGGGCGG   
+chr21_45978668_45978718_      5  6.48e-06       CAGA GGGGTATAAAG GTTCCGACCA
+chr21_32185595_32185645_     19  6.48e-06 CACCAGAGCT GGGATATATAA AGAAGGTTCT
+chr21_32410820_32410870_     22  1.38e-05 AATCACTGAG GATGTATAAAA GTCCCAGGGA
+chr21_31992870_31992920_     17  1.38e-05 CACTATTGAA GATGTATAAAA TTTCATTTGC
+chr21_19617074_19617124_     40  1.41e-05 CCTCGGGACG TGGGTATATAA           
+chr21_31914206_31914256_     16  1.61e-05 CCCACTACTT AGAGTATAAAA TCATTCTGAG
+chr21_46020421_46020471_      3  1.95e-05         GA GACATATAAAA GCCAACATCC
+chr21_32253899_32253949_     18  1.95e-05 CCCACCAGCA AGGATATATAA AAGCTCAGGA
+chr21_45705687_45705737_     38  2.16e-05 CGTGGTCGCG GGGGTATAACA GC        
+chr21_47575506_47575556_     31  3.04e-05 GCTGCCGGTG AGCGTATAAAG GCCCTGGCG 
+chr21_31744582_31744632_     13  3.04e-05 CAGGTCTAAG AGCATATATAA CTTGGAGTCC
+chr21_31768316_31768366_      1  3.67e-05          . AACGTATATAA ATGGTCCTGT
+chr21_26934381_26934431_     28  3.93e-05 AGTCACAAGT GAGTTATAAAA GGGTCGCACG
+chr21_31933633_31933683_      5  5.65e-05       TCAG AGTATATATAA ATGTTCCTGT
+chr21_31710037_31710087_     15  6.24e-05 CCCAGGTTTC TGAGTATATAA TCGCCGCACC
+chr21_36411748_36411798_     23  7.15e-05 AGTTTCAGTT GGCATCtaaaa attatataac
+chr21_46102103_46102153_     37  1.39e-04 TGCCTGGGTC CAGGTATAAAG GCT       
+chr21_46086869_46086919_     38  1.39e-04 TGCCTGGGCC CAGGTATAAAG GC        
+chr21_37838750_37838800_      3  4.81e-04         ga tggttttataa ggggcctcac
+chr21_31962741_31962791_     14  8.57e-04 TATAACTCAG GTTGGATAAAA TAATTTGTAC
+chr21_31973364_31973414_      8  1.47e-03    aaactta aaactctataa acttaaaact
+chr21_28217753_28217803_     27  2.64e-03 GGTGGGGGTG GGGGTTTCACT GGTCCACTAT
+--------------------------------------------------------------------------------
+
+--------------------------------------------------------------------------------
+	Motif GGSRTATAAAA MEME-1 block diagrams
+--------------------------------------------------------------------------------
+SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
+-------------            ----------------  -------------
+chr21_46046964_46047014_          4.5e-07  12_[+1]_27
+chr21_46031920_46031970_          2.2e-06  15_[+1]_24
+chr21_32202076_32202126_          2.7e-06  13_[+1]_26
+chr21_46057197_46057247_          4.9e-06  36_[+1]_3
+chr21_45993530_45993580_          4.9e-06  7_[+1]_32
+chr21_45971413_45971463_          4.9e-06  9_[+1]_30
+chr21_31964683_31964733_          4.9e-06  13_[+1]_26
+chr21_47517957_47518007_          6.5e-06  32_[+1]_7
+chr21_45978668_45978718_          6.5e-06  4_[+1]_35
+chr21_32185595_32185645_          6.5e-06  18_[+1]_21
+chr21_32410820_32410870_          1.4e-05  21_[+1]_18
+chr21_31992870_31992920_          1.4e-05  16_[+1]_23
+chr21_19617074_19617124_          1.4e-05  39_[+1]
+chr21_31914206_31914256_          1.6e-05  15_[+1]_24
+chr21_46020421_46020471_          1.9e-05  2_[+1]_37
+chr21_32253899_32253949_          1.9e-05  17_[+1]_22
+chr21_45705687_45705737_          2.2e-05  37_[+1]_2
+chr21_47575506_47575556_            3e-05  30_[+1]_9
+chr21_31744582_31744632_            3e-05  12_[+1]_27
+chr21_31768316_31768366_          3.7e-05  [+1]_39
+chr21_26934381_26934431_          3.9e-05  27_[+1]_12
+chr21_31933633_31933683_          5.6e-05  4_[+1]_35
+chr21_31710037_31710087_          6.2e-05  14_[+1]_25
+chr21_36411748_36411798_          7.1e-05  22_[+1]_17
+chr21_46102103_46102153_          0.00014  36_[+1]_3
+chr21_46086869_46086919_          0.00014  37_[+1]_2
+chr21_37838750_37838800_          0.00048  2_[+1]_37
+chr21_31962741_31962791_          0.00086  13_[+1]_26
+chr21_31973364_31973414_           0.0015  7_[+1]_32
+chr21_28217753_28217803_           0.0026  26_[+1]_13
+--------------------------------------------------------------------------------
+
+--------------------------------------------------------------------------------
+	Motif GGSRTATAAAA MEME-1 in BLOCKS format
+--------------------------------------------------------------------------------
+BL   MOTIF GGSRTATAAAA width=11 seqs=30
+chr21_46046964_46047014_ (   13) GGGGTATAAAA  1 
+chr21_46031920_46031970_ (   16) AGGGTATAAAA  1 
+chr21_32202076_32202126_ (   14) GAGGTATAAAA  1 
+chr21_46057197_46057247_ (   37) GGCATATAAAA  1 
+chr21_45993530_45993580_ (    8) GGAGTATAAAA  1 
+chr21_45971413_45971463_ (   10) GGCATATAAAA  1 
+chr21_31964683_31964733_ (   14) GGCATATAAAA  1 
+chr21_47517957_47518007_ (   33) GGGGTATAAAG  1 
+chr21_45978668_45978718_ (    5) GGGGTATAAAG  1 
+chr21_32185595_32185645_ (   19) GGGATATATAA  1 
+chr21_32410820_32410870_ (   22) GATGTATAAAA  1 
+chr21_31992870_31992920_ (   17) GATGTATAAAA  1 
+chr21_19617074_19617124_ (   40) TGGGTATATAA  1 
+chr21_31914206_31914256_ (   16) AGAGTATAAAA  1 
+chr21_46020421_46020471_ (    3) GACATATAAAA  1 
+chr21_32253899_32253949_ (   18) AGGATATATAA  1 
+chr21_45705687_45705737_ (   38) GGGGTATAACA  1 
+chr21_47575506_47575556_ (   31) AGCGTATAAAG  1 
+chr21_31744582_31744632_ (   13) AGCATATATAA  1 
+chr21_31768316_31768366_ (    1) AACGTATATAA  1 
+chr21_26934381_26934431_ (   28) GAGTTATAAAA  1 
+chr21_31933633_31933683_ (    5) AGTATATATAA  1 
+chr21_31710037_31710087_ (   15) TGAGTATATAA  1 
+chr21_36411748_36411798_ (   23) GGCATCTAAAA  1 
+chr21_46102103_46102153_ (   37) CAGGTATAAAG  1 
+chr21_46086869_46086919_ (   38) CAGGTATAAAG  1 
+chr21_37838750_37838800_ (    3) TGGTTTTATAA  1 
+chr21_31962741_31962791_ (   14) GTTGGATAAAA  1 
+chr21_31973364_31973414_ (    8) AAACTCTATAA  1 
+chr21_28217753_28217803_ (   27) GGGGTTTCACT  1 
+//
+
+--------------------------------------------------------------------------------
+
+--------------------------------------------------------------------------------
+	Motif GGSRTATAAAA MEME-1 position-specific scoring matrix
+--------------------------------------------------------------------------------
+log-odds matrix: alength= 4 w= 11 n= 1200 bayes= 5.2854 E= 5.1e-040 
+   -14   -179    114   -112 
+     3  -1155    137   -270 
+  -114     20     86    -71 
+     3   -279    122   -170 
+ -1155  -1155   -295    215 
+   156   -179  -1155   -170 
+ -1155  -1155  -1155    220 
+   172   -279  -1155  -1155 
+   125  -1155  -1155     46 
+   167   -179  -1155  -1155 
+   144  -1155    -63   -270 
+--------------------------------------------------------------------------------
+
+--------------------------------------------------------------------------------
+	Motif GGSRTATAAAA MEME-1 position-specific probability matrix
+--------------------------------------------------------------------------------
+letter-probability matrix: alength= 4 w= 11 nsites= 30 E= 5.1e-040 
+ 0.266667  0.066667  0.566667  0.100000 
+ 0.300000  0.000000  0.666667  0.033333 
+ 0.133333  0.266667  0.466667  0.133333 
+ 0.300000  0.033333  0.600000  0.066667 
+ 0.000000  0.000000  0.033333  0.966667 
+ 0.866667  0.066667  0.000000  0.066667 
+ 0.000000  0.000000  0.000000  1.000000 
+ 0.966667  0.033333  0.000000  0.000000 
+ 0.700000  0.000000  0.000000  0.300000 
+ 0.933333  0.066667  0.000000  0.000000 
+ 0.800000  0.000000  0.166667  0.033333 
+--------------------------------------------------------------------------------
+
+--------------------------------------------------------------------------------
+	Motif GGSRTATAAAA MEME-1 regular expression
+--------------------------------------------------------------------------------
+[GA][GA][GC][GA]TATA[AT]AA
+--------------------------------------------------------------------------------
\ No newline at end of file