# HG changeset patch # User iuc # Date 1724926795 0 # Node ID fd05b142b3a3f77e34fe544c4f885c7c0080429b # Parent f33d77dcacce36cb66561a961bbf572415a9dbc6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9 diff -r f33d77dcacce -r fd05b142b3a3 dreme.xml --- a/dreme.xml Sat Apr 09 08:32:58 2022 +0000 +++ b/dreme.xml Thu Aug 29 10:19:55 2024 +0000 @@ -1,11 +1,9 @@ - + - Discriminative Regular Expression Motif Elicitation macros.xml - - python - + - + - + - + - + @@ -63,31 +54,19 @@ - + - - value is not None and value > 0 + + value is not None and value > 0 - - - - - + + + + + - + value == True @@ -102,9 +81,34 @@ - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -115,9 +119,35 @@ - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0 - 5.4.1 + 5.5.6 + 23.0 meme diff -r f33d77dcacce -r fd05b142b3a3 test-data/dreme_output_test1.html --- a/test-data/dreme_output_test1.html Sat Apr 09 08:32:58 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,100 +0,0 @@ - -

Sequences

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Source	Alphabet	Sequence Count

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Control Sequences

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Source	Sequence Count

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Background

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Other Settings

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Strand Handling	- This alphabet only has one strand - Only the given strand is processed - Both the given and reverse complement strands are processed -
# REs to Generalize
Shuffle Seed
E-value Threshold
Max Motif Count
Max Run Time

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Previous Top

DREME version

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Command line

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- - - diff -r f33d77dcacce -r fd05b142b3a3 test-data/dreme_output_test1.txt --- a/test-data/dreme_output_test1.txt Sat Apr 09 08:32:58 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,64 +0,0 @@ -MOTIF UUYUCY DREME-1 - -# Word Pos Neg P-value E-value -# BEST UUYUCY 387 210 2.6e-018 1.2e-013 -# UUUUCC 147 75 1.8e-007 8.1e-003 -# UUUUCU 155 94 2.2e-005 1.0e+000 -# UUCUCU 94 51 1.3e-004 6.1e+000 -# UUCUCC 75 42 1.1e-003 5.0e+001 - -letter-probability matrix: alength= 4 w= 6 nsites= 459 E= 1.2e-013 -0.000000 0.000000 0.000000 1.000000 -0.000000 0.000000 0.000000 1.000000 -0.000000 0.294118 0.000000 0.705882 -0.000000 0.000000 0.000000 1.000000 -0.000000 1.000000 0.000000 0.000000 -0.000000 0.474946 0.000000 0.525054 - - -MOTIF YAGG DREME-2 - -# Word Pos Neg P-value E-value -# BEST YAGG 600 416 1.1e-016 5.1e-012 -# CAGG 441 304 1.5e-010 6.6e-006 -# UAGG 232 165 1.1e-004 4.7e+000 - -letter-probability matrix: alength= 4 w= 4 nsites= 793 E= 5.1e-012 -0.000000 0.692308 0.000000 0.307692 -1.000000 0.000000 0.000000 0.000000 -0.000000 0.000000 1.000000 0.000000 -0.000000 0.000000 1.000000 0.000000 - - -MOTIF GAAGAW DREME-3 - -# Word Pos Neg P-value E-value -# BEST GAAGAW 81 22 8.2e-010 3.4e-005 -# GAAGAU 45 7 2.4e-008 9.9e-004 -# GAAGAA 40 16 7.9e-004 3.3e+001 - -letter-probability matrix: alength= 4 w= 6 nsites= 89 E= 3.4e-005 -0.000000 0.000000 1.000000 0.000000 -1.000000 0.000000 0.000000 0.000000 -1.000000 0.000000 0.000000 0.000000 -0.000000 0.000000 1.000000 0.000000 -1.000000 0.000000 0.000000 0.000000 -0.494382 0.000000 0.000000 0.505618 - - -MOTIF SMUGGA DREME-4 - -# Word Pos Neg P-value E-value -# BEST SMUGGA 110 47 9.1e-008 3.7e-003 -# GAUGGA 22 6 1.7e-003 7.1e+001 -# GCUGGA 33 14 3.6e-003 1.5e+002 -# CCUGGA 32 15 8.6e-003 3.5e+002 -# CAUGGA 29 13 9.1e-003 3.7e+002 - -letter-probability matrix: alength= 4 w= 6 nsites= 119 E= 3.7e-003 -0.000000 0.529412 0.470588 0.000000 -0.428571 0.571429 0.000000 0.000000 -0.000000 0.000000 0.000000 1.000000 -0.000000 0.000000 1.000000 0.000000 -0.000000 0.000000 1.000000 0.000000 -1.000000 0.000000 0.000000 0.000000 diff -r f33d77dcacce -r fd05b142b3a3 test-data/dreme_output_test1.xml --- a/test-data/dreme_output_test1.xml Sat Apr 09 08:32:58 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,44 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff -r f33d77dcacce -r fd05b142b3a3 test-data/dreme_output_test2.html --- a/test-data/dreme_output_test2.html Sat Apr 09 08:32:58 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,50 +0,0 @@ -

Other Settings

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Strand Handling	- This alphabet only has one strand - Only the given strand is processed - Both the given and reverse complement strands are processed -
# REs to Generalize
Shuffle Seed
E-value Threshold
Max Motif Count
Max Run Time

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Previous Top

DREME version

- - (Release date: )
-

- -

Command line

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- -

- - - diff -r f33d77dcacce -r fd05b142b3a3 test-data/dreme_output_test2.txt --- a/test-data/dreme_output_test2.txt Sat Apr 09 08:32:58 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,55 +0,0 @@ -ALPHABET "RNA" RNA-LIKE -A "Adenine" CC0000 -C "Cytosine" 0000CC -G "Guanine" FFB300 -U "Uracil" 008000 -N "Any base" = ACGU -X = ACGU -. = ACGU -V "Not U" = ACG -H "Not G" = ACU -D "Not C" = AGU -B "Not A" = CGU -M "Amino" = AC -R "Purine" = AG -W "Weak" = AU -S "Strong" = CG -Y "Pyrimidine" = CU -K "Keto" = GU -T = U -END ALPHABET - -Background letter frequencies (from dataset): -A 0.221 C 0.245 G 0.221 U 0.312 - - -MOTIF UUYUCY DREME-1 - -# Word Pos Neg P-value E-value -# BEST UUYUCY 387 210 2.6e-018 3.3e-013 -# UUUUCC 147 75 1.8e-007 2.2e-002 -# UUUUCU 155 94 2.2e-005 2.8e+000 -# UUCUCU 94 51 1.3e-004 1.7e+001 -# UUCUCC 75 42 1.1e-003 1.4e+002 - -letter-probability matrix: alength= 4 w= 6 nsites= 459 E= 3.3e-013 -0.000000 0.000000 0.000000 1.000000 -0.000000 0.000000 0.000000 1.000000 -0.000000 0.294118 0.000000 0.705882 -0.000000 0.000000 0.000000 1.000000 -0.000000 1.000000 0.000000 0.000000 -0.000000 0.474946 0.000000 0.525054 - - -MOTIF YAGG DREME-2 - -# Word Pos Neg P-value E-value -# BEST YAGG 600 416 1.1e-016 1.4e-011 -# CAGG 441 304 1.5e-010 1.8e-005 -# UAGG 232 165 1.1e-004 1.3e+001 - -letter-probability matrix: alength= 4 w= 4 nsites= 793 E= 1.4e-011 -0.000000 0.692308 0.000000 0.307692 -1.000000 0.000000 0.000000 0.000000 -0.000000 0.000000 1.000000 0.000000 -0.000000 0.000000 1.000000 0.000000 \ No newline at end of file diff -r f33d77dcacce -r fd05b142b3a3 test-data/dreme_output_test2.xml --- a/test-data/dreme_output_test2.xml Sat Apr 09 08:32:58 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,22 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff -r f33d77dcacce -r fd05b142b3a3 test-data/fimo_output_test1.gff --- a/test-data/fimo_output_test1.gff Sat Apr 09 08:32:58 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ -##gff-version 3 -chrM fimo nucleotide_motif 6529 6536 46.6 + . Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-1-chrM;pvalue=2.18e-05;qvalue=0.142;sequence=TACTAACA; -chrM fimo nucleotide_motif 7741 7748 46.6 + . Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-2-chrM;pvalue=2.18e-05;qvalue=0.142;sequence=TACTAACA; -chrM fimo nucleotide_motif 13656 13663 46.6 + . Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-3-chrM;pvalue=2.18e-05;qvalue=0.142;sequence=TACTAACA; -chrM fimo nucleotide_motif 13740 13747 46.6 + . Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-4-chrM;pvalue=2.18e-05;qvalue=0.142;sequence=TACTAACA; -chrM fimo nucleotide_motif 2299 2306 46.6 - . Name=TACTAAYM_chrM-;Alias=MEME-1;ID=TACTAAYM-MEME-1-5-chrM;pvalue=2.18e-05;qvalue=0.142;sequence=TACTAACA; -chrM fimo nucleotide_motif 861 868 44 + . Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-6-chrM;pvalue=3.96e-05;qvalue=0.185;sequence=TACTAACC; -chrM fimo nucleotide_motif 9346 9353 44 + . Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-7-chrM;pvalue=3.96e-05;qvalue=0.185;sequence=TACTAACC; -chrM fimo nucleotide_motif 3767 3774 41.8 + . Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-8-chrM;pvalue=6.62e-05;qvalue=0.216;sequence=TACTAATA; -chrM fimo nucleotide_motif 5497 5504 41.8 + . Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-9-chrM;pvalue=6.62e-05;qvalue=0.216;sequence=TACTAATA; -chrM fimo nucleotide_motif 10105 10112 41.8 + . Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-10-chrM;pvalue=6.62e-05;qvalue=0.216;sequence=TACTAATA; -chrM fimo nucleotide_motif 10959 10966 40.6 + . Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-11-chrM;pvalue=8.79e-05;qvalue=0.261;sequence=TACTAACT; diff -r f33d77dcacce -r fd05b142b3a3 test-data/fimo_output_test1.html --- a/test-data/fimo_output_test1.html Sat Apr 09 08:32:58 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,34 +0,0 @@ - background file name = --nrdb-- - alphabet = DNA - max stored scores = 100000 - - allow clobber = false - compute q-values = true - parse genomic coord. = false - - - text only = false - scan both strands = true - max strand = false - - - threshold type = p-value - output theshold = 0.0001 - pseudocount = 0.1 - - - alpha = 1 - verbosity = 2 - - - - - -

-This information can be useful in the event you wish to report a -problem with the FIMO software. -

-Go to top - - diff -r f33d77dcacce -r fd05b142b3a3 test-data/fimo_output_test1.txt --- a/test-data/fimo_output_test1.txt Sat Apr 09 08:32:58 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ -motif_id motif_alt_id sequence_name start stop strand score p-value q-value matched_sequence -TACTAAYM MEME-1 chrM 6529 6536 + 12.9701 2.18e-05 0.142 TACTAACA -TACTAAYM MEME-1 chrM 7741 7748 + 12.9701 2.18e-05 0.142 TACTAACA -TACTAAYM MEME-1 chrM 13656 13663 + 12.9701 2.18e-05 0.142 TACTAACA -TACTAAYM MEME-1 chrM 13740 13747 + 12.9701 2.18e-05 0.142 TACTAACA -TACTAAYM MEME-1 chrM 2299 2306 - 12.9701 2.18e-05 0.142 TACTAACA -TACTAAYM MEME-1 chrM 861 868 + 12.2836 3.96e-05 0.185 TACTAACC -TACTAAYM MEME-1 chrM 9346 9353 + 12.2836 3.96e-05 0.185 TACTAACC -TACTAAYM MEME-1 chrM 3767 3774 + 11.7164 6.62e-05 0.216 TACTAATA -TACTAAYM MEME-1 chrM 5497 5504 + 11.7164 6.62e-05 0.216 TACTAATA -TACTAAYM MEME-1 chrM 10105 10112 + 11.7164 6.62e-05 0.216 TACTAATA -TACTAAYM MEME-1 chrM 10959 10966 + 11.6567 8.79e-05 0.261 TACTAACT diff -r f33d77dcacce -r fd05b142b3a3 test-data/fimo_output_test1.xml --- a/test-data/fimo_output_test1.xml Sat Apr 09 08:32:58 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,39 +0,0 @@ ---nrdb-- -false -true -false -false -true -0.0001 -p-value -100000 -0.1 -2 - - - - - - - - - - - - - - - - - - - - - -0.275 -0.225 -0.225 -0.275 - -cisml.xml - diff -r f33d77dcacce -r fd05b142b3a3 test-data/fimo_output_test2.gff --- a/test-data/fimo_output_test2.gff Sat Apr 09 08:32:58 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ -##gff-version 3 -chrM fimo nucleotide_motif 440 446 40.9 + . Name=ACTAAYH_chrM+;Alias=DREME-1;ID=ACTAAYH-DREME-1-1-chrM;pvalue=8.2e-05;qvalue=0.332;sequence=ACTAACA; -chrM fimo nucleotide_motif 2093 2099 40.9 - . Name=ACTAAYH_chrM-;Alias=DREME-1;ID=ACTAAYH-DREME-1-2-chrM;pvalue=8.2e-05;qvalue=0.332;sequence=ACTAACA; -chrM fimo nucleotide_motif 2299 2305 40.9 - . Name=ACTAAYH_chrM-;Alias=DREME-1;ID=ACTAAYH-DREME-1-3-chrM;pvalue=8.2e-05;qvalue=0.332;sequence=ACTAACA; -chrM fimo nucleotide_motif 5186 5192 40.9 + . Name=ACTAAYH_chrM+;Alias=DREME-1;ID=ACTAAYH-DREME-1-4-chrM;pvalue=8.2e-05;qvalue=0.332;sequence=ACTAACA; -chrM fimo nucleotide_motif 6530 6536 40.9 + . Name=ACTAAYH_chrM+;Alias=DREME-1;ID=ACTAAYH-DREME-1-5-chrM;pvalue=8.2e-05;qvalue=0.332;sequence=ACTAACA; -chrM fimo nucleotide_motif 7742 7748 40.9 + . Name=ACTAAYH_chrM+;Alias=DREME-1;ID=ACTAAYH-DREME-1-6-chrM;pvalue=8.2e-05;qvalue=0.332;sequence=ACTAACA; -chrM fimo nucleotide_motif 13657 13663 40.9 + . Name=ACTAAYH_chrM+;Alias=DREME-1;ID=ACTAAYH-DREME-1-7-chrM;pvalue=8.2e-05;qvalue=0.332;sequence=ACTAACA; -chrM fimo nucleotide_motif 13741 13747 40.9 + . Name=ACTAAYH_chrM+;Alias=DREME-1;ID=ACTAAYH-DREME-1-8-chrM;pvalue=8.2e-05;qvalue=0.332;sequence=ACTAACA; -chrM fimo nucleotide_motif 510 516 43.8 + . Name=CCAGCAY_chrM+;Alias=DREME-5;ID=CCAGCAY-DREME-5-1-chrM;pvalue=4.15e-05;qvalue=0.683;sequence=CCAGCAC; -chrM fimo nucleotide_motif 5137 5143 43.8 + . Name=CCAGCAY_chrM+;Alias=DREME-5;ID=CCAGCAY-DREME-5-2-chrM;pvalue=4.15e-05;qvalue=0.683;sequence=CCAGCAC; -chrM fimo nucleotide_motif 4241 4247 40.3 + . Name=CCAGCAY_chrM+;Alias=DREME-5;ID=CCAGCAY-DREME-5-3-chrM;pvalue=9.37e-05;qvalue=1;sequence=CCAGCAT; diff -r f33d77dcacce -r fd05b142b3a3 test-data/fimo_output_test2.html --- a/test-data/fimo_output_test2.html Sat Apr 09 08:32:58 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,33 +0,0 @@ - alphabet = DNA - max stored scores = 100000 - - allow clobber = false - compute q-values = true - parse genomic coord. = false - - - text only = false - scan both strands = true - max strand = false - - - threshold type = p-value - output theshold = 0.0001 - pseudocount = 0.1 - - - alpha = 1 - verbosity = 2 - - - - - -

-This information can be useful in the event you wish to report a -problem with the FIMO software. -

-Go to top - - diff -r f33d77dcacce -r fd05b142b3a3 test-data/fimo_output_test2.txt --- a/test-data/fimo_output_test2.txt Sat Apr 09 08:32:58 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ -motif_id motif_alt_id sequence_name start stop strand score p-value q-value matched_sequence -CCAGCAY DREME-5 chrM 510 516 + 13.5843 4.15e-05 0.683 CCAGCAC -CCAGCAY DREME-5 chrM 5137 5143 + 13.5843 4.15e-05 0.683 CCAGCAC -ACTAAYH DREME-1 chrM 440 446 + 11.7286 8.2e-05 0.332 ACTAACA -ACTAAYH DREME-1 chrM 2093 2099 - 11.7286 8.2e-05 0.332 ACTAACA -ACTAAYH DREME-1 chrM 2299 2305 - 11.7286 8.2e-05 0.332 ACTAACA -ACTAAYH DREME-1 chrM 5186 5192 + 11.7286 8.2e-05 0.332 ACTAACA -ACTAAYH DREME-1 chrM 6530 6536 + 11.7286 8.2e-05 0.332 ACTAACA -ACTAAYH DREME-1 chrM 7742 7748 + 11.7286 8.2e-05 0.332 ACTAACA -ACTAAYH DREME-1 chrM 13657 13663 + 11.7286 8.2e-05 0.332 ACTAACA -ACTAAYH DREME-1 chrM 13741 13747 + 11.7286 8.2e-05 0.332 ACTAACA -CCAGCAY DREME-5 chrM 4241 4247 + 13.1461 9.37e-05 1 CCAGCAT \ No newline at end of file diff -r f33d77dcacce -r fd05b142b3a3 test-data/fimo_output_test2.xml --- a/test-data/fimo_output_test2.xml Sat Apr 09 08:32:58 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,34 +0,0 @@ -true -false -false -true -0.0001 -p-value -100000 -0.1 -2 - - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff -r f33d77dcacce -r fd05b142b3a3 test-data/fimo_output_test3.html --- a/test-data/fimo_output_test3.html Sat Apr 09 08:32:58 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,23 +0,0 @@ - background file name = --uniform-- - alphabet = DNA - max stored scores = 100000 - - allow clobber = false - compute q-values = true - parse genomic coord. = false - - - text only = false - scan both strands = true - max strand = false - - - threshold type = p-value - output theshold = 0.01 - pseudocount = 0.1 - - - alpha = 1 - verbosity = 2 - - \ No newline at end of file diff -r f33d77dcacce -r fd05b142b3a3 test-data/fimo_output_test3.txt --- a/test-data/fimo_output_test3.txt Sat Apr 09 08:32:58 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,40 +0,0 @@ -motif_id motif_alt_id sequence_name start stop strand score p-value q-value matched_sequence -ACTAAYH DREME-1 chrM 440 446 + 12.1831 6.1e-05 0.239 ACTAACA -ACTAAYH DREME-1 chrM 2093 2099 - 12.1831 6.1e-05 0.239 ACTAACA -ACTAAYH DREME-1 chrM 2299 2305 - 12.1831 6.1e-05 0.239 ACTAACA -ACTAAYH DREME-1 chrM 5186 5192 + 12.1831 6.1e-05 0.239 ACTAACA -ACTAAYH DREME-1 chrM 6530 6536 + 12.1831 6.1e-05 0.239 ACTAACA -ACTAAYH DREME-1 chrM 7742 7748 + 12.1831 6.1e-05 0.239 ACTAACA -ACTAAYH DREME-1 chrM 13657 13663 + 12.1831 6.1e-05 0.239 ACTAACA -ACTAAYH DREME-1 chrM 13741 13747 + 12.1831 6.1e-05 0.239 ACTAACA -ACTAAYH DREME-1 chrM 3768 3774 + 11.5915 0.000122 0.239 ACTAATA -ACTAAYH DREME-1 chrM 5498 5504 + 11.5915 0.000122 0.239 ACTAATA -ACTAAYH DREME-1 chrM 7736 7742 + 11.5915 0.000122 0.239 ACTAATA -ACTAAYH DREME-1 chrM 9872 9878 + 11.5915 0.000122 0.239 ACTAATA -ACTAAYH DREME-1 chrM 10106 10112 + 11.5915 0.000122 0.239 ACTAATA -ACTAAYH DREME-1 chrM 10313 10319 + 11.5915 0.000122 0.239 ACTAATA -ACTAAYH DREME-1 chrM 11818 11824 + 11.5915 0.000122 0.239 ACTAATA -ACTAAYH DREME-1 chrM 15903 15909 + 11.5915 0.000122 0.239 ACTAATA -ACTAAYH DREME-1 chrM 7732 7738 + 11.4507 0.000183 0.294 ACTAACT -ACTAAYH DREME-1 chrM 10960 10966 + 11.4507 0.000183 0.294 ACTAACT -ACTAAYH DREME-1 chrM 862 868 + 11.2394 0.000244 0.294 ACTAACC -ACTAAYH DREME-1 chrM 1832 1838 + 11.2394 0.000244 0.294 ACTAACC -ACTAAYH DREME-1 chrM 8679 8685 + 11.2394 0.000244 0.294 ACTAACC -ACTAAYH DREME-1 chrM 8770 8776 + 11.2394 0.000244 0.294 ACTAACC -ACTAAYH DREME-1 chrM 9347 9353 + 11.2394 0.000244 0.294 ACTAACC -ACTAAYH DREME-1 chrM 9359 9365 + 11.2394 0.000244 0.294 ACTAACC -ACTAAYH DREME-1 chrM 10302 10308 + 11.2394 0.000244 0.294 ACTAACC -ACTAAYH DREME-1 chrM 14765 14771 + 11.2394 0.000244 0.294 ACTAACC -ACTAAYH DREME-1 chrM 4466 4472 + 10.8592 0.000305 0.302 ACTAATT -ACTAAYH DREME-1 chrM 11248 11254 + 10.8592 0.000305 0.302 ACTAATT -ACTAAYH DREME-1 chrM 475 481 + 10.6479 0.000366 0.302 ACTAATC -ACTAAYH DREME-1 chrM 7930 7936 + 10.6479 0.000366 0.302 ACTAATC -ACTAAYH DREME-1 chrM 8649 8655 + 10.6479 0.000366 0.302 ACTAATC -ACTAAYH DREME-1 chrM 8670 8676 + 10.6479 0.000366 0.302 ACTAATC -ACTAAYH DREME-1 chrM 10768 10774 + 10.6479 0.000366 0.302 ACTAATC -ACTAAYH DREME-1 chrM 11053 11059 + 10.6479 0.000366 0.302 ACTAATC -ACTAAYH DREME-1 chrM 11101 11107 + 10.6479 0.000366 0.302 ACTAATC -ACTAAYH DREME-1 chrM 12720 12726 + 10.6479 0.000366 0.302 ACTAATC -ACTAAYH DREME-1 chrM 13149 13155 + 10.6479 0.000366 0.302 ACTAATC -ACTAAYH DREME-1 chrM 14216 14222 + 10.6479 0.000366 0.302 ACTAATC -ACTAAYH DREME-1 chrM 678 684 - -1.07042 0.000549 0.366 ACTAAGA \ No newline at end of file diff -r f33d77dcacce -r fd05b142b3a3 test-data/fimo_output_test3.xml --- a/test-data/fimo_output_test3.xml Sat Apr 09 08:32:58 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,32 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - -0.250 -0.250 -0.250 -0.250 - -cisml.xml -