Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002574.1 Hibiscus syriacus cultivar Beakdansim tig00005217_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 52093
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:4975 original size:50 final size:50
Alignment explanation
Indices: 4890--4988 Score: 130
Period size: 50 Copynumber: 2.0 Consensus size: 50
4880 GCACATGAAG
* *
4890 ACTTTGGCACTAAGATGAACCAATACATCATCATTCGGCCAAGGAAGATA
1 ACTTTGGCACCAAGATGAACCAATACATCACCATTCGGCCAAGGAAGATA
* *
4940 ACTTTGGCACCAAGATGAA-CAA-GCATGTCACCATTCGGCCAAGGGAGAT
1 ACTTTGGCACCAAGATGAACCAATACA--TCACCATTCGGCCAAGGAAGAT
4989 GTATCTTCAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
48 2 0.05
49 3 0.07
50 38 0.88
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.20
Consensus pattern (50 bp):
ACTTTGGCACCAAGATGAACCAATACATCACCATTCGGCCAAGGAAGATA
Found at i:9651 original size:21 final size:21
Alignment explanation
Indices: 9625--9676 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
9615 CTTTTCTATC
9625 CTTATTCCATTAATTATTTTA
1 CTTATTCCATTAATTATTTTA
*
9646 CTTATTCAATTAATTATTTTA
1 CTTATTCCATTAATTATTTTA
9667 CTTA-TCCATT
1 CTTATTCCATT
9677 TCTTATACCT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 5 0.17
21 24 0.83
ACGTcount: A:0.29, C:0.15, G:0.00, T:0.56
Consensus pattern (21 bp):
CTTATTCCATTAATTATTTTA
Found at i:12074 original size:77 final size:79
Alignment explanation
Indices: 11973--12121 Score: 189
Period size: 77 Copynumber: 1.9 Consensus size: 79
11963 ATAAAAAAAA
* *
11973 ACTTATTTAATTAATTCATATTAAATATTC-ATT-AAAGACTTATAATATGAATTACAATC-TTT
1 ACTTATTTAATTAATTCAAATTAAATA-TCGATTAAAAGACTTATAATAGGAATTACAATCTTTT
12035 AACGTTTATTTAAAC
65 AACGTTTATTTAAAC
* * * *
12050 ACTTATTTAATT-ATTCCAAATTAAATATCGATTAAAAGAGTTGTAATCGGAATTACATTCTTTT
1 ACTTATTTAATTAATT-CAAATTAAATATCGATTAAAAGACTTATAATAGGAATTACAATCTTTT
*
12114 AATGTTTA
65 AACGTTTA
12122 CTTATTATAT
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
76 5 0.08
77 25 0.41
78 21 0.34
79 10 0.16
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.44
Consensus pattern (79 bp):
ACTTATTTAATTAATTCAAATTAAATATCGATTAAAAGACTTATAATAGGAATTACAATCTTTTA
ACGTTTATTTAAAC
Found at i:24500 original size:21 final size:20
Alignment explanation
Indices: 24476--24514 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
24466 TTTAATACAC
24476 AAGGGATCGATCCGTTTATGA
1 AAGGGATCGATCC-TTTATGA
24497 AAGGGATCGATCCTTTAT
1 AAGGGATCGATCCTTTAT
24515 CAAATAATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (20 bp):
AAGGGATCGATCCTTTATGA
Found at i:24582 original size:21 final size:22
Alignment explanation
Indices: 24558--24616 Score: 86
Period size: 21 Copynumber: 2.8 Consensus size: 22
24548 TCTATTAGAG
24558 GAAGGGATCAATCCTTTTGCT-
1 GAAGGGATCAATCCTTTTGCTC
* *
24579 GAAGGGATCAATCATTTTTCTC
1 GAAGGGATCAATCCTTTTGCTC
24601 G-AGGGATCAATCCTTT
1 GAAGGGATCAATCCTTT
24617 GGTGAGGGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 33 0.97
22 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (22 bp):
GAAGGGATCAATCCTTTTGCTC
Found at i:27751 original size:833 final size:833
Alignment explanation
Indices: 26146--28645 Score: 4892
Period size: 833 Copynumber: 3.0 Consensus size: 833
26136 TTGAATTAGT
26146 TGTTGTTATTGAAATGATTTATAATGCTTAGATATGTTGTTTGGAAGAAGAATTCATGCTTGAAT
1 TGTTGTTATTGAAATGATTTATAATGCTTAGATATGTTGTTTGGAAGAAGAATTCATGCTTGAAT
* *
26211 CAAGTTGGATATCATATCCATGATGATACATGATATTTGACCAATGAAGAAAAATTAGGAAAAAA
66 CAAGTTGGATATCATATCTATGATGATACATGATATTTGACCATTGAAGAAAAATTAGGAAAAAA
26276 TTATTCATTTTTTTAAGACTTGACATAATGAATTGATGATTATAAAACCTTTATAATGTTGTTTG
131 TTATTCATTTTTTTAAGACTTGACATAATGAATTGATGATTATAAAACCTTTATAATGTTGTTTG
26341 GATCAATTTTGAATTATGGAAAGGTTAAGAGACAAATTCGGTAAGTGAATAAATGACATGTTTGA
196 GATCAATTTTGAATTATGGAAAGGTTAAGAGACAAATTCGGTAAGTGAATAAATGACATGTTTGA
26406 TGAGGAAATTTATTAGAAATTAATGTAGAATGCTACAATGAGTTGATAAAAGCTTGAATTTAAGA
261 TGAGGAAATTTATTAGAAATTAATGTAGAATGCTACAATGAGTTGATAAAAGCTTGAATTTAAGA
26471 TTAATGGCAATGTACCATTTTAGAAATATGGAAATATTGGATGAATTTTGAAAGATTTTTTAGAG
326 TTAATGGCAATGTACCATTTTAGAAATATGGAAATATTGGATGAATTTTGAAAGATTTTTTAGAG
26536 AATTATTTATTGTTATGTACCTATGTATGGTAAGGTATTTATATGTACTTTCATTGTATGTGTTT
391 AATTATTTATTGTTATGTACCTATGTATGGTAAGGTATTTATATGTACTTTCATTGTATGTGTTT
26601 TGTATATGATGTAAGTGTAGATCCTGATCAAAATCGAGAACAAAGTAAGCTTAAAACTAAGGATA
456 TGTATATGATGTAAGTGTAGATCCTGATCAAAATCGAGAACAAAGTAAGCTTAAAACTAAGGATA
26666 AAGTTAATAAGTGAAGCTTATATTGCTAATTAAGGTTTGCTAGTTAAGTATACCAGGTGAGTGCA
521 AAGTTAATAAGTGAAGCTTATATTGCTAATTAAGGTTTGCTAGTTAAGTATACCAGGTGAGTGCA
26731 TTATTATATAATAATATTATATGTGATATAAGGAAGGCTTGCAATGAGCCAACTGCTATAGCAAT
586 TTATTATATAATAATATTATATGTGATATAAGGAAGGCTTGCAATGAGCCAACTGCTATAGCAAT
*
26796 CACCAAGTATATGTATCGTTCAAGTATTAAAGTGGAAGCTATAAAAGTTTCTGATGTCGAACCCA
651 CACCAAGTATATGTATCGTTCAAGTAATAAAGTGGAAGCTATAAAAGTTTCTGATGTCGAACCCA
26861 CAGAGAGTGTATGTCACAAAAGTGTTGTTGTTGGAAAAGAGAAAAGATAAGTAATGTGTATTTTT
716 CAGAGAGTGTATGTCACAAAAGTGTTGTTGTTGGAAAAGAGAAAAGATAAGTAATGTGTATTTTT
26926 AGAAAGTAACAGAAAGATAGTAGAGAAATAAAACCAGAATGATAAAAACAGGG
781 AGAAAGTAACAGAAAGATAGTAGAGAAATAAAACCAGAATGATAAAAACAGGG
26979 TGTTGTTATTGAAATGATTTATAATGCTTAGATATGTTGTTTGGAAGAAGAATTCATGCTTGAAT
1 TGTTGTTATTGAAATGATTTATAATGCTTAGATATGTTGTTTGGAAGAAGAATTCATGCTTGAAT
*
27044 CAAGTTGGATACCATATCTATGATGATACATGATATTTGACCATTGAAGAAAAATTAGGAAAAAA
66 CAAGTTGGATATCATATCTATGATGATACATGATATTTGACCATTGAAGAAAAATTAGGAAAAAA
27109 TTATTCATTTTTTTAAGACTTGACATAATGAATTGATGATTATAAAACCTTTATAATGTTGTTTG
131 TTATTCATTTTTTTAAGACTTGACATAATGAATTGATGATTATAAAACCTTTATAATGTTGTTTG
27174 GATCAATTTTGAATTATGGAAAGGTTAAGAGACAAATTCGGTAAGTGAATAAATGACATGTTTGA
196 GATCAATTTTGAATTATGGAAAGGTTAAGAGACAAATTCGGTAAGTGAATAAATGACATGTTTGA
27239 TGAGGAAATTTATTAGAAATTAATGTAGAATGCTACAATGAGTTGATAAAAGCTTGAATTTAAGA
261 TGAGGAAATTTATTAGAAATTAATGTAGAATGCTACAATGAGTTGATAAAAGCTTGAATTTAAGA
27304 TTAATGGCAATGTACCATTTTAGAAATATGGAAATATTGGATGAATTTTGAAAGATTTTTTAGAG
326 TTAATGGCAATGTACCATTTTAGAAATATGGAAATATTGGATGAATTTTGAAAGATTTTTTAGAG
27369 AATTATTTATTGTTATGTACCTATGTATGGTAAGGTATTTATATGTACTTTCATTGTATGTGTTT
391 AATTATTTATTGTTATGTACCTATGTATGGTAAGGTATTTATATGTACTTTCATTGTATGTGTTT
27434 TGTATATGATGTAAGTGTAGATCCTGATCAAAATCGAGAACAAAGTAAGCTTAAAACTAAGGATA
456 TGTATATGATGTAAGTGTAGATCCTGATCAAAATCGAGAACAAAGTAAGCTTAAAACTAAGGATA
27499 AAGTTAATAAGTGAAGCTTATATTGCTAATTAAGGTTTGCTAGTTAAGTATACCAGGTGAGTGCA
521 AAGTTAATAAGTGAAGCTTATATTGCTAATTAAGGTTTGCTAGTTAAGTATACCAGGTGAGTGCA
27564 TTATTATATAATAATATTATATGTGATATAAGGAAGGCTTGCAATGAGCCAACTGCTATAGCAAT
586 TTATTATATAATAATATTATATGTGATATAAGGAAGGCTTGCAATGAGCCAACTGCTATAGCAAT
*
27629 CACCAAGTATATGTATCGTTCAAGTAATAAAGTGGAAGCTATAAAAGTTTCTGATGTTGAACCCA
651 CACCAAGTATATGTATCGTTCAAGTAATAAAGTGGAAGCTATAAAAGTTTCTGATGTCGAACCCA
27694 CAGAGAGTGTATGTCACAAAAGTGTTGTTGTTGGAAAAGAGAAAAGATAAGTAATGTGTATTTTT
716 CAGAGAGTGTATGTCACAAAAGTGTTGTTGTTGGAAAAGAGAAAAGATAAGTAATGTGTATTTTT
*
27759 TGAAAGTAACAGAAAGATAGTAGAGAAATAAAACCAGAATGATAAAAACAGGG
781 AGAAAGTAACAGAAAGATAGTAGAGAAATAAAACCAGAATGATAAAAACAGGG
*
27812 TGTTGTTATTGAAATGATTTATAATGCTTAGATATGTTGTTTGGAAAAAGAATTCATGCTTGAAT
1 TGTTGTTATTGAAATGATTTATAATGCTTAGATATGTTGTTTGGAAGAAGAATTCATGCTTGAAT
27877 CAAGTTGGATATCATATCTATGATGATACATGATATTTGACCATTGAAGAAAAATTAGGAAAAAA
66 CAAGTTGGATATCATATCTATGATGATACATGATATTTGACCATTGAAGAAAAATTAGGAAAAAA
27942 TTATTCATTTTTTTAAGACTTGACATAATGAATTGATGATTATAAAACCTTTATAATGTTGTTTG
131 TTATTCATTTTTTTAAGACTTGACATAATGAATTGATGATTATAAAACCTTTATAATGTTGTTTG
*
28007 GATCAATTTTGAATTATGGAAAGGTTAGGAGACAAATTCGGTAAGTGAATAAATGACATGTTTGA
196 GATCAATTTTGAATTATGGAAAGGTTAAGAGACAAATTCGGTAAGTGAATAAATGACATGTTTGA
28072 TGAGGAAATTTATTAGAAATTAATGTAGAATGCTACAATGAGTTGATAAAAGCTTGAATTTAAGA
261 TGAGGAAATTTATTAGAAATTAATGTAGAATGCTACAATGAGTTGATAAAAGCTTGAATTTAAGA
28137 TTAATGGCAATGTACCATTTTAGAAATATGGAAATATTGGATGAATTTTGAAAGATTTTTTAGAG
326 TTAATGGCAATGTACCATTTTAGAAATATGGAAATATTGGATGAATTTTGAAAGATTTTTTAGAG
* *
28202 AATTATTTATTGTTATGTACCTATGTATGGTAATGTATTTATATGTACTTTAATTGTATGTGTTT
391 AATTATTTATTGTTATGTACCTATGTATGGTAAGGTATTTATATGTACTTTCATTGTATGTGTTT
28267 TGTATATGATGTAAGTGTAGATCCTGATCAAAATCGAGAACAAAGTAAGCTTAAAACTAAGGATA
456 TGTATATGATGTAAGTGTAGATCCTGATCAAAATCGAGAACAAAGTAAGCTTAAAACTAAGGATA
28332 AAGTTAATAAGTGAAGCTTATATTGCTAATTAAGGTTTGCTAGTTAAGTATACCAGGTGAGTGCA
521 AAGTTAATAAGTGAAGCTTATATTGCTAATTAAGGTTTGCTAGTTAAGTATACCAGGTGAGTGCA
28397 TTATTATATAATAATATTATATGTGATATAAGGAAGGCTTGCAATGAGCCAACTGCTATAGCAAT
586 TTATTATATAATAATATTATATGTGATATAAGGAAGGCTTGCAATGAGCCAACTGCTATAGCAAT
28462 CACCAAGTATATGTATCGTTCAAGTAATAAAGTGGAAGCTATAAAAGTTTCTGATGTCGAACCCA
651 CACCAAGTATATGTATCGTTCAAGTAATAAAGTGGAAGCTATAAAAGTTTCTGATGTCGAACCCA
28527 CAGAGAGTGTATGTCACAAAAGTGTTGTTGTTGGAAAAGAGAAAAGATAAGTAATGTGTATTTTT
716 CAGAGAGTGTATGTCACAAAAGTGTTGTTGTTGGAAAAGAGAAAAGATAAGTAATGTGTATTTTT
* *
28592 AGAAAGTAATAGAAAGATAGTAGGGAAATAAAACCAGAATGATAAAAACAGGG
781 AGAAAGTAACAGAAAGATAGTAGAGAAATAAAACCAGAATGATAAAAACAGGG
28645 T
1 T
28646 AATGTTATAG
Statistics
Matches: 1652, Mismatches: 15, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
833 1652 1.00
ACGTcount: A:0.38, C:0.08, G:0.20, T:0.34
Consensus pattern (833 bp):
TGTTGTTATTGAAATGATTTATAATGCTTAGATATGTTGTTTGGAAGAAGAATTCATGCTTGAAT
CAAGTTGGATATCATATCTATGATGATACATGATATTTGACCATTGAAGAAAAATTAGGAAAAAA
TTATTCATTTTTTTAAGACTTGACATAATGAATTGATGATTATAAAACCTTTATAATGTTGTTTG
GATCAATTTTGAATTATGGAAAGGTTAAGAGACAAATTCGGTAAGTGAATAAATGACATGTTTGA
TGAGGAAATTTATTAGAAATTAATGTAGAATGCTACAATGAGTTGATAAAAGCTTGAATTTAAGA
TTAATGGCAATGTACCATTTTAGAAATATGGAAATATTGGATGAATTTTGAAAGATTTTTTAGAG
AATTATTTATTGTTATGTACCTATGTATGGTAAGGTATTTATATGTACTTTCATTGTATGTGTTT
TGTATATGATGTAAGTGTAGATCCTGATCAAAATCGAGAACAAAGTAAGCTTAAAACTAAGGATA
AAGTTAATAAGTGAAGCTTATATTGCTAATTAAGGTTTGCTAGTTAAGTATACCAGGTGAGTGCA
TTATTATATAATAATATTATATGTGATATAAGGAAGGCTTGCAATGAGCCAACTGCTATAGCAAT
CACCAAGTATATGTATCGTTCAAGTAATAAAGTGGAAGCTATAAAAGTTTCTGATGTCGAACCCA
CAGAGAGTGTATGTCACAAAAGTGTTGTTGTTGGAAAAGAGAAAAGATAAGTAATGTGTATTTTT
AGAAAGTAACAGAAAGATAGTAGAGAAATAAAACCAGAATGATAAAAACAGGG
Found at i:32966 original size:41 final size:41
Alignment explanation
Indices: 32921--33028 Score: 153
Period size: 41 Copynumber: 2.6 Consensus size: 41
32911 GCTGCATCAC
* *
32921 TTCACAATCCGATTCAGTTCAATCATAACAACATGCAATAA
1 TTCACAATTCGATTCAATTCAATCATAACAACATGCAATAA
* * * **
32962 TTCACCATTCGACTCAATTCGATCATGGCAACATGCAATAA
1 TTCACAATTCGATTCAATTCAATCATAACAACATGCAATAA
33003 TTCACAATTCGATTCAATTCAATCAT
1 TTCACAATTCGATTCAATTCAATCAT
33029 TGAAACAAGC
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.37, C:0.25, G:0.08, T:0.30
Consensus pattern (41 bp):
TTCACAATTCGATTCAATTCAATCATAACAACATGCAATAA
Found at i:33047 original size:41 final size:41
Alignment explanation
Indices: 32921--33103 Score: 145
Period size: 41 Copynumber: 4.5 Consensus size: 41
32911 GCTGCATCAC
* * *
32921 TTCACAATCCGATTCAGTTCAATCA-TAACAACATGCAATAA
1 TTCACAATTCGATTCAATTCAATCATTGA-AACATGCAATAA
* * * * *
32962 TTCACCATTCGACTCAATTCGATCATGGCAACATGCAATAA
1 TTCACAATTCGATTCAATTCAATCATTGAAACATGCAATAA
* * *
33003 TTCACAATTCGATTCAATTCAATCATTGAAACAAGCATTTA
1 TTCACAATTCGATTCAATTCAATCATTGAAACATGCAATAA
** * * * ***
33044 TTCACAAACCAATTCAATT-AGATCATGGTAACATGTGTTAA
1 TTCACAATTCGATTCAATTCA-ATCATTGAAACATGCAATAA
* *
33085 TTCACAATCCAATTCAATT
1 TTCACAATTCGATTCAATT
33104 TAAATCAAGG
Statistics
Matches: 114, Mismatches: 26, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
40 1 0.01
41 113 0.99
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.31
Consensus pattern (41 bp):
TTCACAATTCGATTCAATTCAATCATTGAAACATGCAATAA
Found at i:33047 original size:82 final size:82
Alignment explanation
Indices: 32921--33126 Score: 200
Period size: 82 Copynumber: 2.5 Consensus size: 82
32911 GCTGCATCAC
* * * ** * *
32921 TTCACAATCCGATTCAGTTCAATCATAACAACATGCAATAATTCACCATTCGACTCAATTCGATC
1 TTCACAATCCGATTCAATTCAATCATAACAACAAGCAATAATTCACAAACCAACTCAATTAGATC
32986 ATGGCAACATGCAATAA
66 ATGGCAACATGCAATAA
* * * * *
33003 TTCACAATTCGATTCAATTCAATCATTGA-AACAAGCATTTATTCACAAACCAATTCAATTAGAT
1 TTCACAATCCGATTCAATTCAATCA-TAACAACAAGCAATAATTCACAAACCAACTCAATTAGAT
* ***
33067 CATGGTAACATGTGTTAA
65 CATGGCAACATGCAATAA
* * *
33085 TTCACAATCCAATTCAATTTAAATCA-AGGCAACAAGCAATAA
1 TTCACAATCCGATTCAA-TTCAATCATA-ACAACAAGCAATAA
33127 CTAATTTACC
Statistics
Matches: 97, Mismatches: 23, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
82 78 0.80
83 19 0.20
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.29
Consensus pattern (82 bp):
TTCACAATCCGATTCAATTCAATCATAACAACAAGCAATAATTCACAAACCAACTCAATTAGATC
ATGGCAACATGCAATAA
Found at i:37268 original size:20 final size:20
Alignment explanation
Indices: 37238--37377 Score: 113
Period size: 20 Copynumber: 7.0 Consensus size: 20
37228 TGCGATTTTC
*
37238 TGACTATCGCAATGCGAATA
1 TGACAATCGCAATGCGAATA
*
37258 TGTA-AATCGCAATGCGAGTA
1 TG-ACAATCGCAATGCGAATA
* *
37278 TGACTATCGCAACGCGAATA
1 TGACAATCGCAATGCGAATA
*
37298 TGTA-AATCGCAATGCGATTA
1 TG-ACAATCGCAATGCGAATA
* * *
37318 TGACTATCGCAATGCGATTC
1 TGACAATCGCAATGCGAATA
* * * *
37338 TGACTATCGCAACGCGATTC
1 TGACAATCGCAATGCGAATA
**
37358 TGACTGTCGCAATGCTGAAT
1 TGACAATCGCAATGC-GAAT
37378 TTCAAATTCT
Statistics
Matches: 101, Mismatches: 14, Indels: 9
0.81 0.11 0.07
Matches are distributed among these distances:
19 2 0.02
20 94 0.93
21 5 0.05
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (20 bp):
TGACAATCGCAATGCGAATA
Found at i:37347 original size:40 final size:40
Alignment explanation
Indices: 37238--37377 Score: 183
Period size: 40 Copynumber: 3.5 Consensus size: 40
37228 TGCGATTTTC
*
37238 TGACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTA
1 TGACTATCGCAATGCGAATATGTAAATCGCAATGCGATTA
*
37278 TGACTATCGCAACGCGAATATGTAAATCGCAATGCGATTA
1 TGACTATCGCAATGCGAATATGTAAATCGCAATGCGATTA
* * * * *
37318 TGACTATCGCAATGCGATTCTG-ACTATCGCAACGCGATTC
1 TGACTATCGCAATGCGAATATGTA-AATCGCAATGCGATTA
*
37358 TGACTGTCGCAATGCTGAAT
1 TGACTATCGCAATGC-GAAT
37378 TTCAAATTCT
Statistics
Matches: 88, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
39 1 0.01
40 84 0.95
41 3 0.03
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (40 bp):
TGACTATCGCAATGCGAATATGTAAATCGCAATGCGATTA
Found at i:37368 original size:60 final size:60
Alignment explanation
Indices: 37235--37377 Score: 173
Period size: 60 Copynumber: 2.4 Consensus size: 60
37225 CGTTGCGATT
37235 TTCTGACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTATGACTATCGCAACGCGA
1 TTCTGACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTATGACTATCGCAACGCGA
* * * * * * *
37295 ATATGTA-AATCGCAATGCGATTATG-ACTATCGCAATGCGATTCTGACTATCGCAACGCGA
1 TTCTG-ACTATCGCAATGCGAATATGTA-AATCGCAATGCGAGTATGACTATCGCAACGCGA
*
37355 TTCTGACTGTCGCAATGCTGAAT
1 TTCTGACTATCGCAATGC-GAAT
37378 TTCAAATTCT
Statistics
Matches: 67, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
59 2 0.03
60 61 0.91
61 4 0.06
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (60 bp):
TTCTGACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTATGACTATCGCAACGCGA
Found at i:38222 original size:24 final size:24
Alignment explanation
Indices: 38190--38243 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
38180 GTATTCGAAA
38190 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
38214 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
38238 TTTGAT
1 TTTGAT
38244 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:38462 original size:14 final size:14
Alignment explanation
Indices: 38433--38469 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
38423 AGAAAAAGAA
38433 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
38448 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
38462 GAAGAAAA
1 GAAGAAAA
38470 TGCCACGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:40527 original size:18 final size:18
Alignment explanation
Indices: 40504--40538 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
40494 AGCAAAAGAT
*
40504 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
40522 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
40539 CAACCGACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:40843 original size:74 final size:74
Alignment explanation
Indices: 40722--40938 Score: 335
Period size: 74 Copynumber: 2.9 Consensus size: 74
40712 TCTTTTGACT
* * * * * *
40722 ATCGCAACGCGAATATGACTATCGCAACGCGAATATGACTATCGCAACGTGAATTTGAATATCGC
1 ATCGCAAAGCGAAAATGACTATCGCAAAGCGAAAATGACTATCGCAACGCGAATTTGACTATCGC
40787 AACGGGATA
66 AACGGGATA
* *
40796 ATCGCAAAGCGAAAATGACTATTGCAAAGCAAAAATGACTATCGCAACGCGAATTTGACTATCGC
1 ATCGCAAAGCGAAAATGACTATCGCAAAGCGAAAATGACTATCGCAACGCGAATTTGACTATCGC
40861 AACGGGATA
66 AACGGGATA
* * *
40870 ATCGCAATGCGAAAATGACTATCGCAATGCGAAAATGACTATCGCAACGCGAATATGACTATCGC
1 ATCGCAAAGCGAAAATGACTATCGCAAAGCGAAAATGACTATCGCAACGCGAATTTGACTATCGC
40935 AACG
66 AACG
40939 CGAATTTAAC
Statistics
Matches: 130, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
74 130 1.00
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.20
Consensus pattern (74 bp):
ATCGCAAAGCGAAAATGACTATCGCAAAGCGAAAATGACTATCGCAACGCGAATTTGACTATCGC
AACGGGATA
Found at i:40886 original size:54 final size:54
Alignment explanation
Indices: 40827--41031 Score: 223
Period size: 54 Copynumber: 3.7 Consensus size: 54
40817 TTGCAAAGCA
*
40827 AAAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGATAATCGCAATGCG
1 AAAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGATAATCGCAACGCG
* ** *
40881 AAAATGACTATCGCAATGCGAAAATGACTATCGCAACGCGAATATGACTATCGCAACGCG
1 AAAATGACTATCGCAACGCGAATTTGACTATCGCAACG-G--GAT-A--ATCGCAACGCG
** * * *
40941 AATTTAACTATCGCAATGCGAATTTGACTATCGCAACGAGATAATCGCAACGCG
1 AAAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGATAATCGCAACGCG
** *
40995 AATTTGATTATCGCAACAG-GAATTTGACTATCGCAAC
1 AAAATGACTATCGCAAC-GCGAATTTGACTATCGCAAC
41032 AAGAAAATCG
Statistics
Matches: 129, Mismatches: 15, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
54 78 0.60
55 2 0.02
56 1 0.01
57 4 0.03
58 1 0.01
60 43 0.33
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (54 bp):
AAAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGATAATCGCAACGCG
Found at i:40894 original size:94 final size:94
Alignment explanation
Indices: 40717--41031 Score: 316
Period size: 94 Copynumber: 3.4 Consensus size: 94
40707 CATATTCTTT
* * * *
40717 TGACTATCGCAACGCGAATATGACTATCGCAACGCGAATATGACTATCGCAACGTGAATTTGAAT
1 TGACTATCGCAACGCGAATATGACTATCGCAACGCGAATTTGACTATCGCAACGGGAAATCGAAT
* **
40782 ATCGCAACGGGATAATCGCAAAGCGAAAA
66 AGCGCAAAAGGATAATCGCAAAGCGAAAA
* * * *
40811 TGACTATTGCAAAGCAAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGATAATCGCA
1 TGACTATCGCAACGCGAATATGACTATCGCAACGCGAATTTGACTATCGCAACGGGA-AATCG-A
* *
40876 AT-GCG-AAAATGACT-ATCGCAATGCGAAAA
64 ATAGCGCAAAAGGA-TAATCGCAAAGCGAAAA
* * * * * *
40905 TGACTATCGCAACGCGAATATGACTATCGCAACGCGAATTTAACTATCGCAATGCGAATTTGACT
1 TGACTATCGCAACGCGAATATGACTATCGCAACGCGAATTTGACTATCGCAACGGGAAATCGAAT
* * * **
40970 ATCGC-AACGAGATAATCGCAACGCGAATT
66 AGCGCAAAAG-GATAATCGCAAAGCGAAAA
* *
40999 TGATTATCGCAACAG-GAATTTGACTATCGCAAC
1 TGACTATCGCAAC-GCGAATATGACTATCGCAAC
41032 AAGAAAATCG
Statistics
Matches: 182, Mismatches: 31, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
92 2 0.01
93 8 0.04
94 162 0.89
95 7 0.04
96 3 0.02
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (94 bp):
TGACTATCGCAACGCGAATATGACTATCGCAACGCGAATTTGACTATCGCAACGGGAAATCGAAT
AGCGCAAAAGGATAATCGCAAAGCGAAAA
Found at i:40988 original size:74 final size:76
Alignment explanation
Indices: 40719--41030 Score: 315
Period size: 74 Copynumber: 4.1 Consensus size: 76
40709 TATTCTTTTG
* * * * *
40719 ACTATCGCAACGCGAATATGACTATCGCAACGCGAATATGACTATCGCAACGTGAATTTGAATAT
1 ACTATCGCAATGCGAAAATGACTATCGCAA-GCGAAAATGAC-ATCGCAACGCGAATTTGACTAT
*
40784 CGCAACGGGA--T
64 CGCAACGGAATTT
* * *
40795 A--ATCGCAAAGCGAAAATGACTATTGCAAAGCAAAAATGACTATCGCAACGCGAATTTGACTAT
1 ACTATCGCAATGCGAAAATGACTATCGC-AAGCGAAAATGAC-ATCGCAACGCGAATTTGACTAT
*
40858 CGCAACGGGA--T
64 CGCAACGGAATTT
*
40869 A--ATCGCAATGCGAAAATGACTATCGCAATGCGAAAATGACTATCGCAACGCGAATATGACTAT
1 ACTATCGCAATGCGAAAATGACTATCGCAA-GCGAAAATGAC-ATCGCAACGCGAATTTGACTAT
40932 CGCAACGCGAATTT
64 CGCAACG-GAATTT
** * *
40946 AACTATCGCAATGCGAATTTGACTATCGCAA-CG-AGAT-A-ATCGCAACGCGAATTTGATTATC
1 -ACTATCGCAATGCGAAAATGACTATCGCAAGCGAAAATGACATCGCAACGCGAATTTGACTATC
41007 GCAACAGGAATTT
65 GCAAC-GGAATTT
41020 GACTATCGCAA
1 -ACTATCGCAA
41031 CAAGAAAATC
Statistics
Matches: 209, Mismatches: 18, Indels: 20
0.85 0.07 0.08
Matches are distributed among these distances:
73 2 0.01
74 168 0.80
75 5 0.02
76 2 0.01
77 4 0.02
78 3 0.01
80 25 0.12
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (76 bp):
ACTATCGCAATGCGAAAATGACTATCGCAAGCGAAAATGACATCGCAACGCGAATTTGACTATCG
CAACGGAATTT
Found at i:41032 original size:20 final size:20
Alignment explanation
Indices: 40717--41031 Score: 272
Period size: 20 Copynumber: 16.6 Consensus size: 20
40707 CATATTCTTT
40717 TGACTATCGCAACGCGAATA
1 TGACTATCGCAACGCGAATA
40737 TGACTATCGCAACGCGAATA
1 TGACTATCGCAACGCGAATA
* *
40757 TGACTATCGCAACGTGAATT
1 TGACTATCGCAACGCGAATA
* *
40777 TGAATATCGCAACG-G--GA
1 TGACTATCGCAACGCGAATA
* *
40794 T-A--ATCGCAAAGCGAAAA
1 TGACTATCGCAACGCGAATA
* * * *
40811 TGACTATTGCAAAGCAAAAA
1 TGACTATCGCAACGCGAATA
*
40831 TGACTATCGCAACGCGAATT
1 TGACTATCGCAACGCGAATA
*
40851 TGACTATCGCAACG-G--GA
1 TGACTATCGCAACGCGAATA
* *
40868 T-A--ATCGCAATGCGAAAA
1 TGACTATCGCAACGCGAATA
* *
40885 TGACTATCGCAATGCGAAAA
1 TGACTATCGCAACGCGAATA
40905 TGACTATCGCAACGCGAATA
1 TGACTATCGCAACGCGAATA
*
40925 TGACTATCGCAACGCGAATT
1 TGACTATCGCAACGCGAATA
* * *
40945 TAACTATCGCAATGCGAATT
1 TGACTATCGCAACGCGAATA
*
40965 TGACTATCGCAA--CG-AGA
1 TGACTATCGCAACGCGAATA
*
40982 T-A--ATCGCAACGCGAATT
1 TGACTATCGCAACGCGAATA
* *
40999 TGATTATCGCAACAG-GAATT
1 TGACTATCGCAAC-GCGAATA
41019 TGACTATCGCAAC
1 TGACTATCGCAAC
41032 AAGAAAATCG
Statistics
Matches: 247, Mismatches: 29, Indels: 38
0.79 0.09 0.12
Matches are distributed among these distances:
14 23 0.09
15 2 0.01
16 5 0.02
17 10 0.04
18 5 0.02
19 2 0.01
20 199 0.81
21 1 0.00
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (20 bp):
TGACTATCGCAACGCGAATA
Found at i:41061 original size:54 final size:55
Alignment explanation
Indices: 40832--41065 Score: 183
Period size: 54 Copynumber: 4.2 Consensus size: 55
40822 AAGCAAAAAT
** * * *
40832 GACTATCGCAAC-GCGAATTTGACTATCGCAACGGGATAATCGCAATGCGAA-AA
1 GACTATCGCAACAGCGAATTTGACTATCGCAACAAGAAAATCGCAAAGCGAATTA
* ** ** *
40885 TGACTATCGCAA-TGCGAAAATGACTATCGCAACGCGAATATGACTATCGCAACGCGAATTTA
1 -GACTATCGCAACAGCGAATTTGACTATCGCAA--C--A-A-GAAAATCGCAAAGCGAA-TTA
* * * * *
40947 -ACTATCGCAA-TGCGAATTTGACTATCGCAACGAGATAATCGCAACGCGAATTT
1 GACTATCGCAACAGCGAATTTGACTATCGCAACAAGAAAATCGCAAAGCGAATTA
* * *
41000 GATTATCGCAACAG-GAATTTGACTATCGCAACAAGAAAATCGCAAAGTGTATTA
1 GACTATCGCAACAGCGAATTTGACTATCGCAACAAGAAAATCGCAAAGCGAATTA
41054 GACTATCGCAAC
1 GACTATCGCAAC
41066 GTGAATATGA
Statistics
Matches: 146, Mismatches: 23, Indels: 22
0.76 0.12 0.12
Matches are distributed among these distances:
53 2 0.01
54 97 0.66
55 2 0.01
56 1 0.01
58 1 0.01
60 42 0.29
62 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (55 bp):
GACTATCGCAACAGCGAATTTGACTATCGCAACAAGAAAATCGCAAAGCGAATTA
Found at i:41207 original size:36 final size:34
Alignment explanation
Indices: 41167--41246 Score: 114
Period size: 30 Copynumber: 2.4 Consensus size: 34
41157 TCAACTTTTA
41167 ATCAATTAAACAAGCACAAATAAGAATTATTTACAC
1 ATCAATTAAACAA--ACAAATAAGAATTATTTACAC
41203 ATCAATT----AAACAAATAAGAATTATTTACAC
1 ATCAATTAAACAAACAAATAAGAATTATTTACAC
41233 ATCAATTAAACAAA
1 ATCAATTAAACAAA
41247 TCAACTCTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
30 28 0.70
32 2 0.05
34 3 0.08
36 7 0.17
ACGTcount: A:0.55, C:0.15, G:0.04, T:0.26
Consensus pattern (34 bp):
ATCAATTAAACAAACAAATAAGAATTATTTACAC
Found at i:41216 original size:30 final size:30
Alignment explanation
Indices: 41182--41247 Score: 132
Period size: 30 Copynumber: 2.2 Consensus size: 30
41172 TTAAACAAGC
41182 ACAAATAAGAATTATTTACACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
41212 ACAAATAAGAATTATTTACACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
41242 ACAAAT
1 ACAAAT
41248 CAACTCTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.55, C:0.14, G:0.03, T:0.29
Consensus pattern (30 bp):
ACAAATAAGAATTATTTACACATCAATTAA
Found at i:42718 original size:21 final size:21
Alignment explanation
Indices: 42637--42723 Score: 84
Period size: 21 Copynumber: 4.1 Consensus size: 21
42627 GAGTGTTGGG
* *
42637 AGGGACCTCTTCAACGATGAC
1 AGGGGCCTCTTGAACGATGAC
* * **
42658 AGTGGCCTCTTGAACGGTGGG
1 AGGGGCCTCTTGAACGATGAC
* ** *
42679 AGGGGACTCTTGAGGGATGAT
1 AGGGGCCTCTTGAACGATGAC
42700 AGGGGCCTCTTGAACGATGAC
1 AGGGGCCTCTTGAACGATGAC
42721 AGG
1 AGG
42724 TGAGTCGGGT
Statistics
Matches: 49, Mismatches: 17, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.23, C:0.20, G:0.37, T:0.21
Consensus pattern (21 bp):
AGGGGCCTCTTGAACGATGAC
Found at i:43185 original size:20 final size:20
Alignment explanation
Indices: 43160--43215 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
43150 TCGCAACACG
*
43160 AATGACTATCGTAACGCGAA
1 AATGACTATCGCAACGCGAA
43180 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
43200 AATGACTATCGCAACG
1 AATGACTATCGCAACG
43216 AGAGAATCGC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.18
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:43284 original size:20 final size:20
Alignment explanation
Indices: 43259--43325 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
43249 CGATTCTTTC
*
43259 GTTGCGATAGTCAAATTCGT
1 GTTGCGATAGTCAATTTCGT
* *
43279 GTTGCGATAGTCATTTTCGC
1 GTTGCGATAGTCAATTTCGT
43299 GTTGCGATAGTC-ATTTCCGT
1 GTTGCGATAGTCAATTT-CGT
43319 GTTGCGA
1 GTTGCGA
43326 AAGTAAACTA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.07
20 38 0.93
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
GTTGCGATAGTCAATTTCGT
Found at i:45870 original size:20 final size:20
Alignment explanation
Indices: 45845--45918 Score: 121
Period size: 20 Copynumber: 3.7 Consensus size: 20
45835 GCGCTTTGAA
*
45845 AATCGCATTGCGACAGTCAG
1 AATCGCATTGCGATAGTCAG
*
45865 AATCGCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
*
45885 AATCGCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
45905 AATCGCATTGCGAT
1 AATCGCATTGCGAT
45919 TTACATATTC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (20 bp):
AATCGCATTGCGATAGTCAG
Found at i:46891 original size:3 final size:3
Alignment explanation
Indices: 46883--46907 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
46873 TCTAATATAA
46883 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
46908 CCATATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Done.