Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003058.1 Hibiscus syriacus cultivar Beakdansim tig00006375_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: 75347
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:18435 original size:29 final size:29
Alignment explanation
Indices: 18354--18462 Score: 155
Period size: 29 Copynumber: 3.7 Consensus size: 29
18344 CCATTATTCC
* *
18354 TTTACTCAACAGTGTTTAACCGTTAATCT
1 TTTACTCAACAGTGTTTAACCTTTCATCT
*
18383 TTTACTCAATAACAATGTTTAACCTTTCATCT
1 TTTACTC---AACAGTGTTTAACCTTTCATCT
18415 TTTACTCAACAGTGTTTAACCTTTCATCT
1 TTTACTCAACAGTGTTTAACCTTTCATCT
*
18444 TTTACTCAACCGTGTTTAA
1 TTTACTCAACAGTGTTTAA
18463 TCGTTCTTCT
Statistics
Matches: 72, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
29 46 0.64
32 26 0.36
ACGTcount: A:0.28, C:0.22, G:0.07, T:0.43
Consensus pattern (29 bp):
TTTACTCAACAGTGTTTAACCTTTCATCT
Found at i:18528 original size:81 final size:81
Alignment explanation
Indices: 18441--18597 Score: 217
Period size: 81 Copynumber: 1.9 Consensus size: 81
18431 TAACCTTTCA
* * * *
18441 TCTTTTACTCAACCGTGTTTAA-TCGTTCTTCTAACTGGAATAATTGACACCTTTCTACCAATTG
1 TCTTTTACTCAACCGTATATAACT-GTTCATCTAACTGGAATAATTGACACCTTTCTACCAAATG
*
18505 CTCAATTAGGCCATTAT
65 CACAATTAGGCCATTAT
* * *
18522 TCTTTTACTCAACGGTATATAACTGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
1 TCTTTTACTCAACCGTATATAACTGTTCATCTAACTGGAATAATTGACACCTTTCTACCAAATGC
*
18587 ACAGTTAGGCC
66 ACAATTAGGCC
18598 TCAAAGGCAC
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
81 65 0.98
82 1 0.02
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (81 bp):
TCTTTTACTCAACCGTATATAACTGTTCATCTAACTGGAATAATTGACACCTTTCTACCAAATGC
ACAATTAGGCCATTAT
Found at i:18652 original size:68 final size:68
Alignment explanation
Indices: 18547--19617 Score: 1527
Period size: 68 Copynumber: 15.8 Consensus size: 68
18537 TATATAACTG
* * *
18547 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
18612 CCT
66 CCT
** * * * * *
18615 TTCATCTAACTGGCGGAAATGAAACATTTATGTCAAATGCACATTTAGGCCTCAATGGCACATAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
18680 CCT
66 CCT
*
18683 TTCATCTAACTGGCATAAATGACA-ACTTTCTGTCAAATGCACAGTTAGGCATCAAAGGCACTTA
1 TTCATCTAACTGGCATAAATGACACA-TTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTA
18747 GCCT
65 GCCT
* * * * * * *
18751 TTCATCTAACTAGAATAAATGATACATTTCTGTCAAAAGCACAGTTAGGCATAAAAGACACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
18816 -CT
66 CCT
* * * * *
18818 TTCATTTAACTAGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAATGCACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
18883 CCT
66 CCT
* * *
18886 TTCATCTAATTGGCATAAATGACACATTTCTATCAAATGCACAATTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
18951 CCT
66 CCT
* * * *
18954 TTCATCTAATTGGTATAAATGACACCTTTCTGTCAAATGCACATTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
19019 CCT
66 CCT
*
19022 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
19087 CCT
66 CCT
* * * * *
19090 TTCATCTAACTGGCATAAATGAAACATTTTTGTCAAATGCACATTTAGGCCTCAATGGCACTTAC
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
19155 CCT
66 CCT
* * *
19158 TTCATCTAACTGTCATAAATGACA-ACTTTCTGTCAAATGCACAATTAGGCATCAAAGGCACTTA
1 TTCATCTAACTGGCATAAATGACACA-TTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTA
19222 GCCT
65 GCCT
* * * *
19226 TTCATCTAACTGGCATAAATGACACATTTATGTCAAATGCACAGTTAGGCATTAAAGACACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
19291 CCT
66 CCT
* * * * *
19294 TTCATGTAACTGGCATAATTGACACCTTTCTTTCAAATGCACAATTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
19359 CCT
66 CCT
* * *
19362 TTCTTCTAATTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGAACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
19427 CCT
66 CCT
* * * * *
19430 TTCATCTAATTGGTAAAAATGACACCTTTCTGTCAAATGCACATTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
19495 CCT
66 CCT
* * * * *
19498 TTCATCTAACTGGTATAAATGATACCTTTCTCTTAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
19563 CCT
66 CCT
* * *
19566 TTCATCTAACTGGAAAAAATGACACATTTCTGTCAAATGCACATTTAGGCCT
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCT
19618 ATTAATCATT
Statistics
Matches: 895, Mismatches: 103, Indels: 10
0.89 0.10 0.01
Matches are distributed among these distances:
67 59 0.07
68 834 0.93
69 2 0.00
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:20283 original size:20 final size:20
Alignment explanation
Indices: 20258--20311 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
20248 TGTGATCAAG
*
20258 TGGTATCGATACCATCCTCA
1 TGGTATCGATACCATCATCA
*
20278 TGGTATCGATACTC-TCATCT
1 TGGTATCGATAC-CATCATCA
20298 TGGTATCGATACCA
1 TGGTATCGATACCA
20312 CTTGAATCGG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 1 0.03
20 28 0.93
21 1 0.03
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (20 bp):
TGGTATCGATACCATCATCA
Found at i:20325 original size:21 final size:21
Alignment explanation
Indices: 20299--20351 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
20289 CTCTCATCTT
20299 GGTATCGATACCACTTGAATC
1 GGTATCGATACCACTTGAATC
20320 GGTATCGATACCACTTGAATC
1 GGTATCGATACCACTTGAATC
20341 GGTATCGATAC
1 GGTATCGATAC
20352 TACTCTATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (21 bp):
GGTATCGATACCACTTGAATC
Found at i:22092 original size:18 final size:18
Alignment explanation
Indices: 22065--22099 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
22055 GATAGTTTTA
*
22065 GCTCGGTTAATAACTTCG
1 GCTCGATTAATAACTTCG
22083 GCTCGATTAATAACTTC
1 GCTCGATTAATAACTTC
22100 TTACAAGTTA
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:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (18 bp):
GCTCGATTAATAACTTCG
Found at i:22940 original size:29 final size:29
Alignment explanation
Indices: 22897--23008 Score: 163
Period size: 29 Copynumber: 3.9 Consensus size: 29
22887 AACCTTGACA
* * *
22897 ATCTTTTACTTAACAATATTTAA-CTGTTC
1 ATCTTTTACTCAACAGTGTTTAACCT-TTC
22926 ATCTTTTACTCAACAGTGTTTAACCTTTC
1 ATCTTTTACTCAACAGTGTTTAACCTTTC
*
22955 ATCTTTTACTCAAGAGTGTTTAACCTTTC
1 ATCTTTTACTCAACAGTGTTTAACCTTTC
*
22984 ATCTTTTACTCAATAGTGTTTAACC
1 ATCTTTTACTCAACAGTGTTTAACC
23009 GTTCTTCTAA
Statistics
Matches: 77, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
29 75 0.97
30 2 0.03
ACGTcount: A:0.27, C:0.21, G:0.07, T:0.46
Consensus pattern (29 bp):
ATCTTTTACTCAACAGTGTTTAACCTTTC
Found at i:23142 original size:81 final size:81
Alignment explanation
Indices: 22985--23221 Score: 300
Period size: 81 Copynumber: 2.9 Consensus size: 81
22975 TAACCTTTCA
* *
22985 TCTTTTACTCAATAGTGTTTAACCGTTCT-TCTAACT-GCATAATTGACACCTTTATGCCAATTA
1 TCTTTTACTCAATAGTATTTAACCGTT-TATCTAACTGGCATAATTGACACCTTTATACCAATTA
*
23048 CACAGTTAAGCCATTAT
65 CACAGTTATGCCATTAT
* * * *
23065 TCTTTTACTCAATTGTATTTAACCATTTATCTAACTGGCATAATTGACACTTTTCTACCAATTAC
1 TCTTTTACTCAATAGTATTTAACCGTTTATCTAACTGGCATAATTGACACCTTTATACCAATTAC
* *
23130 TCAGTTATGCCATTTT
66 ACAGTTATGCCATTAT
* * * * * *
23146 TCTTTTACTCAA-CGATATTTGACCGTTCATCTAACTGGCATAATTAACACCTTTATACCAAATG
1 TCTTTTACTCAATAG-TATTTAACCGTTTATCTAACTGGCATAATTGACACCTTTATACCAATTA
23210 CACAGTTATGCC
65 CACAGTTATGCC
23222 TCAAATGCAC
Statistics
Matches: 135, Mismatches: 19, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
79 1 0.01
80 32 0.24
81 102 0.76
ACGTcount: A:0.29, C:0.23, G:0.09, T:0.39
Consensus pattern (81 bp):
TCTTTTACTCAATAGTATTTAACCGTTTATCTAACTGGCATAATTGACACCTTTATACCAATTAC
ACAGTTATGCCATTAT
Found at i:23281 original size:68 final size:68
Alignment explanation
Indices: 23171--23697 Score: 671
Period size: 68 Copynumber: 7.8 Consensus size: 68
23161 TATTTGACCG
* * * * ** * * *
23171 TTCATCTAACTGGCATAATTAACACCTTTATACCAAATGCACAGTTATGCCTCAAATGCACTTAT
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
23236 CCT
66 CCT
* * * * *
23239 TTCATCTAATTGGTATAAATGACATATGTT-TTTGAAATGCACAGTTAGGCCTCAAAGGCACTTA
1 TTCATCTAACTGGCATAAATGACACAT-TTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTA
23303 GCCT
65 GCCT
* * *
23307 TTCATCTAACTGGCATAAATGACACCTTTCTATCAAATGCACAGTTAGGCCTCGAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
23372 CCT
66 CCT
* * * ** *
23375 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCAGAATTACACCTCAAAGGTACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
23440 CCT
66 CCT
* * * *
23443 ATCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCAAAGTTAAGCCTCAAAGGCAATTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
*
23508 CAT
66 CCT
* * * *
23511 TTCATCTAACTGTCATAAATGACACTTTTTTGTCAAATGCACAGTTAGGCCTCAAAGGAACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
*
23576 TCT
66 CCT
* * * * *
23579 TTCATCTAACTGGCATAAATGATACCTTTCTTTCAATTGCACAGGTT-GGCCTCAAAGGAACTTA
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACA-GTTAGGCCTCAAAGGCACTTA
23643 GCCT
65 GCCT
*
23647 TTCATCTAACTGACATAAATGACACATTTCTGTCAAATGCACAGTTAGGCC
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCC
23698 AATTAATCTT
Statistics
Matches: 398, Mismatches: 57, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
67 5 0.01
68 388 0.97
69 5 0.01
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:24384 original size:20 final size:20
Alignment explanation
Indices: 24359--24414 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
24349 TTGTGATCAA
*
24359 ATGGTATCGATACCATCCTC
1 ATGGTATCGATACCACCCTC
24379 ATGGTATCGATACTC-CCCTC
1 ATGGTATCGATAC-CACCCTC
*
24399 TTGGTATCGATACCAC
1 ATGGTATCGATACCAC
24415 TTGAATTGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.30
Consensus pattern (20 bp):
ATGGTATCGATACCACCCTC
Found at i:24661 original size:40 final size:40
Alignment explanation
Indices: 24615--24981 Score: 203
Period size: 40 Copynumber: 9.3 Consensus size: 40
24605 AATATGAGAG
24615 TGGTGATGTATTGTACAGGATACACACCCAATTACAAGCAA
1 TGGTGATGTATTGTACAGGATACACACCCAATTACAAG-AA
** * * * * *
24656 T-GTGATGTATTGTATGGGCTACACACCTAAATATAAGAG
1 TGGTGATGTATTGTACAGGATACACACCCAATTACAAGAA
* *
24695 TGGTGATGTATTGTAGAGGATACACA-CTAATTACAAGCAA
1 TGGTGATGTATTGTACAGGATACACACCCAATTACAAG-AA
* * * * * ** ** *
24735 -GGTGGTGTATCGTGCGGGGTACAC-CTAAATT-TGAGAG
1 TGGTGATGTATTGTACAGGATACACACCCAATTACAAGAA
* **
24772 TGGTGATGTATTGTA-TGAGATACATGCCCAATTACAAGTAA
1 TGGTGATGTATTGTACAG-GATACACACCCAATTACAAG-AA
* ** ** * * * ** ** *
24813 -GGTAATGTATCATATGGGGTACATACCTAAGAATGAGAG
1 TGGTGATGTATTGTACAGGATACACACCCAATTACAAGAA
*
24852 TGGTGATGTATTGTACAAGATACACACCCAATTACAAGCAA
1 TGGTGATGTATTGTACAGGATACACACCCAATTACAAG-AA
* * * ** **
24893 -GGTGATGTATTGTACAGGGTACACACCTAAATATGAGTG
1 TGGTGATGTATTGTACAGGATACACACCCAATTACAAGAA
* * *
24932 TGGTGAGGTATTGTACAAGATACACACCCAATTATAAGAA
1 TGGTGATGTATTGTACAGGATACACACCCAATTACAAGAA
*
24972 -GGCGATGTAT
1 TGGTGATGTAT
24982 CATACAAGGT
Statistics
Matches: 235, Mismatches: 79, Indels: 26
0.69 0.23 0.08
Matches are distributed among these distances:
37 2 0.01
38 18 0.08
39 47 0.20
40 164 0.70
41 4 0.02
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (40 bp):
TGGTGATGTATTGTACAGGATACACACCCAATTACAAGAA
Found at i:24715 original size:80 final size:80
Alignment explanation
Indices: 24580--24982 Score: 483
Period size: 80 Copynumber: 5.1 Consensus size: 80
24570 CATATATATT
* * * * *
24580 ATGTATCGTACGAGGTACTCACGTAAATATGAGAGTGGTGATGTATTGTACAGGATACACACCCA
1 ATGTATCGTATGGGGTACACACCTAAATATGAGAGTGGTGATGTATTGTACAAGATACACACCCA
*
24645 ATTACAAGCAATGTG
66 ATTACAAGCAAGGTG
* * * * * *
24660 ATGTATTGTATGGGCTACACACCTAAATATAAGAGTGGTGATGTATTGTAGAGGATACACA-CTA
1 ATGTATCGTATGGGGTACACACCTAAATATGAGAGTGGTGATGTATTGTACAAGATACACACCCA
24724 ATTACAAGCAAGGTG
66 ATTACAAGCAAGGTG
* ** * ** **
24739 GTGTATCGTGCGGGGT--ACACCTAAATTTGAGAGTGGTGATGTATTGTATGAGATACATGCCCA
1 ATGTATCGTATGGGGTACACACCTAAATATGAGAGTGGTGATGTATTGTACAAGATACACACCCA
* *
24802 ATTACAAGTAAGGTA
66 ATTACAAGCAAGGTG
* *
24817 ATGTATCATATGGGGTACATACCTAAGA-ATGAGAGTGGTGATGTATTGTACAAGATACACACCC
1 ATGTATCGTATGGGGTACACACCTAA-ATATGAGAGTGGTGATGTATTGTACAAGATACACACCC
24881 AATTACAAGCAAGGTG
65 AATTACAAGCAAGGTG
* ** * *
24897 ATGTATTGTACAGGGTACACACCTAAATATGAGTGTGGTGAGGTATTGTACAAGATACACACCCA
1 ATGTATCGTATGGGGTACACACCTAAATATGAGAGTGGTGATGTATTGTACAAGATACACACCCA
* *
24962 ATTATAAG-AAGGCG
66 ATTACAAGCAAGGTG
24976 ATGTATC
1 ATGTATC
24983 ATACAAGGTA
Statistics
Matches: 271, Mismatches: 47, Indels: 11
0.82 0.14 0.03
Matches are distributed among these distances:
77 36 0.13
78 27 0.10
79 39 0.14
80 168 0.62
81 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (80 bp):
ATGTATCGTATGGGGTACACACCTAAATATGAGAGTGGTGATGTATTGTACAAGATACACACCCA
ATTACAAGCAAGGTG
Found at i:25108 original size:6 final size:6
Alignment explanation
Indices: 25099--25135 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
25089 ATTAATATCA
25099 TTTATT TTTATT TTTATT GTTTA-T TTTATT TTTATT T
1 TTTATT TTTATT TTTATT -TTTATT TTTATT TTTATT T
25136 ATTTACAAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 4 0.14
6 21 0.72
7 4 0.14
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (6 bp):
TTTATT
Found at i:25127 original size:18 final size:19
Alignment explanation
Indices: 25099--25134 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
25089 ATTAATATCA
25099 TTTATTTTTATTTTTATTG
1 TTTATTTTTATTTTTATTG
25118 TTTA-TTTTATTTTTATT
1 TTTATTTTTATTTTTATT
25135 TATTTACAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.81
Consensus pattern (19 bp):
TTTATTTTTATTTTTATTG
Found at i:25140 original size:19 final size:19
Alignment explanation
Indices: 25098--25140 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
25088 TATTAATATC
25098 ATTTATTTTTATTTTTATT
1 ATTTATTTTTATTTTTATT
*
25117 GTTTA-TTTTATTTTTATTT
1 ATTTATTTTTATTTTTA-TT
25136 ATTTA
1 ATTTA
25141 CAAGCCCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (19 bp):
ATTTATTTTTATTTTTATT
Found at i:39413 original size:30 final size:30
Alignment explanation
Indices: 39377--39443 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
39367 TAAAGTTTGG
* *
39377 AAAAGTTTAGAGA-CAAAACAGATCATTTTT
1 AAAAGTTCAGAGACCAAAA-AGATAATTTTT
**
39407 AAAAGTTCAGAGACCAAAATTATAATTTTT
1 AAAAGTTCAGAGACCAAAAAGATAATTTTT
39437 AAAAGTT
1 AAAAGTT
39444 AGGTGTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 27 0.84
31 5 0.16
ACGTcount: A:0.48, C:0.09, G:0.12, T:0.31
Consensus pattern (30 bp):
AAAAGTTCAGAGACCAAAAAGATAATTTTT
Found at i:41949 original size:2 final size:2
Alignment explanation
Indices: 41944--41986 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
41934 TATATATATA
* *
41944 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TA TG TA TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
41986 T
1 T
41987 TATGCGGAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.05, C:0.00, G:0.44, T:0.51
Consensus pattern (2 bp):
TG
Found at i:42617 original size:13 final size:13
Alignment explanation
Indices: 42601--42682 Score: 51
Period size: 15 Copynumber: 5.9 Consensus size: 13
42591 AAATAAATAT
42601 AAAAAAATATAAA
1 AAAAAAATATAAA
* *
42614 AAAATAAAAAGAAGA
1 AAAA-AAATATAA-A
42629 AAAAAATATATAAA
1 AAAAAA-ATATAAA
*
42643 TAAAACAAATA-AAT
1 -AAAA-AAATATAAA
*
42657 AAAATAATAATAAA
1 AAAAAAAT-ATAAA
42671 AAATAAAA-ATAA
1 AAA-AAAATATAA
42683 TATATATATA
Statistics
Matches: 53, Mismatches: 8, Indels: 16
0.69 0.10 0.21
Matches are distributed among these distances:
12 3 0.06
13 13 0.25
14 16 0.30
15 19 0.36
16 2 0.04
ACGTcount: A:0.79, C:0.01, G:0.02, T:0.17
Consensus pattern (13 bp):
AAAAAAATATAAA
Found at i:42652 original size:17 final size:16
Alignment explanation
Indices: 42609--42713 Score: 70
Period size: 17 Copynumber: 6.4 Consensus size: 16
42599 ATAAAAAAAT
*
42609 ATAAAAAAATAAAAAGA
1 ATAAAAAAATAAATA-A
* *
42626 AGAAAAAAATATATAA
1 ATAAAAAAATAAATAA
42642 ATAAAACAAATAAATAA
1 ATAAAA-AAATAAATAA
* *
42659 A-ATAATAATAAA-AA
1 ATAAAAAAATAAATAA
* *
42673 ATAAAAATAATATATAT
1 ATAAAAA-AATAAATAA
* * *
42690 ATATATATAATAAAAAA
1 ATA-AAAAAATAAATAA
42707 ATAAAAA
1 ATAAAAA
42714 TAAAAATAGT
Statistics
Matches: 65, Mismatches: 18, Indels: 11
0.69 0.19 0.12
Matches are distributed among these distances:
14 3 0.05
15 9 0.14
16 16 0.25
17 35 0.54
18 2 0.03
ACGTcount: A:0.75, C:0.01, G:0.02, T:0.22
Consensus pattern (16 bp):
ATAAAAAAATAAATAA
Found at i:42672 original size:56 final size:56
Alignment explanation
Indices: 42590--42726 Score: 145
Period size: 56 Copynumber: 2.4 Consensus size: 56
42580 AATAGTAAGT
42590 AAAATAAATATAAAAAAATATAAAAAAATAAAAAGAAGAAAAAAATATATA-AATAAA
1 AAAAT-AA-ATAAAAAAATATAAAAAAATAAAAAGAAGAAAAAAATATATATAATAAA
* * * * * *
42647 ACAAATAAATAAAATAATA-ATAAAAAATAAAAATAATATATATATATATATAATAAA
1 A-AAATAAATAAAAAAATATA-AAAAAATAAAAAGAAGAAAAAAATATATATAATAAA
42704 AAAATAAA-AATAAAAATAGTAAA
1 AAAATAAATAA-AAAAATA-TAAA
42727 TATATATATA
Statistics
Matches: 67, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
55 3 0.04
56 47 0.70
57 12 0.18
58 5 0.07
ACGTcount: A:0.75, C:0.01, G:0.02, T:0.22
Consensus pattern (56 bp):
AAAATAAATAAAAAAATATAAAAAAATAAAAAGAAGAAAAAAATATATATAATAAA
Found at i:42712 original size:8 final size:8
Alignment explanation
Indices: 42602--42713 Score: 68
Period size: 8 Copynumber: 13.6 Consensus size: 8
42592 AATAAATATA
42602 AAAAAATAT
1 AAAAAA-AT
42611 AAAAAAAT
1 AAAAAAAT
*
42619 AAAAAGAAG
1 AAAAA-AAT
42628 AAAAAAAT
1 AAAAAAAT
* *
42636 ATATAAAT
1 AAAAAAAT
42644 AAAACAAAT
1 AAAA-AAAT
42653 AAATAAAAT
1 AAA-AAAAT
*
42662 --AATAAT
1 AAAAAAAT
42668 -AAAAAAT
1 AAAAAAAT
42675 AAAAATAAT
1 AAAAA-AAT
* * *
42684 ATATATAT
1 AAAAAAAT
* *
42692 ATATATAAT
1 A-AAAAAAT
42701 AAAAAAAT
1 AAAAAAAT
42709 AAAAA
1 AAAAA
42714 TAAAAATAGT
Statistics
Matches: 78, Mismatches: 18, Indels: 15
0.70 0.16 0.14
Matches are distributed among these distances:
6 4 0.05
7 6 0.08
8 34 0.44
9 33 0.42
10 1 0.01
ACGTcount: A:0.76, C:0.01, G:0.02, T:0.21
Consensus pattern (8 bp):
AAAAAAAT
Found at i:42718 original size:5 final size:6
Alignment explanation
Indices: 42590--42721 Score: 62
Period size: 6 Copynumber: 22.0 Consensus size: 6
42580 AATAGTAAGT
* *
42590 AAAATA AATATA AAAA-A ATATAA-A AAAATA AAAAGA AGAAA-A AAATATA
1 AAAATA AAAATA AAAATA A-A-AATA AAAATA AAAATA A-AAATA AAA-ATA
* * *
42639 TAAATA AAACA-A ATAAAT- AAAATA ATAATAA AAAATA AAAAT- AATATA
1 AAAATA AAA-ATA A-AAATA AAAATA AAAAT-A AAAATA AAAATA AAAATA
* * * * *
42687 TATATA TATATA ATAA-A AAAATA AAAATA AAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
42722 GTAAATATAT
Statistics
Matches: 100, Mismatches: 13, Indels: 26
0.72 0.09 0.19
Matches are distributed among these distances:
5 18 0.18
6 64 0.64
7 18 0.18
ACGTcount: A:0.76, C:0.01, G:0.02, T:0.22
Consensus pattern (6 bp):
AAAATA
Found at i:42822 original size:24 final size:22
Alignment explanation
Indices: 42795--42855 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 22
42785 ATAATCTAAA
42795 AAAAATAAAAATATATACTAAA-GT
1 AAAAA-AAAAATATATA--AAATGT
**
42819 AAAAAAGAAAATGCATAAAATGT
1 AAAAAA-AAAATATATAAAATGT
42842 AAAAAAAAAATATA
1 AAAAAAAAAATATA
42856 CATGAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
22 9 0.29
23 9 0.29
24 13 0.42
ACGTcount: A:0.70, C:0.03, G:0.07, T:0.20
Consensus pattern (22 bp):
AAAAAAAAAATATATAAAATGT
Found at i:44032 original size:35 final size:39
Alignment explanation
Indices: 43948--44037 Score: 125
Period size: 39 Copynumber: 2.4 Consensus size: 39
43938 CGAGGGTTTG
*
43948 GTGTTTCAAGAGAAACATTTTCAAAGGTTTTTTGTGTGT
1 GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTGTGTGT
* *
43987 GTGTTTCAAGAGAAACAATTT-GAGGGTTTTTT-T-T-T
1 GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTGTGTGT
44022 GTGTTTCAAGAGAAAC
1 GTGTTTCAAGAGAAAC
44038 TGTCTCAAGA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
35 17 0.35
36 1 0.02
37 1 0.02
38 9 0.19
39 20 0.42
ACGTcount: A:0.28, C:0.08, G:0.23, T:0.41
Consensus pattern (39 bp):
GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTGTGTGT
Found at i:44072 original size:36 final size:36
Alignment explanation
Indices: 44023--44239 Score: 168
Period size: 36 Copynumber: 6.2 Consensus size: 36
44013 TTTTTTTTTG
* *
44023 TGTTTCAAGAGAAACTGTCTCAAGAGGGACAAAATT
1 TGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATT
* *
44059 TGTTTCAAAAGAAAATGTCTCAAGTGAGACAAAACTT
1 TGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * *
44096 AG-TTCTAAAAGAAACTATCTCAAGGGAGACGAAATT
1 TGTTTC-AAAAGAAACTGTCTCAAGAGAGACAAAATT
* *
44132 TGTTTCAAGGAA-AAGA-TAT-TC-A-A-AG----ATTT
1 TGTTTCAA--AAGAA-ACTGTCTCAAGAGAGACAAAATT
* **
44161 TTTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATT
* *
44197 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAGATTT
1 TGTTTCAAAAGAAACTGTCTCAAGAGAGACAA-AATT
44234 TGTTTC
1 TGTTTC
44240 TAGGGAAATT
Statistics
Matches: 144, Mismatches: 20, Indels: 33
0.73 0.10 0.17
Matches are distributed among these distances:
27 1 0.01
28 4 0.03
29 12 0.08
30 1 0.01
31 1 0.01
32 2 0.01
33 2 0.01
35 1 0.01
36 73 0.51
37 44 0.31
38 3 0.02
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (36 bp):
TGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:44253 original size:37 final size:37
Alignment explanation
Indices: 44154--44256 Score: 154
Period size: 36 Copynumber: 2.8 Consensus size: 37
44144 AAGATATTCA
*
44154 AAGATTTTTTTTCAAGGGAAACTGTCTCAAGAGAGAC
1 AAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
* *
44191 AA-AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGAC
1 AAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
* *
44227 AAGATTTTGTTTCTAGGGAAATTGTCTCAA
1 AAGATTTTGTTTCAAGGGAAACTGTCTCAA
44257 AACTCGTTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
36 33 0.57
37 25 0.43
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (37 bp):
AAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
Found at i:44375 original size:37 final size:37
Alignment explanation
Indices: 44325--44509 Score: 126
Period size: 37 Copynumber: 5.3 Consensus size: 37
44315 GGTTTATGTA
*
44325 TCAAGAGAAACTATCTCAAGGGAGACAAAATTTTGTT
1 TCAAGGGAAACTATCTCAAGGGAGACAAAATTTTGTT
* **
44362 TCAAGGGAAACTATCTCAAGAGAGACAAAA-TTAATT
1 TCAAGGGAAACTATCTCAAGGGAGACAAAATTTTGTT
* * * *
44398 TCAAAGGAAA-TGTTTTCAA---TG------TTTATGTT
1 TCAAGGGAAACT-ATCTCAAGGGAGACAAAATTT-TGTT
* *
44427 TCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTT
1 TCAAGGGAAACTATCTCAAGGGAGACAAAATTTTGTT
* * * *
44464 TCAAGGGAAACTACCCCAAGCGAGATAAAATTTAT-TT
1 TCAAGGGAAACTATCTCAAGGGAGACAAAATTT-TGTT
44501 T-AAGGGAAA
1 TCAAGGGAAA
44510 TGTTTTCAAT
Statistics
Matches: 113, Mismatches: 21, Indels: 29
0.69 0.13 0.18
Matches are distributed among these distances:
28 2 0.02
29 15 0.13
30 1 0.01
32 1 0.01
33 1 0.01
35 1 0.01
36 26 0.23
37 62 0.55
38 4 0.04
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.28
Consensus pattern (37 bp):
TCAAGGGAAACTATCTCAAGGGAGACAAAATTTTGTT
Found at i:44400 original size:102 final size:102
Alignment explanation
Indices: 44294--44533 Score: 372
Period size: 102 Copynumber: 2.4 Consensus size: 102
44284 ATATTTTGTG
** * *
44294 TTTCAAGGGAAACATTTTCAAGGTTTATGTATCAAGAGAAACTATCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTT
* *
44359 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAA
66 GTTTCAAGGGAAACTACCCCAAGAGAGACAAAATTAA
* *
44396 TTTCAAAGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTT
* * *
44461 GTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTTA
66 GTTTCAAGGGAAACTACCCCAAGAGAGACAAAATTAA
*
44498 TTTTAAGGGAAATGTTTTCAATGTTTATGTTTCAAG
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAG
44534 GGAGACAAAA
Statistics
Matches: 125, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
102 125 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.32
Consensus pattern (102 bp):
TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTT
GTTTCAAGGGAAACTACCCCAAGAGAGACAAAATTAA
Found at i:44536 original size:87 final size:87
Alignment explanation
Indices: 44442--44620 Score: 286
Period size: 87 Copynumber: 2.1 Consensus size: 87
44432 AGAAACTGTC
* * *
44442 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTTATTTTAAGGG
1 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTCATTTCAAGGG
*
44507 AAATGTTTTCAATGTTTATGTT
66 AAATATTTTCAATGTTTATGTT
* * * *
44529 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAATTATCTCAATCGAGATAAAATTCATTTCAAGGG
1 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTCATTTCAAGGG
44594 AAATATTTTCAATGTTTATGTT
66 AAATATTTTCAATGTTTATGTT
44616 TCAAG
1 TCAAG
44621 AGAAACTGTC
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 84 1.00
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (87 bp):
TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTCATTTCAAGGG
AAATATTTTCAATGTTTATGTT
Found at i:44720 original size:189 final size:189
Alignment explanation
Indices: 44340--44725 Score: 490
Period size: 189 Copynumber: 2.0 Consensus size: 189
44330 AGAAACTATC
*
44340 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAATTTCAAAGG
1 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAATTTCAAAGG
* * * * **
44405 AAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGG
66 AAATATTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTAGTTCCAAAA
* * * * * *
44470 GAAACTACCCCAAGCGAGATAAAATTTATTTTAAGGGAAATGTTTTCAATGTTTATGTT
131 GAAAATACCCCAAGCGAGACAAAATTTATTTCAAGGAAAATGTATTCAATATTTATGTT
* ** * * *
44529 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAATTATCTCAATCGAGATAAAATTCATTTCAAGGG
1 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAATTTCAAAGG
44594 AAATATTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTAGTTCCAAAA
66 AAATATTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTAGTTCCAAAA
** * * * * *
44659 GAAAATGTCTCATGGGAGACGAAA-TTAGTTTCAATGAAAATAG-ATTCAAATATTT-TGTT
131 GAAAATACCCCAAGCGAGACAAAATTTA-TTTCAAGGAAAAT-GTATTC-AATATTTATGTT
44718 TCAAGGGA
1 TCAAGGGA
44726 AACTTGGAAA
Statistics
Matches: 168, Mismatches: 26, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
188 3 0.02
189 158 0.94
190 7 0.04
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (189 bp):
TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAATTTCAAAGG
AAATATTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTAGTTCCAAAA
GAAAATACCCCAAGCGAGACAAAATTTATTTCAAGGAAAATGTATTCAATATTTATGTT
Found at i:45761 original size:31 final size:32
Alignment explanation
Indices: 45673--45784 Score: 138
Period size: 32 Copynumber: 3.5 Consensus size: 32
45663 TTTGCATCAG
* * * *
45673 GATGTTGAAT-TCCCAAAGATGCCCCAATATTC
1 GATGTTGAATCT-CAAAAAATGCCCCAACATTT
*
45705 GATGTTGAATCTCAAAAAATTCCCCAACATTT
1 GATGTTGAATCTCAAAAAATGCCCCAACATTT
*
45737 GATGTTAAATCT-AAAAAATGCCCCAACATTT
1 GATGTTGAATCTCAAAAAATGCCCCAACATTT
45768 GATGTTGAATCTTCAAA
1 GATGTTGAATC-TCAAA
45785 GATGCCCTCA
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
31 28 0.41
32 37 0.54
33 4 0.06
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (32 bp):
GATGTTGAATCTCAAAAAATGCCCCAACATTT
Found at i:46827 original size:69 final size:68
Alignment explanation
Indices: 46712--46848 Score: 202
Period size: 69 Copynumber: 2.0 Consensus size: 68
46702 TCTCTTTCTC
* *
46712 TTGATGCTCCATGATCTTCGAGTGGAGTGATTCAGTAATTCAGAAATGATTCTACTTGATCAATC
1 TTGATGCTCCATGATCTTCGAGTGAAGTGATTAAGTAATTCAGAAATGATTCTAC-TGATCAATC
46777 TCAT
65 TCAT
* * * * *
46781 TTGATGCTCTATGATCTTCGAGTGAAGTGGTTAAGTGATTCGGAAATGATTGTACTGATCAATCT
1 TTGATGCTCCATGATCTTCGAGTGAAGTGATTAAGTAATTCAGAAATGATTCTACTGATCAATCT
46846 CAT
66 CAT
46849 AGTTTGAATC
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
68 13 0.21
69 48 0.79
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.36
Consensus pattern (68 bp):
TTGATGCTCCATGATCTTCGAGTGAAGTGATTAAGTAATTCAGAAATGATTCTACTGATCAATCT
CAT
Found at i:46936 original size:27 final size:27
Alignment explanation
Indices: 46906--46972 Score: 66
Period size: 27 Copynumber: 2.4 Consensus size: 27
46896 GCAACTTGTC
46906 TTCTTTTTTCTTCAATTTTCT-TTTTTT
1 TTCTTTTTTCTTCAATTTT-TATTTTTT
**
46933 TTCTCTTTTT-TTCTCTTTTTATTTTTT
1 TTCT-TTTTTCTTCAATTTTTATTTTTT
*
46960 CTCTTTTTCTCTT
1 TTCTTTTT-TCTT
46973 TTTGCTTTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
26 5 0.15
27 21 0.64
28 7 0.21
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (27 bp):
TTCTTTTTTCTTCAATTTTTATTTTTT
Found at i:46941 original size:8 final size:8
Alignment explanation
Indices: 46930--46975 Score: 58
Period size: 8 Copynumber: 5.6 Consensus size: 8
46920 ATTTTCTTTT
46930 TTTTTCTC
1 TTTTTCTC
46938 TTTTTTTCTC
1 --TTTTTCTC
*
46948 TTTTTAT-
1 TTTTTCTC
46955 TTTTTCTC
1 TTTTTCTC
46963 TTTTTCTC
1 TTTTTCTC
46971 TTTTT
1 TTTTT
46976 GCTTTGATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
7 6 0.18
8 19 0.58
10 8 0.24
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTCTC
Found at i:46944 original size:15 final size:15
Alignment explanation
Indices: 46939--46967 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
46929 TTTTTTCTCT
46939 TTTTTTCTCTTTTTA
1 TTTTTTCTCTTTTTA
46954 TTTTTTCTCTTTTT
1 TTTTTTCTCTTTTT
46968 CTCTTTTTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTTCTCTTTTTA
Found at i:46963 original size:25 final size:23
Alignment explanation
Indices: 46924--46975 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
46914 TCTTCAATTT
* *
46924 TCTTTTT-TTTTCTCTTTTTTTC
1 TCTTTTTATTTTTTCTCTTTTTC
46946 TCTTTTTATTTTTTCTCTTTTTC
1 TCTTTTTATTTTTTCTCTTTTTC
46969 TCTTTTT
1 TCTTTTT
46976 GCTTTGATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 7 0.26
23 20 0.74
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (23 bp):
TCTTTTTATTTTTTCTCTTTTTC
Found at i:46974 original size:15 final size:15
Alignment explanation
Indices: 46941--46974 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
46931 TTTTCTCTTT
*
46941 TTTTCTCTTTTTATT
1 TTTTCTCTTTTTATC
*
46956 TTTTCTCTTTTTCTC
1 TTTTCTCTTTTTATC
46971 TTTT
1 TTTT
46975 TGCTTTGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTCTCTTTTTATC
Found at i:50133 original size:4 final size:4
Alignment explanation
Indices: 50126--50280 Score: 52
Period size: 4 Copynumber: 37.8 Consensus size: 4
50116 ATAGTAAGTA
* * * * * *
50126 AAAT AAAT ATAA- AAAT AAAA AACAT AAAG AAAA AGAAG AAAA AAAT ATAT
1 AAAT AAAT A-AAT AAAT AAAT AA-AT AAAT AAAT A-AAT AAAT AAAT AAAT
* *
50176 AAAT AAAAC AAAT AAAT AAA- ATAAT -AAT AAA- AAAGT AAAA ATAAT
1 AAAT -AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAA-T AAAT A-AAT
* * * * *
50221 ATAT ATAT ATAT ATAAT AAAT AAA- AAAT AAA- AATAGT AAAT ATAT ATAT
1 AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AA-A-T AAAT AAAT AAAT
*
50270 AAAT TAAT AAA
1 AAAT AAAT AAA
50281 ACTGATAATA
Statistics
Matches: 116, Mismatches: 19, Indels: 32
0.69 0.11 0.19
Matches are distributed among these distances:
3 14 0.12
4 79 0.68
5 21 0.18
6 2 0.02
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:50177 original size:25 final size:23
Alignment explanation
Indices: 50149--50225 Score: 59
Period size: 25 Copynumber: 3.1 Consensus size: 23
50139 AATAAAAAAC
50149 ATAAAGAAAAAGAAGAAAAAAATAT
1 ATAAA-AAAAAGAA-AAAAAAATAT
50174 ATAAATAAAACA-AATAAATAAAATA-
1 ATAAA-AAAA-AGAA-AAA-AAAATAT
* *
50199 ATAATAAAAAAGTAAAAATAATAT
1 ATAA-AAAAAAGAAAAAAAAATAT
50223 ATA
1 ATA
50226 TATATATATA
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
23 5 0.12
24 7 0.16
25 23 0.53
26 8 0.19
ACGTcount: A:0.74, C:0.01, G:0.05, T:0.19
Consensus pattern (23 bp):
ATAAAAAAAAGAAAAAAAAATAT
Found at i:50183 original size:24 final size:23
Alignment explanation
Indices: 50156--50225 Score: 63
Period size: 23 Copynumber: 2.9 Consensus size: 23
50146 AACATAAAGA
50156 AAAAGAAGAAAAAAATATATAAAT
1 AAAA-AAGAAAAAAATATATAAAT
*
50180 AAAACAAATAAATAAAATA-AT-AAT
1 -AAA-AAAGAAA-AAAATATATAAAT
50204 AAAAAAGTAAAAATAATATATA
1 AAAAAAG-AAAAA-AATATATA
50226 TATATATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
22 5 0.14
23 10 0.27
24 5 0.14
25 10 0.27
26 7 0.19
ACGTcount: A:0.74, C:0.01, G:0.04, T:0.20
Consensus pattern (23 bp):
AAAAAAGAAAAAAATATATAAAT
Found at i:50218 original size:38 final size:37
Alignment explanation
Indices: 50126--50255 Score: 99
Period size: 38 Copynumber: 3.5 Consensus size: 37
50116 ATAGTAAGTA
* * *
50126 AAAT-AAATATAAAAATAAAA-AACATAAAGAAA-AAG
1 AAATAAAAAATAAAAATAAAACAA-ATAAATAAATAAT
50161 AAGA-AAAAAATATATAAATAAAACAAATAAATAAAATAAT
1 AA-ATAAAAAATA-A-AAATAAAACAAATAAAT-AAATAAT
* * * * *
50201 -AATAAAAAAGTAAAAATAATATATATATATATATAAT
1 AAATAAAAAA-TAAAAATAAAACAAATAAATAAATAAT
50238 AAATAAAAAATAAAAATA
1 AAATAAAAAATAAAAATA
50256 GTAAATATAT
Statistics
Matches: 77, Mismatches: 8, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
35 2 0.03
36 7 0.09
37 15 0.19
38 36 0.47
39 13 0.17
40 4 0.05
ACGTcount: A:0.74, C:0.02, G:0.03, T:0.22
Consensus pattern (37 bp):
AAATAAAAAATAAAAATAAAACAAATAAATAAATAAT
Found at i:50246 original size:37 final size:36
Alignment explanation
Indices: 50196--50331 Score: 138
Period size: 37 Copynumber: 3.8 Consensus size: 36
50186 AATAAATAAA
50196 ATAATAATAAAAAAGTAAAAATAATATATATATATAT
1 ATAATAATAAAAAA-TAAAAATAATATATATATATAT
* *
50233 ATAATAAATAAAAAATAAAAATAGTAAATATATATAT
1 ATAAT-AATAAAAAATAAAAATAATATATATATATAT
* *
50270 A-AATTAATAAAACTGATAATAAA-AAAATA-ATATATAT
1 ATAA-TAATAAAA--AATAA-AAATAATATATATATATAT
*
50307 ATAAT-CTAAAAAATAAAAAT-ATATA
1 ATAATAATAAAAAATAAAAATAATATA
50332 CTAAAGTAAA
Statistics
Matches: 83, Mismatches: 9, Indels: 18
0.75 0.08 0.16
Matches are distributed among these distances:
33 7 0.08
34 4 0.05
36 14 0.17
37 37 0.45
38 18 0.22
39 3 0.04
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.30
Consensus pattern (36 bp):
ATAATAATAAAAAATAAAAATAATATATATATATAT
Found at i:50349 original size:24 final size:23
Alignment explanation
Indices: 50289--50350 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 23
50279 AAACTGATAA
* *
50289 TAAAAAAATAATATATATATAATC
1 TAAAAAAA-AAAATATATATAAAC
*
50313 TAAAAAATAAAAATATATACTAAAG
1 TAAAAAA-AAAAATATATA-TAAAC
*
50338 TAAAAAAGAAAAT
1 TAAAAAAAAAAAT
50351 GCATAAAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
24 21 0.66
25 11 0.34
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (23 bp):
TAAAAAAAAAAATATATATAAAC
Found at i:51028 original size:19 final size:18
Alignment explanation
Indices: 50970--51058 Score: 70
Period size: 19 Copynumber: 4.8 Consensus size: 18
50960 ATGAACTTGA
* * *
50970 AAATAAGCTATAAATATG
1 AAATAAGTTATGAATCTG
50988 AAATTAAGTTATGAATCTG
1 AAA-TAAGTTATGAATCTG
* *
51007 AAATAAGTTTTGAGTCTAG
1 AAATAAGTTATGAATCT-G
* *
51026 AAACAAGTTCTGAATCTG
1 AAATAAGTTATGAATCTG
* *
51044 AGAATGAGTTCTGAA
1 A-AATAAGTTATGAA
51059 ATGTGAAAGT
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
18 17 0.29
19 41 0.71
ACGTcount: A:0.43, C:0.08, G:0.18, T:0.31
Consensus pattern (18 bp):
AAATAAGTTATGAATCTG
Found at i:51087 original size:6 final size:6
Alignment explanation
Indices: 51076--51123 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
51066 AGTACAAATT
* **
51076 ATGAAA ATGAAA TATGAAA GTGACT ATGAAA ATGAAA GATGAAA ATGA
1 ATGAAA ATGAAA -ATGAAA ATGAAA ATGAAA ATGAAA -ATGAAA ATGA
51124 GATATGAAAG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
6 22 0.65
7 12 0.35
ACGTcount: A:0.56, C:0.02, G:0.21, T:0.21
Consensus pattern (6 bp):
ATGAAA
Found at i:51093 original size:13 final size:13
Alignment explanation
Indices: 51075--51132 Score: 73
Period size: 13 Copynumber: 4.5 Consensus size: 13
51065 AAGTACAAAT
51075 TATGAAAATGAAA
1 TATGAAAATGAAA
* *
51088 TATGAAAGTG-AC
1 TATGAAAATGAAA
51100 TATGAAAATGAAA
1 TATGAAAATGAAA
* *
51113 GATGAAAATGAGA
1 TATGAAAATGAAA
51126 TATGAAA
1 TATGAAA
51133 GTTTTGTATT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
12 10 0.27
13 27 0.73
ACGTcount: A:0.55, C:0.02, G:0.21, T:0.22
Consensus pattern (13 bp):
TATGAAAATGAAA
Found at i:51183 original size:18 final size:18
Alignment explanation
Indices: 51162--51226 Score: 53
Period size: 18 Copynumber: 3.4 Consensus size: 18
51152 TGAAAAAGAA
51162 TATGATATGACTATTATG
1 TATGATATGACTATTATG
* *
51180 TATGATATTG-TTTTTCAT-
1 TATGATA-TGACTATT-ATG
51198 TAATTTGATATGACTATTATG
1 T-A--TGATATGACTATTATG
51219 TATGATAT
1 TATGATAT
51227 TGTTTATCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 14
0.67 0.07 0.26
Matches are distributed among these distances:
18 17 0.47
19 5 0.14
20 5 0.14
21 9 0.25
ACGTcount: A:0.31, C:0.05, G:0.14, T:0.51
Consensus pattern (18 bp):
TATGATATGACTATTATG
Found at i:51244 original size:39 final size:39
Alignment explanation
Indices: 51159--51246 Score: 131
Period size: 39 Copynumber: 2.3 Consensus size: 39
51149 GAATGAAAAA
* *
51159 GAATATGATATGACTATTATGTATGATATTGTTTTTCAT
1 GAATTTGATATGACTATTATGTATGATATTGTTTATCAT
*
51198 TAATTTGATATGACTATTATGTATGATATTGTTTATCAT
1 GAATTTGATATGACTATTATGTATGATATTGTTTATCAT
**
51237 GGTTTTGATA
1 GAATTTGATA
51247 AAATCATGAG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.30, C:0.05, G:0.16, T:0.50
Consensus pattern (39 bp):
GAATTTGATATGACTATTATGTATGATATTGTTTATCAT
Found at i:52729 original size:64 final size:63
Alignment explanation
Indices: 52636--52845 Score: 217
Period size: 65 Copynumber: 3.3 Consensus size: 63
52626 TGCACTAAGA
* * * * *
52636 GTGCATCGATGCATCAAGTACATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTAGATGTTTCAAAATATCCACAGTGCATCGATGCATGG-TG
*
52700 GTGCATCGATGCATCAAATGCATTAGATGTTTTCATAAA-ATCCTCAGTGCATCGATGCATGGTA
1 GTGCATCGATGCATCAAATGCATTAGATG-TTTCA-AAATATCCACAGTGCATCGATGCATGGT-
*
52764 T
63 G
* * ** * *
52765 GTGCATCGATGCATGAAATGCATTTGATG-TTCAATTTAATTCATAGTGCATCGATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTAGATGTTTCAAAAT-ATCCACAGTGCATCGATGCATGG--T
52829 G
63 G
*
52830 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
52846 CTCTGAAAAA
Statistics
Matches: 122, Mismatches: 17, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 47 0.39
65 66 0.54
66 4 0.03
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTAGATGTTTCAAAATATCCACAGTGCATCGATGCATGGTG
Found at i:55107 original size:23 final size:22
Alignment explanation
Indices: 55077--55156 Score: 81
Period size: 23 Copynumber: 3.6 Consensus size: 22
55067 GCATGGCCTT
55077 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
55099 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
* * *
55121 GTGTATCGATGCATATTTAAGG
1 GTGCATCGATGCACATTCAAGG
*
55143 ATGCATCGATGCAC
1 GTGCATCGATGCAC
55157 TGTTAGGTGT
Statistics
Matches: 44, Mismatches: 12, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
21 13 0.30
22 15 0.34
23 16 0.36
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.28
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:55131 original size:44 final size:42
Alignment explanation
Indices: 55055--55175 Score: 111
Period size: 43 Copynumber: 2.8 Consensus size: 42
55045 AAAACCCGAT
* ** *
55055 GGATGCATCGATGCA-TGGCCTTGTGCATCGATGCACATTCAA
1 GGATGCATCGATGCACT-GTCAGGTGTATCGATGCACATTCAA
* * * *
55097 GGCGTGCATCGGTGCACCT-TCATGGTGTATCGATGCATATTTAA
1 GG-ATGCATCGATGCA-CTGTCA-GGTGTATCGATGCACATTCAA
*
55141 GGATGCATCGATGCACTGTTAGGTGTATCGATGCA
1 GGATGCATCGATGCACTGTCAGGTGTATCGATGCA
55176 TGAAGAATAA
Statistics
Matches: 63, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
42 18 0.29
43 25 0.40
44 19 0.30
45 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (42 bp):
GGATGCATCGATGCACTGTCAGGTGTATCGATGCACATTCAA
Found at i:55172 original size:20 final size:21
Alignment explanation
Indices: 55120--55176 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
55110 GCACCTTCAT
*
55120 GGTGTATCGATGCATATTTAA
1 GGTGTATCGATGCATAGTTAA
*
55141 GGATGCATCGATGCACT-GTT-A
1 GG-TGTATCGATGCA-TAGTTAA
55162 GGTGTATCGATGCAT
1 GGTGTATCGATGCAT
55177 GAAGAATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 1 0.03
20 11 0.35
21 5 0.16
22 13 0.42
23 1 0.03
ACGTcount: A:0.25, C:0.14, G:0.28, T:0.33
Consensus pattern (21 bp):
GGTGTATCGATGCATAGTTAA
Found at i:59832 original size:14 final size:14
Alignment explanation
Indices: 59813--59841 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
59803 TTTTAGATTC
59813 TTTAAAAGATATTT
1 TTTAAAAGATATTT
59827 TTTAAAAGATATTT
1 TTTAAAAGATATTT
59841 T
1 T
59842 ATGATACTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
TTTAAAAGATATTT
Found at i:65039 original size:65 final size:64
Alignment explanation
Indices: 64920--65129 Score: 205
Period size: 65 Copynumber: 3.2 Consensus size: 64
64910 TTTTTCAGAG
* * * *
64920 TGATGCACCGATGCCCCAATCCATGCATCGATGCAC-CATGA-ATTAAATT-GAACATCGAATGC
1 TGATGCATCGATGCACCAA-CCATGCATCGATGCACTCAGGATATT---TTAAAACATCGAATGC
64982 ATT
62 ATT
* * * *
64985 TCATGCATCGATGC-GCATACCATGTATCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCA
1 TGATGCATCGATGCACCA-ACCATGCATCGATGCACTCAGGATATTT-T-AAAACATCGAATGCA
65048 TT
63 TT
* * * * *
65050 TGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTCAAACATCGAATGCACT
1 TGATGCATCGATGCACCAACCATGCATCGATGCACTCAGGATATTTTAAAACATCGAATGCATT
65114 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
65130 TCTTAGTGCA
Statistics
Matches: 121, Mismatches: 16, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 48 0.40
65 66 0.55
66 5 0.04
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.27
Consensus pattern (64 bp):
TGATGCATCGATGCACCAACCATGCATCGATGCACTCAGGATATTTTAAAACATCGAATGCATT
Found at i:65129 original size:17 final size:19
Alignment explanation
Indices: 65101--65149 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
65091 TATTTTCAAA
65101 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
65119 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
65138 CACCGATGCACT
1 CATCGATGCACT
65150 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:75203 original size:35 final size:35
Alignment explanation
Indices: 75157--75228 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
75147 AATAATTGGG
75157 CAATTCAATATCATGGATTTATGTTTTAATGAATT
1 CAATTCAATATCATGGATTTATGTTTTAATGAATT
75192 CAATTCAATATCATGGATTTATGTTTTAATGAATT
1 CAATTCAATATCATGGATTTATGTTTTAATGAATT
75227 CA
1 CA
75229 GTATGATTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.35, C:0.10, G:0.11, T:0.44
Consensus pattern (35 bp):
CAATTCAATATCATGGATTTATGTTTTAATGAATT
Done.