Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397256.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_56.0, 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: 13963513
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 99179 characters in sequence are not A, C, G, or T
File 28 of 29
Found at i:12623433 original size:15 final size:16
Alignment explanation
Indices: 12623413--12623443 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
12623403 AATAAACATT
12623413 CAAAACAAAA-AAGAA
1 CAAAACAAAAGAAGAA
12623428 CAAAACAAAAGAAGAA
1 CAAAACAAAAGAAGAA
12623444 AGAACAGACC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.77, C:0.13, G:0.10, T:0.00
Consensus pattern (16 bp):
CAAAACAAAAGAAGAA
Found at i:12636753 original size:14 final size:14
Alignment explanation
Indices: 12636730--12636760 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
12636720 TCAACTTGGG
12636730 TTTTTCTCCTTTTT
1 TTTTTCTCCTTTTT
*
12636744 TTTTTTTCCTTTTT
1 TTTTTCTCCTTTTT
12636758 TTT
1 TTT
12636761 CACTTAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTCTCCTTTTT
Found at i:12661094 original size:2 final size:2
Alignment explanation
Indices: 12661087--12661112 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12661077 CACATATACC
12661087 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
12661113 TTCCTTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:12670656 original size:2 final size:2
Alignment explanation
Indices: 12670649--12670675 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12670639 TGGAAAACGC
12670649 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
12670676 TTTCTGCTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:12687015 original size:24 final size:25
Alignment explanation
Indices: 12686988--12687041 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
12686978 GAACGTGGTT
12686988 ATTAAAAT-TTATATAAAAATTT-AA
1 ATTAAAATATTAT-TAAAAATTTGAA
* *
12687012 ATT-AATTATTATTAATAATTTGAA
1 ATTAAAATATTATTAAAAATTTGAA
12687036 ATTAAA
1 ATTAAA
12687042 TTTTTAAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 11 0.44
24 12 0.48
25 2 0.08
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (25 bp):
ATTAAAATATTATTAAAAATTTGAA
Found at i:12702806 original size:434 final size:431
Alignment explanation
Indices: 12701896--12703132 Score: 1569
Period size: 434 Copynumber: 2.9 Consensus size: 431
12701886 ATTTTTTTAA
* * * *
12701896 GTATGAGTTTCGAAATTTTATTGTTAAAAAGACGAAAATCTGATAAGTTACTTAAATTT-TCAAT
1 GTATGAGTCTCGAAATTTTGTTGTTAAAAAGACGAAGATCTGACAAGTTACTTAAATTTCT-AAT
* * ** * * * *
12701960 AGAGTTAGGGAGAGAACCAACTAGATTATTATTAGAGAGTGAAAGTTCGTACAGAGATTTCAATA
65 AGAGTTAGGAAGAGAACCAACCAGATTATTATTAGAGAGTTCAAGTCCATGCAGAGATTTCAACA
* * * *
12702025 TTCCAACTTGTTGAGGTATAACTCCAGAGAGTTTGTTTCCAGACAAGTAGAGAATGGACAGGTTT
130 TTCCAACTTGTTGAGGTATAGCTCCAGAGAGTTTGTTTTCAAACAAGTAGAGAAAGGACAGGTTT
* * * *
12702090 GTCAAGTTTTCTATAAAAAGAGGGATTGAACTTGTCAAAATGTTATTTTGTAGATAGAGCTGAGA
195 GTCAAGTTTTTTATAAAAAGAGGGATTGAACCTGTCAGAATGTTTTTTTGTAGATAGAGCTGAGA
* * * *
12702155 AAGAGACTTTAACTTTTTTATTTCAAAAGGTATA-TTTCTGGAAAAATAATTAATAGACAAGTTA
260 AAGAGACCTTAAC-TTTTTATTTCAAAAGGTATATTTTC-AGAAAAATAATTAATAAACAAGTGA
* * * *
12702219 AGGTAAGTTAGTTTAGATAGATTATCGATATTTGATAGAATGATTCCACTAAAAGAATTTTTAGA
323 AAGTAAGTTAGTTTAGATAGATTACCGATATTTGATAGAATGATTCCACTAAAAGAATTCTTAAA
*
12702284 CAAATCAAGCCAATCAAGTGAACTTAGCATTTCAATTTCTTGAG
388 CAAATCAAGCCAATCAAGTGAACTTAGCATTCCAATTTCTTGAG
12702328 GTATGAGTCTCGAAATTTTGTTGTTAAAAAGACG-AGAATCTGACAAGTTACTTAAATTTCTAAT
1 GTATGAGTCTCGAAATTTTGTTGTTAAAAAGACGAAG-ATCTGACAAGTTACTTAAATTTCTAAT
* * * * * *
12702392 AGAGTTAGGAAGAGAATCGACCAGATTATTATTAGTGAGTTCAAGTCCTTGTAGAAATTTCAACA
65 AGAGTTAGGAAGAGAACCAACCAGATTATTATTAGAGAGTTCAAGTCCATGCAGAGATTTCAACA
* *
12702457 TTCTAACTTGTTGAGGTATAGCTCCAGAGAGCTTGTTTTCAAACAAGTAGAGAAAGGACAGGTTT
130 TTCCAACTTGTTGAGGTATAGCTCCAGAGAGTTTGTTTTCAAACAAGTAGAGAAAGGACAGGTTT
* *
12702522 GTCAAGTTTTTTATAAAAAAAGGGATTGAACCTGTCAGAAT-TTTTTTTGTAGATAGAGTTGAGA
195 GTCAAGTTTTTTATAAAAAGAGGGATTGAACCTGTCAGAATGTTTTTTTGTAGATAGAGCTGAGA
*
12702586 AAGAGACCTTAACTTTCCTATTTCAAAA-GTATATTTTCAGAAAAATAATTAATAAACAAGTCGA
260 AAGAGACCTTAACTTT-TTATTTCAAAAGGTATATTTTCAGAAAAATAATTAATAAACAAGT-GA
* *
12702650 GGGAAGTAAGTTAGTTTATATAGATTACCGATATTTGATGGAATGATTCCACTAAAAGAATTCTT
323 ---AAGTAAGTTAGTTTAGATAGATTACCGATATTTGATAGAATGATTCCACTAAAAGAATTCTT
*
12702715 AAACAAATCAAGCCAATCAAGTGATCTTAGCATTCCAATTTCTTGAG
385 AAACAAATCAAGCCAATCAAGTGAACTTAGCATTCCAATTTCTTGAG
* * * * *
12702762 TTATG-GATC-CTGAAATTTTGTTGTTAAAAAAATGAAGATCTGACAAGTTACTTAATTTTCCAA
1 GTATGAG-TCTC-GAAATTTTGTTGTTAAAAAGACGAAGATCTGACAAGTTACTTAAATTTCTAA
*
12702825 TAGAGTTGGGAAGAGAACCAACCAGATTATTATTAGAGAGTTCAAGTCCATGCAGAGATTTCAAC
64 TAGAGTTAGGAAGAGAACCAACCAGATTATTATTAGAGAGTTCAAGTCCATGCAGAGATTTCAAC
* * * * * * *
12702890 ATTCCAACTTGTTGAGGTAT-GACACTAGAGAGTTTATTTTCGAACAAATAAAGAAAGGATAGGT
129 ATTCCAACTTGTTGAGGTATAG-CTCCAGAGAGTTTGTTTTCAAACAAGTAGAGAAAGGACAGGT
* * ** * *
12702954 TTGTCATGTTTCTTATAGGAAGAGGGATTCAACCTGTCAGAATGTTTTTTTCTAGATAGAGCTGA
193 TTGTCAAGTTTTTTATAAAAAGAGGGATTGAACCTGTCAGAATGTTTTTTTGTAGATAGAGCTGA
* * * * * *
12703019 -AAAGGGGATCATAACTCTTTTTTTTCAAAAGGTATATTTTCAGAAATATAATTGATAGATA-AA
258 GAAA-GAGACCTTAACT-TTTTATTTCAAAAGGTATATTTTCAGAAAAATAATTAATA-A-ACAA
* * * * * * * *
12703082 TTTAGA-TAGGTTAATTTAGATAGATTACTGATATCTGATGGAATGATTCCA
319 GTGAAAGTAAGTTAGTTTAGATAGATTACCGATATTTGATAGAATGATTCCA
12703133 TTGAGAGAAT
Statistics
Matches: 701, Mismatches: 86, Indels: 36
0.85 0.10 0.04
Matches are distributed among these distances:
430 29 0.04
431 49 0.07
432 244 0.35
433 5 0.01
434 303 0.43
435 39 0.06
436 27 0.04
437 4 0.01
438 1 0.00
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.33
Consensus pattern (431 bp):
GTATGAGTCTCGAAATTTTGTTGTTAAAAAGACGAAGATCTGACAAGTTACTTAAATTTCTAATA
GAGTTAGGAAGAGAACCAACCAGATTATTATTAGAGAGTTCAAGTCCATGCAGAGATTTCAACAT
TCCAACTTGTTGAGGTATAGCTCCAGAGAGTTTGTTTTCAAACAAGTAGAGAAAGGACAGGTTTG
TCAAGTTTTTTATAAAAAGAGGGATTGAACCTGTCAGAATGTTTTTTTGTAGATAGAGCTGAGAA
AGAGACCTTAACTTTTTATTTCAAAAGGTATATTTTCAGAAAAATAATTAATAAACAAGTGAAAG
TAAGTTAGTTTAGATAGATTACCGATATTTGATAGAATGATTCCACTAAAAGAATTCTTAAACAA
ATCAAGCCAATCAAGTGAACTTAGCATTCCAATTTCTTGAG
Found at i:12710630 original size:32 final size:32
Alignment explanation
Indices: 12710594--12710656 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
12710584 TGACTGAGAG
*
12710594 TTGCTTTCTTTATTTCTTTTGATGGAATTTAT
1 TTGCTTTCTTTATATCTTTTGATGGAATTTAT
12710626 TTGCTTTCTTTATATCTTTTGATGGAATTTA
1 TTGCTTTCTTTATATCTTTTGATGGAATTTA
12710657 CTTCAAATGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.17, C:0.10, G:0.13, T:0.60
Consensus pattern (32 bp):
TTGCTTTCTTTATATCTTTTGATGGAATTTAT
Found at i:12721924 original size:22 final size:22
Alignment explanation
Indices: 12721883--12721940 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
12721873 CTAGTAAGCC
* *
12721883 AACCAAATATCTATTAATCTTA
1 AACCAAATATATATTAATCTAA
* * *
12721905 AGCCAAATATATGTTGATCTAA
1 AACCAAATATATATTAATCTAA
*
12721927 AAACAAATATATAT
1 AACCAAATATATAT
12721941 ATATATATAT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.33
Consensus pattern (22 bp):
AACCAAATATATATTAATCTAA
Found at i:12723074 original size:28 final size:28
Alignment explanation
Indices: 12723037--12723098 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
12723027 CTCATGGCCA
**
12723037 AAATCCAAAGGTGTTATGACACCTAATC
1 AAATCCAAAGGTACTATGACACCTAATC
* *
12723065 AAATCTAAAGGTACTATGACACCTAAAC
1 AAATCCAAAGGTACTATGACACCTAATC
12723093 -AATCCA
1 AAATCCA
12723099 TCAATTCCCT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 5 0.17
28 24 0.83
ACGTcount: A:0.44, C:0.23, G:0.11, T:0.23
Consensus pattern (28 bp):
AAATCCAAAGGTACTATGACACCTAATC
Found at i:12723456 original size:28 final size:27
Alignment explanation
Indices: 12723420--12723518 Score: 119
Period size: 27 Copynumber: 3.7 Consensus size: 27
12723410 TAACTAAAGA
*
12723420 TGCT-AGGCACCTAACAATATCCAAAGG
1 TGCTAAGGCACCTAACAAT-TCCGAAGG
* * *
12723447 TGTTAAGGCACCTAACAATTCTGAAGA
1 TGCTAAGGCACCTAACAATTCCGAAGG
*
12723474 TGCTAAGGCACTTAACAATTCCGAAGG
1 TGCTAAGGCACCTAACAATTCCGAAGG
* *
12723501 TACTAAGGCATCTAACAA
1 TGCTAAGGCACCTAACAA
12723519 AGTCTAATTA
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
27 46 0.77
28 14 0.23
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.22
Consensus pattern (27 bp):
TGCTAAGGCACCTAACAATTCCGAAGG
Found at i:12723501 original size:54 final size:54
Alignment explanation
Indices: 12723416--12723518 Score: 145
Period size: 54 Copynumber: 1.9 Consensus size: 54
12723406 TACCTAACTA
**
12723416 AAGATGCTAGGCACCTAACAATATCCAAAGGTGTTAAGGCACCTAACAATTCTG
1 AAGATGCTAGGCACCTAACAATATCCAAAGGTACTAAGGCACCTAACAATTCTG
* * *
12723470 AAGATGCTAAGGCACTTAACAAT-TCCGAAGGTACTAAGGCATCTAACAA
1 AAGATGCT-AGGCACCTAACAATATCCAAAGGTACTAAGGCACCTAACAA
12723519 AGTCTAATTA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
54 30 0.70
55 13 0.30
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.21
Consensus pattern (54 bp):
AAGATGCTAGGCACCTAACAATATCCAAAGGTACTAAGGCACCTAACAATTCTG
Found at i:12724639 original size:143 final size:144
Alignment explanation
Indices: 12724376--12724646 Score: 364
Period size: 143 Copynumber: 1.9 Consensus size: 144
12724366 GTGGGGGTCG
* * * *
12724376 ATCTTGGTCTAAAACATAATGCATTTTCTATCTTGAAGGTTTAAGGATCAACCCTTGGAAGGGTA
1 ATCTTGGTCTAAAACAGAATGCATTTTCTATCATGAAGGCTTAAGGATCAACCCTTGGAAGCGTA
** * * ** *
12724441 GGGATTGATCCTAACACTTCCAAAATGTATTTTTCCCCATTCTGCTTTTTGGGATC-ACCCTTTA
66 GGGATCAATCCTAACACTTCCAAAATGCATTTTGCCCCATTCTGCTTCCTAGGATCGACCCTTTA
12724505 AAGGATGGGAGTTA
131 AAGGATGGGAGTTA
** * *
12724519 ATCTTGGTCTAAAGTAGAATGCATTTTCTATCATGGAGGCTTAAGGATCAACCCTTGGAAGCGTG
1 ATCTTGGTCTAAAACAGAATGCATTTTCTATCATGAAGGCTTAAGGATCAACCCTTGGAAGCGTA
* ** *
12724584 GGGGTCAATCCTAGTACTTCCAAAATGCATTTTGCCCCATTTTGCTTCCTAGGATCGACCCTT
66 GGGATCAATCCTAACACTTCCAAAATGCATTTTGCCCCATTCTGCTTCCTAGGATCGACCCTT
12724647 CTAGTTCAAA
Statistics
Matches: 108, Mismatches: 19, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
143 102 0.94
144 6 0.06
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (144 bp):
ATCTTGGTCTAAAACAGAATGCATTTTCTATCATGAAGGCTTAAGGATCAACCCTTGGAAGCGTA
GGGATCAATCCTAACACTTCCAAAATGCATTTTGCCCCATTCTGCTTCCTAGGATCGACCCTTTA
AAGGATGGGAGTTA
Found at i:12736087 original size:2 final size:2
Alignment explanation
Indices: 12736032--12736068 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
12736022 GTGTGTGTAT
*
12736032 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12736069 TAGTTTGGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:12743762 original size:52 final size:51
Alignment explanation
Indices: 12743684--12743784 Score: 148
Period size: 52 Copynumber: 2.0 Consensus size: 51
12743674 AATTGAAACT
*
12743684 AGCTCATCCAGGTGCCAGTCAAGAGATCATTACTGCTTTAATCCCCTCACTA
1 AGCTCATCCAGGTGCCAGTCAAGAGATCATCACTGCTTTAAT-CCCTCACTA
* ** *
12743736 AGCTCATCTAGGTGCCAGTTGAGAGATCATCATTGCTTTAATCCCTCAC
1 AGCTCATCCAGGTGCCAGTCAAGAGATCATCACTGCTTTAATCCCTCAC
12743785 CGAGACCTTG
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
51 7 0.16
52 37 0.84
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.29
Consensus pattern (51 bp):
AGCTCATCCAGGTGCCAGTCAAGAGATCATCACTGCTTTAATCCCTCACTA
Found at i:12745732 original size:22 final size:22
Alignment explanation
Indices: 12745707--12745753 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
12745697 CAAAACAAAA
12745707 ACCACATACAGGGCTCAAACTG
1 ACCACATACAGGGCTCAAACTG
*
12745729 ACCACGTACAGGGCTCAAACTG
1 ACCACATACAGGGCTCAAACTG
12745751 ACC
1 ACC
12745754 TACTAAACTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.34, C:0.34, G:0.19, T:0.13
Consensus pattern (22 bp):
ACCACATACAGGGCTCAAACTG
Found at i:12749894 original size:19 final size:19
Alignment explanation
Indices: 12749867--12749903 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12749857 AAAACAAAAA
*
12749867 AGAAAGGAAAGATAGAGAG
1 AGAAAGGAAAGAAAGAGAG
*
12749886 AGAACGGAAAGAAAGAGA
1 AGAAAGGAAAGAAAGAGA
12749904 AGATAGATGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.35, T:0.03
Consensus pattern (19 bp):
AGAAAGGAAAGAAAGAGAG
Found at i:12759824 original size:13 final size:12
Alignment explanation
Indices: 12759793--12759827 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
12759783 TCATACTAAT
12759793 TAAAAAAATTCA
1 TAAAAAAATTCA
*
12759805 TACAAAAATTCA
1 TAAAAAAATTCA
12759817 TATAAAAAATT
1 TA-AAAAAATT
12759828 TAAATTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 13 0.65
13 7 0.35
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.29
Consensus pattern (12 bp):
TAAAAAAATTCA
Found at i:12770799 original size:26 final size:27
Alignment explanation
Indices: 12770739--12770804 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 27
12770729 GGTTTTAAAT
*
12770739 TATTTAAA-TAAAATTTTATTTTATTA
1 TATTTAAATTAAATTTTTATTTTATTA
*
12770765 TATCT-AATTAAATTTTTATATTT-TTA
1 TATTTAAATTAAATTTTTAT-TTTATTA
12770791 T-TTTAAATTAAATT
1 TATTTAAATTAAATT
12770805 AAATTATATA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 4 0.12
26 27 0.79
27 3 0.09
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (27 bp):
TATTTAAATTAAATTTTTATTTTATTA
Found at i:12770836 original size:18 final size:19
Alignment explanation
Indices: 12770801--12770844 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
12770791 TTTTAAATTA
12770801 AATTAAATTATATAATTAAT
1 AATT-AATTATATAATTAAT
* *
12770821 AATTAATTA-ATTATTATT
1 AATTAATTATATAATTAAT
12770839 AATTAA
1 AATTAA
12770845 AATATCAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 13 0.59
19 5 0.23
20 4 0.18
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
AATTAATTATATAATTAAT
Found at i:12770914 original size:18 final size:19
Alignment explanation
Indices: 12770891--12770926 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
12770881 ATATTTATAT
12770891 TATCATAATA-AATTAATA
1 TATCATAATATAATTAATA
*
12770909 TATCATATTATAATTAAT
1 TATCATAATATAATTAAT
12770927 TATGGTATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (19 bp):
TATCATAATATAATTAATA
Found at i:12771046 original size:20 final size:21
Alignment explanation
Indices: 12771011--12771051 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
12771001 ATATTTATTG
12771011 AATTTAAAATAAAAATTTAAA
1 AATTTAAAATAAAAATTTAAA
*
12771032 AATTTTAAA-AAAAATTTAAA
1 AATTTAAAATAAAAATTTAAA
12771052 TATTATGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
AATTTAAAATAAAAATTTAAA
Found at i:12772757 original size:7 final size:8
Alignment explanation
Indices: 12772741--12772773 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
12772731 TTTAATTTTA
12772741 TTTAAATT
1 TTTAAATT
12772749 TTT-AATT
1 TTTAAATT
12772756 TTTAAATTT
1 TTTAAA-TT
12772765 TTTAAATT
1 TTTAAATT
12772773 T
1 T
12772774 CTCTATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 7 0.30
8 8 0.35
9 8 0.35
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TTTAAATT
Found at i:12772925 original size:10 final size:11
Alignment explanation
Indices: 12772903--12772930 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
12772893 TATATATTTT
12772903 AAATTTTTAAA
1 AAATTTTTAAA
12772914 AAATTTTTAAA
1 AAATTTTTAAA
12772925 AAATTT
1 AAATTT
12772931 CTACAGATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
AAATTTTTAAA
Found at i:12773028 original size:15 final size:16
Alignment explanation
Indices: 12773010--12773044 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
12773000 TTGTTATGTG
*
12773010 AATTTT-ATTTTTAAT
1 AATTTTAATTTTTAAA
12773025 AATTTTAATTTTTAAA
1 AATTTTAATTTTTAAA
12773041 AATT
1 AATT
12773045 AAAAAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
AATTTTAATTTTTAAA
Found at i:12783479 original size:13 final size:13
Alignment explanation
Indices: 12783444--12783486 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
12783434 AAAAATTAAA
*
12783444 AATTTTTAAAATT
1 AATTATTAAAATT
*
12783457 AATATATTAAACTT
1 AAT-TATTAAAATT
12783471 AATTATTAATAATT
1 AATTATTAA-AATT
12783485 AA
1 AA
12783487 AAAATTTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 9 0.36
14 16 0.64
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (13 bp):
AATTATTAAAATT
Found at i:12783998 original size:15 final size:15
Alignment explanation
Indices: 12783962--12784000 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
12783952 AATTACATAT
*
12783962 ATAATAATTTTTAAAA
1 ATAA-AATTATTAAAA
12783978 ATTAAAATTATTAAAA
1 A-TAAAATTATTAAAA
12783994 ATAAAAT
1 ATAAAAT
12784001 CCACATAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 6 0.29
16 12 0.57
17 3 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATAAAATTATTAAAA
Found at i:12784299 original size:21 final size:19
Alignment explanation
Indices: 12784273--12784313 Score: 64
Period size: 21 Copynumber: 2.1 Consensus size: 19
12784263 AATTTACAAA
12784273 AAATAAAATTTGAATAAAATT
1 AAATAAAATTT--ATAAAATT
12784294 AAATAAAATTTATAAAATT
1 AAATAAAATTTATAAAATT
12784313 A
1 A
12784314 TTTTATCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 9 0.45
21 11 0.55
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (19 bp):
AAATAAAATTTATAAAATT
Found at i:12788322 original size:20 final size:20
Alignment explanation
Indices: 12788299--12788340 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
12788289 TTTGGATTAA
*
12788299 ATTTTTTTTCTTTGTTT-TAT
1 ATTTTTTTTATTT-TTTATAT
12788319 ATTTTTTTTATTTTTTATAT
1 ATTTTTTTTATTTTTTATAT
12788339 AT
1 AT
12788341 AAAATATGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (20 bp):
ATTTTTTTTATTTTTTATAT
Found at i:12814758 original size:98 final size:97
Alignment explanation
Indices: 12814587--12814891 Score: 337
Period size: 98 Copynumber: 3.1 Consensus size: 97
12814577 GGTTAAGTTC
* * * * *
12814587 ATTTATATTATCATATTAT-GTATAAATATCCTAAATATTTAAATTTGTTGTTTGAAATAGTTAA
1 ATTTATATTATCATATTATCGTATAAATATCTTAAACAGTTAAATTTGTTATTTTAAATA-TTAA
* * * *
12814651 ATTTATTTAATTTGTATACAATATGTTTAACTT
65 ATTTGTTTAATTTGTATATAACATGTTTAACTA
* * * * *
12814684 ATTTATATTATCATCTTATCATATAAATATCTTAAACAGTAAAATTTATTATTTTAAATGATTGA
1 ATTTATATTATCATATTATCGTATAAATATCTTAAACAGTTAAATTTGTTATTTTAAAT-ATTAA
* *
12814749 ATTTGTTTAATATGTATATAACACGTTTAACTA
65 ATTTGTTTAATTTGTATATAACATGTTTAACTA
* * *
12814782 ATTTATATTATTATATTATCGTACAAATATCTTAAAC-GATTAAATTTGTTATTTTAAACAATTA
1 ATTTATATTATCATATTATCGTATAAATATCTTAAACAG-TTAAATTTGTTATTTTAAA-TATTA
* * * *
12814846 AATTTGTTTAACCTT-TATATAACATGTCTAGCTC
64 AATTTGTTTAA-TTTGTATATAACATGTTTAACTA
12814880 ATTTATATTATC
1 ATTTATATTATC
12814892 GAATTATTAT
Statistics
Matches: 172, Mismatches: 31, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
97 19 0.11
98 151 0.88
99 2 0.01
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.48
Consensus pattern (97 bp):
ATTTATATTATCATATTATCGTATAAATATCTTAAACAGTTAAATTTGTTATTTTAAATATTAAA
TTTGTTTAATTTGTATATAACATGTTTAACTA
Found at i:12815474 original size:3 final size:3
Alignment explanation
Indices: 12815466--12815491 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
12815456 GTTAAAACCC
12815466 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
12815492 ATTAATCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:12816184 original size:15 final size:15
Alignment explanation
Indices: 12816164--12816192 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
12816154 CGTTAAATTT
12816164 ATAAATAAAAATTAA
1 ATAAATAAAAATTAA
12816179 ATAAATAAAAATTA
1 ATAAATAAAAATTA
12816193 CGTACTCGAA
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
ATAAATAAAAATTAA
Found at i:12846074 original size:22 final size:22
Alignment explanation
Indices: 12846009--12846074 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 22
12845999 AAAAACTTAT
12846009 TTAA-ATTTTTTAAA-A-TA-A
1 TTAATATTTTTTAAATAGTATA
*
12846027 TTGAA-ATTTTTTAAATATTATA
1 TT-AATATTTTTTAAATAGTATA
* *
12846049 TTAATATTTTTTATATAGTATT
1 TTAATATTTTTTAAATAGTATA
12846071 TTAA
1 TTAA
12846075 AAAATCAAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
18 2 0.05
19 12 0.30
20 1 0.03
21 4 0.10
22 21 0.52
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (22 bp):
TTAATATTTTTTAAATAGTATA
Found at i:12846850 original size:30 final size:28
Alignment explanation
Indices: 12846815--12846880 Score: 78
Period size: 30 Copynumber: 2.3 Consensus size: 28
12846805 CTAAAGATTT
**
12846815 TTTTTTTAATTTTTAAAAATATAATAATAA
1 TTTTTTTAATTAATAAAAA-ATAA-AATAA
* *
12846845 TTTTTTAAATTAATAAAAAATAAATTAA
1 TTTTTTTAATTAATAAAAAATAAAATAA
12846873 TTTTTTTA
1 TTTTTTTA
12846881 TAATCTCTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 11 0.35
29 4 0.13
30 16 0.52
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
TTTTTTTAATTAATAAAAAATAAAATAA
Found at i:12847155 original size:29 final size:29
Alignment explanation
Indices: 12847096--12847173 Score: 79
Period size: 29 Copynumber: 2.6 Consensus size: 29
12847086 TTTATTTAAT
*
12847096 TTAAAAATATAAAATTTTGATTGAATGTA
1 TTAAAAATATAAAATTTTGATTAAATGTA
*
12847125 TTAAAAGA-ATAAAATTTT-ATTAAAATTTA
1 TTAAAA-ATATAAAATTTTGATT-AAATGTA
*
12847154 TTAAATAATTTAATAATTTT
1 TTAAA-AATATAA-AATTTT
12847174 TTTAAATATT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
28 3 0.07
29 27 0.66
30 5 0.12
31 6 0.15
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (29 bp):
TTAAAAATATAAAATTTTGATTAAATGTA
Found at i:12847216 original size:22 final size:22
Alignment explanation
Indices: 12847201--12847243 Score: 77
Period size: 22 Copynumber: 1.9 Consensus size: 22
12847191 AATAACTTTG
12847201 TAATTTTTAATAAATAAAAATA
1 TAATTTTTAATAAATAAAAATA
12847223 TAATTTTTAATAAATACAAAA
1 TAATTTTTAATAAATA-AAAA
12847244 ATAGAGCAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
TAATTTTTAATAAATAAAAATA
Found at i:12857395 original size:3 final size:3
Alignment explanation
Indices: 12857387--12857416 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
12857377 TTATACTGTT
12857387 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
12857417 CATGAGAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:12863737 original size:2 final size:2
Alignment explanation
Indices: 12863732--12863761 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
12863722 TGTGTGTGTG
12863732 TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12863762 TAAAACCATG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:12874491 original size:40 final size:40
Alignment explanation
Indices: 12874431--12874514 Score: 159
Period size: 40 Copynumber: 2.1 Consensus size: 40
12874421 ATCATATTCT
*
12874431 TTTTGGTAATCCTCGTATTCATCCTTTCTCAAGATGAAAG
1 TTTTGGTAATCCTCGCATTCATCCTTTCTCAAGATGAAAG
12874471 TTTTGGTAATCCTCGCATTCATCCTTTCTCAAGATGAAAG
1 TTTTGGTAATCCTCGCATTCATCCTTTCTCAAGATGAAAG
12874511 TTTT
1 TTTT
12874515 ACTTGCAGGC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (40 bp):
TTTTGGTAATCCTCGCATTCATCCTTTCTCAAGATGAAAG
Found at i:12876716 original size:2 final size:2
Alignment explanation
Indices: 12876706--12876739 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
12876696 AAAGAAGGGA
*
12876706 AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12876740 TTACATAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12902120 original size:14 final size:15
Alignment explanation
Indices: 12902103--12902135 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
12902093 TTTATGAAAC
*
12902103 TAATTTTAATTT-AT
1 TAATTTAAATTTCAT
12902117 TAATTTAAATTTCAT
1 TAATTTAAATTTCAT
12902132 TAAT
1 TAAT
12902136 AATATATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (15 bp):
TAATTTAAATTTCAT
Found at i:12916146 original size:8 final size:8
Alignment explanation
Indices: 12916133--12916161 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
12916123 AAAAGATGGC
12916133 AAAAAAAG
1 AAAAAAAG
12916141 AAAAAAAG
1 AAAAAAAG
12916149 AAAAAAA-
1 AAAAAAAG
12916156 AAAAAA
1 AAAAAA
12916162 GAGCAGCAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 6 0.29
8 15 0.71
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:12916152 original size:14 final size:14
Alignment explanation
Indices: 12916134--12916163 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12916124 AAAGATGGCA
12916134 AAAAAAGAAAAAAAG
1 AAAAAA-AAAAAAAG
12916149 AAAAAAAAAAAAAG
1 AAAAAAAAAAAAAG
12916163 A
1 A
12916164 GCAGCAGCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAAG
Found at i:12917460 original size:20 final size:20
Alignment explanation
Indices: 12917435--12917475 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
12917425 AATAATTAGA
12917435 ATGCAAAATATGAACTTGAC
1 ATGCAAAATATGAACTTGAC
12917455 ATGCAAAATATGAACTTGAC
1 ATGCAAAATATGAACTTGAC
12917475 A
1 A
12917476 GATCAACAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (20 bp):
ATGCAAAATATGAACTTGAC
Found at i:12928395 original size:66 final size:67
Alignment explanation
Indices: 12928320--12928448 Score: 188
Period size: 67 Copynumber: 1.9 Consensus size: 67
12928310 AAAAAATAAA
* * * *
12928320 ATAAATTT-AAAATATGAATATAAATTTTTTATAATTTATCAAATATACTTTTTAAGTTAAAATG
1 ATAAATTTAAAAATATAAACATAAATTTTTTATAATTTATCAAAGATACTTTTTAAATTAAAATG
12928384 AG
66 AG
* * *
12928386 ATAAATTTAAAAATATAAACATAAGTTTTTTATAATTTATTAAAGATATTTTTTAAATTAAAA
1 ATAAATTTAAAAATATAAACATAAATTTTTTATAATTTATCAAAGATACTTTTTAAATTAAAA
12928449 ATATAAATAT
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
66 8 0.15
67 47 0.85
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (67 bp):
ATAAATTTAAAAATATAAACATAAATTTTTTATAATTTATCAAAGATACTTTTTAAATTAAAATG
AG
Found at i:12928461 original size:67 final size:66
Alignment explanation
Indices: 12928311--12928461 Score: 164
Period size: 67 Copynumber: 2.2 Consensus size: 66
12928301 TATATTAGTA
* * *
12928311 AAAAATAAAATAAATTT-AAAATATGAATATAAATTTTTTATAATTTATCAAATATACTTTTTAA
1 AAAAATAAAAT--ATTTAAAAATATAAACATAAATTTTTTATAATTTATCAAAGATACTTTTTAA
*
12928375 GTT
64 ATT
* * *
12928378 -AAAATGAGATAA-ATTTAAAAATATAAACATAAGTTTTTTATAATTTATTAAAGATATTTTTTA
1 AAAAAT-A-A-AATATTTAAAAATATAAACATAAATTTTTTATAATTTATCAAAGATACTTTTTA
12928441 AATT
63 AATT
12928445 AAAAATATAAATATTTA
1 AAAAATA-AAATATTTA
12928462 TTTAAATTTT
Statistics
Matches: 70, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
66 11 0.16
67 51 0.73
68 6 0.09
69 2 0.03
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (66 bp):
AAAAATAAAATATTTAAAAATATAAACATAAATTTTTTATAATTTATCAAAGATACTTTTTAAAT
T
Found at i:12939407 original size:2 final size:2
Alignment explanation
Indices: 12939402--12939451 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
12939392 TCTCTCTCTC
*
12939402 TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12939444 TA TA -A TA T
1 TA TA TA TA T
12939452 CAAACAGTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12945864 original size:36 final size:36
Alignment explanation
Indices: 12945817--12945889 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
12945807 AATAGATGTC
*
12945817 TCTTTGTTATGTTTACTGTCATGAAGCACATACAAG
1 TCTTTGCTATGTTTACTGTCATGAAGCACATACAAG
*
12945853 TCTTTGCTATGTTTACTGTCATGAAGCTCATACAAG
1 TCTTTGCTATGTTTACTGTCATGAAGCACATACAAG
12945889 T
1 T
12945890 ACGTATTTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (36 bp):
TCTTTGCTATGTTTACTGTCATGAAGCACATACAAG
Found at i:12952581 original size:3 final size:3
Alignment explanation
Indices: 12952575--12952607 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
12952565 ATCATCATCA
*
12952575 TCT TCT TCT TCT TCT TCT TCT TCT TCT TTT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
12952608 GGGTTCTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TCT
Found at i:12959760 original size:21 final size:21
Alignment explanation
Indices: 12959710--12959760 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
12959700 ATGTAATAAA
* *
12959710 ATTATAAAAATATTTTTTAAT
1 ATTAAAAAAATATATTTTAAT
* *
12959731 A-TAATAAAATATATTTTATT
1 ATTAAAAAAATATATTTTAAT
12959751 ATTAAAAAAA
1 ATTAAAAAAA
12959761 AAACTTTCTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTAAAAAAATATATTTTAAT
Found at i:12965825 original size:12 final size:12
Alignment explanation
Indices: 12965789--12965840 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
12965779 CAAAACAAGG
*
12965789 TTTTTTCTTTTT
1 TTTTTTCTTGTT
*
12965801 TTTTTTGTGTGTT
1 TTTTTTCT-TGTT
12965814 TTTTTTCTTGTT
1 TTTTTTCTTGTT
**
12965826 TGGTTTCTTTGTT
1 TTTTTTC-TTGTT
12965839 TT
1 TT
12965841 GGGGCTGGGA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
12 16 0.50
13 16 0.50
ACGTcount: A:0.00, C:0.06, G:0.13, T:0.81
Consensus pattern (12 bp):
TTTTTTCTTGTT
Found at i:12967988 original size:3 final size:3
Alignment explanation
Indices: 12967980--12968014 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
12967970 TTGCAGATAA
12967980 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG CATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG -ATG A
12968015 GAGCAATGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.34, C:0.03, G:0.31, T:0.31
Consensus pattern (3 bp):
ATG
Found at i:12969118 original size:78 final size:77
Alignment explanation
Indices: 12968985--12969185 Score: 303
Period size: 78 Copynumber: 2.6 Consensus size: 77
12968975 CATTAAAGGT
* *
12968985 GACAAAGCCTTTCATTTATCAATATTAATCAGGTATCAGAAAAGCGAGGAGTCCATTAATGGTGT
1 GACAAAGCCTTTCATTTATCAATATTAATCAGGTATTAGAAAAG-GAGGACTCCATTAATGGTGT
12969050 TTACTATGATGAC
65 TTACTATGATGAC
* *
12969063 GACAAAGCCTTTCATTTATCAACATTAATCAGGTATTACAAAAGGAAGGACTCCATTAATGGTGT
1 GACAAAGCCTTTCATTTATCAATATTAATCAGGTATTAGAAAAGG-AGGACTCCATTAATGGTGT
**
12969128 TTACTATGATGGT
65 TTACTATGATGAC
** *
12969141 GACAAAGGATTTCATTTAACAATATTAATCAGGTATTAGAAAAGG
1 GACAAAGCCTTTCATTTATCAATATTAATCAGGTATTAGAAAAGG
12969186 GACAAAACAG
Statistics
Matches: 111, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
77 1 0.01
78 110 0.99
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (77 bp):
GACAAAGCCTTTCATTTATCAATATTAATCAGGTATTAGAAAAGGAGGACTCCATTAATGGTGTT
TACTATGATGAC
Found at i:12975217 original size:13 final size:13
Alignment explanation
Indices: 12975199--12975227 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
12975189 TGTTCAGGGA
12975199 CCTCCAACATGGG
1 CCTCCAACATGGG
12975212 CCTCCAACATGGG
1 CCTCCAACATGGG
12975225 CCT
1 CCT
12975228 AATGGGCCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.41, G:0.21, T:0.17
Consensus pattern (13 bp):
CCTCCAACATGGG
Found at i:12975632 original size:2 final size:2
Alignment explanation
Indices: 12975625--12975654 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
12975615 TGAATCATGA
*
12975625 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12975655 GTGATTATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12982309 original size:13 final size:13
Alignment explanation
Indices: 12982293--12982317 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12982283 AACAAACATT
12982293 TAAAAATAAAAAA
1 TAAAAATAAAAAA
12982306 TAAAAATAAAAA
1 TAAAAATAAAAA
12982318 TATTGCTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
TAAAAATAAAAAA
Found at i:12982486 original size:30 final size:28
Alignment explanation
Indices: 12982452--12982529 Score: 77
Period size: 30 Copynumber: 2.7 Consensus size: 28
12982442 TTATTGATAA
*
12982452 ATATTCAAATAAATTTATTATTATTTTATT
1 ATATTCAAATAAATTT-TTATTATATT-TT
**
12982482 ATATTCAGTTAAATTTTATATTATATTTT
1 ATATTCAAATAAATTTT-TATTATATTTT
* *
12982511 A-AATAAAATAAATTTTTAT
1 ATATTCAAATAAATTTTTAT
12982530 AATTAATAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
27 3 0.08
28 11 0.28
29 4 0.10
30 22 0.55
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (28 bp):
ATATTCAAATAAATTTTTATTATATTTT
Found at i:12990981 original size:2 final size:2
Alignment explanation
Indices: 12990974--12990998 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12990964 AGAAACCGAT
12990974 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
12990999 GCAAGAAGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12991108 original size:14 final size:14
Alignment explanation
Indices: 12991086--12991119 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
12991076 TTTAATGAAA
* *
12991086 TTTACATATTATTT
1 TTTATATATTATCT
12991100 TTTATATATTATCT
1 TTTATATATTATCT
12991114 TTTATA
1 TTTATA
12991120 AATATAATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTATATATTATCT
Found at i:12992092 original size:15 final size:14
Alignment explanation
Indices: 12992072--12992103 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
12992062 TTAGGGATAG
12992072 TATAAAATATCTCAT
1 TATAAAATATCT-AT
12992087 TATAAAATATCTAT
1 TATAAAATATCTAT
12992101 TAT
1 TAT
12992104 CATCCCGTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (14 bp):
TATAAAATATCTAT
Found at i:13006354 original size:10 final size:10
Alignment explanation
Indices: 13006328--13006360 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
13006318 TTGATGGGAC
13006328 AAAAGAAAG-
1 AAAAGAAAGA
*
13006337 ATAAGAAAGA
1 AAAAGAAAGA
13006347 AAAAGAAAGA
1 AAAAGAAAGA
13006357 AAAA
1 AAAA
13006361 TTGGGGGAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (10 bp):
AAAAGAAAGA
Found at i:13008361 original size:2 final size:2
Alignment explanation
Indices: 13008354--13008381 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
13008344 TCTGTTACAC
13008354 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
13008382 TTTTACTATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:13020249 original size:12 final size:12
Alignment explanation
Indices: 13020232--13020259 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
13020222 CATTAACAAC
13020232 AGAACATAGGGT
1 AGAACATAGGGT
13020244 AGAACATAGGGT
1 AGAACATAGGGT
13020256 AGAA
1 AGAA
13020260 TCGATAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.46, C:0.07, G:0.32, T:0.14
Consensus pattern (12 bp):
AGAACATAGGGT
Found at i:13038809 original size:22 final size:23
Alignment explanation
Indices: 13038784--13038828 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
13038774 TTTTGTATAA
*
13038784 ATAAAAGAT-TTTAAATTTTAAT
1 ATAAAAGATATTAAAATTTTAAT
*
13038806 ATAAAATATATTAAAATTTTAAT
1 ATAAAAGATATTAAAATTTTAAT
13038829 TTTGTGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
ATAAAAGATATTAAAATTTTAAT
Found at i:13045393 original size:25 final size:25
Alignment explanation
Indices: 13045364--13045416 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
13045354 CTAGTTCATA
13045364 ACTTGGTAGATTTGTTGAAGTTCTG
1 ACTTGGTAGATTTGTTGAAGTTCTG
*
13045389 ACTTGGTGGATTTGTTGAAGTTCTG
1 ACTTGGTAGATTTGTTGAAGTTCTG
13045414 ACT
1 ACT
13045417 CGTGATAGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.19, C:0.09, G:0.28, T:0.43
Consensus pattern (25 bp):
ACTTGGTAGATTTGTTGAAGTTCTG
Found at i:13056888 original size:18 final size:18
Alignment explanation
Indices: 13056865--13056908 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
13056855 CTGAAGCTCT
*
13056865 TCCTCTTCTTCGTCCTCC
1 TCCTCTTCTTCCTCCTCC
*
13056883 TCCTCTTCTTCCTCTTCC
1 TCCTCTTCTTCCTCCTCC
13056901 TCCTCTTC
1 TCCTCTTC
13056909 CTCACCATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.02, T:0.48
Consensus pattern (18 bp):
TCCTCTTCTTCCTCCTCC
Found at i:13056897 original size:9 final size:9
Alignment explanation
Indices: 13056862--13056908 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
13056852 TGGCTGAAGC
13056862 TCTTCCTCT
1 TCTTCCTCT
* *
13056871 TCTTCGTCC
1 TCTTCCTCT
*
13056880 TCCTCCTCT
1 TCTTCCTCT
13056889 TCTTCCTCT
1 TCTTCCTCT
*
13056898 TCCTCCTCT
1 TCTTCCTCT
13056907 TC
1 TC
13056909 CTCACCATCT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.00, C:0.49, G:0.02, T:0.49
Consensus pattern (9 bp):
TCTTCCTCT
Found at i:13066101 original size:11 final size:11
Alignment explanation
Indices: 13066085--13066110 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
13066075 GTGTTTTCTC
13066085 TCTTTTTCTTT
1 TCTTTTTCTTT
13066096 TCTTTTTCTTT
1 TCTTTTTCTTT
13066107 TCTT
1 TCTT
13066111 CTCTCTATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (11 bp):
TCTTTTTCTTT
Found at i:13069669 original size:32 final size:31
Alignment explanation
Indices: 13069633--13069694 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
13069623 TAGAATCTTT
13069633 AAATAAAAAAATTATATATTAATTATAAAATC
1 AAATAAAAAAATTATAT-TTAATTATAAAATC
*** *
13069665 AAATATTTAAATTTTATTTAATTATAAAAT
1 AAATAAAAAAATTATATTTAATTATAAAAT
13069695 TAAAAGCAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 13 0.50
32 13 0.50
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (31 bp):
AAATAAAAAAATTATATTTAATTATAAAATC
Found at i:13079800 original size:1 final size:1
Alignment explanation
Indices: 13079796--13079840 Score: 90
Period size: 1 Copynumber: 45.0 Consensus size: 1
13079786 GCTTAGAAAG
13079796 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
13079841 CAACACAAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:13086149 original size:21 final size:22
Alignment explanation
Indices: 13086124--13086178 Score: 55
Period size: 23 Copynumber: 2.6 Consensus size: 22
13086114 TTTTTTAATT
*
13086124 TTTTACA-T-TAAAATATTAAA
1 TTTTACATTATAAAAAATTAAA
*
13086144 TATTTATATTATAAAAAATTAAA
1 T-TTTACATTATAAAAAATTAAA
13086167 TTTT--ATTATAAA
1 TTTTACATTATAAA
13086179 TATATGAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 9 0.30
21 5 0.17
22 4 0.13
23 12 0.40
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
TTTTACATTATAAAAAATTAAA
Found at i:13129620 original size:27 final size:27
Alignment explanation
Indices: 13129588--13129643 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
13129578 ACATTATAAA
13129588 AATAAAAA-TATAATAAA-AAATCGAAAT
1 AATAAAAATTA-AATAAACAAATC-AAAT
*
13129615 AATAAAACTTAAATAAACAAATCAAAT
1 AATAAAAATTAAATAAACAAATCAAAT
13129642 AA
1 AA
13129644 GATAAAAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 19 0.73
28 7 0.27
ACGTcount: A:0.70, C:0.07, G:0.02, T:0.21
Consensus pattern (27 bp):
AATAAAAATTAAATAAACAAATCAAAT
Found at i:13132417 original size:2 final size:2
Alignment explanation
Indices: 13132400--13132447 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
13132390 TCCCTCAACC
*
13132400 TA TA TA AA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13132441 TA TA TA T
1 TA TA TA T
13132448 TGCCAGTTCC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:13133220 original size:15 final size:14
Alignment explanation
Indices: 13133194--13133226 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
13133184 TTTCCCATTC
13133194 CTTTCCTTTCTTTT
1 CTTTCCTTTCTTTT
13133208 CTTTCCTTTTCTTTT
1 CTTTCC-TTTCTTTT
13133223 CTTT
1 CTTT
13133227 TGAGTTTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (14 bp):
CTTTCCTTTCTTTT
Found at i:13141301 original size:18 final size:18
Alignment explanation
Indices: 13141280--13141322 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
13141270 GTTTCCGGTA
*
13141280 GTTGTTGGGTTTGTTGCT
1 GTTGTTGCGTTTGTTGCT
13141298 GTTGGTT-CGTTTGTTGCT
1 GTT-GTTGCGTTTGTTGCT
13141316 GTTGTTG
1 GTTGTTG
13141323 TTGGTCGGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 3 0.14
18 16 0.73
19 3 0.14
ACGTcount: A:0.00, C:0.07, G:0.37, T:0.56
Consensus pattern (18 bp):
GTTGTTGCGTTTGTTGCT
Found at i:13141447 original size:3 final size:3
Alignment explanation
Indices: 13141439--13141475 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
13141429 GAGAGATATT
* *
13141439 ATG ATG ATG ATG ATG ATG ATG ATG AAG ACG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
13141476 CAATTATGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.38, C:0.03, G:0.32, T:0.27
Consensus pattern (3 bp):
ATG
Found at i:13144674 original size:18 final size:19
Alignment explanation
Indices: 13144636--13144675 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
13144626 CTGATACTGT
*
13144636 TTTTTTATATTATGAATTTA
1 TTTTTTATATTA-GAAATTA
13144656 TTTTTTATATTA-AAATTA
1 TTTTTTATATTAGAAATTA
13144674 TT
1 TT
13144676 AAATAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
20 12 0.63
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (19 bp):
TTTTTTATATTAGAAATTA
Found at i:13144684 original size:30 final size:32
Alignment explanation
Indices: 13144650--13144711 Score: 85
Period size: 30 Copynumber: 2.0 Consensus size: 32
13144640 TTATATTATG
*
13144650 AATTT-ATTTTTTATATTAAAAT-TA-TTAAAT
1 AATTTAATTTTTAATA-TAAAATATATTTAAAT
13144680 AATTTAATTTTTAATATAAAATATATTTAAAT
1 AATTTAATTTTTAATATAAAATATATTTAAAT
13144712 TAACATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 11 0.39
31 11 0.39
32 6 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (32 bp):
AATTTAATTTTTAATATAAAATATATTTAAAT
Found at i:13170065 original size:2 final size:2
Alignment explanation
Indices: 13170058--13170088 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
13170048 ACGACGGAGA
13170058 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
13170089 AGAGAGAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:13170093 original size:2 final size:2
Alignment explanation
Indices: 13170088--13170114 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13170078 GTGTGTGTGT
13170088 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
13170115 CAAGTGAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:13174749 original size:42 final size:42
Alignment explanation
Indices: 13174698--13174782 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
13174688 CCTTCCAAAA
* * *
13174698 ACATTTCTATTTTCTGACTATTATGGCGGTTTGGGTTCTGGT
1 ACATCTCTATTTTCTGACTATTATGCCGGTTTGGGTACTGGT
13174740 ACATCTCTATTTTCTGACTATTATGCCGGTTTGGGTACTGGT
1 ACATCTCTATTTTCTGACTATTATGCCGGTTTGGGTACTGGT
13174782 A
1 A
13174783 ATGTACTGTA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.16, C:0.16, G:0.22, T:0.45
Consensus pattern (42 bp):
ACATCTCTATTTTCTGACTATTATGCCGGTTTGGGTACTGGT
Found at i:13179515 original size:23 final size:23
Alignment explanation
Indices: 13179465--13179518 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
13179455 ACTAGTTATG
* *
13179465 CAATATTTTACTAACCAGTCACA
1 CAATGTTTTACTAACAAGTCACA
* *
13179488 CAATGTTTTATTAACAAGTCACG
1 CAATGTTTTACTAACAAGTCACA
*
13179511 TAATGTTT
1 CAATGTTT
13179519 ATCAATTAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (23 bp):
CAATGTTTTACTAACAAGTCACA
Found at i:13179633 original size:22 final size:22
Alignment explanation
Indices: 13179556--13179635 Score: 74
Period size: 22 Copynumber: 3.6 Consensus size: 22
13179546 ACCAGTCACA
* **
13179556 CAATACTTAAAAATCAATTATA
1 CAATACTTAAAAATAAATTACG
* *
13179578 CAATACTTAAAAATTACTTACG
1 CAATACTTAAAAATAAATTACG
*
13179600 -ACATA-TCAAAAAATAAATTACG
1 CA-ATACT-TAAAAATAAATTACG
13179622 CAATACTTAAAAAT
1 CAATACTTAAAAAT
13179636 CACTAAAACT
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
21 2 0.04
22 42 0.91
23 2 0.04
ACGTcount: A:0.54, C:0.15, G:0.03, T:0.29
Consensus pattern (22 bp):
CAATACTTAAAAATAAATTACG
Found at i:13179825 original size:51 final size:50
Alignment explanation
Indices: 13179735--13179848 Score: 133
Period size: 51 Copynumber: 2.2 Consensus size: 50
13179725 TACTTGGCGA
* * *
13179735 AAAATGCTCAAAATGCTGAAAAGTTTTTTTTCATATATCAAAAATCATT-T
1 AAAATGATTAAAATGCTCAAAAGTTTTTTTT-ATATATCAAAAATCATTCT
* *
13179785 CAAAATGTTTAAAATGCTCAAAAGGTTTTCTTTT-TGTATCAAAAATCATTCT
1 -AAAATGATTAAAATGCTCAAAA-GTTTT-TTTTATATATCAAAAATCATTCT
13179837 AAAATGATTAAA
1 AAAATGATTAAA
13179849 GATTTTTTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
51 45 0.82
52 6 0.11
53 4 0.07
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (50 bp):
AAAATGATTAAAATGCTCAAAAGTTTTTTTTATATATCAAAAATCATTCT
Found at i:13180987 original size:26 final size:25
Alignment explanation
Indices: 13180935--13181022 Score: 88
Period size: 25 Copynumber: 3.4 Consensus size: 25
13180925 TATTGTTGAA
* * *
13180935 AAAAAAAACTATTATATATTATTATG
1 AAAAAAAATTATTATATGTCA-TATG
13180961 AAAAAAAATTATTATATGTCATGATG
1 AAAAAAAATTATTATATGTCAT-ATG
* * *
13180987 -AAAAAAGTTATTACATGTCATATT
1 AAAAAAAATTATTATATGTCATATG
13181011 AAAAAAATATTA
1 AAAAAAA-ATTA
13181023 AAATTATTAT
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
24 2 0.04
25 26 0.50
26 24 0.46
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (25 bp):
AAAAAAAATTATTATATGTCATATG
Found at i:13181042 original size:32 final size:29
Alignment explanation
Indices: 13180994--13181106 Score: 104
Period size: 32 Copynumber: 3.8 Consensus size: 29
13180984 ATGAAAAAAG
**
13180994 TTATTACATGTCATATTAAAAAAATATTAAAA
1 TTATTACACATCATATTAAAAAAATATT---A
* *
13181026 TTATTATACATTATATTAAAAAAATATTA
1 TTATTACACATCATATTAAAAAAATATTA
*
13181055 TTATTACACATCATATTCAAAAAA-ATT-
1 TTATTACACATCATATTAAAAAAATATTA
* * *
13181082 TTACTATACATCATTTTGAAAAAAA
1 TTATTACACATCATATT-AAAAAAA
13181107 AATATTACAT
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
27 14 0.20
28 9 0.13
29 22 0.32
32 24 0.35
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.39
Consensus pattern (29 bp):
TTATTACACATCATATTAAAAAAATATTA
Found at i:13181058 original size:29 final size:29
Alignment explanation
Indices: 13181004--13181106 Score: 111
Period size: 29 Copynumber: 3.5 Consensus size: 29
13180994 TTATTACATG
13181004 TCATATTAAAAAAATATTAAAATTATTATACA
1 TCATATTAAAAAAATATT---ATTATTATACA
* *
13181036 TTATATTAAAAAAATATTATTATTACACA
1 TCATATTAAAAAAATATTATTATTATACA
* *
13181065 TCATATTCAAAAAA-ATT-TTACTATACA
1 TCATATTAAAAAAATATTATTATTATACA
*
13181092 TCATTTTGAAAAAAA
1 TCATATT-AAAAAAA
13181107 AATATTACAT
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
27 14 0.23
28 9 0.15
29 22 0.35
32 17 0.27
ACGTcount: A:0.52, C:0.09, G:0.01, T:0.38
Consensus pattern (29 bp):
TCATATTAAAAAAATATTATTATTATACA
Found at i:13181155 original size:27 final size:27
Alignment explanation
Indices: 13181094--13181165 Score: 78
Period size: 25 Copynumber: 2.8 Consensus size: 27
13181084 ACTATACATC
* *
13181094 ATTTTGAAAAAAAA-ATATTACATGTT
1 ATTTTGAAAAAAAAGTTGTTACATGTT
* *
13181120 ATGTT--AAAAAAAGTTGTTACATTTT
1 ATTTTGAAAAAAAAGTTGTTACATGTT
*
13181145 ATTTTGAAAAAAATGTTGTTA
1 ATTTTGAAAAAAAAGTTGTTA
13181166 TTATATGTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
24 7 0.19
25 13 0.35
26 4 0.11
27 13 0.35
ACGTcount: A:0.44, C:0.03, G:0.11, T:0.42
Consensus pattern (27 bp):
ATTTTGAAAAAAAAGTTGTTACATGTT
Found at i:13186269 original size:41 final size:41
Alignment explanation
Indices: 13186197--13186277 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
13186187 CAGCTTTTCA
* *
13186197 TAAAATATTAATATTAACTTATAAATGAAATATTAATATTT
1 TAAAATATTAATATTAAATTATAAATGAAATATAAATATTT
*
13186238 TAAAATGTTAATGATTAAATTATAAAT-AAATATAAATATT
1 TAAAATATTAAT-ATTAAATTATAAATGAAATATAAATATT
13186278 AATATTAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 23 0.64
42 13 0.36
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (41 bp):
TAAAATATTAATATTAAATTATAAATGAAATATAAATATTT
Found at i:13186302 original size:22 final size:20
Alignment explanation
Indices: 13186265--13186305 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 20
13186255 AATTATAAAT
13186265 AAATATAAATATTAATATTA
1 AAATATAAATATTAATATTA
13186285 AAATGATAAATTATTAATATT
1 AAAT-ATAAA-TATTAATATT
13186306 TTAAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.21
21 5 0.26
22 10 0.53
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
AAATATAAATATTAATATTA
Found at i:13186332 original size:29 final size:29
Alignment explanation
Indices: 13186299--13186395 Score: 101
Period size: 33 Copynumber: 3.3 Consensus size: 29
13186289 GATAAATTAT
13186299 TAATATTTTAAATAAAAAATAAATCATAA
1 TAATATTTTAAATAAAAAATAAATCATAA
*
13186328 TAATATTTAAAAATAAAATAAAATAAATCATAA
1 TAATATTT-TAAAT--AA-AAAATAAATCATAA
* * *
13186361 TAATA-TTTAAATGATAAATAAA--ATAT
1 TAATATTTTAAATAAAAAATAAATCATAA
13186387 TAATATTTT
1 TAATATTTT
13186396 TAAAAATTAA
Statistics
Matches: 58, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
26 8 0.14
27 3 0.05
28 7 0.12
29 9 0.16
30 4 0.07
31 4 0.07
32 4 0.07
33 19 0.33
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.37
Consensus pattern (29 bp):
TAATATTTTAAATAAAAAATAAATCATAA
Found at i:13186356 original size:33 final size:33
Alignment explanation
Indices: 13186314--13186385 Score: 119
Period size: 33 Copynumber: 2.2 Consensus size: 33
13186304 TTTTAAATAA
13186314 AAAATAAATCATAATAATATTTAAA-AATAAAAT
1 AAAATAAATCATAATAATATTTAAATAAT-AAAT
*
13186347 AAAATAAATCATAATAATATTTAAATGATAAAT
1 AAAATAAATCATAATAATATTTAAATAATAAAT
13186380 AAAATA
1 AAAATA
13186386 TTAATATTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
33 35 0.95
34 2 0.05
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (33 bp):
AAAATAAATCATAATAATATTTAAATAATAAAT
Found at i:13186372 original size:26 final size:26
Alignment explanation
Indices: 13186263--13186394 Score: 81
Period size: 33 Copynumber: 4.8 Consensus size: 26
13186253 TAAATTATAA
* *
13186263 ATAAATATAAATATTAATATTAAAATG
1 ATAAATA-AAATAATAATATTTAAATG
* * *
13186290 ATAAAT-TATTAAT-AT-TTTAAATA
1 ATAAATAAAATAATAATATTTAAATG
* *
13186313 AAAAATAAATCATAATAATATTTAAAAATAAA
1 ATAAATAAA--ATAATAATATTT--AAAT--G
13186345 ATAAAATAAATCATAATAATATTTAAATG
1 AT-AAATAAA--ATAATAATATTTAAATG
*
13186374 ATAAATAAAATATTAATATTT
1 ATAAATAAAATAATAATATTT
13186395 TTAAAAATTA
Statistics
Matches: 84, Mismatches: 11, Indels: 21
0.72 0.09 0.18
Matches are distributed among these distances:
23 11 0.13
24 3 0.04
25 4 0.05
26 15 0.18
27 8 0.10
28 10 0.12
29 2 0.02
30 4 0.05
31 4 0.05
32 2 0.02
33 21 0.25
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (26 bp):
ATAAATAAAATAATAATATTTAAATG
Found at i:13186399 original size:21 final size:21
Alignment explanation
Indices: 13186374--13186448 Score: 75
Period size: 21 Copynumber: 3.6 Consensus size: 21
13186364 TATTTAAATG
13186374 ATAAATAAAATATTAATATTT
1 ATAAATAAAATATTAATATTT
* *
13186395 TTAAA-AATTAATGATTGA-A-TT
1 ATAAATAA--AAT-ATTAATATTT
13186416 ATAAATAAAATATTAATATTT
1 ATAAATAAAATATTAATATTT
*
13186437 AAAAATAAAATA
1 ATAAATAAAATA
13186449 CAAATAAATA
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
19 4 0.09
20 6 0.14
21 23 0.53
22 6 0.14
23 4 0.09
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.39
Consensus pattern (21 bp):
ATAAATAAAATATTAATATTT
Found at i:13194853 original size:12 final size:12
Alignment explanation
Indices: 13194836--13194860 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13194826 TAATAGAACT
13194836 TCCCACATTCAA
1 TCCCACATTCAA
13194848 TCCCACATTCAA
1 TCCCACATTCAA
13194860 T
1 T
13194861 TCCAATAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.40, G:0.00, T:0.28
Consensus pattern (12 bp):
TCCCACATTCAA
Found at i:13209869 original size:2 final size:2
Alignment explanation
Indices: 13209862--13209898 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
13209852 AGTGATTTTG
13209862 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13209899 AATTCTTTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:13210762 original size:15 final size:15
Alignment explanation
Indices: 13210742--13210771 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
13210732 GTAGTCAAAG
13210742 CCAATCATGGTGTAT
1 CCAATCATGGTGTAT
13210757 CCAATCATGGTGTAT
1 CCAATCATGGTGTAT
13210772 AGAATCTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (15 bp):
CCAATCATGGTGTAT
Found at i:13210777 original size:15 final size:15
Alignment explanation
Indices: 13210743--13210777 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
13210733 TAGTCAAAGC
*
13210743 CAATCATGGTGTATC
1 CAATCATGGTGTATA
13210758 CAATCATGGTGTATA
1 CAATCATGGTGTATA
*
13210773 GAATC
1 CAATC
13210778 TCATGTGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31
Consensus pattern (15 bp):
CAATCATGGTGTATA
Found at i:13214749 original size:14 final size:14
Alignment explanation
Indices: 13214732--13214760 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
13214722 ACAGACACAT
13214732 ATATATATATATAA
1 ATATATATATATAA
13214746 ATATATATATATAA
1 ATATATATATATAA
13214760 A
1 A
13214761 GAAATTTAAT
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATATATATATATAA
Found at i:13218481 original size:12 final size:12
Alignment explanation
Indices: 13218461--13218491 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
13218451 CAACCACATA
13218461 CCGCCGCCTCCG
1 CCGCCGCCTCCG
*
13218473 CCTCCGCCTCCG
1 CCGCCGCCTCCG
13218485 CCGCCGC
1 CCGCCGC
13218492 AAACCTCAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.68, G:0.23, T:0.10
Consensus pattern (12 bp):
CCGCCGCCTCCG
Found at i:13221358 original size:18 final size:18
Alignment explanation
Indices: 13221327--13221362 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
13221317 CAACATAGGA
*
13221327 CAAATTTATAAAATTTAT
1 CAAATATATAAAATTTAT
*
13221345 CAAATATATGAAATTTAT
1 CAAATATATAAAATTTAT
13221363 ATTACATCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.42
Consensus pattern (18 bp):
CAAATATATAAAATTTAT
Found at i:13227228 original size:30 final size:31
Alignment explanation
Indices: 13227194--13227259 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
13227184 AATCAAACTC
13227194 TTATA-TTTTCATTTTAAGTTAAATAAATCT
1 TTATATTTTTCATTTTAAGTTAAATAAATCT
* *
13227224 TTATATTTTTTATTTTAAGTTAAATAAATTT
1 TTATATTTTTCATTTTAAGTTAAATAAATCT
13227255 TTATA
1 TTATA
13227260 ATTAATGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
30 5 0.15
31 28 0.85
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (31 bp):
TTATATTTTTCATTTTAAGTTAAATAAATCT
Found at i:13239004 original size:23 final size:23
Alignment explanation
Indices: 13238978--13239038 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 23
13238968 TTTATAAATA
**
13238978 TAAAAAAATAAAATTTAATTTTT
1 TAAAAAAATAAAATTTAAAATTT
* *
13239001 TAAATAAAT-ATATTTAAAATTT
1 TAAAAAAATAAAATTTAAAATTT
* *
13239023 TAAAATAATAACATTT
1 TAAAAAAATAAAATTT
13239039 TAATGATCAG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
22 17 0.57
23 13 0.43
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
TAAAAAAATAAAATTTAAAATTT
Found at i:13239032 original size:22 final size:20
Alignment explanation
Indices: 13238982--13239033 Score: 52
Period size: 23 Copynumber: 2.5 Consensus size: 20
13238972 TAAATATAAA
*
13238982 AAAATAA-AATTTAATTTTT
1 AAAATAATAATTTAAATTTT
*
13239001 TAAATAAATATATTTAAAATTTT
1 AAAAT-AATA-ATTT-AAATTTT
13239024 AAAATAATAA
1 AAAATAATAA
13239034 CATTTTAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
19 4 0.15
20 2 0.08
21 2 0.08
22 8 0.31
23 10 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AAAATAATAATTTAAATTTT
Found at i:13249702 original size:14 final size:15
Alignment explanation
Indices: 13249671--13249720 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 15
13249661 TCTACGTATA
13249671 ATAATTTATGTAAATTT
1 ATAATTTAT-T-AATTT
13249688 AGT-ATTTA-TAATTT
1 A-TAATTTATTAATTT
13249702 ATAATTTATTAATTT
1 ATAATTTATTAATTT
13249717 -TAAT
1 ATAAT
13249721 CCAAATCTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
13 1 0.03
14 15 0.50
15 7 0.23
17 6 0.20
18 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (15 bp):
ATAATTTATTAATTT
Found at i:13250121 original size:31 final size:30
Alignment explanation
Indices: 13250086--13250148 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 30
13250076 AATTATTAAT
* * *
13250086 TATAAGAATTTATTTAATTTAAAATAAAAAA
1 TATAAAAATTTAATTAA-ATAAAATAAAAAA
*
13250117 TATAAAAATTTAATTAAATATAATAAAAAA
1 TATAAAAATTTAATTAAATAAAATAAAAAA
13250147 TA
1 TA
13250149 AGAACATATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 13 0.46
31 15 0.54
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (30 bp):
TATAAAAATTTAATTAAATAAAATAAAAAA
Found at i:13250139 original size:27 final size:28
Alignment explanation
Indices: 13250097--13250149 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
13250087 ATAAGAATTT
*
13250097 ATTTAATTTAAAATAA-AAAATATAAAA
1 ATTTAATTTAAAATAATAAAAAATAAAA
13250124 ATTTAA-TTAAATATAATAAAAAATAA
1 ATTTAATTTAAA-ATAATAAAAAATAA
13250150 GAACATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 5 0.22
27 10 0.43
28 8 0.35
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (28 bp):
ATTTAATTTAAAATAATAAAAAATAAAA
Found at i:13251157 original size:29 final size:30
Alignment explanation
Indices: 13251124--13251182 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
13251114 AATTATTAAT
*
13251124 TATTAAA-TTTATTTAATTTAAAATAAAAA
1 TATTAAATTTTATTTAATGTAAAATAAAAA
*
13251153 TATTAAATTTTATTTGATGTAAAATAAAAA
1 TATTAAATTTTATTTAATGTAAAATAAAAA
13251183 AAAATCTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 7 0.26
30 20 0.74
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (30 bp):
TATTAAATTTTATTTAATGTAAAATAAAAA
Found at i:13251209 original size:28 final size:27
Alignment explanation
Indices: 13251142--13251221 Score: 81
Period size: 28 Copynumber: 2.8 Consensus size: 27
13251132 TTATTTAATT
* *
13251142 TAAAATAAAAATATTAAATTTTATTTGATG
1 TAAAATAAAAA-A--AAATTTAATTGGATG
13251172 TAAAATAAAAAAAAATCTTAATTGGATG
1 TAAAATAAAAAAAAAT-TTAATTGGATG
*
13251200 TAATAA-AAAATAAAATTTAATT
1 TAA-AATAAAAAAAAATTTAATT
13251222 TAAAATTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
27 10 0.22
28 21 0.47
29 3 0.07
30 11 0.24
ACGTcount: A:0.56, C:0.01, G:0.06, T:0.36
Consensus pattern (27 bp):
TAAAATAAAAAAAAATTTAATTGGATG
Found at i:13256244 original size:29 final size:29
Alignment explanation
Indices: 13256221--13256277 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
13256211 TTAGTGAGGA
*
13256221 ATCTGCTA-AGGGTAAAATATTAGTAGTTG
1 ATCTGATAGAGGGTAAAATATTAGTAG-TG
*
13256250 ATTTGATAGAGGGTAAAATATTAGTAGT
1 ATCTGATAGAGGGTAAAATATTAGTAGT
13256278 TAACTTGATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.35
Consensus pattern (29 bp):
ATCTGATAGAGGGTAAAATATTAGTAGTG
Found at i:13256286 original size:30 final size:30
Alignment explanation
Indices: 13256229--13256286 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
13256219 GAATCTGCTA
* *
13256229 AGGGTAAAATATTAGTAGTTGATTTGATAG
1 AGGGTAAAATATTAGTAGTTAACTTGATAG
13256259 AGGGTAAAATATTAGTAGTTAACTTGAT
1 AGGGTAAAATATTAGTAGTTAACTTGAT
13256287 GTAGTACTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.36
Consensus pattern (30 bp):
AGGGTAAAATATTAGTAGTTAACTTGATAG
Found at i:13256422 original size:58 final size:60
Alignment explanation
Indices: 13256314--13256429 Score: 155
Period size: 58 Copynumber: 2.0 Consensus size: 60
13256304 CTTGGAATAG
*
13256314 GAAATTGATTCAATATTCTTATTGATTGAACACTAGAGAAGATCTTTATTT-TAGGGTCT
1 GAAATTGATTCAATATTCTTATTGACTGAACACTAGAGAAGATCTTTATTTCTAGGGTCT
* * * * * *
13256373 GAAATTGATTCTATATT-TTGTTGACTGAACATTGGATAATATCTTTATTTCTAGGGT
1 GAAATTGATTCAATATTCTTATTGACTGAACACTAGAGAAGATCTTTATTTCTAGGGT
13256430 GTGGGCATCT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
58 27 0.55
59 22 0.45
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.43
Consensus pattern (60 bp):
GAAATTGATTCAATATTCTTATTGACTGAACACTAGAGAAGATCTTTATTTCTAGGGTCT
Found at i:13258145 original size:17 final size:17
Alignment explanation
Indices: 13258125--13258172 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
13258115 TTGATGTGAA
13258125 ATTTTAATAAATAT-ATT
1 ATTTTAATAAATATGA-T
* *
13258142 ATTTAAATAATTATGAT
1 ATTTTAATAAATATGAT
13258159 ATTTTAATTAAATA
1 ATTTTAA-TAAATA
13258173 AAAAATCTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 19 0.76
18 6 0.24
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
ATTTTAATAAATATGAT
Found at i:13266678 original size:2 final size:2
Alignment explanation
Indices: 13266671--13266695 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13266661 GTCATCACTT
13266671 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
13266696 GAGGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:13279122 original size:2 final size:2
Alignment explanation
Indices: 13279110--13279139 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
13279100 GACAATTATG
*
13279110 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13279140 AATACATTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:13280893 original size:2 final size:2
Alignment explanation
Indices: 13280886--13280914 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
13280876 AAAGCATCAA
13280886 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
13280915 TTCTATCTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:13281904 original size:3 final size:3
Alignment explanation
Indices: 13281896--13281929 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
13281886 GTAGATACGA
*
13281896 ACC ACC ACC ACC ACC ACC ACC ACC ACT ACC ACC A
1 ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC A
13281930 TGTTAGCTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.35, C:0.62, G:0.00, T:0.03
Consensus pattern (3 bp):
ACC
Found at i:13282521 original size:2 final size:2
Alignment explanation
Indices: 13282516--13282545 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
13282506 TCTTGTTAAG
13282516 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13282546 GAAATATGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13291214 original size:19 final size:20
Alignment explanation
Indices: 13291181--13291225 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 20
13291171 CAGAGAGATC
13291181 ATGTATCAATAAAAAATT-AA
1 ATGT-TCAATAAAAAATTCAA
*
13291201 ATGTTCAATCAAAAATTCAA
1 ATGTTCAATAAAAAATTCAA
13291221 ATGTT
1 ATGTT
13291226 AAGTGCTTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.51, C:0.09, G:0.07, T:0.33
Consensus pattern (20 bp):
ATGTTCAATAAAAAATTCAA
Found at i:13295427 original size:151 final size:153
Alignment explanation
Indices: 13295139--13295428 Score: 415
Period size: 151 Copynumber: 1.9 Consensus size: 153
13295129 CTGTGAATGC
* *
13295139 GAAGGAAACAACAAAATTCTAAAGTTCAGATGGATACGTGTAGGATAGAGTAATCTAATTAACAT
1 GAAGGAAACAACAAAATTCTAAAGTTCAAATGGATACGTGTAGGATAGAGTAATCTAACTAACA-
* * * *
13295204 ATATCTTATGATATAAACAAAACTCAGATTTTTGTTTTAATCTCCATAAATGTAAACATATAGTA
65 ATA-CTTATAATATAAACAAAACTCAGATTTTTGTTTTAATCTCCATAAATATAAACAGAAAGTA
13295269 TTTTGTTGCGAAATCTAAATAAAAG
129 TTTTGTTGCGAAATCTAAATAAAAG
* * * *
13295294 GAAGGAAACAACAAGATTCTAGAGTTTAAATGGATACGTGT-GAGATAGGGTAATCTAACTAAC-
1 GAAGGAAACAACAAAATTCTAAAGTTCAAATGGATACGTGTAG-GATAGAGTAATCTAACTAACA
* * *
13295357 ATA-TTATAATGTAAACAAAATTCAGATTTTTGTTTTAATCTCCATAAATATAAGCAGAAAGTAT
65 ATACTTATAATATAAACAAAACTCAGATTTTTGTTTTAATCTCCATAAATATAAACAGAAAGTAT
13295421 TTTGTTGC
130 TTTGTTGC
13295429 AGTGTAAGGC
Statistics
Matches: 121, Mismatches: 13, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
151 62 0.51
153 3 0.02
154 1 0.01
155 55 0.45
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (153 bp):
GAAGGAAACAACAAAATTCTAAAGTTCAAATGGATACGTGTAGGATAGAGTAATCTAACTAACAA
TACTTATAATATAAACAAAACTCAGATTTTTGTTTTAATCTCCATAAATATAAACAGAAAGTATT
TTGTTGCGAAATCTAAATAAAAG
Found at i:13295729 original size:164 final size:163
Alignment explanation
Indices: 13295449--13295819 Score: 419
Period size: 164 Copynumber: 2.3 Consensus size: 163
13295439 AAGGTATTTA
* * * *
13295449 AACAAACATTTTCATAATCCAAGC-AAACCCAGATTTTT-TGTTTAATCTCTGTGAAAGTAAATA
1 AACAAACATTTTCATAATCCAAACAAAACTCAGATTTTTAT-TTTAATCTCTGTCAAAGTAAACA
* * * * *
13295512 CAAGTATAAAGCAGTTCTTGCAGGTTCGAAATCTAAATACAAGGTATGAAACAACAAGACTCTAA
65 CAAGTACAAAGCAGTTCTTGCAGGTCCGAAATCCAAATACAAGGAAGGAAACAACAAGACTCTAA
*
13295577 AGTTTAAATGGA-TACATGTAAGAT-AAGATATTCT
130 AGTCTAAATGGACT-CATGTAAGATAAAG-TATTCT
* * * * *
13295611 AATAAACATTTTCATAGTCTAAACAAAACTTAGATTTTTATTTTAATCT-TGGTCAAAGTATACA
1 AACAAACATTTTCATAATCCAAACAAAACTCAGATTTTTATTTTAATCTCT-GTCAAAGTAAACA
* * * *
13295675 GAAGTACAGAGCAGTTGTTGTAGGGTCCGAAATCCAAATACAAGGAAGGAAACAACAAGACTCTA
65 CAAGTACAAAGCAGTTCTTGCA-GGTCCGAAATCCAAATACAAGGAAGGAAACAACAAGACTCTA
* * * *
13295740 GAGTCTAGATGGACTCGTGTACGATAAAGTATTCT
129 AAGTCTAAATGGACTCATGTAAGATAAAGTATTCT
* *
13295775 AACAAACATTTTCCTAATCGAAACAAAACTCAGAATTTGTTATTT
1 AACAAACATTTTCATAATCCAAACAAAACTCAG-ATTT-TTATTT
13295820 AATTTTCCTG
Statistics
Matches: 173, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
162 21 0.12
163 47 0.27
164 91 0.53
165 8 0.05
166 6 0.03
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (163 bp):
AACAAACATTTTCATAATCCAAACAAAACTCAGATTTTTATTTTAATCTCTGTCAAAGTAAACAC
AAGTACAAAGCAGTTCTTGCAGGTCCGAAATCCAAATACAAGGAAGGAAACAACAAGACTCTAAA
GTCTAAATGGACTCATGTAAGATAAAGTATTCT
Done.