Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001495.1 Hibiscus syriacus cultivar Beakdansim tig00002910_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: 86907
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Found at i:4119 original size:27 final size:27
Alignment explanation
Indices: 4051--4112 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
4041 TTAGTCAAAT
*
4051 AACAAACGCCACAAAAAGCAGCACTGA
1 AACAAACGCCACAAAAAGCACCACTGA
4078 AACAAACGCCACAAAAAGCACCACTGA
1 AACAAACGCCACAAAAAGCACCACTGA
4105 AACAAACG
1 AACAAACG
4113 TCGCAAATGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.53, C:0.31, G:0.13, T:0.03
Consensus pattern (27 bp):
AACAAACGCCACAAAAAGCACCACTGA
Found at i:4583 original size:21 final size:21
Alignment explanation
Indices: 4559--4620 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
4549 TAAACTAGAC
* *
4559 ATCCGTAATAACAAACTTCAA
1 ATCCATAATAACAAACTTAAA
* *
4580 ATCCATAACAAGAAACTTAAA
1 ATCCATAATAACAAACTTAAA
*
4601 ATCCATAATAATAAA-TTAAA
1 ATCCATAATAACAAACTTAAA
4621 GTTTACATTA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
20 5 0.14
21 30 0.86
ACGTcount: A:0.55, C:0.18, G:0.03, T:0.24
Consensus pattern (21 bp):
ATCCATAATAACAAACTTAAA
Found at i:5924 original size:16 final size:16
Alignment explanation
Indices: 5901--5939 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
5891 CATGAAACGA
5901 AGTT-CCCAATTGCTC
1 AGTTCCCCAATTGCTC
*
5916 AGTTCCCCAATTGCTT
1 AGTTCCCCAATTGCTC
5932 AGTTCCCC
1 AGTTCCCC
5940 TAACTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.18, C:0.36, G:0.13, T:0.33
Consensus pattern (16 bp):
AGTTCCCCAATTGCTC
Found at i:6473 original size:22 final size:21
Alignment explanation
Indices: 6434--6475 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
6424 TGTAAATAAA
* *
6434 ATATAATAAATAATATTATTT
1 ATATAAAAAATAAAATTATTT
6455 ATATAAAAACATAAAATTATT
1 ATATAAAAA-ATAAAATTATT
6476 ATTTCAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
ATATAAAAAATAAAATTATTT
Found at i:7563 original size:68 final size:69
Alignment explanation
Indices: 7440--7579 Score: 205
Period size: 68 Copynumber: 2.0 Consensus size: 69
7430 AGCAGCAAAT
* *
7440 GAGTTTGGGTAAATGACGGGAATGAAATAATAGGTAAAGGGGAAAAAATGAAAAAGGGTTAAAGG
1 GAGTTTGGGTAAACGACGGGAATGAAAAAATAGGTAAAGGGGAAAAAATGAAAAAGGGTTAAAGG
7505 G-GC
66 GCGC
* *
7508 GAGTTTGGGTAAACGATGGGAATGGAAAAAAATAGGTCAAGGGG-AAAAATG-AAAAGGGTTAAA
1 GAGTTTGGGTAAACGACGGGAAT-G-AAAAAATAGGTAAAGGGGAAAAAATGAAAAAGGGTTAAA
7571 GGGCGC
64 GGGCGC
7577 GAG
1 GAG
7580 ACTTAGAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
68 36 0.55
69 13 0.20
70 16 0.25
ACGTcount: A:0.43, C:0.04, G:0.36, T:0.16
Consensus pattern (69 bp):
GAGTTTGGGTAAACGACGGGAATGAAAAAATAGGTAAAGGGGAAAAAATGAAAAAGGGTTAAAGG
GCGC
Found at i:7717 original size:41 final size:40
Alignment explanation
Indices: 7620--7724 Score: 115
Period size: 39 Copynumber: 2.6 Consensus size: 40
7610 AAACATAAAC
* * * * *
7620 GCCACTAAAGTACGATTCTATAGCGACGTTTGTAAAAACT
1 GCCACTAAATTACGAGTCTATAGCGACATTTATAAAAAAT
7660 -CCACT-AATGTACGAGTCTATAGCGACATTTATATAAAAAT
1 GCCACTAAAT-TACGAGTCTATAGCGACATTTATA-AAAAAT
* *
7700 GCCACTAAATTATGAGTCTTTAGCG
1 GCCACTAAATTACGAGTCTATAGCG
7725 GCGTTTGTAT
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
38 2 0.04
39 26 0.48
40 5 0.09
41 18 0.33
42 3 0.06
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (40 bp):
GCCACTAAATTACGAGTCTATAGCGACATTTATAAAAAAT
Found at i:8678 original size:3 final size:3
Alignment explanation
Indices: 8672--8744 Score: 146
Period size: 3 Copynumber: 24.3 Consensus size: 3
8662 TAATATATGC
8672 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
8720 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
8745 ATCTCGGGTT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:12138 original size:21 final size:23
Alignment explanation
Indices: 12114--12160 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
12104 TCTATAAAAA
*
12114 TAAAAGTATT-AT-ATTATATTT
1 TAAAAGTATTAATAAATATATTT
*
12135 TAAAATTATTAATAAATATATTT
1 TAAAAGTATTAATAAATATATTT
12158 TAA
1 TAA
12161 GGAATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
22 2 0.09
23 11 0.50
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TAAAAGTATTAATAAATATATTT
Found at i:12175 original size:23 final size:22
Alignment explanation
Indices: 12114--12176 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
12104 TCTATAAAAA
* *
12114 TAAAAGTA-TTATATTATATTT
1 TAAAATTATTTATAATATATTT
*
12135 TAAAATTATTAATAAATATATTT
1 TAAAATTATTTAT-AATATATTT
12158 TAAGGAATT-TTTATAATAT
1 TAA--AATTATTTATAATAT
12177 TATTAGACCA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 7 0.21
22 3 0.09
23 16 0.47
24 4 0.12
25 4 0.12
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (22 bp):
TAAAATTATTTATAATATATTT
Found at i:12404 original size:23 final size:22
Alignment explanation
Indices: 12350--12404 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
12340 ATTGAGTATT
* * * *
12350 TTATTGTAATAATATTATTATA
1 TTATTTTAAAAATATTAATAAA
12372 TTATTATTAAAAATATTAATAAA
1 TTATT-TTAAAAATATTAATAAA
12395 TATATTTTAA
1 T-TATTTTAA
12405 TTATGTTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 5 0.19
23 18 0.67
24 4 0.15
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
TTATTTTAAAAATATTAATAAA
Found at i:13083 original size:69 final size:69
Alignment explanation
Indices: 12961--13096 Score: 213
Period size: 69 Copynumber: 2.0 Consensus size: 69
12951 AACAAATGTA
*
12961 TGGGTAAACGGAGGGAATGAAAAAATAGGTCAAGGGGAAAAAATGAAAAAGGGTTAAAGGG-GCG
1 TGGGTAAACGGAGGGAATGAAAAAATAGGTCAAGGAGAAAAAATGAAAAAGGGTTAAAGGGTGCG
13025 AGTT
66 AGTT
* *
13029 TGGGTAAATGGCGGGAATGAAAAAAAATAGGTCAAGGAG-AAAAATGAAAAAGGGTTAAAGGGTG
1 TGGGTAAACGGAGGGAATG--AAAAAATAGGTCAAGGAGAAAAAATGAAAAAGGGTTAAAGGGTG
13093 CGAG
64 CGAG
13097 ACATAGAAAT
Statistics
Matches: 62, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
68 17 0.27
69 23 0.37
70 22 0.35
ACGTcount: A:0.45, C:0.04, G:0.36, T:0.15
Consensus pattern (69 bp):
TGGGTAAACGGAGGGAATGAAAAAATAGGTCAAGGAGAAAAAATGAAAAAGGGTTAAAGGGTGCG
AGTT
Found at i:13181 original size:41 final size:41
Alignment explanation
Indices: 13133--13524 Score: 176
Period size: 41 Copynumber: 9.6 Consensus size: 41
13123 TTGTAAACAT
*
13133 AAACGCCACTAAAGTACGATTCTATAGCGACGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
* * * *
13174 AAACGCCACTAATGTACGAGTGTATAGCGACATTTATATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
* * * * *
13215 AAATGCCACTAAATTATGAGTCTTTAGCGACGTTTGTATAC
1 AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
* * ** * * * *
13256 AATCGCCTCTAATA-TACTGA-TAAATTGTGACATTTAT-TCAAA
1 AAACGCCACTAA-AGTAC-GAGTCTATAGCGACGTTTGTAT--AA
* * * * * *
13298 AAATGCCATTACAA-TATGAATCTCTTA-C-AGCGTTT-TTTCAA
1 AAACGCCACTA-AAGTACGAGTCT-ATAGCGA-CGTTTGTAT-AA
* * * * ** *
13339 AAATGCCATTATA-TATGTTTCCTATTA-CGAAGTTTGTATAA
1 AAACGCCACTAAAGTACGAGT-CTA-TAGCGACGTTTGTATAA
* * * * *
13380 AAACGCCACTAAATTACGAGTCTTTA-CTAGCATTTGTATAC
1 AAACGCCACTAAAGTACGAGTCTATAGCGA-CGTTTGTATAA
* * * * * *
13421 AAACGACACTAATGTACGAGTCTTTAGCGGCGTTTATATAG
1 AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
** * * *
13462 AAACGCCACTAAAGTACTTGTCTATAGAGACTTTTTTAT-A
1 AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
*
13502 AAACGCCACTAAAGTTCGAGTCT
1 AAACGCCACTAAAGTACGAGTCT
13525 GTGTCGGTGT
Statistics
Matches: 259, Mismatches: 76, Indels: 33
0.70 0.21 0.09
Matches are distributed among these distances:
40 31 0.12
41 198 0.76
42 28 0.11
43 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (41 bp):
AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
Found at i:14193 original size:3 final size:3
Alignment explanation
Indices: 14187--14225 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
14177 TAATATATGC
14187 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
14226 CTCGGTTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:20040 original size:26 final size:27
Alignment explanation
Indices: 19990--20057 Score: 93
Period size: 26 Copynumber: 2.6 Consensus size: 27
19980 TTAGTCAAAT
* * *
19990 AACAAATGCCACAAAAAGTAGCACTGA
1 AACAAACGCCACAAAAAGAACCACTGA
20017 AACAAACGCCACAAAAA-AACCACTGA
1 AACAAACGCCACAAAAAGAACCACTGA
*
20043 AACAAACGCCGCAAA
1 AACAAACGCCACAAA
20058 TGGTAGCGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
26 21 0.57
27 16 0.43
ACGTcount: A:0.54, C:0.28, G:0.12, T:0.06
Consensus pattern (27 bp):
AACAAACGCCACAAAAAGAACCACTGA
Found at i:20273 original size:44 final size:44
Alignment explanation
Indices: 20202--20285 Score: 123
Period size: 44 Copynumber: 1.9 Consensus size: 44
20192 AGGTTGTCCC
*
20202 AAAAACGCCACTAAATGTTCTGACATATAATGGCGTTTGTTCCG
1 AAAAACGCCACTAAATGTTATGACATATAATGGCGTTTGTTCCG
* * * *
20246 AAAAACGCCGCTATATGTTATGTCATATAGTGGCGTTTGT
1 AAAAACGCCACTAAATGTTATGACATATAATGGCGTTTGT
20286 GAATGTAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (44 bp):
AAAAACGCCACTAAATGTTATGACATATAATGGCGTTTGTTCCG
Found at i:20525 original size:21 final size:21
Alignment explanation
Indices: 20501--20553 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
20491 TAAACTAGAC
*
20501 ATCCGTAATAACAAACTTCAA
1 ATCCATAATAACAAACTTCAA
* * *
20522 ATCCATAACAAGAAACTTGAA
1 ATCCATAATAACAAACTTCAA
20543 ATCCATAATAA
1 ATCCATAATAA
20554 TAAATTAAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.51, C:0.21, G:0.06, T:0.23
Consensus pattern (21 bp):
ATCCATAATAACAAACTTCAA
Found at i:22600 original size:23 final size:21
Alignment explanation
Indices: 22556--22618 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 21
22546 TCTATAAAAA
*
22556 TAAAATTATTATATTATATTT
1 TAAAATTATTATAATATATTT
22577 TAAAATTATTAATAAATATATTT
1 TAAAATTATT-AT-AATATATTT
*
22600 TAAGGAATTTTTATAATAT
1 TAA--AATTATTATAATAT
22619 TATTAGACTA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
21 10 0.28
22 2 0.06
23 16 0.44
24 2 0.06
25 6 0.17
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (21 bp):
TAAAATTATTATAATATATTT
Found at i:22856 original size:22 final size:23
Alignment explanation
Indices: 22831--22873 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
22821 ATTAAAAATA
22831 TTAATAAAT-ATATTTAATTATG
1 TTAATAAATAATATTTAATTATG
* *
22853 TTAATAATTAATATTTTATTA
1 TTAATAAATAATATTTAATTA
22874 AAATGATACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TTAATAAATAATATTTAATTATG
Found at i:23530 original size:70 final size:69
Alignment explanation
Indices: 23404--23541 Score: 217
Period size: 70 Copynumber: 2.0 Consensus size: 69
23394 AGCAAATGAG
*
23404 TTTGGGTAAATGACGGGAATGAAAAAATAGGTCAAGGGGAAAAAATGAAAAAGGGTTAAAGGG-G
1 TTTGGGTAAACGACGGGAATGAAAAAATAGGTCAAGGGGAAAAAATGAAAAAGGGTTAAAGGGTG
23468 CGAC
66 CGAC
*
23472 TTTGGGTAAACGGCGGGAATGGAAAAAAAATAGGTCAAGGGG-AAAAATGAAAAAGGGTTAAAGG
1 TTTGGGTAAACGACGGGAAT-G--AAAAAATAGGTCAAGGGGAAAAAATGAAAAAGGGTTAAAGG
23536 GTGCGA
63 GTGCGA
23542 GACTTAGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
68 18 0.28
69 1 0.02
70 23 0.36
71 22 0.34
ACGTcount: A:0.43, C:0.06, G:0.35, T:0.16
Consensus pattern (69 bp):
TTTGGGTAAACGACGGGAATGAAAAAATAGGTCAAGGGGAAAAAATGAAAAAGGGTTAAAGGGTG
CGAC
Found at i:23627 original size:41 final size:41
Alignment explanation
Indices: 23579--23718 Score: 154
Period size: 41 Copynumber: 3.4 Consensus size: 41
23569 TTGTAAACAT
*
23579 AAACGCCACTAAAGTACGATTCTATAGCGACGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
* * * *
23620 AAACGCCACTAATGTATGAGTCTATAGCGACATTTATATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
* * * * * *
23661 AAATGCCACTAAATTATGAGTCTTTAGCGGCGTTTGTATAC
1 AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
* * *
23702 AATCGCCATTAATGTAC
1 AAACGCCACTAAAGTAC
23719 TGGTAAATTA
Statistics
Matches: 80, Mismatches: 19, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 80 1.00
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (41 bp):
AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
Found at i:23866 original size:41 final size:40
Alignment explanation
Indices: 23821--23972 Score: 103
Period size: 41 Copynumber: 3.7 Consensus size: 40
23811 ACGAAGTTTG
23821 TATAAAAATGCCACTAAATTACGAGTCTTTACTGACATTTT
1 TATAAAAA-GCCACTAAATTACGAGTCTTTACTGACATTTT
* * * * *
23862 TATAAAAAGGACACT-AATGTACGAATCTTTAGC-GGCGTTTA
1 TATAAAAA-GCCACTAAAT-TACGAGTCTTTA-CTGACATTTT
* * ** * * **
23903 TATAGAAACGCCACTAAAGTACTTGTCTATAGTGATTTTTT
1 TATA-AAAAGCCACTAAATTACGAGTCTTTACTGACATTTT
*
23944 TATAAAAAGTCACTAAAGTT-CGAGTCTTT
1 TATAAAAAGCCACTAAA-TTACGAGTCTTT
23973 GCCGGCGTTT
Statistics
Matches: 81, Mismatches: 24, Indels: 13
0.69 0.20 0.11
Matches are distributed among these distances:
40 20 0.25
41 55 0.68
42 6 0.07
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (40 bp):
TATAAAAAGCCACTAAATTACGAGTCTTTACTGACATTTT
Found at i:24653 original size:3 final size:3
Alignment explanation
Indices: 24647--24674 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
24637 TAATATATGC
24647 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
24675 ATCTCGGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:28814 original size:21 final size:23
Alignment explanation
Indices: 28790--28836 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
28780 TCTATAAAAA
*
28790 TAAAAGTATT-AT-ATTATATTT
1 TAAAAGTATTAATAAATATATTT
*
28811 TAAAATTATTAATAAATATATTT
1 TAAAAGTATTAATAAATATATTT
28834 TAA
1 TAA
28837 GGAATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
22 2 0.09
23 11 0.50
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TAAAAGTATTAATAAATATATTT
Found at i:28851 original size:23 final size:22
Alignment explanation
Indices: 28790--28852 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
28780 TCTATAAAAA
* *
28790 TAAAAGTA-TTATATTATATTT
1 TAAAATTATTTATAATATATTT
*
28811 TAAAATTATTAATAAATATATTT
1 TAAAATTATTTAT-AATATATTT
28834 TAAGGAATT-TTTATAATAT
1 TAA--AATTATTTATAATAT
28853 TATTAGACTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 7 0.21
22 3 0.09
23 16 0.47
24 4 0.12
25 4 0.12
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (22 bp):
TAAAATTATTTATAATATATTT
Found at i:29782 original size:70 final size:68
Alignment explanation
Indices: 29642--29782 Score: 214
Period size: 69 Copynumber: 2.0 Consensus size: 68
29632 AGCAACAAAT
* *
29642 GAGTTTGGGTAAACGGAGGGAATGAAAAAATAGGTCAAGGGGAAAAAATGAAAAAGGGTTAATGG
1 GAGTTTGGGTAAACGGAGGGAATGAAAAAATAGGTCAAGGAGAAAAAATGAAAAAGGGTTAAAGG
29707 GGC
66 GGC
29710 GAGTTTGGGTAAAC-GACGGGAATGAAAAAAAATAGGTCAAGGAG-AAAAATGAAAAAGGGTTAA
1 GAGTTTGGGTAAACGGA-GGGAATG--AAAAAATAGGTCAAGGAGAAAAAATGAAAAAGGGTTAA
29773 AGGGTGC
63 AGGG-GC
29780 GAG
1 GAG
29783 ACTTAGAAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
67 2 0.03
68 21 0.31
69 22 0.33
70 22 0.33
ACGTcount: A:0.44, C:0.05, G:0.35, T:0.16
Consensus pattern (68 bp):
GAGTTTGGGTAAACGGAGGGAATGAAAAAATAGGTCAAGGAGAAAAAATGAAAAAGGGTTAAAGG
GGC
Found at i:29867 original size:41 final size:41
Alignment explanation
Indices: 29819--29958 Score: 163
Period size: 41 Copynumber: 3.4 Consensus size: 41
29809 TTGTAAACAT
*
29819 AAACGCCACTAAAGTACGATTCTATAGCGACGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
* * *
29860 AAACGCCACTAATGTACGAGTCTATAGCGACATTTATATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
* * * * * *
29901 AAATGCCACTAAATTATGAGTCTTTAGCGGCGTTTGTATAC
1 AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
* * *
29942 AATCGCCTCTAATGTAC
1 AAACGCCACTAAAGTAC
29959 TGATAAATTG
Statistics
Matches: 80, Mismatches: 19, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 80 1.00
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.29
Consensus pattern (41 bp):
AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
Found at i:29974 original size:82 final size:82
Alignment explanation
Indices: 29823--29991 Score: 189
Period size: 82 Copynumber: 2.0 Consensus size: 82
29813 AAACATAAAC
* **
29823 GCCACTAAAGTACGATTCTATAGCGACGTTTGTATAAAAACGCCACTAATGTACGAGTCTATAGC
1 GCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAAAAACGCCACTAATGTACGAGTAAATAGC
29888 GACATTTA-TATAAAAAT
66 GACATTTATTA-AAAAAT
* * * * * * * *
29905 GCCACTAAATTATGAGTCTTTAGCGGCGTTTGTATACAATCGCCTCTAATGTACTGA-TAAATTG
1 GCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAAAAACGCCACTAATGTAC-GAGTAAATAG
*
29969 TGACATTTATTCAAAAAAT
65 CGACATTTATT-AAAAAAT
29988 GCCA
1 GCCA
29992 TTACAATATG
Statistics
Matches: 72, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
82 58 0.81
83 13 0.18
84 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (82 bp):
GCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAAAAACGCCACTAATGTACGAGTAAATAGC
GACATTTATTAAAAAAT
Found at i:30104 original size:41 final size:42
Alignment explanation
Indices: 30059--30202 Score: 120
Period size: 41 Copynumber: 3.5 Consensus size: 42
30049 TATTTCGGAG
*
30059 TTTGTATAAAAACGCCACTAAAT-TATGAGTCTTTA-CTAGCA
1 TTTGTATAAAAACGCCACTAAATGTACGAGTCTTTAGC-AGCA
* * * *
30100 TTTGTATACAAACGACACT-AATGTACGAGTCTTTAGCGGCG
1 TTTGTATAAAAACGCCACTAAATGTACGAGTCTTTAGCAGCA
* * ** * *
30141 TTTATATAGAAACGCCACTAAA-GTACTTGTCTATAGC-GACT
1 TTTGTATAAAAACGCCACTAAATGTACGAGTCTTTAGCAG-CA
*
30182 TTTTTAT-AAAACGCCACTAAA
1 TTTGTATAAAAACGCCACTAAA
30203 GTTTGAGTAT
Statistics
Matches: 85, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
40 17 0.20
41 65 0.76
42 3 0.04
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.32
Consensus pattern (42 bp):
TTTGTATAAAAACGCCACTAAATGTACGAGTCTTTAGCAGCA
Found at i:30857 original size:3 final size:3
Alignment explanation
Indices: 30851--30889 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
30841 TAATATATGC
*
30851 TTA TTA TTA TTA TTA TTA TTA TTT TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
30890 CTCGGTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:33444 original size:17 final size:17
Alignment explanation
Indices: 33422--33458 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
33412 GAAAAGGGAC
33422 AAGACATCATATGAGTT
1 AAGACATCATATGAGTT
33439 AAGACATCATATGAGTT
1 AAGACATCATATGAGTT
33456 AAG
1 AAG
33459 GAAATGGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.27
Consensus pattern (17 bp):
AAGACATCATATGAGTT
Found at i:35017 original size:21 final size:23
Alignment explanation
Indices: 34993--35039 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
34983 TCTATAAAAA
*
34993 TAAAAGTATT-AT-ATTATATTT
1 TAAAAGTATTAATAAATATATTT
*
35014 TAAAATTATTAATAAATATATTT
1 TAAAAGTATTAATAAATATATTT
35037 TAA
1 TAA
35040 GGAATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
22 2 0.09
23 11 0.50
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TAAAAGTATTAATAAATATATTT
Found at i:35054 original size:23 final size:22
Alignment explanation
Indices: 34993--35055 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
34983 TCTATAAAAA
* *
34993 TAAAAGTA-TTATATTATATTT
1 TAAAATTATTTATAATATATTT
*
35014 TAAAATTATTAATAAATATATTT
1 TAAAATTATTTAT-AATATATTT
35037 TAAGGAATT-TTTATAATAT
1 TAA--AATTATTTATAATAT
35056 TATTAGACTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 7 0.21
22 3 0.09
23 16 0.47
24 4 0.12
25 4 0.12
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (22 bp):
TAAAATTATTTATAATATATTT
Found at i:35269 original size:13 final size:13
Alignment explanation
Indices: 35247--35271 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35237 TAATAATATT
35247 ATTATTATATTAC
1 ATTATTATATTAC
35260 ATTATTATATTA
1 ATTATTATATTA
35272 ATAAATATAT
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:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTATTATATTAC
Found at i:35289 original size:23 final size:24
Alignment explanation
Indices: 35263--35313 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
35253 ATATTACATT
35263 ATTATATTAATAAAT-ATATTTTA
1 ATTATATTAATAAATAATATTTTA
* * *
35286 ATTATGTTAATAATTAATATTTTT
1 ATTATATTAATAAATAATATTTTA
35310 ATTA
1 ATTA
35314 AAATGATACT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 13 0.54
24 11 0.46
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (24 bp):
ATTATATTAATAAATAATATTTTA
Found at i:35980 original size:70 final size:68
Alignment explanation
Indices: 35840--35980 Score: 205
Period size: 70 Copynumber: 2.0 Consensus size: 68
35830 AGCAACAAAT
* *
35840 GAGTTTGGGTAAACGGAGGGAATGAAAAAATAGGTCAAGGGGAAAAAATGAAAAAGGGTTAATGG
1 GAGTTTGGGTAAACGGAGGGAATGAAAAAATAGGTCAAGGAGAAAAAATGAAAAAGGGTTAAAGG
35905 GGC
66 GGC
*
35908 GAGTTTGGGTAAAC-GACGGGAATGAAAAAAAATAGGTCAAGGAG-AAAAGTGAAAAAGGGTTAA
1 GAGTTTGGGTAAACGGA-GGGAATG--AAAAAATAGGTCAAGGAGAAAAAATGAAAAAGGGTTAA
35971 AGGGTGC
63 AGGG-GC
35978 GAG
1 GAG
35981 ACTTAGAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
67 2 0.03
68 21 0.32
69 21 0.32
70 22 0.33
ACGTcount: A:0.43, C:0.05, G:0.36, T:0.16
Consensus pattern (68 bp):
GAGTTTGGGTAAACGGAGGGAATGAAAAAATAGGTCAAGGAGAAAAAATGAAAAAGGGTTAAAGG
GGC
Found at i:36065 original size:41 final size:41
Alignment explanation
Indices: 36017--36156 Score: 163
Period size: 41 Copynumber: 3.4 Consensus size: 41
36007 TTGTAAACAT
*
36017 AAACGCCACTAAAGTACGATTCTATAGCGACGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
* * *
36058 AAACGCCACTAATGTACGAGTCTATAGCGACATTTATATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
* * * * * *
36099 AAATGCCACTAAATTATGAGTCTTTAGCGGCGTTTGTATAC
1 AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
* * *
36140 AATCGCCTCTAATGTAC
1 AAACGCCACTAAAGTAC
36157 TGATAAATTG
Statistics
Matches: 80, Mismatches: 19, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 80 1.00
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.29
Consensus pattern (41 bp):
AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
Found at i:36172 original size:82 final size:82
Alignment explanation
Indices: 36021--36189 Score: 189
Period size: 82 Copynumber: 2.0 Consensus size: 82
36011 AAACATAAAC
* **
36021 GCCACTAAAGTACGATTCTATAGCGACGTTTGTATAAAAACGCCACTAATGTACGAGTCTATAGC
1 GCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAAAAACGCCACTAATGTACGAGTAAATAGC
36086 GACATTTA-TATAAAAAT
66 GACATTTATTA-AAAAAT
* * * * * * * *
36103 GCCACTAAATTATGAGTCTTTAGCGGCGTTTGTATACAATCGCCTCTAATGTACTGA-TAAATTG
1 GCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAAAAACGCCACTAATGTAC-GAGTAAATAG
*
36167 TGACATTTATTCAAAAAAT
65 CGACATTTATT-AAAAAAT
36186 GCCA
1 GCCA
36190 TTACAATATG
Statistics
Matches: 72, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
82 58 0.81
83 13 0.18
84 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (82 bp):
GCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAAAAACGCCACTAATGTACGAGTAAATAGC
GACATTTATTAAAAAAT
Found at i:36349 original size:41 final size:40
Alignment explanation
Indices: 36254--36396 Score: 128
Period size: 41 Copynumber: 3.5 Consensus size: 40
36244 CTATTTCGGA
* *
36254 GTTTGTATAAAAACGCCACTAAT-TATGAGTCTTTA-CTAGC
1 GTTTGTAT-AAAACGCCACTAATGTACGAGTCTTTAGC-GGC
* *
36294 ATTTGTATACAAACGACACTAATGTACGAGTCTTTAGCGGC
1 GTTTGTATA-AAACGCCACTAATGTACGAGTCTTTAGCGGC
* * ** * *
36335 GTTTATATAGAAACGCCACTAAAGTACTTGTCTATAGCGAC
1 GTTTGTATA-AAACGCCACTAATGTACGAGTCTTTAGCGGC
* *
36376 TTTTTTATAAAACGCCACTAA
1 GTTTGTATAAAACGCCACTAA
36397 AGTTTGAGTC
Statistics
Matches: 85, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
39 1 0.01
40 31 0.36
41 52 0.61
42 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (40 bp):
GTTTGTATAAAACGCCACTAATGTACGAGTCTTTAGCGGC
Found at i:37052 original size:3 final size:3
Alignment explanation
Indices: 37046--37105 Score: 113
Period size: 3 Copynumber: 20.3 Consensus size: 3
37036 TAATATATGC
37046 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
37094 TTA TTA TT- TTA T
1 TTA TTA TTA TTA T
37106 ATCGGTTTAA
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.04
3 54 0.96
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:44535 original size:21 final size:21
Alignment explanation
Indices: 44511--44563 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
44501 TAAACTAGAC
*
44511 ATCCGTAATAACAAACTTCAA
1 ATCCATAATAACAAACTTCAA
* * *
44532 ATCCATAACAAGAAACTTGAA
1 ATCCATAATAACAAACTTCAA
44553 ATCCATAATAA
1 ATCCATAATAA
44564 TAAATTAAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.51, C:0.21, G:0.06, T:0.23
Consensus pattern (21 bp):
ATCCATAATAACAAACTTCAA
Found at i:46633 original size:21 final size:23
Alignment explanation
Indices: 46608--46654 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
46598 TCTATAAAAA
*
46608 TAAAAATATT-AT-ATTATATTT
1 TAAAAATATTAATAAATATATTT
*
46629 TAAAAGTATTAATAAATATATTT
1 TAAAAATATTAATAAATATATTT
46652 TAA
1 TAA
46655 GGAATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
22 2 0.09
23 11 0.50
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
TAAAAATATTAATAAATATATTT
Found at i:47685 original size:41 final size:41
Alignment explanation
Indices: 47637--47863 Score: 233
Period size: 41 Copynumber: 5.6 Consensus size: 41
47627 TTGTAAACAT
* * *
47637 AAACGCCACTAAAGTACGATTCTATAGCGACGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGACATTTATATAA
*
47678 AAACGCCACTAATGTACGAGTCTATAGCGACATTTATATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGACATTTATATAA
* * * *
47719 AAATGCCACTAAATTACGAGTCTTTA-CTGACATTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGC-GACATTTATATAA
* * * * * *
47760 AAACGACACTAATGTACGAGTCTTTAGCGGCGTTTATATAG
1 AAACGCCACTAAAGTACGAGTCTATAGCGACATTTATATAA
** * ** *
47801 AAACGCCACTAAAGTACTTGTCTATAGTGATTTTTTTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGACATTTATATAA
* *
47842 AAA-GTCACTAAAGTTCGAGTCT
1 AAACGCCACTAAAGTACGAGTCT
47864 TTGCCGGCGT
Statistics
Matches: 152, Mismatches: 32, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
40 16 0.11
41 135 0.89
42 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.31
Consensus pattern (41 bp):
AAACGCCACTAAAGTACGAGTCTATAGCGACATTTATATAA
Found at i:47770 original size:123 final size:122
Alignment explanation
Indices: 47637--47865 Score: 298
Period size: 123 Copynumber: 1.9 Consensus size: 122
47627 TTGTAAACAT
* * * *
47637 AAACGCCACTAAAGTACGATTCTATAGCGACGTTTGTATAAAAACGCCACTAATGTACGAGTCTA
1 AAACGACACTAAAGTACGAGTCTATAGCGACGTTTATATAAAAACGCCACTAAAGTACGAGTCTA
47702 TAGCGACATTTATATAAAAATGCCACTAAA-TTACGAGTCTTTACTGACATTTGTATAA
66 TAGCGACATTTATATAAAAA-GCCACTAAAGTT-CGAGTCTTTACTGACATTTGTATAA
* * * * **
47760 AAACGACACTAATGTACGAGTCTTTAGCGGCGTTTATATAGAAACGCCACTAAAGTACTTGTCTA
1 AAACGACACTAAAGTACGAGTCTATAGCGACGTTTATATAAAAACGCCACTAAAGTACGAGTCTA
* ** * *
47825 TAGTGATTTTTTTATAAAAAGTCACTAAAGTTCGAGTCTTT
66 TAGCGACATTTATATAAAAAGCCACTAAAGTTCGAGTCTTT
47866 GCCGGCGTTT
Statistics
Matches: 90, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
122 17 0.19
123 73 0.81
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Consensus pattern (122 bp):
AAACGACACTAAAGTACGAGTCTATAGCGACGTTTATATAAAAACGCCACTAAAGTACGAGTCTA
TAGCGACATTTATATAAAAAGCCACTAAAGTTCGAGTCTTTACTGACATTTGTATAA
Found at i:47778 original size:82 final size:82
Alignment explanation
Indices: 47637--47863 Score: 260
Period size: 82 Copynumber: 2.8 Consensus size: 82
47627 TTGTAAACAT
* * *
47637 AAACGCCACTAAAGTACGATTCTATAGCGACGTTTGTATAAAAACGCCACTAATGTACGAGTCTA
1 AAACGCCACTAAAGTACGAGTCTATAGCGACATTTGTATAAAAACGACACTAATGTACGAGTCTA
47702 TAGCGACATTTATATAA
66 TAGCGACATTTATATAA
* * *
47719 AAATGCCACTAAATTACGAGTCTTTA-CTGACATTTGTATAAAAACGACACTAATGTACGAGTCT
1 AAACGCCACTAAAGTACGAGTCTATAGC-GACATTTGTATAAAAACGACACTAATGTACGAGTCT
* * * *
47783 TTAGCGGCGTTTATATAG
65 ATAGCGACATTTATATAA
** * ** * * * *
47801 AAACGCCACTAAAGTACTTGTCTATAGTGATTTTTTTATAAAAA-GTCACTAAAGTTCGAGTCT
1 AAACGCCACTAAAGTACGAGTCTATAGCGACATTTGTATAAAAACGACACTAATGTACGAGTCT
47864 TTGCCGGCGT
Statistics
Matches: 121, Mismatches: 22, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
81 17 0.14
82 104 0.86
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.31
Consensus pattern (82 bp):
AAACGCCACTAAAGTACGAGTCTATAGCGACATTTGTATAAAAACGACACTAATGTACGAGTCTA
TAGCGACATTTATATAA
Found at i:48547 original size:3 final size:3
Alignment explanation
Indices: 48541--48583 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
48531 TAATATATGC
48541 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
48584 ATCTCGGGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:58950 original size:21 final size:23
Alignment explanation
Indices: 58926--58972 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
58916 TCTATAAAAA
*
58926 TAAAAGTATT-AT-ATTATATTT
1 TAAAAGTATTAATAAATATATTT
*
58947 TAAAATTATTAATAAATATATTT
1 TAAAAGTATTAATAAATATATTT
58970 TAA
1 TAA
58973 GGAATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
22 2 0.09
23 11 0.50
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TAAAAGTATTAATAAATATATTT
Found at i:58987 original size:23 final size:22
Alignment explanation
Indices: 58926--58988 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
58916 TCTATAAAAA
* *
58926 TAAAAGTA-TTATATTATATTT
1 TAAAATTATTTATAATATATTT
*
58947 TAAAATTATTAATAAATATATTT
1 TAAAATTATTTAT-AATATATTT
58970 TAAGGAATT-TTTATAATAT
1 TAA--AATTATTTATAATAT
58989 TATTAGACTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 7 0.21
22 3 0.09
23 16 0.47
24 4 0.12
25 4 0.12
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (22 bp):
TAAAATTATTTATAATATATTT
Found at i:59916 original size:70 final size:68
Alignment explanation
Indices: 59776--59916 Score: 214
Period size: 69 Copynumber: 2.0 Consensus size: 68
59766 AGCAACAAAT
* *
59776 GAGTTTGGGTAAACGGAGGGAATGAAAAAATAGGTCAAGGGGAAAAAATGAAAAAGGGTTAATGG
1 GAGTTTGGGTAAACGGAGGGAATGAAAAAATAGGTCAAGGAGAAAAAATGAAAAAGGGTTAAAGG
59841 GGC
66 GGC
59844 GAGTTTGGGTAAAC-GACGGGAATGAAAAAAAATAGGTCAAGGAG-AAAAATGAAAAAGGGTTAA
1 GAGTTTGGGTAAACGGA-GGGAATG--AAAAAATAGGTCAAGGAGAAAAAATGAAAAAGGGTTAA
59907 AGGGTGC
63 AGGG-GC
59914 GAG
1 GAG
59917 ACTTAGAAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
67 2 0.03
68 21 0.31
69 22 0.33
70 22 0.33
ACGTcount: A:0.44, C:0.05, G:0.35, T:0.16
Consensus pattern (68 bp):
GAGTTTGGGTAAACGGAGGGAATGAAAAAATAGGTCAAGGAGAAAAAATGAAAAAGGGTTAAAGG
GGC
Found at i:60001 original size:41 final size:41
Alignment explanation
Indices: 59937--60074 Score: 159
Period size: 41 Copynumber: 3.3 Consensus size: 41
59927 TGTAAACTTA
* *
59937 CGACATTTGTAAACATAAACGCCACTAAAGTACGATTCTATAG
1 CGACATTTGTATA-A-AAACGCCACTAAAGTACGAGTCTATAG
* *
59980 CGACGTTTGTATAAAAACGCCACTAATGTACGAGTCTATAG
1 CGACATTTGTATAAAAACGCCACTAAAGTACGAGTCTATAG
* * * * * *
60021 CGTCATTTATATAAAAATGCCACTAAACTATGAGTCTTTAG
1 CGACATTTGTATAAAAACGCCACTAAAGTACGAGTCTATAG
*
60062 CGGCATTTGTATA
1 CGACATTTGTATA
60075 CAATCGCCTC
Statistics
Matches: 81, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
41 69 0.85
42 1 0.01
43 11 0.14
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.30
Consensus pattern (41 bp):
CGACATTTGTATAAAAACGCCACTAAAGTACGAGTCTATAG
Found at i:60237 original size:41 final size:42
Alignment explanation
Indices: 60192--60335 Score: 111
Period size: 41 Copynumber: 3.5 Consensus size: 42
60182 TATTTCGGAG
*
60192 TTTGTATAAAAACGCCACTAAAT-TATGAGTCTTTA-CTAGCA
1 TTTGTATAAAAACGCCACTAAATGTACGAGTCTTTAGC-AGCA
* ** * *
60233 TTTGTATACAAACGAAACT-AATGTACGAGTCTTTAGCGGCG
1 TTTGTATAAAAACGCCACTAAATGTACGAGTCTTTAGCAGCA
* * ** * *
60274 TTTATATAGAAACGCCACTAAA-GTACTTGTCTATAGC-GACT
1 TTTGTATAAAAACGCCACTAAATGTACGAGTCTTTAGCAG-CA
*
60315 TTTTTAT-AAAACGCCACTAAA
1 TTTGTATAAAAACGCCACTAAA
60336 GTTTGAGTCT
Statistics
Matches: 83, Mismatches: 16, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
40 17 0.20
41 63 0.76
42 3 0.04
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (42 bp):
TTTGTATAAAAACGCCACTAAATGTACGAGTCTTTAGCAGCA
Found at i:60958 original size:3 final size:3
Alignment explanation
Indices: 60952--60993 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
60942 TAATATATGC
60952 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
60994 CTCGGTTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:70739 original size:44 final size:43
Alignment explanation
Indices: 70690--70772 Score: 105
Period size: 44 Copynumber: 1.9 Consensus size: 43
70680 GTTTTGTCCC
*
70690 AAAAACGCCACCTA-ATGTTCTGACATATAATGGCGTTTGTTCTG
1 AAAAACGCC-CCTATATGTTATGACAT-TAATGGCGTTTGTTCTG
* * *
70734 AAAAACGCCTCTATATGTTATGCCATTAGTGGCGTTTGT
1 AAAAACGCCCCTATATGTTATGACATTAATGGCGTTTGT
70773 GAATGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
43 15 0.44
44 19 0.56
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (43 bp):
AAAAACGCCCCTATATGTTATGACATTAATGGCGTTTGTTCTG
Found at i:70936 original size:14 final size:15
Alignment explanation
Indices: 70910--70950 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
70900 TTATACAATT
70910 AAAACTAATTTTTCA
1 AAAACTAATTTTTCA
70925 AAAACTAATTTTTCA
1 AAAACTAATTTTTCA
*
70940 AATACT-ATTTT
1 AAAACTAATTTT
70951 CTACTCTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 5 0.20
15 20 0.80
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (15 bp):
AAAACTAATTTTTCA
Found at i:71027 original size:21 final size:21
Alignment explanation
Indices: 71003--71052 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
70993 TAAACTAGAC
*
71003 ATCCGTAACAACAAACTTCAA
1 ATCCATAACAACAAACTTCAA
* *
71024 ATCCATAACAAGAAACTTGAA
1 ATCCATAACAACAAACTTCAA
71045 ATCCATAA
1 ATCCATAA
71053 TAATAAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.50, C:0.24, G:0.06, T:0.20
Consensus pattern (21 bp):
ATCCATAACAACAAACTTCAA
Found at i:72373 original size:16 final size:15
Alignment explanation
Indices: 72347--72376 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
72337 TTCCCCCAAC
72347 TAAAAAAGAAGAAAA
1 TAAAAAAGAAGAAAA
72362 TAAAAGAAGAAGAAA
1 TAAAA-AAGAAGAAA
72377 CATGGTTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.07
Consensus pattern (15 bp):
TAAAAAAGAAGAAAA
Found at i:74000 original size:67 final size:68
Alignment explanation
Indices: 73887--74024 Score: 219
Period size: 67 Copynumber: 2.0 Consensus size: 68
73877 ATCAGCAATT
* *
73887 GAGTTTGGGTAAACGGCGGGAATGAAAAATAGGTCAAGGGGAAAAAATGAAAAAGGGTTAAAGGG
1 GAGTTTGGGTAAACGACGAGAATGAAAAATAGGTCAAGGGGAAAAAATGAAAAAGGGTTAAAGGG
73952 -GC
66 TGC
73954 GAGTTTGGGTAAACGACGAGAATGAAAAAAATA-GTCAAGGGG-AAAAATGAAAAAGGGTTAAAG
1 GAGTTTGGGTAAACGACGAGAATG--AAAAATAGGTCAAGGGGAAAAAATGAAAAAGGGTTAAAG
74017 GGTGC
64 GGTGC
74022 GAG
1 GAG
74025 ACTTAGAAAT
Statistics
Matches: 66, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
67 45 0.68
68 14 0.21
69 7 0.11
ACGTcount: A:0.43, C:0.06, G:0.36, T:0.15
Consensus pattern (68 bp):
GAGTTTGGGTAAACGACGAGAATGAAAAATAGGTCAAGGGGAAAAAATGAAAAAGGGTTAAAGGG
TGC
Found at i:74109 original size:41 final size:40
Alignment explanation
Indices: 74061--74154 Score: 134
Period size: 41 Copynumber: 2.3 Consensus size: 40
74051 TTGTAAAAAT
* * *
74061 AAACGCCACTAAAGTACGATTCTATAGCGACGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGACATTTATAT-A
*
74102 AAACGCCACTAATGTACGAGTCTATAGCGACATTTATATA
1 AAACGCCACTAAAGTACGAGTCTATAGCGACATTTATATA
*
74142 AAATGCCACTAAA
1 AAACGCCACTAAA
74155 TTATGAGTGT
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 12 0.26
41 35 0.74
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.26
Consensus pattern (40 bp):
AAACGCCACTAAAGTACGAGTCTATAGCGACATTTATATA
Found at i:80258 original size:20 final size:20
Alignment explanation
Indices: 80228--80265 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
80218 TGTCTTCTAG
80228 TTTCTATATAGTTATGAATGT
1 TTTCTATATAGTT-TGAATGT
80249 TTTCTA-ATAGTTTGAAT
1 TTTCTATATAGTTTGAAT
80266 AAGATTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.29, C:0.05, G:0.13, T:0.53
Consensus pattern (20 bp):
TTTCTATATAGTTTGAATGT
Found at i:82934 original size:32 final size:31
Alignment explanation
Indices: 82861--82936 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
82851 CTAATGTGAC
* * *
82861 TCTTAGGTAGGCTCTGCGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTGCGACCCTAAGATCAT
** **
82892 TCTCGGGTAGGCCCTGCGACCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGCGACCCTAAGAT-CAT
82924 TCTTAGGTAGGCC
1 TCTTAGGTAGGCC
82937 GCCGCCCAAA
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.66
32 12 0.34
ACGTcount: A:0.16, C:0.26, G:0.30, T:0.28
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGACCCTAAGATCAT
Found at i:86427 original size:21 final size:20
Alignment explanation
Indices: 86392--86436 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
86382 AACAATTCTC
*
86392 TTCATGAAAGATTAAATCCT
1 TTCATGAAAGATTAAACCCT
* *
86412 TTCATGTAAAGGTTAAGCCCT
1 TTCATG-AAAGATTAAACCCT
86433 TTCA
1 TTCA
86437 CCGAAAGGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (20 bp):
TTCATGAAAGATTAAACCCT
Done.