Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003672.1 Hibiscus syriacus cultivar Beakdansim tig00007845_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: 57015
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3115 original size:59 final size:60
Alignment explanation
Indices: 3019--3131 Score: 149
Period size: 59 Copynumber: 1.9 Consensus size: 60
3009 AATACTTCTC
* * *
3019 TTAGGATGAAAACCCGAGAGAGCGTCCTAAGTCGAAAAAAA-AG-GAAAAGAGAAAAATGT
1 TTAGGATGAAAACCCGAAAGAGCGCCCTAAATCGAAAAAAATAGAGAAAA-AGAAAAATGT
* * *
3078 TTAGGGTGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAATAGAGAAAAAGAA
1 TTAGGATGAAAACCCGAAAGAGCGCCCTAAATCGAAAAAAATAGAGAAAAAGAA
3132 CAAAAGAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
59 35 0.76
60 6 0.13
61 5 0.11
ACGTcount: A:0.50, C:0.12, G:0.25, T:0.13
Consensus pattern (60 bp):
TTAGGATGAAAACCCGAAAGAGCGCCCTAAATCGAAAAAAATAGAGAAAAAGAAAAATGT
Found at i:5058 original size:2 final size:2
Alignment explanation
Indices: 5041--5096 Score: 54
Period size: 2 Copynumber: 31.5 Consensus size: 2
5031 AATTACAAAT
*
5041 TA TA -A TA TA TA CA TA TA TA TA -A TA T- TA T- TA TA TA -A T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5077 TA TA -A TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
5097 GAGTTTAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
1 7 0.16
2 38 0.84
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:6177 original size:17 final size:18
Alignment explanation
Indices: 6143--6175 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
6133 TTTTGTTTGT
6143 AATTTATTTAAGTATTTA
1 AATTTATTTAAGTATTTA
6161 AATTT-TTTAA-TATTT
1 AATTTATTTAAGTATTT
6176 TATTTAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
AATTTATTTAAGTATTTA
Found at i:15169 original size:32 final size:31
Alignment explanation
Indices: 15133--15193 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
15123 TTTGGGTCAG
15133 GTTAATACCAGATCAGTTAGATTTTAGGTTGA
1 GTTAATACCAGATCAGTT-GATTTTAGGTTGA
* * * *
15165 GTTAATATCGGATCGGTTGATTTTCGGTT
1 GTTAATACCAGATCAGTTGATTTTAGGTT
15194 TAAATCAACC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 10 0.40
32 15 0.60
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.41
Consensus pattern (31 bp):
GTTAATACCAGATCAGTTGATTTTAGGTTGA
Found at i:15629 original size:23 final size:24
Alignment explanation
Indices: 15597--15641 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
15587 TAGTCGTAAC
* *
15597 ATAAGTAAATTTTATATTATTTTG
1 ATAAGTAAATATAATATTATTTTG
15621 ATAA-TAAATATAATATTATTT
1 ATAAGTAAATATAATATTATTT
15642 CCTTTGTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (24 bp):
ATAAGTAAATATAATATTATTTTG
Found at i:15977 original size:32 final size:32
Alignment explanation
Indices: 15936--16018 Score: 130
Period size: 32 Copynumber: 2.6 Consensus size: 32
15926 GATTGATTTT
15936 CTTTAGGTTCGGGTTAATTTCAGTTCAGGTTG
1 CTTTAGGTTCGGGTTAATTTCAGTTCAGGTTG
* *
15968 CTTTCGGTTCGGGTTAATTTCAGTTCGGGTTG
1 CTTTAGGTTCGGGTTAATTTCAGTTCAGGTTG
* *
16000 CTTTTGGTTCAGGTTAATT
1 CTTTAGGTTCGGGTTAATT
16019 ATGGTTTCAG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.13, C:0.13, G:0.28, T:0.46
Consensus pattern (32 bp):
CTTTAGGTTCGGGTTAATTTCAGTTCAGGTTG
Found at i:16009 original size:16 final size:16
Alignment explanation
Indices: 15879--16014 Score: 85
Period size: 16 Copynumber: 8.5 Consensus size: 16
15869 TTTCAATCTA
15879 TTCGGGTTGCTTTCGG
1 TTCGGGTTGCTTTCGG
* ***
15895 GTCGGGTTAAATTCGG
1 TTCGGGTTGCTTTCGG
* *
15911 TTTGGGTTGCTTTTGG
1 TTCGGGTTGCTTTCGG
** * *
15927 ATT-GATTTTCTTTAGG
1 -TTCGGGTTGCTTTCGG
** *
15943 TTCGGGTTAATTTCAG
1 TTCGGGTTGCTTTCGG
*
15959 TTCAGGTTGCTTTCGG
1 TTCGGGTTGCTTTCGG
** *
15975 TTCGGGTTAATTTCAG
1 TTCGGGTTGCTTTCGG
*
15991 TTCGGGTTGCTTTTGG
1 TTCGGGTTGCTTTCGG
*
16007 TTCAGGTT
1 TTCGGGTT
16015 AATTATGGTT
Statistics
Matches: 85, Mismatches: 33, Indels: 4
0.70 0.27 0.03
Matches are distributed among these distances:
15 2 0.02
16 81 0.95
17 2 0.02
ACGTcount: A:0.10, C:0.12, G:0.31, T:0.46
Consensus pattern (16 bp):
TTCGGGTTGCTTTCGG
Found at i:16303 original size:30 final size:31
Alignment explanation
Indices: 16267--16332 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 31
16257 ATTTTTACCA
* *
16267 CCTAAAATTTTATTAGTTCAAGTTCACC-CT
1 CCTAAAATTTTATAAATTCAAGTTCACCTCT
* *
16297 CCTAAAATTTTATAAATTCGAGTTCGCCTCT
1 CCTAAAATTTTATAAATTCAAGTTCACCTCT
16328 CCTAA
1 CCTAA
16333 CATAAAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 24 0.77
31 7 0.23
ACGTcount: A:0.30, C:0.24, G:0.08, T:0.38
Consensus pattern (31 bp):
CCTAAAATTTTATAAATTCAAGTTCACCTCT
Found at i:17622 original size:16 final size:17
Alignment explanation
Indices: 17587--17623 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
17577 ATAGGATGGA
17587 AAAAATAGTATTATTGT
1 AAAAATAGTATTATTGT
17604 AAAAAT-GTAATTATT-T
1 AAAAATAGT-ATTATTGT
17620 AAAA
1 AAAA
17624 TAATATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (17 bp):
AAAAATAGTATTATTGT
Found at i:18147 original size:4 final size:4
Alignment explanation
Indices: 18138--18170 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
18128 TAAACATGGA
18138 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
18171 CTGACTTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:21657 original size:20 final size:20
Alignment explanation
Indices: 21634--21685 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
21624 AACGCGATCC
21634 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
21654 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
21674 CCAAAATCGCAA
1 CCAGAATCGCAA
21686 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:21702 original size:21 final size:20
Alignment explanation
Indices: 21675--21773 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
21665 AATCAGTTTC
21675 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
21696 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
21717 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
21737 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
21758 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
21774 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:21802 original size:20 final size:20
Alignment explanation
Indices: 21740--21933 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
21730 CGATTTTCCA
* ** *
21740 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
21760 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
21780 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
21800 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
21820 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
21840 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
21860 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
21880 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
21900 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
21921 AAATCGCAACGCG
1 AAATCGCAACGCG
21934 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:21824 original size:60 final size:60
Alignment explanation
Indices: 21740--21933 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
21730 CGATTTTCCA
* ** * *
21740 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
21800 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
21860 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
21921 AAATCGCAACGCG
1 AAATCGCAACGCG
21934 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:22353 original size:33 final size:33
Alignment explanation
Indices: 22314--22384 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
22304 TTCACTTAGA
*
22314 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
22347 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
22380 TTTCA
1 TTTCA
22385 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:22524 original size:14 final size:14
Alignment explanation
Indices: 22505--22559 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
22495 AGAATGACTG
22505 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
22519 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
22538 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
22552 TCGCAACG
1 TCGCAACG
22560 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:22572 original size:33 final size:33
Alignment explanation
Indices: 22505--22575 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
22495 AGAATGACTG
***
22505 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
22538 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
22571 TCGCA
1 TCGCA
22576 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.42, C:0.25, G:0.24, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:22593 original size:19 final size:19
Alignment explanation
Indices: 22571--22668 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
22561 GAAACCAAAA
*
22571 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
22590 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
22604 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
22623 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
22637 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
22656 TCGCGTTGCGATT
1 TCGCGTTGCGATT
22669 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:22612 original size:14 final size:14
Alignment explanation
Indices: 22593--22682 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
22583 TTTCATTTCG
22593 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
22607 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
22626 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
22640 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
22657 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
22673 CGTTGCGATT
1 CGTTGCGATT
22683 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:22618 original size:33 final size:33
Alignment explanation
Indices: 22576--22690 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
22566 CAAAATCGCA
22576 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
22609 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
22642 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
22675 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
22691 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:24615 original size:185 final size:186
Alignment explanation
Indices: 24385--24766 Score: 748
Period size: 185 Copynumber: 2.1 Consensus size: 186
24375 TAGATTGCTT
24385 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
24450 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
24515 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
24570 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
24635 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
24700 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
24756 AGTAAATTTAT
1 AGTAAATTTAT
24767 CCATTCAAGT
Statistics
Matches: 194, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
185 154 0.79
186 40 0.21
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:24699 original size:93 final size:93
Alignment explanation
Indices: 24385--24764 Score: 744
Period size: 93 Copynumber: 4.1 Consensus size: 93
24375 TAGATTGCTT
*
24385 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
24450 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
24478 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
24542 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
24570 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
24635 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
24663 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
24728 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
24756 AGTAAATTT
1 AGTAAATTT
24765 ATCCATTCAA
Statistics
Matches: 285, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.32
93 193 0.68
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:24848 original size:19 final size:19
Alignment explanation
Indices: 24808--24936 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
24798 TAGTTTACTT
* *
24808 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
24828 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
24847 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
24866 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
24880 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
24899 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
24913 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
24932 TCGCA
1 TCGCA
24937 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:24887 original size:33 final size:32
Alignment explanation
Indices: 24844--24936 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
24834 CGCGAAACCA
**
24844 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
24876 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
24909 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
24937 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:24934 original size:52 final size:52
Alignment explanation
Indices: 24808--24936 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
24798 TAGTTTACTT
**
24808 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
24860 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
24913 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
24937 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:24954 original size:19 final size:19
Alignment explanation
Indices: 24932--25066 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
24922 GAAACCAAAA
*
24932 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
24951 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
24967 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
24984 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
25000 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
25017 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
25036 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
25056 TCGTGTTGCGA
1 TCGCGTTGCGA
25067 AAGTAAACTA
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:24973 original size:14 final size:14
Alignment explanation
Indices: 24954--25010 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
24944 TTTCATTTCG
24954 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
24968 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
24985 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTTT
25001 CGTTGCGATT
1 CGTTGCGATT
25011 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.09, C:0.21, G:0.25, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:24979 original size:33 final size:33
Alignment explanation
Indices: 24937--25029 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
24927 CAAAATCGCA
*
24937 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
24970 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
25003 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
25030 TTGGTTTCGC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:26917 original size:38 final size:38
Alignment explanation
Indices: 26874--26946 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
26864 TAATTGATTG
*
26874 TTTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
26912 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
26947 TGTAAAAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.53
Consensus pattern (38 bp):
TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
Found at i:26933 original size:19 final size:19
Alignment explanation
Indices: 26870--26933 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
26860 AGTTTAATTG
26870 ATTG-TTTTTGATTGTTTA
1 ATTGATTTTTGATTGTTTA
* * ** *
26888 ATTGATTTGTAAAAG-TTG
1 ATTGATTTTTGATTGTTTA
*
26906 ATTCAATTTTTGATTGTTTA
1 ATT-GATTTTTGATTGTTTA
26926 ATTGATTT
1 ATTGATTT
26934 GTAAAAGATG
Statistics
Matches: 31, Mismatches: 12, Indels: 5
0.65 0.25 0.10
Matches are distributed among these distances:
18 9 0.29
19 17 0.55
20 5 0.16
ACGTcount: A:0.25, C:0.02, G:0.16, T:0.58
Consensus pattern (19 bp):
ATTGATTTTTGATTGTTTA
Found at i:26947 original size:14 final size:14
Alignment explanation
Indices: 26928--26963 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
26918 ATTGTTTAAT
26928 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
26942 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
26956 TGATTTGT
1 TGATTTGT
26964 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:27086 original size:19 final size:19
Alignment explanation
Indices: 27070--27171 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
27060 AAAAATGACT
27070 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
27089 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
27108 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
27122 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
27141 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
27161 ATCGCAATGCG
1 ATCGCAATGCG
27172 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:27224 original size:19 final size:19
Alignment explanation
Indices: 27200--27525 Score: 405
Period size: 19 Copynumber: 18.4 Consensus size: 19
27190 GATTATCTCG
27200 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
27219 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
27238 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
27252 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
27271 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
27290 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
27309 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
27328 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
27347 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
27361 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
27380 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
27399 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
27413 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
27432 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
27451 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
27465 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
27485 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
27499 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
27518 TTGCGATT
1 TTGCGATT
27526 GTATTTTCCG
Statistics
Matches: 269, Mismatches: 12, Indels: 52
0.81 0.04 0.16
Matches are distributed among these distances:
14 35 0.13
16 31 0.12
17 28 0.10
18 3 0.01
19 160 0.59
20 12 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:27240 original size:52 final size:52
Alignment explanation
Indices: 27178--27497 Score: 550
Period size: 52 Copynumber: 6.0 Consensus size: 52
27168 TGCGTTTATA
*
27178 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
27230 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
27282 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
27339 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
27391 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
27443 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
27496 AT
1 AT
27498 GTTGGGATTT
Statistics
Matches: 257, Mismatches: 5, Indels: 11
0.94 0.02 0.04
Matches are distributed among these distances:
52 182 0.71
53 17 0.07
54 7 0.03
55 8 0.03
57 43 0.17
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:27275 original size:71 final size:72
Alignment explanation
Indices: 27200--27525 Score: 389
Period size: 71 Copynumber: 4.6 Consensus size: 72
27190 GATTATCTCG
27200 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCG-TTGCGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTTCA
27264 TTTCGCA
66 TTTCGCA
* *
27271 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TT-CTTTCG-ATTGCGATT
27336 TTCATTTCGCA
62 TTCATTTCGCA
*
27347 TTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG-ATTGCGATT
*
27405 TTC-TCTCG--
62 TTCATTTCGCA
*
27413 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG-TTGCGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTTCA
27477 TTTCCGCA
66 TTT-CGCA
* *
27485 TTGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
27526 GTATTTTCCG
Statistics
Matches: 227, Mismatches: 11, Indels: 38
0.82 0.04 0.14
Matches are distributed among these distances:
66 12 0.05
67 25 0.11
68 14 0.06
69 13 0.06
70 3 0.01
71 109 0.48
72 12 0.05
73 6 0.03
74 8 0.04
76 25 0.11
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (72 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTTCA
TTTCGCA
Found at i:27443 original size:161 final size:157
Alignment explanation
Indices: 27178--27497 Score: 552
Period size: 161 Copynumber: 2.0 Consensus size: 157
27168 TGCGTTTATA
27178 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
* *
27243 ATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGT
66 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG-
27308 ATTGCGATTTTAATTT-CGCATTGCGATTTTC
127 -TTGCGATTTTAATTTCCGCATTGCGATTTTC
*
27339 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
27404 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
66 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
*
27469 GATTTTCATTTCCGCATTGCGATTTTC
131 GATTTTAATTTCCGCATTGCGATTTTC
27496 AT
1 AT
27498 GTTGGGATTT
Statistics
Matches: 154, Mismatches: 4, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
156 14 0.09
157 17 0.11
158 4 0.03
159 3 0.02
161 116 0.75
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (157 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
GATTTTAATTTCCGCATTGCGATTTTC
Found at i:27469 original size:33 final size:33
Alignment explanation
Indices: 27219--27525 Score: 280
Period size: 33 Copynumber: 8.8 Consensus size: 33
27209 TCATTTCGCA
*
27219 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
27252 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * *
27288 CATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCG
1 --TTGCGATTTTCATTTCGCATTGCGA--TT-CTCTCG
27326 CATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
27361 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
27397 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
27432 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
27465 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
* *
27499 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
27526 GTATTTTCCG
Statistics
Matches: 235, Mismatches: 20, Indels: 38
0.80 0.07 0.13
Matches are distributed among these distances:
31 9 0.04
32 5 0.02
33 87 0.37
34 29 0.12
35 13 0.06
36 11 0.05
37 2 0.01
38 67 0.29
39 3 0.01
40 9 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:29845 original size:12 final size:12
Alignment explanation
Indices: 29828--29852 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29818 TCTTCGGGGA
29828 CTTTTTCTTCTT
1 CTTTTTCTTCTT
29840 CTTTTTCTTCTT
1 CTTTTTCTTCTT
29852 C
1 C
29853 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:30061 original size:24 final size:24
Alignment explanation
Indices: 30027--30073 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
30017 CTGAAACATC
30027 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
30051 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
30074 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:30775 original size:20 final size:20
Alignment explanation
Indices: 30747--31115 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
30737 AAATTTCAGT
* * * *
30747 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
30767 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
30787 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
30807 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
30827 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
30847 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
30867 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
30887 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
30907 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
30927 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
30947 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
30967 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
30987 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
31007 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
31027 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
31047 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
31067 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
31087 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
31107 GTTGCGATT
1 GTTGCGATT
31116 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:32871 original size:60 final size:60
Alignment explanation
Indices: 32761--32878 Score: 141
Period size: 60 Copynumber: 2.0 Consensus size: 60
32751 CATTTGACAC
* * * * *
32761 GATGCCTTCAAGTTCCCAGGGAAAGCATTCAACTGCGAGCTTCTTCGACCTCAATGTCAA
1 GATGCCTTCAAGTTCCAAGGGAAAGCATTCAACTACGAACTTATTCGACCTAAATGTCAA
* *
32821 GATGCCTTCAAGTT-CAAGGGGAAGGCATTCAACTAAC-AACTTATTTGACCTAAATGTC
1 GATGCCTTCAAGTTCCAA-GGGAAAGCATTCAACT-ACGAACTTATTCGACCTAAATGTC
32879 GGCATCATGA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
59 2 0.04
60 46 0.94
61 1 0.02
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (60 bp):
GATGCCTTCAAGTTCCAAGGGAAAGCATTCAACTACGAACTTATTCGACCTAAATGTCAA
Found at i:34837 original size:90 final size:89
Alignment explanation
Indices: 34684--34862 Score: 288
Period size: 90 Copynumber: 2.0 Consensus size: 89
34674 GAGTATATAA
*
34684 TCATTATATACTCAACAAAATTATTTATATATGAATTCAATATTGAAATTACCTCAAAAATAGCA
1 TCATTATATACTCAACAAAATTATTTATATATAAATTCAATATTGAAATTACCTCAAAAATAGC-
34749 GGAAGAT-CAACAAGATTTTCACGAT
65 GGAA-ATACAACAAGATTTTCACGAT
* *
34774 TCATTATATACTCAACAAAATTATTTTTATATAAATTCAGTATTGAAATTACCTCAAAAATAGCG
1 TCATTATATACTCAACAAAATTATTTATATATAAATTCAATATTGAAATTACCTCAAAAATAGCG
*
34839 GAAATACCAACAAGTTTTTCACGA
66 GAAATA-CAACAAGATTTTCACGA
34863 ACGGACGTAA
Statistics
Matches: 83, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
88 2 0.02
89 4 0.05
90 77 0.93
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.33
Consensus pattern (89 bp):
TCATTATATACTCAACAAAATTATTTATATATAAATTCAATATTGAAATTACCTCAAAAATAGCG
GAAATACAACAAGATTTTCACGAT
Found at i:37130 original size:19 final size:19
Alignment explanation
Indices: 37093--37136 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
37083 TTGTTTCTAG
* *
37093 TTTTTTGATTGGTTGCTTT
1 TTTTTTGACTGGATGCTTT
37112 TGTTTTTGACTGGAT-CTTT
1 T-TTTTTGACTGGATGCTTT
37131 TTTTTT
1 TTTTTT
37137 CTTGTGTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 5 0.23
19 6 0.27
20 11 0.50
ACGTcount: A:0.07, C:0.07, G:0.18, T:0.68
Consensus pattern (19 bp):
TTTTTTGACTGGATGCTTT
Found at i:37620 original size:2 final size:2
Alignment explanation
Indices: 37613--37660 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
37603 ACATACATAC
* *
37613 AT AT AT AT AT AT AT AT AT AC AT AC 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 AT AT AT AT
37655 AT AT AT
1 AT AT AT
37661 GTACACACCA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:37637 original size:24 final size:24
Alignment explanation
Indices: 37605--37655 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
37595 GGTAAGATAC
37605 ATACATACATATATATATATATAT
1 ATACATACATATATATATATATAT
37629 ATACATACATATATATATATATAT
1 ATACATACATATATATATATATAT
37653 ATA
1 ATA
37656 TATATGTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (24 bp):
ATACATACATATATATATATATAT
Found at i:40840 original size:4 final size:4
Alignment explanation
Indices: 40831--40867 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
40821 TTATCCATAA
*
40831 ACAT ACAT ACAC ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
40868 TATAAGAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.22
Consensus pattern (4 bp):
ACAT
Found at i:41286 original size:21 final size:21
Alignment explanation
Indices: 41260--41314 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
41250 TAGAGGGTAG
* *
41260 GGTTTTAGTGTTTGAAGCATA
1 GGTTTTAGGGTTTGAAGAATA
41281 GGTTTTAGGGTTTGAAGAATA
1 GGTTTTAGGGTTTGAAGAATA
*
41302 AGTTTTAGGGTTT
1 GGTTTTAGGGTTT
41315 TAGATTTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.24, C:0.02, G:0.31, T:0.44
Consensus pattern (21 bp):
GGTTTTAGGGTTTGAAGAATA
Found at i:50536 original size:22 final size:22
Alignment explanation
Indices: 50511--50591 Score: 90
Period size: 22 Copynumber: 3.7 Consensus size: 22
50501 CAATACACGG
*
50511 AAGTGCCTTAGCACTGGTACTA
1 AAGTGCCTTAGCACTGATACTA
* * *
50533 AAGTGCCTCAGCACTAATACGA
1 AAGTGCCTTAGCACTGATACTA
* * * *
50555 AAATGCATTTGCACTGACACTA
1 AAGTGCCTTAGCACTGATACTA
50577 AAGTGCCTTAGCACT
1 AAGTGCCTTAGCACT
50592 ACTGACATAT
Statistics
Matches: 45, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (22 bp):
AAGTGCCTTAGCACTGATACTA
Found at i:53494 original size:19 final size:20
Alignment explanation
Indices: 53470--53515 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
53460 CAAAAAGACC
53470 CAATTTC-ACATTCTAACAT
1 CAATTTCAACATTCTAACAT
53489 CAATTTCAACATTCTAACAT
1 CAATTTCAACATTCTAACAT
*
53509 TAATTTC
1 CAATTTC
53516 CATCATAGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.37, C:0.24, G:0.00, T:0.39
Consensus pattern (20 bp):
CAATTTCAACATTCTAACAT
Done.