Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001968.1 Hibiscus syriacus cultivar Beakdansim tig00003976_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: 55014
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:4094 original size:21 final size:21
Alignment explanation
Indices: 4070--4135 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
4060 GTAAGTAATC
*
4070 GCAACGCGAATTGGGAAAATT
1 GCAACGCGAATTGGGAAAATA
* ** *
4091 GCAATGCGAA-TAAGTAAATA
1 GCAACGCGAATTGGGAAAATA
*
4111 GCAACGCGAATTGGGAAAATC
1 GCAACGCGAATTGGGAAAATA
4132 GCAA
1 GCAA
4136 TGCGGTACTG
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 15 0.44
21 19 0.56
ACGTcount: A:0.42, C:0.15, G:0.26, T:0.17
Consensus pattern (21 bp):
GCAACGCGAATTGGGAAAATA
Found at i:4095 original size:40 final size:41
Alignment explanation
Indices: 4049--4139 Score: 148
Period size: 41 Copynumber: 2.2 Consensus size: 41
4039 TGCGATTTTT
* *
4049 TCGCAATGCGAGTAAGT-AATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATAGCAACGCGAATTGGGAAAA
*
4089 TTGCAATGCGAATAAGTAAATAGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATAGCAACGCGAATTGGGAAAA
4130 TCGCAATGCG
1 TCGCAATGCG
4140 GTACTGACTA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
40 15 0.33
41 31 0.67
ACGTcount: A:0.38, C:0.16, G:0.26, T:0.19
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATAGCAACGCGAATTGGGAAAA
Found at i:4756 original size:20 final size:20
Alignment explanation
Indices: 4719--4775 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
4709 GATTCTCTCT
*
4719 TTGCGATAGTCGA-ATTCGCG
1 TTGCGATAGTC-ATTTTCGCG
*
4739 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCATTTTCGCG
**
4759 TTGCGATTTTCATTTTC
1 TTGCGATAGTCATTTTC
4776 AGAAACTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 1 0.03
20 31 0.97
ACGTcount: A:0.16, C:0.18, G:0.23, T:0.44
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCG
Found at i:6101 original size:18 final size:18
Alignment explanation
Indices: 6080--6124 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
6070 TCCACTTCGG
*
6080 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
6098 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
6116 GAGCCATCA
1 GAGCCATCA
6125 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:6644 original size:19 final size:20
Alignment explanation
Indices: 6607--6649 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
6597 AGTTTACATT
6607 CGATAGCCATTTCCGCGTTG
1 CGATAGCCATTTCCGCGTTG
*
6627 CGATAGTCATTT-CGCGTTG
1 CGATAGCCATTTCCGCGTTG
6646 CGAT
1 CGAT
6650 TTTAAGTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.16, C:0.26, G:0.26, T:0.33
Consensus pattern (20 bp):
CGATAGCCATTTCCGCGTTG
Found at i:9232 original size:24 final size:24
Alignment explanation
Indices: 9205--9258 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
9195 GTATTCGAAA
* *
9205 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
9229 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
9253 TTTGAT
1 TTTGAT
9259 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:9448 original size:12 final size:12
Alignment explanation
Indices: 9431--9455 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9421 TCATAATCCT
9431 GAAGAAGAAAAA
1 GAAGAAGAAAAA
9443 GAAGAAGAAAAA
1 GAAGAAGAAAAA
9455 G
1 G
9456 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:11765 original size:19 final size:19
Alignment explanation
Indices: 11743--11834 Score: 78
Period size: 19 Copynumber: 5.4 Consensus size: 19
11733 GGAAATTACT
11743 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
11762 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
11776 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
11795 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
11809 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
11828 ATCGCAA
1 ATCGCAA
11835 CGAGGGAATC
Statistics
Matches: 55, Mismatches: 8, Indels: 20
0.66 0.10 0.24
Matches are distributed among these distances:
14 18 0.33
15 2 0.04
16 4 0.07
17 4 0.07
18 2 0.04
19 25 0.45
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:11785 original size:33 final size:33
Alignment explanation
Indices: 11743--11854 Score: 163
Period size: 33 Copynumber: 3.4 Consensus size: 33
11733 GGAAATTACT
11743 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
11776 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
11808 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
11842 ATCGCAACGCGAA
1 ATCGCAATGCGAA
11855 TTTAATTTCG
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
32 1 0.01
33 67 0.97
34 1 0.01
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:11872 original size:19 final size:20
Alignment explanation
Indices: 11850--11892 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
11840 GAATCGCAAC
11850 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
11869 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
11889 GCGA
1 GCGA
11893 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:11877 original size:14 final size:14
Alignment explanation
Indices: 11878--11911 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
11868 TGCGATTTTC
11878 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
11892 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
11906 ATTTTC
1 ATTTTC
11912 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:12051 original size:14 final size:14
Alignment explanation
Indices: 12032--12068 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
12022 CATCAATTAA
12032 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
12046 ACAAATCACCTTTT
1 ACAAATCAACTTTT
12060 ACAAATCAA
1 ACAAATCAA
12069 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:12598 original size:20 final size:20
Alignment explanation
Indices: 12573--12625 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
12563 TCGCTATGTA
12573 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
12593 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
12613 TATCTCGTTGCGA
1 AATCGCGTTGCGA
12626 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:12659 original size:20 final size:20
Alignment explanation
Indices: 12634--12687 Score: 92
Period size: 20 Copynumber: 2.7 Consensus size: 20
12624 GATTTTGTAT
12634 TATCGCATTGCGATAGT-AA
1 TATCGCATTGCGATAGTCAA
12653 GTATCGCATTGCGATAGTCAA
1 -TATCGCATTGCGATAGTCAA
12674 TATCGCATTGCGAT
1 TATCGCATTGCGAT
12688 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 31 0.94
21 2 0.06
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTCAA
Found at i:12672 original size:61 final size:61
Alignment explanation
Indices: 12574--12690 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
12564 CGCTATGTAA
* * * * * *
12574 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAATATCGCATTGCGATTTTGTATT
* * *
12635 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAATATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAATATCGCATTGCGATTTT
12691 CCCAATTCGC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAATATCGCATTGCGATTTTGTATT
Found at i:12706 original size:61 final size:61
Alignment explanation
Indices: 12574--12708 Score: 146
Period size: 61 Copynumber: 2.2 Consensus size: 61
12564 CGCTATGTAA
* * * * * * ** *
12574 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAATATCGCATTGCGATTTTCCAAT
* * *
12635 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAATATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAATATCGCATTGCGATTTT-CCAAT
12697 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
12709 TTACTTATTC
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
61 58 0.97
62 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAATATCGCATTGCGATTTTCCAAT
Found at i:12798 original size:21 final size:21
Alignment explanation
Indices: 12758--12798 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
12748 ACTGTATACC
**
12758 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
12779 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
12799 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:13272 original size:3 final size:3
Alignment explanation
Indices: 13266--13305 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
13256 TACTATTAAA
*
13266 TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT
13306 CACTTAATCT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:26802 original size:56 final size:57
Alignment explanation
Indices: 26705--26813 Score: 159
Period size: 57 Copynumber: 1.9 Consensus size: 57
26695 GATGCATTCT
* *
26705 CCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTTGATGCAAAAG
1 CCATGCATCGATGCACTCAGAATATTTTCAAAACATCGAATGCATTTCATGCAAAAG
**
26762 CCATGCATCGATGCACGT-AGGCTATTTTC-AAACATCGAATGCATTTCATGCA
1 CCATGCATCGATGCAC-TCAGAATATTTTCAAAACATCGAATGCATTTCATGCA
26814 TCGATGCACA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
56 22 0.47
57 24 0.51
58 1 0.02
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (57 bp):
CCATGCATCGATGCACTCAGAATATTTTCAAAACATCGAATGCATTTCATGCAAAAG
Found at i:30261 original size:15 final size:15
Alignment explanation
Indices: 30239--30276 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
30229 GAAAATGAGT
30239 AAAG-AAAAAAGAGC
1 AAAGAAAAAAAGAGC
30253 AAAGAAAAAAAGAGC
1 AAAGAAAAAAAGAGC
30268 AAAGAAAAA
1 AAAGAAAAA
30277 CAAAGAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 4 0.17
15 19 0.83
ACGTcount: A:0.76, C:0.05, G:0.18, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAAAGAGC
Found at i:30293 original size:29 final size:29
Alignment explanation
Indices: 30230--30308 Score: 74
Period size: 29 Copynumber: 2.7 Consensus size: 29
30220 AAAAACAATG
* * *
30230 AAAATGAGTAAAGAAAAAAGAGCAAAGAA
1 AAAAAGAGCAAAGAAAAAAAAGCAAAGAA
30259 AAAAAGAGCAAAGAAAAACAAAG-AAA-AA
1 AAAAAGAGCAAAGAAAAA-AAAGCAAAGAA
*
30287 AATAAAGAG-AAACAAAGAAAAA
1 AA-AAAGAGCAAAGAAA-AAAAA
30309 TAGGACAAGA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
28 13 0.30
29 27 0.63
30 3 0.07
ACGTcount: A:0.75, C:0.05, G:0.16, T:0.04
Consensus pattern (29 bp):
AAAAAGAGCAAAGAAAAAAAAGCAAAGAA
Found at i:31519 original size:37 final size:37
Alignment explanation
Indices: 31464--31716 Score: 258
Period size: 37 Copynumber: 7.1 Consensus size: 37
31454 TTGGGTGTTG
** *
31464 TTTCTCTCGAAACAAAATTTTGTCTCACTTGAGCCATT
1 TTTCTCTTAAAAC-AAATTTTGTCTCACTTGAGACATT
*
31502 TTTCTCTTAAAACAAATTTCGTCTCACTTGAGACATT
1 TTTCTCTTAAAACAAATTTTGTCTCACTTGAGACATT
* ** *
31539 TTCCT-TTGGAAAA-AAA--TT-TCAAAGTT--G---TT
1 TTTCTCTT--AAAACAAATTTTGTCTCACTTGAGACATT
* *
31568 TTTCT-TAAAAACAAATTTTGTTTCACTTGAGACATT
1 TTTCTCTTAAAACAAATTTTGTCTCACTTGAGACATT
* *
31604 TGTCTCTTAAAACAAATTTTGTCTCACTTGATACATT
1 TTTCTCTTAAAACAAATTTTGTCTCACTTGAGACATT
* *
31641 TTCCTCTTAAAACAAATTTCGTCTCACTTGAGACATT
1 TTTCTCTTAAAACAAATTTTGTCTCACTTGAGACATT
* *
31678 TTCCTCTTAAAACAAATTTCGTCTCACTTGAGACATT
1 TTTCTCTTAAAACAAATTTTGTCTCACTTGAGACATT
31715 TT
1 TT
31717 CCTTCTGAAC
Statistics
Matches: 180, Mismatches: 23, Indels: 25
0.79 0.10 0.11
Matches are distributed among these distances:
27 4 0.02
28 3 0.02
29 7 0.04
30 2 0.01
31 4 0.02
32 1 0.01
33 1 0.01
34 5 0.03
35 1 0.01
36 8 0.04
37 129 0.72
38 15 0.08
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (37 bp):
TTTCTCTTAAAACAAATTTTGTCTCACTTGAGACATT
Found at i:31658 original size:102 final size:102
Alignment explanation
Indices: 31473--31660 Score: 290
Period size: 102 Copynumber: 1.8 Consensus size: 102
31463 GTTTCTCTCG
* *
31473 AAACAAAATTTTGTCTCACTTGAGCCATTTTTCTCTTAAAACAAATTTCGTCTCACTTGAGACAT
1 AAACAAAATTTTGTCTCACTTGAGACATTTGTCTCTTAAAACAAATTTCGTCTCACTTGAGACAT
31538 TTTCCTTTGGAAAAAAATTTCAAAGTTGTTTTTCTTAA
66 TTTCCTTT-GAAAAAAATTTCAAAGTTGTTTTTCTTAA
* * *
31576 AAAC-AAATTTTGTTTCACTTGAGACATTTGTCTCTTAAAACAAATTTTGTCTCACTTGATACAT
1 AAACAAAATTTTGTCTCACTTGAGACATTTGTCTCTTAAAACAAATTTCGTCTCACTTGAGACAT
31640 TTTCCTCTT-AAAACAAATTTC
66 TTTCCT-TTGAAAA-AAATTTC
31661 GTCTCACTTG
Statistics
Matches: 78, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
101 4 0.05
102 68 0.87
103 6 0.08
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (102 bp):
AAACAAAATTTTGTCTCACTTGAGACATTTGTCTCTTAAAACAAATTTCGTCTCACTTGAGACAT
TTTCCTTTGAAAAAAATTTCAAAGTTGTTTTTCTTAA
Found at i:31717 original size:37 final size:37
Alignment explanation
Indices: 31570--31733 Score: 240
Period size: 37 Copynumber: 4.4 Consensus size: 37
31560 AAGTTGTTTT
* *
31570 TCTTAAAAACAAATTTTGTTTCACTTGAGACATTTGT-C
1 TCTT-AAAACAAATTTCGTCTCACTTGAGACATTT-TCC
* *
31608 TCTTAAAACAAATTTTGTCTCACTTGATACATTTTCC
1 TCTTAAAACAAATTTCGTCTCACTTGAGACATTTTCC
31645 TCTTAAAACAAATTTCGTCTCACTTGAGACATTTTCC
1 TCTTAAAACAAATTTCGTCTCACTTGAGACATTTTCC
31682 TCTTAAAACAAATTTCGTCTCACTTGAGACATTTTCC
1 TCTTAAAACAAATTTCGTCTCACTTGAGACATTTTCC
* *
31719 TTCTGAACACAAATT
1 -TCTTAAAACAAATT
31734 CCAAAGTTGT
Statistics
Matches: 118, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
36 1 0.01
37 101 0.86
38 16 0.14
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.40
Consensus pattern (37 bp):
TCTTAAAACAAATTTCGTCTCACTTGAGACATTTTCC
Found at i:31936 original size:36 final size:36
Alignment explanation
Indices: 31834--31948 Score: 92
Period size: 36 Copynumber: 3.2 Consensus size: 36
31824 AAATATATAG
* *
31834 AACAAAATTGATCTCACATGAGATAGTTTTCC-TAA
1 AACAAAATTAATCTCACTTGAGATAGTTTTCCTTAA
* ** * * * * *
31869 GAACAAATTTTGTCACGCTAGAGACAATTTTCCTTAA
1 -AACAAAATTAATCTCACTTGAGATAGTTTTCCTTAA
*
31906 AACAAAATTAATCTCACTTGAGATTGTTTT-CTCTAA
1 AACAAAATTAATCTCACTTGAGATAGTTTTCCT-TAA
31942 AA-AAAAT
1 AACAAAAT
31949 GAATTTTGTC
Statistics
Matches: 59, Mismatches: 18, Indels: 5
0.72 0.22 0.06
Matches are distributed among these distances:
35 7 0.12
36 49 0.83
37 3 0.05
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (36 bp):
AACAAAATTAATCTCACTTGAGATAGTTTTCCTTAA
Found at i:32116 original size:66 final size:66
Alignment explanation
Indices: 31994--32209 Score: 296
Period size: 65 Copynumber: 3.3 Consensus size: 66
31984 ACAAAGTTTG
* * *
31994 TCTCCCTTGAGACAGTTTCCCTTGAAACACAAAATCTTT-AATTATGTTTCCATTGAAACAAATT
1 TCTCTCTTGAGACAGTTTCTCTTG-AA-ACAAAATCTTTGAATT-TGTTTCCCTTGAAACAAATT
*
32058 TTTT
63 TTTA
* *
32062 TCTCTCTTGAGACATTTTCTCTTGAAACAAAATCTTTGAATTTATTTCCCTTGAAACAAA-TTTT
1 TCTCTCTTGAGACAGTTTCTCTTGAAACAAAATCTTTGAATTTGTTTCCCTTGAAACAAATTTTT
32126 A
66 A
*
32127 TCTCTCTTGAGACAGTTTCTCTTGAAACAACATCTTTGAATTTGTTTCCCTTGAAACAAA-TTTT
1 TCTCTCTTGAGACAGTTTCTCTTGAAACAAAATCTTTGAATTTGTTTCCCTTGAAACAAATTTTT
*
32191 G
66 A
32192 TCTC-CTTTGAGACAGTTT
1 TCTCTC-TTGAGACAGTTT
32210 ACAGTTTCCC
Statistics
Matches: 136, Mismatches: 10, Indels: 7
0.89 0.07 0.05
Matches are distributed among these distances:
64 1 0.01
65 81 0.60
66 27 0.20
67 6 0.04
68 21 0.15
ACGTcount: A:0.28, C:0.20, G:0.10, T:0.42
Consensus pattern (66 bp):
TCTCTCTTGAGACAGTTTCTCTTGAAACAAAATCTTTGAATTTGTTTCCCTTGAAACAAATTTTT
A
Found at i:32266 original size:36 final size:36
Alignment explanation
Indices: 32210--32389 Score: 279
Period size: 36 Copynumber: 5.0 Consensus size: 36
32200 GAGACAGTTT
*
32210 ACAGTTTCCCTTGAACCAAATTTTGTCTCCCTTGAG
1 ACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAG
* *
32246 ATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAG
1 ACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAG
*
32282 ACAGTTTCCCTTGAAACAAATTTTGTCACCCTTGAG
1 ACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAG
* *
32318 ATAGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAG
1 ACAGTTTCCCTTGAAACAAA-TTTTGTCTCCCTTGAG
* *
32355 ACAGTTTCCCTTGAAACACATTTTATCTCCCTTGA
1 ACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGA
32390 AACAAATTTT
Statistics
Matches: 130, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
36 98 0.75
37 32 0.25
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (36 bp):
ACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAG
Found at i:32389 original size:94 final size:93
Alignment explanation
Indices: 32288--32479 Score: 294
Period size: 94 Copynumber: 2.1 Consensus size: 93
32278 TGAGACAGTT
* * * *
32288 TCCCTTGAAACAAATTTTGTCACCCTTGAGATAGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTG
1 TCCCTTGAAACAAATTTTGGCACCCTTGAGACAGTTTCCCTTGAAACAAA-TTTTGTCTCCCTTA
* *
32353 AGACAGTTTCCCTTGAAACACATTTTATC
65 AGACAATTTCCCTTGAAACAAATTTTATC
* *
32382 TCCCTTGAAACAAATTTTGGCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCCCTTAA
1 TCCCTTGAAACAAATTTTGGCACCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTAA
*
32447 GACAATTTCCCTTGAAACAAATTTTGTC
66 GACAATTTCCCTTGAAACAAATTTTATC
32475 TCCCT
1 TCCCT
32480 CGAGACAGTC
Statistics
Matches: 89, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
93 43 0.48
94 46 0.52
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (93 bp):
TCCCTTGAAACAAATTTTGGCACCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTAA
GACAATTTCCCTTGAAACAAATTTTATC
Found at i:32398 original size:130 final size:129
Alignment explanation
Indices: 32252--32497 Score: 402
Period size: 130 Copynumber: 1.9 Consensus size: 129
32242 TGAGATAATT
* *
32252 TCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCACCCTTGA
1 TCCCTTGAAACAAATTTTGGCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCACCCTTAA
* * * * *
32317 GATAGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACACATTTTATC
66 GACAATTTCCCTTGAAACAAA-TTTTGTCTCCCTCGAGACAGTCTCCCTTGAAACACATTTTATC
* *
32382 TCCCTTGAAACAAATTTTGGCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCCCTTAA
1 TCCCTTGAAACAAATTTTGGCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCACCCTTAA
32447 GACAATTTCCCTTGAAACAAATTTTGTCTCCCTCGAGACAGTCTCCCTTGA
66 GACAATTTCCCTTGAAACAAATTTTGTCTCCCTCGAGACAGTCTCCCTTGA
32498 GACAGTTTCC
Statistics
Matches: 107, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
129 27 0.25
130 80 0.75
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.36
Consensus pattern (129 bp):
TCCCTTGAAACAAATTTTGGCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCACCCTTAA
GACAATTTCCCTTGAAACAAATTTTGTCTCCCTCGAGACAGTCTCCCTTGAAACACATTTTATC
Found at i:32414 original size:57 final size:58
Alignment explanation
Indices: 32324--32444 Score: 190
Period size: 57 Copynumber: 2.1 Consensus size: 58
32314 TGAGATAGTT
* * *
32324 TCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACACATTTTATC
1 TCCCTTGAAACAAAGTTTTGGCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTATC
* *
32382 TCCCTTGAAACAAA-TTTTGGCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTTGTC
1 TCCCTTGAAACAAAGTTTTGGCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTATC
32439 TCCCTT
1 TCCCTT
32445 AAGACAATTT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
57 44 0.76
58 14 0.24
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (58 bp):
TCCCTTGAAACAAAGTTTTGGCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTATC
Found at i:32432 original size:36 final size:36
Alignment explanation
Indices: 32382--32497 Score: 178
Period size: 36 Copynumber: 3.2 Consensus size: 36
32372 ACATTTTATC
*
32382 TCCCTTGAAACAAATTTTGGCTCCCTTGAGACAGTT
1 TCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTT
* * *
32418 TCTCTTGAAACAAATTTTGTCTCCCTTAAGACAATT
1 TCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTT
* *
32454 TCCCTTGAAACAAATTTTGTCTCCCTCGAGACAGTC
1 TCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTT
32490 TCCCTTGA
1 TCCCTTGA
32498 GACAGTTTCC
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 71 1.00
ACGTcount: A:0.26, C:0.27, G:0.13, T:0.34
Consensus pattern (36 bp):
TCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTT
Found at i:32510 original size:15 final size:15
Alignment explanation
Indices: 32472--32512 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
32462 AACAAATTTT
*
32472 GTCTCCCTCGAGACA
1 GTCTCCCTTGAGACA
32487 GTCTCCCTTGAGACA
1 GTCTCCCTTGAGACA
*
32502 GTTTCCCTTGA
1 GTCTCCCTTGA
32513 AACAACCTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.17, C:0.34, G:0.20, T:0.29
Consensus pattern (15 bp):
GTCTCCCTTGAGACA
Found at i:36596 original size:29 final size:29
Alignment explanation
Indices: 36563--36624 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
36553 TTAGGTCAGT
36563 GACTTTATTACAAAGATTTAAAATTTGAA
1 GACTTTATTACAAAGATTTAAAATTTGAA
36592 GACTTTATTACAAAGATTTAAAATTTGAA
1 GACTTTATTACAAAGATTTAAAATTTGAA
36621 GACT
1 GACT
36625 CAATATTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (29 bp):
GACTTTATTACAAAGATTTAAAATTTGAA
Found at i:37474 original size:19 final size:19
Alignment explanation
Indices: 37434--37487 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 19
37424 GCAAAAAATG
* *
37434 GTATCGATACTATAATGGA
1 GTATCGATACCATAATAGA
37453 GTATCGATACCATAATATAGTA
1 GTATCGATACCAT-A-ATAG-A
37475 GTATCGATACCAT
1 GTATCGATACCAT
37488 GGTAGGGGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 12 0.40
20 1 0.03
21 3 0.10
22 14 0.47
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (19 bp):
GTATCGATACCATAATAGA
Found at i:37909 original size:54 final size:53
Alignment explanation
Indices: 37835--38165 Score: 298
Period size: 54 Copynumber: 6.1 Consensus size: 53
37825 TTGGCACAAA
* *
37835 GTGTGCAACTCACAGAATTCATCAT-ATGTTGATGAACAACCGTTTCGGCACTAT
1 GTGTGCAACTCAGA-AATTCATCATGA-GTTGATGAACAACCGTTACGGCACTAT
* * *
37889 ATGTGCAACTCATGAAATTCATCAT-ATGTTTATGAACAACCGTTTCGGCACTAT
1 GTGTGCAACTCA-GAAATTCATCATGA-GTTGATGAACAACCGTTACGGCACTAT
* *
37943 GTGTGCAACTCACGGAATTCATCATGAGTTGATGAACAAACG-TACAGGCACTAT
1 GTGTGCAACTCA-GAAATTCATCATGAGTTGATGAACAACCGTTAC-GGCACTAT
* * **
37997 GTGTGCAAC-CTATGGAATTCATCATGAGATT-ATGAACAACCGTAAATGCACTAT
1 GTGTGCAACTC-A-GAAATTCATCATGAG-TTGATGAACAACCGTTACGGCACTAT
* * * * * *
38051 ATGTGTAACCCACAGAATTCATCATGAGATGATGAACAACCG-TACAGACACTAT
1 GTGTGCAACTCAGA-AATTCATCATGAGTTGATGAACAACCGTTAC-GGCACTAT
* * ** *
38105 GTGTGCAACCCACGAAATTCATCATGCGTTGATGAATGACCGTATA-GGCACTAC
1 GTGTGCAACTCA-GAAATTCATCATGAGTTGATGAACAACCGT-TACGGCACTAT
38159 GTGTGCA
1 GTGTGCA
38166 TCTTAATAAA
Statistics
Matches: 232, Mismatches: 32, Indels: 26
0.80 0.11 0.09
Matches are distributed among these distances:
53 5 0.02
54 218 0.94
55 7 0.03
56 2 0.01
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (53 bp):
GTGTGCAACTCAGAAATTCATCATGAGTTGATGAACAACCGTTACGGCACTAT
Found at i:38016 original size:108 final size:107
Alignment explanation
Indices: 37835--38165 Score: 389
Period size: 108 Copynumber: 3.1 Consensus size: 107
37825 TTGGCACAAA
* *
37835 GTGTGCAACTCACAGAATTCATCAT-ATGTTGATGAACAACCGTTTC-GGCACTATATGTGCAA-
1 GTGTGCAACTCACAGAATTCATCATGA-GTTGATGAACAACCG-TACAGGCACTATGTGTGCAAC
* *
37897 CTCATGAAATTCATCATATGTTTATGAACAACCGTTTCGGCACTAT
64 CT-ATGAAATTCATCATA-GTTTATGAACAACCGTATAGGCACTAT
* *
37943 GTGTGCAACTCACGGAATTCATCATGAGTTGATGAACAAACGTACAGGCACTATGTGTGCAACCT
1 GTGTGCAACTCACAGAATTCATCATGAGTTGATGAACAACCGTACAGGCACTATGTGTGCAACCT
* * * *
38008 ATGGAATTCATCATGAGATTATGAACAACCGTAAATGCACTAT
66 ATGAAATTCATCAT-AGTTTATGAACAACCGTATAGGCACTAT
* * * * * *
38051 ATGTGTAACCCACAGAATTCATCATGAGATGATGAACAACCGTACAGACACTATGTGTGCAACCC
1 GTGTGCAACTCACAGAATTCATCATGAGTTGATGAACAACCGTACAGGCACTATGTGTGCAACCT
* * * ** *
38116 ACGAAATTCATCATGCGTTGATGAATGACCGTATAGGCACTAC
66 ATGAAATTCATCAT-AGTTTATGAACAACCGTATAGGCACTAT
38159 GTGTGCA
1 GTGTGCA
38166 TCTTAATAAA
Statistics
Matches: 189, Mismatches: 30, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
107 2 0.01
108 183 0.97
109 4 0.02
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (107 bp):
GTGTGCAACTCACAGAATTCATCATGAGTTGATGAACAACCGTACAGGCACTATGTGTGCAACCT
ATGAAATTCATCATAGTTTATGAACAACCGTATAGGCACTAT
Found at i:40148 original size:13 final size:14
Alignment explanation
Indices: 40132--40161 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
40122 CAAAATTATT
40132 TAAATAAATTC-AA
1 TAAATAAATTCTAA
40145 TAAATAAATTCTAA
1 TAAATAAATTCTAA
40159 TAA
1 TAA
40162 TTTAAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (14 bp):
TAAATAAATTCTAA
Found at i:40315 original size:2 final size:2
Alignment explanation
Indices: 40304--40351 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
40294 TAAATATGTT
40304 TA TA -A TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40343 TA TA TA TA T
1 TA TA TA TA T
40352 CGGGGGTGGG
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 3 0.07
2 40 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40317 original size:17 final size:17
Alignment explanation
Indices: 40308--40351 Score: 74
Period size: 15 Copynumber: 2.7 Consensus size: 17
40298 TATGTTTATA
40308 ATATATATATATAT-AT
1 ATATATATATATATAAT
40324 AT-TATATATATATAAT
1 ATATATATATATATAAT
40340 ATATATATATAT
1 ATATATATATAT
40352 CGGGGGTGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 11 0.42
16 6 0.23
17 9 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATATATATATATAAT
Found at i:40319 original size:19 final size:19
Alignment explanation
Indices: 40304--40351 Score: 75
Period size: 17 Copynumber: 2.7 Consensus size: 19
40294 TAAATATGTT
40304 TATA-ATATATATATAT-A
1 TATATATATATATATATAA
40321 TATAT-TATATATATATAA
1 TATATATATATATATATAA
40339 TATATATATATAT
1 TATATATATATAT
40352 CGGGGGTGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 15 0.54
18 6 0.21
19 7 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TATATATATATATATATAA
Found at i:40320 original size:13 final size:13
Alignment explanation
Indices: 40304--40350 Score: 71
Period size: 13 Copynumber: 3.8 Consensus size: 13
40294 TAAATATGTT
40304 TATA-ATAT-ATA
1 TATATATATAATA
*
40315 TATATATATATTA
1 TATATATATAATA
40328 TATATATATAATA
1 TATATATATAATA
40341 TATATATATA
1 TATATATATA
40351 TCGGGGGTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
11 4 0.12
12 4 0.12
13 24 0.75
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TATATATATAATA
Found at i:41223 original size:194 final size:192
Alignment explanation
Indices: 40866--41340 Score: 558
Period size: 194 Copynumber: 2.5 Consensus size: 192
40856 TAAACCGATT
* * * *** *
40866 TATTATACCGGTAACATTGAAATTTA-CTATTACATTATAATTATCATTTTGATG-TTTTGGAAT
1 TATTATACCGGTTACATTAAAAATTACCTATTACATTATAATTATGGGTTTGATGTTTTTGGGAT
* * * *
40929 CAACACAATTT-TAAATGTATCAACACTTTATGCGGCACCTCGTTGGGCATTCATCTGGAAAAAA
66 CGACAC-TTTTATAAATGTATCGACACTTTATGCGGCACCTCGTTGGGCATTAATCTGGAAAAAA
* * * * *
40993 GTATCGGCACATATTTAAAAAGTGTCGATACATTATGTTGACCTATTCTCAAATAAAATCGGTA
130 GTATCGACACATAATTAAAAAGTGTCGA-ACATTATGTAGACCTATTATCAAATAAAATCAGTA
*
41057 TATTATAACGGTTACATTACAAAATTACCTA-TACATTATAATTATGGGTTTGATGTTTTTGGGA
1 TATTATACCGGTTACATTA-AAAATTACCTATTACATTATAATTATGGGTTTGATGTTTTTGGGA
* *
41121 TCGAGACTTTTTATAAATGTATCGACACTTTATGCGTGCATCC-CTTTTGGGCATTAATTCTGGA
65 TCGACAC-TTTTATAAATGTATCGACACTTTATGCG-GCA-CCTC-GTTGGGCATTAA-TCTGGA
* **
41185 CAAAAGTATCGACACA-AATTAAACAAGTG-CG-ACATTATGTAGACCTATTATCTCATAAAATC
125 AAAAAGTATCGACACATAATTAAA-AAGTGTCGAACATTATGTAGACCTATTATCAAATAAAATC
41247 AGTA
189 AGTA
*
41251 TATTTTACCGGTTACATTGAAAAATTACCTATTAC-TTATAATTATGGGTTTCGATGTTTTTGGG
1 TATTATACCGGTTACATT-AAAAATTACCTATTACATTATAATTATGGGTTT-GATGTTTTTGGG
*
41315 ATCGATACTTTTATAAA--TATCGACAC
64 ATCGACACTTTTATAAATGTATCGACAC
41341 ATATGCTTAC
Statistics
Matches: 246, Mismatches: 26, Indels: 23
0.83 0.09 0.08
Matches are distributed among these distances:
191 16 0.07
192 36 0.15
193 18 0.07
194 104 0.42
195 27 0.11
196 20 0.08
197 25 0.10
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (192 bp):
TATTATACCGGTTACATTAAAAATTACCTATTACATTATAATTATGGGTTTGATGTTTTTGGGAT
CGACACTTTTATAAATGTATCGACACTTTATGCGGCACCTCGTTGGGCATTAATCTGGAAAAAAG
TATCGACACATAATTAAAAAGTGTCGAACATTATGTAGACCTATTATCAAATAAAATCAGTA
Found at i:44041 original size:19 final size:19
Alignment explanation
Indices: 44017--44065 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
44007 ATTACATTCA
44017 TATACAAAATTATAAATCG
1 TATACAAAATTATAAATCG
*
44036 TATACAAAATTATGAATCG
1 TATACAAAATTATAAATCG
44055 TATACAAAATT
1 TATACAAAATT
44066 TCACCTATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.51, C:0.10, G:0.06, T:0.33
Consensus pattern (19 bp):
TATACAAAATTATAAATCG
Found at i:45935 original size:193 final size:195
Alignment explanation
Indices: 45674--46152 Score: 618
Period size: 193 Copynumber: 2.5 Consensus size: 195
45664 GATTTTGATC
* * **
45674 TCGATTCTTTTTATAAATGTATCGACACTTTATGGGTGCACCCTTTTGGGCATTCATTCTGGACA
1 TCGATACTTTTAATAAATGTATCGACACTTTAT-GGTGCACCAGTTT-GGCATTCATTCTGGACA
* *
45739 AAAAGTATCGACATAAATT-AAAAGTGTTGATACATTATGTAGACCTATTTTCTCATAAAACCAA
64 AAAAGTATCGACATAAATTAAAAAGTGTTCATACATTATGTAGAACTATTTTCTCAT-AAACCAA
* *
45803 TAAATTTATATCGGTTACATTGTTAATTTACCTATTACATTGTAA-T-TTGGTTTCGATG-TTTT
128 TAAATTTATA-CGGTTACATTGTTAATTTACCTATTACATTATAATTATTGGATTCGATGTTTTT
45865 GGGA
192 GGGA
* *
45869 TCGATA-TAATTT-A-GAATGCATCGACACTTTATGCGTGCACCAGTTTGGCATTCATTCTGGAC
1 TCGATACT--TTTAATAAATGTATCGACACTTTATG-GTGCACCAGTTTGGCATTCATTCTGGAC
* * *
45931 AAAAAGTATCGACACAAATTTAAAAAGTG-TCATACATTATGTATAACTATTTTCTCATAAACCG
63 AAAAAGTATCGACATAAA-TTAAAAAGTGTTCATACATTATGTAGAACTATTTTCTCATAAACCA
* * *
45995 GTAAATTTGTACGGTTACATTGTTAATTTACCTATTACATTATAATTATTTGATTCGATGTTTTT
127 ATAAATTTATACGGTTACATTGTTAATTTACCTATTACATTATAATTATTGGATTCGATGTTTTT
46060 GGGA
192 GGGA
* * * *
46064 TCGATACTTTTAATAAATGTATCGACACTTTAT--TGCATCGGTTGGGCATTCATTCTAGACAAA
1 TCGATACTTTTAATAAATGTATCGACACTTTATGGTGCACCAGTTTGGCATTCATTCTGGACAAA
* *
46127 AAGAATCGACATAATTTAAAAAGTGT
66 AAGTATCGACATAAATTAAAAAGTGT
46153 CGATTGTGTT
Statistics
Matches: 248, Mismatches: 24, Indels: 26
0.83 0.08 0.09
Matches are distributed among these distances:
192 43 0.17
193 87 0.35
194 69 0.28
195 28 0.11
196 21 0.08
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (195 bp):
TCGATACTTTTAATAAATGTATCGACACTTTATGGTGCACCAGTTTGGCATTCATTCTGGACAAA
AAGTATCGACATAAATTAAAAAGTGTTCATACATTATGTAGAACTATTTTCTCATAAACCAATAA
ATTTATACGGTTACATTGTTAATTTACCTATTACATTATAATTATTGGATTCGATGTTTTTGGGA
Found at i:46054 original size:194 final size:194
Alignment explanation
Indices: 45674--46232 Score: 617
Period size: 193 Copynumber: 2.9 Consensus size: 194
45664 GATTTTGATC
* * **
45674 TCGATTCTTTTTATAAATGTATCGACACTTTATGGGTGCACCCTTTTGGGCATTCATTCTGGACA
1 TCGATACTTTTAATAAATGTATCGACACTTTAT-GGTGCACCAGTTT-GGCATTCATTCTGGACA
* * * *
45739 AAAAGTATCGACATAAA-TT-AAAAGTGTTGATACATTATGTAGACCTATTTTCTCATAAAACCA
64 AAAAGTATCGACA-AAATTTAAAAAGTG-TCATACATTATGTATAACTATTTTCTCAT-AAACCG
* * *
45802 ATAAATTTATATCGGTTACATTGTTAATTTACCTATTACATTGTAA-T-TTGGTTTCGATG-TTT
126 GTAAATTTATA-CGGTTACATTGTTAATTTACCTATTACATTATAATTATTGGATTCGATGTTTT
45864 TGGGA
190 TGGGA
* *
45869 TCGATA-TAATTT-A-GAATGCATCGACACTTTATGCGTGCACCAGTTTGGCATTCATTCTGGAC
1 TCGATACT--TTTAATAAATGTATCGACACTTTATG-GTGCACCAGTTTGGCATTCATTCTGGAC
45931 AAAAAGTATCGACACAAATTTAAAAAGTGTCATACATTATGTATAACTATTTTCTCATAAACCGG
63 AAAAAGTATCGACA-AAATTTAAAAAGTGTCATACATTATGTATAACTATTTTCTCATAAACCGG
* *
45996 TAAATTTGTACGGTTACATTGTTAATTTACCTATTACATTATAATTATTTGATTCGATGTTTTTG
127 TAAATTTATACGGTTACATTGTTAATTTACCTATTACATTATAATTATTGGATTCGATGTTTTTG
46061 GGA
192 GGA
* * * *
46064 TCGATACTTTTAATAAATGTATCGACACTTTAT--TGCATCGGTTGGGCATTCATTCTAGACAAA
1 TCGATACTTTTAATAAATGTATCGACACTTTATGGTGCACCAGTTTGGCATTCATTCTGGACAAA
* * * * * *
46127 AAGAATCGACATAATTTAAAAAGTGTC---GATTGTGT-TAAC-AGTTTTCTAATTAAAACGGTA
66 AAGTATCGACAAAATTTAAAAAGTGTCATACATTATGTATAACTA-TTTTCTCA-TAAACCGGTA
* * * ** * *
46187 TATATCTACGGTTACATTGAAAATTTACCTATTCCGTTATAATTAT
129 AATTTATACGGTTACATTGTTAATTTACCTATTACATTATAATTAT
46233 CTCAAATTTT
Statistics
Matches: 317, Mismatches: 34, Indels: 32
0.83 0.09 0.08
Matches are distributed among these distances:
187 1 0.00
188 11 0.03
189 54 0.17
192 48 0.15
193 85 0.27
194 69 0.22
195 28 0.09
196 21 0.07
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.38
Consensus pattern (194 bp):
TCGATACTTTTAATAAATGTATCGACACTTTATGGTGCACCAGTTTGGCATTCATTCTGGACAAA
AAGTATCGACAAAATTTAAAAAGTGTCATACATTATGTATAACTATTTTCTCATAAACCGGTAAA
TTTATACGGTTACATTGTTAATTTACCTATTACATTATAATTATTGGATTCGATGTTTTTGGGA
Found at i:47908 original size:11 final size:11
Alignment explanation
Indices: 47892--47916 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
47882 TATACATAAC
47892 AATGTTCAAAT
1 AATGTTCAAAT
47903 AATGTTCAAAT
1 AATGTTCAAAT
47914 AAT
1 AAT
47917 CAAACCCACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (11 bp):
AATGTTCAAAT
Found at i:48350 original size:16 final size:17
Alignment explanation
Indices: 48328--48370 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
48318 ATTCACATAA
48328 AAAATTAAATCGTATAC
1 AAAATTAAATCGTATAC
* *
48345 AAATTATAAATCTTATAC
1 AAAAT-TAAATCGTATAC
48363 AAAATTAA
1 AAAATTAA
48371 CCCTACATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.56, C:0.09, G:0.02, T:0.33
Consensus pattern (17 bp):
AAAATTAAATCGTATAC
Found at i:49906 original size:18 final size:18
Alignment explanation
Indices: 49883--49921 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
49873 TCCTCCTCAT
*
49883 TTCCTCCATCTTTTCTTC
1 TTCCTCCATATTTTCTTC
49901 TTCCTCCATATTTTCTTC
1 TTCCTCCATATTTTCTTC
49919 TTC
1 TTC
49922 ATATTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.08, C:0.36, G:0.00, T:0.56
Consensus pattern (18 bp):
TTCCTCCATATTTTCTTC
Found at i:52762 original size:179 final size:176
Alignment explanation
Indices: 52356--52722 Score: 533
Period size: 176 Copynumber: 2.1 Consensus size: 176
52346 CAAAAACTTA
* * ** *
52356 TCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAAGTATCGACACTTTTAACATATCTGGTGG
1 TCTTTTAAATTCCAAAAGTGTCGATACTTATAACAAA-TATCGACATTTTTAACATATCCAGTAG
* *
52421 CGCTTTACTGGTTTTGTCATTTTTAGACCGGTTTAATCATATTTTTACCTGTATATTATTATAGA
65 CGCTTTACTGGTTTTGTCATTTTTAGACCGCTTTAATCATATTTTTACATGTATATTATTATAGA
*
52486 TCGATCATTTTAAAGTATCGACACTTTATAGGCGCTATTACTGCTTC
130 TCGATCATTTTAAAGTATCGACACTTTATAGGCACTATTACTGCTTC
*
52533 TCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAATATCGACATTTTTAACATATCCAGTAGC
1 TCTTTTAAATTCCAAAAGTGTCGATACTTATAACAAATATCGACATTTTTAACATATCCAGTAGC
* * * *
52598 GCTTTACCT-GTTTTGTCATTTTTATACTGCTTTTATCATATTTTTACATGT-TATTTGTTAT-G
66 GCTTTA-CTGGTTTTGTCATTTTTAGACCGCTTTAATCATATTTTTACATGTATA-TTATTATAG
52660 AATCGATACATTTTATAAAGTATCGACACTTTATAGGCACTATTACTGCTTC
129 -ATCGAT-CA-TTT-TAAAGTATCGACACTTTATAGGCACTATTACTGCTTC
52712 TCTTTTAAATT
1 TCTTTTAAATT
52723 TTAACATACC
Statistics
Matches: 173, Mismatches: 11, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
175 3 0.02
176 79 0.46
177 41 0.24
178 3 0.02
179 47 0.27
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (176 bp):
TCTTTTAAATTCCAAAAGTGTCGATACTTATAACAAATATCGACATTTTTAACATATCCAGTAGC
GCTTTACTGGTTTTGTCATTTTTAGACCGCTTTAATCATATTTTTACATGTATATTATTATAGAT
CGATCATTTTAAAGTATCGACACTTTATAGGCACTATTACTGCTTC
Found at i:52772 original size:20 final size:20
Alignment explanation
Indices: 52744--52782 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
52734 GTGGTGCTTT
*
52744 ACCGATTTTGTCATTTTTAG
1 ACCGATTTTATCATTTTTAG
*
52764 ACCGTTTTTATCATTTTTA
1 ACCGATTTTATCATTTTTA
52783 CTTGTTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.15, G:0.10, T:0.54
Consensus pattern (20 bp):
ACCGATTTTATCATTTTTAG
Found at i:52851 original size:140 final size:141
Alignment explanation
Indices: 52579--52862 Score: 414
Period size: 140 Copynumber: 2.0 Consensus size: 141
52569 ATATCGACAT
* *
52579 TTTTAACATATCCAGTAGCGCTTTACCTGTTTTGTCATTTTTATACTGCTTTTATCATATTTTTA
1 TTTTAACATATCCAGTAGCGCTTTACCTGTTTTGTCATTTTTAGACCGCTTTTATCA-ATTTTTA
52644 CATGTTATTTGTTATGAATCGATACATTTTATAAAGTATCGACACTTTATAGGCACTATTACTGC
65 CATGTTATTTGTTATGAATCGATACATTTTATAAAGTATCGACACTTTATAGGCACTATTACTGC
52709 TTCTCTTTTAAA
130 TTCTCTTTTAAA
* * * *
52721 TTTTAACATA-CCGGTGGTGCTTTACC-GATTTTGTCATTTTTAGACCGTTTTTATC-ATTTTTA
1 TTTTAACATATCCAGTAGCGCTTTACCTG-TTTTGTCATTTTTAGACCGCTTTTATCAATTTTTA
* * **
52783 CTTGTTATATTGTTATGGATC-ATACATTTTTATAAAGTATCGACACTTTATAGGCGTTATTACT
65 CATGTTAT-TTGTTATGAATCGATACA-TTTTATAAAGTATCGACACTTTATAGGCACTATTACT
52847 GCTTCTCTTTTAAA
128 GCTTCTCTTTTAAA
52861 TT
1 TT
52863 CTAAAAGTTT
Statistics
Matches: 129, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
139 19 0.15
140 63 0.49
141 37 0.29
142 10 0.08
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.48
Consensus pattern (141 bp):
TTTTAACATATCCAGTAGCGCTTTACCTGTTTTGTCATTTTTAGACCGCTTTTATCAATTTTTAC
ATGTTATTTGTTATGAATCGATACATTTTATAAAGTATCGACACTTTATAGGCACTATTACTGCT
TCTCTTTTAAA
Found at i:52895 original size:20 final size:20
Alignment explanation
Indices: 52866--52915 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
52856 TTAAATTCTA
*
52866 AAAGTTTCGATACTTATAAT
1 AAAGTATCGATACTTATAAT
52886 AAAGTATCGATACTTATAAT
1 AAAGTATCGATACTTATAAT
52906 AAAGTATCGA
1 AAAGTATCGA
52916 CTTTCAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (20 bp):
AAAGTATCGATACTTATAAT
Done.