Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003139.1 Hibiscus syriacus cultivar Beakdansim tig00006589_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: 92499
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1925 original size:18 final size:18
Alignment explanation
Indices: 1902--1937 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1892 AAGCAAAAGG
*
1902 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
1920 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
1938 CAACCGGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:2337 original size:20 final size:20
Alignment explanation
Indices: 2294--2338 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
2284 TCGCAAACTG
*
2294 AATTTGACTATCGCGTAGCG
1 AATTTGACTATCGCGTAGCA
*
2314 AATTTGACTTTCGCGTTA-CA
1 AATTTGACTATCGCG-TAGCA
2334 AATTT
1 AATTT
2339 ACCTTCAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.38
Consensus pattern (20 bp):
AATTTGACTATCGCGTAGCA
Found at i:2441 original size:25 final size:25
Alignment explanation
Indices: 2403--2454 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
2393 AAATCAATTA
*
2403 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
*
2428 AACATTGTTATGGGTATATTATTTG
1 AACATTGTTATGGGTACATTATTTG
2453 AA
1 AA
2455 AAAATAATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.06, G:0.21, T:0.44
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:2860 original size:18 final size:18
Alignment explanation
Indices: 2839--2875 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2829 GTAATTGGAG
2839 TTTGAATTTCAATTTCAA
1 TTTGAATTTCAATTTCAA
* *
2857 TTTGAGTTTGAATTTCAA
1 TTTGAATTTCAATTTCAA
2875 T
1 T
2876 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.08, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTCAATTTCAA
Found at i:2882 original size:24 final size:24
Alignment explanation
Indices: 2831--2883 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
2821 TTTCATATGT
* * *
2831 AATTGGAGTTTGAATTTCAATTTC
1 AATTTGAGTTTGAATTTCAATATA
2855 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTCAATATA
2879 AATTT
1 AATTT
2884 CGGCTCCACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTCAATATA
Found at i:3230 original size:39 final size:39
Alignment explanation
Indices: 3187--3273 Score: 165
Period size: 39 Copynumber: 2.2 Consensus size: 39
3177 TCCGATGCTC
3187 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
*
3226 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
3265 ATCAAAATC
1 ATCAAAATC
3274 TACAACTTGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.47, C:0.21, G:0.15, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:3471 original size:20 final size:20
Alignment explanation
Indices: 3446--3488 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
3436 ATGTTGCGAT
* *
3446 CAACGCGAAATTTAAATTCG
1 CAACGCGAAAGTCAAATTCG
3466 CAACGCGAAAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
3486 CAA
1 CAA
3489 ACCGAAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.42, C:0.23, G:0.16, T:0.19
Consensus pattern (20 bp):
CAACGCGAAAGTCAAATTCG
Found at i:3661 original size:66 final size:60
Alignment explanation
Indices: 3591--3727 Score: 184
Period size: 66 Copynumber: 2.2 Consensus size: 60
3581 TTTTAGAAAC
*
3591 AACAAATCAACTTTTACAAATCAATTAAACAAGTCAAAAAATAATTCTTATTTACAAATCAAATT
1 AACAAATCAACTTTTACAAATCAATT----AA-TCAAAAAATAAATCTTATTTACAAATC-AATT
3656 A
60 A
* **
3657 AACAAATCAACTTTTACAAATCAATTAATCAAAAAATAAATCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAATCAAAAAATAAATCTTATTTACAAATCAATTA
3717 AACAAATCAAC
1 AACAAATCAAC
3728 ATAAAATTCA
Statistics
Matches: 67, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
60 16 0.24
61 23 0.34
62 2 0.03
66 26 0.39
ACGTcount: A:0.52, C:0.18, G:0.01, T:0.30
Consensus pattern (60 bp):
AACAAATCAACTTTTACAAATCAATTAATCAAAAAATAAATCTTATTTACAAATCAATTA
Found at i:3753 original size:61 final size:60
Alignment explanation
Indices: 3591--3747 Score: 158
Period size: 66 Copynumber: 2.5 Consensus size: 60
3581 TTTTAGAAAC
* *
3591 AACAAATCAACTTTTACAAATCAATTAAACAAGTCAAAAAATAATTCTTATTTACAAATCAAATT
1 AACAAATCAAC-TATACAAATCAATT--A-AA--CAAAAAATAAATCTTATTTACAAATCAAATT
3656 A
60 A
* * * **
3657 AACAAATCAACTTTTACAAATCAATTAATCAAAAAATAAATCTTATTTCCTCATC-AATTA
1 AACAAATCAAC-TATACAAATCAATTAAACAAAAAATAAATCTTATTTACAAATCAAATTA
3717 AACAAATCAAC-ATA-AAATTCAATTAAACAAA
1 AACAAATCAACTATACAAA-TCAATTAAACAAA
3748 GAAAAAAAAG
Statistics
Matches: 83, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
57 3 0.04
58 14 0.17
60 16 0.19
61 22 0.27
63 1 0.01
64 1 0.01
66 26 0.31
ACGTcount: A:0.54, C:0.17, G:0.01, T:0.29
Consensus pattern (60 bp):
AACAAATCAACTATACAAATCAATTAAACAAAAAATAAATCTTATTTACAAATCAAATTA
Found at i:5110 original size:21 final size:21
Alignment explanation
Indices: 5086--5181 Score: 97
Period size: 21 Copynumber: 4.6 Consensus size: 21
5076 GGCGGGACCA
*
5086 CTTGAACGATGACAGGGGCCT
1 CTTGAACGATGAGAGGGGCCT
* * *
5107 CTTGAACGGTGGGAGGGGCTT
1 CTTGAACGATGAGAGGGGCCT
*
5128 CTTCG-ATGATGAGAGGGGCCT
1 CTT-GAACGATGAGAGGGGCCT
*
5149 CTTGAACGAT-AGGAGGTGCCT
1 CTTGAACGATGA-GAGGGGCCT
*
5170 CTTGAATGATGA
1 CTTGAACGATGA
5182 TAGGTGCATC
Statistics
Matches: 60, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
20 2 0.03
21 56 0.93
22 2 0.03
ACGTcount: A:0.22, C:0.18, G:0.36, T:0.24
Consensus pattern (21 bp):
CTTGAACGATGAGAGGGGCCT
Found at i:5164 original size:42 final size:42
Alignment explanation
Indices: 5086--5181 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 42
5076 GGCGGGACCA
* * * *
5086 CTTGAACGATGACAGGGGCCTCTTGAACGGTGGGAGGGGCTT
1 CTTGAATGATGACAGGGGCCTCTTGAACGATAGGAGGGGCCT
* *
5128 CTTCG-ATGATGAGAGGGGCCTCTTGAACGATAGGAGGTGCCT
1 CTT-GAATGATGACAGGGGCCTCTTGAACGATAGGAGGGGCCT
5170 CTTGAATGATGA
1 CTTGAATGATGA
5182 TAGGTGCATC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
41 1 0.02
42 44 0.96
43 1 0.02
ACGTcount: A:0.22, C:0.18, G:0.36, T:0.24
Consensus pattern (42 bp):
CTTGAATGATGACAGGGGCCTCTTGAACGATAGGAGGGGCCT
Found at i:7650 original size:22 final size:22
Alignment explanation
Indices: 7622--7672 Score: 86
Period size: 22 Copynumber: 2.3 Consensus size: 22
7612 GATGGAGATA
7622 GACGGATTTCGTCAGAA-ATGGG
1 GACGGATTTCGTC-GAAGATGGG
7644 GACGGATTTCGTCGAAGATGGG
1 GACGGATTTCGTCGAAGATGGG
7666 GACGGAT
1 GACGGAT
7673 GTCGCCGTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 3 0.11
22 25 0.89
ACGTcount: A:0.25, C:0.14, G:0.39, T:0.22
Consensus pattern (22 bp):
GACGGATTTCGTCGAAGATGGG
Found at i:7825 original size:20 final size:20
Alignment explanation
Indices: 7800--7844 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
7790 GCGTAAAAAC
*
7800 ATTTGACTTTCACGTTGCGA
1 ATTTGACTATCACGTTGCGA
*
7820 ATTTGACTATCGCGTTGCGA
1 ATTTGACTATCACGTTGCGA
7840 ATTTG
1 ATTTG
7845 GAAAATCGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.40
Consensus pattern (20 bp):
ATTTGACTATCACGTTGCGA
Found at i:8304 original size:64 final size:64
Alignment explanation
Indices: 8199--8325 Score: 218
Period size: 64 Copynumber: 2.0 Consensus size: 64
8189 AATATTGAGA
* * *
8199 GCCCTCCCACCCACATTCCACGTTGTATCAAATATCATGCAAATTGTTGGGAAGAAACCAAACT
1 GCCCTCCCACCCACATTCCACGTTGCAACAAATATCATGCAAATTGTTGGAAAGAAACCAAACT
*
8263 GCCCTCCCACCCACATTCCACGTTGCAACAAATATCCTGCAAATTGTTGGAAAGAAACCAAAC
1 GCCCTCCCACCCACATTCCACGTTGCAACAAATATCATGCAAATTGTTGGAAAGAAACCAAAC
8326 AACAGAACAC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 59 1.00
ACGTcount: A:0.34, C:0.31, G:0.13, T:0.21
Consensus pattern (64 bp):
GCCCTCCCACCCACATTCCACGTTGCAACAAATATCATGCAAATTGTTGGAAAGAAACCAAACT
Found at i:9668 original size:42 final size:42
Alignment explanation
Indices: 9552--9913 Score: 415
Period size: 42 Copynumber: 8.7 Consensus size: 42
9542 CAAAATACTA
* * * *
9552 TACTTTAGTGGCGTTTTTATA-AAAACGCCGCTATA-AACTAG
1 TACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGAA-TCG
* **
9593 TA-TTTTAGTGGCGTTTTTATA-CAAACGTTGCTATAGAGAT-G
1 TACTTTT-GTGGCGTTTTAATACCAAACGCCGCTATAGA-ATCG
* * *
9634 TACTTTTGTGGCGTTTTAATACCAAACGACGCTATAGACTCA
1 TACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGAATCG
* *
9676 TACTTTAGTGGCATTTT--TACACAAACGCCGCTATAGACA-CG
1 TACTTTTGTGGCGTTTTAATAC-CAAACGCCGCTATAGA-ATCG
9717 TACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGACA-CG
1 TACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGA-ATCG
*
9759 TACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGATTCG
1 TACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGAATCG
*
9801 TACTTTAGTGGCGTTTT--TACACAAACGCCGCTATAGACA-CG
1 TACTTTTGTGGCGTTTTAATAC-CAAACGCCGCTATAGA-ATCG
* *
9842 TACTTTTGTGGCGTTTTAATAACAAACGCCGCTATAGACTCG
1 TACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGAATCG
*
9884 TACTTTAGTGGCGTTTTAATACCAAACGCC
1 TACTTTTGTGGCGTTTTAATACCAAACGCC
9914 ACAATTGTCA
Statistics
Matches: 281, Mismatches: 24, Indels: 31
0.84 0.07 0.09
Matches are distributed among these distances:
40 9 0.03
41 109 0.39
42 157 0.56
43 6 0.02
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (42 bp):
TACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGAATCG
Found at i:9687 original size:83 final size:83
Alignment explanation
Indices: 9552--9913 Score: 441
Period size: 83 Copynumber: 4.4 Consensus size: 83
9542 CAAAATACTA
* * * *
9552 TACTTTAGTGGCGTTTTTATA-AAAACGCCGCTATA-A-ACTAGTATTTTAGTGGCGTTTTTATA
1 TACTTTAGTGGCGTTTTAATACCAAACGCCGCTATAGACAC-A-TACTTTAGTGGCGTTTTAATA
**
9614 CAAACGTTGCTATAGAGAT-G
64 CAAACGCCGCTATAGA-ATCG
* * * * * *
9634 TACTTTTGTGGCGTTTTAATACCAAACGACGCTATAGACTCATACTTTAGTGGCATTTTTACACA
1 TACTTTAGTGGCGTTTTAATACCAAACGCCGCTATAGACACATACTTTAGTGGCGTTTTAATACA
9699 AACGCCGCTATAGACA-CG
66 AACGCCGCTATAGA-ATCG
* * *
9717 TACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACC
1 TACTTTAGTGGCGTTTTAATACCAAACGCCGCTATAGACACATACTTTAGTGGCGTTTTAATA-C
*
9782 AAACGCCGCTATAGATTCG
65 AAACGCCGCTATAGAATCG
* *
9801 TACTTTAGTGGCGTTTT--TACACAAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATAA
1 TACTTTAGTGGCGTTTTAATAC-CAAACGCCGCTATAGACACATACTTTAGTGGCGTTTTAAT-A
*
9864 CAAACGCCGCTATAGACTCG
64 CAAACGCCGCTATAGAATCG
9884 TACTTTAGTGGCGTTTTAATACCAAACGCC
1 TACTTTAGTGGCGTTTTAATACCAAACGCC
9914 ACAATTGTCA
Statistics
Matches: 249, Mismatches: 21, Indels: 18
0.86 0.07 0.06
Matches are distributed among these distances:
82 22 0.09
83 178 0.71
84 45 0.18
85 4 0.02
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (83 bp):
TACTTTAGTGGCGTTTTAATACCAAACGCCGCTATAGACACATACTTTAGTGGCGTTTTAATACA
AACGCCGCTATAGAATCG
Found at i:9912 original size:125 final size:125
Alignment explanation
Indices: 9533--9913 Score: 547
Period size: 125 Copynumber: 3.1 Consensus size: 125
9523 CGTTTTTGAA
* * * * * *
9533 CAAACGCCGCAAAATACT-ATACTTTAGTGGCGTTTTTATAAAAACGCCGCTATAAACTA-GTA-
1 CAAACGCCGCTATAGACTCATACTTTAGTGGCGTTTTTACACAAACGCCGCTATAGAC-ACGTAC
* ** *
9595 TTTTAGTGGCGTTTTTAT-ACAAACGTTGCTATAGAGAT-GTACTTTTGTGGCGTTTTAATAC
65 TTTT-GTGGCGTTTTAATAACAAACGCCGCTATAGA-CTCGTACTTTTGTGGCGTTTTAATAC
* *
9656 CAAACGACGCTATAGACTCATACTTTAGTGGCATTTTTACACAAACGCCGCTATAGACACGTACT
1 CAAACGCCGCTATAGACTCATACTTTAGTGGCGTTTTTACACAAACGCCGCTATAGACACGTACT
* *
9721 TTTGTGGCGTTTTAATACCAAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATAC
66 TTTGTGGCGTTTTAATAACAAACGCCGCTATAGACTCGTACTTTTGTGGCGTTTTAATAC
* *
9781 CAAACGCCGCTATAGATTCGTACTTTAGTGGCGTTTTTACACAAACGCCGCTATAGACACGTACT
1 CAAACGCCGCTATAGACTCATACTTTAGTGGCGTTTTTACACAAACGCCGCTATAGACACGTACT
*
9846 TTTGTGGCGTTTTAATAACAAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTAATAC
66 TTTGTGGCGTTTTAATAACAAACGCCGCTATAGACTCGTACTTTTGTGGCGTTTTAATAC
9906 CAAACGCC
1 CAAACGCC
9914 ACAATTGTCA
Statistics
Matches: 232, Mismatches: 21, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
123 15 0.06
124 50 0.22
125 167 0.72
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.32
Consensus pattern (125 bp):
CAAACGCCGCTATAGACTCATACTTTAGTGGCGTTTTTACACAAACGCCGCTATAGACACGTACT
TTTGTGGCGTTTTAATAACAAACGCCGCTATAGACTCGTACTTTTGTGGCGTTTTAATAC
Found at i:13608 original size:21 final size:21
Alignment explanation
Indices: 13566--13624 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
13556 TGATTTATTA
**
13566 TTATGGATTTCATTTTTCTTG
1 TTATGGATTTCAAGTTTCTTG
* *
13587 TTATGGATTTTAAGTTTGTTG
1 TTATGGATTTCAAGTTTCTTG
* *
13608 TTATCGATGTCAAGTTT
1 TTATGGATTTCAAGTTT
13625 ATTGGAAAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.19, C:0.07, G:0.19, T:0.56
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTCTTG
Found at i:13824 original size:43 final size:43
Alignment explanation
Indices: 13777--14001 Score: 301
Period size: 43 Copynumber: 5.3 Consensus size: 43
13767 ACCAGATCTT
* *
13777 TTGCGGTGTTTGTGGGAAAAACGCCGCTAAATATCAAGACCTA
1 TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATATCAACACCTA
* *
13820 TTGCGGCGTTTAT-GGACAAAACGCTGCTAAATATCAACACCTA
1 TTGCGGCGTTTGTGGGA-AAAACGCCGCTAAATATCAACACCTA
* * * *
13863 TTGCGGTGTTTGTGGAAAAAACGCCGCTAAATCTCAACACATA
1 TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATATCAACACCTA
* * *
13906 TTGCGACGTTTGTTGGAAAAACGCCGCTAAATCTCAACACCTA
1 TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATATCAACACCTA
* * *
13949 TTGCGGCGTTTGTTGGAAAAA-GCCACCAAATATCAACACCTA
1 TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATATCAACACCTA
13991 TTGCGGCGTTT
1 TTGCGGCGTTT
14002 TTTGTTACCA
Statistics
Matches: 161, Mismatches: 19, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
42 32 0.20
43 127 0.79
44 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.26
Consensus pattern (43 bp):
TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATATCAACACCTA
Found at i:15760 original size:29 final size:29
Alignment explanation
Indices: 15718--15777 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
15708 GTGTTGCCGT
15718 AGGTCGCCATGGCATCCAGGCAAGCTTGG
1 AGGTCGCCATGGCATCCAGGCAAGCTTGG
* *
15747 AGGTCGCCATGGCATCCGGGCGAGCTTGG
1 AGGTCGCCATGGCATCCAGGCAAGCTTGG
15776 AG
1 AG
15778 TCTCTGCATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.18, C:0.27, G:0.38, T:0.17
Consensus pattern (29 bp):
AGGTCGCCATGGCATCCAGGCAAGCTTGG
Found at i:15937 original size:29 final size:28
Alignment explanation
Indices: 15895--15978 Score: 132
Period size: 29 Copynumber: 2.9 Consensus size: 28
15885 GGCAACGTGG
15895 GTAGGTCGCCAGGGAATCCCAGCGACATT
1 GTAGGTCGCCAGGG-ATCCCAGCGACATT
15924 GTAGGTCGCCAGGGCATCCCAGCGACATT
1 GTAGGTCGCCAGGG-ATCCCAGCGACATT
*
15953 GTAGGTCGCCAAGGGATCCCAACGAC
1 GTAGGTCGCC-AGGGATCCCAGCGAC
15979 CTATGCCTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
29 48 0.92
30 4 0.08
ACGTcount: A:0.24, C:0.30, G:0.31, T:0.15
Consensus pattern (28 bp):
GTAGGTCGCCAGGGATCCCAGCGACATT
Found at i:16073 original size:12 final size:11
Alignment explanation
Indices: 16053--16088 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
16043 GAAATCAGCT
16053 GCATTATTGCA
1 GCATTATTGCA
*
16064 GCACTTATTGCT
1 GCA-TTATTGCA
16076 GCATTATTGCA
1 GCATTATTGCA
16087 GC
1 GC
16089 CCGTGAACGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.36
Consensus pattern (11 bp):
GCATTATTGCA
Found at i:16222 original size:15 final size:15
Alignment explanation
Indices: 16202--16232 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
16192 AGAAAGAAAG
16202 GGAGAAAATAGCAAA
1 GGAGAAAATAGCAAA
*
16217 GGAGAAGATAGCAAA
1 GGAGAAAATAGCAAA
16232 G
1 G
16233 AAAAGAGGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.06, G:0.32, T:0.06
Consensus pattern (15 bp):
GGAGAAAATAGCAAA
Found at i:16311 original size:8 final size:9
Alignment explanation
Indices: 16281--16318 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
16271 GGTAAGTTTT
16281 TTTTAATTA
1 TTTTAATTA
16290 TTTTAATTA
1 TTTTAATTA
*
16299 GTTT-ATTA
1 TTTTAATTA
16307 TTTTAAATTA
1 TTTT-AATTA
16317 TT
1 TT
16319 AGTTTGTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 7 0.28
9 12 0.48
10 6 0.24
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (9 bp):
TTTTAATTA
Found at i:16440 original size:28 final size:27
Alignment explanation
Indices: 16401--16453 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
16391 ATATTAAAAA
16401 AATAATTAATTAGTGTGTTAGTTAGTCT
1 AATAATTAATTAGTGTG-TAGTTAGTCT
* *
16429 AATATTTAATTAGTTTGTAGTTAGT
1 AATAATTAATTAGTGTGTAGTTAGT
16454 TAAATAGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.32, C:0.02, G:0.17, T:0.49
Consensus pattern (27 bp):
AATAATTAATTAGTGTGTAGTTAGTCT
Found at i:16459 original size:27 final size:29
Alignment explanation
Indices: 16400--16464 Score: 82
Period size: 27 Copynumber: 2.3 Consensus size: 29
16390 TATATTAAAA
16400 AAATAATTAATTAGTGTGTTAGTTAGTCT
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
* *
16429 -AATATTTAATTAGTTTG-TAGTTAGT-T
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
*
16455 AAATAGTTAA
1 AAATAATTAA
16465 GTTATATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 1 0.03
27 16 0.50
28 15 0.47
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.46
Consensus pattern (29 bp):
AAATAATTAATTAGTGTGTTAGTTAGTCT
Found at i:16600 original size:26 final size:28
Alignment explanation
Indices: 16573--16634 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 28
16563 ATAAAAGAAT
*
16573 AATTATT-TAAATTAGTTTATTGTTATA
1 AATTATTATAAATTAGTTTATTATTATA
*
16600 AATTATTAGTTAATTAGTTTATTATTATA
1 AATTATTA-TAAATTAGTTTATTATTATA
16629 AATTAT
1 AATTAT
16635 GGTAAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 7 0.23
29 24 0.77
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (28 bp):
AATTATTATAAATTAGTTTATTATTATA
Found at i:16684 original size:21 final size:21
Alignment explanation
Indices: 16659--16698 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
16649 GTTAATTAGT
16659 TTGTTAGTTTAAGTTATATTA
1 TTGTTAGTTTAAGTTATATTA
*
16680 TTGTTAGTTTACGTTATAT
1 TTGTTAGTTTAAGTTATAT
16699 CATATAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.03, G:0.15, T:0.57
Consensus pattern (21 bp):
TTGTTAGTTTAAGTTATATTA
Found at i:16944 original size:30 final size:30
Alignment explanation
Indices: 16876--17001 Score: 94
Period size: 30 Copynumber: 4.4 Consensus size: 30
16866 ATTAGTTAAT
* * *
16876 TAGTTTTTTAGTAGTAAATTATAATTAAA-AA
1 TAGTTTATTAGT-TTAAGTTAT-ATTAAAGAA
*
16907 TCA-TTTATTAGTTTAATTTATATTAAAGAA
1 T-AGTTTATTAGTTTAAGTTATATTAAAGAA
*
16937 TAGTTTATTA-ATTAACGTTATATTAAAGAA
1 TAGTTTATTAGTTTAA-GTTATATTAAAGAA
16967 TA---T-TTA----AAGTTATATTAAAGAA
1 TAGTTTATTAGTTTAAGTTATATTAAAGAA
16989 TAGTTTATTAGTT
1 TAGTTTATTAGTT
17002 GTTTAAGGGA
Statistics
Matches: 79, Mismatches: 5, Indels: 24
0.73 0.05 0.22
Matches are distributed among these distances:
22 16 0.20
23 2 0.03
25 1 0.01
26 6 0.08
27 1 0.01
29 11 0.14
30 32 0.41
31 9 0.11
32 1 0.01
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.47
Consensus pattern (30 bp):
TAGTTTATTAGTTTAAGTTATATTAAAGAA
Found at i:16978 original size:22 final size:23
Alignment explanation
Indices: 16948--16995 Score: 80
Period size: 22 Copynumber: 2.1 Consensus size: 23
16938 AGTTTATTAA
*
16948 TTAACGTTATATTAAAGAATA-T
1 TTAAAGTTATATTAAAGAATAGT
16970 TTAAAGTTATATTAAAGAATAGT
1 TTAAAGTTATATTAAAGAATAGT
16993 TTA
1 TTA
16996 TTAGTTGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.46, C:0.02, G:0.10, T:0.42
Consensus pattern (23 bp):
TTAAAGTTATATTAAAGAATAGT
Found at i:18295 original size:18 final size:18
Alignment explanation
Indices: 18272--18307 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
18262 TATTTTTAAT
18272 TATTATTTAAATTAAATA
1 TATTATTTAAATTAAATA
* *
18290 TATTATTTGATTTAAATA
1 TATTATTTAAATTAAATA
18308 AATTTTATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
TATTATTTAAATTAAATA
Found at i:18304 original size:23 final size:23
Alignment explanation
Indices: 18276--18321 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
18266 TTTAATTATT
18276 ATTTAAATTAAA-TATATTATTTG
1 ATTTAAA-TAAATTATATTATTTG
*
18299 ATTTAAATAAATTTTATTATTTG
1 ATTTAAATAAATTATATTATTTG
18322 TAATTTTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (23 bp):
ATTTAAATAAATTATATTATTTG
Found at i:18320 original size:18 final size:21
Alignment explanation
Indices: 18270--18320 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
18260 GTTATTTTTA
18270 ATTATTATTTAAATTAAATAT
1 ATTATTATTTAAATTAAATAT
18291 ATTATTTGATTTAAA-TAAAT-T
1 ATTA-TT-ATTTAAATTAAATAT
18312 -TTATTATTT
1 ATTATTATTT
18321 GTAATTTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
18 4 0.14
19 2 0.07
20 3 0.11
21 5 0.18
22 7 0.25
23 7 0.25
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
ATTATTATTTAAATTAAATAT
Found at i:19314 original size:14 final size:14
Alignment explanation
Indices: 19295--19339 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
19285 AAGTCGTAAC
19295 TCATTACTATCAAA
1 TCATTACTATCAAA
19309 TCATTAC--T-AAA
1 TCATTACTATCAAA
*
19320 TCATTAATATCAAA
1 TCATTACTATCAAA
19334 TCATTA
1 TCATTA
19340 AATATTAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
11 9 0.33
12 1 0.04
13 1 0.04
14 16 0.59
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (14 bp):
TCATTACTATCAAA
Found at i:19355 original size:21 final size:22
Alignment explanation
Indices: 19295--19349 Score: 67
Period size: 25 Copynumber: 2.4 Consensus size: 22
19285 AAGTCGTAAC
*
19295 TCATTACTATCAAATCATTACTAAA
1 TCATTAATATCAAATCA-T--TAAA
19320 TCATTAATATCAAATCATTAAA
1 TCATTAATATCAAATCATTAAA
19342 T-ATTAATA
1 TCATTAATA
19350 ATAAATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 7 0.24
22 5 0.17
24 1 0.03
25 16 0.55
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (22 bp):
TCATTAATATCAAATCATTAAA
Found at i:19360 original size:21 final size:22
Alignment explanation
Indices: 19311--19360 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
19301 CTATCAAATC
*
19311 ATTACTAAATCATTAATATCAA
1 ATTATTAAATCATTAATATCAA
*
19333 ATCATTAAAT-ATTAATAAT-AA
1 ATTATTAAATCATTAAT-ATCAA
19354 ATTATTA
1 ATTATTA
19361 TTACTAATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (22 bp):
ATTATTAAATCATTAATATCAA
Found at i:19432 original size:49 final size:49
Alignment explanation
Indices: 19370--20087 Score: 650
Period size: 49 Copynumber: 13.3 Consensus size: 49
19360 ATTACTAATC
* *
19370 ATTAATAATCATTACTATCAAATTATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
* * * * * *
19419 ATCATTAATCATTACTAAATCATTAAT-ATCAAATCATTAAATGTTAATAATAAT-TTT
1 ATTACTAATCATTACT--ATCA--AATCATTAAA-AATT-AA---TAATAAT-TTCATT
* * * *
19476 ATTATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCAT-T--ACTATCAAATCATTAAAAATTAATAATAATTTCATT
19528 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAAT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTC------A-T--T
19586 CATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 -ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
*
19637 GTTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAAT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTC------A-T--T
19695 CATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 -ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
*
19746 GTTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
* *
19795 ATTACTAATCATTACTAAATCATTAAT-ATCAAATCATTAAATATTAATAATAATTTCATAATTA
1 ATTACTAATCATTACT--ATCA--AATCATTAAA-AATT--A-A-TAA---TAATTTC---A-T-
19859 CT
49 -T
19861 AATCATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ----ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
19914 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTAATAAT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTC-------AT--T
*
19972 CATTACTAATCATTACTATCAAATCATTAAAAAATAATAATAATTTCATT
1 -ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
*
20022 ATTACTAATTATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
20071 ATTACTAATCATTACTA
1 ATTACTAATCATTACTA
20088 AATCATTAAT
Statistics
Matches: 569, Mismatches: 30, Indels: 140
0.77 0.04 0.19
Matches are distributed among these distances:
49 254 0.45
50 11 0.02
51 11 0.02
52 30 0.05
53 15 0.03
54 4 0.01
55 6 0.01
56 12 0.02
57 26 0.05
58 8 0.01
59 63 0.11
60 90 0.16
62 3 0.01
63 2 0.00
64 2 0.00
66 7 0.01
67 5 0.01
68 4 0.01
70 16 0.03
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (49 bp):
ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
Found at i:19458 original size:60 final size:59
Alignment explanation
Indices: 19307--19495 Score: 281
Period size: 60 Copynumber: 3.2 Consensus size: 59
19297 ATTACTATCA
*
19307 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATTATTATTACT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTATTATTACT
* * * * * *
19366 AATCATTAAT-AATCATTACTATCAAATTATTAAAAATTAATAATAATTTCATTATCATT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTT-ATTATTACT
*
19425 AATCATTACTAAATCATTAATATCAAATCATTAAATGTTAATAATAATTTTATTATTACT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAA-TTTATTATTACT
19485 AATCATTACTA
1 AATCATTACTA
19496 TCAAATCATT
Statistics
Matches: 113, Mismatches: 14, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
58 35 0.31
59 25 0.22
60 50 0.44
61 3 0.03
ACGTcount: A:0.47, C:0.11, G:0.01, T:0.42
Consensus pattern (59 bp):
AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTATTATTACT
Found at i:19496 original size:109 final size:109
Alignment explanation
Indices: 19376--20210 Score: 921
Period size: 109 Copynumber: 7.6 Consensus size: 109
19366 AATCATTAAT
* * *
19376 AATCATTACTATCAAATTATTAAAAATTAATAATAATTTCATTATCATTAATCATTACTAAATCA
1 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCA
*
19441 TTAATATCAAATCATTAAATGTTAATAATAATTTTATTATTACT-
66 TTAATATCAAATCATTAAAT-TTAATAATAATTTAATTATTACTA
19485 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTATCAAA
1 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC--T-AAA
* * * * * * * *
19550 TCATTAA-A--AATTAATAATAATTTCATTATTA-CTAATCATTACTA
63 TCATTAATATCAAATCATTA-AATTTAATAATAATTTAATTATTACTA
*
19594 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTGTTACTAATCATTACTATCAAA
1 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC--T-AAA
* * * * * * * *
19659 TCATTAA-A--AATTAATAATAATTTCATTATTA-CTAATCATTACTA
63 TCATTAATATCAAATCATTA-AATTTAATAATAATTTAATTATTACTA
*
19703 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTGTTACTAATCATTACTATCAAA
1 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC--T-AAA
* * * * * * * *
19768 TCATTAA-A--AATTAATAATAATTTCATTATTA-CTAATCATTACTA
63 TCATTAATATCAAATCATTA-AATTTAATAATAATTTAATTATTACTA
* * *
19812 AATCATTAATATCAAATCATTAAATATTAATAATAATTTCATAATTACTAATCATTACT-AATCA
1 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCA
* * *
19876 TTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT-
66 TTAATATCAAATCATT-AAATTTAATAATAATTTAATTATTACTA
*
19920 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTAATAATCATTACT-AATCA
1 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCA
* ** *
19984 TTACTATCAAATCATTAAAAAATAATAATAATTTCATTATTACT-
66 TTAATATCAAATCATT-AAATTTAATAATAATTTAATTATTACTA
*
20028 AATTATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCA
1 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCA
20093 TTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCTTTACTA
66 TTAATATCAAATCATTAAAT-TTAATAATAATTT-A--A-T--T-A---TTACTA
* *
20148 AATCATTACTATCAAATCATTAAATATTAATAATAATTTCATCATTACTAATCATTACTAAAT
1 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAAT
20211 TTTATAAATA
Statistics
Matches: 661, Mismatches: 42, Indels: 35
0.90 0.06 0.05
Matches are distributed among these distances:
105 8 0.01
106 1 0.00
107 1 0.00
108 186 0.28
109 381 0.58
110 3 0.00
111 2 0.00
112 11 0.02
113 1 0.00
115 1 0.00
116 1 0.00
119 5 0.01
120 60 0.09
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (109 bp):
AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCA
TTAATATCAAATCATTAAATTTAATAATAATTTAATTATTACTA
Found at i:19603 original size:60 final size:60
Alignment explanation
Indices: 19528--19653 Score: 236
Period size: 60 Copynumber: 2.1 Consensus size: 60
19518 TAATTTCATT
19528 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
*
19587 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTGTTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
19647 ATTACTA
1 ATTACTA
19654 TCAAATCATT
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
59 6 0.09
60 59 0.91
ACGTcount: A:0.45, C:0.13, G:0.01, T:0.40
Consensus pattern (60 bp):
ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
Found at i:19707 original size:60 final size:60
Alignment explanation
Indices: 19638--19762 Score: 234
Period size: 60 Copynumber: 2.1 Consensus size: 60
19628 AATTTCATTG
19638 TTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA
1 TTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA
*
19697 TTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTGTTACTAATCA
1 TTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA
19757 TTACTA
1 TTACTA
19763 TCAAATCATT
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
59 5 0.08
60 59 0.92
ACGTcount: A:0.45, C:0.14, G:0.01, T:0.41
Consensus pattern (60 bp):
TTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA
Found at i:19816 original size:60 final size:59
Alignment explanation
Indices: 19747--20208 Score: 667
Period size: 60 Copynumber: 8.1 Consensus size: 59
19737 AATTTCATTG
19747 TTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA
1 TTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA
* * *
19806 TTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATAATTACTAATCA
1 TTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA
19866 TTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTC------A-T--T-A
1 TTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA
*
19915 TTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTAATAATCA
1 TTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA
*
19974 TTACTAATCATTACTATCAAATCATTAAAAAATAATAATAATTTCATTATTAC---T-A
1 TTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA
20029 --A-T--T-ATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA
1 TTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA
* * *
20082 TTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCT
1 TTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA
* *
20142 TTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATCATTACTAATCA
1 TTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA
20202 TTACTAA
1 TTACTAA
20209 ATTTTATAAA
Statistics
Matches: 367, Mismatches: 14, Indels: 44
0.86 0.03 0.10
Matches are distributed among these distances:
49 89 0.24
50 2 0.01
52 3 0.01
53 3 0.01
55 3 0.01
56 3 0.01
58 1 0.00
59 98 0.27
60 165 0.45
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.41
Consensus pattern (59 bp):
TTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA
Found at i:19870 original size:10 final size:10
Alignment explanation
Indices: 19855--19881 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
19845 TAATTTCATA
19855 ATTACTAATC
1 ATTACTAATC
19865 ATTACTAATC
1 ATTACTAATC
19875 ATTACTA
1 ATTACTA
19882 TCAAATCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (10 bp):
ATTACTAATC
Found at i:19888 original size:24 final size:24
Alignment explanation
Indices: 19861--19941 Score: 72
Period size: 24 Copynumber: 3.3 Consensus size: 24
19851 CATAATTACT
19861 AATCATTACTAATCATTACTATCA
1 AATCATTACTAATCATTACTATCA
** * * * **
19885 AATCATTAAAAATTAATAATAATTT
1 AATCATTACTAATCATTACT-ATCA
* *
19910 CATTATTACTAATCATTACTATCA
1 AATCATTACTAATCATTACTATCA
19934 AATCATTA
1 AATCATTA
19942 AAAATTAATA
Statistics
Matches: 38, Mismatches: 18, Indels: 2
0.66 0.31 0.03
Matches are distributed among these distances:
24 23 0.61
25 15 0.39
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.40
Consensus pattern (24 bp):
AATCATTACTAATCATTACTATCA
Found at i:20055 original size:24 final size:24
Alignment explanation
Indices: 19969--20056 Score: 59
Period size: 24 Copynumber: 3.6 Consensus size: 24
19959 CATTATTAAT
** *
19969 AATCATTACTAATCATTACTATCA
1 AATCATTAAAAATTATTACTATCA
* * * **
19993 AATCATTAAAAAATAATAATAATTT
1 AATCATTAAAAATTATTACT-ATCA
* * **
20018 CATTATTACTAATTATTACTATCA
1 AATCATTAAAAATTATTACTATCA
20042 AATCATTAAAAATTA
1 AATCATTAAAAATTA
20057 ATAATAATTT
Statistics
Matches: 42, Mismatches: 21, Indels: 2
0.65 0.32 0.03
Matches are distributed among these distances:
24 27 0.64
25 15 0.36
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (24 bp):
AATCATTAAAAATTATTACTATCA
Found at i:20095 original size:21 final size:21
Alignment explanation
Indices: 20071--20210 Score: 57
Period size: 21 Copynumber: 7.0 Consensus size: 21
20061 TAATTTCATT
20071 ATTACTAATCATTACTAAATC
1 ATTACTAATCATTACTAAATC
* * *
20092 ATTAAT-ATCAAATCATTAAAT-
1 ATTACTAATC--ATTACTAAATC
* * * *
20113 ATTAATAATAATT--T-CATT
1 ATTACTAATCATTACTAAATC
*
20131 ATTACTAATCTTTACTAAATC
1 ATTACTAATCATTACTAAATC
* *
20152 ATTACT-ATCAAATCATTAAAT-
1 ATTACTAATC--ATTACTAAATC
* * *
20173 ATTAATAATAATT--T-CATC
1 ATTACTAATCATTACTAAATC
20191 ATTACTAATCATTACTAAAT
1 ATTACTAATCATTACTAAAT
20211 TTTATAAATA
Statistics
Matches: 84, Mismatches: 21, Indels: 28
0.63 0.16 0.21
Matches are distributed among these distances:
17 4 0.05
18 23 0.27
20 12 0.14
21 26 0.31
22 19 0.23
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTACTAATCATTACTAAATC
Found at i:23300 original size:28 final size:28
Alignment explanation
Indices: 23269--23322 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
23259 ATAATCTAAT
* *
23269 ATATAACTTAAACTAACAAATTAATATA
1 ATATAACTCAAACTAACAAACTAATATA
23297 ATATAACTCAAACTAACAAACTAATA
1 ATATAACTCAAACTAACAAACTAATA
23323 ATTTATACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (28 bp):
ATATAACTCAAACTAACAAACTAATATA
Found at i:23329 original size:28 final size:28
Alignment explanation
Indices: 23265--23329 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
23255 TTATATAATC
* *
23265 TAATATATAACTTAAACTAACAAATTAA
1 TAATATATAACTCAAACTAACAAACTAA
23293 T-ATAATATAACTCAAACTAACAAACTAA
1 TAAT-ATATAACTCAAACTAACAAACTAA
*
23321 TAATTTATA
1 TAATATATA
23330 CTAACAAACT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 2 0.06
28 28 0.88
29 2 0.06
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.32
Consensus pattern (28 bp):
TAATATATAACTCAAACTAACAAACTAA
Found at i:24055 original size:29 final size:29
Alignment explanation
Indices: 23977--24060 Score: 116
Period size: 29 Copynumber: 2.9 Consensus size: 29
23967 GTTGGATGCC
** *
23977 GGGCGTGCATGGCGACCTATAAGGTCACT
1 GGGCGTGCATGGCGACCTACCATGTCACT
*
24006 GGGCGTGCATGGCGACCTACCATGTCTCCT
1 GGGCGTGCATGGCGACCTACCATGTC-ACT
24036 -GGCGTGCATGGCGACCTACCATGTC
1 GGGCGTGCATGGCGACCTACCATGTC
24061 GGTGAAGCTT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 48 0.96
30 2 0.04
ACGTcount: A:0.17, C:0.30, G:0.32, T:0.21
Consensus pattern (29 bp):
GGGCGTGCATGGCGACCTACCATGTCACT
Found at i:24148 original size:29 final size:29
Alignment explanation
Indices: 24106--24161 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
24096 ACAAGGTTGC
24106 TAGGTCGCTGGGAGTGCATGGCGACCTTG
1 TAGGTCGCTGGGAGTGCATGGCGACCTTG
*
24135 TAGGTCGCTGGGAGTGCTTGGCGACCT
1 TAGGTCGCTGGGAGTGCATGGCGACCT
24162 ATGGTTGGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.12, C:0.21, G:0.41, T:0.25
Consensus pattern (29 bp):
TAGGTCGCTGGGAGTGCATGGCGACCTTG
Found at i:24705 original size:20 final size:20
Alignment explanation
Indices: 24675--24724 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
24665 CTATTTTGTA
* *
24675 AATTGATTTTATAAATCTTT
1 AATTTATTTTATAAATCTAT
* *
24695 GATTTATTTTATACATCTAT
1 AATTTATTTTATAAATCTAT
24715 AATTTATTTT
1 AATTTATTTT
24725 TTGTTATTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.58
Consensus pattern (20 bp):
AATTTATTTTATAAATCTAT
Found at i:37411 original size:83 final size:83
Alignment explanation
Indices: 37289--37491 Score: 230
Period size: 83 Copynumber: 2.4 Consensus size: 83
37279 GAACAAACAA
* * * * *
37289 ATTTGCTATAGATTACTGGTGATACGAA-GAATTTTGAGAAATACAAGCTGGCAAAGAACGGA-C
1 ATTTGCTATAGACTACTGGTGATAC-AAGGAGTTTCGAGAAATACAAGCTAGAAAAGAAC-GATC
*
37352 AAGACATTTCTAAGGAGGCC
64 AAAACATTTCTAAGGAGGCC
* ** *
37372 ATTTGCTATATACTACCAGTGATACAAGGAGTTTCGAGAAATATAAGCTAGAAAAGAACGATCAA
1 ATTTGCTATAGACTACTGGTGATACAAGGAGTTTCGAGAAATACAAGCTAGAAAAGAACGATCAA
* *
37437 AACATTTGTAAGGAGGCT
66 AACATTTCTAAGGAGGCC
** * *
37455 ATTCACAATAGACTACTGGTGATATAAGGAGTTTCGA
1 ATTTGCTATAGACTACTGGTGATACAAGGAGTTTCGA
37492 TAAACATAAT
Statistics
Matches: 99, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
82 4 0.04
83 95 0.96
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (83 bp):
ATTTGCTATAGACTACTGGTGATACAAGGAGTTTCGAGAAATACAAGCTAGAAAAGAACGATCAA
AACATTTCTAAGGAGGCC
Found at i:41186 original size:24 final size:24
Alignment explanation
Indices: 41159--41204 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
41149 TTCATATATG
* *
41159 AAACATTTTATTAGAAATCAAACC
1 AAACATTCTATTAAAAATCAAACC
41183 AAACATTCTATTAAAAATCAAA
1 AAACATTCTATTAAAAATCAAA
41205 ATTCAAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.54, C:0.15, G:0.02, T:0.28
Consensus pattern (24 bp):
AAACATTCTATTAAAAATCAAACC
Found at i:45093 original size:60 final size:61
Alignment explanation
Indices: 44942--45087 Score: 199
Period size: 60 Copynumber: 2.4 Consensus size: 61
44932 GTCATTCGAT
* * * *
44942 TATTATAAGTTACAAAATTGTCA-TCTAACTATAGAGTATTGCTTTGTTGAGTCCCTCGAC
1 TATTAAAAGTTAAAAAATGGTCACTCTAACTATAGAGTATTGCTTTGTTGAGTCCCCCGAC
* *
45002 TATTAAAACTTAAAAAATGGTC-CTCTAACTAT-GTAGTATTGTTTTGTTGAGTCCCCCGAC
1 TATTAAAAGTTAAAAAATGGTCACTCTAACTATAG-AGTATTGCTTTGTTGAGTCCCCCGAC
*
45062 TATTAAAAGTTATAAAATGGTCACTC
1 TATTAAAAGTTAAAAAATGGTCACTC
45088 GACTATTCAT
Statistics
Matches: 75, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
59 1 0.01
60 71 0.95
61 3 0.04
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.37
Consensus pattern (61 bp):
TATTAAAAGTTAAAAAATGGTCACTCTAACTATAGAGTATTGCTTTGTTGAGTCCCCCGAC
Found at i:46402 original size:23 final size:21
Alignment explanation
Indices: 46354--46398 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
46344 CTTTTTTAAG
46354 ATAATATATATTATTGAAATA
1 ATAATATATATTATTGAAATA
*
46375 ATAATGTATAGTTAGTTG-AATA
1 ATAATATATA-TTA-TTGAAATA
46397 AT
1 AT
46399 TAATTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 9 0.43
22 9 0.43
23 3 0.14
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (21 bp):
ATAATATATATTATTGAAATA
Found at i:51847 original size:20 final size:20
Alignment explanation
Indices: 51822--51888 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
51812 AAATCACAAT
51822 GCGATACTGACTATCGCAAC
1 GCGATACTGACTATCGCAAC
* *
51842 GCGATAAT-ACAAAATCGCAAC
1 GCGATACTGAC--TATCGCAAC
*
51863 GCGATACTGACTTTCGCAAC
1 GCGATACTGACTATCGCAAC
*
51883 GAGATA
1 GCGATA
51889 ATACAGAATC
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 2 0.05
20 19 0.50
21 15 0.39
22 2 0.05
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.19
Consensus pattern (20 bp):
GCGATACTGACTATCGCAAC
Found at i:51860 original size:21 final size:20
Alignment explanation
Indices: 51834--51902 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 20
51824 GATACTGACT
51834 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATAC-AA
* *
51855 ATCGCAACGCGATACTGAC-T
1 ATCGCAACGCGATAAT-ACAA
* *
51875 TTCGCAACGAGATAATACAGA
1 ATCGCAACGCGATAATACA-A
51896 ATCGCAA
1 ATCGCAA
51903 TGTGATTTTC
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
19 2 0.05
20 13 0.34
21 21 0.55
22 2 0.05
ACGTcount: A:0.41, C:0.25, G:0.17, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGATAATACAA
Found at i:51899 original size:41 final size:41
Alignment explanation
Indices: 51811--51902 Score: 139
Period size: 41 Copynumber: 2.2 Consensus size: 41
51801 GCGAATTGGG
* * *
51811 AAAATCACAATGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGAGATAATAC
*
51852 AAAATCGCAACGCGATACTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGAGATAATAC
*
51893 AGAATCGCAA
1 AAAATCGCAA
51903 TGTGATTTTC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.18
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCGCAACGAGATAATAC
Found at i:52562 original size:20 final size:20
Alignment explanation
Indices: 52537--52589 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
52527 GCGCTATGTA
52537 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
52557 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
52577 TATCTCGTTGCGA
1 AATCGCGTTGCGA
52590 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:52623 original size:20 final size:20
Alignment explanation
Indices: 52598--52651 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
52588 GATTTTGTAT
52598 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
52618 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
52638 TATCGCATTGCGAT
1 TATCGCATTGCGAT
52652 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:52636 original size:61 final size:61
Alignment explanation
Indices: 52538--52654 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
52528 CGCTATGTAA
* * * * *
52538 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
52599 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
52655 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:52670 original size:61 final size:61
Alignment explanation
Indices: 52538--52672 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
52528 CGCTATGTAA
* * * * * ** *
52538 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
52599 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
52661 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
52673 TTACTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:52762 original size:21 final size:21
Alignment explanation
Indices: 52722--52762 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
52712 ACTGTAGACC
**
52722 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
52743 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
52763 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:53683 original size:2 final size:2
Alignment explanation
Indices: 53676--53749 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
53666 CTTTATTTTA
53676 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53718 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53750 GCATTTTGGT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56895 original size:29 final size:29
Alignment explanation
Indices: 56863--56927 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
56853 ACTAATTCAA
* *
56863 AAATAATAAAAATAT-TTTATATTTAATTT
1 AAATAATAAAAATATATTAATA-TTAATGT
* *
56892 AAATTATAAAAGTATATTAATATTAATGT
1 AAATAATAAAAATATATTAATATTAATGT
56921 AAA-AATA
1 AAATAATA
56928 TATTTTAGCA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 3 0.10
29 22 0.73
30 5 0.17
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (29 bp):
AAATAATAAAAATATATTAATATTAATGT
Found at i:56907 original size:24 final size:23
Alignment explanation
Indices: 56880--56932 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
56870 AAAAATATTT
56880 TATATTTAAT-TTAAAT-TATAAAA
1 TATATTTAATATT-AATGTA-AAAA
56903 GTATA-TTAATATTAATGTAAAAA
1 -TATATTTAATATTAATGTAAAAA
56926 TATATTT
1 TATATTT
56933 TAGCATATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
22 4 0.15
23 14 0.54
24 8 0.31
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (23 bp):
TATATTTAATATTAATGTAAAAA
Found at i:59918 original size:3 final size:3
Alignment explanation
Indices: 59910--59974 Score: 76
Period size: 3 Copynumber: 20.7 Consensus size: 3
59900 ATGAAATCTT
* *
59910 TAA TAA TAA TAAA TAA TAA TAA TAA CTTA TAA TAA TAA TAA TAA TATT
1 TAA TAA TAA T-AA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TA-A
*
59958 TTA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA
59975 CATTAAAATA
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
3 47 0.89
4 6 0.11
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:59931 original size:16 final size:16
Alignment explanation
Indices: 59910--59972 Score: 72
Period size: 16 Copynumber: 3.8 Consensus size: 16
59900 ATGAAATCTT
59910 TAATAATAATAAATAA
1 TAATAATAATAAATAA
59926 TAATAATAACTTATAATAA
1 TAATAATAA--TA-AATAA
** *
59945 TAATAATAATATTTTA
1 TAATAATAATAAATAA
59961 TAATAATAATAA
1 TAATAATAATAA
59973 TACATTAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
16 22 0.55
17 2 0.05
18 2 0.05
19 14 0.35
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (16 bp):
TAATAATAATAAATAA
Found at i:59934 original size:19 final size:18
Alignment explanation
Indices: 59910--59974 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 18
59900 ATGAAATCTT
59910 TAATAATAATAAATAATAA
1 TAATAATAAT-AATAATAA
*
59929 TAATAACTTATAATAATAA
1 TAATAA-TAATAATAATAA
* *
59948 TAATAATATTTTATAATAA
1 TAATAATA-ATAATAATAA
59967 TAATAATA
1 TAATAATA
59975 CATTAAAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
18 1 0.03
19 36 0.90
20 3 0.08
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
TAATAATAATAATAATAA
Found at i:59949 original size:22 final size:22
Alignment explanation
Indices: 59915--59974 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
59905 ATCTTTAATA
59915 ATAATAAATAATAATAATAACTT
1 ATAAT-AATAATAATAATAACTT
**
59938 ATAATAATAATAATAATATTTT
1 ATAATAATAATAATAATAACTT
59960 ATAATAATAATAATA
1 ATAATAATAATAATA
59975 CATTAAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 30 0.86
23 5 0.14
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
ATAATAATAATAATAATAACTT
Found at i:59984 original size:19 final size:19
Alignment explanation
Indices: 59920--59985 Score: 78
Period size: 19 Copynumber: 3.3 Consensus size: 19
59910 TAATAATAAT
59920 AAATAATAATAATAACTTATA
1 AAATAATAATAAT-ACTT-TA
*
59941 ATAATAATAATAATATTTTA
1 A-AATAATAATAATACTTTA
* *
59961 TAATAATAATAATACATTA
1 AAATAATAATAATACTTTA
59980 AAATAA
1 AAATAA
59986 CTATTGAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
19 21 0.54
20 2 0.05
21 4 0.10
22 12 0.31
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (19 bp):
AAATAATAATAATACTTTA
Found at i:61260 original size:14 final size:14
Alignment explanation
Indices: 61241--61271 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
61231 GTGAAATTCT
61241 AAATATTTAAATAA
1 AAATATTTAAATAA
*
61255 AAATATTTATATAA
1 AAATATTTAAATAA
61269 AAA
1 AAA
61272 ATCATCGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATATTTAAATAA
Found at i:61360 original size:24 final size:24
Alignment explanation
Indices: 61314--61362 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
61304 AATTATATGT
* *
61314 TTTTTAATAAAATTTATATATAAA
1 TTTTTAATAAAATTTAAAGATAAA
61338 TTTTT-ATAAAATTTAAAAGATAAA
1 TTTTTAATAAAATTT-AAAGATAAA
61362 T
1 T
61363 GGGTAGAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (24 bp):
TTTTTAATAAAATTTAAAGATAAA
Found at i:61456 original size:32 final size:32
Alignment explanation
Indices: 61398--61490 Score: 80
Period size: 32 Copynumber: 2.8 Consensus size: 32
61388 CATGTATTAT
* * * **
61398 TTTAATTATAAATAATATT-AATTTTTACATTA
1 TTTAACTAAAAAT-ATATTAAAATTTTACAACA
*
61430 TTTATCTAAAAATATATTAAAATTTTACAACA
1 TTTAACTAAAAATATATTAAAATTTTACAACA
* *
61462 TTTAACTAAATAAGCATATGAAAATTTTA
1 TTTAACTAAA-AA-TATATTAAAATTTTA
61491 ATAGATAAAC
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
31 5 0.10
32 29 0.59
33 2 0.04
34 13 0.27
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.44
Consensus pattern (32 bp):
TTTAACTAAAAATATATTAAAATTTTACAACA
Found at i:62740 original size:16 final size:17
Alignment explanation
Indices: 62719--62751 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
62709 AAGAAGTTGT
*
62719 CACCAAC-CTTCAATTC
1 CACCAACGCATCAATTC
62735 CACCAACGCATCAATTC
1 CACCAACGCATCAATTC
62752 TCGAATCAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.33, C:0.42, G:0.03, T:0.21
Consensus pattern (17 bp):
CACCAACGCATCAATTC
Found at i:66464 original size:6 final size:6
Alignment explanation
Indices: 66450--66480 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
66440 TCGAGACAGT
*
66450 GTGAGA GTGATA GTGAGA GTGAGA GTGAGA G
1 GTGAGA GTGAGA GTGAGA GTGAGA GTGAGA G
66481 AGGGAGAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.32, C:0.00, G:0.48, T:0.19
Consensus pattern (6 bp):
GTGAGA
Found at i:71842 original size:30 final size:30
Alignment explanation
Indices: 71806--71878 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
71796 AAAATCGAAT
*
71806 TAAACGGGGACGGAAAAAAATTGTTTATGC
1 TAAACGGGGACGGAAAAAAATCGTTTATGC
* *
71836 TAAACGGGGACGGAGAAAAATCGTTTATGT
1 TAAACGGGGACGGAAAAAAATCGTTTATGC
71866 TAAACGGGGACGG
1 TAAACGGGGACGG
71879 GGACAGGGAC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.37, C:0.11, G:0.32, T:0.21
Consensus pattern (30 bp):
TAAACGGGGACGGAAAAAAATCGTTTATGC
Found at i:73259 original size:30 final size:30
Alignment explanation
Indices: 73223--73295 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
73213 AAAATCGAAT
*
73223 TAAACGGGGACGGAAAAAAATTGTTTATGC
1 TAAACGGGGACGGAAAAAAATCGTTTATGC
* *
73253 TAAACGGGGACGGAGAAAAATCGTTTATGT
1 TAAACGGGGACGGAAAAAAATCGTTTATGC
73283 TAAACGGGGACGG
1 TAAACGGGGACGG
73296 GGACAGGGAC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.37, C:0.11, G:0.32, T:0.21
Consensus pattern (30 bp):
TAAACGGGGACGGAAAAAAATCGTTTATGC
Found at i:80152 original size:18 final size:18
Alignment explanation
Indices: 80129--80186 Score: 77
Period size: 18 Copynumber: 3.4 Consensus size: 18
80119 TATTCTGACA
80129 AAAAATATTAGAATAATT
1 AAAAATATTAGAATAATT
*
80147 -AAAA-A-TAGAATATTT
1 AAAAATATTAGAATAATT
*
80162 TAAAATATTAGAATAATT
1 AAAAATATTAGAATAATT
80180 AAAAATA
1 AAAAATA
80187 GAATATTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 9 0.26
16 5 0.15
17 5 0.15
18 15 0.44
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (18 bp):
AAAAATATTAGAATAATT
Found at i:80155 original size:15 final size:15
Alignment explanation
Indices: 80137--80201 Score: 76
Period size: 15 Copynumber: 4.1 Consensus size: 15
80127 CAAAAAATAT
80137 TAGAATAATTAAAAA
1 TAGAATAATTAAAAA
*
80152 TAGAATATTTTAAAATA
1 TAGAATA-ATTAAAA-A
80169 TTAGAATAATTAAAAA
1 -TAGAATAATTAAAAA
* *
80185 TAGAATATTTTAAAA
1 TAGAATAATTAAAAA
80200 TA
1 TA
80202 TTAATATTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
15 22 0.51
16 7 0.16
17 7 0.16
18 7 0.16
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (15 bp):
TAGAATAATTAAAAA
Found at i:80166 original size:16 final size:16
Alignment explanation
Indices: 80145--80212 Score: 77
Period size: 16 Copynumber: 4.2 Consensus size: 16
80135 ATTAGAATAA
80145 TTAAAAATAGAATATT
1 TTAAAAATAGAATATT
*
80161 TTAAAATATTAGAATA-A
1 TTAAAA-A-TAGAATATT
80178 TTAAAAATAGAATATT
1 TTAAAAATAGAATATT
*
80194 TT-AAAATATTAATATT
1 TTAAAAATA-GAATATT
80210 TTA
1 TTA
80213 TAATTATTCT
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
15 13 0.30
16 17 0.39
17 7 0.16
18 7 0.16
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (16 bp):
TTAAAAATAGAATATT
Found at i:80167 original size:33 final size:33
Alignment explanation
Indices: 80130--80204 Score: 150
Period size: 33 Copynumber: 2.3 Consensus size: 33
80120 ATTCTGACAA
80130 AAAATATTAGAATAATTAAAAATAGAATATTTT
1 AAAATATTAGAATAATTAAAAATAGAATATTTT
80163 AAAATATTAGAATAATTAAAAATAGAATATTTT
1 AAAATATTAGAATAATTAAAAATAGAATATTTT
80196 AAAATATTA
1 AAAATATTA
80205 ATATTTTATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (33 bp):
AAAATATTAGAATAATTAAAAATAGAATATTTT
Found at i:92471 original size:15 final size:16
Alignment explanation
Indices: 92449--92485 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
92439 TCTTATCTTT
*
92449 TATTTAATATTTTAAA
1 TATTTAATATATTAAA
92465 T-TTTAATATATTAAA
1 TATTTAATATATTAAA
92480 TATTTA
1 TATTTA
92486 TCAATTATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTTAATATATTAAA
Done.