Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003225.1 Hibiscus syriacus cultivar Beakdansim tig00006791_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: 60455
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2529 original size:13 final size:13
Alignment explanation
Indices: 2511--2553 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
2501 GCCGGTCAAC
2511 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
2524 GGTCAATGGGTCG
1 GGTCAACGGGTCG
*
2537 GGTCAACAGGTCG
1 GGTCAACGGGTCG
2550 GGTC
1 GGTC
2554 GGGCCGGGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.16, C:0.21, G:0.44, T:0.19
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:2586 original size:9 final size:9
Alignment explanation
Indices: 2572--2597 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
2562 TCGGGTTATG
2572 ACCGGTCAA
1 ACCGGTCAA
2581 ACCGGTCAA
1 ACCGGTCAA
2590 ACCGGTCA
1 ACCGGTCA
2598 TTTTTCCTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.31, C:0.35, G:0.23, T:0.12
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:4054 original size:18 final size:19
Alignment explanation
Indices: 4019--4059 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
4009 AATACCCAAA
4019 AATAATATTAATACA-TTT
1 AATAATATTAATACATTTT
*
4037 AATATTATT-ATACAATTTT
1 AATAATATTAATAC-ATTTT
4056 AATA
1 AATA
4060 CTTTTTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 4 0.20
18 9 0.45
19 7 0.35
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (19 bp):
AATAATATTAATACATTTT
Found at i:4127 original size:22 final size:23
Alignment explanation
Indices: 4097--4176 Score: 83
Period size: 22 Copynumber: 3.5 Consensus size: 23
4087 ATATATTTAT
*
4097 TAATATTTTAATAATATTATATTA
1 TAAT-TTTTAATAATATTATAATA
* *
4121 T-ATTTTTAGTATTATTATAATA
1 TAATTTTTAATAATATTATAATA
* * *
4143 TAATTATT-ATATTATAATAATA
1 TAATTTTTAATAATATTATAATA
4165 TAATTTTTAATA
1 TAATTTTTAATA
4177 TTAATATACT
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
22 36 0.77
23 10 0.21
24 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (23 bp):
TAATTTTTAATAATATTATAATA
Found at i:4148 original size:14 final size:14
Alignment explanation
Indices: 4131--4160 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4121 TATTTTTAGT
4131 ATTATTATAATATA
1 ATTATTATAATATA
*
4145 ATTATTATATTATA
1 ATTATTATAATATA
4159 AT
1 AT
4161 AATATAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATTATTATAATATA
Found at i:4694 original size:25 final size:24
Alignment explanation
Indices: 4621--4680 Score: 104
Period size: 24 Copynumber: 2.5 Consensus size: 24
4611 CCCTCCATGG
*
4621 TCAAAATTCTCTTCAGTATTATTC
1 TCAAAATTCTCTTCACTATTATTC
4645 TCAAAATTCTCTTCACTATTATTC
1 TCAAAATTCTCTTCACTATTATTC
4669 TCAAAATT-TCTT
1 TCAAAATTCTCTT
4681 GCCATTTCTA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
23 4 0.11
24 31 0.89
ACGTcount: A:0.30, C:0.22, G:0.02, T:0.47
Consensus pattern (24 bp):
TCAAAATTCTCTTCACTATTATTC
Found at i:7336 original size:20 final size:21
Alignment explanation
Indices: 7311--7366 Score: 80
Period size: 20 Copynumber: 2.8 Consensus size: 21
7301 ATTTTCTAGG
7311 AAAAGGAT-GATCCCTTTTGA
1 AAAAGGATCGATCCCTTTTGA
7331 AAAAGGATCGATCCCTTTTG-
1 AAAAGGATCGATCCCTTTTGA
* *
7351 TAAAGGATCAATCCCT
1 AAAAGGATCGATCCCT
7367 AAAAAAAGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 22 0.67
21 11 0.33
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.29
Consensus pattern (21 bp):
AAAAGGATCGATCCCTTTTGA
Found at i:9433 original size:24 final size:23
Alignment explanation
Indices: 9406--9481 Score: 73
Period size: 26 Copynumber: 3.1 Consensus size: 23
9396 TTTTTCTAAC
*
9406 ATATGGCTTTATAT-TGTATAAACA
1 ATAT-GCTTTAAATGTGTATAAA-A
9430 ATATGCTTTAAATGTGTATAAAA
1 ATATGCTTTAAATGTGTATAAAA
* *
9453 ATAGTAGGATTTAATTGTGTATAAAA
1 ATA-T--GCTTTAAATGTGTATAAAA
9479 ATA
1 ATA
9482 GTAGAATCTA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
23 12 0.27
24 13 0.29
26 20 0.44
ACGTcount: A:0.42, C:0.04, G:0.14, T:0.39
Consensus pattern (23 bp):
ATATGCTTTAAATGTGTATAAAA
Found at i:9471 original size:26 final size:26
Alignment explanation
Indices: 9436--9499 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 26
9426 AACAATATGC
* *
9436 TTTAAATGTGTATAAAAATAGTAGGA
1 TTTAATTGTGTATAAAAATAGTAGAA
9462 TTTAATTGTGTATAAAAATAGTAGAA
1 TTTAATTGTGTATAAAAATAGTAGAA
* *
9488 TCTAATAGTGTA
1 TTTAATTGTGTA
9500 CAAACAACAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.44, C:0.02, G:0.17, T:0.38
Consensus pattern (26 bp):
TTTAATTGTGTATAAAAATAGTAGAA
Found at i:10199 original size:26 final size:25
Alignment explanation
Indices: 10169--10262 Score: 91
Period size: 26 Copynumber: 3.6 Consensus size: 25
10159 AACAACATAT
*
10169 TTTAAGTATGCATAAAAATAATAGAA
1 TTTAA-TATGTATAAAAATAATAGAA
* *
10195 TTTAATAGTGTATAAAAATAGTAGGA
1 TTTAATA-TGTATAAAAATAATAGAA
*
10221 TTTAATTGTGTATAAAAATAATA-AGA
1 TTTAA-TATGTATAAAAATAATAGA-A
*
10247 TTTAATGGTGTATAAA
1 TTTAAT-ATGTATAAA
10263 CAACATGTTT
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
25 3 0.05
26 54 0.93
27 1 0.02
ACGTcount: A:0.48, C:0.01, G:0.15, T:0.36
Consensus pattern (25 bp):
TTTAATATGTATAAAAATAATAGAA
Found at i:10433 original size:63 final size:64
Alignment explanation
Indices: 10355--10500 Score: 197
Period size: 63 Copynumber: 2.3 Consensus size: 64
10345 ATAAAATAAT
* *
10355 ATGTTTTAAATGTGTATAAATAATATACGATTTAATAAT-TTTTAGGGTTTAGTTGTATAAAAAC
1 ATGTTTTAAATGTGTATAAA-AATATACGATTTAATAATGTTTTAGGGTGTAATTGTATAAAAAC
* * * * *
10419 AT-TTTTAAATGTGTATAAAAGTTTATGTTTTAATAGTGTTTTAGGGTGTAATTGTATAAAAAC
1 ATGTTTTAAATGTGTATAAAAATATACGATTTAATAATGTTTTAGGGTGTAATTGTATAAAAAC
*
10482 ATGTTTTAAACGTGTATAA
1 ATGTTTTAAATGTGTATAA
10501 GTAGTACGGT
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
62 13 0.18
63 42 0.58
64 17 0.24
ACGTcount: A:0.37, C:0.03, G:0.16, T:0.45
Consensus pattern (64 bp):
ATGTTTTAAATGTGTATAAAAATATACGATTTAATAATGTTTTAGGGTGTAATTGTATAAAAAC
Found at i:10785 original size:20 final size:21
Alignment explanation
Indices: 10760--10852 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
10750 TTTTCCCAAT
*
10760 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
10780 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
10801 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
10821 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
10842 TCGCAATGCGA
1 TCGCAATGCGA
10853 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:10805 original size:41 final size:41
Alignment explanation
Indices: 10760--10852 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
10750 TTTTCCCAAT
10760 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
10801 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
10842 TCGCAATGCGA
1 TCGCAATGCGA
10853 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:10865 original size:41 final size:41
Alignment explanation
Indices: 10779--10913 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
10769 GAATAAGTAA
* *
10779 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
10820 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
10861 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
10902 TTCGCAACGCGA
1 ATCGCAACGCGA
10914 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:10866 original size:20 final size:20
Alignment explanation
Indices: 10841--10935 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
10831 AATTGGGAAA
*
10841 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
10861 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
10882 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
10902 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
10922 TTCGCAACGTGATA
1 ATCGCAACGCGATA
10936 ATACATAATC
Statistics
Matches: 60, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:11151 original size:22 final size:22
Alignment explanation
Indices: 11123--11166 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
11113 CACTCTCTCA
*
11123 CCCATCTTCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
**
11145 CCCATCTCCGGTGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
11167 TATCTAAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.20, C:0.41, G:0.16, T:0.23
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:11422 original size:20 final size:20
Alignment explanation
Indices: 11397--11434 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
11387 TGATTCTCTC
11397 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
11417 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
11435 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:12766 original size:18 final size:18
Alignment explanation
Indices: 12745--12789 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
12735 TCCACTTCGG
*
12745 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
12763 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
12781 GAGCCATCA
1 GAGCCATCA
12790 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:13316 original size:19 final size:20
Alignment explanation
Indices: 13273--13317 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
13263 CGCAACACGA
*
13273 AAATGACTATCGCAATGCGG
1 AAATGACTATCACAATGCGG
*
13293 AAATGGCTATCACAATGC-G
1 AAATGACTATCACAATGCGG
13312 AAATGA
1 AAATGA
13318 AAATCGCAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.40, C:0.18, G:0.22, T:0.20
Consensus pattern (20 bp):
AAATGACTATCACAATGCGG
Found at i:13336 original size:14 final size:14
Alignment explanation
Indices: 13317--13374 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
13307 ATGCGAAATG
13317 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
13331 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
*
13347 ATGAAATCACAACGAC
1 A--AAATCGCAACGAC
13363 AAAATCGCAACG
1 AAAATCGCAACG
13375 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 8 0.22
18 8 0.22
ACGTcount: A:0.50, C:0.24, G:0.16, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:13347 original size:33 final size:33
Alignment explanation
Indices: 13305--13391 Score: 149
Period size: 32 Copynumber: 2.7 Consensus size: 33
13295 ATGGCTATCA
13305 CAATGCGAAATGAAAATCGCAACGACAAAATCG
1 CAATGCGAAATGAAAATCGCAACGACAAAATCG
*
13338 CAATGCGAAATG-AAATCACAACGACAAAATCG
1 CAATGCGAAATGAAAATCGCAACGACAAAATCG
*
13370 CAACGCGAAATGAAAATCGCAA
1 CAATGCGAAATGAAAATCGCAA
13392 TGCGATTTGT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
32 30 0.60
33 20 0.40
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.11
Consensus pattern (33 bp):
CAATGCGAAATGAAAATCGCAACGACAAAATCG
Found at i:13427 original size:14 final size:14
Alignment explanation
Indices: 13408--13465 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
13398 TTGTGTTTCG
13408 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
13422 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
13438 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
13454 CGTTGCGATTTT
1 CGTTGCGATTTT
13466 CATTTCACAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:13442 original size:32 final size:33
Alignment explanation
Indices: 13403--13471 Score: 131
Period size: 32 Copynumber: 2.1 Consensus size: 33
13393 GCGATTTGTG
13403 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
13435 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
13468 TTTC
1 TTTC
13472 ACATTGCGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 27 0.75
33 9 0.25
ACGTcount: A:0.09, C:0.19, G:0.23, T:0.49
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:13479 original size:33 final size:32
Alignment explanation
Indices: 13410--13479 Score: 113
Period size: 32 Copynumber: 2.2 Consensus size: 32
13400 GTGTTTCGCG
* *
13410 TTGCGATTTTGTCGTTGCGATTTCATTTCGCG
1 TTGCGATTTTGTCGTTGCGATTTCATTTCACA
13442 TTGCGATTTTGTCGTTGCGATTTTCATTTCACA
1 TTGCGATTTTGTCGTTGCGA-TTTCATTTCACA
13475 TTGCG
1 TTGCG
13480 TTAGCCATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 20 0.57
33 15 0.43
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (32 bp):
TTGCGATTTTGTCGTTGCGATTTCATTTCACA
Found at i:15543 original size:14 final size:14
Alignment explanation
Indices: 15524--15573 Score: 55
Period size: 14 Copynumber: 3.2 Consensus size: 14
15514 CGAAATGGCT
15524 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
15538 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
15557 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
15571 ATC
1 ATC
15574 ACAATGCGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
14 14 0.45
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.35
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.12
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:15550 original size:33 final size:33
Alignment explanation
Indices: 15505--15582 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 33
15495 AAAATAGACT
* ***
15505 ATCGCAACGCGAAATGGCTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
15538 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
*
15571 ATCACAATGCGA
1 ATCGCAATGCGA
15583 TTTTCATTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:15570 original size:19 final size:19
Alignment explanation
Indices: 15534--15570 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
15524 ATCGCAACGA
* *
15534 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAACGAGAAAT
15553 GAAAATCGCAACGAGAAA
1 GAAAATCGCAACGAGAAA
15571 ATCACAATGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.16, G:0.22, T:0.11
Consensus pattern (19 bp):
GAAAATCGCAACGAGAAAT
Found at i:15679 original size:19 final size:19
Alignment explanation
Indices: 15609--15676 Score: 100
Period size: 19 Copynumber: 3.5 Consensus size: 19
15599 CGATTTTCTT
*
15609 GTTGCGATAACCATTTTCGC
1 GTTGCGATAGCCA-TTTCGC
*
15629 GTTGTGATAGCCATTTCGC
1 GTTGCGATAGCCATTTCGC
*
15648 GTTGCGATAGTCATTTCGC
1 GTTGCGATAGCCATTTCGC
15667 GTTGCGATAG
1 GTTGCGATAG
15677 TCAAATGAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
19 33 0.75
20 11 0.25
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.35
Consensus pattern (19 bp):
GTTGCGATAGCCATTTCGC
Found at i:16763 original size:24 final size:24
Alignment explanation
Indices: 16736--16789 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
16726 GTATTCGAAA
* *
16736 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
16760 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
16784 TTTGAT
1 TTTGAT
16790 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:16981 original size:12 final size:12
Alignment explanation
Indices: 16964--16988 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16954 ATATAATCCT
16964 GAAGAAGAAAAA
1 GAAGAAGAAAAA
16976 GAAGAAGAAAAA
1 GAAGAAGAAAAA
16988 G
1 G
16989 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:19302 original size:19 final size:19
Alignment explanation
Indices: 19280--19429 Score: 132
Period size: 19 Copynumber: 8.7 Consensus size: 19
19270 GGAAATTACT
19280 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
19299 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
19313 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
19332 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
19346 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
19365 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
19379 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
19398 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
19417 ATCGCAACGCGAA
1 ATCGCAATGCGAA
19430 TTTAATTTCG
Statistics
Matches: 103, Mismatches: 13, Indels: 30
0.71 0.09 0.21
Matches are distributed among these distances:
14 27 0.26
15 3 0.03
16 6 0.06
17 6 0.06
18 3 0.03
19 58 0.56
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:19322 original size:33 final size:33
Alignment explanation
Indices: 19280--19404 Score: 198
Period size: 33 Copynumber: 3.8 Consensus size: 33
19270 GGAAATTACT
19280 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
19313 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
19345 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
19379 ATCGCAATGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
19405 TGCGAAATGA
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 81 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:19387 original size:66 final size:66
Alignment explanation
Indices: 19281--19404 Score: 239
Period size: 66 Copynumber: 1.9 Consensus size: 66
19271 GAAATTACTA
19281 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
19346 T
66 T
*
19347 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAA
19405 TGCGAAATGA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 57 1.00
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.15
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
T
Found at i:19627 original size:14 final size:14
Alignment explanation
Indices: 19608--19644 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
19598 CATCAATTAA
19608 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
19622 ACAAATCACCTTTT
1 ACAAATCAACTTTT
19636 ACAAATCAA
1 ACAAATCAA
19645 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:21068 original size:21 final size:21
Alignment explanation
Indices: 21002--21068 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
20992 GTGAATCGGG
*
21002 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
21022 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
21044 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
21065 CTCT
1 CTCT
21069 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:21087 original size:42 final size:41
Alignment explanation
Indices: 21002--21124 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
20992 GTGAATCGGG
* * * * *
21002 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
21044 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
21086 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
21125 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:23202 original size:33 final size:33
Alignment explanation
Indices: 23145--23243 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
23135 ACGAGATAAT
*
23145 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
23179 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
23212 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
23244 GCGAAATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:23237 original size:19 final size:19
Alignment explanation
Indices: 23120--23285 Score: 136
Period size: 20 Copynumber: 9.1 Consensus size: 19
23110 TCTTTTGGTT
*
23120 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
23139 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
23159 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
23177 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
23193 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
23211 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
23226 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
23246 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
23265 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
23284 GA
1 GA
23286 TTTTGGTTTC
Statistics
Matches: 119, Mismatches: 15, Indels: 26
0.74 0.09 0.16
Matches are distributed among these distances:
14 19 0.16
15 3 0.03
16 2 0.02
17 1 0.01
18 4 0.03
19 43 0.36
20 45 0.38
21 2 0.02
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:23315 original size:18 final size:18
Alignment explanation
Indices: 23281--23360 Score: 78
Period size: 18 Copynumber: 4.5 Consensus size: 18
23271 AAAATCGCAA
*
23281 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-ATTTCGCGT
23300 TGCGATTTTATTTCGCGT
1 TGCGATTTTATTTCGCGT
*
23318 TGCGA--TTA--TCTCGT
1 TGCGATTTTATTTCGCGT
*
23332 TGCGATAGTTATTTCCGCGT
1 TGCGAT-TTTATTT-CGCGT
23352 TGCGATTTT
1 TGCGATTTT
23361 CATTCTCGAA
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
14 10 0.20
16 3 0.06
17 3 0.06
18 13 0.25
19 12 0.24
20 10 0.20
ACGTcount: A:0.11, C:0.17, G:0.25, T:0.46
Consensus pattern (18 bp):
TGCGATTTTATTTCGCGT
Found at i:23945 original size:21 final size:21
Alignment explanation
Indices: 23912--24012 Score: 59
Period size: 20 Copynumber: 4.9 Consensus size: 21
23902 TGCGAAAGTA
* * *
23912 AGTATCTCGTTGCGATTTTTT
1 AGTATCGCATTGCGATTTTTC
* **
23933 ATTATCGCATTGCGA-TAGTC
1 AGTATCGCATTGCGATTTTTC
*
23953 AGTATCGCATTGCGATTTTCCC
1 AGTATCGCATTGCGATTTT-TC
* *
23975 AAT-TCGCGTTGCGATTTACTT-
1 AGTATCGCATTGCGATTT--TTC
23996 A-T-TCGCATTGCGATTTT
1 AGTATCGCATTGCGATTTT
24013 CCCAATTCGC
Statistics
Matches: 62, Mismatches: 14, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
18 1 0.02
20 30 0.48
21 27 0.44
22 3 0.05
23 1 0.02
ACGTcount: A:0.19, C:0.20, G:0.19, T:0.43
Consensus pattern (21 bp):
AGTATCGCATTGCGATTTTTC
Found at i:23968 original size:20 final size:20
Alignment explanation
Indices: 23875--23968 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
23865 CGCTATGTAA
*
23875 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* *
23895 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
23915 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
23936 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
23956 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
23969 TTTCCCAATT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:23987 original size:41 final size:41
Alignment explanation
Indices: 23896--24030 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
23886 AAAGTCAGTA
* * * ** *
23896 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
23936 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
23978 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
24019 TCGCGTTGCGAT
1 TCGCGTTGCGAT
24031 TTACTTATTC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 3 0.04
41 74 0.94
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:24022 original size:21 final size:20
Alignment explanation
Indices: 23957--24049 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
23947 ATAGTCAGTA
*
23957 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACCAAT
* **
23978 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACCAAT
*
23998 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACCAAT
* **
24019 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACCAAT
24039 TCGCATTGCGA
1 TCGCATTGCGA
24050 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACCAAT
Found at i:24031 original size:41 final size:41
Alignment explanation
Indices: 23957--24049 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
23947 ATAGTCAGTA
23957 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
23998 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
24039 TCGCATTGCGA
1 TCGCATTGCGA
24050 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:28623 original size:31 final size:31
Alignment explanation
Indices: 28588--28650 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 31
28578 AAATAATAAT
28588 TACAA-TTTCTAATATTTTTAATTTATTAAAA
1 TACAATTTTCTAATATTTTTAATTTA-TAAAA
* * *
28619 TACAATTTTCTTATTTTTTTTATTTATAAAA
1 TACAATTTTCTAATATTTTTAATTTATAAAA
28650 T
1 T
28651 TATAAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 11 0.39
32 17 0.61
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (31 bp):
TACAATTTTCTAATATTTTTAATTTATAAAA
Found at i:28733 original size:22 final size:22
Alignment explanation
Indices: 28693--28753 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
28683 ATAAATAATA
*
28693 TTAAATAAATTAT-TATAATATT
1 TTAAATAAATAATAT-TAATATT
*
28715 TTAAA-ATAATAATATTAATCTT
1 TTAAATA-AATAATATTAATATT
*
28737 TTTAATAAATAATATTA
1 TTAAATAAATAATATTA
28754 TTTATTGTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
21 1 0.03
22 30 0.91
23 2 0.06
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
TTAAATAAATAATATTAATATT
Found at i:38286 original size:60 final size:58
Alignment explanation
Indices: 38220--38345 Score: 155
Period size: 60 Copynumber: 2.1 Consensus size: 58
38210 ACCATTTTAA
* * *
38220 AACTTTTAATAGTCGAAGGACTCAACAAAGTAAT-GTCATATAGTCAAGGGATCATTATGT
1 AACTTTTAATAGTAGAAGAACTCAACAAAG-AATACTC-TATAGTCAAGGGATCATT-TGT
* *
38280 AACTTTTAATAGTAGGAGAACTCAACAAAGCATCACTCTATAGTCAAGGGATCATTTGT
1 AACTTTTAATAGTAGAAGAACTCAACAAAGAAT-ACTCTATAGTCAAGGGATCATTTGT
38339 ATACTTT
1 A-ACTTT
38346 ACCCTTTAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
59 6 0.10
60 50 0.86
61 2 0.03
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (58 bp):
AACTTTTAATAGTAGAAGAACTCAACAAAGAATACTCTATAGTCAAGGGATCATTTGT
Found at i:39090 original size:115 final size:106
Alignment explanation
Indices: 38860--39098 Score: 298
Period size: 115 Copynumber: 2.2 Consensus size: 106
38850 AAAATAATAG
* * *
38860 TTAAGCTACTACACATGTAATTTACCTTTTTAATTGAAAGTACCCTAAGACAGAATGCTAAGACT
1 TTAA-CTACTAAACATGTAATTTACATTTTTAATTGAAAGTACCCTAAGACAGAATGCTAAGACA
* * *
38925 GTCAACTTGCTGCATTGAATGCTAAGAGTAAACACATGTAGT
65 GTCAACTTGCTGCACTGAATGCTAAGAGCAAACACATGCAGT
* * *
38967 TTAGCTACTAAACATGTAGTTTAGCATTTTTCAATTGAAAGTAGCCTAAGACAGAATGCTAAGAG
1 TTAACTACTAAACATGTAATTTA-CATTTTT-AATTGAAAGTACCCTAAGACAGAATGCT-A-AG
*
39032 TAAACACAGTCAATTTGCTGCACTGAATGCTAAGAGCAAACACATGCAGT
62 -----ACAGTCAACTTGCTGCACTGAATGCTAAGAGCAAACACATGCAGT
39082 TTAACTACTAAACATGT
1 TTAACTACTAAACATGT
39099 CCTTTTTCTG
Statistics
Matches: 112, Mismatches: 11, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
106 17 0.15
107 9 0.08
108 27 0.24
109 1 0.01
110 2 0.02
115 56 0.50
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (106 bp):
TTAACTACTAAACATGTAATTTACATTTTTAATTGAAAGTACCCTAAGACAGAATGCTAAGACAG
TCAACTTGCTGCACTGAATGCTAAGAGCAAACACATGCAGT
Found at i:40409 original size:21 final size:20
Alignment explanation
Indices: 40371--40419 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
40361 GAATTATAAA
40371 TTTATATAATATAAAATAGT
1 TTTATATAATATAAAATAGT
* *
40391 TTTATAATAATCTAGAATA-T
1 TTTAT-ATAATATAAAATAGT
*
40411 TCTATATAA
1 TTTATATAA
40420 AGATTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 4 0.16
20 10 0.40
21 11 0.44
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (20 bp):
TTTATATAATATAAAATAGT
Found at i:42293 original size:18 final size:18
Alignment explanation
Indices: 42276--42309 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
42266 TATTCGAATA
42276 ATTT-AATCGAATATAAT
1 ATTTAAATCGAATATAAT
42293 ATTTAAATCGAATATAA
1 ATTTAAATCGAATATAA
42310 AATCTTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (18 bp):
ATTTAAATCGAATATAAT
Found at i:43551 original size:22 final size:22
Alignment explanation
Indices: 43521--43582 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
43511 CTGCTGGGAG
* * *
43521 CATATGGGTATCGGTACTCTTT
1 CATACGGGTATCGATACTCCTT
43543 CATACGGGTATCGATACTCCTT
1 CATACGGGTATCGATACTCCTT
* *
43565 CGTAGGGGTATCGATACT
1 CATACGGGTATCGATACT
43583 ACTTGTATAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (22 bp):
CATACGGGTATCGATACTCCTT
Found at i:54018 original size:17 final size:18
Alignment explanation
Indices: 53971--54018 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
53961 TGGTAAAGTA
*
53971 AAATACAAATAAATAAAT
1 AAATACAAATAAAAAAAT
*
53989 AAA-ACAAACAAAAAAAT
1 AAATACAAATAAAAAAAT
54006 AAATA-AAATAAAA
1 AAATACAAATAAAA
54019 TAAAAAAGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 22 0.85
18 4 0.15
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (18 bp):
AAATACAAATAAAAAAAT
Found at i:54116 original size:14 final size:13
Alignment explanation
Indices: 54097--54148 Score: 59
Period size: 14 Copynumber: 3.8 Consensus size: 13
54087 ACTACATTAT
54097 AAATAAAAAATAAA
1 AAATAAAAAA-AAA
54111 AAATAATAAAAAAA
1 AAATAA-AAAAAAA
* *
54125 TAATAAAAAAAAC
1 AAATAAAAAAAAA
54138 AAATGAAAAAA
1 AAAT-AAAAAA
54149 TTAGGCAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
13 9 0.27
14 20 0.61
15 4 0.12
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.13
Consensus pattern (13 bp):
AAATAAAAAAAAA
Found at i:54119 original size:21 final size:20
Alignment explanation
Indices: 54095--54149 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 20
54085 AAACTACATT
54095 ATAAATAAAAAATAAAAAATA
1 ATAAATAAAAAATAAAAAA-A
54116 ATAAA-AAAATAATAAAAAAA
1 ATAAATAAAA-AATAAAAAAA
*
54136 ACAAATGAAAAAAT
1 ATAAAT-AAAAAAT
54150 TAGGCAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
20 9 0.30
21 17 0.57
22 4 0.13
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.16
Consensus pattern (20 bp):
ATAAATAAAAAATAAAAAAA
Found at i:54122 original size:11 final size:11
Alignment explanation
Indices: 54095--54135 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
54085 AAACTACATT
54095 ATAAATAAAA-A
1 ATAAA-AAAATA
54106 AT-AAAAAATA
1 ATAAAAAAATA
54116 ATAAAAAAATA
1 ATAAAAAAATA
54127 ATAAAAAAA
1 ATAAAAAAA
54136 ACAAATGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 4 0.14
10 5 0.18
11 19 0.68
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (11 bp):
ATAAAAAAATA
Found at i:54146 original size:24 final size:25
Alignment explanation
Indices: 54097--54149 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
54087 ACTACATTAT
54097 AAATAAAAAATAAAAAATAATAAAA
1 AAATAAAAAATAAAAAATAATAAAA
* *
54122 AAATAATAAAA-AAAACA-AATGAAA
1 AAATAA-AAAATAAAAAATAATAAAA
54146 AAAT
1 AAAT
54150 TAGGCAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 10 0.40
25 11 0.44
26 4 0.16
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.15
Consensus pattern (25 bp):
AAATAAAAAATAAAAAATAATAAAA
Found at i:57233 original size:5 final size:5
Alignment explanation
Indices: 57218--57256 Score: 53
Period size: 5 Copynumber: 7.6 Consensus size: 5
57208 CTAAACATTC
57218 TTTCTT TTTCT TTTCT TTTCTT TTTCT TTTCT TTT-T TTT
1 TTTC-T TTTCT TTTCT TTTC-T TTTCT TTTCT TTTCT TTT
57257 AACTTAGAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 4 0.12
5 19 0.59
6 9 0.28
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (5 bp):
TTTCT
Found at i:57234 original size:11 final size:11
Alignment explanation
Indices: 57218--57253 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
57208 CTAAACATTC
57218 TTTCTTTT-TCT
1 TTTCTTTTCT-T
57229 TTTCTTTTCTT
1 TTTCTTTTCTT
57240 TTTCTTTTCTT
1 TTTCTTTTCTT
57251 TTT
1 TTT
57254 TTTAACTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 23 0.96
12 1 0.04
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTCTTTTCTT
Found at i:57239 original size:16 final size:16
Alignment explanation
Indices: 57218--57256 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
57208 CTAAACATTC
57218 TTTCTTTTTCTTTTCT
1 TTTCTTTTTCTTTTCT
57234 TTTCTTTTTCTTTTCT
1 TTTCTTTTTCTTTTCT
57250 TTT-TTTT
1 TTTCTTTT
57257 AACTTAGAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 4 0.17
16 19 0.83
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (16 bp):
TTTCTTTTTCTTTTCT
Done.