Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1518
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: 37110
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Found at i:1716 original size:2 final size:2
Alignment explanation
Indices: 1709--1759 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1699 ATCTGCTCTT
1709 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1751 TA TA TA TA T
1 TA TA TA TA T
1760 CTTGCTGCAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2394 original size:38 final size:39
Alignment explanation
Indices: 2343--2448 Score: 187
Period size: 38 Copynumber: 2.7 Consensus size: 39
2333 CAACCCTACC
2343 AAACTTACCATACCCAACCCAATAACCCAATCC-AAGTT
1 AAACTTACCATACCCAACCCAATAACCCAATCCAAAGTT
*
2381 AAACTTACCATACCCAACCTAATAACCCAATCCAAAGTT
1 AAACTTACCATACCCAACCCAATAACCCAATCCAAAGTT
*
2420 AAACTTACCATACTCAACCCAATAACCCA
1 AAACTTACCATACCCAACCCAATAACCCA
2449 TAACCAAACA
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
38 32 0.50
39 32 0.50
ACGTcount: A:0.43, C:0.36, G:0.02, T:0.19
Consensus pattern (39 bp):
AAACTTACCATACCCAACCCAATAACCCAATCCAAAGTT
Found at i:2701 original size:21 final size:21
Alignment explanation
Indices: 2675--2733 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
2665 AAGTTTTAAG
2675 ATTTTTATTTAAATTTAATTA
1 ATTTTTATTTAAATTTAATTA
** **
2696 ATTTTTAAATATCTTTAAATTA
1 ATTTTTATTTAAATTT-AATTA
*
2718 A-TTTTATTTAATTTTA
1 ATTTTTATTTAAATTTA
2734 TGTATTTTTA
Statistics
Matches: 29, Mismatches: 8, Indels: 3
0.73 0.20 0.08
Matches are distributed among these distances:
20 1 0.03
21 22 0.76
22 6 0.21
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
ATTTTTATTTAAATTTAATTA
Found at i:2733 original size:31 final size:31
Alignment explanation
Indices: 2683--2762 Score: 79
Period size: 31 Copynumber: 2.5 Consensus size: 31
2673 AGATTTTTAT
* *
2683 TTAAATTTAATTAATTTTTAAATATCTTTAAA
1 TTAATTTTATTTAA-TTTTAAATATCTTTAAA
** *
2715 TTAATTTTATTTAATTTTATGTATTTTTAAA
1 TTAATTTTATTTAATTTTAAATATCTTTAAA
*
2746 TTATATAATTATTTAAT
1 TTA-AT-TTTATTTAAT
2763 ATTTTTATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
31 17 0.43
32 14 0.35
33 9 0.22
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (31 bp):
TTAATTTTATTTAATTTTAAATATCTTTAAA
Found at i:4097 original size:54 final size:53
Alignment explanation
Indices: 4013--4118 Score: 160
Period size: 54 Copynumber: 2.0 Consensus size: 53
4003 GTTACTAAGG
4013 ATGCAGATTCCATATATTGGTGTGCATTTCCCCTGCTTTATTAGATTCACTACA
1 ATGCAGATTCCATATATTGGTGTG-ATTTCCCCTGCTTTATTAGATTCACTACA
* *
4067 ATGCAGATTGCATATATTGCCGTGTG-TTTCCCCTTCTTTATTAGATTCACTA
1 ATGCAGATTCCATATATTG--GTGTGATTTCCCCTGCTTTATTAGATTCACTA
4119 GAAATTTTTA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
54 43 0.90
56 5 0.10
ACGTcount: A:0.23, C:0.22, G:0.15, T:0.41
Consensus pattern (53 bp):
ATGCAGATTCCATATATTGGTGTGATTTCCCCTGCTTTATTAGATTCACTACA
Found at i:5400 original size:15 final size:14
Alignment explanation
Indices: 5368--5415 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
5358 TTTTTTTCAC
*
5368 TTTTTC-TTTTTCT
1 TTTTTCGTTTTTTT
*
5381 TTTTTGGTTGTTTTT
1 TTTTTCGTT-TTTTT
*
5396 TTTTTCGTTTTTCT
1 TTTTTCGTTTTTTT
5410 TTTTTC
1 TTTTTC
5416 ACCCTTCTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 5 0.17
14 12 0.41
15 12 0.41
ACGTcount: A:0.00, C:0.10, G:0.08, T:0.81
Consensus pattern (14 bp):
TTTTTCGTTTTTTT
Found at i:5727 original size:29 final size:30
Alignment explanation
Indices: 5695--5751 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
5685 TTCTTTTTTT
* *
5695 AAAAAATTACAAATAAATTATAA-ATTTAA
1 AAAAAATTAAAAATAAATAATAATATTTAA
*
5724 AAAAATTTAAAAATAAATAATAATATTT
1 AAAAAATTAAAAATAAATAATAATATTT
5752 TTAAAATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (30 bp):
AAAAAATTAAAAATAAATAATAATATTTAA
Found at i:5757 original size:29 final size:28
Alignment explanation
Indices: 5690--5758 Score: 66
Period size: 29 Copynumber: 2.4 Consensus size: 28
5680 GGATATTCTT
* * *
5690 TTTTTAAAAAATTACAAATAAATTATAAA
1 TTTTT-AAAATTTAAAAATAAATAATAAA
**
5719 TTTAAAAAAATTTAAAAATAAATAATAATA
1 TTT-TTAAAATTTAAAAATAAATAATAA-A
5749 TTTTTAAAAT
1 TTTTTAAAAT
5759 ATTATAATTT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
29 27 0.87
30 4 0.13
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (28 bp):
TTTTTAAAATTTAAAAATAAATAATAAA
Found at i:7805 original size:2 final size:2
Alignment explanation
Indices: 7798--7831 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
7788 GAGCATTACC
*
7798 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
7832 GGAGGGAGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:8136 original size:19 final size:20
Alignment explanation
Indices: 8098--8137 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
8088 TGATTTTTAT
8098 AAATTATTTATGTATTAAATA
1 AAATTATTTATG-ATTAAATA
*
8119 AAATTTTTTATG-TTAAATA
1 AAATTATTTATGATTAAATA
8138 TAATATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
21 11 0.61
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (20 bp):
AAATTATTTATGATTAAATA
Found at i:8228 original size:29 final size:30
Alignment explanation
Indices: 8165--8230 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 30
8155 TAAATTATTT
*
8165 ATTTTAA-AAATATTTTTATGAAATATTTA
1 ATTTTAATAAATATTTTTATGAAATATATA
* * * *
8194 AATTTAATATATATTTTTAT-ATATGTATA
1 ATTTTAATAAATATTTTTATGAAATATATA
8223 ATTTTAAT
1 ATTTTAAT
8231 CATGATAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
29 19 0.63
30 11 0.37
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (30 bp):
ATTTTAATAAATATTTTTATGAAATATATA
Found at i:9146 original size:20 final size:21
Alignment explanation
Indices: 9123--9208 Score: 54
Period size: 20 Copynumber: 4.1 Consensus size: 21
9113 AGACATGATG
*
9123 TAAAAATATAAT-ATATTTAA
1 TAAAAATAAAATAATATTTAA
* *
9143 TAAATATAAAATAATATTT-T
1 TAAAAATAAAATAATATTTAA
*
9163 TAGTATAATAAAAT-ATATTTAA
1 TA--AAAATAAAATAATATTTAA
* *
9185 -AATATTAAAATAATAAATTTAA
1 TAAAAATAAAATAAT--ATTTAA
9207 TA
1 TA
9209 TACATATTAT
Statistics
Matches: 51, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
19 9 0.18
20 14 0.27
21 13 0.25
22 14 0.27
23 1 0.02
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (21 bp):
TAAAAATAAAATAATATTTAA
Found at i:9164 original size:23 final size:22
Alignment explanation
Indices: 9130--9182 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
9120 ATGTAAAAAT
*
9130 ATAATATATTTAATAAATATAAA
1 ATAATATTTTTAATAAA-ATAAA
* *
9153 ATAATATTTTTAGTATAATAAA
1 ATAATATTTTTAATAAAATAAA
9175 AT-ATATTT
1 ATAATATTT
9183 AAAATATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 6 0.22
22 7 0.26
23 14 0.52
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
ATAATATTTTTAATAAAATAAA
Found at i:9225 original size:41 final size:39
Alignment explanation
Indices: 9130--9225 Score: 102
Period size: 41 Copynumber: 2.4 Consensus size: 39
9120 ATGTAAAAAT
* ** *
9130 ATAATATATTTAATAAATATAAAATAATATTTTTAGTATA
1 ATAATATATTTTA-AAATATAAAATAATAAATTTAATATA
*
9170 ATAAAATATATTTAAAATATTAAAATAATAAATTTAATATA
1 ATAATATAT-TTTAAAATA-TAAAATAATAAATTTAATATA
*
9211 CATATTATATTTTAA
1 -ATAATATATTTTAA
9226 TTTAAAATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
40 13 0.28
41 26 0.57
42 7 0.15
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (39 bp):
ATAATATATTTTAAAATATAAAATAATAAATTTAATATA
Found at i:9435 original size:2 final size:2
Alignment explanation
Indices: 9428--9466 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
9418 ACCGGGGGAA
9428 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9467 GAGAGAGAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9471 original size:2 final size:2
Alignment explanation
Indices: 9466--9492 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9456 ATATATATAT
9466 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
9493 AGGGGAGGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9983 original size:15 final size:16
Alignment explanation
Indices: 9948--9985 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
9938 TTAAAAATTT
*
9948 ATTTAAAAATAAATCA
1 ATTTTAAAATAAATCA
*
9964 ATTTTAAAATATAT-A
1 ATTTTAAAATAAATCA
9979 ATTTTAA
1 ATTTTAA
9986 TAGGTAGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTTTAAAATAAATCA
Found at i:10061 original size:16 final size:15
Alignment explanation
Indices: 10040--10071 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
10030 TATTATTACA
10040 TACTTTATTATTTTAT
1 TACTTTATT-TTTTAT
10056 TACTTTATTTTTTAT
1 TACTTTATTTTTTAT
10071 T
1 T
10072 TTTTATTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (15 bp):
TACTTTATTTTTTAT
Found at i:10071 original size:7 final size:8
Alignment explanation
Indices: 10043--10083 Score: 50
Period size: 7 Copynumber: 5.2 Consensus size: 8
10033 TATTACATAC
10043 TTTATTAT
1 TTTATTAT
*
10051 TTTATTAC
1 TTTATTAT
10059 TTTATT-T
1 TTTATTAT
10066 TTTATT-T
1 TTTATTAT
10073 TTTATTGAT
1 TTTATT-AT
10082 TT
1 TT
10084 AAACATTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
7 13 0.45
8 13 0.45
9 3 0.10
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (8 bp):
TTTATTAT
Found at i:11512 original size:18 final size:18
Alignment explanation
Indices: 11489--11527 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
11479 GCCATGTAAC
11489 AAAGGAATGTATAAACCT
1 AAAGGAATGTATAAACCT
*
11507 AAAGGAATGTATAAGCCT
1 AAAGGAATGTATAAACCT
11525 AAA
1 AAA
11528 AAAGGCTATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.51, C:0.10, G:0.18, T:0.21
Consensus pattern (18 bp):
AAAGGAATGTATAAACCT
Found at i:14431 original size:27 final size:26
Alignment explanation
Indices: 14393--14453 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
14383 TTGATGACCG
14393 ACATTTAGAACCTTCTA-ACCCTGAAT-A
1 ACATTT-GAACC-TCTAGACCCT-AATCA
*
14420 ACATTTGCAACCTCTAGAGCCTAATCA
1 ACATTTG-AACCTCTAGACCCTAATCA
14447 ACATTTG
1 ACATTTG
14454 GGTCATGGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
26 8 0.27
27 22 0.73
ACGTcount: A:0.34, C:0.26, G:0.10, T:0.30
Consensus pattern (26 bp):
ACATTTGAACCTCTAGACCCTAATCA
Found at i:16739 original size:22 final size:20
Alignment explanation
Indices: 16714--16756 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
16704 AAATTATTTT
*
16714 TATTTAAATTTAATTATAAAAA
1 TATTTAAATAT-A-TATAAAAA
16736 TATTTAAATATATATAAAAA
1 TATTTAAATATATATAAAAA
16756 T
1 T
16757 TACTTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
21 1 0.05
22 10 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TATTTAAATATATATAAAAA
Found at i:18740 original size:18 final size:19
Alignment explanation
Indices: 18705--18740 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
18695 ATGATCAAAC
18705 CTTATTTCATAGTATTTAA
1 CTTATTTCATAGTATTTAA
*
18724 CTTATTT-ATATTATTTA
1 CTTATTTCATAGTATTTA
18741 TAAATGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.31, C:0.08, G:0.03, T:0.58
Consensus pattern (19 bp):
CTTATTTCATAGTATTTAA
Found at i:23350 original size:16 final size:16
Alignment explanation
Indices: 23331--23383 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
23321 AACTCGTTCA
23331 GGTTCGAGTTTTTTCG
1 GGTTCGAGTTTTTTCG
*
23347 GGTTC-AGATTTTTTTG
1 GGTTCGAG-TTTTTTCG
* * *
23363 CGTTCGAGCTTGTTCG
1 GGTTCGAGTTTTTTCG
23379 GGTTC
1 GGTTC
23384 AGGCTTTTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 2 0.07
16 25 0.86
17 2 0.07
ACGTcount: A:0.08, C:0.15, G:0.30, T:0.47
Consensus pattern (16 bp):
GGTTCGAGTTTTTTCG
Found at i:23368 original size:32 final size:32
Alignment explanation
Indices: 23332--23405 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
23322 ACTCGTTCAG
* * *
23332 GTTCGAGTTTTTTCGGGTTCAGATTTTTTTGC
1 GTTCGAGCTTGTTCGGGTTCAGACTTTTTTGC
* *
23364 GTTCGAGCTTGTTCGGGTTCAGGCTTTTTTGG
1 GTTCGAGCTTGTTCGGGTTCAGACTTTTTTGC
*
23396 GTTTGAGCTT
1 GTTCGAGCTT
23406 ATTTGGATTC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.08, C:0.14, G:0.30, T:0.49
Consensus pattern (32 bp):
GTTCGAGCTTGTTCGGGTTCAGACTTTTTTGC
Found at i:23397 original size:16 final size:16
Alignment explanation
Indices: 23339--23398 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 16
23329 CAGGTTCGAG
**
23339 TTTTTTCGGGTTCAGAT
1 TTTTTT-GGGTTCAGGC
*
23356 TTTTTTGCGTTC-GAGC
1 TTTTTTGGGTTCAG-GC
* *
23372 TTGTTCGGGTTCAGGC
1 TTTTTTGGGTTCAGGC
23388 TTTTTTGGGTT
1 TTTTTTGGGTT
23399 TGAGCTTATT
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
15 1 0.03
16 25 0.76
17 7 0.21
ACGTcount: A:0.07, C:0.13, G:0.28, T:0.52
Consensus pattern (16 bp):
TTTTTTGGGTTCAGGC
Found at i:23417 original size:32 final size:32
Alignment explanation
Indices: 23332--23418 Score: 84
Period size: 32 Copynumber: 2.7 Consensus size: 32
23322 ACTCGTTCAG
* * * **
23332 GTTCGAGTTTTTTCGGGTTCAGATTTTTTTGC
1 GTTCGAGCTTATTCGGATTCAGGCTTTTTTGC
* * *
23364 GTTCGAGCTTGTTCGGGTTCAGGCTTTTTTGG
1 GTTCGAGCTTATTCGGATTCAGGCTTTTTTGC
* *
23396 GTTTGAGCTTATTTGGATTCAGG
1 GTTCGAGCTTATTCGGATTCAGG
23419 TTCAAATTTA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.10, C:0.13, G:0.30, T:0.47
Consensus pattern (32 bp):
GTTCGAGCTTATTCGGATTCAGGCTTTTTTGC
Found at i:24819 original size:16 final size:16
Alignment explanation
Indices: 24798--24895 Score: 92
Period size: 16 Copynumber: 6.1 Consensus size: 16
24788 CTTGGCTTTA
24798 GGTTCTCTCGGGTTCG
1 GGTTCTCTCGGGTTCG
* *
24814 GGTTCTTTCAGGTTCG
1 GGTTCTCTCGGGTTCG
*
24830 GGTTCTTTCGGGTTCG
1 GGTTCTCTCGGGTTCG
* * *
24846 AGCTT-TTTTGGGTTCG
1 -GGTTCTCTCGGGTTCG
*
24862 GGCTT-TCTCGAGTTCG
1 GG-TTCTCTCGGGTTCG
*
24878 GGTTGTCTCGGGTTCG
1 GGTTCTCTCGGGTTCG
24894 GG
1 GG
24896 CTATTTCAGG
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
15 3 0.04
16 63 0.91
17 3 0.04
ACGTcount: A:0.03, C:0.19, G:0.37, T:0.41
Consensus pattern (16 bp):
GGTTCTCTCGGGTTCG
Found at i:24907 original size:16 final size:16
Alignment explanation
Indices: 24805--24908 Score: 84
Period size: 16 Copynumber: 6.5 Consensus size: 16
24795 TTAGGTTCTC
*
24805 TCGGGTTCGGGTTCTT
1 TCGGGTTCGGGCTCTT
* *
24821 TCAGGTTCGGGTTCTT
1 TCGGGTTCGGGCTCTT
* *
24837 TCGGGTTCGAGCTTTT
1 TCGGGTTCGGGCTCTT
*
24853 TTGGGTTCGGGCT-TT
1 TCGGGTTCGGGCTCTT
* * * *
24868 CTCGAGTTCGGGTTGTC
1 -TCGGGTTCGGGCTCTT
*
24885 TCGGGTTCGGGCTATT
1 TCGGGTTCGGGCTCTT
*
24901 TCAGGTTC
1 TCGGGTTC
24909 AAATAATTTT
Statistics
Matches: 70, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
15 2 0.03
16 67 0.96
17 1 0.01
ACGTcount: A:0.05, C:0.19, G:0.35, T:0.41
Consensus pattern (16 bp):
TCGGGTTCGGGCTCTT
Found at i:25837 original size:18 final size:18
Alignment explanation
Indices: 25811--25850 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
25801 ACACTTGGAA
25811 TTTTCTTTTT-TTATTTAT
1 TTTTCTTTTTATTA-TTAT
*
25829 TTTTGTTTTTATTATTAT
1 TTTTCTTTTTATTATTAT
25847 TTTT
1 TTTT
25851 AATTCAGGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.12, C:0.03, G:0.03, T:0.82
Consensus pattern (18 bp):
TTTTCTTTTTATTATTAT
Found at i:27411 original size:13 final size:13
Alignment explanation
Indices: 27393--27419 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
27383 ATCCTTCATA
27393 TATCGATACAATG
1 TATCGATACAATG
27406 TATCGATACAATG
1 TATCGATACAATG
27419 T
1 T
27420 GAGTTTTAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:27488 original size:19 final size:20
Alignment explanation
Indices: 27464--27514 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
27454 TATTTTAGTG
*
27464 TGTATCGATACAATG-AACA
1 TGTATCGATACAAAGTAACA
*
27483 TGTATCGATACAAAGTAATA
1 TGTATCGATACAAAGTAACA
27503 TGTATCGATACA
1 TGTATCGATACA
27515 TCTGGGTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (20 bp):
TGTATCGATACAAAGTAACA
Found at i:30186 original size:13 final size:13
Alignment explanation
Indices: 30168--30192 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30158 AAAGAACGCA
30168 ATATCGATACAAT
1 ATATCGATACAAT
30181 ATATCGATACAA
1 ATATCGATACAA
30193 AGAACGCAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.08, T:0.28
Consensus pattern (13 bp):
ATATCGATACAAT
Found at i:30195 original size:33 final size:33
Alignment explanation
Indices: 30153--30244 Score: 130
Period size: 33 Copynumber: 2.8 Consensus size: 33
30143 CCCTTGTATT
*
30153 GATACAAAGAACGCAATATCGATACAATATATC
1 GATACAAAGAACGCAGTATCGATACAATATATC
* *
30186 GATACAAAGAACGCAGTATCGATAAAATGTATC
1 GATACAAAGAACGCAGTATCGATACAATATATC
** *
30219 GATATTAAGAACTCAGTATCGATACA
1 GATACAAAGAACGCAGTATCGATACA
30245 TCTGGGTTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.46, C:0.16, G:0.15, T:0.23
Consensus pattern (33 bp):
GATACAAAGAACGCAGTATCGATACAATATATC
Found at i:30457 original size:19 final size:19
Alignment explanation
Indices: 30433--30478 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
30423 AACTAAGAAC
*
30433 AATCATCAAAAAATCACAA
1 AATCATAAAAAAATCACAA
30452 AATCATAAAAAAATCACAA
1 AATCATAAAAAAATCACAA
30471 AATCATAA
1 AATCATAA
30479 GATCAATCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.65, C:0.17, G:0.00, T:0.17
Consensus pattern (19 bp):
AATCATAAAAAAATCACAA
Found at i:34529 original size:19 final size:19
Alignment explanation
Indices: 34505--34562 Score: 80
Period size: 19 Copynumber: 3.0 Consensus size: 19
34495 TTTGTATTGA
34505 TACATTGTATCGATACATG
1 TACATTGTATCGATACATG
* *
34524 TACATTATATTGATACATG
1 TACATTGTATCGATACATG
*
34543 GACAATTGTATCGATACATG
1 TAC-ATTGTATCGATACATG
34563 AAACTGGCAG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 19 0.58
20 14 0.42
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (19 bp):
TACATTGTATCGATACATG
Found at i:34616 original size:20 final size:20
Alignment explanation
Indices: 34591--34644 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
34581 CTACTGCTGT
*
34591 TTGTATCGATACATGGT-ACA
1 TTGTATCGATACATGATGA-A
*
34611 TTGTATTGATACATGATGAA
1 TTGTATCGATACATGATGAA
34631 TTGTATCGATACAT
1 TTGTATCGATACAT
34645 TGCTTGTAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (20 bp):
TTGTATCGATACATGATGAA
Done.