Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1067
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: 39872
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Found at i:1717 original size:2 final size:2
Alignment explanation
Indices: 1710--1764 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1700 ATCTGCTCTT
1710 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
1752 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
1765 CTTGCTGCAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2403 original size:39 final size:39
Alignment explanation
Indices: 2349--2455 Score: 196
Period size: 39 Copynumber: 2.7 Consensus size: 39
2339 CAACCCTACC
2349 AAACTTACCATACCCAACCCAATAACCCAATCCAAAGTT
1 AAACTTACCATACCCAACCCAATAACCCAATCCAAAGTT
*
2388 AAACTTACCATACCCAACCTAATAACCCAATCCAAAGTT
1 AAACTTACCATACCCAACCCAATAACCCAATCCAAAGTT
*
2427 AAACTTACCATACTCAACCCAATAACCCA
1 AAACTTACCATACCCAACCCAATAACCCA
2456 TAACCAAACA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 65 1.00
ACGTcount: A:0.44, C:0.36, G:0.02, T:0.19
Consensus pattern (39 bp):
AAACTTACCATACCCAACCCAATAACCCAATCCAAAGTT
Found at i:2707 original size:21 final size:21
Alignment explanation
Indices: 2683--2741 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
2673 AGTTTTAAAG
2683 ATTTTTATTTAAATTTAATTA
1 ATTTTTATTTAAATTTAATTA
** **
2704 ATTTTTAAATATCTTTAAATTA
1 ATTTTTATTTAAATTT-AATTA
*
2726 A-TTTTATTTAATTTTA
1 ATTTTTATTTAAATTTA
2742 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:2710 original size:31 final size:32
Alignment explanation
Indices: 2670--2740 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
2660 ATGAAAATAG
* * *
2670 TTAAGTTTTAAAGAT-TTTTATTTAAATTTAA
1 TTAATTTTTAAAGATCTTTAAATTAAATTTAA
* * *
2701 TTAATTTTTAAATATCTTTAAATTAATTTTAT
1 TTAATTTTTAAAGATCTTTAAATTAAATTTAA
2733 TTAATTTT
1 TTAATTTT
2741 ATGTATTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (32 bp):
TTAATTTTTAAAGATCTTTAAATTAAATTTAA
Found at i:2722 original size:41 final size:41
Alignment explanation
Indices: 2676--2754 Score: 99
Period size: 41 Copynumber: 1.9 Consensus size: 41
2666 ATAGTTAAGT
*
2676 TTTAAA-GATTTTTATTTAAATTTAAT-TAATTTTTAAATATC
1 TTTAAATGAATTTTATTT-AATTTAATGT-ATTTTTAAATATC
* *
2717 TTTAAATTAATTTTATTTAATTTTATGTATTTTTAAAT
1 TTTAAATGAATTTTATTTAATTTAATGTATTTTTAAAT
2755 TATATAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
41 23 0.70
42 10 0.30
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (41 bp):
TTTAAATGAATTTTATTTAATTTAATGTATTTTTAAATATC
Found at i:2741 original size:31 final size:31
Alignment explanation
Indices: 2691--2770 Score: 79
Period size: 31 Copynumber: 2.5 Consensus size: 31
2681 AGATTTTTAT
* *
2691 TTAAATTTAATTAATTTTTAAATATCTTTAAA
1 TTAATTTTATTTAA-TTTTAAATATCTTTAAA
** *
2723 TTAATTTTATTTAATTTTATGTATTTTTAAA
1 TTAATTTTATTTAATTTTAAATATCTTTAAA
*
2754 TTATATAATTATTTAAT
1 TTA-AT-TTTATTTAAT
2771 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:4106 original size:54 final size:53
Alignment explanation
Indices: 4022--4127 Score: 160
Period size: 54 Copynumber: 2.0 Consensus size: 53
4012 GTTACTAAGG
4022 ATGCAGATTCCATATATTGGTGTGCATTTCCCCTGCTTTATTAGATTCACTACA
1 ATGCAGATTCCATATATTGGTGTG-ATTTCCCCTGCTTTATTAGATTCACTACA
* *
4076 ATGCAGATTGCATATATTGCCGTGTG-TTTCCCCTTCTTTATTAGATTCACTA
1 ATGCAGATTCCATATATTG--GTGTGATTTCCCCTGCTTTATTAGATTCACTA
4128 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:5403 original size:16 final size:14
Alignment explanation
Indices: 5377--5425 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
5367 TTTTTTTCAC
5377 TTTTTC-TTTTTCT
1 TTTTTCGTTTTTCT
* *
5390 TTTTTGGTTGTTTTTT
1 TTTTTCG-T-TTTTCT
5406 TTTTTCGTTTTTCT
1 TTTTTCGTTTTTCT
5420 TTTTTC
1 TTTTTC
5426 ACCCTTCTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
13 5 0.17
14 11 0.38
15 2 0.07
16 11 0.38
ACGTcount: A:0.00, C:0.10, G:0.08, T:0.82
Consensus pattern (14 bp):
TTTTTCGTTTTTCT
Found at i:5738 original size:29 final size:30
Alignment explanation
Indices: 5706--5762 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
5696 TCTTTTTTTT
*
5706 AAAAAATTACAAA-TAAATTATAA-ATTTAA
1 AAAAAATTA-AAAGTAAATAATAATATTTAA
*
5735 AAAAATTTAAAAGTAAATAATAATATTT
1 AAAAAATTAAAAGTAAATAATAATATTT
5763 TTAAAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 3 0.12
29 17 0.71
30 4 0.17
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (30 bp):
AAAAAATTAAAAGTAAATAATAATATTTAA
Found at i:7816 original size:2 final size:2
Alignment explanation
Indices: 7809--7842 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
7799 GAGCATTACC
*
7809 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
7843 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:8147 original size:19 final size:20
Alignment explanation
Indices: 8109--8148 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
8099 TGATTTTTAT
8109 AAATTATTTATGTATTAAATA
1 AAATTATTTATG-ATTAAATA
*
8130 AAATTTTTTATG-TTAAATA
1 AAATTATTTATGATTAAATA
8149 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:8239 original size:29 final size:29
Alignment explanation
Indices: 8176--8240 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
8166 TAAATTATTT
*
8176 ATTTTAA-AATATTTTTATGAAATATTTA
1 ATTTTAATAATATTTTTATGAAATATATA
* * *
8204 AATTTAATATATATTTTTAT-ATATGTATA
1 ATTTTAATA-ATATTTTTATGAAATATATA
8233 ATTTTAAT
1 ATTTTAAT
8241 CATTATAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 6 0.20
29 14 0.47
30 10 0.33
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (29 bp):
ATTTTAATAATATTTTTATGAAATATATA
Found at i:9156 original size:20 final size:21
Alignment explanation
Indices: 9133--9218 Score: 54
Period size: 20 Copynumber: 4.1 Consensus size: 21
9123 AGACATGATG
*
9133 TAAAAATATAAT-ATATTTAA
1 TAAAAATAAAATAATATTTAA
* *
9153 TAAATATAAAATAATATTT-T
1 TAAAAATAAAATAATATTTAA
*
9173 TAGTATAATAAAAT-ATATTTAA
1 TA--AAAATAAAATAATATTTAA
* *
9195 -AATATTAAAATAATAAATTTAA
1 TAAAAATAAAATAAT--ATTTAA
9217 TA
1 TA
9219 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:9174 original size:23 final size:22
Alignment explanation
Indices: 9140--9192 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
9130 ATGTAAAAAT
*
9140 ATAATATATTTAATAAATATAAA
1 ATAATATTTTTAATAAA-ATAAA
* *
9163 ATAATATTTTTAGTATAATAAA
1 ATAATATTTTTAATAAAATAAA
9185 AT-ATATTT
1 ATAATATTT
9193 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:9235 original size:41 final size:39
Alignment explanation
Indices: 9140--9235 Score: 102
Period size: 41 Copynumber: 2.4 Consensus size: 39
9130 ATGTAAAAAT
* ** *
9140 ATAATATATTTAATAAATATAAAATAATATTTTTAGTATA
1 ATAATATATTTTA-AAATATAAAATAATAAATTTAATATA
*
9180 ATAAAATATATTTAAAATATTAAAATAATAAATTTAATATA
1 ATAATATAT-TTTAAAATA-TAAAATAATAAATTTAATATA
*
9221 CATATTATATTTTAA
1 -ATAATATATTTTAA
9236 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:9445 original size:2 final size:2
Alignment explanation
Indices: 9438--9470 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
9428 ACCGGGGGAA
9438 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 A
9471 GAGAGAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9475 original size:2 final size:2
Alignment explanation
Indices: 9470--9498 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9460 ATATATATAT
9470 AG 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 AG A
9499 AGGGGAGGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9986 original size:15 final size:16
Alignment explanation
Indices: 9951--9988 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
9941 TTAAAAATTT
*
9951 ATTTAAAAATAAATCA
1 ATTTTAAAATAAATCA
*
9967 ATTTTAAAATATAT-A
1 ATTTTAAAATAAATCA
9982 ATTTTAA
1 ATTTTAA
9989 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:10064 original size:16 final size:15
Alignment explanation
Indices: 10043--10074 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
10033 TATTATTACA
10043 TACTTTATTATTTTAT
1 TACTTTATT-TTTTAT
10059 TACTTTATTTTTTAT
1 TACTTTATTTTTTAT
10074 T
1 T
10075 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:10074 original size:7 final size:8
Alignment explanation
Indices: 10046--10086 Score: 50
Period size: 7 Copynumber: 5.2 Consensus size: 8
10036 TATTACATAC
10046 TTTATTAT
1 TTTATTAT
*
10054 TTTATTAC
1 TTTATTAT
10062 TTTATT-T
1 TTTATTAT
10069 TTTATT-T
1 TTTATTAT
10076 TTTATTGAT
1 TTTATT-AT
10085 TT
1 TT
10087 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:11515 original size:18 final size:18
Alignment explanation
Indices: 11492--11530 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
11482 GCCATGTAAC
11492 AAAGGAATGTATAAACCT
1 AAAGGAATGTATAAACCT
*
11510 AAAGGAATGTATAAGCCT
1 AAAGGAATGTATAAACCT
11528 AAA
1 AAA
11531 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:14439 original size:27 final size:26
Alignment explanation
Indices: 14401--14461 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
14391 TTGATGACCG
14401 ACATTTAGAACCTTCTA-ACCCTGAAT-A
1 ACATTT-GAACC-TCTAGACCCT-AATCA
*
14428 ACATTTGCAACCTCTAGAGCCTAATCA
1 ACATTTG-AACCTCTAGACCCTAATCA
14455 ACATTTG
1 ACATTTG
14462 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:16747 original size:22 final size:20
Alignment explanation
Indices: 16722--16764 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
16712 AAATTATTTT
*
16722 TATTTAAATTTAATTATAAAAA
1 TATTTAAATAT-A-TATAAAAA
16744 TATTTAAATATATATAAAAA
1 TATTTAAATATATATAAAAA
16764 T
1 T
16765 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:18748 original size:18 final size:19
Alignment explanation
Indices: 18713--18748 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
18703 ATGATCAAAC
18713 CTTATTTCATAGTATTTAA
1 CTTATTTCATAGTATTTAA
*
18732 CTTATTT-ATATTATTTA
1 CTTATTTCATAGTATTTA
18749 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:23358 original size:16 final size:16
Alignment explanation
Indices: 23339--23391 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
23329 AACTCGTTCA
23339 GGTTCGAGTTTTTTCG
1 GGTTCGAGTTTTTTCG
*
23355 GGTTC-AGATTTTTTTG
1 GGTTCGAG-TTTTTTCG
* * *
23371 CGTTCGAGCTTGTTCG
1 GGTTCGAGTTTTTTCG
23387 GGTTC
1 GGTTC
23392 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:23376 original size:32 final size:32
Alignment explanation
Indices: 23340--23413 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
23330 ACTCGTTCAG
* * *
23340 GTTCGAGTTTTTTCGGGTTCAGATTTTTTTGC
1 GTTCGAGCTTGTTCGGGTTCAGACTTTTTTGC
* *
23372 GTTCGAGCTTGTTCGGGTTCAGGCTTTTTTGG
1 GTTCGAGCTTGTTCGGGTTCAGACTTTTTTGC
*
23404 GTTTGAGCTT
1 GTTCGAGCTT
23414 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:23405 original size:16 final size:16
Alignment explanation
Indices: 23347--23406 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 16
23337 CAGGTTCGAG
**
23347 TTTTTTCGGGTTCAGAT
1 TTTTTT-GGGTTCAGGC
*
23364 TTTTTTGCGTTC-GAGC
1 TTTTTTGGGTTCAG-GC
* *
23380 TTGTTCGGGTTCAGGC
1 TTTTTTGGGTTCAGGC
23396 TTTTTTGGGTT
1 TTTTTTGGGTT
23407 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:23425 original size:32 final size:32
Alignment explanation
Indices: 23340--23426 Score: 84
Period size: 32 Copynumber: 2.7 Consensus size: 32
23330 ACTCGTTCAG
* * * **
23340 GTTCGAGTTTTTTCGGGTTCAGATTTTTTTGC
1 GTTCGAGCTTATTCGGATTCAGGCTTTTTTGC
* * *
23372 GTTCGAGCTTGTTCGGGTTCAGGCTTTTTTGG
1 GTTCGAGCTTATTCGGATTCAGGCTTTTTTGC
* *
23404 GTTTGAGCTTATTTGGATTCAGG
1 GTTCGAGCTTATTCGGATTCAGG
23427 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:24828 original size:16 final size:16
Alignment explanation
Indices: 24807--24904 Score: 92
Period size: 16 Copynumber: 6.1 Consensus size: 16
24797 CTTGGCTTTA
24807 GGTTCTCTCGGGTTCG
1 GGTTCTCTCGGGTTCG
* *
24823 GGTTCTTTCAGGTTCG
1 GGTTCTCTCGGGTTCG
*
24839 GGTTCTTTCGGGTTCG
1 GGTTCTCTCGGGTTCG
* * *
24855 AGCTT-TTTTGGGTTCG
1 -GGTTCTCTCGGGTTCG
*
24871 GGCTT-TCTCGAGTTCG
1 GG-TTCTCTCGGGTTCG
*
24887 GGTTGTCTCGGGTTCG
1 GGTTCTCTCGGGTTCG
24903 GG
1 GG
24905 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:24916 original size:16 final size:16
Alignment explanation
Indices: 24814--24917 Score: 84
Period size: 16 Copynumber: 6.5 Consensus size: 16
24804 TTAGGTTCTC
*
24814 TCGGGTTCGGGTTCTT
1 TCGGGTTCGGGCTCTT
* *
24830 TCAGGTTCGGGTTCTT
1 TCGGGTTCGGGCTCTT
* *
24846 TCGGGTTCGAGCTTTT
1 TCGGGTTCGGGCTCTT
*
24862 TTGGGTTCGGGCT-TT
1 TCGGGTTCGGGCTCTT
* * * *
24877 CTCGAGTTCGGGTTGTC
1 -TCGGGTTCGGGCTCTT
*
24894 TCGGGTTCGGGCTATT
1 TCGGGTTCGGGCTCTT
*
24910 TCAGGTTC
1 TCGGGTTC
24918 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:25846 original size:18 final size:18
Alignment explanation
Indices: 25820--25859 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
25810 ACACTTGGAA
25820 TTTTCTTTTT-TTATTTAT
1 TTTTCTTTTTATTA-TTAT
*
25838 TTTTGTTTTTATTATTAT
1 TTTTCTTTTTATTATTAT
25856 TTTT
1 TTTT
25860 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:27419 original size:13 final size:13
Alignment explanation
Indices: 27401--27427 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
27391 ATCCTTCATA
27401 TATCGATACAATG
1 TATCGATACAATG
27414 TATCGATACAATG
1 TATCGATACAATG
27427 T
1 T
27428 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:27496 original size:19 final size:20
Alignment explanation
Indices: 27472--27522 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
27462 TATTTTAGTG
*
27472 TGTATCGATACAATG-AACA
1 TGTATCGATACAAAGTAACA
*
27491 TGTATCGATACAAAGTAATA
1 TGTATCGATACAAAGTAACA
27511 TGTATCGATACA
1 TGTATCGATACA
27523 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:30197 original size:13 final size:13
Alignment explanation
Indices: 30179--30203 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30169 AAAGAACGCA
30179 ATATCGATACAAT
1 ATATCGATACAAT
30192 ATATCGATACAA
1 ATATCGATACAA
30204 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:30206 original size:33 final size:33
Alignment explanation
Indices: 30164--30255 Score: 130
Period size: 33 Copynumber: 2.8 Consensus size: 33
30154 CCCTTGTATT
*
30164 GATACAAAGAACGCAATATCGATACAATATATC
1 GATACAAAGAACGCAGTATCGATACAATATATC
* *
30197 GATACAAAGAACGCAGTATCGATAAAATGTATC
1 GATACAAAGAACGCAGTATCGATACAATATATC
** *
30230 GATATTAAGAACTCAGTATCGATACA
1 GATACAAAGAACGCAGTATCGATACA
30256 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:30468 original size:19 final size:19
Alignment explanation
Indices: 30444--30489 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
30434 AACTAAGAAC
*
30444 AATCATCAAAAAATCACAA
1 AATCATAAAAAAATCACAA
30463 AATCATAAAAAAATCACAA
1 AATCATAAAAAAATCACAA
30482 AATCATAA
1 AATCATAA
30490 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:32862 original size:33 final size:33
Alignment explanation
Indices: 32825--32891 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
32815 TTCAATGATT
32825 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
32858 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
32891 T
1 T
32892 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:32863 original size:13 final size:13
Alignment explanation
Indices: 32845--32869 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
32835 CATAAAATGT
32845 TGTATCGATACAA
1 TGTATCGATACAA
32858 TGTATCGATACA
1 TGTATCGATACA
32870 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:32953 original size:13 final size:13
Alignment explanation
Indices: 32935--32959 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
32925 ATTACTCACA
32935 TGTATCGATACAT
1 TGTATCGATACAT
32948 TGTATCGATACA
1 TGTATCGATACA
32960 CTGATTTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:33024 original size:52 final size:52
Alignment explanation
Indices: 32968--33088 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
32958 CACTGATTTT
*
32968 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
33020 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
33072 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
33089 TAACTTTTCA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:38188 original size:19 final size:19
Alignment explanation
Indices: 38164--38221 Score: 80
Period size: 19 Copynumber: 3.0 Consensus size: 19
38154 TTTGTATTGA
38164 TACATTGTATCGATACATG
1 TACATTGTATCGATACATG
* *
38183 TACATTATATTGATACATG
1 TACATTGTATCGATACATG
*
38202 GACAATTGTATCGATACATG
1 TAC-ATTGTATCGATACATG
38222 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:38275 original size:20 final size:20
Alignment explanation
Indices: 38250--38303 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
38240 CTACTGCTGT
*
38250 TTGTATCGATACATGGT-ACA
1 TTGTATCGATACATGATGA-A
*
38270 TTGTATTGATACATGATGAA
1 TTGTATCGATACATGATGAA
38290 TTGTATCGATACAT
1 TTGTATCGATACAT
38304 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.