Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1669
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: 38316
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Found at i:70 original size:22 final size:21
Alignment explanation
Indices: 45--89 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
35 GTAAGTTTTT
* *
45 AATTTTATTTTTAATGATAAAA
1 AATTTCATTATTAAT-ATAAAA
*
67 AATTTCATTATTACTATAAAA
1 AATTTCATTATTAATATAAAA
88 AA
1 AA
90 ATGAATTGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (21 bp):
AATTTCATTATTAATATAAAA
Found at i:1017 original size:30 final size:30
Alignment explanation
Indices: 983--1050 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 30
973 CAAAGTGCCC
*
983 TTAATTTTTAAATAAATTATCAAAATAATA
1 TTAATTTTAAAATAAATTATCAAAATAATA
* *
1013 TTAA-TTTAAAATAAATTATCGAAATATTA
1 TTAATTTTAAAATAAATTATCAAAATAATA
1042 TT-ATTTTAA
1 TTAATTTTAA
1051 CTCATAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 1 0.03
29 29 0.85
30 4 0.12
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (30 bp):
TTAATTTTAAAATAAATTATCAAAATAATA
Found at i:1524 original size:37 final size:36
Alignment explanation
Indices: 1446--1541 Score: 104
Period size: 38 Copynumber: 2.5 Consensus size: 36
1436 AAATATTTAA
*
1446 TTTAAACTTTTAATTAAATTATAAGTGTCTAATTATTT
1 TTTAAA-TTTAAATTAAATTATAAGTGTCTAATTA-TT
1484 TTTAAATTTAAATTAAAGGTTATAA-TAGTCTAATTATT
1 TTTAAATTTAAATTAAA--TTATAAGT-GTCTAATTATT
* *
1522 TTAAAATTTAAGTTATAATT
1 TTTAAATTTAAATTA-AATT
1542 GTTTAATTAT
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
37 12 0.24
38 22 0.43
39 17 0.33
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (36 bp):
TTTAAATTTAAATTAAATTATAAGTGTCTAATTATT
Found at i:1537 original size:31 final size:32
Alignment explanation
Indices: 1493--1552 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
1483 TTTTAAATTT
1493 AAATTAAAGGTTATAATAGTCTAATTATTTTA
1 AAATTAAAGGTTATAATAGTCTAATTATTTTA
* * *
1525 AAATTTAA-GTTATAATTGTTTAATTATT
1 AAATTAAAGGTTATAATAGTCTAATTATT
1553 AAGAGTTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 18 0.72
32 7 0.28
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (32 bp):
AAATTAAAGGTTATAATAGTCTAATTATTTTA
Found at i:1711 original size:110 final size:110
Alignment explanation
Indices: 1539--1759 Score: 406
Period size: 110 Copynumber: 2.0 Consensus size: 110
1529 TTAAGTTATA
* *
1539 ATTGTTTAATTATTAAGAGTTATAATTGTCCAACGTGGAATTCGCTTACTAGTTTAGCAATTTAA
1 ATTGTCTAATTATTAAGAGTTATAATTGACCAACGTGGAATTCGCTTACTAGTTTAGCAATTTAA
1604 AATAATTATAATTTTAAAAATAATTAGATGATTACAATCTAAATT
66 AATAATTATAATTTTAAAAATAATTAGATGATTACAATCTAAATT
*
1649 ATTGTCTAATTATTAAGAGTTATAATTGACCAACGTGGAATTCGCTTACTAGTTTAGTAATTTAA
1 ATTGTCTAATTATTAAGAGTTATAATTGACCAACGTGGAATTCGCTTACTAGTTTAGCAATTTAA
*
1714 AATAATTATAATTTTAAAAATAATTAGATGATTACAATCTCAATT
66 AATAATTATAATTTTAAAAATAATTAGATGATTACAATCTAAATT
1759 A
1 A
1760 AAATTTTAAA
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
110 107 1.00
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (110 bp):
ATTGTCTAATTATTAAGAGTTATAATTGACCAACGTGGAATTCGCTTACTAGTTTAGCAATTTAA
AATAATTATAATTTTAAAAATAATTAGATGATTACAATCTAAATT
Found at i:1786 original size:37 final size:36
Alignment explanation
Indices: 1716--1838 Score: 139
Period size: 37 Copynumber: 3.4 Consensus size: 36
1706 TAATTTAAAA
*
1716 TAATTATAATTTTAAAAATAATTAGATGATTACAATC
1 TAATTAAAATTTT-AAAATAATTAGATGATTACAATC
* *
1753 TCAATTAAAATTTTAAAATAATTAGAAGGTTACAATC
1 T-AATTAAAATTTTAAAATAATTAGATGATTACAATC
1790 T--TT--AATTTTAAAATAATTAGATGATTACAA-C
1 TAATTAAAATTTTAAAATAATTAGATGATTACAATC
*
1821 TTAAACTAAAATTTTAAA
1 -T-AATTAAAATTTTAAA
1839 TTAAACAAAT
Statistics
Matches: 73, Mismatches: 6, Indels: 14
0.78 0.06 0.15
Matches are distributed among these distances:
31 1 0.01
32 26 0.36
34 2 0.03
35 1 0.01
37 32 0.44
38 11 0.15
ACGTcount: A:0.49, C:0.07, G:0.06, T:0.39
Consensus pattern (36 bp):
TAATTAAAATTTTAAAATAATTAGATGATTACAATC
Found at i:1797 original size:32 final size:33
Alignment explanation
Indices: 1722--1819 Score: 126
Period size: 32 Copynumber: 2.8 Consensus size: 33
1712 AAAATAATTA
1722 TAATTTTAAAAATAATTAGATGATTACAATCTCAAT
1 TAATTTT-AAAATAATTAGATGATTACAATCT--AT
* *
1758 TAAAATTTTAAAATAATTAGAAGGTTACAATCT-T
1 T--AATTTTAAAATAATTAGATGATTACAATCTAT
1792 TAATTTTAAAATAATTAGATGATTACAA
1 TAATTTTAAAATAATTAGATGATTACAA
1820 CTTAAACTAA
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
32 25 0.45
34 2 0.04
36 1 0.02
37 22 0.39
38 6 0.11
ACGTcount: A:0.48, C:0.06, G:0.07, T:0.39
Consensus pattern (33 bp):
TAATTTTAAAATAATTAGATGATTACAATCTAT
Found at i:2039 original size:39 final size:41
Alignment explanation
Indices: 1996--2073 Score: 115
Period size: 39 Copynumber: 1.9 Consensus size: 41
1986 AATACCAACA
1996 TAATAATATAATTAAAAAATACT-TA-TATAATAATAACCT
1 TAATAATATAATTAAAAAATACTATACTATAATAATAACCT
* *
2035 TAATAATATTATTAAAAAATATTAATACTATAATAATAA
1 TAATAATATAATTAAAAAATACT-ATACTATAATAATAA
2074 TAGTAGGTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
39 21 0.62
41 2 0.06
42 11 0.32
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (41 bp):
TAATAATATAATTAAAAAATACTATACTATAATAATAACCT
Found at i:2542 original size:21 final size:21
Alignment explanation
Indices: 2516--2590 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
2506 TTTTACAATT
*
2516 TGTATCGATACAATAAGTGAA
1 TGTATCGATACAATAACTGAA
* * *
2537 TGTATCGATACATTCACT-TA
1 TGTATCGATACAATAACTGAA
**
2557 TGTATCGATAC-ATATTTGAAA
1 TGTATCGATACAATAACTG-AA
2578 TGTATCGATACAA
1 TGTATCGATACAA
2591 GACCATGTCG
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
19 2 0.05
20 12 0.29
21 27 0.64
22 1 0.02
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (21 bp):
TGTATCGATACAATAACTGAA
Found at i:3469 original size:10 final size:10
Alignment explanation
Indices: 3454--3478 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3444 ATGATTTATT
3454 TTATGAAAAA
1 TTATGAAAAA
3464 TTATGAAAAA
1 TTATGAAAAA
3474 TTATG
1 TTATG
3479 TTGAATGACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (10 bp):
TTATGAAAAA
Found at i:6308 original size:13 final size:13
Alignment explanation
Indices: 6290--6314 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6280 AGATTGCACA
6290 GTATCGATACATT
1 GTATCGATACATT
6303 GTATCGATACAT
1 GTATCGATACAT
6315 GACCAAATGT
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):
GTATCGATACATT
Found at i:6327 original size:20 final size:21
Alignment explanation
Indices: 6302--6354 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
6292 ATCGATACAT
**
6302 TGTATCGATACATGACCA-AA
1 TGTATCGATACATGAAAAGAA
*
6322 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACATGAAAAGAA
6343 TGTATCGATACA
1 TGTATCGATACA
6355 GGTTATTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGAAAAGAA
Found at i:6451 original size:33 final size:32
Alignment explanation
Indices: 6395--6462 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
6385 CTTTAACTGT
*
6395 TTGTATCGATACACCCAATATGTATCGATACA
1 TTGTATCGATACACCCAAAATGTATCGATACA
*
6427 TTGTATGGATACATCCCAAAATGTATCGATACA
1 TTGTATCGATACA-CCCAAAATGTATCGATACA
6460 TTG
1 TTG
6463 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 12 0.36
33 21 0.64
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (32 bp):
TTGTATCGATACACCCAAAATGTATCGATACA
Found at i:12616 original size:13 final size:13
Alignment explanation
Indices: 12594--12631 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
12584 CAGCATTCTC
* *
12594 TGTATTGATACAT
1 TGTATCGATACAG
12607 TGTATCGATACAG
1 TGTATCGATACAG
12620 TGTATCGATACA
1 TGTATCGATACA
12632 AAGAGTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:13097 original size:20 final size:21
Alignment explanation
Indices: 13065--13116 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 21
13055 CCCCTAGGCA
*
13065 GCACCCACCAGGTCGCGACC-G
1 GCACCC-CCAGGTCGCAACCGG
13086 GCACCCCCAGGTCGCAACCGG
1 GCACCCCCAGGTCGCAACCGG
13107 GCAGCCCCCA
1 GCA-CCCCCA
13117 CACTAGCAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 12 0.43
21 10 0.36
22 6 0.21
ACGTcount: A:0.19, C:0.50, G:0.27, T:0.04
Consensus pattern (21 bp):
GCACCCCCAGGTCGCAACCGG
Found at i:15111 original size:13 final size:13
Alignment explanation
Indices: 15093--15117 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15083 AGATTGCACA
15093 GTATCGATACATT
1 GTATCGATACATT
15106 GTATCGATACAT
1 GTATCGATACAT
15118 GACCAAATGT
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):
GTATCGATACATT
Found at i:15130 original size:20 final size:21
Alignment explanation
Indices: 15105--15156 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
15095 ATCGATACAT
**
15105 TGTATCGATACATGACCA-AA
1 TGTATCGATACATGAAAAGAA
*
15125 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACATGAAAAGAA
15146 TGTATCGATAC
1 TGTATCGATAC
15157 GGGTCATTGG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.29
Consensus pattern (21 bp):
TGTATCGATACATGAAAAGAA
Found at i:15236 original size:13 final size:13
Alignment explanation
Indices: 15218--15243 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
15208 ACACCCAATA
15218 TGTATCGATACAT
1 TGTATCGATACAT
15231 TGTATCGATACAT
1 TGTATCGATACAT
15244 CCCAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:15239 original size:32 final size:33
Alignment explanation
Indices: 15198--15265 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
15188 CCTTAACTGT
*
15198 TTGTATCGATACA-CCCAATATGTATCGATACA
1 TTGTATCGATACATCCCAAAATGTATCGATACA
15230 TTGTATCGATACATCCCAAAATGTATCGATACA
1 TTGTATCGATACATCCCAAAATGTATCGATACA
15263 TTG
1 TTG
15266 GCTTGTAACG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 13 0.38
33 21 0.62
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACATCCCAAAATGTATCGATACA
Found at i:18065 original size:26 final size:26
Alignment explanation
Indices: 18022--18125 Score: 82
Period size: 25 Copynumber: 4.2 Consensus size: 26
18012 ATTTTGAACC
*
18022 AAAAAAGAAAGAGAGAAAAAGGAAA-
1 AAAAAAGAAAGAGAGAAAAAAGAAAG
18047 AAAAAAGAAATGA-AGGAAAAAAGAAAG
1 AAAAAAGAAA-GAGA-GAAAAAAGAAAG
18074 --AAAA-AAAGA-AGAAAAAAGAAAG
1 AAAAAAGAAAGAGAGAAAAAAGAAAG
* * *
18096 -GAAAAGAAA-A-AAAAAGAAAGTAAG
1 AAAAAAGAAAGAGAGAAA-AAAGAAAG
18120 AAAAAA
1 AAAAAA
18126 AGATGGCCTA
Statistics
Matches: 68, Mismatches: 4, Indels: 14
0.79 0.05 0.16
Matches are distributed among these distances:
22 12 0.18
23 12 0.18
24 13 0.19
25 19 0.28
26 12 0.18
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (26 bp):
AAAAAAGAAAGAGAGAAAAAAGAAAG
Found at i:18073 original size:20 final size:20
Alignment explanation
Indices: 18022--18115 Score: 93
Period size: 20 Copynumber: 4.5 Consensus size: 20
18012 ATTTTGAACC
*
18022 AAAAAAGAAAGAGAGAAAAAGG
1 AAAAAAGAAAGA-A-AAGAAGG
*
18044 AAAAAA-AAAGAAATGAAGG
1 AAAAAAGAAAGAAAAGAAGG
*
18063 AAAAAAGAAAGAAAAAAAGAAG
1 AAAAAAGAAAGAAAAGAAG--G
*
18085 AAAAAAGAAAGGAAAAGAA-A
1 AAAAAAGAAA-GAAAAGAAGG
18105 AAAAAAGAAAG
1 AAAAAAGAAAG
18116 TAAGAAAAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
19 12 0.19
20 21 0.34
21 5 0.08
22 17 0.27
23 7 0.11
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.01
Consensus pattern (20 bp):
AAAAAAGAAAGAAAAGAAGG
Found at i:18089 original size:38 final size:40
Alignment explanation
Indices: 18022--18114 Score: 120
Period size: 38 Copynumber: 2.4 Consensus size: 40
18012 ATTTTGAACC
* *
18022 AAAAAAGAAAGAGAGAAAAAGGAAAAAAAAAGAAATG-AAGG
1 AAAAAAGAAAGA-A-AAAAAGGAAAAAAAAAGAAAGGAAAAG
*
18063 AAAAAAGAAAGAAAAAAA-GAAGAAAAAAGAAAGGAAAAG
1 AAAAAAGAAAGAAAAAAAGGAAAAAAAAAGAAAGGAAAAG
18102 AAAAAA-AAAGAAA
1 AAAAAAGAAAGAAA
18115 GTAAGAAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
38 21 0.44
39 14 0.29
40 1 0.02
41 12 0.25
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.01
Consensus pattern (40 bp):
AAAAAAGAAAGAAAAAAAGGAAAAAAAAAGAAAGGAAAAG
Found at i:18120 original size:28 final size:27
Alignment explanation
Indices: 18037--18126 Score: 99
Period size: 28 Copynumber: 3.1 Consensus size: 27
18027 AGAAAGAGAG
*
18037 AAAAAGGAAAAAAAAAGAAATGAAGGAAA
1 AAAAAAGAAAAAAAAAGAAAT-AA-GAAA
*
18066 AAAGAAAGAAAAAAAGAAGAAAAAAGAAA
1 AAA-AAAGAAAAAAA-AAGAAATAAGAAA
**
18095 GGAAAAGAAAAAAAAAGAAAGTAAGAAA
1 AAAAAAGAAAAAAAAAGAAA-TAAGAAA
18123 AAAA
1 AAAA
18127 GATGGCCTAG
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
27 6 0.12
28 19 0.37
29 8 0.16
30 12 0.24
31 6 0.12
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (27 bp):
AAAAAAGAAAAAAAAAGAAATAAGAAA
Found at i:18121 original size:38 final size:37
Alignment explanation
Indices: 18022--18126 Score: 113
Period size: 38 Copynumber: 2.7 Consensus size: 37
18012 ATTTTGAACC
* *
18022 AAAAAAGAAAGAGAGAAAAAGGAAAAAAAAAGAAATGAAGG
1 AAAAAAGAAAGA-A-AAAAA-G-AAAAAAAAGAAAGGAAAG
18063 AAAAAAGAAAGAAAAAAAGAAGAAAAAAGAAAGGAAAAG
1 AAAAAAGAAAGAAAAAAAGAA-AAAAAAGAAAGG-AAAG
**
18102 AAAAAA-AAAGAAAGTAAGAAAAAAA
1 AAAAAAGAAAGAAAAAAAGAAAAAAA
18127 GATGGCCTAG
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
37 7 0.12
38 24 0.41
39 14 0.24
40 1 0.02
41 12 0.21
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (37 bp):
AAAAAAGAAAGAAAAAAAGAAAAAAAAGAAAGGAAAG
Found at i:18125 original size:20 final size:19
Alignment explanation
Indices: 18038--18126 Score: 85
Period size: 20 Copynumber: 4.6 Consensus size: 19
18028 GAAAGAGAGA
18038 AAAAGGAAAAAAAAAGAAAT
1 AAAA-GAAAAAAAAAGAAAT
* *
18058 GAAGGAAAAAAGAAAGAAA-
1 AAAAGAAAAAA-AAAGAAAT
* *
18077 AAAAGAAGAAAAAAGAAAGG
1 AAAAGAAAAAAAAAGAAA-T
18097 AAAAGAAAAAAAAAGAAAGT
1 AAAAGAAAAAAAAAGAAA-T
18117 --AAGAAAAAAA
1 AAAAGAAAAAAA
18127 GATGGCCTAG
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
18 17 0.29
19 15 0.25
20 27 0.46
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (19 bp):
AAAAGAAAAAAAAAGAAAT
Found at i:25403 original size:18 final size:18
Alignment explanation
Indices: 25380--25414 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
25370 AAAAGAAAGG
25380 CTTAAACCTAATAAAAAA
1 CTTAAACCTAATAAAAAA
25398 CTTAAACCTAATAAAAA
1 CTTAAACCTAATAAAAA
25415 TCATAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.60, C:0.17, G:0.00, T:0.23
Consensus pattern (18 bp):
CTTAAACCTAATAAAAAA
Found at i:25421 original size:18 final size:18
Alignment explanation
Indices: 25382--25421 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
25372 AAGAAAGGCT
*
25382 TAAACCTAATAAAAAACT
1 TAAACCTAATAAAAAACA
*
25400 TAAACCTAATAAAAATCA
1 TAAACCTAATAAAAAACA
25418 TAAA
1 TAAA
25422 TTAACATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (18 bp):
TAAACCTAATAAAAAACA
Found at i:26226 original size:10 final size:10
Alignment explanation
Indices: 26200--26250 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
26190 AATCTTGATC
*
26200 TTTTCTTCTT
1 TTTTTTTCTT
26210 CTTTTTTTCTT
1 -TTTTTTTCTT
26221 TTTTTTTCTT
1 TTTTTTTCTT
* *
26231 TCTTTCTCTT
1 TTTTTTTCTT
*
26241 TTTTCTTCTT
1 TTTTTTTCTT
26251 CATAAAGGCA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
10 25 0.74
11 9 0.26
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:26240 original size:20 final size:18
Alignment explanation
Indices: 26198--26250 Score: 70
Period size: 20 Copynumber: 2.8 Consensus size: 18
26188 GCAATCTTGA
26198 TCTTTTCTTCTTCTTTTTT
1 TCTTTT-TTCTTCTTTTTT
*
26217 TCTTTTTTTTTCTTTCTTT
1 TCTTTTTTCTTCTTT-TTT
26236 CTCTTTTTTCTTCTT
1 -TCTTTTTTCTTCTT
26251 CATAAAGGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 8 0.27
19 9 0.30
20 13 0.43
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (18 bp):
TCTTTTTTCTTCTTTTTT
Found at i:26578 original size:34 final size:33
Alignment explanation
Indices: 26534--26759 Score: 267
Period size: 34 Copynumber: 6.7 Consensus size: 33
26524 AGGTTTGGTA
*
26534 AAATCCACCATTTAATCAACAATGGCAACCTACC
1 AAAT-CACCATTTAATCAACAATGGTAACCTACC
*
26568 AAATCTACCATTTAGTCAACAATGGTAAGCC-ACC
1 AAATC-ACCATTTAATCAACAATGGTAA-CCTACC
* *
26602 AAATCACCCATTTAATCAATAATGGTAAGCTACC
1 AAATCA-CCATTTAATCAACAATGGTAACCTACC
** *
26636 AAATTTCTCATTTAATCAACAATGGTAAGCTACC
1 AAATCAC-CATTTAATCAACAATGGTAACCTACC
* * *
26670 AAATCTCTCATTTAGTCAACAATGGCAAACC-ACC
1 AAATCAC-CATTTAATCAACAATGG-TAACCTACC
*
26704 AAATCACCCATTTAATCAACAATGGTAAACTACC
1 AAATCA-CCATTTAATCAACAATGGTAACCTACC
26738 AAATCACCATTTAATCAACAAT
1 AAATCACCATTTAATCAACAAT
26760 TCTCCCACTT
Statistics
Matches: 168, Mismatches: 16, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
33 23 0.14
34 139 0.83
35 6 0.04
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (33 bp):
AAATCACCATTTAATCAACAATGGTAACCTACC
Found at i:26683 original size:102 final size:101
Alignment explanation
Indices: 26534--26759 Score: 346
Period size: 102 Copynumber: 2.2 Consensus size: 101
26524 AGGTTTGGTA
* *
26534 AAATCCACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCC
1 AAAT-CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACC
* *
26599 ACCAAATCACCCATTTAATCAATAATGGTAAGCTACC
65 ACCAAATCACCCATTTAATCAACAATGGTAAACTACC
** * *
26636 AAATTTCTCATTTAATCAACAATGGTAAGCTACCAAATCT-CTCATTTAGTCAACAATGGCAAAC
1 AAATCAC-CATTTAATCAACAATGGCAACCTACCAAATCTAC-CATTTAGTCAACAATGGCAAAC
26700 CACCAAATCACCCATTTAATCAACAATGGTAAACTACC
64 CACCAAATCACCCATTTAATCAACAATGGTAAACTACC
26738 AAATCACCATTTAATCAACAAT
1 AAATCACCATTTAATCAACAAT
26760 TCTCCCACTT
Statistics
Matches: 112, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
101 17 0.15
102 95 0.85
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (101 bp):
AAATCACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCA
CCAAATCACCCATTTAATCAACAATGGTAAACTACC
Found at i:31214 original size:34 final size:33
Alignment explanation
Indices: 31166--31385 Score: 273
Period size: 34 Copynumber: 6.5 Consensus size: 33
31156 TGGTAAAAAC
*
31166 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
31199 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
31233 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
31267 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
31301 CTCCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 CACCATTTAATCAACAATGG-TAACCTACCAAAT
*
31334 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
31368 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
31386 AGAGAGGATA
Statistics
Matches: 163, Mismatches: 16, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
33 47 0.29
34 114 0.70
35 2 0.01
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:31334 original size:101 final size:101
Alignment explanation
Indices: 31166--31385 Score: 352
Period size: 101 Copynumber: 2.2 Consensus size: 101
31156 TGGTAAAAAC
* *
31166 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
* *
31231 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** * *
31267 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCT-CCATTTAGTCAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCA
31331 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
31368 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
31386 AGAGAGGATA
Statistics
Matches: 108, Mismatches: 10, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
100 15 0.14
101 63 0.58
102 30 0.28
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:31344 original size:67 final size:67
Alignment explanation
Indices: 31166--31385 Score: 291
Period size: 67 Copynumber: 3.3 Consensus size: 67
31156 TGGTAAAAAC
* *
31166 CACCATTTAATCAACAATGGC-AACCTACCAAATCTA-CCATTTAGTCAACAATGGTAAGCCACC
1 CACCATTTAATCAACAATGGCAAACC-ACCAAATC-ACCCATTTAATCAACAATGGTAAGCTACC
31229 AAAT
64 AAAT
* * * * ** *
31233 CACCCATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAGCTACCA
31298 AAT
65 AAT
* * *
31301 CTCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACCAA
1 CACCATTTAATCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAGCTACCAA
31366 AT
66 AT
31368 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
31386 AGAGAGGATA
Statistics
Matches: 129, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
67 74 0.57
68 53 0.41
69 2 0.02
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:31428 original size:21 final size:19
Alignment explanation
Indices: 31401--31451 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 19
31391 GGATAGATTC
*
31401 TTCTCTTTCTTTTTACTTT
1 TTCTCTTTCTTTTTATTTT
* *
31420 TTCTCTCTTCGTATTATTTT
1 TTCTCT-TTCTTTTTATTTT
31440 TT-TCTTTCTTTT
1 TTCTCTTTCTTTT
31452 GTTTTTCTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 5 0.19
19 9 0.35
20 12 0.46
ACGTcount: A:0.06, C:0.20, G:0.02, T:0.73
Consensus pattern (19 bp):
TTCTCTTTCTTTTTATTTT
Found at i:31968 original size:29 final size:29
Alignment explanation
Indices: 31925--32001 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 29
31915 TTTATTTAAA
* *
31925 ATAAAAGCTTCTTTAAATACAA-AAAAAT
1 ATAAAAACTTATTTAAATACAATAAAAAT
* * * *
31953 CATAAAAACTTATTTAGACACAATACAAGT
1 -ATAAAAACTTATTTAAATACAATAAAAAT
*
31983 ATAAAGACTTATTTAAATA
1 ATAAAAACTTATTTAAATA
32002 ATAAAATAAA
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
29 34 0.89
30 4 0.11
ACGTcount: A:0.53, C:0.12, G:0.05, T:0.30
Consensus pattern (29 bp):
ATAAAAACTTATTTAAATACAATAAAAAT
Found at i:33541 original size:2 final size:2
Alignment explanation
Indices: 33534--33592 Score: 57
Period size: 2 Copynumber: 30.0 Consensus size: 2
33524 TAAAATTTAT
* * *
33534 TA TA TA TA TA TG TA AA TA TA TA TT TA T- 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
* * *
33575 TG TT TA TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA
33593 AATTTCAAAA
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:33661 original size:22 final size:23
Alignment explanation
Indices: 33635--33683 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 23
33625 ACTTTTAAAA
33635 ATTAAATAAATATAA-AAA-TATT
1 ATTAAA-AAATATAATAAATTATT
*
33657 -TTTAAAAATATAATAAATTATT
1 ATTAAAAAATATAATAAATTATT
33679 ATTAA
1 ATTAA
33684 TTAGGTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
20 8 0.36
21 7 0.32
22 4 0.18
23 3 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
ATTAAAAAATATAATAAATTATT
Found at i:36998 original size:14 final size:14
Alignment explanation
Indices: 36975--37016 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
36965 TATTATTAAT
*
36975 TATTTAAATAATAA
1 TATTTTAATAATAA
*
36989 TATTTTAATAAAAA
1 TATTTTAATAATAA
*
37003 T-TTTTAAAAATAA
1 TATTTTAATAATAA
37016 T
1 T
37017 TATTAATATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TATTTTAATAATAA
Found at i:37046 original size:23 final size:25
Alignment explanation
Indices: 37020--37065 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
37010 AAATAATTAT
*
37020 TAATATT-TTT-ATTTTTAATAAAA
1 TAATATTATTTAATTTATAATAAAA
37043 TAATATTATTTAATTTATAATAA
1 TAATATTATTTAATTTATAATAA
37066 TAAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
24 3 0.15
25 10 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TAATATTATTTAATTTATAATAAAA
Found at i:37067 original size:23 final size:23
Alignment explanation
Indices: 37020--37088 Score: 58
Period size: 23 Copynumber: 3.1 Consensus size: 23
37010 AAATAATTAT
*
37020 TAATATT-TTT-ATTTTTAATAAAA
1 TAATATTATTTAATTTATAAT--AA
37043 TAATATTATTTAATTTATAATAA
1 TAATATTATTTAATTTATAATAA
* *
37066 TAA-ATAAATTAA--TATAATAA
1 TAATATTATTTAATTTATAATAA
37086 TAA
1 TAA
37089 GAATAATAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
20 11 0.27
22 7 0.17
23 12 0.29
24 3 0.07
25 8 0.20
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TAATATTATTTAATTTATAATAA
Found at i:37451 original size:9 final size:9
Alignment explanation
Indices: 37439--37477 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
37429 TATTAAAAAT
37439 AATATAATA
1 AATATAATA
37448 AATATAATA
1 AATATAATA
*
37457 TAATATATTTA
1 -AATATA-ATA
37468 AATATAATA
1 AATATAATA
37477 A
1 A
37478 TTTAATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 12 0.46
10 12 0.46
11 2 0.08
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (9 bp):
AATATAATA
Found at i:37454 original size:14 final size:14
Alignment explanation
Indices: 37432--37486 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
37422 TAATAAATAT
*
37432 TAAAAATAATATAA
1 TAAATATAATATAA
37446 TAAATATAATATAA
1 TAAATATAATATAA
* *
37460 TATATTTAAATATAA
1 TAAATAT-AATATAA
*
37475 T-AATTTAATATA
1 TAAATATAATATA
37487 TTTATTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
13 6 0.17
14 22 0.61
15 8 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TAAATATAATATAA
Found at i:37464 original size:21 final size:20
Alignment explanation
Indices: 37392--37477 Score: 67
Period size: 21 Copynumber: 4.5 Consensus size: 20
37382 TTTAAACATC
*
37392 ATATAA-AAATATAAAATAA
1 ATATAATAAATATATAATAA
* *
37411 ATA-AA-ATAT-TTTAATAA
1 ATATAATAAATATATAATAA
37428 ATATTAA-AAATAATATAATAA
1 ATA-TAATAAAT-ATATAATAA
*
37449 ATATAATATAATATAT-TTAA
1 ATATAATA-AATATATAATAA
37469 ATATAATAA
1 ATATAATAA
37478 TTTAATATAT
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
17 9 0.16
18 5 0.09
19 9 0.16
20 14 0.25
21 15 0.27
22 3 0.05
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
ATATAATAAATATATAATAA
Found at i:38076 original size:21 final size:22
Alignment explanation
Indices: 38051--38101 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 22
38041 AAATTTTTGA
*
38051 AATAAAAATA-TATTAATTAAT
1 AATAAAAATATTATAAATTAAT
**
38072 AAT-AATTTATTATAAATTAAT
1 AATAAAAATATTATAAATTAAT
38093 AA-AAAAATA
1 AATAAAAATA
38102 AAATCTTAGA
Statistics
Matches: 23, Mismatches: 5, Indels: 4
0.72 0.16 0.12
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
AATAAAAATATTATAAATTAAT
Done.