Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12
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: 24583705
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1509421 characters in sequence are not A, C, G, or T
File 5 of 75
Found at i:1243954 original size:24 final size:23
Alignment explanation
Indices: 1243919--1243965 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
1243909 TTTTATGTTT
*
1243919 TATAAATTATATAATATATCTATA
1 TATAAATAATATAATATAT-TATA
*
1243943 TATAAATAATATATTATATTATA
1 TATAAATAATATAATATATTATA
1243966 AACATAGAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
TATAAATAATATAATATATTATA
Found at i:1248507 original size:23 final size:23
Alignment explanation
Indices: 1248467--1248513 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
1248457 CCAAGTTATT
*
1248467 ACCCAACCCAAAGTAAAATTAAA
1 ACCCAACCCAAAGTAAAATGAAA
*
1248490 ACCCAACCC-AATTAAAAATGAAA
1 ACCCAACCCAAAGT-AAAATGAAA
1248513 A
1 A
1248514 TAAAATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.57, C:0.26, G:0.04, T:0.13
Consensus pattern (23 bp):
ACCCAACCCAAAGTAAAATGAAA
Found at i:1251723 original size:23 final size:24
Alignment explanation
Indices: 1251693--1251736 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
1251683 AATATTTTTT
*
1251693 TTTATTTTTTTATTT-TTAAAATA
1 TTTATTTTTGTATTTATTAAAATA
1251716 TTT-TTTTTGTATTTATTAAAA
1 TTTATTTTTGTATTTATTAAAA
1251737 ATCGGGCCGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (24 bp):
TTTATTTTTGTATTTATTAAAATA
Found at i:1252844 original size:28 final size:30
Alignment explanation
Indices: 1252790--1252855 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
1252780 AGGGGTCTGG
* * *
1252790 TTATAAAAATTGTACTTTATTCCTTTAA-AA
1 TTAT-AAAATTGTAATTTAATCATTTAATAA
1252820 TTATAAAATT-TAATTTAATCATTTAATAA
1 TTATAAAATTGTAATTTAATCATTTAATAA
1252849 TTATAAA
1 TTATAAA
1252856 GATATAGACT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 13 0.41
29 15 0.47
30 4 0.12
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (30 bp):
TTATAAAATTGTAATTTAATCATTTAATAA
Found at i:1255054 original size:2 final size:2
Alignment explanation
Indices: 1255047--1255083 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1255037 CGACTTTTCT
1255047 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1255084 TTGTTAATAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1259781 original size:21 final size:20
Alignment explanation
Indices: 1259752--1259790 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1259742 TTGAAAAAAC
*
1259752 ACAAAAATAAAGATAGAAATA
1 ACAAAAAT-AAGAAAGAAATA
*
1259773 ACAAGAATAAGAAAGAAA
1 ACAAAAATAAGAAAGAAA
1259791 GAGATATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.72, C:0.05, G:0.13, T:0.10
Consensus pattern (20 bp):
ACAAAAATAAGAAAGAAATA
Found at i:1263970 original size:18 final size:19
Alignment explanation
Indices: 1263923--1263970 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
1263913 CTAATTAATT
* *
1263923 ATTTTTAAAATAAATGGTA
1 ATTTTTTAAATAAATAGTA
*
1263942 AGTTTTT-AATAAA-AGTA
1 ATTTTTTAAATAAATAGTA
1263959 ATTTTTTAAATA
1 ATTTTTTAAATA
1263971 TTTTTTAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 9 0.38
18 10 0.42
19 5 0.21
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (19 bp):
ATTTTTTAAATAAATAGTA
Found at i:1264075 original size:20 final size:20
Alignment explanation
Indices: 1264050--1264095 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
1264040 ATTTTTAATA
1264050 AAAGTAGGGGGATTGCAATT
1 AAAGTAGGGGGATTGCAATT
1264070 AAAGTAGGGGGATTGCAATT
1 AAAGTAGGGGGATTGCAATT
1264090 AAAGTA
1 AAAGTA
1264096 TAATTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.39, C:0.04, G:0.33, T:0.24
Consensus pattern (20 bp):
AAAGTAGGGGGATTGCAATT
Found at i:1264143 original size:63 final size:63
Alignment explanation
Indices: 1264070--1264190 Score: 242
Period size: 63 Copynumber: 1.9 Consensus size: 63
1264060 GATTGCAATT
1264070 AAAGTAGGGGGATTGCAATTAAAGTATAATTTTTTTAGAGGTTAAAATATAATTTTATTAATA
1 AAAGTAGGGGGATTGCAATTAAAGTATAATTTTTTTAGAGGTTAAAATATAATTTTATTAATA
1264133 AAAGTAGGGGGATTGCAATTAAAGTATAATTTTTTTAGAGGTTAAAATATAATTTTAT
1 AAAGTAGGGGGATTGCAATTAAAGTATAATTTTTTTAGAGGTTAAAATATAATTTTAT
1264191 CATATATTAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.40, C:0.02, G:0.18, T:0.40
Consensus pattern (63 bp):
AAAGTAGGGGGATTGCAATTAAAGTATAATTTTTTTAGAGGTTAAAATATAATTTTATTAATA
Found at i:1264666 original size:39 final size:39
Alignment explanation
Indices: 1264612--1264695 Score: 168
Period size: 39 Copynumber: 2.2 Consensus size: 39
1264602 TTTTTGTCCC
1264612 AATTAAGTTGGTATCACTTTGTTTTGTGTTTCCAATTTT
1 AATTAAGTTGGTATCACTTTGTTTTGTGTTTCCAATTTT
1264651 AATTAAGTTGGTATCACTTTGTTTTGTGTTTCCAATTTT
1 AATTAAGTTGGTATCACTTTGTTTTGTGTTTCCAATTTT
1264690 AATTAA
1 AATTAA
1264696 TTATTTAAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.24, C:0.10, G:0.14, T:0.52
Consensus pattern (39 bp):
AATTAAGTTGGTATCACTTTGTTTTGTGTTTCCAATTTT
Found at i:1277883 original size:18 final size:18
Alignment explanation
Indices: 1277862--1277897 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1277852 ATTATCTTCA
1277862 ATATGATTATTAGATTTC
1 ATATGATTATTAGATTTC
*
1277880 ATATGGTTATTAGATTTC
1 ATATGATTATTAGATTTC
1277898 TTCATGTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.14, T:0.50
Consensus pattern (18 bp):
ATATGATTATTAGATTTC
Found at i:1279583 original size:2 final size:2
Alignment explanation
Indices: 1279570--1279616 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
1279560 CAGTGGTGAG
* *
1279570 CT CT CG CT CT CT CT CT CT CT CT CT CT GT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1279612 CT CT C
1 CT CT C
1279617 CCTGTTCATT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.04, T:0.47
Consensus pattern (2 bp):
CT
Found at i:1283568 original size:79 final size:79
Alignment explanation
Indices: 1283437--1283602 Score: 262
Period size: 79 Copynumber: 2.1 Consensus size: 79
1283427 GCTCATTTTT
* * *
1283437 AAACTTGGTAGGAACCTAAAGGATATTTACACTATTTGAATTATTCGAGTTATTCAAATTATAAA
1 AAACTTGATAGGAACCTAAAAGATATTTACACCATTTGAATTATTCGAGTTATTCAAATTATAAA
1283502 ATTAAACTCGGTTC
66 ATTAAACTCGGTTC
* * *
1283516 AAACTTGATAGGGACCTAAAA-AGTATTTACACCATTTGAATTATTTGAGTTATTCAATTTATAA
1 AAACTTGATAGGAACCTAAAAGA-TATTTACACCATTTGAATTATTCGAGTTATTCAAATTATAA
1283580 AATTAAACTCGGTTC
65 AATTAAACTCGGTTC
1283595 AAACTTGA
1 AAACTTGA
1283603 ATAACTCGAT
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
78 1 0.01
79 79 0.99
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.36
Consensus pattern (79 bp):
AAACTTGATAGGAACCTAAAAGATATTTACACCATTTGAATTATTCGAGTTATTCAAATTATAAA
ATTAAACTCGGTTC
Found at i:1288089 original size:15 final size:16
Alignment explanation
Indices: 1288069--1288106 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1288059 CTTTCAAAAA
*
1288069 AAAAATT-AAATCTTT
1 AAAAATTCAAATATTT
1288084 AAAAATTCAAATATTT
1 AAAAATTCAAATATTT
1288100 ATAAAAT
1 A-AAAAT
1288107 AAAAATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 7 0.35
16 8 0.40
17 5 0.25
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (16 bp):
AAAAATTCAAATATTT
Found at i:1291372 original size:4 final size:4
Alignment explanation
Indices: 1291363--1291441 Score: 61
Period size: 4 Copynumber: 18.0 Consensus size: 4
1291353 GCAAATGAAT
* *
1291363 AAAG AAAG AAAG AAAC AAGACG AAATAG AAAGG AAAG AAAG AAAAG AAAA
1 AAAG AAAG AAAG AAAG AA-A-G -AA-AG AAA-G AAAG AAAG -AAAG AAAG
1291413 AGAAG AAA- AAAG AAAGG AAAG AAAG AAAG
1 A-AAG AAAG AAAG AAA-G AAAG AAAG AAAG
1291442 GAGAAAGACA
Statistics
Matches: 62, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
3 3 0.05
4 37 0.60
5 18 0.29
6 1 0.02
7 3 0.05
ACGTcount: A:0.72, C:0.03, G:0.24, T:0.01
Consensus pattern (4 bp):
AAAG
Found at i:1291403 original size:9 final size:8
Alignment explanation
Indices: 1291389--1291441 Score: 54
Period size: 9 Copynumber: 6.2 Consensus size: 8
1291379 AAGACGAAAT
1291389 AGAAAGGAA
1 AGAAA-GAA
1291398 AGAAAGAAA
1 AGAAAG-AA
*
1291407 AGAAAAAGA
1 AGAAAGA-A
1291416 AGAAA-AA
1 AGAAAGAA
1291423 AGAAAGGAA
1 AGAAA-GAA
1291432 AGAAAGAA
1 AGAAAGAA
1291440 AG
1 AG
1291442 GAGAAAGACA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
7 6 0.15
8 8 0.21
9 25 0.64
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (8 bp):
AGAAAGAA
Found at i:1291427 original size:29 final size:33
Alignment explanation
Indices: 1291363--1291441 Score: 115
Period size: 34 Copynumber: 2.4 Consensus size: 33
1291353 GCAAATGAAT
*
1291363 AAAGAAAGAAAGAAACAAGACGAAATAGAAAGG
1 AAAGAAAGAAAGAAACAAGAAGAAATAGAAAGG
*
1291396 AAAGAAAGAAAAGAAA-AAGAAGAAAAAAGAAAGG
1 AAAGAAAG-AAAGAAACAAGAAG-AAATAGAAAGG
1291430 AAAGAAAGAAAG
1 AAAGAAAGAAAG
1291442 GAGAAAGACA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
33 17 0.40
34 25 0.60
ACGTcount: A:0.72, C:0.03, G:0.24, T:0.01
Consensus pattern (33 bp):
AAAGAAAGAAAGAAACAAGAAGAAATAGAAAGG
Found at i:1295445 original size:13 final size:12
Alignment explanation
Indices: 1295427--1295465 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1295417 TAAAAACCAT
1295427 AAAATTTATAAA
1 AAAATTTATAAA
*
1295439 CAAAATTAATAAA
1 -AAAATTTATAAA
*
1295452 AAAAGTTATAAA
1 AAAATTTATAAA
1295464 AA
1 AA
1295466 TTTTTTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (12 bp):
AAAATTTATAAA
Found at i:1295495 original size:14 final size:15
Alignment explanation
Indices: 1295460--1295495 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1295450 AAAAAAGTTA
1295460 TAAAAATTTTTTATT
1 TAAAAATTTTTTATT
*
1295475 TATAAATTTTTTA-T
1 TAAAAATTTTTTATT
1295489 TAAAAAT
1 TAAAAAT
1295496 AATAATGCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TAAAAATTTTTTATT
Found at i:1295602 original size:8 final size:8
Alignment explanation
Indices: 1295589--1295628 Score: 53
Period size: 8 Copynumber: 4.8 Consensus size: 8
1295579 TTTTAATAAA
1295589 AATTTTAT
1 AATTTTAT
1295597 AATTTTAT
1 AATTTTAT
*
1295605 AATTTTAA
1 AATTTTAT
1295613 AATTTTTAT
1 AA-TTTTAT
1295622 AAATTTT
1 -AATTTT
1295629 GTTTATATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 17 0.61
9 9 0.32
10 2 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
AATTTTAT
Found at i:1295610 original size:16 final size:18
Alignment explanation
Indices: 1295588--1295628 Score: 59
Period size: 16 Copynumber: 2.4 Consensus size: 18
1295578 TTTTTAATAA
*
1295588 AAATTTTATAA-TTTTAT
1 AAATTTTAAAATTTTTAT
1295605 -AATTTTAAAATTTTTAT
1 AAATTTTAAAATTTTTAT
1295622 AAATTTT
1 AAATTTT
1295629 GTTTATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 9 0.43
17 6 0.29
18 6 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
AAATTTTAAAATTTTTAT
Found at i:1295634 original size:30 final size:29
Alignment explanation
Indices: 1295600--1295656 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
1295590 ATTTTATAAT
1295600 TTTATAATTTTAAAATTTTTATAAATTTTG
1 TTTATAATTTTAAAATTTTTA-AAATTTTG
* **
1295630 TTTATATTTTTATGATTTTTAAAATTT
1 TTTATAATTTTAAAATTTTTAAAATTT
1295657 AAAATGGCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 6 0.25
30 18 0.75
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (29 bp):
TTTATAATTTTAAAATTTTTAAAATTTTG
Found at i:1302320 original size:1 final size:1
Alignment explanation
Indices: 1302314--1302353 Score: 53
Period size: 1 Copynumber: 40.0 Consensus size: 1
1302304 GGCCAAATTT
* * *
1302314 AAAAAAAAAAAAAAAAAAAAAAAAAACAAACAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1302354 GGGGAGAGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.93, C:0.05, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:1320609 original size:111 final size:108
Alignment explanation
Indices: 1320389--1320681 Score: 400
Period size: 111 Copynumber: 2.7 Consensus size: 108
1320379 ATATTTGGCA
* * * *
1320389 ATTTGGTTAAACGAG--AAATCGAAACCCAACACATTAGGGCACGTTCCTCGAATTTC-CAAACG
1 ATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACTTTTCTCGAATTTCTCAAACG
* * *
1320451 CAAAACATTACC-TTTTTGTAATTTTTAAAAGGATATTTAGCT
66 CAAAATATTGCCTTTTTTGTAATTTTTAAAAGGACATTTAGCT
*
1320493 ATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACTTTTTCTCGAATTTCTCAAAT
1 ATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCAC-TTTTCTCGAATTTCTCAAAC
1320558 GCAAAATATTGCCTTATTTTG-AGATTTTTTAAAAGGACATTTAGCT
65 GCAAAATATTGCCTT-TTTTGTA-A-TTTTTAAAAGGACATTTAGCT
* *
1320604 ATTTGGTTGAACGAGAAAAATCAAAACCCAGCACATTAGGGCACGTCTTCTCGAATTT-TCAAAC
1 ATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCAC-TTTTCTCGAATTTCTCAAAC
*
1320668 GCTAAATATTGCCT
65 GCAAAATATTGCCT
1320682 CAATTAGAAA
Statistics
Matches: 168, Mismatches: 13, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
104 14 0.08
106 26 0.15
107 12 0.07
108 15 0.09
109 2 0.01
110 24 0.14
111 75 0.45
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (108 bp):
ATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACTTTTCTCGAATTTCTCAAACG
CAAAATATTGCCTTTTTTGTAATTTTTAAAAGGACATTTAGCT
Found at i:1321474 original size:21 final size:20
Alignment explanation
Indices: 1321428--1321474 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
1321418 ATAAATGAGC
1321428 CAATAAT-AGTAATAATAAT
1 CAATAATAAGTAATAATAAT
*
1321447 -AA-CATAAGTAATAATAAT
1 CAATAATAAGTAATAATAAT
1321465 ACAATAATAA
1 -CAATAATAA
1321475 TAGCAATATC
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
17 2 0.09
18 14 0.64
20 2 0.09
21 4 0.18
ACGTcount: A:0.62, C:0.06, G:0.04, T:0.28
Consensus pattern (20 bp):
CAATAATAAGTAATAATAAT
Found at i:1321500 original size:18 final size:16
Alignment explanation
Indices: 1321432--1321500 Score: 50
Period size: 18 Copynumber: 3.9 Consensus size: 16
1321422 ATGAGCCAAT
1321432 AATAGTAATAATAATA-
1 AATA-TAATAATAATAC
1321448 ACATAAGTAATAATAATAC
1 A-AT-A-TAATAATAATAC
**
1321467 AATAATAATAGCAATATC
1 AAT-ATAATAATAATA-C
1321485 AGATATAATAATAATA
1 A-ATATAATAATAATA
1321501 GCGAAAGTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
16 1 0.02
17 11 0.25
18 29 0.66
19 3 0.07
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.29
Consensus pattern (16 bp):
AATATAATAATAATAC
Found at i:1324858 original size:25 final size:25
Alignment explanation
Indices: 1324822--1324875 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
1324812 ACACACCACA
*
1324822 GCTCGCAAGAGCGTCCCGATAATTG
1 GCTCGCAAGAGCGTCCCGATAAATG
* *
1324847 GCTC-CAATGAGCTTCCTGATAAATG
1 GCTCGCAA-GAGCGTCCCGATAAATG
1324872 GCTC
1 GCTC
1324876 TCCGGAGCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 3 0.12
25 22 0.88
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (25 bp):
GCTCGCAAGAGCGTCCCGATAAATG
Found at i:1324883 original size:25 final size:26
Alignment explanation
Indices: 1324855--1324917 Score: 87
Period size: 25 Copynumber: 2.5 Consensus size: 26
1324845 TGGCTCCAAT
1324855 GAGCTTCCT-GATAAATGGCTCTCCG
1 GAGCTTCCTCGATAAATGGCTCTCCG
* *
1324880 GAGCTT-CTCGATTAATGGCTCTCTG
1 GAGCTTCCTCGATAAATGGCTCTCCG
1324905 GAGCTT-CTCGATA
1 GAGCTTCCTCGATA
1324918 TTTGACTCTC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 2 0.06
25 32 0.94
ACGTcount: A:0.19, C:0.25, G:0.24, T:0.32
Consensus pattern (26 bp):
GAGCTTCCTCGATAAATGGCTCTCCG
Found at i:1324926 original size:25 final size:25
Alignment explanation
Indices: 1324873--1324945 Score: 67
Period size: 25 Copynumber: 2.9 Consensus size: 25
1324863 TGATAAATGG
* * *
1324873 CTCTCCGGAGCTTCTCGAT-TAATGG
1 CTCTCAGGAGCTTCTCGATAT-TTGA
*
1324898 CTCTCTGGAGCTTCTCGATATTTGA
1 CTCTCAGGAGCTTCTCGATATTTGA
* * *
1324923 CTCTCACGAGCTTCCCGTTATTT
1 CTCTCAGGAGCTTCTCGATATTT
1324946 AGCTCTTATG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
25 39 0.98
26 1 0.03
ACGTcount: A:0.15, C:0.29, G:0.19, T:0.37
Consensus pattern (25 bp):
CTCTCAGGAGCTTCTCGATATTTGA
Found at i:1325010 original size:27 final size:27
Alignment explanation
Indices: 1324980--1325066 Score: 99
Period size: 27 Copynumber: 3.3 Consensus size: 27
1324970 TGGCTCTTAC
*
1324980 GAGCTTCCTAATTTAAAGCTCTCTCAT
1 GAGCTTCCCAATTTAAAGCTCTCTCAT
* *
1325007 GAGCCTCCCGATTTAAAGCTCTCTCAT
1 GAGCTTCCCAATTTAAAGCTCTCTCAT
* **
1325034 GAGCTTCCC-GTTTATGGCTCTCT-A-
1 GAGCTTCCCAATTTAAAGCTCTCTCAT
1325058 GAGCTTCCC
1 GAGCTTCCC
1325067 GATATTACCT
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
24 9 0.17
25 1 0.02
26 11 0.21
27 32 0.60
ACGTcount: A:0.20, C:0.31, G:0.16, T:0.33
Consensus pattern (27 bp):
GAGCTTCCCAATTTAAAGCTCTCTCAT
Found at i:1325061 original size:24 final size:25
Alignment explanation
Indices: 1324997--1325138 Score: 98
Period size: 24 Copynumber: 5.7 Consensus size: 25
1324987 CTAATTTAAA
* **
1324997 GCTCTCTCATGAGCCTCCCGATTTAAA
1 GCTCTCT-ATGAGCTTCCCG-TTTATG
1325024 GCTCTCTCATGAGCTTCCCGTTTATG
1 GCTCTCT-ATGAGCTTCCCGTTTATG
1325050 GCTCTCTA-GAGCTTCCCGATATTA--
1 GCTCTCTATGAGCTTCCCG-T-TTATG
* * * **
1325074 CCTCGC-ATAAGCTTCCCAATTATG
1 GCTCTCTATGAGCTTCCCGTTTATG
*
1325098 GCTCT-TATGAGCTTCCCGTTACATG
1 GCTCTCTATGAGCTTCCCGTT-TATG
*
1325123 GCTCAC-ATGAGCTTCC
1 GCTCTCTATGAGCTTCC
1325139 TATTATATGG
Statistics
Matches: 92, Mismatches: 15, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
22 3 0.03
23 1 0.01
24 36 0.39
25 19 0.21
26 14 0.15
27 19 0.21
ACGTcount: A:0.19, C:0.32, G:0.17, T:0.32
Consensus pattern (25 bp):
GCTCTCTATGAGCTTCCCGTTTATG
Found at i:1325132 original size:25 final size:25
Alignment explanation
Indices: 1325031--1325184 Score: 104
Period size: 25 Copynumber: 6.3 Consensus size: 25
1325021 AAAGCTCTCT
*
1325031 CATGAGCTTCCCGTT-TATGGCTCT
1 CATGAGCTTCCCGTTATATGGCTCA
* ** *
1325055 C-TAGAGCTTCCCGATAT-TACCTCG
1 CAT-GAGCTTCCCGTTATATGGCTCA
* ** *
1325079 CATAAGCTTCCCAAT-TATGGCTCT
1 CATGAGCTTCCCGTTATATGGCTCA
* *
1325103 TATGAGCTTCCCGTTACATGGCTCA
1 CATGAGCTTCCCGTTATATGGCTCA
**
1325128 CATGAGCTTCCTATTATATGGCTCGA
1 CATGAGCTTCCCGTTATATGGCTC-A
* *
1325154 -AAGAGCTACCCGTTTATAT-GCTCA
1 CATGAGCTTCCCG-TTATATGGCTCA
1325178 CATGAGC
1 CATGAGC
1325185 ATTCTTGAAT
Statistics
Matches: 98, Mismatches: 24, Indels: 15
0.72 0.18 0.11
Matches are distributed among these distances:
23 2 0.02
24 43 0.44
25 46 0.47
26 7 0.07
ACGTcount: A:0.22, C:0.28, G:0.18, T:0.32
Consensus pattern (25 bp):
CATGAGCTTCCCGTTATATGGCTCA
Found at i:1325144 original size:48 final size:46
Alignment explanation
Indices: 1325031--1325184 Score: 114
Period size: 48 Copynumber: 3.2 Consensus size: 46
1325021 AAAGCTCTCT
* * * *
1325031 CATGAGCTTCCCGT-TTATGGCTCTCTAGAGCTTCCCGATATTACCTCG
1 CATGAGCTTCCC-TATTATGGCTCT-TAGAGCTTCCCGTTAAT-GCTCA
* *
1325079 CATAAGCTTCCCAATTATGGCTCTTATGAGCTTCCCGTTACATGGCTCA
1 CATGAGCTTCCCTATTATGGCTCTTA-GAGCTTCCCGTTA-AT-GCTCA
** *
1325128 CATGAGCTT-CCTATTATATGGCTCGAAAGAGCTACCCGTTTATATGCTCA
1 CATGAGCTTCCCTA-T-TATGGCTC-TTAGAGCTTCCCG-TTA-ATGCTCA
1325178 CATGAGC
1 CATGAGC
1325185 ATTCTTGAAT
Statistics
Matches: 86, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
47 2 0.02
48 36 0.42
49 13 0.15
50 29 0.34
51 6 0.07
ACGTcount: A:0.22, C:0.28, G:0.18, T:0.32
Consensus pattern (46 bp):
CATGAGCTTCCCTATTATGGCTCTTAGAGCTTCCCGTTAATGCTCA
Found at i:1325231 original size:17 final size:19
Alignment explanation
Indices: 1325193--1325231 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1325183 GCATTCTTGA
*
1325193 ATATGAATTGACAGATATT
1 ATATGAATTGACAGAGATT
1325212 ATATGAATTGAC-G-GATT
1 ATATGAATTGACAGAGATT
1325229 ATA
1 ATA
1325232 ATTTTGTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 1 0.05
19 12 0.63
ACGTcount: A:0.41, C:0.05, G:0.18, T:0.36
Consensus pattern (19 bp):
ATATGAATTGACAGAGATT
Found at i:1329989 original size:15 final size:16
Alignment explanation
Indices: 1329949--1329990 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
1329939 TAAAATTTAC
1329949 TTATTAAAATAATAATT
1 TTATTAAAA-AATAATT
*
1329966 TTATAAAAAAAT-ATT
1 TTATTAAAAAATAATT
*
1329981 TTTTTAAAAA
1 TTATTAAAAA
1329991 CTCACTAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 11 0.50
16 3 0.14
17 8 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTATTAAAAAATAATT
Found at i:1331525 original size:4 final size:4
Alignment explanation
Indices: 1331516--1331546 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
1331506 TTAGATTTTT
*
1331516 ATTA ATTA ATTA ACTA ATTA ATTA ATTA ATT
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATT
1331547 CATGGGCCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (4 bp):
ATTA
Found at i:1331726 original size:15 final size:16
Alignment explanation
Indices: 1331698--1331727 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1331688 ATATATTCCG
1331698 TTAATTGTATATAATT
1 TTAATTGTATATAATT
1331714 TTAATTG-ATATAAT
1 TTAATTGTATATAAT
1331728 AACAAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (16 bp):
TTAATTGTATATAATT
Found at i:1347742 original size:2 final size:2
Alignment explanation
Indices: 1347735--1347760 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1347725 AGTATTTTTC
1347735 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1347761 TCTCTTGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1348028 original size:15 final size:15
Alignment explanation
Indices: 1347998--1348027 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1347988 AAGTTTAATT
1347998 ATTAATATTATTAAA
1 ATTAATATTATTAAA
1348013 ATTAAT-TTATTAAA
1 ATTAATATTATTAAA
1348027 A
1 A
1348028 AAATAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTAATATTATTAAA
Found at i:1353379 original size:18 final size:18
Alignment explanation
Indices: 1353343--1353381 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1353333 CATAATTTTA
* *
1353343 TAATTTTTATATAATTTT
1 TAATTTTTATACAACTTT
*
1353361 TAATTTTTTTACAACTTT
1 TAATTTTTATACAACTTT
1353379 TAA
1 TAA
1353382 AAATTCTAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (18 bp):
TAATTTTTATACAACTTT
Found at i:1361769 original size:21 final size:21
Alignment explanation
Indices: 1361680--1361773 Score: 62
Period size: 21 Copynumber: 4.5 Consensus size: 21
1361670 CCCGTCTCCT
1361680 CACCACCACCTGTCCATTCTC
1 CACCACCACCTGTCCATTCTC
* * ** ** *
1361701 CACCTCCACCGGTTAAGCCAC
1 CACCACCACCTGTCCATTCTC
* * ** * *
1361722 CACCAGCACCAGTTTACTCCC
1 CACCACCACCTGTCCATTCTC
*
1361743 CTCCACCACCTGTCCATTCTC
1 CACCACCACCTGTCCATTCTC
1361764 CACCACCACC
1 CACCACCACC
1361774 GGTTAAGTCA
Statistics
Matches: 51, Mismatches: 22, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.21, C:0.52, G:0.07, T:0.19
Consensus pattern (21 bp):
CACCACCACCTGTCCATTCTC
Found at i:1363278 original size:14 final size:14
Alignment explanation
Indices: 1363259--1363304 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
1363249 ATTAATAATA
*
1363259 ATATATGTGTGTAT
1 ATATATATGTGTAT
*
1363273 ATATATATGTGTGT
1 ATATATATGTGTAT
* *
1363287 ATATATATATATAT
1 ATATATATGTGTAT
1363301 ATAT
1 ATAT
1363305 GAAGAAAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (14 bp):
ATATATATGTGTAT
Found at i:1363280 original size:16 final size:16
Alignment explanation
Indices: 1363259--1363296 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
1363249 ATTAATAATA
1363259 ATATATGTGTGTATAT
1 ATATATGTGTGTATAT
1363275 ATATATGTGTGTATAT
1 ATATATGTGTGTATAT
1363291 ATATAT
1 ATATAT
1363297 ATATATATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (16 bp):
ATATATGTGTGTATAT
Found at i:1363285 original size:18 final size:18
Alignment explanation
Indices: 1363259--1363300 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1363249 ATTAATAATA
*
1363259 ATATATGTGTGTATATAT
1 ATATATGTGTATATATAT
*
1363277 ATATGTGTGTATATATAT
1 ATATATGTGTATATATAT
1363295 ATATAT
1 ATATAT
1363301 ATATGAAGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (18 bp):
ATATATGTGTATATATAT
Found at i:1363628 original size:15 final size:16
Alignment explanation
Indices: 1363608--1363638 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1363598 AATACTGAAA
1363608 TTTC-AACCTTTTATT
1 TTTCAAACCTTTTATT
1363623 TTTCAAACCTTTTATT
1 TTTCAAACCTTTTATT
1363639 ATTGAAACGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.23, C:0.19, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTCAAACCTTTTATT
Found at i:1363646 original size:16 final size:16
Alignment explanation
Indices: 1363612--1363646 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1363602 CTGAAATTTC
*
1363612 AACCTTTTATTTTTCA
1 AACCTTTTATTATTCA
*
1363628 AACCTTTTATTATTGA
1 AACCTTTTATTATTCA
1363644 AAC
1 AAC
1363647 GTTAGAAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.31, C:0.17, G:0.03, T:0.49
Consensus pattern (16 bp):
AACCTTTTATTATTCA
Found at i:1366005 original size:2 final size:2
Alignment explanation
Indices: 1365998--1366028 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1365988 TTAAAATGTT
1365998 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1366029 TGTTAATGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1367752 original size:26 final size:26
Alignment explanation
Indices: 1367723--1367773 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
1367713 TAAATATTTT
*
1367723 TTTATTTTTAATCACATATATATATA
1 TTTATTTTTAATCAAATATATATATA
*
1367749 TTTATTTTTAGTCAAATATATATAT
1 TTTATTTTTAATCAAATATATATAT
1367774 TATATATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.55
Consensus pattern (26 bp):
TTTATTTTTAATCAAATATATATATA
Found at i:1367767 original size:22 final size:22
Alignment explanation
Indices: 1367740--1367796 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
1367730 TTAATCACAT
* *
1367740 ATATATATATTTATTTTTAGTCAA
1 ATATATATA-TTATATATA-TCAA
*
1367764 ATATATATATTATATATATTAA
1 ATATATATATTATATATATCAA
1367786 ATATATATATT
1 ATATATATATT
1367797 TGATATGGGC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
22 14 0.47
23 7 0.23
24 9 0.30
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
ATATATATATTATATATATCAA
Found at i:1367802 original size:24 final size:24
Alignment explanation
Indices: 1367740--1367802 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
1367730 TTAATCACAT
* *
1367740 ATATATATATTTATTTTTAGTCAA
1 ATATATATATTTATATATAGTCAA
*
1367764 ATATATATA-TTATATATA-TTAA
1 ATATATATATTTATATATAGTCAA
1367786 ATATATATATTTGATAT
1 ATATATATATTT-ATAT
1367803 GGGCCGGGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 12 0.35
23 9 0.26
24 13 0.38
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (24 bp):
ATATATATATTTATATATAGTCAA
Found at i:1371228 original size:16 final size:16
Alignment explanation
Indices: 1371204--1371253 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
1371194 AATTTTATCA
*
1371204 TTATTAATTTAAAATT
1 TTATAAATTTAAAATT
1371220 TTATAAATTATAAAA-T
1 TTATAAATT-TAAAATT
* *
1371236 GTCTAAA-TTAAAATT
1 TTATAAATTTAAAATT
1371251 TTA
1 TTA
1371254 CCATTTTAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
14 5 0.19
15 3 0.11
16 14 0.52
17 5 0.19
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (16 bp):
TTATAAATTTAAAATT
Found at i:1371672 original size:23 final size:23
Alignment explanation
Indices: 1371642--1371686 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
1371632 TTTATATTCG
1371642 AATAAGTGATTCGAGTCAACTCA
1 AATAAGTGATTCGAGTCAACTCA
1371665 AATAAGTGATTCGAGTCAACTC
1 AATAAGTGATTCGAGTCAACTC
1371687 GAATGAGTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.27
Consensus pattern (23 bp):
AATAAGTGATTCGAGTCAACTCA
Found at i:1372965 original size:11 final size:11
Alignment explanation
Indices: 1372946--1372994 Score: 82
Period size: 11 Copynumber: 4.5 Consensus size: 11
1372936 AAAAATTAAA
1372946 AAAAGTATTTTT
1 AAAA-TATTTTT
1372958 AAAATATTTTT
1 AAAATATTTTT
1372969 AAAATATTTTT
1 AAAATATTTTT
1372980 AAAATA-TTTT
1 AAAATATTTTT
1372990 AAAAT
1 AAAAT
1372995 TTAAAAAAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.24
11 24 0.65
12 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (11 bp):
AAAATATTTTT
Found at i:1373018 original size:11 final size:11
Alignment explanation
Indices: 1372932--1373018 Score: 74
Period size: 11 Copynumber: 8.1 Consensus size: 11
1372922 ATTTTTAAAA
1372932 TTTAAAAA-AT
1 TTTAAAAATAT
**
1372942 TAAAAAAAGTAT
1 TTTAAAAA-TAT
*
1372954 TTTTAAAATAT
1 TTTAAAAATAT
*
1372965 TTTTAAAATAT
1 TTTAAAAATAT
*
1372976 TTTTAAAATAT
1 TTTAAAAATAT
1372987 TTT--AAA-AT
1 TTTAAAAATAT
*
1372995 TTAAAAAAGTAT
1 TTTAAAAA-TAT
1373007 TTTAAAAATAT
1 TTTAAAAATAT
1373018 T
1 T
1373019 AAAAAAAAAC
Statistics
Matches: 64, Mismatches: 7, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
8 4 0.06
9 3 0.05
10 9 0.14
11 32 0.50
12 16 0.25
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (11 bp):
TTTAAAAATAT
Found at i:1373022 original size:21 final size:19
Alignment explanation
Indices: 1372958--1373023 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 19
1372948 AAGTATTTTT
*
1372958 AAAATATTTTTAAAATATTTTT
1 AAAATA-TTTTAAAA-A-TTTA
1372980 AAAATATTTT-AAAATTTAA
1 AAAATATTTTAAAAATTT-A
1372999 AAAAGTATTTTAAAAATATTA
1 AAAA-TATTTTAAAAAT-TTA
1373020 AAAA
1 AAAA
1373024 AAAACTCAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
18 3 0.08
19 5 0.13
20 9 0.23
21 14 0.36
22 8 0.21
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
AAAATATTTTAAAAATTTA
Found at i:1373370 original size:11 final size:11
Alignment explanation
Indices: 1373354--1373378 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1373344 TACAATCTTG
1373354 AAAGCCTTTGA
1 AAAGCCTTTGA
1373365 AAAGCCTTTGA
1 AAAGCCTTTGA
1373376 AAA
1 AAA
1373379 AAATGGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (11 bp):
AAAGCCTTTGA
Found at i:1373908 original size:11 final size:12
Alignment explanation
Indices: 1373894--1373925 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1373884 AAATGCGGAA
1373894 AATAAAATA-AT
1 AATAAAATATAT
1373905 AATAAAATATAT
1 AATAAAATATAT
1373917 AA-AAAATAT
1 AATAAAATAT
1373926 GTATATGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 16 0.80
12 4 0.20
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
AATAAAATATAT
Found at i:1374012 original size:3 final size:3
Alignment explanation
Indices: 1374004--1374068 Score: 55
Period size: 3 Copynumber: 21.7 Consensus size: 3
1373994 ATAGGTATAG
* *
1374004 TAA TAA TAA TAA CAA TAA TAA TAAA TAA T-A TAA TAG TAA TAA TTAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA -TAA
*
1374050 T-A TAA -CA TAA TTAA TAA TA
1 TAA TAA TAA TAA -TAA TAA TA
1374069 TATGAAAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
2 5 0.10
3 36 0.72
4 9 0.18
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1374027 original size:18 final size:18
Alignment explanation
Indices: 1374004--1374068 Score: 55
Period size: 19 Copynumber: 3.4 Consensus size: 18
1373994 ATAGGTATAG
1374004 TAATAATAATAACAATAA
1 TAATAATAATAACAATAA
1374022 TAATAAATAATATA-ATAGTAA
1 TAAT-AATAATA-ACA-A-TAA
1374043 TAATTAAT-ATAAC-ATAA
1 TAA-TAATAATAACAATAA
1374060 TTAATAATA
1 -TAATAATA
1374069 TATGAAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 16
0.71 0.00 0.29
Matches are distributed among these distances:
17 7 0.18
18 8 0.21
19 9 0.23
20 5 0.13
21 9 0.23
22 1 0.03
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.34
Consensus pattern (18 bp):
TAATAATAATAACAATAA
Found at i:1379201 original size:23 final size:23
Alignment explanation
Indices: 1379175--1379238 Score: 110
Period size: 23 Copynumber: 2.8 Consensus size: 23
1379165 GATTCGAGTT
*
1379175 ATTCGAGTCAATTCGAATAAGTG
1 ATTCGAGTCAACTCGAATAAGTG
*
1379198 ATTCGAGTCAACTCAAATAAGTG
1 ATTCGAGTCAACTCGAATAAGTG
1379221 ATTCGAGTCAACTCGAAT
1 ATTCGAGTCAACTCGAAT
1379239 GAGTTCGAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (23 bp):
ATTCGAGTCAACTCGAATAAGTG
Found at i:1380575 original size:30 final size:30
Alignment explanation
Indices: 1380541--1380612 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 30
1380531 ACCAAAAATT
1380541 TATTTTAAAAAT-TTAAAAAATTAAAAAAA
1 TATTTTAAAAATATTAAAAAATTAAAAAAA
**
1380570 GTATTTTAAAAATATTTTAAAATTAAAAAAA
1 -TATTTTAAAAATATTAAAAAATTAAAAAAA
1380601 T-TTTTAAAAATA
1 TATTTTAAAAATA
1380613 AATATATTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
29 11 0.28
30 13 0.33
31 15 0.38
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (30 bp):
TATTTTAAAAATATTAAAAAATTAAAAAAA
Found at i:1380597 original size:17 final size:17
Alignment explanation
Indices: 1380575--1380621 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
1380565 AAAAAGTATT
1380575 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
*
1380592 TTAAAAAAATTTTTAAAA
1 TTAAAAATA-TTTTAAAA
* *
1380610 ATAAATATATTT
1 TTAAAAATATTT
1380622 ATTATATCGG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAAAAATATTTTAAAA
Found at i:1380605 original size:18 final size:19
Alignment explanation
Indices: 1380577--1380614 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
1380567 AAAGTATTTT
*
1380577 AAAAATATTTTAAAATTAA
1 AAAAATATTTTAAAAATAA
1380596 AAAAAT-TTTTAAAAATAA
1 AAAAATATTTTAAAAATAA
1380614 A
1 A
1380615 TATATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAAATATTTTAAAAATAA
Found at i:1386119 original size:12 final size:12
Alignment explanation
Indices: 1386102--1386132 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1386092 TTTACATTGT
*
1386102 TTTTAAAATATG
1 TTTTAAAATATA
1386114 TTTTAAAATATA
1 TTTTAAAATATA
1386126 TTTTAAA
1 TTTTAAA
1386133 TAAGTCGATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (12 bp):
TTTTAAAATATA
Found at i:1387694 original size:30 final size:30
Alignment explanation
Indices: 1387641--1387723 Score: 80
Period size: 31 Copynumber: 2.8 Consensus size: 30
1387631 AAGTTTTCGT
***
1387641 TTTGGTCACTTAACTA-AAAAAAG-TTACAA
1 TTTGGTCACTTAACTATTCGAAAGTTTAC-A
1387670 TTTGGTCACTTAACTATTCGAAAGTTTACA
1 TTTGGTCACTTAACTATTCGAAAGTTTACA
* * *
1387700 TTTAAGTTACTAAACTATTCGAAA
1 TTT-GGTCACTTAACTATTCGAAA
1387724 ATTTTTATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
29 16 0.36
30 8 0.18
31 21 0.47
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (30 bp):
TTTGGTCACTTAACTATTCGAAAGTTTACA
Found at i:1389177 original size:16 final size:16
Alignment explanation
Indices: 1389152--1389183 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1389142 TGATTTTCAA
1389152 TTTCTCTTTCTTTTTT
1 TTTCTCTTTCTTTTTT
*
1389168 TTTCTTTTTCTTTTTT
1 TTTCTCTTTCTTTTTT
1389184 CTCATTCATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTCTCTTTCTTTTTT
Found at i:1389443 original size:19 final size:19
Alignment explanation
Indices: 1389406--1389443 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1389396 GATTTTTTTA
*
1389406 AAAATAAATCAATAAAATG
1 AAAATAAATAAATAAAATG
1389425 AAAATAAA-AAATAATAATG
1 AAAATAAATAAATAA-AATG
1389444 GAGAGAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.21
Consensus pattern (19 bp):
AAAATAAATAAATAAAATG
Found at i:1392630 original size:31 final size:31
Alignment explanation
Indices: 1392595--1392656 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
1392585 TTACACAATG
*
1392595 GTCACTAAATTATTTGAAAGTTTTCATTTAA
1 GTCACTAAACTATTTGAAAGTTTTCATTTAA
* *
1392626 GTCACTGAACTATTTGAAAGTTTTTATTTAA
1 GTCACTAAACTATTTGAAAGTTTTCATTTAA
1392657 AGTATTGGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.45
Consensus pattern (31 bp):
GTCACTAAACTATTTGAAAGTTTTCATTTAA
Found at i:1395709 original size:3 final size:3
Alignment explanation
Indices: 1395703--1395728 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1395693 TCACAGTGAT
1395703 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
1395729 TGATTCTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1398256 original size:26 final size:26
Alignment explanation
Indices: 1398226--1398277 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1398216 ATGTCATTAA
*
1398226 ATAATTAAAATGAGACCAT-AAATAAT
1 ATAATAAAAATG-GACCATAAAATAAT
*
1398252 ATAATAAAAATGGTCCATAAAATAAT
1 ATAATAAAAATGGACCATAAAATAAT
1398278 TTTTCTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.58, C:0.08, G:0.08, T:0.27
Consensus pattern (26 bp):
ATAATAAAAATGGACCATAAAATAAT
Found at i:1398592 original size:2 final size:2
Alignment explanation
Indices: 1398585--1398616 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1398575 CTTTAAAGAG
1398585 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
1398617 AGATTCCTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1417986 original size:22 final size:22
Alignment explanation
Indices: 1417961--1418002 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1417951 AAATATATAA
1417961 ATTAAATTAATAAA-ATTAAAAT
1 ATTAAA-TAATAAATATTAAAAT
*
1417983 ATTAAATATTAAATATTAAA
1 ATTAAATAATAAATATTAAA
1418003 TCCATAGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
ATTAAATAATAAATATTAAAAT
Found at i:1417991 original size:7 final size:7
Alignment explanation
Indices: 1417961--1418003 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
1417951 AAATATATAA
1417961 ATTAAATT
1 ATTAAA-T
*
1417969 AATAAA-
1 ATTAAAT
1417975 ATTAAAAT
1 ATT-AAAT
1417983 ATTAAAT
1 ATTAAAT
1417990 ATTAAAT
1 ATTAAAT
1417997 ATTAAAT
1 ATTAAAT
1418004 CCATAGCTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
6 2 0.06
7 21 0.68
8 8 0.26
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
ATTAAAT
Found at i:1421952 original size:4 final size:4
Alignment explanation
Indices: 1421943--1421992 Score: 100
Period size: 4 Copynumber: 12.5 Consensus size: 4
1421933 ACTTGAAACT
1421943 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1421991 TG
1 TG
1421993 AGAATAATAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 46 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:1429008 original size:3 final size:3
Alignment explanation
Indices: 1428992--1429037 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
1428982 GAAACTTGGG
*
1428992 CAT CAT CAAT -AT CAT CAT CAT C-T CCCT CAT CAT CAT CAT CAT CAT
1 CAT CAT C-AT CAT CAT CAT CAT CAT -CAT CAT CAT CAT CAT CAT CAT
1429037 C
1 C
1429038 TGTATCCTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
2 3 0.08
3 32 0.84
4 3 0.08
ACGTcount: A:0.30, C:0.37, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:1431311 original size:48 final size:49
Alignment explanation
Indices: 1431238--1431331 Score: 120
Period size: 47 Copynumber: 1.9 Consensus size: 49
1431228 ATTTTGTTTT
* **
1431238 TTTTTTATATTTTTATAAATTTTAAAGTTATTTTTAACACAATTTTTATA
1 TTTTTTATATTTTGATAAATTTTAAAAATA-TTTTAACACAATTTTTATA
* *
1431288 TTTTTTA-ATTTTGAT-CATTTTAAAAATATTTTAACACCATTTTT
1 TTTTTTATATTTTGATAAATTTTAAAAATATTTTAACACAATTTTT
1431332 GAAGTTATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
47 15 0.38
48 10 0.26
49 7 0.18
50 7 0.18
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59
Consensus pattern (49 bp):
TTTTTTATATTTTGATAAATTTTAAAAATATTTTAACACAATTTTTATA
Found at i:1431412 original size:16 final size:17
Alignment explanation
Indices: 1431391--1431422 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1431381 GAATGAATAT
1431391 AAATTATT-ATAATTTA
1 AAATTATTAATAATTTA
1431407 AAATTATTAATAATTT
1 AAATTATTAATAATTT
1431423 CATATAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AAATTATTAATAATTTA
Found at i:1445034 original size:16 final size:16
Alignment explanation
Indices: 1445013--1445043 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1445003 GATATCACCA
*
1445013 TTAAAGTATTAATACC
1 TTAAAGTATCAATACC
1445029 TTAAAGTATCAATAC
1 TTAAAGTATCAATAC
1445044 ATTGGGAGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.35
Consensus pattern (16 bp):
TTAAAGTATCAATACC
Found at i:1445212 original size:7 final size:7
Alignment explanation
Indices: 1445200--1445244 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
1445190 CCAAGAATAA
1445200 TTCATGT
1 TTCATGT
1445207 TTCATGTT
1 TTCATG-T
1445215 TTCATGT
1 TTCATGT
**
1445222 TTCATAC
1 TTCATGT
*
1445229 TGCATGT
1 TTCATGT
1445236 TTCATGT
1 TTCATGT
1445243 TT
1 TT
1445245 TCTTCTGTAC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
7 24 0.77
8 7 0.23
ACGTcount: A:0.16, C:0.16, G:0.13, T:0.56
Consensus pattern (7 bp):
TTCATGT
Found at i:1445536 original size:20 final size:20
Alignment explanation
Indices: 1445511--1445574 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 20
1445501 ATATTTTTAA
1445511 TTATGTAGTGATTCAAAGAC
1 TTATGTAGTGATTCAAAGAC
* ***
1445531 TTATGTAAT-ATTTTTAG--
1 TTATGTAGTGATTCAAAGAC
1445548 TTATGTAGTGATTCAAAGAC
1 TTATGTAGTGATTCAAAGAC
*
1445568 TTGTGTA
1 TTATGTA
1445575 ATTTTTTTAA
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
17 8 0.25
18 5 0.16
19 5 0.16
20 14 0.44
ACGTcount: A:0.31, C:0.06, G:0.19, T:0.44
Consensus pattern (20 bp):
TTATGTAGTGATTCAAAGAC
Found at i:1445538 original size:37 final size:37
Alignment explanation
Indices: 1445488--1445597 Score: 175
Period size: 37 Copynumber: 3.0 Consensus size: 37
1445478 TTTATGTGTT
*
1445488 AAAGACCTATGTAATATTTTTAATTATGTAGTGATTC
1 AAAGACTTATGTAATATTTTTAATTATGTAGTGATTC
*
1445525 AAAGACTTATGTAATATTTTTAGTTATGTAGTGATTC
1 AAAGACTTATGTAATATTTTTAATTATGTAGTGATTC
* * *
1445562 AAAGACTTGTGTAATTTTTTTAATTATATAGTGATT
1 AAAGACTTATGTAATATTTTTAATTATGTAGTGATT
1445598 TAAATGGTTA
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.46
Consensus pattern (37 bp):
AAAGACTTATGTAATATTTTTAATTATGTAGTGATTC
Found at i:1445632 original size:9 final size:9
Alignment explanation
Indices: 1445608--1445676 Score: 68
Period size: 9 Copynumber: 7.8 Consensus size: 9
1445598 TAAATGGTTA
*
1445608 AGGTCAAAT
1 AGGTTAAAT
* *
1445617 CGGTTAAGT
1 AGGTTAAAT
1445626 AGGTTAAAT
1 AGGTTAAAT
*
1445635 TGGTTAAAT
1 AGGTTAAAT
*
1445644 CGGTT-AAT
1 AGGTTAAAT
*
1445652 CGGTTAAAT
1 AGGTTAAAT
1445661 AGGTTAAAT
1 AGGTTAAAT
*
1445670 CGGTTAA
1 AGGTTAA
1445677 TTTTTAACCA
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
8 8 0.16
9 42 0.84
ACGTcount: A:0.35, C:0.07, G:0.25, T:0.33
Consensus pattern (9 bp):
AGGTTAAAT
Found at i:1445634 original size:18 final size:18
Alignment explanation
Indices: 1445608--1445676 Score: 95
Period size: 18 Copynumber: 3.9 Consensus size: 18
1445598 TAAATGGTTA
* *
1445608 AGGTCAAATCGGTTAAGT
1 AGGTTAAATCGGTTAAAT
*
1445626 AGGTTAAATTGGTTAAAT
1 AGGTTAAATCGGTTAAAT
*
1445644 CGGTT-AATCGGTTAAAT
1 AGGTTAAATCGGTTAAAT
1445661 AGGTTAAATCGGTTAA
1 AGGTTAAATCGGTTAA
1445677 TTTTTAACCA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
17 15 0.34
18 29 0.66
ACGTcount: A:0.35, C:0.07, G:0.25, T:0.33
Consensus pattern (18 bp):
AGGTTAAATCGGTTAAAT
Found at i:1445677 original size:26 final size:27
Alignment explanation
Indices: 1445613--1445676 Score: 94
Period size: 26 Copynumber: 2.4 Consensus size: 27
1445603 GGTTAAGGTC
* *
1445613 AAATCGGTTAAGTAGGTTAAATTGGTT
1 AAATCGGTTAAATAGGTTAAATAGGTT
*
1445640 AAATCGGTT-AATCGGTTAAATAGGTT
1 AAATCGGTTAAATAGGTTAAATAGGTT
1445666 AAATCGGTTAA
1 AAATCGGTTAA
1445677 TTTTTAACCA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 23 0.70
27 10 0.30
ACGTcount: A:0.36, C:0.06, G:0.23, T:0.34
Consensus pattern (27 bp):
AAATCGGTTAAATAGGTTAAATAGGTT
Found at i:1445852 original size:12 final size:12
Alignment explanation
Indices: 1445835--1445859 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1445825 AACTAATTCG
1445835 GGTCGGTTAACC
1 GGTCGGTTAACC
1445847 GGTCGGTTAACC
1 GGTCGGTTAACC
1445859 G
1 G
1445860 AATGCACACC
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:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:1449496 original size:15 final size:16
Alignment explanation
Indices: 1449469--1449498 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1449459 GGGTTTTTGT
1449469 GGAGAAGAAAAAGAAA
1 GGAGAAGAAAAAGAAA
1449485 GGAGAA-AAAAAGAA
1 GGAGAAGAAAAAGAA
1449499 GAAAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (16 bp):
GGAGAAGAAAAAGAAA
Found at i:1449501 original size:11 final size:11
Alignment explanation
Indices: 1449471--1449526 Score: 53
Period size: 11 Copynumber: 5.0 Consensus size: 11
1449461 GTTTTTGTGG
1449471 AGAAGAAAAAGAA
1 AGAAG-AAAA-AA
*
1449484 AGGAGAAAAAA
1 AGAAGAAAAAA
1449495 AGAAGAAAAAA
1 AGAAGAAAAAA
*
1449506 A-AATAAAAAA
1 AGAAGAAAAAA
1449516 TAG-AGAAAAAA
1 -AGAAGAAAAAA
1449527 GGACGAGATC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
10 8 0.22
11 21 0.57
12 4 0.11
13 4 0.11
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.04
Consensus pattern (11 bp):
AGAAGAAAAAA
Found at i:1449513 original size:21 final size:23
Alignment explanation
Indices: 1449471--1449526 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 23
1449461 GTTTTTGTGG
1449471 AGAAGAAAAAGAAAGGAGAAAAAA-
1 AGAAGAAAAA-AAA-GAGAAAAAAT
*
1449495 AGAAGAAAAAAAA-ATAAAAAAT
1 AGAAGAAAAAAAAGAGAAAAAAT
1449517 AG-AGAAAAAA
1 AGAAGAAAAAA
1449527 GGACGAGATC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 15 0.50
22 2 0.07
23 3 0.10
24 10 0.33
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.04
Consensus pattern (23 bp):
AGAAGAAAAAAAAGAGAAAAAAT
Found at i:1449522 original size:24 final size:25
Alignment explanation
Indices: 1449470--1449526 Score: 59
Period size: 24 Copynumber: 2.4 Consensus size: 25
1449460 GGTTTTTGTG
*
1449470 GAGAAGAAAAAGAAAGGAGAAAAAA
1 GAGAAGAAAAAGAAAAGAGAAAAAA
*
1449495 -AGAAGAAAAA-AAAATA-AAAAATA
1 GAGAAGAAAAAGAAAAGAGAAAAA-A
1449518 GAGAA-AAAA
1 GAGAAGAAAA
1449527 GGACGAGATC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
22 5 0.18
23 9 0.32
24 14 0.50
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (25 bp):
GAGAAGAAAAAGAAAAGAGAAAAAA
Found at i:1451934 original size:271 final size:272
Alignment explanation
Indices: 1451451--1451995 Score: 1083
Period size: 271 Copynumber: 2.0 Consensus size: 272
1451441 TTTTAATTGA
1451451 AACGATTAGATCAACGAATCAATAATACGAAGGATTCCATCTTCGATTAAATTTAAAAACCAATG
1 AACGATTAGATCAACGAATCAATAATACGAAGGATTCCATCTTCGATTAAATTTAAAAACCAATG
1451516 TTTGTTAGCACAAAAGCTTTGACTCAAAGCACAAAAATGGGACTCCCTCACCAAACGCGGTATTC
66 TTTGTTAGCACAAAAGCTTTGACTCAAAGCACAAAAATGGGACTCCCTCACCAAACGCGGTATTC
1451581 AATTTTGTTTGACTAAAAAGACAATTTATTAATTATTTATATACTTATAAAAAATAATATTAGAT
131 AATTTTGTTTGACTAAAAAGACAATTTATTAATTATTTATATACTTATAAAAAATAATATTAGAT
1451646 AAATGATTAAATTTTAGTTTTAGTCCTTTTAATTTGCTTAAGTTTTAAATTTAATCTTTTTTCTT
196 AAATGATTAAATTTTAGTTTTAGTCCTTTTAATTTGCTTAAGTTTTAAATTTAATCTTTTTTCTT
1451711 T-ATTTAAATAT
261 TAATTTAAATAT
1451722 AACGATTAGATCAACGAATCAATAATACGAAGGATTCCATCTTCGATTAAATTTAAAAACCAATG
1 AACGATTAGATCAACGAATCAATAATACGAAGGATTCCATCTTCGATTAAATTTAAAAACCAATG
1451787 TTTGTTAGCACAAAAGCTTTGACTCAAAGCACAAAAATGGGACTCCCTCACCAAACGCGGTATTC
66 TTTGTTAGCACAAAAGCTTTGACTCAAAGCACAAAAATGGGACTCCCTCACCAAACGCGGTATTC
1451852 AATTTTGTTTGACTAAAAAGACAATTTATTAATTATTTATATACTTATAAAAAATAATATTAGAT
131 AATTTTGTTTGACTAAAAAGACAATTTATTAATTATTTATATACTTATAAAAAATAATATTAGAT
1451917 AAATGATTAAATTTTAGTTTTAGTCCTTTTAATTTGCTTAAGTTTTAAATTTAATCTTTTTTCTT
196 AAATGATTAAATTTTAGTTTTAGTCCTTTTAATTTGCTTAAGTTTTAAATTTAATCTTTTTTCTT
1451982 TAATTTAAATAT
261 TAATTTAAATAT
1451994 AA
1 AA
1451996 TTTGGTCATT
Statistics
Matches: 273, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
271 261 0.96
272 12 0.04
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (272 bp):
AACGATTAGATCAACGAATCAATAATACGAAGGATTCCATCTTCGATTAAATTTAAAAACCAATG
TTTGTTAGCACAAAAGCTTTGACTCAAAGCACAAAAATGGGACTCCCTCACCAAACGCGGTATTC
AATTTTGTTTGACTAAAAAGACAATTTATTAATTATTTATATACTTATAAAAAATAATATTAGAT
AAATGATTAAATTTTAGTTTTAGTCCTTTTAATTTGCTTAAGTTTTAAATTTAATCTTTTTTCTT
TAATTTAAATAT
Found at i:1483681 original size:16 final size:17
Alignment explanation
Indices: 1483661--1483700 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
1483651 TTAATTGTTT
1483661 TATTTATTTATTTGAAA
1 TATTTATTTATTTGAAA
*
1483678 -ATTTATTTATTTTAAA
1 TATTTATTTATTTGAAA
1483694 TATTTAT
1 TATTTAT
1483701 GATAAAACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
TATTTATTTATTTGAAA
Found at i:1483951 original size:5 final size:5
Alignment explanation
Indices: 1483941--1483971 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
1483931 TAACTCCGAG
1483941 TATAA TATAA TATAA TATAA TATAA TATAA T
1 TATAA TATAA TATAA TATAA TATAA TATAA T
1483972 GAAAGGGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TATAA
Found at i:1487428 original size:23 final size:23
Alignment explanation
Indices: 1487402--1487450 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
1487392 ATAATAACTC
1487402 AAAATAAGTTTATTTAAATTTAA
1 AAAATAAGTTTATTTAAATTTAA
1487425 AAAATAAGTTTATTTAAATTTAA
1 AAAATAAGTTTATTTAAATTTAA
1487448 AAA
1 AAA
1487451 CTTTCTTCCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (23 bp):
AAAATAAGTTTATTTAAATTTAA
Found at i:1490734 original size:29 final size:29
Alignment explanation
Indices: 1490690--1490745 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
1490680 ATAGTGACCA
* * *
1490690 GATCAAATTAGTCCCTCTATTATTAAATG
1 GATCAAATTAGCCCCTATACTATTAAATG
*
1490719 GATCAATTTAGCCCCTATACTATTAAA
1 GATCAAATTAGCCCCTATACTATTAAA
1490746 AAGAATCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.36
Consensus pattern (29 bp):
GATCAAATTAGCCCCTATACTATTAAATG
Found at i:1503482 original size:24 final size:24
Alignment explanation
Indices: 1503455--1503503 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
1503445 AAAAATATGA
* *
1503455 CAACGGTGGCGCTTGCACCAGCGG
1 CAACGGCGGCGCTTACACCAGCGG
1503479 CAACGGCGGCGCTTACACCAGCGG
1 CAACGGCGGCGCTTACACCAGCGG
1503503 C
1 C
1503504 GATGCAAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.18, C:0.37, G:0.35, T:0.10
Consensus pattern (24 bp):
CAACGGCGGCGCTTACACCAGCGG
Found at i:1507582 original size:51 final size:50
Alignment explanation
Indices: 1507484--1507603 Score: 145
Period size: 51 Copynumber: 2.4 Consensus size: 50
1507474 TCCTCTTCTG
* * * *
1507484 GGTTCTGCTTTAAACCATTGGCACTTCTCTTAGTTGTATGCCGCTCTCCT
1 GGTTCTGCTTTAAACCATTGGCACTTCTCCTAGGTGCACGCCGCTCTCCT
* **
1507534 CGGTTCTGCTTTAAACCATTGGCGCTTCTCCTAGGTGCACGCTTCTCTCCT
1 -GGTTCTGCTTTAAACCATTGGCACTTCTCCTAGGTGCACGCCGCTCTCCT
*
1507585 GGGT-T-CTTTAAACCATTGG
1 GGTTCTGCTTTAAACCATTGG
1507604 AAACCGAGAC
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
48 14 0.23
49 1 0.02
50 3 0.05
51 43 0.70
ACGTcount: A:0.14, C:0.28, G:0.20, T:0.38
Consensus pattern (50 bp):
GGTTCTGCTTTAAACCATTGGCACTTCTCCTAGGTGCACGCCGCTCTCCT
Found at i:1509650 original size:27 final size:27
Alignment explanation
Indices: 1509620--1510003 Score: 626
Period size: 27 Copynumber: 14.2 Consensus size: 27
1509610 ACATTGGTCA
*
1509620 ATTTATTGCTCGACTCAGTAGCAGTAG
1 ATTTCTTGCTCGACTCAGTAGCAGTAG
1509647 ATTTCTTGCTCGACTCAGTAGCAGTAG
1 ATTTCTTGCTCGACTCAGTAGCAGTAG
*
1509674 ATTTCTTGCTTGACTCAGTAGCAGTAG
1 ATTTCTTGCTCGACTCAGTAGCAGTAG
*
1509701 ATTTCTTGCTTGACTCAGTAGCAGTAG
1 ATTTCTTGCTCGACTCAGTAGCAGTAG
* *
1509728 ATTTCTTGCTTGACTCGGTAGCAGTA-
1 ATTTCTTGCTCGACTCAGTAGCAGTAG
*
1509754 AGTTTCTTGCTCGACTCGGTAGCAGTAG
1 A-TTTCTTGCTCGACTCAGTAGCAGTAG
1509782 ATTTCTTGCTCGACTCAGTAGCAGTAG
1 ATTTCTTGCTCGACTCAGTAGCAGTAG
*
1509809 GTTTCTTGCTCGACTCAGTAGCAGTAG
1 ATTTCTTGCTCGACTCAGTAGCAGTAG
* * *
1509836 ATTTCTTGCTTGAATCAGTAACAGTAG
1 ATTTCTTGCTCGACTCAGTAGCAGTAG
1509863 ATTTCTTGCTCGACTCAGTAGCAGTAG
1 ATTTCTTGCTCGACTCAGTAGCAGTAG
1509890 ATTTCTTGCTCGACTCAGTAGCAGTAG
1 ATTTCTTGCTCGACTCAGTAGCAGTAG
1509917 ATTTCTTGCTCGACTCAGTAGCAGTAG
1 ATTTCTTGCTCGACTCAGTAGCAGTAG
*
1509944 ATTTCTTGCTCAACTCAGTAGCAGTAG
1 ATTTCTTGCTCGACTCAGTAGCAGTAG
* **
1509971 ATTTCTTGCTGGACTCAGTAGCTTTAG
1 ATTTCTTGCTCGACTCAGTAGCAGTAG
1509998 ATTTCT
1 ATTTCT
1510004 CTTGTGATTT
Statistics
Matches: 337, Mismatches: 18, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
26 1 0.00
27 335 0.99
28 1 0.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.35
Consensus pattern (27 bp):
ATTTCTTGCTCGACTCAGTAGCAGTAG
Found at i:1513788 original size:20 final size:19
Alignment explanation
Indices: 1513763--1513801 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
1513753 ACGTGTTTAA
1513763 TTTTTAATTAGTTGTTTTTT
1 TTTTTAATTAG-TGTTTTTT
*
1513783 TTTTTAATTTGTGTTTTTT
1 TTTTTAATTAGTGTTTTTT
1513802 AATTACTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.13, C:0.00, G:0.10, T:0.77
Consensus pattern (19 bp):
TTTTTAATTAGTGTTTTTT
Found at i:1516660 original size:315 final size:315
Alignment explanation
Indices: 1516037--1516679 Score: 1071
Period size: 315 Copynumber: 2.0 Consensus size: 315
1516027 ACTAAATCTT
*
1516037 AATTC-GAAATATTAACACTCATATATATCTCAATCCATTTAGTATAGAATAATCTTAAACATAA
1 AATTCAGAAATATTAACACTC--A-ATATCTCAATCCATTTAGAATAGAATAATCTTAAACATAA
* * *
1516101 AACTTGAAATAAATTTAAAATTTTAGACTTTTAAGGATAGATTTAAATATCTTTAATGTTATGAT
63 AACTTGAAATAAACTTAAAATTTTAGACTTTTAAAGATAGATTTAAATATCTTTAATGTCATGAT
*
1516166 CATGTGGATTTAATTTGCACTTAATTTAGTCTTAGTAATGTTTGATAGAAATATGATCAATGATT
128 CATGTGGATTTAATTTGCACTTAATCTAGTCTTAGTAATGTTTGATAGAAATATGATCAATGATT
1516231 TTGATACCCATAGATATAAGATCTAACCCTAGTTATTATAAATTAAATTTTGTATGTTGGCACGA
193 TTGATACCCATAGATATAAGATCTAACCCTAGTTATTATAAATTAAATTTTGTATGTTGGCACGA
* * * *
1516296 GGTATAAGATTTGATCCGATGTAATTTGCTTTTTCTTTGATTGTTGAAGGAGTCGGAC
258 GGTATAAGATTTAATCCGATGTAATTTACTTTTCCTTTCATTGTTGAAGGAGTCGGAC
1516354 AATTCAGAAATATTAACACTC-ATATCTCAATCCATTTAGAATAGAATCAAATCTTAAACATAAA
1 AATTCAGAAATATTAACACTCAATATCTCAATCCATTTAGAATAGAAT--AATCTTAAACATAAA
* *
1516418 ACTTGAAATAAACTTAAAATTTTATACTTTTAAAGATAGATTTAAGTATCTTCT-ATGTCATGAT
64 ACTTGAAATAAACTTAAAATTTTAGACTTTTAAAGATAGATTTAAATATCTT-TAATGTCATGAT
*
1516482 CATGTGGATTTAATTTGCACTTAATCTAGTCTTCGTAATG-TTGATAGAAATATGATCAATGATT
128 CATGTGGATTTAATTTGCACTTAATCTAGTCTTAGTAATGTTTGATAGAAATATGATCAATGATT
1516546 TTGATACCCATAGATATAAGATCTAACCCTAGTTATTATAAATTAAATTTTGTATGTTGGCACGA
193 TTGATACCCATAGATATAAGATCTAACCCTAGTTATTATAAATTAAATTTTGTATGTTGGCACGA
1516611 GGTATACA-ATTTAATCCGATGTAATTTACTTTTCCTTTCATTGTTGAAGGAGTCGGAC
258 GGTATA-AGATTTAATCCGATGTAATTTACTTTTCCTTTCATTGTTGAAGGAGTCGGAC
*
1516669 AATTCAAAAAT
1 AATTCAGAAAT
1516680 TTATTGAGAT
Statistics
Matches: 308, Mismatches: 13, Indels: 12
0.92 0.04 0.04
Matches are distributed among these distances:
314 25 0.08
315 151 0.49
316 111 0.36
317 6 0.02
318 15 0.05
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.39
Consensus pattern (315 bp):
AATTCAGAAATATTAACACTCAATATCTCAATCCATTTAGAATAGAATAATCTTAAACATAAAAC
TTGAAATAAACTTAAAATTTTAGACTTTTAAAGATAGATTTAAATATCTTTAATGTCATGATCAT
GTGGATTTAATTTGCACTTAATCTAGTCTTAGTAATGTTTGATAGAAATATGATCAATGATTTTG
ATACCCATAGATATAAGATCTAACCCTAGTTATTATAAATTAAATTTTGTATGTTGGCACGAGGT
ATAAGATTTAATCCGATGTAATTTACTTTTCCTTTCATTGTTGAAGGAGTCGGAC
Found at i:1519082 original size:29 final size:30
Alignment explanation
Indices: 1519049--1519111 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
1519039 CTTAATGTGT
*
1519049 AATTTTATAAATG-AACTTTGATTTTATAC
1 AATTTTATAAATGAAACTTTGATTTGATAC
* * *
1519078 AATTTTATACATGAAATTTTGATTTGATCC
1 AATTTTATAAATGAAACTTTGATTTGATAC
1519108 AATT
1 AATT
1519112 ATTGATATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 12 0.41
30 17 0.59
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.48
Consensus pattern (30 bp):
AATTTTATAAATGAAACTTTGATTTGATAC
Found at i:1521512 original size:6 final size:6
Alignment explanation
Indices: 1521503--1521532 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
1521493 TAATATATTT
1521503 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA
1521533 GTAGGTGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
ATAAAA
Found at i:1523896 original size:132 final size:133
Alignment explanation
Indices: 1523755--1524019 Score: 523
Period size: 132 Copynumber: 2.0 Consensus size: 133
1523745 TAGATGTAGC
1523755 TTGAGTTTGAATCGTACTAATTGTATTGCTATTAGAGTTTTACTCTCCTCTTATAATTCACCAAA
1 TTGAGTTTGAATCGTACTAATTGTATTGCTATTAGAGTTTTACTCTCCTCTTATAATTCACCAAA
1523820 AAAATATTTATAAATTATATTATATTGTTTTGAATATATTTTGTCATTTTTATATC-TTTATGTA
66 AAAATATTTATAAATTATATTATATTGTTTTGAATATATTTTGTCATTTTTATATCTTTTATGTA
1523884 TAT
131 TAT
1523887 TTGAGTTTGAATCGTACTAATTGTATTGCTATTAGAGTTTTACTCTCCTCTTATAATTCACCAAA
1 TTGAGTTTGAATCGTACTAATTGTATTGCTATTAGAGTTTTACTCTCCTCTTATAATTCACCAAA
1523952 AAAATATTTATAAATTATATTATATTGTTTTGAATATATTTTGTCATTTTTATATCTTTTATGTA
66 AAAATATTTATAAATTATATTATATTGTTTTGAATATATTTTGTCATTTTTATATCTTTTATGTA
1524017 TAT
131 TAT
1524020 AAAAAGAGTA
Statistics
Matches: 132, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
132 121 0.92
133 11 0.08
ACGTcount: A:0.31, C:0.10, G:0.09, T:0.50
Consensus pattern (133 bp):
TTGAGTTTGAATCGTACTAATTGTATTGCTATTAGAGTTTTACTCTCCTCTTATAATTCACCAAA
AAAATATTTATAAATTATATTATATTGTTTTGAATATATTTTGTCATTTTTATATCTTTTATGTA
TAT
Found at i:1527915 original size:20 final size:20
Alignment explanation
Indices: 1527890--1527929 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1527880 TATATTTTTT
*
1527890 TAGAGAA-AGGAAGGTGGTAA
1 TAGAGAATA-GAAAGTGGTAA
1527910 TAGAGAATAGAAAGTGGTAA
1 TAGAGAATAGAAAGTGGTAA
1527930 GGATTTGTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.47, C:0.00, G:0.35, T:0.17
Consensus pattern (20 bp):
TAGAGAATAGAAAGTGGTAA
Found at i:1536360 original size:22 final size:22
Alignment explanation
Indices: 1536334--1536421 Score: 141
Period size: 22 Copynumber: 4.2 Consensus size: 22
1536324 CCTTCTCTCA
1536334 TTTTATCGCATTTAATATAATT
1 TTTTATCGCATTTAATATAATT
1536356 TTTTATCGCATTTAATATAA--
1 TTTTATCGCATTTAATATAATT
1536376 TTTTATCGCATTTAATATAATT
1 TTTTATCGCATTTAATATAATT
1536398 TTTTAT---ATTTAATATAATT
1 TTTTATCGCATTTAATATAATT
1536417 TTTTA
1 TTTTA
1536422 ACAGCCCGAT
Statistics
Matches: 64, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
19 18 0.28
20 20 0.31
22 26 0.41
ACGTcount: A:0.33, C:0.07, G:0.03, T:0.57
Consensus pattern (22 bp):
TTTTATCGCATTTAATATAATT
Found at i:1536381 original size:20 final size:20
Alignment explanation
Indices: 1536333--1536418 Score: 120
Period size: 20 Copynumber: 4.2 Consensus size: 20
1536323 CCCTTCTCTC
1536333 ATTTTATCGCATTTAATATA
1 ATTTTATCGCATTTAATATA
1536353 ATTTTTTATCGCATTTAATATA
1 A--TTTTATCGCATTTAATATA
1536375 ATTTTATCGCATTTAATATA
1 ATTTTATCGCATTTAATATA
***
1536395 ATTTT-TTATATTTAATATA
1 ATTTTATCGCATTTAATATA
1536414 ATTTT
1 ATTTT
1536419 TTAACAGCCC
Statistics
Matches: 61, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
19 16 0.26
20 25 0.41
22 20 0.33
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.56
Consensus pattern (20 bp):
ATTTTATCGCATTTAATATA
Found at i:1536392 original size:42 final size:39
Alignment explanation
Indices: 1536333--1536418 Score: 145
Period size: 42 Copynumber: 2.1 Consensus size: 39
1536323 CCCTTCTCTC
1536333 ATTTTATCGCATTTAATATAATTTTTTATCGCATTTAATATA
1 ATTTTATCGCATTTAATATAATTTTTTAT---ATTTAATATA
1536375 ATTTTATCGCATTTAATATAATTTTTTATATTTAATATA
1 ATTTTATCGCATTTAATATAATTTTTTATATTTAATATA
1536414 ATTTT
1 ATTTT
1536419 TTAACAGCCC
Statistics
Matches: 44, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
39 15 0.34
42 29 0.66
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.56
Consensus pattern (39 bp):
ATTTTATCGCATTTAATATAATTTTTTATATTTAATATA
Found at i:1538273 original size:20 final size:21
Alignment explanation
Indices: 1538248--1538288 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1538238 TATTTTTAAC
*
1538248 ATTTTTTAATTTTTAAAAATA
1 ATTTTATAATTTTTAAAAATA
* *
1538269 ATTTTATATTTTTTGAAAAT
1 ATTTTATAATTTTTAAAAAT
1538289 TTGAAATTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
ATTTTATAATTTTTAAAAATA
Found at i:1539993 original size:30 final size:30
Alignment explanation
Indices: 1539957--1540018 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
1539947 GTACTATTTT
1539957 TTGATATTCTTTACTATATATTATATGGGC
1 TTGATATTCTTTACTATATATTATATGGGC
1539987 TTGATATTCTTTACTATATATTATATGGGC
1 TTGATATTCTTTACTATATATTATATGGGC
1540017 TT
1 TT
1540019 AAGTGTTTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.26, C:0.10, G:0.13, T:0.52
Consensus pattern (30 bp):
TTGATATTCTTTACTATATATTATATGGGC
Found at i:1542969 original size:18 final size:18
Alignment explanation
Indices: 1542931--1542992 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
1542921 GCCTAGTCAC
*
1542931 CCACCAACCCACCACCATCA
1 CCACC-ACCC-CCACCCTCA
*
1542951 CCACCACCCTCACCCTCA
1 CCACCACCCCCACCCTCA
*
1542969 CC-CTCACCCCCATCCTCA
1 CCAC-CACCCCCACCCTCA
1542987 TCCACC
1 -CCACC
1542993 CACTAAGCCC
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
17 1 0.03
18 21 0.60
19 7 0.20
20 6 0.17
ACGTcount: A:0.24, C:0.65, G:0.00, T:0.11
Consensus pattern (18 bp):
CCACCACCCCCACCCTCA
Found at i:1542985 original size:12 final size:12
Alignment explanation
Indices: 1542937--1542986 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
1542927 TCACCCACCA
*
1542937 ACCCACCACCATC
1 ACCC-CCACCCTC
*
1542950 ACCACCACCCTC
1 ACCCCCACCCTC
*
1542962 ACCCTCACCCTC
1 ACCCCCACCCTC
*
1542974 ACCCCCATCCTC
1 ACCCCCACCCTC
1542986 A
1 A
1542987 TCCACCCACT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
12 28 0.90
13 3 0.10
ACGTcount: A:0.24, C:0.64, G:0.00, T:0.12
Consensus pattern (12 bp):
ACCCCCACCCTC
Found at i:1543106 original size:24 final size:24
Alignment explanation
Indices: 1543021--1543119 Score: 65
Period size: 24 Copynumber: 4.1 Consensus size: 24
1543011 CACTCCTCCT
* * * *
1543021 CCAGTTCATCCACCACCCAAGGCG
1 CCAGTTCAACCACCAACCAAGCCA
* *
1543045 CCAGTGCAACCACCAACCAAGCCC
1 CCAGTTCAACCACCAACCAAGCCA
* ** * *
1543069 CCAACTTC-TGCTCCACCCAAGCCA
1 CC-AGTTCAACCACCAACCAAGCCA
* *
1543093 CCAGTTCAACCTCCAACTAAGCCA
1 CCAGTTCAACCACCAACCAAGCCA
1543117 CCA
1 CCA
1543120 ACCAAACCTC
Statistics
Matches: 56, Mismatches: 17, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
23 4 0.07
24 49 0.88
25 3 0.05
ACGTcount: A:0.29, C:0.47, G:0.11, T:0.12
Consensus pattern (24 bp):
CCAGTTCAACCACCAACCAAGCCA
Found at i:1543150 original size:24 final size:24
Alignment explanation
Indices: 1543123--1543181 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
1543113 GCCACCAACC
* *
1543123 AAACCTCCAACTCAACCCCCGCCT
1 AAACCACCAACTCAACCCCCGACT
*
1543147 AAACCACCAACTCAGCCCCCGACT
1 AAACCACCAACTCAACCCCCGACT
*
1543171 AAGCCACCAAC
1 AAACCACCAAC
1543182 CAAGCCTCCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.34, C:0.51, G:0.07, T:0.08
Consensus pattern (24 bp):
AAACCACCAACTCAACCCCCGACT
Found at i:1543154 original size:60 final size:60
Alignment explanation
Indices: 1543098--1543217 Score: 170
Period size: 60 Copynumber: 2.0 Consensus size: 60
1543088 AGCCACCAGT
*
1543098 TCAACCTCCAACTAAGCCACCAACCAAACCTCCAACTCAACCCCCGCCTAAACCACCAAC
1 TCAACCCCCAACTAAGCCACCAACCAAACCTCCAACTCAACCCCCGCCTAAACCACCAAC
* * * * *
1543158 TCAGCCCCCGACTAAGCCACCAACCAAGCCTCCAACTCAGCCCCCGACC-AAGCCACCAAC
1 TCAACCCCCAACTAAGCCACCAACCAAACCTCCAACTCAACCCCCG-CCTAAACCACCAAC
1543218 ACACCCACCA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
60 51 0.96
61 2 0.04
ACGTcount: A:0.33, C:0.51, G:0.07, T:0.08
Consensus pattern (60 bp):
TCAACCCCCAACTAAGCCACCAACCAAACCTCCAACTCAACCCCCGCCTAAACCACCAAC
Found at i:1543187 original size:24 final size:25
Alignment explanation
Indices: 1543129--1543187 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 25
1543119 AACCAAACCT
* *
1543129 CCAACTCAA-CCCCCGCCTAAACCA
1 CCAACTCAAGCCCCCGACTAAGCCA
1543153 CCAACTC-AGCCCCCGACTAAGCCA
1 CCAACTCAAGCCCCCGACTAAGCCA
1543177 CCAAC-CAAGCC
1 CCAACTCAAGCC
1543188 TCCAACTCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 2 0.06
24 29 0.94
ACGTcount: A:0.32, C:0.53, G:0.08, T:0.07
Consensus pattern (25 bp):
CCAACTCAAGCCCCCGACTAAGCCA
Found at i:1543199 original size:24 final size:24
Alignment explanation
Indices: 1543054--1543227 Score: 68
Period size: 24 Copynumber: 7.2 Consensus size: 24
1543044 GCCAGTGCAA
* *
1543054 CCACCAACCAAGCCCCCAACTTCTG
1 CCACCAACCAAGCCACCAAC-TCAG
* * ** *
1543079 -CTCCACCCAAGCCACCAGTTCAA
1 CCACCAACCAAGCCACCAACTCAG
* * *
1543102 CCTCCAACTAAGCCACCAAC-CAAA
1 CCACCAACCAAGCCACCAACTC-AG
* * ** * *
1543126 CCTCCAACTCAA-CCCCCGCCTAAA
1 CCACCAAC-CAAGCCACCAACTCAG
* * *
1543150 CCACCAACTC-AGCCCCCGACTAAG
1 CCACCAAC-CAAGCCACCAACTCAG
*
1543174 CCACCAACCAAGCCTCCAACTCAG
1 CCACCAACCAAGCCACCAACTCAG
* * * *
1543198 CCCCCGACCAAGCCACCAACACAC
1 CCACCAACCAAGCCACCAACTCAG
1543222 CCACCA
1 CCACCA
1543228 TCTCATCCTC
Statistics
Matches: 114, Mismatches: 29, Indels: 13
0.73 0.19 0.08
Matches are distributed among these distances:
23 5 0.04
24 107 0.94
25 2 0.02
ACGTcount: A:0.32, C:0.52, G:0.07, T:0.09
Consensus pattern (24 bp):
CCACCAACCAAGCCACCAACTCAG
Found at i:1548582 original size:20 final size:21
Alignment explanation
Indices: 1548557--1548597 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1548547 TATTTTTAAC
*
1548557 ATTTTTTAATTTTTAAAAATA
1 ATTTTATAATTTTTAAAAATA
* *
1548578 ATTTTATATTTTTTGAAAAT
1 ATTTTATAATTTTTAAAAAT
1548598 TTGAAATTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
ATTTTATAATTTTTAAAAATA
Found at i:1552120 original size:23 final size:23
Alignment explanation
Indices: 1552061--1552114 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
1552051 AACAAATAAT
** *
1552061 AATAAAACATAAACAATTATTTTA
1 AATAAAACATTTA-AATTAATTTA
*
1552085 AATTAAACATTTAAATTAATTTA
1 AATAAAACATTTAAATTAATTTA
1552108 AATAAAA
1 AATAAAA
1552115 TTTTTATTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 15 0.60
24 10 0.40
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (23 bp):
AATAAAACATTTAAATTAATTTA
Found at i:1554075 original size:23 final size:23
Alignment explanation
Indices: 1554045--1554089 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
1554035 AGATTTTTCC
1554045 TAAATATTATCACTAAATAAATT
1 TAAATATTATCACTAAATAAATT
*
1554068 TAAATATTATTACTAAATAAAT
1 TAAATATTATCACTAAATAAAT
1554090 CAAAATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (23 bp):
TAAATATTATCACTAAATAAATT
Found at i:1554095 original size:23 final size:23
Alignment explanation
Indices: 1554046--1554095 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
1554036 GATTTTTCCT
**
1554046 AAATATTATCACTAAATAAATTT
1 AAATATTATCACTAAATAAATCA
*
1554069 AAATATTATTACTAAATAAATCA
1 AAATATTATCACTAAATAAATCA
1554092 AAAT
1 AAAT
1554096 TTAAAAGTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (23 bp):
AAATATTATCACTAAATAAATCA
Found at i:1568107 original size:15 final size:17
Alignment explanation
Indices: 1568083--1568117 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1568073 TTATTTATTA
1568083 TTTATGTTATTCA-GAT
1 TTTATGTTATTCAGGAT
1568099 TTTAT-TTATTCAGGAT
1 TTTATGTTATTCAGGAT
1568115 TTT
1 TTT
1568118 CCTTACAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.23, C:0.06, G:0.11, T:0.60
Consensus pattern (17 bp):
TTTATGTTATTCAGGAT
Done.