Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold93
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: 1685797
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 216 characters in sequence are not A, C, G, or T
File 12 of 14
Found at i:1412355 original size:13 final size:13
Alignment explanation
Indices: 1412337--1412365 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1412327 ATACCGATTG
1412337 CATTGTATCGATA
1 CATTGTATCGATA
1412350 CATTGTATCGATA
1 CATTGTATCGATA
1412363 CAT
1 CAT
1412366 GACCAAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:1412378 original size:20 final size:21
Alignment explanation
Indices: 1412353--1412405 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
1412343 ATCGATACAT
**
1412353 TGTATCGATACATGACCA-AA
1 TGTATCGATACATGAAAAGAA
*
1412373 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACATGAAAAGAA
1412394 TGTATCGATACA
1 TGTATCGATACA
1412406 GGTCATTGGC
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:1412475 original size:13 final size:13
Alignment explanation
Indices: 1412457--1412481 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1412447 ACACACAATA
1412457 TGTATCGATACAT
1 TGTATCGATACAT
1412470 TGTATCGATACA
1 TGTATCGATACA
1412482 CCATAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1412478 original size:32 final size:33
Alignment explanation
Indices: 1412437--1412504 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
1412427 GTAGCCAAAT
*
1412437 TTGTATCGATACA-CACAATATGTATCGATACA
1 TTGTATCGATACACCACAAAATGTATCGATACA
*
1412469 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACACCACAAAATGTATCGATACA
1412502 TTG
1 TTG
1412505 GCTTGTAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACACCACAAAATGTATCGATACA
Found at i:1415455 original size:13 final size:13
Alignment explanation
Indices: 1415437--1415464 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1415427 ACAACATTCC
1415437 TTGTATCGATACA
1 TTGTATCGATACA
1415450 TTGTATCGATACA
1 TTGTATCGATACA
1415463 TT
1 TT
1415465 AGGTACTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1417928 original size:13 final size:13
Alignment explanation
Indices: 1417910--1417936 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1417900 ACATGCTGCT
1417910 TTGTATCGATACA
1 TTGTATCGATACA
1417923 TTGTATCGATACA
1 TTGTATCGATACA
1417936 T
1 T
1417937 GGACAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1420355 original size:21 final size:21
Alignment explanation
Indices: 1420329--1420372 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1420319 GTCAGTATCT
1420329 CAAGATA-ATCAGTGACAATTA
1 CAAGATACATC-GTGACAATTA
*
1420350 CAAGATACATCGTGACTATTA
1 CAAGATACATCGTGACAATTA
1420371 CA
1 CA
1420373 TTTTTCTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.25
Consensus pattern (21 bp):
CAAGATACATCGTGACAATTA
Found at i:1426697 original size:23 final size:23
Alignment explanation
Indices: 1426645--1426697 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
1426635 AAGATTTATT
*
1426645 TTAATATATTAATAATATATAAA
1 TTAATATATTAATAATAAATAAA
*
1426668 TTTATATATT-ATCAATAAATTAAA
1 TTAATATATTAAT-AATAAA-TAAA
1426692 -TAATAT
1 TTAATAT
1426698 TATTTTATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
22 2 0.08
23 19 0.76
24 4 0.16
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
TTAATATATTAATAATAAATAAA
Found at i:1426718 original size:29 final size:30
Alignment explanation
Indices: 1426686--1426743 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
1426676 TTATCAATAA
1426686 ATTAAATAATA-TTAT-TTTATTATTAAAAC
1 ATTAAA-AATATTTATATTTATTATTAAAAC
* *
1426715 ATTAAAATTATTTATATTTATTTTTAAAA
1 ATTAAAAATATTTATATTTATTATTAAAA
1426744 TTTTTTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 3 0.12
29 10 0.40
30 12 0.48
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (30 bp):
ATTAAAAATATTTATATTTATTATTAAAAC
Found at i:1426744 original size:22 final size:23
Alignment explanation
Indices: 1426716--1426760 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
1426706 TATTAAAACA
*
1426716 TTAAAATTATTT-ATATTTATTT
1 TTAAAATTATTTAATAATTATTT
*
1426738 TTAAAATTTTTTAATAATTATTT
1 TTAAAATTATTTAATAATTATTT
1426761 ACAACTTACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TTAAAATTATTTAATAATTATTT
Found at i:1426978 original size:7 final size:7
Alignment explanation
Indices: 1426956--1426997 Score: 66
Period size: 7 Copynumber: 5.7 Consensus size: 7
1426946 TAAAAATAAT
1426956 TATTTAA
1 TATTTAA
1426963 TAAATTTAA
1 T--ATTTAA
1426972 TATTTAA
1 TATTTAA
1426979 TATTTAA
1 TATTTAA
1426986 TATTTAA
1 TATTTAA
1426993 TATTT
1 TATTT
1426998 TTTTTACCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 26 0.79
9 7 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
TATTTAA
Found at i:1427431 original size:31 final size:30
Alignment explanation
Indices: 1427378--1427436 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
1427368 AAAAATAATG
*
1427378 ATATATTTAAATTTTATATTTAAAATTAAAT
1 ATATATTTAAATTTAATATTT-AAATTAAAT
*
1427409 ATATATTTTAAA-TTAATTTTTAAATTAA
1 ATATA-TTTAAATTTAATATTTAAATTAA
1427437 CATACAAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 7 0.28
31 12 0.48
32 6 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (30 bp):
ATATATTTAAATTTAATATTTAAATTAAAT
Found at i:1427911 original size:17 final size:17
Alignment explanation
Indices: 1427889--1427921 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1427879 TAAAATAAAA
*
1427889 TAAAAAATATATTAATC
1 TAAAAAATATAATAATC
1427906 TAAAAAATATAATAAT
1 TAAAAAATATAATAAT
1427922 TAATAAGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAAAAATATAATAATC
Found at i:1429256 original size:32 final size:31
Alignment explanation
Indices: 1429197--1429257 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
1429187 TACTTTAATG
*
1429197 ACCTAAATAACCCAAAAATAATTATTTAAAT
1 ACCTAAATAACCCAAAAATAATAATTTAAAT
* * *
1429228 ACCTCAAATAACCCTAGAATTATAATTTAA
1 ACCT-AAATAACCCAAAAATAATAATTTAA
1429258 GCCATTGAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 4 0.16
32 21 0.84
ACGTcount: A:0.51, C:0.18, G:0.02, T:0.30
Consensus pattern (31 bp):
ACCTAAATAACCCAAAAATAATAATTTAAAT
Found at i:1429587 original size:16 final size:17
Alignment explanation
Indices: 1429561--1429593 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1429551 TAGAAAAATA
1429561 AAAAAATAACTTAAACT
1 AAAAAATAACTTAAACT
1429578 AAAAAA-AACTTAAACT
1 AAAAAATAACTTAAACT
1429594 CATCATAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.67, C:0.12, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAAAATAACTTAAACT
Found at i:1429629 original size:15 final size:16
Alignment explanation
Indices: 1429598--1429630 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1429588 TAAACTCATC
*
1429598 ATAACTCAAGTTTAAA
1 ATAACTCAAGTTCAAA
1429614 ATAACT-AAGTTCAAA
1 ATAACTCAAGTTCAAA
1429629 AT
1 AT
1429631 GATCAAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.52, C:0.12, G:0.06, T:0.30
Consensus pattern (16 bp):
ATAACTCAAGTTCAAA
Found at i:1429762 original size:14 final size:14
Alignment explanation
Indices: 1429735--1429771 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1429725 AAATAAAAAC
1429735 TTAATTTAACAATT
1 TTAATTTAACAATT
* *
1429749 TTATTTTAATAATT
1 TTAATTTAACAATT
1429763 TTAATTTAA
1 TTAATTTAA
1429772 AAAATATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (14 bp):
TTAATTTAACAATT
Found at i:1431093 original size:23 final size:24
Alignment explanation
Indices: 1431070--1431115 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1431060 TTATCGATAA
1431070 TTCATAATT-TATCGATACATTAAT
1 TTCA-AATTGTATCGATACATTAAT
*
1431094 TTGAAATTGTATCGATACATTA
1 TTCAAATTGTATCGATACATTA
1431116 TGAATTGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (24 bp):
TTCAAATTGTATCGATACATTAAT
Found at i:1431123 original size:20 final size:21
Alignment explanation
Indices: 1431061--1431133 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 21
1431051 GATTTGAAAT
*
1431061 TATCGATA-ATTCAT-AATT-
1 TATCGATACATTAATGAATTG
1431079 TATCGATACATTAATTTGAAATTG
1 TATCGATACATTAA--TG-AATTG
1431103 TATCGATACATT-ATGAATTG
1 TATCGATACATTAATGAATTG
1431123 TATCGATACAT
1 TATCGATACAT
1431134 GGCTACGAGA
Statistics
Matches: 48, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
18 8 0.17
19 4 0.08
20 16 0.33
21 3 0.06
23 5 0.10
24 12 0.25
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41
Consensus pattern (21 bp):
TATCGATACATTAATGAATTG
Found at i:1431636 original size:14 final size:14
Alignment explanation
Indices: 1431617--1431643 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1431607 CTTTAGTGTA
1431617 CATTATAAAAATAG
1 CATTATAAAAATAG
1431631 CATTATAAAAATA
1 CATTATAAAAATA
1431644 CCAATAGACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.07, G:0.04, T:0.30
Consensus pattern (14 bp):
CATTATAAAAATAG
Found at i:1433670 original size:110 final size:110
Alignment explanation
Indices: 1433477--1433691 Score: 376
Period size: 110 Copynumber: 2.0 Consensus size: 110
1433467 AGTGGCAGAT
*
1433477 AAAGAAGACCTCAATAGCAATTAAACTTTTAAGAGCAATTTGTGACAAAAACAAGTAAACATCAT
1 AAAGAAGACCTCAATAGCAATTAAACTCTTAAGAGCAATTTGTGACAAAAACAAGTAAACATCAT
*
1433542 AACAAAAATGAACCCAAATCGAACAATAATATCAAGTGAAGTAGA
66 AACAAAAATGAAACCAAATCGAACAATAATATCAAGTGAAGTAGA
* * * *
1433587 AAAGAAGACTTCAATAGCAATTGAACTCTTAAGAGCAATTTGTGACAAAAACAAGTAAATATCCT
1 AAAGAAGACCTCAATAGCAATTAAACTCTTAAGAGCAATTTGTGACAAAAACAAGTAAACATCAT
1433652 AACAAAAATGAAACCAAATCGAACAATAATATCAAGTGAA
66 AACAAAAATGAAACCAAATCGAACAATAATATCAAGTGAA
1433692 AATACCAAAT
Statistics
Matches: 99, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
110 99 1.00
ACGTcount: A:0.52, C:0.15, G:0.13, T:0.20
Consensus pattern (110 bp):
AAAGAAGACCTCAATAGCAATTAAACTCTTAAGAGCAATTTGTGACAAAAACAAGTAAACATCAT
AACAAAAATGAAACCAAATCGAACAATAATATCAAGTGAAGTAGA
Found at i:1434831 original size:20 final size:20
Alignment explanation
Indices: 1434806--1434843 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1434796 TTTTAACCCA
1434806 ATTGTATCGATACATTCTTC
1 ATTGTATCGATACATTCTTC
* *
1434826 ATTGTATTGATACGTTCT
1 ATTGTATCGATACATTCT
1434844 GGGTTTTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.13, T:0.47
Consensus pattern (20 bp):
ATTGTATCGATACATTCTTC
Found at i:1434844 original size:51 final size:52
Alignment explanation
Indices: 1434754--1434890 Score: 186
Period size: 51 Copynumber: 2.7 Consensus size: 52
1434744 TTCTAGAATA
* * *
1434754 AAATGTATCGATACATTTTTCATTGTATCAATACTTTCTGGG-TTTTAACCC
1 AAATGTATCGATACATTCTTCATTGTATCGATACGTTCTGGGTTTTTAACCC
* * *
1434805 AATTGTATCGATACATTCTTCATTGTATTGATACGTTCTGGGTTTTTGACCC
1 AAATGTATCGATACATTCTTCATTGTATCGATACGTTCTGGGTTTTTAACCC
* * *
1434857 AAATGTATCAATATATTCTTCAATGTATCGATAC
1 AAATGTATCGATACATTCTTCATTGTATCGATAC
1434891 ATCTAGTTAA
Statistics
Matches: 74, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
51 37 0.50
52 37 0.50
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (52 bp):
AAATGTATCGATACATTCTTCATTGTATCGATACGTTCTGGGTTTTTAACCC
Found at i:1440032 original size:13 final size:13
Alignment explanation
Indices: 1440014--1440039 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1440004 CAATTTTTTG
1440014 TGTATCGATACAT
1 TGTATCGATACAT
1440027 TGTATCGATACAT
1 TGTATCGATACAT
1440040 ACTTTGTGTA
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:1440051 original size:32 final size:33
Alignment explanation
Indices: 1439994--1440057 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1439984 TACAAGCCAA
**
1439994 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
1440027 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
1440058 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:1440730 original size:40 final size:41
Alignment explanation
Indices: 1440684--1440774 Score: 116
Period size: 39 Copynumber: 2.3 Consensus size: 41
1440674 TTTTCTTTCT
1440684 CCCTTAACTAAAG-TAATTTTAACAAATTCATACATTCTCC
1 CCCTTAACTAAAGATAATTTTAACAAATTCATACATTCTCC
* * *
1440724 CCCTTAA-T-AAGATAATTTTAGCAAATTTATGCATTCTCC
1 CCCTTAACTAAAGATAATTTTAACAAATTCATACATTCTCC
* *
1440763 CCTTTTACTAAA
1 CCCTTAACTAAA
1440775 AAAAAATCTC
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
38 3 0.07
39 30 0.70
40 8 0.19
41 2 0.05
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.37
Consensus pattern (41 bp):
CCCTTAACTAAAGATAATTTTAACAAATTCATACATTCTCC
Found at i:1442630 original size:13 final size:13
Alignment explanation
Indices: 1442612--1442649 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1442602 ATAATCCCCC
1442612 TGTATCGATACAG
1 TGTATCGATACAG
*
1442625 TGTATCGATACAT
1 TGTATCGATACAG
1442638 TGTATCGATACA
1 TGTATCGATACA
1442650 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1448251 original size:13 final size:13
Alignment explanation
Indices: 1448233--1448258 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1448223 CAATTTTTTG
1448233 TGTATCGATACAT
1 TGTATCGATACAT
1448246 TGTATCGATACAT
1 TGTATCGATACAT
1448259 ACTTTGTGTA
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:1448270 original size:32 final size:33
Alignment explanation
Indices: 1448213--1448276 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1448203 TACAAGCCAA
**
1448213 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
1448246 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
1448277 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:1448353 original size:20 final size:20
Alignment explanation
Indices: 1448307--1448380 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
1448297 ATCCCAATGA
***
1448307 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGAAT
1448328 CATGTATCGATACATTGCAA-
1 CATGTATCGATACATTG-AAT
*
1448348 CATGTATCGATACTTTGAAT
1 CATGTATCGATACATTGAAT
*
1448368 TATGTATCGATAC
1 CATGTATCGATAC
1448381 TTTTAAGGGT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.04
20 29 0.63
21 15 0.33
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.39
Consensus pattern (20 bp):
CATGTATCGATACATTGAAT
Found at i:1452657 original size:18 final size:18
Alignment explanation
Indices: 1452617--1452658 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
1452607 AATTTCCTTA
*
1452617 TTTTT-TTTGTCTTTGTT
1 TTTTTCTTTGTCTTTCTT
* *
1452634 TCTTTCTTTTTCTTTCTT
1 TTTTTCTTTGTCTTTCTT
1452652 TTTTTCT
1 TTTTTCT
1452659 CTCTACTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.81
Consensus pattern (18 bp):
TTTTTCTTTGTCTTTCTT
Found at i:1453311 original size:166 final size:165
Alignment explanation
Indices: 1452988--1453526 Score: 556
Period size: 166 Copynumber: 3.2 Consensus size: 165
1452978 AGAAAAATTC
* * * *** * * *
1452988 AAAATTTATG-AAATAAATTAAATTTTTCAAAAATGATTTAATGGGAGTTAAATGACAATA-TTA
1 AAAATTTATGAAAATAAA-TGAATTTTTGAAAACTGATTTAACATGAATTAAATAATAATATTTA
* ** * * * * * *
1453051 GATGAATTTTAAAAATTTTAGATC-AAGAAAAATC-CTCTCGAAAACATCTATGGTATAGAAAAC
65 -ATAAATTTTAAAAA-TAAAAAACAAAGAAAAATCTCTCT-AAAAACATTTACGGAATAGAAAAC
* * *
1453114 TCGATTTTTTTG-AAATAGG-GAAATATCAAGGAAAAAATGA
127 TC-A-TATTTTGAAAATAGGAG-ATTTTCAAGGAAAAAATGA
* * *
1453154 AAAACTCATGAAAATAAATGAATTTTTGAAAACTGATTTAACATGAATTAAATAATAATATTTGA
1 AAAATTTATGAAAATAAATGAATTTTTGAAAACTGATTTAACATGAATTAAATAATAATATTTAA
* * * *
1453219 TAAATTTTAAAAATAAAAAACCAAGAAAAATCTCATC-GAAAATATTTACGGAATAGAAAACTTT
66 TAAATTTTAAAAATAAAAAACAAAGAAAAATCTC-TCTAAAAACATTTACGGAATAGAAAAC-TC
* *
1453283 ATATTTTGGAAACA-AGG-GATTTTCAAGGAAAAATTAA
129 ATATTTT-GAAA-ATAGGAGATTTTCAAGGAAAAAATGA
* ** *
1453320 AAAATTTATGAAAATAAATGAATTTTTTAAAAAGGATCTAACATGAATTAAATAATAATATTTAA
1 AAAATTTATGAAAATAAATGAATTTTTGAAAACTGATTTAACATGAATTAAATAATAATATTTAA
* * * *
1453385 TAAATTTTAAAAATTAAAAACAAAGAAAAATCTCTCTAAAAACATTTATGGAGTAGAAAACTCCT
66 TAAATTTTAAAAATAAAAAACAAAGAAAAATCTCTCTAAAAACATTTACGGAATAGAAAACTCAT
1453450 ATTTTGAAAATAGGAGATTTTCAAGGAAAAAATTGA
131 ATTTTGAAAATAGGAGATTTTCAAGGAAAAAA-TGA
*
1453486 AAAATTTATGAAAATAAATGAATTTTTGAAAACTAATTTAA
1 AAAATTTATGAAAATAAATGAATTTTTGAAAACTGATTTAA
1453527 TATTGTCGTA
Statistics
Matches: 311, Mismatches: 49, Indels: 26
0.81 0.13 0.07
Matches are distributed among these distances:
163 1 0.00
164 7 0.02
165 34 0.11
166 249 0.80
167 17 0.05
168 3 0.01
ACGTcount: A:0.50, C:0.07, G:0.11, T:0.32
Consensus pattern (165 bp):
AAAATTTATGAAAATAAATGAATTTTTGAAAACTGATTTAACATGAATTAAATAATAATATTTAA
TAAATTTTAAAAATAAAAAACAAAGAAAAATCTCTCTAAAAACATTTACGGAATAGAAAACTCAT
ATTTTGAAAATAGGAGATTTTCAAGGAAAAAATGA
Found at i:1456007 original size:8 final size:8
Alignment explanation
Indices: 1455994--1456019 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1455984 CAAATCACTA
1455994 TGCTGATT
1 TGCTGATT
1456002 TGCTGATT
1 TGCTGATT
1456010 TGCTGATT
1 TGCTGATT
1456018 TG
1 TG
1456020 GAGTGGCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.27, T:0.50
Consensus pattern (8 bp):
TGCTGATT
Found at i:1456701 original size:52 final size:52
Alignment explanation
Indices: 1456631--1456751 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
1456621 GAAAATTTAT
*
1456631 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
1456683 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
1456735 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
1456752 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:1456764 original size:52 final size:51
Alignment explanation
Indices: 1456631--1456771 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
1456621 GAAAATTTAT
1456631 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
1456683 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
1456735 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
1456772 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:1456778 original size:13 final size:13
Alignment explanation
Indices: 1456760--1456784 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1456750 CAAAGATCAG
1456760 TGTATCGATACAA
1 TGTATCGATACAA
1456773 TGTATCGATACA
1 TGTATCGATACA
1456785 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1456867 original size:13 final size:13
Alignment explanation
Indices: 1456849--1456873 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1456839 CAAAAAAATA
1456849 TGTATCGATACAT
1 TGTATCGATACAT
1456862 TGTATCGATACA
1 TGTATCGATACA
1456874 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1456869 original size:33 final size:33
Alignment explanation
Indices: 1456827--1456893 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1456817 AGTAGCTTAA
1456827 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1456860 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1456893 A
1 A
1456894 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1457835 original size:171 final size:171
Alignment explanation
Indices: 1457623--1458017 Score: 673
Period size: 171 Copynumber: 2.3 Consensus size: 171
1457613 TTTTAGAGAT
* *
1457623 GATGAAGGTGCCAATATGCTGATTCAAGACCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
1 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
1457688 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACAATATTGGGCCTAAAGATGAGAAAAAGGA
66 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACAATATTGGGCCTAAAGATGAGAAAAAGGA
*
1457753 TGTCAACGTGCTGATTCAAGGCTAGCTACATTGAACTTAAA
131 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
* * *
1457794 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATGATGAGAAAA
1 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
* *
1457859 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGA
66 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACAATATTGGGCCTAAAGATGAGAAAAAGGA
1457924 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
131 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
* *
1457965 GATGGAAAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
1 GAT-GAAGA--TGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAG
1458018 GTGCCAATGT
Statistics
Matches: 210, Mismatches: 11, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
171 166 0.79
172 4 0.02
174 40 0.19
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.25
Consensus pattern (171 bp):
GATGAAGATGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
GTGATAAAGATGCCAATATGTTGATTCATGGCCAACAATATTGGGCCTAAAGATGAGAAAAAGGA
TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
Found at i:1458074 original size:49 final size:49
Alignment explanation
Indices: 1457932--1458400 Score: 584
Period size: 49 Copynumber: 9.6 Consensus size: 49
1457922 GATGTCAACG
* *
1457932 TGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-GAAGA--TGCCAATA
* *
1457984 TGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A-G--G-TGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1458027 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* * *
1458076 TGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A-G--G-TGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
*
1458119 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* * * *
1458168 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* *
1458217 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGATGCCAATA
* * *
1458269 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* *
1458318 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGATGCCAATA
* *
1458370 TGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTA
1458401 GAGGGGTTGC
Statistics
Matches: 368, Mismatches: 31, Indels: 36
0.85 0.07 0.08
Matches are distributed among these distances:
43 70 0.19
44 5 0.01
45 2 0.01
46 3 0.01
47 1 0.00
48 5 0.01
49 164 0.45
50 3 0.01
51 3 0.01
52 112 0.30
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.25
Consensus pattern (49 bp):
TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
Found at i:1458310 original size:101 final size:101
Alignment explanation
Indices: 1457864--1458400 Score: 743
Period size: 101 Copynumber: 5.4 Consensus size: 101
1457854 GAAAAGTGAT
* * * * *
1457864 AAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCA
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT--G---AAGG-TGCCA
* * *
1457929 ACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
60 ATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGA
*
1457971 AAATG-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGCCAATGTG
1 AAA-GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTG
*
1458029 CTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G-
65 CTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGA
1458064 -AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATGTGC
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGC
1458122 TGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-G-
66 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGA
1458156 -AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGC
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGC
1458220 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGA
66 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGA
* *
1458256 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGC
1458321 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGA
66 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGA
* * *
1458357 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA
1458401 GAGGGGTTGC
Statistics
Matches: 406, Mismatches: 13, Indels: 28
0.91 0.03 0.06
Matches are distributed among these distances:
91 1 0.00
92 130 0.32
94 1 0.00
95 41 0.10
96 5 0.01
98 48 0.12
99 1 0.00
101 141 0.35
103 1 0.00
107 36 0.09
108 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.25
Consensus pattern (101 bp):
AAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGC
TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGA
Found at i:1458501 original size:32 final size:33
Alignment explanation
Indices: 1458405--1458497 Score: 163
Period size: 33 Copynumber: 2.8 Consensus size: 33
1458395 GGCTTAGAGG
1458405 GGTTGCCACCGACTTGTGTGGGCTTTGGAAGAA
1 GGTTGCCACCGACTTGTGTGGGCTTTGGAAGAA
1458438 GGTTGCCACCGACTTGTGTGGGCTTTAGGAAG-A
1 GGTTGCCACCGACTTGTGTGGGCTTT-GGAAGAA
1458471 -GTTGCCACCGACTTGTGTGGGCTTTGG
1 GGTTGCCACCGACTTGTGTGGGCTTTGG
1458498 GAAGGAAAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
31 2 0.03
32 25 0.42
33 27 0.46
34 5 0.08
ACGTcount: A:0.15, C:0.19, G:0.37, T:0.29
Consensus pattern (33 bp):
GGTTGCCACCGACTTGTGTGGGCTTTGGAAGAA
Found at i:1458587 original size:33 final size:34
Alignment explanation
Indices: 1458499--1459072 Score: 340
Period size: 33 Copynumber: 15.9 Consensus size: 34
1458489 GGGCTTTGGG
*
1458499 AAGGAAAAAAAGATGCCACGGAGTTGTGGAC-TTAA
1 AAGG-AAAAAAG-TGCCACGGAGTTGTGGGCTTTAA
1458534 AAGTGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AAG-GAAAAA-AGTGCCACGGAGTTGTGGGCTTTAA
1458570 AA-GAAAAAAGTGCCACGGAGTTGTGGGCTTTGAA
1 AAGGAAAAAAGTGCCACGGAGTTGTGGGCTTT-AA
1458604 AAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AA-GGAAAAA-AGTGCCACGGAGTTGTGGGCTTTAA
* *
1458640 ACGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAA
1 AAGGAAAAAAGTGCCACGGAGTTGTGGGCTTTAA
*
1458674 AA-GAAAAAGGTGCCACGGAGTTGTGGGCTTTGAA
1 AAGGAAAAAAGTGCCACGGAGTTGTGGGCTTT-AA
** * ***
1458708 AAGGAAAAAAGAGTGCCACAAAGTCGTAGGTGCCACAGA
1 AAGG-AAAAA-AGTGCCACGGAGTTGT-GG-GCTTTA-A
** ** *** * * **** **
1458747 GTTGTGGGCTTTAAAAG-AAAAAGGTGCCACGGAG-TTGTGGGC
1 ----AAGG--AAAAAAGTGCCACGGAGTTGTGG-GCTT-T--AA
*** * * *
1458789 TTTGAAAAGGAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGG
1 AAGGAAA---A-AA-G-TGCCACGGA-GT-TGTGGGCTTTA-A
* * *
1458832 AAGGGAGAAAGATGCCACGGAGTTGTGGAC-TTAA
1 AAGGAAAAAAG-TGCCACGGAGTTGTGGGCTTTAA
1458866 AAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AA-GGAAAAA-AGTGCCACGGAGTTGTGGGCTTTAA
1458902 AA-GAAAAAAGTGCCACGGAGTTGTGGGCTTTGAA
1 AAGGAAAAAAGTGCCACGGAGTTGTGGGCTTT-AA
*
1458936 AAGGGAAAAAGAGTGCCACGAAGTTGTGGGCTTTAA
1 AA-GGAAAAA-AGTGCCACGGAGTTGTGGGCTTTAA
*
1458972 ACA-GAAAAAGGTGCCACGGAGTTGTGGGCTTTGAA
1 A-AGGAAAAAAGTGCCACGGAGTTGTGGGCTTT-AA
*
1459007 AA-GAAGAAAGAGTGCCACGAAGTTGTGGGCTTTAA
1 AAGGAA-AAA-AGTGCCACGGAGTTGTGGGCTTTAA
* * *
1459042 AA-GAAGAAGGTGCCACGGAGTTGTGGACTTT
1 AAGGAAAAAAGTGCCACGGAGTTGTGGGCTTT
1459073 GAGACAAAAT
Statistics
Matches: 424, Mismatches: 71, Indels: 90
0.72 0.12 0.15
Matches are distributed among these distances:
33 95 0.22
34 78 0.18
35 77 0.18
36 68 0.16
37 59 0.14
38 14 0.03
39 6 0.01
40 3 0.01
41 4 0.01
42 3 0.01
43 8 0.02
44 5 0.01
45 4 0.01
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.20
Consensus pattern (34 bp):
AAGGAAAAAAGTGCCACGGAGTTGTGGGCTTTAA
Found at i:1458613 original size:104 final size:105
Alignment explanation
Indices: 1458486--1459071 Score: 600
Period size: 104 Copynumber: 5.4 Consensus size: 105
1458476 CACCGACTTG
** *
1458486 TGTGGGCTTTGGGAA-GGAAAAAAAGATGCCACGGAGTTGTGGACTTAAAAGTGAAAAAGAGTGC
1 TGTGGGCTTTGAAAAGGGAAAAAGAG-TGCCACGGAGTTGTGGACTTAAAAGTGAAAAAGAGTGC
1458550 CACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGT
65 CACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGT
* *
1458591 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACG-GAAAAAG-GTGC
1 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGAC-TTAAAAGTGAAAAAGAGTGC
*
1458654 CACGGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGT
65 CACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGT
* ** * * * *
1458695 TGTGGGCTTTGAAAAGGAAAAAAGAGTGCCACAAAGTCGTAGGTGC-CACAGAGTTGTGGGCTTT
1 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGT-GG-ACTTA-A-A--AGT--G----
* * * * * *
1458759 AAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAGAAGGTTGCCACCGACTT
54 --AA-AAAGA-GTGCCACGGAGTTGTGGGCTTT-AAAAGAAAAAAG-TGCCACGGA-GT
* * *
1458818 GTGTGGGCTTT-AGGAAGGGAGAAAGA-TGCCACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTG
1 -TGTGGGCTTTGA-AAAGGGAAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGTGAAAAAGAGTG
1458881 CCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGT
64 CCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGT
* * * **
1458923 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGAAGTTGTGGGCTTTAAACAGAAAAAG-GTGCC
1 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGTGAAAAAGAGTGCC
*
1458987 ACGGAGTTGTGGGCTTTGAAAAGAAGAAAGAGTGCCACGAAGT
66 ACGGAGTTGTGGGCTTT-AAAAGAA-AAA-AGTGCCACGGAGT
*
1459030 TGTGGGCTTT-AAAA--GAAGAAG-GTGCCACGGAGTTGTGGACTT
1 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGACTT
1459072 TGAGACAAAA
Statistics
Matches: 406, Mismatches: 44, Indels: 64
0.79 0.09 0.12
Matches are distributed among these distances:
103 19 0.05
104 130 0.32
105 77 0.19
106 33 0.08
107 31 0.08
108 23 0.06
109 4 0.01
110 2 0.00
111 1 0.00
116 1 0.00
117 2 0.00
118 4 0.01
120 23 0.06
121 12 0.03
122 11 0.03
123 13 0.03
124 20 0.05
ACGTcount: A:0.33, C:0.12, G:0.34, T:0.20
Consensus pattern (105 bp):
TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGTGAAAAAGAGTGCC
ACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGT
Found at i:1458616 original size:70 final size:69
Alignment explanation
Indices: 1458486--1459074 Score: 389
Period size: 70 Copynumber: 8.2 Consensus size: 69
1458476 CACCGACTTG
* * * *
1458486 TGTGGGCTTTGGGAAGGAAAAAAAGATGCCACGGAGTTGTGGAC-TTAAAAGTGAAAAAGAGTGC
1 TGTGGGCTTT-GAAAAGAAAAAGAG-TGCCACGGAGTTGTGGGCTTTAAAA--GAAAAAGAGTGC
1458550 CACGGAGT
62 CACGGAGT
1458558 TGTGGGCTTT-AAAAGAAAAA-AGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCC
1 TGTGGGCTTTGAAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAA--GAAAAAGAGTGCC
1458621 ACGGAGT
63 ACGGAGT
*
1458628 TGTGGGCTTT-AAACGGAAAAAG-GTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAG-GTGCCAC
1 TGTGGGCTTTGAAA-AGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGAGTGCCAC
1458690 GGAGT
65 GGAGT
** * * *** * *** * *
1458695 TGTGGGCTTTGAAAAGGAAAAAAGAGTGCCACAAAGTCGTAGG-TGCCACAG-AGTTGTGGGCTT
1 TGTGGGCTTTGAAAA-G-AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGAGTGC--
* * * *
1458758 TAAAAGAAAAAGG
62 --CACG---GAGT
* **** * *
1458771 TGCCACGGAG-TTGTGGGCTTTGAAAAGGAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGGAAG
1 TG---TGG-GCTT-T--GAAAAGAAAA--AG-A-G-TGCCACGGA-GT-TGTGGGCTTTA--AA-
* *
1458835 GGAGAAAGA-TGCCACGGAGT
49 AGAAAAAGAGTGCCACGGAGT
*
1458855 TGTGGAC-TT-AAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAA-AGTGCCA
1 TGTGGGCTTTGAAAA--GAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGAGTGCCA
1458917 CGGAGT
64 CGGAGT
*
1458923 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGAAGTTGTGGGCTTTAAACAGAAAAAG-GTGCC
1 TGTGGGCTTTGAAAA--GAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA-AGAAAAAGAGTGCC
1458987 ACGGAGT
63 ACGGAGT
* *
1458994 TGTGGGCTTTGAAAAGAAGAAAGAGTGCCACGAAGTTGTGGGCTTTAAAAGAAGAAG-GTGCCAC
1 TGTGGGCTTTGAAAAGAA-AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGAGTGCCAC
1459058 GGAGT
65 GGAGT
*
1459063 TGTGGACTTTGA
1 TGTGGGCTTTGA
1459075 GACAAAATGC
Statistics
Matches: 412, Mismatches: 61, Indels: 91
0.73 0.11 0.16
Matches are distributed among these distances:
67 23 0.06
68 52 0.13
69 54 0.13
70 132 0.32
71 73 0.18
72 11 0.03
73 10 0.02
74 1 0.00
75 1 0.00
76 6 0.01
78 5 0.01
79 5 0.01
80 7 0.02
81 3 0.01
82 3 0.01
83 1 0.00
84 5 0.01
85 7 0.02
86 1 0.00
87 6 0.01
88 1 0.00
90 1 0.00
91 3 0.01
92 1 0.00
ACGTcount: A:0.33, C:0.12, G:0.34, T:0.21
Consensus pattern (69 bp):
TGTGGGCTTTGAAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGAGTGCCACG
GAGT
Found at i:1458848 original size:38 final size:37
Alignment explanation
Indices: 1458749--1459066 Score: 117
Period size: 35 Copynumber: 9.1 Consensus size: 37
1458739 GCCACAGAGT
* * * *
1458749 TGTGGGCTTT-AAAA-GAAAAAGGTGCCACGGA-GT-
1 TGTGGGCTTTGAAAAGGAGAAAGATGCCACCGACTTG
* *
1458782 TGTGGGCTTTGAAAAGGAGAAGGTTGCCACCGACTTG
1 TGTGGGCTTTGAAAAGGAGAAAGATGCCACCGACTTG
* * * *
1458819 TGTGGGCTTTAGGAAGGGAGAAAGATGCCACGGA-GT-
1 TGTGGGCTTT-GAAAAGGAGAAAGATGCCACCGACTTG
* * * *
1458855 TGTGGAC-TT-AAAAGGGAAAAAGAGTGCCACGGA-GT-
1 TGTGGGCTTTGAAAA-GGAGAAAGA-TGCCACCGACTTG
* * * *
1458890 TGTGGGCTTT-AAAAGAAAAAAG-TGCCACGGA-GT-
1 TGTGGGCTTTGAAAAGGAGAAAGATGCCACCGACTTG
* **
1458923 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCA-CGAAGT-
1 TGTGGGCTTTGAAAA-GGAGAAAGA-TGCCACCGACTTG
* * * *
1458960 TGTGGGCTTT-AAACA-GAAAAAGGTGCCACGGA-GT-
1 TGTGGGCTTTGAAA-AGGAGAAAGATGCCACCGACTTG
* **
1458994 TGTGGGCTTTGAAAAGAAGAAAGAGTGCCA-CGAAGT-
1 TGTGGGCTTTGAAAAGGAGAAAGA-TGCCACCGACTTG
* * * *
1459030 TGTGGGCTTT-AAAAGAAG-AAGGTGCCACGGAGTTG
1 TGTGGGCTTTGAAAAGGAGAAAGATGCCACCGACTTG
1459065 TG
1 TG
1459067 GACTTTGAGA
Statistics
Matches: 235, Mismatches: 29, Indels: 40
0.77 0.10 0.13
Matches are distributed among these distances:
33 38 0.16
34 40 0.17
35 75 0.32
36 35 0.15
37 29 0.12
38 18 0.08
ACGTcount: A:0.32, C:0.12, G:0.35, T:0.21
Consensus pattern (37 bp):
TGTGGGCTTTGAAAAGGAGAAAGATGCCACCGACTTG
Found at i:1458916 original size:191 final size:191
Alignment explanation
Indices: 1458546--1459074 Score: 560
Period size: 191 Copynumber: 2.8 Consensus size: 191
1458536 GTGAAAAAGA
*
1458546 GTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
1 GTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
* * *
1458611 AAAGAGTGCCACGGAGTTGTGGGCTTTAAACGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAA
66 AAAGAGTGCCACCGAGTTGTGGGCTTTAAACGGAAAAAGATGCCACGGAGTTGTGGACTTTAAAA
1458676 GAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTGCCACAAAGTCGTAG
131 GAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTGCCACAAAGTCGTAG
*
1458737 GTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAA-GG-A
1 GTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
* * * *
1458800 GAAG-GTTGCCACCGACTTGTGTGGGCTTTAGGAAGGGAGAAAGATGCCACGGAGTTGTGGAC-T
66 AAAGAG-TGCCACCGA-GT-TGTGGGCTTTA--AACGGAAAAAGATGCCACGGAGTTGTGGACTT
1458863 TAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAA-G-AAAAA-AGTG-C-C--A--C
126 TAAAA--GAAAAAG-GTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTGCCACAAAGTC
1458918 ----
188 GTAG
*
1458918 --G-----GAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGAAGTTGTGGGCTTT-AAACA
1 GTGCCACAGAGTTGTGGGCTTT-AAAA--GAAAAA-AGTGCCACGGAGTTGTGGGCTTTGAAA-A
* * * *
1458975 --GAAAAAG-GTGCCACGGAGTTGTGGGCTTTGAAA-AGAAGAAAGAGTGCCACGAAGTTGTGGG
61 GGGAAAAAGAGTGCCACCGAGTTGTGGGCTTT-AAACGGAA-AAAGA-TGCCACGGAGTTGTGGA
* *
1459036 CTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGACTTTGA
123 CTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGA
1459075 GACAAAATGC
Statistics
Matches: 299, Mismatches: 20, Indels: 55
0.80 0.05 0.15
Matches are distributed among these distances:
173 23 0.08
174 28 0.09
175 30 0.10
176 8 0.03
177 18 0.06
178 27 0.09
179 1 0.00
185 1 0.00
187 1 0.00
188 1 0.00
189 13 0.04
190 4 0.01
191 73 0.24
192 11 0.04
193 27 0.09
194 11 0.04
195 22 0.07
ACGTcount: A:0.32, C:0.13, G:0.34, T:0.21
Consensus pattern (191 bp):
GTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
AAAGAGTGCCACCGAGTTGTGGGCTTTAAACGGAAAAAGATGCCACGGAGTTGTGGACTTTAAAA
GAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTGCCACAAAGTCGTAG
Found at i:1458926 original size:228 final size:225
Alignment explanation
Indices: 1458512--1459071 Score: 668
Period size: 228 Copynumber: 2.6 Consensus size: 225
1458502 GAAAAAAAGA
*
1458512 TGCCACGGAGTTGTGGACTTAAAAGTGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAA
1 TGCCACAGAGTTGTGGACTTAAAAG-GAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAA
* * *
1458577 AAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAC
65 AAGTGCCACCGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGACTTAAAAC
*
1458642 GGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGA
130 GGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTGA
1458707 AAAGGAAAAAAGAGTGCCACAAAGTCGTAGG
195 AAAGGAAAAAAGAGTGCCACAAAGTCGTAGG
* * *
1458738 TGCCACAGAGTTGTGGGCTTTAAAA-GAAAAAG-GTGCCACGGAGTTGTGGGCTTTGAAAAGGAG
1 TGCCACAGAGTTGTGGAC-TTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAGAAA
* * * *
1458801 AAGGTTGCCACCGACTTGTGTGGGCTTT-AGGAAGGGAGAAAGA-TGCCACGGAGTTGTGGACTT
64 AAAG-TGCCACCGA-GT-TGTGGGCTTTGA-AAAGGGAAAAAGAGTGCCACGGAGTTGTGGACTT
*
1458864 AAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGG
125 AAAACGGAAAAAG-GTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGG
* * *
1458929 CTTTGAAAAGGGAAAAAGAGTGCCACGAAGTTGT-GG
189 CTTTGAAAAGGAAAAAAGAGTGCCACAAAGTCGTAGG
*
1458965 -G---C----TT-T--A---AACA-GAAAAAG-GTGCCACGGAGTTGTGGGCTTTGAAAAGAAGA
1 TGCCACAGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAGAA-A
*
1459014 AAGAGTGCCA-CGAAGTTGTGGGCTTT-AAAA--GAAGAAG-GTGCCACGGAGTTGTGGACTT
64 AA-AGTGCCACCG-AGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGACTT
1459072 TGAGACAAAA
Statistics
Matches: 298, Mismatches: 25, Indels: 40
0.82 0.07 0.11
Matches are distributed among these distances:
208 25 0.08
210 2 0.01
211 11 0.04
212 42 0.14
213 8 0.03
214 1 0.00
218 1 0.00
219 2 0.01
223 1 0.00
224 22 0.07
225 16 0.05
226 25 0.08
227 40 0.13
228 102 0.34
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.21
Consensus pattern (225 bp):
TGCCACAGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAA
AGTGCCACCGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGACTTAAAACG
GAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTGAA
AAGGAAAAAAGAGTGCCACAAAGTCGTAGG
Found at i:1459009 original size:141 final size:139
Alignment explanation
Indices: 1458737--1459074 Score: 452
Period size: 141 Copynumber: 2.4 Consensus size: 139
1458727 AAAGTCGTAG
* *
1458737 GTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAGA
1 GTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAA
** ** *
1458802 AGGTTGCCACCGACTTGTGTGGGCTTTAGGAAGGGAGAAAGATGCCACGGAGTTGTGGACTTAAA
66 AGGTTGCCACCGAAGTGTGTGGGCTTTA-GAACAGAAAAAGATGCCACGGAGTTGTGGACTTAAA
1458867 AGGGAA-AAAGA
130 A--GAAGAAAGA
*
1458878 GTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
1 GTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAA-GG-A
* *
1458943 AAAGAG-TGCCA-CGAAGT-TGTGGGCTTTA-AACAGAAAAAGGTGCCACGGAGTTGTGGGCTTT
64 AAAG-GTTGCCACCGAAGTGTGTGGGCTTTAGAACAGAAAAAGATGCCACGGAGTTGTGGAC-TT
1459004 GAAAAGAAGAAAGA
127 -AAAAGAAGAAAGA
* * *
1459018 GTGCCACGAAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGACTTTGA
1 GTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGA
1459075 GACAAAATGC
Statistics
Matches: 177, Mismatches: 14, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
139 28 0.16
140 60 0.34
141 73 0.41
142 6 0.03
143 9 0.05
144 1 0.01
ACGTcount: A:0.32, C:0.13, G:0.35, T:0.21
Consensus pattern (139 bp):
GTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAA
AGGTTGCCACCGAAGTGTGTGGGCTTTAGAACAGAAAAAGATGCCACGGAGTTGTGGACTTAAAA
GAAGAAAGA
Found at i:1459130 original size:62 final size:64
Alignment explanation
Indices: 1459031--1459196 Score: 184
Period size: 62 Copynumber: 2.7 Consensus size: 64
1459021 CCACGAAGTT
* * * *
1459031 GTGGGCTTTAAAAGAAGAAGG-TGCCACGGAGTTGTGGACTTTGAGACA-A-AATGCCACTGAGT
1 GTGGACTTTAAAAG-AGAAGGATGCCACTGAGTCGTGGACTTTGAG-CAGAGAATGCCACTCAGT
1459093 C
64 C
* *
1459094 GTGGACTTT-AAAGAGAAGGATGCCACTGCGTCGTGGACTTTGAGCAGAGATTGCCACTCAGTC
1 GTGGACTTTAAAAGAGAAGGATGCCACTGAGTCGTGGACTTTGAGCAGAGAATGCCACTCAGTC
* *
1459157 GTGGACTTTGAAAAGAG-A--TTGCCACTGAGTCGTAGACTTT
1 GTGGACTTT-AAAAGAGAAGGATGCCACTGAGTCGTGGACTTT
1459197 TTTTGACCTT
Statistics
Matches: 89, Mismatches: 9, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
61 8 0.09
62 45 0.51
63 29 0.33
64 1 0.01
65 6 0.07
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.25
Consensus pattern (64 bp):
GTGGACTTTAAAAGAGAAGGATGCCACTGAGTCGTGGACTTTGAGCAGAGAATGCCACTCAGTC
Found at i:1459158 original size:31 final size:31
Alignment explanation
Indices: 1459064--1459196 Score: 123
Period size: 31 Copynumber: 4.3 Consensus size: 31
1459054 CCACGGAGTT
* *
1459064 GTGGACTTTGAGACA-A-AATGCCACTGAGTC
1 GTGGACTTTGAG-CAGAGATTGCCACTCAGTC
*
1459094 GTGGACTTTAAAG-AGAAGGA-TGCCACTGC-GTC
1 GTGGACTTT-GAGCAG-A-GATTGCCACT-CAGTC
1459126 GTGGACTTTGAGCAGAGATTGCCACTCAGTC
1 GTGGACTTTGAGCAGAGATTGCCACTCAGTC
** *
1459157 GTGGACTTTGAAAAGAGATTGCCACTGAGTC
1 GTGGACTTTGAGCAGAGATTGCCACTCAGTC
*
1459188 GTAGACTTT
1 GTGGACTTT
1459197 TTTTGACCTT
Statistics
Matches: 87, Mismatches: 7, Indels: 17
0.78 0.06 0.15
Matches are distributed among these distances:
29 1 0.01
30 12 0.14
31 52 0.60
32 21 0.24
33 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.26
Consensus pattern (31 bp):
GTGGACTTTGAGCAGAGATTGCCACTCAGTC
Found at i:1459218 original size:9 final size:9
Alignment explanation
Indices: 1459206--1459232 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
1459196 TTTTTGACCT
1459206 TTTTTTTTA
1 TTTTTTTTA
1459215 TTTTTTTTA
1 TTTTTTTTA
1459224 TTTTTTTTA
1 TTTTTTTTA
1459233 AAAAAAGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:1464048 original size:2 final size:2
Alignment explanation
Indices: 1464041--1464078 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1464031 GGATGATTTC
*
1464041 TA TA TA TA TA TA TA TA TA TA TA TA TA TT 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
1464079 AAGAAAGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1467137 original size:16 final size:16
Alignment explanation
Indices: 1467116--1467146 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1467106 TGCACATTTT
*
1467116 AACATGTGCCTGAGGC
1 AACATGCGCCTGAGGC
1467132 AACATGCGCCTGAGG
1 AACATGCGCCTGAGG
1467147 TGAAGTTATG
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:0.26, C:0.26, G:0.32, T:0.16
Consensus pattern (16 bp):
AACATGCGCCTGAGGC
Found at i:1475404 original size:13 final size:13
Alignment explanation
Indices: 1475386--1475411 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1475376 TTATTCAATA
1475386 TATCGATACATTG
1 TATCGATACATTG
1475399 TATCGATACATTG
1 TATCGATACATTG
1475412 ATCTTTGTAT
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):
TATCGATACATTG
Found at i:1479298 original size:20 final size:20
Alignment explanation
Indices: 1479250--1479301 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
1479240 GTATCGATAC
* **
1479250 AATGTATCAATACATGACTA
1 AATGTATCGATACATGAAAA
*
1479270 AATGTATCGATACTTGAAAA
1 AATGTATCGATACATGAAAA
1479290 AATGTATCGATA
1 AATGTATCGATA
1479302 AAAGTCATTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (20 bp):
AATGTATCGATACATGAAAA
Found at i:1479377 original size:20 final size:20
Alignment explanation
Indices: 1479336--1479387 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1479326 TAGCTAAATT
*
1479336 TGTATCGATACA-CACAATA
1 TGTATCGATACATCACAAAA
1479355 TGTATCGATACATCACAAAA
1 TGTATCGATACATCACAAAA
1479375 TGTATCGATACAT
1 TGTATCGATACAT
1479388 TGGCTTGTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 12 0.39
20 19 0.61
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (20 bp):
TGTATCGATACATCACAAAA
Found at i:1486175 original size:49 final size:49
Alignment explanation
Indices: 1486014--1486329 Score: 274
Period size: 49 Copynumber: 6.6 Consensus size: 49
1486004 CGAAGAATGA
* * * * *
1486014 CAATGTGCTGATTCAAGGCCAGCGACATTAGAATTGAAGAAGAA--TGC
1 CAATGTGCTGATTCAAGGCCAGCGATATCAGACTTAAAGATGAAGGTGC
** * * ** * * *
1486061 CAATGTGCTGAGACAAGGCCAGCAACATTGGGC-TAAGGAATGTTAAAGATGC
1 CAATGTGCTGATTCAAGGCCAGCGATATCAGACTTAAAG-ATG---AAGGTGC
* *
1486113 CAATATGCTGATTCAAGGCCAACGATATCAGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGATATCAGACTTAAAGATGAAGGTGC
** * *
1486162 CAATGTATTGATTCAAGGCCAGCGATATCGGACTTAAAGATGAACGTGC
1 CAATGTGCTGATTCAAGGCCAGCGATATCAGACTTAAAGATGAAGGTGC
* * *
1486211 CAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGA-CAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGATATCAGACTTAAAGATGAAGGTGC
* * **
1486259 CAATATGCTGATTTAAGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGATATCAGACTTAAAGATGAAGGTGC
*
1486302 CAATATGCTGATTCAAGGCCAGCGATAT
1 CAATGTGCTGATTCAAGGCCAGCGATAT
1486330 TGGACTTAGA
Statistics
Matches: 224, Mismatches: 38, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
43 34 0.15
44 1 0.00
46 3 0.01
47 29 0.13
48 37 0.17
49 84 0.38
50 2 0.01
52 30 0.13
53 4 0.02
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCGATATCAGACTTAAAGATGAAGGTGC
Found at i:1486437 original size:29 final size:29
Alignment explanation
Indices: 1486359--1486715 Score: 454
Period size: 29 Copynumber: 12.3 Consensus size: 29
1486349 CACCAACTTG
* *
1486359 TGTGGGCTTTTGAAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAAGATGCCACTGACT
* *
1486388 TGTGGGC-TTTGAGAATG-TGCCACTAACT
1 TGTGGGCTTTTGA-AAAGATGCCACTGACT
1486416 TGTGGGCTTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTTGAAAAGATGCCACTGACT
* * *
1486445 TGTGGGCTTTTTG-AAGGTTGCCACTCACT
1 TGTGGGC-TTTTGAAAAGATGCCACTGACT
* * *
1486474 TGTGGGC-TTTGAGAAGGTGCCACTAACT
1 TGTGGGCTTTTGAAAAGATGCCACTGACT
*
1486502 TATGGGCTTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTTGAAAAGATGCCACTGACT
* *
1486531 TATGGGCTTTTTG-AAGGATGCCACTGACT
1 TGTGGGC-TTTTGAAAAGATGCCACTGACT
*
1486560 TGTGGGCTTTTGAGAAGATGCCACTGACT
1 TGTGGGCTTTTGAAAAGATGCCACTGACT
* *
1486589 TATGGGCTTTTGAAAAGATGCCGCTGACT
1 TGTGGGCTTTTGAAAAGATGCCACTGACT
* *
1486618 TGTGGGCTTTTGAAAAAGGTGCCACCGACT
1 TGTGGGCTTTTG-AAAAGATGCCACTGACT
*
1486648 TGTGGGCTTTTGAAAATATGCCACTGACT
1 TGTGGGCTTTTGAAAAGATGCCACTGACT
* *
1486677 TGTAGGATTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTTGAAAAGATGCCACTGACT
1486706 TGTGGGCTTT
1 TGTGGGCTTT
1486716 GGAAGGTGAG
Statistics
Matches: 285, Mismatches: 34, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
27 4 0.01
28 48 0.17
29 197 0.69
30 36 0.13
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.32
Consensus pattern (29 bp):
TGTGGGCTTTTGAAAAGATGCCACTGACT
Found at i:1486494 original size:86 final size:88
Alignment explanation
Indices: 1486359--1486715 Score: 489
Period size: 86 Copynumber: 4.1 Consensus size: 88
1486349 CACCAACTTG
* *
1486359 TGTGGGC-TTTTGAAAGGTTGCCACTGACTTGTGGGC-TTTGAGAATG-TGCCACTAACTTGTGG
1 TGTGGGCTTTTTGAAAGGTTGCCACTCACTTGTGGGCTTTTGAGAA-GATGCCACTAACTTATGG
1486421 GCTTTTGAAAAGATGCCACTGACT
65 GCTTTTGAAAAGATGCCACTGACT
*
1486445 TGTGGGCTTTTTG-AAGGTTGCCACTCACTTGTGGGC-TTTGAGAAGGTGCCACTAACTTATGGG
1 TGTGGGCTTTTTGAAAGGTTGCCACTCACTTGTGGGCTTTTGAGAAGATGCCACTAACTTATGGG
1486508 CTTTTGAAAAGATGCCACTGACT
66 CTTTTGAAAAGATGCCACTGACT
* * * *
1486531 TATGGGCTTTTTG-AAGGATGCCACTGACTTGTGGGCTTTTGAGAAGATGCCACTGACTTATGGG
1 TGTGGGCTTTTTGAAAGGTTGCCACTCACTTGTGGGCTTTTGAGAAGATGCCACTAACTTATGGG
*
1486595 CTTTTGAAAAGATGCCGCTGACT
66 CTTTTGAAAAGATGCCACTGACT
* * * *
1486618 TGTGGGC-TTTTGAAAAAGG-TGCCAC-CGACTTGTGGGCTTTTGAAAATATGCCACTGACTTGT
1 TGTGGGCTTTTTG--AAAGGTTGCCACTC-ACTTGTGGGCTTTTGAGAAGATGCCACTAACTTAT
* *
1486680 AGGATTTTGAAAAGATGCCACTGACT
63 GGGCTTTTGAAAAGATGCCACTGACT
1486706 TGTGGGCTTT
1 TGTGGGCTTT
1486716 GGAAGGTGAG
Statistics
Matches: 247, Mismatches: 16, Indels: 13
0.89 0.06 0.05
Matches are distributed among these distances:
85 1 0.00
86 114 0.46
87 58 0.23
88 68 0.28
89 6 0.02
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.32
Consensus pattern (88 bp):
TGTGGGCTTTTTGAAAGGTTGCCACTCACTTGTGGGCTTTTGAGAAGATGCCACTAACTTATGGG
CTTTTGAAAAGATGCCACTGACT
Found at i:1500416 original size:24 final size:26
Alignment explanation
Indices: 1500365--1500417 Score: 74
Period size: 24 Copynumber: 2.1 Consensus size: 26
1500355 GAAAATGAGG
1500365 TTGGAGTGTCCCCTCGGAAGAATAAAA
1 TTGGAGTGT-CCCTCGGAAGAATAAAA
*
1500392 TTGGAGTGT-CCTC-GATGAATAAAA
1 TTGGAGTGTCCCTCGGAAGAATAAAA
1500416 TT
1 TT
1500418 TTGATATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 12 0.48
25 4 0.16
27 9 0.36
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (26 bp):
TTGGAGTGTCCCTCGGAAGAATAAAA
Found at i:1502651 original size:52 final size:52
Alignment explanation
Indices: 1502503--1502631 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
1502493 CGAAATATGA
1502503 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
* *
1502555 AAATTTGCCTGTATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
1502607 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1502632 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
Found at i:1502658 original size:13 final size:13
Alignment explanation
Indices: 1502640--1502664 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1502630 CAAAGATCAG
1502640 TGTATCGATACAA
1 TGTATCGATACAA
1502653 TGTATCGATACA
1 TGTATCGATACA
1502665 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1502751 original size:32 final size:32
Alignment explanation
Indices: 1502710--1502777 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
1502700 AGCTTCGTAG
*
1502710 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTAACGATACAAAACTTATGTAT
*
1502742 CGATACATTGTAACGATACAATACTTATGTAT
1 CGATACATTGTAACGATACAAAACTTATGTAT
1502774 CGAT
1 CGAT
1502778 GCAAATCGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (32 bp):
CGATACATTGTAACGATACAAAACTTATGTAT
Found at i:1502777 original size:19 final size:18
Alignment explanation
Indices: 1502718--1502782 Score: 59
Period size: 19 Copynumber: 3.8 Consensus size: 18
1502708 AGCGATACAT
1502718 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
1502737 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
*
1502750 TGTAACGATACAATACTTA
1 TGTATCGATACAA-ACTTA
*
1502769 TGTATCGATGCAAA
1 TGTATCGATACAAA
1502783 TCGTTGAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 13
0.70 0.06 0.25
Matches are distributed among these distances:
13 10 0.27
14 1 0.03
16 2 0.05
18 2 0.05
19 22 0.59
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.32
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:1503594 original size:53 final size:50
Alignment explanation
Indices: 1503537--1503682 Score: 170
Period size: 49 Copynumber: 2.9 Consensus size: 50
1503527 TGAGAAGAAT
* * * **
1503537 GCCAATGTGTTGATTCAAGGCCAACAACATTGGGTTTTAAAGATGACGAAGGC
1 GCCAATATGTTGATTCAAGGCCAGCGACATTGGGACTTAAAGAT---GAAGGC
* * * *
1503590 GCCAATATGCTGATTCAAGGCCAGCGATACT-GGACTTAAAGATGAAGGT
1 GCCAATATGTTGATTCAAGGCCAGCGACATTGGGACTTAAAGATGAAGGC
1503639 GCCAATATGTTGATTCAAGGCCAGCGACATT-GGACTTAAAGATG
1 GCCAATATGTTGATTCAAGGCCAGCGACATTGGGACTTAAAGATG
1503683 GTGAGGATAG
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
49 46 0.57
52 10 0.12
53 25 0.31
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (50 bp):
GCCAATATGTTGATTCAAGGCCAGCGACATTGGGACTTAAAGATGAAGGC
Found at i:1503920 original size:43 final size:43
Alignment explanation
Indices: 1503814--1504170 Score: 309
Period size: 43 Copynumber: 7.8 Consensus size: 43
1503804 ATAAGAAAAA
* ** * *
1503814 TGCCAATGTGCTGAGGCAAGGCCCGCGACATTGGTCTTAAAGACCAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT--A-A--AGG
* * *
1503862 TGCCAATATGCTGATTCCATGCCAGCGATATTGGACTTAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGG
*
1503905 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC-T-----TAAAGG
* * *
1503954 TGCCGATATGTTGATTCAAGGCCAGCGATATTGGACTTAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGG
* * * *
1503997 TGCCAATGTGCTGATTTAGGGCCAGCGACATTGGTCTTAAAGACAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT----A-AAGG
* * *
1504045 TGCCAATATGCTGATTCAAGGCCAACGATATTAGACTTAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGG
* *
1504088 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC-T-----TAAAGG
* *
1504137 CGCCAATATGCTGATTCAAGGCCAGCGATATTGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGG
1504171 GCTGAGAAAG
Statistics
Matches: 255, Mismatches: 37, Indels: 33
0.78 0.11 0.10
Matches are distributed among these distances:
43 109 0.43
44 3 0.01
45 1 0.00
46 1 0.00
47 1 0.00
48 66 0.26
49 74 0.29
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (43 bp):
TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGG
Found at i:1504111 original size:91 final size:92
Alignment explanation
Indices: 1503814--1504170 Score: 538
Period size: 91 Copynumber: 3.9 Consensus size: 92
1503804 ATAAGAAAAA
** * * **
1503814 TGCCAATGTGCTGAGGCAAGGCCCGCGACATTGGTCTTAAAGA-CCAGGTGCCAATATGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATT
* *
1503878 CCATGCCAGCGATATTGGACTTAAAGG
66 CAAGGCCAGCGATATTGGACTTAAAGG
* *
1503905 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAAGGTGCCGATATGTTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATT
1503970 CAAGGCCAGCGATATTGGACTTAAAGG
66 CAAGGCCAGCGATATTGGACTTAAAGG
* * * *
1503997 TGCCAATGTGCTGATTTAGGGCCAGCGACATTGGTCTTAAAGA-CAAGGTGCCAATATGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATT
* *
1504061 CAAGGCCAACGATATTAGACTTAAAGG
66 CAAGGCCAGCGATATTGGACTTAAAGG
* *
1504088 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATAAAGGCGCCAATATGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATT
1504153 CAAGGCCAGCGATATTGG
66 CAAGGCCAGCGATATTGG
1504171 GCTGAGAAAG
Statistics
Matches: 238, Mismatches: 26, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
91 121 0.51
92 117 0.49
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (92 bp):
TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATT
CAAGGCCAGCGATATTGGACTTAAAGG
Found at i:1504122 original size:183 final size:183
Alignment explanation
Indices: 1503814--1504170 Score: 588
Period size: 183 Copynumber: 2.0 Consensus size: 183
1503804 ATAAGAAAAA
* *
1503814 TGCCAATGTGCTGAGGCAAGGCCCGCGACATTGGTCTTAAAGACCAGGTGCCAATATGCTGATTC
1 TGCCAATGTGCTGAGGCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTC
* * * * *
1503879 CATGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTA
66 AAGGCCAACGATATTAGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTA
* * *
1503944 AAGATAAAGGTGCCGATATGTTGATTCAAGGCCAGCGATATTGGACTTAAAGG
131 AAGATAAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGG
*** *
1503997 TGCCAATGTGCTGATTTAGGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTC
1 TGCCAATGTGCTGAGGCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTC
1504062 AAGGCCAACGATATTAGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTA
66 AAGGCCAACGATATTAGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTA
1504127 AAGATAAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGG
131 AAGATAAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGG
1504171 GCTGAGAAAG
Statistics
Matches: 160, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
183 160 1.00
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (183 bp):
TGCCAATGTGCTGAGGCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTC
AAGGCCAACGATATTAGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTA
AAGATAAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGG
Found at i:1504217 original size:33 final size:33
Alignment explanation
Indices: 1504174--1504337 Score: 265
Period size: 33 Copynumber: 5.0 Consensus size: 33
1504164 ATATTGGGCT
1504174 GAGAAAGGTTGCCACCGACTTGTGTGGGCTTTA
1 GAGAAAGGTTGCCACCGACTTGTGTGGGCTTTA
*
1504207 GAGAATGGTTGCCACCGACTTGTGTGGGCTTTA
1 GAGAAAGGTTGCCACCGACTTGTGTGGGCTTTA
* *
1504240 GAGAATGGTTGCCACCGACTTGTGTGGGCTTTG
1 GAGAAAGGTTGCCACCGACTTGTGTGGGCTTTA
* *
1504273 GAAAAAGGTTGCCACCGACTTGTGTGGGCTTTT
1 GAGAAAGGTTGCCACCGACTTGTGTGGGCTTTA
* *
1504306 GAAAAAGGTTGCCACCGACTTGTGTAGGCTTT
1 GAGAAAGGTTGCCACCGACTTGTGTGGGCTTT
1504338 TAAAAAGAAG
Statistics
Matches: 125, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 125 1.00
ACGTcount: A:0.20, C:0.18, G:0.32, T:0.29
Consensus pattern (33 bp):
GAGAAAGGTTGCCACCGACTTGTGTGGGCTTTA
Found at i:1504391 original size:34 final size:33
Alignment explanation
Indices: 1504337--1504819 Score: 290
Period size: 34 Copynumber: 15.2 Consensus size: 33
1504327 GTGTAGGCTT
* *
1504337 TTAAAAAGAAGAAAGATGCCACGGAGTTGTGGAC
1 TTAAAAGGAAAAAAG-TGCCACGGAGTTGTGGAC
*
1504371 TTAAAAGGGAAAAAAGTGCCACGGAGTTGTGGGC
1 TTAAAA-GGAAAAAAGTGCCACGGAGTTGTGGAC
* *
1504405 TTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGAC
1 -TTAAAAGGAAAAAAGTGCCACGGAGTTGTGGAC
* *
1504439 TTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGC
1 TTAAAAGGAAAAA-AGTGCCACGGAGTTGTGGAC
1504473 TTAAAAGG------GTGCCACGGAGTTGTGGAC
1 TTAAAAGGAAAAAAGTGCCACGGAGTTGTGGAC
*
1504500 TTAAAAGG-AAAAGGTGCCACGGAGTTGTGGAC
1 TTAAAAGGAAAAAAGTGCCACGGAGTTGTGGAC
* **
1504532 TTTAAAGGAAAAAAGGGTGCCACGGAGTCATGGAC
1 TTAAAAGGAAAAAA--GTGCCACGGAGTTGTGGAC
* *
1504567 TTAAAAGG------GTTCCACGGAGTTGTGGGC
1 TTAAAAGGAAAAAAGTGCCACGGAGTTGTGGAC
* *
1504594 TT--TA--AAAAGAGTGCCACGGAGTTGTGGAC
1 TTAAAAGGAAAAAAGTGCCACGGAGTTGTGGAC
** * * *
1504623 TTTGAA-GAAAAGA-TGCCACTGAGTCGTGGAC
1 TTAAAAGGAAAAAAGTGCCACGGAGTTGTGGAC
* * * *
1504654 TT---TGG-AAAGAGATGCCACTGAATTGTGGAC
1 TTAAAAGGAAAAAAG-TGCCACGGAGTTGTGGAC
** * * ** **
1504684 TT-TGA-G-ACAAGGTGCCACTAAGTCATGGAC
1 TTAAAAGGAAAAAAGTGCCACGGAGTTGTGGAC
* * *
1504714 TTTAAAGGAAAAAAGGGTGCCACGGAGTTATGGGC
1 TTAAAAGGAAAAAA--GTGCCACGGAGTTGTGGAC
* * *
1504749 TT--TA--AAAAGAGTGCCACAGAGTTGTGGAC
1 TTAAAAGGAAAAAAGTGCCACGGAGTTGTGGAC
* *
1504778 TTCGAAAA-GAAAAAGGTGCCACGGAGTCGTGGAC
1 TT--AAAAGGAAAAAAGTGCCACGGAGTTGTGGAC
1504812 TTAAAAGG
1 TTAAAAGG
1504820 GTATTTGAAG
Statistics
Matches: 357, Mismatches: 56, Indels: 73
0.73 0.12 0.15
Matches are distributed among these distances:
25 1 0.00
27 43 0.12
28 5 0.01
29 38 0.11
30 34 0.10
31 29 0.08
32 37 0.10
33 21 0.06
34 95 0.27
35 54 0.15
ACGTcount: A:0.34, C:0.14, G:0.32, T:0.21
Consensus pattern (33 bp):
TTAAAAGGAAAAAAGTGCCACGGAGTTGTGGAC
Found at i:1504436 original size:68 final size:66
Alignment explanation
Indices: 1504336--1504819 Score: 335
Period size: 61 Copynumber: 7.6 Consensus size: 66
1504326 TGTGTAGGCT
*
1504336 TTTAAAAAGAAGAAAGATGCCACGGAGTTGTGGACTTAAAAGGGAAAAAAGTGCCACGGAGTTGT
1 TTTAAAAAGAA-AAAGGTGCCACGGAGTTGTGGACTTAAAA-GG-AAAAAGTGCCACGGAGTTGT
1504401 GGGC
63 GGGC
*
1504405 TTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTG
1 TTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGG-AAAA-AGTGCCACGGAGTTGTG
1504470 GGC
64 GGC
* *
1504473 -TT-AAAAG-----GGTGCCACGGAGTTGTGGACTTAAAAGGAAAAGGTGCCACGGAGTTGTGGA
1 TTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGTGCCACGGAGTTGTGGG
1504531 C
66 C
* ** *
1504532 TTTAAAGGAA-AAAAGGGTGCCACGGAGTCATGGACTTAAAAGG-----GTTCCACGGAGTTGTG
1 TTTAAA--AAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGTGCCACGGAGTTGTG
1504591 GGC
64 GGC
** * *
1504594 TTTAAAAAG----A-GTGCCACGGAGTTGTGGACTTTGAA-G-AAAAGATGCCACTGAGTCGTGG
1 TTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAG-TGCCACGGAGTTGTGG
*
1504652 AC
65 GC
* * * * * ** * * ** ** *
1504654 TTT----GGAAAGAGATGCCACTGAATTGTGGACTT-TGA-GACAAGGTGCCACTAAGTCATGGA
1 TTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGTGCCACGGAGTTGTGGG
1504713 C
66 C
* * * * * *
1504714 TTTAAAGGAA-AAAAGGGTGCCACGGAGTTATGGGCTT-TAA--AAAGAGTGCCACAGAGTTGTG
1 TTTAAA--AAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGTGCCACGGAGTTGTG
*
1504775 GAC
64 GGC
** *
1504778 TTCGAAAAGAAAAAGGTGCCACGGAGTCGTGGACTTAAAAGG
1 TTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGG
1504820 GTATTTGAAG
Statistics
Matches: 332, Mismatches: 51, Indels: 67
0.74 0.11 0.15
Matches are distributed among these distances:
55 1 0.00
56 22 0.07
59 19 0.06
60 47 0.14
61 50 0.15
62 25 0.08
63 25 0.08
64 23 0.07
65 22 0.07
66 5 0.02
67 35 0.11
68 47 0.14
69 11 0.03
ACGTcount: A:0.33, C:0.14, G:0.32, T:0.21
Consensus pattern (66 bp):
TTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGTGCCACGGAGTTGTGGG
C
Found at i:1504478 original size:27 final size:27
Alignment explanation
Indices: 1504448--1504685 Score: 152
Period size: 27 Copynumber: 8.0 Consensus size: 27
1504438 CTTAGAAGGA
*
1504448 AAAAGAGTGCCACGGAGTTGTGGGCTT
1 AAAAGAGTGCCACGGAGTTGTGGACTT
*
1504475 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGAGTGCCACGGAGTTGTGGACTT
1504502 AAAAGGAAAAGGTGCCACGGAGTTGTGGACTTT
1 AAAA-G---A-GTGCCACGGAGTTGTGGAC-TT
* **
1504535 AAAGGAAAAAAGGGTGCCACGGAGTCATGGACTT
1 -------AAAAGAGTGCCACGGAGTTGTGGACTT
* * *
1504569 AAAAGGGTTCCACGGAGTTGTGGGCTTT
1 AAAAGAGTGCCACGGAGTTGTGGAC-TT
1504597 AAAAAGAGTGCCACGGAGTTGTGGACTTT
1 -AAAAGAGTGCCACGGAGTTGTGGAC-TT
* * *
1504626 GAAGAAAAGATGCCACTGAGTCGTGGACTTT
1 -AA-AAGAG-TGCCACGGAGTTGTGGAC-TT
* * *
1504657 GGAAAGAGATGCCACTGAATTGTGGACTT
1 -AAAAGAG-TGCCACGGAGTTGTGGACTT
1504686 TGAGACAAGG
Statistics
Matches: 173, Mismatches: 21, Indels: 32
0.77 0.09 0.14
Matches are distributed among these distances:
27 50 0.29
28 3 0.02
29 29 0.17
30 25 0.14
31 21 0.12
32 19 0.11
33 2 0.01
34 2 0.01
35 17 0.10
39 1 0.01
40 4 0.02
ACGTcount: A:0.30, C:0.14, G:0.33, T:0.22
Consensus pattern (27 bp):
AAAAGAGTGCCACGGAGTTGTGGACTT
Found at i:1504572 original size:94 final size:95
Alignment explanation
Indices: 1504386--1504819 Score: 417
Period size: 94 Copynumber: 4.6 Consensus size: 95
1504376 AGGGAAAAAA
*
1504386 GTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGAC-TTAGAAGGAAA
1 GTGCCACGGAGTTGTGGAC-TT-AAAAGAAAAAGGTGCCACGGAGTTGTGGACTTTA-AAGGAAA
* ** *
1504450 AAGAGTGCCACGGAGTTGTGGGC-TT-AAAAGG
63 AAGGGTGCCACGGAGTCATGGACTTTAAAAAGG
*
1504481 GTGCCACGGAGTTGTGGACTTAAAAGGAAAAGGTGCCACGGAGTTGTGGACTTTAAAGGAAAAAA
1 GTGCCACGGAGTTGTGGACTTAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTTAAAGG-AAAAA
1504546 GGGTGCCACGGAGTCATGGAC-TT-AAAAGG
65 GGGTGCCACGGAGTCATGGACTTTAAAAAGG
* * * * *
1504575 GTTCCACGGAGTTGTGGGCTT-TAA-AAAGA-GTGCCACGGAGTTGTGGACTTTGAA-G-AAAA-
1 GTGCCACGGAGTTGTGGACTTAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTTAAAGGAAAAAG
* * * **
1504634 GATGCCACTGAGTCGTGGACTTTGGAAAGAG
66 GGTGCCACGGAGTCATGGACTTTAAAAAG-G
* * * ** * ** **
1504665 ATGCCACTGAATTGTGGACTT-TGAG-ACAAGGTGCCACTAAGTCATGGACTTTAAAGGAAAAAA
1 GTGCCACGGAGTTGTGGACTTAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTTAAAGG-AAAAA
* * *
1504728 GGGTGCCACGGAGTTATGGGCTTTAAAAAGA
65 GGGTGCCACGGAGTCATGGACTTTAAAAAGG
* * *
1504759 GTGCCACAGAGTTGTGGACTTCGAAAAGAAAAAGGTGCCACGGAGTCGTGGACTTAAAAGG
1 GTGCCACGGAGTTGTGGACTT--AAAAGAAAAAGGTGCCACGGAGTTGTGGACTTTAAAGG
1504820 GTATTTGAAG
Statistics
Matches: 277, Mismatches: 47, Indels: 27
0.79 0.13 0.08
Matches are distributed among these distances:
87 17 0.06
88 6 0.02
89 4 0.01
90 22 0.08
91 44 0.16
92 4 0.01
93 35 0.13
94 76 0.27
95 40 0.14
97 2 0.01
98 27 0.10
ACGTcount: A:0.32, C:0.14, G:0.33, T:0.21
Consensus pattern (95 bp):
GTGCCACGGAGTTGTGGACTTAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTTAAAGGAAAAAG
GGTGCCACGGAGTCATGGACTTTAAAAAGG
Found at i:1504669 original size:30 final size:30
Alignment explanation
Indices: 1504543--1504716 Score: 128
Period size: 30 Copynumber: 5.9 Consensus size: 30
1504533 TTAAAGGAAA
* * *
1504543 AAAGGGTGCCACGGAGTCATGGAC-TT-A-
1 AAAGAGTGCCACTGAGTCGTGGACTTTGAG
* * * * * *
1504570 AAAGGGTTCCACGGAGTTGTGGGCTTT-AA
1 AAAGAGTGCCACTGAGTCGTGGACTTTGAG
* *
1504599 AAAGAGTGCCACGGAGTTGTGGACTTTGAAG
1 AAAGAGTGCCACTGAGTCGTGGACTTTG-AG
1504630 AAA-AGATGCCACTGAGTCGTGGACTTTG-G
1 AAAGAG-TGCCACTGAGTCGTGGACTTTGAG
* *
1504659 AAAGAGATGCCACTGAATTGTGGACTTTGAG
1 AAAGAG-TGCCACTGAGTCGTGGACTTTGAG
* *
1504690 ACAAG-GTGCCACTAAGTCATGGACTTT
1 A-AAGAGTGCCACTGAGTCGTGGACTTT
1504717 AAAGGAAAAA
Statistics
Matches: 123, Mismatches: 16, Indels: 13
0.81 0.11 0.09
Matches are distributed among these distances:
27 20 0.16
28 3 0.02
29 28 0.23
30 42 0.34
31 27 0.22
32 3 0.02
ACGTcount: A:0.29, C:0.16, G:0.31, T:0.24
Consensus pattern (30 bp):
AAAGAGTGCCACTGAGTCGTGGACTTTGAG
Found at i:1504714 original size:60 final size:60
Alignment explanation
Indices: 1504599--1504716 Score: 166
Period size: 60 Copynumber: 2.0 Consensus size: 60
1504589 TGGGCTTTAA
* * *
1504599 AAAGAGTGCCACGGAGTTGTGGACTTTGAAGAAAAGATGCCACTGAGTCGTGGACTTTGG
1 AAAGAGTGCCACGGAATTGTGGACTTTGAAGAAAAGATGCCACTAAGTCATGGACTTTGG
* * *
1504659 AAAGAGATGCCACTGAATTGTGGACTTTG-AGACAAGGTGCCACTAAGTCATGGACTTT
1 AAAGAG-TGCCACGGAATTGTGGACTTTGAAGAAAAGATGCCACTAAGTCATGGACTTT
1504717 AAAGGAAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
60 31 0.61
61 20 0.39
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.25
Consensus pattern (60 bp):
AAAGAGTGCCACGGAATTGTGGACTTTGAAGAAAAGATGCCACTAAGTCATGGACTTTGG
Found at i:1506133 original size:10 final size:9
Alignment explanation
Indices: 1506098--1506157 Score: 50
Period size: 9 Copynumber: 6.6 Consensus size: 9
1506088 TTACACATTC
1506098 TTTTTTTTG
1 TTTTTTTTG
* *
1506107 TGTATTTT-
1 TTTTTTTTG
*
1506115 TTGTTTTTG
1 TTTTTTTTG
1506124 TTTTTGTTTG
1 TTTTT-TTTG
1506134 TTTTTTTTG
1 TTTTTTTTG
* *
1506143 TGTTGTTTTC
1 T-TTTTTTTG
1506153 TTTTT
1 TTTTT
1506158 ACTTTTGTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
8 5 0.13
9 18 0.46
10 16 0.41
ACGTcount: A:0.02, C:0.02, G:0.15, T:0.82
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:1506139 original size:25 final size:25
Alignment explanation
Indices: 1506098--1506156 Score: 68
Period size: 24 Copynumber: 2.3 Consensus size: 25
1506088 TTACACATTC
*
1506098 TTTTTTTTGTGTATTTTTTGTTTTTG
1 TTTTTTTTGTGTATTTTTTG-TGTTG
1506124 TTTTTGTTTGT-T-TTTTTTGTGTTG
1 TTTTT-TTTGTGTATTTTTTGTGTTG
1506148 TTTTCTTTT
1 TTTT-TTTT
1506157 TACTTTTGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
24 11 0.37
25 8 0.27
26 6 0.20
27 5 0.17
ACGTcount: A:0.02, C:0.02, G:0.15, T:0.81
Consensus pattern (25 bp):
TTTTTTTTGTGTATTTTTTGTGTTG
Found at i:1506157 original size:35 final size:36
Alignment explanation
Indices: 1506098--1506169 Score: 101
Period size: 35 Copynumber: 2.0 Consensus size: 36
1506088 TTACACATTC
* * **
1506098 TTTTTTTTGTGTATTTTTTGTTTTTGTTTTTGTTTG
1 TTTTTTTTGTGTATGTTTTCTTTTTACTTTTGTTTG
1506134 TTTTTTTTGTGT-TGTTTTCTTTTTACTTTTGTTTG
1 TTTTTTTTGTGTATGTTTTCTTTTTACTTTTGTTTG
1506169 T
1 T
1506170 GTGTTTACTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 20 0.62
36 12 0.38
ACGTcount: A:0.03, C:0.03, G:0.15, T:0.79
Consensus pattern (36 bp):
TTTTTTTTGTGTATGTTTTCTTTTTACTTTTGTTTG
Found at i:1506163 original size:26 final size:25
Alignment explanation
Indices: 1506134--1506189 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
1506124 TTTTTGTTTG
* *
1506134 TTTTTTTTGTGTTGTTTTCTTTTTAC
1 TTTTTTTTGTG-TGTTTACTTTTGAC
*
1506160 TTTTGTTTGTGTGTTTACTTTTGAC
1 TTTTTTTTGTGTGTTTACTTTTGAC
1506185 TTTTT
1 TTTTT
1506190 CATTATTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 16 0.62
26 10 0.38
ACGTcount: A:0.05, C:0.07, G:0.14, T:0.73
Consensus pattern (25 bp):
TTTTTTTTGTGTGTTTACTTTTGAC
Found at i:1513162 original size:13 final size:13
Alignment explanation
Indices: 1513144--1513227 Score: 60
Period size: 13 Copynumber: 5.5 Consensus size: 13
1513134 AGCTTCGTAG
1513144 CGATACATTGTAT
1 CGATACATTGTAT
1513157 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
1513176 CGATACATTGTAT
1 CGATACATTGTAT
1513189 CGATACAACACTTATGTAT
1 CGAT---ACA--T-TGTAT
1513208 CGATACATTGTAT
1 CGATACATTGTAT
1513221 CGATACA
1 CGATACA
1513228 ACACTTATGT
Statistics
Matches: 59, Mismatches: 0, Indels: 24
0.71 0.00 0.29
Matches are distributed among these distances:
13 26 0.44
14 1 0.02
15 2 0.03
16 8 0.14
17 2 0.03
18 1 0.02
19 19 0.32
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:1513176 original size:19 final size:18
Alignment explanation
Indices: 1513152--1513248 Score: 97
Period size: 19 Copynumber: 5.8 Consensus size: 18
1513142 AGCGATACAT
1513152 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
1513171 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
1513184 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
1513203 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
1513216 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
1513235 TGTATCGATACAAA
1 TGTATCGATACAAA
1513249 TCGTTGAAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 25
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.33
14 2 0.03
16 4 0.06
18 3 0.05
19 35 0.53
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:1513185 original size:32 final size:32
Alignment explanation
Indices: 1513144--1513246 Score: 197
Period size: 32 Copynumber: 3.2 Consensus size: 32
1513134 AGCTTCGTAG
*
1513144 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
1513176 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
1513208 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
1513240 CGATACA
1 CGATACA
1513247 AATCGTTGAA
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
32 70 1.00
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:1514366 original size:43 final size:43
Alignment explanation
Indices: 1514305--1514619 Score: 369
Period size: 43 Copynumber: 6.9 Consensus size: 43
1514295 TAAAGACCAA
*
1514305 GTGCCAATATGCTGATTCAATGCCAGCGATATTGGACTTAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
* *
1514348 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----TAAAG
1514397 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
* * *
1514440 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A-AAG
*
1514488 GTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
* * *
1514531 GTGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----TAAAG
* *
1514580 GCGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTA
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA
1514620 GAAAGGTTGC
Statistics
Matches: 236, Mismatches: 19, Indels: 34
0.82 0.07 0.12
Matches are distributed among these distances:
43 115 0.49
44 3 0.01
47 1 0.00
48 40 0.17
49 77 0.33
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.24
Consensus pattern (43 bp):
GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
Found at i:1514531 original size:22 final size:22
Alignment explanation
Indices: 1514506--1514573 Score: 52
Period size: 22 Copynumber: 3.1 Consensus size: 22
1514496 ATGCTGATTC
1514506 AAGGCCAACGATATTGGACTTA
1 AAGGCCAACGATATTGGACTTA
* ** *
1514528 AAGGTGCCAATG-TGCT-GA-TTC
1 AA-G-GCCAACGATATTGGACTTA
*
1514549 AAGGCCAACGACATTGGACTTA
1 AAGGCCAACGATATTGGACTTA
1514571 AAG
1 AAG
1514574 ATAAAGGCGC
Statistics
Matches: 32, Mismatches: 9, Indels: 10
0.63 0.18 0.20
Matches are distributed among these distances:
19 6 0.19
20 2 0.06
21 6 0.19
22 9 0.28
23 3 0.09
24 6 0.19
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.22
Consensus pattern (22 bp):
AAGGCCAACGATATTGGACTTA
Found at i:1514549 original size:91 final size:92
Alignment explanation
Indices: 1514258--1514619 Score: 593
Period size: 91 Copynumber: 4.0 Consensus size: 92
1514248 ATGAGAAGAA
** * * **
1514258 TGCCAATGTGCTGAGGCAAGGCCCGCGACATTGGTCTTAAAGACCAA-GTGCCAATATGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATT
*
1514322 CAATGCCAGCGATATTGGACTTAAAGG
66 CAAGGCCAGCGATATTGGACTTAAAGG
1514349 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATT
1514414 CAAGGCCAGCGATATTGGACTTAAAGG
66 CAAGGCCAGCGATATTGGACTTAAAGG
* *
1514441 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA-CAAGGTGCCAATATGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATT
*
1514505 CAAGGCCAACGATATTGGACTTAAAGG
66 CAAGGCCAGCGATATTGGACTTAAAGG
* *
1514532 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATAAAGGCGCCAATATGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATT
*
1514597 CAAGGCCAGCGATATTGGGCTTA
66 CAAGGCCAGCGATATTGGACTTA
1514620 GAAAGGTTGC
Statistics
Matches: 253, Mismatches: 16, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
91 128 0.51
92 125 0.49
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (92 bp):
TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATT
CAAGGCCAGCGATATTGGACTTAAAGG
Found at i:1514566 original size:183 final size:183
Alignment explanation
Indices: 1514258--1514619 Score: 636
Period size: 183 Copynumber: 2.0 Consensus size: 183
1514248 ATGAGAAGAA
*
1514258 TGCCAATGTGCTGAGGCAAGGCCCGCGACATTGGTCTTAAAGACCAAGTGCCAATATGCTGATTC
1 TGCCAATGTGCTGAGGCAAGGCCAGCGACATTGGTCTTAAAGACCAAGTGCCAATATGCTGATTC
* * *
1514323 AATGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTA
66 AAGGCCAACGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTA
*
1514388 AAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGG
131 AAGATAAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGG
**
1514441 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA-CAAGGTGCCAATATGCTGATT
1 TGCCAATGTGCTGAGGCAAGGCCAGCGACATTGGTCTTAAAGACCAA-GTGCCAATATGCTGATT
1514505 CAAGGCCAACGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTT
65 CAAGGCCAACGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTT
*
1514570 AAAGATAAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTA
130 AAAGATAAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA
1514620 GAAAGGTTGC
Statistics
Matches: 170, Mismatches: 8, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
182 3 0.02
183 167 0.98
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (183 bp):
TGCCAATGTGCTGAGGCAAGGCCAGCGACATTGGTCTTAAAGACCAAGTGCCAATATGCTGATTC
AAGGCCAACGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTA
AAGATAAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGG
Found at i:1514661 original size:33 final size:33
Alignment explanation
Indices: 1514619--1514781 Score: 245
Period size: 33 Copynumber: 4.9 Consensus size: 33
1514609 TATTGGGCTT
*
1514619 AGAAAGGTTGCCACCGACTTGTGTAGGCTTTAG
1 AGAAAGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
1514652 AGAATGGTTGCCACCAACTTGTGTGGGCTTTAG
1 AGAAAGGTTGCCACCGACTTGTGTGGGCTTTAG
* * *
1514685 AGAATGGTTGCCACTGACTTTTGTGGGCTTTAG
1 AGAAAGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
1514718 AAAAAGGTTGCCACCGACTTGTGTGGGCTTTTG
1 AGAAAGGTTGCCACCGACTTGTGTGGGCTTTAG
*
1514751 AAAAAGGTTGCCACCGACTTGTGTGGGCTTT
1 AGAAAGGTTGCCACCGACTTGTGTGGGCTTT
1514782 TAAAAAGGAG
Statistics
Matches: 119, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 119 1.00
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.31
Consensus pattern (33 bp):
AGAAAGGTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:1514829 original size:27 final size:27
Alignment explanation
Indices: 1514797--1514969 Score: 94
Period size: 27 Copynumber: 5.6 Consensus size: 27
1514787 AGGAGAAAGA
1514797 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
1514824 TGCCACAGAGTTATGGACTTAAAAGGGAAAAAGAG
1 TGCCACGGAGTTGTGGACTTAAAA--G-----G-G
*
1514859 TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGG
1 TGCCACGGAGTTGTGGAC-TT-AAAAG-----GG
* *
1514893 TGCCATGGAGTTGTGGACTTAGAAGGAAAAAGAG
1 TGCCACGGAGTTGTGGACTT-------AAAAGGG
*
1514927 TGCCACGGAGTTGTGGGCTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
1514954 TGCCACGGAGTTGTGG
1 TGCCACGGAGTTGTGG
1514970 CCCAGACAAA
Statistics
Matches: 119, Mismatches: 11, Indels: 32
0.73 0.07 0.20
Matches are distributed among these distances:
27 44 0.37
29 1 0.01
33 2 0.02
34 37 0.31
35 23 0.19
36 2 0.02
37 4 0.03
39 6 0.05
ACGTcount: A:0.31, C:0.13, G:0.35, T:0.21
Consensus pattern (27 bp):
TGCCACGGAGTTGTGGACTTAAAAGGG
Found at i:1514863 original size:35 final size:34
Alignment explanation
Indices: 1514817--1514952 Score: 175
Period size: 34 Copynumber: 4.0 Consensus size: 34
1514807 TTGTGGACTT
* * *
1514817 AAAAGGGTGCCACAGAGTTATGGACTTAAAAGGGA
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAA-GGA
* *
1514852 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGA
1 AAAAGAGTGCCACGGAGTTGTGGAC-TTAAAAGGA
* *
1514887 AAAAG-GTGCCATGGAGTTGTGGACTTAGAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
*
1514920 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGG
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGG
1514953 GTGCCACGGA
Statistics
Matches: 87, Mismatches: 12, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
33 12 0.14
34 41 0.47
35 28 0.32
36 6 0.07
ACGTcount: A:0.36, C:0.11, G:0.34, T:0.19
Consensus pattern (34 bp):
AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
Found at i:1514936 original size:68 final size:68
Alignment explanation
Indices: 1514817--1514950 Score: 207
Period size: 68 Copynumber: 2.0 Consensus size: 68
1514807 TTGTGGACTT
*
1514817 AAAAGGGTGCCACAGAGTTATGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AAAAAGGTGCCACAGAGTTATGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGC-TTAA
1514882 AAAG
65 AAAG
** * *
1514886 AAAAAGGTGCCATGGAGTTGTGGACTTAGAA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAA
1 AAAAAGGTGCCACAGAGTTATGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAA
1514950 A
66 A
1514951 GGGTGCCACG
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
67 6 0.10
68 28 0.47
69 26 0.43
ACGTcount: A:0.37, C:0.11, G:0.33, T:0.19
Consensus pattern (68 bp):
AAAAAGGTGCCACAGAGTTATGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAA
AAG
Found at i:1517646 original size:20 final size:20
Alignment explanation
Indices: 1517621--1517675 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
1517611 ATTTGCCTGC
1517621 ATGTATCGATACATTGAACA
1 ATGTATCGATACATTGAACA
*
1517641 ATGTATCGATACATTGAATA
1 ATGTATCGATACATTGAACA
1517661 ATGTATCGATACATT
1 ATGTATCGATACATT
1517676 TCCTTGGAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACATTGAACA
Found at i:1517763 original size:19 final size:19
Alignment explanation
Indices: 1517704--1517763 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
1517694 TAGTGATACA
*
1517704 TTGTATCGATACAACACT-T
1 TTGTATCGATACAA-ATTGT
* *
1517723 ATGTATCGATACATTTATTGT
1 TTGTATCGATACA--AATTGT
1517744 TTGTATCGATACAAATTGT
1 TTGTATCGATACAAATTGT
1517763 T
1 T
1517764 GAAATTCAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
19 18 0.55
20 2 0.06
21 13 0.39
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.43
Consensus pattern (19 bp):
TTGTATCGATACAAATTGT
Found at i:1528088 original size:29 final size:29
Alignment explanation
Indices: 1528040--1528411 Score: 405
Period size: 28 Copynumber: 13.1 Consensus size: 29
1528030 TCCAAAGCAA
1528040 ACAAGTCAGTGGCACCCTTTTCAAAAGCCC
1 ACAAGTCAGTGGCA-CCTTTTCAAAAGCCC
*
1528070 ACAATTCAGTGGCACCTTTTCAAAAGCCC
1 ACAAGTCAGTGGCACCTTTTCAAAAGCCC
1528099 ACAAGTCAGTGGCACCTTTTCAAAAGCCC
1 ACAAGTCAGTGGCACCTTTTCAAAAGCCC
*
1528128 ACAAGTCAGTGGCACATTTTC-AAAGCCC
1 ACAAGTCAGTGGCACCTTTTCAAAAGCCC
* ** *
1528156 ACAAGTTAGTAGTAACC-TTT-AGAAGCCC
1 ACAAGTCAGT-GGCACCTTTTCAAAAGCCC
**
1528184 ACAAGTCAGTGGCATATTTTC-AAAGCCC
1 ACAAGTCAGTGGCACCTTTTCAAAAGCCC
* *
1528212 ACAAGTTAGTGGCATCTTTTC-AAAGCCC
1 ACAAGTCAGTGGCACCTTTTCAAAAGCCC
** *
1528240 ACAAGTCAGTGGCATATTTTC-ATAGCCC
1 ACAAGTCAGTGGCACCTTTTCAAAAGCCC
**
1528268 ACAAGTCAGTGGCATTTTTTC-AAAGCCC
1 ACAAGTCAGTGGCACCTTTTCAAAAGCCC
*
1528296 ACAAGTCAGTGGCAACC--CTCAAAAAGCCC
1 ACAAGTCAGTGGC-ACCTTTTC-AAAAGCCC
*
1528325 ACTAA-TCAGTGGCAACC--TTCAGAAGCCC
1 AC-AAGTCAGTGGC-ACCTTTTCAAAAGCCC
1528353 ACAAGTCAGTGGCACCTTTTC-AAAGCCC
1 ACAAGTCAGTGGCACCTTTTCAAAAGCCC
* *
1528381 ACAAGTTAGTGCCAACC-TTT-AAAAGCCC
1 ACAAGTCAGTGGC-ACCTTTTCAAAAGCCC
1528409 ACA
1 ACA
1528412 CGAGTTGGTG
Statistics
Matches: 300, Mismatches: 29, Indels: 28
0.84 0.08 0.08
Matches are distributed among these distances:
27 9 0.03
28 180 0.60
29 96 0.32
30 15 0.05
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (29 bp):
ACAAGTCAGTGGCACCTTTTCAAAAGCCC
Found at i:1528502 original size:43 final size:43
Alignment explanation
Indices: 1528437--1528518 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
1528427 TTCTTCTAAG
* * *
1528437 TCCAATATCGCTGGCTTGGAATCAGCATATTGTCACCTTTAAT
1 TCCAATATCGCTGCCTTGGAATCAGCACATTGGCACCTTTAAT
*
1528480 TCCAATATTGCTAGCCTT-GAATCAGCACATTGGCACCTT
1 TCCAATATCGCT-GCCTTGGAATCAGCACATTGGCACCTT
1528519 CATCTTTAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
43 30 0.88
44 4 0.12
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.33
Consensus pattern (43 bp):
TCCAATATCGCTGCCTTGGAATCAGCACATTGGCACCTTTAAT
Found at i:1529469 original size:20 final size:20
Alignment explanation
Indices: 1529444--1529508 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 20
1529434 CGAGGAAAAT
1529444 TATCGATACATTATTTAATG
1 TATCGATACATTATTTAATG
1529464 TATCGATAC---A-TT-A--
1 TATCGATACATTATTTAATG
*
1529477 TATCGATACATTATTCAATG
1 TATCGATACATTATTTAATG
1529497 TATCGATACATT
1 TATCGATACATT
1529509 TTATCGATAC
Statistics
Matches: 37, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
13 9 0.24
15 1 0.03
16 3 0.08
17 2 0.05
18 1 0.03
20 21 0.57
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (20 bp):
TATCGATACATTATTTAATG
Found at i:1529482 original size:13 final size:13
Alignment explanation
Indices: 1529464--1529521 Score: 56
Period size: 13 Copynumber: 4.9 Consensus size: 13
1529454 TTATTTAATG
1529464 TATCGATACATTA
1 TATCGATACATTA
1529477 TATCGATACATTA
1 TATCGATACATTA
*
1529490 T-TC---A-A-TG
1 TATCGATACATTA
*
1529497 TATCGATACATTT
1 TATCGATACATTA
1529510 TATCGATACATT
1 TATCGATACATT
1529522 GATCTTTGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
7 2 0.05
8 3 0.08
9 1 0.03
11 1 0.03
12 3 0.08
13 27 0.73
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (13 bp):
TATCGATACATTA
Found at i:1529482 original size:33 final size:33
Alignment explanation
Indices: 1529444--1529521 Score: 138
Period size: 33 Copynumber: 2.4 Consensus size: 33
1529434 CGAGGAAAAT
*
1529444 TATCGATACATTATTTAATGTATCGATACATTA
1 TATCGATACATTATTCAATGTATCGATACATTA
*
1529477 TATCGATACATTATTCAATGTATCGATACATTT
1 TATCGATACATTATTCAATGTATCGATACATTA
1529510 TATCGATACATT
1 TATCGATACATT
1529522 GATCTTTGTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (33 bp):
TATCGATACATTATTCAATGTATCGATACATTA
Found at i:1529532 original size:33 final size:32
Alignment explanation
Indices: 1529443--1529536 Score: 118
Period size: 33 Copynumber: 2.8 Consensus size: 32
1529433 CCGAGGAAAA
1529443 TTATCGATACATTAT-TTAATGTATCGATACATT
1 TTATCGATACATTATCTT--TGTATCGATACATT
* **
1529476 ATATCGATACATTATTCAATGTATCGATACATT
1 TTATCGATACATTA-TCTTTGTATCGATACATT
1529509 TTATCGATACATTGATCTTTGTATCGAT
1 TTATCGATACATT-ATCTTTGTATCGAT
1529537 GCATCTGGGA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
33 50 0.96
34 2 0.04
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.44
Consensus pattern (32 bp):
TTATCGATACATTATCTTTGTATCGATACATT
Found at i:1535832 original size:23 final size:23
Alignment explanation
Indices: 1535773--1535845 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 23
1535763 TCAAAATAAC
*
1535773 AAAAAAAAG-GTCAAAAGCAAAAGT
1 AAAAAAAAGTG-CAAAAG-AAAAAT
* *
1535797 ACAAAATA-T-CAAAAGAAAAAT
1 AAAAAAAAGTGCAAAAGAAAAAT
*
1535818 AAAAAAAAGTGCAAAAGCAAAAT
1 AAAAAAAAGTGCAAAAGAAAAAT
1535841 AAAAA
1 AAAAA
1535846 GGAAACAACA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
21 11 0.28
22 7 0.17
23 16 0.40
24 6 0.15
ACGTcount: A:0.71, C:0.08, G:0.11, T:0.10
Consensus pattern (23 bp):
AAAAAAAAGTGCAAAAGAAAAAT
Found at i:1537106 original size:17 final size:18
Alignment explanation
Indices: 1537071--1537107 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
1537061 TTATGTCAAA
1537071 TCCCTAGATAGCTTGACC
1 TCCCTAGATAGCTTGACC
1537089 TCCCTAG-TA-CTATGACC
1 TCCCTAGATAGCT-TGACC
1537106 TC
1 TC
1537108 TTCAAAGTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 2 0.11
17 9 0.50
18 7 0.39
ACGTcount: A:0.22, C:0.35, G:0.14, T:0.30
Consensus pattern (18 bp):
TCCCTAGATAGCTTGACC
Found at i:1537228 original size:55 final size:55
Alignment explanation
Indices: 1537112--1537522 Score: 374
Period size: 55 Copynumber: 7.5 Consensus size: 55
1537102 GACCTCTTCA
*** * *
1537112 AAGTCCACAACTCCGTGGCATATGTTTTCAAGTCCACAAC-TCCGTGGCATTCTTTAA
1 AAGTCCACAACTCCGTGGCA-CCCTTTT-AAGTCCACAACTTCCGTGGCACTCTTT-T
* * *
1537169 AAGTCCACAATTCTGTGGCACCCTTTTAAGTCCACAACTTCAGTGGCACTCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTTCCGTGGCACTCTTTT
* *
1537224 AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAAC-TCCGTGACAC-CATTTT
1 AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTTCCGTGGCACTC-TTTT
* * * ***
1537278 AAGTCCACAATTCCGTGGCATCCATTTCAAGTCCACAAC-TCCGTGGTGTTCTTTT
1 AAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTTCCGTGGCACTCTTTT
**
1537333 AAAGTCCACAACTATGTGGCACCCTTTTAAGTCCACAACTT-CGTGGCACTCTTTT
1 -AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTTCCGTGGCACTCTTTT
* *
1537388 ATGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTT-CGTGGCA-TCCTTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTTCCGTGGCACT-C-TTTT
** * * ** *
1537443 AAACCCACAAGTCAGTGGCA-CCTTCCAAAGTCCACAACTT-CATGGCA-TCCTTTTT
1 AAGTCCACAACTCCGTGGCACCCTT-TTAAGTCCACAACTTCCGTGGCACT-C-TTTT
* * **
1537498 AAGCCCACAAGTTAGTGGCACCCTT
1 AAGTCCACAACTCCGTGGCACCCTT
1537523 CCAAAGCCCA
Statistics
Matches: 301, Mismatches: 43, Indels: 21
0.82 0.12 0.06
Matches are distributed among these distances:
53 2 0.01
54 79 0.26
55 162 0.54
56 40 0.13
57 18 0.06
ACGTcount: A:0.25, C:0.30, G:0.15, T:0.30
Consensus pattern (55 bp):
AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTTCCGTGGCACTCTTTT
Found at i:1537249 original size:27 final size:27
Alignment explanation
Indices: 1537112--1537507 Score: 395
Period size: 27 Copynumber: 14.4 Consensus size: 27
1537102 GACCTCTTCA
**
1537112 AAGTCCACAACTCCGTGGCATATGTTTT
1 AAGTCCACAACTCCGTGGCAT-CCTTTT
* *
1537140 CAAGTCCACAACTCCGTGGCATTCTTTAA
1 -AAGTCCACAACTCCGTGGCATCCTTT-T
* * *
1537169 AAGTCCACAATTCTGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
*
1537196 AAGTCCACAACTTCAGTGGCA-CTCTTTT
1 AAGTCCACAAC-TCCGTGGCATC-CTTTT
1537224 AAGTCCACAACTCCGTGGCATCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
*
1537251 AAGTCCACAACTCCGTGACA-CCATTTT
1 AAGTCCACAACTCCGTGGCATCC-TTTT
* *
1537278 AAGTCCACAATTCCGTGGCATCCATTTC
1 AAGTCCACAACTCCGTGGCATCC-TTTT
** *
1537306 AAGTCCACAACTCCGTGGTGTTCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
** *
1537333 AAAGTCCACAACTATGTGGCACCCTTTT
1 -AAGTCCACAACTCCGTGGCATCCTTTT
*
1537361 AAGTCCACAACTTCGTGGCA-CTCTTTT
1 AAGTCCACAACTCCGTGGCATC-CTTTT
*
1537388 ATGTCCACAACTCCGTGGCATCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
*
1537415 AAGTCCACAACTTCGTGGCATCCTTTTT
1 AAGTCCACAACTCCGTGGCATCC-TTTT
** * * **
1537443 AAACCCACAAGTCAGTGGCA-CCTTCCA
1 AAGTCCACAACTCCGTGGCATCCTT-TT
* *
1537470 AAGTCCACAACTTCATGGCATCCTTTTT
1 AAGTCCACAACTCCGTGGCATCC-TTTT
*
1537498 AAGCCCACAA
1 AAGTCCACAA
1537508 GTTAGTGGCA
Statistics
Matches: 307, Mismatches: 47, Indels: 27
0.81 0.12 0.07
Matches are distributed among these distances:
26 5 0.02
27 151 0.49
28 128 0.42
29 23 0.07
ACGTcount: A:0.25, C:0.31, G:0.14, T:0.30
Consensus pattern (27 bp):
AAGTCCACAACTCCGTGGCATCCTTTT
Found at i:1537314 original size:110 final size:108
Alignment explanation
Indices: 1537111--1537507 Score: 415
Period size: 110 Copynumber: 3.6 Consensus size: 108
1537101 TGACCTCTTC
** * *
1537111 AAAGTCCACAACTCCGTGGCATATGTTTTCAAGTCCACAACTCCGTGGCATTCTTTAAAAGTCCA
1 AAAGTCCACAACTCCGTGGCAT-CCTTTT-AAGTCCACAACTCCGTGGCA-CCTTT-TAAGTCCA
* *
1537176 CAATTCTGTGGCACCCTTTTAAGTCCACAACTTCAGTGGCACTCTTTT
62 CAATTCCGTGGCATCCTTTTAAGTCCACAACTTC-GTGGCACTCTTTT
*
1537224 -AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGACACCATTTTAAGTCCACAA
1 AAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCACC-TTTTAAGTCCACAA
* * ***
1537288 TTCCGTGGCATCCATTTCAAGTCCACAACTCCGTGGTGTTCTTTT
65 TTCCGTGGCATCC-TTTTAAGTCCACAACTTCGTGGCACTCTTTT
** * * *
1537333 AAAGTCCACAACTATGTGGCACCCTTTTAAGTCCACAACTTCGTGGCACTCTTTTATGTCCACAA
1 AAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCAC-CTTTTAAGTCCACAA
*
1537398 CTCCGTGGCATCCTTTTAAGTCCACAACTTCGTGGCA-TCCTTTTT
65 TTCCGTGGCATCCTTTTAAGTCCACAACTTCGTGGCACT-C-TTTT
* * * ** * * *
1537443 AAA-CCCACAAGTCAGTGGCA-CCTTCCAAAGTCCACAACTTCATGGCATCCTTTTTAAGCCCAC
1 AAAGTCCACAACTCCGTGGCATCCTT-TTAAGTCCACAACTCCGTGGCA-CC-TTTTAAGTCCAC
1537506 AA
63 AA
1537508 GTTAGTGGCA
Statistics
Matches: 243, Mismatches: 32, Indels: 21
0.82 0.11 0.07
Matches are distributed among these distances:
108 5 0.02
109 86 0.35
110 126 0.52
111 5 0.02
112 21 0.09
ACGTcount: A:0.25, C:0.30, G:0.14, T:0.30
Consensus pattern (108 bp):
AAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCACCTTTTAAGTCCACAAT
TCCGTGGCATCCTTTTAAGTCCACAACTTCGTGGCACTCTTTT
Found at i:1537516 original size:137 final size:135
Alignment explanation
Indices: 1537112--1537522 Score: 413
Period size: 137 Copynumber: 3.0 Consensus size: 135
1537102 GACCTCTTCA
** * *
1537112 AAGTCCACAACTCCGTGGCATATGTTTTCAAGTCCACAACTCCGTGGCATTCTTTAAAAGTCCAC
1 AAGTCCACAACTCCGTGGCAT-CCTTTT-AAGTCCACAACTTCGTGGCATCCTTTAAAA-TCCAC
* * * *
1537177 AATTCTGTGGCACCCTTTTAAGTCCACAACTTCAGTGGCA-CTCTTTTAAGTCCACAACTCCGTG
63 AACTCAGTGGCA-CCTTTAAAGTCCACAACTTCA-TGGCACCT-TTTTAAGTCCACAACTTCGTG
1537241 GCA-TCCTTTT
125 GCACTCCTTTT
* * *
1537251 AAGTCCACAACTCCGTGACA-CCATTTTAAGTCCACAA-TTCCGTGGCATCCATTTCAAGTCCAC
1 AAGTCCACAACTCCGTGGCATCC-TTTTAAGTCCACAACTT-CGTGGCATCC-TTTAAAATCCAC
* ** * * *
1537314 AACTCCGTGGTGTTCTTTTAAAGTCCACAACTAT-GTGGCACCCTTTTAAGTCCACAACTTCGTG
63 AACTCAGT-G-GCACCTTTAAAGTCCACAACT-TCATGGCACCTTTTTAAGTCCACAACTTCGTG
1537378 GCACT-CTTTT
125 GCACTCCTTTT
* * *
1537388 ATGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTTCGTGGCATCCTTTTTAAACCCACAA
1 AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTTCGTGGCATCC-TTTAAAATCCACAA
* * * * *
1537453 GTCAGTGGCACCTTCCAAAGTCCACAACTTCATGGCATCCTTTTTAAGCCCACAAGTTAGTGGCA
65 CTCAGTGGCACCTT-TAAAGTCCACAACTTCATGGCA-CCTTTTTAAGTCCACAACTTCGTGGCA
1537518 C-CCTT
128 CTCCTT
1537523 CCAAAGCCCA
Statistics
Matches: 225, Mismatches: 33, Indels: 30
0.78 0.11 0.10
Matches are distributed among these distances:
135 5 0.02
136 20 0.09
137 147 0.65
138 32 0.14
139 21 0.09
ACGTcount: A:0.25, C:0.30, G:0.15, T:0.30
Consensus pattern (135 bp):
AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTTCGTGGCATCCTTTAAAATCCACAAC
TCAGTGGCACCTTTAAAGTCCACAACTTCATGGCACCTTTTTAAGTCCACAACTTCGTGGCACTC
CTTTT
Found at i:1537529 original size:28 final size:28
Alignment explanation
Indices: 1537446--1537806 Score: 206
Period size: 28 Copynumber: 12.2 Consensus size: 28
1537436 CCTTTTTAAA
1537446 CCCACAAGTCAGTGGCA-CCTTCCAAAG
1 CCCACAAGTCAGTGGCACCCTTCCAAAG
* * * ***
1537473 TCCACAACTTCA-TGGCATCCTTTTTAAG
1 CCCACAA-GTCAGTGGCACCCTTCCAAAG
*
1537501 CCCACAAGTTAGTGGCACCCTTCCAAAG
1 CCCACAAGTCAGTGGCACCCTTCCAAAG
1537529 CCCACAAGTCAGTGGCACCCTTCCAAAG
1 CCCACAAGTCAGTGGCACCCTTCCAAAG
*** *
1537557 CCCACAAGTCAGTGGCATTATTTCAAAG
1 CCCACAAGTCAGTGGCACCCTTCCAAAG
* * *
1537585 CCCACACAAGTCGGTGGCAACTCAATT-GAAAG
1 -CC-CACAAGTCAGTGGC-AC-C-CTTCCAAAG
* * *
1537617 CCCACATAAGTCGGTGGCAACCTATTTCAAAG
1 CCCAC--AAGTCAGTGGC-ACC-CTTCCAAAG
* * **
1537649 CCCACACAAGTCGGTGGTAACCCATTTGAAAG
1 -CC-CACAAGTCAGTGG-CACCC-TTCCAAAG
* **
1537681 CCCACACAAGTCGGTGGCAACCCATTTTAAAG
1 -CC-CACAAGTCAGTGGC-ACCC-TTCCAAAG
** *
1537713 CCCACACAAGTTGGTGGCAACCCATTTCAAAG
1 -CC-CACAAGTCAGTGGC-ACCC-TTCCAAAG
* * *
1537745 CCCATAAGTCAGTGGCATCCTTTCAAAG
1 CCCACAAGTCAGTGGCACCCTTCCAAAG
* *
1537773 CCCACAAGTCAGTGGCATCATTCTCAAAG
1 CCCACAAGTCAGTGGCACCCTTC-CAAAG
1537802 CCCAC
1 CCCAC
1537807 TGTCGTAACG
Statistics
Matches: 280, Mismatches: 37, Indels: 32
0.80 0.11 0.09
Matches are distributed among these distances:
27 13 0.05
28 107 0.38
29 15 0.05
30 27 0.10
31 9 0.03
32 101 0.36
33 5 0.02
34 3 0.01
ACGTcount: A:0.30, C:0.32, G:0.18, T:0.20
Consensus pattern (28 bp):
CCCACAAGTCAGTGGCACCCTTCCAAAG
Found at i:1537538 original size:83 final size:83
Alignment explanation
Indices: 1537141--1537563 Score: 238
Period size: 82 Copynumber: 5.1 Consensus size: 83
1537131 ATATGTTTTC
* * * * * ** **
1537141 AAGTCCACAACTCCGTGGCATTCTTTAAAAGTCCACAA-TTCTGTGGCA-CCCTTTTAAGTCCAC
1 AAGTCCACAACTCCATGGCATCCTTT-TAAGCCCACAACTT-AGTGGCATCCCTTCCAAACCCAC
* * **
1537204 AACTTCAGTGGCACTCTT-TT
64 AA-GTCAGTGGCACCCTTCCA
* * ** * * ** **
1537224 AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGACA-CCATTTTAAGTCCACAA
1 AAGTCCACAACTCCATGGCATCCTTTTAAGCCCACAACTTAGTGGCATCCCTTCCAAACCCACAA
* * * *
1537288 TTCCGTGGCATCCATTTC-
66 GTCAGTGGCA-CCCTTCCA
* ** * * ** **
1537306 AAGTCCACAACTCCGTGGTGTTCTTTTAAAGTCCACAAC-TATGTGGCA-CCCTTTTAAGTCCAC
1 AAGTCCACAACTCCATGGCATCCTTTT-AAGCCCACAACTTA-GTGGCATCCCTTCCAAACCCAC
* * **
1537369 AACTTC-GTGGCACTCTT-TT
64 AA-GTCAGTGGCACCCTTCCA
* * * * * **
1537388 ATGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTTCGTGGCATCCTTTTTAAACCCACAA
1 AAGTCCACAACTCCATGGCATCCTTTTAAGCCCACAACTTAGTGGCATCCCTTCCAAACCCACAA
1537453 GTCAGTGGCA-CCTTCCA
66 GTCAGTGGCACCCTTCCA
* *
1537470 AAGTCCACAACTTCATGGCATCCTTTTTAAGCCCACAAGTTAGTGGCA-CCCTTCCAAAGCCCAC
1 AAGTCCACAACTCCATGGCATCC-TTTTAAGCCCACAACTTAGTGGCATCCCTTCCAAA-CCCAC
1537534 AAGTCAGTGGCACCCTTCCA
64 AAGTCAGTGGCACCCTTCCA
*
1537554 AAGCCCACAA
1 AAGTCCACAA
1537564 GTCAGTGGCA
Statistics
Matches: 284, Mismatches: 42, Indels: 27
0.80 0.12 0.08
Matches are distributed among these distances:
81 31 0.11
82 132 0.46
83 102 0.36
84 19 0.07
ACGTcount: A:0.26, C:0.32, G:0.15, T:0.28
Consensus pattern (83 bp):
AAGTCCACAACTCCATGGCATCCTTTTAAGCCCACAACTTAGTGGCATCCCTTCCAAACCCACAA
GTCAGTGGCACCCTTCCA
Found at i:1537622 original size:32 final size:32
Alignment explanation
Indices: 1537503--1537806 Score: 275
Period size: 32 Copynumber: 10.0 Consensus size: 32
1537493 TTTTTAAGCC
** *
1537503 CACAAGTTAGTGGC-ACCC-TTCCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
1537531 CACAAGTCAGTGGC-ACCC-TTCCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* **
1537559 CACAAGTCAGTGGC-A-TTATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * *
1537589 CACAAGTCGGTGGCAACTCAATTGAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
1537621 CATAAGTCGGTGGCAACCTATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
1537653 CACAAGTCGGTGGTAACCCATTTGAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1537685 CACAAGTCGGTGGCAACCCATTTTAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1537717 CACAAGTTGGTGGCAACCCATTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * *
1537747 CATAAGTCAGTGGC-ATCC-TTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
1537775 CACAAGTCAGTGGC-A-TCATTCTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATT-TCAAAGCCCA
1537806 C
1 C
1537807 TGTCGTAACG
Statistics
Matches: 240, Mismatches: 27, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
27 1 0.00
28 75 0.31
29 11 0.05
30 26 0.11
31 4 0.02
32 123 0.51
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.19
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
Found at i:1540852 original size:52 final size:52
Alignment explanation
Indices: 1540774--1540902 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
1540764 CGAAATATGA
*
1540774 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTAGGC
*
1540826 AAATTTGCCTGTATGTATCGATACATTTTATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTAGGC
* *
1540878 AAACTTACCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1540903 AAGATCAGTG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTAGGC
Found at i:1540929 original size:13 final size:13
Alignment explanation
Indices: 1540911--1540935 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1540901 CAAAGATCAG
1540911 TGTATCGATACAA
1 TGTATCGATACAA
1540924 TGTATCGATACA
1 TGTATCGATACA
1540936 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1541002 original size:19 final size:19
Alignment explanation
Indices: 1540978--1541062 Score: 92
Period size: 19 Copynumber: 4.7 Consensus size: 19
1540968 TAGCTTACAT
1540978 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
*
1540997 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
*
1541016 TGTATTGATAC---A--T-
1 TGTATCGATACAAAACTTA
*
1541029 TGTATCGATACAACACTTTA
1 TGTATCGATACAAAAC-TTA
1541049 TGTATCGATACAAA
1 TGTATCGATACAAA
1541063 TCGTTGACAT
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
13 10 0.18
14 1 0.02
16 2 0.04
19 29 0.53
20 13 0.24
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:1541038 original size:32 final size:33
Alignment explanation
Indices: 1540997--1541060 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 33
1540987 ACAAAACTTA
*
1540997 TGTATCGATACAACAC-TTATGTATTGATACAT
1 TGTATCGATACAACACTTTATGTATCGATACAT
1541029 TGTATCGATACAACACTTTATGTATCGATACA
1 TGTATCGATACAACACTTTATGTATCGATACA
1541061 AATCGTTGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 16 0.53
33 14 0.47
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.36
Consensus pattern (33 bp):
TGTATCGATACAACACTTTATGTATCGATACAT
Found at i:1541368 original size:28 final size:28
Alignment explanation
Indices: 1541294--1541873 Score: 746
Period size: 28 Copynumber: 20.2 Consensus size: 28
1541284 AGTGTCTACA
1541294 CCCACAAGTCAGTGGCATCCTTCTCAAAG
1 CCCACAAGTCAGTGGCATCCTT-TCAAAG
*
1541323 CCCATACAAATCAGTGGCATCCTTTCAAAG
1 CCC--ACAAGTCAGTGGCATCCTTTCAAAG
*
1541353 CCCACAAGTTAGTGGCATCCTTTCAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
* *
1541381 CCCACAAGTCAATGGCATCCTTTCAAAA
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
* * * *
1541409 CCCATAAGTTAGTGACATCTTTTCAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
* * *
1541437 CCCATAAGTCGGTGGCATTCTTCTCAAAG
1 CCCACAAGTCAGTGGCATCCTT-TCAAAG
1541466 CCCACAAGTCAGTGGCATCCTTCTCAAAG
1 CCCACAAGTCAGTGGCATCCTT-TCAAAG
*
1541495 CCCACACAAATCAGTGGCATCCTTTCAAAG
1 -CC-CACAAGTCAGTGGCATCCTTTCAAAG
*
1541525 CCCATAAGTCAGTGGCATCCTTTCAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
* *
1541553 CTCACAAGTCAGTGGCATCCTTTTAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
*
1541581 CTCACAAGTCAGTGGCATCCTTTCAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
* * *
1541609 CCTAGAAGTTAGTGGCATCCTTCTCAAAG
1 CCCACAAGTCAGTGGCATCCTT-TCAAAG
*
1541638 CCCACAAGTTAGTGGCATCCTTCTCAAAG
1 CCCACAAGTCAGTGGCATCCTT-TCAAAG
*
1541667 CCCACAAGTCAGTGGCATCCTTCTCAATG
1 CCCACAAGTCAGTGGCATCCTT-TCAAAG
* *
1541696 CCCAAAAGTTAGTGGCATCCTTCTCAAAG
1 CCCACAAGTCAGTGGCATCCTT-TCAAAG
*
1541725 CCCACAAGTCAATGGCATCCTTCTCAAAG
1 CCCACAAGTCAGTGGCATCCTT-TCAAAG
* * *
1541754 CCCATATAAATCAGTGGCATCTTTTCAAAG
1 CCC--ACAAGTCAGTGGCATCCTTTCAAAG
*
1541784 CCAACAAGTCAGTGGCATCCTTTCAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
* *
1541812 CCCACAAGTCAGTGGCATCTTTTTAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
* *
1541840 CCCATAAGTCAATGGCATCCTTTCAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
1541868 CCCACA
1 CCCACA
1541874 CAAGTCGGTG
Statistics
Matches: 486, Mismatches: 57, Indels: 17
0.87 0.10 0.03
Matches are distributed among these distances:
28 257 0.53
29 152 0.31
30 25 0.05
31 52 0.11
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.24
Consensus pattern (28 bp):
CCCACAAGTCAGTGGCATCCTTTCAAAG
Found at i:1541607 original size:172 final size:170
Alignment explanation
Indices: 1541294--1541871 Score: 809
Period size: 172 Copynumber: 3.4 Consensus size: 170
1541284 AGTGTCTACA
*
1541294 CCCACAAGTCAGTGGCATCCTTCTCAAAGCCCATACAAATCAGTGGCATCCTTTCAAAGCCCACA
1 CCCACAAGTCAGTGGCATCCTTCTCAAAGCCC--ACAAATCAGTGGCATCCTTTCAAAGCCCAAA
* * *
1541359 AGTTAGTGGCATCCTTTCAAAGCCCACAAGTCAATGGCATCCTTTCAAAACCCATAAGTTAGTGA
64 AGTTAGTGGCATCCTTTCAAAGCCCACAAGTCAATGGCATCCTTTCAAAGCCCATAAGTCAGTGG
* * * *
1541424 CATCTTTTCAAAGCCCATAAGTCGGTGGCATTCTTCTCAAAG
129 CATCTTTTCAAAGCCAACAAGTCAGTGGCATCCTTCTCAAAG
*
1541466 CCCACAAGTCAGTGGCATCCTTCTCAAAGCCCACACAAATCAGTGGCATCCTTTCAAAGCCCATA
1 CCCACAAGTCAGTGGCATCCTTCTCAAAG-CC-CACAAATCAGTGGCATCCTTTCAAAGCCCAAA
* * * * * *
1541531 AGTCAGTGGCATCCTTTCAAAGCTCACAAGTCAGTGGCATCCTTTTAAAGCTCACAAGTCAGTGG
64 AGTTAGTGGCATCCTTTCAAAGCCCACAAGTCAATGGCATCCTTTCAAAGCCCATAAGTCAGTGG
* * * *
1541596 CATCCTTTCAAAGCCTAGAAGTTAGTGGCATCCTTCTCAAAG
129 CATCTTTTCAAAGCCAACAAGTCAGTGGCATCCTTCTCAAAG
* * *
1541638 CCCACAAGTTAGTGGCATCCTTCTCAAAGCCCACAAGTCAGTGGCATCCTTCTCAATGCCCAAAA
1 CCCACAAGTCAGTGGCATCCTTCTCAAAGCCCACAAATCAGTGGCATCCTT-TCAAAGCCCAAAA
*
1541703 GTTAGTGGCATCCTTCTCAAAGCCCACAAGTCAATGGCATCCTTCTCAAAGCCCATATAAATCAG
65 GTTAGTGGCATCCTT-TCAAAGCCCACAAGTCAATGGCATCCTT-TCAAAGCCC--ATAAGTCAG
1541768 TGGCATCTTTTCAAAGCCAACAAGTCAGTGGCATCCTT-TCAAAG
126 TGGCATCTTTTCAAAGCCAACAAGTCAGTGGCATCCTTCTCAAAG
* * * * *
1541812 CCCACAAGTCAGTGGCAT-CTTTTTAAAGCCCATAAGTCAATGGCATCCTTTCAAAGCCCA
1 CCCACAAGTCAGTGGCATCCTTCTCAAAGCCCACAAATCAGTGGCATCCTTTCAAAGCCCA
1541872 CACAAGTCGG
Statistics
Matches: 362, Mismatches: 37, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
170 19 0.05
171 27 0.07
172 214 0.59
173 37 0.10
174 24 0.07
175 41 0.11
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (170 bp):
CCCACAAGTCAGTGGCATCCTTCTCAAAGCCCACAAATCAGTGGCATCCTTTCAAAGCCCAAAAG
TTAGTGGCATCCTTTCAAAGCCCACAAGTCAATGGCATCCTTTCAAAGCCCATAAGTCAGTGGCA
TCTTTTCAAAGCCAACAAGTCAGTGGCATCCTTCTCAAAG
Found at i:1541755 original size:259 final size:256
Alignment explanation
Indices: 1541294--1541873 Score: 863
Period size: 259 Copynumber: 2.2 Consensus size: 256
1541284 AGTGTCTACA
* *
1541294 CCCACAAGTCAGTGGCATCCTTCTCAAAGCCCATACAAATCAGTGGCATCCTTTCAAAGCCCACA
1 CCCACAAGTCAGTGGCATCCTT-TTAAAGCCC--ACAAGTCAGTGGCATCCTTTCAAAGCCCACA
* *
1541359 AGTTAGTGGCATCCTTTCAAAGCCCACAAGTCAATGGCATCCTTTCAAAACCCATAAGTTAGTGA
63 AGTTAGTGGCATCCTTTCAAAGCCCACAAGTCAATGGCATCCTTTCAAAACCCACAAGTCAGTGA
* * * * *
1541424 CATCTTTTCAAAGCCCATAAGTCGGTGGCATTCTTCTCAAAGCCCACAAGTCAGTGGCATCCTTC
128 CATCTTCTCAAAGCCCAAAAGTCAGTGGCATCCTTCTCAAAGCCCACAAGTCAATGGCATCCTTC
* *
1541489 TCAAAGCCCACACAAATCAGTGGCATCCTTTCAAAGCCCATAAGTCAGTGGCATCCTTTCAAAG
193 TCAAAGCCCACACAAATCAGTGGCATCCTTTCAAAGCCAACAAGTCAGTGGCATCCTTTCAAAG
* * * *
1541553 CTCACAAGTCAGTGGCATCCTTTTAAAGCTCACAAGTCAGTGGCATCCTTTCAAAGCCTAGAAGT
1 CCCACAAGTCAGTGGCATCCTTTTAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGT
* * * *
1541618 TAGTGGCATCCTTCTCAAAGCCCACAAGTTAGTGGCATCCTTCTCAAAGCCCACAAGTCAGTGGC
66 TAGTGGCATCCTT-TCAAAGCCCACAAGTCAATGGCATCCTT-TCAAAACCCACAAGTCAGTGAC
* *
1541683 ATCCTTCTCAATGCCCAAAAGTTAGTGGCATCCTTCTCAAAGCCCACAAGTCAATGGCATCCTTC
129 AT-CTTCTCAAAGCCCAAAAGTCAGTGGCATCCTTCTCAAAGCCCACAAGTCAATGGCATCCTTC
* * *
1541748 TCAAAGCCCATATAAATCAGTGGCATCTTTTCAAAGCCAACAAGTCAGTGGCATCCTTTCAAAG
193 TCAAAGCCCACACAAATCAGTGGCATCCTTTCAAAGCCAACAAGTCAGTGGCATCCTTTCAAAG
* * *
1541812 CCCACAAGTCAGTGGCATCTTTTTAAAGCCCATAAGTCAATGGCATCCTTTCAAAGCCCACA
1 CCCACAAGTCAGTGGCATCCTTTTAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACA
1541874 CAAGTCGGTG
Statistics
Matches: 287, Mismatches: 31, Indels: 6
0.89 0.10 0.02
Matches are distributed among these distances:
256 44 0.15
257 26 0.09
258 27 0.09
259 190 0.66
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.24
Consensus pattern (256 bp):
CCCACAAGTCAGTGGCATCCTTTTAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGT
TAGTGGCATCCTTTCAAAGCCCACAAGTCAATGGCATCCTTTCAAAACCCACAAGTCAGTGACAT
CTTCTCAAAGCCCAAAAGTCAGTGGCATCCTTCTCAAAGCCCACAAGTCAATGGCATCCTTCTCA
AAGCCCACACAAATCAGTGGCATCCTTTCAAAGCCAACAAGTCAGTGGCATCCTTTCAAAG
Found at i:1542076 original size:48 final size:48
Alignment explanation
Indices: 1542018--1542139 Score: 208
Period size: 48 Copynumber: 2.5 Consensus size: 48
1542008 GGCACCTTTA
*
1542018 TTAGCTCAATGTCGTTGGCCTTGAATCAGCACATTGTCCATTTTTCCC
1 TTAGCTCAATGTCGTTGGCCTTGAATCAGCACATTGTCCACTTTTCCC
*
1542066 TTAGCTCAATGTCGTTGGCCTTAAATCAGCACATTGTCCACTTTTCCC
1 TTAGCTCAATGTCGTTGGCCTTGAATCAGCACATTGTCCACTTTTCCC
* *
1542114 ATAGCTCGATGTCGTTGGCCTTGAAT
1 TTAGCTCAATGTCGTTGGCCTTGAAT
1542140 TGGCATATTG
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 69 1.00
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.36
Consensus pattern (48 bp):
TTAGCTCAATGTCGTTGGCCTTGAATCAGCACATTGTCCACTTTTCCC
Found at i:1546217 original size:137 final size:139
Alignment explanation
Indices: 1545964--1546231 Score: 337
Period size: 137 Copynumber: 1.9 Consensus size: 139
1545954 TACTTTCAAC
* *
1545964 GTGAAAGTATCTCGGTACCTCTAAAGGACTTAATATAAAAAGGGTGAACCTATCCAAAATACCCA
1 GTGAAAGTATCCCGGTACCCCTAAAGGAC---ATATAAAAAGGGTGAACCTATCCAAAATACCCA
* ** * * *
1546029 CCTTCAGCATAAAAGCAGATCTGGTGATAACCTAAGACTCGATTTTTAAAAATTATAAAAATGCC
63 CCTTCAGCATAAAAGCAGACCCAGTGATAACCTAAGACTCGATTCTAAAAAATTACAAAAATGCC
1546094 CTTACCTTTGAT
128 CTTACCTTTGAT
* * * *
1546106 GTGAAAGTATCCCGGTACCCCTAAAGGAC-TAT-AAAGGGGTGAACTTATCCTAAATACCGACCT
1 GTGAAAGTATCCCGGTACCCCTAAAGGACATATAAAAAGGGTGAACCTATCCAAAATACCCACCT
* *
1546169 TC-GACATAAATGC-GAACCCAGTGATAACCTAAGACTCGATTCTAAAAAATTACGAAAATGCCC
66 TCAG-CATAAAAGCAG-ACCCAGTGATAACCTAAGACTCGATTCTAAAAAATTACAAAAATGCCC
1546232 CTATAGGTAT
Statistics
Matches: 110, Mismatches: 14, Indels: 9
0.83 0.11 0.07
Matches are distributed among these distances:
136 2 0.02
137 78 0.71
138 3 0.03
142 27 0.25
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.25
Consensus pattern (139 bp):
GTGAAAGTATCCCGGTACCCCTAAAGGACATATAAAAAGGGTGAACCTATCCAAAATACCCACCT
TCAGCATAAAAGCAGACCCAGTGATAACCTAAGACTCGATTCTAAAAAATTACAAAAATGCCCTT
ACCTTTGAT
Found at i:1547757 original size:12 final size:12
Alignment explanation
Indices: 1547734--1547775 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
1547724 TATTTTCTCC
*
1547734 TTTTTCTTTCTT
1 TTTTTCTCTCTT
* *
1547746 TTTTTTTGTCTT
1 TTTTTCTCTCTT
1547758 TTTTTCTCTCTT
1 TTTTTCTCTCTT
1547770 TTTTTC
1 TTTTTC
1547776 AGCTGAACCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (12 bp):
TTTTTCTCTCTT
Found at i:1548912 original size:168 final size:167
Alignment explanation
Indices: 1548402--1549039 Score: 526
Period size: 168 Copynumber: 3.8 Consensus size: 167
1548392 ATGAAGAAGG
* * * *
1548402 ATGAATTTTTGAAAACTGAATTAGTATGAAATAAATAATAATGTTTGATG-ATTTATT-AAAATT
1 ATGAATTTTTGAAAACTGAATTAATATAAAATAAATAATAATATTTAATGAATTT-TTAAAAATT
* ** * * * * * * * * * * *
1548465 GAAAACCAAGAAAACTGCC-CTCGAAAAAATTTATGGAGTAGAAAACACC-ATATTTTAAAA-AA
65 AAAAATTAAAAAAAAT-CCTCACAAAAAAAATTACGAAGAAGAAAACCCCGTTATTTGAAAATAA
* * * * *
1548527 AATGGAGTTTCGACGAAAAAAATCAAAAACT-CATGAAAATGA
129 GA-GGA-TTTC-AAGAAAAAAAT-AAAAAATGAATGAAAATAA
* ** * * * * * *
1548569 ATGAATATTTTAAAACCAACCAAATTAATGTGAGATAAATAATGATGTTTGATGAA-TTTTAAAA
1 ATGAAT-TTTT-GAA--AACTGAATTAATATAAAATAAATAATAATATTTAATGAATTTTTAAAA
** * * * * * * *
1548633 ATT-AAAACCAAAAAAAATCCCTTTA-AAAAAAATTTA-TAGAGTAGAAAACACAG-TATTTTAA
62 ATTAAAAATTAAAAAAAAT-CC-TCACAAAAAAAATTACGA-AGAAGAAAACCCCGTTATTTGAA
* * * * *
1548694 AAAAATAGAAATTTCAAGGAAAAAATAAAAAATGAATGAAAATGA
124 AATAAGAG-GATTTCAAGAAAAAAATAAAAAATGAATGAAAATAA
* * *
1548739 ATGAATTTTTTAAAACT-AAGTTAATATAAAATAAATAATAATATTTGATGAATTTTTAAGAATT
1 ATGAATTTTTGAAAACTGAA-TTAATATAAAATAAATAATAATATTTAATGAATTTTTAAAAATT
* * * * *
1548803 AAAAATTAAGAAAAATCTTCCCTAAAAAATTTACGAAGAAGAAAACCCCGTTATTTGAAAATAAG
65 AAAAATTAAAAAAAATCCTCACAAAAAAAATTACGAAGAAGAAAACCCCGTTATTTGAAAATAAG
1548868 AGGATTTCAAGCAAAAAAATAAAAAATGAATGAAAATAA
130 AGGATTTCAAG-AAAAAAATAAAAAATGAATGAAAATAA
* *
1548907 ATGAATTTTTGAACACTGAATTAATATAAAATGAATAATAATATTTAATGAATTTTTAAAAATTA
1 ATGAATTTTTGAAAACTGAATTAATATAAAATAAATAATAATATTTAATGAATTTTTAAAAATTA
* *
1548972 AAAATTAAAAAAAATCCTCACAAAAAAAATTACGGAGAAGAAAACCCTGTTATTTGAAAATAAGA
66 AAAATTAAAAAAAATCCTCACAAAAAAAATTACGAAGAAGAAAACCCCGTTATTTGAAAATAAGA
1549037 GGA
131 GGA
1549040 ATTCGGAAAG
Statistics
Matches: 391, Mismatches: 59, Indels: 41
0.80 0.12 0.08
Matches are distributed among these distances:
165 2 0.01
166 31 0.08
167 46 0.12
168 175 0.45
169 14 0.04
170 42 0.11
171 76 0.19
172 5 0.01
ACGTcount: A:0.53, C:0.08, G:0.11, T:0.28
Consensus pattern (167 bp):
ATGAATTTTTGAAAACTGAATTAATATAAAATAAATAATAATATTTAATGAATTTTTAAAAATTA
AAAATTAAAAAAAATCCTCACAAAAAAAATTACGAAGAAGAAAACCCCGTTATTTGAAAATAAGA
GGATTTCAAGAAAAAAATAAAAAATGAATGAAAATAA
Found at i:1549325 original size:28 final size:28
Alignment explanation
Indices: 1549294--1549354 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
1549284 AATTTATACA
*
1549294 ATTTGACACATTAATTAAAAAATACGGT
1 ATTTGACACATTAATTAAAAAATACGAT
1549322 ATTTGACACATTAATTAAAAAATACGAT
1 ATTTGACACATTAATTAAAAAATACGAT
1549350 ATTTG
1 ATTTG
1549355 TCATACTGTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (28 bp):
ATTTGACACATTAATTAAAAAATACGAT
Done.