Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr1
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: 35726063
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1821929 characters in sequence are not A, C, G, or T
File 19 of 109
Found at i:6317249 original size:85 final size:86
Alignment explanation
Indices: 6317002--6317235 Score: 337
Period size: 86 Copynumber: 2.7 Consensus size: 86
6316992 GTGTTTTTGT
*
6317002 GAAAAGTGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGT-GAGAAAAGCGTCGCTAAAGGTCT
1 GAAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGA-AAAAGCGTCGCTAAAGGTCT
**
6317066 TGAGCTATAGCAACATTTGTTG
65 TGAGCTATAGCGGCATTTGTTG
** * * *
6317088 GAAAAGCGCCGCTAAAGGTCTTGATCTATAGTAGCGTTTGTGTAAAAAGCGTCGCTAAAGATTTT
1 GAAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAAAAGCGTCGCTAAAGGTCTT
*
6317153 GAGCTATAGCGGCGTTTG-TG
66 GAGCTATAGCGGCATTTGTTG
* * *
6317173 GAGAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAAAAACGTTGCTAAAGGTC
1 GAAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAAAAGCGTCGCTAAAGGTC
6317236 GTGGTCTTTA
Statistics
Matches: 130, Mismatches: 17, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
85 57 0.44
86 72 0.55
87 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.27
Consensus pattern (86 bp):
GAAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAAAAGCGTCGCTAAAGGTCTT
GAGCTATAGCGGCATTTGTTG
Found at i:6320641 original size:9 final size:9
Alignment explanation
Indices: 6320625--6320666 Score: 66
Period size: 9 Copynumber: 4.7 Consensus size: 9
6320615 GAGTTAAACG
6320625 AATCGAGTT
1 AATCGAGTT
*
6320634 ATTCGAGTT
1 AATCGAGTT
6320643 AATCGAGTT
1 AATCGAGTT
6320652 AATCGAGTT
1 AATCGAGTT
*
6320661 ATTCGA
1 AATCGA
6320667 ATCAACTCGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (9 bp):
AATCGAGTT
Found at i:6320737 original size:9 final size:9
Alignment explanation
Indices: 6320720--6320756 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
6320710 TGAGTTTTCG
6320720 AATTCGAAT
1 AATTCGAAT
*
6320729 AACTCGAAT
1 AATTCGAAT
6320738 AATTCGAAT
1 AATTCGAAT
6320747 AATTCGAAT
1 AATTCGAAT
6320756 A
1 A
6320757 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:6321015 original size:29 final size:31
Alignment explanation
Indices: 6320969--6321027 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 31
6320959 AAACCTTTTA
*
6320969 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
6320999 TTTT-CCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
6321028 TCCCACCTCC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.20, C:0.39, G:0.00, T:0.41
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:6325700 original size:29 final size:29
Alignment explanation
Indices: 6325655--6325719 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 29
6325645 TTGAAAATTT
* *
6325655 TAAAATTAATTTAAATATATACGTTTAGG
1 TAAAATTAAGTTAAATATATACCTTTAGG
6325684 TAAAATTAACGTT-AATATATACCTTTAGG
1 TAAAATTAA-GTTAAATATATACCTTTAGG
6325713 TAAAATT
1 TAAAATT
6325720 TTAAAATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 31 0.94
30 2 0.06
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.40
Consensus pattern (29 bp):
TAAAATTAAGTTAAATATATACCTTTAGG
Found at i:6326445 original size:18 final size:19
Alignment explanation
Indices: 6326419--6326454 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
6326409 TATATAAAAT
6326419 ATAAAAATAATT-ATTTTA
1 ATAAAAATAATTAATTTTA
*
6326437 ATAATAATAATTAATTTT
1 ATAAAAATAATTAATTTT
6326455 GATGAAATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATAAAAATAATTAATTTTA
Found at i:6326702 original size:23 final size:24
Alignment explanation
Indices: 6326676--6326721 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
6326666 AACTTTTAGC
6326676 ATATATTAACCT-TTTTAAAACTA
1 ATATATTAACCTATTTTAAAACTA
* *
6326699 ATATTTTAACCTATTTTTAAACT
1 ATATATTAACCTATTTTAAAACT
6326722 TTACNNNNNN
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (24 bp):
ATATATTAACCTATTTTAAAACTA
Found at i:6328378 original size:5 final size:6
Alignment explanation
Indices: 6328357--6328397 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
6328347 GGTTTTCTCC
* *
6328357 AAAATG AAAAAG AAAAAG AAAAAG AAAAAGG AAAAGG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA-G AAAAAG AAAA
6328398 TGACCTGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
6 27 0.84
7 5 0.16
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:6331466 original size:27 final size:27
Alignment explanation
Indices: 6331388--6331450 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
6331378 CTACCCCGTG
* *
6331388 TTTACTGTCTCAACGGACTACACTGTA
1 TTTACTGTCTCGACGAACTACACTGTA
6331415 TTTACTGTCTCGACGAACTACACTGTA
1 TTTACTGTCTCGACGAACTACACTGTA
6331442 TTTACTGTC
1 TTTACTGTC
6331451 CTGATGAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.24, C:0.25, G:0.14, T:0.37
Consensus pattern (27 bp):
TTTACTGTCTCGACGAACTACACTGTA
Found at i:6333944 original size:5 final size:5
Alignment explanation
Indices: 6333934--6333959 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
6333924 ATGAAGTAAA
6333934 AAAAG AAAAG AAAAG AAAAG AAAAG A
1 AAAAG AAAAG AAAAG AAAAG AAAAG A
6333960 TATTTAGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:6333971 original size:117 final size:116
Alignment explanation
Indices: 6333842--6334062 Score: 361
Period size: 117 Copynumber: 1.9 Consensus size: 116
6333832 CATTTGTAAT
* * *
6333842 ATATTTATTTAATTACTTTATAAGTAAATATATGTTTATTATATTATATTATTATCATTATTATT
1 ATATTTAGTTAATTACTTTATAAGTAAATAGATATTTATTATATTATATTATTATCATTATTATT
*
6333907 TTTAAATAATATATATAATGAAGTAAAAAAAGAAAAGAAAAGAAAAGAAAAG
66 GTTAAATAATATATATAATGAAGTAAAAAAA-AAAAGAAAAGAAAAGAAAAG
* *
6333959 ATATTTAGTTAATTACTTTTTAAGTAAGTAGATATTTATTATATTATATTATTATCATTATTATT
1 ATATTTAGTTAATTACTTTATAAGTAAATAGATATTTATTATATTATATTATTATCATTATTATT
* *
6334024 GTTAACTAATATATATAATGAAGTAAAATAAAAAAGAAA
66 GTTAAATAATATATATAATGAAGTAAAAAAAAAAAGAAA
6334063 CAAACAAACA
Statistics
Matches: 96, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
116 8 0.08
117 88 0.92
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.42
Consensus pattern (116 bp):
ATATTTAGTTAATTACTTTATAAGTAAATAGATATTTATTATATTATATTATTATCATTATTATT
GTTAAATAATATATATAATGAAGTAAAAAAAAAAAGAAAAGAAAAGAAAAG
Found at i:6334080 original size:21 final size:21
Alignment explanation
Indices: 6334056--6334095 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
6334046 GTAAAATAAA
6334056 AAAGAA-ACAAACAAACAAAAC
1 AAAGAAGA-AAACAAACAAAAC
*
6334077 AAAGAAGAAAAGAAACAAA
1 AAAGAAGAAAACAAACAAA
6334096 GAGTAATTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.78, C:0.12, G:0.10, T:0.00
Consensus pattern (21 bp):
AAAGAAGAAAACAAACAAAAC
Found at i:6334548 original size:11 final size:11
Alignment explanation
Indices: 6334532--6334556 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
6334522 GAATTTACGG
6334532 TAGAAATTGAA
1 TAGAAATTGAA
6334543 TAGAAATTGAA
1 TAGAAATTGAA
6334554 TAG
1 TAG
6334557 GAAAATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.20, T:0.28
Consensus pattern (11 bp):
TAGAAATTGAA
Found at i:6335085 original size:22 final size:23
Alignment explanation
Indices: 6335048--6335091 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
6335038 GCTTTGCCGA
*
6335048 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACTTTATGTGCCGTATT
6335071 TCAGGCAC-TTATGTGCCGTAT
1 TCAGGCACTTTATGTGCCGTAT
6335092 ACTGATCAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.39
Consensus pattern (23 bp):
TCAGGCACTTTATGTGCCGTATT
Found at i:6344661 original size:9 final size:9
Alignment explanation
Indices: 6344568--6344731 Score: 60
Period size: 9 Copynumber: 18.0 Consensus size: 9
6344558 AATATAATAG
*
6344568 TATAATATT
1 TATAATTTT
*
6344577 TATATAGTTT
1 TATA-ATTTT
*
6344587 TATTATTTT
1 TATAATTTT
6344596 TATAAATTTT
1 TAT-AATTTT
*
6344606 CAT-ATTTT
1 TATAATTTT
6344614 TA-AAGTTATCCGT
1 TATAA-TT-T---T
*
6344627 TATTATTTT
1 TATAATTTT
*
6344636 TATAACTTT
1 TATAATTTT
6344645 TACCTAATTTT
1 TA--TAATTTT
6344656 TATAATTTCT
1 TATAATTT-T
6344666 T-T-A-TTT
1 TATAATTTT
*
6344672 TAT-CTTTT
1 TATAATTTT
*
6344680 TGTAATTTT
1 TATAATTTT
6344689 TAT-A-TTT
1 TATAATTTT
6344696 TATAA-TTT
1 TATAATTTT
*
6344704 TA-ATTCTTT
1 TATAAT-TTT
*
6344713 TATATTTTT
1 TATAATTTT
6344722 TAATAATTTT
1 T-ATAATTTT
6344732 CACAAAATTT
Statistics
Matches: 118, Mismatches: 17, Indels: 39
0.68 0.10 0.22
Matches are distributed among these distances:
6 2 0.02
7 10 0.08
8 20 0.17
9 45 0.38
10 26 0.22
11 8 0.07
12 1 0.01
13 5 0.04
14 1 0.01
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (9 bp):
TATAATTTT
Found at i:6344685 original size:24 final size:24
Alignment explanation
Indices: 6344652--6344720 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 24
6344642 TTTTACCTAA
6344652 TTTTTATAATTTCTT-TATTTTATC
1 TTTTTATAATTT-TTATATTTTATC
* *
6344676 TTTTTGTAATTTTTATATTTTATA
1 TTTTTATAATTTTTATATTTTATC
* *
6344700 ATTTTA-ATTCTTTTATATTTT
1 TTTTTATAAT-TTTTATATTTT
6344721 TTAATAATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
23 4 0.11
24 34 0.89
ACGTcount: A:0.23, C:0.04, G:0.01, T:0.71
Consensus pattern (24 bp):
TTTTTATAATTTTTATATTTTATC
Found at i:6353738 original size:51 final size:51
Alignment explanation
Indices: 6353678--6353780 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
6353668 TGCAAAATCA
6353678 TATGATTTACCAAACTAAAAATTTGGTTTTCAAAATTAAAACTCTAGAAAG
1 TATGATTTACCAAACTAAAAATTTGGTTTTCAAAATTAAAACTCTAGAAAG
6353729 TATGATTTACCAAACTAAAAATTTGGTTTTCAAAATTAAAACTCTAGAAAG
1 TATGATTTACCAAACTAAAAATTTGGTTTTCAAAATTAAAACTCTAGAAAG
6353780 T
1 T
6353781 TCCATTACAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.34
Consensus pattern (51 bp):
TATGATTTACCAAACTAAAAATTTGGTTTTCAAAATTAAAACTCTAGAAAG
Found at i:6354097 original size:14 final size:14
Alignment explanation
Indices: 6354078--6354104 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6354068 TAATCAACAA
6354078 TTATTTAATTAAAT
1 TTATTTAATTAAAT
6354092 TTATTTAATTAAA
1 TTATTTAATTAAA
6354105 AATTAATTAT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTATTTAATTAAAT
Found at i:6360775 original size:26 final size:25
Alignment explanation
Indices: 6360746--6360804 Score: 59
Period size: 26 Copynumber: 2.3 Consensus size: 25
6360736 CATTGTATTC
*
6360746 ATATTTATAT-ACATAAAATTTAATAA
1 ATATTTATATAACA-AAAA-CTAATAA
6360772 ATATCTT-TATAACAAAAACTAATAA
1 ATAT-TTATATAACAAAAACTAATAA
6360797 ATACTTTA
1 ATA-TTTA
6360805 GTTGCTACTG
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
25 11 0.39
26 12 0.43
27 5 0.18
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (25 bp):
ATATTTATATAACAAAAACTAATAA
Found at i:6371622 original size:13 final size:13
Alignment explanation
Indices: 6371604--6371646 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
6371594 TAGATTTTTC
6371604 CTAAATATTATCA
1 CTAAATATTATCA
*
6371617 CTAAATA--AT-T
1 CTAAATATTATCA
6371627 CTAAATATTATCA
1 CTAAATATTATCA
6371640 CTAAATA
1 CTAAATA
6371647 ATTCTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 7 0.28
11 2 0.08
12 2 0.08
13 14 0.56
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:6371634 original size:23 final size:23
Alignment explanation
Indices: 6371604--6371655 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
6371594 TAGATTTTTC
6371604 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
6371627 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
6371650 CTAAAT
1 CTAAAT
6371656 TTAAAAATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.38
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATT
Found at i:6371668 original size:23 final size:23
Alignment explanation
Indices: 6371604--6371668 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 23
6371594 TAGATTTTTC
** *
6371604 CTAAATATTATCACTAAATAATT
1 CTAAATATTAAAAATAAATAATT
** *
6371627 CTAAATATTATCACTAAATAATT
1 CTAAATATTAAAAATAAATAATT
6371650 CTAAAT-TTAAAAATCAAAT
1 CTAAATATTAAAAAT-AAAT
6371669 TTAAACTAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
22 5 0.13
23 33 0.87
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (23 bp):
CTAAATATTAAAAATAAATAATT
Found at i:6375714 original size:5 final size:6
Alignment explanation
Indices: 6375698--6375722 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
6375688 GTAGAAATGC
6375698 TAAAAA TAAAAA TAAAAA TAAAAA T
1 TAAAAA TAAAAA TAAAAA TAAAAA T
6375723 GAGGGGTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
TAAAAA
Found at i:6385539 original size:89 final size:89
Alignment explanation
Indices: 6385425--6385594 Score: 261
Period size: 89 Copynumber: 1.9 Consensus size: 89
6385415 AATTAAGTCC
* * * *
6385425 TTTTTTTTGCATTCAATTGGGTACTTGAACTT-TCAGAATGCATCAAAAAGACCCTCAAAATTTT
1 TTTTTTTTGCAATCAATTAGGTACTT-AAATTGTCAAAATGCATCAAAAAGACCCTCAAAATTTT
6385489 CCAAAAAAAGCAATTAAGCCCCTAT
65 CCAAAAAAAGCAATTAAGCCCCTAT
* *
6385514 TTTTTTTTGCAATCAATTAGGTACTTAAATTGTCAAAATGCATCAAAAAGACCCTCAAATTTTTT
1 TTTTTTTTGCAATCAATTAGGTACTTAAATTGTCAAAATGCATCAAAAAGACCCTCAAAATTTTC
*
6385579 CAAAAAAGGCAATTAA
66 CAAAAAAAGCAATTAA
6385595 ACTCCTTTTT
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
88 4 0.05
89 69 0.95
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.34
Consensus pattern (89 bp):
TTTTTTTTGCAATCAATTAGGTACTTAAATTGTCAAAATGCATCAAAAAGACCCTCAAAATTTTC
CAAAAAAAGCAATTAAGCCCCTAT
Found at i:6385782 original size:27 final size:27
Alignment explanation
Indices: 6385752--6385809 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
6385742 AAAACAACAA
**
6385752 AAAATATAAAAATTATTAAACTTTAAT
1 AAAATATAAAAATTATTAAAAATTAAT
* *
6385779 AAAATATAAAATTTTTTAAAAATTAAT
1 AAAATATAAAAATTATTAAAAATTAAT
6385806 AAAA
1 AAAA
6385810 ATTAGAAAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (27 bp):
AAAATATAAAAATTATTAAAAATTAAT
Found at i:6385853 original size:20 final size:20
Alignment explanation
Indices: 6385825--6385870 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
6385815 AAAGAAAAAA
6385825 TATAAAAATATT-TAAAA-TT
1 TATAAAAA-ATTGTAAAATTT
6385844 TATAAAAAATTGTAAAATTT
1 TATAAAAAATTGTAAAATTT
6385864 TATAAAA
1 TATAAAA
6385871 TGCATCAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.12
19 13 0.52
20 9 0.36
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
TATAAAAAATTGTAAAATTT
Found at i:6385886 original size:19 final size:19
Alignment explanation
Indices: 6385864--6385901 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
6385854 TGTAAAATTT
6385864 TATAAAATGCATCAAAAAG
1 TATAAAATGCATCAAAAAG
6385883 TATAAAATGCATCAAAAAG
1 TATAAAATGCATCAAAAAG
6385902 GCCTTTTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.58, C:0.11, G:0.11, T:0.21
Consensus pattern (19 bp):
TATAAAATGCATCAAAAAG
Found at i:6390894 original size:13 final size:13
Alignment explanation
Indices: 6390876--6390901 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6390866 CGTCAAGTCC
6390876 TAGCTACAGGATG
1 TAGCTACAGGATG
6390889 TAGCTACAGGATG
1 TAGCTACAGGATG
6390902 CTACATTTGT
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:0.31, T:0.23
Consensus pattern (13 bp):
TAGCTACAGGATG
Found at i:6399094 original size:20 final size:21
Alignment explanation
Indices: 6399069--6399109 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
6399059 ATGTTGAATT
6399069 AATTGA-TGAATTACAAGTTA
1 AATTGATTGAATTACAAGTTA
*
6399089 AATTGATTGAATTTCAAGTTA
1 AATTGATTGAATTACAAGTTA
6399110 GAAGTTAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.39
Consensus pattern (21 bp):
AATTGATTGAATTACAAGTTA
Found at i:6399992 original size:22 final size:23
Alignment explanation
Indices: 6399951--6399996 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
6399941 GGATTTATAT
6399951 TATTCTGGATATGTTAGGTTGGA
1 TATTCTGGATATGTTAGGTTGGA
* *
6399974 TATTCTGG-TGTGTTTGGTTGGA
1 TATTCTGGATATGTTAGGTTGGA
6399996 T
1 T
6399997 CCGTGTATCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.15, C:0.04, G:0.33, T:0.48
Consensus pattern (23 bp):
TATTCTGGATATGTTAGGTTGGA
Found at i:6401067 original size:15 final size:15
Alignment explanation
Indices: 6401049--6401084 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
6401039 CGAAAATCCG
6401049 TTTTATTAATGTTAA
1 TTTTATTAATGTTAA
6401064 TTTTATTAATGTTAA
1 TTTTATTAATGTTAA
6401079 TTTTAT
1 TTTTAT
6401085 AAAAGATGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.64
Consensus pattern (15 bp):
TTTTATTAATGTTAA
Found at i:6402311 original size:19 final size:18
Alignment explanation
Indices: 6402289--6402326 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
6402279 TATAATAATG
*
6402289 ATAACAATAATAAATAGTA
1 ATAAAAATAAT-AATAGTA
6402308 ATAAAAATAATAATAGTA
1 ATAAAAATAATAATAGTA
6402326 A
1 A
6402327 ATTAATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.26
Consensus pattern (18 bp):
ATAAAAATAATAATAGTA
Found at i:6404722 original size:44 final size:44
Alignment explanation
Indices: 6404650--6405087 Score: 217
Period size: 44 Copynumber: 9.5 Consensus size: 44
6404640 TATCTCCGTG
* * *
6404650 AAGTTGCAGTGGAGCAAGA-TGAACCTACAAATCCTATATCCCTG
1 AAGTTGCAGTGGATC-AGATTGAAGCTACAAATCCTATATCCCTA
* * *
6404694 AAGTTGCAGTGGATC-GTATTGAAGCTACAATTCCTATACCCCAA
1 AAGTTGCAGTGGATCAG-ATTGAAGCTACAAATCCTATATCCCTA
* * * * *
6404738 AAGTTGTAGTGGGTCAGAATGAAACTACAATGACAAATCCTATATCCTTA
1 AAGTTGCAGTGGATCAGATTG-AA--GC--T-ACAAATCCTATATCCCTA
* * * * *
6404788 AAGTTACAGTGGATC-GAATTAAAGCTACAAATCTTATACCCCTG
1 AAGTTGCAGTGGATCAG-ATTGAAGCTACAAATCCTATATCCCTA
* * * *
6404832 AAGTTGCAGTAGG-TCGGATTGAATCTACCATAGCAAGTCTTATCTCCCTA
1 AAGTTGCAGT-GGATCAGATTGAAGCTA-C--A--AA-TCCTATATCCCTA
* * * * * *
6404882 AACTTGCAGTCGAACAAGA-TGAAGCTACAAATCTTATA-CCATTG
1 AAGTTGCAGTGGATC-AGATTGAAGCTACAAATCCTATATCC-CTA
* * * *
6404926 AATTTGCAGTGGGTCAGATTGAAGTTACCATAA-CGAACTTTATCTCTCTA
1 AAGTTGCAGTGGATCAGATTGAAGCTA-CA-AATC---CTATATC-C-CTA
* * * * * *
6404976 AAGTTTCAGCGGAGCA-AGGTGAACCTACAAATCTTATATCCCTA
1 AAGTTGCAGTGGATCAGA-TTGAAGCTACAAATCCTATATCCCTA
* * *
6405020 AAGTTGTAGTGGATCAGATTGAAGCTACAAATCCTATACCCCTG
1 AAGTTGCAGTGGATCAGATTGAAGCTACAAATCCTATATCCCTA
* *
6405064 AAGTTGCAGTGGGTCGGATTGAAG
1 AAGTTGCAGTGGATCAGATTGAAG
6405088 TTACCATAGC
Statistics
Matches: 292, Mismatches: 70, Indels: 64
0.69 0.16 0.15
Matches are distributed among these distances:
42 1 0.00
43 6 0.02
44 165 0.57
45 15 0.05
46 7 0.02
47 4 0.01
48 5 0.02
49 13 0.04
50 74 0.25
51 2 0.01
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (44 bp):
AAGTTGCAGTGGATCAGATTGAAGCTACAAATCCTATATCCCTA
Found at i:6404836 original size:94 final size:93
Alignment explanation
Indices: 6404675--6405049 Score: 308
Period size: 94 Copynumber: 4.0 Consensus size: 93
6404665 AAGATGAACC
* * * * *
6404675 TACAAATCCTATATCCCTGAAGTTGCAGTGGATCGTA-TTGAAGCTACAATTCCTATACCCCAAA
1 TACAAATCCTATATCCCTAAAGTTGCAGTGGATC-AAGTTGAAGCTACAAATCTTATACCCCTAA
* * *
6404739 AGTTGTAGTGGGTCAGAATGAAACTACAA
65 AGTTGCAGTGGGTCAGATTGAAGCTACAA
* * * *
6404768 TGACAAATCCTATATCCTTAAAGTTACAGTGGATCGAA-TTAAAGCTACAAATCTTATACCCCTG
1 T-ACAAATCCTATATCCCTAAAGTTGCAGTGGATC-AAGTTGAAGCTACAAATCTTATACCCCTA
* * * *
6404832 AAGTTGCAGTAGGTCGGATTGAATCTACCA
64 AAGTTGCAGTGGGTCAGATTGAAGCTACAA
* * * * * * * ** *
6404862 TAGCAAGTCTTATCTCCCTAAACTTGCAGTCGAACAAGATGAAGCTACAAATCTTATACCATTGA
1 TA-CAAATCCTATATCCCTAAAGTTGCAGTGGATCAAGTTGAAGCTACAAATCTTATACCCCTAA
* * *
6404927 ATTTGCAGTGGGTCAGATTGAAGTTACCA
65 AGTTGCAGTGGGTCAGATTGAAGCTACAA
* * * * * * * *
6404956 TAACGAA--CTTTATCTCTCTAAAGTTTCAGCGGAGCAAGGTGAACCTACAAATCTTATATCCCT
1 T-ACAAATCCTATATC-C-CTAAAGTTGCAGTGGATCAAGTTGAAGCTACAAATCTTATACCCCT
* *
6405019 AAAGTTGTAGTGGATCAGATTGAAGCTACAA
63 AAAGTTGCAGTGGGTCAGATTGAAGCTACAA
6405050 ATCCTATACC
Statistics
Matches: 223, Mismatches: 53, Indels: 11
0.78 0.18 0.04
Matches are distributed among these distances:
92 4 0.02
93 5 0.02
94 213 0.96
95 1 0.00
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (93 bp):
TACAAATCCTATATCCCTAAAGTTGCAGTGGATCAAGTTGAAGCTACAAATCTTATACCCCTAAA
GTTGCAGTGGGTCAGATTGAAGCTACAA
Found at i:6405105 original size:94 final size:94
Alignment explanation
Indices: 6405007--6405181 Score: 237
Period size: 94 Copynumber: 1.9 Consensus size: 94
6404997 AACCTACAAA
* *
6405007 TCTTATATCCCTAAAGTTGTAGT-GGATC-AGATTGAAGCTACAAATCCTATACCCCTGAAGTTG
1 TCTTATATCCCTAAAGTTGTAGTAGG-GCAAGA-TGAAGCTACAAATCCTATACCCCTGAAGTTA
* *
6405070 CAGTGGGTCGGATTGAAGTTACCATAGCGAG
64 AAGTGGATCGGATTGAAGTTACCATAGCGAG
* * * * *
6405101 TCTTATCTCCCTAAAGTTGTAGTAGGGCAAGATGAAGCTGCAAATCCTATATCTCTGTAGTTAAA
1 TCTTATATCCCTAAAGTTGTAGTAGGGCAAGATGAAGCTACAAATCCTATACCCCTGAAGTTAAA
6405166 GTGGATCGGATTGAAG
66 GTGGATCGGATTGAAG
6405182 AGACAATTCC
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
94 65 0.93
95 5 0.07
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (94 bp):
TCTTATATCCCTAAAGTTGTAGTAGGGCAAGATGAAGCTACAAATCCTATACCCCTGAAGTTAAA
GTGGATCGGATTGAAGTTACCATAGCGAG
Found at i:6405117 original size:138 final size:138
Alignment explanation
Indices: 6404869--6405217 Score: 364
Period size: 138 Copynumber: 2.5 Consensus size: 138
6404859 CCATAGCAAG
* * * * * * * *
6404869 TCTTATCTCCCTAAACTTGCAGTCGAACAAGA-TGAAGCTACAAATCTTATACCATTGAATTTGC
1 TCTTATATCCCTAAAGTTGAAGTGGATC-AGATTGAAGCTACAAATCCTATACCACTGAAGTTGC
* * * *
6404933 AGTGGGTCAGATTGAAGTTACCATAACGAACTTTATCTCTCTAAAGTT-TCAG-CGGAGCAAGGT
65 AGTGGGTCGGATTGAAGTTACCATAACGAACTTTATCTCCCTAAAGTTGT-AGTAGG-GCAAGAT
6404996 GAACCTACAAA
128 GAACCTACAAA
* *
6405007 TCTTATATCCCTAAAGTTGTAGTGGATCAGATTGAAGCTACAAATCCTATACCCCTGAAGTTGCA
1 TCTTATATCCCTAAAGTTGAAGTGGATCAGATTGAAGCTACAAATCCTATACCACTGAAGTTGCA
* *
6405072 GTGGGTCGGATTGAAGTTACCATAGCG-AGTCTTATCTCCCTAAAGTTGTAGTAGGGCAAGATGA
66 GTGGGTCGGATTGAAGTTACCATAACGAACT-TTATCTCCCTAAAGTTGTAGTAGGGCAAGATGA
* *
6405136 AGCTGCAAA
130 ACCTACAAA
* * ** * * ** * * *
6405145 TCCTATATCTCTGTAGTTAAAGTGGATCGGATTGAAGAGACAATTCCTATACCTCTGAAGTTACA
1 TCTTATATCCCTAAAGTTGAAGTGGATCAGATTGAAGCTACAAATCCTATACCACTGAAGTTGCA
*
6405210 GTAGGTCG
66 GTGGGTCG
6405218 TAATGAAATT
Statistics
Matches: 177, Mismatches: 30, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
137 5 0.03
138 169 0.95
139 3 0.02
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (138 bp):
TCTTATATCCCTAAAGTTGAAGTGGATCAGATTGAAGCTACAAATCCTATACCACTGAAGTTGCA
GTGGGTCGGATTGAAGTTACCATAACGAACTTTATCTCCCTAAAGTTGTAGTAGGGCAAGATGAA
CCTACAAA
Found at i:6405265 original size:232 final size:228
Alignment explanation
Indices: 6404587--6405267 Score: 583
Period size: 232 Copynumber: 2.9 Consensus size: 228
6404577 ACATCTTAAC
* * * * * * * * *
6404587 TCCTATACCCCTAAAATAGCAGTGGGTCGGATTGAAGCTA-AAGTGGCGAATCTTATCTCCGTGA
1 TCCTATACCCCTGAAGTTGCAGTGGGTCGGATTGAAGTTACCA-TAGCGAGTCTTATCTCCCTAA
* * *
6404651 AGTTGCAGTGGAGCAAGATGAACCTACAAATCCTATATCCCTGAAGTTGCAGTGGATCGTATTGA
65 AGTTGCAGTGG-GCAAGATGAAGCTACAAATCCTATATCTCTGAAGTTGCAGTGGATCGGATTGA
* * * ** * * *
6404716 AGCTACAATTCCTATACCCCAAAAGTTGTAGTGGGTCAGAATGAAACTACAATGACAAATCCTAT
129 AGATACAATTCCTATACCTCTAAAGTTACAGTAGGTC-GAATGAAA-TATAATG-CAAATCTTAT
*
6404781 AT-CCTTAAAGTTACAGTGGATCGAATTAAAGCTACAAA
191 ATCCCTT-AAGTTGCAGTGGATCGAATTAAAGCTACAAA
* * *
6404819 TCTTATACCCCTGAAGTTGCAGTAGGTCGGATTGAA-TCTACCATAGCAAGTCTTATCTCCCTAA
1 TCCTATACCCCTGAAGTTGCAGTGGGTCGGATTGAAGT-TACCATAGCGAGTCTTATCTCCCTAA
* ** * * * * *
6404883 ACTTGCAGTCGAACAAGATGAAGCTACAAATCTTATACCAT-TGAATTTGCAGTGGGTCAGATTG
65 AGTTGCAGT-GGGCAAGATGAAGCTACAAATCCTATATC-TCTGAAGTTGCAGTGGATCGGATTG
* * * * * * * **
6404947 AAGTTACCATAACGAACTTTATCTCTCTAAAGTTTCAG-CGG-AGCAAGGTG-AACCT-A--CAA
128 AAGATACAAT-TC---CTATA-C-CTCTAAAGTTACAGTAGGTCG-AA--TGAAATATAATGCAA
* * *
6405006 ATCTTATATCCCTAAAGTTGTAGTGGATC-AGATTGAAGCTACAAA
184 ATCTTATATCCCTTAAGTTGCAGTGGATCGA-ATTAAAGCTACAAA
6405051 TCCTATACCCCTGAAGTTGCAGTGGGTCGGATTGAAGTTACCATAGCGAGTCTTATCTCCCTAAA
1 TCCTATACCCCTGAAGTTGCAGTGGGTCGGATTGAAGTTACCATAGCGAGTCTTATCTCCCTAAA
* * * **
6405116 GTTGTAGTAGGGCAAGATGAAGCTGCAAATCCTATATCTCTGTAGTTAAAGTGGATCGGATTGAA
66 GTTGCAGT-GGGCAAGATGAAGCTACAAATCCTATATCTCTGAAGTTGCAGTGGATCGGATTGAA
* * * * *
6405181 GAGACAATTCCTATACCTCTGAAGTTACAGTAGGTCGTAATGAAATTATAATGGCGAATCTTTTT
130 GATACAATTCCTATACCTCTAAAGTTACAGTAGGTCG-AATGAAA-TATAAT-GCAAATCTTATA
*
6405246 TCCCTTAATTTGCAGTGGATCG
192 TCCCTTAAGTTGCAGTGGATCG
6405268 GAATGAAATT
Statistics
Matches: 347, Mismatches: 76, Indels: 51
0.73 0.16 0.11
Matches are distributed among these distances:
226 14 0.04
227 5 0.01
228 8 0.02
229 1 0.00
231 3 0.01
232 284 0.82
233 7 0.02
235 2 0.01
236 6 0.02
237 5 0.01
238 12 0.03
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (228 bp):
TCCTATACCCCTGAAGTTGCAGTGGGTCGGATTGAAGTTACCATAGCGAGTCTTATCTCCCTAAA
GTTGCAGTGGGCAAGATGAAGCTACAAATCCTATATCTCTGAAGTTGCAGTGGATCGGATTGAAG
ATACAATTCCTATACCTCTAAAGTTACAGTAGGTCGAATGAAATATAATGCAAATCTTATATCCC
TTAAGTTGCAGTGGATCGAATTAAAGCTACAAA
Found at i:6405298 original size:50 final size:50
Alignment explanation
Indices: 6405202--6405314 Score: 149
Period size: 50 Copynumber: 2.3 Consensus size: 50
6405192 TATACCTCTG
* * * *
6405202 AAGTTACAGTAGG-TCGTAATGAAATTATAATGGCGAATCTTTTTTCCCTT
1 AAGTTGCAGT-GGATCGGAATGAAATTACAATGGCGAATCTTTTTTCCCTA
*
6405252 AATTTGCAGTGGATCGGAATGAAATTACAATGGCGAAT-TTTATTTCCCTA
1 AAGTTGCAGTGGATCGGAATGAAATTACAATGGCGAATCTTT-TTTCCCTA
6405302 AAGTTGCAGTGGA
1 AAGTTGCAGTGGA
6405315 GCAAGATGAA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
49 5 0.09
50 50 0.91
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (50 bp):
AAGTTGCAGTGGATCGGAATGAAATTACAATGGCGAATCTTTTTTCCCTA
Found at i:6405331 original size:50 final size:50
Alignment explanation
Indices: 6405219--6405331 Score: 122
Period size: 50 Copynumber: 2.3 Consensus size: 50
6405209 AGTAGGTCGT
* * * * * *
6405219 AATGAAATTATAATGGCGAATCTTTTTTCCCTTAATTTGCAGTGGATCGG
1 AATGAAACTACAATGGCGAATCTTTTTTCCCTAAAGTTGCAGTGGAGCAG
*
6405269 AATGAAATTACAATGGCGAAT-TTTATTTCCCTAAAGTTGCAGTGGAGCA-
1 AATGAAACTACAATGGCGAATCTTT-TTTCCCTAAAGTTGCAGTGGAGCAG
*
6405318 AGATGAAGCTACAA
1 A-ATGAAACTACAA
6405332 ATATTATATC
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
49 4 0.07
50 50 0.93
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (50 bp):
AATGAAACTACAATGGCGAATCTTTTTTCCCTAAAGTTGCAGTGGAGCAG
Found at i:6406598 original size:21 final size:21
Alignment explanation
Indices: 6406569--6406608 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
6406559 TTTTATTGTA
*
6406569 GTTTCAATTTAGTCTCCTGTTC
1 GTTTCAATTGAGTC-CCTGTTC
6406591 GTTT-AATTGAGTCCCTGT
1 GTTTCAATTGAGTCCCTGT
6406609 ACTTGCCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 8 0.47
22 4 0.24
ACGTcount: A:0.15, C:0.20, G:0.17, T:0.47
Consensus pattern (21 bp):
GTTTCAATTGAGTCCCTGTTC
Found at i:6406787 original size:16 final size:17
Alignment explanation
Indices: 6406768--6406808 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
6406758 TATGTAATTA
6406768 TTTTATTATCAT-ACAT
1 TTTTATTATCATGACAT
*
6406784 TTTTA-TATCATGCCAT
1 TTTTATTATCATGACAT
*
6406800 TATTATTAT
1 TTTTATTAT
6406809 TATTATCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 6 0.29
16 12 0.57
17 3 0.14
ACGTcount: A:0.29, C:0.12, G:0.02, T:0.56
Consensus pattern (17 bp):
TTTTATTATCATGACAT
Found at i:6414169 original size:18 final size:18
Alignment explanation
Indices: 6414146--6414181 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
6414136 TATGTAATCA
6414146 TTTTGCTAACCCAAGGTC
1 TTTTGCTAACCCAAGGTC
6414164 TTTTGCTAACCCAAGGTC
1 TTTTGCTAACCCAAGGTC
6414182 AAAATAGGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.33
Consensus pattern (18 bp):
TTTTGCTAACCCAAGGTC
Found at i:6417225 original size:18 final size:18
Alignment explanation
Indices: 6417202--6417236 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
6417192 AGAAATAGCT
*
6417202 GCAAAATAATACATAAAA
1 GCAAAACAATACATAAAA
6417220 GCAAAACAATACATAAA
1 GCAAAACAATACATAAA
6417237 TGCTTAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.66, C:0.14, G:0.06, T:0.14
Consensus pattern (18 bp):
GCAAAACAATACATAAAA
Found at i:6420417 original size:3 final size:3
Alignment explanation
Indices: 6420409--6420700 Score: 500
Period size: 3 Copynumber: 97.3 Consensus size: 3
6420399 NNNNNNNNNN
6420409 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
6420457 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
6420505 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
6420553 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
6420601 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
6420649 ATA ACTTA ATA ACA AGA A-A ATA A-A AT- TTA ATA AAA ATAA ATA ATA
1 ATA A--TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA
6420694 ATA ATA A
1 ATA ATA A
6420701 AAAGACTAAA
Statistics
Matches: 277, Mismatches: 6, Indels: 12
0.94 0.02 0.04
Matches are distributed among these distances:
2 5 0.02
3 266 0.96
4 3 0.01
5 3 0.01
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:6421016 original size:19 final size:19
Alignment explanation
Indices: 6420992--6421055 Score: 119
Period size: 19 Copynumber: 3.4 Consensus size: 19
6420982 AATCATATCT
6420992 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
6421011 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
6421030 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
6421049 TCTAAGA
1 TCTAAGA
6421056 AGATTACATA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 43 1.00
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:6421638 original size:124 final size:125
Alignment explanation
Indices: 6421485--6421736 Score: 488
Period size: 124 Copynumber: 2.0 Consensus size: 125
6421475 TTTCATATAT
6421485 AAAATTACACAAAATCAAAGTTCATGTATAGTTTTAATATTTATACCAGAATAAAAATATATATG
1 AAAATTACAC-AAATCAAAGTTCATGTATAGTTTTAATATTTATACCAGAATAAAAATATATATG
6421550 AAAATTTAGAAAAAAAAACTTAAAATTTTTAAAAATAGATAAACTATTTGGAACAGGCTCC
65 AAAATTTAGAAAAAAAAACTTAAAATTTTTAAAAATAGATAAACTATTTGGAACAGGCTCC
6421611 AAAATTACAC-AATCAAAGTTCATGTATAGTTTTAATATTTATACCAGAATAAAAATATATATGA
1 AAAATTACACAAATCAAAGTTCATGTATAGTTTTAATATTTATACCAGAATAAAAATATATATGA
6421675 AAATTTAGAAAAAAAAACTTAAAATTTTTAAAAATAGATAAACTATTTGGAACAGGCTCC
66 AAATTTAGAAAAAAAAACTTAAAATTTTTAAAAATAGATAAACTATTTGGAACAGGCTCC
6421735 AA
1 AA
6421737 TTTCGAAAAT
Statistics
Matches: 126, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
124 116 0.92
126 10 0.08
ACGTcount: A:0.51, C:0.10, G:0.09, T:0.31
Consensus pattern (125 bp):
AAAATTACACAAATCAAAGTTCATGTATAGTTTTAATATTTATACCAGAATAAAAATATATATGA
AAATTTAGAAAAAAAAACTTAAAATTTTTAAAAATAGATAAACTATTTGGAACAGGCTCC
Found at i:6435970 original size:81 final size:82
Alignment explanation
Indices: 6435834--6435997 Score: 321
Period size: 81 Copynumber: 2.0 Consensus size: 82
6435824 ATTTGTATTG
6435834 TATTACATTTTTTTCCATCCATAATGTACTTATTCCAATTATATAAAAAAGTTGATCTATTTTTT
1 TATTACATTTTTTTCCATCCATAATGTACTTATTCCAATTATATAAAAAAGTTGATCTATTTTTT
6435899 TTACATCAATAATATAC
66 TTACATCAATAATATAC
6435916 TATTACA-TTTTTTCCATCCATAATGTACTTATTCCAATTATATAAAAAAGTTGATCTATTTTTT
1 TATTACATTTTTTTCCATCCATAATGTACTTATTCCAATTATATAAAAAAGTTGATCTATTTTTT
6435980 TTACATCAATAATATAC
66 TTACATCAATAATATAC
6435997 T
1 T
6435998 TAATTACAAT
Statistics
Matches: 82, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
81 75 0.91
82 7 0.09
ACGTcount: A:0.35, C:0.15, G:0.04, T:0.46
Consensus pattern (82 bp):
TATTACATTTTTTTCCATCCATAATGTACTTATTCCAATTATATAAAAAAGTTGATCTATTTTTT
TTACATCAATAATATAC
Found at i:6440475 original size:49 final size:49
Alignment explanation
Indices: 6440380--6440475 Score: 122
Period size: 49 Copynumber: 2.0 Consensus size: 49
6440370 CTCACGGTGG
* * **
6440380 TTATACGGTCACGGGTTGAAGTATAACTAGGGCTCCTGGTTAATGGTAA
1 TTATACGGTCACGAGTTAAAGTATAACTAGGGCTCCCAGTTAATGGTAA
* *
6440429 TTATACGGTCACGAGTTAAAGTATAACTGGGGAC-CCCAGTTGATGGT
1 TTATACGGTCACGAGTTAAAGTATAACTAGGG-CTCCCAGTTAATGGT
6440476 GGTTATGTGG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
49 39 0.98
50 1 0.03
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (49 bp):
TTATACGGTCACGAGTTAAAGTATAACTAGGGCTCCCAGTTAATGGTAA
Found at i:6443547 original size:28 final size:27
Alignment explanation
Indices: 6443507--6443564 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 27
6443497 GAATCAAACA
*
6443507 CAGAATTAGAAATGATTTTCTTTACTTT
1 CAGAATCAGAAATGATTTTC-TTACTTT
6443535 CAGAATCAGAAATGATTTTCTTACTTT
1 CAGAATCAGAAATGATTTTCTTACTTT
6443562 CAG
1 CAG
6443565 TAGGAAAGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 10 0.34
28 19 0.66
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (27 bp):
CAGAATCAGAAATGATTTTCTTACTTT
Found at i:6453143 original size:6 final size:6
Alignment explanation
Indices: 6453132--6453158 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
6453122 AGGTTTCTAA
6453132 AAATGG AAATGG AAATGG AAATGG AAA
1 AAATGG AAATGG AAATGG AAATGG AAA
6453159 CTTGTAATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.30, T:0.15
Consensus pattern (6 bp):
AAATGG
Found at i:6453351 original size:25 final size:27
Alignment explanation
Indices: 6453300--6453359 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 27
6453290 AAATTTCTCG
*
6453300 AAATTTTACCGGGGGTAAAATCATC-A
1 AAATTTTACCGGGGATAAAATCATCAA
**
6453326 AAATTTTACC-GGGATAAAATTGTCAA
1 AAATTTTACCGGGGATAAAATCATCAA
6453352 AAATTTTA
1 AAATTTTA
6453360 ATGGAAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
25 11 0.37
26 19 0.63
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.32
Consensus pattern (27 bp):
AAATTTTACCGGGGATAAAATCATCAA
Found at i:6461804 original size:7 final size:6
Alignment explanation
Indices: 6461778--6461802 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
6461768 ATGCATTCAA
6461778 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
6461803 TAAAATGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:6481191 original size:9 final size:9
Alignment explanation
Indices: 6481177--6481204 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
6481167 TATAGTTTGA
6481177 TATTCGAAT
1 TATTCGAAT
6481186 TATTCGAAT
1 TATTCGAAT
6481195 TATTCGAAT
1 TATTCGAAT
6481204 T
1 T
6481205 TGAAAACTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:6490023 original size:53 final size:53
Alignment explanation
Indices: 6489966--6490073 Score: 216
Period size: 53 Copynumber: 2.0 Consensus size: 53
6489956 GTTGCAAAAT
6489966 TGATTGCAAAGGAAGGGAAATTAGCCACATTAAAATTAACTTTTAGTGAGGTC
1 TGATTGCAAAGGAAGGGAAATTAGCCACATTAAAATTAACTTTTAGTGAGGTC
6490019 TGATTGCAAAGGAAGGGAAATTAGCCACATTAAAATTAACTTTTAGTGAGGTC
1 TGATTGCAAAGGAAGGGAAATTAGCCACATTAAAATTAACTTTTAGTGAGGTC
6490072 TG
1 TG
6490074 TTTGATATCC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (53 bp):
TGATTGCAAAGGAAGGGAAATTAGCCACATTAAAATTAACTTTTAGTGAGGTC
Found at i:6494603 original size:18 final size:19
Alignment explanation
Indices: 6494576--6494626 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
6494566 GACATGTGAC
*
6494576 AAAAAATAATAAATA-AAT
1 AAAAATTAATAAATAGAAT
6494594 AAAAATTAATAAA-AGTAAT
1 AAAAATTAATAAATAG-AAT
*
6494613 AAAAATTATTAAAT
1 AAAAATTAATAAAT
6494627 TTTAATTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 1 0.04
18 12 0.43
19 15 0.54
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (19 bp):
AAAAATTAATAAATAGAAT
Found at i:6494604 original size:10 final size:10
Alignment explanation
Indices: 6494580--6494678 Score: 53
Period size: 10 Copynumber: 9.9 Consensus size: 10
6494570 TGTGACAAAA
*
6494580 AATAATAAATA
1 AATAA-AAATT
6494591 AATAAAAATT
1 AATAAAAATT
*
6494601 AAT-AAAAGT
1 AATAAAAATT
6494610 AATAAAAATT
1 AATAAAAATT
* **
6494620 ATTAAATTTT
1 AATAAAAATT
6494630 AATTAAAAA-T
1 AA-TAAAAATT
*
6494640 AA-AAAATTTAT
1 AATAAAA-AT-T
*
6494651 AAAAAAAATT
1 AATAAAAATT
*
6494661 -ATAAAATTT
1 AATAAAAATT
*
6494670 TATAAAAAT
1 AATAAAAAT
6494679 CGAAAAAAAT
Statistics
Matches: 67, Mismatches: 14, Indels: 15
0.70 0.15 0.16
Matches are distributed among these distances:
8 4 0.06
9 15 0.22
10 31 0.46
11 13 0.19
12 4 0.06
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (10 bp):
AATAAAAATT
Found at i:6494632 original size:20 final size:20
Alignment explanation
Indices: 6494591--6494678 Score: 76
Period size: 19 Copynumber: 4.5 Consensus size: 20
6494581 ATAATAAATA
*
6494591 AATAAAAATTAATAAAA--GT
1 AATAAAAATTAA-AAAATTTT
**
6494610 AATAAAAATTATTAAATTTT
1 AATAAAAATTAAAAAATTTT
6494630 AATTAAAAA-TAAAAAATTTAT
1 AA-TAAAAATTAAAAAATTT-T
* *
6494651 AAAAAAAATTATAAAATTTT
1 AATAAAAATTAAAAAATTTT
6494671 -ATAAAAAT
1 AATAAAAAT
6494679 CGAAAAAAAT
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
18 3 0.05
19 18 0.32
20 17 0.30
21 18 0.32
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (20 bp):
AATAAAAATTAAAAAATTTT
Found at i:6494638 original size:21 final size:20
Alignment explanation
Indices: 6494591--6494678 Score: 85
Period size: 21 Copynumber: 4.5 Consensus size: 20
6494581 ATAATAAATA
*
6494591 AATAAAAATTAATAAAA--GT
1 AATAAAAATT-ATAAAATTTT
*
6494610 AATAAAAATTATTAAATTTT
1 AATAAAAATTATAAAATTTT
*
6494630 AATTAAAAA-TAAAAAATTTAT
1 AA-TAAAAATTATAAAATTT-T
*
6494651 AAAAAAAATTATAAAATTTT
1 AATAAAAATTATAAAATTTT
6494671 -ATAAAAAT
1 AATAAAAAT
6494679 CGAAAAAAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
18 5 0.09
19 17 0.30
20 17 0.30
21 18 0.32
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (20 bp):
AATAAAAATTATAAAATTTT
Found at i:6494684 original size:29 final size:30
Alignment explanation
Indices: 6494648--6494734 Score: 92
Period size: 29 Copynumber: 3.0 Consensus size: 30
6494638 ATAAAAAATT
6494648 TATA-AAAAAAATTATAAAATTTTATAAAA
1 TATAGAAAAAAATTATAAAATTTTATAAAA
* * *
6494677 -ATCGAAAAAAA-TAT-AAAGTATATAGAAA
1 TATAGAAAAAAATTATAAAATTTTATA-AAA
*
6494705 TATAGAAAAAAATTTATAGAATTTTATAAA
1 TATAGAAAAAAA-TTATAAAATTTTATAAA
6494735 GTTGTAAGAA
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
27 8 0.18
28 8 0.18
29 17 0.38
31 5 0.11
32 7 0.16
ACGTcount: A:0.62, C:0.01, G:0.06, T:0.31
Consensus pattern (30 bp):
TATAGAAAAAAATTATAAAATTTTATAAAA
Found at i:6494692 original size:40 final size:41
Alignment explanation
Indices: 6494613--6494693 Score: 105
Period size: 41 Copynumber: 2.0 Consensus size: 41
6494603 TAAAAGTAAT
* *
6494613 AAAAATTATTAAATTTTAATTAAAAATAAAAAATTTATAAA
1 AAAAATTATAAAATTTTAATTAAAAATAAAAAATATATAAA
6494654 AAAAATTATAAAATTTT-A-TAAAAATCGAAAAAA-ATATAAA
1 AAAAATTATAAAATTTTAATTAAAAAT--AAAAAATATATAAA
6494694 GTATATAGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
39 7 0.19
40 7 0.19
41 22 0.61
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (41 bp):
AAAAATTATAAAATTTTAATTAAAAATAAAAAATATATAAA
Found at i:6495011 original size:37 final size:37
Alignment explanation
Indices: 6494963--6495043 Score: 101
Period size: 37 Copynumber: 2.2 Consensus size: 37
6494953 GTTAAAGAAT
* * *
6494963 TTTTTTTATTTTTA-TAAAAGTTTACAATTTTTTATAA
1 TTTTTATATTTTTATTAAAAGTTAAC-AGTTTTTATAA
*
6495000 TTTTTATATTTTTATTGAAAGTTAACAGTTTTTATAA
1 TTTTTATATTTTTATTAAAAGTTAACAGTTTTTATAA
*
6495037 ATTTTAT
1 TTTTTAT
6495044 TGATATTTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
37 29 0.76
38 9 0.24
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.60
Consensus pattern (37 bp):
TTTTTATATTTTTATTAAAAGTTAACAGTTTTTATAA
Found at i:6500272 original size:27 final size:27
Alignment explanation
Indices: 6500249--6500305 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
6500239 CAGGTTGCGG
* *
6500249 CTATTTGATAGGCGCAACTAGTTGAGC
1 CTATCTGACAGGCGCAACTAGTTGAGC
* *
6500276 CTATCTGACAGGCGCGACTAGTTGTGC
1 CTATCTGACAGGCGCAACTAGTTGAGC
6500303 CTA
1 CTA
6500306 ACTCAGAGGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (27 bp):
CTATCTGACAGGCGCAACTAGTTGAGC
Found at i:6500315 original size:27 final size:27
Alignment explanation
Indices: 6500258--6500319 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
6500248 GCTATTTGAT
* * *
6500258 AGGCGCAACTAGTTGAGCCTATCTGAC
1 AGGCGCGACTAGTTGAGCCTAACTCAC
* *
6500285 AGGCGCGACTAGTTGTGCCTAACTCAG
1 AGGCGCGACTAGTTGAGCCTAACTCAC
6500312 AGGCGCGA
1 AGGCGCGA
6500320 ATGGTGGGGC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.24, C:0.26, G:0.31, T:0.19
Consensus pattern (27 bp):
AGGCGCGACTAGTTGAGCCTAACTCAC
Found at i:6500468 original size:16 final size:16
Alignment explanation
Indices: 6500434--6500468 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
6500424 AAAATCAAAT
* *
6500434 AAAATTACATTATATA
1 AAAATTACATTAAAAA
6500450 AAAATTACATTAAAAA
1 AAAATTACATTAAAAA
6500466 AAA
1 AAA
6500469 TCACAAAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATTACATTAAAAA
Found at i:6500945 original size:27 final size:27
Alignment explanation
Indices: 6500901--6500977 Score: 118
Period size: 27 Copynumber: 2.9 Consensus size: 27
6500891 CACACACCAT
* * *
6500901 TCGCGCCTACCTGCCAGGCTCGATTAG
1 TCGCGCCTATCTGACAGGCGCGATTAG
6500928 TCGCGCCTATCTGACAGGCGCGATTAG
1 TCGCGCCTATCTGACAGGCGCGATTAG
*
6500955 TCACGCCTATCTGACAGGCGCGA
1 TCGCGCCTATCTGACAGGCGCGA
6500978 CCATTTTTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.18, C:0.34, G:0.27, T:0.21
Consensus pattern (27 bp):
TCGCGCCTATCTGACAGGCGCGATTAG
Found at i:6507085 original size:23 final size:22
Alignment explanation
Indices: 6507052--6507138 Score: 95
Period size: 23 Copynumber: 3.8 Consensus size: 22
6507042 GGACTCACCA
6507052 CAGCTCGTATGAGCTTACCGTTT
1 CAGCTC-TATGAGCTTACCGTTT
* *
6507075 TAGCTCTTATGAGCTTACTGTTT
1 CAGCTC-TATGAGCTTACCGTTT
*
6507098 CAGCTCTACGGAGCTTACCG-TT
1 CAGCTCTA-TGAGCTTACCGTTT
*
6507120 CAGCTCGATAGAGCTTACC
1 CAGCTCTAT-GAGCTTACC
6507139 ATTTACTGGC
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
22 20 0.37
23 34 0.63
ACGTcount: A:0.20, C:0.26, G:0.21, T:0.33
Consensus pattern (22 bp):
CAGCTCTATGAGCTTACCGTTT
Found at i:6508079 original size:13 final size:13
Alignment explanation
Indices: 6508061--6508085 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6508051 ACATGTTTGG
6508061 ATATGAAATTGAT
1 ATATGAAATTGAT
6508074 ATATGAAATTGA
1 ATATGAAATTGA
6508086 CATTGAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (13 bp):
ATATGAAATTGAT
Found at i:6510927 original size:41 final size:41
Alignment explanation
Indices: 6510882--6510984 Score: 98
Period size: 41 Copynumber: 2.5 Consensus size: 41
6510872 CATCGGCATA
* *
6510882 AAGCCTACTAATCACAAATCCAGATATGATACACCAGCACG
1 AAGCCTACTAAGCACAAAGCCAGATATGATACACCAGCACG
* * * * * **
6510923 AAGCCTGCTAGGCATAAAGCCTGATCTGATACACCAGCATA
1 AAGCCTACTAAGCACAAAGCCAGATATGATACACCAGCACG
* * *
6510964 AAGCCTGCTAGGCACAGAGCC
1 AAGCCTACTAAGCACAAAGCC
6510985 TGAATATCAC
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.36, C:0.29, G:0.18, T:0.17
Consensus pattern (41 bp):
AAGCCTACTAAGCACAAAGCCAGATATGATACACCAGCACG
Found at i:6510985 original size:41 final size:41
Alignment explanation
Indices: 6510894--6510987 Score: 125
Period size: 41 Copynumber: 2.3 Consensus size: 41
6510884 GCCTACTAAT
* * * *
6510894 CACAAATCCAGATATGATACACCAGCACGAAGCCTGCTAGG
1 CACAAAGCCTGATCTGATACACCAGCACAAAGCCTGCTAGG
* *
6510935 CATAAAGCCTGATCTGATACACCAGCATAAAGCCTGCTAGG
1 CACAAAGCCTGATCTGATACACCAGCACAAAGCCTGCTAGG
*
6510976 CACAGAGCCTGA
1 CACAAAGCCTGA
6510988 ATATCACTGA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.35, C:0.29, G:0.20, T:0.16
Consensus pattern (41 bp):
CACAAAGCCTGATCTGATACACCAGCACAAAGCCTGCTAGG
Found at i:6513555 original size:23 final size:22
Alignment explanation
Indices: 6513500--6513555 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
6513490 TCGAATTGAG
* *
6513500 TAATTCAAATTTTAATTTCGAA
1 TAATTCAAATTTTAAATTCAAA
6513522 TCAAATT-AAATTTTACAATTCAAA
1 T--AATTCAAATTTTA-AATTCAAA
6513546 TAATTCAAAT
1 TAATTCAAAT
6513556 ATATGATTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
22 5 0.18
23 12 0.43
24 11 0.39
ACGTcount: A:0.46, C:0.11, G:0.02, T:0.41
Consensus pattern (22 bp):
TAATTCAAATTTTAAATTCAAA
Found at i:6513584 original size:15 final size:15
Alignment explanation
Indices: 6513560--6513589 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6513550 TCAAATATAT
6513560 GATTGGTGTAAATAC
1 GATTGGTGTAAATAC
*
6513575 GATTGTTGTAAATAC
1 GATTGGTGTAAATAC
6513590 AATTTTGCTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.37
Consensus pattern (15 bp):
GATTGGTGTAAATAC
Found at i:6518916 original size:2 final size:2
Alignment explanation
Indices: 6518905--6518938 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
6518895 AATTAGCTGG
6518905 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6518939 TAGTCATGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:6524998 original size:15 final size:16
Alignment explanation
Indices: 6524964--6524999 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
6524954 TAAATATTTA
*
6524964 ATATAAAGAAAATCAT
1 ATATAAAGAAAATAAT
6524980 ATATAAAGAAAA-AAT
1 ATATAAAGAAAATAAT
6524995 ATATA
1 ATATA
6525000 TCAAACAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (16 bp):
ATATAAAGAAAATAAT
Found at i:6527915 original size:30 final size:30
Alignment explanation
Indices: 6527879--6527940 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
6527869 TGTGGTAAAT
*
6527879 TTGACATAGTGAATAAAAGTTGAAGGAGGA
1 TTGACATAGTGAATAAAAATTGAAGGAGGA
6527909 TTGACATAGTGAATAAAAATTGAAGGAGGA
1 TTGACATAGTGAATAAAAATTGAAGGAGGA
6527939 TT
1 TT
6527941 ATGAAATGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.44, C:0.03, G:0.27, T:0.26
Consensus pattern (30 bp):
TTGACATAGTGAATAAAAATTGAAGGAGGA
Found at i:6537009 original size:24 final size:25
Alignment explanation
Indices: 6536973--6537020 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
6536963 AAAATAATTT
* *
6536973 AAATTAATCAGAGTTCGACTGAAAC
1 AAATAAATCAGAGTTCAACTGAAAC
*
6536998 AAATAAAT-AGAGTTTAACTGAAA
1 AAATAAATCAGAGTTCAACTGAAA
6537021 GATTATCTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.25
Consensus pattern (25 bp):
AAATAAATCAGAGTTCAACTGAAAC
Found at i:6537239 original size:76 final size:78
Alignment explanation
Indices: 6537138--6537295 Score: 302
Period size: 76 Copynumber: 2.1 Consensus size: 78
6537128 ATAAATATAA
6537138 TTAATTATTATTATATTTGAAAAATATAAATTTAATTTGATAAATGTTATTAATATGTGTTTTTT
1 TTAATTATTATTATATTTGAAAAATATAAATTTAATTTGATAAATGTTATTAATATGTGTTTTTT
6537203 TTAGAACTATATT
66 TTAGAACTATATT
6537216 TTAATTATTA-T-TATTTGAAAAATATAAATTTAATTTGATAAATGTTATTAATATGTGTTTTTT
1 TTAATTATTATTATATTTGAAAAATATAAATTTAATTTGATAAATGTTATTAATATGTGTTTTTT
6537279 TTAGAACTATATT
66 TTAGAACTATATT
6537292 TTAA
1 TTAA
6537296 GCTTAATAAC
Statistics
Matches: 80, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
76 69 0.86
77 1 0.01
78 10 0.12
ACGTcount: A:0.39, C:0.01, G:0.08, T:0.53
Consensus pattern (78 bp):
TTAATTATTATTATATTTGAAAAATATAAATTTAATTTGATAAATGTTATTAATATGTGTTTTTT
TTAGAACTATATT
Found at i:6541737 original size:14 final size:14
Alignment explanation
Indices: 6541714--6541753 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
6541704 ACAGAAAAGT
*
6541714 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
6541728 AAATCATTTTACGG
1 AAAACATTTTACAG
6541742 AAAACATTTTAC
1 AAAACATTTTAC
6541754 TGGCAAACAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:6541745 original size:34 final size:35
Alignment explanation
Indices: 6541679--6541745 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
6541669 CAAACACCAA
* *
6541679 AAAATATTTTCCAGTAAATTATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
6541714 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
6541746 CATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:6543061 original size:32 final size:32
Alignment explanation
Indices: 6543025--6543110 Score: 95
Period size: 33 Copynumber: 2.7 Consensus size: 32
6543015 ACTTTTTCGA
* *
6543025 AAAATATTTT-CAGGAAATCTGCCAAACAGCAG
1 AAAATATTTTACAGTAAATCT-CCAAACACCAG
*
6543057 AAAATATTTTACA-TAGATTCATCCAAACACCAG
1 AAAATATTTTACAGTA-AATC-TCCAAACACCAG
*
6543090 AAAATATTTTCCAGTAAATCT
1 AAAATATTTTACAGTAAATCT
6543111 TTCAGTAAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
32 12 0.27
33 30 0.67
34 3 0.07
ACGTcount: A:0.44, C:0.19, G:0.09, T:0.28
Consensus pattern (32 bp):
AAAATATTTTACAGTAAATCTCCAAACACCAG
Found at i:6552528 original size:22 final size:22
Alignment explanation
Indices: 6552500--6552550 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
6552490 NNNNNNNNNN
*
6552500 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAACGAAA
6552522 TTGAGAGAATTTTGGAACGAAA
1 TTGAGAGAATTTTGGAACGAAA
6552544 TTGAGAG
1 TTGAGAG
6552551 GATTAGAGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.39, C:0.02, G:0.31, T:0.27
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAACGAAA
Found at i:6553432 original size:61 final size:61
Alignment explanation
Indices: 6553307--6553432 Score: 137
Period size: 61 Copynumber: 2.1 Consensus size: 61
6553297 TCATAAATAC
* * * * * * * **
6553307 AAAATTTCAACAAATGTAGCCCTTAATATTTACAAAATTTGTCATTTTAGTTCTAATTTTA
1 AAAAATTCAACAAATGTAACCCTCAATATTTACAAAATCTGTCAATTTAATTCTAACTCAA
* *
6553368 AAAAATTCAATAAATTTAACCCTCAATATTTACAAAATCTGTCAATTTAA-TCTTAACTCAA
1 AAAAATTCAACAAATGTAACCCTCAATATTTACAAAATCTGTCAATTTAATTC-TAACTCAA
6553429 AAAA
1 AAAA
6553433 TTTAAAAAAT
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
60 2 0.04
61 51 0.96
ACGTcount: A:0.44, C:0.15, G:0.04, T:0.37
Consensus pattern (61 bp):
AAAAATTCAACAAATGTAACCCTCAATATTTACAAAATCTGTCAATTTAATTCTAACTCAA
Found at i:6554787 original size:2 final size:2
Alignment explanation
Indices: 6554780--6554816 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
6554770 TGGATTTGAA
6554780 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
6554817 TATGCCTGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:6573414 original size:30 final size:30
Alignment explanation
Indices: 6573380--6573441 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
6573370 CTTAACAAGA
6573380 AAATGCCTCTAAAAT-AATAAAAAAATTAAC
1 AAATGCCTCTAAAATAAAT-AAAAAATTAAC
* * *
6573410 AAATGCCTTTAAACTAAATACAAAATTAAC
1 AAATGCCTCTAAAATAAATAAAAAATTAAC
6573440 AA
1 AA
6573442 TAAAAATAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 25 0.89
31 3 0.11
ACGTcount: A:0.58, C:0.15, G:0.03, T:0.24
Consensus pattern (30 bp):
AAATGCCTCTAAAATAAATAAAAAATTAAC
Found at i:6581659 original size:2 final size:2
Alignment explanation
Indices: 6581652--6581690 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
6581642 ACATTAGATA
6581652 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6581691 AGTACCNNNN
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6581845 original size:29 final size:29
Alignment explanation
Indices: 6581803--6581861 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
6581793 AGTATCAAAT
6581803 AACGTATTAAACCATTAAAATTTAATTTA
1 AACGTATTAAACCATTAAAATTTAATTTA
6581832 AACGTATTAAACCATTAAAATTTAATTTA
1 AACGTATTAAACCATTAAAATTTAATTTA
6581861 A
1 A
6581862 CTTAAATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.37
Consensus pattern (29 bp):
AACGTATTAAACCATTAAAATTTAATTTA
Found at i:6586376 original size:30 final size:30
Alignment explanation
Indices: 6586337--6586394 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
6586327 ATGTTATGAA
* *
6586337 TTAATTGTAT-TTGATTTACTTTTGGCATAT
1 TTAAATGTATATTGATTGA-TTTTGGCATAT
6586367 TTAAATGTATATTGATTGATTTTGGCAT
1 TTAAATGTATATTGATTGATTTTGGCAT
6586395 CAATTTGACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 18 0.72
31 7 0.28
ACGTcount: A:0.26, C:0.05, G:0.16, T:0.53
Consensus pattern (30 bp):
TTAAATGTATATTGATTGATTTTGGCATAT
Found at i:6601990 original size:21 final size:21
Alignment explanation
Indices: 6601964--6602012 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
6601954 ATTCATAGTT
*
6601964 TTTTTTAATCTAAAATTTTGA
1 TTTTTTAATCTAAAATTTTAA
* *
6601985 TTTTTTATTGTAAAATTTTAA
1 TTTTTTAATCTAAAATTTTAA
*
6602006 TATTTTA
1 TTTTTTA
6602013 TTGTTTATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (21 bp):
TTTTTTAATCTAAAATTTTAA
Found at i:6602013 original size:21 final size:21
Alignment explanation
Indices: 6601974--6602016 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
6601964 TTTTTTAATC
* *
6601974 TAAAATTTTGATTTTTTATTG
1 TAAAATTTTAATATTTTATTG
6601995 TAAAATTTTAATATTTTATTG
1 TAAAATTTTAATATTTTATTG
6602016 T
1 T
6602017 TTATAACATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (21 bp):
TAAAATTTTAATATTTTATTG
Found at i:6608106 original size:14 final size:14
Alignment explanation
Indices: 6608087--6608116 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
6608077 AAAAGTAAAG
6608087 AGTATTTATAGAGC
1 AGTATTTATAGAGC
6608101 AGTATTTATAGAGC
1 AGTATTTATAGAGC
6608115 AG
1 AG
6608117 ATTAGAACTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (14 bp):
AGTATTTATAGAGC
Found at i:6611540 original size:3 final size:3
Alignment explanation
Indices: 6611532--6611560 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
6611522 ATATTAAGCC
6611532 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
6611561 TTGCAAATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:6628060 original size:48 final size:48
Alignment explanation
Indices: 6628002--6628098 Score: 131
Period size: 48 Copynumber: 2.0 Consensus size: 48
6627992 ACCAGTAATT
* * *
6628002 ATACGTAACATATAACATATACAGAGTCATATTAACTTACTCTTTTCA
1 ATACATAACATATAACACATACAGAGTCATATTAACTCACTCTTTTCA
* * * *
6628050 ATACATAACATATATCACGTACAGAGTTATATTAACTCCCTCTTTTCA
1 ATACATAACATATAACACATACAGAGTCATATTAACTCACTCTTTTCA
6628098 A
1 A
6628099 ATCCTTCCTG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (48 bp):
ATACATAACATATAACACATACAGAGTCATATTAACTCACTCTTTTCA
Found at i:6630681 original size:5 final size:5
Alignment explanation
Indices: 6630671--6630695 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
6630661 AAGTCTCATG
6630671 TATGC TATGC TATGC TATGC TATGC
1 TATGC TATGC TATGC TATGC TATGC
6630696 ACACGCCCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (5 bp):
TATGC
Found at i:6632641 original size:27 final size:25
Alignment explanation
Indices: 6632603--6632662 Score: 84
Period size: 27 Copynumber: 2.3 Consensus size: 25
6632593 TTATTAGGGA
*
6632603 TAAAATCGTCAAAATTTTACCGAGAGG
1 TAAAATTGTCAAAATTTTACCG-GA-G
*
6632630 TAAAATTGTCAAAATTTTACTGGAG
1 TAAAATTGTCAAAATTTTACCGGAG
6632655 TAAAATTG
1 TAAAATTG
6632663 AGATGAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 9 0.29
26 2 0.06
27 20 0.65
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.32
Consensus pattern (25 bp):
TAAAATTGTCAAAATTTTACCGGAG
Found at i:6634323 original size:26 final size:28
Alignment explanation
Indices: 6634291--6634344 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
6634281 TATAATTTTT
6634291 ATAATTTTTA-A-TATTTAATTTTAAAA
1 ATAATTTTTATAGTATTTAATTTTAAAA
* *
6634317 ATAATTTTTATAGTTTTTTATTTTAAAA
1 ATAATTTTTATAGTATTTAATTTTAAAA
6634345 TTTAAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 10 0.42
27 1 0.04
28 13 0.54
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (28 bp):
ATAATTTTTATAGTATTTAATTTTAAAA
Found at i:6634328 original size:35 final size:35
Alignment explanation
Indices: 6634282--6634352 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 35
6634272 ATATTGTGTT
*
6634282 ATAATTTTTATAATTTTTAATATTT-AATTTTAAAA
1 ATAATTTTTATAATTTTTAAT-TTTAAAATTTAAAA
* *
6634317 ATAATTTTTATAGTTTTTTATTTTAAAATTTAAAA
1 ATAATTTTTATAATTTTTAATTTTAAAATTTAAAA
6634352 A
1 A
6634353 AAGTTAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
34 3 0.09
35 29 0.91
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (35 bp):
ATAATTTTTATAATTTTTAATTTTAAAATTTAAAA
Found at i:6634335 original size:45 final size:46
Alignment explanation
Indices: 6634241--6634347 Score: 118
Period size: 45 Copynumber: 2.4 Consensus size: 46
6634231 ACATATAACA
6634241 TTTATTAATTTTTAAAATTTTAAATTAAAAAATATTGTGTTATAATT
1 TTTA-TAATTTTTAAAATTTTAAATTAAAAAATATTGTGTTATAATT
* * * *
6634288 TTTATAATTTTTAATA-TTTAATTTTAAAAATAATT-T-TTATAGTT
1 TTTATAATTTTTAAAATTTTAAATTAAAAAAT-ATTGTGTTATAATT
6634332 TTT-T-A-TTTTAAAATTT
1 TTTATAATTTTTAAAATTT
6634348 AAAAAAAGTT
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
41 7 0.13
42 3 0.06
43 1 0.02
44 10 0.19
45 14 0.26
46 14 0.26
47 4 0.08
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (46 bp):
TTTATAATTTTTAAAATTTTAAATTAAAAAATATTGTGTTATAATT
Found at i:6638620 original size:26 final size:26
Alignment explanation
Indices: 6638582--6638633 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
6638572 ACTTAACAGA
*
6638582 TCTTTTAAGGAGACGACCCCTTGATG
1 TCTTTTAAAGAGACGACCCCTTGATG
**
6638608 TCTTTTAAAGAGACGACTTCTTGATG
1 TCTTTTAAAGAGACGACCCCTTGATG
6638634 CCTTCAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTTTTAAAGAGACGACCCCTTGATG
Found at i:6647539 original size:17 final size:17
Alignment explanation
Indices: 6647514--6647553 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 17
6647504 AAAAGAATAC
6647514 CAAAGAGAAAAGAA-AGAA
1 CAAA-AGAAAAGAAGA-AA
6647532 CAAAAGAAAAGAAGAAA
1 CAAAAGAAAAGAAGAAA
6647549 CAAAA
1 CAAAA
6647554 TAAGAGCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.75, C:0.07, G:0.17, T:0.00
Consensus pattern (17 bp):
CAAAAGAAAAGAAGAAA
Found at i:6651681 original size:26 final size:27
Alignment explanation
Indices: 6651619--6651684 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
6651609 ATTTTACTTC
6651619 AGTAAAATTTTGATAATTTTACCCCCT
1 AGTAAAATTTTGATAATTTTACCCCCT
* *
6651646 AATAATATTTTGA-AGATTTTA-CCCCT
1 AGTAAAATTTTGATA-ATTTTACCCCCT
*
6651672 GGTAAAATTTTGA
1 AGTAAAATTTTGA
6651685 GAAAATTCAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
26 16 0.48
27 17 0.52
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.41
Consensus pattern (27 bp):
AGTAAAATTTTGATAATTTTACCCCCT
Found at i:6652404 original size:41 final size:42
Alignment explanation
Indices: 6652306--6652415 Score: 125
Period size: 42 Copynumber: 2.6 Consensus size: 42
6652296 CGCTTTTATG
* *
6652306 AAAATCCTTCCAGTTGGAAGCGTTTTCAGGTGAAATTCAGAA
1 AAAACCCTTCCAGTTGGAAGCATTTTCAGGTGAAATTCAGAA
* * * * *
6652348 AAAACACGTCTAGTTGTAAGCATTTTCAGGTG-ATTTGCA-AA
1 AAAACCCTTCCAGTTGGAAGCATTTTCAGGTGAAATT-CAGAA
*
6652389 AAAACCCTTCCAGTTGGAAGCACTTTC
1 AAAACCCTTCCAGTTGGAAGCATTTTC
6652416 TGCCACATCA
Statistics
Matches: 55, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
41 27 0.49
42 28 0.51
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (42 bp):
AAAACCCTTCCAGTTGGAAGCATTTTCAGGTGAAATTCAGAA
Found at i:6655427 original size:16 final size:17
Alignment explanation
Indices: 6655387--6655427 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
6655377 ATAGAATAAA
6655387 TTTAATTTTAATTGTGAT
1 TTTAA-TTTAATTGTGAT
*
6655405 TTT-ATTTAATTTTG-T
1 TTTAATTTAATTGTGAT
6655420 TTTAATTT
1 TTTAATTT
6655428 GTTTAATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 4 0.19
16 13 0.62
17 1 0.05
18 3 0.14
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.68
Consensus pattern (17 bp):
TTTAATTTAATTGTGAT
Found at i:6655868 original size:32 final size:32
Alignment explanation
Indices: 6655820--6655882 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
6655810 CAGTGAATTA
*
6655820 AAAAAATAAAAATGATGTAAGATGATATCATT
1 AAAAAATAAAAATGATGTAAGATAATATCATT
* *
6655852 AAAAAATACAAGTGATGTAAGATAATATCAT
1 AAAAAATAAAAATGATGTAAGATAATATCAT
6655883 GGAGAAACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.56, C:0.05, G:0.13, T:0.27
Consensus pattern (32 bp):
AAAAAATAAAAATGATGTAAGATAATATCATT
Found at i:6656476 original size:39 final size:38
Alignment explanation
Indices: 6656380--6656481 Score: 107
Period size: 39 Copynumber: 2.6 Consensus size: 38
6656370 ATACAAAAAA
* *
6656380 TTATTTAATTATATAAATTATTACAAATTTCATAATAT
1 TTATATAATTATATAAAATATTACAAATTTCATAATAT
* * * *
6656418 TTATAATAATTGTATAAAATATTACAATTTTCGTAATTCTT
1 TTAT-ATAATTATATAAAATATTACAAATTTCATAA-T-AT
*
6656459 TTATGTAATTATA-AAAATATTAC
1 TTATATAATTATATAAAATATTAC
6656482 TGAATTATAT
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
38 4 0.08
39 36 0.68
40 8 0.15
41 5 0.09
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (38 bp):
TTATATAATTATATAAAATATTACAAATTTCATAATAT
Found at i:6656506 original size:19 final size:19
Alignment explanation
Indices: 6656465--6656506 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
6656455 TCTTTTATGT
*
6656465 AATTATAAAAATATTACTG
1 AATTATAAAAATATTACTA
*
6656484 AATTATATAAATTATTA-TA
1 AATTATA-AAAATATTACTA
6656503 AATT
1 AATT
6656507 TGATTATATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
AATTATAAAAATATTACTA
Found at i:6656766 original size:9 final size:10
Alignment explanation
Indices: 6656736--6656770 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
6656726 TAATATTGTA
6656736 TTTATCAGTT
1 TTTATCAGTT
6656746 TTTATCAGTT
1 TTTATCAGTT
* *
6656756 TTTATTATTT
1 TTTATCAGTT
6656766 TTTAT
1 TTTAT
6656771 TCTAAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.20, C:0.06, G:0.06, T:0.69
Consensus pattern (10 bp):
TTTATCAGTT
Found at i:6669364 original size:13 final size:15
Alignment explanation
Indices: 6669346--6669378 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
6669336 ACAATGGGTG
6669346 AAAAAAAATT-ATA-
1 AAAAAAAATTGATAT
6669359 AAAAAAAATTGATAT
1 AAAAAAAATTGATAT
6669374 AAAAA
1 AAAAA
6669379 TTAAATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.56
14 3 0.17
15 5 0.28
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (15 bp):
AAAAAAAATTGATAT
Found at i:6669748 original size:24 final size:25
Alignment explanation
Indices: 6669716--6669762 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
6669706 TTTTATGATT
*
6669716 ATTTTTTTATA-CAAATTTTTTATG
1 ATTTTTTTAAAGCAAATTTTTTATG
*
6669740 ATTTTTTTAAAGCAGATTTTTTA
1 ATTTTTTTAAAGCAAATTTTTTA
6669763 ATGAGTAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.60
Consensus pattern (25 bp):
ATTTTTTTAAAGCAAATTTTTTATG
Found at i:6673782 original size:22 final size:22
Alignment explanation
Indices: 6673730--6673784 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
6673720 TAAAGAAATA
*
6673730 AAAAGAAAAAATTAAATTGTTC
1 AAAAGAAAAAATTAAATTGCTC
* *
6673752 AACATAAAAAATT-AATTGCTC
1 AAAAGAAAAAATTAAATTGCTC
6673773 AAAACGAAAAAA
1 AAAA-GAAAAAA
6673785 ATATAGGGAC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.62, C:0.09, G:0.07, T:0.22
Consensus pattern (22 bp):
AAAAGAAAAAATTAAATTGCTC
Found at i:6676425 original size:29 final size:29
Alignment explanation
Indices: 6676373--6676447 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
6676363 CGGACTGACG
* *
6676373 CATGGTCGTGTGGCTCATATGGCC-AGGCA
1 CATGGTCGTGTGGCTCACACGGCCTA-GCA
6676402 CATGGTCGTGTGGCTCACACGGCCTAGCA
1 CATGGTCGTGTGGCTCACACGGCCTAGCA
** *
6676431 CAAAGTCATGTGGCTCA
1 CATGGTCGTGTGGCTCA
6676448 GCCTGGGCAG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 39 0.98
30 1 0.03
ACGTcount: A:0.20, C:0.27, G:0.31, T:0.23
Consensus pattern (29 bp):
CATGGTCGTGTGGCTCACACGGCCTAGCA
Found at i:6677030 original size:17 final size:16
Alignment explanation
Indices: 6676977--6677033 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 16
6676967 AATCTAGAGT
6676977 AAAAGAA-AGAAAAGAA
1 AAAAGAAGAG-AAAGAA
*
6676993 AAAAAAAG-GAAAGGGAA
1 AAAAGAAGAGAAA--GAA
6677010 AAAAGAAGAGAAAGAA
1 AAAAGAAGAGAAAGAA
6677026 TAAAAGAA
1 -AAAAGAA
6677034 CGTTTAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
15 3 0.09
16 10 0.29
17 17 0.50
18 4 0.12
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (16 bp):
AAAAGAAGAGAAAGAA
Found at i:6688676 original size:41 final size:41
Alignment explanation
Indices: 6688627--6688720 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
6688617 ATCGGCTTTT
6688627 AGCCTGCTAGACTTATAGTCCGAAATGTTTCACCGGCATCA
1 AGCCTGCTAGACTTATAGTCCGAAATGTTTCACCGGCATCA
* *
6688668 AGCTTGCTAGCCTTATAGTCCGAAATGTTTCACCGGCATCA
1 AGCCTGCTAGACTTATAGTCCGAAATGTTTCACCGGCATCA
6688709 AGCCTGCTAGAC
1 AGCCTGCTAGAC
6688721 ATAAAGTCTG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.27
Consensus pattern (41 bp):
AGCCTGCTAGACTTATAGTCCGAAATGTTTCACCGGCATCA
Found at i:6688742 original size:41 final size:41
Alignment explanation
Indices: 6688627--6688745 Score: 123
Period size: 41 Copynumber: 2.9 Consensus size: 41
6688617 ATCGGCTTTT
* * * *
6688627 AGCCTGCTAGACTTATAGTCCGAAATGTTTCACCGGCATCA
1 AGCCTGCTAGACATAAAGTCCGAAATATCTCACCGGCATCA
* * * * * *
6688668 AGCTTGCTAGCCTTATAGTCCGAAATGTTTCACCGGCATCA
1 AGCCTGCTAGACATAAAGTCCGAAATATCTCACCGGCATCA
*
6688709 AGCCTGCTAGACATAAAGTCTG-AATCATCTCACCGGC
1 AGCCTGCTAGACATAAAGTCCGAAAT-ATCTCACCGGC
6688746 GATAAAGCTT
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
40 3 0.04
41 65 0.96
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (41 bp):
AGCCTGCTAGACATAAAGTCCGAAATATCTCACCGGCATCA
Found at i:6703545 original size:27 final size:27
Alignment explanation
Indices: 6703506--6703569 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
6703496 AAGCAATTCG
6703506 CTAGTCA-CATGTCCACCAGGCAG-TCTA
1 CTAGTCATC-TGTCCACCAGGCAGCTC-A
6703533 CTAGTCATCTGTCCACCAGGCAGCTCA
1 CTAGTCATCTGTCCACCAGGCAGCTCA
*
6703560 CCAGTCATCT
1 CTAGTCATCT
6703570 ATTCTACGGT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
27 31 0.91
28 3 0.09
ACGTcount: A:0.23, C:0.36, G:0.17, T:0.23
Consensus pattern (27 bp):
CTAGTCATCTGTCCACCAGGCAGCTCA
Found at i:6705097 original size:81 final size:81
Alignment explanation
Indices: 6704962--6705129 Score: 309
Period size: 81 Copynumber: 2.1 Consensus size: 81
6704952 ATCTTGGCAA
* *
6704962 ATTGAGTTAATTCTTAGGTATAGAGGCATCTTATACTTCTACTAGTTTGTTTCTTTCTTAAAGGA
1 ATTGAGTTAATTCTTAGGTATAGAGGCACCTTATACTTCTACTAGTTTGTTTCTTTCTCAAAGGA
*
6705027 ATTACATAGATGATTT
66 AATACATAGATGATTT
6705043 ATTGAGTTAATTCTTAGGTATAGAGGCACCTTATACTTCTACTAGTTTGTTTCTTTCTCAAAGGA
1 ATTGAGTTAATTCTTAGGTATAGAGGCACCTTATACTTCTACTAGTTTGTTTCTTTCTCAAAGGA
6705108 AATACATAGATGATTT
66 AATACATAGATGATTT
6705124 ATTGAG
1 ATTGAG
6705130 GAAGGCTCAT
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
81 84 1.00
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (81 bp):
ATTGAGTTAATTCTTAGGTATAGAGGCACCTTATACTTCTACTAGTTTGTTTCTTTCTCAAAGGA
AATACATAGATGATTT
Found at i:6705151 original size:81 final size:81
Alignment explanation
Indices: 6704962--6705151 Score: 222
Period size: 81 Copynumber: 2.3 Consensus size: 81
6704952 ATCTTGGCAA
* * * * * * *
6704962 ATTGAGTTAATTCTTAGGTATAGAGGCATCTTATACTTCTACTAGTTTGTTTCTTTCTTAAAGGA
1 ATTGAGTGAACTCATAGGCATACAGGCACCTTATACTTCTACTAGTTTGTTTCTTTCTCAAAGGA
*
6705027 ATTACATAGATGATTT
66 AATACATAGATGATTT
* * * * *
6705043 ATTGAGTTAATTCTTAGGTATAGAGGCACCTTATACTTCTACTAGTTTGTTTCTTTCTCAAAGGA
1 ATTGAGTGAACTCATAGGCATACAGGCACCTTATACTTCTACTAGTTTGTTTCTTTCTCAAAGGA
6705108 AATACATAGATGATTT
66 AATACATAGATGATTT
*
6705124 ATTGAG-GAAGGCTCATATGCAT-CAGGCA
1 ATTGAGTGAA--CTCATAGGCATACAGGCA
6705152 AAAGGTACTC
Statistics
Matches: 98, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
80 2 0.02
81 89 0.91
82 7 0.07
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.39
Consensus pattern (81 bp):
ATTGAGTGAACTCATAGGCATACAGGCACCTTATACTTCTACTAGTTTGTTTCTTTCTCAAAGGA
AATACATAGATGATTT
Found at i:6708313 original size:2 final size:2
Alignment explanation
Indices: 6708306--6708331 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6708296 TATTAAAGCT
6708306 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
6708332 CATGTATGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6719178 original size:15 final size:16
Alignment explanation
Indices: 6719155--6719185 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
6719145 TTTAGTATTA
6719155 TATATATTTAAAAATT
1 TATATATTTAAAAATT
6719171 TATA-ATTTAAAAATT
1 TATATATTTAAAAATT
6719186 ACATCGATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TATATATTTAAAAATT
Found at i:6724367 original size:21 final size:21
Alignment explanation
Indices: 6724343--6724396 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
6724333 ATTTCTTTTG
6724343 AACCTCTGCTTCTCGGGCTGC
1 AACCTCTGCTTCTCGGGCTGC
*
6724364 AACCTCTACTTCTCGGGCTGC
1 AACCTCTGCTTCTCGGGCTGC
*
6724385 AGCCTCTGCTTC
1 AACCTCTGCTTC
6724397 CCTCGCTGCC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.11, C:0.39, G:0.20, T:0.30
Consensus pattern (21 bp):
AACCTCTGCTTCTCGGGCTGC
Found at i:6732619 original size:17 final size:17
Alignment explanation
Indices: 6732585--6732618 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
6732575 TGGGAATTAC
*
6732585 ATTTTTTTTAATTTAAA
1 ATTTTATTTAATTTAAA
6732602 ATTTTATTT-ATTTAAA
1 ATTTTATTTAATTTAAA
6732618 A
1 A
6732619 ACATTAGTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTTTATTTAATTTAAA
Found at i:6733736 original size:42 final size:38
Alignment explanation
Indices: 6733657--6733738 Score: 101
Period size: 38 Copynumber: 2.1 Consensus size: 38
6733647 TTGGTTTTAT
*
6733657 AAATAAGATAATTATTAATTAAAAATTAAAAAACTTGA
1 AAATAAGATAATTATTAATTAAAAATAAAAAAACTTGA
* *
6733695 AAATAATATATTTATTAATTAAAATAATAAAAAAAAGCTTGA
1 AAATAAGATAATTATTAATT-AAA-AAT-AAAAAAA-CTTGA
6733737 AA
1 AA
6733739 CAACATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
38 18 0.49
39 3 0.08
40 3 0.08
41 6 0.16
42 7 0.19
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (38 bp):
AAATAAGATAATTATTAATTAAAAATAAAAAAACTTGA
Done.