Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 110 of 230
Found at i:31875483 original size:25 final size:25
Alignment explanation
Indices: 31875455--31875502 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
31875445 TATGCACTTT
**
31875455 ATTTTAATGTTTTATATTTATTCAC
1 ATTTTAATAATTTATATTTATTCAC
* *
31875480 ATTTTTATAATTTCTATTTATTC
1 ATTTTAATAATTTATATTTATTC
31875503 TTATTTTGTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.27, C:0.08, G:0.02, T:0.62
Consensus pattern (25 bp):
ATTTTAATAATTTATATTTATTCAC
Found at i:31877269 original size:14 final size:14
Alignment explanation
Indices: 31877250--31877278 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
31877240 GGGCTTATTC
31877250 ATAAAAAGTAAAAA
1 ATAAAAAGTAAAAA
31877264 ATAAAAAGTAAAAA
1 ATAAAAAGTAAAAA
31877278 A
1 A
31877279 AAAGATGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (14 bp):
ATAAAAAGTAAAAA
Found at i:31877292 original size:16 final size:16
Alignment explanation
Indices: 31877273--31877308 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
31877263 AATAAAAAGT
31877273 AAAAAAAAAGATGAAC
1 AAAAAAAAAGATGAAC
31877289 AAAAAAAAAGATGAAC
1 AAAAAAAAAGATGAAC
31877305 AAAA
1 AAAA
31877309 TATTTGATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.78, C:0.06, G:0.11, T:0.06
Consensus pattern (16 bp):
AAAAAAAAAGATGAAC
Found at i:31898565 original size:78 final size:79
Alignment explanation
Indices: 31898465--31898671 Score: 303
Period size: 78 Copynumber: 2.6 Consensus size: 79
31898455 TCCTCGTTCA
* * * *
31898465 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AATGCCTTCGGGAC-TAACCCGGAT
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAACCCGGAT
31898528 TTAACAACTCGCACG
65 TTAACAACTCGCACG
* *
31898543 AATGCCTTCGGGACTTAACCCGGATTTA-AAACTCGCACGAATGCCTTCGGGCTTAACCCGGATT
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGGCTTAACCCGGATT
*
31898607 TAATAACTCGCACG
66 TAACAACTCGCACG
* *
31898621 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGG
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGG
31898672 ATCTTAGTCC
Statistics
Matches: 116, Mismatches: 10, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
77 9 0.08
78 89 0.77
79 18 0.16
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (79 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGGCTTAACCCGGATT
TAACAACTCGCACG
Found at i:31898657 original size:40 final size:40
Alignment explanation
Indices: 31898465--31898724 Score: 298
Period size: 40 Copynumber: 6.6 Consensus size: 40
31898455 TCCTCGTTCA
* * * * *
31898465 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
31898504 AATGCCTTCGGGAC-TAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
31898543 AATGCCTTCGGGACTTAACCCGGATTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
31898582 AATGCCTTCGGG-CTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
31898621 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * *
31898661 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
31898701 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
31898725 CAGCATTCAA
Statistics
Matches: 196, Mismatches: 18, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
38 35 0.18
39 75 0.38
40 78 0.40
41 8 0.04
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:31898733 original size:41 final size:41
Alignment explanation
Indices: 31898656--31898733 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
31898646 TTAGTATCTC
* * *
31898656 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
31898697 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
31898734 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:31905631 original size:120 final size:119
Alignment explanation
Indices: 31905409--31905671 Score: 316
Period size: 120 Copynumber: 2.2 Consensus size: 119
31905399 TCCTCGTTCA
* * **
31905409 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGATT
1 AATGCCTTCGGGACTTAGCCCGGATTTAACAACTCACACAATGCCTTCGGGACTTAACCCGGATT
* * * *
31905474 TAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTA-ACAAC-TCGCAC
66 TAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATATAC-ACTTAGCAC
* *
31905527 GAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGA
1 -AATGCCTTCGGGACTTAGCCCGGATTTAACAACTCACAC-AATGCCTTCGGGACTTAACCCGGA
** * ** *
31905592 TTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
64 TTTAACAACTCGCACAAAGGCCTTCGGGA-CTTAACCCGGATATATACACTTAGCAC
*
31905648 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
31905672 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
119 36 0.30
120 80 0.66
121 6 0.05
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (119 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAACAACTCACACAATGCCTTCGGGACTTAACCCGGATT
TAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATATACACTTAGCAC
Found at i:31905632 original size:40 final size:40
Alignment explanation
Indices: 31905409--31905618 Score: 314
Period size: 40 Copynumber: 5.3 Consensus size: 40
31905399 TCCTCGTTCA
* * * ** *
31905409 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
31905448 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
31905488 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
31905528 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
** * *
31905568 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
31905608 AAGGCCTTCGG
1 AATGCCTTCGG
31905619 ATCTTAGTCC
Statistics
Matches: 159, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 33 0.21
40 126 0.79
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:31905655 original size:80 final size:80
Alignment explanation
Indices: 31905412--31905671 Score: 267
Period size: 80 Copynumber: 3.3 Consensus size: 80
31905402 TCGTTCAAAT
* * * ** * * *
31905412 GCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AATGCCTTCGGGACTTAACCCGGATTTA
1 GCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
* *
31905476 ACAACTCGCACGAAT
66 ACAACTAGCACGAAA
* * *
31905491 GCCTTCGGGACTTAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTA
1 GCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
* *
31905556 ACAACTCGCACGAAT
66 ACAACTAGCACGAAA
** * **
31905571 GCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAGTCCGGATAT
1 GCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGA-CTTAACCCGGATAT
*
31905635 ATTC-ACTTAGCAC-AAA
65 A-ACAAC-TAGCACGAAA
*
31905651 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
31905672 CAGCATTCAA
Statistics
Matches: 159, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
79 33 0.21
80 120 0.75
81 6 0.04
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
ACAACTAGCACGAAA
Found at i:31905680 original size:41 final size:41
Alignment explanation
Indices: 31905603--31905680 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
31905593 TTAGTATCTC
* * *
31905603 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
31905644 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
31905681 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:31911995 original size:28 final size:28
Alignment explanation
Indices: 31911932--31912082 Score: 205
Period size: 28 Copynumber: 5.4 Consensus size: 28
31911922 ATATTAAGTC
*
31911932 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
31911959 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* *
31911987 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTATATAATCAAACT
* *
31912015 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
31912043 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
31912072 CGCACACTTAG
1 CGCACACTTAG
31912083 CGCCAATCTC
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 22 0.19
28 76 0.67
29 15 0.13
ACGTcount: A:0.32, C:0.28, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:31914168 original size:11 final size:10
Alignment explanation
Indices: 31914152--31914181 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
31914142 TTCGTAACGT
31914152 AAAAAAAAGTC
1 AAAAAAAA-TC
31914163 AAAAAAAATC
1 AAAAAAAATC
31914173 AAAAAAAAT
1 AAAAAAAAT
31914182 TGAGTTGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.58
11 8 0.42
ACGTcount: A:0.80, C:0.07, G:0.03, T:0.10
Consensus pattern (10 bp):
AAAAAAAATC
Found at i:31915444 original size:48 final size:47
Alignment explanation
Indices: 31915365--31915470 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
31915355 GAGTGTCATG
*
31915365 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
31915413 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
31915461 GAAAAAGAAA
1 GAAAAAGAAA
31915471 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:31917187 original size:20 final size:20
Alignment explanation
Indices: 31917141--31917187 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
31917131 AGCTCGTTTC
*
31917141 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
31917161 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
31917181 CAGCTCA
1 CAGCTCA
31917188 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:31919485 original size:16 final size:16
Alignment explanation
Indices: 31919464--31919495 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
31919454 TAATGTGTTT
31919464 TGCTGCTGTTGTTTAA
1 TGCTGCTGTTGTTTAA
31919480 TGCTGCTGTTGTTTAA
1 TGCTGCTGTTGTTTAA
31919496 ATGCAGAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.25, T:0.50
Consensus pattern (16 bp):
TGCTGCTGTTGTTTAA
Found at i:31927889 original size:10 final size:10
Alignment explanation
Indices: 31927874--31927911 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
31927864 TTGGGTTAAG
31927874 ATTGAGCTGA
1 ATTGAGCTGA
31927884 ATTGAGCTCGA
1 ATTGAGCT-GA
31927895 A-TGAGCTGA
1 ATTGAGCTGA
*
31927904 CTTGAGCT
1 ATTGAGCT
31927912 CGAGTGAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 20 0.80
11 3 0.12
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (10 bp):
ATTGAGCTGA
Found at i:31927899 original size:20 final size:20
Alignment explanation
Indices: 31927876--31927922 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
31927866 GGGTTAAGAT
31927876 TGAGCTGAATTGAGCTCGAA
1 TGAGCTGAATTGAGCTCGAA
* *
31927896 TGAGCTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
31927916 TGAGCTG
1 TGAGCTG
31927923 GAAACGAGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.23, C:0.17, G:0.34, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:31929455 original size:12 final size:12
Alignment explanation
Indices: 31929438--31929462 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31929428 TTTCACTCTT
31929438 CTCTTTTTCAAA
1 CTCTTTTTCAAA
31929450 CTCTTTTTCAAA
1 CTCTTTTTCAAA
31929462 C
1 C
31929463 CCTCTCTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.28, G:0.00, T:0.48
Consensus pattern (12 bp):
CTCTTTTTCAAA
Found at i:31931707 original size:13 final size:13
Alignment explanation
Indices: 31931664--31931715 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
31931654 AAAGAGTTCG
*
31931664 AAAAAAAAATCCGA
1 AAAAAAAAAT-TGA
* *
31931678 AAAAAAAAGA-AGG
1 AAAAAAAA-ATTGA
31931691 AAAAAAAAATTGA
1 AAAAAAAAATTGA
31931704 AAAAAAAAATTG
1 AAAAAAAAATTG
31931716 CATACGGTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
12 1 0.03
13 22 0.69
14 8 0.25
15 1 0.03
ACGTcount: A:0.75, C:0.04, G:0.12, T:0.10
Consensus pattern (13 bp):
AAAAAAAAATTGA
Found at i:31931764 original size:1 final size:1
Alignment explanation
Indices: 31931758--31931784 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
31931748 AAATATCCGT
31931758 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
31931785 GAGTCTGGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:31931880 original size:22 final size:19
Alignment explanation
Indices: 31931855--31931898 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
31931845 CCTTTGAGTG
31931855 AAATTTCACACTATTAAAAAAA
1 AAATTTC-CA-TA-TAAAAAAA
*
31931877 AAATTTCGATATAAAAAAA
1 AAATTTCCATATAAAAAAA
31931896 AAA
1 AAA
31931899 GTGTTTCGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 11 0.52
20 2 0.10
21 1 0.05
22 7 0.33
ACGTcount: A:0.64, C:0.09, G:0.02, T:0.25
Consensus pattern (19 bp):
AAATTTCCATATAAAAAAA
Found at i:31932781 original size:16 final size:16
Alignment explanation
Indices: 31932760--31932797 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
31932750 GTGAGCGAGA
31932760 AAATGAAAAGAAAAAG
1 AAATGAAAAGAAAAAG
31932776 AAATG-AAAGAAAAAG
1 AAATGAAAAGAAAAAG
31932791 AAGATGA
1 AA-ATGA
31932798 GTGTGAGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.08
Consensus pattern (16 bp):
AAATGAAAAGAAAAAG
Found at i:31932912 original size:17 final size:18
Alignment explanation
Indices: 31932880--31932913 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
31932870 AAAAGAGAGT
*
31932880 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
31932898 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
31932914 GGAGTGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:31936029 original size:11 final size:11
Alignment explanation
Indices: 31936014--31936048 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
31936004 TTTTTGCTCG
31936014 ATTTTTTTTCA
1 ATTTTTTTTCA
* *
31936025 CTTTTTTTTGA
1 ATTTTTTTTCA
31936036 ATTTTTTTTCA
1 ATTTTTTTTCA
31936047 AT
1 AT
31936049 CAATTTTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.17, C:0.09, G:0.03, T:0.71
Consensus pattern (11 bp):
ATTTTTTTTCA
Found at i:31937563 original size:10 final size:10
Alignment explanation
Indices: 31937548--31937585 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
31937538 TTGGGTTAAG
31937548 ATTGAGCTGA
1 ATTGAGCTGA
31937558 ATTGAGCTCGA
1 ATTGAGCT-GA
31937569 A-TGAGCTGA
1 ATTGAGCTGA
*
31937578 CTTGAGCT
1 ATTGAGCT
31937586 CGAGTGAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 20 0.80
11 3 0.12
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (10 bp):
ATTGAGCTGA
Found at i:31937573 original size:20 final size:20
Alignment explanation
Indices: 31937550--31937596 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
31937540 GGGTTAAGAT
31937550 TGAGCTGAATTGAGCTCGAA
1 TGAGCTGAATTGAGCTCGAA
* *
31937570 TGAGCTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
31937590 TGAGCTG
1 TGAGCTG
31937597 GAAACGAGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.23, C:0.17, G:0.34, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:31942250 original size:20 final size:19
Alignment explanation
Indices: 31942223--31942276 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 19
31942213 ATTTTTTTAA
31942223 TTTTTATTTAATTTTAACT
1 TTTTTATTTAATTTTAACT
** *
31942242 TTTTCTATTTTTTTTTTACT
1 TTTT-TATTTAATTTTAACT
*
31942262 TTTTTACTTAATTTT
1 TTTTTATTTAATTTT
31942277 TTGTGGAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTTATTTAATTTTAACT
Found at i:31950001 original size:12 final size:13
Alignment explanation
Indices: 31949969--31950002 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
31949959 GCTGTTTCAA
*
31949969 TTTCTTTATTTAT
1 TTTCTTTGTTTAT
31949982 TTTCTTTGTTTAT
1 TTTCTTTGTTTAT
31949995 TTT-TTTGT
1 TTTCTTTGT
31950003 GCCGATTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.09, C:0.06, G:0.06, T:0.79
Consensus pattern (13 bp):
TTTCTTTGTTTAT
Found at i:31953965 original size:20 final size:20
Alignment explanation
Indices: 31953942--31953988 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
31953932 GGGTTAAGAT
31953942 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTTGAA
* * *
31953962 TGAGTTGACTTGAGCTTGAG
1 TGAGCTGAATTGAGCTTGAA
31953982 TGAGCTG
1 TGAGCTG
31953989 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.11, G:0.34, T:0.32
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTTGAA
Found at i:31958549 original size:20 final size:20
Alignment explanation
Indices: 31958503--31958549 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
31958493 AGCTCGTTTC
*
31958503 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
31958523 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
31958543 CAGCTCA
1 CAGCTCA
31958550 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:31962502 original size:23 final size:22
Alignment explanation
Indices: 31962451--31962502 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
31962441 CCTCGTCTTT
*
31962451 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
31962473 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
31962496 TTCTTTT
1 TTCTTTT
31962503 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:31969129 original size:17 final size:17
Alignment explanation
Indices: 31969107--31969141 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
31969097 AAAGAAAGAC
31969107 AGAAAAAGA-AATCGAAA
1 AGAAAAAGAGAAT-GAAA
31969124 AGAAAAAGAGAATGAAA
1 AGAAAAAGAGAATGAAA
31969141 A
1 A
31969142 AGAGCAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.82
18 3 0.18
ACGTcount: A:0.71, C:0.03, G:0.20, T:0.06
Consensus pattern (17 bp):
AGAAAAAGAGAATGAAA
Found at i:31978052 original size:21 final size:21
Alignment explanation
Indices: 31978028--31978086 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 21
31978018 TTAAAACAAG
31978028 TGAAGAAAAAGAAAAAGAGAA
1 TGAAGAAAAAGAAAAAGAGAA
* *
31978049 TGAA-AAAGAGCAAAAAGAGAT
1 TGAAGAAAAAG-AAAAAGAGAA
31978070 TGAGAGTGAAAAAGAAA
1 TGA-A--GAAAAAGAAA
31978087 TTGAAGAAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
20 5 0.17
21 16 0.53
22 1 0.03
24 3 0.10
25 5 0.17
ACGTcount: A:0.64, C:0.02, G:0.25, T:0.08
Consensus pattern (21 bp):
TGAAGAAAAAGAAAAAGAGAA
Found at i:31978065 original size:27 final size:27
Alignment explanation
Indices: 31978033--31978084 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
31978023 ACAAGTGAAG
31978033 AAAAAGAAAAAGAGAATGAAAAAGAGC
1 AAAAAGAAAAAGAGAATGAAAAAGAGC
* ** *
31978060 AAAAAGAGATTGAGAGTGAAAAAGA
1 AAAAAGAAAAAGAGAATGAAAAAGA
31978085 AATTGAAGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.65, C:0.02, G:0.25, T:0.08
Consensus pattern (27 bp):
AAAAAGAAAAAGAGAATGAAAAAGAGC
Found at i:31986071 original size:30 final size:30
Alignment explanation
Indices: 31986037--31986133 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
31986027 AGCTCACTCC
31986037 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
31986067 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
31986097 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
31986127 TAGCTCA
1 TAGCTCA
31986134 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:31991121 original size:22 final size:22
Alignment explanation
Indices: 31991091--31991134 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
31991081 TTTGGTATTT
31991091 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
31991113 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
31991135 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:31994836 original size:29 final size:29
Alignment explanation
Indices: 31994803--31994875 Score: 119
Period size: 29 Copynumber: 2.5 Consensus size: 29
31994793 ATGTATTAGT
* *
31994803 TTAGGACATATTTAAAACACTTGAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
*
31994832 TTAGGACATAATTAAAACACCTAAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
31994861 TTAGGACATATTTAA
1 TTAGGACATATTTAA
31994876 TAATATCTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.30
Consensus pattern (29 bp):
TTAGGACATATTTAAAACACCTAAACTAA
Found at i:31998181 original size:30 final size:30
Alignment explanation
Indices: 31998145--31998241 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
31998135 AGCTCACTCC
31998145 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
31998175 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
31998205 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
31998235 TAGCTCA
1 TAGCTCA
31998242 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:31999874 original size:15 final size:14
Alignment explanation
Indices: 31999854--31999888 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
31999844 GTTCGTAACG
31999854 AAAAAAAAGGAAATA
1 AAAAAAAAGGAAA-A
*
31999869 AAAAAAAATGAAAA
1 AAAAAAAAGGAAAA
31999883 AAAAAA
1 AAAAAA
31999889 TTTTTTGAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.86, C:0.00, G:0.09, T:0.06
Consensus pattern (14 bp):
AAAAAAAAGGAAAA
Found at i:31999988 original size:9 final size:9
Alignment explanation
Indices: 31999974--31999998 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
31999964 AAGAAATTCA
31999974 AAAAAAATC
1 AAAAAAATC
31999983 AAAAAAATC
1 AAAAAAATC
31999992 AAAAAAA
1 AAAAAAA
31999999 GGAAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAAAAATC
Found at i:32000017 original size:13 final size:13
Alignment explanation
Indices: 32000001--32000058 Score: 53
Period size: 15 Copynumber: 4.2 Consensus size: 13
31999991 CAAAAAAAGG
32000001 AAAAAAAAGTGAA
1 AAAAAAAAGTGAA
* *
32000014 AAAAAAAATTGAGTT
1 AAAAAAAAGTGA--A
*
32000029 AAAAAAAAGAAGAA
1 AAAAAAAAG-TGAA
32000043 AAAACAAAAGTGAA
1 AAAA-AAAAGTGAA
32000057 AA
1 AA
32000059 GTCTTGTGAG
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
13 11 0.31
14 9 0.26
15 13 0.37
16 2 0.06
ACGTcount: A:0.74, C:0.02, G:0.14, T:0.10
Consensus pattern (13 bp):
AAAAAAAAGTGAA
Found at i:32000986 original size:37 final size:37
Alignment explanation
Indices: 32000935--32001005 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
32000925 CATTCTTGTA
32000935 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
32000972 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
32001006 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:32001005 original size:6 final size:6
Alignment explanation
Indices: 32000945--32000994 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
32000935 AAGAGAAAAC
*
32000945 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
32000994 A
1 A
32000995 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:32001087 original size:11 final size:12
Alignment explanation
Indices: 32001055--32001085 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
32001045 TTGAGAGAAC
32001055 TTGAAAAAGCCT
1 TTGAAAAAGCCT
32001067 TTGAAAAAGCCT
1 TTGAAAAAGCCT
32001079 TTGAAAA
1 TTGAAAA
32001086 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:32003300 original size:30 final size:30
Alignment explanation
Indices: 32003266--32003362 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
32003256 AGCTCACTCC
32003266 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
32003296 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
32003326 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
32003356 TAGCTCA
1 TAGCTCA
32003363 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:32005295 original size:16 final size:16
Alignment explanation
Indices: 32005256--32005296 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
32005246 ATACAACCTC
*
32005256 TTTTTTTTATGCACAA
1 TTTTTTTTTTGCACAA
*
32005272 ATTTTTTTTTGCACAA
1 TTTTTTTTTTGCACAA
32005288 TTTTTTTTT
1 TTTTTTTTT
32005297 CAATTCACGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.20, C:0.10, G:0.05, T:0.66
Consensus pattern (16 bp):
TTTTTTTTTTGCACAA
Found at i:32006854 original size:22 final size:22
Alignment explanation
Indices: 32006824--32006867 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
32006814 TTTGGTATTT
32006824 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
32006846 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
32006868 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:32010571 original size:20 final size:20
Alignment explanation
Indices: 32010525--32010571 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
32010515 AGCTCGTTTC
*
32010525 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
32010545 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
32010565 CAGCTCA
1 CAGCTCA
32010572 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:32012078 original size:11 final size:11
Alignment explanation
Indices: 32012048--32012118 Score: 54
Period size: 11 Copynumber: 6.0 Consensus size: 11
32012038 ATTGGAGTAA
32012048 CAAAAAAAA-T
1 CAAAAAAAATT
32012058 CAAAAAAAATT
1 CAAAAAAAATT
32012069 CGAAAAAAATTTGATT
1 C-AAAAAAA----ATT
*
32012085 GAAAAAAAAATT
1 -CAAAAAAAATT
*
32012097 CAAAAAAAAGT
1 CAAAAAAAATT
*
32012108 GAAAAAAAATT
1 CAAAAAAAATT
32012119 GAGCAAAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
10 9 0.18
11 20 0.41
12 10 0.20
16 10 0.20
ACGTcount: A:0.69, C:0.06, G:0.07, T:0.18
Consensus pattern (11 bp):
CAAAAAAAATT
Found at i:32012128 original size:38 final size:38
Alignment explanation
Indices: 32012049--32012131 Score: 107
Period size: 39 Copynumber: 2.2 Consensus size: 38
32012039 TTGGAGTAAC
* *
32012049 AAAAAAAATCAAAAAAAATTCGAAAAAAATTTGATTG-AA
1 AAAAAAAATCAAAAAAAAGTCGAAAAAAAATTGA--GCAA
*
32012088 AAAAAAATTCAAAAAAAAGT-GAAAAAAAATTGAGCAA
1 AAAAAAAATCAAAAAAAAGTCGAAAAAAAATTGAGCAA
32012125 AAAAAAA
1 AAAAAAA
32012132 GAAAAGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
36 1 0.03
37 9 0.22
38 12 0.30
39 18 0.45
ACGTcount: A:0.71, C:0.05, G:0.08, T:0.16
Consensus pattern (38 bp):
AAAAAAAATCAAAAAAAAGTCGAAAAAAAATTGAGCAA
Found at i:32012129 original size:39 final size:38
Alignment explanation
Indices: 32012049--32012131 Score: 96
Period size: 38 Copynumber: 2.2 Consensus size: 38
32012039 TTGGAGTAAC
* * **
32012049 AAAAAAAATCAAAAAAAATTCGAAAAAAATTTGATTGAA
1 AAAAAAAATCAAAAAAAAGTCGAAAAAAAATTGA-CAAA
*
32012088 AAAAAAATTCAAAAAAAAGT-GAAAAAAAATTGAGCAAA
1 AAAAAAAATCAAAAAAAAGTCGAAAAAAAATTGA-CAAA
32012126 AAAAAA
1 AAAAAA
32012132 GAAAAGAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
38 20 0.53
39 18 0.47
ACGTcount: A:0.71, C:0.05, G:0.08, T:0.16
Consensus pattern (38 bp):
AAAAAAAATCAAAAAAAAGTCGAAAAAAAATTGACAAA
Found at i:32013227 original size:6 final size:6
Alignment explanation
Indices: 32013194--32013301 Score: 56
Period size: 6 Copynumber: 17.7 Consensus size: 6
32013184 AAAGAAATTG
* * * ** *
32013194 AAAG-A AAACAA AAAGAA AACGAA GAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * **
32013241 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA TATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA -AAAGAA
32013292 AAAGAA AAAG
1 AAAGAA AAAG
32013302 CGAAAAAAGA
Statistics
Matches: 71, Mismatches: 28, Indels: 7
0.67 0.26 0.07
Matches are distributed among these distances:
5 3 0.04
6 58 0.82
7 6 0.08
8 4 0.06
ACGTcount: A:0.69, C:0.04, G:0.19, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:32013255 original size:18 final size:18
Alignment explanation
Indices: 32013198--32013256 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
32013188 AAATTGAAAG
* *
32013198 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAATCGA
* * *
32013216 AGAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAATCGA
32013234 AAAAGAAAAAGAAATCGA
1 AAAAGAAAAAGAAATCGA
32013252 AAAAG
1 AAAAG
32013257 TGAGAGAAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.71, C:0.07, G:0.17, T:0.05
Consensus pattern (18 bp):
AAAAGAAAAAGAAATCGA
Found at i:32013461 original size:48 final size:47
Alignment explanation
Indices: 32013382--32013487 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
32013372 GAGTGTCATG
*
32013382 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
32013430 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
32013478 GAAAAAGAAA
1 GAAAAAGAAA
32013488 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:32015202 original size:20 final size:20
Alignment explanation
Indices: 32015156--32015202 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
32015146 AGCTCGTTTC
*
32015156 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
32015176 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
32015196 CAGCTCA
1 CAGCTCA
32015203 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:32022019 original size:15 final size:15
Alignment explanation
Indices: 32021999--32022027 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
32021989 CGTAGCTTCG
32021999 AAAAAAAAATTGCAA
1 AAAAAAAAATTGCAA
32022014 AAAAAAAAATTGCA
1 AAAAAAAAATTGCA
32022028 TACGGTCTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.72, C:0.07, G:0.07, T:0.14
Consensus pattern (15 bp):
AAAAAAAAATTGCAA
Found at i:32024306 original size:24 final size:25
Alignment explanation
Indices: 32024279--32024332 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
32024269 ATGAGTGATA
*
32024279 AAAAAAGAGA-GAGTGATTCAAAA-G
1 AAAAAAGAAACGAGTGA-TCAAAATG
*
32024303 -AAAAAGAAACGAGTGATGAAAATG
1 AAAAAAGAAACGAGTGATCAAAATG
32024327 AAAAAA
1 AAAAAA
32024333 AGAATTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 13 0.52
24 7 0.28
25 5 0.20
ACGTcount: A:0.63, C:0.04, G:0.22, T:0.11
Consensus pattern (25 bp):
AAAAAAGAAACGAGTGATCAAAATG
Found at i:32029433 original size:46 final size:46
Alignment explanation
Indices: 32029381--32029474 Score: 145
Period size: 46 Copynumber: 2.0 Consensus size: 46
32029371 ATAGTGTGGC
*
32029381 GTTCATCATAAACCAAGGTTCTTATCA-TCATTGATAGTGGGTCGAG
1 GTTCATCATAAACCAAGGTTCCTATCATTC-TTGATAGTGGGTCGAG
**
32029427 GTTCATCATATGCCAAGGTTCCTATCATTCTTGATAGTGGGTCGAG
1 GTTCATCATAAACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAG
32029473 GT
1 GT
32029475 CTTTTCTTTG
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
46 42 0.95
47 2 0.05
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.34
Consensus pattern (46 bp):
GTTCATCATAAACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAG
Found at i:32039245 original size:13 final size:13
Alignment explanation
Indices: 32039227--32039255 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
32039217 AATAGTTGTG
32039227 TGTTATTTAATTA
1 TGTTATTTAATTA
32039240 TGTTATTTAATTA
1 TGTTATTTAATTA
32039253 TGT
1 TGT
32039256 AGGTTAGCCG
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:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:32040519 original size:11 final size:11
Alignment explanation
Indices: 32040503--32040538 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
32040493 AAAAGAGAAG
32040503 AAATTCAAAAA
1 AAATTCAAAAA
32040514 AAATTCAAAAA
1 AAATTCAAAAA
*
32040525 AAATTGAAAAA
1 AAATTCAAAAA
32040536 AAA
1 AAA
32040539 GAAAAAAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.75, C:0.06, G:0.03, T:0.17
Consensus pattern (11 bp):
AAATTCAAAAA
Found at i:32041525 original size:15 final size:14
Alignment explanation
Indices: 32041502--32041549 Score: 69
Period size: 15 Copynumber: 3.3 Consensus size: 14
32041492 AAATTGAGAG
32041502 AAGAAAAAAAGAAA
1 AAGAAAAAAAGAAA
*
32041516 TAAGAGAAAAAGAAA
1 -AAGAAAAAAAGAAA
32041531 AAGAAATAAAAGAAA
1 AAGAAA-AAAAGAAA
32041546 AAGA
1 AAGA
32041550 TGAAAATGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 5 0.17
15 25 0.83
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (14 bp):
AAGAAAAAAAGAAA
Found at i:32041531 original size:21 final size:21
Alignment explanation
Indices: 32041498--32041549 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
32041488 AATGAAATTG
*
32041498 AGAGAAGAA-AAAAAGAAATA
1 AGAGAAAAAGAAAAAGAAATA
32041518 AGAGAAAAAGAAAAAGAAATA
1 AGAGAAAAAGAAAAAGAAATA
*
32041539 AAAGAAAAAGA
1 AGAGAAAAAGA
32041550 TGAAAATGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 8 0.28
21 21 0.72
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (21 bp):
AGAGAAAAAGAAAAAGAAATA
Found at i:32043711 original size:13 final size:13
Alignment explanation
Indices: 32043693--32043721 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
32043683 AATAGTTGTG
32043693 TGTTATTTAATTA
1 TGTTATTTAATTA
32043706 TGTTATTTAATTA
1 TGTTATTTAATTA
32043719 TGT
1 TGT
32043722 AGGTTAGCCG
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:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:32048740 original size:20 final size:20
Alignment explanation
Indices: 32048717--32048770 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
32048707 AGTTTTTCCC
*
32048717 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
32048737 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
32048757 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
32048771 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:32048752 original size:30 final size:30
Alignment explanation
Indices: 32048717--32048790 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
32048707 AGTTTTTCCC
32048717 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
32048747 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
32048777 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
32048791 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:32048780 original size:20 final size:20
Alignment explanation
Indices: 32048717--32048781 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
32048707 AGTTTTTCCC
* * * *
32048717 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
32048737 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
32048756 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
32048777 AGCTC
1 AGCTC
32048782 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:32051476 original size:12 final size:12
Alignment explanation
Indices: 32051455--32051647 Score: 54
Period size: 12 Copynumber: 16.7 Consensus size: 12
32051445 AGAAAAGGAG
*
32051455 AAAGAGATTGAA
1 AAAGAAATTGAA
32051467 AAAGAAATTG--
1 AAAGAAATTGAA
**
32051477 AAAGAAA-ACAA
1 AAAGAAATTGAA
**
32051488 AAAGAAAACGAA
1 AAAGAAATTGAA
**
32051500 AAAGAAAAAGAA
1 AAAGAAATTGAA
** *
32051512 ATTGCAAA-AGAA
1 AAAG-AAATTGAA
*
32051524 AAAGAAATCGAA
1 AAAGAAATTGAA
** *
32051536 AAAGTGA--GAG
1 AAAGAAATTGAA
*
32051546 AAAGAAAATGAAGA
1 AAAGAAATTG-A-A
32051560 AAAGAAAATTGAA
1 AAAG-AAATTGAA
32051573 AAAGAAATTG--
1 AAAGAAATTGAA
32051583 --AG-AA-TGAA
1 AAAGAAATTGAA
32051591 AAA-AAATTGAA
1 AAAGAAATTGAA
*
32051602 AAAGAAAAAGTGAAA
1 AAAG--AAATTG-AA
32051617 AAAGAAATTGAA
1 AAAGAAATTGAA
* **
32051629 AGAGAGCTTG-A
1 AAAGAAATTGAA
32051640 AAAGAAAT
1 AAAGAAAT
32051648 CAAGTGAAAA
Statistics
Matches: 135, Mismatches: 26, Indels: 41
0.67 0.13 0.20
Matches are distributed among these distances:
6 2 0.01
7 2 0.01
8 2 0.01
10 17 0.13
11 23 0.17
12 54 0.40
13 14 0.10
14 10 0.07
15 11 0.08
ACGTcount: A:0.66, C:0.03, G:0.20, T:0.11
Consensus pattern (12 bp):
AAAGAAATTGAA
Found at i:32051493 original size:11 final size:12
Alignment explanation
Indices: 32051477--32051539 Score: 67
Period size: 12 Copynumber: 5.3 Consensus size: 12
32051467 AAAGAAATTG
32051477 AAAGAAAAC-AA
1 AAAGAAAACGAA
32051488 AAAGAAAACGAA
1 AAAGAAAACGAA
*
32051500 AAAGAAAAAGAA
1 AAAGAAAACGAA
**
32051512 ATTGCAAAA-GAA
1 AAAG-AAAACGAA
*
32051524 AAAGAAATCGAA
1 AAAGAAAACGAA
32051536 AAAG
1 AAAG
32051540 TGAGAGAAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
11 12 0.28
12 27 0.63
13 4 0.09
ACGTcount: A:0.73, C:0.06, G:0.16, T:0.05
Consensus pattern (12 bp):
AAAGAAAACGAA
Found at i:32051507 original size:18 final size:18
Alignment explanation
Indices: 32051481--32051539 Score: 82
Period size: 18 Copynumber: 3.3 Consensus size: 18
32051471 AAATTGAAAG
* *
32051481 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAATCGA
* *
32051499 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAATCGA
32051517 AAAAGAAAAAGAAATCGA
1 AAAAGAAAAAGAAATCGA
32051535 AAAAG
1 AAAAG
32051540 TGAGAGAAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.73, C:0.07, G:0.15, T:0.05
Consensus pattern (18 bp):
AAAAGAAAAAGAAATCGA
Found at i:32051509 original size:6 final size:6
Alignment explanation
Indices: 32051477--32051611 Score: 58
Period size: 6 Copynumber: 21.7 Consensus size: 6
32051467 AAAGAAATTG
* * ** *
32051477 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** * *
32051524 AAAGAA ATCGAA AAAGTGAGA GAAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAA--GA-A -AAAGAA AAAG-A-A AAAGAA AA-AGAA
** * * **
32051573 AAAGAA ATTGAG AATGAA AAA-AA ATTGAA AAAGAA AAAG
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG
32051612 TGAAAAAAGA
Statistics
Matches: 93, Mismatches: 28, Indels: 17
0.67 0.20 0.12
Matches are distributed among these distances:
5 6 0.06
6 67 0.72
7 8 0.09
8 8 0.09
9 1 0.01
10 3 0.03
ACGTcount: A:0.70, C:0.03, G:0.19, T:0.09
Consensus pattern (6 bp):
AAAGAA
Found at i:32051597 original size:17 final size:18
Alignment explanation
Indices: 32051463--32051611 Score: 80
Period size: 18 Copynumber: 8.4 Consensus size: 18
32051453 AGAAAGAGAT
32051463 TGAAAAAGAAATTGAAAGAAA
1 TGAAAAAGAAATTG--A-AAA
** **
32051484 ACAAAAAGAAAACGAAAA
1 TGAAAAAGAAATTGAAAA
*
32051502 AGAAAAAGAAATTGCAAAA
1 TGAAAAAGAAATTG-AAAA
*
32051521 -GAAAAAGAAATCGAAAA
1 TGAAAAAGAAATTGAAAA
* ** *
32051538 AGTGAGAGAAA--GAAAA
1 TGAAAAAGAAATTGAAAA
*
32051554 TG---AAGAAA-AGAAAA
1 TGAAAAAGAAATTGAAAA
*
32051568 TTGAAAAAGAAATTGAGAA
1 -TGAAAAAGAAATTGAAAA
32051587 TGAAAAA-AAATTGAAAA
1 TGAAAAAGAAATTGAAAA
*
32051604 AGAAAAAG
1 TGAAAAAG
32051612 TGAAAAAAGA
Statistics
Matches: 102, Mismatches: 17, Indels: 21
0.73 0.12 0.15
Matches are distributed among these distances:
13 5 0.05
14 5 0.05
15 2 0.02
16 6 0.06
17 19 0.19
18 46 0.45
19 9 0.09
21 10 0.10
ACGTcount: A:0.68, C:0.03, G:0.19, T:0.10
Consensus pattern (18 bp):
TGAAAAAGAAATTGAAAA
Found at i:32051615 original size:14 final size:15
Alignment explanation
Indices: 32051533--32051623 Score: 50
Period size: 14 Copynumber: 6.3 Consensus size: 15
32051523 AAAAGAAATC
*
32051533 GAAAAAGTGAGAGAAA
1 GAAAAAGTGA-AAAAA
32051549 G-AAAA-TGAAGAAAA
1 GAAAAAGTGAA-AAAA
*
32051563 G-AAAATTG-AAAAA
1 GAAAAAGTGAAAAAA
** * *
32051576 GAAATTGAGAATGAAA
1 GAAAAAGTGAA-AAAA
*
32051592 -AAAAATTG-AAAAA
1 GAAAAAGTGAAAAAA
32051605 GAAAAAGTGAAAAAA
1 GAAAAAGTGAAAAAA
32051620 GAAA
1 GAAA
32051624 TTGAAAGAGA
Statistics
Matches: 56, Mismatches: 12, Indels: 15
0.67 0.14 0.18
Matches are distributed among these distances:
13 9 0.16
14 23 0.41
15 20 0.36
16 4 0.07
ACGTcount: A:0.68, C:0.00, G:0.21, T:0.11
Consensus pattern (15 bp):
GAAAAAGTGAAAAAA
Found at i:32051663 original size:33 final size:33
Alignment explanation
Indices: 32051626--32051688 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
32051616 AAAAGAAATT
32051626 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
32051659 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
32051689 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:32053510 original size:30 final size:30
Alignment explanation
Indices: 32053465--32053538 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
32053455 AGTTTTTCCC
32053465 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* * *
32053495 AGCTTGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
32053525 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
32053539 TGGCTTAAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
29 4 0.11
30 34 0.89
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:32053528 original size:20 final size:20
Alignment explanation
Indices: 32053465--32053529 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
32053455 AGTTTTTCCC
* * * *
32053465 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
* *
32053485 AGCTTAATTTAGCTT-GTTT
1 AGCTCAATTTAGCTTACTTT
32053504 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
32053525 AGCTC
1 AGCTC
32053530 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
19 1 0.03
20 31 0.89
21 3 0.09
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:32056002 original size:56 final size:56
Alignment explanation
Indices: 32055897--32056003 Score: 153
Period size: 56 Copynumber: 1.9 Consensus size: 56
32055887 ATTAATGCCA
* * * * *
32055897 TCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCCCTTTAAATGCCGT
1 TCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCACATTAAATGCCGT
32055953 TCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCACATTAAAT
1 TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCACATTAAAT
32056004 CAGCAAGCAG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
55 21 0.47
56 24 0.53
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.40
Consensus pattern (56 bp):
TCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCACATTAAATGCCGT
Found at i:32056653 original size:20 final size:20
Alignment explanation
Indices: 32056628--32056682 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
32056618 ACGAGTTAAA
* *
32056628 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
32056648 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
32056668 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
32056683 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:32059731 original size:20 final size:20
Alignment explanation
Indices: 32059708--32059754 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
32059698 GGGTTAAGAT
*
32059708 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
32059728 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
*
32059748 TGGGCTG
1 TGAGCTG
32059755 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.19, C:0.13, G:0.38, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:32062662 original size:17 final size:16
Alignment explanation
Indices: 32062642--32062681 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
32062632 TTTACCTTGA
* *
32062642 TTTTTTTGGTCACCTTT
1 TTTTTTTGCTCA-ATTT
32062659 TTTTTTTGCTCAATTT
1 TTTTTTTGCTCAATTT
32062675 TTTTTTT
1 TTTTTTT
32062682 CACTTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.07, C:0.12, G:0.07, T:0.72
Consensus pattern (16 bp):
TTTTTTTGCTCAATTT
Found at i:32062675 original size:15 final size:14
Alignment explanation
Indices: 32062657--32062752 Score: 67
Period size: 15 Copynumber: 6.8 Consensus size: 14
32062647 TTGGTCACCT
32062657 TTTTTTTTTGCTCAA
1 TTTTTTTTTG-TCAA
*
32062672 TTTTTTTTT-TCAC
1 TTTTTTTTTGTCAA
*
32062685 TTTTTTTTTGAAT-AT
1 TTTTTTTTTG--TCAA
*
32062700 TTTTTTTTTCAATCAA
1 TTTTTTTTT--GTCAA
*
32062716 TTTTTTTTTTTCGAA
1 TTTTTTTTTGTC-AA
32062731 TTTTTTTTTG---A
1 TTTTTTTTTGTCAA
32062742 TTTTTTTTTGT
1 TTTTTTTTTGT
32062753 TACTCCAATA
Statistics
Matches: 67, Mismatches: 6, Indels: 19
0.73 0.07 0.21
Matches are distributed among these distances:
11 11 0.16
13 12 0.18
14 2 0.03
15 31 0.46
16 11 0.16
ACGTcount: A:0.14, C:0.07, G:0.05, T:0.74
Consensus pattern (14 bp):
TTTTTTTTTGTCAA
Found at i:32062704 original size:44 final size:44
Alignment explanation
Indices: 32062656--32062750 Score: 126
Period size: 45 Copynumber: 2.2 Consensus size: 44
32062646 TTTGGTCACC
* *
32062656 TTTTTTTTTTGC--TCAA-TTTTTTTTTTC-ACTTTTTTTTTGAA
1 TTTTTTTTTTTCAATCAATTTTTTTTTTTCGAATTTTTTTTTG-A
32062697 TATTTTTTTTTTCAATCAATTTTTTTTTTTCGAATTTTTTTTTGA
1 T-TTTTTTTTTTCAATCAATTTTTTTTTTTCGAATTTTTTTTTGA
32062742 TTTTTTTTT
1 TTTTTTTTT
32062751 GTTACTCCAA
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
41 1 0.02
42 10 0.21
44 12 0.26
45 13 0.28
46 11 0.23
ACGTcount: A:0.14, C:0.07, G:0.04, T:0.75
Consensus pattern (44 bp):
TTTTTTTTTTTCAATCAATTTTTTTTTTTCGAATTTTTTTTTGA
Found at i:32062744 original size:11 final size:12
Alignment explanation
Indices: 32062718--32062751 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
32062708 TCAATCAATT
32062718 TTTTTTTTTCGAA
1 TTTTTTTTT-GAA
32062731 TTTTTTTTTG-A
1 TTTTTTTTTGAA
32062742 TTTTTTTTTG
1 TTTTTTTTTG
32062752 TTACTCCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
12 1 0.05
13 9 0.43
ACGTcount: A:0.09, C:0.03, G:0.09, T:0.79
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:32062750 original size:12 final size:13
Alignment explanation
Indices: 32062717--32062750 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
32062707 TTCAATCAAT
32062717 TTTTTTTTTTCGA
1 TTTTTTTTTTCGA
*
32062730 ATTTTTTTTT-GA
1 TTTTTTTTTTCGA
32062742 TTTTTTTTT
1 TTTTTTTTT
32062751 GTTACTCCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.09, C:0.03, G:0.06, T:0.82
Consensus pattern (13 bp):
TTTTTTTTTTCGA
Found at i:32064259 original size:20 final size:20
Alignment explanation
Indices: 32064236--32064282 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
32064226 GGGTTAAGAT
*
32064236 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
32064256 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
*
32064276 TGGGCTG
1 TGAGCTG
32064283 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.19, C:0.13, G:0.38, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:32066822 original size:4 final size:4
Alignment explanation
Indices: 32066813--32066840 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
32066803 TATCACTAAG
32066813 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
32066841 AATAAAACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:32074361 original size:13 final size:13
Alignment explanation
Indices: 32074341--32074374 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
32074331 AAATTGATTG
*
32074341 AAAAAAAAATTCA
1 AAAAAAAAAGTCA
*
32074354 AAAAAAAAAGTGA
1 AAAAAAAAAGTCA
32074367 AAAAAAAA
1 AAAAAAAA
32074375 TCGAGCAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.82, C:0.03, G:0.06, T:0.09
Consensus pattern (13 bp):
AAAAAAAAAGTCA
Found at i:32074414 original size:29 final size:27
Alignment explanation
Indices: 32074339--32074424 Score: 90
Period size: 29 Copynumber: 3.2 Consensus size: 27
32074329 AAAAATTGAT
32074339 TGAAAAAAAAATTCAA--AAAAAAAA-G
1 TGAAAAAAAAA-TCAAGCAAAAAAAAGG
*
32074364 TGAAAAAAAAATCGAGCAAAAAAAAGG
1 TGAAAAAAAAATCAAGCAAAAAAAAGG
**
32074391 TGACCAAAAAAAATCAAGTTAAAAAAA-G
1 TGA--AAAAAAAATCAAGCAAAAAAAAGG
32074419 TGAAAA
1 TGAAAA
32074425 GTCTTGCGAG
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
24 3 0.06
25 11 0.21
26 11 0.21
27 4 0.08
28 4 0.08
29 19 0.37
ACGTcount: A:0.69, C:0.07, G:0.13, T:0.12
Consensus pattern (27 bp):
TGAAAAAAAAATCAAGCAAAAAAAAGG
Found at i:32082712 original size:23 final size:22
Alignment explanation
Indices: 32082661--32082712 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
32082651 CCTCGTCTTT
*
32082661 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
32082683 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
32082706 TTCTTTT
1 TTCTTTT
32082713 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:32084994 original size:20 final size:20
Alignment explanation
Indices: 32084966--32085035 Score: 97
Period size: 20 Copynumber: 3.5 Consensus size: 20
32084956 CTTATTTTTT
*
32084966 TTAGTTCATTCGAGCTCAAA
1 TTAGCTCATTCGAGCTCAAA
*
32084986 TTAGCTCATTCGAGCTCAAG
1 TTAGCTCATTCGAGCTCAAA
*
32085006 TCAGCTCATTCGAGCTC-AA
1 TTAGCTCATTCGAGCTCAAA
32085025 TTCAGCTCATT
1 TT-AGCTCATT
32085036 AAGCTCGTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
19 2 0.05
20 42 0.95
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.33
Consensus pattern (20 bp):
TTAGCTCATTCGAGCTCAAA
Found at i:32085001 original size:10 final size:9
Alignment explanation
Indices: 32084988--32085041 Score: 54
Period size: 10 Copynumber: 5.6 Consensus size: 9
32084978 AGCTCAAATT
32084988 AGCTCATTC
1 AGCTCATTC
*
32084997 GAGCTCAAGTC
1 -AGCTC-ATTC
32085008 AGCTCATTC
1 AGCTCATTC
32085017 GAGCTCAATTC
1 -AGCTC-ATTC
*
32085028 AGCTCATTA
1 AGCTCATTC
32085037 AGCTC
1 AGCTC
32085042 GTTATTAGCT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
9 11 0.29
10 20 0.53
11 7 0.18
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.28
Consensus pattern (9 bp):
AGCTCATTC
Found at i:32090527 original size:20 final size:20
Alignment explanation
Indices: 32090504--32090550 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
32090494 GGGTTAAGAT
*
32090504 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
32090524 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
32090544 TGAGCTG
1 TGAGCTG
32090551 GAAACAAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:32092240 original size:48 final size:48
Alignment explanation
Indices: 32092185--32092290 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
32092175 TTGTCTTTTC
*
32092185 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
32092233 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
32092281 TTTCTTTTTC
1 TTTCTTTTTC
32092291 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:32093363 original size:25 final size:24
Alignment explanation
Indices: 32093335--32093402 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
32093325 TTTAACTTGA
* * *
32093335 TTTTTTTTGCTTACTTTTTTTTTC
1 TTTTTTTTGCTCAATTTTTTTTAC
32093359 TTTTTTTTGCTCAATTTTTTTTAC
1 TTTTTTTTGCTCAATTTTTTTTAC
*
32093383 TTTTTTTT--TGAATTTTTTTT
1 TTTTTTTTGCTCAATTTTTTTT
32093403 GAATTTCGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
22 11 0.28
24 29 0.73
ACGTcount: A:0.09, C:0.09, G:0.04, T:0.78
Consensus pattern (24 bp):
TTTTTTTTGCTCAATTTTTTTTAC
Found at i:32093398 original size:11 final size:11
Alignment explanation
Indices: 32093371--32093408 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
32093361 TTTTTTGCTC
32093371 AATTTTTTTT-
1 AATTTTTTTTG
*
32093381 ACTTTTTTTTTG
1 A-ATTTTTTTTG
32093393 AATTTTTTTTG
1 AATTTTTTTTG
32093404 AATTT
1 AATTT
32093409 CGATTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 1 0.04
11 22 0.92
12 1 0.04
ACGTcount: A:0.18, C:0.03, G:0.05, T:0.74
Consensus pattern (11 bp):
AATTTTTTTTG
Found at i:32094496 original size:20 final size:20
Alignment explanation
Indices: 32094473--32094526 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
32094463 AGTTTTTCCC
*
32094473 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
32094493 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
32094513 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
32094527 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:32094508 original size:30 final size:30
Alignment explanation
Indices: 32094473--32094546 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
32094463 AGTTTTTCCC
32094473 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
32094503 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
32094533 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
32094547 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:32094536 original size:20 final size:20
Alignment explanation
Indices: 32094473--32094537 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
32094463 AGTTTTTCCC
* * * *
32094473 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
32094493 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
32094512 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
32094533 AGCTC
1 AGCTC
32094538 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:32096119 original size:19 final size:20
Alignment explanation
Indices: 32096081--32096120 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
32096071 AAAAAATGAA
**
32096081 AATTTTTTTTGTTGTAATTT
1 AATTTTTTTCCTTGTAATTT
32096101 AATTTTTTTCCTTGT-ATTT
1 AATTTTTTTCCTTGTAATTT
32096120 A
1 A
32096121 GCTTACTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.20, C:0.05, G:0.07, T:0.68
Consensus pattern (20 bp):
AATTTTTTTCCTTGTAATTT
Found at i:32096170 original size:12 final size:12
Alignment explanation
Indices: 32096153--32096178 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
32096143 AAAAAAATTG
32096153 AAATTCAAAAAA
1 AAATTCAAAAAA
32096165 AAATTCAAAAAA
1 AAATTCAAAAAA
32096177 AA
1 AA
32096179 GTGAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (12 bp):
AAATTCAAAAAA
Found at i:32096201 original size:27 final size:26
Alignment explanation
Indices: 32096171--32096245 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 26
32096161 AAAAAAATTC
32096171 AAAAAAAAGTGAAAAAAAATCGAGCAA
1 AAAAAAAAGTGAAAAAAAAT-GAGCAA
** *
32096198 AAAAAAAGAAAGAAAAAAAGTGAGCAA
1 AAAAAAA-AGTGAAAAAAAATGAGCAA
*
32096225 AAAAAATCAAGTTAAAAAAAA
1 AAAAAA--AAGTGAAAAAAAA
32096246 GTGAAAAGTC
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
27 19 0.50
28 18 0.47
29 1 0.03
ACGTcount: A:0.73, C:0.05, G:0.13, T:0.08
Consensus pattern (26 bp):
AAAAAAAAGTGAAAAAAAATGAGCAA
Found at i:32098985 original size:11 final size:10
Alignment explanation
Indices: 32098958--32098984 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
32098948 GAAGAAATTC
32098958 AAAAAAATCA
1 AAAAAAATCA
32098968 AAAAAAATCA
1 AAAAAAATCA
32098978 AAAAAAA
1 AAAAAAA
32098985 AGAAAAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.85, C:0.07, G:0.00, T:0.07
Consensus pattern (10 bp):
AAAAAAATCA
Found at i:32100075 original size:6 final size:6
Alignment explanation
Indices: 32100043--32100150 Score: 76
Period size: 6 Copynumber: 17.7 Consensus size: 6
32100033 AAAGAAATTG
* * ** *
32100043 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* ** * *
32100090 AAAGAA ATCA-AA AAAGTG AAAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
32100141 AAAGAA AAAG
1 AAAGAA AAAG
32100151 CGAAAAAAGA
Statistics
Matches: 77, Mismatches: 20, Indels: 11
0.71 0.19 0.10
Matches are distributed among these distances:
5 4 0.05
6 61 0.79
7 8 0.10
8 4 0.05
ACGTcount: A:0.73, C:0.04, G:0.17, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:32100130 original size:14 final size:13
Alignment explanation
Indices: 32100111--32100148 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
32100101 AAAAGTGAAA
32100111 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
32100123 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
32100138 GAAAAAGAAAA
1 GAAAAAGAAAA
32100149 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:32100185 original size:12 final size:12
Alignment explanation
Indices: 32100154--32100185 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
32100144 GAAAAAGCGA
*
32100154 AAAAAGAATTTG
1 AAAAAGAGTTTG
32100166 AAAAAGAGTTTG
1 AAAAAGAGTTTG
32100178 AAAAAGAG
1 AAAAAGAG
32100186 AAGAGTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.19
Consensus pattern (12 bp):
AAAAAGAGTTTG
Found at i:32103352 original size:22 final size:22
Alignment explanation
Indices: 32103327--32103368 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
32103317 AAAGAGATTG
*
32103327 AAAAAG-AAATTAAAAGAAAAC
1 AAAAAGAAAATGAAAAGAAAAC
32103348 AAAAAGAAAATGAAAAGAAAA
1 AAAAAGAAAATGAAAAGAAAA
32103369 AGAAATTGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.79, C:0.02, G:0.12, T:0.07
Consensus pattern (22 bp):
AAAAAGAAAATGAAAAGAAAAC
Found at i:32103362 original size:6 final size:6
Alignment explanation
Indices: 32103338--32103476 Score: 61
Period size: 6 Copynumber: 22.8 Consensus size: 6
32103328 AAAAGAAATT
* * ** *
32103338 AAAAG- AAAACA AAAAGA AAATG- AAAAGA AAAAGA AATTGC AAAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
* * * * * *
32103384 AAAAGA AATCA-A AAAAGT GAGAGA AAAAGA AAATGAA GAAAAGA AAATTGA
1 AAAAGA AA-AAGA AAAAGA AAAAGA AAAAGA AAAAG-A -AAAAGA AAA-AGA
** * *
32103435 AAAAGA AATTGA GAATGA AAAA-A AAAATTGA AAAAGA AAAAG
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAA--GA AAAAGA AAAAG
32103477 TGAAAAAAGA
Statistics
Matches: 96, Mismatches: 28, Indels: 19
0.67 0.20 0.13
Matches are distributed among these distances:
5 14 0.15
6 65 0.68
7 8 0.08
8 9 0.09
ACGTcount: A:0.71, C:0.02, G:0.17, T:0.09
Consensus pattern (6 bp):
AAAAGA
Found at i:32103381 original size:18 final size:17
Alignment explanation
Indices: 32103342--32103392 Score: 75
Period size: 17 Copynumber: 2.9 Consensus size: 17
32103332 GAAATTAAAA
* *
32103342 GAAAACAAAAAGAAAAT
1 GAAAAGAAAAAGAAATT
32103359 GAAAAGAAAAAGAAATT
1 GAAAAGAAAAAGAAATT
32103376 GCAAAAGAAAAAGAAAT
1 G-AAAAGAAAAAGAAAT
32103393 CAAAAAAGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 16 0.52
18 15 0.48
ACGTcount: A:0.73, C:0.04, G:0.16, T:0.08
Consensus pattern (17 bp):
GAAAAGAAAAAGAAATT
Found at i:32103436 original size:27 final size:27
Alignment explanation
Indices: 32103406--32103494 Score: 92
Period size: 27 Copynumber: 3.1 Consensus size: 27
32103396 AAAAGTGAGA
32103406 GAAAAAGAAAATGAAGAAAAGAAAATT
1 GAAAAAGAAAATGAAGAAAAGAAAATT
* *
32103433 GAAAAAGAAATTGAGAATGAAAAAAAAAATT
1 GAAAAAGAAAAT--GAA-G-AAAAGAAAATT
32103464 GAAAAAGAAAAAGTGAA-AAAAG-AAATT
1 GAAAAAG-AAAA-TGAAGAAAAGAAAATT
32103491 GAAA
1 GAAA
32103495 GAGAGCTTGA
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
27 20 0.38
28 4 0.08
29 3 0.06
30 1 0.02
31 20 0.38
32 3 0.06
33 1 0.02
ACGTcount: A:0.70, C:0.00, G:0.18, T:0.12
Consensus pattern (27 bp):
GAAAAAGAAAATGAAGAAAAGAAAATT
Found at i:32103462 original size:19 final size:19
Alignment explanation
Indices: 32103434--32103475 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
32103424 AAGAAAATTG
* * *
32103434 AAAAAGAAATTGAGAATGA
1 AAAAAAAAATTGAAAAAGA
32103453 AAAAAAAAATTGAAAAAGA
1 AAAAAAAAATTGAAAAAGA
32103472 AAAA
1 AAAA
32103476 GTGAAAAAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.12
Consensus pattern (19 bp):
AAAAAAAAATTGAAAAAGA
Found at i:32103528 original size:33 final size:33
Alignment explanation
Indices: 32103491--32103553 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
32103481 AAAAGAAATT
32103491 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
32103524 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
32103554 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:32105367 original size:30 final size:30
Alignment explanation
Indices: 32105332--32105405 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
32105322 AGTTTTTCCC
*
32105332 AGCTCGATTT-AGCTCACA-TGAGCTTATTTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTACTTT
*
32105362 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTACTTT
32105392 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
32105406 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.41
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTACTTT
Found at i:32113209 original size:24 final size:25
Alignment explanation
Indices: 32113156--32113209 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
32113146 AACAAATTAT
* *
32113156 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
32113181 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
32113204 TTTTTT
1 TTTTTT
32113210 TATCACTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:32117697 original size:15 final size:14
Alignment explanation
Indices: 32117661--32117715 Score: 65
Period size: 15 Copynumber: 3.8 Consensus size: 14
32117651 TCTATTGATC
32117661 GAGAAAAAGAAAAA
1 GAGAAAAAGAAAAA
*
32117675 GAGAAAAACAAAAA
1 GAGAAAAAGAAAAA
*
32117689 GAGTGAAAAGAAAAA
1 GAG-AAAAAGAAAAA
*
32117704 GAAAGAAAAGAA
1 GAGA-AAAAGAA
32117716 TGAGGAGAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
14 16 0.47
15 18 0.53
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (14 bp):
GAGAAAAAGAAAAA
Found at i:32125551 original size:21 final size:23
Alignment explanation
Indices: 32125506--32125552 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
32125496 TCACCTGCAA
* *
32125506 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
32125529 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
32125550 TAA
1 TAA
32125553 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:32127328 original size:18 final size:18
Alignment explanation
Indices: 32127307--32127341 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
32127297 TTTTTCTTTT
32127307 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
32127325 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
32127342 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:32136085 original size:23 final size:22
Alignment explanation
Indices: 32136034--32136085 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
32136024 CCTCGTCTTT
*
32136034 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
32136056 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
32136079 TTCTTTT
1 TTCTTTT
32136086 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:32140830 original size:28 final size:28
Alignment explanation
Indices: 32140790--32140853 Score: 128
Period size: 28 Copynumber: 2.3 Consensus size: 28
32140780 GAGATTGGCG
32140790 CTAAGTGTGCGAGCTTGATTATGTAGCA
1 CTAAGTGTGCGAGCTTGATTATGTAGCA
32140818 CTAAGTGTGCGAGCTTGATTATGTAGCA
1 CTAAGTGTGCGAGCTTGATTATGTAGCA
32140846 CTAAGTGT
1 CTAAGTGT
32140854 AGCACTAAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.25, C:0.14, G:0.28, T:0.33
Consensus pattern (28 bp):
CTAAGTGTGCGAGCTTGATTATGTAGCA
Found at i:32140856 original size:12 final size:12
Alignment explanation
Indices: 32140839--32140864 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
32140829 AGCTTGATTA
32140839 TGTAGCACTAAG
1 TGTAGCACTAAG
32140851 TGTAGCACTAAG
1 TGTAGCACTAAG
32140863 TG
1 TG
32140865 GGCGAGCTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (12 bp):
TGTAGCACTAAG
Found at i:32140870 original size:40 final size:40
Alignment explanation
Indices: 32140811--32140893 Score: 157
Period size: 40 Copynumber: 2.1 Consensus size: 40
32140801 AGCTTGATTA
*
32140811 TGTAGCACTAAGTGTGCGAGCTTGATTATGTAGCACTAAG
1 TGTAGCACTAAGTGGGCGAGCTTGATTATGTAGCACTAAG
32140851 TGTAGCACTAAGTGGGCGAGCTTGATTATGTAGCACTAAG
1 TGTAGCACTAAGTGGGCGAGCTTGATTATGTAGCACTAAG
32140891 TGT
1 TGT
32140894 GCGAGTTTGA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.30
Consensus pattern (40 bp):
TGTAGCACTAAGTGGGCGAGCTTGATTATGTAGCACTAAG
Found at i:32140870 original size:68 final size:68
Alignment explanation
Indices: 32140790--32140921 Score: 237
Period size: 68 Copynumber: 1.9 Consensus size: 68
32140780 GAGATTGGCG
* *
32140790 CTAAGTGTGCGAGCTTGATTATGTAGCACTAAGTGTGCGAGCTTGATTATGTAGCACTAAGTGTA
1 CTAAGTGGGCGAGCTTGATTATGTAGCACTAAGTGTGCGAGCTTGATTATATAGCACTAAGTGTA
32140855 GCA
66 GCA
*
32140858 CTAAGTGGGCGAGCTTGATTATGTAGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGT
1 CTAAGTGGGCGAGCTTGATTATGTAGCACTAAGTGTGCGAGCTTGATTATATAGCACTAAGTGT
32140922 GCGAGTTGAT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 61 1.00
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.32
Consensus pattern (68 bp):
CTAAGTGGGCGAGCTTGATTATGTAGCACTAAGTGTGCGAGCTTGATTATATAGCACTAAGTGTA
GCA
Done.