Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009624.1 Hibiscus syriacus cultivar Beakdansim tig00117016_pilon, whole genome shotgun sequence
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: 8249038
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 28 of 38
Found at i:5587806 original size:14 final size:14
Alignment explanation
Indices: 5587559--5587806 Score: 119
Period size: 14 Copynumber: 17.7 Consensus size: 14
5587549 AAGAAAAGAA
*
5587559 AAAAATGAAATGAA-
1 AAAAATGAAA-AAAG
5587573 AAAAATG-AAAAAG
1 AAAAATGAAAAAAG
* * *
5587586 AAAAAAG-AGAGAG
1 AAAAATGAAAAAAG
*
5587599 AAAAA-GAAAAAGG
1 AAAAATGAAAAAAG
5587612 AAAAGA-GAAAAAAG
1 AAAA-ATGAAAAAAG
*
5587626 GAAAA-GAATATATAA-
1 AAAAATGAA-A-A-AAG
*
5587641 AATAAAAG-AAAAAG
1 AA-AAATGAAAAAAG
*
5587655 AAAAATGAAAAATG
1 AAAAATGAAAAAAG
5587669 AAAAATGAAAAAATG
1 AAAAATGAAAAAA-G
5587684 AAAAAT-AAAAAAGGG
1 AAAAATGAAAAAA--G
** **
5587699 AAAAGGGAAAAGGG
1 AAAAATGAAAAAAG
*
5587713 AAAAAAAGAAAAAAG
1 -AAAAATGAAAAAAG
*
5587728 AAAAAAGAAAAAAG
1 AAAAATGAAAAAAG
5587742 AGAAAA-GAGAAAAGAG
1 A-AAAATGA-AAAA-AG
*
5587758 AAAAGA-GAAAAGAG
1 AAAA-ATGAAAAAAG
*
5587772 AAAAAT-AAAGAA-
1 AAAAATGAAAAAAG
5587784 AAAAA-GAAAAAAG
1 AAAAATGAAAAAAG
*
5587797 AAAATTGAAA
1 AAAAATGAAA
5587807 GGAGGGTTCA
Statistics
Matches: 185, Mismatches: 27, Indels: 44
0.72 0.11 0.17
Matches are distributed among these distances:
12 13 0.07
13 43 0.23
14 73 0.39
15 39 0.21
16 16 0.09
17 1 0.01
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (14 bp):
AAAAATGAAAAAAG
Found at i:5589894 original size:65 final size:64
Alignment explanation
Indices: 5589720--5589932 Score: 157
Period size: 65 Copynumber: 3.2 Consensus size: 64
5589710 TGAAACAAAT
* * * * *
5589720 TTTGTCTCACTTGAGACAAT-TTCTCT-TGAAAC-ATAAACCTTCAGATTGTTTTTCTTAAAAAC
1 TTTGTCTCACTTGAGACAATCTTCCCTAAGAAACGA-ACA-TTTGAGATTG-TTTTCTTAAAAA-
5589782 AAA
62 AAA
* *
5589785 TTTCGTCTCACTTGAGACAATCTTCCTTAAGATACGAACATTTGAGATTGTATTTCTTAAAAAAA
1 TTT-GTCTCACTTGAGACAATCTTCCCTAAGAAACGAACATTTGAGATTGT-TTTCTTAAAAAAA
5589850 A
64 A
* * ** * * * * *
5589851 TATGTCTCACTTGAGACAGT-TTCCCCTAA-AAACTCAGATTTTGAAATTGTTTCACTTGAAACA
1 TTTGTCTCACTTGAGACAATCTT-CCCTAAGAAACGAACA-TTTGAGATTGTTT-TCTTAAAAAA
5589914 AA
63 AA
5589916 TTTGATCTCACTTGAGA
1 TTTG-TCTCACTTGAGA
5589933 TTGTTTTCCT
Statistics
Matches: 120, Mismatches: 19, Indels: 17
0.77 0.12 0.11
Matches are distributed among these distances:
64 9 0.08
65 46 0.38
66 35 0.29
67 23 0.19
68 6 0.05
69 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (64 bp):
TTTGTCTCACTTGAGACAATCTTCCCTAAGAAACGAACATTTGAGATTGTTTTCTTAAAAAAAA
Found at i:5589973 original size:102 final size:102
Alignment explanation
Indices: 5589826--5590036 Score: 273
Period size: 102 Copynumber: 2.1 Consensus size: 102
5589816 ATACGAACAT
* * ** *
5589826 TTGAGATTGTATTTCTTAAAAAAAATATGTCTCACTTGAGACAGTTTCCCCTAAAAACTCAGATT
1 TTGAGATTGTATTTCCTAAAAAAAATATATCTCACTTGAGACAGTTTCCCCTAAAAACAAAAATT
*
5589891 TTGAAATTGTTTCACTTGAAAC-AAATTTGATCTCAC
66 TTGAAATTGTTTCACTCGAAACAAAATTTGATCTCAC
* * * **
5589927 TTGAGATTGT-TTTCCTAAAAACAAATATTATCTCGCTTGAGGCAGTTTTCCCTTGAAACAAAAA
1 TTGAGATTGTATTTCCTAAAAA-AAATA-TATCTCACTTGAGACAGTTTCCCCTAAAAACAAAAA
*
5589991 TTTTGAAATTGTTTCACTCGAAACAAAATTTTATCTCAC
64 TTTTGAAATTGTTTCACTCGAAACAAAATTTGATCTCAC
*
5590030 CTGAGAT
1 TTGAGAT
5590037 AGCTTCTCTT
Statistics
Matches: 94, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
100 10 0.11
101 15 0.16
102 50 0.53
103 19 0.20
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.36
Consensus pattern (102 bp):
TTGAGATTGTATTTCCTAAAAAAAATATATCTCACTTGAGACAGTTTCCCCTAAAAACAAAAATT
TTGAAATTGTTTCACTCGAAACAAAATTTGATCTCAC
Found at i:5589975 original size:36 final size:36
Alignment explanation
Indices: 5589909--5589977 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
5589899 GTTTCACTTG
**
5589909 AAACAAATTTGATCTCACTTGAGATTGTTTTCCTAA
1 AAACAAATTTGATCTCACTTGAGACAGTTTTCCTAA
* *
5589945 AAACAAATATT-ATCTCGCTTGAGGCAGTTTTCC
1 AAACAAAT-TTGATCTCACTTGAGACAGTTTTCC
5589978 CTTGAAACAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
36 26 0.93
37 2 0.07
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (36 bp):
AAACAAATTTGATCTCACTTGAGACAGTTTTCCTAA
Found at i:5592614 original size:318 final size:318
Alignment explanation
Indices: 5592025--5592980 Score: 1522
Period size: 318 Copynumber: 3.0 Consensus size: 318
5592015 TATTAAATAA
*
5592025 TTCGAAACAAATTAATCAATGTTCAATAAATGGATCATAATTTAATTTTCTATTCGAATTTCAAT
1 TTCGAAACAAATTAATCAATGTTCAATAAATGGATCATAATTTAATTTTCTATTAGAATTTCAAT
*
5592090 TTCCACTATTGCGACAACGTATAAGCGAC-AAGGTACCAATTTTGGGCGCGGTGGGAGTGCTTAC
66 TTCCACTATTGCGACAACGTATAAGCGACTAA-GTACCAATTTTGGGCGCGGTGGGGGTGCTTAC
*
5592154 CCTTCCCCACGCGTAATCAACTCCCAAACCTAAAATGAATCTTTGATAAGCGCATGCCAGTCTTT
130 CCTTCCCCACGCGTAATCAACTCCCGAACCTAAAATGAATCTTTGATAAGCGCATGCCAGTCTTT
* *
5592219 TATCTTAAAAATGATTTTTCTTAAAAATT-TTTAAAAGAAGTTTTTAGGTGTTCGACCTACCTAA
195 TGTCTTAAAAATGATTTTTCTT-AAAATTGTTTAAAAGACGTTTTTAGGTGTTCGACCTACCTAA
* *
5592283 CCCAAAAGTTGATGGCGACTCCAAATCAATTTAATCAAAATAAACACAAAAGTTCAATTT
259 CCCAAAGGTTGATGGCGACTCCAAATCAATTTAATCAAAATAAACACAAAAATTCAATTT
* * *
5592343 TTCGAAACAAATTGATCAATGTTCAGTAAATGGATCATAATTTACTTTTCTATTAGAATTTCAAT
1 TTCGAAACAAATTAATCAATGTTCAATAAATGGATCATAATTTAATTTTCTATTAGAATTTCAAT
*
5592408 TTCCACTATTGCGACAACGTATAAGCGACTAAGAACCAATTTTGGGCGCGGTGGGGGTGCTTACC
66 TTCCACTATTGCGACAACGTATAAGCGACTAAGTACCAATTTTGGGCGCGGTGGGGGTGCTTACC
* * * * **
5592473 CTTCCCCAGGTGTAACCAACTCCCGAACCTAAAATGAATCTTTGATAAGCGCATACCAAACTTTT
131 CTTCCCCACGCGTAATCAACTCCCGAACCTAAAATGAATCTTTGATAAGCGCATGCCAGTCTTTT
* * * *
5592538 GTCTTAAAAATAATTTTACTTAAAATTGTTTAAAAGACGTTTTTAGGTGTTCGACCTAACTAATC
196 GTCTTAAAAATGATTTTTCTTAAAATTGTTTAAAAGACGTTTTTAGGTGTTCGACCTACCTAACC
*
5592603 CAAAGGTTGATGGCGACTCCAAATCAATTTAATCAATATAAACACAAAAATTCAATTT
261 CAAAGGTTGATGGCGACTCCAAATCAATTTAATCAAAATAAACACAAAAATTCAATTT
*
5592661 TTCGAAACAAATTAATCAATGTTCAATAAATGGATCATAATTTAATTTTCTATTTGAATTTCAAT
1 TTCGAAACAAATTAATCAATGTTCAATAAATGGATCATAATTTAATTTTCTATTAGAATTTCAAT
* * * * *
5592726 TTCCACTATTACGACAACGTATAAACGACTAGGTACCAATTTTGGGAGCAGTGGGGGTGCTTACC
66 TTCCACTATTGCGACAACGTATAAGCGACTAAGTACCAATTTTGGGCGCGGTGGGGGTGCTTACC
* * * * *
5592791 CTTCTCCACGCATAATCAACTCCCGAACCTAAAATGAATATTTGACAAGCGCATGCCAGTCTTTC
131 CTTCCCCACGCGTAATCAACTCCCGAACCTAAAATGAATCTTTGATAAGCGCATGCCAGTCTTTT
* * *
5592856 GTCTTAAAAATGATTTTTCTTAAAATTGTTTAAAAAACATTTTTAGGTGGTCGACCTACCTAACC
196 GTCTTAAAAATGATTTTTCTTAAAATTGTTTAAAAGACGTTTTTAGGTGTTCGACCTACCTAACC
* *
5592921 CAAAGGTTGGA-GGTGACTCCAAATCAATTTAATCAAAATAAACACAAAAATTAAATTT
261 CAAAGGTT-GATGGCGACTCCAAATCAATTTAATCAAAATAAACACAAAAATTCAATTT
5592979 TT
1 TT
5592981 ACAAAATAAG
Statistics
Matches: 582, Mismatches: 53, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
317 6 0.01
318 572 0.98
319 4 0.01
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (318 bp):
TTCGAAACAAATTAATCAATGTTCAATAAATGGATCATAATTTAATTTTCTATTAGAATTTCAAT
TTCCACTATTGCGACAACGTATAAGCGACTAAGTACCAATTTTGGGCGCGGTGGGGGTGCTTACC
CTTCCCCACGCGTAATCAACTCCCGAACCTAAAATGAATCTTTGATAAGCGCATGCCAGTCTTTT
GTCTTAAAAATGATTTTTCTTAAAATTGTTTAAAAGACGTTTTTAGGTGTTCGACCTACCTAACC
CAAAGGTTGATGGCGACTCCAAATCAATTTAATCAAAATAAACACAAAAATTCAATTT
Found at i:5594489 original size:41 final size:41
Alignment explanation
Indices: 5594444--5594705 Score: 231
Period size: 41 Copynumber: 6.3 Consensus size: 41
5594434 CATTTTTTCA
* * * *
5594444 ACAAACGCCGCAACAGAGTAGTACTTTAGTGGCGTTTCTAT
1 ACAAACGCCGCAATAGACTTGTACTTTAGTGGCGTTTTTAT
* * *
5594485 ACAAACGTCGCTATAGACTTGTACTTTAGTGGCATTTTTAT
1 ACAAACGCCGCAATAGACTTGTACTTTAGTGGCGTTTTTAT
* * * * * *
5594526 ATAAACACC-CTATACAATTGTACTTTAGTGGCGTTTTTGTTT
1 ACAAACGCCGCAATAGACTTGTACTTTAGTGGCG-TTTT-TAT
*
5594568 ATAAACGCCGCGAA-AGACTTGTACTTTAGTGGCGTTTTTAT
1 ACAAACGCCGC-AATAGACTTGTACTTTAGTGGCGTTTTTAT
** * * *
5594609 ACAAACATCGCTATACACTTGTACTTTAGTGACGTTTTTAT
1 ACAAACGCCGCAATAGACTTGTACTTTAGTGGCGTTTTTAT
* * * * * *
5594650 ACAAATGCTGCTATACACTAGTACTTTAGTGGCGTTTGTATTT
1 ACAAACGCCGCAATAGACTTGTACTTTAGTGGCGTTT-T-TAT
*
5594693 ATAAACGCCGCAA
1 ACAAACGCCGCAA
5594706 ATTTATAAGT
Statistics
Matches: 178, Mismatches: 36, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
40 22 0.12
41 110 0.62
42 15 0.08
43 30 0.17
44 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (41 bp):
ACAAACGCCGCAATAGACTTGTACTTTAGTGGCGTTTTTAT
Found at i:5594574 original size:83 final size:84
Alignment explanation
Indices: 5594464--5594682 Score: 250
Period size: 83 Copynumber: 2.7 Consensus size: 84
5594454 CAACAGAGTA
* * *
5594464 GTACTTTAGTGGCG--TTTCTATACAAACGTCGCTATAGACTTGTACTTTAGTGGCATTTTTATA
1 GTACTTTAGTGGCGTTTTTCTATACAAACGCCGCGAAAGACTTGTACTTTAGTGGCATTTTTATA
*
5594527 TAAACA-CCCTATACAATT
66 CAAACATCCCTATACAATT
* * * *
5594545 GTACTTTAGTGGCGTTTTTGTTTATAAACGCCGCGAAAGACTTGTACTTTAGTGGCGTTTTTATA
1 GTACTTTAGTGGCGTTTTTCTATACAAACGCCGCGAAAGACTTGTACTTTAGTGGCATTTTTATA
* *
5594610 CAAACATCGCTATACACTT
66 CAAACATCCCTATACAATT
* * * * * * *
5594629 GTACTTTAGTGACG-TTTT-TATACAAATGCTGCTATACACTAGTACTTTAGTGGC
1 GTACTTTAGTGGCGTTTTTCTATACAAACGCCGCGAAAGACTTGTACTTTAGTGGC
5594683 GTTTGTATTT
Statistics
Matches: 116, Mismatches: 19, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
81 14 0.12
82 28 0.24
83 51 0.44
84 23 0.20
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.38
Consensus pattern (84 bp):
GTACTTTAGTGGCGTTTTTCTATACAAACGCCGCGAAAGACTTGTACTTTAGTGGCATTTTTATA
CAAACATCCCTATACAATT
Found at i:5594599 original size:124 final size:125
Alignment explanation
Indices: 5594446--5594705 Score: 362
Period size: 124 Copynumber: 2.1 Consensus size: 125
5594436 TTTTTTCAAC
* * *
5594446 AAACGCCGCAACAGAGTAGTACTTTAGTGGCGTTTCTATACAAACGTCGCTATAGACTTGTACTT
1 AAACGCCGCAACAGACTAGTACTTTAGTGGCGTTTCTATACAAACATCGCTATACACTTGTACTT
* * * * *
5594511 TAGTGGCATTTTTATATAAACAC-CCTATACAATTGTACTTTAGTGGCGTTTTTGTTTAT
66 TAGTGACATTTTTATACAAACACTCCTATACAATAGTACTTTAGTGGCGTTTGTATTTAT
* *
5594570 AAACGCCGCGAA-AGACTTGTACTTTAGTGGCGTTTTTATACAAACATCGCTATACACTTGTACT
1 AAACGCCGC-AACAGACTAGTACTTTAGTGGCGTTTCTATACAAACATCGCTATACACTTGTACT
* ** * *
5594634 TTAGTGACGTTTTTATACAAATGCTGCTATACACTAGTACTTTAGTGGCGTTTGTATTTAT
65 TTAGTGACATTTTTATACAAACACTCCTATACAATAGTACTTTAGTGGCGTTTGTATTTAT
5594695 AAACGCCGCAA
1 AAACGCCGCAA
5594706 ATTTATAAGT
Statistics
Matches: 119, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
124 77 0.65
125 42 0.35
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (125 bp):
AAACGCCGCAACAGACTAGTACTTTAGTGGCGTTTCTATACAAACATCGCTATACACTTGTACTT
TAGTGACATTTTTATACAAACACTCCTATACAATAGTACTTTAGTGGCGTTTGTATTTAT
Found at i:5597659 original size:20 final size:20
Alignment explanation
Indices: 5597634--5597688 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
5597624 AGTTTGTTTG
5597634 GAATTTTATCATTTTTAAAT
1 GAATTTTATCATTTTTAAAT
*
5597654 GAATTTCATCATTTTTAAAT
1 GAATTTTATCATTTTTAAAT
*
5597674 GAATTTTCTCATTTT
1 GAATTTTATCATTTT
5597689 AGCTTAGTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.31, C:0.09, G:0.05, T:0.55
Consensus pattern (20 bp):
GAATTTTATCATTTTTAAAT
Found at i:5598286 original size:43 final size:42
Alignment explanation
Indices: 5598187--5598360 Score: 201
Period size: 42 Copynumber: 4.1 Consensus size: 42
5598177 GTTTCGATTA
* * *
5598187 GCGGCGTTTGTTCTAAAAACGCCACTATAGAAT-TTACCTTTT
1 GCGGCGTTTGTTCAAAAAACGCCGCTATAG-ATCTGACCTTTT
* *
5598229 GCGGCGTTTGTTCAAAAAATGCTGCTATAGATTCTGACCTTTT
1 GCGGCGTTTGTTCAAAAAACGCCGCTATAGA-TCTGACCTTTT
* *
5598272 GTGGCGTTTTTTCAAAAAACGCCGCTATAGATCTGACCTTTT
1 GCGGCGTTTGTTCAAAAAACGCCGCTATAGATCTGACCTTTT
* * * *
5598314 GCGGTGTTTGTATC-TAAAACGCTGCTATAGAAC-GACCTTTT
1 GCGGCGTTTGT-TCAAAAAACGCCGCTATAGATCTGACCTTTT
5598355 GCGGCG
1 GCGGCG
5598361 CTATAGATCT
Statistics
Matches: 113, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
41 14 0.12
42 62 0.55
43 37 0.33
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (42 bp):
GCGGCGTTTGTTCAAAAAACGCCGCTATAGATCTGACCTTTT
Found at i:5598338 original size:85 final size:83
Alignment explanation
Indices: 5598187--5598360 Score: 217
Period size: 85 Copynumber: 2.1 Consensus size: 83
5598177 GTTTCGATTA
* * *
5598187 GCGGCGTTTGTTCTAAAAACGCCACTATAGAATTTACCTTTTGCGGCGTTTGTTCAAAAAATGCT
1 GCGGCGTTTGTTCAAAAAACGCCACTATAGAATTGACCTTTTGCGGCGTTTGTTCAAAAAACGCT
*
5598252 GCTATAGATTCTGACCTTTT
66 GCTATAGA-AC-GACCTTTT
* * * * *
5598272 GTGGCGTTTTTTCAAAAAACGCCGCTATAG-ATCTGACCTTTTGCGGTGTTTGTATC-TAAAACG
1 GCGGCGTTTGTTCAAAAAACGCCACTATAGAAT-TGACCTTTTGCGGCGTTTGT-TCAAAAAACG
5598335 CTGCTATAGAACGACCTTTT
64 CTGCTATAGAACGACCTTTT
5598355 GCGGCG
1 GCGGCG
5598361 CTATAGATCT
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
83 13 0.17
84 3 0.04
85 59 0.77
86 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (83 bp):
GCGGCGTTTGTTCAAAAAACGCCACTATAGAATTGACCTTTTGCGGCGTTTGTTCAAAAAACGCT
GCTATAGAACGACCTTTT
Found at i:5598366 original size:23 final size:24
Alignment explanation
Indices: 5598337--5598381 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
5598327 CTAAAACGCT
*
5598337 GCTATAGAAC-GACCTTTTGCGGC
1 GCTATAGAACTGACATTTTGCGGC
*
5598360 GCTATAGATCTGACATTTTGCG
1 GCTATAGAACTGACATTTTGCG
5598382 ACGTTTGTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.31
Consensus pattern (24 bp):
GCTATAGAACTGACATTTTGCGGC
Found at i:5598422 original size:43 final size:42
Alignment explanation
Indices: 5598367--5598643 Score: 183
Period size: 43 Copynumber: 6.5 Consensus size: 42
5598357 GGCGCTATAG
* * *
5598367 ATCTGACATTTTGCGACGTTTGTTCTAAAAACACCGCTAAAA
1 ATCTGACCTTTTGCGGCGTTTGTTCTAAAAACGCCGCTAAAA
* * *
5598409 ATTCTGACCTTTTGCAGCGTTTGTATCT-AAAACGCCACTATAGA
1 A-TCTGACCTTTTGCGGCGTTTGT-TCTAAAAACGCCGCTA-AAA
* * *
5598453 A--TGACCTTTTGTGGCGTTTTGTTCTAAAAACGCCGCTATAG
1 ATCTGACCTTTTGCGGCG-TTTGTTCTAAAAACGCCGCTAAAA
* * ** *
5598494 ATCTGACATTTTACGGCGTTTGTTCCGAAAACGCCGCTATATAT
1 ATCTGACCTTTTGCGGCGTTTGTTCTAAAAACGCCGCTA-A-AA
* *
5598538 ATC-GA-CTTTTAGCGGCGTTTGTTCCT-AAAATGCCGCTATAGAT
1 ATCTGACCTTTT-GCGGCGTTTGTT-CTAAAAACGCCGCTA-A-AA
* * * * * *
5598581 ATC-GACCTTTAGCGGCATTTGTTCCAAAAGCGTCGC-AATAG
1 ATCTGACCTTTTGCGGCGTTTGTTCTAAAAACGCCGCTAA-AA
*
5598622 ATCTTGACCTATTGCGGCGTTT
1 ATC-TGACCTTTTGCGGCGTTT
5598644 TTTGTTCTCA
Statistics
Matches: 185, Mismatches: 35, Indels: 29
0.74 0.14 0.12
Matches are distributed among these distances:
41 22 0.12
42 42 0.23
43 106 0.57
44 15 0.08
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (42 bp):
ATCTGACCTTTTGCGGCGTTTGTTCTAAAAACGCCGCTAAAA
Found at i:5598441 original size:108 final size:108
Alignment explanation
Indices: 5598252--5598468 Score: 292
Period size: 108 Copynumber: 2.0 Consensus size: 108
5598242 AAAAAATGCT
* * * * * * * *
5598252 GCTATAGATTCTGACCTTTTGTGGCGTTTTTTCAAAAAACGCCGCTATAGATCTGACCTTTTGCG
1 GCTATAGATTCTGACATTTTGCGACGTTTGTTCAAAAAACACCGCTAAAAATCTGACCTTTTGCA
* **
5598317 GTGTTTGTATCTAAAACGCTGCTATAGAACGACCTTTTGCGGC
66 GCGTTTGTATCTAAAACGCCACTATAGAACGACCTTTTGCGGC
*
5598360 GCTATAGA-TCTGACATTTTGCGACGTTTGTTCTAAAAACACCGCTAAAAATTCTGACCTTTTGC
1 GCTATAGATTCTGACATTTTGCGACGTTTGTTCAAAAAACACCGCTAAAAA-TCTGACCTTTTGC
* *
5598424 AGCGTTTGTATCTAAAACGCCACTATAGAATGACCTTTTGTGGC
65 AGCGTTTGTATCTAAAACGCCACTATAGAACGACCTTTTGCGGC
5598468 G
1 G
5598469 TTTTGTTCTA
Statistics
Matches: 94, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
107 34 0.36
108 60 0.64
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (108 bp):
GCTATAGATTCTGACATTTTGCGACGTTTGTTCAAAAAACACCGCTAAAAATCTGACCTTTTGCA
GCGTTTGTATCTAAAACGCCACTATAGAACGACCTTTTGCGGC
Found at i:5598483 original size:150 final size:150
Alignment explanation
Indices: 5598225--5598494 Score: 348
Period size: 150 Copynumber: 1.8 Consensus size: 150
5598215 AGAATTTACC
* ** * * * ** *
5598225 TTTTGCGGCGTTTGTTCAAAAAATGCTGCTATAGATTCTGACCTTTTGTGGCGTTTTTTCAAAAA
1 TTTTGCGACGTTTGTTCAAAAAACACCGCTAAAAATTCTGACCTTTTGCAGCGTTTTATCAAAAA
* * * *
5598290 ACGCCGCTATAGATCTGACCTTTTGCGGTGTTTGTATCTAAAACGCTGCTATAGAACGACCTTTT
66 ACGCCACTATAGATATGACCTTTTGCGGCGTTTGTATCTAAAACGCCGCTATAGAACGACCTTTT
5598355 GCGGCGCTATAGATCTGACA
131 GCGGCGCTATAGATCTGACA
* *
5598375 TTTTGCGACGTTTGTTCTAAAAACACCGCTAAAAATTCTGACCTTTTGCAGCGTTTGTATC-TAA
1 TTTTGCGACGTTTGTTCAAAAAACACCGCTAAAAATTCTGACCTTTTGCAGCGTTT-TATCAAAA
*
5598439 AACGCCACTATAGA-ATGACCTTTTGTGGCGTTTTGT-TCTAAAAACGCCGCTATAGA
65 AACGCCACTATAGATATGACCTTTTGCGGCG-TTTGTATCT-AAAACGCCGCTATAGA
5598495 TCTGACATTT
Statistics
Matches: 101, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
149 16 0.16
150 82 0.81
151 3 0.03
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (150 bp):
TTTTGCGACGTTTGTTCAAAAAACACCGCTAAAAATTCTGACCTTTTGCAGCGTTTTATCAAAAA
ACGCCACTATAGATATGACCTTTTGCGGCGTTTGTATCTAAAACGCCGCTATAGAACGACCTTTT
GCGGCGCTATAGATCTGACA
Found at i:5598559 original size:85 final size:83
Alignment explanation
Indices: 5598361--5598580 Score: 221
Period size: 85 Copynumber: 2.6 Consensus size: 83
5598351 TTTTGCGGCG
* * * * * * * *
5598361 CTATAGATCTGACATTTTGCGACGTTTGTTCTAAAAACACCGCTAAAAATTCTGACCTTTTGCAG
1 CTATAGA-ATGACCTTTTGCGGCGTTTGTTCTAAAAACGCCGCTATAGA-TCTGACATTTTACAG
*
5598426 CGTTTGTATCTAAAACGCCA
64 CGTTTGTATCGAAAACGCCA
* *
5598446 CTATAGAATGACCTTTTGTGGCGTTTTGTTCTAAAAACGCCGCTATAGATCTGACATTTTACGGC
1 CTATAGAATGACCTTTTGCGGCG-TTTGTTCTAAAAACGCCGCTATAGATCTGACATTTTACAGC
*
5598511 GTTTGT-TCCGAAAACGCCG
65 GTTTGTAT-CGAAAACGCCA
* *
5598530 CTATATATATCGA-CTTTTAGCGGCGTTTGTTCCT-AAAATGCCGCTATAGAT
1 CTATAGA-AT-GACCTTTT-GCGGCGTTTGTT-CTAAAAACGCCGCTATAGAT
5598581 ATCGACCTTT
Statistics
Matches: 114, Mismatches: 15, Indels: 12
0.81 0.11 0.09
Matches are distributed among these distances:
83 1 0.01
84 46 0.40
85 58 0.51
86 9 0.08
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.34
Consensus pattern (83 bp):
CTATAGAATGACCTTTTGCGGCGTTTGTTCTAAAAACGCCGCTATAGATCTGACATTTTACAGCG
TTTGTATCGAAAACGCCA
Found at i:5598639 original size:86 final size:85
Alignment explanation
Indices: 5598370--5598643 Score: 204
Period size: 85 Copynumber: 3.2 Consensus size: 85
5598360 GCTATAGATC
* * * * * * * * *
5598370 TGACATTTTGCGACGTTTGTTCTAAAAACACCGCTAAAAATTCTGAC-CTTTTGCAGCGTTTGTA
1 TGACCTTTTGCGGCGTTTGTTCTAAAAACGCCGCTATAGA-TATGACAC-TTTACGGCATTTGT-
* * *
5598434 T-CTAAAACGCCACTATAGA-A-
63 TCCGAAAACGCCGCAATAGATAT
* * * *
5598454 TGACCTTTTGTGGCGTTTTGTTCTAAAAACGCCGCTATAGATCTGACATTTTACGGCGTTTGTTC
1 TGACCTTTTGCGGCG-TTTGTTCTAAAAACGCCGCTATAGATATGACACTTTACGGCATTTGTTC
* *
5598519 CGAAAACGCCGCTATATATAT
65 CGAAAACGCCGCAATAGATAT
* *
5598540 CGA-CTTTTAGCGGCGTTTGTTCCT-AAAATGCCGCTATAGATATCGAC-CTTTAGCGGCATTTG
1 TGACCTTTT-GCGGCGTTTGTT-CTAAAAACGCCGCTATAGATAT-GACACTTTA-CGGCATTTG
* *
5598602 TTCC-AAAAGCGTCGCAATAGATCT
62 TTCCGAAAA-CGCCGCAATAGATAT
*
5598626 TGACCTATTGCGGCGTTT
1 TGACCTTTTGCGGCGTTT
5598644 TTTGTTCTCA
Statistics
Matches: 155, Mismatches: 24, Indels: 20
0.78 0.12 0.10
Matches are distributed among these distances:
83 1 0.01
84 45 0.29
85 59 0.38
86 46 0.30
87 4 0.03
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (85 bp):
TGACCTTTTGCGGCGTTTGTTCTAAAAACGCCGCTATAGATATGACACTTTACGGCATTTGTTCC
GAAAACGCCGCAATAGATAT
Found at i:5599312 original size:35 final size:34
Alignment explanation
Indices: 5599266--5599374 Score: 148
Period size: 35 Copynumber: 3.1 Consensus size: 34
5599256 CAATCCTCAG
*
5599266 TTTCATTCTAAACCACAAATTCCAAAGTAATTCAA
1 TTTCATTCTAAACC-CAAATTCCAAAATAATTCAA
5599301 TTTCATTCTAAACCCTAAATTCCAAAATAATTCAA
1 TTTCATTCTAAACCC-AAATTCCAAAATAATTCAA
* *
5599336 TTAT-ATTCTAAAACCCAAATTCTAAAATACTTCAA
1 TT-TCATTCT-AAACCCAAATTCCAAAATAATTCAA
5599371 TTTC
1 TTTC
5599375 TATTTTTTAT
Statistics
Matches: 67, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
34 2 0.03
35 58 0.87
36 7 0.10
ACGTcount: A:0.42, C:0.22, G:0.01, T:0.35
Consensus pattern (34 bp):
TTTCATTCTAAACCCAAATTCCAAAATAATTCAA
Found at i:5600019 original size:20 final size:20
Alignment explanation
Indices: 5599996--5600051 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
5599986 ACAGATTCCA
*
5599996 AAATTGCAACG-TGAATATGT
1 AAATCGCAACGAT-AATATGT
5600016 AAATCGCAACGATAATATGT
1 AAATCGCAACGATAATATGT
*
5600036 AAATCGCAACGCTAAT
1 AAATCGCAACGATAAT
5600052 TACCGATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 32 0.97
21 1 0.03
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.25
Consensus pattern (20 bp):
AAATCGCAACGATAATATGT
Found at i:5600080 original size:37 final size:37
Alignment explanation
Indices: 5600038--5600121 Score: 132
Period size: 37 Copynumber: 2.3 Consensus size: 37
5600028 TAATATGTAA
* *
5600038 ATCGCAACGCTAATTACCGATATAGGTAAACAGTATT
1 ATCGCAACGCTAATTACCAATATAGGTAAACAGTACT
* *
5600075 ATCGCAAAGCTAATTACCAATATATGTAAACAGTACT
1 ATCGCAACGCTAATTACCAATATAGGTAAACAGTACT
5600112 ATCGCAACGC
1 ATCGCAACGC
5600122 GATTTTCAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.25
Consensus pattern (37 bp):
ATCGCAACGCTAATTACCAATATAGGTAAACAGTACT
Found at i:5600164 original size:57 final size:58
Alignment explanation
Indices: 5600076--5600199 Score: 187
Period size: 57 Copynumber: 2.2 Consensus size: 58
5600066 AACAGTATTA
* * *
5600076 TCGCAAAGCTAATTACCAATATATGTAAACAGTACTATCGCAACGCGATTTTC-AAAT
1 TCGCAACGCTAATTACCAATATATATAAACAGTACTACCGCAACGCGATTTTCTAAAT
* **
5600133 TCGCAACGCTAATTACCGATATATATAAACAGTGTTACCGCAACGCGATTTTCTAAAT
1 TCGCAACGCTAATTACCAATATATATAAACAGTACTACCGCAACGCGATTTTCTAAAT
5600191 TCGCAACGC
1 TCGCAACGC
5600200 GAATATGTAA
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
57 47 0.78
58 13 0.22
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.27
Consensus pattern (58 bp):
TCGCAACGCTAATTACCAATATATATAAACAGTACTACCGCAACGCGATTTTCTAAAT
Found at i:5600210 original size:21 final size:20
Alignment explanation
Indices: 5600171--5600219 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
5600161 ACAGTGTTAC
* *
5600171 CGCAACGCGATTTTCTAAATT
1 CGCAACGCGAATATCTAAA-T
*
5600192 CGCAACGCGAATATGTAAAT
1 CGCAACGCGAATATCTAAAT
*
5600212 CTCAACGC
1 CGCAACGC
5600220 TAATTACCGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (20 bp):
CGCAACGCGAATATCTAAAT
Found at i:5600324 original size:134 final size:134
Alignment explanation
Indices: 5600083--5600332 Score: 367
Period size: 134 Copynumber: 1.9 Consensus size: 134
5600073 TTATCGCAAA
* *
5600083 GCTAATTACCAATATATGTAAACAGTACTATCGCAACGCGATTTTCAAATTCGCAACGCTAATTA
1 GCTAATTACCAATATAGGTAAACAGTACTATCGCAACGCGATTTACAAATTCGCAACGCTAATTA
* * * *
5600148 CCGATATATATAAACAGTGTTACCGCAACGCGATTTTCTAAATTCGCAACGCGAATATGTAAATC
66 CCGATATAGATAAACAGTGTTACCGCAACGAGAATATCTAAA-TCGCAACGCGAATATGTAAATC
5600213 TCAAC
130 TCAAC
* * *
5600218 GCTAATTACCGATATAGGTAAACAGTACTATTG-AACGCGATTTACAAATTCGTAACGCTAATTA
1 GCTAATTACCAATATAGGTAAACAGTACTATCGCAACGCGATTTACAAATTCGCAACGCTAATTA
* * * *
5600282 CCGATATAGGTAAACAGTGTTATCGCAACGATAATATGTAAATCGCAACGC
66 CCGATATAGATAAACAGTGTTACCGCAACGAGAATATCTAAATCGCAACGC
5600333 TAATTACCGA
Statistics
Matches: 102, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
133 9 0.09
134 63 0.62
135 30 0.29
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (134 bp):
GCTAATTACCAATATAGGTAAACAGTACTATCGCAACGCGATTTACAAATTCGCAACGCTAATTA
CCGATATAGATAAACAGTGTTACCGCAACGAGAATATCTAAATCGCAACGCGAATATGTAAATCT
CAAC
Found at i:5600420 original size:114 final size:113
Alignment explanation
Indices: 5600191--5600425 Score: 362
Period size: 114 Copynumber: 2.1 Consensus size: 113
5600181 TTTTCTAAAT
* * *
5600191 TCGCAACGCGAATATGTAAATCTCAACGCTAATTACCGATATAGGTAAACAGTACTATTGAACGC
1 TCGCAACGAGAATATGTAAATCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGAACGC
* **
5600256 GATTTACAAATTCGTAACGCTAATTACCGATATAGGTAAACAGTGTTA
66 GATTTACAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTA
* **
5600304 TCGCAACGATAATATGTAAATCGCAACGCTAATTACCGATATAGGTAAACAGTGTTATCGCAACG
1 TCGCAACGAGAATATGTAAATCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCG-AACG
* *
5600369 CGATTTTCAAATTCGCAACGCTAATTACCGATGTAGGTAAACAGTACTA
65 CGATTTACAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTA
5600418 TCGCAACG
1 TCGCAACG
5600426 CGATTTTGGA
Statistics
Matches: 110, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
113 54 0.49
114 56 0.51
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.26
Consensus pattern (113 bp):
TCGCAACGAGAATATGTAAATCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGAACGC
GATTTACAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTA
Found at i:5600427 original size:57 final size:57
Alignment explanation
Indices: 5600214--5600432 Score: 300
Period size: 57 Copynumber: 3.9 Consensus size: 57
5600204 ATGTAAATCT
* *
5600214 CAACGCTAATTACCGATATAGGTAAACAGTACTATTG-AACGCGATTTACAAATTCG
1 CAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGCGATTTTCAAATTCG
* ** ** *
5600270 TAACGCTAATTACCGATATAGGTAAACAGTGTTATCGCAACGATAATATGT-AAA-TCG
1 CAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACG-CGAT-TTTCAAATTCG
**
5600327 CAACGCTAATTACCGATATAGGTAAACAGTGTTATCGCAACGCGATTTTCAAATTCG
1 CAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGCGATTTTCAAATTCG
*
5600384 CAACGCTAATTACCGATGTAGGTAAACAGTACTATCGCAACGCGATTTT
1 CAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGCGATTTT
5600433 GGAAACTGTG
Statistics
Matches: 143, Mismatches: 15, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
55 2 0.01
56 38 0.27
57 97 0.68
58 5 0.03
59 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (57 bp):
CAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGCGATTTTCAAATTCG
Found at i:5601203 original size:36 final size:34
Alignment explanation
Indices: 5601137--5601249 Score: 154
Period size: 35 Copynumber: 3.2 Consensus size: 34
5601127 GTTCCTCCTT
* *
5601137 AAATTGAAATATTTTAGAATTTGGGTTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGG-TTTAGAATG
*
5601172 TAATTGAATTATTTTTGGAATTTAGGGTTTAGAATG
1 AAATTGAATTA-TTTTGGAATTT-GGGTTTAGAATG
*
5601208 AAATTGAATTACTTTGGAATTTGGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTT-GGGTTTAGAATG
5601243 AAATTGA
1 AAATTGA
5601250 GGAATATCTT
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
35 38 0.54
36 29 0.41
37 3 0.04
ACGTcount: A:0.35, C:0.01, G:0.22, T:0.42
Consensus pattern (34 bp):
AAATTGAATTATTTTGGAATTTGGGTTTAGAATG
Found at i:5602314 original size:2 final size:2
Alignment explanation
Indices: 5602307--5602336 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5602297 TTGTTTTGTA
5602307 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5602337 TATTTTGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5602997 original size:182 final size:182
Alignment explanation
Indices: 5602566--5603238 Score: 1071
Period size: 182 Copynumber: 3.7 Consensus size: 182
5602556 TGTCGATTTA
* * * *
5602566 TGTCGATACTTTATAAAAATGTATCAATCCACATCAATATAACAAGTAAAAATATGAAAAAACCG
1 TGTCGATACTTTATAAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGAAAAAACCG
* * * *
5602631 GTCTCGAAAAGACAAAACCGGTAAAGCGCTACCGGATATATTGAAATTGTCGATACTTTAATATA
66 GTCTCGAAAGGACAAAACCGGTATAGAGCTACCGGATATATTGAAAGTGTCGATACTTTAATATA
*
5602696 AGTATCGACACTTTGTGAATTTAAAAGAGAAGTA-TTTTAGCGCCTATAAAG
131 AGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAG
*
5602747 TGTCGATACTTTATAAAAATGTATCGATCCACAACGATATAACATGTAAAAATATGAAAAAACCG
1 TGTCGATACTTTATAAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGAAAAAACCG
* * *
5602812 GTCTCTAAAGGACAAAACCGGTATAGAGCGACTGGATATATTGAAAGTGTCGATACTTTAATATA
66 GTCTCGAAAGGACAAAACCGGTATAGAGCTACCGGATATATTGAAAGTGTCGATACTTTAATATA
5602877 AGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAG
131 AGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAG
* *
5602929 TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
1 TGTCGATACTTTATAAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGAAAAAACCG
* * * *
5602994 GTCTCTAAAGGACAAAACCGGTATAGAGCAACCGAATATATTGAAAATGTCGATACTTTAATATA
66 GTCTCGAAAGGACAAAACCGGTATAGAGCTACCGGATATATTGAAAGTGTCGATACTTTAATATA
*
5603059 AGTATCGACCCTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAG
131 AGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAG
* * * * * *
5603111 TGTCGATACTTTATAAAAATGCATCGATCCATAACGATATAACAGATAAAAATATGACAAAATCA
1 TGTCGATACTTTATAAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGAAAAAACCG
* *
5603176 GTCTCGAAATGACAAAACCGGTA-AAACGCTACCGGATATATTGAAAGTGTCGATACTTTAATA
66 GTCTCGAAAGGACAAAACCGGTATAGA-GCTACCGGATATATTGAAAGTGTCGATACTTTAATA
5603239 AGTACGCGTA
Statistics
Matches: 458, Mismatches: 32, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
181 154 0.34
182 304 0.66
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.27
Consensus pattern (182 bp):
TGTCGATACTTTATAAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGAAAAAACCG
GTCTCGAAAGGACAAAACCGGTATAGAGCTACCGGATATATTGAAAGTGTCGATACTTTAATATA
AGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAG
Found at i:5605208 original size:22 final size:23
Alignment explanation
Indices: 5605156--5605212 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 23
5605146 GAACATTTTT
* *
5605156 ATTTTTTTATATAAAATGATAGT
1 ATTTTATTATATAAAATGATAGA
* *
5605179 ATAGTTATTATATAAAATTATA-A
1 AT-TTTATTATATAAAATGATAGA
5605202 ATTTTATTATA
1 ATTTTATTATA
5605213 AATGCAGGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
22 8 0.29
23 4 0.14
24 16 0.57
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (23 bp):
ATTTTATTATATAAAATGATAGA
Found at i:5605512 original size:18 final size:18
Alignment explanation
Indices: 5605491--5605527 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
5605481 GTAATTGGAG
5605491 TTTGAATTTGAATTTCAA
1 TTTGAATTTGAATTTCAA
*
5605509 TTTGAGTTTGAATTTCAA
1 TTTGAATTTGAATTTCAA
5605527 T
1 T
5605528 ATAAATTTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.05, G:0.14, T:0.51
Consensus pattern (18 bp):
TTTGAATTTGAATTTCAA
Found at i:5606275 original size:200 final size:198
Alignment explanation
Indices: 5605763--5606530 Score: 987
Period size: 200 Copynumber: 3.9 Consensus size: 198
5605753 TAAAGTTTCT
*
5605763 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCAAAAAACATCGAAAC-CAAATATTATAA
1 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCAAAAAACATCGAAACTGAAA-ATTATAA
* * * *
5605827 TGTAATAGGTAAATTTACAATGTAACCGATATAAATATACTGATTTTATGAGCAAATTGGTCAGC
65 TGTAATAGGTAAATTTACAATGTAACCGATATAAATATACCGATTTTATGAGAAAATAGGTCAAC
* * * **
5605892 ATAAATG-ATCGACACCTTTTAAATTTGTTTCGATACTTTTTGTCC-GA-GCCTTTGCTC-AACG
130 AT-AATGTATCGACA-CTTTTAAATTTGTGTCGATACATTTTGTCCAAATG-AATT-C-CAAACG
* * *
5605953 AGCTTCACG
190 GGGTACACG
** *
5605962 CATAAAAGTGTCGATACATTTA-AAATTGTATCAATCCAAAAAACATCGAAACTGAAAATTATAA
1 CAT-AAAGTGTCGATACATTTATAAAAAGTATCGATCCAAAAAACATCGAAACTGAAAATTATAA
* * *
5606026 TGTAATAGGTAAATATACAATGTAACCGGTATAAATATACTTG-TTTTATGAGAAAATAGGT-AT
65 TGTAATAGGTAAATTTACAATGTAACCGATATAAATATAC-CGATTTTATGAGAAAATAGGTCA-
*
5606089 ACATAATGTATCGACACTGTTTAAATTTGTGTCGATACATTTTATCCATAATGAATTCCAAACGG
128 ACATAATGTATCGACACT-TTTAAATTTGTGTCGATACATTTTGTCCA-AATGAATTCCAAACGG
*
5606154 GGTACACA
191 GGTACACG
* * **
5606162 CATAAAGTGTCGCTACATTTTTAAAAAGTATCGATCTC-AAAAACATCGAAACTGGTAATTATAA
1 CATAAAGTGTCGATACATTTATAAAAAGTATCGATC-CAAAAAACATCGAAACTGAAAATTATAA
* * *
5606226 TGTAATAGGTAAATTTACAATGTAACCAATATAAGTATACCGATTTTATGAGAAAATAGGTGAAC
65 TGTAATAGGTAAATTTACAATGTAACCGATATAAATATACCGATTTTATGAGAAAATAGGTCAAC
* * * *
5606291 ATAATGTATCGACACTTTTTAGATTTGTGTCGATACATCTTGTCCAGAATGAATGCAAAACGGGG
130 ATAATGTATCGACAC-TTTTAAATTTGTGTCGATACATTTTGTCCA-AATGAATTCCAAACGGGG
*
5606356 TGCACG
193 TACACG
* *
5606362 CATAAACTGTCGATACATTTATAAAAAGTATCGATCCAAAAAACATCGAAACCGAAAATTATAAT
1 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCAAAAAACATCGAAACTGAAAATTATAAT
* * *
5606427 GTAATAGGTAAATTTACAATGTAACCGATATAAATATACCGGTTTTATGAGAAAATATGTTAACA
66 GTAATAGGTAAATTTACAATGTAACCGATATAAATATACCGATTTTATGAGAAAATAGGTCAACA
* *
5606492 TATTGTATCGACACTTTTAAATTTGTGTCGATACTTTTT
131 TAATGTATCGACACTTTTAAATTTGTGTCGATACATTTT
5606531 TAAATTACGC
Statistics
Matches: 499, Mismatches: 54, Indels: 32
0.85 0.09 0.05
Matches are distributed among these distances:
198 7 0.01
199 167 0.33
200 318 0.64
201 6 0.01
202 1 0.00
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (198 bp):
CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCAAAAAACATCGAAACTGAAAATTATAAT
GTAATAGGTAAATTTACAATGTAACCGATATAAATATACCGATTTTATGAGAAAATAGGTCAACA
TAATGTATCGACACTTTTAAATTTGTGTCGATACATTTTGTCCAAATGAATTCCAAACGGGGTAC
ACG
Found at i:5606513 original size:399 final size:399
Alignment explanation
Indices: 5605763--5606530 Score: 1091
Period size: 399 Copynumber: 1.9 Consensus size: 399
5605753 TAAAGTTTCT
5605763 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCAAAAAACATCGAAACCAAATATTATAAT
1 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCAAAAAACATCGAAACCAAATATTATAAT
* * * * *
5605828 GTAATAGGTAAATTTACAATGTAACCGATATAAATATACTGATTTTATGAGCAAATTGGTCAGCA
66 GTAATAGGTAAATTTACAATGTAACCAATATAAATATACCGATTTTATGAGAAAATAGGTCAACA
* * * ** * ** *
5605893 TAAATGATCGACACCTTTTAAATTTGTTTCGATACTTTTTGTCCGAGCCTTTGCTCAACGAGCTT
131 TAAATGATCGACACCTTTTAAATTTGTGTCGATACATCTTGTCCGAGAATATGCAAAACGAGCTG
* ** *
5605958 CACGCATAAAAGTGTCGATACATTTAAAATTGTATCAATCCAAAAAACATCGAAACTGAAAATTA
196 CACGCATAAAACTGTCGATACATTTAAAAAAGTATCAATCCAAAAAACATCGAAACCGAAAATTA
* **
5606023 TAATGTAATAGGTAAATATACAATGTAACCGGTATAAATATACTTGTTTTATGAGAAAATAGGTA
261 TAATGTAATAGGTAAATATACAATGTAACCGATATAAATATACCGGTTTTATGAGAAAATAGGTA
5606088 TACATAATGTATCGACACTGTTTAAATTTGTGTCGATACATTTTATCCATAATGAATTCCAAACG
326 TACATAATGTATCGACACTGTTTAAATTTGTGTCGATACATTTTATCCATAATGAATTCCAAACG
5606153 GGGTACACA
391 GGGTACACA
* * ***
5606162 CATAAAGTGTCGCTACATTTTTAAAAAGTATCGATCTC-AAAAACATCGAAA-CTGGTAATTATA
1 CATAAAGTGTCGATACATTTATAAAAAGTATCGATC-CAAAAAACATCGAAACCAAAT-ATTATA
* *
5606225 ATGTAATAGGTAAATTTACAATGTAACCAATATAAGTATACCGATTTTATGAGAAAATAGGTGAA
64 ATGTAATAGGTAAATTTACAATGTAACCAATATAAATATACCGATTTTATGAGAAAATAGGTCAA
* *
5606290 CAT-AATGTATCGACACTTTTTAGATTTGTGTCGATACATCTTGTCC-AGAATGAATGCAAAACG
129 CATAAATG-ATCGACACCTTTTAAATTTGTGTCGATACATCTTGTCCGAGAAT--ATGCAAAACG
* * *
5606353 GGGTGCACGCAT-AAACTGTCGATACATTTATAAAAAGTATCGATCCAAAAAACATCGAAACCGA
191 AGCTGCACGCATAAAACTGTCGATACATTTA-AAAAAGTATCAATCCAAAAAACATCGAAACCGA
*
5606417 AAATTATAATGTAATAGGTAAATTTACAATGTAACCGATATAAATATACCGGTTTTATGAGAAAA
255 AAATTATAATGTAATAGGTAAATATACAATGTAACCGATATAAATATACCGGTTTTATGAGAAAA
* * *
5606482 TATGT-TAACATATTGTATCGACACT-TTTAAATTTGTGTCGATACTTTTT
320 TAGGTAT-ACATAATGTATCGACACTGTTTAAATTTGTGTCGATACATTTT
5606531 TAAATTACGC
Statistics
Matches: 325, Mismatches: 37, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
398 9 0.03
399 188 0.58
400 128 0.39
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (399 bp):
CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCAAAAAACATCGAAACCAAATATTATAAT
GTAATAGGTAAATTTACAATGTAACCAATATAAATATACCGATTTTATGAGAAAATAGGTCAACA
TAAATGATCGACACCTTTTAAATTTGTGTCGATACATCTTGTCCGAGAATATGCAAAACGAGCTG
CACGCATAAAACTGTCGATACATTTAAAAAAGTATCAATCCAAAAAACATCGAAACCGAAAATTA
TAATGTAATAGGTAAATATACAATGTAACCGATATAAATATACCGGTTTTATGAGAAAATAGGTA
TACATAATGTATCGACACTGTTTAAATTTGTGTCGATACATTTTATCCATAATGAATTCCAAACG
GGGTACACA
Found at i:5606885 original size:31 final size:31
Alignment explanation
Indices: 5606818--5606887 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
5606808 TCTTTTGGTA
5606818 TTCGGGTCAGATTTTTTAAAAAAATTTCAGG
1 TTCGGGTCAGATTTTTTAAAAAAATTTCAGG
* ** *
5606849 ATCGGGTTGGATTTTTTAAAAAATATTT-GGG
1 TTCGGGTCAGATTTTTTAAAAAA-ATTTCAGG
5606880 TTCGGGTC
1 TTCGGGTC
5606888 GGGTCGGGTT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
31 28 0.88
32 4 0.12
ACGTcount: A:0.27, C:0.09, G:0.24, T:0.40
Consensus pattern (31 bp):
TTCGGGTCAGATTTTTTAAAAAAATTTCAGG
Found at i:5607494 original size:16 final size:18
Alignment explanation
Indices: 5607469--5607512 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
5607459 ACAGGTTTCG
*
5607469 GATTCTAATTC-CT-ACA
1 GATTCCAATTCACTCACA
*
5607485 GATTCCAATTCATTCACA
1 GATTCCAATTCACTCACA
5607503 GATTCCAATT
1 GATTCCAATT
5607513 TTCCTCATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 10 0.42
17 1 0.04
18 13 0.54
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.36
Consensus pattern (18 bp):
GATTCCAATTCACTCACA
Found at i:5611504 original size:200 final size:198
Alignment explanation
Indices: 5611151--5611627 Score: 622
Period size: 200 Copynumber: 2.4 Consensus size: 198
5611141 CATAATATAG
*
5611151 AGTGTCGATACATTTATTAAAAGTATCGATACCAATAACATCGAAACCGATAATTATAATGTAAT
1 AGTGTCGATACATTTATTAAAAGTATCGATCCCAA-AACATCGAAACCGATAATTATAATGTAAT
* * * ** *
5611216 AGGTAAATTTACAATGTAACTGGTATAAATATACTTGTTTTATAAAAAAATAGGCCAGCATAAAG
65 AGGTAAATTTACAATGTAACCGATAGAAATATACCGGTTTTATAAAAAAATAGGCCAGAATAAAG
*
5611281 TATCGACACTATTTAAATTTGTGTCGATACTTTTTGTCCATAATGAATGCCAAACGAGGTGCACG
130 TATCGACACTATTTAAATTTGTGTCGATA-TTTTTGTCCAGAATGAATGCCAAACGAGGTGCACG
5611346 CATAA
194 CATAA
* * *
5611351 AGTGTCGATACATTTATTAAAAGTTTCGATCCCACAAACATCGAAACCGATAATTACAATGTGAT
1 AGTGTCGATACATTTATTAAAAGTATCGATCCCA-AAACATCGAAACCGATAATTATAATGTAAT
* * * *
5611416 AGGTAAATTTACAATGTACCCGATAGAAATATACCGGTTTTATGAGAAAATATA-TCTA-AATAA
65 AGGTAAATTTACAATGTAACCGATAGAAATATACCGGTTTTAT-A-AAAAAATAGGCCAGAATAA
* * * * * * *
5611479 TGTATCGACACTTTTTAAGTTTGTGTCGATATTTTTTTCCAGAATGAATGTCTAACGAGGTGCAT
128 AGTATCGACACTATTTAAATTTGTGTCGATATTTTTGTCCAGAATGAATGCCAAACGAGGTGCAC
5611544 GCATAA
193 GCATAA
* * * *
5611550 AGTATCGATACATTTA--AAATTGTATCGATCCGAAAAACATCGAAACCGATAATTATAATTTAA
1 AGTGTCGATACATTTATTAAA-AGTATCGATCC-CAAAACATCGAAACCGATAATTATAATGTAA
5611613 TAGGT-AATTTACAAT
64 TAGGTAAATTTACAAT
5611628 ATTATCGGTA
Statistics
Matches: 243, Mismatches: 29, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
197 13 0.05
198 40 0.16
199 51 0.21
200 128 0.53
201 4 0.02
202 7 0.03
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (198 bp):
AGTGTCGATACATTTATTAAAAGTATCGATCCCAAAACATCGAAACCGATAATTATAATGTAATA
GGTAAATTTACAATGTAACCGATAGAAATATACCGGTTTTATAAAAAAATAGGCCAGAATAAAGT
ATCGACACTATTTAAATTTGTGTCGATATTTTTGTCCAGAATGAATGCCAAACGAGGTGCACGCA
TAA
Found at i:5611703 original size:23 final size:23
Alignment explanation
Indices: 5611670--5611717 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
5611660 AAATAGATCA
*
5611670 ATATAAACGCTACCTATTATATT
1 ATATAAACGCTACCTAATATATT
*
5611693 ATATAAGCGCTACCTAATATATT
1 ATATAAACGCTACCTAATATATT
5611716 AT
1 AT
5611718 TGTACTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.38
Consensus pattern (23 bp):
ATATAAACGCTACCTAATATATT
Found at i:5611763 original size:87 final size:87
Alignment explanation
Indices: 5611670--5611832 Score: 290
Period size: 87 Copynumber: 1.9 Consensus size: 87
5611660 AAATAGATCA
* * *
5611670 ATATAAACGCTACCTATTATATTATATAAGCGCTACCTAATATATTATTGTACTTAATAATATTT
1 ATATAAACGCTACATATTACATTATATAAGCGCTACCTAATATATTATTATACTTAATAATATTT
5611735 TCGGTTAAATGCTTATTTTATT
66 TCGGTTAAATGCTTATTTTATT
*
5611757 ATATAAATGCTACATATTACATTATATAAGCGCTACCTAATATATTATTATACTTAATAATATTT
1 ATATAAACGCTACATATTACATTATATAAGCGCTACCTAATATATTATTATACTTAATAATATTT
5611822 TCGGTTAAATG
66 TCGGTTAAATG
5611833 ATATAACATA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.43
Consensus pattern (87 bp):
ATATAAACGCTACATATTACATTATATAAGCGCTACCTAATATATTATTATACTTAATAATATTT
TCGGTTAAATGCTTATTTTATT
Found at i:5611803 original size:23 final size:23
Alignment explanation
Indices: 5611753--5611804 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
5611743 ATGCTTATTT
* *
5611753 TATTATATAAATGCTACATATTA
1 TATTATATAAACGCTACATAATA
* * *
5611776 CATTATATAAGCGCTACCTAATA
1 TATTATATAAACGCTACATAATA
5611799 TATTAT
1 TATTAT
5611805 TATACTTAAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.13, G:0.06, T:0.40
Consensus pattern (23 bp):
TATTATATAAACGCTACATAATA
Found at i:5622353 original size:3 final size:3
Alignment explanation
Indices: 5622245--5622337 Score: 125
Period size: 3 Copynumber: 31.3 Consensus size: 3
5622235 TTCCTTTTAT
* * * * * *
5622245 TTA TTA TTA TTA -TA TTA TTG TTG TTG TTG TTG TTG TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5622292 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5622338 CTTTTATCTT
Statistics
Matches: 87, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
2 2 0.02
3 85 0.98
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5622701 original size:12 final size:12
Alignment explanation
Indices: 5622684--5622708 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5622674 AAAGCTTTAT
5622684 TATTTTATTCGA
1 TATTTTATTCGA
5622696 TATTTTATTCGA
1 TATTTTATTCGA
5622708 T
1 T
5622709 TTATATCCGA
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:0.08, G:0.08, T:0.60
Consensus pattern (12 bp):
TATTTTATTCGA
Found at i:5633705 original size:14 final size:14
Alignment explanation
Indices: 5633686--5633722 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
5633676 AGAAAAACGA
5633686 AAAAAATTAAAAGG
1 AAAAAATTAAAAGG
5633700 AAAAAATTAAAAGG
1 AAAAAATTAAAAGG
5633714 AAAAAATTA
1 AAAAAATTA
5633723 GAGAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.73, C:0.00, G:0.11, T:0.16
Consensus pattern (14 bp):
AAAAAATTAAAAGG
Found at i:5633730 original size:13 final size:14
Alignment explanation
Indices: 5633679--5633733 Score: 67
Period size: 14 Copynumber: 3.9 Consensus size: 14
5633669 AGAGAGGAGA
5633679 AAAACGAAAAAAATT
1 AAAA-GAAAAAAATT
*
5633694 AAAAGGAAAAAATT
1 AAAAGAAAAAAATT
*
5633708 AAAAGGAAAAAATT
1 AAAAGAAAAAAATT
*
5633722 -AGAGAAAAAAAT
1 AAAAGAAAAAAAT
5633734 AAGCTCTTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
13 10 0.27
14 23 0.62
15 4 0.11
ACGTcount: A:0.73, C:0.02, G:0.13, T:0.13
Consensus pattern (14 bp):
AAAAGAAAAAAATT
Found at i:5634413 original size:24 final size:24
Alignment explanation
Indices: 5634386--5634431 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
5634376 ATTTTAAAAA
5634386 TATTTTTAGGATTTATCTTTTGAT
1 TATTTTTAGGATTTATCTTTTGAT
5634410 TATTTTTAGGATTTATCTTTTG
1 TATTTTTAGGATTTATCTTTTG
5634432 GGTGATTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.20, C:0.04, G:0.13, T:0.63
Consensus pattern (24 bp):
TATTTTTAGGATTTATCTTTTGAT
Found at i:5639623 original size:108 final size:108
Alignment explanation
Indices: 5639399--5639615 Score: 434
Period size: 108 Copynumber: 2.0 Consensus size: 108
5639389 AACATTAGAT
5639399 AGTACATCATCCACATACTATTCATTAATAGGGGCATTAGATTTTGGGTTTTTAAAACCCAACAG
1 AGTACATCATCCACATACTATTCATTAATAGGGGCATTAGATTTTGGGTTTTTAAAACCCAACAG
5639464 TAATGGTAATCGAGCCCTAGTAATACCTGAAACTCCTGATAAA
66 TAATGGTAATCGAGCCCTAGTAATACCTGAAACTCCTGATAAA
5639507 AGTACATCATCCACATACTATTCATTAATAGGGGCATTAGATTTTGGGTTTTTAAAACCCAACAG
1 AGTACATCATCCACATACTATTCATTAATAGGGGCATTAGATTTTGGGTTTTTAAAACCCAACAG
5639572 TAATGGTAATCGAGCCCTAGTAATACCTGAAACTCCTGATAAA
66 TAATGGTAATCGAGCCCTAGTAATACCTGAAACTCCTGATAAA
5639615 A
1 A
5639616 TTTCATCAAA
Statistics
Matches: 109, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
108 109 1.00
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.29
Consensus pattern (108 bp):
AGTACATCATCCACATACTATTCATTAATAGGGGCATTAGATTTTGGGTTTTTAAAACCCAACAG
TAATGGTAATCGAGCCCTAGTAATACCTGAAACTCCTGATAAA
Found at i:5648372 original size:111 final size:111
Alignment explanation
Indices: 5648178--5648400 Score: 446
Period size: 111 Copynumber: 2.0 Consensus size: 111
5648168 TGATAAGCAT
5648178 GTTGTTATTAAATAATTTGGATTTTTCCTTATAGATCCTCAAATTTTAGCTTTGTCTAGGTCCAT
1 GTTGTTATTAAATAATTTGGATTTTTCCTTATAGATCCTCAAATTTTAGCTTTGTCTAGGTCCAT
5648243 GTTGCATCGACGAACTTCCCAATATGCTTTATGCTCTATCTCCATA
66 GTTGCATCGACGAACTTCCCAATATGCTTTATGCTCTATCTCCATA
5648289 GTTGTTATTAAATAATTTGGATTTTTCCTTATAGATCCTCAAATTTTAGCTTTGTCTAGGTCCAT
1 GTTGTTATTAAATAATTTGGATTTTTCCTTATAGATCCTCAAATTTTAGCTTTGTCTAGGTCCAT
5648354 GTTGCATCGACGAACTTCCCAATATGCTTTATGCTCTATCTCCATA
66 GTTGCATCGACGAACTTCCCAATATGCTTTATGCTCTATCTCCATA
5648400 G
1 G
5648401 GTAAGTGACA
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
111 112 1.00
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (111 bp):
GTTGTTATTAAATAATTTGGATTTTTCCTTATAGATCCTCAAATTTTAGCTTTGTCTAGGTCCAT
GTTGCATCGACGAACTTCCCAATATGCTTTATGCTCTATCTCCATA
Found at i:5675926 original size:313 final size:314
Alignment explanation
Indices: 5675357--5675983 Score: 1060
Period size: 313 Copynumber: 2.0 Consensus size: 314
5675347 ACATTGTACC
*
5675357 AACCTTGGACGACTTGAATCCTAGTATCATTTGACCAACCATTCATGCAACCTATTTTAAGATGA
1 AACCTTGGACGACTTGAATCCTAGTATCATTTGACCAACCATTCATGCAACATATTTTAAGATGA
* * *
5675422 AGCCGGTGATGTTTTAGATGTTGCATTTAATGAGGTAGTATAGCGGTCCATTTACTAAAGACCCA
66 AGCCAGTGATGTTTTAGATGTTGCATTTAATGAGGCAATATAGCGGTCCATTTACTAAAGACCCA
* * * *
5675487 AGGGCACATCTTAGAGTAGTCATGGAAGTGTGTGACTCATTTTTACATAAAGGAGTACCTGAGGA
131 AGGGCACATCTTAGAGCAGTCATGGAAGTGTGCGACTCACTTGTACATAAAGGAGTACCTGAGGA
*
5675552 AGCATTGAACCTGAAGTGTTACCTTACTCCCTACGTGATAAATCTAGAGCATGGCATAACTCTTT
196 AGCATTGAACCTGAAGTGTTACCTTACTCCCTACGTGATAAATCTAGAGCACGGCATAACTCTTT
***
5675617 GTTTTCAGGTGCTATAGCATCATGGAATAAATTAACACAATTTTTTGTTGAGAT
261 GCCGTCAGGTGCTATAGCATCATGGAATAAATTAACACAATTTTTTGTTGAGAT
* *
5675671 AACCTTGGACGACTTGAATCCT-GATATCATTTGACCAACCATTCATGCAACATATTTTGAGCTG
1 AACCTTGGACGACTTGAATCCTAG-TATCATTTGACCAACCATTCATGCAACATATTTTAAGATG
*
5675735 AAGCCAGTGAT-TTTTAGATGTTGCATTTAATGAGGCAATATAGCGGTCCATTTACTAAAGATCC
65 AAGCCAGTGATGTTTTAGATGTTGCATTTAATGAGGCAATATAGCGGTCCATTTACTAAAGACCC
* *
5675799 AAGGGCACATCTTAGAGCAGTCATGGAGGTGTGCGACTCACTTGTACATCAAGGAGTACCTGAGG
130 AAGGGCACATCTTAGAGCAGTCATGGAAGTGTGCGACTCACTTGTACATAAAGGAGTACCTGAGG
* *
5675864 AAGTATTGAACCTGAAGTGTTTCCTTACTCCCTACGTGATAAATCTAGAGCACGGCATAACTCTT
195 AAGCATTGAACCTGAAGTGTTACCTTACTCCCTACGTGATAAATCTAGAGCACGGCATAACTCTT
5675929 TGCCGTCAGGTGCTATAGCATCATGGAATAAATTAACACAATTTTTTGTTGAGAT
260 TGCCGTCAGGTGCTATAGCATCATGGAATAAATTAACACAATTTTTTGTTGAGAT
5675984 CCAATCCGAC
Statistics
Matches: 293, Mismatches: 19, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
313 224 0.76
314 69 0.24
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.31
Consensus pattern (314 bp):
AACCTTGGACGACTTGAATCCTAGTATCATTTGACCAACCATTCATGCAACATATTTTAAGATGA
AGCCAGTGATGTTTTAGATGTTGCATTTAATGAGGCAATATAGCGGTCCATTTACTAAAGACCCA
AGGGCACATCTTAGAGCAGTCATGGAAGTGTGCGACTCACTTGTACATAAAGGAGTACCTGAGGA
AGCATTGAACCTGAAGTGTTACCTTACTCCCTACGTGATAAATCTAGAGCACGGCATAACTCTTT
GCCGTCAGGTGCTATAGCATCATGGAATAAATTAACACAATTTTTTGTTGAGAT
Found at i:5680907 original size:55 final size:55
Alignment explanation
Indices: 5680752--5680908 Score: 206
Period size: 55 Copynumber: 2.9 Consensus size: 55
5680742 TTACCGAAAG
* **
5680752 GGCACTGTGTGTGCAACCCCACGAAATTCATAATGAGTTTAACAATTTTCGTATT
1 GGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATGAATTTTCGTATT
* * * *
5680807 GGCACTATGTGCGCAACCTCACGAAATTCATAATAAGTTTATGAATTTTCTTATT
1 GGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATGAATTTTCGTATT
* * ** *
5680862 GGTACTATGTGTACAACCCCACTTAATTCATAATGAGTTTGTGAATT
1 GGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATGAATT
5680909 ACCGTATACG
Statistics
Matches: 87, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
55 87 1.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (55 bp):
GGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATGAATTTTCGTATT
Found at i:5687867 original size:17 final size:18
Alignment explanation
Indices: 5687841--5687881 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
5687831 CAAATAATAG
5687841 GGTTTATGAT-ACATTAA
1 GGTTTATGATCACATTAA
* *
5687858 GGTTTGTGATCACATTAG
1 GGTTTATGATCACATTAA
5687876 GGTTTA
1 GGTTTA
5687882 CAAAATTGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.27, C:0.07, G:0.24, T:0.41
Consensus pattern (18 bp):
GGTTTATGATCACATTAA
Found at i:5700904 original size:55 final size:55
Alignment explanation
Indices: 5700813--5700959 Score: 179
Period size: 55 Copynumber: 2.7 Consensus size: 55
5700803 ACCGAAATGG
* * * * *
5700813 CACTGTGTGTGCAACCTCACAAAATTCGTAATGAGTTTATGAATATCCGTATTGA
1 CACTATGTGTGCAACCTCACTAAATTCATAATGAGTTTATAAATATCCATATTGA
* * * *
5700868 CACTATGTGTGCAACCTCACTAAATTCATAACGAGTTTATAAATTTCTATATTGG
1 CACTATGTGTGCAACCTCACTAAATTCATAATGAGTTTATAAATATCCATATTGA
* *
5700923 CAATATGTGTGCAACCCCACGT-AATTCATAATGAGTT
1 CACTATGTGTGCAACCTCAC-TAAATTCATAATGAGTT
5700960 GTGAATTACC
Statistics
Matches: 79, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
55 78 0.99
56 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (55 bp):
CACTATGTGTGCAACCTCACTAAATTCATAATGAGTTTATAAATATCCATATTGA
Found at i:5708931 original size:30 final size:29
Alignment explanation
Indices: 5708875--5708942 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 29
5708865 TGTCAAGGGG
5708875 GACCACCAAACTTTCAATTGAATCAATCA
1 GACCACCAAACTTTCAATTGAATCAATCA
* * *
5708904 GACCACCCAACTATTTAATTGATTCAATCA
1 GACCACCAAACT-TTCAATTGAATCAATCA
* *
5708934 AACAACCAA
1 GACCACCAA
5708943 CCGTTAATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 11 0.34
30 21 0.66
ACGTcount: A:0.43, C:0.28, G:0.06, T:0.24
Consensus pattern (29 bp):
GACCACCAAACTTTCAATTGAATCAATCA
Found at i:5709108 original size:374 final size:377
Alignment explanation
Indices: 5708501--5709253 Score: 1156
Period size: 374 Copynumber: 2.0 Consensus size: 377
5708491 AAATCAATGT
* * **
5708501 GACCACCGAACTTCCAAATGAATCAATCAGACCACCCATCTATTTAATTGATTCAATCAAACAGT
1 GACCACCAAACTTCCAAATGAATCAATCAGACCACCCAACTATTTAATTGATTCAATCAAACAAC
** * * *
5708566 CGGCTATTAATTTTTAACGGAGGTGGTGATGTGTCCGTTAATAAAATTGGCATAATTATATATTT
66 CAACCATTAATTTTTAACAGAAGTGGTGATGTGTCCGTTAATAAAATTGGCATAATTATATATTT
* * *
5708631 GGTTCTTAATATTTACATATTCTGTCAATTTTGACACTATTTTAATTTAATTAAATAAATTTAAC
131 GGTTCTTAATATTTACATATTCTATCAATTTCGACACTATTTTAATTCAATTAAATAAATTTAAC
* * * * * *
5708696 TATCCAATTTGTATGTGACACGTGTTAATACATGATTGGAAGGTTTTATTTAT-AATTTTAAATT
196 TATCCAATTAGAACGTGACACATGTCAATACATGATTGGAAGATTTTATTTATGAATTTTAAATT
* *
5708760 ATTTAATTAAATAAATTTTCTATCCAATCATGT-GTGACACGTGTCACCACCCAATTGAAATT-A
261 ATTTAATTAAATAAATTTTCTATCCAATCAAGTAGTGACACGTCTCACCACCCAATTG-AATTGA
*
5708823 AAATAAAGGGATTCAACA-TGCTTGCAAGGGGAAT-AGAACCTGTGTCAAGGGG
325 AAATAAAGGGATCCAACATTGCTTGCAAGGGGAATCA-AACCTGTGTCAAGGGG
* *
5708875 GACCACCAAACTTTCAATTGAATCAATCAGACCACCCAACTATTTAATTGATTCAATCAAACAAC
1 GACCACCAAACTTCCAAATGAATCAATCAGACCACCCAACTATTTAATTGATTCAATCAAACAAC
* * * * *
5708940 CAACCGTTAATTTTTAACAGAAGTGGTGTTGTTTTCGTTAATGAAATTGGCATAATTATATATTT
66 CAACCATTAATTTTTAACAGAAGTGGTGATGTGTCCGTTAATAAAATTGGCATAATTATATATTT
* * *
5709005 GGTTCTTAATATTTATATATTCTATCAATTTCGTCATTATTTTAATTCAATTAAATAAATTTAAC
131 GGTTCTTAATATTTACATATTCTATCAATTTCGACACTATTTTAATTCAATTAAATAAATTTAAC
5709070 TATCCAATTAGAACGTGACACATGTCAATACATGATTGGAAGATTTTATTTATGAATTTTAAATT
196 TATCCAATTAGAACGTGACACATGTCAATACATGATTGGAAGATTTTATTTATGAATTTTAAATT
* *
5709135 ATTTAATTAAATAATTTTTCTATCCAATCAAGTAGTGACACTTCTCACCACCCAATTGAATTGAA
261 ATTTAATTAAATAAATTTTCTATCCAATCAAGTAGTGACACGTCTCACCACCCAATTGAATTGAA
5709200 AATAAAGGGATCCAACATTGCTTGCAAGGGGAATCAAACCTGTGTCAAGGGG
326 AATAAAGGGATCCAACATTGCTTGCAAGGGGAATCAAACCTGTGTCAAGGGG
5709252 GA
1 GA
5709254 AAAGCTACCC
Statistics
Matches: 341, Mismatches: 33, Indels: 7
0.90 0.09 0.02
Matches are distributed among these distances:
374 220 0.65
375 46 0.13
376 40 0.12
377 34 0.10
378 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (377 bp):
GACCACCAAACTTCCAAATGAATCAATCAGACCACCCAACTATTTAATTGATTCAATCAAACAAC
CAACCATTAATTTTTAACAGAAGTGGTGATGTGTCCGTTAATAAAATTGGCATAATTATATATTT
GGTTCTTAATATTTACATATTCTATCAATTTCGACACTATTTTAATTCAATTAAATAAATTTAAC
TATCCAATTAGAACGTGACACATGTCAATACATGATTGGAAGATTTTATTTATGAATTTTAAATT
ATTTAATTAAATAAATTTTCTATCCAATCAAGTAGTGACACGTCTCACCACCCAATTGAATTGAA
AATAAAGGGATCCAACATTGCTTGCAAGGGGAATCAAACCTGTGTCAAGGGG
Found at i:5709786 original size:109 final size:109
Alignment explanation
Indices: 5709597--5709859 Score: 334
Period size: 109 Copynumber: 2.4 Consensus size: 109
5709587 AATTTTGAAA
** * * *
5709597 TTAATTCGGTTCAGTGAATAATTTT-AAAAAAAATGGTTTGATTAACCAAACTGAATTAACCAAA
1 TTAATTCGGTTCAGTGAATAATTTTCAAATTAATTGGTTCGATTAACCAAACTGAAATAACCAAA
*
5709661 ATTTTCCTTCTATTAATTCGATTAATAATTTT-AAAAAAATCGG
66 ATTTTCCTTCAATTAATTCGATTAATAATTTTCAAAAAAATCGG
* *
5709704 TTAATTCGGTTCAGTGAATAATTTTCAAATTAATTCGGTTCGATTAACCGAACTGAAATAACCGA
1 TTAATTCGGTTCAGTGAATAATTTTCAAATTAATT-GGTTCGATTAACCAAACTGAAATAACCAA
* * * * *
5709769 ATTTTTGCTTCAATTAATTCGGTTGATAATTTTCAAAAAATTCGG
65 AATTTTCCTTCAATTAATTCGATTAATAATTTTCAAAAAAATCGG
* * * *
5709814 TTAATTCGGTTCGGTTAATCATTCTCAAATTAATTTGGTTCG-TTAA
1 TTAATTCGGTTCAGTGAATAATTTTCAAATTAA-TTGGTTCGATTAA
5709860 TAATTTTCAA
Statistics
Matches: 135, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
107 25 0.19
108 6 0.04
109 57 0.42
110 45 0.33
111 2 0.01
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (109 bp):
TTAATTCGGTTCAGTGAATAATTTTCAAATTAATTGGTTCGATTAACCAAACTGAAATAACCAAA
ATTTTCCTTCAATTAATTCGATTAATAATTTTCAAAAAAATCGG
Found at i:5709869 original size:28 final size:29
Alignment explanation
Indices: 5709814--5709882 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
5709804 AAAAATTCGG
* *
5709814 TTAATTCGGTTCGGTTAATCATTCTCAAA
1 TTAATTTGGTTCGGTTAATAATTCTCAAA
*
5709843 TTAATTTGGTTC-GTTAATAATTTTCAAA
1 TTAATTTGGTTCGGTTAATAATTCTCAAA
*
5709871 TAAATTTTGGTT
1 TTAA-TTTGGTT
5709883 GGATTAACAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 17 0.49
29 18 0.51
ACGTcount: A:0.29, C:0.10, G:0.13, T:0.48
Consensus pattern (29 bp):
TTAATTTGGTTCGGTTAATAATTCTCAAA
Found at i:5714561 original size:21 final size:21
Alignment explanation
Indices: 5714537--5714589 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
5714527 TGTCTCAAAA
* *
5714537 GACCTCATGTATGTCCCGGAG
1 GACCTCATATATGTCCCGAAG
*
5714558 GACCTCGTATATGTCCCGAAG
1 GACCTCATATATGTCCCGAAG
5714579 GACCTCATATA
1 GACCTCATATA
5714590 ACCCTCGACT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (21 bp):
GACCTCATATATGTCCCGAAG
Found at i:5714746 original size:14 final size:16
Alignment explanation
Indices: 5714727--5714765 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 16
5714717 TTCTCTTATA
5714727 ATCACATATATC-T-T
1 ATCACATATATCATGT
5714741 ATCACATA-A-CATGT
1 ATCACATATATCATGT
5714755 ATCACATATAT
1 ATCACATATAT
5714766 ACATAATCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
12 1 0.05
13 2 0.10
14 17 0.81
15 1 0.05
ACGTcount: A:0.41, C:0.21, G:0.03, T:0.36
Consensus pattern (16 bp):
ATCACATATATCATGT
Found at i:5721567 original size:21 final size:21
Alignment explanation
Indices: 5721538--5721600 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
5721528 ATGTAAGATT
* * *
5721538 TATCTTGAAGGACCTCATGTA
1 TATCCTGAAAGACCTCATATA
5721559 TATCCTGAAAGACCTCATATA
1 TATCCTGAAAGACCTCATATA
5721580 TATCCCT-AAAGACCTCATATA
1 TAT-CCTGAAAGACCTCATATA
5721601 ACCCTCAACT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 35 0.92
22 3 0.08
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.30
Consensus pattern (21 bp):
TATCCTGAAAGACCTCATATA
Found at i:5722341 original size:18 final size:19
Alignment explanation
Indices: 5722318--5722355 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
5722308 ATGGTAATGA
5722318 TACCC-TAGGTATCGATAC
1 TACCCTTAGGTATCGATAC
5722336 TACCCTTTAGGTATCGATAC
1 TACCC-TTAGGTATCGATAC
5722356 CCCTTGAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
20 13 0.72
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (19 bp):
TACCCTTAGGTATCGATAC
Found at i:5722359 original size:18 final size:19
Alignment explanation
Indices: 5722323--5722360 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
5722313 AATGATACCC
5722323 TAGGTATCGATACTACCCTT
1 TAGGTATCGATAC-ACCCTT
5722343 TAGGTATCGATAC-CCCTT
1 TAGGTATCGATACACCCTT
5722361 GAATATCTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
20 13 0.72
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (19 bp):
TAGGTATCGATACACCCTT
Found at i:5725534 original size:31 final size:31
Alignment explanation
Indices: 5725496--5725598 Score: 93
Period size: 31 Copynumber: 3.3 Consensus size: 31
5725486 CTAATGTGAC
5725496 TCTTGGGTAGACT-CTGCGGCCCTGAGAATTT
1 TCTTGGGTAG-CTCCTGCGGCCCTGAGAATTT
* * *
5725527 TCTTGGGTAGGTCCTGCGGCCCTGATATTTT
1 TCTTGGGTAGCTCCTGCGGCCCTGAGAATTT
* * ** * *
5725558 TCTTGGCTAGGC-CCCGTAGCCCCGAGAACTT
1 TCTTGGGTA-GCTCCTGCGGCCCTGAGAATTT
5725589 TCTTGGGTAG
1 TCTTGGGTAG
5725599 GCTCTCAGGC
Statistics
Matches: 57, Mismatches: 13, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
30 2 0.04
31 54 0.95
32 1 0.02
ACGTcount: A:0.14, C:0.25, G:0.29, T:0.32
Consensus pattern (31 bp):
TCTTGGGTAGCTCCTGCGGCCCTGAGAATTT
Found at i:5730404 original size:21 final size:19
Alignment explanation
Indices: 5730367--5730406 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
5730357 TTTAATAATA
*
5730367 AATTTTTTTAAATAAAAAC
1 AATTTTTTTAAAAAAAAAC
5730386 AATTTTTAATTAAAAAAAAAC
1 AATTTTT--TTAAAAAAAAAC
5730407 TTAACTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
21 11 0.61
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTTTTTTAAAAAAAAAC
Found at i:5736918 original size:13 final size:13
Alignment explanation
Indices: 5736900--5736951 Score: 77
Period size: 13 Copynumber: 4.0 Consensus size: 13
5736890 GTCATAAATC
*
5736900 TATGACGCGCATT
1 TATGACACGCATT
*
5736913 TATGACACACATT
1 TATGACACGCATT
5736926 TATGACACGCATT
1 TATGACACGCATT
*
5736939 TATGACGCGCATT
1 TATGACACGCATT
5736952 GAGCGTCATT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 35 1.00
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (13 bp):
TATGACACGCATT
Found at i:5737029 original size:85 final size:85
Alignment explanation
Indices: 5736921--5737076 Score: 224
Period size: 85 Copynumber: 1.8 Consensus size: 85
5736911 TTTATGACAC
* * * *
5736921 ACATTTATGACACGCATTTATGACGCGCATTGAGCGTCATTGAAGCCCCCGTCA-TAAATTAAGA
1 ACATTTATGACACGCATGTATGACGCACAATGAGCGTCATTGAAGCCCCCGTCATTAAA-AAAGA
5736985 TGACACATATTTGTGTGTCAT
65 TGACACATATTTGTGTGTCAT
** * *
5737006 ACATTTATGACACGCATGTATGACTTACAATGAGCGTCATTGAAGCTCCTGTCATTAAAAAAGAT
1 ACATTTATGACACGCATGTATGACGCACAATGAGCGTCATTGAAGCCCCCGTCATTAAAAAAGAT
5737071 GACACA
66 GACACA
5737077 CATTCAGGGG
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
85 58 0.94
86 4 0.06
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.29
Consensus pattern (85 bp):
ACATTTATGACACGCATGTATGACGCACAATGAGCGTCATTGAAGCCCCCGTCATTAAAAAAGAT
GACACATATTTGTGTGTCAT
Found at i:5737115 original size:2 final size:2
Alignment explanation
Indices: 5737108--5737140 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5737098 TTTCGTAAAT
5737108 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5737141 TAGATTCACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5746504 original size:2 final size:2
Alignment explanation
Indices: 5746497--5746537 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
5746487 CAAGTGATGA
5746497 AT 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 AT A
5746538 GATCACAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5753876 original size:27 final size:27
Alignment explanation
Indices: 5753846--5753929 Score: 75
Period size: 27 Copynumber: 3.1 Consensus size: 27
5753836 GTTTCGGCAC
5753846 TATGTGTGCAACCCACAGAATTCATCA
1 TATGTGTGCAACCCACAGAATTCATCA
* * * **
5753873 TATGTTGATG-AA-CAACCG-TTTCGGCA
1 TATG-TG-TGCAACCCACAGAATTCATCA
5753899 CTATGTGTGCAACCCACAGAATTCATCA
1 -TATGTGTGCAACCCACAGAATTCATCA
5753927 TAT
1 TAT
5753930 ATTGATGAAC
Statistics
Matches: 41, Mismatches: 10, Indels: 12
0.65 0.16 0.19
Matches are distributed among these distances:
25 2 0.05
26 9 0.22
27 19 0.46
28 9 0.22
29 2 0.05
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.29
Consensus pattern (27 bp):
TATGTGTGCAACCCACAGAATTCATCA
Found at i:5753889 original size:31 final size:31
Alignment explanation
Indices: 5753854--5753943 Score: 72
Period size: 27 Copynumber: 3.2 Consensus size: 31
5753844 ACTATGTGTG
5753854 CAACCCACAGAATTCATCATATGTTGATGAA
1 CAACCCACAGAATTCATCATATGTTGATGAA
* **
5753885 CAA--C-C-G-TTTCGGCACTATG-TG-TG--
1 CAACCCACAGAATTCATCA-TATGTTGATGAA
*
5753908 CAACCCACAGAATTCATCATATATTGATGAA
1 CAACCCACAGAATTCATCATATGTTGATGAA
5753939 CAACC
1 CAACC
5753944 ATTTCGGTAC
Statistics
Matches: 42, Mismatches: 7, Indels: 20
0.61 0.10 0.29
Matches are distributed among these distances:
23 3 0.07
25 3 0.07
26 8 0.19
27 9 0.21
28 8 0.19
29 3 0.07
31 8 0.19
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (31 bp):
CAACCCACAGAATTCATCATATGTTGATGAA
Found at i:5754231 original size:54 final size:54
Alignment explanation
Indices: 5753787--5754208 Score: 592
Period size: 54 Copynumber: 7.8 Consensus size: 54
5753777 TTTTCGTATG
* * *
5753787 GGCACTATGTGTGCAACCCATGGAATTCATTATATGTTGATGAACAATCGTTTC
1 GGCACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCGTTTC
*
5753841 GGCACTATGTGTGCAACCCACAGAATTCATCATATGTTGATGAACAACCGTTTC
1 GGCACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCGTTTC
* * *
5753895 GGCACTATGTGTGCAACCCACAGAATTCATCATATATTGATGAACAACCATTTC
1 GGCACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCGTTTC
* * * *
5753949 GGTACTATGTGTGTAACTCACGAAATTCATCATATGTTGATGAACAACCGTTTC
1 GGCACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCGTTTC
* * * *
5754003 GGCACTATGTGTGTAACCCAAGGAATTCATAATATTTTGATGAACAACCGTTTC
1 GGCACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCGTTTC
* * * * * *
5754057 GACACTATGTGTGGAACCCAAGTAATTCATCATATGTTAATGAACAACTGTTTC
1 GGCACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCGTTTC
* * *
5754111 GGTACTATGTGTGTAACCCACGAAATTCATCATATGTTGATGAACAACCGTTTC
1 GGCACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCGTTTC
* * * *
5754165 GGCACTACGTGTGAAACCCATGGAATTCATCATATGTTTATGAA
1 GGCACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAA
5754209 TGATCGTATG
Statistics
Matches: 329, Mismatches: 39, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 329 1.00
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (54 bp):
GGCACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCGTTTC
Found at i:5754262 original size:56 final size:56
Alignment explanation
Indices: 5754188--5754347 Score: 223
Period size: 56 Copynumber: 2.9 Consensus size: 56
5754178 AAACCCATGG
* * *
5754188 AATTCATCATATGTTTATGAATGAT-CGTATGGGCACTGTGTGTGCAAAAACTAAGC
1 AATTCATAATAAGTTTATGAATG-TCCGTATGGGCACTGTGTGTGCAAAAACTAAGA
* *
5754244 AATTCATAATAAGTTTATGAATGTCCGTATGGGCACTGTGTGTGTAAAAACTAATA
1 AATTCATAATAAGTTTATGAATGTCCGTATGGGCACTGTGTGTGCAAAAACTAAGA
* * **
5754300 AATTCATAATAAGTTTATGAATTTCCATATGGGCACTACGTGTGCAAA
1 AATTCATAATAAGTTTATGAATGTCCGTATGGGCACTGTGTGTGCAAA
5754348 CTATAGAGTT
Statistics
Matches: 93, Mismatches: 10, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
55 1 0.01
56 92 0.99
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.33
Consensus pattern (56 bp):
AATTCATAATAAGTTTATGAATGTCCGTATGGGCACTGTGTGTGCAAAAACTAAGA
Found at i:5754286 original size:162 final size:161
Alignment explanation
Indices: 5753739--5754286 Score: 550
Period size: 162 Copynumber: 3.4 Consensus size: 161
5753729 AATGGAACCG
* * **** * *
5753739 TGTGTTCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTATGTGTGCAAC
1 TGTGTGCAAAACCAAG-AATTCATAATAAGTTTATGAACAACCGTATCGGCAC-ATGTGTGTAAC
* * * * *
5753804 CCATGGAATTCATTATATGTTGATGAACAATCGTTTCGGCACTATGTGTGCAACCCACA-GAATT
64 CCACGAAATTCATCATATGTTGATGAACAACCGTTTCGGCACTATGTGTGAAACCCA-AGGAATT
*
5753868 CATCATATGTTGATGAACAACCGTTTCGGCACTA
128 CATCATATGTTTATGAACAACCGTTTCGGCACTA
* * * * * *
5753902 TGTGTGC-AACCCACAGAATTCATCATATA-TTGATGAACAACCATTTCGGTACTATGTGTGTAA
1 TGTGTGCAAAACCA-AGAATTCATAATA-AGTTTATGAACAACCGTATCGGCAC-ATGTGTGTAA
* *
5753965 CTCACGAAATTCATCATATGTTGATGAACAACCGTTTCGGCACTATGTGTGTAACCCAAGGAATT
63 CCCACGAAATTCATCATATGTTGATGAACAACCGTTTCGGCACTATGTGTGAAACCCAAGGAATT
* *
5754030 CATAATAT-TTTGATGAACAACCGTTTCGACACTA
128 CATCATATGTTT-ATGAACAACCGTTTCGGCACTA
* * * * * * * *
5754064 TGTGTG-GAACCCAAGTAATTCATCATATGTTAATGAACAACTGTTTCGGTACTATGTGTGTAAC
1 TGTGTGCAAAACCAAG-AATTCATAATAAGTTTATGAACAACCGTATCGGCAC-ATGTGTGTAAC
* *
5754128 CCACGAAATTCATCATATGTTGATGAACAACCGTTTCGGCACTACGTGTGAAACCCATGGAATTC
64 CCACGAAATTCATCATATGTTGATGAACAACCGTTTCGGCACTATGTGTGAAACCCAAGGAATTC
** * * * *
5754193 ATCATATGTTTATGAATGATCGTATGGGCACTG
129 ATCATATGTTTATGAACAACCGTTTCGGCACTA
* *** *
5754226 TGTGTGCAAAAACTAAGCAATTCATAATAAGTTTATGAATGTCCGTATGGGCAC-TGTGTGT
1 TGTGTGC-AAAACCAAG-AATTCATAATAAGTTTATGAACAACCGTATCGGCACATGTGTGT
5754287 GTAAAAACTA
Statistics
Matches: 322, Mismatches: 53, Indels: 21
0.81 0.13 0.05
Matches are distributed among these distances:
161 5 0.02
162 273 0.85
163 12 0.04
164 32 0.10
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (161 bp):
TGTGTGCAAAACCAAGAATTCATAATAAGTTTATGAACAACCGTATCGGCACATGTGTGTAACCC
ACGAAATTCATCATATGTTGATGAACAACCGTTTCGGCACTATGTGTGAAACCCAAGGAATTCAT
CATATGTTTATGAACAACCGTTTCGGCACTA
Found at i:5754490 original size:29 final size:29
Alignment explanation
Indices: 5754444--5754501 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
5754434 GAAGTGCATA
5754444 ACGGTGCATCAAAAGCATAAAAGGATGCC
1 ACGGTGCATCAAAAGCATAAAAGGATGCC
* * * *
5754473 ACGGTGCATTAAAGGCATGAAATGATGCC
1 ACGGTGCATCAAAAGCATAAAAGGATGCC
5754502 CTAAATGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.38, C:0.19, G:0.26, T:0.17
Consensus pattern (29 bp):
ACGGTGCATCAAAAGCATAAAAGGATGCC
Found at i:5756910 original size:54 final size:54
Alignment explanation
Indices: 5756632--5756903 Score: 341
Period size: 54 Copynumber: 5.0 Consensus size: 54
5756622 TATGTGTATC
* ** * * * *
5756632 ATAGGCACTAGGTGTATAACCCAC-ATAATTCATCATACGTTAATGAGCGACCAT
1 ATAGGCACTAAGTGTGCAACCCACGA-AATTCATCATATGTTGATGAACGACCGT
* * *
5756686 TTAGGCACTAAGTGTGCAACCCACGTAATTCATCATATGTTGATGAATGACCGT
1 ATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCGT
* * * * *
5756740 ATAGGCACTAAATGTACAACCCAC-AGAACTCATCATATGCTGATGAACGACCAT
1 ATAGGCACTAAGTGTGCAACCCACGA-AATTCATCATATGTTGATGAACGACCGT
*
5756794 ATAGGCACTAAGTGTGTAACCCACGAAATTCATCATATGTTGATGAACGACCGT
1 ATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCGT
* * *
5756848 ATAGGCACTAAGTATGCAACCCACGAAATTCATCATATATTGATAAACGACCGT
1 ATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCGT
5756902 AT
1 AT
5756904 CAGCACTTCG
Statistics
Matches: 187, Mismatches: 28, Indels: 6
0.85 0.13 0.03
Matches are distributed among these distances:
54 186 0.99
55 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.25
Consensus pattern (54 bp):
ATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCGT
Found at i:5762711 original size:21 final size:21
Alignment explanation
Indices: 5762680--5762754 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
5762670 TCAGATGAGG
*
5762680 AGTATCAATACTGATGCAATT
1 AGTATCGATACTGATGCAATT
* *
5762701 AGTGTCGATACTGAT---ATG
1 AGTATCGATACTGATGCAATT
* *
5762719 GGTATCGATATTGATGCAATT
1 AGTATCGATACTGATGCAATT
5762740 AGTATCGATACTGAT
1 AGTATCGATACTGAT
5762755 ATGGGTATCG
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
18 14 0.33
21 28 0.67
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.35
Consensus pattern (21 bp):
AGTATCGATACTGATGCAATT
Found at i:5762728 original size:18 final size:18
Alignment explanation
Indices: 5762705--5762768 Score: 74
Period size: 18 Copynumber: 3.4 Consensus size: 18
5762695 GCAATTAGTG
5762705 TCGATACTGATATGGGTA
1 TCGATACTGATATGGGTA
* **
5762723 TCGATATTGATGCAATTAGTA
1 TCGATACTGAT---ATGGGTA
5762744 TCGATACTGATATGGGTA
1 TCGATACTGATATGGGTA
5762762 TCGATAC
1 TCGATAC
5762769 CATGGAATCC
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
18 22 0.59
21 15 0.41
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.34
Consensus pattern (18 bp):
TCGATACTGATATGGGTA
Found at i:5762735 original size:39 final size:39
Alignment explanation
Indices: 5762681--5762768 Score: 149
Period size: 39 Copynumber: 2.3 Consensus size: 39
5762671 CAGATGAGGA
* *
5762681 GTATCAATACTGATGCAATTAGTGTCGATACTGATATGG
1 GTATCGATACTGATGCAATTAGTATCGATACTGATATGG
*
5762720 GTATCGATATTGATGCAATTAGTATCGATACTGATATGG
1 GTATCGATACTGATGCAATTAGTATCGATACTGATATGG
5762759 GTATCGATAC
1 GTATCGATAC
5762769 CATGGAATCC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.31, C:0.12, G:0.23, T:0.34
Consensus pattern (39 bp):
GTATCGATACTGATGCAATTAGTATCGATACTGATATGG
Found at i:5763385 original size:162 final size:162
Alignment explanation
Indices: 5763193--5763502 Score: 482
Period size: 162 Copynumber: 1.9 Consensus size: 162
5763183 TACTATAGAT
* *
5763193 ACTAAGTGTGCAACCCACATATTTCATCATATGTTGATGAACGA-CTGTATAGGCACTAAGTGTG
1 ACTAAGTGTGCAACCCACAAAATTCATCATATGTTGATGAACGACCT-TATAGGCACTAAGTGTG
* * * *
5763257 CACCCCACGGAAA-TCATCATTTGTTTATGAAC-AACCGTATAGGCACTAAGTGTGCAACCCACA
65 AAACCCAC-GAAATTCATCATTTGTTGATGAACGAA-CGTATAAGCACTAAGTGTGCAACCCACA
*
5763320 GAATTCATCATATGTTGATGAACGACCGTATAAGC
128 GAATTCATAATATGTTGATGAACGACCGTATAAGC
*
5763355 ACTAAGTGTGCAACCCACAAAATTCATCATATGTTGATGAACGACCTTATAGGCACTATGTGTGA
1 ACTAAGTGTGCAACCCACAAAATTCATCATATGTTGATGAACGACCTTATAGGCACTAAGTGTGA
*
5763420 AACCCACGAAATTCATCATTTGTTGATGAACGAATGTATAAGCACTAAGTGTGCAACCCACAGAA
66 AACCCACGAAATTCATCATTTGTTGATGAACGAACGTATAAGCACTAAGTGTGCAACCCACAGAA
*
5763485 TTCATAATATGTTTATGA
131 TTCATAATATGTTGATGA
5763503 GCAACCATGT
Statistics
Matches: 135, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
161 4 0.03
162 127 0.94
163 4 0.03
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (162 bp):
ACTAAGTGTGCAACCCACAAAATTCATCATATGTTGATGAACGACCTTATAGGCACTAAGTGTGA
AACCCACGAAATTCATCATTTGTTGATGAACGAACGTATAAGCACTAAGTGTGCAACCCACAGAA
TTCATAATATGTTGATGAACGACCGTATAAGC
Found at i:5763528 original size:54 final size:54
Alignment explanation
Indices: 5763193--5763502 Score: 424
Period size: 54 Copynumber: 5.7 Consensus size: 54
5763183 TACTATAGAT
* * *
5763193 ACTAAGTGTGCAACCCACATATTTCATCATATGTTGATGAACGACTGTATAGGC
1 ACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCGTATAGGC
* * * * * *
5763247 ACTAAGTGTGCACCCCACGGAAATCATCATTTGTTTATGAACAACCGTATAGGC
1 ACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCGTATAGGC
*
5763301 ACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCGTATAAGC
1 ACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCGTATAGGC
* *
5763355 ACTAAGTGTGCAACCCACAAAATTCATCATATGTTGATGAACGACCTTATAGGC
1 ACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCGTATAGGC
* * * ** *
5763409 ACTATGTGTGAAACCCAC-GAAATTCATCATTTGTTGATGAACGAATGTATAAGC
1 ACTAAGTGTGCAACCCACAG-AATTCATCATATGTTGATGAACGACCGTATAGGC
* *
5763463 ACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGA
1 ACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGA
5763503 GCAACCATGT
Statistics
Matches: 222, Mismatches: 32, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
54 221 1.00
55 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (54 bp):
ACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCGTATAGGC
Found at i:5766154 original size:175 final size:175
Alignment explanation
Indices: 5765863--5766215 Score: 690
Period size: 175 Copynumber: 2.0 Consensus size: 175
5765853 ATTTTACAAC
5765863 TTTAAAGTTGAACTTTTTTATATAACAAAAAGGGAGAGATGTATGGGTTTGAAAAATTCAATTTC
1 TTTAAAGTTGAACTTTTTTATATAACAAAAAGGGAGAGATGTATGGGTTTGAAAAATTCAATTTC
5765928 TTAACGAAAAAGGGGAGCTAAACATTTTCATACTTTTTCCAACAATTGATATATTTTTTCATTAA
66 TTAACGAAAAAGGGGAGCTAAACATTTTCATACTTTTTCCAACAATTGATATATTTTTTCATTAA
5765993 ATATTTTATTAAAGGAGAGTTTTTACC-AAAATAATTTTCAAATGT
131 ATATTTTATTAAAGGAGAG-TTTTACCAAAAATAATTTTCAAATGT
5766038 TTTAAAGTTGAACTTTTTTATATAACAAAAAGGGAGAGATGTATGGGTTTGAAAAATTCAATTTC
1 TTTAAAGTTGAACTTTTTTATATAACAAAAAGGGAGAGATGTATGGGTTTGAAAAATTCAATTTC
5766103 TTAACGAAAAAGGGGAGCTAAACATTTTCATACTTTTTCCAACAATTGATATATTTTTTCATTAA
66 TTAACGAAAAAGGGGAGCTAAACATTTTCATACTTTTTCCAACAATTGATATATTTTTTCATTAA
5766168 ATATTTTATTAAAGGAGAGTTTTACCAAAAATAATTTTCAAATGT
131 ATATTTTATTAAAGGAGAGTTTTACCAAAAATAATTTTCAAATGT
5766213 TTT
1 TTT
5766216 GTTATATCAA
Statistics
Matches: 177, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
174 7 0.04
175 170 0.96
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (175 bp):
TTTAAAGTTGAACTTTTTTATATAACAAAAAGGGAGAGATGTATGGGTTTGAAAAATTCAATTTC
TTAACGAAAAAGGGGAGCTAAACATTTTCATACTTTTTCCAACAATTGATATATTTTTTCATTAA
ATATTTTATTAAAGGAGAGTTTTACCAAAAATAATTTTCAAATGT
Found at i:5766427 original size:20 final size:20
Alignment explanation
Indices: 5766383--5766421 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5766373 ACGTACAAAA
* *
5766383 AGTATCGATATTGTTCTTAC
1 AGTATCGATAATGTTCGTAC
5766403 AGTATCGATAATGTTCGTA
1 AGTATCGATAATGTTCGTA
5766422 TGGTATTGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (20 bp):
AGTATCGATAATGTTCGTAC
Found at i:5767214 original size:2 final size:2
Alignment explanation
Indices: 5767207--5767256 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
5767197 AATCCTAACA
5767207 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5767249 AT AT AT AT
1 AT AT AT AT
5767257 TGATATTGGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5771432 original size:30 final size:28
Alignment explanation
Indices: 5771396--5771452 Score: 87
Period size: 30 Copynumber: 2.0 Consensus size: 28
5771386 AAAAAAATTG
5771396 TAATAATAATAATAAAATATAAGATAACGA
1 TAATAATAATAATAAAATA-AA-ATAACGA
*
5771426 TAATAATAATAATATAATAAAATAACG
1 TAATAATAATAATAAAATAAAATAACG
5771453 GAAAAAAACC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 6 0.23
29 2 0.08
30 18 0.69
ACGTcount: A:0.63, C:0.04, G:0.05, T:0.28
Consensus pattern (28 bp):
TAATAATAATAATAAAATAAAATAACGA
Found at i:5771814 original size:86 final size:86
Alignment explanation
Indices: 5771650--5771854 Score: 256
Period size: 87 Copynumber: 2.3 Consensus size: 86
5771640 CGTCTAAGGG
* * * * *
5771650 TGACACGGCTCCTACGTGATGAGGAAATCTGGTCATCTTTAGGGATGATAACTCGTTCCTACGTA
1 TGACACGGCT-CTACGTGATGA-GAGATCTGGCCATCTTAAAGGATGATAACACGTTCCTACGTA
5771715 ATGGGACGACTGGTTATC-A-GGT
64 ATGGGACGACTGG-TATCTATGGT
*
5771737 TGACACGGCTCTTACGTGATGAGAGATCTGGCCATC-TAAAGG-TGATAACACGGTTCCTACGTG
1 TGACACGGCTC-TACGTGATGAGAGATCTGGCCATCTTAAAGGATGATAACAC-GTTCCTACGTA
5771800 ATGAGGACGACTGGTATCTATGGT
64 ATG-GGACGACTGGTATCTATGGT
*
5771824 TGACACGGCTCTACGTGATGAAGAGGTCTGG
1 TGACACGGCTCTACGTGATG-AGAGATCTGG
5771855 TCTGGGGATG
Statistics
Matches: 105, Mismatches: 7, Indels: 12
0.85 0.06 0.10
Matches are distributed among these distances:
84 8 0.08
85 21 0.20
86 33 0.31
87 43 0.41
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (86 bp):
TGACACGGCTCTACGTGATGAGAGATCTGGCCATCTTAAAGGATGATAACACGTTCCTACGTAAT
GGGACGACTGGTATCTATGGT
Found at i:5771855 original size:41 final size:42
Alignment explanation
Indices: 5771733--5771855 Score: 115
Period size: 45 Copynumber: 2.9 Consensus size: 42
5771723 ACTGGTTATC
* *
5771733 AGGTTGACACGGCTCTTACGTGATG-AGAGATCTGGCCATCTAA
1 AGGTTGACACGGCTC-TACGTGATGAAGAGGTCTGG-TATCTAA
* * * * *
5771776 AGGTGATAACACGGTTCCTACGTGATGAGGACGACTGGTATCT-A
1 AGGT--TGACACGGCT-CTACGTGATGAAGAGGTCTGGTATCTAA
*
5771820 TGGTTGACACGGCTCTACGTGATGAAGAGGTCTGGT
1 AGGTTGACACGGCTCTACGTGATGAAGAGGTCTGGT
5771856 CTGGGGATGA
Statistics
Matches: 63, Mismatches: 13, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
41 19 0.30
42 8 0.13
43 4 0.06
44 4 0.06
45 21 0.33
46 7 0.11
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (42 bp):
AGGTTGACACGGCTCTACGTGATGAAGAGGTCTGGTATCTAA
Found at i:5772944 original size:20 final size:20
Alignment explanation
Indices: 5772919--5772957 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
5772909 TCCTTTATTT
5772919 ATTTTTCTTC-TTCATTTTTC
1 ATTTTT-TTCATTCATTTTTC
*
5772939 ATTTTTTTCATTCCTTTTT
1 ATTTTTTTCATTCATTTTT
5772958 TTTTTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.10, C:0.18, G:0.00, T:0.72
Consensus pattern (20 bp):
ATTTTTTTCATTCATTTTTC
Found at i:5786282 original size:3 final size:3
Alignment explanation
Indices: 5786276--5786336 Score: 65
Period size: 3 Copynumber: 21.0 Consensus size: 3
5786266 AAAAAAATTG
* **
5786276 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TAA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5786320 TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA
5786337 CGGAAAAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 5 0.10
3 40 0.83
4 3 0.06
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:5788169 original size:15 final size:15
Alignment explanation
Indices: 5788128--5788184 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 15
5788118 TTGAAAAGAT
5788128 ATAATAA-AAAAATA
1 ATAATAATAAAAATA
**
5788142 GTATAATTTTAAAAATA
1 --ATAATAATAAAAATA
5788159 ATAATAAT-AAAATAA
1 ATAATAATAAAAAT-A
5788174 ATAATAATAAA
1 ATAATAATAAA
5788185 TAAAAAGGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
14 5 0.15
15 15 0.44
16 7 0.21
17 7 0.21
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (15 bp):
ATAATAATAAAAATA
Found at i:5788175 original size:18 final size:19
Alignment explanation
Indices: 5788154--5788189 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
5788144 ATAATTTTAA
5788154 AAATAATAAT-AATAAAAT
1 AAATAATAATAAATAAAAT
5788172 AAATAATAATAAATAAAA
1 AAATAATAATAAATAAAA
5788190 AGGGAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (19 bp):
AAATAATAATAAATAAAAT
Found at i:5788213 original size:15 final size:15
Alignment explanation
Indices: 5788151--5788217 Score: 52
Period size: 15 Copynumber: 4.6 Consensus size: 15
5788141 AGTATAATTT
5788151 TAAA-AATAATAATAA
1 TAAATAATAA-AATAA
*
5788166 TAAAATAA-ATAATAA
1 T-AAATAATAAAATAA
***
5788181 TAAATAA-AAAGGGA
1 TAAATAATAAAATAA
5788195 -AAATAATAAAATAA
1 TAAATAATAAAATAA
5788209 TAAATAATA
1 TAAATAATA
5788218 GTAGTAAAGA
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
13 6 0.15
14 13 0.32
15 15 0.38
16 4 0.10
17 2 0.05
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (15 bp):
TAAATAATAAAATAA
Found at i:5788987 original size:12 final size:12
Alignment explanation
Indices: 5788970--5788997 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
5788960 CCTAAAACAA
5788970 AAATAATATTCT
1 AAATAATATTCT
5788982 AAATAATATTCT
1 AAATAATATTCT
5788994 AAAT
1 AAAT
5788998 CCTAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (12 bp):
AAATAATATTCT
Found at i:5789041 original size:75 final size:75
Alignment explanation
Indices: 5788918--5789130 Score: 311
Period size: 76 Copynumber: 2.8 Consensus size: 75
5788908 TAAAACATCT
* * * * **
5788918 TAAATCCTAATTAAAACATTAAAAACTATTTAAACTAAAATACCTAAAACAAAAATAATAT-TCT
1 TAAATCCTAATTAAAATACT-AAAACTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
*
5788982 AAATAATATTC
65 AAATAATATCC
5788993 TAAATCCTAATTAAAATACTAAAACTTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1 TAAATCCTAATTAAAATACTAAAAC-TATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
5789058 AAATAATATCC
65 AAATAATATCC
* *
5789069 TAAAACTTAATTAAAATACTAAAACATATTTAAACTAAAATACCTAAAACAAAGATAAAATA
1 TAAATCCTAATTAAAATACTAAAAC-TATTTAAACTAAAATACCTAAAACAAAGATAAAATA
5789131 AAATGTTTAA
Statistics
Matches: 126, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
74 5 0.04
75 51 0.40
76 70 0.56
ACGTcount: A:0.58, C:0.13, G:0.01, T:0.28
Consensus pattern (75 bp):
TAAATCCTAATTAAAATACTAAAACTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAA
AATAATATCC
Found at i:5789127 original size:25 final size:24
Alignment explanation
Indices: 5789080--5789134 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
5789070 AAAACTTAAT
* ** *
5789080 TAAAATACTAAAACATATTTAAAC
1 TAAAATACTAAAACAAAGATAAAA
5789104 TAAAATACCTAAAACAAAGATAAAA
1 TAAAATA-CTAAAACAAAGATAAAA
5789129 TAAAAT
1 TAAAAT
5789135 GTTTAATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 7 0.27
25 19 0.73
ACGTcount: A:0.64, C:0.11, G:0.02, T:0.24
Consensus pattern (24 bp):
TAAAATACTAAAACAAAGATAAAA
Found at i:5790462 original size:21 final size:21
Alignment explanation
Indices: 5790420--5790462 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
5790410 TTTCTGGGCT
*
5790420 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
5790441 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
5790462 A
1 A
5790463 ACGAACATGG
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:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:5790535 original size:23 final size:22
Alignment explanation
Indices: 5790491--5790535 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
5790481 AATGCCAGAG
*
5790491 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
5790513 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
5790536 AAATTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:5792223 original size:103 final size:103
Alignment explanation
Indices: 5791998--5792215 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
5791988 GTTGAGGGTC
*
5791998 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTATGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
5792063 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
5792101 TATGTGGTCCTTCGGGACATATATGTATTCTATGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTATGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
5792166 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
5792204 TATGTGGTCCTT
1 TATGTGGTCCTT
5792216 ATGGACATTA
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTATGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:5792299 original size:23 final size:23
Alignment explanation
Indices: 5792231--5792291 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
5792221 CATTATTATA
*
5792231 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTATG
*
5792254 CGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTATG
*
5792277 TGGCACTTCGGTGCA
1 TGGCACTACGGTGCA
5792292 TTTATATGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.26, G:0.28, T:0.26
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTATG
Found at i:5792357 original size:17 final size:18
Alignment explanation
Indices: 5792337--5792371 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
5792327 CCTCCATAAA
5792337 CTCACATATATAT-AGTT
1 CTCACATATATATGAGTT
5792354 CTCACATATATATGAGTT
1 CTCACATATATATGAGTT
5792372 GTGGTGATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (18 bp):
CTCACATATATATGAGTT
Found at i:5795559 original size:21 final size:21
Alignment explanation
Indices: 5795517--5795559 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5795507 TTTATGGGCT
* *
5795517 AGGGGAATCGATACCCATTCA
1 AGGGCAATCGATACCCACTCA
*
5795538 AGGGCAATCGATACCCCCTCA
1 AGGGCAATCGATACCCACTCA
5795559 A
1 A
5795560 ACGAACATGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.30, G:0.21, T:0.16
Consensus pattern (21 bp):
AGGGCAATCGATACCCACTCA
Found at i:5795632 original size:23 final size:22
Alignment explanation
Indices: 5795588--5795632 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
5795578 AATGCCAGAG
*
5795588 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
5795610 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
5795633 AAATTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:5796016 original size:17 final size:17
Alignment explanation
Indices: 5795994--5796047 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 17
5795984 TGTGATATGT
5795994 TATGATGATATAAAAGA
1 TATGATGATATAAAAGA
5796011 TATGAT-ATGATAATAA-A
1 TATGATGAT-ATAA-AAGA
5796028 TTAT-ATGAATATAAAAGA
1 -TATGATG-ATATAAAAGA
5796046 TA
1 TA
5796048 AGTTATGTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
16 2 0.06
17 17 0.55
18 10 0.32
19 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.13, T:0.33
Consensus pattern (17 bp):
TATGATGATATAAAAGA
Found at i:5797279 original size:103 final size:103
Alignment explanation
Indices: 5797095--5797318 Score: 340
Period size: 103 Copynumber: 2.1 Consensus size: 103
5797085 GTCAAGGGTC
5797095 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
5797160 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
* *
5797198 TATGTGGTTCTTCGGGACATATTTGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
5797263 TTGATCCCTAGTATATGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCC-----TA-GCATATGTATATGATTCTTAAGGAATGA
*
5797307 TATATGGTCCTT
1 TATGTGGTCCTT
5797319 ATGGACATTA
Statistics
Matches: 108, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
103 70 0.65
108 1 0.01
109 37 0.34
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:5797384 original size:23 final size:23
Alignment explanation
Indices: 5797333--5797394 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
5797323 ACATTATTAT
*
5797333 ATGGCACTACGGTACAATTCTAC
1 ATGGCACTACGGTGCAATTCTAC
* * *
5797356 ACGGCACTACGGTGTAATTCTAT
1 ATGGCACTACGGTGCAATTCTAC
* *
5797379 GTGGCACTTCGGTGCA
1 ATGGCACTACGGTGCA
5797395 TTTATATGAG
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.27
Consensus pattern (23 bp):
ATGGCACTACGGTGCAATTCTAC
Found at i:5797402 original size:23 final size:23
Alignment explanation
Indices: 5797325--5797402 Score: 57
Period size: 23 Copynumber: 3.3 Consensus size: 23
5797315 CCTTATGGAC
* *
5797325 ATTATTATATGGCACTACGGTACA
1 ATTA-TATGTGGCACTACGGTGCA
* *** *
5797349 ATTCTACACGGCACTACGGTGTA
1 ATTATATGTGGCACTACGGTGCA
* *
5797372 ATTCTATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
5797395 TTTATATG
1 ATTATATG
5797403 AGCTGTGGTG
Statistics
Matches: 42, Mismatches: 12, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
23 39 0.93
24 3 0.07
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.35
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:5799332 original size:14 final size:14
Alignment explanation
Indices: 5799313--5799339 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5799303 AAATATGTTA
5799313 TTTTTCTACACTGT
1 TTTTTCTACACTGT
5799327 TTTTTCTACACTG
1 TTTTTCTACACTG
5799340 CATTGTTCAA
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:0.15, C:0.22, G:0.07, T:0.56
Consensus pattern (14 bp):
TTTTTCTACACTGT
Found at i:5806545 original size:80 final size:80
Alignment explanation
Indices: 5806410--5806720 Score: 444
Period size: 80 Copynumber: 3.9 Consensus size: 80
5806400 TGTAAGTCCT
* *
5806410 TACGGACCTAAGGATATCTTGGGTAGGTCCCATGGTATATCCTTAGGTTGCTTCCCTTTGCTGTG
1 TACGGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTG
5806475 TGCATAAGGTAACCC
66 TGCATAAGGTAACCC
* *
5806490 TACGGACCTAAGGATATCTTAGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGTTGTG
1 TACGGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTG
5806555 TGCATAAGGTAACCC
66 TGCATAAGGTAACCC
* * * *
5806570 TACGGACCTAAGGATATCTTGGGTAGGGCCCAAGGTATATTCTTAGGTTGGTTCCCTTAGTTGTG
1 TACGGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTG
* *
5806635 TGCTTAAAGTAACCC
66 TGCATAAGGTAACCC
* * * * *
5806650 TACGGATCTAAGGATGTCCTTGGGTAGAT-CCAAGGTATATTCTTAGGTTGGCTCCCCTTTTTGC
1 TACGGACCTAAGGATAT-CTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGG-TTCCC--TTTGC
5806714 TGTGTGC
62 TGTGTGC
5806721 TGAGGGCAAG
Statistics
Matches: 210, Mismatches: 17, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
80 187 0.89
81 13 0.06
83 10 0.05
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (80 bp):
TACGGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTG
TGCATAAGGTAACCC
Found at i:5808515 original size:23 final size:23
Alignment explanation
Indices: 5808489--5808539 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
5808479 GAAGAAAAAT
5808489 GAGTCTCGTCTTTAATTGAAACG
1 GAGTCTCGTCTTTAATTGAAACG
5808512 GAGTCTCGTCTTTAATTGAAACG
1 GAGTCTCGTCTTTAATTGAAACG
5808535 GAGTC
1 GAGTC
5808540 CCGCCACTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (23 bp):
GAGTCTCGTCTTTAATTGAAACG
Found at i:5809063 original size:19 final size:19
Alignment explanation
Indices: 5809041--5809077 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5809031 TCTAATAAAA
*
5809041 TAAAATAAAAATTATAATT
1 TAAAATAAAAATAATAATT
*
5809060 TAAAATAATAATAATAAT
1 TAAAATAAAAATAATAAT
5809078 AAATAAAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAATAAAAATAATAATT
Found at i:5809179 original size:18 final size:18
Alignment explanation
Indices: 5809156--5809198 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
5809146 TTGTTTTTTA
*
5809156 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
* *
5809174 AAATAAAGGAAAATAATT
1 AAATAAAAGAAAAGAATT
5809192 AAATAAA
1 AAATAAA
5809199 CAAATTAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:5809889 original size:63 final size:63
Alignment explanation
Indices: 5809820--5809940 Score: 208
Period size: 63 Copynumber: 1.9 Consensus size: 63
5809810 TAAAACATCT
5809820 TAAATCCTAATTAAAACACTTAAAAC-TATTTAAACTAAAATACCTAAAACAAAAATAATATTC
1 TAAATCCTAATTAAAACAC-TAAAACTTATTTAAACTAAAATACCTAAAACAAAAATAATATTC
* *
5809883 TAAATCCTAATTAAAATACTAAAACTTATTTAAACTAAAATACCTAAAACAAAGATAA
1 TAAATCCTAATTAAAACACTAAAACTTATTTAAACTAAAATACCTAAAACAAAAATAA
5809941 AATATAATGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
62 6 0.11
63 49 0.89
ACGTcount: A:0.56, C:0.15, G:0.01, T:0.28
Consensus pattern (63 bp):
TAAATCCTAATTAAAACACTAAAACTTATTTAAACTAAAATACCTAAAACAAAAATAATATTC
Found at i:5814185 original size:21 final size:20
Alignment explanation
Indices: 5814159--5814217 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 20
5814149 TTTATCCAAT
5814159 AAACTTGACATCCATAACAAC
1 AAACTTGA-ATCCATAACAAC
5814180 AAACTTGAAATCCATAACAAC
1 AAACTTG-AATCCATAACAAC
*
5814201 CAACTTGAACTCCATAA
1 AAACTTGAA-TCCATAA
5814218 TAATAAATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
20 2 0.06
21 32 0.91
22 1 0.03
ACGTcount: A:0.47, C:0.27, G:0.05, T:0.20
Consensus pattern (20 bp):
AAACTTGAATCCATAACAAC
Found at i:5816084 original size:16 final size:16
Alignment explanation
Indices: 5816063--5816095 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
5816053 ACTGCCAGTA
5816063 AATCTTGCATCAATAT
1 AATCTTGCATCAATAT
5816079 AATCTTGCATCAATAT
1 AATCTTGCATCAATAT
5816095 A
1 A
5816096 TGATAATCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.18, G:0.06, T:0.36
Consensus pattern (16 bp):
AATCTTGCATCAATAT
Found at i:5821583 original size:41 final size:41
Alignment explanation
Indices: 5821471--5821584 Score: 165
Period size: 41 Copynumber: 2.8 Consensus size: 41
5821461 TATTAAAAGT
* * *
5821471 CCACTAAAGTACGAGTCTTTAGCAGCGTTTATATAAAAACA
1 CCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACA
* * *
5821512 TCACTAAAGTAAGAGTCTATAGTGGCGTTTGTATAAAAACA
1 CCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACA
*
5821553 CCACTAAAGTACGTGTCTATAGCGGCGTTTGT
1 CCACTAAAGTACGAGTCTATAGCGGCGTTTGT
5821585 GTATAGTACA
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 63 1.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (41 bp):
CCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACA
Found at i:5823655 original size:21 final size:21
Alignment explanation
Indices: 5823629--5823684 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
5823619 GCGAATAAGT
5823629 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
5823650 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
*
5823671 AAATCGCAATGCGA
1 AAATCGCAACGCGA
5823685 TACTGACTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.39, C:0.20, G:0.27, T:0.14
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:5823698 original size:20 final size:20
Alignment explanation
Indices: 5823673--5823786 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
5823663 AATTGGGAAA
*
5823673 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
5823693 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
5823713 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
5823734 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
5823754 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
5823774 TTCGCAACGCGAT
1 ATCGCAACGCGAT
5823787 TTACATAGCG
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
19 2 0.02
20 65 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:5823748 original size:61 final size:61
Alignment explanation
Indices: 5823670--5823786 Score: 171
Period size: 61 Copynumber: 1.9 Consensus size: 61
5823660 GCGAATTGGG
* * * *
5823670 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
5823731 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
5823787 TTACATAGCG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:5824322 original size:19 final size:19
Alignment explanation
Indices: 5824284--5824350 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
5824274 TTCGAGAATG
5824284 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
5824304 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
5824323 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
5824342 AAAATCGCA
1 AAAATCGCA
5824351 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 30 0.73
20 11 0.27
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:5824397 original size:33 final size:33
Alignment explanation
Indices: 5824360--5824447 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 33
5824350 ATTGCGATTT
* * *
5824360 TCATTTCGCGTTACGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTAGTCGCGATAG
*
5824393 TCATTTCGCGTTGCGATTCTCTAGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTAGTCGCGATAG
5824426 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
5824448 ATTATCTCGT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 35 0.70
34 15 0.30
ACGTcount: A:0.14, C:0.24, G:0.24, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTAGTCGCGATAG
Found at i:5824449 original size:20 final size:20
Alignment explanation
Indices: 5824416--5824472 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
5824406 CGATTCTCTA
**
5824416 GTTGCGATAGTCATTTCCGC
1 GTTGCGATTCTCATTTCCGC
*
5824436 GTTGCGATTCTCATTAT-CTC
1 GTTGCGATTCTCATT-TCCGC
*
5824456 GTTGCGATTTTCATTTC
1 GTTGCGATTCTCATTTC
5824473 AACCAAAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (20 bp):
GTTGCGATTCTCATTTCCGC
Found at i:5826517 original size:42 final size:42
Alignment explanation
Indices: 5826457--5826579 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
5826447 GCCCGACTCG
* * *
5826457 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
5826499 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
5826541 ACTGTCATCGTTGAAGAAGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAG-AGTCCACTCCCACCGTTCAAGAG
5826580 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 61 0.92
43 5 0.08
ACGTcount: A:0.24, C:0.37, G:0.17, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:5826537 original size:21 final size:21
Alignment explanation
Indices: 5826513--5826579 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
5826503 TCATTCCTCG
5826513 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
5826534 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
5826555 AGAAGT-CCCTCCCACCATTCA
1 AG-AGTCCCCTCCCACCGTTCA
5826576 AGAG
1 AGAG
5826580 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 2 0.06
21 28 0.88
22 2 0.06
ACGTcount: A:0.25, C:0.36, G:0.19, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:5826717 original size:21 final size:21
Alignment explanation
Indices: 5826684--5826743 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 21
5826674 TGCGAAAGTA
* * *
5826684 AGTATCTCGTTGCGATTTTTT
1 AGTATCGCATTGCGATTTTTC
* **
5826705 ATTATCGCATTGCGA-TAGTC
1 AGTATCGCATTGCGATTTTTC
5826725 AGTATCGCATTGCGATTTT
1 AGTATCGCATTGCGATTTT
5826744 CCCAATTCAT
Statistics
Matches: 29, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (21 bp):
AGTATCGCATTGCGATTTTTC
Found at i:5826759 original size:41 final size:41
Alignment explanation
Indices: 5826729--5826821 Score: 132
Period size: 41 Copynumber: 2.3 Consensus size: 41
5826719 ATAGTCAGTA
* * *
5826729 TCGCATTGCGATTTTCCCAATTCATGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCACGTTGCGATTCACGTAT
* * *
5826770 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCACGTTGCGATTCACGTAT
5826811 TCGCATTGCGA
1 TCGCATTGCGA
5826822 ATTGGGAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.18, C:0.24, G:0.17, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCACGTTGCGATTCACGTAT
Done.