Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 15 of 182
Found at i:5146056 original size:27 final size:27
Alignment explanation
Indices: 5146026--5146077 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
5146016 GGCCAATCAC
* *
5146026 ATTGGTGGCACTAAAGGTGCCAAAGAG
1 ATTGGCGGCACCAAAGGTGCCAAAGAG
*
5146053 ATTGGCGGCACCAATGGTGCCAAAG
1 ATTGGCGGCACCAAAGGTGCCAAAG
5146078 GACTAAAATG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.31, C:0.19, G:0.33, T:0.17
Consensus pattern (27 bp):
ATTGGCGGCACCAAAGGTGCCAAAGAG
Found at i:5146535 original size:19 final size:19
Alignment explanation
Indices: 5146511--5146566 Score: 78
Period size: 18 Copynumber: 3.0 Consensus size: 19
5146501 TCTAATTAAG
5146511 TAATAACTCTATTTTAATT
1 TAATAACTCTATTTTAATT
* * *
5146530 TAATAA-ACTATTCTCATT
1 TAATAACTCTATTTTAATT
5146548 TAATAACTCTATTTTAATT
1 TAATAACTCTATTTTAATT
5146567 AAAATAGAGT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
18 15 0.50
19 15 0.50
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (19 bp):
TAATAACTCTATTTTAATT
Found at i:5146568 original size:18 final size:18
Alignment explanation
Indices: 5146506--5146568 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
5146496 AGAATTCTAA
*
5146506 TTAAGTAATAACTCTATT
1 TTAATTAATAACTCTATT
*
5146524 TTAATTTAATAA-ACTATT
1 TTAA-TTAATAACTCTATT
* *
5146542 CTCATTTAATAACTCTATT
1 -TTAATTAATAACTCTATT
5146561 TTAATTAA
1 TTAATTAA
5146569 AATAGAGTTA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
18 22 0.63
19 13 0.37
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.48
Consensus pattern (18 bp):
TTAATTAATAACTCTATT
Found at i:5146618 original size:19 final size:18
Alignment explanation
Indices: 5146563--5146618 Score: 67
Period size: 18 Copynumber: 3.0 Consensus size: 18
5146553 ACTCTATTTT
5146563 AATTAAAATAGAGTTATTA
1 AATTAAAATAG-GTTATTA
* * *
5146582 AATGAGAATAGTTTATTA
1 AATTAAAATAGGTTATTA
5146600 AATTAAAATAGCGTTATTA
1 AATTAAAATAG-GTTATTA
5146619 CTTAATTAGA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
18 15 0.50
19 15 0.50
ACGTcount: A:0.48, C:0.02, G:0.12, T:0.38
Consensus pattern (18 bp):
AATTAAAATAGGTTATTA
Found at i:5147276 original size:26 final size:27
Alignment explanation
Indices: 5147244--5147310 Score: 118
Period size: 26 Copynumber: 2.5 Consensus size: 27
5147234 GTTTTTTGAT
5147244 ATATTTTGGTAAATAAAAAAA-TTATA
1 ATATTTTGGTAAATAAAAAAATTTATA
5147270 ATATTTTGGTAAATAAAAAAATTTATA
1 ATATTTTGGTAAATAAAAAAATTTATA
*
5147297 ATATTTTGTTAAAT
1 ATATTTTGGTAAAT
5147311 TTTTATTTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
26 21 0.54
27 18 0.46
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.43
Consensus pattern (27 bp):
ATATTTTGGTAAATAAAAAAATTTATA
Found at i:5147591 original size:13 final size:13
Alignment explanation
Indices: 5147573--5147601 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
5147563 TTAAGCCGTA
5147573 TTTTAATAATAAT
1 TTTTAATAATAAT
5147586 TTTTAATAATAAT
1 TTTTAATAATAAT
5147599 TTT
1 TTT
5147602 AAATTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTTAATAATAAT
Found at i:5151105 original size:45 final size:45
Alignment explanation
Indices: 5151007--5151194 Score: 229
Period size: 45 Copynumber: 4.2 Consensus size: 45
5150997 AATAATAACA
* * * * *
5151007 GATACACGGTGG-ATCAGCACATAGC-ACCACCCTTATAGTCAAT
1 GATACCCGGTGGAATCAGCACACAACAACCACCTTTATAATCAAT
* * * *
5151050 GATACTCGGTGGAATCAGCACATAGCAACCACCTTCATAATCAAT
1 GATACCCGGTGGAATCAGCACACAACAACCACCTTTATAATCAAT
* *
5151095 -AGTACCCGGTGGAATCAGCACACAACAATCACCTTTAAAATCAAT
1 GA-TACCCGGTGGAATCAGCACACAACAACCACCTTTATAATCAAT
*
5151140 GATACCCGGTGGAATCAGCACACAACAACCACTTTTATAATCAAT
1 GATACCCGGTGGAATCAGCACACAACAACCACCTTTATAATCAAT
*
5151185 GGTACCCGGT
1 GATACCCGGT
5151195 ACACGTAATA
Statistics
Matches: 127, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
43 11 0.09
44 14 0.11
45 101 0.80
46 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.21
Consensus pattern (45 bp):
GATACCCGGTGGAATCAGCACACAACAACCACCTTTATAATCAAT
Found at i:5155671 original size:4 final size:4
Alignment explanation
Indices: 5155662--5155688 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
5155652 TTTTAATATT
5155662 TTAA TTAA TTAA TTAA TTAA TTAA TTA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTA
5155689 GATATTAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:5159515 original size:13 final size:12
Alignment explanation
Indices: 5159486--5159525 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
5159476 TTATTGCCAT
*
5159486 GTTTTCGTTTTC
1 GTTTTCTTTTTC
5159498 GTTTTCTATTTTC
1 GTTTTCT-TTTTC
*
5159511 TTTTTCTTTTTC
1 GTTTTCTTTTTC
5159523 GTT
1 GTT
5159526 GCTGGTTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 13 0.54
13 11 0.46
ACGTcount: A:0.03, C:0.15, G:0.10, T:0.72
Consensus pattern (12 bp):
GTTTTCTTTTTC
Found at i:5160751 original size:15 final size:15
Alignment explanation
Indices: 5160731--5160768 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
5160721 CACTACAGGG
5160731 GTCACACGGCCGTGT
1 GTCACACGGCCGTGT
*
5160746 GTCACAGGGCCGTGT
1 GTCACACGGCCGTGT
5160761 GTCACACG
1 GTCACACG
5160769 TGGCTGAGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.16, C:0.32, G:0.34, T:0.18
Consensus pattern (15 bp):
GTCACACGGCCGTGT
Found at i:5162483 original size:26 final size:26
Alignment explanation
Indices: 5162447--5162515 Score: 102
Period size: 26 Copynumber: 2.7 Consensus size: 26
5162437 TTTACATCGT
*
5162447 TGCTCACACGAGCTGTGAAATGGGTA
1 TGCTCACACGAGCTGTGAAATGGGCA
* *
5162473 TGCTTACACGAGCTGTGAAATGGGCC
1 TGCTCACACGAGCTGTGAAATGGGCA
*
5162499 TGCTCATACGAGCTGTG
1 TGCTCACACGAGCTGTG
5162516 GGTCGGAATG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.23, C:0.22, G:0.30, T:0.25
Consensus pattern (26 bp):
TGCTCACACGAGCTGTGAAATGGGCA
Found at i:5163984 original size:20 final size:19
Alignment explanation
Indices: 5163959--5164036 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 19
5163949 TTGTACAGGT
5163959 TTGCACTTCGGTGCCTTTGA
1 TTGCACTT-GGTGCCTTTGA
* *
5163979 TTGCACATTTGTGCCTTTGC
1 TTGCAC-TTGGTGCCTTTGA
*
5163999 TTGCACTTTGGTGCCTCTGA
1 TTGCAC-TTGGTGCCTTTGA
*
5164019 TTGCACATTTGTGCCTTT
1 TTGCAC-TTGGTGCCTTT
5164037 TTCTGCACTT
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
20 46 0.96
21 2 0.04
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.44
Consensus pattern (19 bp):
TTGCACTTGGTGCCTTTGA
Found at i:5164043 original size:20 final size:20
Alignment explanation
Indices: 5163980--5164044 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 20
5163970 TGCCTTTGAT
*
5163980 TGCACATTTGTGCC-TTTGC
1 TGCACATTTGTGCCTTTTTC
**
5163999 TTGCAC-TTTGGTGCCTCTGAT-
1 -TGCACATTT-GTGCCT-TTTTC
5164020 TGCACATTTGTGCCTTTTTC
1 TGCACATTTGTGCCTTTTTC
5164040 TGCAC
1 TGCAC
5164045 TTCGTTTCCT
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
19 5 0.14
20 26 0.74
21 3 0.09
22 1 0.03
ACGTcount: A:0.11, C:0.26, G:0.20, T:0.43
Consensus pattern (20 bp):
TGCACATTTGTGCCTTTTTC
Found at i:5164046 original size:40 final size:40
Alignment explanation
Indices: 5163959--5164036 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 40
5163949 TTGTACAGGT
*
5163959 TTGCACTTCGGTGCCTTTGATTGCACATTTGTGCCTTTGC
1 TTGCACTTCGGTGCCTCTGATTGCACATTTGTGCCTTTGC
*
5163999 TTGCACTTTGGTGCCTCTGATTGCACATTTGTGCCTTT
1 TTGCACTTCGGTGCCTCTGATTGCACATTTGTGCCTTT
5164037 TTCTGCACTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.44
Consensus pattern (40 bp):
TTGCACTTCGGTGCCTCTGATTGCACATTTGTGCCTTTGC
Found at i:5170665 original size:12 final size:12
Alignment explanation
Indices: 5170648--5170695 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
5170638 GTTCACTAAC
*
5170648 AAGCTCGTTTAA
1 AAGCTCGTTTAT
5170660 AAGCTCGTTTAT
1 AAGCTCGTTTAT
**
5170672 TGGCTCGTTTAT
1 AAGCTCGTTTAT
5170684 AAGCTCGTTTAT
1 AAGCTCGTTTAT
5170696 TAACTCATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.42
Consensus pattern (12 bp):
AAGCTCGTTTAT
Found at i:5170677 original size:24 final size:24
Alignment explanation
Indices: 5170650--5170696 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
5170640 TCACTAACAA
5170650 GCTCGTTTAAAAGCTCGTTTATTG
1 GCTCGTTTAAAAGCTCGTTTATTG
*
5170674 GCTCGTTTATAAGCTCGTTTATT
1 GCTCGTTTAAAAGCTCGTTTATT
5170697 AACTCATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.45
Consensus pattern (24 bp):
GCTCGTTTAAAAGCTCGTTTATTG
Found at i:5170706 original size:24 final size:24
Alignment explanation
Indices: 5170655--5170707 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
5170645 AACAAGCTCG
* ** *
5170655 TTTAAAAGCTCGTTTATTGGCTCG
1 TTTATAAGCTCGTTTATTAACTCA
5170679 TTTATAAGCTCGTTTATTAACTCA
1 TTTATAAGCTCGTTTATTAACTCA
5170703 TTTAT
1 TTTAT
5170708 TTATTAATGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.25, C:0.15, G:0.13, T:0.47
Consensus pattern (24 bp):
TTTATAAGCTCGTTTATTAACTCA
Found at i:5175391 original size:51 final size:51
Alignment explanation
Indices: 5175333--5175433 Score: 150
Period size: 51 Copynumber: 2.0 Consensus size: 51
5175323 GATGTCCAGG
* * *
5175333 TGGCTTGTGATCAAGGTGTCTCGACTTCTAGCCAAAGTCAGA-ACGTACAGT
1 TGGCTTGTAATCAAGGTGTCTCAACTACTAGCCAAAGTCAGACA-GTACAGT
*
5175384 TGGCTTGTAATCAAGGTGTCTCAACTACTAGTCAAAGTCAGACAGTACAG
1 TGGCTTGTAATCAAGGTGTCTCAACTACTAGCCAAAGTCAGACAGTACAG
5175434 GTGTCATGTG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 44 0.98
52 1 0.02
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.27
Consensus pattern (51 bp):
TGGCTTGTAATCAAGGTGTCTCAACTACTAGCCAAAGTCAGACAGTACAGT
Found at i:5180703 original size:41 final size:41
Alignment explanation
Indices: 5180641--5180718 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
5180631 GATTTTTATC
* *
5180641 AAATCTATTTTACAATCATTACCTATTTATGCTATGTTAAG
1 AAATCTATTTTACAATAATTACCTACTTATGCTATGTTAAG
5180682 AAATCTATTTTACAATAATTACCTACTTATGCTATGT
1 AAATCTATTTTACAATAATTACCTACTTATGCTATGT
5180719 CTGTTTTCCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (41 bp):
AAATCTATTTTACAATAATTACCTACTTATGCTATGTTAAG
Found at i:5186114 original size:29 final size:29
Alignment explanation
Indices: 5186082--5186143 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
5186072 GCCACGTGTT
*
5186082 ATGTTAGTCTTGAGAGAGAAAGTTGTGAG
1 ATGTTAGTCTTGAGAGAGAAAATTGTGAG
5186111 ATGTTAGTCTTGAGAGAGAAAATTGTGAG
1 ATGTTAGTCTTGAGAGAGAAAATTGTGAG
5186140 ATGT
1 ATGT
5186144 AAATATCAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.32, C:0.03, G:0.32, T:0.32
Consensus pattern (29 bp):
ATGTTAGTCTTGAGAGAGAAAATTGTGAG
Found at i:5190672 original size:13 final size:13
Alignment explanation
Indices: 5190654--5190711 Score: 71
Period size: 13 Copynumber: 4.5 Consensus size: 13
5190644 TCATCGGGTG
5190654 GAAATGGATATAT
1 GAAATGGATATAT
* * *
5190667 GAAATGGTTCTAC
1 GAAATGGATATAT
*
5190680 GAAATGGTTATAT
1 GAAATGGATATAT
*
5190693 GACATGGATATAT
1 GAAATGGATATAT
5190706 GAAATG
1 GAAATG
5190712 AACATTTAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.40, C:0.05, G:0.24, T:0.31
Consensus pattern (13 bp):
GAAATGGATATAT
Found at i:5193150 original size:39 final size:39
Alignment explanation
Indices: 5193099--5193210 Score: 136
Period size: 40 Copynumber: 2.8 Consensus size: 39
5193089 ACAAGGTTGG
* * * *
5193099 ATCTTATTATATTATCTGAGAATCTACAATAGAGGATAA
1 ATCTCATTATATTATCCGAGAATCTGCAATAAAGGATAA
* * *
5193138 ATCTCATTATATTACCCCGAGAATCTGCAACAAAGGCTAA
1 ATCTCATTATATTA-TCCGAGAATCTGCAATAAAGGATAA
5193178 ATCTCATTATATT-TCCCGAGAATCTGCAATAAA
1 ATCTCATTATATTAT-CCGAGAATCTGCAATAAA
5193211 TGCTAGATCT
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
39 30 0.48
40 32 0.52
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (39 bp):
ATCTCATTATATTATCCGAGAATCTGCAATAAAGGATAA
Found at i:5193221 original size:39 final size:40
Alignment explanation
Indices: 5193099--5193227 Score: 154
Period size: 39 Copynumber: 3.3 Consensus size: 40
5193089 ACAAGGTTGG
* * * * *
5193099 ATCTTATTATATTAT-CTGAGAATCTACAATAGAGGATAA
1 ATCTCATTATATTATCCCGAGAATCTGCAATAAAGGCTAA
* *
5193138 ATCTCATTATATTACCCCGAGAATCTGCAACAAAGGCTAA
1 ATCTCATTATATTATCCCGAGAATCTGCAATAAAGGCTAA
* *
5193178 ATCTCATTATATT-TCCCGAGAATCTGCAATAAATGCTAG
1 ATCTCATTATATTATCCCGAGAATCTGCAATAAAGGCTAA
*
5193217 ATCTCGTTATA
1 ATCTCATTATA
5193228 ATCTATAATA
Statistics
Matches: 77, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
39 45 0.58
40 32 0.42
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (40 bp):
ATCTCATTATATTATCCCGAGAATCTGCAATAAAGGCTAA
Found at i:5194238 original size:15 final size:14
Alignment explanation
Indices: 5194214--5194248 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
5194204 TAACCTAAAT
5194214 TAATTAAATTAAACA
1 TAATTAAATT-AACA
*
5194229 TAATTTAATTAACA
1 TAATTAAATTAACA
5194243 TAATTA
1 TAATTA
5194249 GTCCTTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (14 bp):
TAATTAAATTAACA
Found at i:5201182 original size:4 final size:4
Alignment explanation
Indices: 5201173--5201233 Score: 113
Period size: 4 Copynumber: 15.2 Consensus size: 4
5201163 TCTATTTATA
*
5201173 TATG TATG TATG TATG TATG TATG TACG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5201221 TATG TATG TATG T
1 TATG TATG TATG T
5201234 TAGATTAACT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 55 1.00
ACGTcount: A:0.25, C:0.02, G:0.25, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:5206522 original size:99 final size:99
Alignment explanation
Indices: 5206351--5206552 Score: 386
Period size: 99 Copynumber: 2.0 Consensus size: 99
5206341 AAATCTATTG
*
5206351 AAATACCCTCAAAGACCAACTCCGAAATTGGTAATGGTTGTAATAGGTCGGCTAGATGGAGGAAA
1 AAATACCCTCAAAGACCAACTCCGAAATTGGTAATGGTTGTAATAGGTCGACTAGATGGAGGAAA
*
5206416 GAATCCTTCATTTGTTGGCAGATCTGGCACTCAA
66 GAATCCTTCATTTGTTGGCAGATCTGACACTCAA
5206450 AAATACCCTCAAAGACCAACTCCGAAATTGGTAATGGTTGTAATAGGTCGACTAGATGGAGGAAA
1 AAATACCCTCAAAGACCAACTCCGAAATTGGTAATGGTTGTAATAGGTCGACTAGATGGAGGAAA
5206515 GAATCCTTCATTTGTTGGCAGATCTGACACTCAA
66 GAATCCTTCATTTGTTGGCAGATCTGACACTCAA
5206549 AAAT
1 AAAT
5206553 GAAGTGATGA
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
99 101 1.00
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (99 bp):
AAATACCCTCAAAGACCAACTCCGAAATTGGTAATGGTTGTAATAGGTCGACTAGATGGAGGAAA
GAATCCTTCATTTGTTGGCAGATCTGACACTCAA
Found at i:5215785 original size:40 final size:39
Alignment explanation
Indices: 5215687--5215949 Score: 278
Period size: 40 Copynumber: 6.6 Consensus size: 39
5215677 TCCTCGTTCA
* * * *
5215687 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
5215726 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
5215765 GAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
5215805 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
5215845 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
5215885 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
5215926 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
5215950 CAGCATTCAA
Statistics
Matches: 197, Mismatches: 21, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
39 40 0.20
40 145 0.74
41 12 0.06
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:5215909 original size:120 final size:119
Alignment explanation
Indices: 5215687--5215949 Score: 307
Period size: 120 Copynumber: 2.2 Consensus size: 119
5215677 TCCTCGTTCA
* * *
5215687 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATT
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
* * *
5215752 TAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAAC-TCGCAC
66 TAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTTAGCAC
* * * * *
5215805 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGA
1 -AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGACATAACCCGG-
* * ** * *
5215870 ATTT-GTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
63 ATTTAATAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAATAACTTAGCAC
*
5215926 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
5215950 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 37 0.31
120 75 0.62
121 9 0.07
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
TAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTTAGCAC
Found at i:5215958 original size:41 final size:41
Alignment explanation
Indices: 5215881--5215958 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
5215871 TTTGTATCTC
* * *
5215881 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
5215922 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
5215959 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:5223681 original size:39 final size:40
Alignment explanation
Indices: 5223636--5223860 Score: 242
Period size: 40 Copynumber: 5.7 Consensus size: 40
5223626 GCTCCTCGTT
* * * *
5223636 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
5223676 C-AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
5223715 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
5223755 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
5223795 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
5223836 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
5223861 CAGCATTCAA
Statistics
Matches: 159, Mismatches: 20, Indels: 12
0.83 0.10 0.06
Matches are distributed among these distances:
39 39 0.25
40 105 0.66
41 15 0.09
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:5223869 original size:41 final size:41
Alignment explanation
Indices: 5223792--5223869 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
5223782 TTTGTATCTC
* * *
5223792 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
5223833 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
5223870 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:5235624 original size:25 final size:25
Alignment explanation
Indices: 5235596--5235755 Score: 128
Period size: 25 Copynumber: 6.4 Consensus size: 25
5235586 GTTTGCCGCG
*
5235596 AAGGTTTTCCAAAGAATTCACCACA
1 AAGGCTTTCCAAAGAATTCACCACA
*
5235621 AAGGCTTTCCAAAAAATTCACCACA
1 AAGGCTTTCCAAAGAATTCACCACA
* ***
5235646 AAGGCCTTT-CAGAGAATTTGTCACA
1 AAGG-CTTTCCAAAGAATTCACCACA
* *
5235671 AAGGCGTTCCATAGAATTCACCACA
1 AAGGCTTTCCAAAGAATTCACCACA
* * * *
5235696 AAGGCATTCCAGAGTATTCTA-TACA
1 AAGGCTTTCCAAAGAATTC-ACCACA
** *
5235721 AAGGCTTTTTAGATG-ATTCACCACA
1 AAGGCTTTCCA-AAGAATTCACCACA
5235746 AAGGCATTTC
1 AAGGC-TTTC
5235756 AGAAATCCAT
Statistics
Matches: 106, Mismatches: 23, Indels: 11
0.76 0.16 0.08
Matches are distributed among these distances:
24 4 0.04
25 93 0.88
26 9 0.08
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (25 bp):
AAGGCTTTCCAAAGAATTCACCACA
Found at i:5235674 original size:50 final size:51
Alignment explanation
Indices: 5235608--5235758 Score: 164
Period size: 50 Copynumber: 3.0 Consensus size: 51
5235598 GGTTTTCCAA
* *
5235608 AGAATTC-ACCACAAAGGCTTTCCAAAAAATTCACCACAAAGGCCTTTCAG
1 AGAATTCTATCACAAAGGCTTTCCAAAAAATTCACCACAAAGGCATTTCAG
* * * * *
5235658 AGAATT-TGTCACAAAGGCGTTCCATAGAATTCACCACAAAGGCATTCCAG
1 AGAATTCTATCACAAAGGCTTTCCAAAAAATTCACCACAAAGGCATTTCAG
* ** * **
5235708 AGTATTCTAT-ACAAAGGCTTTTTAGATGATTCACCACAAAGGCATTTCAG
1 AGAATTCTATCACAAAGGCTTTCCAAAAAATTCACCACAAAGGCATTTCAG
5235758 A
1 A
5235759 AATCCATGTT
Statistics
Matches: 83, Mismatches: 16, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
50 81 0.98
51 2 0.02
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (51 bp):
AGAATTCTATCACAAAGGCTTTCCAAAAAATTCACCACAAAGGCATTTCAG
Found at i:5237451 original size:39 final size:38
Alignment explanation
Indices: 5237408--5237507 Score: 119
Period size: 39 Copynumber: 2.6 Consensus size: 38
5237398 TGAATATAAT
* * *
5237408 AATTATAATTACCATAATTATATTAATGTTAGACCGAAA
1 AATTATAATTACAATAATTATAATAATATTAGACCG-AA
* * ** *
5237447 AATTACAATTACAATAATTATAATAATATTCGATTGTA
1 AATTATAATTACAATAATTATAATAATATTAGACCGAA
5237485 AATTATAATTACAATAATTATAA
1 AATTATAATTACAATAATTATAA
5237508 CAAGGATTTC
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
38 23 0.44
39 29 0.56
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.38
Consensus pattern (38 bp):
AATTATAATTACAATAATTATAATAATATTAGACCGAA
Found at i:5240938 original size:52 final size:48
Alignment explanation
Indices: 5240812--5240944 Score: 124
Period size: 52 Copynumber: 2.6 Consensus size: 48
5240802 AATTCTTTTA
* *
5240812 TTTATTATTTATGTCTTATTAATTTAATTAATTAAAGATAAAATAATCT
1 TTTA-TATTTATCTCTTATTAATTTAATTAATTAAAGATAAAATAAACT
* * * *
5240861 TTTA-ATATTATCACTTCATTAATTTAATTCAATTGATGATAATATAAAACT
1 TTTATAT-TTATCTCTT-ATTAATTTAATT-AATTAAAGATAAAAT-AAACT
*
5240912 TTTATCATTTATCTCTTAATTTATTTAAATTAA
1 TTTAT-ATTTATCTCTT-ATTAATTT-AATTAA
5240945 CTATCGAGCG
Statistics
Matches: 68, Mismatches: 9, Indels: 11
0.77 0.10 0.12
Matches are distributed among these distances:
47 2 0.03
48 7 0.10
49 16 0.24
50 12 0.18
51 8 0.12
52 17 0.25
53 6 0.09
ACGTcount: A:0.39, C:0.08, G:0.03, T:0.50
Consensus pattern (48 bp):
TTTATATTTATCTCTTATTAATTTAATTAATTAAAGATAAAATAAACT
Found at i:5241361 original size:14 final size:14
Alignment explanation
Indices: 5241342--5241369 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5241332 AAATAAATCT
5241342 GAATTTTTTTACCC
1 GAATTTTTTTACCC
5241356 GAATTTTTTTACCC
1 GAATTTTTTTACCC
5241370 CTATTCCCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.07, T:0.50
Consensus pattern (14 bp):
GAATTTTTTTACCC
Found at i:5243177 original size:40 final size:40
Alignment explanation
Indices: 5243133--5243272 Score: 142
Period size: 40 Copynumber: 3.5 Consensus size: 40
5243123 AAAACACACC
* ***
5243133 AATTTGGCACCCAGTGCCTCATCGGATAATTTGAAGTAAT
1 AATTTGACACCCAGTGCCTCATCGGATAATCCAAAGTAAT
* * *
5243173 AATTTGACACCCAGTGTCTCATCGGCTAAACCAAAGT-A-
1 AATTTGACACCCAGTGCCTCATCGGATAATCCAAAGTAAT
* * * *
5243211 AA-TTGGCACCCAGTGCCTCATTGAATTAATCCAAAGTAGT
1 AATTTGACACCCAGTGCCTCATCGGA-TAATCCAAAGTAAT
*
5243251 AAATTGACACCCAGTGCCTCAT
1 AATTTGACACCCAGTGCCTCAT
5243273 TGACTCAAAG
Statistics
Matches: 81, Mismatches: 15, Indels: 7
0.79 0.15 0.07
Matches are distributed among these distances:
37 18 0.22
38 12 0.15
39 1 0.01
40 32 0.40
41 18 0.22
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.26
Consensus pattern (40 bp):
AATTTGACACCCAGTGCCTCATCGGATAATCCAAAGTAAT
Found at i:5243478 original size:24 final size:24
Alignment explanation
Indices: 5243433--5243479 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
5243423 TATATATACC
5243433 AATTCAATCAATATAAATTCAATA
1 AATTCAATCAATATAAATTCAATA
5243457 AATTC-ATCACATACTAAA-TCAAT
1 AATTCAATCA-ATA-TAAATTCAAT
5243480 CCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (24 bp):
AATTCAATCAATATAAATTCAATA
Found at i:5245600 original size:17 final size:15
Alignment explanation
Indices: 5245562--5245595 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
5245552 TAGATGTATT
5245562 TAACTTTTATAATAA
1 TAACTTTTATAATAA
5245577 TAA-TTTTATAATAA
1 TAACTTTTATAATAA
5245591 TAACT
1 TAACT
5245596 CTTTTTCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (15 bp):
TAACTTTTATAATAA
Found at i:5245668 original size:22 final size:23
Alignment explanation
Indices: 5245614--5245668 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 23
5245604 ATTACTTATA
5245614 ATAATTTTATTTTTATATACAAT
1 ATAATTTTATTTTTATATACAAT
*** *
5245637 A-AAAAATATTTTTTTATA-AAT
1 ATAATTTTATTTTTATATACAAT
5245658 ATAATTTTATT
1 ATAATTTTATT
5245669 ATAAAATTTA
Statistics
Matches: 24, Mismatches: 7, Indels: 3
0.71 0.21 0.09
Matches are distributed among these distances:
21 4 0.17
22 19 0.79
23 1 0.04
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
ATAATTTTATTTTTATATACAAT
Found at i:5246847 original size:23 final size:24
Alignment explanation
Indices: 5246821--5246875 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 24
5246811 GGTTCTTAGT
*
5246821 TACATTGT-GTGCCATCCATAGCC
1 TACATTATAGTGCCATCCATAGCC
5246844 TACATACTTATAGTGCCATCCATAGCC
1 TAC--A-TTATAGTGCCATCCATAGCC
5246871 TACAT
1 TACAT
5246876 ACTTATAGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
23 3 0.11
24 1 0.04
25 2 0.07
26 3 0.11
27 18 0.67
ACGTcount: A:0.27, C:0.29, G:0.13, T:0.31
Consensus pattern (24 bp):
TACATTATAGTGCCATCCATAGCC
Found at i:5246867 original size:27 final size:27
Alignment explanation
Indices: 5246829--5246883 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
5246819 GTTACATTGT
5246829 GTGCCATCCATAGCCTACATACTTATA
1 GTGCCATCCATAGCCTACATACTTATA
5246856 GTGCCATCCATAGCCTACATACTTATA
1 GTGCCATCCATAGCCTACATACTTATA
5246883 G
1 G
5246884 ACCAAGGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.29
Consensus pattern (27 bp):
GTGCCATCCATAGCCTACATACTTATA
Found at i:5255723 original size:22 final size:23
Alignment explanation
Indices: 5255678--5255723 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
5255668 ACAAAGAATG
*
5255678 CGGAGGTGTTTGCATCACCCATAA
1 CGGAGGTGTTTGAAT-ACCCATAA
5255702 CGGAGGTGTTTGAAT-CCCATAA
1 CGGAGGTGTTTGAATACCCATAA
5255724 GGCGATGGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 7 0.33
24 14 0.67
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (23 bp):
CGGAGGTGTTTGAATACCCATAA
Found at i:5257498 original size:24 final size:22
Alignment explanation
Indices: 5257446--5257499 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
5257436 ACAGATTGTT
*
5257446 ATAA-AAAATTATAAAATAAAA
1 ATAATAAAATTACAAAATAAAA
5257467 ATAATAAAATTACATAAATGAAAA
1 ATAATAAAATTACA-AAAT-AAAA
*
5257491 A-AATTAAAT
1 ATAATAAAAT
5257500 AATATTCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 4 0.14
22 8 0.29
23 11 0.39
24 5 0.18
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (22 bp):
ATAATAAAATTACAAAATAAAA
Found at i:5258238 original size:42 final size:42
Alignment explanation
Indices: 5258192--5258301 Score: 116
Period size: 42 Copynumber: 2.6 Consensus size: 42
5258182 TATATAAGTA
* * *** *
5258192 ATATATTATAAAATAGTATAATTTTATAAATAATTCAAATTT
1 ATATAATATAAAATAATATAAACATATAAATAATTCAAATAT
* *
5258234 ATATAAAAATAAAA-ATTATAAACATATAAATAATTCAAATAT
1 ATAT-AATATAAAATAATATAAACATATAAATAATTCAAATAT
*
5258276 ATATAATAAAAAATAATATAAA-ATAT
1 ATATAATATAAAATAATATAAACATAT
5258302 TAAAATTTGG
Statistics
Matches: 56, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
41 11 0.20
42 38 0.68
43 7 0.12
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (42 bp):
ATATAATATAAAATAATATAAACATATAAATAATTCAAATAT
Found at i:5258637 original size:20 final size:20
Alignment explanation
Indices: 5258592--5258638 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
5258582 TCATTGTTCA
*
5258592 AGGTTC-GGGTTTTAGGTTT
1 AGGTTCAGGGTTTGAGGTTT
5258611 AGAGTTCAGGGTTTGA-GTTT
1 AG-GTTCAGGGTTTGAGGTTT
5258631 GAGGTTCA
1 -AGGTTCA
5258639 TGTTTTAGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 2 0.08
20 13 0.54
21 9 0.38
ACGTcount: A:0.17, C:0.06, G:0.36, T:0.40
Consensus pattern (20 bp):
AGGTTCAGGGTTTGAGGTTT
Found at i:5262214 original size:27 final size:27
Alignment explanation
Indices: 5262181--5262233 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
5262171 AGACCACCCG
* *
5262181 TGTTTAATGTCCTAGTGGGCTACCCCA
1 TGTTTAATGTCCCAGTGGACTACCCCA
5262208 TGTTTAATGTCCCAGTGGACTACCCC
1 TGTTTAATGTCCCAGTGGACTACCCC
5262234 GTCTTCACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.19, C:0.28, G:0.21, T:0.32
Consensus pattern (27 bp):
TGTTTAATGTCCCAGTGGACTACCCCA
Found at i:5265037 original size:143 final size:145
Alignment explanation
Indices: 5264776--5265063 Score: 449
Period size: 143 Copynumber: 2.0 Consensus size: 145
5264766 CTTGATTAAA
*
5264776 ATCATCTTTTGAAATCGTGCATTGAAACTTTTATTTTTATTTTATTTTATTTTATTCAGTTAAAT
1 ATCATCTTTTGAAATCGTGCATTGAAACTTTTATTTTCATTTTATTTTATTTTATTCAGTTAAAT
* * * *
5264841 TTTAGTTTTTAATTACTTCCTCAAAATCAAAATATTTTTAATCACCAATGTG-TTTGAATTTCAT
66 TTTAGTTTTTAATGACTTCCTCAAAATCAAAATATTTTTAATCACCAAAGTGTTTTAAATTGCA-
*
5264905 TTCATAAATAATTTTC
130 CTCATAAATAATTTTC
*
5264921 ATCATCTTTTGAAATCGTGCATTGGAACTTTTATTTTCATTTTA-TTTATTTTACTT-AGTTAAA
1 ATCATCTTTTGAAATCGTGCATTGAAACTTTTATTTTCATTTTATTTTATTTTA-TTCAGTTAAA
**
5264984 -TTTAGTTTTTAATGACTTCCTCAAAATCAAAATATTTTTCTTCACCAAAGTGTTTTAAATTGCA
65 TTTTAGTTTTTAATGACTTCCTCAAAATCAAAATATTTTTAATCACCAAAGTGTTTTAAATTGCA
5265048 CTCATAAATAATTTTC
130 CTCATAAATAATTTTC
5265064 TTTCACAGTC
Statistics
Matches: 132, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
143 63 0.48
144 25 0.19
145 44 0.33
ACGTcount: A:0.31, C:0.13, G:0.07, T:0.49
Consensus pattern (145 bp):
ATCATCTTTTGAAATCGTGCATTGAAACTTTTATTTTCATTTTATTTTATTTTATTCAGTTAAAT
TTTAGTTTTTAATGACTTCCTCAAAATCAAAATATTTTTAATCACCAAAGTGTTTTAAATTGCAC
TCATAAATAATTTTC
Found at i:5265860 original size:37 final size:37
Alignment explanation
Indices: 5265799--5265944 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
5265789 TACGTATGAT
* *
5265799 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
5265834 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
5265871 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
5265908 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
5265945 TAAAGCTACC
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 92 0.88
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:5276138 original size:24 final size:24
Alignment explanation
Indices: 5276106--5276151 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
5276096 GTAGAGAAGG
*
5276106 GAAGGAGCATGTTGAAGCAATAAC
1 GAAGGAGCATGTGGAAGCAATAAC
5276130 GAAGGAGCATGTGGAAGCAATA
1 GAAGGAGCATGTGGAAGCAATA
5276152 GCGCTTGATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.41, C:0.11, G:0.33, T:0.15
Consensus pattern (24 bp):
GAAGGAGCATGTGGAAGCAATAAC
Found at i:5276708 original size:230 final size:230
Alignment explanation
Indices: 5276305--5276765 Score: 823
Period size: 230 Copynumber: 2.0 Consensus size: 230
5276295 CTAGAGATAG
** * *
5276305 AAACAATTAAAGATTCTGCTGTTGCAAAGATATCGTACCCTTCAAGGCTAGAAGAGAAATAAAAG
1 AAACAATTAAAGATTCTGCCATTGCAAAGATACCGTAACCTTCAAGGCTAGAAGAGAAATAAAAG
*
5276370 TGGGATGGAAATGAGGTTGTAAGTTTTTTAAACTTGTTCAAAAAATTAGATGTCAACCTGCATTT
66 TGGGATGGAAACGAGGTTGTAAGTTTTTTAAACTTGTTCAAAAAATTAGATGTCAACCTGCATTT
5276435 GATTGAAAAAGTTCCTAAGTATGCCAAAATTTTAAAGGAAATCATGTCTAGGCATAGGAAAATTA
131 GATTGAAAAAGTTCCTAAGTATGCCAAAATTTTAAAGGAAATCATGTCTAGGCATAGGAAAATTA
5276500 AGGTAGGAGAACAAGTTAACATGAGCACTTATTGT
196 AGGTAGGAGAACAAGTTAACATGAGCACTTATTGT
*
5276535 AAACAATTAAAGATTTTGCCATTGCAAAGATACCGTAACCTTCAAGGCTAGAAGAGAAATAAAAG
1 AAACAATTAAAGATTCTGCCATTGCAAAGATACCGTAACCTTCAAGGCTAGAAGAGAAATAAAAG
* *
5276600 TGGGATGGAAACGAGGTTGTAAGTTTTTTAAACTTGTTCAAAACATTAGATGTCAACCTGTATTT
66 TGGGATGGAAACGAGGTTGTAAGTTTTTTAAACTTGTTCAAAAAATTAGATGTCAACCTGCATTT
*
5276665 GATTGAAAAAGTTCCTAAGTATGCCAAAATTTTAAAGGAAATCATGTCTAGGCGTAGGAAAATTA
131 GATTGAAAAAGTTCCTAAGTATGCCAAAATTTTAAAGGAAATCATGTCTAGGCATAGGAAAATTA
* *
5276730 AGGTAGGAGAACAAGTTAACATGAGCTCTTCTTGT
196 AGGTAGGAGAACAAGTTAACATGAGCACTTATTGT
5276765 A
1 A
5276766 GTGTTCTTAT
Statistics
Matches: 220, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
230 220 1.00
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (230 bp):
AAACAATTAAAGATTCTGCCATTGCAAAGATACCGTAACCTTCAAGGCTAGAAGAGAAATAAAAG
TGGGATGGAAACGAGGTTGTAAGTTTTTTAAACTTGTTCAAAAAATTAGATGTCAACCTGCATTT
GATTGAAAAAGTTCCTAAGTATGCCAAAATTTTAAAGGAAATCATGTCTAGGCATAGGAAAATTA
AGGTAGGAGAACAAGTTAACATGAGCACTTATTGT
Found at i:5278881 original size:20 final size:20
Alignment explanation
Indices: 5278856--5278930 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
5278846 ACTGAATTTA
5278856 CACTTCGGTGCCTCTTTTTG
1 CACTTCGGTGCCTCTTTTTG
* *
5278876 CACTTCGGTGCCT-TTGATCG
1 CACTTCGGTGCCTCTT-TTTG
* *
5278896 TACATTC-GTGCCTCTATTTG
1 CAC-TTCGGTGCCTCTTTTTG
*
5278916 CACTTCGATGCCTCT
1 CACTTCGGTGCCTCT
5278931 GTTATACATC
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
19 5 0.12
20 34 0.79
21 4 0.09
ACGTcount: A:0.11, C:0.31, G:0.19, T:0.40
Consensus pattern (20 bp):
CACTTCGGTGCCTCTTTTTG
Found at i:5280765 original size:17 final size:18
Alignment explanation
Indices: 5280726--5280767 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
5280716 CTAATTCTTT
5280726 CAAAATCCTCTAAACTCC
1 CAAAATCCTCTAAACTCC
*
5280744 TAAAATCCT-TAAAAC-CC
1 CAAAATCCTCT-AAACTCC
5280761 CAAAATC
1 CAAAATC
5280768 TCATTTTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.45, C:0.33, G:0.00, T:0.21
Consensus pattern (18 bp):
CAAAATCCTCTAAACTCC
Found at i:5283608 original size:63 final size:63
Alignment explanation
Indices: 5283509--5283636 Score: 256
Period size: 63 Copynumber: 2.0 Consensus size: 63
5283499 TTGATCTGTC
5283509 GTAATTCGGTGTAGTAGATTAAACTAGTTTTTGCACTTTAGGAGCTTGAACATAAGCATTTTA
1 GTAATTCGGTGTAGTAGATTAAACTAGTTTTTGCACTTTAGGAGCTTGAACATAAGCATTTTA
5283572 GTAATTCGGTGTAGTAGATTAAACTAGTTTTTGCACTTTAGGAGCTTGAACATAAGCATTTTA
1 GTAATTCGGTGTAGTAGATTAAACTAGTTTTTGCACTTTAGGAGCTTGAACATAAGCATTTTA
5283635 GT
1 GT
5283637 TAAGTTTTAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (63 bp):
GTAATTCGGTGTAGTAGATTAAACTAGTTTTTGCACTTTAGGAGCTTGAACATAAGCATTTTA
Found at i:5286011 original size:15 final size:15
Alignment explanation
Indices: 5285991--5286019 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5285981 GGTTGAGAGC
5285991 TTTTTTGAAGGAATT
1 TTTTTTGAAGGAATT
5286006 TTTTTTGAAGGAAT
1 TTTTTTGAAGGAAT
5286020 GGATAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTTTTGAAGGAATT
Found at i:5296833 original size:15 final size:15
Alignment explanation
Indices: 5296813--5296842 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5296803 ATCGGGTCTT
5296813 ATCCTCCTGAAGTTG
1 ATCCTCCTGAAGTTG
5296828 ATCCTCCTGAAGTTG
1 ATCCTCCTGAAGTTG
5296843 CAATGAGGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (15 bp):
ATCCTCCTGAAGTTG
Found at i:5297232 original size:220 final size:220
Alignment explanation
Indices: 5296828--5297240 Score: 648
Period size: 220 Copynumber: 1.9 Consensus size: 220
5296818 CCTGAAGTTG
* * **
5296828 ATCCTCCTGAAGTTGCAATGAGGTAGGCTGAAGATGGCAGATCTTATCTCCCTGAAGTTGTAGTG
1 ATCCTCCTGAAGTTGCAATGAGGTAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTACAGTG
** *
5296893 GAACAGATTAAAGCTGATAATCCTATCTCCCTGAAGTTGCAGTGAAGCGGATTAAAACCTTAGAT
66 GAACAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTGCAGTGAAGCGAATTAAAACCTTAGAT
**
5296958 CTTATCTCTCTGAAGTTGCAGAGAGCAGATTGCATCTAGTCTTACCTCCCTGAAGTTGCAGTGGA
131 CTTATCTCTCTGAAGTTGCAGAGAGCAGATCACATCTAGTCTTACCTCCCTGAAGTTGCAGTGGA
5297023 GCAGACTAAGTAAGCATCTATTCTT
196 GCAGACTAAGTAAGCATCTATTCTT
*
5297048 ATCCTCCTGAAGTTGCAGTGAGGTAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTACAGTG
1 ATCCTCCTGAAGTTGCAATGAGGTAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTACAGTG
* *
5297113 GAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGAATTAAAACCTTAGAT
66 GAACAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTGCAGTGAAGCGAATTAAAACCTTAGAT
* * * * * *
5297178 CTTATTTCTTTGAAGTTGCGGAGATCAGATCACATCTATTTTTATCCT-CCTGAAGTTGCAGTG
131 CTTATCTCTCTGAAGTTGCAGAGAGCAGATCACATCTAGTCTTA-CCTCCCTGAAGTTGCAGTG
5297241 AGGTAGACTG
Statistics
Matches: 174, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
220 171 0.98
221 3 0.02
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (220 bp):
ATCCTCCTGAAGTTGCAATGAGGTAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTACAGTG
GAACAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTGCAGTGAAGCGAATTAAAACCTTAGAT
CTTATCTCTCTGAAGTTGCAGAGAGCAGATCACATCTAGTCTTACCTCCCTGAAGTTGCAGTGGA
GCAGACTAAGTAAGCATCTATTCTT
Found at i:5297244 original size:173 final size:173
Alignment explanation
Indices: 5297037--5297413 Score: 623
Period size: 173 Copynumber: 2.2 Consensus size: 173
5297027 ACTAAGTAAG
5297037 CATCTATTCTTATCCTCCTGAAGTTGCAGTGAGGTAGACTGAAGATGGCAAATCTTATCTCCCTG
1 CATCTATTCTTATCCTCCTGAAGTTGCAGTGAGGTAGACTGAAGATGGCAAATCTTATCTCCCTG
5297102 AAGTTACAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTGCAGTGGAGC-GAATT
66 AAGTTACAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTGCAGTGGAGCAG-ATT
* * * * *
5297166 AAAACCTTAGATCTTATTTCTTTGAAGTTGCGGAGATCAGATCA
130 AAAACCTTAGATCTTATTTCTCTAAAGTTACGGAGAGCAAATCA
*
5297210 CATCTATTTTTATCCTCCTGAAGTTGCAGTGAGGTAGACTGAAGATGGCAAATCTTATCTCCCTG
1 CATCTATTCTTATCCTCCTGAAGTTGCAGTGAGGTAGACTGAAGATGGCAAATCTTATCTCCCTG
* *
5297275 AAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTA
66 AAGTTACAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTA
* *
5297340 AAACCTTGGATCTTATTTCTCTAAAGTTACGGAGAGCAAATCG
131 AAACCTTAGATCTTATTTCTCTAAAGTTACGGAGAGCAAATCA
*
5297383 CATCTATTCTTAT-TTCCCTGAAGTTGCAGTG
1 CATCTATTCTTATCCT-CCTGAAGTTGCAGTG
5297414 GAGCAGACTA
Statistics
Matches: 190, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
172 1 0.01
173 188 0.99
174 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (173 bp):
CATCTATTCTTATCCTCCTGAAGTTGCAGTGAGGTAGACTGAAGATGGCAAATCTTATCTCCCTG
AAGTTACAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTA
AAACCTTAGATCTTATTTCTCTAAAGTTACGGAGAGCAAATCA
Found at i:5297367 original size:44 final size:44
Alignment explanation
Indices: 5296868--5297344 Score: 281
Period size: 44 Copynumber: 10.9 Consensus size: 44
5296858 AAGATGGCAG
* * * *
5296868 ATCTTATCTCCCTGAAGTTGTAGTGGAACAGATTAAAGCTGATA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCGATA
* * * *
5296912 ATCCTATCTCCCTGAAGTTGCAGTGAAGCGGATTAAAACC-TTA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCGATA
* * ** *
5296955 GATCTTATCTCTCTGAAGTTGCAG-AGAGCAGATT-GCATC--TA
1 -ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCGATA
* * * *
5296996 GTCTTACCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGC-ATCTA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AACCGA--TA
* * * * **
5297043 TTCTTATC-CTCCTGAAGTTGCAGT-GAGGTAGACTGAAGATGGCA-A
1 ATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAAAACCG-ATA
* * *
5297088 ATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCCAATA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCGATA
* *
5297132 ATCCTATCTCCCTGAAGTTGCAGTGGAGC-GAATTAAAACC-TTA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAG-ATTAAAACCGATA
* ** * * * *
5297175 GATCTTATTTCTTTGAAGTTGC-G-GAGATCAGA-TCACATC--TA
1 -ATCTTATCTCCCTGAAGTTGCAGTG-GAGCAGATTAAAACCGATA
* * * * * **
5297216 TTTTTATC-CTCCTGAAGTTGCAGT-GAGGTAGACTGAAGATGGCA-A
1 ATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAAAACCG-ATA
*
5297261 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCGATA
*
5297305 ATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACC
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACC
5297345 TTGGATCTTA
Statistics
Matches: 327, Mismatches: 74, Indels: 64
0.70 0.16 0.14
Matches are distributed among these distances:
39 1 0.00
40 36 0.11
41 16 0.05
42 7 0.02
43 22 0.07
44 156 0.48
45 50 0.15
46 10 0.03
47 26 0.08
48 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (44 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCGATA
Found at i:5302044 original size:25 final size:24
Alignment explanation
Indices: 5302016--5302068 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
5302006 GGTTGTGTTT
*
5302016 ATTTATTATGGACTTTGATTTGGAC
1 ATTTATTATGGACTTTGACTT-GAC
* *
5302041 ATTTATTTTGGATTTTGACTTGAC
1 ATTTATTATGGACTTTGACTTGAC
5302065 ATTT
1 ATTT
5302069 TTCTACATGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 7 0.28
25 18 0.72
ACGTcount: A:0.23, C:0.08, G:0.17, T:0.53
Consensus pattern (24 bp):
ATTTATTATGGACTTTGACTTGAC
Found at i:5306090 original size:18 final size:18
Alignment explanation
Indices: 5306067--5306266 Score: 184
Period size: 18 Copynumber: 11.1 Consensus size: 18
5306057 TAAGACACGT
*
5306067 ATAATAACATATGTTCAC
1 ATAATAACATAGGTTCAC
***
5306085 ATAATAACATAGGTTTGT
1 ATAATAACATAGGTTCAC
*
5306103 ATGATAACATAGGTTCAC
1 ATAATAACATAGGTTCAC
* *
5306121 ATAACAACATAGGTTCCC
1 ATAATAACATAGGTTCAC
**
5306139 ATAATAACATAGGTTCGT
1 ATAATAACATAGGTTCAC
** * *
5306157 ACGATAACATAAGCTCAC
1 ATAATAACATAGGTTCAC
* **
5306175 ATGATAACATAGGTTTGC
1 ATAATAACATAGGTTCAC
*
5306193 ATAACAACATAGGTTCAC
1 ATAATAACATAGGTTCAC
* **
5306211 ATAATATCATAGGTTCGT
1 ATAATAACATAGGTTCAC
* **
5306229 ATAATAACATAAGTTTGC
1 ATAATAACATAGGTTCAC
*
5306247 ATAAGAACATAGGTTCAC
1 ATAATAACATAGGTTCAC
5306265 AT
1 AT
5306267 GAAATATGGG
Statistics
Matches: 141, Mismatches: 41, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 141 1.00
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (18 bp):
ATAATAACATAGGTTCAC
Found at i:5306149 original size:54 final size:54
Alignment explanation
Indices: 5306067--5306262 Score: 212
Period size: 54 Copynumber: 3.6 Consensus size: 54
5306057 TAAGACACGT
* * *
5306067 ATAATAACATATGTTCACATAATAACATAGGTTTGTATGATAACATAGGTTCAC
1 ATAATAACATAGGTTCGCATAATAACATAGGTTCGTATGATAACATAGGTTCAC
* * * * *
5306121 ATAACAACATAGGTTCCCATAATAACATAGGTTCGTACGATAACATAAGCTCAC
1 ATAATAACATAGGTTCGCATAATAACATAGGTTCGTATGATAACATAGGTTCAC
* * * ** * * **
5306175 ATGATAACATAGGTTTGCATAACAACATAGGTTCACATAATATCATAGGTTCGT
1 ATAATAACATAGGTTCGCATAATAACATAGGTTCGTATGATAACATAGGTTCAC
* * *
5306229 ATAATAACATAAGTTTGCATAAGAACATAGGTTC
1 ATAATAACATAGGTTCGCATAATAACATAGGTTC
5306263 ACATGAAATA
Statistics
Matches: 118, Mismatches: 24, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 118 1.00
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (54 bp):
ATAATAACATAGGTTCGCATAATAACATAGGTTCGTATGATAACATAGGTTCAC
Found at i:5327707 original size:28 final size:29
Alignment explanation
Indices: 5327601--5327726 Score: 130
Period size: 30 Copynumber: 4.3 Consensus size: 29
5327591 ATACAACATG
* * *
5327601 CAGTATC-AGTCTGGGCCTGAGCCCTATA
1 CAGTATCAAGTGTGGGCCTTAGCCCAATA
* * *
5327629 CAGTAGCAACGAGTGGGCCATAGCCCAATA
1 CAGTATCAA-GTGTGGGCCTTAGCCCAATA
* *
5327659 CAGTAACAGAGTGTGGGCCTTAACCCAATA
1 CAGTATCA-AGTGTGGGCCTTAGCCCAATA
*
5327689 CAGTATC-AGTGTGGGCCTTAGCCCAAAA
1 CAGTATCAAGTGTGGGCCTTAGCCCAATA
5327717 CAGTAATCAA
1 CAGT-ATCAA
5327727 TACAAATGCA
Statistics
Matches: 80, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
28 29 0.36
29 4 0.05
30 46 0.57
31 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.24, T:0.20
Consensus pattern (29 bp):
CAGTATCAAGTGTGGGCCTTAGCCCAATA
Found at i:5327878 original size:26 final size:26
Alignment explanation
Indices: 5327849--5327910 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
5327839 CAAAGCTAAT
*
5327849 AGTATCAGTAATGCAATA-ACACTGCC
1 AGTATCAGTAATACAATAGA-ACTGCC
* *
5327875 AGTAACAGTAATACAATAGAGCTGCC
1 AGTATCAGTAATACAATAGAACTGCC
*
5327901 AGTATGAGTA
1 AGTATCAGTA
5327911 TCGCATCAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 29 0.97
27 1 0.03
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (26 bp):
AGTATCAGTAATACAATAGAACTGCC
Found at i:5328232 original size:26 final size:26
Alignment explanation
Indices: 5328160--5328244 Score: 91
Period size: 27 Copynumber: 3.2 Consensus size: 26
5328150 ATTTCGGTTG
*
5328160 TTTTACACTTCGAGGATATTTCT-GTAA
1 TTTTAC-CTTCGAGGGTATTT-TAGTAA
*
5328187 TCTTACCCTTCGAGGGTATTTTAGTAA
1 TTTTA-CCTTCGAGGGTATTTTAGTAA
* * *
5328214 TTTTACCATCGAGGGTATTTCAATAA
1 TTTTACCTTCGAGGGTATTTTAGTAA
5328240 TTTTA
1 TTTTA
5328245 GAGGCCCATT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
26 24 0.48
27 25 0.50
28 1 0.02
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (26 bp):
TTTTACCTTCGAGGGTATTTTAGTAA
Found at i:5332210 original size:30 final size:30
Alignment explanation
Indices: 5332176--5332284 Score: 85
Period size: 30 Copynumber: 3.4 Consensus size: 30
5332166 AGAAAACCGA
5332176 GGTACCCAGAACTCTTAACTCTTAACTGAT
1 GGTACCCAGAACTCTTAACTCTTAACTGAT
**** * *
5332206 GGTACCCAGAACGAAGATCTATCTTGGAGAAAACCGA-
1 GGTACCCAGAACTCTTAAC--TCTT------AACTGAT
5332243 GGTACCCAGAACTCTTAACTCTTAACTGAT
1 GGTACCCAGAACTCTTAACTCTTAACTGAT
5332273 GGTACCCAGAAC
1 GGTACCCAGAAC
5332285 GAAGATCTAT
Statistics
Matches: 58, Mismatches: 12, Indels: 18
0.66 0.14 0.20
Matches are distributed among these distances:
29 5 0.09
30 26 0.45
32 4 0.07
35 4 0.07
37 14 0.24
38 5 0.09
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (30 bp):
GGTACCCAGAACTCTTAACTCTTAACTGAT
Found at i:5332256 original size:67 final size:67
Alignment explanation
Indices: 5332148--5332311 Score: 328
Period size: 67 Copynumber: 2.4 Consensus size: 67
5332138 TAATGACCAT
5332148 AACGAAGATCTATCTTGGAGAAAACCGAGGTACCCAGAACTCTTAACTCTTAACTGATGGTACCC
1 AACGAAGATCTATCTTGGAGAAAACCGAGGTACCCAGAACTCTTAACTCTTAACTGATGGTACCC
5332213 AG
66 AG
5332215 AACGAAGATCTATCTTGGAGAAAACCGAGGTACCCAGAACTCTTAACTCTTAACTGATGGTACCC
1 AACGAAGATCTATCTTGGAGAAAACCGAGGTACCCAGAACTCTTAACTCTTAACTGATGGTACCC
5332280 AG
66 AG
5332282 AACGAAGATCTATCTTGGAGAAAACCGAGG
1 AACGAAGATCTATCTTGGAGAAAACCGAGG
5332312 CTCCTAGCAA
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 97 1.00
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (67 bp):
AACGAAGATCTATCTTGGAGAAAACCGAGGTACCCAGAACTCTTAACTCTTAACTGATGGTACCC
AG
Found at i:5334450 original size:42 final size:42
Alignment explanation
Indices: 5334402--5334493 Score: 157
Period size: 42 Copynumber: 2.2 Consensus size: 42
5334392 ATTTTAAGAA
*
5334402 GTTTTATGTATCAGCTTATAATTCCAGTAATTATTAACAGAT
1 GTTTTATGTATCAACTTATAATTCCAGTAATTATTAACAGAT
* *
5334444 TTTTTATGTATCAATTTATAATTCCAGTAATTATTAACAGAT
1 GTTTTATGTATCAACTTATAATTCCAGTAATTATTAACAGAT
5334486 GTTTTATG
1 GTTTTATG
5334494 AAAAGCAATT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.47
Consensus pattern (42 bp):
GTTTTATGTATCAACTTATAATTCCAGTAATTATTAACAGAT
Found at i:5335404 original size:28 final size:30
Alignment explanation
Indices: 5335294--5335407 Score: 121
Period size: 30 Copynumber: 3.9 Consensus size: 30
5335284 GGCATACAAC
* * **
5335294 ATACAGTATC--AGTCTGGGCCTGAGCCTT
1 ATACAGTATCAGAGTGTGGGCCTTAGCCCA
*
5335322 ATACAGTAGT-AGAGTGTGGGCCATAGCCCA
1 ATACAGTA-TCAGAGTGTGGGCCTTAGCCCA
* *
5335352 ATACTGTAACAGAGTGTGGGCCTTAGCCCA
1 ATACAGTATCAGAGTGTGGGCCTTAGCCCA
5335382 ATACAGTATCA-A-TGTGGGCCTTAGCC
1 ATACAGTATCAGAGTGTGGGCCTTAGCC
5335408 AAAAATAGTA
Statistics
Matches: 72, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
28 22 0.31
29 2 0.03
30 48 0.67
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (30 bp):
ATACAGTATCAGAGTGTGGGCCTTAGCCCA
Found at i:5335848 original size:26 final size:27
Alignment explanation
Indices: 5335802--5335860 Score: 70
Period size: 26 Copynumber: 2.2 Consensus size: 27
5335792 TATAACGGTC
5335802 ATTTTACCCTATAGGGCTATTTCAGT-
1 ATTTTACCCTATAGGGCTATTTCAGTA
*
5335828 ATTTTACCCT-TCGAGGG-TATTTGAGTA
1 ATTTTACCCTAT--AGGGCTATTTCAGTA
5335855 ATTTTA
1 ATTTTA
5335861 GTGCCCATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 1 0.03
26 18 0.62
27 10 0.34
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.44
Consensus pattern (27 bp):
ATTTTACCCTATAGGGCTATTTCAGTA
Found at i:5336607 original size:11 final size:11
Alignment explanation
Indices: 5336591--5336615 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5336581 TGCCAGTAGA
5336591 GAAAAGAAAAG
1 GAAAAGAAAAG
5336602 GAAAAGAAAAG
1 GAAAAGAAAAG
5336613 GAA
1 GAA
5336616 GGGGGAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (11 bp):
GAAAAGAAAAG
Found at i:5338622 original size:73 final size:73
Alignment explanation
Indices: 5338542--5338840 Score: 571
Period size: 73 Copynumber: 4.1 Consensus size: 73
5338532 GGAATCTCTT
5338542 AAAAATTAAATTCTTTTGTAAGTTAGCATTACTTGAGATGAGAAATGAATTAAGTTTAGGGGTGC
1 AAAAATTAAATTCTTTTGTAAGTTAGCATTACTTGAGATGAGAAATGAATTAAGTTTAGGGGTGC
5338607 GGAAACTA
66 GGAAACTA
5338615 AAAAATTAAATTCTTTTGTAAGTTAGCATTACTTGAGATGAGAAATGAATTAAGTTTAGGGGTGC
1 AAAAATTAAATTCTTTTGTAAGTTAGCATTACTTGAGATGAGAAATGAATTAAGTTTAGGGGTGC
5338680 GGAAACTA
66 GGAAACTA
*
5338688 AAAAATTAAATTCTTTTGTAAGTTAGCTTTACTTGAGATGAGAAATGAATTAAGTTTAGGGGTGC
1 AAAAATTAAATTCTTTTGTAAGTTAGCATTACTTGAGATGAGAAATGAATTAAGTTTAGGGGTGC
5338753 GGAAACTA
66 GGAAACTA
* *
5338761 AAAAATTAAATTCTTTTGTAAGTTAGCTTTACTTGAGATGAGAAATGAATTAAGTTTAGGGGTGT
1 AAAAATTAAATTCTTTTGTAAGTTAGCATTACTTGAGATGAGAAATGAATTAAGTTTAGGGGTGC
5338826 GGAAACTA
66 GGAAACTA
5338834 AAAAATT
1 AAAAATT
5338841 TATAGACTTT
Statistics
Matches: 224, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 224 1.00
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.34
Consensus pattern (73 bp):
AAAAATTAAATTCTTTTGTAAGTTAGCATTACTTGAGATGAGAAATGAATTAAGTTTAGGGGTGC
GGAAACTA
Found at i:5339653 original size:27 final size:26
Alignment explanation
Indices: 5339617--5339667 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
5339607 CTCATCCATT
5339617 TCTCTCATTTTCACTTCTCCCATTTGC
1 TCTCTCATTTTCACTT-TCCCATTTGC
* *
5339644 TCTCTTATTTTCCCTTTCCCATTT
1 TCTCTCATTTTCACTTTCCCATTT
5339668 TTTGATTGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.10, C:0.35, G:0.02, T:0.53
Consensus pattern (26 bp):
TCTCTCATTTTCACTTTCCCATTTGC
Found at i:5350027 original size:62 final size:62
Alignment explanation
Indices: 5349925--5350799 Score: 1723
Period size: 62 Copynumber: 14.1 Consensus size: 62
5349915 TTACCTCTTT
* *
5349925 AGAATTACATATACATACTTTCTTTTAAGAACCATCCCTTAAGACTTATTCAATTTCATCATA
1 AGAA-TACATATACATACTATCTTTTAAGAACCGTCCCTTAAGACTTATTCAATTTCATCATA
5349988 AGAATACATATACATACTATCTTTTAAGAACCGTCCCTTAAGACTTATTCAATTTCATCATA
1 AGAATACATATACATACTATCTTTTAAGAACCGTCCCTTAAGACTTATTCAATTTCATCATA
5350050 AGAATACATATACATACTATCTTTTAAGAACCGTCCCTTAAGACTTATTCAATTTCATCATA
1 AGAATACATATACATACTATCTTTTAAGAACCGTCCCTTAAGACTTATTCAATTTCATCATA
5350112 AGAATACATATACATACTATCTTTTAAGAACCGTCCCTTAAGACTTATTCAATTTCATCATA
1 AGAATACATATACATACTATCTTTTAAGAACCGTCCCTTAAGACTTATTCAATTTCATCATA
5350174 AGAATACATATACATACTATCTTTTAAGAACCGTCCCTTAAGACTTATTCAATTTCATCATA
1 AGAATACATATACATACTATCTTTTAAGAACCGTCCCTTAAGACTTATTCAATTTCATCATA
5350236 AGAATACATATACATACTATCTTTTAAGAACCGTCCCTTAAGACTTATTCAATTTCATCATA
1 AGAATACATATACATACTATCTTTTAAGAACCGTCCCTTAAGACTTATTCAATTTCATCATA
5350298 AGAATACATATACATACTATCTTTTAAGAACCGTCCCTTAAGACTTATTCAATTTCATCATA
1 AGAATACATATACATACTATCTTTTAAGAACCGTCCCTTAAGACTTATTCAATTTCATCATA
5350360 AGAATACATATACATACTATCTTTTAAGAACCGTCCCTTAAGACTTATTCAATTTCATCATA
1 AGAATACATATACATACTATCTTTTAAGAACCGTCCCTTAAGACTTATTCAATTTCATCATA
5350422 AGAATACATATACATACTATCTTTTAAGAACCGTCCCTTAAGACTTATTCAATTTCATCATA
1 AGAATACATATACATACTATCTTTTAAGAACCGTCCCTTAAGACTTATTCAATTTCATCATA
5350484 AGAATACATATACATACTATCTTTTAAGAACCGTCCCTTAAGACTTATTCAATTTCATCATA
1 AGAATACATATACATACTATCTTTTAAGAACCGTCCCTTAAGACTTATTCAATTTCATCATA
5350546 AGAATACATATACATACTATCTTTTAAGAACCGTCCCTTAAGACTTATTCAATTTCATCATA
1 AGAATACATATACATACTATCTTTTAAGAACCGTCCCTTAAGACTTATTCAATTTCATCATA
5350608 AGAATACATATACATACTATCTTTTAAGAACCGTCCCTTAAGACTTATTCAATTTCATCATA
1 AGAATACATATACATACTATCTTTTAAGAACCGTCCCTTAAGACTTATTCAATTTCATCATA
5350670 AGAATACATATACATACTATCTTTTAAGAACCGTCCCTTAAGACTTATTCAATTTCATCATA
1 AGAATACATATACATACTATCTTTTAAGAACCGTCCCTTAAGACTTATTCAATTTCATCATA
5350732 AGAATACATATACATACTATCTTTTAAGAACCGTCCCTTAAGACTTATTCAATTTCATCATA
1 AGAATACATATACATACTATCTTTTAAGAACCGTCCCTTAAGACTTATTCAATTTCATCATA
5350794 AGAATA
1 AGAATA
5350800 ACCAAACCAA
Statistics
Matches: 810, Mismatches: 2, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
62 806 1.00
63 4 0.00
ACGTcount: A:0.37, C:0.21, G:0.06, T:0.36
Consensus pattern (62 bp):
AGAATACATATACATACTATCTTTTAAGAACCGTCCCTTAAGACTTATTCAATTTCATCATA
Found at i:5350848 original size:50 final size:50
Alignment explanation
Indices: 5350773--5350872 Score: 173
Period size: 50 Copynumber: 2.0 Consensus size: 50
5350763 CGTCCCTTAA
*
5350773 GACTTATTCAATTTCATCATAAGAATAACCAAACCAAGTTCACTTTAGAT
1 GACTTATTCAATTTCATCATAAGAATAACCAAACCAAGTTCACTTCAGAT
* *
5350823 GACTTATTCAATTTCATCATAAGAATAACCAAACCGAGTTTACTTCAGAT
1 GACTTATTCAATTTCATCATAAGAATAACCAAACCAAGTTCACTTCAGAT
5350873 TTATCAGATC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (50 bp):
GACTTATTCAATTTCATCATAAGAATAACCAAACCAAGTTCACTTCAGAT
Found at i:5352891 original size:40 final size:40
Alignment explanation
Indices: 5352836--5353157 Score: 374
Period size: 40 Copynumber: 8.1 Consensus size: 40
5352826 TTATTATATT
* *
5352836 AATGCACATGCGTGCCCCTATTTGTACTTCGCTACCCCTG
1 AATGCACATACGTGCCCCTATTTGTACTTCGGTACCCCTG
* * * *
5352876 AATGCACATACGTGCCCTTGTTTGTACTTTGGTACCCCTA
1 AATGCACATACGTGCCCCTATTTGTACTTCGGTACCCCTG
* * *
5352916 AATGCACATATGTGCCCCTATTTGTACTTTGGTACCCCTA
1 AATGCACATACGTGCCCCTATTTGTACTTCGGTACCCCTG
* * * * * *
5352956 AATTCTCATACATGCCCCTTTTTGTACTTCGATACCCTTG
1 AATGCACATACGTGCCCCTATTTGTACTTCGGTACCCCTG
** *
5352996 AATGCACATACGTGCCCCTATTTGTACTTTAGTAACCCTG
1 AATGCACATACGTGCCCCTATTTGTACTTCGGTACCCCTG
* * * *
5353036 AATGCACATACGTGCCTCTTTTTGTACTTTGGTACCCCTA
1 AATGCACATACGTGCCCCTATTTGTACTTCGGTACCCCTG
* *
5353076 AATGCACATACGTGCCCTTATTTGCACTTCGGTACCCCTG
1 AATGCACATACGTGCCCCTATTTGTACTTCGGTACCCCTG
* * * * * *
5353116 AATCCACATACATGCCCTTGTTTGTATTTCAGTACCCCTG
1 AATGCACATACGTGCCCCTATTTGTACTTCGGTACCCCTG
5353156 AA
1 AA
5353158 GTCATATACA
Statistics
Matches: 238, Mismatches: 44, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 238 1.00
ACGTcount: A:0.21, C:0.30, G:0.15, T:0.34
Consensus pattern (40 bp):
AATGCACATACGTGCCCCTATTTGTACTTCGGTACCCCTG
Found at i:5352953 original size:20 final size:20
Alignment explanation
Indices: 5352896--5352955 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
5352886 CGTGCCCTTG
5352896 TTTGTACTTTGGTACCCCTA
1 TTTGTACTTTGGTACCCCTA
** * * *
5352916 AATGCACATAT-GTGCCCCTA
1 TTTGTAC-TTTGGTACCCCTA
5352936 TTTGTACTTTGGTACCCCTA
1 TTTGTACTTTGGTACCCCTA
5352956 AATTCTCATA
Statistics
Matches: 28, Mismatches: 10, Indels: 4
0.67 0.24 0.10
Matches are distributed among these distances:
19 2 0.07
20 24 0.86
21 2 0.07
ACGTcount: A:0.20, C:0.27, G:0.15, T:0.38
Consensus pattern (20 bp):
TTTGTACTTTGGTACCCCTA
Found at i:5353155 original size:120 final size:120
Alignment explanation
Indices: 5352836--5353157 Score: 441
Period size: 120 Copynumber: 2.7 Consensus size: 120
5352826 TTATTATATT
* * *
5352836 AATGCACATGCGTGCCCCTATTTGTACTTCGCTACCCCTGAATGCACATACGTGCCCTTGTTTGT
1 AATGCACATACGTGCCCTTATTTGTACTTCGATACCCCTGAATGCACATACGTGCCCTTGTTTGT
* * *
5352901 ACTTTGGTACCCCTAAATGCACATATGTGCCCCTATTTGTACTTTGGTACCCCTA
66 ACTTTAGTACCCCTGAATGCACATACGTGCCCCTATTTGTACTTTGGTACCCCTA
* * * * * *
5352956 AATTCTCATACATGCCCCTT-TTTGTACTTCGATACCCTTGAATGCACATACGTGCCCCTATTTG
1 AATGCACATACGTG-CCCTTATTTGTACTTCGATACCCCTGAATGCACATACGTGCCCTTGTTTG
* * *
5353020 TACTTTAGTAACCCTGAATGCACATACGTGCCTCTTTTTGTACTTTGGTACCCCTA
65 TACTTTAGTACCCCTGAATGCACATACGTGCCCCTATTTGTACTTTGGTACCCCTA
* * * *
5353076 AATGCACATACGTGCCCTTATTTGCACTTCGGTACCCCTGAATCCACATACATGCCCTTGTTTGT
1 AATGCACATACGTGCCCTTATTTGTACTTCGATACCCCTGAATGCACATACGTGCCCTTGTTTGT
5353141 A-TTTCAGTACCCCTGAA
66 ACTTT-AGTACCCCTGAA
5353158 GTCATATACA
Statistics
Matches: 173, Mismatches: 26, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
119 8 0.05
120 161 0.93
121 4 0.02
ACGTcount: A:0.21, C:0.30, G:0.15, T:0.34
Consensus pattern (120 bp):
AATGCACATACGTGCCCTTATTTGTACTTCGATACCCCTGAATGCACATACGTGCCCTTGTTTGT
ACTTTAGTACCCCTGAATGCACATACGTGCCCCTATTTGTACTTTGGTACCCCTA
Found at i:5356974 original size:40 final size:40
Alignment explanation
Indices: 5356930--5357190 Score: 288
Period size: 40 Copynumber: 6.5 Consensus size: 40
5356920 ATTATTGTAG
* * **
5356930 GAATGCACTTACATGCCCCTATTTGTACTTCAATACCCCT
1 GAATGCACATACATGCCCCTGTTTGTACTTCGGTACCCCT
*
5356970 GAATGCACATACATGCCCCTGTTTATACTTCGGTACCCCT
1 GAATGCACATACATGCCCCTGTTTGTACTTCGGTACCCCT
** * * * *
5357010 GAATGCACATATGTGCCCCTATTTGTACATCAGTACCCTT
1 GAATGCACATACATGCCCCTGTTTGTACTTCGGTACCCCT
* * * * *
5357050 GAATCCACATACATGCTCTTTTTTGTACTTTGGTACCCCT
1 GAATGCACATACATGCCCCTGTTTGTACTTCGGTACCCCT
* * *
5357090 GAATTCACATACATGCCCCTGTTTGTACTTTGGTGCCCCT
1 GAATGCACATACATGCCCCTGTTTGTACTTCGGTACCCCT
* * *
5357130 GAATGCACATACGTGCCCTTGTTTGTACTTCGGTACTCCT
1 GAATGCACATACATGCCCCTGTTTGTACTTCGGTACCCCT
* * * *
5357170 AAAGGCATATACATGCTCCTG
1 GAATGCACATACATGCCCCTG
5357191 ATTCTATTTT
Statistics
Matches: 182, Mismatches: 39, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 182 1.00
ACGTcount: A:0.22, C:0.29, G:0.15, T:0.33
Consensus pattern (40 bp):
GAATGCACATACATGCCCCTGTTTGTACTTCGGTACCCCT
Found at i:5357145 original size:20 final size:20
Alignment explanation
Indices: 5357085--5357147 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
5357075 TACTTTGGTA
* *
5357085 CCCCTGAATTCACATACATG
1 CCCCTGAATGCACATACGTG
** * * **
5357105 CCCCTGTTTGTACTTTGGTG
1 CCCCTGAATGCACATACGTG
5357125 CCCCTGAATGCACATACGTG
1 CCCCTGAATGCACATACGTG
5357145 CCC
1 CCC
5357148 TTGTTTGTAC
Statistics
Matches: 29, Mismatches: 14, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.19, C:0.35, G:0.17, T:0.29
Consensus pattern (20 bp):
CCCCTGAATGCACATACGTG
Found at i:5357182 original size:120 final size:120
Alignment explanation
Indices: 5356963--5357187 Score: 317
Period size: 120 Copynumber: 1.9 Consensus size: 120
5356953 TGTACTTCAA
*
5356963 TACCCCTGAATGCACATACATGCCCCTGTTTATACTTCGGTACCCCTGAATGCACATATGTGCCC
1 TACCCCTGAATGCACATACATGCCCCTGTTTATACTTCGGTACCCCTGAATGCACATACGTGCCC
* *
5357028 CTATTTGTACATCAGTACCCTTGAATCCACATACATGCTCTTTTTTGTACTTTGG
66 CTATTTGTACATCAGTACCCTTAAAGCCACATACATGCTCTTTTTTGTACTTTGG
* * * *
5357083 TACCCCTGAATTCACATACATGCCCCTGTTTGTACTTTGGTGCCCCTGAATGCACATACGTGCCC
1 TACCCCTGAATGCACATACATGCCCCTGTTTATACTTCGGTACCCCTGAATGCACATACGTGCCC
* * * * * *
5357148 TTGTTTGTACTTCGGTACTCC-TAAAGGCATATACATGCTC
66 CTATTTGTACATCAGTAC-CCTTAAAGCCACATACATGCTC
5357188 CTGATTCTAT
Statistics
Matches: 91, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
120 89 0.98
121 2 0.02
ACGTcount: A:0.22, C:0.29, G:0.16, T:0.33
Consensus pattern (120 bp):
TACCCCTGAATGCACATACATGCCCCTGTTTATACTTCGGTACCCCTGAATGCACATACGTGCCC
CTATTTGTACATCAGTACCCTTAAAGCCACATACATGCTCTTTTTTGTACTTTGG
Found at i:5359228 original size:64 final size:64
Alignment explanation
Indices: 5359127--5359259 Score: 248
Period size: 64 Copynumber: 2.1 Consensus size: 64
5359117 ATGCATAGAT
*
5359127 AAAAATAACTAAAGTTTTAATGAAGGGTATTTTAGTCATTAAATAATAAAAAGAATAAAAAGGG
1 AAAAATAACTAAAGTTTTAATGAAGGGTATTTTAGTCATTAAATAATAAAAAGAATAAAAAGAG
*
5359191 AAAAATAACTAAAGTTTTAATGAAGGGTATTTTAGTCATTGAATAATAAAAAGAATAAAAAGAG
1 AAAAATAACTAAAGTTTTAATGAAGGGTATTTTAGTCATTAAATAATAAAAAGAATAAAAAGAG
5359255 AAAAA
1 AAAAA
5359260 GATGGAAAAA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 67 1.00
ACGTcount: A:0.55, C:0.03, G:0.15, T:0.27
Consensus pattern (64 bp):
AAAAATAACTAAAGTTTTAATGAAGGGTATTTTAGTCATTAAATAATAAAAAGAATAAAAAGAG
Found at i:5360196 original size:50 final size:50
Alignment explanation
Indices: 5360087--5360376 Score: 278
Period size: 50 Copynumber: 5.7 Consensus size: 50
5360077 ATTTCGGTAA
* *
5360087 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGACATCCTTGAGATCGTG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAGA-C--G
* * *
5360143 AGAGGTCCCATGTAAGGCCATGTCTGGGAAATGACATTGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
* * *
5360193 AGAGGTCCCATGTAAGACCATGTCTGGGACACGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
** * * *
5360243 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
** * * * * * *
5360293 AGAACTCCCATGTAAGACCATATCTGGGATATGACATTGGTA--GTACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGACG
* ** *
5360342 AAACATCCCATGTAAGACCATGTTTGGGACATGGC
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGC
5360377 TTTCGCATGT
Statistics
Matches: 199, Mismatches: 34, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
48 1 0.01
49 32 0.16
50 122 0.61
52 1 0.01
53 4 0.02
55 2 0.01
56 37 0.19
ACGTcount: A:0.28, C:0.22, G:0.29, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
Found at i:5367750 original size:56 final size:50
Alignment explanation
Indices: 5367656--5367951 Score: 236
Period size: 49 Copynumber: 5.8 Consensus size: 50
5367646 ATTTGGGTAA
* * *
5367656 AGAGATCCCATGTAAGACCATGTCTGGGACATGACATTGGCATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA--C-T--GA-CACG
* * *
5367712 AGAGGTCCCATGCAAAACCATGTCTAGGACATGGCATTGGCACTGACACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGACACG
* * * * *
5367762 AGAGGTCCCATGTAAGACCATGTGTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGACACG
** * * ** * *
5367812 AGAACTCCCATGTAAGACCATATCTTGGTTATGGCATTGGCAGT-ACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGACACG
* ** * ** * *
5367861 AAACATCCCATGTAAGACCATATCTGGGTTATGGCATTGGCAGT-ACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGACACG
* ** * *
5367910 AAACATCTCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
5367952 TGTTATTATC
Statistics
Matches: 206, Mismatches: 34, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
49 86 0.42
50 79 0.38
51 2 0.01
53 1 0.00
54 1 0.00
56 37 0.18
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGACACG
Found at i:5374482 original size:41 final size:41
Alignment explanation
Indices: 5374425--5374535 Score: 127
Period size: 41 Copynumber: 2.7 Consensus size: 41
5374415 ATCGGAGTGT
* **
5374425 AAATAGGGGCACGTATGTGCAATTTAGGGGTATTGAAGTAC
1 AAATAGGGGCACGTATGTGCAATTCAGGGGTACCGAAGTAC
*
5374466 AAATAGGGGC-CTGTATGTGCAATTCATGGGTACCGAAGTAC
1 AAATAGGGGCAC-GTATGTGCAATTCAGGGGTACCGAAGTAC
** *
5374507 -AATCAGGGGCACACATCTGCAATTCAGGG
1 AAAT-AGGGGCACGTATGTGCAATTCAGGG
5374536 AATAATTAAC
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
40 4 0.07
41 54 0.92
42 1 0.02
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (41 bp):
AAATAGGGGCACGTATGTGCAATTCAGGGGTACCGAAGTAC
Found at i:5376474 original size:11 final size:11
Alignment explanation
Indices: 5376458--5376487 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
5376448 GAATTATTAT
5376458 TTTAATGTTTA
1 TTTAATGTTTA
5376469 TTTAATGTTTA
1 TTTAATGTTTA
5376480 TTTAATGT
1 TTTAATGT
5376488 CTATAAGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (11 bp):
TTTAATGTTTA
Found at i:5382846 original size:27 final size:26
Alignment explanation
Indices: 5382816--5382875 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
5382806 CCACAGCATG
*
5382816 TGTGAGCAAACCTATTTTCACAGCTCA
1 TGTGAGCAAACCTA-ATTCACAGCTCA
** *
5382843 TGTGAGC-ATTCTAATTCACAGCTCG
1 TGTGAGCAAACCTAATTCACAGCTCA
5382868 TGTGAGCA
1 TGTGAGCA
5382876 TACATGTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
25 17 0.61
26 4 0.14
27 7 0.25
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (26 bp):
TGTGAGCAAACCTAATTCACAGCTCA
Found at i:5393415 original size:22 final size:22
Alignment explanation
Indices: 5393364--5393429 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
5393354 GGTATTTGGG
* *
5393364 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
5393385 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
5393407 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
5393430 TCAAAGAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:5395337 original size:63 final size:63
Alignment explanation
Indices: 5395270--5395388 Score: 220
Period size: 63 Copynumber: 1.9 Consensus size: 63
5395260 AGCAAGAAGA
*
5395270 AAAGAAATAGAATCGATGAATCAAACGAAATTGAGAAGAAAGAAAAGGTGAGAATCGGTCAAC
1 AAAGAAATAGAATCGATGAATCAAACGAAATTGAGAAGAAAGAAAAGATGAGAATCGGTCAAC
*
5395333 AAAGAAATAGAATCGATGAATCAAACGAAATTGAGAAGAAAGAAAAGATGCGAATC
1 AAAGAAATAGAATCGATGAATCAAACGAAATTGAGAAGAAAGAAAAGATGAGAATC
5395389 TGCCAAGGAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 54 1.00
ACGTcount: A:0.54, C:0.09, G:0.23, T:0.14
Consensus pattern (63 bp):
AAAGAAATAGAATCGATGAATCAAACGAAATTGAGAAGAAAGAAAAGATGAGAATCGGTCAAC
Found at i:5399970 original size:18 final size:17
Alignment explanation
Indices: 5399948--5399981 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5399938 ACCTCTTCTT
5399948 TTTTTTTTAATTCTGAA
1 TTTTTTTTAATTCTGAA
*
5399965 TTTTTTTTACTTCTGAA
1 TTTTTTTTAATTCTGAA
5399982 ACTTCTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.09, G:0.06, T:0.65
Consensus pattern (17 bp):
TTTTTTTTAATTCTGAA
Found at i:5400082 original size:11 final size:11
Alignment explanation
Indices: 5400066--5400097 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
5400056 AAATTGAATA
5400066 CAATTTTTTTT
1 CAATTTTTTTT
5400077 CAATTTTTTTT
1 CAATTTTTTTT
*
5400088 TAATTTTTTT
1 CAATTTTTTT
5400098 CCCTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (11 bp):
CAATTTTTTTT
Found at i:5403918 original size:30 final size:30
Alignment explanation
Indices: 5403884--5403980 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
5403874 TAAACTAAAA
*
5403884 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
5403914 TGAGCTGAGGCTAAACTCTTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
5403944 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
5403973 ATGAGCTA
1 -TGAGCTA
5403981 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:5404620 original size:100 final size:100
Alignment explanation
Indices: 5404447--5404647 Score: 402
Period size: 100 Copynumber: 2.0 Consensus size: 100
5404437 AACTAAGTTG
5404447 GATCAAGGGATAATTGGTTAAAAACGATGGTAGGCACTTAAACACATTATTCCTCATCCAAAACA
1 GATCAAGGGATAATTGGTTAAAAACGATGGTAGGCACTTAAACACATTATTCCTCATCCAAAACA
5404512 TTTTAATTTCTTTAATCGAATATAGTAACTCATTT
66 TTTTAATTTCTTTAATCGAATATAGTAACTCATTT
5404547 GATCAAGGGATAATTGGTTAAAAACGATGGTAGGCACTTAAACACATTATTCCTCATCCAAAACA
1 GATCAAGGGATAATTGGTTAAAAACGATGGTAGGCACTTAAACACATTATTCCTCATCCAAAACA
5404612 TTTTAATTTCTTTAATCGAATATAGTAACTCATTT
66 TTTTAATTTCTTTAATCGAATATAGTAACTCATTT
5404647 G
1 G
5404648 GTCCTTTGTC
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 101 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (100 bp):
GATCAAGGGATAATTGGTTAAAAACGATGGTAGGCACTTAAACACATTATTCCTCATCCAAAACA
TTTTAATTTCTTTAATCGAATATAGTAACTCATTT
Found at i:5406275 original size:12 final size:12
Alignment explanation
Indices: 5406260--5406302 Score: 86
Period size: 12 Copynumber: 3.6 Consensus size: 12
5406250 TTCTTTTTGC
5406260 TTTTCAAAGGCT
1 TTTTCAAAGGCT
5406272 TTTTCAAAGGCT
1 TTTTCAAAGGCT
5406284 TTTTCAAAGGCT
1 TTTTCAAAGGCT
5406296 TTTTCAA
1 TTTTCAA
5406303 GTTCTCTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.44
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:5406379 original size:6 final size:6
Alignment explanation
Indices: 5406363--5406412 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
5406353 TTTCTTTTTA
*
5406363 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
5406412 T
1 T
5406413 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:5406395 original size:37 final size:37
Alignment explanation
Indices: 5406352--5406422 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
5406342 CTTGCCTCTC
5406352 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
5406389 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
5406423 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:5406423 original size:16 final size:16
Alignment explanation
Indices: 5406348--5406408 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
5406338 GCCTCTTGCC
*
5406348 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
5406364 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
5406380 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
5406396 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
5406409 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:5407438 original size:12 final size:13
Alignment explanation
Indices: 5407407--5407438 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
5407397 TTTAACTCGA
5407407 TTTTTTTTGTCAC
1 TTTTTTTTGTCAC
5407420 TTTTTTTT-TC-C
1 TTTTTTTTGTCAC
5407431 TTTTTTTT
1 TTTTTTTT
5407439 CGATTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 9 0.47
12 2 0.11
13 8 0.42
ACGTcount: A:0.03, C:0.12, G:0.03, T:0.81
Consensus pattern (13 bp):
TTTTTTTTGTCAC
Found at i:5407445 original size:11 final size:11
Alignment explanation
Indices: 5407421--5407462 Score: 50
Period size: 10 Copynumber: 3.8 Consensus size: 11
5407411 TTTTGTCACT
*
5407421 TTTTTTTTC-C
1 TTTTTTTTCGA
5407431 TTTTTTTTCGA
1 TTTTTTTTCGA
*
5407442 TTTTTTTTTGAA
1 TTTTTTTTCG-A
5407454 TTTTTTTTC
1 TTTTTTTTC
5407463 TGAATTTCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
10 9 0.33
11 9 0.33
12 9 0.33
ACGTcount: A:0.07, C:0.10, G:0.05, T:0.79
Consensus pattern (11 bp):
TTTTTTTTCGA
Found at i:5407446 original size:12 final size:12
Alignment explanation
Indices: 5407403--5407462 Score: 56
Period size: 12 Copynumber: 5.2 Consensus size: 12
5407393 TTTTTTTAAC
5407403 TCGATTTTTTTT
1 TCGATTTTTTTT
5407415 GTC-ACTTTTTTTT
1 -TCGA-TTTTTTTT
*
5407428 TC--CTTTTTTT
1 TCGATTTTTTTT
5407438 TCGATTTTTTTT
1 TCGATTTTTTTT
*
5407450 T-GAATTTTTTT
1 TCGATTTTTTTT
5407461 TC
1 TC
5407463 TGAATTTCTT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
10 9 0.22
11 10 0.25
12 11 0.28
13 10 0.25
ACGTcount: A:0.08, C:0.12, G:0.07, T:0.73
Consensus pattern (12 bp):
TCGATTTTTTTT
Found at i:5407458 original size:13 final size:13
Alignment explanation
Indices: 5407431--5407469 Score: 57
Period size: 11 Copynumber: 3.2 Consensus size: 13
5407421 TTTTTTTTCC
5407431 TTTTTTTTC-G-A
1 TTTTTTTTCTGAA
5407442 TTTTTTTT-TGAA
1 TTTTTTTTCTGAA
5407454 TTTTTTTTCTGAA
1 TTTTTTTTCTGAA
5407467 TTT
1 TTT
5407470 CTTCTCCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 9 0.36
12 9 0.36
13 7 0.28
ACGTcount: A:0.13, C:0.05, G:0.08, T:0.74
Consensus pattern (13 bp):
TTTTTTTTCTGAA
Found at i:5408195 original size:35 final size:35
Alignment explanation
Indices: 5408149--5408216 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
5408139 CTCTTTGAAC
*
5408149 AAAGTTCATTCAAATGGTCAAAAGTCAAAAGTCCT
1 AAAGTTCATTCAAATGATCAAAAGTCAAAAGTCCT
5408184 AAAGTTCATTCAAATGATCAAAAGTCAAAAGTC
1 AAAGTTCATTCAAATGATCAAAAGTCAAAAGTC
5408217 AAAAGTCCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.25
Consensus pattern (35 bp):
AAAGTTCATTCAAATGATCAAAAGTCAAAAGTCCT
Found at i:5408233 original size:35 final size:35
Alignment explanation
Indices: 5408149--5408235 Score: 113
Period size: 35 Copynumber: 2.5 Consensus size: 35
5408139 CTCTTTGAAC
* * *
5408149 AAAGTTCATTCAAATGGTCAAAAGTCAAAAGTCCT
1 AAAGTCCATTCAAATGATCAAAAGTCAAAAGTCCA
*
5408184 AAAGTTCATTCAAATGATCAAAAGTCAAAAGT-CA
1 AAAGTCCATTCAAATGATCAAAAGTCAAAAGTCCA
*
5408218 AAAGTCCTTTACAAATGA
1 AAAGTCCATT-CAAATGA
5408236 AAGAAAACAA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
34 9 0.19
35 38 0.81
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.25
Consensus pattern (35 bp):
AAAGTCCATTCAAATGATCAAAAGTCAAAAGTCCA
Found at i:5422603 original size:29 final size:29
Alignment explanation
Indices: 5422547--5422603 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
5422537 TTATGGAAGA
* * *
5422547 GGTGGAGAACTTGTTCGTTAAGAGTTCGC
1 GGTGAAGAACTTGTTCATTAAGAATTCGC
*
5422576 GGTGAAGAACTTGTTCATTGAGAATTCG
1 GGTGAAGAACTTGTTCATTAAGAATTCG
5422604 TGCCAAGGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.25, C:0.12, G:0.32, T:0.32
Consensus pattern (29 bp):
GGTGAAGAACTTGTTCATTAAGAATTCGC
Found at i:5425326 original size:615 final size:614
Alignment explanation
Indices: 5424021--5427319 Score: 4651
Period size: 613 Copynumber: 5.4 Consensus size: 614
5424011 CGTTGTTGTG
* * * * * *
5424021 ACTTTTATTTCCTTTCACTTTTACTTTAAATTTTGTTTTGTTGCCCCTAATCACATAAATGCAAG
1 ACTTTTATTTGCTTTTAGTTTTACTTTAAATTTTGTTTTGTTGCTCCTAATCACATAACTGAAAG
* * ** * * *
5424086 CCATCTTTTAGT-AAAAA-A-A-ATATCTCATTATAATTATATTTTTAATCCATCGGCTACCCAA
66 CCATATTTTAGTCAAAAATATATATATGTCATTATAATTATATTAATAATCCTTCGGCAACCCTA
* * * * *
5424147 CAAACTCGTTCAAATGTGTTTTGAAAA--C-ATAA-TGGTTTGGTTTTCTTCAAAAAATAGTTTA
131 CAAACTCGTTCAAATGTGTTCTGAAAACTCTTTAACT-ATTTGATTTTCTTC-AAAATTAGTTTA
* * *
5424208 A-TTTATTTAGAAAAGAAA-AAAGAGTAAACTAAACAGTTGGTCACCCAACTTTTACAAATTTTC
194 ATTTTAATTAGAAAAGAAACAAA-AGTAAACTACATAGTTGGTCACCCAACTTTTACAAATTTTC
* * * *
5424271 ATTTTAGATATCTAGAA-AAAAAAGTTGTAAAATAGTCATCAATGTTAGAGTATGTTAATTTTGG
258 ATTTTAGATATCTAGAAGAAAAAAGTTGTAAAATAGACATCAATGTTACAGTATTTTCATTTTGG
* ** *** *
5424335 TCACTCCCGTTGAAACAGGTATTTGAAAACACACTTGGAATTTGTTGTAAATTTTGATTTTCCAC
323 TCACTCCCATTGAAATGGGTAACGGAAAACCCACTTGGAATTTGTTGTAAATTTTGATTTTCCAC
* * * *
5424400 CTAGTAATGTAATTTCCATGTCTTTATTAGACATAAAACTAAATAACTATCATTTTAGTCA-TTT
388 CTAGTAATGTAATTTCCATGTCATTATTATACATACAACTAAAT-ATTATCATTTTAGTCACTTT
* * * *
5424464 CATTCTTTTACCTATAAATGAATAAGAACCTAAAAATTGAGGAAATTTTTCATTGCTTATTTCAA
452 -ATTCTTTTATCTATAAATGAATAAGAACCTAAAAATTGGGGAGATTTTTCATTGCTTATTTCAG
* * * * * * * *
5424529 TGCCGCTCT-AATGCACTAGTTTTTTTGTTTTATTGTTTATGTATAATCTTAACCATCCTAGAAC
516 TGCCTCTCTGAA-GCACTAG--TTTTT-TCTTCTTGTTTTTGTACAATCTTAGCTATCCTAGTAC
* * ** *
5424593 GAAAAATGTTGAAGCCCACAAATACTATGGTTGTTTTC
577 GAACAATGTTGTAGCTGACAAATACTATGGTTGTTTAC
* ** * * *
5424631 ACGTTTATTTGCTTTTAGTTTTACTTTAAATTCAGTTTTGTTGCTCGTGATCACATAAATGAAAG
1 ACTTTTATTTGCTTTTAGTTTTACTTTAAATTTTGTTTTGTTGCTCCTAATCACATAACTGAAAG
** * *
5424696 CCATATTTT-GTCAAAAATATATATAAT-TCATTATAATTATATTGTTAATCCTCCGGCTACCCT
66 CCATATTTTAGTCAAAAATATATAT-ATGTCATTATAATTATATTAATAATCCTTCGGCAACCCT
* * *
5424759 ACAAACTCATTCATATGTGTT-TAGAAAACTCTTTAACTATTTGGTTTTCTTCAAAATTAGTTTA
130 ACAAACTCGTTCAAATGTGTTCT-GAAAACTCTTTAACTATTTGATTTTCTTCAAAATTAGTTTA
* **
5424823 A-TTTAATTAGAAAAGAAATAAGGGTAAACTACATAGTTGGTCACCCAACTTTTACAAATTTTCA
194 ATTTTAATTAGAAAAGAAACAAAAGTAAACTACATAGTTGGTCACCCAACTTTTACAAATTTTCA
* * * *
5424887 TTTTAGATATCTAGCAAAAAGAAGAAGTTGTAAAATAGGCATCGATGTTACAGTATTATCATTTT
259 TTTTAGATATCTAG-AAGAA-AA-AAGTTGTAAAATAGACATCAATGTTACAGTATTTTCATTTT
* * * * * **
5424952 GTTCACTCCCATTTAAATGGGTAAC-AAAAACCCACTTGGAATTTTTTGTAAAATTTGACATTCC
321 GGTCACTCCCATTGAAATGGGTAACGGAAAACCCACTTGGAATTTGTTGTAAATTTTGATTTTCC
5425016 ACCTAGTAATGTAATTTCCATGTCATTATTATACATACAACTAAATATTATCATTTTAGTCACTT
386 ACCTAGTAATGTAATTTCCATGTCATTATTATACATACAACTAAATATTATCATTTTAGTCACTT
*
5425081 TGTTCTTTTATCTATAAATGAATAAGAACCTAAAAATTGGGGAGATTTTTCATTGCTTATTTCAG
451 TATTCTTTTATCTATAAATGAATAAGAACCTAAAAATTGGGGAGATTTTTCATTGCTTATTTCAG
5425146 TGCCTCTCTGAAGCACTAGTTTTTTCTTCTTGTTTTTGTACAATCTTAGCTATCCTAGTACGAAC
516 TGCCTCTCTGAAGCACTAGTTTTTTCTTCTTGTTTTTGTACAATCTTAGCTATCCTAGTACGAAC
5425211 AATGTTGTAGCTGACAAATACTATGGTTGTTTAC
581 AATGTTGTAGCTGACAAATACTATGGTTGTTTAC
* * * *
5425245 ACTTTTATTTGCTTTTAGTTTTCCTTTACATTTTGTTTTGTTGCTCCTAATCGCATAACTGGAAG
1 ACTTTTATTTGCTTTTAGTTTTACTTTAAATTTTGTTTTGTTGCTCCTAATCACATAACTGAAAG
*
5425310 CCATATTTTAGTCAAAAATATATATATGTCATTATAATTATATTAATAATCCTTTGGCAACCCTA
66 CCATATTTTAGTCAAAAATATATATATGTCATTATAATTATATTAATAATCCTTCGGCAACCCTA
* *
5425375 CAAACTCGTTTAAATGTGTTCTGGAAACTCTTTAACTATTTGATTTTCTTCAAAATTAGTTTAAT
131 CAAACTCGTTCAAATGTGTTCTGAAAACTCTTTAACTATTTGATTTTCTTCAAAATTAGTTTAAT
*
5425440 TTTAATTAGAAAAGAAACAAAAGTAAACTGCATAGTTGGTCACCCAACTTTTACAAATTTTCATT
196 TTTAATTAGAAAAGAAACAAAAGTAAACTACATAGTTGGTCACCCAACTTTTACAAATTTTCATT
* * * *
5425505 GTAGATATCTAGAAGAAAAAATTTGTAAAATAAACATCAATGTTACAATATTTTCATTTTGGTCA
261 TTAGATATCTAGAAGAAAAAAGTTGTAAAATAGACATCAATGTTACAGTATTTTCATTTTGGTCA
* *
5425570 CTCCCATTGAAATGGGCAACGGAAAA-CAACTTGGAATTTGTTGTAAATTTTGATTTTCCACCTA
326 CTCCCATTGAAATGGGTAACGGAAAACCCACTTGGAATTTGTTGTAAATTTTGATTTTCCACCTA
*
5425634 GTAATGTAATTTCCATGTCATTATTATACATACAACTAAATATTATCATTTTAGTCACTTTGTTC
391 GTAATGTAATTTCCATGTCATTATTATACATACAACTAAATATTATCATTTTAGTCACTTTATTC
5425699 TTTTATCTATAAATGAATAAGAACCTAAAAATTGGGGAGATTTTTCATTGCTTATTTCAGTGCCT
456 TTTTATCTATAAATGAATAAGAACCTAAAAATTGGGGAGATTTTTCATTGCTTATTTCAGTGCCT
*
5425764 CTCTGAAGCACTAGTTTTTTCTTCTTGTTTTTGTACAATCTTAGTTATCCTAGTACGAACAATGT
521 CTCTGAAGCACTAGTTTTTTCTTCTTGTTTTTGTACAATCTTAGCTATCCTAGTACGAACAATGT
5425829 TGTAGCTGACAAATACTATGGTTGTTTAC
586 TGTAGCTGACAAATACTATGGTTGTTTAC
* * *
5425858 ACTTTTATTTGCTTTTAGTTTTCCTTTACATTTTGTTTTGTTGCTCCTAATCGCATAACTGAAAG
1 ACTTTTATTTGCTTTTAGTTTTACTTTAAATTTTGTTTTGTTGCTCCTAATCACATAACTGAAAG
* * *
5425923 ACAGATTTTAGTCAAAAATATATATATGTCATTATAATTATATTAATAATCCTTTGGCAACCCTA
66 CCATATTTTAGTCAAAAATATATATATGTCATTATAATTATATTAATAATCCTTCGGCAACCCTA
* *
5425988 CAAACTCGTTTAAATGTGTTCTGGAAACTCTTTAACTATTTGATTTTCTTCAAAATTAGTTTAAT
131 CAAACTCGTTCAAATGTGTTCTGAAAACTCTTTAACTATTTGATTTTCTTCAAAATTAGTTTAAT
*
5426053 TTTAATTAGAAAAGAAACAAAAGTAAACTGCATAGTTGGTCACCCAACTTTTACAAATTTTCATT
196 TTTAATTAGAAAAGAAACAAAAGTAAACTACATAGTTGGTCACCCAACTTTTACAAATTTTCATT
* * * *
5426118 GTAGATATCTAGAAGAAAAAATTTGTAAAATAAACATCAATGTTACAATATTTTCATTTTGGTCA
261 TTAGATATCTAGAAGAAAAAAGTTGTAAAATAGACATCAATGTTACAGTATTTTCATTTTGGTCA
* *
5426183 CTCCCATTGAAATGGGCAACGGAAAA-CAACTTGGAATTTGTTGTAAATTTTGATTTTCCACCTA
326 CTCCCATTGAAATGGGTAACGGAAAACCCACTTGGAATTTGTTGTAAATTTTGATTTTCCACCTA
*
5426247 GTAATGTAATTTCCATGTCATTATTATACATACAACTAAATATTATCATTTTAGTCACTTCATTC
391 GTAATGTAATTTCCATGTCATTATTATACATACAACTAAATATTATCATTTTAGTCACTTTATTC
*
5426312 TTTTATCTATAAATGAATAAGAACCTAAAAATTGGGGAGATTTTTCATTGCTTATTTTAGTGCCT
456 TTTTATCTATAAATGAATAAGAACCTAAAAATTGGGGAGATTTTTCATTGCTTATTTCAGTGCCT
*
5426377 CTCTGAAGCACTAGTTTTTTCTTCTTGTTTTTGTACAATCTTAGTTATCCTAGTACGAACAATGT
521 CTCTGAAGCACTAGTTTTTTCTTCTTGTTTTTGTACAATCTTAGCTATCCTAGTACGAACAATGT
5426442 TGTAGCTGACAAATACTATGGTTGTTTAC
586 TGTAGCTGACAAATACTATGGTTGTTTAC
* * *
5426471 ACTTTTATTTGCTTTTAGTTTTCCTTTACATTTTGTTTTGTTGCTCCTAATCGCATAACTGAAAG
1 ACTTTTATTTGCTTTTAGTTTTACTTTAAATTTTGTTTTGTTGCTCCTAATCACATAACTGAAAG
* * *
5426536 ACAGATTTTAGTCAAAAATATATATATGTCATTATAATTATATTAATAATCCTTTGGCAACCCTA
66 CCATATTTTAGTCAAAAATATATATATGTCATTATAATTATATTAATAATCCTTCGGCAACCCTA
* *
5426601 CAAACTCGTTTAAATGTGTTCTGGAAACTCTTTAACTATTTGATTTTCTTCAAAATTAGTTTAAT
131 CAAACTCGTTCAAATGTGTTCTGAAAACTCTTTAACTATTTGATTTTCTTCAAAATTAGTTTAAT
* *
5426666 TTTAATTAGAAAAGAAACAAAAGTAAACTGCATAGTTGGTCACCAAACTTTTACAAATTTTCATT
196 TTTAATTAGAAAAGAAACAAAAGTAAACTACATAGTTGGTCACCCAACTTTTACAAATTTTCATT
* * * *
5426731 TTAGATATCTACAAGAAAAAAGTTGTAAAATAGACATCGATGTTATAGTATTTTCATTTTGGCCA
261 TTAGATATCTAGAAGAAAAAAGTTGTAAAATAGACATCAATGTTACAGTATTTTCATTTTGGTCA
* *
5426796 CTCCCATTGAAATGAGTAACGGAAAACCCACTCGGAATTTGTTGTAAATTTTGATTTTCCACCTA
326 CTCCCATTGAAATGGGTAACGGAAAACCCACTTGGAATTTGTTGTAAATTTTGATTTTCCACCTA
* * *
5426861 GTAATGTAATTTCCATGTCATTATTATACATAAAACTAAATATTATCATTTTAGTTACTTCATTC
391 GTAATGTAATTTCCATGTCATTATTATACATACAACTAAATATTATCATTTTAGTCACTTTATTC
* * *
5426926 TTTTATCTATGAATGAATAAGAACCTAAAAA-TGAGGGAAATTTTTCACTGCTTA-TTCGAGTGC
456 TTTTATCTATAAATGAATAAGAACCTAAAAATTG-GGGAGATTTTTCATTGCTTATTTC-AGTGC
**** * * * * **
5426989 CT-AGAAAATGCACTAGTTTTCCTT-TTCTTATTTATCTACAATCTTATCCGTCCTAGTACGAAC
519 CTCTCTGAA-GCACTAGTTTT--TTCTTCTTGTTTTTGTACAATCTTAGCTATCCTAGTACGAAC
* ** * *
5427052 AATGTTGAAGCCCACAAATACTATGGTTTTTTTC
581 AATGTTGTAGCTGACAAATACTATGGTTGTTTAC
* * * * * *
5427086 ACTTTTATTTCCTTTTGGTTTTACTTTAAATTTTGTTTTCTAGCTCCTAACCACATCAA-TAAAA
1 ACTTTTATTTGCTTTTAGTTTTACTTTAAATTTTGTTTTGTTGCTCCTAATCACAT-AACTGAAA
* ** ** * *
5427150 ACCATATTAAAGTC-AAAA-ATATATATGTCATTATAATTATATTGTTAATCCTTCGACTACCCT
65 GCCATATTTTAGTCAAAAATATATATATGTCATTATAATTATATTAATAATCCTTCGGCAACCCT
* * *
5427213 ACAAACTCGTTCAATTGTGTTTTGAAAACTTTTTAACTATTTGATTTTCTT-AAAACTTAGTTTA
130 ACAAACTCGTTCAAATGTGTTCTGAAAACTCTTTAACTATTTGATTTTCTTCAAAA-TTAGTTTA
* ** *
5427277 A-TTTAATTAGAAAA-AAATAAGGGTAAACTACACAGTTGGTCAC
194 ATTTTAATTAGAAAAGAAACAAAAGTAAACTACATAGTTGGTCAC
5427320 TCAATGTAAC
Statistics
Matches: 2481, Mismatches: 178, Indels: 59
0.91 0.07 0.02
Matches are distributed among these distances:
609 2 0.00
610 68 0.03
611 25 0.01
612 19 0.01
613 1419 0.57
614 306 0.12
615 317 0.13
616 97 0.04
617 92 0.04
618 83 0.03
619 53 0.02
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (614 bp):
ACTTTTATTTGCTTTTAGTTTTACTTTAAATTTTGTTTTGTTGCTCCTAATCACATAACTGAAAG
CCATATTTTAGTCAAAAATATATATATGTCATTATAATTATATTAATAATCCTTCGGCAACCCTA
CAAACTCGTTCAAATGTGTTCTGAAAACTCTTTAACTATTTGATTTTCTTCAAAATTAGTTTAAT
TTTAATTAGAAAAGAAACAAAAGTAAACTACATAGTTGGTCACCCAACTTTTACAAATTTTCATT
TTAGATATCTAGAAGAAAAAAGTTGTAAAATAGACATCAATGTTACAGTATTTTCATTTTGGTCA
CTCCCATTGAAATGGGTAACGGAAAACCCACTTGGAATTTGTTGTAAATTTTGATTTTCCACCTA
GTAATGTAATTTCCATGTCATTATTATACATACAACTAAATATTATCATTTTAGTCACTTTATTC
TTTTATCTATAAATGAATAAGAACCTAAAAATTGGGGAGATTTTTCATTGCTTATTTCAGTGCCT
CTCTGAAGCACTAGTTTTTTCTTCTTGTTTTTGTACAATCTTAGCTATCCTAGTACGAACAATGT
TGTAGCTGACAAATACTATGGTTGTTTAC
Found at i:5428562 original size:25 final size:25
Alignment explanation
Indices: 5428524--5428639 Score: 96
Period size: 25 Copynumber: 4.7 Consensus size: 25
5428514 AGGGTTACTG
* *
5428524 ATTCAGCTCTTATGAGCTTACCGAT
1 ATTCAACTCGTATGAGCTTACCGAT
* *
5428549 ACTCAACTCGTATGAGCTTACCGGT
1 ATTCAACTCGTATGAGCTTACCGAT
* *
5428574 ATTCAGCTCAG-AGGAGCTTACC-ATT
1 ATTCAACTC-GTATGAGCTTACCGA-T
* * *
5428599 ATTCAGCTCGGAGGAGCTTACCG-T
1 ATTCAACTCGTATGAGCTTACCGAT
5428623 -TTACAACTCGTATGAGC
1 ATT-CAACTCGTATGAGC
5428640 ATACATGTAC
Statistics
Matches: 75, Mismatches: 11, Indels: 11
0.77 0.11 0.11
Matches are distributed among these distances:
23 2 0.03
24 13 0.17
25 59 0.79
26 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (25 bp):
ATTCAACTCGTATGAGCTTACCGAT
Found at i:5429964 original size:13 final size:13
Alignment explanation
Indices: 5429946--5429976 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
5429936 CACATGGGCG
5429946 TGTGGCTTGGCCA
1 TGTGGCTTGGCCA
*
5429959 TGTGGCTTGGCCG
1 TGTGGCTTGGCCA
5429972 TGTGG
1 TGTGG
5429977 TACAAGTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.03, C:0.19, G:0.45, T:0.32
Consensus pattern (13 bp):
TGTGGCTTGGCCA
Found at i:5431950 original size:600 final size:604
Alignment explanation
Indices: 5430385--5431952 Score: 2191
Period size: 600 Copynumber: 2.6 Consensus size: 604
5430375 TTTTACAAAT
* *
5430385 TTTCATTTTAGTTATCTAG--AAAAAAA-TTGGTAAAATAGGCATCGATGTTACAGTACTTTCAT
1 TTTCATTTTAGATATCTAGAAAAAAAAAGTT-GTAAAATAGGCATCGATGTTACAGTATTTTCAT
* *
5430447 TTTGGTCACTCCTGTTGAAGTGGGTAACGAAAAACCACTTGGAATTTGTTGTAAATTTTGACTTT
65 TTTGGTCACTCCTGTTGAAATGGGTAACGAAAACCCACTTGGAATTTGTTGTAAATTTTGACTTT
*
5430512 CCACCTAGTAATGTAATTTCCATGTCATTA-T-T--AT---AC---AT-ATTATCATATTAGTCA
130 CCACCTAGTAATGTAATTTCCATGTCATTATTATACATACAACTAAATAATTATCATTTTAGTCA
* * *
5430566 CTTCATTATTTTATCTATAAATGAATAAGAACCTAAAAATTGGGGAAATTTTTTATTGCTTATTT
195 CTTCATTCTTTTATCTATAAATGAATAAGAACCTAAAAATTGGGGAAATTTTTCATTGATTATTT
* * * ** * *
5430631 TAGTGCCTCTCTAATGCACTA-G-TTTTTTCTTCTTGTTTTTGTTTAATCTTAACTATCCTAGTA
260 CAGTGCCTCTCTAATGCACTAGGTTTTTTTTTTCTTGTTTATGTACAATCTTAACCATCCTAGAA
* * *
5430694 TGAACAATATTAAAGACGACAAATACTATGGTTGTTTTCACTTTTATTCGCTTTTAGTTTTACTT
325 TGAACAATGTT-GAGGCGACAAATACTATGGTTGTTTTCACTTTTATTCGCTTTTAGTTTTACTT
* *
5430759 TAAATTCTATTTTGTTGCTCATGATCACATAAATGAAAGCCAGATTTTAGTCAAAAATGTACATA
389 TAAATTCTATTTTGTTGCTCATGATCACATAAATGAAAGCCAGATTTTAGTAAAAAATGCACATA
* *
5430824 TGTCATTATAATTATATTGGTATTCCTTTGGCTACCCTACAAAATCATTCAAATGTGTTTTGAAA
454 TGTCATTATAATTATATTGGTAATCCTTTGGCTACCCTACAAAATCATTCAAATGTGCTTTGAAA
5430889 ACTCTTAAACTATTTGATTTTCTTCAAAATTAGTTTAATTTTAATTAGAAAAGAAATAAGGGTAA
519 ACTCTTAAACTATTTGATTTTCTTCAAAATTAGTTTAATTTTAATTAGAAAAGAAATAAGGGTAA
5430954 ACTACACAATTGGTTACCCAACTTTTATAAAC
584 ACTACACAATTGGTT-----AC-----T-AAC
*
5430986 TTTCATTTTAGATATCTA-AAAGAAAAAAGTTGTAAAATAGGCATC-AGTGTTACAATATTTTCA
1 TTTCATTTTAGATATCTAGAAA-AAAAAAGTTGTAAAATAGGCATCGA-TGTTACAGTATTTTCA
5431049 TTTTGGTCACTCCTGTTGAAATGGGTAACTGAAAACCCACTTGGAATTTGTTGTAAATTTTGACT
64 TTTTGGTCACTCCTGTTGAAATGGGTAAC-GAAAACCCACTTGGAATTTGTTGTAAATTTTGACT
* * * *
5431114 TTCTACCTAGTAATGTAATTTCTACGTCATAATTATACATACAACTAAATAATTATCATTTTAGT
128 TTCCACCTAGTAATGTAATTTCCATGTCATTATTATACATACAACTAAATAATTATCATTTTAGT
* * * *
5431179 CACTTCATTCTTTTATCTATAAATGAATAAGAACCTCAAAATTGGGGGAATTTATGATTGATTAT
193 CACTTCATTCTTTTATCTATAAATGAATAAGAACCTAAAAATTGGGGAAATTTTTCATTGATTAT
* * *
5431244 TTCAGTCCCTCTCTAATGTACTAGGTTTTTTCTTT-TTGTTTATGTACAATCTTAACCATCCTAG
258 TTCAGTGCCTCTCTAATGCACTAGGTTTTTTTTTTCTTGTTTATGTACAATCTTAACCATCCTAG
* * **
5431308 TAA-AAACAATGTTGAAGGCAACAAATACTATGGTTGTTTTCACTTTTATTTTCTTTTAGTTTTA
323 -AATGAACAATGTTG-AGGCGACAAATACTATGGTTGTTTTCACTTTTATTCGCTTTTAGTTTTA
* *
5431372 CTTTAAATTCTGTTTTGTTGCTCTTGATCACATAAATGAAAGCCAGATTTTAGTAAAAAATGCAC
386 CTTTAAATTCTATTTTGTTGCTCATGATCACATAAATGAAAGCCAGATTTTAGTAAAAAATGCAC
*
5431437 ATATGTCATTATAATTATATTGGTAATCCTTTGGCTACCCTACAAACTCATTCAAATGTGCTTTG
451 ATATGTCATTATAATTATATTGGTAATCCTTTGGCTACCCTACAAAATCATTCAAATGTGCTTTG
* *
5431502 AAAACTCTTTAACTATTTGATTTTCTTCAAAATTAGTTTAA-TTTAATTAGAAAATAAATAAGGG
516 AAAACTCTTAAACTATTTGATTTTCTTCAAAATTAGTTTAATTTTAATTAGAAAAGAAATAAGGG
*
5431566 TAAACTACACAGTTGG-T-C-AAC
581 TAAACTACACAATTGGTTACTAAC
* * *
5431587 -TTCATTTTAGATATCTAGAAAAAAAAAGTTGTAAAATAGACAACGATGTTACAGT-TTGTTCAC
1 TTTCATTTTAGATATCTAGAAAAAAAAAGTTGTAAAATAGGCATCGATGTTACAGTATT-TTCAT
* *
5431650 TTTGGTCACTCCCGTTGAAATGGGTAACGGAAAACCCACTTGGAATTTGTTGTAAATTTTGATTT
65 TTTGGTCACTCCTGTTGAAATGGGTAAC-GAAAACCCACTTGGAATTTGTTGTAAATTTTGACTT
* *
5431715 TCCACTTAGTGATGTAATTTCCATGTCATTATTATACATACAACTAAATAATTATCATTTTAGTC
129 TCCACCTAGTAATGTAATTTCCATGTCATTATTATACATACAACTAAATAATTATCATTTTAGTC
* * * * *
5431780 ACCTGATTCGTTTATCTATAAATGAATAAGAACCTAAAAATTGCGGAAATTTTTCATTGGTTATT
194 ACTTCATTCTTTTATCTATAAATGAATAAGAACCTAAAAATTGGGGAAATTTTTCATTGATTATT
** * * *
5431845 TCAGTGCAACTGTGATGCAGTAGGTTTTTTTTTTCTTGTTTATGTACAATCTTAACCATCCTAGA
259 TCAGTGCCTCTCTAATGCACTAGGTTTTTTTTTTCTTGTTTATGTACAATCTTAACCATCCTAGA
* *
5431910 ATGAACAATGTTGAGGCCGACAACTACTAT-GTTTTTTTCACTT
324 ATGAACAATGTTGAGG-CGACAAATACTATGGTTGTTTTCACTT
5431953 ACATATCAAT
Statistics
Matches: 863, Mismatches: 77, Indels: 55
0.87 0.08 0.06
Matches are distributed among these distances:
599 2 0.00
600 270 0.31
601 74 0.09
602 2 0.00
603 62 0.07
604 64 0.07
605 1 0.00
606 1 0.00
608 3 0.00
611 2 0.00
614 3 0.00
615 129 0.15
616 242 0.28
617 8 0.01
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.40
Consensus pattern (604 bp):
TTTCATTTTAGATATCTAGAAAAAAAAAGTTGTAAAATAGGCATCGATGTTACAGTATTTTCATT
TTGGTCACTCCTGTTGAAATGGGTAACGAAAACCCACTTGGAATTTGTTGTAAATTTTGACTTTC
CACCTAGTAATGTAATTTCCATGTCATTATTATACATACAACTAAATAATTATCATTTTAGTCAC
TTCATTCTTTTATCTATAAATGAATAAGAACCTAAAAATTGGGGAAATTTTTCATTGATTATTTC
AGTGCCTCTCTAATGCACTAGGTTTTTTTTTTCTTGTTTATGTACAATCTTAACCATCCTAGAAT
GAACAATGTTGAGGCGACAAATACTATGGTTGTTTTCACTTTTATTCGCTTTTAGTTTTACTTTA
AATTCTATTTTGTTGCTCATGATCACATAAATGAAAGCCAGATTTTAGTAAAAAATGCACATATG
TCATTATAATTATATTGGTAATCCTTTGGCTACCCTACAAAATCATTCAAATGTGCTTTGAAAAC
TCTTAAACTATTTGATTTTCTTCAAAATTAGTTTAATTTTAATTAGAAAAGAAATAAGGGTAAAC
TACACAATTGGTTACTAAC
Found at i:5432294 original size:30 final size:30
Alignment explanation
Indices: 5432258--5432322 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
5432248 CAACTTAACG
*
5432258 AACAAATGCCTCTAAAATAATAACAAAATT
1 AACAAATACCTCTAAAATAATAACAAAATT
*
5432288 AACAAATACCTTTAAAATAATAACAAAATT
1 AACAAATACCTCTAAAATAATAACAAAATT
5432318 AACAA
1 AACAA
5432323 TAAAATAAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.60, C:0.15, G:0.02, T:0.23
Consensus pattern (30 bp):
AACAAATACCTCTAAAATAATAACAAAATT
Found at i:5432377 original size:11 final size:11
Alignment explanation
Indices: 5432359--5432398 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
5432349 ACAATAACAA
5432359 CAAAATAGTAG
1 CAAAATAGTAG
*
5432370 CAACATAGTAG
1 CAAAATAGTAG
* *
5432381 TAAAATTGTAG
1 CAAAATAGTAG
5432392 CAAAATA
1 CAAAATA
5432399 AGGAGAAAAC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.53, C:0.10, G:0.15, T:0.23
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:5432407 original size:22 final size:22
Alignment explanation
Indices: 5432360--5432407 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
5432350 CAATAACAAC
* *
5432360 AAAATAGTAGCAACATAGTAGT
1 AAAATAGTAGCAAAATAGGAGT
*
5432382 AAAATTGTAGCAAAATAAGGAG-
1 AAAATAGTAGCAAAAT-AGGAGT
5432404 AAAA
1 AAAA
5432408 CAACACCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.56, C:0.06, G:0.19, T:0.19
Consensus pattern (22 bp):
AAAATAGTAGCAAAATAGGAGT
Found at i:5432428 original size:21 final size:22
Alignment explanation
Indices: 5432392--5432433 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
5432382 AAAATTGTAG
* *
5432392 CAAAATAAGGAGAAAACAACAC
1 CAAAATAAGCAGAAAAAAACAC
5432414 CAAAATAA-CAGAAAAAAACA
1 CAAAATAAGCAGAAAAAAACA
5432434 GAAAAAAAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.69, C:0.17, G:0.10, T:0.05
Consensus pattern (22 bp):
CAAAATAAGCAGAAAAAAACAC
Found at i:5438271 original size:4 final size:4
Alignment explanation
Indices: 5438262--5438289 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
5438252 TTAAACTAAG
5438262 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
5438290 AATAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:5438759 original size:11 final size:11
Alignment explanation
Indices: 5438743--5438771 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
5438733 CAACTCAAAA
5438743 TTTTTTTTGA-
1 TTTTTTTTGAC
5438753 TTTTTTTTGAC
1 TTTTTTTTGAC
5438764 TTTTTTTT
1 TTTTTTTT
5438772 CGCTACGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.07, C:0.03, G:0.07, T:0.83
Consensus pattern (11 bp):
TTTTTTTTGAC
Found at i:5440308 original size:20 final size:19
Alignment explanation
Indices: 5440285--5440349 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
5440275 AAGCTCAAAC
5440285 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
5440305 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
5440325 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
5440345 GAGCT
1 GAGCT
5440350 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:5442122 original size:86 final size:86
Alignment explanation
Indices: 5442012--5442186 Score: 350
Period size: 86 Copynumber: 2.0 Consensus size: 86
5442002 GAAAGGTAAT
5442012 GAAGTTGGAACCAATCCGTGGATGGAATCTTGCAAACCTGAAACAAAGAAAAATCACAAGGTAAT
1 GAAGTTGGAACCAATCCGTGGATGGAATCTTGCAAACCTGAAACAAAGAAAAATCACAAGGTAAT
5442077 TTCGAAAGGGGGTTAGCAAAA
66 TTCGAAAGGGGGTTAGCAAAA
5442098 GAAGTTGGAACCAATCCGTGGATGGAATCTTGCAAACCTGAAACAAAGAAAAATCACAAGGTAAT
1 GAAGTTGGAACCAATCCGTGGATGGAATCTTGCAAACCTGAAACAAAGAAAAATCACAAGGTAAT
5442163 TTCGAAAGGGGGTTAGCAAAA
66 TTCGAAAGGGGGTTAGCAAAA
5442184 GAA
1 GAA
5442187 TTCCTCTCTT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 89 1.00
ACGTcount: A:0.42, C:0.15, G:0.25, T:0.18
Consensus pattern (86 bp):
GAAGTTGGAACCAATCCGTGGATGGAATCTTGCAAACCTGAAACAAAGAAAAATCACAAGGTAAT
TTCGAAAGGGGGTTAGCAAAA
Found at i:5442302 original size:21 final size:21
Alignment explanation
Indices: 5442273--5442409 Score: 51
Period size: 21 Copynumber: 6.7 Consensus size: 21
5442263 CAAGCTCTCT
* *
5442273 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-ATTTC
* **
5442294 TTCTTTTTCAATTTTCATTTC
1 TTCATTTTCTTTTTTCATTTC
5442315 TTCATTTTCTTTTTCTCTCACTTT-
1 TTCATTTTC-TTTT-T-TCA-TTTC
*
5442339 TTCAATTTC-TTTTTC-TTT-
1 TTCATTTTCTTTTTTCATTTC
* *
5442357 TGCAATTTC-TTTTTC-TTT-
1 TTCATTTTCTTTTTTCATTTC
*
5442375 TTCGTTTTCTTTTTGT--TTTC
1 TTCATTTTCTTTTT-TCATTTC
*
5442395 TTTCAATTTCTTTTT
1 -TTCATTTTCTTTTT
5442410 CAATCTCTTT
Statistics
Matches: 92, Mismatches: 15, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
18 26 0.28
19 7 0.08
20 6 0.07
21 33 0.36
22 5 0.05
23 1 0.01
24 11 0.12
25 3 0.03
ACGTcount: A:0.09, C:0.18, G:0.03, T:0.69
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCATTTC
Found at i:5442350 original size:12 final size:12
Alignment explanation
Indices: 5442293--5442419 Score: 55
Period size: 12 Copynumber: 10.6 Consensus size: 12
5442283 TTTTTCGCTT
5442293 TTTCTTTTTCAA
1 TTTCTTTTTCAA
*
5442305 TTTTCATTTCTTCAT
1 -TTTC-TTT-TTCAA
**
5442320 TTTCTTTTTCTC
1 TTTCTTTTTCAA
**
5442332 TCACTTTTTCAA
1 TTTCTTTTTCAA
*
5442344 TTTCTTTTTC-T
1 TTTCTTTTTCAA
** **
5442355 TTTGCAATTTCTT
1 TTT-CTTTTTCAA
**
5442368 TTTCTTTTTCGT
1 TTTCTTTTTCAA
*
5442380 TTTCTTTTT--G
1 TTTCTTTTTCAA
*
5442390 TTT-TCTTTCAA
1 TTTCTTTTTCAA
5442401 TTTCTTTTTCAA
1 TTTCTTTTTCAA
*
5442413 TCTCTTT
1 TTTCTTT
5442420 CTCCTTTTCT
Statistics
Matches: 87, Mismatches: 20, Indels: 15
0.71 0.16 0.12
Matches are distributed among these distances:
9 4 0.05
10 3 0.03
11 6 0.07
12 52 0.60
13 11 0.13
14 7 0.08
15 4 0.05
ACGTcount: A:0.10, C:0.19, G:0.02, T:0.69
Consensus pattern (12 bp):
TTTCTTTTTCAA
Found at i:5442356 original size:18 final size:18
Alignment explanation
Indices: 5442290--5442410 Score: 98
Period size: 18 Copynumber: 6.4 Consensus size: 18
5442280 TCTTTTTTCG
5442290 CTTTTTCTTTTTCAATTTT
1 CTTTTTCTTTTTCAA-TTT
* **
5442309 CATTTCTTCATTTTCTTTTT
1 C-TTT-TTCTTTTTCAATTT
* **
5442329 CTCTCACTTTTTCAATTT
1 CTTTTTCTTTTTCAATTT
*
5442347 CTTTTTCTTTTGCAATTT
1 CTTTTTCTTTTTCAATTT
**
5442365 CTTTTTCTTTTTCGTTTT
1 CTTTTTCTTTTTCAATTT
*
5442383 CTTTTTGTTTTCTTTCAATTT
1 C-TTTT-TCTT-TTTCAATTT
5442404 CTTTTTC
1 CTTTTTC
5442411 AATCTCTTTC
Statistics
Matches: 77, Mismatches: 20, Indels: 10
0.72 0.19 0.09
Matches are distributed among these distances:
18 39 0.51
19 8 0.10
20 14 0.18
21 16 0.21
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.69
Consensus pattern (18 bp):
CTTTTTCTTTTTCAATTT
Found at i:5442410 original size:6 final size:6
Alignment explanation
Indices: 5442290--5442397 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
5442280 TCTTTTTTCG
* * * **
5442290 CTTTTT CTTTTT CAATTTT CATTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
5442341 CAATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
5442389 -GTTTT CTTT
1 CTTTTT CTTT
5442398 CAATTTCTTT
Statistics
Matches: 75, Mismatches: 24, Indels: 6
0.71 0.23 0.06
Matches are distributed among these distances:
5 4 0.05
6 58 0.77
7 10 0.13
8 3 0.04
ACGTcount: A:0.08, C:0.19, G:0.03, T:0.70
Consensus pattern (6 bp):
CTTTTT
Done.