Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold125
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: 3608436
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 25 characters in sequence are not A, C, G, or T
File 14 of 18
Found at i:2387930 original size:24 final size:26
Alignment explanation
Indices: 2387902--2387967 Score: 73
Period size: 28 Copynumber: 2.5 Consensus size: 26
2387892 TGTGCACATC
2387902 ATTTTATATAAAT-TT-TTTATATTT
1 ATTTTATATAAATATTATTTATATTT
*
2387926 ATTTTTATTTAAAATATTATTTATATTT
1 A-TTTTATAT-AAATATTATTTATATTT
2387954 ATATTTATAATAAA
1 AT-TTTAT-ATAAA
2387968 AATAAAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
24 1 0.03
25 7 0.21
26 4 0.12
27 3 0.09
28 18 0.53
29 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (26 bp):
ATTTTATATAAATATTATTTATATTT
Found at i:2388710 original size:20 final size:20
Alignment explanation
Indices: 2388687--2388770 Score: 77
Period size: 20 Copynumber: 4.4 Consensus size: 20
2388677 AATAATATAA
* *
2388687 ATAAAAATACCAATAGTAAT
1 ATAAAAATAACAATACTAAT
*
2388707 ATAAAATTAACAATACTAAT
1 ATAAAAATAACAATACTAAT
* *
2388727 ATAAATA-AAC-ATAATAAT
1 ATAAAAATAACAATACTAAT
* *
2388745 ATAAAATTAAGAATA-TAA-
1 ATAAAAATAACAATACTAAT
2388763 ATAAAAAT
1 ATAAAAAT
2388771 GAATAATATT
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
18 19 0.37
19 8 0.15
20 25 0.48
ACGTcount: A:0.64, C:0.06, G:0.02, T:0.27
Consensus pattern (20 bp):
ATAAAAATAACAATACTAAT
Found at i:2388711 original size:38 final size:36
Alignment explanation
Indices: 2388663--2388808 Score: 120
Period size: 38 Copynumber: 3.9 Consensus size: 36
2388653 TAAAACAAAC
*
2388663 ATAATA-ATAAATCTAATAATATAAATAAAAATACCAATA
1 ATAATATA-AAAT-TAACAATATAAATAAAAATA-C-ATA
*
2388702 GTAATATAAAATTAACAATACTAATATAAATAA-ACATA
1 ATAATATAAAATTAACAATA-TAA-ATAAA-AATACATA
*
2388740 ATAATATAAAATTAAGAATATAAATAAAAATGA-ATA
1 ATAATATAAAATTAACAATATAAATAAAAAT-ACATA
* *
2388776 ATATTATAATAAATTTAACAAAATAAA-AAAAAT
1 ATA--AT-ATAAAATTAACAATATAAATAAAAAT
2388809 CATGTCCACG
Statistics
Matches: 91, Mismatches: 7, Indels: 19
0.78 0.06 0.16
Matches are distributed among these distances:
35 2 0.02
36 11 0.12
37 4 0.04
38 36 0.40
39 29 0.32
40 7 0.08
41 2 0.02
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (36 bp):
ATAATATAAAATTAACAATATAAATAAAAATACATA
Found at i:2388778 original size:19 final size:20
Alignment explanation
Indices: 2388742--2388779 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
2388732 TAAACATAAT
*
2388742 AATATAAAATTAAGAATATA
1 AATATAAAATGAAGAATATA
*
2388762 AATA-AAAATGAATAATAT
1 AATATAAAATGAAGAATAT
2388780 TATAATAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (20 bp):
AATATAAAATGAAGAATATA
Found at i:2390507 original size:2 final size:2
Alignment explanation
Indices: 2390500--2390538 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2390490 TCTCCATTGG
2390500 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2390539 AATGTAAGTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2392228 original size:36 final size:37
Alignment explanation
Indices: 2392149--2392228 Score: 112
Period size: 36 Copynumber: 2.2 Consensus size: 37
2392139 ATCATTGATC
*
2392149 CAATTTACCCCCAAAATTGTATCATACAAAGTATTAA
1 CAATTTACCCCCAAAATTCTATCATACAAAGTATTAA
2392186 -ATATTTA-CCCC-AAATATCTATCATACAAAGTATTAA
1 CA-ATTTACCCCCAAAAT-TCTATCATACAAAGTATTAA
2392222 CAATTTA
1 CAATTTA
2392229 GTAGTTGATA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
35 4 0.10
36 29 0.74
37 6 0.15
ACGTcount: A:0.44, C:0.20, G:0.04, T:0.33
Consensus pattern (37 bp):
CAATTTACCCCCAAAATTCTATCATACAAAGTATTAA
Found at i:2394771 original size:21 final size:20
Alignment explanation
Indices: 2394729--2394771 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
2394719 TTATTTTAAA
**
2394729 TTTAATTATAAAAGAATTTT
1 TTTAATTATAAAAGAAGCTT
*
2394749 TTTAATTATAAAAATAAGCTT
1 TTTAATTAT-AAAAGAAGCTT
2394770 TT
1 TT
2394772 AAATCCATCT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (20 bp):
TTTAATTATAAAAGAAGCTT
Found at i:2397050 original size:20 final size:20
Alignment explanation
Indices: 2397025--2397064 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2397015 TTAAAATAGC
*
2397025 TCCATTTTCAGATGATATGA
1 TCCATTATCAGATGATATGA
2397045 TCCATTATCAGATGATATGA
1 TCCATTATCAGATGATATGA
2397065 AGTTTCATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (20 bp):
TCCATTATCAGATGATATGA
Found at i:2401379 original size:134 final size:134
Alignment explanation
Indices: 2401139--2401409 Score: 515
Period size: 134 Copynumber: 2.0 Consensus size: 134
2401129 GCCAACAGTC
*
2401139 ATGAAACAAAGCACCACGGGCGTTCTCTTGACCAAGCATACAAGCCTTTTGGTTTCTACTTTTGG
1 ATGAAACAAAGCACCACGGGCATTCTCTTGACCAAGCATACAAGCCTTTTGGTTTCTACTTTTGG
2401204 GTTTCAATGTAGAAAAACATAACAATCAGTGCACGGAAATTATACTGACTTGTCCCAGCAAATGT
66 GTTTCAATGTAGAAAAACATAACAATCAGTGCACGGAAATTATACTGACTTGTCCCAGCAAATGT
2401269 TTAA
131 TTAA
*
2401273 ATGAAACAAAGCACCATGGGCATTCTCTTGACCAAGCATACAAGCCTTTTGGTTTCTACTTTTGG
1 ATGAAACAAAGCACCACGGGCATTCTCTTGACCAAGCATACAAGCCTTTTGGTTTCTACTTTTGG
*
2401338 GTTTCAATGTAGAAAAACATAACAATCAGTGCATGGAAATTATACTGACTTGTCCCAGCAAATGT
66 GTTTCAATGTAGAAAAACATAACAATCAGTGCACGGAAATTATACTGACTTGTCCCAGCAAATGT
2401403 TTAA
131 TTAA
2401407 ATG
1 ATG
2401410 TTACTATTGC
Statistics
Matches: 134, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
134 134 1.00
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (134 bp):
ATGAAACAAAGCACCACGGGCATTCTCTTGACCAAGCATACAAGCCTTTTGGTTTCTACTTTTGG
GTTTCAATGTAGAAAAACATAACAATCAGTGCACGGAAATTATACTGACTTGTCCCAGCAAATGT
TTAA
Found at i:2402460 original size:22 final size:22
Alignment explanation
Indices: 2402432--2402473 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
2402422 AAATATATTT
2402432 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTATA
2402454 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
2402474 AATTAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTATA
Found at i:2410345 original size:2 final size:2
Alignment explanation
Indices: 2410338--2410362 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2410328 AATTAAACAA
2410338 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2410363 ATTTCTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2411742 original size:21 final size:21
Alignment explanation
Indices: 2411690--2411736 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
2411680 ACCGGTCACA
* *
2411690 ACTCCGACAACCCCGACCACG
1 ACTCCGACGACCCCAACCACG
*
2411711 ACTCCGACGACCCCAACTACG
1 ACTCCGACGACCCCAACCACG
2411732 ACTCC
1 ACTCC
2411737 TGCGACATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.28, C:0.51, G:0.13, T:0.09
Consensus pattern (21 bp):
ACTCCGACGACCCCAACCACG
Found at i:2413077 original size:7 final size:7
Alignment explanation
Indices: 2413065--2413097 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
2413055 ACCAAACCAA
2413065 AAAAAAT
1 AAAAAAT
2413072 AAAAAAT
1 AAAAAAT
2413079 AAAAAAAT
1 -AAAAAAT
2413087 AAAAAAT
1 AAAAAAT
2413094 AAAA
1 AAAA
2413098 TTTTAAAACG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:2413105 original size:15 final size:15
Alignment explanation
Indices: 2413064--2413097 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
2413054 TACCAAACCA
2413064 AAAAAAATAAAAAAT
1 AAAAAAATAAAAAAT
2413079 AAAAAAATAAAAAAT
1 AAAAAAATAAAAAAT
2413094 AAAA
1 AAAA
2413098 TTTTAAAACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (15 bp):
AAAAAAATAAAAAAT
Found at i:2420695 original size:3 final size:3
Alignment explanation
Indices: 2420681--2420710 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
2420671 TTTCTACCAA
*
2420681 CAG CAA CAG CAG CAG CAG CAG CAG CAG CAG
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
2420711 TTTCTTTTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.37, C:0.33, G:0.30, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:2420772 original size:36 final size:37
Alignment explanation
Indices: 2420680--2420764 Score: 109
Period size: 39 Copynumber: 2.3 Consensus size: 37
2420670 ATTTCTACCA
* *
2420680 ACAGCAACAGCAGCAGCAGCAGCAGCAGCAGTTTCTTTT
1 ACAGCAACAGCAACAGCAGCAGCAGCAGCAG--TATTTT
*
2420719 GCAGCAACAGCAACAGCAGCAGCAGCAGCAG-ATTTT
1 ACAGCAACAGCAACAGCAGCAGCAGCAGCAGTATTTT
*
2420755 ACCGCAACAG
1 ACAGCAACAG
2420765 TATCAGCAAC
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
36 12 0.29
39 29 0.71
ACGTcount: A:0.34, C:0.29, G:0.24, T:0.13
Consensus pattern (37 bp):
ACAGCAACAGCAACAGCAGCAGCAGCAGCAGTATTTT
Found at i:2436117 original size:12 final size:13
Alignment explanation
Indices: 2436093--2436129 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
2436083 ATTCGAATCG
2436093 TATTAAA-TTAAA
1 TATTAAATTTAAA
2436105 T-TTAAATTTAAA
1 TATTAAATTTAAA
*
2436117 TATAAAATTTAAA
1 TATTAAATTTAAA
2436130 ATTTTTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
11 5 0.23
12 7 0.32
13 10 0.45
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
TATTAAATTTAAA
Found at i:2439300 original size:52 final size:53
Alignment explanation
Indices: 2439221--2439333 Score: 174
Period size: 53 Copynumber: 2.1 Consensus size: 53
2439211 TCTATTAATT
* ** *
2439221 ACTTTAAGATATGTTAAAATA-TTTTTTTTATTTGTTGTTTATGCATTTAAATG
1 ACTTT-AGATATGTCAAAATATTTTTTTTTATTTGTCATTTATGCATTTAAATA
2439274 ACTTTAGATATGTCAAAATATTTTTTTTTATTTGTCATTTATGCATTTAAATA
1 ACTTTAGATATGTCAAAATATTTTTTTTTATTTGTCATTTATGCATTTAAATA
2439327 ACTTTAG
1 ACTTTAG
2439334 TATAGAATAT
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
52 14 0.25
53 41 0.75
ACGTcount: A:0.31, C:0.06, G:0.10, T:0.53
Consensus pattern (53 bp):
ACTTTAGATATGTCAAAATATTTTTTTTTATTTGTCATTTATGCATTTAAATA
Found at i:2443039 original size:2 final size:2
Alignment explanation
Indices: 2443032--2443056 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2443022 CAAAAGCAAA
2443032 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2443057 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2443061 original size:2 final size:2
Alignment explanation
Indices: 2443056--2443088 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2443046 ATATATATAT
2443056 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2443089 AGAAAATCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2446075 original size:2 final size:2
Alignment explanation
Indices: 2446062--2446091 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2446052 GACCAATGCA
*
2446062 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2446092 CTCTTTGGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2447024 original size:22 final size:23
Alignment explanation
Indices: 2446978--2447026 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
2446968 GTATAAATTT
* * *
2446978 ATATATTTTTATTATATTAAATA
1 ATATAATTTTATTAAATAAAATA
2447001 ATATAATTTT-TTAAATAAAATA
1 ATATAATTTTATTAAATAAAATA
2447023 ATAT
1 ATAT
2447027 TTAATTTATC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
ATATAATTTTATTAAATAAAATA
Found at i:2448562 original size:2 final size:2
Alignment explanation
Indices: 2448555--2448606 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
2448545 TTACAGGTTG
2448555 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2448597 AT AT AT AT AT
1 AT AT AT AT AT
2448607 CATGCAAAGG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2450109 original size:2 final size:2
Alignment explanation
Indices: 2450102--2450135 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
2450092 TAAAAATTAA
*
2450102 AT AT AT AT AT AT AT AT AT AT AT AT GAA AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT A
2450136 CTACCATTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 28 0.97
3 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:2451968 original size:66 final size:66
Alignment explanation
Indices: 2451896--2452029 Score: 241
Period size: 66 Copynumber: 2.0 Consensus size: 66
2451886 CACAAGGTTT
2451896 AATTGTAATGGATTAAAGAACAGAGCACCTTAATAACATACAATTAAAATGAAACAGAGGCTAGG
1 AATTGTAATGGATTAAAGAACAGAGCACCTTAATAACATACAATTAAAATGAAACAGAGGCTAGG
2451961 A
66 A
* * *
2451962 AATTGTAATGGATTAAAGAATAGAGCGCCTTAATAACATCCAATTAAAATGAAACAGAGGCTAGG
1 AATTGTAATGGATTAAAGAACAGAGCACCTTAATAACATACAATTAAAATGAAACAGAGGCTAGG
2452027 A
66 A
2452028 AA
1 AA
2452030 CAGCACTCTG
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.48, C:0.12, G:0.19, T:0.22
Consensus pattern (66 bp):
AATTGTAATGGATTAAAGAACAGAGCACCTTAATAACATACAATTAAAATGAAACAGAGGCTAGG
A
Found at i:2457025 original size:21 final size:20
Alignment explanation
Indices: 2456999--2457043 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
2456989 ATAGTTTAAA
2456999 AGAAGAGAAAAGAGAGAGATG
1 AGAAGAGAAAAGAGAGAGA-G
* *
2457020 AGAAGAGAAGAGAGAGTGAG
1 AGAAGAGAAAAGAGAGAGAG
2457040 AGAA
1 AGAA
2457044 CTTGCTAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.56, C:0.00, G:0.40, T:0.04
Consensus pattern (20 bp):
AGAAGAGAAAAGAGAGAGAG
Found at i:2458142 original size:2 final size:2
Alignment explanation
Indices: 2458135--2458159 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2458125 TACTTTAACC
2458135 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2458160 GTAAGTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2459443 original size:2 final size:2
Alignment explanation
Indices: 2459438--2459469 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2459428 CTCTATAAAA
2459438 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2459470 TAAATCTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2459911 original size:21 final size:21
Alignment explanation
Indices: 2459850--2459917 Score: 77
Period size: 21 Copynumber: 3.2 Consensus size: 21
2459840 ATTGAATCAA
*
2459850 ATTTAAATAA-AAAAATTTATA
1 ATTTAAATAATAAAAA-TTATT
* *
2459871 ATTAAAATTAATTAAAATTATT
1 ATTTAAA-TAATAAAAATTATT
2459893 ATTTAAATAATAAAAATTATT
1 ATTTAAATAATAAAAATTATT
2459914 -TTTA
1 ATTTA
2459918 TTTAAATTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
20 4 0.10
21 19 0.47
22 13 0.32
23 4 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATTTAAATAATAAAAATTATT
Found at i:2459938 original size:24 final size:22
Alignment explanation
Indices: 2459861--2459939 Score: 61
Period size: 24 Copynumber: 3.4 Consensus size: 22
2459851 TTTAAATAAA
* *
2459861 AAAATTTATAATTAAAATTAATT
1 AAAATTT-TTATTTAAATTAATT
* *
2459884 AAAATTATTATTTAAA-TAATAA
1 AAAATTTTTATTTAAATTAAT-T
2459906 AAATTATTTTTATTTAAATTTAATT
1 AAA--ATTTTTATTTAAA-TTAATT
2459931 ATAAATTTT
1 A-AAATTTT
2459940 AATATAATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
21 4 0.09
22 10 0.23
23 6 0.14
24 17 0.39
25 1 0.02
26 6 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AAAATTTTTATTTAAATTAATT
Found at i:2459947 original size:18 final size:18
Alignment explanation
Indices: 2459926--2459982 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 18
2459916 TATTTAAATT
2459926 TAATTATAAATTTTAATA
1 TAATTATAAATTTTAATA
* *
2459944 TAATAATAATTTTTAATA
1 TAATTATAAATTTTAATA
* * **
2459962 TTATTTTAAATAATAATA
1 TAATTATAAATTTTAATA
2459980 TAA
1 TAA
2459983 ATTTTTAAAT
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TAATTATAAATTTTAATA
Found at i:2459949 original size:47 final size:46
Alignment explanation
Indices: 2459855--2459952 Score: 110
Period size: 47 Copynumber: 2.1 Consensus size: 46
2459845 ATCAAATTTA
*
2459855 AATAAAAAAATTTATAATTAAAATTAATTAAAATTATTATTTAAAT
1 AATAAAAAAATTTATAATTAAAATTAATTAAAATTATTATATAAAT
* * * *
2459901 AATAAAAATTATTTTTATTTAAATTTAATTATAAATT-TTA-ATATAAT
1 AATAAAAA-AATTTATAATTAAAATTAATTA-AAATTATTATATA-AAT
2459948 AATAA
1 AATAA
2459953 TTTTTAATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
46 10 0.23
47 29 0.66
48 5 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (46 bp):
AATAAAAAAATTTATAATTAAAATTAATTAAAATTATTATATAAAT
Found at i:2460220 original size:3 final size:3
Alignment explanation
Indices: 2460212--2460241 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2460202 GATAAAACAA
2460212 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2460242 TATTATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2460246 original size:3 final size:3
Alignment explanation
Indices: 2460240--2460276 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2460230 AATAATAATA
2460240 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
2460277 GGATATTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2471212 original size:30 final size:31
Alignment explanation
Indices: 2471160--2471228 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 31
2471150 ATCAAAACTT
* *
2471160 ATTTAATTATTTATTATATTATTAAAATATTA
1 ATTTAAATATTTATTATATTATT-AAATAATA
*
2471192 TTTTAAATATTT-TT-TATTATTAAATAATA
1 ATTTAAATATTTATTATATTATTAAATAATA
2471221 ATTTAAAT
1 ATTTAAAT
2471229 TTAATCTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 14 0.42
30 7 0.21
31 2 0.06
32 10 0.30
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (31 bp):
ATTTAAATATTTATTATATTATTAAATAATA
Found at i:2472920 original size:17 final size:15
Alignment explanation
Indices: 2472880--2472930 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
2472870 AAGAAGATCA
* *
2472880 TTAAATTATTTTAAAT
1 TTAAAATATTTT-ATT
*
2472896 TTAATAT-TTTTATT
1 TTAAAATATTTTATT
2472910 ATTAAAATATTTTATT
1 -TTAAAATATTTTATT
2472926 TTAAA
1 TTAAA
2472931 TTAAATTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
14 2 0.07
15 15 0.52
16 12 0.41
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTAAAATATTTTATT
Found at i:2472924 original size:16 final size:16
Alignment explanation
Indices: 2472898--2472930 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2472888 TTTTAAATTT
2472898 AATATTTTTATTATTAA
1 AATATTTTTATT-TTAA
2472915 AATA-TTTTATTTTAA
1 AATATTTTTATTTTAA
2472930 A
1 A
2472931 TTAAATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 7 0.44
17 4 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
AATATTTTTATTTTAA
Found at i:2473199 original size:17 final size:18
Alignment explanation
Indices: 2473161--2473207 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
2473151 AATTTAAATT
*
2473161 ATTATTAATT-AATTAAG
1 ATTATGAATTAAATTAAG
*
2473178 TTTATGAATTAAATTAA-
1 ATTATGAATTAAATTAAG
*
2473195 ATTATGATTTAAA
1 ATTATGAATTAAA
2473208 AAATTTAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 19 0.76
18 6 0.24
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (18 bp):
ATTATGAATTAAATTAAG
Found at i:2473333 original size:21 final size:19
Alignment explanation
Indices: 2473301--2473339 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
2473291 TAATATTTTT
2473301 ATAATTAAATTTAAATAAA
1 ATAATTAAATTTAAATAAA
2473320 ATAATTTAATATTTAAATAA
1 ATAA-TTAA-ATTTAAATAA
2473340 TACTTTAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 4 0.22
21 10 0.56
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
ATAATTAAATTTAAATAAA
Found at i:2474290 original size:23 final size:22
Alignment explanation
Indices: 2474244--2474290 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
2474234 TTGATCATAT
*
2474244 AATAAATAAATTTTTTAATTTA
1 AATAAATAAATTTTTAAATTTA
2474266 AATAAA-AAATTAATTTAAATTTA
1 AATAAATAAATT--TTTAAATTTA
2474289 AA
1 AA
2474291 ATTCAAACTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 5 0.23
22 6 0.27
23 11 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AATAAATAAATTTTTAAATTTA
Found at i:2474568 original size:22 final size:22
Alignment explanation
Indices: 2474530--2474591 Score: 83
Period size: 21 Copynumber: 2.9 Consensus size: 22
2474520 CATAGTTTTT
*
2474530 ATAATATTTT-ATATAATTTCG
1 ATAATCTTTTGATATAATTTCG
2474551 ATAATCTTTTGATATAATTTCG
1 ATAATCTTTTGATATAATTTCG
* *
2474573 ATAAAC-TATGATATAATTT
1 ATAATCTTTTGATATAATTT
2474592 TAATAATCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 21 0.57
22 16 0.43
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (22 bp):
ATAATCTTTTGATATAATTTCG
Found at i:2475143 original size:6 final size:6
Alignment explanation
Indices: 2475132--2475161 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
2475122 AAGCTAAGTG
*
2475132 TAAATT TAAATT TAAATT TGAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT
2475162 GAATATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (6 bp):
TAAATT
Found at i:2475170 original size:12 final size:12
Alignment explanation
Indices: 2475132--2475171 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
2475122 AAGCTAAGTG
*
2475132 TAAATTTAAATT
1 TAAATTTGAATT
2475144 TAAATTTGAATT
1 TAAATTTGAATT
2475156 TAAA-TTGAATAT
1 TAAATTTGAAT-T
2475168 TAAA
1 TAAA
2475172 AATTTTAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 6 0.23
12 20 0.77
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (12 bp):
TAAATTTGAATT
Found at i:2476284 original size:14 final size:13
Alignment explanation
Indices: 2476257--2476304 Score: 55
Period size: 14 Copynumber: 3.7 Consensus size: 13
2476247 TGAATTTTTA
2476257 TTAAATAT-ATAT
1 TTAAATATAATAT
2476269 TTAAATATTAATAT
1 TTAAATA-TAATAT
*
2476283 TT-AATATAATTTT
1 TTAAATATAA-TAT
2476296 TTAAATATA
1 TTAAATATA
2476305 TAAAAATATC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
12 10 0.32
13 9 0.29
14 12 0.39
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTAAATATAATAT
Found at i:2476302 original size:21 final size:21
Alignment explanation
Indices: 2476278--2476343 Score: 66
Period size: 21 Copynumber: 3.1 Consensus size: 21
2476268 TTTAAATATT
2476278 AATATTTAATATAATTTTTTA
1 AATATTTAATATAATTTTTTA
*
2476299 AATATATAA-A-AATATCTTTTAA
1 AATATTTAATATAAT-T-TTTT-A
*
2476321 AATATTAAATAT-ATTTTTTA
1 AATATTTAATATAATTTTTTA
2476341 AAT
1 AAT
2476344 GTAAATTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 11
0.73 0.06 0.22
Matches are distributed among these distances:
19 3 0.08
20 6 0.16
21 16 0.43
22 9 0.24
23 3 0.08
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
AATATTTAATATAATTTTTTA
Found at i:2478414 original size:2 final size:2
Alignment explanation
Indices: 2478407--2478440 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2478397 AAGAAAAACC
2478407 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2478441 TTCACAACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2478878 original size:33 final size:35
Alignment explanation
Indices: 2478794--2478887 Score: 95
Period size: 33 Copynumber: 2.7 Consensus size: 35
2478784 AATCTAAAGG
* * **
2478794 TTATTTTATTATTTATTATATTTTAAAATATTATA
1 TTATTTTATTATTAATTATAATTTAAAATAAAATA
* *
2478829 TTTTTATTTTTA-TAATTA-AATTT-AAATAAAATA
1 TTATT-TTATTATTAATTATAATTTAAAATAAAATA
*
2478862 TTATTTTATTATTAATTATAGTTTAA
1 TTATTTTATTATTAATTATAATTTAA
2478888 GTTAAATCAA
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
32 5 0.11
33 18 0.39
34 8 0.17
35 10 0.22
36 5 0.11
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (35 bp):
TTATTTTATTATTAATTATAATTTAAAATAAAATA
Found at i:2480852 original size:17 final size:17
Alignment explanation
Indices: 2480815--2480867 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
2480805 AAATATTTCG
*
2480815 AATTAAAT-ATTAATA-
1 AATTAAATAAATAATAT
2480830 AA-TAAATAAATAATAT
1 AATTAAATAAATAATAT
2480846 AATTAAAATAAA-AATAT
1 AATT-AAATAAATAATAT
2480863 AATTA
1 AATTA
2480868 CTTAAGTGCT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.15
15 8 0.24
16 3 0.09
17 10 0.30
18 7 0.21
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AATTAAATAAATAATAT
Found at i:2487933 original size:2 final size:2
Alignment explanation
Indices: 2487926--2487952 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2487916 ACAAGAACCA
2487926 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2487953 ATGATGATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2488833 original size:25 final size:26
Alignment explanation
Indices: 2488796--2488846 Score: 61
Period size: 24 Copynumber: 2.0 Consensus size: 26
2488786 AATTACTATT
* *
2488796 TATATATTAATAATATTTTTATTTAAA
1 TATATATTAATAA-ATATTAATTTAAA
2488823 TATA-ATT-ATAAATATTAATTTAAA
1 TATATATTAATAAATATTAATTTAAA
2488847 ATTATTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 11 0.50
25 4 0.18
26 3 0.14
27 4 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
TATATATTAATAAATATTAATTTAAA
Found at i:2488836 original size:12 final size:12
Alignment explanation
Indices: 2488816--2488857 Score: 52
Period size: 11 Copynumber: 3.6 Consensus size: 12
2488806 TAATATTTTT
2488816 ATTTAAATA-TA
1 ATTTAAATATTA
2488827 ATTATAAATATTA
1 ATT-TAAATATTA
2488840 ATTTAAA-ATTA
1 ATTTAAATATTA
*
2488851 TTTTAAA
1 ATTTAAA
2488858 CAATAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 13 0.46
12 10 0.36
13 5 0.18
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTTAAATATTA
Found at i:2489800 original size:3 final size:3
Alignment explanation
Indices: 2489792--2489824 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2489782 CAATTTGAAT
2489792 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2489825 TTCTATTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2490391 original size:2 final size:2
Alignment explanation
Indices: 2490384--2490423 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2490374 AAAATCGCTA
2490384 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2490424 GAACAACAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2499023 original size:64 final size:64
Alignment explanation
Indices: 2498922--2499050 Score: 222
Period size: 64 Copynumber: 2.0 Consensus size: 64
2498912 AAATTATTGT
* * *
2498922 AAGAAAGATCCATCTGGCTGCAAAGAAGTACAATAGATTACAGCTAACTAGACTTGAAACGTTA
1 AAGAAAGATCCATCTGGCTGCAAAGAAGTACAATAGATTACAACTAACAAGACTTGAAACATTA
*
2498986 AAGAAAGATCCATCTGGCTGCAAAGAAGTATAATAGATTACAACTAACAAGACTTGAAACATTA
1 AAGAAAGATCCATCTGGCTGCAAAGAAGTACAATAGATTACAACTAACAAGACTTGAAACATTA
2499050 A
1 A
2499051 GGTACATTAT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.45, C:0.16, G:0.17, T:0.22
Consensus pattern (64 bp):
AAGAAAGATCCATCTGGCTGCAAAGAAGTACAATAGATTACAACTAACAAGACTTGAAACATTA
Found at i:2503312 original size:5 final size:5
Alignment explanation
Indices: 2503294--2503342 Score: 52
Period size: 5 Copynumber: 10.4 Consensus size: 5
2503284 ATTTAATAAT
*
2503294 TTAT- TTAT- TTATA TTATA TT-TA -TATA TTTTA TTATA TTATAA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTAT-A TTATA
2503341 TT
1 TT
2503343 TAAAATATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
3 1 0.03
4 12 0.31
5 21 0.54
6 5 0.13
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (5 bp):
TTATA
Found at i:2503328 original size:23 final size:24
Alignment explanation
Indices: 2503297--2503341 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
2503287 TAATAATTTA
*
2503297 TTTATTTATATTATATTTATATAT
1 TTTATTTATATTATAATTATATAT
2503321 TTTA-TTATATTATAATTATAT
1 TTTATTTATATTATAATTATAT
2503342 TTAAAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
TTTATTTATATTATAATTATATAT
Found at i:2503373 original size:18 final size:18
Alignment explanation
Indices: 2503345--2503404 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 18
2503335 ATTATATTTA
2503345 AAATATTTAATATTATTAT
1 AAAT-TTTAATATTATTAT
*
2503364 AAATTTTAATA-AATTA-
1 AAATTTTAATATTATTAT
2503380 ATAA-TTT-ATATTA-TAT
1 A-AATTTTAATATTATTAT
2503396 AAATTTTAA
1 AAATTTTAA
2503405 AATATTTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
15 7 0.21
16 9 0.26
17 7 0.21
18 7 0.21
19 4 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AAATTTTAATATTATTAT
Found at i:2503871 original size:2 final size:2
Alignment explanation
Indices: 2503864--2503898 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2503854 TCATGTTGTG
2503864 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2503899 ACTGTCATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2507617 original size:18 final size:18
Alignment explanation
Indices: 2507594--2507635 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2507584 GAAAAGCACC
2507594 AACAATTAAGGAAAGATT
1 AACAATTAAGGAAAGATT
*
2507612 AACAATTAAGGACAGATT
1 AACAATTAAGGAAAGATT
*
2507630 AGCAAT
1 AACAAT
2507636 CAAATGAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.52, C:0.10, G:0.17, T:0.21
Consensus pattern (18 bp):
AACAATTAAGGAAAGATT
Found at i:2515414 original size:2 final size:2
Alignment explanation
Indices: 2515407--2515431 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2515397 AAATGTGTAT
2515407 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
2515432 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2519044 original size:2 final size:2
Alignment explanation
Indices: 2519037--2519070 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2519027 TCCTTCAATA
2519037 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2519071 TTTGAATAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2530991 original size:31 final size:28
Alignment explanation
Indices: 2530956--2531017 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 28
2530946 TTATAAATAT
*
2530956 TAATAAAAAATAATTTTAATATTATTTTAAA
1 TAATAAAAAA-AATTTTAA-ATT-TTATAAA
*
2530987 TAATAATAAAAATTTTAAATTTTATAAA
1 TAATAAAAAAAATTTTAAATTTTATAAA
2531015 TAA
1 TAA
2531018 AATTAATATC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 9 0.31
29 3 0.10
30 8 0.28
31 9 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
TAATAAAAAAAATTTTAAATTTTATAAA
Found at i:2531025 original size:34 final size:33
Alignment explanation
Indices: 2530925--2531025 Score: 91
Period size: 31 Copynumber: 3.0 Consensus size: 33
2530915 TTTTTATCGT
*
2530925 AAAAATATTATTTAAATTTTATTATAAATATTAATA
1 AAAAATAAT-TTTAAATTTTA-TATAAA-ATTAATA
* * *
2530961 AAAAATAATTTT-AATATTATTTTAAA-TAATA
1 AAAAATAATTTTAAATTTTATATAAAATTAATA
*
2530992 ATAAA-AATTTTAAATTTTATAAATAAAATTAATA
1 AAAAATAATTTTAAATTTTAT--ATAAAATTAATA
2531026 TCATAAATAT
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
30 6 0.11
31 16 0.30
32 1 0.02
33 8 0.15
34 11 0.21
35 3 0.06
36 8 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (33 bp):
AAAAATAATTTTAAATTTTATATAAAATTAATA
Found at i:2536775 original size:12 final size:12
Alignment explanation
Indices: 2536758--2536785 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
2536748 TCACCTCTCT
2536758 TATCTATATTTA
1 TATCTATATTTA
2536770 TATCTATATTTA
1 TATCTATATTTA
2536782 TATC
1 TATC
2536786 ATAGCCGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.57
Consensus pattern (12 bp):
TATCTATATTTA
Found at i:2537318 original size:15 final size:14
Alignment explanation
Indices: 2537274--2537329 Score: 62
Period size: 15 Copynumber: 4.0 Consensus size: 14
2537264 AATTAAAAAT
2537274 ATTAT-AATTTAAA
1 ATTATAAATTTAAA
**
2537287 ATTATAAATAAATAA
1 ATTATAAATTTA-AA
2537302 ATTATAAATATTAAA
1 ATTATAAAT-TTAAA
2537317 ATTA-AAATTTAAA
1 ATTATAAATTTAAA
2537330 TCTATTAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
13 10 0.28
14 8 0.22
15 17 0.47
16 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
ATTATAAATTTAAA
Found at i:2537510 original size:18 final size:19
Alignment explanation
Indices: 2537478--2537519 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
2537468 ATCGATTAAT
*
2537478 ATATACCTAAAAAAAGTAC
1 ATATACCTAAAAAAAGTAA
2537497 ATATACCT-AAAAAAGTAA
1 ATATACCTAAAAAAAGTAA
2537515 ATATA
1 ATATA
2537520 TATATATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.60, C:0.12, G:0.05, T:0.24
Consensus pattern (19 bp):
ATATACCTAAAAAAAGTAA
Found at i:2538876 original size:14 final size:14
Alignment explanation
Indices: 2538845--2538890 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
2538835 TAGTTGGTAT
*
2538845 TTTAACATTTTATA
1 TTTAATATTTTATA
2538859 TTTAATATTATTAT-
1 TTTAATATT-TTATA
2538873 TTTAAT-TTTTATA
1 TTTAATATTTTATA
2538886 TTTAA
1 TTTAA
2538891 AATATAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 4 0.14
13 7 0.24
14 14 0.48
15 4 0.14
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTAATATTTTATA
Found at i:2538938 original size:26 final size:26
Alignment explanation
Indices: 2538886--2538939 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
2538876 AATTTTTATA
* * *
2538886 TTTAAAATATAATTTTTTATTAAATT
1 TTTAAAATATAAATTATTAATAAATT
2538912 TTTAAAA-ATAAATTATTAATAATATT
1 TTTAAAATATAAATTATTAATAA-ATT
2538938 TT
1 TT
2538940 ATTTAAACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 12 0.50
26 12 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
TTTAAAATATAAATTATTAATAAATT
Found at i:2539587 original size:13 final size:13
Alignment explanation
Indices: 2539569--2539603 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
2539559 TTAAAATAAT
**
2539569 TATATATTTTAAA
1 TATATATTAAAAA
2539582 TATATATTAAAAA
1 TATATATTAAAAA
2539595 TATATATTA
1 TATATATTA
2539604 TTTTATTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TATATATTAAAAA
Found at i:2539934 original size:2 final size:2
Alignment explanation
Indices: 2539916--2539952 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
2539906 TGGGTTCACC
* *
2539916 TA TA CA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2539953 TCAATTAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:2546471 original size:11 final size:12
Alignment explanation
Indices: 2546452--2546490 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
2546442 ATGGAAAGAA
2546452 AGAAGAAAAAAAC
1 AGAA-AAAAAAAC
2546465 A-AAAAAAAAAC
1 AGAAAAAAAAAC
2546476 AGAAAAAGAAAAC
1 AGAAAAA-AAAAC
2546489 AG
1 AG
2546491 TGCACCTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 9 0.38
12 7 0.29
13 8 0.33
ACGTcount: A:0.79, C:0.08, G:0.13, T:0.00
Consensus pattern (12 bp):
AGAAAAAAAAAC
Found at i:2549372 original size:25 final size:24
Alignment explanation
Indices: 2549341--2549398 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
2549331 CTCATCCAAC
2549341 AATTAAAAATTTTAATTTTTTTATT
1 AATTAAAAATTTTAA-TTTTTTATT
* *
2549366 AATTAAAATTTTTTATTTTTTATT
1 AATTAAAAATTTTAATTTTTTATT
*
2549390 AATAAAAAA
1 AATTAAAAA
2549399 ATTACTTCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 16 0.55
25 13 0.45
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
AATTAAAAATTTTAATTTTTTATT
Found at i:2550991 original size:24 final size:23
Alignment explanation
Indices: 2550966--2551049 Score: 71
Period size: 25 Copynumber: 3.4 Consensus size: 23
2550956 GACTAAAAAT
*
2550966 TATTTATTAAGATATATTAATTAT
1 TATTTATTAA-ATATATTAATTAA
*
2550990 TA-TAATTAAATATTAATTACATTAA
1 TATTTATTAAATA-T-ATTA-ATTAA
* *
2551015 AATTTTTTAAATATATATAATTAA
1 TATTTATTAAATATAT-TAATTAA
2551039 TATTTTATTAA
1 TA-TTTATTAA
2551050 CTTTTAAATT
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
22 3 0.06
23 7 0.15
24 14 0.30
25 15 0.32
26 8 0.17
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (23 bp):
TATTTATTAAATATATTAATTAA
Found at i:2551123 original size:13 final size:15
Alignment explanation
Indices: 2551098--2551129 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
2551088 TAAAATAATA
2551098 AATAAATAATA-TTT
1 AATAAATAATATTTT
2551112 AATAAA-AATATTTT
1 AATAAATAATATTTT
2551126 AATA
1 AATA
2551130 TAATTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AATAAATAATATTTT
Found at i:2551145 original size:19 final size:21
Alignment explanation
Indices: 2551123--2551169 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 21
2551113 ATAAAAATAT
2551123 TTTAATATA-ATTTT-TTATA
1 TTTAATATATATTTTATTATA
2551142 TTTAATATATTATTTTAATTATA
1 TTTAATATA-TATTTT-ATTATA
2551165 TTTAA
1 TTTAA
2551170 AAATAAGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.38
21 5 0.21
23 10 0.42
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTAATATATATTTTATTATA
Found at i:2551470 original size:22 final size:23
Alignment explanation
Indices: 2551428--2551473 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
2551418 AAAAAACTAT
*
2551428 ATATATTAAAATTTATTTTTTAA
1 ATATATTAAAATTTATATTTTAA
2551451 ATATATT-AAATATTA-ATTTTAA
1 ATATATTAAAAT-TTATATTTTAA
2551473 A
1 A
2551474 AATAATTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
ATATATTAAAATTTATATTTTAA
Found at i:2551476 original size:24 final size:23
Alignment explanation
Indices: 2551428--2551481 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
2551418 AAAAAACTAT
* **
2551428 ATATATTAAAATTTATTTTTTAA
1 ATATATTAAAATTAATTTTAAAA
2551451 ATATATTAAATATTAATTTTAAAA
1 ATATATTAAA-ATTAATTTTAAAA
2551475 ATA-ATTA
1 ATATATTA
2551482 TATAAATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 14 0.52
24 13 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
ATATATTAAAATTAATTTTAAAA
Found at i:2551492 original size:13 final size:13
Alignment explanation
Indices: 2551462--2551504 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
2551452 TATATTAAAT
*
2551462 ATTAATTTTA-AA
1 ATTAATTATATAA
*
2551474 AATAATTATATAA
1 ATTAATTATATAA
*
2551487 ATTAATTAAATAA
1 ATTAATTATATAA
2551500 ATTAA
1 ATTAA
2551505 ATTTACTGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
12 8 0.31
13 18 0.69
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATTAATTATATAA
Found at i:2557965 original size:2 final size:2
Alignment explanation
Indices: 2557958--2557998 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2557948 TTGGAATTGT
2557958 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2557999 CCAAAAAGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2561975 original size:17 final size:19
Alignment explanation
Indices: 2561942--2561988 Score: 66
Period size: 17 Copynumber: 2.7 Consensus size: 19
2561932 TTTAAAAAAT
2561942 TTTAAT-TTAAATAAATAA
1 TTTAATATTAAATAAATAA
2561960 -TTAATATTAAAT-AATAA
1 TTTAATATTAAATAAATAA
2561977 TTTAA-ATTAAAT
1 TTTAATATTAAAT
2561989 TAATTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 17 0.63
18 10 0.37
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TTTAATATTAAATAAATAA
Found at i:2562950 original size:18 final size:20
Alignment explanation
Indices: 2562929--2562969 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
2562919 TTATTAATAA
*
2562929 ATTAAA-TAATATTATTT-T
1 ATTAAACTAAAATTATTTAT
2562947 ATTAAACTAAAATTATTTAT
1 ATTAAACTAAAATTATTTAT
2562967 ATT
1 ATT
2562970 TAATTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 10 0.50
20 4 0.20
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTAAACTAAAATTATTTAT
Found at i:2563132 original size:2 final size:2
Alignment explanation
Indices: 2563127--2563154 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2563117 AGATTAAAAA
2563127 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2563155 GTAAATTGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2563404 original size:17 final size:19
Alignment explanation
Indices: 2563371--2563412 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
2563361 TGGTGAACAA
*
2563371 ATATTTAAATTTTATTATT
1 ATATTTAAATTTAATTATT
2563390 -TATTT-AATTTAATTATT
1 ATATTTAAATTTAATTATT
2563407 ATATTT
1 ATATTT
2563413 TATGTTGCGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
ATATTTAAATTTAATTATT
Found at i:2564069 original size:2 final size:2
Alignment explanation
Indices: 2564062--2564093 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2564052 GCTCTCATAA
*
2564062 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2564094 TTCATTAGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2565788 original size:2 final size:2
Alignment explanation
Indices: 2565781--2565817 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2565771 ACAATACTTA
2565781 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2565818 AATATGATCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2571550 original size:41 final size:41
Alignment explanation
Indices: 2571488--2571569 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
2571478 ACTCGAATCC
* *
2571488 AGCTTCACTGTTCCAAGATTTTCCTTCAAGAGCAGCCAAAT
1 AGCTTCACTGTTCCAAGATTTTCCTTCAAGACCAGCAAAAT
* *
2571529 AGCTTCATTGTTCCAATATTTTCCTTCAAGACCAGCAAAAT
1 AGCTTCACTGTTCCAAGATTTTCCTTCAAGACCAGCAAAAT
2571570 GCCTGCAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (41 bp):
AGCTTCACTGTTCCAAGATTTTCCTTCAAGACCAGCAAAAT
Found at i:2575075 original size:16 final size:14
Alignment explanation
Indices: 2575038--2575076 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
2575028 AAAAGTTAAA
*
2575038 ATTAAAATAAATAT
1 ATTAAAATTAATAT
2575052 ATTAAAATTAATATT
1 ATTAAAATTAATA-T
2575067 ATATAAAATT
1 AT-TAAAATT
2575077 TAATCTCGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 12 0.55
15 3 0.14
16 7 0.32
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATTAAAATTAATAT
Found at i:2582343 original size:2 final size:2
Alignment explanation
Indices: 2582336--2582371 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2582326 AAGAAGAAGA
2582336 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2582372 GGTGTTAGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2582897 original size:18 final size:20
Alignment explanation
Indices: 2582874--2582916 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
2582864 TTGCTTTTTC
2582874 TTTAATTATCAT-ATTA-AA
1 TTTAATTATCATAATTAGAA
*
2582892 TTTAATTATTATAATTAGAA
1 TTTAATTATCATAATTAGAA
2582912 TTTAA
1 TTTAA
2582917 ATTAAATATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.50
19 4 0.18
20 7 0.32
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (20 bp):
TTTAATTATCATAATTAGAA
Found at i:2585246 original size:17 final size:17
Alignment explanation
Indices: 2585207--2585246 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
2585197 CTACTATAAA
*
2585207 TTAAATATTAAGTCGAT
1 TTAAATACTAAGTCGAT
*
2585224 TT-AATACTAAGTCTAT
1 TTAAATACTAAGTCGAT
2585240 TTAAATA
1 TTAAATA
2585247 TTCTTTTACC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.42
Consensus pattern (17 bp):
TTAAATACTAAGTCGAT
Found at i:2589831 original size:17 final size:17
Alignment explanation
Indices: 2589809--2589845 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
2589799 GATTCTGTTA
2589809 AATATAAATACATATTT
1 AATATAAATACATATTT
*
2589826 AATATAAATATATATTT
1 AATATAAATACATATTT
2589843 AAT
1 AAT
2589846 TTTTTAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (17 bp):
AATATAAATACATATTT
Found at i:2592415 original size:13 final size:13
Alignment explanation
Indices: 2592399--2592429 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2592389 TATATTTTAT
2592399 ATATTAAATATAA
1 ATATTAAATATAA
*
2592412 ATATTAAATATGA
1 ATATTAAATATAA
2592425 ATATT
1 ATATT
2592430 TTAAAAAAAT
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:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (13 bp):
ATATTAAATATAA
Found at i:2593988 original size:2 final size:2
Alignment explanation
Indices: 2593981--2594020 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
2593971 CCGCTTGAGA
2593981 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2594021 GTGACCTTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2595267 original size:2 final size:2
Alignment explanation
Indices: 2595260--2595294 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2595250 CACAGGATGT
*
2595260 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2595295 GCTCATGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2596975 original size:23 final size:25
Alignment explanation
Indices: 2596922--2596975 Score: 58
Period size: 23 Copynumber: 2.2 Consensus size: 25
2596912 GTAATGTTAT
* *
2596922 AATTATTATTTTATAATTTTAATTT
1 AATTATTATTTAATAATTTTAATTG
**
2596947 TTTTATTA-TTAAT-ATTTTAATTG
1 AATTATTATTTAATAATTTTAATTG
2596970 AATTAT
1 AATTAT
2596976 AATCCAACAA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
23 13 0.57
24 4 0.17
25 6 0.26
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (25 bp):
AATTATTATTTAATAATTTTAATTG
Found at i:2604244 original size:21 final size:21
Alignment explanation
Indices: 2604215--2604274 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
2604205 TAATATTTAT
2604215 AATTA-TTTTAATAATTTAAA
1 AATTATTTTTAATAATTTAAA
* *
2604235 AATTATTTTTTAT-ATTTTAA
1 AATTATTTTTAATAATTTAAA
*
2604255 AATATATATTTAATAATTTA
1 AAT-TATTTTTAATAATTTA
2604275 TATTATAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
20 14 0.44
21 14 0.44
22 4 0.12
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
AATTATTTTTAATAATTTAAA
Found at i:2604806 original size:15 final size:16
Alignment explanation
Indices: 2604771--2604800 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2604761 ATTTTTAAAT
2604771 AAAATAAAATAAATTA
1 AAAATAAAATAAATTA
2604787 AAAAT-AAATAAATT
1 AAAATAAAATAAATT
2604801 TTAAATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AAAATAAAATAAATTA
Found at i:2604951 original size:14 final size:15
Alignment explanation
Indices: 2604922--2604954 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2604912 ATCTATTAAA
*
2604922 TTAAATTGATTAATT
1 TTAAATTAATTAATT
2604937 TTAAATTAATT-ATT
1 TTAAATTAATTAATT
2604951 TTAA
1 TTAA
2604955 TTTATTATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TTAAATTAATTAATT
Found at i:2606043 original size:23 final size:23
Alignment explanation
Indices: 2605996--2606041 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
2605986 AAAAATACTA
2605996 AATTTATATTTATTAATTTTTTT
1 AATTTATATTTATTAATTTTTTT
2606019 AATTTAT-TTTAATTTAATTTTTT
1 AATTTATATTT-A-TTAATTTTTT
2606042 AAAAATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 3 0.14
23 8 0.38
24 10 0.48
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (23 bp):
AATTTATATTTATTAATTTTTTT
Found at i:2608207 original size:21 final size:21
Alignment explanation
Indices: 2608140--2608208 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
2608130 TTGTATTATC
*
2608140 ATTAAA-TAATTTAAA-TTGA
1 ATTAAATTAATTTAAATTTAA
* *
2608159 ATTATATTAATTAAAATTATAA
1 ATTAAATTAATTTAAATT-TAA
* *
2608181 A-AAAATTGATTTAAATTTAA
1 ATTAAATTAATTTAAATTTAA
2608201 ATTAAATT
1 ATTAAATT
2608209 TATCAATTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
19 5 0.13
20 12 0.32
21 18 0.47
22 3 0.08
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (21 bp):
ATTAAATTAATTTAAATTTAA
Found at i:2613075 original size:15 final size:14
Alignment explanation
Indices: 2613057--2613107 Score: 59
Period size: 15 Copynumber: 3.6 Consensus size: 14
2613047 TATATTTAAT
2613057 ATATATTTAAATAA
1 ATATATTTAAATAA
**
2613071 A-ATATAAAAATAA
1 ATATATTTAAATAA
*
2613084 ATATATTTCAATTAA
1 ATATATTT-AAATAA
2613099 ATATATTTA
1 ATATATTTA
2613108 TTTATTTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
13 11 0.37
14 6 0.20
15 13 0.43
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
ATATATTTAAATAA
Found at i:2613109 original size:19 final size:17
Alignment explanation
Indices: 2613087--2613125 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2613077 AAAATAAATA
2613087 TATTTCAATTAAATATATT
1 TATTT-AATTAAA-ATATT
*
2613106 TATTTATTTAAAATATT
1 TATTTAATTAAAATATT
2613123 TAT
1 TAT
2613126 CTTATTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 6 0.32
19 5 0.26
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTTAATTAAAATATT
Found at i:2613121 original size:17 final size:19
Alignment explanation
Indices: 2613095--2613131 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
2613085 TATATTTCAA
2613095 TTAAATATATTTAT-TTAT
1 TTAAATATATTTATCTTAT
2613113 TTAAA-ATATTTATCTTAT
1 TTAAATATATTTATCTTAT
2613131 T
1 T
2613132 ATAATCATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (19 bp):
TTAAATATATTTATCTTAT
Found at i:2623610 original size:79 final size:78
Alignment explanation
Indices: 2623506--2623662 Score: 251
Period size: 79 Copynumber: 2.0 Consensus size: 78
2623496 CAAGAGGGAG
* ** * * *
2623506 AAAAAAAAGGTATCAATGAGCAGAGAAACTGAATTATTGGTAGATAATTTCAGGAAGATCAAAAT
1 AAAAAAAAGCTATCAATGAAAAGAGAAACTGAATTATTGCTAGAAAATTTCAGAAAGATCAAAAT
2623571 CAGAAAAAAAAAA
66 CAGAAAAAAAAAA
2623584 AAAAAAAAGCCTATCAATGAAAAGAGAAACTGAATTATTGCTAGAAAATTTCAGAAAGATCAAAA
1 AAAAAAAAG-CTATCAATGAAAAGAGAAACTGAATTATTGCTAGAAAATTTCAGAAAGATCAAAA
2623649 TCAGAAAAAAAAAA
65 TCAGAAAAAAAAAA
2623663 TGCAAACAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
78 9 0.12
79 63 0.88
ACGTcount: A:0.57, C:0.09, G:0.15, T:0.18
Consensus pattern (78 bp):
AAAAAAAAGCTATCAATGAAAAGAGAAACTGAATTATTGCTAGAAAATTTCAGAAAGATCAAAAT
CAGAAAAAAAAAA
Found at i:2623675 original size:17 final size:17
Alignment explanation
Indices: 2623653--2623685 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2623643 TCAAAATCAG
2623653 AAAAAAAAAATGCAAAC
1 AAAAAAAAAATGCAAAC
2623670 AAAAAAAAAATGCAAA
1 AAAAAAAAAATGCAAA
2623686 TGCTAACCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.79, C:0.09, G:0.06, T:0.06
Consensus pattern (17 bp):
AAAAAAAAAATGCAAAC
Found at i:2626293 original size:2 final size:2
Alignment explanation
Indices: 2626286--2626310 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2626276 AGTTTTCTTT
2626286 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2626311 TTTATATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2626958 original size:24 final size:24
Alignment explanation
Indices: 2626919--2626967 Score: 57
Period size: 25 Copynumber: 2.0 Consensus size: 24
2626909 AAATTTTTAT
2626919 TTTAAATTTTTGATAA-AAAAATA
1 TTTAAATTTTTGATAATAAAAATA
*
2626942 TTTAAGATTATTT-ATAATAAATATA
1 TTTAA-ATT-TTTGATAATAAAAATA
2626967 T
1 T
2626968 AAAATATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
23 5 0.23
24 7 0.32
25 10 0.45
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (24 bp):
TTTAAATTTTTGATAATAAAAATA
Found at i:2627505 original size:24 final size:24
Alignment explanation
Indices: 2627473--2627552 Score: 58
Period size: 24 Copynumber: 3.4 Consensus size: 24
2627463 TAATCTCAAA
*
2627473 TTATTTTAAAATTATTAAATTTTT
1 TTATATTAAAATTATTAAATTTTT
*
2627497 TTATATT--AA-TATTTAATTATTT
1 TTATATTAAAATTATTAAATT-TTT
* * ** *
2627519 TTATTATTAAATTTAATAAAAATAT
1 TTA-TATTAAAATTATTAAATTTTT
2627544 TTATATTAA
1 TTATATTAA
2627553 TTAAATAATA
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
21 8 0.19
22 8 0.19
23 4 0.09
24 12 0.28
25 6 0.14
26 5 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TTATATTAAAATTATTAAATTTTT
Found at i:2627519 original size:22 final size:22
Alignment explanation
Indices: 2627485--2627535 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
2627475 ATTTTAAAAT
*
2627485 TATTAAATTTTTTTA-TATTAA
1 TATTTAATTTTTTTATTATTAA
2627506 TATTTAATTATTTTTATTATTAA
1 TATTTAATT-TTTTTATTATTAA
2627529 -ATTTAAT
1 TATTTAAT
2627536 AAAAATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 8 0.30
22 13 0.48
23 6 0.22
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TATTTAATTTTTTTATTATTAA
Found at i:2627568 original size:21 final size:20
Alignment explanation
Indices: 2627531--2627580 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
2627521 ATTATTAAAT
2627531 TTAA-TAAA-AATATTTATA
1 TTAATTAAATAATATTTATA
2627549 TTAATTAAATAATAATTTATA
1 TTAATTAAATAAT-ATTTATA
2627570 TTAAATTAAAT
1 TT-AATTAAAT
2627581 CGGTCTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 4 0.14
19 4 0.14
20 3 0.11
21 9 0.32
22 8 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTAATTAAATAATATTTATA
Found at i:2627577 original size:22 final size:22
Alignment explanation
Indices: 2627496--2627580 Score: 75
Period size: 22 Copynumber: 3.8 Consensus size: 22
2627486 ATTAAATTTT
* * *
2627496 TTTATATTAATATTTAATTAT-T
1 TTTATATTAA-ATTAAATAATAA
* *
2627518 TTTATTATTAAATTTAATAAAAATA
1 TTTA-TATTAAATTAAAT-AATA-A
2627543 TTTATATT-AATTAAATAATAA
1 TTTATATTAAATTAAATAATAA
2627564 TTTATATTAAATTAAAT
1 TTTATATTAAATTAAAT
2627581 CGGTCTAAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
21 9 0.17
22 22 0.42
23 14 0.26
24 4 0.08
25 4 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTATATTAAATTAAATAATAA
Found at i:2627690 original size:17 final size:16
Alignment explanation
Indices: 2627670--2627701 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
2627660 ATTTATATAA
2627670 TTTTTATTTAAATTTAT
1 TTTTTA-TTAAATTTAT
2627687 TTTTTATTAAATTTA
1 TTTTTATTAAATTTA
2627702 AAAATCTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTTTATTAAATTTAT
Found at i:2632723 original size:18 final size:18
Alignment explanation
Indices: 2632700--2632737 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
2632690 TAAGTTATAA
2632700 TGATATGCTTTGCTCCAT
1 TGATATGCTTTGCTCCAT
2632718 TGATATGCTTTGCTCCAT
1 TGATATGCTTTGCTCCAT
2632736 TG
1 TG
2632738 CAGAGATTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.16, C:0.21, G:0.18, T:0.45
Consensus pattern (18 bp):
TGATATGCTTTGCTCCAT
Found at i:2638466 original size:11 final size:12
Alignment explanation
Indices: 2638450--2638478 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
2638440 AATGTTTTCA
2638450 ATTTTTTATT-T
1 ATTTTTTATTAT
2638461 ATTTTTTATTAT
1 ATTTTTTATTAT
2638473 ATTTTT
1 ATTTTT
2638479 ATAATAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
ATTTTTTATTAT
Found at i:2638545 original size:19 final size:20
Alignment explanation
Indices: 2638521--2638593 Score: 76
Period size: 23 Copynumber: 3.4 Consensus size: 20
2638511 GAGTAAAATA
2638521 ATAATTAATAAAAAAT-TTT
1 ATAATTAATAAAAAATATTT
*
2638540 ATAATTAATAAATTAATATTT
1 ATAATTAATAAA-AAATATTT
2638561 ATTAATTTAATAAAAATATTATATT
1 A-TAA-TTAATAAAAA-A-TAT-TT
2638586 ATAATTAA
1 ATAATTAA
2638594 GATATATTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
19 12 0.27
20 3 0.07
21 4 0.09
22 4 0.09
23 13 0.29
24 6 0.13
25 3 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATAATTAATAAAAAATATTT
Found at i:2638602 original size:38 final size:42
Alignment explanation
Indices: 2638525--2638603 Score: 103
Period size: 38 Copynumber: 2.0 Consensus size: 42
2638515 AAAATAATAA
* * *
2638525 TTAATAAAAAATTTTATAATTAATAAATTAATATTTATTAAT
1 TTAATAAAAAATATTATAATTAATAAATTAAGATATATTAAT
2638567 TTAAT-AAAAATATTAT-ATT-AT-AATTAAGATATATTAA
1 TTAATAAAAAATATTATAATTAATAAATTAAGATATATTAA
2638604 CATTTTAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
38 14 0.41
39 2 0.06
40 3 0.09
41 10 0.29
42 5 0.15
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (42 bp):
TTAATAAAAAATATTATAATTAATAAATTAAGATATATTAAT
Found at i:2639443 original size:22 final size:21
Alignment explanation
Indices: 2639383--2639443 Score: 63
Period size: 19 Copynumber: 3.0 Consensus size: 21
2639373 TGATTATTTA
* *
2639383 TTTATTATTTTATAAAATATT
1 TTTATTAATTTAAAAAATATT
* *
2639404 TTTA-T-ATTTAATATATATT
1 TTTATTAATTTAAAAAATATT
2639423 TTTATTAAATTTAAAAAATAT
1 TTTATT-AATTTAAAAAATAT
2639444 ATATTAATTA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
19 14 0.45
20 2 0.06
21 4 0.13
22 11 0.35
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTATTAATTTAAAAAATATT
Found at i:2640318 original size:2 final size:2
Alignment explanation
Indices: 2640311--2640336 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2640301 TCTTTCAAAA
2640311 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2640337 TTAGGGTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2641246 original size:23 final size:24
Alignment explanation
Indices: 2641220--2641267 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
2641210 CCTAATTTAG
2641220 ATTTA-TAAGTTTTTTAAATAATA
1 ATTTAGTAAGTTTTTTAAATAATA
**
2641243 ATTTAGTATTTTTTTTAAATAATA
1 ATTTAGTAAGTTTTTTAAATAATA
2641267 A
1 A
2641268 AATAGATCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (24 bp):
ATTTAGTAAGTTTTTTAAATAATA
Found at i:2651950 original size:26 final size:25
Alignment explanation
Indices: 2651901--2651950 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
2651891 AAAAAGTCAA
* **
2651901 TATATTTAATAATTTATATTATATT
1 TATATTTAATAATTAATAAAATATT
2651926 TATATTTACATAATTAATAAAATAT
1 TATATTTA-ATAATTAATAAAATAT
2651951 AAATTAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (25 bp):
TATATTTAATAATTAATAAAATATT
Done.