Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 3 of 318
Found at i:665970 original size:30 final size:30
Alignment explanation
Indices: 665928--665985 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
665918 GTATATAATT
665928 ATATTAAATTAAAATTCATATATTAAATTAC
1 ATATTAAATTAAAATTCATATA-TAAATTAC
*
665959 ATATT-AATTAAAATTCATGTATAAATT
1 ATATTAAATTAAAATTCATATATAAATT
665986 TAATATTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 6 0.23
30 15 0.58
31 5 0.19
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (30 bp):
ATATTAAATTAAAATTCATATATAAATTAC
Found at i:665983 original size:29 final size:28
Alignment explanation
Indices: 665916--665985 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 28
665906 AATCACTTTT
665916 ATGTATATAATTATATTAAATTAAAATTC
1 ATGTATA-AATTATATTAAATTAAAATTC
*
665945 ATATATTAAATTACATATT-AATTAAAATTC
1 ATGTA-TAAATT--ATATTAAATTAAAATTC
665975 ATGTATAAATT
1 ATGTATAAATT
665986 TAATATTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
29 14 0.39
30 17 0.47
31 5 0.14
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (28 bp):
ATGTATAAATTATATTAAATTAAAATTC
Found at i:666156 original size:27 final size:25
Alignment explanation
Indices: 666126--666188 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 25
666116 CTCTTGAAAT
666126 AAACATAAAAAAAAAAGTTAAGTATCA
1 AAACATAAAAAAAAAA-TTAA-TATCA
* *
666153 AAACACAATAAAAAAAATTAATGTCA
1 AAACATAA-AAAAAAAATTAATATCA
*
666179 AAATATAAAA
1 AAACATAAAA
666189 GCATAAACAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
25 2 0.06
26 10 0.32
27 11 0.35
28 8 0.26
ACGTcount: A:0.68, C:0.08, G:0.05, T:0.19
Consensus pattern (25 bp):
AAACATAAAAAAAAAATTAATATCA
Found at i:666578 original size:18 final size:18
Alignment explanation
Indices: 666555--666654 Score: 80
Period size: 18 Copynumber: 5.3 Consensus size: 18
666545 GTTAATGATC
*
666555 AAATTTAGCTAAAAAAT-T
1 AAATTTAAC-AAAAAATAT
666573 AAATTTAACAAAAAATAT
1 AAATTTAACAAAAAATAT
*
666591 AAATATTAA-AAATTAAATTT
1 AAAT-TTAACAAA--AAATAT
666611 AACATTATACCACAAAAAAT-T
1 AA-ATT-TA--ACAAAAAATAT
*
666632 TAATTTAACAAAAAATAT
1 AAATTTAACAAAAAATAT
666650 AAATT
1 AAATT
666655 AAAAATTAAA
Statistics
Matches: 68, Mismatches: 4, Indels: 20
0.74 0.04 0.22
Matches are distributed among these distances:
17 16 0.24
18 21 0.31
19 6 0.09
20 11 0.16
21 6 0.09
22 4 0.06
23 1 0.01
24 3 0.04
ACGTcount: A:0.60, C:0.07, G:0.01, T:0.32
Consensus pattern (18 bp):
AAATTTAACAAAAAATAT
Found at i:666606 original size:32 final size:31
Alignment explanation
Indices: 666566--666667 Score: 106
Period size: 27 Copynumber: 3.4 Consensus size: 31
666556 AATTTAGCTA
666566 AAAAATTAAATTTAACAAAAAATATAAATATT
1 AAAAATTAAATTTAACAAAAAATATAAA-ATT
* ** **
666598 AAAAATTAAATTTAAC----ATTATACCACA
1 AAAAATTAAATTTAACAAAAAATATAAAATT
*
666625 AAAAATTTAATTTAACAAAAAATAT-AAATT
1 AAAAATTAAATTTAACAAAAAATATAAAATT
666655 AAAAATTAAATTT
1 AAAAATTAAATTT
666668 TGCAATAACT
Statistics
Matches: 54, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
27 16 0.30
28 5 0.09
30 13 0.24
31 4 0.07
32 16 0.30
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (31 bp):
AAAAATTAAATTTAACAAAAAATATAAAATT
Found at i:668266 original size:51 final size:51
Alignment explanation
Indices: 668195--668406 Score: 343
Period size: 51 Copynumber: 4.2 Consensus size: 51
668185 CTGATCACAT
668195 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
* * * * *
668246 TTATCACTTTTCATTGATCAGATAAGTGTAGCTAAAGCTACCACTTGTCAT
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
668297 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
* * *
668348 TTATCACTTGTCATTGATCAGATAAGTGTAGCTAAAGCTACCATTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
*
668399 TTGTCACT
1 TTATCACT
668407 GATCAGAAGT
Statistics
Matches: 147, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 147 1.00
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.34
Consensus pattern (51 bp):
TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
Found at i:668318 original size:102 final size:102
Alignment explanation
Indices: 668192--668390 Score: 389
Period size: 102 Copynumber: 2.0 Consensus size: 102
668182 ACACTGATCA
*
668192 CATTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTATCACTTTT
1 CATTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTATCACTTGT
668257 CATTGATCAGATAAGTGTAGCTAAAGCTACCACTTGT
66 CATTGATCAGATAAGTGTAGCTAAAGCTACCACTTGT
668294 CATTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTATCACTTGT
1 CATTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTATCACTTGT
668359 CATTGATCAGATAAGTGTAGCTAAAGCTACCA
66 CATTGATCAGATAAGTGTAGCTAAAGCTACCA
668391 TTTATCACTT
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
102 96 1.00
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (102 bp):
CATTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTATCACTTGT
CATTGATCAGATAAGTGTAGCTAAAGCTACCACTTGT
Found at i:668547 original size:20 final size:22
Alignment explanation
Indices: 668514--668561 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
668504 ATCATACATT
668514 ATATAATTCATAAAATT-AA-C
1 ATATAATTCATAAAATTCAACC
*
668534 ATATAA-TCATTAAACTTCAACC
1 ATATAATTCA-TAAAATTCAACC
668556 ATATAA
1 ATATAA
668562 ACTTACCTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 3 0.12
20 12 0.50
21 2 0.08
22 7 0.29
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (22 bp):
ATATAATTCATAAAATTCAACC
Found at i:678609 original size:13 final size:14
Alignment explanation
Indices: 678578--678612 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
678568 AAATCCAAAG
678578 CTATTTTTTTAACT
1 CTATTTTTTTAACT
*
678592 TTATTTTTTTAA-T
1 CTATTTTTTTAACT
678605 CTATTTTT
1 CTATTTTT
678613 CATTTCTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (14 bp):
CTATTTTTTTAACT
Found at i:680946 original size:18 final size:19
Alignment explanation
Indices: 680909--680946 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
680899 ATAAAATCAA
* *
680909 ATAATAAATATGTAATTTT
1 ATAATAAAAATATAATTTT
680928 ATAATAAAAATAT-ATTTT
1 ATAATAAAAATATAATTTT
680946 A
1 A
680947 CATATATCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (19 bp):
ATAATAAAAATATAATTTT
Found at i:685799 original size:17 final size:17
Alignment explanation
Indices: 685763--685801 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
685753 AAACTTATTT
**
685763 TTAAAAATTAAAAATCA
1 TTAAAAATTAAAAAAAA
*
685780 TTAAAATTTAAAAAAAA
1 TTAAAAATTAAAAAAAA
685797 TTAAA
1 TTAAA
685802 TGCTAGCGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
TTAAAAATTAAAAAAAA
Found at i:686173 original size:35 final size:34
Alignment explanation
Indices: 686134--686203 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 34
686124 ATGCTGATAA
686134 GCCACTTAAATAAATCTAAATCCCAATATCTATTT
1 GCCACTTAAATAAATCTAAATCCCAATATCT-TTT
*
686169 GCCACTTAAATAAATTTAAATCCCAATATCTTTT
1 GCCACTTAAATAAATCTAAATCCCAATATCTTTT
686203 G
1 G
686204 AAAAATTATG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 4 0.12
35 30 0.88
ACGTcount: A:0.39, C:0.21, G:0.04, T:0.36
Consensus pattern (34 bp):
GCCACTTAAATAAATCTAAATCCCAATATCTTTT
Found at i:696118 original size:26 final size:26
Alignment explanation
Indices: 696079--696132 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
696069 AAGGGGGTTT
696079 AATTTTTTTCTTTA-TCATTTTTATAA
1 AATTTTTTTCTTTACT-ATTTTTATAA
696105 AATTTTATTT-TTTACTATTTTTATAA
1 AATTTT-TTTCTTTACTATTTTTATAA
696131 AA
1 AA
696133 AAATTAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
26 22 0.85
27 4 0.15
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (26 bp):
AATTTTTTTCTTTACTATTTTTATAA
Found at i:696175 original size:19 final size:20
Alignment explanation
Indices: 696153--696204 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
696143 TCAATAAATT
696153 TTAAATTTTTAT-ATTTTTA
1 TTAAATTTTTATAATTTTTA
* * *
696172 TTAAAATTTAATAATTTTTC
1 TTAAATTTTTATAATTTTTA
*
696192 TAAAATTTATTAT
1 TTAAATTT-TTAT
696205 TTATAATTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 10 0.40
20 12 0.48
21 3 0.12
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (20 bp):
TTAAATTTTTATAATTTTTA
Found at i:701619 original size:20 final size:20
Alignment explanation
Indices: 701594--701637 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
701584 ATATTATTAA
*
701594 ATTATT-TTGAAATAATAAAT
1 ATTATTATTCAAAT-ATAAAT
*
701614 ATTATTATTCAAATTTAAAT
1 ATTATTATTCAAATATAAAT
701634 ATTA
1 ATTA
701638 AAAAACATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (20 bp):
ATTATTATTCAAATATAAAT
Found at i:702300 original size:19 final size:18
Alignment explanation
Indices: 702256--702300 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 18
702246 TTTGAAGAAA
702256 GTGAATTTAAAATTCAAC
1 GTGAATTTAAAATTCAAC
*
702274 GTGAATTTAAAATTCGAC
1 GTGAATTTAAAATTCAAC
702292 GTAGAATTT
1 GT-GAATTT
702301 GTGTCTGACA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 19 0.76
19 6 0.24
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.36
Consensus pattern (18 bp):
GTGAATTTAAAATTCAAC
Found at i:715628 original size:83 final size:85
Alignment explanation
Indices: 715502--715671 Score: 299
Period size: 83 Copynumber: 2.0 Consensus size: 85
715492 AAAGAGCATG
* *
715502 AGTTGGTTAGAAGTGAGGGGGGAGGGGGGAACTTAATGGTTTTTACAGCTTTTTTCCCTACTTAT
1 AGTTGGTTAGAAGTGA-GAGGGAGGGGGGAACTTAATGGTTTTTACAGCTTTTTTCCCCACTTAT
715567 CGCACTTATCGCACAAAGACT
65 CGCACTTATCGCACAAAGACT
715588 AGTTGGTTAGAAGTGA-AGGG-GGGGGGAACTTAATGGTTTTTACAGCTTTTTTCCCCACTTATC
1 AGTTGGTTAGAAGTGAGAGGGAGGGGGGAACTTAATGGTTTTTACAGCTTTTTTCCCCACTTATC
715651 GCACTTATCGCACAAAGACT
66 GCACTTATCGCACAAAGACT
715671 A
1 A
715672 AAAATAAGTG
Statistics
Matches: 82, Mismatches: 2, Indels: 3
0.94 0.02 0.03
Matches are distributed among these distances:
83 63 0.77
84 3 0.04
86 16 0.20
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.31
Consensus pattern (85 bp):
AGTTGGTTAGAAGTGAGAGGGAGGGGGGAACTTAATGGTTTTTACAGCTTTTTTCCCCACTTATC
GCACTTATCGCACAAAGACT
Found at i:715830 original size:16 final size:16
Alignment explanation
Indices: 715809--715841 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
715799 CATGTAATGG
715809 CTTATAAAGTTTTGAT
1 CTTATAAAGTTTTGAT
715825 CTTATAAAGTTTTGAT
1 CTTATAAAGTTTTGAT
715841 C
1 C
715842 ATTAGCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.09, G:0.12, T:0.48
Consensus pattern (16 bp):
CTTATAAAGTTTTGAT
Found at i:726837 original size:20 final size:20
Alignment explanation
Indices: 726812--726861 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
726802 TGGCTTAAAA
726812 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
726832 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
726849 GTGGTAGTGGATT
1 TTGGTAGTGGATT
726862 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:731476 original size:20 final size:20
Alignment explanation
Indices: 731451--731500 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
731441 TGGCTTAAAA
731451 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
731471 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
731488 GTGGTAGTGGATT
1 TTGGTAGTGGATT
731501 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:742615 original size:309 final size:309
Alignment explanation
Indices: 742056--742679 Score: 1248
Period size: 309 Copynumber: 2.0 Consensus size: 309
742046 AAAATGCAGC
742056 AGATGGGTCTTTACCCTAATGAAGTGACATATATTTCTGTGTTATCTGCATGTAGTCATATGGGT
1 AGATGGGTCTTTACCCTAATGAAGTGACATATATTTCTGTGTTATCTGCATGTAGTCATATGGGT
742121 TTGGTTGATGAAGCAAAGAGCTACTTTGATCTCATGATAACAAAGCACAATATATCACCCGATGT
66 TTGGTTGATGAAGCAAAGAGCTACTTTGATCTCATGATAACAAAGCACAATATATCACCCGATGT
742186 CATTCACTATTCATGCATGGTAGATACTCTTGGTCGAGCAGGAATGATTTCCGAAGCTTATGATT
131 CATTCACTATTCATGCATGGTAGATACTCTTGGTCGAGCAGGAATGATTTCCGAAGCTTATGATT
742251 TGATACAGAGAATGCCCTTTGTTGCCACTGCTTCTATGTGGGGTTCACTTTTAGCTTGTTGTAGA
196 TGATACAGAGAATGCCCTTTGTTGCCACTGCTTCTATGTGGGGTTCACTTTTAGCTTGTTGTAGA
742316 TTCCATGGGAATCTTGAAATAGCTCAGATAGCAGCTAAGCATTTATTTG
261 TTCCATGGGAATCTTGAAATAGCTCAGATAGCAGCTAAGCATTTATTTG
742365 AGATGGGTCTTTACCCTAATGAAGTGACATATATTTCTGTGTTATCTGCATGTAGTCATATGGGT
1 AGATGGGTCTTTACCCTAATGAAGTGACATATATTTCTGTGTTATCTGCATGTAGTCATATGGGT
742430 TTGGTTGATGAAGCAAAGAGCTACTTTGATCTCATGATAACAAAGCACAATATATCACCCGATGT
66 TTGGTTGATGAAGCAAAGAGCTACTTTGATCTCATGATAACAAAGCACAATATATCACCCGATGT
742495 CATTCACTATTCATGCATGGTAGATACTCTTGGTCGAGCAGGAATGATTTCCGAAGCTTATGATT
131 CATTCACTATTCATGCATGGTAGATACTCTTGGTCGAGCAGGAATGATTTCCGAAGCTTATGATT
742560 TGATACAGAGAATGCCCTTTGTTGCCACTGCTTCTATGTGGGGTTCACTTTTAGCTTGTTGTAGA
196 TGATACAGAGAATGCCCTTTGTTGCCACTGCTTCTATGTGGGGTTCACTTTTAGCTTGTTGTAGA
742625 TTCCATGGGAATCTTGAAATAGCTCAGATAGCAGCTAAGCATTTATTTG
261 TTCCATGGGAATCTTGAAATAGCTCAGATAGCAGCTAAGCATTTATTTG
742674 AGATGG
1 AGATGG
742680 AACCTGATAA
Statistics
Matches: 315, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
309 315 1.00
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (309 bp):
AGATGGGTCTTTACCCTAATGAAGTGACATATATTTCTGTGTTATCTGCATGTAGTCATATGGGT
TTGGTTGATGAAGCAAAGAGCTACTTTGATCTCATGATAACAAAGCACAATATATCACCCGATGT
CATTCACTATTCATGCATGGTAGATACTCTTGGTCGAGCAGGAATGATTTCCGAAGCTTATGATT
TGATACAGAGAATGCCCTTTGTTGCCACTGCTTCTATGTGGGGTTCACTTTTAGCTTGTTGTAGA
TTCCATGGGAATCTTGAAATAGCTCAGATAGCAGCTAAGCATTTATTTG
Found at i:745337 original size:13 final size:13
Alignment explanation
Indices: 745321--745347 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
745311 GACAAATCAA
745321 CTCGACACTAACT
1 CTCGACACTAACT
745334 CTCGACACTAACT
1 CTCGACACTAACT
745347 C
1 C
745348 ACAATTGATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.41, G:0.07, T:0.22
Consensus pattern (13 bp):
CTCGACACTAACT
Found at i:755362 original size:28 final size:28
Alignment explanation
Indices: 755310--755393 Score: 125
Period size: 28 Copynumber: 3.0 Consensus size: 28
755300 CACTTTGTGC
755310 TATTCTGGTGTGTTTTGGATGGATTATAT
1 TATTCTGGTGTGTTTTGGA-GGATTATAT
755339 TATTCTGGTGT-TTTTGGGAGGATTATAT
1 TATTCTGGTGTGTTTT-GGAGGATTATAT
* *
755367 GATACTGGTGTGTTTTGGAGGATTATA
1 TATTCTGGTGTGTTTTGGAGGATTATA
755394 CTGGTGTGTT
Statistics
Matches: 51, Mismatches: 2, Indels: 5
0.88 0.03 0.09
Matches are distributed among these distances:
28 33 0.65
29 18 0.35
ACGTcount: A:0.19, C:0.04, G:0.30, T:0.48
Consensus pattern (28 bp):
TATTCTGGTGTGTTTTGGAGGATTATAT
Found at i:755363 original size:23 final size:24
Alignment explanation
Indices: 755337--755407 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 24
755327 GATGGATTAT
755337 ATTATTCTGGTGT-TTTTGGGAGG
1 ATTATTCTGGTGTGTTTTGGGAGG
755360 ATTATATGATACTGGTGTGTTTT-GGAGG
1 A-T-TAT--T-CTGGTGTGTTTTGGGAGG
*
755388 ATTATACTGGTGTGTTTTGG
1 ATTATTCTGGTGTGTTTTGG
755408 TTGGACATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 13
0.74 0.02 0.24
Matches are distributed among these distances:
23 13 0.32
24 2 0.05
25 3 0.08
26 3 0.08
27 2 0.05
28 13 0.32
29 4 0.10
ACGTcount: A:0.17, C:0.04, G:0.32, T:0.46
Consensus pattern (24 bp):
ATTATTCTGGTGTGTTTTGGGAGG
Found at i:755645 original size:21 final size:21
Alignment explanation
Indices: 755597--755683 Score: 104
Period size: 21 Copynumber: 4.1 Consensus size: 21
755587 GGCTATACTG
*
755597 ATCAGGCACTTTATGTGTCGT
1 ATCAGGCACCTTATGTGTCGT
*
755618 ATTTCAGGCACCTTGTGTGTCGT
1 A--TCAGGCACCTTATGTGTCGT
**
755641 ATCAGGCACCTCGTGTGTCGT
1 ATCAGGCACCTTATGTGTCGT
*
755662 TTCAGGCA-CTTATGTGTCGT
1 ATCAGGCACCTTATGTGTCGT
755682 AT
1 AT
755684 ACTGATCAGG
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
20 11 0.19
21 27 0.47
23 19 0.33
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.37
Consensus pattern (21 bp):
ATCAGGCACCTTATGTGTCGT
Found at i:756923 original size:46 final size:48
Alignment explanation
Indices: 756765--756951 Score: 163
Period size: 46 Copynumber: 3.9 Consensus size: 48
756755 TGGTTGGACC
756765 ATGGCATCA-A-TGTGATATGTGA-TCTGTGTAAGACCATAGCTGGGCT
1 ATGGCATCAGAGTGTGATATGTGATTC-GTGTAAGACCATAGCTGGGCT
* * * *
756811 ATGGCATCAGAGATATGTGATTATGTGCTTCCGTATAAGACCATATCTGGGAT
1 ATGGCATCAGAG---TGTGA-TATGTGATT-CGTGTAAGACCATAGCTGGGCT
* *
756864 ATGGCATC--AGTGTGATATGTGATTCGTGTAATACCATGGCTGGGCT
1 ATGGCATCAGAGTGTGATATGTGATTCGTGTAAGACCATAGCTGGGCT
* * *
756910 ATGGC-TACGGTGTGTGATATGTGACTAT-GTGCAAGACCATAG
1 ATGGCAT-CAGAGTGTGATATGTGA-T-TCGTGTAAGACCATAG
756952 TTTTACTATG
Statistics
Matches: 114, Mismatches: 14, Indels: 23
0.75 0.09 0.15
Matches are distributed among these distances:
45 1 0.01
46 32 0.28
47 9 0.08
48 18 0.16
49 12 0.11
50 1 0.01
51 7 0.06
52 6 0.05
53 27 0.24
54 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (48 bp):
ATGGCATCAGAGTGTGATATGTGATTCGTGTAAGACCATAGCTGGGCT
Found at i:768000 original size:12 final size:12
Alignment explanation
Indices: 767985--768009 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
767975 TTAATTTTCA
767985 TTTTATTAATTT
1 TTTTATTAATTT
767997 TTTTATTAATTT
1 TTTTATTAATTT
768009 T
1 T
768010 ACTGATTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTATTAATTT
Found at i:772803 original size:13 final size:14
Alignment explanation
Indices: 772755--772802 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
772745 TATAACTAAA
*
772755 AAAATAACATTGTAAT
1 AAAATAA-ATT-TAAC
772771 AAACATAAATTTAAC
1 AAA-ATAAATTTAAC
*
772786 AAAATAATTTTAAC
1 AAAATAAATTTAAC
772800 AAA
1 AAA
772803 TGAACTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 13 0.45
15 6 0.21
16 6 0.21
17 4 0.14
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.29
Consensus pattern (14 bp):
AAAATAAATTTAAC
Found at i:772887 original size:29 final size:31
Alignment explanation
Indices: 772833--772901 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
772823 TGAGAAATAG
772833 AGGGACTAAATTCCTAGAAAT-AAA-AGTAT
1 AGGGACTAAATTCCTAGAAATAAAAGAGTAT
*
772862 AGGGACTAAATT-CTA-AATTTACAAAGAGTAT
1 AGGGACTAAATTCCTAGAA-ATA-AAAGAGTAT
772893 AGGGACTAA
1 AGGGACTAA
772902 TGTCATGTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
27 2 0.06
28 4 0.11
29 12 0.34
30 3 0.09
31 14 0.40
ACGTcount: A:0.46, C:0.10, G:0.19, T:0.25
Consensus pattern (31 bp):
AGGGACTAAATTCCTAGAAATAAAAGAGTAT
Found at i:783693 original size:16 final size:16
Alignment explanation
Indices: 783672--783702 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
783662 AGGAGTAATA
*
783672 TATCTATATCTATATC
1 TATCTATATATATATC
783688 TATCTATATATATAT
1 TATCTATATATATAT
783703 ATAATGAGCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.13, G:0.00, T:0.52
Consensus pattern (16 bp):
TATCTATATATATATC
Found at i:785823 original size:21 final size:21
Alignment explanation
Indices: 785799--785849 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
785789 GACACCGTCC
785799 GTGACGGCGATGACTCACCTT
1 GTGACGGCGATGACTCACCTT
* *
785820 GTGACGTCGATGTCTCACCTT
1 GTGACGGCGATGACTCACCTT
**
785841 CCGACGGCG
1 GTGACGGCG
785850 GAGAATCCAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.16, C:0.31, G:0.29, T:0.24
Consensus pattern (21 bp):
GTGACGGCGATGACTCACCTT
Found at i:786637 original size:15 final size:16
Alignment explanation
Indices: 786617--786646 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
786607 GTTTTAGAGA
786617 AATGGAAA-ATAATTG
1 AATGGAAATATAATTG
786632 AATGGAAATATAATT
1 AATGGAAATATAATT
786647 ATAAATTCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.30
Consensus pattern (16 bp):
AATGGAAATATAATTG
Found at i:793354 original size:22 final size:21
Alignment explanation
Indices: 793324--793367 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
793314 AAACAATGTT
793324 AAATTTATTAATAT-TGATTTA
1 AAATTTATTAATATAT-ATTTA
*
793345 AAATATTATTTATATATATTTA
1 AAAT-TTATTAATATATATTTA
793367 A
1 A
793368 CTATTAAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 4 0.20
22 15 0.75
23 1 0.05
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
AAATTTATTAATATATATTTA
Found at i:793897 original size:24 final size:24
Alignment explanation
Indices: 793847--793898 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
793837 TTCGTAGGTC
* *
793847 AAATAAATTATGCTAATAAATGCT
1 AAATAAATTATACTAATAAATACT
* *
793871 AAATATATTATACTAATAAATATT
1 AAATAAATTATACTAATAAATACT
793895 AAAT
1 AAAT
793899 GTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:797219 original size:23 final size:23
Alignment explanation
Indices: 797191--797236 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
797181 TTATTTTGAG
797191 GTTTTCATGGTAGTAATAAAAAT
1 GTTTTCATGGTAGTAATAAAAAT
797214 GTTTTCATGGTAGTAATAAAAAT
1 GTTTTCATGGTAGTAATAAAAAT
797237 CATTCACACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.04, G:0.17, T:0.39
Consensus pattern (23 bp):
GTTTTCATGGTAGTAATAAAAAT
Found at i:797242 original size:22 final size:23
Alignment explanation
Indices: 797194--797242 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
797184 TTTTGAGGTT
**
797194 TTCATGGTAGTAATAAAAATGTT
1 TTCATGGTAGTAATAAAAATGCA
797217 TTCATGGTAGTAATAAAAAT-CA
1 TTCATGGTAGTAATAAAAATGCA
797239 TTCA
1 TTCA
797243 CACACAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.37
Consensus pattern (23 bp):
TTCATGGTAGTAATAAAAATGCA
Found at i:803473 original size:18 final size:20
Alignment explanation
Indices: 803450--803486 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
803440 AGTCCCCCAA
803450 AAAATAAAA-C-CATAAAAT
1 AAAATAAAATCTCATAAAAT
803468 AAAATAAAATCTCATAAAA
1 AAAATAAAATCTCATAAAA
803487 ACCTCCCGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 1 0.06
20 7 0.41
ACGTcount: A:0.70, C:0.11, G:0.00, T:0.19
Consensus pattern (20 bp):
AAAATAAAATCTCATAAAAT
Found at i:804358 original size:23 final size:23
Alignment explanation
Indices: 804328--804380 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
804318 AATATTGATT
804328 ATTTTTTAAAAAATA-TTTTTTAA
1 ATTTTTTAAAAAATACTTTTTT-A
* *
804351 ATTTTTT-ACATATACTTTTTTA
1 ATTTTTTAAAAAATACTTTTTTA
804373 ATTTTTTA
1 ATTTTTTA
804381 TGAGGTGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 13 0.50
23 13 0.50
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (23 bp):
ATTTTTTAAAAAATACTTTTTTA
Found at i:807339 original size:13 final size:13
Alignment explanation
Indices: 807321--807346 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
807311 AAATAATGAA
807321 ATAACTAAATAAT
1 ATAACTAAATAAT
807334 ATAACTAAATAAT
1 ATAACTAAATAAT
807347 GACAGATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (13 bp):
ATAACTAAATAAT
Found at i:811050 original size:21 final size:22
Alignment explanation
Indices: 811021--811066 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
811011 GATATGTTAA
811021 AAATATTTTAATTAT-TATTTG
1 AAATATTTTAATTATATATTTG
*
811042 AAATTTTTTAATTATAATATTTG
1 AAATATTTTAATTAT-ATATTTG
811065 AA
1 AA
811067 TTTATACTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 14 0.64
23 8 0.36
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (22 bp):
AAATATTTTAATTATATATTTG
Found at i:813587 original size:18 final size:19
Alignment explanation
Indices: 813534--813576 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
813524 GATGAATCAT
*
813534 ATAGAAAGAG--ATAGAAA
1 ATAGAAAGAGAAAAAGAAA
813551 ATAGAAAGAGAAAAAGAAA
1 ATAGAAAGAGAAAAAGAAA
813570 A-AGAAAG
1 ATAGAAAG
813577 GGGAAGAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 10 0.43
18 6 0.26
19 7 0.30
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.07
Consensus pattern (19 bp):
ATAGAAAGAGAAAAAGAAA
Found at i:814009 original size:3 final size:3
Alignment explanation
Indices: 814001--814027 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
813991 AAGGAAGAGG
814001 AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA
814028 TGAGAGCTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:820896 original size:22 final size:21
Alignment explanation
Indices: 820864--820919 Score: 78
Period size: 21 Copynumber: 2.6 Consensus size: 21
820854 TAGACTAATA
820864 TAAA-TAAAAAAATTTAAAGAC
1 TAAATTAAAAAAATTT-AAGAC
820885 TAAATTAAAAAAAATTTAAGAC
1 TAAATT-AAAAAAATTTAAGAC
*
820907 AAAATTAAAAAAA
1 TAAATTAAAAAAA
820920 GTGTTATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 11 0.34
22 11 0.34
23 10 0.31
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.23
Consensus pattern (21 bp):
TAAATTAAAAAAATTTAAGAC
Found at i:820899 original size:23 final size:22
Alignment explanation
Indices: 820869--820919 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
820859 TAATATAAAT
*
820869 AAAAAAATTTAAAGACTAAATTA
1 AAAAAAATTT-AAGACAAAATTA
820892 AAAAAAATTTAAGACAAAATTA
1 AAAAAAATTTAAGACAAAATTA
820914 AAAAAA
1 AAAAAA
820920 GTGTTATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 17 0.63
23 10 0.37
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.22
Consensus pattern (22 bp):
AAAAAAATTTAAGACAAAATTA
Found at i:821659 original size:31 final size:33
Alignment explanation
Indices: 821599--821660 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
821589 TTGTATTTTA
* *
821599 CTTTATTTATTCAAAAAAAATAAGTAAATTAAT
1 CTTTATATATTCAAAAAAAAGAAGTAAATTAAT
*
821632 CTTTATATATT-AAATAAAAGAA-TAAATTA
1 CTTTATATATTCAAAAAAAAGAAGTAAATTA
821661 GTTTATTCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 7 0.27
32 9 0.35
33 10 0.38
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (33 bp):
CTTTATATATTCAAAAAAAAGAAGTAAATTAAT
Found at i:822850 original size:12 final size:12
Alignment explanation
Indices: 822833--822857 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
822823 ACATTATAGA
822833 TTTTATATAAAT
1 TTTTATATAAAT
822845 TTTTATATAAAT
1 TTTTATATAAAT
822857 T
1 T
822858 ATATAATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTTATATAAAT
Found at i:830454 original size:31 final size:30
Alignment explanation
Indices: 830419--830496 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 30
830409 TTAAAAGTCA
830419 AAAAGTACAAAGACTAAAATTGAAT-AAATAG
1 AAAAGTACAAAGACTAAAATTG-ATCAAAT-G
* * * *
830450 AAAAGTGCAAGGACTCAAATTGATCAAATT
1 AAAAGTACAAAGACTAAAATTGATCAAATG
830480 AAAA-TACAAAGACTAAA
1 AAAAGTACAAAGACTAAA
830497 TTTACAACTT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
29 10 0.26
30 6 0.15
31 23 0.59
ACGTcount: A:0.58, C:0.10, G:0.13, T:0.19
Consensus pattern (30 bp):
AAAAGTACAAAGACTAAAATTGATCAAATG
Found at i:833144 original size:17 final size:17
Alignment explanation
Indices: 833122--833170 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
833112 TTATCATTCC
833122 TCAATTTTATAATTTAA
1 TCAATTTTATAATTTAA
*
833139 TCAATTTAAT-ATTTAA
1 TCAATTTTATAATTTAA
833155 TAACAA-TTTATAATTT
1 T--CAATTTTATAATTT
833171 TATTATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 7 0.26
17 13 0.48
18 7 0.26
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (17 bp):
TCAATTTTATAATTTAA
Found at i:833170 original size:18 final size:16
Alignment explanation
Indices: 833122--833170 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 16
833112 TTATCATTCC
833122 TCAATTTTATAATTTAA
1 TCAA-TTTATAATTTAA
833139 TCAATTTA-ATATTTAA
1 TCAATTTATA-ATTTAA
833155 TAACAATTTATAATTT
1 T--CAATTTATAATTT
833171 TATTATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 1 0.04
16 11 0.39
17 4 0.14
18 11 0.39
19 1 0.04
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (16 bp):
TCAATTTATAATTTAA
Found at i:833820 original size:18 final size:17
Alignment explanation
Indices: 833765--833820 Score: 53
Period size: 18 Copynumber: 3.3 Consensus size: 17
833755 TATTTTAAAA
*
833765 TAATTGAATAAAAACAT
1 TAATAGAATAAAAACAT
833782 TAA-AG-ATAACAAACAT
1 TAATAGAATAA-AAACAT
* *
833798 AAATAGAATAATAAATAT
1 TAATAGAATAA-AAACAT
833816 TAATA
1 TAATA
833821 ATAGGATAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
15 4 0.13
16 9 0.29
17 5 0.16
18 13 0.42
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.27
Consensus pattern (17 bp):
TAATAGAATAAAAACAT
Found at i:837543 original size:6 final size:6
Alignment explanation
Indices: 837534--837562 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
837524 GAAATCAACA
837534 TTTCAC TTTCAC TTTCAC TTTCAC TTTCA
1 TTTCAC TTTCAC TTTCAC TTTCAC TTTCA
837563 AATTCAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.31, G:0.00, T:0.52
Consensus pattern (6 bp):
TTTCAC
Found at i:837568 original size:18 final size:18
Alignment explanation
Indices: 837534--837568 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
837524 GAAATCAACA
**
837534 TTTCACTTTCACTTTCAC
1 TTTCACTTTCAAATTCAC
837552 TTTCACTTTCAAATTCA
1 TTTCACTTTCAAATTCA
837569 AAAAACAAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.29, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTCACTTTCAAATTCAC
Found at i:849994 original size:13 final size:15
Alignment explanation
Indices: 849967--850000 Score: 54
Period size: 13 Copynumber: 2.4 Consensus size: 15
849957 GTATGATTAT
849967 ATTTATTTTTCGTGA
1 ATTTATTTTTCGTGA
849982 ATTT-TTTTT-GTGA
1 ATTTATTTTTCGTGA
849995 ATTTAT
1 ATTTAT
850001 AACTCTACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 8 0.44
14 6 0.33
15 4 0.22
ACGTcount: A:0.21, C:0.03, G:0.12, T:0.65
Consensus pattern (15 bp):
ATTTATTTTTCGTGA
Found at i:855679 original size:8 final size:8
Alignment explanation
Indices: 855662--855695 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
855652 TTATTAATAA
855662 ATTT-ATT
1 ATTTAATT
855669 ATTTAATT
1 ATTTAATT
855677 ATTTAATT
1 ATTTAATT
855685 ATTTAATT
1 ATTTAATT
855693 ATT
1 ATT
855696 AAAAATCATC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 4 0.15
8 22 0.85
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (8 bp):
ATTTAATT
Found at i:867954 original size:63 final size:63
Alignment explanation
Indices: 867850--867976 Score: 245
Period size: 63 Copynumber: 2.0 Consensus size: 63
867840 ACCGCCTAAA
*
867850 GTATTGGTCTGGAGAGGAGCTTTGATCAAATATGAATTTATTGAGTTAGGAAAATAAACAATT
1 GTATTGGTCTGGAGAGGAGCTTTGATCAAATATGAACTTATTGAGTTAGGAAAATAAACAATT
867913 GTATTGGTCTGGAGAGGAGCTTTGATCAAATATGAACTTATTGAGTTAGGAAAATAAACAATT
1 GTATTGGTCTGGAGAGGAGCTTTGATCAAATATGAACTTATTGAGTTAGGAAAATAAACAATT
867976 G
1 G
867977 AAGCGAAATT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.36, C:0.07, G:0.24, T:0.32
Consensus pattern (63 bp):
GTATTGGTCTGGAGAGGAGCTTTGATCAAATATGAACTTATTGAGTTAGGAAAATAAACAATT
Found at i:872664 original size:6 final size:6
Alignment explanation
Indices: 872648--872678 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
872638 AGAAACAAGA
*
872648 AAGAAC GAGAAC AAGAAC AAGAAC AAGAAC A
1 AAGAAC AAGAAC AAGAAC AAGAAC AAGAAC A
872679 GAAAAAAAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.65, C:0.16, G:0.19, T:0.00
Consensus pattern (6 bp):
AAGAAC
Found at i:873752 original size:71 final size:68
Alignment explanation
Indices: 873625--873758 Score: 151
Period size: 71 Copynumber: 1.9 Consensus size: 68
873615 ATAGACAATA
* * * * * * *
873625 TAATGGTTTTGCCTTTTAATTTAATAAATAAATATTTATCAGAATGACGTAATTTTGCCTTTTTA
1 TAATGATTTTGACTTTTAATTTAAAAAATAAACATTTATCAAAACGACGTAATTTTGCATTTTTA
873690 AGT
66 AGT
* **
873693 TAATGATTTTGACTTTTAACTTTAGAAAATATAAACATTTATCAAAACGATGTGGTTTTGCATTT
1 TAATGATTTTGACTTTTAA-TTTA-AAAA-ATAAACATTTATCAAAACGACGTAATTTTGCATTT
873758 T
63 T
873759 CTTATTCGAA
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
68 17 0.32
69 4 0.08
70 3 0.06
71 29 0.55
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.46
Consensus pattern (68 bp):
TAATGATTTTGACTTTTAATTTAAAAAATAAACATTTATCAAAACGACGTAATTTTGCATTTTTA
AGT
Found at i:883701 original size:45 final size:46
Alignment explanation
Indices: 883613--883701 Score: 128
Period size: 45 Copynumber: 1.9 Consensus size: 46
883603 AAATAGATAT
* *
883613 TTTCCAAAGTTTTAAAAAAATATACTTAAATAATACTAAGGTAAGTG
1 TTTCCAAAGTTTTAAAAAAATATA-TTAAATAACACCAAGGTAAGTG
883660 TTTCTCAAAGTTTT-AAAAAATAT-TTAAATAACACCAAGGTAA
1 TTTC-CAAAGTTTTAAAAAAATATATTAAATAACACCAAGGTAA
883702 CTGCAAATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
45 17 0.44
47 13 0.33
48 9 0.23
ACGTcount: A:0.47, C:0.10, G:0.09, T:0.34
Consensus pattern (46 bp):
TTTCCAAAGTTTTAAAAAAATATATTAAATAACACCAAGGTAAGTG
Found at i:895807 original size:16 final size:17
Alignment explanation
Indices: 895777--895810 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
895767 GGAAGTTGGA
895777 GGAGAGGGGAAGGGATG
1 GGAGAGGGGAAGGGATG
*
895794 GGAG-GGGGAGGGGATG
1 GGAGAGGGGAAGGGATG
895810 G
1 G
895811 CTTTTGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.24, C:0.00, G:0.71, T:0.06
Consensus pattern (17 bp):
GGAGAGGGGAAGGGATG
Found at i:897574 original size:23 final size:23
Alignment explanation
Indices: 897543--897600 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
897533 CTTACTTCGT
*
897543 AAATAATTTATATTAAATAT-TTA
1 AAAT-ATTTATATTAAACATATTA
*
897566 AAAGTATTTAAATTAAACATATTA
1 AAA-TATTTATATTAAACATATTA
*
897590 TAATATTTATA
1 AAATATTTATA
897601 AACTTGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 23 0.79
24 6 0.21
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
AAATATTTATATTAAACATATTA
Found at i:899435 original size:24 final size:24
Alignment explanation
Indices: 899403--899459 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
899393 ATTGAATCCA
* *
899403 AAAAAAGAAGGGGAGATGGTATTT
1 AAAAAAGAAGGGAAGATGATATTT
899427 AAAAAAGAAGGGAAGATGATATTT
1 AAAAAAGAAGGGAAGATGATATTT
899451 AAAAAAGAA
1 AAAAAAGAA
899460 AGAAAAGCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.56, C:0.00, G:0.26, T:0.18
Consensus pattern (24 bp):
AAAAAAGAAGGGAAGATGATATTT
Found at i:902427 original size:29 final size:28
Alignment explanation
Indices: 902388--902471 Score: 114
Period size: 28 Copynumber: 3.0 Consensus size: 28
902378 CACTTTGTGC
902388 TATTCTGGTGTGTTTTGGATGGATTATAT
1 TATTCTGGTGTGTTTTGGA-GGATTATAT
* *
902417 TATTCTGGTGTGTTTGGGAGGACTATAT
1 TATTCTGGTGTGTTTTGGAGGATTATAT
* * *
902445 GATACTGGTGTGTTTTGGAGAATTATA
1 TATTCTGGTGTGTTTTGGAGGATTATA
902472 CTGGTGTGTT
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 30 0.62
29 18 0.38
ACGTcount: A:0.20, C:0.05, G:0.30, T:0.45
Consensus pattern (28 bp):
TATTCTGGTGTGTTTTGGAGGATTATAT
Found at i:902471 original size:28 final size:28
Alignment explanation
Indices: 902392--902485 Score: 108
Period size: 28 Copynumber: 3.5 Consensus size: 28
902382 TTGTGCTATT
* *
902392 CTGGTGTGTTTTGGATGGATTATATTATT
1 CTGGTGTGTTTTGGA-GGATTATATGATA
* *
902421 CTGGTGTGTTTGGGAGGACTATATGATA
1 CTGGTGTGTTTTGGAGGATTATATGATA
902449 CTGGTGTGTTTTGGA-GA--AT-T-ATA
1 CTGGTGTGTTTTGGAGGATTATATGATA
902472 CTGGTGTGTTTTGG
1 CTGGTGTGTTTTGG
902486 TTGGACATTT
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
23 17 0.28
24 1 0.02
25 2 0.03
27 2 0.03
28 24 0.40
29 14 0.23
ACGTcount: A:0.17, C:0.05, G:0.33, T:0.45
Consensus pattern (28 bp):
CTGGTGTGTTTTGGAGGATTATATGATA
Found at i:902748 original size:21 final size:21
Alignment explanation
Indices: 902688--902748 Score: 50
Period size: 21 Copynumber: 2.8 Consensus size: 21
902678 AGGCACTTTA
*
902688 TGTGTCGTATTTCAGGCACCTTG
1 TGTGTCGT-TTT-AGGCACCTCG
**** *
902711 TGTGTCGCAGCATGCACCTCG
1 TGTGTCGTTTTAGGCACCTCG
902732 TGTGTCGTTTTAGGCAC
1 TGTGTCGTTTTAGGCAC
902749 TTATGTGTCG
Statistics
Matches: 27, Mismatches: 11, Indels: 2
0.68 0.28 0.05
Matches are distributed among these distances:
21 20 0.74
23 7 0.26
ACGTcount: A:0.13, C:0.25, G:0.28, T:0.34
Consensus pattern (21 bp):
TGTGTCGTTTTAGGCACCTCG
Found at i:902930 original size:23 final size:23
Alignment explanation
Indices: 902886--902930 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
902876 ATCAATTAAA
*
902886 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
902909 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
902931 CACATATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:904098 original size:5 final size:5
Alignment explanation
Indices: 904088--904159 Score: 64
Period size: 5 Copynumber: 14.8 Consensus size: 5
904078 TGTTAAAAAA
* *
904088 ATATT ATATT ATAGTA ATGATT ATGTT -T-TT ATATT ATATT ATTATT
1 ATATT ATATT ATA-TT AT-ATT ATATT ATATT ATATT ATATT A-TATT
904134 A-A-T ATATT ATATT ATATT ATA-T ATAT
1 ATATT ATATT ATATT ATATT ATATT ATAT
904160 ACATAAAACA
Statistics
Matches: 56, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
3 4 0.07
4 8 0.14
5 32 0.57
6 11 0.20
7 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (5 bp):
ATATT
Found at i:904141 original size:19 final size:19
Alignment explanation
Indices: 904117--904159 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
904107 ATTATGTTTT
904117 TATATTATATTATTATTA-A
1 TATATTATATTA-TATTATA
904136 TATATTATATTATATTATA
1 TATATTATATTATATTATA
904155 TATAT
1 TATAT
904160 ACATAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATTATATTATATTATA
Found at i:904191 original size:17 final size:17
Alignment explanation
Indices: 904169--904202 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
904159 TACATAAAAC
*
904169 AAAAGAAAGAATAGAAA
1 AAAAGAAAGAAAAGAAA
904186 AAAAGAAAGAAAAGAAA
1 AAAAGAAAGAAAAGAAA
904203 CAGAATAGAA
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:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (17 bp):
AAAAGAAAGAAAAGAAA
Found at i:904198 original size:9 final size:9
Alignment explanation
Indices: 904169--904202 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
904159 TACATAAAAC
904169 AAAAGAAAG
1 AAAAGAAAG
*
904178 AATAGAAA-
1 AAAAGAAAG
904186 AAAAGAAAG
1 AAAAGAAAG
904195 AAAAGAAA
1 AAAAGAAA
904203 CAGAATAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:905132 original size:46 final size:44
Alignment explanation
Indices: 905072--905186 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
905062 ACAGGACAGA
* *
905072 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
905118 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
905162 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
905187 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:905167 original size:44 final size:45
Alignment explanation
Indices: 905072--905205 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
905062 ACAGGACAGA
* *
905072 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
905118 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
905162 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
905206 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:910244 original size:5 final size:5
Alignment explanation
Indices: 910234--910305 Score: 64
Period size: 5 Copynumber: 14.8 Consensus size: 5
910224 TGTTAAAAAA
* *
910234 ATATT ATATT ATAGTA ATGATT ATGTT -T-TT ATATT ATATT ATTATT
1 ATATT ATATT ATA-TT AT-ATT ATATT ATATT ATATT ATATT A-TATT
910280 A-A-T ATATT ATATT ATATT ATA-T ATAT
1 ATATT ATATT ATATT ATATT ATATT ATAT
910306 ACATAAAACA
Statistics
Matches: 56, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
3 4 0.07
4 8 0.14
5 32 0.57
6 11 0.20
7 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (5 bp):
ATATT
Found at i:910287 original size:19 final size:19
Alignment explanation
Indices: 910263--910305 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
910253 ATTATGTTTT
910263 TATATTATATTATTATTA-A
1 TATATTATATTA-TATTATA
910282 TATATTATATTATATTATA
1 TATATTATATTATATTATA
910301 TATAT
1 TATAT
910306 ACATAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATTATATTATATTATA
Found at i:910338 original size:18 final size:19
Alignment explanation
Indices: 910310--910349 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
910300 ATATATACAT
*
910310 AAAACAAAAGAAAGAATAG
1 AAAACAAAAGAAAGAAAAG
910329 AAAA-AAAAGAAAGAAAAG
1 AAAACAAAAGAAAGAAAAG
910347 AAA
1 AAA
910350 CAGAATAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.80, C:0.03, G:0.15, T:0.03
Consensus pattern (19 bp):
AAAACAAAAGAAAGAAAAG
Found at i:911278 original size:46 final size:44
Alignment explanation
Indices: 911218--911332 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
911208 ACAGGACAGA
* *
911218 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
911264 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
911308 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
911333 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:911313 original size:44 final size:45
Alignment explanation
Indices: 911218--911351 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
911208 ACAGGACAGA
* *
911218 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
911264 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
911308 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
911352 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:915922 original size:14 final size:14
Alignment explanation
Indices: 915903--915932 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
915893 AACACTTATA
915903 ATTGAGGTAAAAGT
1 ATTGAGGTAAAAGT
915917 ATTGAGGTAAAAGT
1 ATTGAGGTAAAAGT
915931 AT
1 AT
915933 CATGCGGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.27, T:0.30
Consensus pattern (14 bp):
ATTGAGGTAAAAGT
Found at i:934868 original size:25 final size:23
Alignment explanation
Indices: 934806--934869 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 23
934796 TCTTTCAATT
*
934806 TAATTTATTTAAAT-TTGAAAAA
1 TAATTTTTTTAAATATTGAAAAA
*
934828 T-ATCTTTTTT-ATTATTGATAAAAA
1 TAAT-TTTTTTAAATATTG--AAAAA
934852 TAATTTTTTTAAATATTG
1 TAATTTTTTTAAATATTG
934870 TTTTTGTTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
21 4 0.12
22 9 0.27
24 12 0.36
25 8 0.24
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.53
Consensus pattern (23 bp):
TAATTTTTTTAAATATTGAAAAA
Found at i:952157 original size:18 final size:19
Alignment explanation
Indices: 952113--952158 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
952103 ACTTTTTAAA
952113 AATATTATTATATTAATAT
1 AATATTATTATATTAATAT
* * *
952132 AA-AATATTATATT-TTTT
1 AATATTATTATATTAATAT
952149 AATATTATTA
1 AATATTATTA
952159 AACATACATA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
17 4 0.18
18 16 0.73
19 2 0.09
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
AATATTATTATATTAATAT
Found at i:952279 original size:15 final size:14
Alignment explanation
Indices: 952254--952293 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
952244 TTTTAACTTT
952254 ATTTT-AATAATAA
1 ATTTTAAATAATAA
952267 ATTTTAAAATAAT-A
1 ATTTT-AAATAATAA
952281 ATTTTAAATAATA
1 ATTTTAAATAATA
952294 TTCTTCACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 12 0.50
14 6 0.25
15 6 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAAATAATAA
Found at i:952667 original size:25 final size:26
Alignment explanation
Indices: 952634--952684 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
952624 TTCAATTTTT
* *
952634 TATATTATTTTTTTGTTTTT-TTAAA
1 TATAATATTTTTTTATTTTTATTAAA
952659 TATAATATTTTTTTATTTTTATTAAA
1 TATAATATTTTTTTATTTTTATTAAA
952685 AATATTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (26 bp):
TATAATATTTTTTTATTTTTATTAAA
Found at i:953283 original size:33 final size:33
Alignment explanation
Indices: 953246--953342 Score: 109
Period size: 33 Copynumber: 3.1 Consensus size: 33
953236 GTTTTTTATA
953246 ATTATTTTAAAATTAATTTGTTAGTAATTTAGG
1 ATTATTTTAAAATTAATTTGTTAGTAATTTAGG
* *
953279 ATTATGTTAAAATT-TTTTG-T-GT--TTGTA--
1 ATTATTTTAAAATTAATTTGTTAGTAATT-TAGG
*
953306 ATTATTTTAAAATTAATTTATTAGTAATTTAGG
1 ATTATTTTAAAATTAATTTGTTAGTAATTTAGG
953339 ATTA
1 ATTA
953343 AGTTATAAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
27 13 0.25
28 5 0.10
29 3 0.06
30 4 0.08
31 3 0.06
32 6 0.12
33 17 0.33
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (33 bp):
ATTATTTTAAAATTAATTTGTTAGTAATTTAGG
Found at i:953322 original size:60 final size:61
Alignment explanation
Indices: 953230--953363 Score: 200
Period size: 60 Copynumber: 2.2 Consensus size: 61
953220 TGAATGTAAT
* * *
953230 TTTTTTGTTTTTTATAATTATTTTAAAATTAATTTGTTAGTAATTTAGGATTATGTTA-AAA
1 TTTTTTG-TGTTTATAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAA
*
953291 TTTTTTGTGTTTGTAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAA
1 TTTTTTGTGTTTATAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAA
*
953352 -TTGTTGTGTTTA
1 TTTTTTGTGTTTA
953364 GTTTAGTATT
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
60 56 0.85
61 10 0.15
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.57
Consensus pattern (61 bp):
TTTTTTGTGTTTATAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAA
Found at i:953686 original size:27 final size:27
Alignment explanation
Indices: 953643--953695 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
953633 CCCACCATTT
953643 GCGCCTCAGAGATAGGCTCGACTAGTC
1 GCGCCTCAGAGATAGGCTCGACTAGTC
953670 GCGCCTCAGAGGA-AGGCTCGACTAGT
1 GCGCCTCAGA-GATAGGCTCGACTAGT
953696 AACGCCCCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 23 0.92
28 2 0.08
ACGTcount: A:0.23, C:0.28, G:0.32, T:0.17
Consensus pattern (27 bp):
GCGCCTCAGAGATAGGCTCGACTAGTC
Found at i:953701 original size:27 final size:27
Alignment explanation
Indices: 953644--953701 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
953634 CCACCATTTG
**
953644 CGCCTCAGAGATAGGCTCGACTAGTCG
1 CGCCTCAGAGATAGGCTCGACTAGTAA
953671 CGCCTCAGAGGA-AGGCTCGACTAGTAA
1 CGCCTCAGA-GATAGGCTCGACTAGTAA
953698 CGCC
1 CGCC
953702 CCTAACCCGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 26 0.93
28 2 0.07
ACGTcount: A:0.24, C:0.31, G:0.29, T:0.16
Consensus pattern (27 bp):
CGCCTCAGAGATAGGCTCGACTAGTAA
Found at i:956225 original size:18 final size:19
Alignment explanation
Indices: 956202--956240 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
956192 ATATATAGAT
956202 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
956220 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
956239 AT
1 AT
956241 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:960196 original size:29 final size:30
Alignment explanation
Indices: 960133--960206 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 30
960123 AATAATGCTT
* * * *
960133 ATAGGTCGATTTTGAAATTTATTTAGGTAT
1 ATAGGCCGATTTTGAAAATTATTTAGGGAA
*
960163 TTAGGCCGATTTT-AAAATTATTTAGGGAA
1 ATAGGCCGATTTTGAAAATTATTTAGGGAA
*
960192 ATAGGCTGATTTTGA
1 ATAGGCCGATTTTGA
960207 GGGAAAGCTA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 24 0.67
30 12 0.33
ACGTcount: A:0.31, C:0.05, G:0.22, T:0.42
Consensus pattern (30 bp):
ATAGGCCGATTTTGAAAATTATTTAGGGAA
Found at i:961024 original size:23 final size:21
Alignment explanation
Indices: 960965--961030 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
960955 TTCAAATATT
*
960965 TTTATATGTGAAATATTTTAA
1 TTTATATGTGAAATATATTAA
* * *
960986 TTAATTATTTGAAATATCATTATG
1 TTTA-TATGTGAAATAT-ATTA-A
*
961010 TTTATATGTGAAATATTTTAA
1 TTTATATGTGAAATATATTAA
961031 ATACACGTAT
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
21 3 0.09
22 14 0.41
23 14 0.41
24 3 0.09
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.52
Consensus pattern (21 bp):
TTTATATGTGAAATATATTAA
Found at i:961695 original size:5 final size:5
Alignment explanation
Indices: 961685--961721 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
961675 AATTATTTGA
*
961685 AAAAT AAAAT AAAAT AAAAT TAAA- AAAAT AAAA- AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
961722 CTCTAAATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
4 7 0.24
5 22 0.76
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:976044 original size:17 final size:16
Alignment explanation
Indices: 976014--976060 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
976004 AACATGTCAA
* *
976014 TTTGTGTGTATTTTAT
1 TTTGTTTGTTTTTTAT
976030 GTTTGTTTGTTTTTTAT
1 -TTTGTTTGTTTTTTAT
976047 TTT-TTTGATTTTTT
1 TTTGTTTG-TTTTTT
976061 TTGAATGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 4 0.15
16 9 0.33
17 14 0.52
ACGTcount: A:0.09, C:0.00, G:0.15, T:0.77
Consensus pattern (16 bp):
TTTGTTTGTTTTTTAT
Found at i:976053 original size:15 final size:18
Alignment explanation
Indices: 976024--976060 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
976014 TTTGTGTGTA
976024 TTTTATGTTTGTTTG-TT
1 TTTTATGTTTGTTTGATT
976041 TTTTAT-TTT-TTTGATT
1 TTTTATGTTTGTTTGATT
976057 TTTT
1 TTTT
976061 TTGAATGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 4 0.21
16 9 0.47
17 6 0.32
ACGTcount: A:0.08, C:0.00, G:0.11, T:0.81
Consensus pattern (18 bp):
TTTTATGTTTGTTTGATT
Found at i:982131 original size:12 final size:12
Alignment explanation
Indices: 982116--982160 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
982106 TAAAAATGGC
*
982116 ATTAAAATTAGT
1 ATTAAAATTAAT
982128 ATTAAAATTAAT
1 ATTAAAATTAAT
*
982140 AATAAAATTTAAT
1 ATTAAAA-TTAAT
982153 ATCTAAAA
1 AT-TAAAA
982161 ATATCTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 17 0.61
13 6 0.21
14 5 0.18
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (12 bp):
ATTAAAATTAAT
Found at i:983577 original size:28 final size:29
Alignment explanation
Indices: 983537--983613 Score: 111
Period size: 28 Copynumber: 2.7 Consensus size: 29
983527 GAATTAACCG
*
983537 AAAAAGTTCGGTTCGGTTA-TTTTTTTGA
1 AAAAAATTCGGTTCGGTTATTTTTTTTGA
*
983565 AAAAAATTTGGTTCGGTTATTTTTTTTGA
1 AAAAAATTCGGTTCGGTTATTTTTTTTGA
*
983594 AAACAAATTCAGTTCGGTTA
1 AAA-AAATTCGGTTCGGTTA
983614 ACGGTTAAGG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
28 17 0.40
29 12 0.28
30 14 0.33
ACGTcount: A:0.30, C:0.08, G:0.18, T:0.44
Consensus pattern (29 bp):
AAAAAATTCGGTTCGGTTATTTTTTTTGA
Found at i:983837 original size:19 final size:20
Alignment explanation
Indices: 983809--983848 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
983799 TTAATCCATT
*
983809 TTTAATATTTT-CAAAAAAA
1 TTTAACATTTTACAAAAAAA
983828 TTTAACATTTTAACAAAAAAA
1 TTTAACATTTT-ACAAAAAAA
983849 ATTATTAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
21 8 0.44
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (20 bp):
TTTAACATTTTACAAAAAAA
Found at i:990434 original size:15 final size:15
Alignment explanation
Indices: 990416--990450 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
990406 ATATCGACTC
990416 AAAAAAGAAGAAAAG
1 AAAAAAGAAGAAAAG
*
990431 AAAAAATAAGAAAAG
1 AAAAAAGAAGAAAAG
990446 AAAAA
1 AAAAA
990451 CCCTTTCCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (15 bp):
AAAAAAGAAGAAAAG
Found at i:1001876 original size:13 final size:14
Alignment explanation
Indices: 1001849--1001882 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
1001839 CTCCCTCTTG
1001849 TTTTCTCCCCTTCTC
1 TTTTC-CCCCTTCTC
1001864 TTTTCCCCC-TCTC
1 TTTTCCCCCTTCTC
1001877 TTTTCC
1 TTTTCC
1001883 ATTTTAAGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.53
14 4 0.21
15 5 0.26
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (14 bp):
TTTTCCCCCTTCTC
Found at i:1004295 original size:11 final size:11
Alignment explanation
Indices: 1004279--1004303 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1004269 TGTCTTTTTT
1004279 AGTCAAATGAG
1 AGTCAAATGAG
1004290 AGTCAAATGAG
1 AGTCAAATGAG
1004301 AGT
1 AGT
1004304 TGCAATTATT
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:0.44, C:0.08, G:0.28, T:0.20
Consensus pattern (11 bp):
AGTCAAATGAG
Found at i:1018049 original size:13 final size:13
Alignment explanation
Indices: 1018031--1018093 Score: 85
Period size: 13 Copynumber: 4.9 Consensus size: 13
1018021 TTTGGTAATT
1018031 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
1018044 CTTTTG-AAAGTG
1 CTTTTGAAAAGTG
*
1018056 C-TGTGAAAAAGTG
1 CTTTTG-AAAAGTG
1018069 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
*
1018082 TTTTTGAAAAGT
1 CTTTTGAAAAGT
1018094 TTAGTTTAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
11 3 0.07
12 7 0.16
13 31 0.70
14 3 0.07
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.38
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Found at i:1019270 original size:22 final size:22
Alignment explanation
Indices: 1019242--1019294 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
1019232 TAATACCAAA
1019242 CCCCATACCCCCACTACAACAG
1 CCCCATACCCCCACTACAACAG
*
1019264 CCCCATACCTCCACTACAACAG
1 CCCCATACCCCCACTACAACAG
*
1019286 TCCCATACC
1 CCCCATACC
1019295 GTCTGACACC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.30, C:0.53, G:0.04, T:0.13
Consensus pattern (22 bp):
CCCCATACCCCCACTACAACAG
Found at i:1019602 original size:26 final size:25
Alignment explanation
Indices: 1019565--1019621 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 25
1019555 GTGTTCTTGG
*
1019565 TTCTTTTTTATTTT-TATTTAGTTTTT
1 TTCTTTTGTATTTTCT-TTTA-TTTTT
1019591 TTCTTTTGTATTTTCTTTTATTTTT
1 TTCTTTTGTATTTTCTTTTATTTTT
1019616 TTCTTT
1 TTCTTT
1019622 CTATTCGCGA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 11 0.38
26 17 0.59
27 1 0.03
ACGTcount: A:0.09, C:0.07, G:0.04, T:0.81
Consensus pattern (25 bp):
TTCTTTTGTATTTTCTTTTATTTTT
Found at i:1019604 original size:13 final size:13
Alignment explanation
Indices: 1019565--1019621 Score: 53
Period size: 13 Copynumber: 4.5 Consensus size: 13
1019555 GTGTTCTTGG
*
1019565 TTCTTTTTTATTT
1 TTCTTTTGTATTT
* * *
1019578 TTATTTAGTTTTT
1 TTCTTTTGTATTT
1019591 TTCTTTTGTA-TT
1 TTCTTTTGTATTT
* *
1019603 TTCTTTTATTTTT
1 TTCTTTTGTATTT
1019616 TTCTTT
1 TTCTTT
1019622 CTATTCGCGA
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
12 10 0.29
13 24 0.71
ACGTcount: A:0.09, C:0.07, G:0.04, T:0.81
Consensus pattern (13 bp):
TTCTTTTGTATTT
Found at i:1019604 original size:25 final size:26
Alignment explanation
Indices: 1019565--1019621 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
1019555 GTGTTCTTGG
*
1019565 TTCTTTTTTATTTTT-ATTTAGTTTTT
1 TTCTTTTGTATTTTTCATTTA-TTTTT
*
1019591 TTCTTTTGTA-TTTTCTTTTATTTTT
1 TTCTTTTGTATTTTTCATTTATTTTT
1019616 TTCTTT
1 TTCTTT
1019622 CTATTCGCGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 15 0.54
26 13 0.46
ACGTcount: A:0.09, C:0.07, G:0.04, T:0.81
Consensus pattern (26 bp):
TTCTTTTGTATTTTTCATTTATTTTT
Found at i:1019617 original size:20 final size:18
Alignment explanation
Indices: 1019565--1019617 Score: 52
Period size: 20 Copynumber: 2.8 Consensus size: 18
1019555 GTGTTCTTGG
*
1019565 TTCTTTTTTATTTTTATT
1 TTCTTTTTTTTTTTTATT
**
1019583 TAGTTTTTTTCTTTTGTATT
1 TTCTTTTTTT-TTTT-TATT
*
1019603 TTCTTTTATTTTTTT
1 TTCTTTTTTTTTTTT
1019618 CTTTCTATTC
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
18 8 0.30
19 8 0.30
20 11 0.41
ACGTcount: A:0.09, C:0.06, G:0.04, T:0.81
Consensus pattern (18 bp):
TTCTTTTTTTTTTTTATT
Found at i:1020552 original size:3 final size:3
Alignment explanation
Indices: 1020530--1020593 Score: 65
Period size: 3 Copynumber: 20.3 Consensus size: 3
1020520 TTTTTATTTA
* * * *
1020530 TAT TAT TGT TAG TAT CAT TAT TAT TAT TAT CTCCAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -T--AT TAT TAT TAT TAT
1020578 TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT T
1020594 CTCTTGTTAT
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
3 46 0.92
4 1 0.02
5 1 0.02
6 2 0.04
ACGTcount: A:0.30, C:0.08, G:0.03, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:1020955 original size:15 final size:15
Alignment explanation
Indices: 1020935--1020965 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1020925 TATTATTTTC
1020935 TATTTATTACTATTA
1 TATTTATTACTATTA
1020950 TATTTATTACTATTA
1 TATTTATTACTATTA
1020965 T
1 T
1020966 TAATATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTTATTACTATTA
Found at i:1021063 original size:3 final size:3
Alignment explanation
Indices: 1021048--1021101 Score: 56
Period size: 3 Copynumber: 18.3 Consensus size: 3
1021038 CACACTTAGC
* * * * *
1021048 TAT TAT TAC TAT TAT TAT TTT TAC TAT TAT AAT TAT TAT TAA TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1021095 TAT TAT T
1 TAT TAT T
1021102 CTCTTACATT
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1023098 original size:62 final size:62
Alignment explanation
Indices: 1023032--1023215 Score: 323
Period size: 62 Copynumber: 3.0 Consensus size: 62
1023022 CACGTATCTC
*
1023032 TTCATTCATTAACATTACATTTCATTACATACAATAAATTTCCTAAAATCCAAAAATACGCG
1 TTCATGCATTAACATTACATTTCATTACATACAATAAATTTCCTAAAATCCAAAAATACGCG
*
1023094 TTCATGCATTAACATTACATTTTATTACATACAATAAATTTCCTAAAATCCAAAAATACGCG
1 TTCATGCATTAACATTACATTTCATTACATACAATAAATTTCCTAAAATCCAAAAATACGCG
* * *
1023156 TTCATGCATCAACATTACATTTCATTGCATACAATAAATTTCCTAAAATCCAAAAGTACG
1 TTCATGCATTAACATTACATTTCATTACATACAATAAATTTCCTAAAATCCAAAAATACG
1023216 TCGAGTTTAG
Statistics
Matches: 116, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 116 1.00
ACGTcount: A:0.41, C:0.21, G:0.05, T:0.33
Consensus pattern (62 bp):
TTCATGCATTAACATTACATTTCATTACATACAATAAATTTCCTAAAATCCAAAAATACGCG
Found at i:1026326 original size:86 final size:87
Alignment explanation
Indices: 1026181--1026358 Score: 286
Period size: 86 Copynumber: 2.1 Consensus size: 87
1026171 AGTAAAAATT
*
1026181 GAAGACAAACCTTGCCACTCTCGTTTATAGTAGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCT
1 GAAGACAAACCTTGCCACTCTCGTTTATAGCAGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCT
1026246 GCACTGA-CAGCGAAGCAGATC
66 GCACTGAGCAGCGAAGCAGATC
* * *
1026267 GAAGACAAACCTTGCCTCTCTCGTTTGTAGCAGAGCTGGTTGAAGATATCAGATCTTGCCTTCCT
1 GAAGACAAACCTTGCCACTCTCGTTTATAGCAGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCT
* * *
1026332 GTATTTAGCAGCGAAGCAGATC
66 GCACTGAGCAGCGAAGCAGATC
1026354 GAAGA
1 GAAGA
1026359 TGGCAGATTT
Statistics
Matches: 84, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
86 65 0.77
87 19 0.23
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.26
Consensus pattern (87 bp):
GAAGACAAACCTTGCCACTCTCGTTTATAGCAGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCT
GCACTGAGCAGCGAAGCAGATC
Found at i:1026475 original size:46 final size:46
Alignment explanation
Indices: 1026417--1027007 Score: 250
Period size: 46 Copynumber: 13.2 Consensus size: 46
1026407 ACTCTATCTC
*
1026417 CCTGTATCTGGCAGTGGAATAGATTGAAGATTGCAGATCTTGCCTT
1 CCTGTATCTGGCAGTGGAATAGATTGAAGATTGCAGATCTTACCTT
* * * * * * *
1026463 CCTGTATTTGGCAG-CGAAGCAGATCGAAGATGGCAGATTTTACCTC
1 CCTGTATCTGGCAGTGGAA-TAGATTGAAGATTGCAGATCTTACCTT
* * * ** * * * *
1026509 CCTG-A-CT-ACAGTGGAGTACATTGAAG-CCG-ATAACTCTATCTC
1 CCTGTATCTGGCAGTGGAATAGATTGAAGATTGCAGATCT-TACCTT
* * *
1026551 CCTGTATCTGGCAGTGGAATAGATTGAATATTGCAGATATTGCCTT
1 CCTGTATCTGGCAGTGGAATAGATTGAAGATTGCAGATCTTACCTT
* * * * *
1026597 CCTGTAT-TCGGCAG-CGAAGCAGATCGAAGATGGCAGATTTTACC-T
1 CCTGTATCT-GGCAGTGGAA-TAGATTGAAGATTGCAGATCTTACCTT
* * * * * *
1026642 CACTG-A-CT-ACAGTGGAGTACATTGAAG---CCA-ATAACTCTATCTC
1 C-CTGTATCTGGCAGTGGAATAGATTGAAGATTGCAGAT--CT-TACCTT
* *
1026685 CCTGTATCTAGCAGTGGAATAGATTGAAGATTGCAGATCTTGCCTT
1 CCTGTATCTGGCAGTGGAATAGATTGAAGATTGCAGATCTTACCTT
* * * * * * *
1026731 CCTGTATTTGGCAG-CGAAGCAGATCGAAGATGGCAGATTTTACCTC
1 CCTGTATCTGGCAGTGGAA-TAGATTGAAGATTGCAGATCTTACCTT
* * * ** * * *
1026777 CCTG-A-CT-ACAGTGGAGTACATTGAAG-CCG-ATAACTCTATC-T
1 CCTGTATCTGGCAGTGGAATAGATTGAAGATTGCAGATCT-TACCTT
*
1026818 CACTGTATCTGGCAGTGGAATAGATTGAAGATTGCAGATCTTGCCTT
1 C-CTGTATCTGGCAGTGGAATAGATTGAAGATTGCAGATCTTACCTT
* * * * * *
1026865 CCTGTAT-TAGGCAG-CGAAGCAGATCGAAGATGGCAGATTTTACCTC
1 CCTGTATCT-GGCAGTGGAA-TAGATTGAAGATTGCAGATCTTACCTT
* * * ** * * * *
1026911 CCTGTGA-CT-ACAGTGGAGTACATTGAAG-CCG-ATAACTCTATCTC
1 CCTGT-ATCTGGCAGTGGAATAGATTGAAGATTGCAGATCT-TACCTT
*
1026955 CCTGTATCTGGCAGTGGAATAGATTGAAGATTGCAGATCTTGCCTT
1 CCTGTATCTGGCAGTGGAATAGATTGAAGATTGCAGATCTTACCTT
*
1027001 CTTGTAT
1 CCTGTAT
1027008 TAGGTAGGAA
Statistics
Matches: 382, Mismatches: 119, Indels: 88
0.65 0.20 0.15
Matches are distributed among these distances:
39 2 0.01
40 2 0.01
41 8 0.02
42 23 0.06
43 38 0.10
44 27 0.07
45 93 0.24
46 168 0.44
47 17 0.04
48 2 0.01
49 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.29
Consensus pattern (46 bp):
CCTGTATCTGGCAGTGGAATAGATTGAAGATTGCAGATCTTACCTT
Found at i:1026546 original size:134 final size:134
Alignment explanation
Indices: 1026306--1027008 Score: 1273
Period size: 134 Copynumber: 5.2 Consensus size: 134
1026296 GCAGAGCTGG
*
1026306 TTGAAGATAT-CAGATCTTGCCTTCCTGTATTTAGCAGCGAAGCAGATCGAAGATGGCAGATTTT
1 TTGAAGAT-TGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTT
*
1026370 ACCTCCCTGACTACAGTGGAGTACATTGAGGCCGATAACTCTATCTCCCTGTATCTGGCAGTGGA
65 ACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATCTGGCAGTGGA
1026435 ATAGA
130 ATAGA
1026440 TTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTA
1 TTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTA
1026505 CCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATCTGGCAGTGGAA
66 CCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATCTGGCAGTGGAA
1026570 TAGA
131 TAGA
* * *
1026574 TTGAATATTGCAGATATTGCCTTCCTGTATTCGGCAGCGAAGCAGATCGAAGATGGCAGATTTTA
1 TTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTA
* * *
1026639 CCTCACTGACTACAGTGGAGTACATTGAAGCCAATAACTCTATCTCCCTGTATCTAGCAGTGGAA
66 CCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATCTGGCAGTGGAA
1026704 TAGA
131 TAGA
1026708 TTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTA
1 TTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTA
*
1026773 CCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCACTGTATCTGGCAGTGGAA
66 CCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATCTGGCAGTGGAA
1026838 TAGA
131 TAGA
*
1026842 TTGAAGATTGCAGATCTTGCCTTCCTGTATTAGGCAGCGAAGCAGATCGAAGATGGCAGATTTTA
1 TTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTA
1026907 CCTCCCTGTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATCTGGCAGTGG
66 CCTCCC--TGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATCTGGCAGTGG
1026972 AATAGA
129 AATAGA
*
1026978 TTGAAGATTGCAGATCTTGCCTTCTTGTATT
1 TTGAAGATTGCAGATCTTGCCTTCCTGTATT
1027009 AGGTAGGAAG
Statistics
Matches: 548, Mismatches: 18, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
133 1 0.00
134 455 0.83
136 92 0.17
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (134 bp):
TTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTA
CCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATCTGGCAGTGGAA
TAGA
Found at i:1027603 original size:229 final size:229
Alignment explanation
Indices: 1027191--1027628 Score: 714
Period size: 229 Copynumber: 1.9 Consensus size: 229
1027181 ATATTGATGT
* *
1027191 GAAATAGATCGAAGATAGCAGGTCCTGCCTTCCTATATTGGTAGGAAGTGGATTGAAAAACAGAC
1 GAAATAGATCGAAGATAGCAGATCCTGCCTCCCTATATTGGTAGGAAGTGGATTGAAAAACAGAC
* * * * *
1027256 TCTATCTCCCTGTATTTAGCAGTGGAATAGATTGCAGGTCGAAGACGGCAGACTTTACCTCCCTG
66 TCTATCTCCCTGTATTTAGCAGTAGAACAGATTGAAGATCAAAGACGGCAGACTTTACCTCCCTG
* * **
1027321 ACTACAGTGGAGTACGTTGAAGCCGATAACTCTATCTCCCTGTATTGGGCAGTGGAATAGATTGA
131 ACTACAATGGAGTACATTGAAGCCGATAACTCTATCTCCCTACATTGGGCAGTGGAATAGATTGA
1027386 AGATTGCAGATCTTGCCTTCCTGTATTCGGCAAC
196 AGATTGCAGATCTTGCCTTCCTGTATTCGGCAAC
1027420 GAAATAGATCGAAGATAGCAGATCCTGCCTCCCTATATTGGTAGGAAGTGGATTGAAAAACAGAC
1 GAAATAGATCGAAGATAGCAGATCCTGCCTCCCTATATTGGTAGGAAGTGGATTGAAAAACAGAC
* * *
1027485 TCTATCTCCCTGTATTTGGCAGTAGAACAGATTGAAGATCAAAGATGGCAGATTTTACCTCCCTG
66 TCTATCTCCCTGTATTTAGCAGTAGAACAGATTGAAGATCAAAGACGGCAGACTTTACCTCCCTG
* *
1027550 ACTACAATGGAGTACATTGAAGCCGATGACTCTATCTCCCTACATTTGGCAGTGGAATAGATTGA
131 ACTACAATGGAGTACATTGAAGCCGATAACTCTATCTCCCTACATTGGGCAGTGGAATAGATTGA
* *
1027615 AGATTTCAGGTCTT
196 AGATTGCAGATCTT
1027629 ATCTCCCTAA
Statistics
Matches: 191, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
229 191 1.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (229 bp):
GAAATAGATCGAAGATAGCAGATCCTGCCTCCCTATATTGGTAGGAAGTGGATTGAAAAACAGAC
TCTATCTCCCTGTATTTAGCAGTAGAACAGATTGAAGATCAAAGACGGCAGACTTTACCTCCCTG
ACTACAATGGAGTACATTGAAGCCGATAACTCTATCTCCCTACATTGGGCAGTGGAATAGATTGA
AGATTGCAGATCTTGCCTTCCTGTATTCGGCAAC
Found at i:1027990 original size:22 final size:22
Alignment explanation
Indices: 1027962--1028014 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
1027952 TAATACCAAA
1027962 CCCCATACCCCCACTACAACAG
1 CCCCATACCCCCACTACAACAG
*
1027984 CCCCATACCTCCACTACAACAG
1 CCCCATACCCCCACTACAACAG
*
1028006 TCCCATACC
1 CCCCATACC
1028015 GTCTGACACC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.30, C:0.53, G:0.04, T:0.13
Consensus pattern (22 bp):
CCCCATACCCCCACTACAACAG
Found at i:1028322 original size:26 final size:25
Alignment explanation
Indices: 1028285--1028341 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 25
1028275 GTGTTCTTGG
*
1028285 TTCTTTTTTATTTT-TATTTAGTTTTT
1 TTCTTTTGTATTTTCT-TTTA-TTTTT
1028311 TTCTTTTGTATTTTCTTTTATTTTT
1 TTCTTTTGTATTTTCTTTTATTTTT
1028336 TTCTTT
1 TTCTTT
1028342 CTCTTCGCGA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 11 0.38
26 17 0.59
27 1 0.03
ACGTcount: A:0.09, C:0.07, G:0.04, T:0.81
Consensus pattern (25 bp):
TTCTTTTGTATTTTCTTTTATTTTT
Found at i:1028324 original size:13 final size:13
Alignment explanation
Indices: 1028285--1028341 Score: 53
Period size: 13 Copynumber: 4.5 Consensus size: 13
1028275 GTGTTCTTGG
*
1028285 TTCTTTTTTATTT
1 TTCTTTTGTATTT
* * *
1028298 TTATTTAGTTTTT
1 TTCTTTTGTATTT
1028311 TTCTTTTGTA-TT
1 TTCTTTTGTATTT
* *
1028323 TTCTTTTATTTTT
1 TTCTTTTGTATTT
1028336 TTCTTT
1 TTCTTT
1028342 CTCTTCGCGA
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
12 10 0.29
13 24 0.71
ACGTcount: A:0.09, C:0.07, G:0.04, T:0.81
Consensus pattern (13 bp):
TTCTTTTGTATTT
Found at i:1028324 original size:25 final size:26
Alignment explanation
Indices: 1028285--1028341 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
1028275 GTGTTCTTGG
*
1028285 TTCTTTTTTATTTTT-ATTTAGTTTTT
1 TTCTTTTGTATTTTTCATTTA-TTTTT
*
1028311 TTCTTTTGTA-TTTTCTTTTATTTTT
1 TTCTTTTGTATTTTTCATTTATTTTT
1028336 TTCTTT
1 TTCTTT
1028342 CTCTTCGCGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 15 0.54
26 13 0.46
ACGTcount: A:0.09, C:0.07, G:0.04, T:0.81
Consensus pattern (26 bp):
TTCTTTTGTATTTTTCATTTATTTTT
Found at i:1028337 original size:20 final size:18
Alignment explanation
Indices: 1028285--1028337 Score: 52
Period size: 20 Copynumber: 2.8 Consensus size: 18
1028275 GTGTTCTTGG
*
1028285 TTCTTTTTTATTTTTATT
1 TTCTTTTTTTTTTTTATT
**
1028303 TAGTTTTTTTCTTTTGTATT
1 TTCTTTTTTT-TTTT-TATT
*
1028323 TTCTTTTATTTTTTT
1 TTCTTTTTTTTTTTT
1028338 CTTTCTCTTC
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
18 8 0.30
19 8 0.30
20 11 0.41
ACGTcount: A:0.09, C:0.06, G:0.04, T:0.81
Consensus pattern (18 bp):
TTCTTTTTTTTTTTTATT
Found at i:1029277 original size:3 final size:3
Alignment explanation
Indices: 1029255--1029327 Score: 83
Period size: 3 Copynumber: 23.3 Consensus size: 3
1029245 TTTTTATTTA
* * * *
1029255 TAT TAT TGT TAG TAT CAT TAT TAT TAT TAT TAT CTCCAT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -T--AT TAT TAT TAT
1029303 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
1029328 CTCTTGTTAT
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
3 55 0.93
4 1 0.02
5 1 0.02
6 2 0.03
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:1029366 original size:20 final size:19
Alignment explanation
Indices: 1029329--1029380 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
1029319 ATTATTATTC
1029329 TCTTGTTATA-T-TACTAT
1 TCTTGTTATATTATACTAT
1029346 TCTTGTTATATTATCACTAT
1 TCTTGTTATATTAT-ACTAT
* *
1029366 TTTTCTTACTATTAT
1 TCTTGTTA-TATTAT
1029381 TATTACTACA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 10 0.34
18 1 0.03
19 1 0.03
20 11 0.38
21 6 0.21
ACGTcount: A:0.23, C:0.13, G:0.04, T:0.60
Consensus pattern (19 bp):
TCTTGTTATATTATACTAT
Found at i:1029698 original size:15 final size:15
Alignment explanation
Indices: 1029678--1029708 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1029668 TATTATTTTC
1029678 TATTTATTACTATTA
1 TATTTATTACTATTA
1029693 TATTTATTACTATTA
1 TATTTATTACTATTA
1029708 T
1 T
1029709 TAATATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTTATTACTATTA
Found at i:1029808 original size:15 final size:15
Alignment explanation
Indices: 1029790--1029827 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1029780 CACACTTAGC
1029790 TATTATTACTATTAT
1 TATTATTACTATTAT
*
1029805 TATTTTTACTATTAT
1 TATTATTACTATTAT
*
1029820 AATTATTA
1 TATTATTA
1029828 TTAATCTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTATTACTATTAT
Done.