Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 75 of 214
Found at i:21349336 original size:20 final size:20
Alignment explanation
Indices: 21349313--21349366 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
21349303 AGTTTTTCCC
*
21349313 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
21349333 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
21349353 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
21349367 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:21349348 original size:30 final size:30
Alignment explanation
Indices: 21349313--21349386 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
21349303 AGTTTTTCCC
21349313 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
21349343 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
21349373 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
21349387 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:21349376 original size:20 final size:20
Alignment explanation
Indices: 21349313--21349377 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
21349303 AGTTTTTCCC
* * * *
21349313 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
21349333 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
21349352 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
21349373 AGCTC
1 AGCTC
21349378 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:21351009 original size:12 final size:13
Alignment explanation
Indices: 21350992--21351066 Score: 62
Period size: 13 Copynumber: 5.5 Consensus size: 13
21350982 TTGGAGTAAC
21350992 AAAAAAAA-TCAA
1 AAAAAAAATTCAA
21351004 AAAAAAAATTCGAA
1 AAAAAAAATTC-AA
* *
21351018 AAAAAATTGATTGAAA
1 AAAAAA--AATT-CAA
21351034 AAAAAAAATTCAA
1 AAAAAAAATTCAA
* * *
21351047 AAAAATAAGTGAA
1 AAAAAAAATTCAA
21351060 AAAAAAA
1 AAAAAAA
21351067 TCGAGCAAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
12 8 0.16
13 20 0.40
14 11 0.22
16 11 0.22
ACGTcount: A:0.75, C:0.04, G:0.07, T:0.15
Consensus pattern (13 bp):
AAAAAAAATTCAA
Found at i:21351011 original size:14 final size:14
Alignment explanation
Indices: 21350992--21351051 Score: 61
Period size: 15 Copynumber: 4.3 Consensus size: 14
21350982 TTGGAGTAAC
21350992 AAAAAAAA-TC-AA
1 AAAAAAAATTCAAA
21351004 AAAAAAAATTCGAAA
1 AAAAAAAATTC-AAA
** *
21351019 AAAAATTGATTGAAA
1 AAAAA-AAATTCAAA
21351034 AAAAAAAATTCAAA
1 AAAAAAAATTCAAA
21351048 AAAA
1 AAAA
21351052 TAAGTGAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
12 8 0.21
13 2 0.05
14 10 0.26
15 15 0.39
16 3 0.08
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.15
Consensus pattern (14 bp):
AAAAAAAATTCAAA
Found at i:21351065 original size:30 final size:30
Alignment explanation
Indices: 21351002--21351066 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
21350992 AAAAAAAATC
* * **
21351002 AAAAAAAAAATTCGAAAAAAAATTGATTGA
1 AAAAAAAAAATTCAAAAAAAAAGTGATAAA
21351032 AAAAAAAAAATTCAAAAAAATAAGTGA-AAA
1 AAAAAAAAAATTCAAAAAAA-AAGTGATAAA
21351062 AAAAA
1 AAAAA
21351067 TCGAGCAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.74, C:0.03, G:0.08, T:0.15
Consensus pattern (30 bp):
AAAAAAAAAATTCAAAAAAAAAGTGATAAA
Found at i:21351077 original size:29 final size:28
Alignment explanation
Indices: 21351044--21351119 Score: 80
Period size: 30 Copynumber: 2.6 Consensus size: 28
21351034 AAAAAAAATT
* *
21351044 CAAAAAAATAAGTGAAAAAAAAATCGAG
1 CAAAAAAAAAAGTGAAAAAAAAATCAAG
* *
21351072 CAAAAAAAAAGGGTGACCAAAAAAATCAAG
1 CAAAAAAAAA-AGTGA-AAAAAAAATCAAG
**
21351102 TTAAAAAAAAAGTGAAAA
1 CAAAAAAAAAAGTGAAAA
21351120 GTCTTGCGAG
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
28 11 0.29
29 8 0.21
30 19 0.50
ACGTcount: A:0.67, C:0.08, G:0.14, T:0.11
Consensus pattern (28 bp):
CAAAAAAAAAAGTGAAAAAAAAATCAAG
Found at i:21351078 original size:43 final size:42
Alignment explanation
Indices: 21350992--21351081 Score: 103
Period size: 43 Copynumber: 2.1 Consensus size: 42
21350982 TTGGAGTAAC
* *
21350992 AAAAAAAATCAAAAAAAAAATTCGAAAAAAAATTGATTG-AAAA
1 AAAAAAAATCAAAAAAAAAAGTCGAAAAAAAATCGA--GCAAAA
* *
21351035 AAAAAAATTCAAAAAAATAAGT-GAAAAAAAAATCGAGCAAAA
1 AAAAAAAATCAAAAAAAAAAGTCG-AAAAAAAATCGAGCAAAA
21351077 AAAAA
1 AAAAA
21351082 GGGTGACCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
41 1 0.02
42 10 0.24
43 30 0.73
ACGTcount: A:0.73, C:0.06, G:0.08, T:0.13
Consensus pattern (42 bp):
AAAAAAAATCAAAAAAAAAAGTCGAAAAAAAATCGAGCAAAA
Found at i:21352060 original size:15 final size:16
Alignment explanation
Indices: 21352040--21352071 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
21352030 AGAAAATGAA
21352040 AAAGAAAAAGAA-ATG
1 AAAGAAAAAGAAGATG
21352055 AAAGAAAAAGAAGATG
1 AAAGAAAAAGAAGATG
21352071 A
1 A
21352072 GTGTGAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAGAAGATG
Found at i:21352186 original size:17 final size:18
Alignment explanation
Indices: 21352154--21352187 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21352144 AAAAGAGAGT
*
21352154 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
21352172 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
21352188 GGAGTGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:21353476 original size:20 final size:20
Alignment explanation
Indices: 21353453--21353506 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
21353443 AGTTTTTCCC
*
21353453 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
21353473 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
21353493 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
21353507 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:21353488 original size:30 final size:30
Alignment explanation
Indices: 21353453--21353526 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
21353443 AGTTTTTCCC
21353453 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
21353483 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
21353513 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
21353527 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:21353516 original size:20 final size:20
Alignment explanation
Indices: 21353453--21353517 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
21353443 AGTTTTTCCC
* * * *
21353453 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
21353473 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
21353492 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
21353513 AGCTC
1 AGCTC
21353518 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:21358985 original size:19 final size:18
Alignment explanation
Indices: 21358949--21358988 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
21358939 TTTCCACTCG
*
21358949 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
21358967 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
21358986 TTT
1 TTT
21358989 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:21360071 original size:16 final size:16
Alignment explanation
Indices: 21360050--21360105 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
21360040 CTTCTTCTTC
21360050 TTTTTTTCACGAAATT
1 TTTTTTTCACGAAATT
*
21360066 TTTTTTTCATG-AATT
1 TTTTTTTCACGAAATT
*
21360081 TTTTTTTCACGAAAAT
1 TTTTTTTCACGAAATT
21360097 TTTTTTTCA
1 TTTTTTTCA
21360106 ACTTGATATC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
15 14 0.39
16 22 0.61
ACGTcount: A:0.23, C:0.11, G:0.05, T:0.61
Consensus pattern (16 bp):
TTTTTTTCACGAAATT
Found at i:21360163 original size:12 final size:13
Alignment explanation
Indices: 21360143--21360179 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
21360133 ATGGAAACCA
21360143 AATTTTTTTTTTG
1 AATTTTTTTTTTG
21360156 AATTTTTTTTTTG
1 AATTTTTTTTTTG
*
21360169 AGTTTTTTTTT
1 AATTTTTTTTT
21360180 CGAGAAACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.14, C:0.00, G:0.08, T:0.78
Consensus pattern (13 bp):
AATTTTTTTTTTG
Found at i:21360550 original size:46 final size:46
Alignment explanation
Indices: 21360497--21360590 Score: 163
Period size: 46 Copynumber: 2.0 Consensus size: 46
21360487 CAAAGAAAAG
*
21360497 ACCTCGACCCACTATCAA-GAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATG-ATGATAAGAACCTTGGTATATGATGA
21360543 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
21360589 AC
1 AC
21360591 GCCACACTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 45 0.98
47 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.24
Consensus pattern (46 bp):
ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
Found at i:21365417 original size:20 final size:19
Alignment explanation
Indices: 21365394--21365458 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
21365384 AAGCTCAAAC
21365394 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
21365414 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
21365434 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
21365454 GAGCT
1 GAGCT
21365459 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:21367272 original size:33 final size:33
Alignment explanation
Indices: 21367234--21367296 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
21367224 GATTACTCAC
21367234 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
21367267 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
21367297 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:21367320 original size:6 final size:6
Alignment explanation
Indices: 21367311--21367418 Score: 76
Period size: 6 Copynumber: 17.8 Consensus size: 6
21367301 TCTTTTTTCG
* * * **
21367311 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
* * ** *
21367362 -TATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
21367409 -GTTTT CTTTT
1 CTTTTT CTTTT
21367419 AATTTATTTT
Statistics
Matches: 75, Mismatches: 23, Indels: 8
0.71 0.22 0.08
Matches are distributed among these distances:
5 8 0.11
6 55 0.73
7 9 0.12
8 3 0.04
ACGTcount: A:0.06, C:0.18, G:0.03, T:0.73
Consensus pattern (6 bp):
CTTTTT
Found at i:21367323 original size:21 final size:21
Alignment explanation
Indices: 21367294--21367349 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
21367284 CAAGCTCTCT
*
21367294 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
21367315 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
21367336 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
21367350 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:21367323 original size:27 final size:26
Alignment explanation
Indices: 21367293--21367403 Score: 86
Period size: 28 Copynumber: 4.2 Consensus size: 26
21367283 TCAAGCTCTC
21367293 TTTCAATTTCTTTTTTCGCTTTTTCTT
1 TTTCAATTTCTTTTTTC-CTTTTTCTT
* *
21367320 TTTCAATTTTCTTTTCTTCATTTTCTTTT
1 TTTCAA-TTTCTTTT-TTCCTTTT-TCTT
*
21367349 TCTCTCACTTT-TTTATTT-CTTTTTCTT
1 T-T-TCAATTTCTTT-TTTCCTTTTTCTT
* *
21367376 TTGCAATTTC-TTTTT-CTTTTTCGT
1 TTTCAATTTCTTTTTTCCTTTTTCTT
21367400 TTTC
1 TTTC
21367404 TTTTTGTTTT
Statistics
Matches: 68, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
24 14 0.21
25 7 0.10
26 1 0.01
27 10 0.15
28 16 0.24
29 12 0.18
30 5 0.07
31 3 0.04
ACGTcount: A:0.08, C:0.19, G:0.03, T:0.70
Consensus pattern (26 bp):
TTTCAATTTCTTTTTTCCTTTTTCTT
Found at i:21367342 original size:14 final size:14
Alignment explanation
Indices: 21367293--21367349 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
21367283 TCAAGCTCTC
21367293 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
21367306 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
21367320 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
21367334 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
21367348 TT
1 TT
21367350 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:21367349 original size:15 final size:15
Alignment explanation
Indices: 21367313--21367369 Score: 50
Period size: 17 Copynumber: 3.9 Consensus size: 15
21367303 TTTTTTCGCT
*
21367313 TTTTCTTTTTC--AA
1 TTTTCTTTTTCTTCA
21367326 TTTTC-TTTTCTTCA
1 TTTTCTTTTTCTTCA
21367340 TTTTCTTTTTCTCTCA
1 TTTTCTTTTTCT-TCA
21367356 CTTTT-TTATTTCTT
1 -TTTTCTT-TTTCTT
21367370 TTTCTTTTGC
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
12 5 0.14
13 5 0.14
14 6 0.16
15 6 0.16
16 6 0.16
17 9 0.24
ACGTcount: A:0.09, C:0.19, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTCTTTTTCTTCA
Found at i:21368594 original size:20 final size:20
Alignment explanation
Indices: 21368548--21368594 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
21368538 AGCTCGTTTC
*
21368548 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
21368568 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
21368588 CAGCTCA
1 CAGCTCA
21368595 GTCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:21370106 original size:11 final size:12
Alignment explanation
Indices: 21370090--21370147 Score: 55
Period size: 14 Copynumber: 4.6 Consensus size: 12
21370080 TTGGAGTAAC
*
21370090 AAAAAAATTTGA
1 AAAAAAATTCGA
21370102 AAAAAAATTCGAAA
1 AAAAAAATTCG--A
*
21370116 AAAAAAATTTGA
1 AAAAAAATTCGA
21370128 TTAAAAAAATTC-A
1 --AAAAAAATTCGA
21370141 AAAAAAA
1 AAAAAAA
21370148 GTGAAAAGTC
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
11 7 0.18
12 11 0.28
13 1 0.03
14 20 0.51
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.21
Consensus pattern (12 bp):
AAAAAAATTCGA
Found at i:21370118 original size:14 final size:14
Alignment explanation
Indices: 21370101--21370147 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
21370091 AAAAAATTTG
21370101 AAAAAAAATTCGAA
1 AAAAAAAATTCGAA
* *
21370115 AAAAAAAATTTGAT
1 AAAAAAAATTCGAA
*
21370129 TAAAAAAATTC-AA
1 AAAAAAAATTCGAA
21370142 AAAAAA
1 AAAAAA
21370148 GTGAAAAGTC
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
13 6 0.22
14 21 0.78
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.19
Consensus pattern (14 bp):
AAAAAAAATTCGAA
Found at i:21370123 original size:26 final size:26
Alignment explanation
Indices: 21370090--21370147 Score: 91
Period size: 26 Copynumber: 2.2 Consensus size: 26
21370080 TTGGAGTAAC
21370090 AAAAAAATTTGA-AAAAAAATTCGAAA
1 AAAAAAATTTGATAAAAAAATTC-AAA
21370116 AAAAAAATTTGATTAAAAAAATTCAAA
1 AAAAAAATTTGA-TAAAAAAATTCAAA
21370143 AAAAA
1 AAAAA
21370148 GTGAAAAGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
26 12 0.40
27 8 0.27
28 10 0.33
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.21
Consensus pattern (26 bp):
AAAAAAATTTGATAAAAAAATTCAAA
Found at i:21371226 original size:17 final size:17
Alignment explanation
Indices: 21371169--21371226 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
21371159 GAAATTGAAA
* *
21371169 GAAAACAAAAAGAAAAC
1 GAAAAAAAAAAGAAATC
* *
21371186 GAAGAAGAAAAAGAAATT
1 GAA-AAAAAAAAGAAATC
*
21371204 GCAAAAAAAAAGAAATC
1 GAAAAAAAAAAGAAATC
21371221 GAAAAA
1 GAAAAA
21371227 GTGAGAGAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
17 20 0.61
18 13 0.39
ACGTcount: A:0.72, C:0.07, G:0.16, T:0.05
Consensus pattern (17 bp):
GAAAAAAAAAAGAAATC
Found at i:21371251 original size:14 final size:14
Alignment explanation
Indices: 21371223--21371283 Score: 63
Period size: 14 Copynumber: 4.2 Consensus size: 14
21371213 AAGAAATCGA
21371223 AAAAGTGAGAGAAAAG
1 AAAAGTGA-A-AAAAG
21371239 AAAA-TGAAGAAAAG
1 AAAAGTGAA-AAAAG
*
21371253 AAAATTGAAAAACA-
1 AAAAGTGAAAAA-AG
21371267 AAAAGTGAAAAAAG
1 AAAAGTGAAAAAAG
21371281 AAA
1 AAA
21371284 TTGAAAGAGA
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
13 1 0.02
14 28 0.68
15 8 0.20
16 4 0.10
ACGTcount: A:0.70, C:0.02, G:0.20, T:0.08
Consensus pattern (14 bp):
AAAAGTGAAAAAAG
Found at i:21371431 original size:48 final size:47
Alignment explanation
Indices: 21371352--21371457 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
21371342 GAGTGTCATG
*
21371352 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
21371400 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
21371448 GAAAAAGAAA
1 GAAAAAGAAA
21371458 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:21373169 original size:20 final size:20
Alignment explanation
Indices: 21373123--21373169 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
21373113 AGCTCGTTTC
*
21373123 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
21373143 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
21373163 CAGCTCA
1 CAGCTCA
21373170 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:21374563 original size:15 final size:15
Alignment explanation
Indices: 21374545--21374610 Score: 50
Period size: 15 Copynumber: 4.6 Consensus size: 15
21374535 TAAACTTGAT
21374545 TTTTTTTTGCTCACC
1 TTTTTTTTGCTCACC
* ***
21374560 TTTTTTTTTCTTTTC
1 TTTTTTTTGCTCACC
21374575 TTTTTTTTGCTCGA--
1 TTTTTTTTGCTC-ACC
*
21374589 TTTTTTTT--TCACT
1 TTTTTTTTGCTCACC
21374602 TTTTTTTTG
1 TTTTTTTTG
21374611 AATTTTTTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
11 1 0.03
12 2 0.05
13 8 0.20
14 8 0.20
15 21 0.52
ACGTcount: A:0.05, C:0.15, G:0.06, T:0.74
Consensus pattern (15 bp):
TTTTTTTTGCTCACC
Found at i:21374604 original size:12 final size:12
Alignment explanation
Indices: 21374588--21374650 Score: 54
Period size: 12 Copynumber: 4.8 Consensus size: 12
21374578 TTTTTGCTCG
21374588 ATTTTTTTTTCA
1 ATTTTTTTTTCA
* *
21374600 CTTTTTTTTTGA
1 ATTTTTTTTTCA
21374612 ATTTTTTTTCAATCAA
1 ATTTTTTTT---TC-A
21374628 ATTTTTTTTTTCGA
1 A-TTTTTTTTTC-A
21374642 ATTTTTTTT
1 ATTTTTTTT
21374651 GATTTTTTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
12 18 0.44
13 8 0.20
14 4 0.10
15 1 0.02
16 2 0.05
17 8 0.20
ACGTcount: A:0.17, C:0.08, G:0.03, T:0.71
Consensus pattern (12 bp):
ATTTTTTTTTCA
Found at i:21374609 original size:30 final size:28
Alignment explanation
Indices: 21374544--21374609 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 28
21374534 TTAAACTTGA
21374544 TTTTTTTTTGCTCACCTTTTTTTTTCTTT
1 TTTTTTTTTGCTCA-CTTTTTTTTTCTTT
**
21374573 TCTTTTTTTTGCTCGA-TTTTTTTTTCACT
1 T-TTTTTTTTGCTC-ACTTTTTTTTTCTTT
21374602 TTTTTTTT
1 TTTTTTTT
21374610 GAATTTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 7 0.21
29 13 0.39
30 12 0.36
31 1 0.03
ACGTcount: A:0.05, C:0.15, G:0.05, T:0.76
Consensus pattern (28 bp):
TTTTTTTTTGCTCACTTTTTTTTTCTTT
Found at i:21374618 original size:14 final size:14
Alignment explanation
Indices: 21374589--21374650 Score: 58
Period size: 14 Copynumber: 4.5 Consensus size: 14
21374579 TTTTGCTCGA
*
21374589 TTTTTTTTTC--AC
1 TTTTTTTTTCGAAT
21374601 TTTTTTTTT-GAAT
1 TTTTTTTTTCGAAT
* *
21374614 TTTTTTTCAATCAAAT
1 TTTTTTT--TTCGAAT
21374630 TTTTTTTTTCGAAT
1 TTTTTTTTTCGAAT
21374644 TTTTTTT
1 TTTTTTT
21374651 GATTTTTTTG
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
12 9 0.22
13 8 0.20
14 12 0.30
15 1 0.03
16 10 0.25
ACGTcount: A:0.16, C:0.08, G:0.03, T:0.73
Consensus pattern (14 bp):
TTTTTTTTTCGAAT
Found at i:21376954 original size:10 final size:10
Alignment explanation
Indices: 21376939--21376976 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
21376929 GCTCGTTTCC
*
21376939 AGCTCACTCG
1 AGCTCAATCG
21376949 AGCTCAAGTC-
1 AGCTCAA-TCG
21376959 AGCTCAATCG
1 AGCTCAATCG
21376969 AGCTCAAT
1 AGCTCAAT
21376977 TTAGCTACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (10 bp):
AGCTCAATCG
Found at i:21376963 original size:20 final size:20
Alignment explanation
Indices: 21376938--21376975 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
21376928 AGCTCGTTTC
*
21376938 CAGCTCACTCGAGCTCAAGT
1 CAGCTCAATCGAGCTCAAGT
21376958 CAGCTCAATCGAGCTCAA
1 CAGCTCAATCGAGCTCAA
21376976 TTTAGCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.18
Consensus pattern (20 bp):
CAGCTCAATCGAGCTCAAGT
Found at i:21376982 original size:20 final size:20
Alignment explanation
Indices: 21376939--21376999 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
21376929 GCTCGTTTCC
* * *
21376939 AGCTCACTCGAGCTCAAGTC
1 AGCTCAATCGAGCTCAATTT
21376959 AGCTCAATCGAGCTCAATTT
1 AGCTCAATCGAGCTCAATTT
21376979 AGCTACAATTC-AGCTC-ATTT
1 AGCT-CAA-TCGAGCTCAATTT
21376999 A
1 A
21377000 TTTTATTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 26 0.72
21 8 0.22
22 2 0.06
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (20 bp):
AGCTCAATCGAGCTCAATTT
Found at i:21376993 original size:11 final size:10
Alignment explanation
Indices: 21376949--21376995 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
21376939 AGCTCACTCG
*
21376949 AGCTCAAGTC
1 AGCTCAATTC
21376959 AGCTCAA-TC
1 AGCTCAATTC
*
21376968 GAGCTCAATTT
1 -AGCTCAATTC
21376979 AGCTACAATTC
1 AGCT-CAATTC
21376990 AGCTCA
1 AGCTCA
21376996 TTTATTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 2 0.06
10 20 0.62
11 10 0.31
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.26
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:21377500 original size:13 final size:13
Alignment explanation
Indices: 21377482--21377506 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21377472 GTATTGATCA
21377482 TGTGTTCACACCT
1 TGTGTTCACACCT
21377495 TGTGTTCACACC
1 TGTGTTCACACC
21377507 ATGATGACCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:21380607 original size:24 final size:25
Alignment explanation
Indices: 21380554--21380607 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
21380544 AACAAATTCT
* *
21380554 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
21380579 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
21380602 TTTTTT
1 TTTTTT
21380608 TATCACTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:21384372 original size:18 final size:18
Alignment explanation
Indices: 21384349--21384420 Score: 65
Period size: 18 Copynumber: 3.9 Consensus size: 18
21384339 CTAGACCGTA
21384349 TGCAATTTTTTTTTTTTT
1 TGCAATTTTTTTTTTTTT
* *
21384367 TGCAATTTTTTTTTCCTTC
1 TGCAATTTTTTTTT-TTTT
**
21384386 T-CTTTTTTTTTTTTTTT
1 TGCAATTTTTTTTTTTTT
* *
21384403 TTCGGATTTTTTTTTTTT
1 TGC-AATTTTTTTTTTTT
21384421 CGAAACTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
17 3 0.07
18 25 0.58
19 15 0.35
ACGTcount: A:0.07, C:0.10, G:0.06, T:0.78
Consensus pattern (18 bp):
TGCAATTTTTTTTTTTTT
Found at i:21384430 original size:16 final size:16
Alignment explanation
Indices: 21384395--21384454 Score: 63
Period size: 15 Copynumber: 3.9 Consensus size: 16
21384385 CTCTTTTTTT
* **
21384395 TTTTTTTTTTCGGATT
1 TTTTTTTTTTCGAAAC
21384411 TTTTTTTTTTCGAAAC
1 TTTTTTTTTTCGAAAC
21384427 -TTTTTTTTT--AAAC
1 TTTTTTTTTTCGAAAC
21384440 TTTTTTTTTTTCGAA
1 -TTTTTTTTTTCGAA
21384455 GCTACGATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
13 4 0.11
15 18 0.49
16 13 0.35
17 2 0.05
ACGTcount: A:0.15, C:0.08, G:0.07, T:0.70
Consensus pattern (16 bp):
TTTTTTTTTTCGAAAC
Found at i:21384447 original size:13 final size:14
Alignment explanation
Indices: 21384412--21384448 Score: 58
Period size: 13 Copynumber: 2.6 Consensus size: 14
21384402 TTTCGGATTT
21384412 TTTTTTTTTCGAAAC
1 TTTTTTTTTC-AAAC
21384427 TTTTTTTTT-AAAC
1 TTTTTTTTTCAAAC
21384440 TTTTTTTTT
1 TTTTTTTTT
21384449 TTCGAAGCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 13 0.59
15 9 0.41
ACGTcount: A:0.16, C:0.08, G:0.03, T:0.73
Consensus pattern (14 bp):
TTTTTTTTTCAAAC
Found at i:21384448 original size:14 final size:15
Alignment explanation
Indices: 21384411--21384449 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
21384401 TTTTCGGATT
21384411 TTTTTTTTTTCGAAAC
1 TTTTTTTTTTC-AAAC
21384427 -TTTTTTTTT-AAAC
1 TTTTTTTTTTCAAAC
21384440 TTTTTTTTTT
1 TTTTTTTTTT
21384450 TCGAAGCTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 4 0.18
14 9 0.41
15 9 0.41
ACGTcount: A:0.15, C:0.08, G:0.03, T:0.74
Consensus pattern (15 bp):
TTTTTTTTTTCAAAC
Found at i:21386998 original size:20 final size:19
Alignment explanation
Indices: 21386975--21387039 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
21386965 AAGCTCAAAC
21386975 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
21386995 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
21387015 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
21387035 GAGCT
1 GAGCT
21387040 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:21389968 original size:21 final size:21
Alignment explanation
Indices: 21389923--21389985 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
21389913 TTTGAACCAT
* *
21389923 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
21389945 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
21389966 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
21389986 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:21396648 original size:20 final size:20
Alignment explanation
Indices: 21396605--21396648 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
21396595 GGGTTAAGAT
* *
21396605 TGAGTTGAATTGAGCTTGAA
1 TGAGTTGAATTCAGCTCGAA
* *
21396625 TGAGTTGACTTCAGCTCGAG
1 TGAGTTGAATTCAGCTCGAA
21396645 TGAG
1 TGAG
21396649 CTGGAAACAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.11, G:0.32, T:0.32
Consensus pattern (20 bp):
TGAGTTGAATTCAGCTCGAA
Found at i:21400724 original size:20 final size:19
Alignment explanation
Indices: 21400701--21400765 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
21400691 AAGCTCAAAC
21400701 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
21400721 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
21400741 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
21400761 GAGCT
1 GAGCT
21400766 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:21402053 original size:17 final size:18
Alignment explanation
Indices: 21402031--21402064 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21402021 ACAACACTCC
*
21402031 TTTCTT-CTTCACTCTCG
1 TTTCTTCCTTCAATCTCG
21402048 TTTCTTCCTTCAATCTC
1 TTTCTTCCTTCAATCTC
21402065 ACTCTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.09, C:0.35, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTCTTCCTTCAATCTCG
Found at i:21402172 original size:15 final size:16
Alignment explanation
Indices: 21402147--21402178 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
21402137 TATCTCACAC
21402147 TCATCTTCTTTTTCTT
1 TCATCTTCTTTTTCTT
21402163 TCAT-TTCTTTTTCTT
1 TCATCTTCTTTTTCTT
21402178 T
1 T
21402179 TTCATTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (16 bp):
TCATCTTCTTTTTCTT
Found at i:21403154 original size:32 final size:30
Alignment explanation
Indices: 21403097--21403233 Score: 101
Period size: 33 Copynumber: 4.6 Consensus size: 30
21403087 CTCGCAAGAC
* *
21403097 TTTTCA-CTTTTTTTTTAACTTGATTTTTTT
1 TTTTCACCTTTTTTTTT-GCTCGATTTTTTT
21403127 TTTGCTCACCTTTTTTTTTGCTCGATTTTTTT
1 TTT--TCACCTTTTTTTTTGCTCGATTTTTTT
*
21403159 TTTTCA-CTTTTTTTTT--T-GAATTTTTT
1 TTTTCACCTTTTTTTTTGCTCGATTTTTTT
* *
21403185 TTTTCAATCAATTTTTTTTT-TTCGAATTTTTTT
1 TTTTC-A-C-CTTTTTTTTTGCTCG-ATTTTTTT
*
21403218 TTTTGA--TTTTTTTTTG
1 TTTTCACCTTTTTTTTTG
21403234 TTACTCCAAT
Statistics
Matches: 90, Mismatches: 6, Indels: 23
0.76 0.05 0.19
Matches are distributed among these distances:
26 13 0.14
27 2 0.02
28 9 0.10
29 10 0.11
30 15 0.17
31 1 0.01
32 19 0.21
33 21 0.23
ACGTcount: A:0.12, C:0.10, G:0.06, T:0.72
Consensus pattern (30 bp):
TTTTCACCTTTTTTTTTGCTCGATTTTTTT
Found at i:21403155 original size:15 final size:15
Alignment explanation
Indices: 21403121--21403174 Score: 67
Period size: 16 Copynumber: 3.6 Consensus size: 15
21403111 TTAACTTGAT
21403121 TTTTTTTTTGCTCACC
1 TTTTTTTTTGCTCA-C
21403137 TTTTTTTTTGCTCGA-
1 TTTTTTTTTGCTC-AC
*
21403152 TTTTTTTTT-TTCAC
1 TTTTTTTTTGCTCAC
21403166 TTTTTTTTT
1 TTTTTTTTT
21403175 TGAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
13 1 0.03
14 11 0.31
15 9 0.26
16 13 0.37
17 1 0.03
ACGTcount: A:0.06, C:0.15, G:0.06, T:0.74
Consensus pattern (15 bp):
TTTTTTTTTGCTCAC
Found at i:21403214 original size:13 final size:13
Alignment explanation
Indices: 21403197--21403232 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
21403187 TTCAATCAAT
21403197 TTTTTTTTTTCGAA
1 TTTTTTTTTTCG-A
*
21403211 TTTTTTTTTTTGA
1 TTTTTTTTTTCGA
21403224 TTTTTTTTT
1 TTTTTTTTT
21403233 GTTACTCCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.08, C:0.03, G:0.06, T:0.83
Consensus pattern (13 bp):
TTTTTTTTTTCGA
Found at i:21404862 original size:20 final size:19
Alignment explanation
Indices: 21404839--21404903 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
21404829 AAGCTCAAAC
21404839 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
21404859 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
21404879 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
21404899 GAGCT
1 GAGCT
21404904 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:21408074 original size:25 final size:25
Alignment explanation
Indices: 21408046--21408094 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
21408036 AATAGGTGCG
*
21408046 TAAAAAAAAGTTCGAAAA-AAAAAAT
1 TAAAAAAAAATT-GAAAAGAAAAAAT
21408071 TAAAAAAAAATTGAAAAGAAAAAA
1 TAAAAAAAAATTGAAAAGAAAAAA
21408095 AATTGCATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.76, C:0.02, G:0.08, T:0.14
Consensus pattern (25 bp):
TAAAAAAAAATTGAAAAGAAAAAAT
Found at i:21408075 original size:11 final size:12
Alignment explanation
Indices: 21408047--21408093 Score: 51
Period size: 11 Copynumber: 3.8 Consensus size: 12
21408037 ATAGGTGCGT
*
21408047 AAAAAAAAGTTCG
1 AAAAAAAAATT-G
21408060 AAAAAAAAAATT-
1 -AAAAAAAAATTG
21408072 AAAAAAAAATTG
1 AAAAAAAAATTG
21408084 AAAAGAAAAA
1 AAAA-AAAAA
21408094 AAATTGCATA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
11 11 0.37
12 4 0.13
13 5 0.17
14 10 0.33
ACGTcount: A:0.77, C:0.02, G:0.09, T:0.13
Consensus pattern (12 bp):
AAAAAAAAATTG
Found at i:21408075 original size:12 final size:13
Alignment explanation
Indices: 21408047--21408094 Score: 55
Period size: 14 Copynumber: 3.7 Consensus size: 13
21408037 ATAGGTGCGT
*
21408047 AAAAAAAAGTTCGA
1 AAAAAAAAATT-GA
21408061 AAAAAAAAATT--
1 AAAAAAAAATTGA
21408072 AAAAAAAAATTGA
1 AAAAAAAAATTGA
21408085 AAAGAAAAAA
1 AAA-AAAAAA
21408095 AATTGCATAC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 11 0.37
13 3 0.10
14 16 0.53
ACGTcount: A:0.77, C:0.02, G:0.08, T:0.12
Consensus pattern (13 bp):
AAAAAAAAATTGA
Found at i:21411311 original size:17 final size:18
Alignment explanation
Indices: 21411289--21411329 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
21411279 CGTTTCTTTT
21411289 TCTTTTGAATCACTC-TC
1 TCTTTTGAATCACTCATC
**
21411306 TCTTTTTTATCACTCATC
1 TCTTTTGAATCACTCATC
21411324 T-TTTTG
1 TCTTTTG
21411330 TTTTCTTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.15, C:0.24, G:0.05, T:0.56
Consensus pattern (18 bp):
TCTTTTGAATCACTCATC
Found at i:21411313 original size:24 final size:25
Alignment explanation
Indices: 21411260--21411313 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
21411250 AACAAATTCT
* *
21411260 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
21411285 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
21411308 TTTTTT
1 TTTTTT
21411314 ATCACTCATC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:21413582 original size:15 final size:15
Alignment explanation
Indices: 21413558--21413614 Score: 82
Period size: 14 Copynumber: 3.9 Consensus size: 15
21413548 TAGACCGTAT
21413558 GCAATTTTTTTTTT-
1 GCAATTTTTTTTTTC
21413572 GCAATTTTTTTTTTC
1 GCAATTTTTTTTTTC
*
21413587 G-GATTTTTTTTTTC
1 GCAATTTTTTTTTTC
*
21413601 GAAATTTTTTTTTT
1 GCAATTTTTTTTTT
21413615 AACTTTTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
14 27 0.69
15 12 0.31
ACGTcount: A:0.14, C:0.07, G:0.09, T:0.70
Consensus pattern (15 bp):
GCAATTTTTTTTTTC
Found at i:21413621 original size:28 final size:28
Alignment explanation
Indices: 21413559--21413631 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 28
21413549 AGACCGTATG
*
21413559 CAATTTTTTTTTT-GCAATTTTTTTTTT
1 CAATTTTTTTTTTCGAAATTTTTTTTTT
*
21413586 CGGATTTTTTTTTTCGAAATTTTTTTTTT
1 C-AATTTTTTTTTTCGAAATTTTTTTTTT
21413615 -AACTTTTTTTTTTCGAA
1 CAA-TTTTTTTTTTCGAA
21413632 GCTACGATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
27 2 0.05
28 25 0.62
29 13 0.32
ACGTcount: A:0.16, C:0.08, G:0.07, T:0.68
Consensus pattern (28 bp):
CAATTTTTTTTTTCGAAATTTTTTTTTT
Found at i:21413627 original size:13 final size:14
Alignment explanation
Indices: 21413560--21413628 Score: 79
Period size: 14 Copynumber: 4.9 Consensus size: 14
21413550 GACCGTATGC
21413560 AATTTTTTTTTTGC-
1 AATTTTTTTTTT-CA
*
21413574 AATTTTTTTTTTCG
1 AATTTTTTTTTTCA
*
21413588 GATTTTTTTTTTCGA
1 AATTTTTTTTTTC-A
21413603 AATTTTTTTTTT-A
1 AATTTTTTTTTTCA
*
21413616 ACTTTTTTTTTTC
1 AATTTTTTTTTTC
21413629 GAAGCTACGA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
13 13 0.27
14 24 0.50
15 11 0.23
ACGTcount: A:0.14, C:0.07, G:0.06, T:0.72
Consensus pattern (14 bp):
AATTTTTTTTTTCA
Found at i:21420281 original size:20 final size:19
Alignment explanation
Indices: 21420256--21420310 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 19
21420246 TGTGGTTCAA
*
21420256 CTCATTCGAGCTCAAGTTAG
1 CTCATTC-AGCTCAAGTCAG
21420276 CTCATTCATGCTCAAGTCAG
1 CTCATTCA-GCTCAAGTCAG
21420296 CTCATTCAAGCTCAA
1 CTCATTC-AGCTCAA
21420311 TTTAACTCGT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.29
Consensus pattern (19 bp):
CTCATTCAGCTCAAGTCAG
Found at i:21422322 original size:13 final size:12
Alignment explanation
Indices: 21422292--21422351 Score: 70
Period size: 12 Copynumber: 5.1 Consensus size: 12
21422282 GTATTACGGT
*
21422292 ATTGTAAAAAAA
1 ATTGAAAAAAAA
21422304 A-T-AAAAAAAA
1 ATTGAAAAAAAA
21422314 ACTTGAAAAAAAA
1 A-TTGAAAAAAAA
*
21422327 TTTGAAAAAAAA
1 ATTGAAAAAAAA
*
21422339 ATTCAAAAAAAA
1 ATTGAAAAAAAA
21422351 A
1 A
21422352 GTTTGTATTC
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
10 8 0.20
11 1 0.02
12 24 0.59
13 8 0.20
ACGTcount: A:0.73, C:0.03, G:0.05, T:0.18
Consensus pattern (12 bp):
ATTGAAAAAAAA
Found at i:21422432 original size:18 final size:18
Alignment explanation
Indices: 21422408--21422452 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
21422398 AAAAGAAGAA
* *
21422408 GAAAAAAAATTCGAAATT
1 GAAAAAAAAATCAAAATT
21422426 -AAAAAAAAATCAAAATT
1 GAAAAAAAAATCAAAATT
21422443 GAAAAAAAAA
1 GAAAAAAAAA
21422453 AGAGTGATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.73, C:0.04, G:0.07, T:0.16
Consensus pattern (18 bp):
GAAAAAAAAATCAAAATT
Found at i:21424844 original size:20 final size:20
Alignment explanation
Indices: 21424819--21424873 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
21424809 TGTGGTTCAA
*
21424819 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
21424839 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
21424859 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
21424874 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:21426959 original size:20 final size:20
Alignment explanation
Indices: 21426934--21426988 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
21426924 TGTGGTTCAA
*
21426934 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
21426954 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
21426974 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
21426989 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:21428814 original size:12 final size:11
Alignment explanation
Indices: 21428784--21428813 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
21428774 AAAAAAAAGG
*
21428784 AAAAGAAATTC
1 AAAAAAAATTC
21428795 AAAAAAAATTC
1 AAAAAAAATTC
21428806 AAAAAAAA
1 AAAAAAAA
21428814 AATTTGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.77, C:0.07, G:0.03, T:0.13
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:21430362 original size:16 final size:15
Alignment explanation
Indices: 21430343--21430372 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
21430333 AGTATCAATT
21430343 TTTGATTGGTGATGAC
1 TTTGATTGG-GATGAC
21430359 TTTGATTGGGATGA
1 TTTGATTGGGATGA
21430373 TGGATTGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.20, C:0.03, G:0.33, T:0.43
Consensus pattern (15 bp):
TTTGATTGGGATGAC
Found at i:21432658 original size:20 final size:20
Alignment explanation
Indices: 21432633--21432687 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
21432623 TGTGGTTCAA
*
21432633 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
21432653 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
21432673 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
21432688 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:21434649 original size:34 final size:33
Alignment explanation
Indices: 21434585--21434650 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
21434575 TTAAAGATGT
* *
21434585 TGTTCTACATGCATGGAACGGCAATTAATGAGA
1 TGTTCCACATGCATGGAACGACAATTAATGAGA
*
21434618 TGTTCCACATGCAATGG-ACGACATTTAAATGAG
1 TGTTCCACATGC-ATGGAACGACAATT-AATGAG
21434651 GGAGAGTGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 18 0.64
34 10 0.36
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (33 bp):
TGTTCCACATGCATGGAACGACAATTAATGAGA
Found at i:21436568 original size:11 final size:11
Alignment explanation
Indices: 21436554--21436593 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
21436544 GAATACAAAT
21436554 TTTTTTTTGAA
1 TTTTTTTTGAA
21436565 TTTTTTTTGAA
1 TTTTTTTTGAA
*
21436576 TTTTTTTCG-A
1 TTTTTTTTGAA
21436586 TTTTTTTT
1 TTTTTTTT
21436594 CCTTTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 8 0.30
11 19 0.70
ACGTcount: A:0.12, C:0.03, G:0.07, T:0.78
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:21436599 original size:10 final size:11
Alignment explanation
Indices: 21436552--21436603 Score: 54
Period size: 10 Copynumber: 4.8 Consensus size: 11
21436542 TTGAATACAA
*
21436552 ATTTTTTTTTG
1 ATTTTTTTTCG
21436563 AATTTTTTTT-G
1 -ATTTTTTTTCG
*
21436574 AATTTTTTTCG
1 ATTTTTTTTCG
21436585 ATTTTTTTTC-
1 ATTTTTTTTCG
*
21436595 CTTTTTTTT
1 ATTTTTTTT
21436604 ACAATATCGA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
10 16 0.44
11 11 0.31
12 9 0.25
ACGTcount: A:0.12, C:0.06, G:0.06, T:0.77
Consensus pattern (11 bp):
ATTTTTTTTCG
Found at i:21437617 original size:20 final size:20
Alignment explanation
Indices: 21437571--21437617 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
21437561 AGCTCGTTTC
*
21437571 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
21437591 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
21437611 CAGCTCA
1 CAGCTCA
21437618 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:21437751 original size:18 final size:18
Alignment explanation
Indices: 21437728--21437763 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
21437718 TAAGTTAGTT
21437728 AATTTGTTAAAATCTGGA
1 AATTTGTTAAAATCTGGA
21437746 AATTTGTTAAAATCTGGA
1 AATTTGTTAAAATCTGGA
21437764 CAAACAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.17, T:0.39
Consensus pattern (18 bp):
AATTTGTTAAAATCTGGA
Found at i:21439495 original size:56 final size:56
Alignment explanation
Indices: 21439390--21439496 Score: 153
Period size: 56 Copynumber: 1.9 Consensus size: 56
21439380 ATTAATGCCG
* * * * *
21439390 TCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCCCTTTAAATGTCGT
1 TCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCACATTAAATGTCGT
21439446 TCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCACATTAAAT
1 TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCACATTAAAT
21439497 CAACAAGCAG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
55 21 0.47
56 24 0.53
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.41
Consensus pattern (56 bp):
TCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCACATTAAATGTCGT
Found at i:21440147 original size:20 final size:20
Alignment explanation
Indices: 21440122--21440176 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
21440112 ACGAGTTAAA
* *
21440122 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
21440142 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
21440162 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
21440177 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:21440798 original size:11 final size:11
Alignment explanation
Indices: 21440784--21440808 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
21440774 CTTTTTCACT
21440784 TTTTTTTTGAA
1 TTTTTTTTGAA
21440795 TTTTTTTTGAA
1 TTTTTTTTGAA
21440806 TTT
1 TTT
21440809 CGATTTTTTT
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:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:21445305 original size:14 final size:13
Alignment explanation
Indices: 21445286--21445321 Score: 63
Period size: 13 Copynumber: 2.7 Consensus size: 13
21445276 AAAGAGTTCG
21445286 AAAAAAAAATTGA
1 AAAAAAAAATTGA
21445299 AAAAAAAAATTGA
1 AAAAAAAAATTGA
21445312 AAAGAAAAAA
1 AAA-AAAAAA
21445322 AAAATTGCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.11
Consensus pattern (13 bp):
AAAAAAAAATTGA
Found at i:21449152 original size:24 final size:24
Alignment explanation
Indices: 21449097--21449153 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 24
21449087 GGATAACTAA
* **
21449097 GAAAGGGTATTTGGTTTTTGGTAC
1 GAAATGGTATTTGGGATTTGGTAC
***
21449121 GTTTTGGTATTTGGGATTTGGTAC
1 GAAATGGTATTTGGGATTTGGTAC
21449145 GAAATGGTA
1 GAAATGGTA
21449154 ATGGTTTAAA
Statistics
Matches: 24, Mismatches: 9, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.04, G:0.33, T:0.42
Consensus pattern (24 bp):
GAAATGGTATTTGGGATTTGGTAC
Found at i:21451779 original size:17 final size:18
Alignment explanation
Indices: 21451740--21451781 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
21451730 AAAGAAGAAA
21451740 ACAAAA-AGATGAGTGAT
1 ACAAAAGAGATGAGTGAT
*
21451757 AAAAAAGAGA-GAGTGAT
1 ACAAAAGAGATGAGTGAT
*
21451774 TCAAAAGA
1 ACAAAAGA
21451782 AAAAGAAACG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.57, C:0.05, G:0.24, T:0.14
Consensus pattern (18 bp):
ACAAAAGAGATGAGTGAT
Found at i:21451784 original size:24 final size:25
Alignment explanation
Indices: 21451757--21451810 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
21451747 GATGAGTGAT
*
21451757 AAAAAAGAGA-GAGTGATTCAAAA-G
1 AAAAAAGAAACGAGTGA-TCAAAATG
*
21451781 -AAAAAGAAACGAGTGATGAAAATG
1 AAAAAAGAAACGAGTGATCAAAATG
21451805 AAAAAA
1 AAAAAA
21451811 AGAATTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 13 0.52
24 7 0.28
25 5 0.20
ACGTcount: A:0.63, C:0.04, G:0.22, T:0.11
Consensus pattern (25 bp):
AAAAAAGAAACGAGTGATCAAAATG
Found at i:21452712 original size:10 final size:10
Alignment explanation
Indices: 21452697--21452734 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
21452687 GCTCGTTTCC
*
21452697 AGCTCACTCG
1 AGCTCAATCG
21452707 AGCTCAAGTC-
1 AGCTCAA-TCG
21452717 AGCTCAATCG
1 AGCTCAATCG
21452727 AGCTCAAT
1 AGCTCAAT
21452735 TTAGCTTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (10 bp):
AGCTCAATCG
Found at i:21452740 original size:20 final size:20
Alignment explanation
Indices: 21452696--21452733 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
21452686 AGCTCGTTTC
*
21452696 CAGCTCACTCGAGCTCAAGT
1 CAGCTCAATCGAGCTCAAGT
21452716 CAGCTCAATCGAGCTCAA
1 CAGCTCAATCGAGCTCAA
21452734 TTTAGCTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.18
Consensus pattern (20 bp):
CAGCTCAATCGAGCTCAAGT
Found at i:21454481 original size:12 final size:13
Alignment explanation
Indices: 21454464--21454495 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
21454454 TTGGAGTAAC
21454464 AAAAAAATC-AAA
1 AAAAAAATCGAAA
21454476 AAAAAAATCGAAA
1 AAAAAAATCGAAA
21454489 AAAAAAA
1 AAAAAAA
21454496 ATTGATTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.84, C:0.06, G:0.03, T:0.06
Consensus pattern (13 bp):
AAAAAAATCGAAA
Found at i:21455444 original size:18 final size:18
Alignment explanation
Indices: 21455423--21455457 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
21455413 AGAAAAGAAA
21455423 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
21455441 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
21455458 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:21457115 original size:10 final size:10
Alignment explanation
Indices: 21457100--21457137 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
21457090 GCTCGTTTCC
*
21457100 AGCTCACTCG
1 AGCTCAATCG
21457110 AGCTCAAGTC-
1 AGCTCAA-TCG
21457120 AGCTCAATCG
1 AGCTCAATCG
21457130 AGCTCAAT
1 AGCTCAAT
21457138 TTAGCTTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (10 bp):
AGCTCAATCG
Found at i:21457143 original size:20 final size:20
Alignment explanation
Indices: 21457099--21457136 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
21457089 AGCTCGTTTC
*
21457099 CAGCTCACTCGAGCTCAAGT
1 CAGCTCAATCGAGCTCAAGT
21457119 CAGCTCAATCGAGCTCAA
1 CAGCTCAATCGAGCTCAA
21457137 TTTAGCTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.18
Consensus pattern (20 bp):
CAGCTCAATCGAGCTCAAGT
Found at i:21462537 original size:30 final size:30
Alignment explanation
Indices: 21462503--21462599 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
21462493 AGCTCACTCC
21462503 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
21462533 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
21462563 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
21462593 TAGCTCA
1 TAGCTCA
21462600 TTTTAGTTTT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:21463530 original size:22 final size:20
Alignment explanation
Indices: 21463498--21463546 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
21463488 GCCGAATTTA
21463498 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATT-GTG
* *
21463521 TGAACATTTTTATTATTGTG
1 TGAACATTTTAATCATTGTG
21463541 TGAACA
1 TGAACA
21463547 CCTAGATGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 7 0.29
23 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TGAACATTTTAATCATTGTG
Found at i:21464231 original size:20 final size:20
Alignment explanation
Indices: 21464202--21464266 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
21464192 GTTCGTAACG
* *
21464202 AAAAAAAAAAGAATTC-AAA
1 AAAAAAAAAAAAAATCGAAA
21464221 AAAAAATAAAAAAAATCGAAA
1 AAAAAA-AAAAAAAATCGAAA
* *
21464242 AAAAGGAAAAAAAAGT-GAAA
1 AAAA-AAAAAAAAAATCGAAA
21464262 AAAAA
1 AAAAA
21464267 TCGAGTTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
19 6 0.16
20 16 0.42
21 15 0.39
22 1 0.03
ACGTcount: A:0.80, C:0.03, G:0.09, T:0.08
Consensus pattern (20 bp):
AAAAAAAAAAAAAATCGAAA
Found at i:21464242 original size:11 final size:10
Alignment explanation
Indices: 21464219--21464267 Score: 57
Period size: 10 Copynumber: 4.9 Consensus size: 10
21464209 AAAGAATTCA
21464219 AAAAAAAAT-
1 AAAAAAAATG
21464228 AAAAAAAATCG
1 AAAAAAAAT-G
*
21464239 -AAAAAAAGG
1 AAAAAAAATG
21464248 AAAAAAAAGTG
1 AAAAAAAA-TG
21464259 AAAAAAAAT
1 AAAAAAAAT
21464268 CGAGTTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
9 10 0.29
10 15 0.44
11 9 0.26
ACGTcount: A:0.80, C:0.02, G:0.10, T:0.08
Consensus pattern (10 bp):
AAAAAAAATG
Found at i:21465325 original size:11 final size:12
Alignment explanation
Indices: 21465293--21465323 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
21465283 TTGAGAGAAC
21465293 TTGAAAAAGCCT
1 TTGAAAAAGCCT
21465305 TTGAAAAAGCCT
1 TTGAAAAAGCCT
21465317 TTGAAAA
1 TTGAAAA
21465324 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:21467534 original size:30 final size:30
Alignment explanation
Indices: 21467500--21467596 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
21467490 AGCTCACTCC
21467500 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
21467530 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
21467560 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
21467590 TAGCTCA
1 TAGCTCA
21467597 TTTTAGTTTT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:21468526 original size:22 final size:20
Alignment explanation
Indices: 21468494--21468542 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
21468484 GCCGAATTTA
21468494 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATT-GTG
* *
21468517 TGAACATTTTTATTATTGTG
1 TGAACATTTTAATCATTGTG
21468537 TGAACA
1 TGAACA
21468543 CCTAGATGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 7 0.29
23 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TGAACATTTTAATCATTGTG
Found at i:21473907 original size:20 final size:21
Alignment explanation
Indices: 21473867--21473922 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
21473857 ACCAATAAAA
21473867 TAAATGAGCT-GAATTGTAGC
1 TAAATGAGCTCGAATTGTAGC
21473887 TAAATTGAGCTCG-ATTG-AGC
1 TAAA-TGAGCTCGAATTGTAGC
21473907 TGAAATGAGCTC-AATT
1 T-AAATGAGCTCGAATT
21473923 AAGCTGGTCG
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
20 18 0.56
21 13 0.41
22 1 0.03
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.30
Consensus pattern (21 bp):
TAAATGAGCTCGAATTGTAGC
Found at i:21475994 original size:33 final size:33
Alignment explanation
Indices: 21475956--21476018 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
21475946 GATTACTCAC
21475956 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
21475989 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
21476019 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:21476045 original size:21 final size:21
Alignment explanation
Indices: 21476016--21476071 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
21476006 CAAGCTCTCT
*
21476016 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
21476037 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
21476058 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
21476072 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:21476064 original size:14 final size:14
Alignment explanation
Indices: 21476015--21476071 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
21476005 TCAAGCTCTC
21476015 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
21476028 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
21476042 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
21476056 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
21476070 TT
1 TT
21476072 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:21476099 original size:18 final size:18
Alignment explanation
Indices: 21476078--21476136 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
21476068 TTTTCTCTCA
21476078 CTTTTTCGATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
21476096 CTTTTGCAATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
21476114 CTTCTTCGTTTTCTTTTT
1 CTTTTTCGATTTCTTTTT
*
21476132 GTTTT
1 CTTTT
21476137 CTTTCAATTT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.05, C:0.17, G:0.07, T:0.71
Consensus pattern (18 bp):
CTTTTTCGATTTCTTTTT
Found at i:21476153 original size:6 final size:6
Alignment explanation
Indices: 21476033--21476140 Score: 65
Period size: 6 Copynumber: 17.7 Consensus size: 6
21476023 TCTTTTTTCG
* * * **
21476033 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** * *
21476084 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTCTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
21476132 -GTTTT CTTT
1 CTTTTT CTTT
21476141 CAATTTCTTT
Statistics
Matches: 72, Mismatches: 27, Indels: 6
0.69 0.26 0.06
Matches are distributed among these distances:
5 4 0.06
6 56 0.78
7 9 0.12
8 3 0.04
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.70
Consensus pattern (6 bp):
CTTTTT
Found at i:21477195 original size:15 final size:15
Alignment explanation
Indices: 21477177--21477229 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
21477167 TTAACTTGAT
21477177 TTTTTTTTTGCTCAC
1 TTTTTTTTTGCTCAC
* *
21477192 TTTTTTTTCT-TTCTC
1 TTTTTTTT-TGCTCAC
21477207 TTTTTTTTTGCTCGA-
1 TTTTTTTTTGCTC-AC
21477222 TTTTTTTT
1 TTTTTTTT
21477230 CACTTTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
14 1 0.03
15 29 0.94
16 1 0.03
ACGTcount: A:0.04, C:0.15, G:0.06, T:0.75
Consensus pattern (15 bp):
TTTTTTTTTGCTCAC
Found at i:21477198 original size:30 final size:31
Alignment explanation
Indices: 21477162--21477234 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 31
21477152 CTTTTCACTT
21477162 TTTTTTTAACTTGAT-TTTTTTTTTGCTC-AC
1 TTTTTTT-ACTTGATCTTTTTTTTTGCTCGAC
* ** *
21477192 TTTTTTTTCTTTCTCTTTTTTTTTGCTCGAT
1 TTTTTTTACTTGATCTTTTTTTTTGCTCGAC
21477223 TTTTTTTCACTT
1 TTTTTTT-ACTT
21477235 TTTTTTGAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 4 0.11
30 20 0.57
31 8 0.23
32 3 0.09
ACGTcount: A:0.08, C:0.15, G:0.05, T:0.71
Consensus pattern (31 bp):
TTTTTTTACTTGATCTTTTTTTTTGCTCGAC
Found at i:21477247 original size:10 final size:11
Alignment explanation
Indices: 21477221--21477257 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
21477211 TTTTTGCTCG
*
21477221 ATTTTTTTTCA
1 ATTTTTTTTGA
*
21477232 CTTTTTTTTGA
1 ATTTTTTTTGA
21477243 ATTTTTTTTGA
1 ATTTTTTTTGA
21477254 ATTT
1 ATTT
21477258 CGATTTTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.73
Consensus pattern (11 bp):
ATTTTTTTTGA
Found at i:21478653 original size:20 final size:21
Alignment explanation
Indices: 21478613--21478668 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
21478603 ACCAATAAAA
21478613 TAAATGAGCT-GAATTGTAGC
1 TAAATGAGCTCGAATTGTAGC
21478633 TAAATTGAGCTCG-ATTG-AGC
1 TAAA-TGAGCTCGAATTGTAGC
21478653 TGAAATGAGCTC-AATT
1 T-AAATGAGCTCGAATT
21478669 AAGCTGGTCG
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
20 18 0.56
21 13 0.41
22 1 0.03
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.30
Consensus pattern (21 bp):
TAAATGAGCTCGAATTGTAGC
Found at i:21480739 original size:33 final size:33
Alignment explanation
Indices: 21480701--21480763 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
21480691 GATTACTCAC
21480701 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
21480734 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
21480764 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:21480790 original size:21 final size:21
Alignment explanation
Indices: 21480761--21480816 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
21480751 CAAGCTCTCT
*
21480761 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
21480782 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
21480803 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
21480817 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:21480809 original size:14 final size:14
Alignment explanation
Indices: 21480760--21480816 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
21480750 TCAAGCTCTC
21480760 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
21480773 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
21480787 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
21480801 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
21480815 TT
1 TT
21480817 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:21480844 original size:18 final size:18
Alignment explanation
Indices: 21480823--21480881 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
21480813 TTTTCTCTCA
21480823 CTTTTTCGATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
21480841 CTTTTGCAATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
21480859 CTTCTTCGTTTTCTTTTT
1 CTTTTTCGATTTCTTTTT
*
21480877 GTTTT
1 CTTTT
21480882 CTTTCAATTT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.05, C:0.17, G:0.07, T:0.71
Consensus pattern (18 bp):
CTTTTTCGATTTCTTTTT
Found at i:21480898 original size:6 final size:6
Alignment explanation
Indices: 21480778--21480885 Score: 65
Period size: 6 Copynumber: 17.7 Consensus size: 6
21480768 TCTTTTTTCG
* * * **
21480778 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** * *
21480829 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTCTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
21480877 -GTTTT CTTT
1 CTTTTT CTTT
21480886 CAATTTCTTT
Statistics
Matches: 72, Mismatches: 27, Indels: 6
0.69 0.26 0.06
Matches are distributed among these distances:
5 4 0.06
6 56 0.78
7 9 0.12
8 3 0.04
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.70
Consensus pattern (6 bp):
CTTTTT
Found at i:21481932 original size:14 final size:14
Alignment explanation
Indices: 21481915--21481964 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
21481905 TTAACTTGAT
21481915 TTTTTTTTGCTCAC
1 TTTTTTTTGCTCAC
*
21481929 TTTTTTTT-CTTTCTC
1 TTTTTTTTGC--TCAC
21481944 TTTTTTTTGCTCGA-
1 TTTTTTTTGCTC-AC
21481958 TTTTTTT
1 TTTTTTT
21481965 CACTTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
13 1 0.03
14 17 0.57
15 11 0.37
16 1 0.03
ACGTcount: A:0.04, C:0.16, G:0.06, T:0.74
Consensus pattern (14 bp):
TTTTTTTTGCTCAC
Found at i:21481982 original size:10 final size:11
Alignment explanation
Indices: 21481958--21481992 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
21481948 TTTTGCTCGA
* *
21481958 TTTTTTTCACT
1 TTTTTTTGAAT
21481969 TTTTTTTGAAT
1 TTTTTTTGAAT
21481980 TTTTTTTGAAT
1 TTTTTTTGAAT
21481991 TT
1 TT
21481993 CGATTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.14, C:0.06, G:0.06, T:0.74
Consensus pattern (11 bp):
TTTTTTTGAAT
Found at i:21483387 original size:20 final size:21
Alignment explanation
Indices: 21483347--21483402 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
21483337 ACCAATAAAA
21483347 TAAATGAGCT-GAATTGTAGC
1 TAAATGAGCTCGAATTGTAGC
21483367 TAAATTGAGCTCG-ATTG-AGC
1 TAAA-TGAGCTCGAATTGTAGC
21483387 TGAAATGAGCTC-AATT
1 T-AAATGAGCTCGAATT
21483403 AAGCTGGTCG
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
20 18 0.56
21 13 0.41
22 1 0.03
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.30
Consensus pattern (21 bp):
TAAATGAGCTCGAATTGTAGC
Found at i:21485456 original size:33 final size:33
Alignment explanation
Indices: 21485418--21485480 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
21485408 GATTACTCAC
21485418 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
21485451 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
21485481 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:21485568 original size:18 final size:18
Alignment explanation
Indices: 21485545--21485611 Score: 73
Period size: 18 Copynumber: 3.6 Consensus size: 18
21485535 TCACTTTTCG
21485545 ATTTCTTTTTCTT-TTGCA
1 ATTTCTTTTTCTTCTT-CA
*
21485563 ATTTCTTTTTCTTCTTCG
1 ATTTCTTTTTCTTCTTCA
* *
21485581 TTTTCTTTTTGTTTCTTTCA
1 ATTTCTTTTT-CTTC-TTCA
21485601 ATTTCTTTTTC
1 ATTTCTTTTTC
21485612 AATCTCTTCT
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
18 23 0.57
19 5 0.12
20 12 0.30
ACGTcount: A:0.07, C:0.18, G:0.04, T:0.70
Consensus pattern (18 bp):
ATTTCTTTTTCTTCTTCA
Found at i:21485611 original size:6 final size:6
Alignment explanation
Indices: 21485495--21485590 Score: 50
Period size: 6 Copynumber: 15.0 Consensus size: 6
21485485 TCTTTTTTCG
*
21485495 CTTTTT CTTTTT CAATTTT C-TTTT CTTCATTT CTTTTCT CTCACTTTT
1 CTTTTT CTTTTT C-TTTTT CTTTTT CTT--TTT CTTTT-T CT---TTTT
** * ** * *
21485543 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTCTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
21485591 GTTTCTTTCA
Statistics
Matches: 67, Mismatches: 15, Indels: 16
0.68 0.15 0.16
Matches are distributed among these distances:
5 5 0.07
6 43 0.64
7 8 0.12
8 6 0.09
9 2 0.03
10 3 0.04
ACGTcount: A:0.07, C:0.21, G:0.03, T:0.69
Consensus pattern (6 bp):
CTTTTT
Found at i:21486641 original size:14 final size:14
Alignment explanation
Indices: 21486624--21486685 Score: 53
Period size: 14 Copynumber: 4.6 Consensus size: 14
21486614 TTAACTTGAT
21486624 TTTTTTTTGCTCAC
1 TTTTTTTTGCTCAC
* *
21486638 TTTTTTTCT-TTCTC
1 TTTTTTT-TGCTCAC
21486652 TTTTTTTTGCTCGA-
1 TTTTTTTTGCTC-AC
21486666 -TTTTTTT--TCAC
1 TTTTTTTTGCTCAC
21486677 TTTTTTTTG
1 TTTTTTTTG
21486686 AATTTTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 13
0.69 0.07 0.24
Matches are distributed among these distances:
10 1 0.03
11 2 0.05
12 7 0.18
13 8 0.21
14 19 0.50
15 1 0.03
ACGTcount: A:0.05, C:0.16, G:0.06, T:0.73
Consensus pattern (14 bp):
TTTTTTTTGCTCAC
Found at i:21486683 original size:28 final size:28
Alignment explanation
Indices: 21486608--21486684 Score: 77
Period size: 28 Copynumber: 2.7 Consensus size: 28
21486598 ACTTTTCACT
*
21486608 TTTTTTTTAACTTGATTTTTTTTTGCTCA
1 TTTTTTTTCACTT-ATTTTTTTTTGCTCA
* * *
21486637 CTTTTTTTC-TTTCTCTTTTTTTTGCTCGA
1 TTTTTTTTCACTTAT-TTTTTTTTGCTC-A
21486666 TTTTTTTTCACTT-TTTTTT
1 TTTTTTTTCACTTATTTTTT
21486685 GAATTTTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
27 1 0.03
28 19 0.49
29 17 0.44
30 2 0.05
ACGTcount: A:0.08, C:0.14, G:0.05, T:0.73
Consensus pattern (28 bp):
TTTTTTTTCACTTATTTTTTTTTGCTCA
Done.