Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A01
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: 104050246
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4660000 characters in sequence are not A, C, G, or T
File 9 of 316
Found at i:2662150 original size:10 final size:11
Alignment explanation
Indices: 2662126--2662171 Score: 60
Period size: 11 Copynumber: 4.3 Consensus size: 11
2662116 GGTTTCGACA
2662126 ATTATTATATT
1 ATTATTATATT
2662137 ATTATTAT-TT
1 ATTATTATATT
2662147 ATTATTATATT
1 ATTATTATATT
*
2662158 -TATATAATATT
1 AT-TATTATATT
2662169 ATT
1 ATT
2662172 GATAGGTACT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
10 11 0.35
11 19 0.61
12 1 0.03
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
ATTATTATATT
Found at i:2662333 original size:25 final size:28
Alignment explanation
Indices: 2662283--2662338 Score: 73
Period size: 25 Copynumber: 2.1 Consensus size: 28
2662273 TTTTTAATGC
*
2662283 TATGTATACACTTTGTAATATTATTA-T
1 TATGTATACACTTTGTAATATCATTAGT
*
2662310 TATGTATATA-TTT-TAATATCATTAGT
1 TATGTATACACTTTGTAATATCATTAGT
2662336 TAT
1 TAT
2662339 ACATTTTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 10 0.38
26 7 0.27
27 9 0.35
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.54
Consensus pattern (28 bp):
TATGTATACACTTTGTAATATCATTAGT
Found at i:2662638 original size:11 final size:11
Alignment explanation
Indices: 2662616--2662646 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
2662606 ATATTTATTT
2662616 TATATATATATG
1 TATATAT-TATG
2662628 TATATATTATG
1 TATATATTATG
2662639 TATATATT
1 TATATATT
2662647 TTAACATTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.63
12 7 0.37
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (11 bp):
TATATATTATG
Found at i:2664883 original size:43 final size:43
Alignment explanation
Indices: 2664824--2664981 Score: 220
Period size: 43 Copynumber: 3.8 Consensus size: 43
2664814 TTTATTGGAA
2664824 AAAAACGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGG
1 AAAAACGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGG
2664867 AAAAACGCCGCT--A----AAGGCTTTTAGCGGCGTTTGTGGG
1 AAAAACGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGG
* ** *
2664904 GAAAGTGCCGCTAAAGGTCAAGGCTTTTAGCGGAGTTTGTGGG
1 AAAAACGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGG
* *
2664947 AAAAGCGCCGCTAACGGTCAAGGCTTTTAGCGGCG
1 AAAAACGCCGCTAAAGGTCAAGGCTTTTAGCGGCG
2664982 CTTTTTCTAC
Statistics
Matches: 101, Mismatches: 8, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
37 33 0.33
39 1 0.01
41 1 0.01
43 66 0.65
ACGTcount: A:0.25, C:0.19, G:0.34, T:0.23
Consensus pattern (43 bp):
AAAAACGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGG
Found at i:2664893 original size:37 final size:37
Alignment explanation
Indices: 2664843--2664960 Score: 146
Period size: 37 Copynumber: 3.0 Consensus size: 37
2664833 GCTAAAGGTC
*
2664843 AAGGCTTTTAGCGGCGTTTGTGGGAAAAACGCCGCTA
1 AAGGCTTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTA
* *
2664880 AAGGCTTTTAGCGGCGTTTGTGGGGAAAGTGCCGCTAAA
1 AAGGCTTTTAGCGGCGTTTGTGGGAAAAGCGCCGCT--A
*
2664919 GGTCAAGGCTTTTAGCGGAGTTTGTGGGAAAAGCGCCGCTA
1 ----AAGGCTTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTA
2664960 A
1 A
2664961 CGGTCAAGGC
Statistics
Matches: 69, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
37 34 0.49
39 1 0.01
41 1 0.01
43 33 0.48
ACGTcount: A:0.24, C:0.17, G:0.35, T:0.25
Consensus pattern (37 bp):
AAGGCTTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTA
Found at i:2665133 original size:32 final size:31
Alignment explanation
Indices: 2665056--2665137 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
2665046 CTTCCTGCAT
* * *
2665056 TAAAATCCAACCAAATACAACAAATATAATA
1 TAAAATACAACCAAAAACAACAAATATAACA
* * * *
2665087 TAAAATGCAGCCAAAAACAGCAAATTTAACA
1 TAAAATACAACCAAAAACAACAAATATAACA
2665118 TAAAAATACAACCAAAAACA
1 T-AAAATACAACCAAAAACA
2665138 TTAATTCTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
31 26 0.62
32 16 0.38
ACGTcount: A:0.61, C:0.20, G:0.04, T:0.16
Consensus pattern (31 bp):
TAAAATACAACCAAAAACAACAAATATAACA
Found at i:2669964 original size:14 final size:15
Alignment explanation
Indices: 2669940--2669969 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
2669930 CACAAACTTC
2669940 AGAATTTATGTATTT
1 AGAATTTATGTATTT
2669955 AGAA-TTATGTATTT
1 AGAATTTATGTATTT
2669969 A
1 A
2669970 TATAAACACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (15 bp):
AGAATTTATGTATTT
Found at i:2672414 original size:29 final size:29
Alignment explanation
Indices: 2672363--2672418 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
2672353 TAGTGTTTAT
*
2672363 GTTTTATGTTTTAAAATTTAGGGTTTAGG
1 GTTTAATGTTTTAAAATTTAGGGTTTAGG
*
2672392 GTTTAATG-TTTAAGATTTAAGGGTTTA
1 GTTTAATGTTTTAAAATTT-AGGGTTTA
2672419 CAGAAAGCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 9 0.38
29 15 0.62
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (29 bp):
GTTTAATGTTTTAAAATTTAGGGTTTAGG
Found at i:2672753 original size:41 final size:40
Alignment explanation
Indices: 2672708--2673000 Score: 318
Period size: 41 Copynumber: 7.2 Consensus size: 40
2672698 AACTTTTTGC
* *
2672708 GGCGTTTGGACCAAAAACGCCGCTATTAATCAGTTTTTAGT
1 GGCGTTTGGA-TAAAAACGCCGCTATTGATCAGTTTTTAGT
* *
2672749 GGCGTTTTGGATAAAAACGCCACAATTGATCAGTTTTTAGT
1 GGCG-TTTGGATAAAAACGCCGCTATTGATCAGTTTTTAGT
* * * *
2672790 GGCGTTTTGGATAAAAGCACCACAATT-ATTCAGTTTTTAGT
1 GGCG-TTTGGATAAAAACGCCGCTATTGA-TCAGTTTTTAGT
*
2672831 GGCGTTTGGGATAAAAACGCCGCAATTGATCAGTTTTTAGT
1 GGCGTTT-GGATAAAAACGCCGCTATTGATCAGTTTTTAGT
* *
2672872 GGCGTTTGGGATTAAAACGCCGCTATTGATCAGCTTTTAGT
1 GGCGTTT-GGATAAAAACGCCGCTATTGATCAGTTTTTAGT
* ** *
2672913 GGCGTTTTGCGAAAAACGCCGCTATTGACCAGTTTTTAGT
1 GGCGTTTGGATAAAAACGCCGCTATTGATCAGTTTTTAGT
* ** * * * *
2672953 GGCGTTTTTGCCAAAAACGCCGCTATAGTTTAGCTTTTAGT
1 GGCG-TTTGGATAAAAACGCCGCTATTGATCAGTTTTTAGT
2672994 GGCGTTT
1 GGCGTTT
2673001 CGGACAAACG
Statistics
Matches: 223, Mismatches: 24, Indels: 11
0.86 0.09 0.04
Matches are distributed among these distances:
40 38 0.17
41 178 0.80
42 7 0.03
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (40 bp):
GGCGTTTGGATAAAAACGCCGCTATTGATCAGTTTTTAGT
Found at i:2672795 original size:82 final size:82
Alignment explanation
Indices: 2672708--2673000 Score: 351
Period size: 82 Copynumber: 3.6 Consensus size: 82
2672698 AACTTTTTGC
* *
2672708 GGCG-TTTGGACCAAAAACGCCGCTATTAATCAGTTTTTAGTGGCGTTTTGGATAAAAACGCCAC
1 GGCGTTTTGGA-CAAAAACGCCGCTATTAATCAGCTTTTAGTGGCGTTTTGGATAAAAACGCCGC
2672772 AATTGATCAGTTTTTAGT
65 AATTGATCAGTTTTTAGT
* * * * * * * *
2672790 GGCGTTTTGGATAAAAGCACCACAATTATTCAGTTTTTAGTGGCGTTTGGGATAAAAACGCCGCA
1 GGCGTTTTGGACAAAAACGCCGCTATTAATCAGCTTTTAGTGGCGTTTTGGATAAAAACGCCGCA
2672855 ATTGATCAGTTTTTAGT
66 ATTGATCAGTTTTTAGT
* ** *
2672872 GGCGTTTGGGATTAAAACGCCGCTATTGATCAGCTTTTAGTGGCGTTTTGCG--AAAAACGCCGC
1 GGCGTTTTGGACAAAAACGCCGCTATTAATCAGCTTTTAGTGGCGTTTTG-GATAAAAACGCCGC
* *
2672935 TATTGACCAGTTTTTAGT
65 AATTGATCAGTTTTTAGT
* * * *
2672953 GGCGTTTTTGCCAAAAACGCCGCTA-TAGTTTAGCTTTTAGTGGCGTTT
1 GGCGTTTTGGACAAAAACGCCGCTATTA-ATCAGCTTTTAGTGGCGTTT
2673001 CGGACAAACG
Statistics
Matches: 180, Mismatches: 28, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
80 1 0.01
81 65 0.36
82 107 0.59
83 7 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (82 bp):
GGCGTTTTGGACAAAAACGCCGCTATTAATCAGCTTTTAGTGGCGTTTTGGATAAAAACGCCGCA
ATTGATCAGTTTTTAGT
Found at i:2678293 original size:16 final size:16
Alignment explanation
Indices: 2678272--2678330 Score: 66
Period size: 16 Copynumber: 3.5 Consensus size: 16
2678262 ATATTTATAT
2678272 ATTTTTTATTAATTTA
1 ATTTTTTATTAATTTA
2678288 ATTTTTATAGTTAAATTTA
1 ATTTTT-TA-TT-AATTTA
*
2678307 ATTTTTTA-AAATATTA
1 ATTTTTTATTAAT-TTA
2678323 ATTTTTTA
1 ATTTTTTA
2678331 ACGATACTGA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
15 3 0.08
16 17 0.45
17 2 0.05
18 4 0.11
19 12 0.32
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.63
Consensus pattern (16 bp):
ATTTTTTATTAATTTA
Found at i:2680637 original size:30 final size:30
Alignment explanation
Indices: 2680568--2680637 Score: 70
Period size: 30 Copynumber: 2.4 Consensus size: 30
2680558 AATATACGGG
* * *
2680568 AATA-AGTTGCTCGCACGAGCTGACAGTAT
1 AATAGAGTTGCTCACACAAGCTAACAGTAT
** * *
2680597 ACCAGGGTTGCTCACACAAGCTAACATTAT
1 AATAGAGTTGCTCACACAAGCTAACAGTAT
2680627 AATAGAGTTGC
1 AATAGAGTTGC
2680638 CCAAAAAAGC
Statistics
Matches: 30, Mismatches: 10, Indels: 1
0.73 0.24 0.02
Matches are distributed among these distances:
29 2 0.07
30 28 0.93
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.24
Consensus pattern (30 bp):
AATAGAGTTGCTCACACAAGCTAACAGTAT
Found at i:2682264 original size:131 final size:131
Alignment explanation
Indices: 2681965--2682362 Score: 478
Period size: 131 Copynumber: 3.0 Consensus size: 131
2681955 TTGCCTCGCC
* * *
2681965 TTAGAAAACACGAGTGAAATTCTGAAGGGATACTT-GATTATTTTGAACAAACGGGAGATTGCAA
1 TTAGAAAACATGAGTGAAATTCTGAAGGG--ACTTCGATTATTTTGAACAAACGAGAAATTGCAA
* * *
2682029 CCCAGCACGATAGGGCACTATTCCCCGAATTGCCAAACATCGAACATTTCTTTCGTTTTAAATAG
64 CCCAGCACGATAGGGCACTATTCCCCGAATTGCCAAACATCGAACATTTCCTTCGTTTCAAAGAG
2682094 TTT
129 TTT
* * * * * **
2682097 TTAGAAAACGTGAGTGAAATTCCGAAGGAATCTTCGATTGTTTTGAACAAACGAAAAAGCGCAAC
1 TTAGAAAACATGAGTGAAATTCTGAAGGGA-CTTCGATTATTTTGAACAAACGAGAAATTGCAAC
* * * * * *
2682162 CCAGCACGATAAGGCACGATT-CTCAAATCGCCAAACATCGAACATTTCCTTCGTTTCAAAGATT
65 CCAGCACGATAGGGCACTATTCCCCGAATTGCCAAACATCGAACATTTCCTTCGTTTCAAAGAGT
2682226 TT
130 TT
* * * *
2682228 TTAGGAACCATGAGTGAAATTCTAAAGGGACGTTCGATTATTTTGAGCAAACGAGAAATTGCAAC
1 TTAGAAAACATGAGTGAAATTCTGAAGGGAC-TTCGATTATTTTGAACAAACGAGAAATTGCAAC
* * ** *
2682293 CCAGCACGATAGGGCACTATTCCGCGGATTGCCAAACATCGAACATCGCCTTCGTTTTGAAAG-G
65 CCAGCACGATAGGGCACTATTCCCCGAATTGCCAAACATCGAACATTTCCTTCG-TTTCAAAGAG
2682357 TTT
129 TTT
2682360 TTA
1 TTA
2682363 AATGAATAAT
Statistics
Matches: 221, Mismatches: 40, Indels: 10
0.82 0.15 0.04
Matches are distributed among these distances:
130 2 0.01
131 112 0.51
132 100 0.45
133 7 0.03
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (131 bp):
TTAGAAAACATGAGTGAAATTCTGAAGGGACTTCGATTATTTTGAACAAACGAGAAATTGCAACC
CAGCACGATAGGGCACTATTCCCCGAATTGCCAAACATCGAACATTTCCTTCGTTTCAAAGAGTT
T
Found at i:2684430 original size:18 final size:19
Alignment explanation
Indices: 2684403--2684439 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
2684393 TGAATTGATT
2684403 TCCTCTTTTTTTCAATCGG
1 TCCTCTTTTTTTCAATCGG
2684422 TCCTC-TTTTTTCAATCGG
1 TCCTCTTTTTTTCAATCGG
2684440 GCCCCCTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.11, C:0.27, G:0.11, T:0.51
Consensus pattern (19 bp):
TCCTCTTTTTTTCAATCGG
Found at i:2688442 original size:18 final size:18
Alignment explanation
Indices: 2688419--2688453 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2688409 AGGCGCAACC
*
2688419 AACTTTTTTTTATATTAA
1 AACTTTTTTTTAAATTAA
2688437 AACTTTTTTTTAAATTA
1 AACTTTTTTTTAAATTA
2688454 TTATTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (18 bp):
AACTTTTTTTTAAATTAA
Found at i:2688535 original size:13 final size:13
Alignment explanation
Indices: 2688517--2688541 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2688507 CCGTGTAGAG
2688517 ATACAAAAATGGT
1 ATACAAAAATGGT
2688530 ATACAAAAATGG
1 ATACAAAAATGG
2688542 CAATTTATAA
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:0.56, C:0.08, G:0.16, T:0.20
Consensus pattern (13 bp):
ATACAAAAATGGT
Found at i:2688685 original size:60 final size:60
Alignment explanation
Indices: 2688619--2688736 Score: 209
Period size: 60 Copynumber: 2.0 Consensus size: 60
2688609 TACTAAACTG
* **
2688619 AACACAACAATTTATAACATTATCCTAAATTACTATTAAATTAATTTTAAAATAATTACA
1 AACACAACAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTACA
2688679 AACACAACAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
1 AACACAACAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
2688737 TAAAAAAATT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.35
Consensus pattern (60 bp):
AACACAACAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTACA
Found at i:2689289 original size:34 final size:35
Alignment explanation
Indices: 2689245--2689311 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
2689235 CAGTAAAATA
* *
2689245 TTTTCCGTAAAATGATTT-TTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
2689279 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
2689312 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.07, G:0.13, T:0.48
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:2689315 original size:14 final size:15
Alignment explanation
Indices: 2689239--2689315 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
2689229 GATTGCCAGT
* *
2689239 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
2689253 AAAATGATTTT-TGG
1 AAAATGATTTTCTGG
*
2689267 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
2689287 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
2689302 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
2689316 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 20 0.40
15 16 0.32
16 1 0.02
18 1 0.02
19 4 0.08
20 8 0.16
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:2691607 original size:61 final size:61
Alignment explanation
Indices: 2691535--2691658 Score: 239
Period size: 61 Copynumber: 2.0 Consensus size: 61
2691525 CGGATATTTA
*
2691535 TTTGTATATTTTTAACTGTAACATTACTCTTAATTAAGTAATTGGTTCAGTTGATGTTTTT
1 TTTGTATATTTTTAACTGTAACATCACTCTTAATTAAGTAATTGGTTCAGTTGATGTTTTT
2691596 TTTGTATATTTTTAACTGTAACATCACTCTTAATTAAGTAATTGGTTCAGTTGATGTTTTT
1 TTTGTATATTTTTAACTGTAACATCACTCTTAATTAAGTAATTGGTTCAGTTGATGTTTTT
2691657 TT
1 TT
2691659 GTAACTGAAT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.26, C:0.09, G:0.13, T:0.52
Consensus pattern (61 bp):
TTTGTATATTTTTAACTGTAACATCACTCTTAATTAAGTAATTGGTTCAGTTGATGTTTTT
Found at i:2692370 original size:20 final size:20
Alignment explanation
Indices: 2692332--2692371 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2692322 TACTTATAAT
*
2692332 AAACACTTTTGGGACAAAAA
1 AAACACTTTTGAGACAAAAA
*
2692352 AAACACTTTTGAGATAAAAA
1 AAACACTTTTGAGACAAAAA
2692372 CATTGTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.23
Consensus pattern (20 bp):
AAACACTTTTGAGACAAAAA
Found at i:2699736 original size:112 final size:112
Alignment explanation
Indices: 2699534--2699763 Score: 433
Period size: 112 Copynumber: 2.0 Consensus size: 112
2699524 AAGTGCCATG
*
2699534 GAGGCCCTTCTATTATGAGCCAAATTATATTTTACCCCTCTATTGAAAAAAGTAGAAATGGATGA
1 GAGG-CCTTCTATTATGAGCCAAATTATATTTTACCCCTCTACTGAAAAAAGTAGAAATGGATGA
2699599 AAATTTTAATTGAAAGAATCAGGATTAATTTGCTCAATTTTGAGTAAA
65 AAATTTTAATTGAAAGAATCAGGATTAATTTGCTCAATTTTGAGTAAA
*
2699647 GAGGCCTTCTATTATGAGCCAGATTATATTTTACCCCTCTACTGAAAAAAGTAGAAATGGATGAA
1 GAGGCCTTCTATTATGAGCCAAATTATATTTTACCCCTCTACTGAAAAAAGTAGAAATGGATGAA
2699712 AATTTTAATTGAAAGAATCAGGATTAATTTGCTCAATTTTGAGTAAA
66 AATTTTAATTGAAAGAATCAGGATTAATTTGCTCAATTTTGAGTAAA
2699759 GAGGC
1 GAGGC
2699764 AAAATACAAT
Statistics
Matches: 115, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
112 111 0.97
113 4 0.03
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (112 bp):
GAGGCCTTCTATTATGAGCCAAATTATATTTTACCCCTCTACTGAAAAAAGTAGAAATGGATGAA
AATTTTAATTGAAAGAATCAGGATTAATTTGCTCAATTTTGAGTAAA
Found at i:2701550 original size:14 final size:14
Alignment explanation
Indices: 2701531--2701558 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2701521 TTCAATTTGG
2701531 TACCTATATTTTTT
1 TACCTATATTTTTT
2701545 TACCTATATTTTTT
1 TACCTATATTTTTT
2701559 CTTTGTCTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.00, T:0.64
Consensus pattern (14 bp):
TACCTATATTTTTT
Found at i:2704053 original size:16 final size:16
Alignment explanation
Indices: 2704034--2704068 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
2704024 ATAATAAAAC
2704034 TGTAATGAAATAGAGT
1 TGTAATGAAATAGAGT
*
2704050 TGTAATGTAATAGAGT
1 TGTAATGAAATAGAGT
2704066 TGT
1 TGT
2704069 GATCAGTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.26, T:0.37
Consensus pattern (16 bp):
TGTAATGAAATAGAGT
Found at i:2705302 original size:24 final size:24
Alignment explanation
Indices: 2705257--2705303 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2705247 ATATTAAAAG
*
2705257 ATATATATATAAAATGTATACATA
1 ATATATATATAAAATATATACATA
*
2705281 ATATA-ATATTAAAATATTTACAT
1 ATATATATA-TAAAATATATACAT
2705304 GGCATATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (24 bp):
ATATATATATAAAATATATACATA
Found at i:2705856 original size:39 final size:39
Alignment explanation
Indices: 2705813--2705963 Score: 178
Period size: 39 Copynumber: 3.9 Consensus size: 39
2705803 GATTCCACTC
* *
2705813 CCCCCATGCTACTTTGTTTTATTATTAATCAAAAAC-ACT
1 CCCCCATACTATTTTGTTTTATTATTAAT-AAAAACTACT
* * * *
2705852 CCCCCATGCTATTTTGTTTTATTGTTAATTAAAACTATT
1 CCCCCATACTATTTTGTTTTATTATTAATAAAAACTACT
* * *
2705891 TCCCCATACTATTTTGTTTTATTGTTAATTAAAACTACT
1 CCCCCATACTATTTTGTTTTATTATTAATAAAAACTACT
* * *
2705930 TCCTCATACTATTTTGTTTTATTATTAATTAAAA
1 CCCCCATACTATTTTGTTTTATTATTAATAAAAA
2705964 TCATACTTTA
Statistics
Matches: 102, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
38 5 0.05
39 97 0.95
ACGTcount: A:0.29, C:0.19, G:0.05, T:0.47
Consensus pattern (39 bp):
CCCCCATACTATTTTGTTTTATTATTAATAAAAACTACT
Found at i:2705913 original size:78 final size:78
Alignment explanation
Indices: 2705814--2705963 Score: 212
Period size: 78 Copynumber: 1.9 Consensus size: 78
2705804 ATTCCACTCC
* * *
2705814 CCCCATGCTACTTTGTTTTATTATTAATCAAAAAC-ACTCCCCCATGCTATTTTGTTTTATTGTT
1 CCCCATACTACTTTGTTTTATTATTAAT-AAAAACTACTCCCCCATACTATTTTGTTTTATTATT
2705878 AATTAAAACTATTT
65 AATTAAAACTATTT
* * * * *
2705892 CCCCATACTATTTTGTTTTATTGTTAATTAAAACTACTTCCTCATACTATTTTGTTTTATTATTA
1 CCCCATACTACTTTGTTTTATTATTAATAAAAACTACTCCCCCATACTATTTTGTTTTATTATTA
2705957 ATTAAAA
66 ATTAAAA
2705964 TCATACTTTA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
77 5 0.08
78 58 0.92
ACGTcount: A:0.29, C:0.18, G:0.05, T:0.47
Consensus pattern (78 bp):
CCCCATACTACTTTGTTTTATTATTAATAAAAACTACTCCCCCATACTATTTTGTTTTATTATTA
ATTAAAACTATTT
Found at i:2723664 original size:13 final size:13
Alignment explanation
Indices: 2723646--2723687 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
2723636 CCGGCTCCGT
*
2723646 CCGCCGCCATCCA
1 CCGCCGCCAGCCA
*
2723659 CCGCCGCCGGCCA
1 CCGCCGCCAGCCA
*
2723672 CCGCCGCCGGCCA
1 CCGCCGCCAGCCA
2723685 CCG
1 CCG
2723688 TGAAAATTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.10, C:0.62, G:0.26, T:0.02
Consensus pattern (13 bp):
CCGCCGCCAGCCA
Found at i:2724123 original size:38 final size:39
Alignment explanation
Indices: 2724069--2724323 Score: 205
Period size: 39 Copynumber: 6.5 Consensus size: 39
2724059 CCGCTACAGA
2724069 ACGCCAAATCTGTATC-TCGATCTGCTCTCGCCTACG-G
1 ACGCCAAATCTGTATCTTCGATCTGCTCTCGCCTACGAG
*
2724106 ACGCCAAATCTGTTATCTTCGAT-TG-TTTCTGCGC-ACGAG
1 ACGCCAAATCTG-TATCTTCGATCTGCTCTC-GC-CTACGAG
2724145 ACGCCAAATCTGTATCTTCGATCTGCTCTCGCCTACAGAG
1 ACGCCAAATCTGTATCTTCGATCTGCTCTCGCCTAC-GAG
* * * *
2724185 A-GCCAAATCTGTTTTTTCGATCTGCTTTCCGCCCTACAAG
1 ACGCCAAATCTGTATCTTCGATCTGCTCT-CG-CCTACGAG
* *
2724225 ATGCCAAATC---A-CTTC-ATCTGCTCTCCCCGCTACAGAG
1 ACGCCAAATCTGTATCTTCGATCTGCTCT-CGC-CTAC-GAG
2724262 A-G-CAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAG
1 ACGCCAAATCTG-TATCTTCGATCTGCTCT-CG-C-CTAC-GAG
*
2724304 ATGCCAAAT-TGTTATCTTCG
1 ACGCCAAATCTG-TATCTTCG
2724324 CCAAATCTTA
Statistics
Matches: 183, Mismatches: 12, Indels: 40
0.78 0.05 0.17
Matches are distributed among these distances:
35 7 0.04
36 15 0.08
37 21 0.11
38 22 0.12
39 50 0.27
40 16 0.09
41 24 0.13
42 11 0.06
43 12 0.07
44 5 0.03
ACGTcount: A:0.22, C:0.31, G:0.17, T:0.30
Consensus pattern (39 bp):
ACGCCAAATCTGTATCTTCGATCTGCTCTCGCCTACGAG
Found at i:2724258 original size:36 final size:41
Alignment explanation
Indices: 2724059--2724409 Score: 160
Period size: 39 Copynumber: 8.5 Consensus size: 41
2724049 TTCACTCTCT
*
2724059 CCGCTACAGA-ACGCCAAATCTGTATC-TCGATCTGCTCT-CG
1 CCGCTACAGAGATGCCAAATC--TATCTTCGATCTGCTCTCCG
* * *
2724099 -C-CTAC-G-GACGCCAAATCTGTTATCTTCGAT-TG-TTTCTG
1 CCGCTACAGAGATGCCAAATC---TATCTTCGATCTGCTCTCCG
*
2724137 -CGC-AC-GAGACGCCAAATCTGTATCTTCGATCTGCTCT-CG
1 CCGCTACAGAGATGCCAAATC--TATCTTCGATCTGCTCTCCG
* * *
2724176 -C-CTACAGAGA-GCCAAATCTGTTTTTTCGATCTGCTTTCCG
1 CCGCTACAGAGATGCCAAATC--TATCTTCGATCTGCTCTCCG
2724216 CC-CTACA-AGATGCCAAATC-A-CTTC-ATCTGCTCTCC-
1 CCGCTACAGAGATGCCAAATCTATCTTCGATCTGCTCTCCG
2724251 CCGCTACAGAGA-G-CAAATCTGTTATCTTCGATCTGCTCTCCG
1 CCGCTACAGAGATGCCAAATC---TATCTTCGATCTGCTCTCCG
*
2724293 CCGCTACAGAGATGCCAAATTGTTATCTTCGCCAAATCTTATCTTCGATCTGCCTCCG
1 CCGCTACAGAGATGCCAAA-T-CTATCTTCG---------ATC-T-G--CT--CTCCG
2724351 CCGCTACAGAGATGCC-AATC-ATCTTCGATCTGCTCTCCG
1 CCGCTACAGAGATGCCAAATCTATCTTCGATCTGCTCTCCG
*
2724390 CCCGCTACAGAGACGCCAAA
1 -CCGCTACAGAGATGCCAAA
2724410 CACCATTCTC
Statistics
Matches: 251, Mismatches: 17, Indels: 85
0.71 0.05 0.24
Matches are distributed among these distances:
35 8 0.03
36 16 0.06
37 19 0.08
38 26 0.10
39 54 0.22
40 30 0.12
41 29 0.12
42 12 0.05
43 10 0.04
44 5 0.02
45 4 0.02
52 3 0.01
53 1 0.00
54 8 0.03
56 3 0.01
57 2 0.01
58 21 0.08
ACGTcount: A:0.22, C:0.33, G:0.17, T:0.28
Consensus pattern (41 bp):
CCGCTACAGAGATGCCAAATCTATCTTCGATCTGCTCTCCG
Found at i:2724259 original size:77 final size:78
Alignment explanation
Indices: 2724085--2724312 Score: 235
Period size: 77 Copynumber: 2.9 Consensus size: 78
2724075 AATCTGTATC
* * *
2724085 TCGATCTGCTCTCGCCTAC-G-GACGCCAAATCTGTTATCTTCGAT-TG-TTTCTG-CGC-AC-G
1 TCGATCTGCTCTCCCCTACAGAGA-G-CAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAG
*
2724143 AGACGCCAAATCTGTATCT
64 AGATGCCAAATC---A-CT
* * *
2724162 TCGATCTGCTCTCGCCTACAGAGAGCCAAATCTGTT-TTTTCGATCTGCTTTCCGCC-CTACA-A
1 TCGATCTGCTCTCCCCTACAGAGAG-CAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGA
2724224 GATGCCAAATCACT
65 GATGCCAAATCACT
2724238 TC-ATCTGCTCTCCCCGCTACAGAGAGCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAG
1 TCGATCTGCTCT-CCC-CTACAGAGAGCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAG
2724302 AGATGCCAAAT
64 AGATGCCAAAT
2724313 TGTTATCTTC
Statistics
Matches: 133, Mismatches: 6, Indels: 22
0.83 0.04 0.14
Matches are distributed among these distances:
75 9 0.07
76 16 0.12
77 55 0.41
78 20 0.15
79 19 0.14
80 14 0.11
ACGTcount: A:0.21, C:0.32, G:0.18, T:0.29
Consensus pattern (78 bp):
TCGATCTGCTCTCCCCTACAGAGAGCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAG
ATGCCAAATCACT
Found at i:2724377 original size:38 final size:40
Alignment explanation
Indices: 2724333--2724408 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
2724323 GCCAAATCTT
*
2724333 ATCTTCGATCTGC-CTCCG-CCGCTACAGAGATGCCAATC
1 ATCTTCGATCTGCTCTCCGCCCGCTACAGAGACGCCAATC
2724371 ATCTTCGATCTGCTCTCCGCCCGCTACAGAGACGCCAA
1 ATCTTCGATCTGCTCTCCGCCCGCTACAGAGACGCCAA
2724409 ACACCATTCT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
38 13 0.37
39 5 0.14
40 17 0.49
ACGTcount: A:0.21, C:0.38, G:0.18, T:0.22
Consensus pattern (40 bp):
ATCTTCGATCTGCTCTCCGCCCGCTACAGAGACGCCAATC
Found at i:2724489 original size:39 final size:38
Alignment explanation
Indices: 2724443--2724565 Score: 119
Period size: 37 Copynumber: 3.2 Consensus size: 38
2724433 TCTCATCGCC
2724443 CCCCGCTACAGAGA-CCCAATCTGTATCCTCGATC-GCTCT
1 CCCCGCTACAGAGATCCCAATC---ATCCTCGATCTGCTCT
* *
2724482 CCCCGCTACA-AGATGCCAATCATCTTCGATCTGCTCT
1 CCCCGCTACAGAGATCCCAATCATCCTCGATCTGCTCT
* * * *
2724519 CGCCGCTACAGA-AGCCAAATCATCTTCCGATCTGCTCT
1 CCCCGCTACAGAGATCCCAATCATCCT-CGATCTGCTCT
2724557 CCGCCGCTA
1 CC-CCGCTA
2724566 AGGAGCCAAT
Statistics
Matches: 72, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
36 9 0.12
37 25 0.35
38 16 0.22
39 22 0.31
ACGTcount: A:0.21, C:0.40, G:0.15, T:0.24
Consensus pattern (38 bp):
CCCCGCTACAGAGATCCCAATCATCCTCGATCTGCTCT
Found at i:2724573 original size:38 final size:38
Alignment explanation
Indices: 2724471--2724574 Score: 137
Period size: 37 Copynumber: 2.8 Consensus size: 38
2724461 ATCTGTATCC
*
2724471 TCGATC-GCTCTCC-CCGCTACAAGATGCC-AATCATCT
1 TCGATCTGCTCTCCGCCGCTACAGGA-GCCAAATCATCT
*
2724507 TCGATCTGCTCT-CGCCGCTACAGAAGCCAAATCATCT
1 TCGATCTGCTCTCCGCCGCTACAGGAGCCAAATCATCT
2724544 TCCGATCTGCTCTCCGCCGCTA-AGGAGCCAA
1 T-CGATCTGCTCTCCGCCGCTACAGGAGCCAA
2724575 TCTGTTATCT
Statistics
Matches: 60, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
36 10 0.17
37 23 0.38
38 19 0.32
39 8 0.13
ACGTcount: A:0.22, C:0.38, G:0.17, T:0.23
Consensus pattern (38 bp):
TCGATCTGCTCTCCGCCGCTACAGGAGCCAAATCATCT
Found at i:2732709 original size:19 final size:20
Alignment explanation
Indices: 2732670--2732711 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
2732660 TTATGGCCTT
2732670 TAATGCATAATGATATGATG
1 TAATGCATAATGATATGATG
2732690 TAATGCA-AATG-TATGAATG
1 TAATGCATAATGATATG-ATG
2732709 TAA
1 TAA
2732712 AGGAGGCATC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 4 0.19
19 10 0.48
20 7 0.33
ACGTcount: A:0.43, C:0.05, G:0.19, T:0.33
Consensus pattern (20 bp):
TAATGCATAATGATATGATG
Found at i:2735664 original size:20 final size:20
Alignment explanation
Indices: 2735628--2735673 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
2735618 TCGGATCACC
*
2735628 TAAAA-ATTTAGTTATTTTAA
1 TAAAACATTTAG-TAATTTAA
*
2735648 TAAAACATTTA-TAATTTAC
1 TAAAACATTTAGTAATTTAA
2735667 TAAAACA
1 TAAAACA
2735674 ACAATTTTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 13 0.57
20 5 0.22
21 5 0.22
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (20 bp):
TAAAACATTTAGTAATTTAA
Found at i:2736726 original size:12 final size:12
Alignment explanation
Indices: 2736704--2736764 Score: 61
Period size: 12 Copynumber: 5.1 Consensus size: 12
2736694 ATAAAAAAAC
*
2736704 AATACTATATATA
1 AATA-TATACATA
*
2736717 AATATATATATA
1 AATATATACATA
*
2736729 TATATATACATA
1 AATATATACATA
* *
2736741 AAAATATACATT
1 AATATATACATA
2736753 AATATATA-ATA
1 AATATATACATA
2736764 A
1 A
2736765 TAATAGTAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
11 3 0.07
12 34 0.83
13 4 0.10
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (12 bp):
AATATATACATA
Found at i:2736996 original size:12 final size:12
Alignment explanation
Indices: 2736972--2737051 Score: 74
Period size: 12 Copynumber: 6.6 Consensus size: 12
2736962 GAGAGGGCAT
2736972 ATATAATATAATA
1 ATATAA-ATAATA
2736985 ATATAAATAATA
1 ATATAAATAATA
* *
2736997 ATATATACATGAGA
1 ATATA-A-ATAATA
2737011 A-AT-AATAATA
1 ATATAAATAATA
2737021 ATATAAATAATA
1 ATATAAATAATA
* *
2737033 GTAAAAATAATA
1 ATATAAATAATA
*
2737045 AAATAAA
1 ATATAAA
2737052 AAAATAAAAC
Statistics
Matches: 54, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
10 5 0.09
11 3 0.06
12 32 0.59
13 9 0.17
14 5 0.09
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (12 bp):
ATATAAATAATA
Found at i:2737398 original size:26 final size:26
Alignment explanation
Indices: 2737365--2737480 Score: 99
Period size: 26 Copynumber: 4.8 Consensus size: 26
2737355 TAGCCTTTCC
2737365 AAAACAAAAAACAACCCCTATTCCAA
1 AAAACAAAAAACAACCCCTATTCCAA
* **
2737391 AAAACAAAAAACTA-CCCTCCTCCAA
1 AAAACAAAAAACAACCCCTATTCCAA
*
2737416 AAAAC---AAAC--CTCC--TT-CAA
1 AAAACAAAAAACAACCCCTATTCCAA
*
2737434 AAAACAAAAAA-AACACCTCTCTTCCAA
1 AAAACAAAAAACAAC-CC-CTATTCCAA
2737461 AAAACAAAAAACAACCCCTA
1 AAAACAAAAAACAACCCCTA
2737481 AAAAACAAAG
Statistics
Matches: 71, Mismatches: 7, Indels: 24
0.70 0.07 0.24
Matches are distributed among these distances:
18 8 0.11
19 1 0.01
21 5 0.07
22 5 0.07
23 1 0.01
24 1 0.01
25 14 0.20
26 17 0.24
27 16 0.23
28 3 0.04
ACGTcount: A:0.56, C:0.32, G:0.00, T:0.12
Consensus pattern (26 bp):
AAAACAAAAAACAACCCCTATTCCAA
Found at i:2737399 original size:25 final size:25
Alignment explanation
Indices: 2737361--2737480 Score: 78
Period size: 25 Copynumber: 5.0 Consensus size: 25
2737351 AAACTAGCCT
*
2737361 TTCCAAAACA-AAAAACAACCCCTA
1 TTCCAAAAAACAAAAACAACCCCTA
* *
2737385 TTCCAAAAAACAAAAAACTA-CCCTC
1 TTCCAAAAAAC-AAAAACAACCCCTA
* *
2737410 CTCCAAAAAAC--AAAC--CTCC--
1 TTCCAAAAAACAAAAACAACCCCTA
* *
2737429 TT-CAAAAAACAAAAAAAACACCTCTC
1 TTCCAAAAAACAAAAACAAC-CC-CTA
2737455 TTCCAAAAAACAAAAAACAACCCCTA
1 TTCCAAAAAAC-AAAAACAACCCCTA
2737481 AAAAACAAAG
Statistics
Matches: 73, Mismatches: 10, Indels: 24
0.68 0.09 0.22
Matches are distributed among these distances:
18 8 0.11
19 1 0.01
20 3 0.04
21 2 0.03
22 5 0.07
23 1 0.01
24 10 0.14
25 14 0.19
26 11 0.15
27 10 0.14
28 8 0.11
ACGTcount: A:0.54, C:0.33, G:0.00, T:0.13
Consensus pattern (25 bp):
TTCCAAAAAACAAAAACAACCCCTA
Found at i:2737418 original size:18 final size:18
Alignment explanation
Indices: 2737395--2737441 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
2737385 TTCCAAAAAA
* *
2737395 CAAAAAACTACCCTCCTC
1 CAAAAAACAAACCTCCTC
*
2737413 CAAAAAACAAACCTCCTT
1 CAAAAAACAAACCTCCTC
2737431 CAAAAAACAAA
1 CAAAAAACAAA
2737442 AAAAACACCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.53, C:0.34, G:0.00, T:0.13
Consensus pattern (18 bp):
CAAAAAACAAACCTCCTC
Found at i:2737420 original size:44 final size:43
Alignment explanation
Indices: 2737369--2737467 Score: 114
Period size: 45 Copynumber: 2.2 Consensus size: 43
2737359 CTTTCCAAAA
2737369 CAAAAAACAACC-CCTATTCCAAAAAAC-AAAAAACTACC-CTCCTC
1 CAAAAAACAACCTCC--TT-CAAAAAACAAAAAAAC-ACCTCTCCTC
*
2737413 CAAAAAACAAACCTCCTTCAAAAAACAAAAAAAACACCTCTCTTC
1 CAAAAAAC-AACCTCCTTCAAAAAAC-AAAAAAACACCTCTCCTC
2737458 CAAAAAACAA
1 CAAAAAACAA
2737468 AAAACAACCC
Statistics
Matches: 49, Mismatches: 1, Indels: 10
0.82 0.02 0.17
Matches are distributed among these distances:
43 8 0.16
44 15 0.31
45 24 0.49
46 2 0.04
ACGTcount: A:0.55, C:0.32, G:0.00, T:0.13
Consensus pattern (43 bp):
CAAAAAACAACCTCCTTCAAAAAACAAAAAAACACCTCTCCTC
Found at i:2737444 original size:27 final size:27
Alignment explanation
Indices: 2737413--2737471 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
2737403 TACCCTCCTC
2737413 CAAAAAACAA-ACCTC-CTT-CAAAAAA
1 CAAAAAA-AACACCTCTCTTCCAAAAAA
2737438 CAAAAAAAACACCTCTCTTCCAAAAAA
1 CAAAAAAAACACCTCTCTTCCAAAAAA
2737465 CAAAAAA
1 CAAAAAA
2737472 CAACCCCTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
24 2 0.06
25 12 0.39
26 3 0.10
27 14 0.45
ACGTcount: A:0.61, C:0.27, G:0.00, T:0.12
Consensus pattern (27 bp):
CAAAAAAAACACCTCTCTTCCAAAAAA
Found at i:2737624 original size:4 final size:4
Alignment explanation
Indices: 2737615--2737649 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
2737605 GGCCAAGGTT
2737615 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
2737650 TTGTGTTTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:2739475 original size:44 final size:44
Alignment explanation
Indices: 2739284--2740292 Score: 1446
Period size: 44 Copynumber: 23.2 Consensus size: 44
2739274 TCCTTGAAAC
* **
2739284 AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAATAGATCGA
1 AGATAACAGATTTGGCATCTCTGTAGCGGCGGAGAGCAGATCGA
* *
2739328 AGAT----GATTTGGCATCTCTATAGCGGCGGAGAGTAGATCGA
1 AGATAACAGATTTGGCATCTCTGTAGCGGCGGAGAGCAGATCGA
*
2739368 AGAT----GATTTGGCATCTCTGTAGCGGCGGAGAGTAGATCGA
1 AGATAACAGATTTGGCATCTCTGTAGCGGCGGAGAGCAGATCGA
*
2739408 AGAT----GATTTGGCATCTCTGTAGCGGCGGAGAGCAGATCAA
1 AGATAACAGATTTGGCATCTCTGTAGCGGCGGAGAGCAGATCGA
2739448 AGATAACAGATTTGGCATCTCTGTAGCGGCGGAGAGCAGATCGA
1 AGATAACAGATTTGGCATCTCTGTAGCGGCGGAGAGCAGATCGA
** * *
2739492 AGATAACAGATTTGGTGTCTTTGTAGCGGCGGAGAACAGATCGA
1 AGATAACAGATTTGGCATCTCTGTAGCGGCGGAGAGCAGATCGA
* *
2739536 AGATAACAGATTTGACATCTCTGTAGCGGCGGAGAGTAGATCGA
1 AGATAACAGATTTGGCATCTCTGTAGCGGCGGAGAGCAGATCGA
* * * *
2739580 AGGTAACAAGATTTGGCGTCTCTGTAGCGGCGGTGAGCAGATCAA
1 AGATAAC-AGATTTGGCATCTCTGTAGCGGCGGAGAGCAGATCGA
* * *
2739625 AGAT----GATTTGGCATCGCTGTAGCAGTGGAGAGCAGATCGA
1 AGATAACAGATTTGGCATCTCTGTAGCGGCGGAGAGCAGATCGA
* *
2739665 AGATAACAGATTTGGCGTCTCTGTAGCGGCAGAGAGCAGATC-A
1 AGATAACAGATTTGGCATCTCTGTAGCGGCGGAGAGCAGATCGA
* * *
2739708 AGGATAACAAATTTGGCGTCTATGTAGCGGCGGAGAGCAGATCGA
1 A-GATAACAGATTTGGCATCTCTGTAGCGGCGGAGAGCAGATCGA
*
2739753 AGATAACAGATTTAGCATCTCTGTAGCGGCGGAGAGCAGATCGA
1 AGATAACAGATTTGGCATCTCTGTAGCGGCGGAGAGCAGATCGA
*
2739797 AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
1 AGATAACAGATTTGGCATCTCTGTAGCGGCGGAGAGCAGATCGA
* **
2739841 AGATAACATATTTGGCATCTCTGTAGCGGC-GAGAGCAGATTAA
1 AGATAACAGATTTGGCATCTCTGTAGCGGCGGAGAGCAGATCGA
2739884 AGATAACAGATTTGGCATCTCTGTAGCGGCGGAGAGCAGATCGA
1 AGATAACAGATTTGGCATCTCTGTAGCGGCGGAGAGCAGATCGA
*
2739928 A-AGTAACAAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
1 AGA-TAAC-AGATTTGGCATCTCTGTAGCGGCGGAGAGCAGATCGA
*
2739973 AGATAACAGATTTGGCATCTCTGTAGCGGCAGAGAGCAGATCGA
1 AGATAACAGATTTGGCATCTCTGTAGCGGCGGAGAGCAGATCGA
2740017 AGATAACAGATTTGGCATCTCTGTAGCGGCGGAGAGCAGATCGA
1 AGATAACAGATTTGGCATCTCTGTAGCGGCGGAGAGCAGATCGA
*
2740061 A-AGTAACAAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
1 AGA-TAAC-AGATTTGGCATCTCTGTAGCGGCGGAGAGCAGATCGA
* *
2740106 AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAACAGATCGA
1 AGATAACAGATTTGGCATCTCTGTAGCGGCGGAGAGCAGATCGA
*
2740150 AGATAACAGATTTGGCATCTCTGTAGCGGCGGAGAGCAAATCGA
1 AGATAACAGATTTGGCATCTCTGTAGCGGCGGAGAGCAGATCGA
* *
2740194 AGATAACAGATTTGGCATCTCCGTAGCAGCGGAGAGCAGATCGA
1 AGATAACAGATTTGGCATCTCTGTAGCGGCGGAGAGCAGATCGA
* * *
2740238 AGATAATAGATTTGGCATCTCTATAGCGGCAGAGAGCAGATCGA
1 AGATAACAGATTTGGCATCTCTGTAGCGGCGGAGAGCAGATCGA
*
2740282 AAATAACAGAT
1 AGATAACAGAT
2740293 CGGTGTTCCT
Statistics
Matches: 877, Mismatches: 70, Indels: 36
0.89 0.07 0.04
Matches are distributed among these distances:
40 148 0.17
43 44 0.05
44 564 0.64
45 119 0.14
46 2 0.00
ACGTcount: A:0.30, C:0.17, G:0.31, T:0.22
Consensus pattern (44 bp):
AGATAACAGATTTGGCATCTCTGTAGCGGCGGAGAGCAGATCGA
Found at i:2740617 original size:4 final size:4
Alignment explanation
Indices: 2740608--2740638 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
2740598 CCCAAACACA
2740608 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
2740639 AACCTTGGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:2740736 original size:38 final size:38
Alignment explanation
Indices: 2740640--2740726 Score: 174
Period size: 38 Copynumber: 2.3 Consensus size: 38
2740630 ATAAATAAAA
2740640 ACCTTGGCCACCTACTCCACCACCCTTGTTGGCCACCC
1 ACCTTGGCCACCTACTCCACCACCCTTGTTGGCCACCC
2740678 ACCTTGGCCACCTACTCCACCACCCTTGTTGGCCACCC
1 ACCTTGGCCACCTACTCCACCACCCTTGTTGGCCACCC
2740716 ACCTTGGCCAC
1 ACCTTGGCCAC
2740727 ATAAACCACC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.16, C:0.49, G:0.14, T:0.21
Consensus pattern (38 bp):
ACCTTGGCCACCTACTCCACCACCCTTGTTGGCCACCC
Found at i:2740847 original size:25 final size:25
Alignment explanation
Indices: 2740818--2740925 Score: 90
Period size: 25 Copynumber: 4.5 Consensus size: 25
2740808 TTTTAGGGGT
2740818 TGTTTTTTGTTTTTTGGAAGAGAGG
1 TGTTTTTTGTTTTTTGGAAGAGAGG
2740843 TGTTTTTTTTGTTTTTTGG-AG-GA-G
1 TG--TTTTTTGTTTTTTGGAAGAGAGG
*
2740867 -G---TTTGTTTTTTGGAGGAG-GG
1 TGTTTTTTGTTTTTTGGAAGAGAGG
* *
2740887 TAGTTTTTTG-TTTTTGGAATAGGGG
1 T-GTTTTTTGTTTTTTGGAAGAGAGG
2740912 TTGTTTTTTGTTTT
1 -TGTTTTTTGTTTT
2740926 GGAAAGGCTA
Statistics
Matches: 67, Mismatches: 3, Indels: 25
0.71 0.03 0.26
Matches are distributed among these distances:
18 12 0.18
19 1 0.01
20 2 0.03
22 1 0.01
23 1 0.01
24 11 0.16
25 18 0.27
26 6 0.09
27 15 0.22
ACGTcount: A:0.11, C:0.00, G:0.31, T:0.57
Consensus pattern (25 bp):
TGTTTTTTGTTTTTTGGAAGAGAGG
Found at i:2740855 original size:27 final size:25
Alignment explanation
Indices: 2740802--2740878 Score: 92
Period size: 27 Copynumber: 3.2 Consensus size: 25
2740792 CATTCAAGAC
2740802 TTTGTTTTTT--AGG-GG-TTGTTT
1 TTTGTTTTTTGGAGGAGGTTTGTTT
2740823 TTTGTTTTTTGGAAGAGAGGTGTT-TTT
1 TTTGTTTTTTGG-AG-GAGGT-TTGTTT
2740850 TTTGTTTTTTGGAGGAGGTTTGTTT
1 TTTGTTTTTTGGAGGAGGTTTGTTT
2740875 TTTG
1 TTTG
2740879 GAGGAGGGTA
Statistics
Matches: 48, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
21 10 0.21
24 4 0.08
25 13 0.27
26 4 0.08
27 15 0.31
28 2 0.04
ACGTcount: A:0.09, C:0.00, G:0.30, T:0.61
Consensus pattern (25 bp):
TTTGTTTTTTGGAGGAGGTTTGTTT
Found at i:2740873 original size:18 final size:18
Alignment explanation
Indices: 2740850--2740896 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
2740840 AGGTGTTTTT
2740850 TTTGTTTTTTGGAGGAGG
1 TTTGTTTTTTGGAGGAGG
2740868 TTTGTTTTTTGGAGGAGG
1 TTTGTTTTTTGGAGGAGG
* *
2740886 GTAGTTTTTTG
1 TTTGTTTTTTG
2740897 TTTTTGGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.11, C:0.00, G:0.36, T:0.53
Consensus pattern (18 bp):
TTTGTTTTTTGGAGGAGG
Found at i:2740910 original size:24 final size:23
Alignment explanation
Indices: 2740868--2740941 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 23
2740858 TTGGAGGAGG
*
2740868 TTTGTTTTTTGGAGGAGGGTAGTTT
1 TTTG-TTTTTGGA-AAGGGTAGTTT
*
2740893 TTTGTTTTTGGAATAGGGGTTGTTT
1 TTTGTTTTTGGAA-A-GGGTAGTTT
*
2740918 TTTG-TTTTGGAAAGGCTAGTTT
1 TTTGTTTTTGGAAAGGGTAGTTT
2740940 TT
1 TT
2740942 GGAGATTAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
22 9 0.21
23 1 0.02
24 17 0.40
25 16 0.37
ACGTcount: A:0.14, C:0.01, G:0.31, T:0.54
Consensus pattern (23 bp):
TTTGTTTTTGGAAAGGGTAGTTT
Found at i:2740916 original size:43 final size:45
Alignment explanation
Indices: 2740824--2740921 Score: 114
Period size: 43 Copynumber: 2.2 Consensus size: 45
2740814 GGGTTGTTTT
* * *
2740824 TTGTTTTTTGGAAGAGAGGTGTTTTTTTTGTTTTTTGGAGGAGGT
1 TTGTTTTTTGGAAGAGAGGTGTGTTTTTTGTTTTTTGGAAGAGGG
*
2740869 TTGTTTTTTGG-AG-GAGG-GTAGTTTTTTG-TTTTTGGAATAGGGG
1 TTGTTTTTTGGAAGAGAGGTGT-GTTTTTTGTTTTTTGGAAGA-GGG
2740912 TTGTTTTTTG
1 TTGTTTTTTG
2740922 TTTTGGAAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
42 11 0.23
43 23 0.49
44 2 0.04
45 11 0.23
ACGTcount: A:0.12, C:0.00, G:0.34, T:0.54
Consensus pattern (45 bp):
TTGTTTTTTGGAAGAGAGGTGTGTTTTTTGTTTTTTGGAAGAGGG
Found at i:2741255 original size:3 final size:3
Alignment explanation
Indices: 2741236--2741323 Score: 62
Period size: 3 Copynumber: 29.3 Consensus size: 3
2741226 GAGCTTTGTT
* *
2741236 TTA TT- TTA TTA TT- TTA TTA TTT TTA CTA TTA TT- TATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
2741279 TTA TTA TT- TCTCA TGTA TATA TTA TTA TT- TATA TTA TTA -TA TTA
1 TTA TTA TTA T-T-A T-TA T-TA TTA TTA TTA T-TA TTA TTA TTA TTA
2741323 T
1 T
2741324 ATATGCCCTC
Statistics
Matches: 69, Mismatches: 6, Indels: 20
0.73 0.06 0.21
Matches are distributed among these distances:
2 9 0.13
3 51 0.74
4 7 0.10
5 2 0.03
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:2741301 original size:21 final size:18
Alignment explanation
Indices: 2741236--2741323 Score: 90
Period size: 18 Copynumber: 4.7 Consensus size: 18
2741226 GAGCTTTGTT
2741236 TTATT-TTATTATTTTATTA
1 TTATTATTATTA-TTTA-TA
* *
2741255 TTTTTACTATTATTTATA
1 TTATTATTATTATTTATA
*
2741273 TTATTATTATTATTTCTCA
1 TTATTATTATTATTTAT-A
2741292 TGTATATATTATTATTTATA
1 T-TAT-TATTATTATTTATA
2741312 TTATTA-TATTAT
1 TTATTATTATTAT
2741324 ATATGCCCTC
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
17 6 0.10
18 18 0.31
19 13 0.22
20 10 0.17
21 12 0.20
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (18 bp):
TTATTATTATTATTTATA
Found at i:2741326 original size:27 final size:26
Alignment explanation
Indices: 2741240--2741327 Score: 81
Period size: 27 Copynumber: 3.3 Consensus size: 26
2741230 TTTGTTTTAT
* * *
2741240 TTTATTATTTTATTATTTTTACTATTA
1 TTTA-TATATTATTATTTATATTATTA
* *
2741267 TTTATATTATTATTA-TTAT-TTCTCA
1 TTTATA-TATTATTATTTATATTATTA
*
2741292 TGTATATATTATTATTTATATTATTA
1 TTTATATATTATTATTTATATTATTA
2741318 TATTATATAT
1 T-TTATATAT
2741328 GCCCTCCCCA
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
24 8 0.17
25 12 0.25
26 10 0.21
27 18 0.38
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (26 bp):
TTTATATATTATTATTTATATTATTA
Found at i:2742205 original size:132 final size:132
Alignment explanation
Indices: 2741980--2742219 Score: 345
Period size: 132 Copynumber: 1.8 Consensus size: 132
2741970 AACGGAAACG
* * * * *
2741980 ATGTTCGATGTTTAGCAATTCGGGGAATCGTGCCCTATCGTGTTAGGTTGTAATTTCTTGTTTGC
1 ATGTTCGACGTTCAGCAATTCGGGGAATCGTGCCCTATCGTGCTAGGTTGCAATTTCTCGTTTGC
* * * * *
2742045 CCAAAATAATCGGATGTCTCTTTAGAATTTCGTTCATGTTTTCTAAAAACCTTTTAAAACGAAGG
66 CCAAAATAATCGAATATCCCTTTAGAATTTCATTCACGTTTTCTAAAAACCTTTTAAAACGAAGG
2742110 AA
131 AA
* * *
2742112 ATGTTCGACGTTCGGCAATTCGGGGAATCGTGCCCTATCGTGCTGGGTTGCAATTTCTCGTTTGT
1 ATGTTCGACGTTCAGCAATTCGGGGAATCGTGCCCTATCGTGCTAGGTTGCAATTTCTCGTTTGC
* *
2742177 GCAAAATAATCGAATATCCCTTTGGAATTTCATTCACGTTTTC
66 CCAAAATAATCGAATATCCCTTTAGAATTTCATTCACGTTTTC
2742220 CAAAGCGAGA
Statistics
Matches: 93, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
132 93 1.00
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (132 bp):
ATGTTCGACGTTCAGCAATTCGGGGAATCGTGCCCTATCGTGCTAGGTTGCAATTTCTCGTTTGC
CCAAAATAATCGAATATCCCTTTAGAATTTCATTCACGTTTTCTAAAAACCTTTTAAAACGAAGG
AA
Found at i:2744715 original size:19 final size:19
Alignment explanation
Indices: 2744653--2744715 Score: 62
Period size: 18 Copynumber: 3.4 Consensus size: 19
2744643 AACAATTTAA
*
2744653 TTTTTTTAT-TTCTTTAT-
1 TTTTTTTCTCTTCTTTATC
*
2744670 TTTTCTTCTCTTCTTT-TC
1 TTTTTTTCTCTTCTTTATC
2744688 TTTTATTTCTC-TCTTTATC
1 TTTT-TTTCTCTTCTTTATC
2744707 TTATTTTTC
1 TT-TTTTTC
2744716 ACTACAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
17 8 0.21
18 15 0.39
19 13 0.34
20 2 0.05
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTTTTTCTCTTCTTTATC
Found at i:2747293 original size:32 final size:32
Alignment explanation
Indices: 2747252--2747316 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 32
2747242 ACATGGATCC
2747252 TTTGTTCAATCA-TTGCAAATGTAAATTCTCTT
1 TTTGTTCAATCATTTGC-AATGTAAATTCTCTT
*
2747284 TTTGTTCAATCATTTTCAATGTAAATTCTCTT
1 TTTGTTCAATCATTTGCAATGTAAATTCTCTT
2747316 T
1 T
2747317 CTCTTGCTGG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 28 0.90
33 3 0.10
ACGTcount: A:0.26, C:0.15, G:0.08, T:0.51
Consensus pattern (32 bp):
TTTGTTCAATCATTTGCAATGTAAATTCTCTT
Found at i:2751038 original size:21 final size:21
Alignment explanation
Indices: 2751012--2751052 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2751002 ATCTGCTCAA
* *
2751012 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
2751033 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
2751053 TTGCTCGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:2756157 original size:27 final size:27
Alignment explanation
Indices: 2756127--2756178 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
2756117 ATTACTCCGA
*
2756127 TCAATTTTTAAAA-AAAAATTAATTTAC
1 TCAA-TTTCAAAATAAAAATTAATTTAC
*
2756154 TCAATTTCAAAATTAAAATTAATTT
1 TCAATTTCAAAATAAAAATTAATTT
2756179 TATTTTCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (27 bp):
TCAATTTCAAAATAAAAATTAATTTAC
Found at i:2772284 original size:20 final size:20
Alignment explanation
Indices: 2772259--2772296 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2772249 TTGTCTAAAT
2772259 TTTCTTTCACTTTCTCTCAC
1 TTTCTTTCACTTTCTCTCAC
*
2772279 TTTCTTTCATTTTCTCTC
1 TTTCTTTCACTTTCTCTC
2772297 TCTGCTTTTT
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:0.08, C:0.32, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTCTTTCACTTTCTCTCAC
Found at i:2774304 original size:6 final size:6
Alignment explanation
Indices: 2774290--2774352 Score: 54
Period size: 6 Copynumber: 10.5 Consensus size: 6
2774280 AATGACTTTG
* * * * * *
2774290 CCTCCT CCTCTT CCTCCT CCTTCT CCTTCT CCTTCT CCTTCT CCTTCT
1 CCTCCT CCTCCT CCTCCT CCTCCT CCTCCT CCTCCT CCTCCT CCTCCT
* *
2774338 CCTTCT CCTTCT CCT
1 CCTCCT CCTCCT CCT
2774353 TGAAAATTGT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 54 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (6 bp):
CCTCCT
Found at i:2774353 original size:6 final size:6
Alignment explanation
Indices: 2774301--2774353 Score: 97
Period size: 6 Copynumber: 8.8 Consensus size: 6
2774291 CTCCTCCTCT
*
2774301 TCCTCC TCCTTC TCCTTC TCCTTC TCCTTC TCCTTC TCCTTC TCCTTC
1 TCCTTC TCCTTC TCCTTC TCCTTC TCCTTC TCCTTC TCCTTC TCCTTC
2774349 TCCTT
1 TCCTT
2774354 GAAAATTGTT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (6 bp):
TCCTTC
Found at i:2800869 original size:26 final size:27
Alignment explanation
Indices: 2800830--2800881 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
2800820 CAAAAGTTGG
2800830 TAAAAAAAATTTTG-GACCCTTAAAAGC
1 TAAAAAAAATTTTGAG-CCCTTAAAAGC
2800857 TAAAAAAAA-TTTGAGCCCTTAAAAG
1 TAAAAAAAATTTTGAGCCCTTAAAAG
2800882 TTGGTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.50, C:0.13, G:0.12, T:0.25
Consensus pattern (27 bp):
TAAAAAAAATTTTGAGCCCTTAAAAGC
Found at i:2806471 original size:22 final size:22
Alignment explanation
Indices: 2806446--2806491 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
2806436 AAAATACTGA
* *
2806446 TTAAAACGTGTTGAATTGTTAT
1 TTAAAAAGTGTTAAATTGTTAT
2806468 TTAAAAAGTGTTAAATTGTTAT
1 TTAAAAAGTGTTAAATTGTTAT
2806490 TT
1 TT
2806492 TTTAACGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (22 bp):
TTAAAAAGTGTTAAATTGTTAT
Found at i:2807799 original size:29 final size:30
Alignment explanation
Indices: 2807740--2807797 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
2807730 TCCGAGCCTT
*
2807740 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
2807770 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
2807798 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:2808027 original size:13 final size:13
Alignment explanation
Indices: 2808009--2808040 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
2807999 TTTCCAGCAA
2808009 TTATGAATTTATT
1 TTATGAATTTATT
2808022 TTATGAATTTATT
1 TTATGAATTTATT
*
2808035 TGATGA
1 TTATGA
2808041 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:2808248 original size:50 final size:50
Alignment explanation
Indices: 2808135--2808376 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
2808125 ATTTGGGTAA
* * *
2808135 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
2808191 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
2808241 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
2808291 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
2808341 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
2808377 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:2808324 original size:100 final size:103
Alignment explanation
Indices: 2808135--2808384 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
2808125 ATTTGGGTAA
2808135 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
2808200 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
2808241 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
2808303 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
2808341 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
2808385 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:2818934 original size:29 final size:30
Alignment explanation
Indices: 2818875--2818932 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
2818865 TCCGAGCCTT
*
2818875 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
2818905 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
2818933 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:2819162 original size:13 final size:13
Alignment explanation
Indices: 2819144--2819175 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
2819134 TTTCCAGCAA
2819144 TTATGAATTTATT
1 TTATGAATTTATT
2819157 TTATGAATTTATT
1 TTATGAATTTATT
*
2819170 TGATGA
1 TTATGA
2819176 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:2819383 original size:50 final size:50
Alignment explanation
Indices: 2819270--2819511 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
2819260 ATTTGGGTAA
* * *
2819270 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
2819326 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
2819376 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
2819426 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
2819476 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
2819512 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:2819459 original size:100 final size:103
Alignment explanation
Indices: 2819270--2819519 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
2819260 ATTTGGGTAA
2819270 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
2819335 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
2819376 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
2819438 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
2819476 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
2819520 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:2829814 original size:25 final size:26
Alignment explanation
Indices: 2829777--2829826 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
2829767 CAAAAGTTGG
2829777 TAAAAAAATTTTG-GACCCTTAAAAGC
1 TAAAAAAATTTTGAG-CCCTTAAAAGC
2829803 TAAAAAAA-TTTGAGCCCTTAAAAG
1 TAAAAAAATTTTGAGCCCTTAAAAG
2829827 TTGGTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.48, C:0.14, G:0.12, T:0.26
Consensus pattern (26 bp):
TAAAAAAATTTTGAGCCCTTAAAAGC
Found at i:2832275 original size:33 final size:32
Alignment explanation
Indices: 2832137--2832283 Score: 105
Period size: 33 Copynumber: 4.4 Consensus size: 32
2832127 ATAACTCAGT
* *
2832137 TATGGTCTTATCATCAGAATGCCATAGCCCAGC
1 TATGGTCTTA-CATTAGAATGCCATAGCCCAAC
* * * *
2832170 TATGGTCTTACATATAAATACTACCATGGTCCAAC
1 TATGGTCTTACAT-TAGA-A-TGCCATAGCCCAAC
* * * * * * * **
2832205 CATAGTCTTACGTTTATAGTGCCATAACCTAGT
1 TATGGTCTTAC-ATTAGAATGCCATAGCCCAAC
2832238 TATGGTCTTATCATTAGAATGCCATAGCCCAAC
1 TATGGTCTTA-CATTAGAATGCCATAGCCCAAC
2832271 TATGGTCTTACAT
1 TATGGTCTTACAT
2832284 ATAAACACGG
Statistics
Matches: 82, Mismatches: 27, Indels: 11
0.68 0.22 0.09
Matches are distributed among these distances:
32 6 0.07
33 51 0.62
34 2 0.02
35 22 0.27
36 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (32 bp):
TATGGTCTTACATTAGAATGCCATAGCCCAAC
Found at i:2832298 original size:101 final size:101
Alignment explanation
Indices: 2832111--2832350 Score: 365
Period size: 101 Copynumber: 2.4 Consensus size: 101
2832101 AATTCATCAT
* * * *
2832111 TTACATTCGTAGTGCGATAA-CTCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAGCTATGG
1 TTACGTTCATAGTGCCATAACCT-AGTTATGGTCTTATCATCAGAATGCCATAGCCCAACTATGG
* *
2832175 TCTTACATATAAATACTACCATGGTCCAACCATAGTC
65 TCTTACATATAAACACGACCATGGTCCAACCATAGTC
* *
2832212 TTACGTTTATAGTGCCATAACCTAGTTATGGTCTTATCATTAGAATGCCATAGCCCAACTATGGT
1 TTACGTTCATAGTGCCATAACCTAGTTATGGTCTTATCATCAGAATGCCATAGCCCAACTATGGT
* *
2832277 CTTACATATAAACACGGCCATGGTCCAACCATGGTC
66 CTTACATATAAACACGACCATGGTCCAACCATAGTC
*
2832313 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATC
1 TTACGTTCATAGTGCCATAACCTAGTTATGGTCTTATC
2832351 CGTCAATTCA
Statistics
Matches: 126, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
101 124 0.98
102 2 0.02
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (101 bp):
TTACGTTCATAGTGCCATAACCTAGTTATGGTCTTATCATCAGAATGCCATAGCCCAACTATGGT
CTTACATATAAACACGACCATGGTCCAACCATAGTC
Found at i:2835854 original size:30 final size:30
Alignment explanation
Indices: 2835820--2835877 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
2835810 TTTGAGATTT
*
2835820 GGGGCAAAAGTGTAAATATATAAAAGTTTA
1 GGGGCAAAAGTGTAAATATACAAAAGTTTA
*
2835850 GGGGCAAAAGTGTAAATATGCAAAAGTT
1 GGGGCAAAAGTGTAAATATACAAAAGTT
2835878 CGAGTCAAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.45, C:0.05, G:0.26, T:0.24
Consensus pattern (30 bp):
GGGGCAAAAGTGTAAATATACAAAAGTTTA
Found at i:2836306 original size:42 final size:41
Alignment explanation
Indices: 2836208--2836403 Score: 173
Period size: 41 Copynumber: 4.7 Consensus size: 41
2836198 CATTGAATGT
* * *
2836208 AAGGGGTTGCTAAGTGCAGATTCCCTGAATCACT-AATCAAA
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGAATC-TA
* * *
2836249 AAGGGGTTGCTAAGTGCTGATTCCCCGAATTATTGATTCTA
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGAATCTA
* * *
2836290 AAGGTGGTTGCTAAGTGCTGATTCCACCGTATC-CTTGATTGTGA
1 AAGG-GGTTGCTAAGTGCTGATTCC-CCGAATCAC-TGAATCT-A
* * * * *
2836334 AAGGGGTTGATATGTGTTGATTCCCCGTATCACTGAATAT-
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGAATCTA
*
2836374 AAGGTGGTTGCTAAGTGTTGATTCCACCGA
1 AAGG-GGTTGCTAAGTGCTGATTCC-CCGA
2836404 GTAACGGTTA
Statistics
Matches: 129, Mismatches: 18, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
40 4 0.03
41 53 0.41
42 38 0.29
43 29 0.22
44 5 0.04
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.32
Consensus pattern (41 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGAATCTA
Found at i:2836396 original size:84 final size:85
Alignment explanation
Indices: 2836248--2836402 Score: 222
Period size: 85 Copynumber: 1.8 Consensus size: 85
2836238 CACTAATCAA
* * * * *
2836248 AAAGGGGTTGCTAAGTGCTGATTCCCCGAATTATTGATTCTAAAGGTGGTTGCTAAGTGCTGATT
1 AAAGGGGTTGATAAGTGCTGATTCCCCGAATCACTGAATATAAAGGTGGTTGCTAAGTGCTGATT
2836313 CCACCGTATCCTTGATTGTG
66 CCACCGTATCCTTGATTGTG
* * * *
2836333 AAAGGGGTTGATATGTGTTGATTCCCCGTATCACTGAATAT-AAGGTGGTTGCTAAGTGTTGATT
1 AAAGGGGTTGATAAGTGCTGATTCCCCGAATCACTGAATATAAAGGTGGTTGCTAAGTGCTGATT
2836397 CCACCG
66 CCACCG
2836403 AGTAACGGTT
Statistics
Matches: 61, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
84 28 0.46
85 33 0.54
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (85 bp):
AAAGGGGTTGATAAGTGCTGATTCCCCGAATCACTGAATATAAAGGTGGTTGCTAAGTGCTGATT
CCACCGTATCCTTGATTGTG
Found at i:2839099 original size:42 final size:43
Alignment explanation
Indices: 2839040--2839204 Score: 147
Period size: 43 Copynumber: 3.9 Consensus size: 43
2839030 TTAGGGTTAC
*
2839040 TGAGATTACGTGTAAGACCATATCTAGGATA-TGGCATCGATA
1 TGAGATTACATGTAAGACCATATCTAGGATATTGGCATCGATA
* * * *
2839082 TGAGACTT-CGTGTAAGACCATGTCTGGGACATTGGCATCGATA
1 TGAGA-TTACATGTAAGACCATATCTAGGATATTGGCATCGATA
* * * ** * * *
2839125 TGTGATTTCATGTAAGACTATGGCTGGGCTATTGGCATCAATA
1 TGAGATTACATGTAAGACCATATCTAGGATATTGGCATCGATA
** * *
2839168 CAATATTACATGTAATACCATATCTAGGATA-TGGCAT
1 TGAGATTACATGTAAGACCATATCTAGGATATTGGCAT
2839205 TGTTACGGTA
Statistics
Matches: 99, Mismatches: 21, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
42 33 0.33
43 66 0.67
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (43 bp):
TGAGATTACATGTAAGACCATATCTAGGATATTGGCATCGATA
Found at i:2841673 original size:30 final size:30
Alignment explanation
Indices: 2841604--2841684 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 30
2841594 GATATACGGG
* * *
2841604 AATA-AGTTGCTCGCACGAGCTGACAGTAT
1 AATAGAGTTGCTCACACAAGCTAACAGTAT
** * *
2841633 ACCAGGGTTGCTCACACAAGCTAACATTAT
1 AATAGAGTTGCTCACACAAGCTAACAGTAT
2841663 AATAGAGTTGCTCACACAAGCT
1 AATAGAGTTGCTCACACAAGCT
2841685 GGTATTATAT
Statistics
Matches: 41, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
29 2 0.05
30 39 0.95
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.23
Consensus pattern (30 bp):
AATAGAGTTGCTCACACAAGCTAACAGTAT
Found at i:2844317 original size:26 final size:26
Alignment explanation
Indices: 2844286--2844335 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
2844276 CCTTTTTACT
*
2844286 TTTCCCTCAAAACTTTTACTCCCCAC
1 TTTCCCCCAAAACTTTTACTCCCCAC
2844312 TTTCCCCCAAAACTTTTACTCCCC
1 TTTCCCCCAAAACTTTTACTCCCC
2844336 TCCCCTCCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.22, C:0.44, G:0.00, T:0.34
Consensus pattern (26 bp):
TTTCCCCCAAAACTTTTACTCCCCAC
Found at i:2847828 original size:27 final size:29
Alignment explanation
Indices: 2847758--2847829 Score: 85
Period size: 27 Copynumber: 2.5 Consensus size: 29
2847748 CCGAATATAA
*
2847758 TAAATATATATTTTTAATTTTTAATTATTTT
1 TAAA-ATAAATTTTTAATTTTT-ATTATTTT
* *
2847789 TAAAAT-ACTTTTTTATTTTT-TTATTTT
1 TAAAATAAATTTTTAATTTTTATTATTTT
2847816 TAAAATAAATTTTT
1 TAAAATAAATTTTT
2847830 GGTGTTTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 13 0.36
28 6 0.17
29 11 0.31
30 2 0.06
31 4 0.11
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (29 bp):
TAAAATAAATTTTTAATTTTTATTATTTT
Found at i:2853753 original size:16 final size:16
Alignment explanation
Indices: 2853732--2853778 Score: 69
Period size: 15 Copynumber: 2.9 Consensus size: 16
2853722 GGACCAACCT
2853732 TATTAATTAATTTTAC
1 TATTAATTAATTTTAC
*
2853748 TATTAAATTAATTTT-T
1 TATT-AATTAATTTTAC
2853764 TATTAATTAATTTTA
1 TATTAATTAATTTTA
2853779 GAGATAGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 10 0.36
16 8 0.29
17 10 0.36
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (16 bp):
TATTAATTAATTTTAC
Found at i:2865284 original size:42 final size:42
Alignment explanation
Indices: 2865228--2865324 Score: 108
Period size: 42 Copynumber: 2.3 Consensus size: 42
2865218 ATTAAAAACA
* * *
2865228 ATTTAATAAATAAA-TAATAAATAATAAAATCATATTTTAATATT
1 ATTTAA-ATATAAATTAATAAA-AATAAAAT-ATAATTTAATAGT
*
2865272 A-TTAAATATAAATTAATAAAAATAATATATAATTTAATAGT
1 ATTTAAATATAAATTAATAAAAATAAAATATAATTTAATAGT
*
2865313 ATTTTAATATAA
1 ATTTAAATATAA
2865325 TTCAAATATT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
41 12 0.26
42 22 0.48
43 11 0.24
44 1 0.02
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (42 bp):
ATTTAAATATAAATTAATAAAAATAAAATATAATTTAATAGT
Found at i:2868118 original size:25 final size:25
Alignment explanation
Indices: 2868090--2868151 Score: 97
Period size: 25 Copynumber: 2.5 Consensus size: 25
2868080 TTGAGCCTTG
2868090 TAACAGGAAGCTTATCCGAGCAATA
1 TAACAGGAAGCTTATCCGAGCAATA
* *
2868115 TAACATGAAGCTTATCCGGGCAATA
1 TAACAGGAAGCTTATCCGAGCAATA
*
2868140 TAACGGGAAGCT
1 TAACAGGAAGCT
2868152 CACAAAGAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.21
Consensus pattern (25 bp):
TAACAGGAAGCTTATCCGAGCAATA
Found at i:2868196 original size:24 final size:24
Alignment explanation
Indices: 2868134--2868216 Score: 87
Period size: 24 Copynumber: 3.4 Consensus size: 24
2868124 GCTTATCCGG
*
2868134 GCAATATAACGGGAAGCTCACAAAGA
1 GCAAT-TAACGGGTAGCTC-CAAAGA
* *
2868160 GTCTA-TAATGGGTAGCTCCAAAGA
1 G-CAATTAACGGGTAGCTCCAAAGA
* *
2868184 GCAATTAACGGGTAGATCCGAAGA
1 GCAATTAACGGGTAGCTCCAAAGA
2868208 GCAATTAAC
1 GCAATTAAC
2868217 AGGAAGTACA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
23 2 0.04
24 32 0.67
25 11 0.23
26 1 0.02
27 2 0.04
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (24 bp):
GCAATTAACGGGTAGCTCCAAAGA
Found at i:2879425 original size:32 final size:32
Alignment explanation
Indices: 2879389--2879453 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
2879379 ACATGGATCC
*
2879389 TTTGTTCAATTATTGTAAATGTAAATTCTCTT
1 TTTGTTCAATCATTGTAAATGTAAATTCTCTT
*
2879421 TTTGTTCAATCATTGTCAATGTAAATTCTCTT
1 TTTGTTCAATCATTGTAAATGTAAATTCTCTT
2879453 T
1 T
2879454 CTCTTGCTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.26, C:0.12, G:0.09, T:0.52
Consensus pattern (32 bp):
TTTGTTCAATCATTGTAAATGTAAATTCTCTT
Found at i:2883495 original size:32 final size:32
Alignment explanation
Indices: 2883459--2883522 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
2883449 GAGCGTTAGT
* *
2883459 TCAATTGGTATGAGTATTGTTCTCAATACAAG
1 TCAATTGGTATGACTATTATTCTCAATACAAG
2883491 TCAATTGGTATGACTATTATTCTCAATACAAG
1 TCAATTGGTATGACTATTATTCTCAATACAAG
2883523 AAAATATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.38
Consensus pattern (32 bp):
TCAATTGGTATGACTATTATTCTCAATACAAG
Found at i:2884979 original size:141 final size:143
Alignment explanation
Indices: 2884806--2885369 Score: 374
Period size: 145 Copynumber: 3.9 Consensus size: 143
2884796 TGCGTGCTGA
* * * *
2884806 CGTGTAGCATTGAGAAATGCCTTCTTTTTCTTGGGGGGGAGGGGTAGGCTGGCGACTTTTTGAGC
1 CGTGTAGCATCGAGAAATGTCTTCTTTTTCTTGGGGGGGAGGGGTAGGCTGGCGAGTTTTTGTGC
*
2884871 GATCCTCGTAAATGATATGGAAATCTTGTAAATGCTTGATCAAGGATGCTTATTTTTTGTGTCAT
66 GATCCTCGTAAATGATACGGAAATCTTGTAAATGCTTGATCAAGGATGCTTATTTTTTGTGTCAT
2884936 GTGTGC-G-TGCG
131 GTGTGCAGATGCG
* * *
2884947 TGTGTAGCATCGAGAAATGTCTTCTTTTTCTTGGGTTGGGGGGGGGGAGGTAGGCGGGCGAGTTT
1 CGTGTAGCATCGAGAAATGTCTTCTTTTTC-----TTGGGGGGGAGG-GGTAGGCTGGCGAGTTT
* ** * * * * * *
2885012 TTGTGTGGATTGTCATAAATGAAACGGAAAT-TGAGTAAATGCTTGTTAAAGGTTGCTT-TTTTT
60 TTGTG-CGATCCTCGTAAATGATACGGAAATCT-TGTAAATGCTTGATCAAGGATGCTTATTTTT
*
2885075 TTTGTCATATGTGTGTGCATGCATGCG
123 TGTGTC--A--TGTGTGCA-G-ATGCG
* *
2885102 CGTGTATCATCGAGAAATGTCTTCTTTTTCTT------GACGGGGTA-G-TGGGTGAGTTTTTGT
1 CGTGTAGCATCGAGAAATGTCTTCTTTTTCTTGGGGGGGA-GGGGTAGGCT-GGCGAGTTTTTGT
* * * * * * * *
2885159 GTGATCCTCGTAAATGATACAGAAATCGTGCAAATGCTTGGTCACGGATGCTTATATTTTGTCTC
64 GCGATCCTCGTAAATGATACGGAAATCTTGTAAATGCTTGATCAAGGATGCTTATTTTTTGTGTC
* *
2885224 ATGTGTGTGCGCGGTGCG
129 A--TGTGTGC-AGATGCG
* * * * *
2885242 CATGTGTGTTTAGCATTGGGAAATGTCTTATTTTTCTT-GGGGGCAGGCG--GG-T---GAGTTT
1 C----GTG--TAGCATCGAGAAATGTCTTCTTTTTCTTGGGGGGGAGGGGTAGGCTGGCGAGTTT
* ** *** * * *
2885300 TTGCGCGATCCTCACAAGCAAAACGAAAATCGTGTAAATGCTTGATCAAGGATGCTTATTTTTTG
60 TTGTGCGATCCTCGTAAATGATACGGAAATCTTGTAAATGCTTGATCAAGGATGCTTATTTTTTG
2885365 TGTCA
125 TGTCA
2885370 CTAGACATTA
Statistics
Matches: 328, Mismatches: 62, Indels: 62
0.73 0.14 0.14
Matches are distributed among these distances:
140 5 0.02
141 38 0.12
142 38 0.12
143 22 0.07
144 8 0.02
145 63 0.19
146 35 0.11
147 30 0.09
148 40 0.12
149 3 0.01
150 5 0.02
151 8 0.02
153 1 0.00
155 32 0.10
ACGTcount: A:0.21, C:0.13, G:0.30, T:0.36
Consensus pattern (143 bp):
CGTGTAGCATCGAGAAATGTCTTCTTTTTCTTGGGGGGGAGGGGTAGGCTGGCGAGTTTTTGTGC
GATCCTCGTAAATGATACGGAAATCTTGTAAATGCTTGATCAAGGATGCTTATTTTTTGTGTCAT
GTGTGCAGATGCG
Found at i:2885000 original size:147 final size:148
Alignment explanation
Indices: 2884806--2885134 Score: 343
Period size: 148 Copynumber: 2.2 Consensus size: 148
2884796 TGCGTGCTGA
* * *
2884806 CGTGTAGCATTGAGAAATGCCTTCTTTTTC---TTGGGGGGGAGGGGTAGGCTGGCGACTTTTTG
1 CGTGTAGCATCGAGAAATGTCTTCTTTTTCTTGTTGGGGGGGAGGGGTAGGCGGGCGACTTTTTG
* * * * *
2884868 AG-CGATCCTCGTAAATGATATGGAAATCT-TGTAAATGCTTGATCAAGGATGCTTATTTTTTGT
66 AGTCGATCCTCATAAATGAAACGGAAAT-TGAGTAAATGCTTGATAAAGGATGCTT-TTTTTTGT
2884931 GTC-A-TGTGTGC-G-TGCG
129 GTCAAGTGTGTGCAGATGCG
* * *
2884947 TGTGTAGCATCGAGAAATGTCTTCTTTTTCTTGGGTTGGGGGGGGGGAGGTAGGCGGGCGAGTTT
1 CGTGTAGCATCGAGAAATGTCTTCTTTTTCTT--GTTGGGGGGGAGG-GGTAGGCGGGCGACTTT
* * ** * * *
2885012 TTGTGTGGATTGTCATAAATGAAACGGAAATTGAGTAAATGCTTGTTAAAGGTTGCTTTTTTTTT
63 TTGAGTCGATCCTCATAAATGAAACGGAAATTGAGTAAATGCTTGATAAAGGATGCTTTTTTTTG
2885077 TGTCATATGTGTGTGCATGCATGCG
128 TGTCA-A-GTGTGTGCA-G-ATGCG
*
2885102 CGTGTATCATCGAGAAATGTCTTCTTTTTCTTG
1 CGTGTAGCATCGAGAAATGTCTTCTTTTTCTTG
2885135 ACGGGGTAGT
Statistics
Matches: 152, Mismatches: 20, Indels: 20
0.79 0.10 0.10
Matches are distributed among these distances:
141 27 0.18
146 11 0.07
147 30 0.20
148 40 0.26
149 1 0.01
151 7 0.05
153 2 0.01
155 34 0.22
ACGTcount: A:0.20, C:0.12, G:0.30, T:0.37
Consensus pattern (148 bp):
CGTGTAGCATCGAGAAATGTCTTCTTTTTCTTGTTGGGGGGGAGGGGTAGGCGGGCGACTTTTTG
AGTCGATCCTCATAAATGAAACGGAAATTGAGTAAATGCTTGATAAAGGATGCTTTTTTTTGTGT
CAAGTGTGTGCAGATGCG
Found at i:2894047 original size:3 final size:3
Alignment explanation
Indices: 2894039--2894071 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2894029 AGAAACGAAA
2894039 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2894072 TTATCCACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2894404 original size:18 final size:19
Alignment explanation
Indices: 2894358--2894405 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
2894348 ATTGGATTTT
*
2894358 ATAATATTATATATTTTTAA
1 ATAAT-TTATATATATTTAA
*
2894378 AAAATTT-TATAATATTTAA
1 ATAATTTATAT-ATATTTAA
2894397 ATAATTTAT
1 ATAATTTAT
2894406 TTAATTTGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 3 0.13
19 15 0.65
20 5 0.22
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATAATTTATATATATTTAA
Found at i:2899728 original size:2 final size:2
Alignment explanation
Indices: 2899721--2899746 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2899711 AACCAGAAAA
2899721 AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC
2899747 TGTTTTGTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2899821 original size:20 final size:20
Alignment explanation
Indices: 2899796--2899833 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2899786 TTGTCTAAAT
2899796 TTTCTTTCACTTTCTCTCAC
1 TTTCTTTCACTTTCTCTCAC
*
2899816 TTTCTTTCATTTTCTCTC
1 TTTCTTTCACTTTCTCTC
2899834 TCTGCTTTTT
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:0.08, C:0.32, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTCTTTCACTTTCTCTCAC
Found at i:2900802 original size:24 final size:24
Alignment explanation
Indices: 2900760--2900806 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2900750 ATTTTGAAAA
*
2900760 CTAAAAAGTAAAGGAACTAAATTC
1 CTAAAAAATAAAGGAACTAAATTC
2900784 CTAAAAAATAGAAGG-ACTAAATT
1 CTAAAAAATA-AAGGAACTAAATT
2900807 TTAATTTTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.55, C:0.11, G:0.13, T:0.21
Consensus pattern (24 bp):
CTAAAAAATAAAGGAACTAAATTC
Found at i:2910822 original size:32 final size:32
Alignment explanation
Indices: 2910781--2910842 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
2910771 AATTTGAAAC
2910781 CCGAGAAGCCAATTCTGAGGAGAATCCACATT
1 CCGAGAAGCCAATTCTGAGGAGAATCCACATT
*
2910813 CCGAGAAGCCAATTCTGAGGGGAATCCACA
1 CCGAGAAGCCAATTCTGAGGAGAATCCACA
2910843 ATTTGAAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.34, C:0.26, G:0.24, T:0.16
Consensus pattern (32 bp):
CCGAGAAGCCAATTCTGAGGAGAATCCACATT
Found at i:2911599 original size:98 final size:98
Alignment explanation
Indices: 2911425--2911621 Score: 331
Period size: 98 Copynumber: 2.0 Consensus size: 98
2911415 GTACAATAAA
* * *
2911425 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTCATCCAAAATTTAAGAAATCACACCCAATACGTTAAGGCACAATT
* *
2911490 CCTCTAGAATCCCAAATTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
*
2911523 ACTTTAAAAGAACATCCACTTATCCAAAATTTAAGAAATCACACCCAATACGTTAAGGCACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAAATTTAAGAAATCACACCCAATACGTTAAGGCACAATT
*
2911588 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
2911621 A
1 A
2911622 TTATTTTTTT
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 92 1.00
ACGTcount: A:0.38, C:0.25, G:0.09, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAAATTTAAGAAATCACACCCAATACGTTAAGGCACAATT
CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
Found at i:2912950 original size:19 final size:19
Alignment explanation
Indices: 2912926--2913089 Score: 169
Period size: 19 Copynumber: 8.8 Consensus size: 19
2912916 AATCATATAT
2912926 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
2912945 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
*
2912964 TCTAATATTGCATATCATA
1 TCTAAGATTGCATATCATA
2912983 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
**
2913004 TCTTGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
2913023 TCTAAGATTGCATATCCTA
1 TCTAAGATTGCATATCATA
* * *
2913042 ---AAAAAT---TATGATA
1 TCTAAGATTGCATATCATA
**
2913055 TCTTGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
2913074 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
2913090 CTAAAAAATT
Statistics
Matches: 115, Mismatches: 22, Indels: 16
0.75 0.14 0.10
Matches are distributed among these distances:
13 5 0.04
16 6 0.05
19 87 0.76
21 17 0.15
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:2913014 original size:40 final size:40
Alignment explanation
Indices: 2912926--2913037 Score: 183
Period size: 40 Copynumber: 2.9 Consensus size: 40
2912916 AATCATATAT
2912926 TCTAAGATTGCATATCATATCTAAGATT--ATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
*
2912964 TCTAATATTGCATATCATATCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
**
2913004 TCTTGGATTGCATATCATATCTAAGATTGCATAT
1 TCTAAGATTGCATATCATATCTAAGATTGCATAT
2913038 CCTAAAAAAT
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
38 27 0.40
40 41 0.60
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (40 bp):
TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
Found at i:2913063 original size:51 final size:51
Alignment explanation
Indices: 2913001--2913102 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
2912991 TGCATATATC
2913001 ATATCTTGGATTGCATATCATATCTAAGATTGCATATCCTAAAAAATTATG
1 ATATCTTGGATTGCATATCATATCTAAGATTGCATATCCTAAAAAATTATG
2913052 ATATCTTGGATTGCATATCATATCTAAGATTGCATATCCTAAAAAATTATG
1 ATATCTTGGATTGCATATCATATCTAAGATTGCATATCCTAAAAAATTATG
2913103 TTTCCATATG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (51 bp):
ATATCTTGGATTGCATATCATATCTAAGATTGCATATCCTAAAAAATTATG
Found at i:2913689 original size:30 final size:30
Alignment explanation
Indices: 2913650--2913706 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
2913640 TTTTATAAAT
2913650 AATTAATATTT-AT-TACTTAAAAATATTTAA
1 AATTAATATTTCATATA-TT-AAAATATTTAA
*
2913680 AATTTATATTTCATATATTAAAATATT
1 AATTAATATTTCATATATTAAAATATT
2913707 AACAACAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
30 18 0.75
31 4 0.17
32 2 0.08
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (30 bp):
AATTAATATTTCATATATTAAAATATTTAA
Found at i:2913963 original size:101 final size:100
Alignment explanation
Indices: 2913809--2914013 Score: 340
Period size: 101 Copynumber: 2.0 Consensus size: 100
2913799 TAACATGTCT
2913809 AAAATTGACATTTTATTTCTCAAAAAACTTTTTGAAAGCAATGCTAAACATTCAAATTTTAAAAC
1 AAAATTGACATTTTATTTCTCAAAAAACTTTTTGAAAGCAATGCTAAACATTCAAATTTTAAAAC
2913874 AAACTTCTCAAAAGCACTTTTAAACAACACTTTTC
66 AAACTTCTCAAAAGCACTTTTAAACAACACTTTTC
* *
2913909 AAAATTGACATTTTATTTCTCAAAATTACTTTTT-AACAGCAATGCTAAAGATTCAAATTTTAAA
1 AAAATTGACATTTTATTTCTCAAAA-AACTTTTTGAA-AGCAATGCTAAACATTCAAATTTTAAA
* **
2913973 ACAAGCTTCTCAAAAGCACTTTTTTACAACACTTTTC
64 ACAAACTTCTCAAAAGCACTTTTAAACAACACTTTTC
2914010 AAAA
1 AAAA
2914014 GCATTGTCAA
Statistics
Matches: 98, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
100 27 0.28
101 71 0.72
ACGTcount: A:0.42, C:0.18, G:0.05, T:0.35
Consensus pattern (100 bp):
AAAATTGACATTTTATTTCTCAAAAAACTTTTTGAAAGCAATGCTAAACATTCAAATTTTAAAAC
AAACTTCTCAAAAGCACTTTTAAACAACACTTTTC
Found at i:2918373 original size:15 final size:15
Alignment explanation
Indices: 2918353--2918387 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
2918343 TTTTCGTCTC
2918353 TTTTATCACAAACAA
1 TTTTATCACAAACAA
2918368 TTTTATCACAAACAA
1 TTTTATCACAAACAA
2918383 TTTTA
1 TTTTA
2918388 CCGACGTGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (15 bp):
TTTTATCACAAACAA
Found at i:2932566 original size:51 final size:52
Alignment explanation
Indices: 2932507--2932622 Score: 137
Period size: 51 Copynumber: 2.2 Consensus size: 52
2932497 ATTGGTATAA
***
2932507 TAATAAATTTAGCCTTTAAAATTTACACATTCTAAT-AATTT-GATCTTAATT
1 TAATAAATTTAGCCAGCAAAATTTACACATTCTAATCAATTTGGATC-TAATT
** * **
2932558 TAATAAATTTAGCCAGCAGCATTTACACATTTTTGTCAATTTGGATCTAATT
1 TAATAAATTTAGCCAGCAAAATTTACACATTCTAATCAATTTGGATCTAATT
2932610 TAATAAATTTAGC
1 TAATAAATTTAGC
2932623 TTGCAACAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
51 28 0.51
52 23 0.42
53 4 0.07
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (52 bp):
TAATAAATTTAGCCAGCAAAATTTACACATTCTAATCAATTTGGATCTAATT
Found at i:2942514 original size:24 final size:24
Alignment explanation
Indices: 2942469--2942522 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
2942459 CATTAAAATT
* * *
2942469 TTTAATTTTATATTGGGATAATTAG
1 TTTAATTATATATTGAGATAA-TAA
*
2942494 TTTAATTAT-TATTGAGTTAATAA
1 TTTAATTATATATTGAGATAATAA
2942517 TTTAAT
1 TTTAAT
2942523 ATCAATATCA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 8 0.32
24 9 0.36
25 8 0.32
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (24 bp):
TTTAATTATATATTGAGATAATAA
Found at i:2943608 original size:1 final size:1
Alignment explanation
Indices: 2943602--2943627 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
2943592 AAATACTATC
2943602 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
2943628 TGCAGTCTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2949990 original size:28 final size:29
Alignment explanation
Indices: 2949956--2950016 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
2949946 AACTTATTTT
*
2949956 ATTGTTAA-TTTGTTATTATTTTAAAGAC
1 ATTGTTAATTTTATTATTATTTTAAAGAC
* *
2949984 ATTGTTAATTTTATTATTATTTTAGAGTC
1 ATTGTTAATTTTATTATTATTTTAAAGAC
2950013 ATTG
1 ATTG
2950017 CTTGTTAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 8 0.28
29 21 0.72
ACGTcount: A:0.30, C:0.03, G:0.11, T:0.56
Consensus pattern (29 bp):
ATTGTTAATTTTATTATTATTTTAAAGAC
Found at i:2950131 original size:18 final size:17
Alignment explanation
Indices: 2950094--2950127 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2950084 GAAATATTAT
2950094 TTTGATGTTTTAGTATA
1 TTTGATGTTTTAGTATA
*
2950111 TTTGATGTATTA-TATA
1 TTTGATGTTTTAGTATA
2950127 T
1 T
2950128 ATTTTAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.59
Consensus pattern (17 bp):
TTTGATGTTTTAGTATA
Found at i:2953783 original size:119 final size:119
Alignment explanation
Indices: 2953642--2953873 Score: 403
Period size: 119 Copynumber: 1.9 Consensus size: 119
2953632 TTTAAATTTT
*
2953642 TTAAACGAGAAAAAGGCCTCCGCAGTCCCTCTCAATTTCGAAATTGAGAAGATTTGT-CTCTTTA
1 TTAAACGAGAAAAAGGCCTCCGCAGTCCCTCTCAATTTCAAAATTGAGAAGATTTGTCCT-TTTA
*
2953706 AAAAATTAAAGCAATTTAATTCTTGTCAATTTTAAAAGTGAGCAATTAAAAATAA
65 AAAAATCAAAGCAATTTAATTCTTGTCAATTTTAAAAGTGAGCAATTAAAAATAA
* *
2953761 TTAAACGATAAAAAGGTCTCCGCAGTCCCTCTCAATTTCAAAATTGAGAAGATTTGTCCTTTTAA
1 TTAAACGAGAAAAAGGCCTCCGCAGTCCCTCTCAATTTCAAAATTGAGAAGATTTGTCCTTTTAA
*
2953826 AAAATCAAAGCAATTTAATTCTTGTCAATTTTGAAAGTGAGCAATTAA
66 AAAATCAAAGCAATTTAATTCTTGTCAATTTTAAAAGTGAGCAATTAA
2953874 GAATCACGAC
Statistics
Matches: 107, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
119 105 0.98
120 2 0.02
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (119 bp):
TTAAACGAGAAAAAGGCCTCCGCAGTCCCTCTCAATTTCAAAATTGAGAAGATTTGTCCTTTTAA
AAAATCAAAGCAATTTAATTCTTGTCAATTTTAAAAGTGAGCAATTAAAAATAA
Found at i:2956940 original size:20 final size:19
Alignment explanation
Indices: 2956904--2956949 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
2956894 TTATTTAAAT
2956904 TTAATTATAAAAAATATATA
1 TTAA-TATAAAAAATATATA
* *
2956924 TTAATATAAAATCATATATT
1 TTAATATAAAA-AATATATA
2956944 TTAATA
1 TTAATA
2956950 CTATTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
TTAATATAAAAAATATATA
Found at i:2961739 original size:27 final size:28
Alignment explanation
Indices: 2961682--2961743 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
2961672 TTTGATTGTG
* *
2961682 TTTTTTTTTAAAAAAGATTTGTTTTCAA
1 TTTTATTTTAAAAAAGATTTGTTTACAA
* **
2961710 TTTTATTTTAAAAATGATTT-TTTAGGA
1 TTTTATTTTAAAAAAGATTTGTTTACAA
2961737 TTTTATT
1 TTTTATT
2961744 AAAAAATAGC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 11 0.38
28 18 0.62
ACGTcount: A:0.31, C:0.02, G:0.08, T:0.60
Consensus pattern (28 bp):
TTTTATTTTAAAAAAGATTTGTTTACAA
Found at i:2966758 original size:17 final size:17
Alignment explanation
Indices: 2966728--2966761 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2966718 TTGGATGAAC
*
2966728 TTATATTATAATTTTAT
1 TTATAATATAATTTTAT
*
2966745 TTATAATATTATTTTAT
1 TTATAATATAATTTTAT
2966762 ATCTTGCATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATAATATAATTTTAT
Found at i:2967274 original size:20 final size:20
Alignment explanation
Indices: 2967227--2967264 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2967217 TTAATAATGT
2967227 TAAAATT-TTAATTTTAACC
1 TAAAATTCTTAATTTTAACC
2967246 TAAAATTCTTAATTTTAAC
1 TAAAATTCTTAATTTTAAC
2967265 TTAATTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (20 bp):
TAAAATTCTTAATTTTAACC
Found at i:2967855 original size:14 final size:14
Alignment explanation
Indices: 2967838--2967872 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
2967828 TATACAATAT
2967838 CAAAATAATACTAA
1 CAAAATAATACTAA
*
2967852 CAAAATAATATTAA
1 CAAAATAATACTAA
*
2967866 CATAATA
1 CAAAATA
2967873 GTAAAATGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (14 bp):
CAAAATAATACTAA
Found at i:2977746 original size:20 final size:20
Alignment explanation
Indices: 2977721--2977761 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
2977711 AATAAACATC
2977721 TATACACATTCGCGCTTAGT
1 TATACACATTCGCGCTTAGT
2977741 TATACACATTCGCGCTTAGT
1 TATACACATTCGCGCTTAGT
2977761 T
1 T
2977762 TGACAACAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (20 bp):
TATACACATTCGCGCTTAGT
Found at i:2978119 original size:26 final size:26
Alignment explanation
Indices: 2978089--2978139 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
2978079 AAATATTGGT
2978089 GACTAAATTTATTAAATCAAGATGAG
1 GACTAAATTTATTAAATCAAGATGAG
2978115 GACTAAATTTATTAAATCAAGATGA
1 GACTAAATTTATTAAATCAAGATGA
2978140 AATTATAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.47, C:0.08, G:0.14, T:0.31
Consensus pattern (26 bp):
GACTAAATTTATTAAATCAAGATGAG
Found at i:2979156 original size:22 final size:22
Alignment explanation
Indices: 2979103--2979145 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2979093 CCCCAGTTTT
2979103 TACTGGTTTAGTCCGTTCTTTG
1 TACTGGTTTAGTCCGTTCTTTG
2979125 TACTGGTTTAGTCCGTTCTTT
1 TACTGGTTTAGTCCGTTCTTT
2979146 TGTCGTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.19, G:0.21, T:0.51
Consensus pattern (22 bp):
TACTGGTTTAGTCCGTTCTTTG
Found at i:2985482 original size:22 final size:22
Alignment explanation
Indices: 2985457--2985502 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
2985447 AAAAAGATAC
*
2985457 AAATA-AAATAATATTTAATTAA
1 AAATACAAATAATA-TTAAATAA
2985479 AAATACAAATAATATTAAATAA
1 AAATACAAATAATATTAAATAA
2985501 AA
1 AA
2985503 TATCGAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (22 bp):
AAATACAAATAATATTAAATAA
Found at i:2986848 original size:21 final size:21
Alignment explanation
Indices: 2986832--2986873 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2986822 GTTATAATTT
2986832 TTTTATTTACCAATATATATA
1 TTTTATTTACCAATATATATA
*
2986853 TTTTATTTACCAAAATATATA
1 TTTTATTTACCAATATATATA
2986874 AAAAAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (21 bp):
TTTTATTTACCAATATATATA
Done.