Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold245
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: 689785
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.33
Warning! 23636 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:396710 original size:29 final size:30
Alignment explanation
Indices: 396651--396710 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
396641 GTTGGGAGGG
** *
396651 GAGTAAAAGTTTTTTGGGAAAAGTGGAAAA
1 GAGTAAAAGTTTTGAGGGAAAAGTGAAAAA
396681 GAGTAAAAGTTTTGAGGGAAAAGT-AAAAA
1 GAGTAAAAGTTTTGAGGGAAAAGTGAAAAA
396710 G
1 G
396711 GTTTGGGAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 5 0.19
30 22 0.81
ACGTcount: A:0.47, C:0.00, G:0.30, T:0.23
Consensus pattern (30 bp):
GAGTAAAAGTTTTGAGGGAAAAGTGAAAAA
Found at i:396767 original size:9 final size:9
Alignment explanation
Indices: 396753--396784 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
396743 TATAGTTTGA
396753 TATTCGAAT
1 TATTCGAAT
396762 TATTCGAAT
1 TATTCGAAT
*
396771 TATTCGAGT
1 TATTCGAAT
396780 TATTC
1 TATTC
396785 AAATCCGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (9 bp):
TATTCGAAT
Found at i:398547 original size:16 final size:16
Alignment explanation
Indices: 398509--398548 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 16
398499 CGACCACAAG
398509 GAAAAAAAAGAGAAAA
1 GAAAAAAAAGAGAAAA
398525 GAGAAAAAAA-AGAAAA
1 GA-AAAAAAAGAGAAAA
398541 CGAAAAAA
1 -GAAAAAA
398549 TAAAACACCC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (16 bp):
GAAAAAAAAGAGAAAA
Found at i:398553 original size:18 final size:16
Alignment explanation
Indices: 398509--398553 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
398499 CGACCACAAG
*
398509 GAAAAAAAAGAGAAAA
1 GAAAAAAAAAAGAAAA
*
398525 GAGAAAAAAAAGAAAA
1 GAAAAAAAAAAGAAAA
398541 CGAAAAAATAAAA
1 -GAAAAAA-AAAA
398554 CACCCAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.58
17 6 0.25
18 4 0.17
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (16 bp):
GAAAAAAAAAAGAAAA
Found at i:399367 original size:17 final size:17
Alignment explanation
Indices: 399345--399379 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
399335 CCTCAACCTG
399345 TTTTACCTTTACTAACA
1 TTTTACCTTTACTAACA
399362 TTTTACCTTTACTAACA
1 TTTTACCTTTACTAACA
399379 T
1 T
399380 ATTATGCAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.23, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTTACCTTTACTAACA
Found at i:412237 original size:2 final size:2
Alignment explanation
Indices: 412230--412254 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
412220 ATAATAAATT
412230 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
412255 CAATTTCCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:414549 original size:82 final size:83
Alignment explanation
Indices: 414425--414595 Score: 326
Period size: 82 Copynumber: 2.1 Consensus size: 83
414415 AACTATTATT
*
414425 TTATAAATTAAAATTTTATATAAAAAAAATATTTGAATTGAATGGTTGTATAGTTTTATTTATTC
1 TTATATATTAAAATTTTATATAAAAAAAATATTTGAATTGAATGGTTGTATAGTTTTATTTATTC
414490 TATTAATTTAAGGTTAAA
66 TATTAATTTAAGGTTAAA
414508 TTATATATTAAAA-TTTATATAAAAAAAATATTTGAATTGAATGGTTGTATAGTTTTATTTATTC
1 TTATATATTAAAATTTTATATAAAAAAAATATTTGAATTGAATGGTTGTATAGTTTTATTTATTC
414572 TATTAATTTAAGGTTAAA
66 TATTAATTTAAGGTTAAA
414590 TTATAT
1 TTATAT
414596 CATAGGTTTC
Statistics
Matches: 87, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
82 75 0.86
83 12 0.14
ACGTcount: A:0.42, C:0.01, G:0.09, T:0.48
Consensus pattern (83 bp):
TTATATATTAAAATTTTATATAAAAAAAATATTTGAATTGAATGGTTGTATAGTTTTATTTATTC
TATTAATTTAAGGTTAAA
Found at i:421747 original size:23 final size:23
Alignment explanation
Indices: 421721--421838 Score: 181
Period size: 23 Copynumber: 5.3 Consensus size: 23
421711 AAAAGTGCCA
421721 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
421744 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
421767 CACTGATATGTAGCC----CTAC
1 CACTGATATGTAGCCGAAGCTAC
*
421786 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
421809 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
421832 CACTGAT
1 CACTGAT
421839 CAATAACACT
Statistics
Matches: 86, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
19 19 0.22
23 67 0.78
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:421797 original size:42 final size:43
Alignment explanation
Indices: 421721--421837 Score: 146
Period size: 42 Copynumber: 2.6 Consensus size: 43
421711 AAAAGTGCCA
421721 CACTGATATGTAGCCGAAGCTACCACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCC--A-CTACCACTGAAATGTAGCCGAAGCTAC
* *
421767 CACTGATATGTAGCC-CTACCACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCACTACCACTGAAATGTAGCCGAAGCTAC
*
421809 CACTGAAATGTAGCCGAAGCTACCACTGA
1 CACTGATATGTAGCC--A-CTACCACTGA
421838 TCAATAACAC
Statistics
Matches: 64, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
42 39 0.61
46 25 0.39
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.21
Consensus pattern (43 bp):
CACTGATATGTAGCCACTACCACTGAAATGTAGCCGAAGCTAC
Found at i:422305 original size:30 final size:30
Alignment explanation
Indices: 422271--422339 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
422261 TCCTTGACTC
422271 AAACTTTTGAAAAATTACTA-TTTTGCCCCT
1 AAACTTTTGAAAAATTAC-ACTTTTGCCCCT
* * * *
422301 AAACTTTTGCATATTTACACTTTTGCCCTT
1 AAACTTTTGAAAAATTACACTTTTGCCCCT
422331 AAACTTTTG
1 AAACTTTTG
422340 CATATTTACA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 1 0.03
30 33 0.97
ACGTcount: A:0.29, C:0.20, G:0.07, T:0.43
Consensus pattern (30 bp):
AAACTTTTGAAAAATTACACTTTTGCCCCT
Found at i:422324 original size:16 final size:16
Alignment explanation
Indices: 422303--422351 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
422293 TTGCCCCTAA
422303 ACTTTTGCATATTTAC
1 ACTTTTGCATATTTAC
** *
422319 ACTTTTGC--CCTTAA
1 ACTTTTGCATATTTAC
422333 ACTTTTGCATATTTAC
1 ACTTTTGCATATTTAC
422349 ACT
1 ACT
422352 ATTTCCCCAA
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
14 11 0.44
16 14 0.56
ACGTcount: A:0.24, C:0.22, G:0.06, T:0.47
Consensus pattern (16 bp):
ACTTTTGCATATTTAC
Found at i:422340 original size:30 final size:30
Alignment explanation
Indices: 422291--422359 Score: 113
Period size: 30 Copynumber: 2.3 Consensus size: 30
422281 AAAATTACTA
422291 TTTTGCCCCTAAACTTTTGCATATTTACAC
1 TTTTGCCCCTAAACTTTTGCATATTTACAC
*
422321 TTTTGCCCTTAAACTTTTGCATATTTACAC
1 TTTTGCCCCTAAACTTTTGCATATTTACAC
422351 TATTT-CCCC
1 T-TTTGCCCC
422360 AAAGCTCGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 33 0.92
31 3 0.08
ACGTcount: A:0.22, C:0.28, G:0.06, T:0.45
Consensus pattern (30 bp):
TTTTGCCCCTAAACTTTTGCATATTTACAC
Found at i:422836 original size:24 final size:21
Alignment explanation
Indices: 422772--422823 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
422762 AAGTGAGTTA
*
422772 GACAAAAAGAGAAGCAACTTG
1 GACAAAAAGAGAAGTAACTTG
422793 GACAAAAAGAGAAGTAACTTG
1 GACAAAAAGAGAAGTAACTTG
422814 GACAAAAAGA
1 GACAAAAAGA
422824 AACGAAGTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.56, C:0.12, G:0.23, T:0.10
Consensus pattern (21 bp):
GACAAAAAGAGAAGTAACTTG
Found at i:445637 original size:16 final size:16
Alignment explanation
Indices: 445613--445645 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
445603 TCTAAAATAT
445613 AGTAAAATATTAAAAA
1 AGTAAAATATTAAAAA
*
445629 AGTATAATATTAAAAA
1 AGTAAAATATTAAAAA
445645 A
1 A
445646 CAATTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (16 bp):
AGTAAAATATTAAAAA
Found at i:448361 original size:21 final size:21
Alignment explanation
Indices: 448315--448354 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
448305 ATTTAATCCT
* *
448315 TTTAGCACAA-AATTTGTATG
1 TTTACCACAACAATTTATATG
448335 TTTACCACAACAATTTATAT
1 TTTACCACAACAATTTATAT
448355 TTATACCTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.40
Consensus pattern (21 bp):
TTTACCACAACAATTTATATG
Found at i:451027 original size:9 final size:9
Alignment explanation
Indices: 451013--451043 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
451003 GTTAAACGAA
451013 TCGAGTTAT
1 TCGAGTTAT
*
451022 TCGAGTTAA
1 TCGAGTTAT
451031 TCGAGTTAT
1 TCGAGTTAT
451040 TCGA
1 TCGA
451044 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:451114 original size:9 final size:9
Alignment explanation
Indices: 451097--451133 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
451087 TGAGTTTTCG
451097 AATTCGAAT
1 AATTCGAAT
*
451106 AACTCGAAT
1 AATTCGAAT
451115 AATTCGAAT
1 AATTCGAAT
451124 AATTCGAAT
1 AATTCGAAT
451133 A
1 A
451134 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:452096 original size:5 final size:5
Alignment explanation
Indices: 452086--452111 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
452076 CTCGAAAATT
452086 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
452112 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:452625 original size:44 final size:43
Alignment explanation
Indices: 452572--452709 Score: 206
Period size: 43 Copynumber: 3.2 Consensus size: 43
452562 ATAGAAATAC
*
452572 ACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTCCTACAA
1 ACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTCCCACAA
*
452615 ACGCCGGCTAAAGGTC-TGTTCTTTAGCGGCGCTATTCCCACAA
1 ACGCC-GCTAAAGGTCATGTTCTTTAGCGGCGCTTTTCCCACAA
* * * *
452658 ACGCCGATAAATGTCATGTTCTTTCGCGGCGTTTTTCCCACAA
1 ACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTCCCACAA
452701 ACGCCGCTA
1 ACGCCGCTA
452710 TTGTTTGGTG
Statistics
Matches: 85, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
42 8 0.09
43 67 0.79
44 10 0.12
ACGTcount: A:0.21, C:0.30, G:0.21, T:0.28
Consensus pattern (43 bp):
ACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTCCCACAA
Found at i:452837 original size:44 final size:44
Alignment explanation
Indices: 452690--452825 Score: 254
Period size: 44 Copynumber: 3.1 Consensus size: 44
452680 TTCGCGGCGT
*
452690 TTTTCCCACAAACGCCGCTATTGTTTGGTGACCTTTAGCGGTGC
1 TTTTCCAACAAACGCCGCTATTGTTTGGTGACCTTTAGCGGTGC
452734 TTTTCCAACAAACGCCGCTATTGTTTGGTGACCTTTAGCGGTGC
1 TTTTCCAACAAACGCCGCTATTGTTTGGTGACCTTTAGCGGTGC
*
452778 TTTTCCAACAAACGCCGCTATTGTTTGGTGACCTTTAGCGGCGC
1 TTTTCCAACAAACGCCGCTATTGTTTGGTGACCTTTAGCGGTGC
452822 TTTT
1 TTTT
452826 TCTAAAAACG
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 90 1.00
ACGTcount: A:0.17, C:0.26, G:0.22, T:0.35
Consensus pattern (44 bp):
TTTTCCAACAAACGCCGCTATTGTTTGGTGACCTTTAGCGGTGC
Found at i:453170 original size:21 final size:21
Alignment explanation
Indices: 453146--453195 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
453136 TTCTGCTCTG
453146 CTCTGCTTCCCTCGCTGCCGC
1 CTCTGCTTCCCTCGCTGCCGC
453167 CTCTGCTTCCCTCGCTGCCGC
1 CTCTGCTTCCCTCGCTGCCGC
453188 CTCTGCTT
1 CTCTGCTT
453196 TAATTAAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.00, C:0.50, G:0.18, T:0.32
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCCGC
Found at i:453578 original size:8 final size:8
Alignment explanation
Indices: 453562--453592 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
453552 ATTCGGGCCT
*
453562 ACAATGCA
1 ACAAGGCA
453570 ACAAGGCA
1 ACAAGGCA
453578 ACAAGGCA
1 ACAAGGCA
453586 ACAAGGC
1 ACAAGGC
453593 CTTCATGAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.48, C:0.26, G:0.23, T:0.03
Consensus pattern (8 bp):
ACAAGGCA
Found at i:455668 original size:38 final size:37
Alignment explanation
Indices: 455626--455719 Score: 143
Period size: 38 Copynumber: 2.5 Consensus size: 37
455616 CCCAAATCCC
*
455626 TAACCCCTAACCCTTAAATCCACCTAACCCTTAAAGCA
1 TAACCCCTAACCC-TAAATCCACCTAACCCCTAAAGCA
*
455664 TAACCCCTAACTCCTAAATCCCCCTAACCCCTAAAGCA
1 TAACCCCTAAC-CCTAAATCCACCTAACCCCTAAAGCA
455702 TAACCCCTAACCCCTAAA
1 TAACCCCTAA-CCCTAAA
455720 CCTTAAATCC
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
38 49 0.94
39 3 0.06
ACGTcount: A:0.36, C:0.43, G:0.02, T:0.19
Consensus pattern (37 bp):
TAACCCCTAACCCTAAATCCACCTAACCCCTAAAGCA
Found at i:455672 original size:45 final size:44
Alignment explanation
Indices: 455623--455729 Score: 136
Period size: 38 Copynumber: 2.5 Consensus size: 44
455613 AACCCCAAAT
*
455623 CCCTAACCCCTAACCCTTAAATCCACCTAACCCTTAAAGCATAAC
1 CCCTAACCCCTAA-CCTTAAATCCACCTAACCCCTAAAGCATAAC
*
455668 CCCTAA---CT--CC-TAAATCCCCCTAACCCCTAAAGCATAAC
1 CCCTAACCCCTAACCTTAAATCCACCTAACCCCTAAAGCATAAC
455706 CCCTAACCCCTAAACCTTAAATCC
1 CCCTAACCCCT-AACCTTAAATCC
455730 CAAACCCTAA
Statistics
Matches: 53, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
38 32 0.60
39 2 0.04
41 2 0.04
42 2 0.04
44 2 0.04
45 13 0.25
ACGTcount: A:0.35, C:0.44, G:0.02, T:0.20
Consensus pattern (44 bp):
CCCTAACCCCTAACCTTAAATCCACCTAACCCCTAAAGCATAAC
Found at i:456364 original size:39 final size:38
Alignment explanation
Indices: 456283--456374 Score: 121
Period size: 39 Copynumber: 2.4 Consensus size: 38
456273 ATAATTTATC
* * *
456283 CCCCTAACCCCTAAATTCCCCTAACCCCTAAAGCATAG
1 CCCCTAACCCTTAAATCCCCCTAACCCCTAAAGCATAA
* * *
456321 CCCCTAACTCTTAAATCCCCTCTAACCCTTAAATCATAA
1 CCCCTAACCCTTAAATCCCC-CTAACCCCTAAAGCATAA
456360 CCCCTAACCCTTAAA
1 CCCCTAACCCTTAAA
456375 CCTTAAATCT
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
38 17 0.37
39 29 0.63
ACGTcount: A:0.33, C:0.42, G:0.02, T:0.23
Consensus pattern (38 bp):
CCCCTAACCCTTAAATCCCCCTAACCCCTAAAGCATAA
Found at i:456368 original size:21 final size:20
Alignment explanation
Indices: 456283--456374 Score: 79
Period size: 21 Copynumber: 4.8 Consensus size: 20
456273 ATAATTTATC
*
456283 CCCCTAACCCCTAAAT--T-
1 CCCCTAACCCTTAAATCATA
* *
456300 CCCCTAACCCCTAAAGCATA
1 CCCCTAACCCTTAAATCATA
*
456320 GCCCCTAACTCTTAAATC---
1 -CCCCTAACCCTTAAATCATA
456338 CCCTCTAACCCTTAAATCATAA
1 CCC-CTAACCCTTAAATCAT-A
456360 CCCCTAACCCTTAAA
1 CCCCTAACCCTTAAA
456375 CCTTAAATCT
Statistics
Matches: 61, Mismatches: 5, Indels: 14
0.76 0.06 0.17
Matches are distributed among these distances:
17 18 0.30
18 13 0.21
19 1 0.02
21 26 0.43
22 3 0.05
ACGTcount: A:0.33, C:0.42, G:0.02, T:0.23
Consensus pattern (20 bp):
CCCCTAACCCTTAAATCATA
Found at i:456941 original size:41 final size:41
Alignment explanation
Indices: 456881--456958 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
456871 TTTTTTTATT
*
456881 ATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAAGCCCGAGC
*
456922 ATTAGCGGTGCTATT-TCAAAAACGCCGCTAAAAGCCC
1 ATTAGCGGCGCT-TTCTCAAAAACGCCGCTAAAAGCCC
456959 CAAAACTCAG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
41 32 0.94
42 2 0.06
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.19
Consensus pattern (41 bp):
ATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAAGCCCGAGC
Found at i:457048 original size:39 final size:39
Alignment explanation
Indices: 457005--457117 Score: 129
Period size: 40 Copynumber: 2.8 Consensus size: 39
456995 TTTGCAGCGC
*
457005 TTTTCAAAAAACGCCACTAATGCTTATTTTTAGCGACGT
1 TTTTCAAAAAGCGCCACTAATGCTTATTTTTAGCGACGT
* * * *
457044 TTTTCAAAAAGCGTCACTAATGCTCCATCTTTAGCGGCGT
1 TTTTCAAAAAGCGCCACTAATGCT-TATTTTTAGCGACGT
* *
457084 TTTT-AGAAGAGCGCCGCTAATGCTTGATTTTTAG
1 TTTTCA-AAAAGCGCCACTAATGCTT-ATTTTTAG
457118 TGGCGCTTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
39 23 0.38
40 38 0.62
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (39 bp):
TTTTCAAAAAGCGCCACTAATGCTTATTTTTAGCGACGT
Found at i:457229 original size:23 final size:23
Alignment explanation
Indices: 457195--457240 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
457185 ATTTCAACTC
*
457195 AAAAAATCTACATTGTTAATGTT
1 AAAAAATCTACATGGTTAATGTT
*
457218 AAAAAATTTACATGGTTAATGTT
1 AAAAAATCTACATGGTTAATGTT
457241 TCGTGAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (23 bp):
AAAAAATCTACATGGTTAATGTT
Found at i:460100 original size:35 final size:34
Alignment explanation
Indices: 460061--460126 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
460051 CGTACAAACT
*
460061 CAAACCCCGAAAATAAAGCCCTAACTCTCATAGAG
1 CAAA-CCCGAAAATAAAACCCTAACTCTCATAGAG
* * *
460096 CAAACCTGAAAATAAAACTCTAATTCTCATA
1 CAAACCCGAAAATAAAACCCTAACTCTCATA
460127 AAGTTCTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
34 23 0.85
35 4 0.15
ACGTcount: A:0.45, C:0.27, G:0.08, T:0.20
Consensus pattern (34 bp):
CAAACCCGAAAATAAAACCCTAACTCTCATAGAG
Found at i:478471 original size:47 final size:47
Alignment explanation
Indices: 478400--478494 Score: 183
Period size: 46 Copynumber: 2.0 Consensus size: 47
478390 TTATACAATA
478400 TTTGGAATTCAGTCCTTAGATTTTTTTTAATTTGAAATTTATCGTGT
1 TTTGGAATTCAGTCCTTAGATTTTTTTTAATTTGAAATTTATCGTGT
478447 TTTGGAATTC-GTCCTTAGATTTTTTTTAATTTGAAATTTATCGTGT
1 TTTGGAATTCAGTCCTTAGATTTTTTTTAATTTGAAATTTATCGTGT
478493 TT
1 TT
478495 ATTTTTTAAC
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 38 0.79
47 10 0.21
ACGTcount: A:0.22, C:0.08, G:0.15, T:0.55
Consensus pattern (47 bp):
TTTGGAATTCAGTCCTTAGATTTTTTTTAATTTGAAATTTATCGTGT
Found at i:480087 original size:3 final size:3
Alignment explanation
Indices: 480081--480137 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
480071 TTTTTTACAC
480081 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
480129 TAT TAT TAT
1 TAT TAT TAT
480138 AGCCATATAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:483643 original size:29 final size:30
Alignment explanation
Indices: 483585--483643 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
483575 TATTTTTTAG
*
483585 TTAAATTTGACCCTTAATTTTTTAAAAAAT
1 TTAAATTTGACCCATAATTTTTTAAAAAAT
*
483615 TTAAATTTGA-CCATCATTTTTTAAAAAAT
1 TTAAATTTGACCCATAATTTTTTAAAAAAT
483644 AGAATCGTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 17 0.63
30 10 0.37
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.46
Consensus pattern (30 bp):
TTAAATTTGACCCATAATTTTTTAAAAAAT
Found at i:485058 original size:26 final size:26
Alignment explanation
Indices: 485029--485080 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
485019 ACATATATTT
485029 TATATTTATAAAAA-ATTTATGTAAAA
1 TATATTTATAAAAATA-TTATGTAAAA
*
485055 TATATTTATAAAAGTATTATGTAAAA
1 TATATTTATAAAAATATTATGTAAAA
485081 ATAAATAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 23 0.96
27 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (26 bp):
TATATTTATAAAAATATTATGTAAAA
Found at i:489893 original size:30 final size:31
Alignment explanation
Indices: 489820--489895 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 31
489810 CTGGCCCAAT
* *
489820 TTGGTACTCAAACTTGACAGTTTTTTCTAAT
1 TTGGTACTTAAACTTGACAGTTTTTTCTAAG
* * *
489851 TTAGTACCTAAACTTGACA-TTTTTTTTAAG
1 TTGGTACTTAAACTTGACAGTTTTTTCTAAG
*
489881 TTGGTATTTAAACTT
1 TTGGTACTTAAACTT
489896 TTTGGAGTCC
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
30 21 0.57
31 16 0.43
ACGTcount: A:0.28, C:0.13, G:0.12, T:0.47
Consensus pattern (31 bp):
TTGGTACTTAAACTTGACAGTTTTTTCTAAG
Found at i:492424 original size:27 final size:27
Alignment explanation
Indices: 492381--492444 Score: 92
Period size: 27 Copynumber: 2.3 Consensus size: 27
492371 TATATTTAAT
*
492381 ATATAATATATATTTGATTCAAAATAAA
1 ATAT-ATATAAATTTGATTCAAAATAAA
*
492409 ATATATATAAATTTGATTGAAAATAAA
1 ATATATATAAATTTGATTCAAAATAAA
*
492436 AAATATATA
1 ATATATATA
492445 TTTAATATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
27 29 0.88
28 4 0.12
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.38
Consensus pattern (27 bp):
ATATATATAAATTTGATTCAAAATAAA
Found at i:500490 original size:2 final size:2
Alignment explanation
Indices: 500485--500511 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
500475 AATAAATCCT
500485 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
500512 ATGTCTCTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:505547 original size:14 final size:14
Alignment explanation
Indices: 505528--505557 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
505518 GAAAACTTTG
*
505528 ATTAAAATTTTAAA
1 ATTAAAATATTAAA
505542 ATTAAAATATTAAA
1 ATTAAAATATTAAA
505556 AT
1 AT
505558 AATTATATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
ATTAAAATATTAAA
Found at i:511960 original size:11 final size:12
Alignment explanation
Indices: 511930--511963 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
511920 CGGTTGGCCC
511930 ATATTAATTTTT
1 ATATTAATTTTT
511942 ATATTAATTTTT
1 ATATTAATTTTT
511954 ATA-TAATTTT
1 ATATTAATTTT
511964 AAAAAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:511976 original size:17 final size:18
Alignment explanation
Indices: 511956--511989 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
511946 TAATTTTTAT
511956 ATAATTT-TAAAAAATAA
1 ATAATTTATAAAAAATAA
*
511973 ATAATTTATCAAAAATA
1 ATAATTTATAAAAAATA
511990 CTAAAAACAT
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:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (18 bp):
ATAATTTATAAAAAATAA
Found at i:516098 original size:19 final size:19
Alignment explanation
Indices: 516076--516114 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
516066 ATAATTAAGC
516076 TTAAAGATAATAATATATA
1 TTAAAGATAATAATATATA
516095 TTAAAGATAATAATATATA
1 TTAAAGATAATAATATATA
516114 T
1 T
516115 AATATTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (19 bp):
TTAAAGATAATAATATATA
Found at i:519833 original size:28 final size:28
Alignment explanation
Indices: 519808--519869 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
519798 TAGCTCTTTC
*
519808 TAATTCATTGTCCCTTCCGTTCTCTTAT
1 TAATTCATTGTCCCTTCCATTCTCTTAT
*
519836 TTATTCATTGTCCCTTCCATTCTCTTAT
1 TAATTCATTGTCCCTTCCATTCTCTTAT
*
519864 TTATTC
1 TAATTC
519870 CTTTGTTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.15, C:0.27, G:0.05, T:0.53
Consensus pattern (28 bp):
TAATTCATTGTCCCTTCCATTCTCTTAT
Found at i:535575 original size:106 final size:107
Alignment explanation
Indices: 535382--535576 Score: 268
Period size: 106 Copynumber: 1.8 Consensus size: 107
535372 GGGGAGTGTT
* * * *
535382 GGGTTTTGGCGGGAAGAGTCGATGGGTGTTTGTGGTGGTTGGCAGGTGCGCCCGTGTCGGGGTCT
1 GGGTTTTGGCAGGAAGAGTCGATGGGTGTTCGTGGTGGTTGGCAGGTACGCCCGTGTCGGAGTCT
**
535447 GAAACCGCCATCTTACTTGGCGGTTGCAGCAGTAGAAGAAGG
66 GAAACCGCCATCTTACACGGCGGTTGCAGCAGTAGAAGAAGG
* * * * *
535489 GGGTTTTGGCAGGAAGTGTCGGTGGGTG-TCGTGTTGGTTGGGAGGTACGCCCGTGTCTGAGTCT
1 GGGTTTTGGCAGGAAGAGTCGATGGGTGTTCGTGGTGGTTGGCAGGTACGCCCGTGTCGGAGTCT
535553 GAAACCGCCA-CTTGACACGGCGGT
66 GAAACCGCCATCTT-ACACGGCGGT
535577 CTCAGCGGTT
Statistics
Matches: 76, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
105 3 0.04
106 48 0.63
107 25 0.33
ACGTcount: A:0.15, C:0.18, G:0.42, T:0.26
Consensus pattern (107 bp):
GGGTTTTGGCAGGAAGAGTCGATGGGTGTTCGTGGTGGTTGGCAGGTACGCCCGTGTCGGAGTCT
GAAACCGCCATCTTACACGGCGGTTGCAGCAGTAGAAGAAGG
Found at i:538602 original size:13 final size:13
Alignment explanation
Indices: 538586--538610 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
538576 TTTTGGGGAA
538586 AATTTTTGGGTTT
1 AATTTTTGGGTTT
538599 AATTTTTGGGTT
1 AATTTTTGGGTT
538611 CCGCCATGAA
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:0.00, G:0.24, T:0.60
Consensus pattern (13 bp):
AATTTTTGGGTTT
Found at i:538962 original size:23 final size:23
Alignment explanation
Indices: 538925--538969 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
538915 TCATAAAGTG
538925 TGTAATATCCCAAAAATTACTAT
1 TGTAATATCCCAAAAATTACTAT
538948 TGTAATA-CCCTAAAAATTACTA
1 TGTAATATCCC-AAAAATTACTA
538970 CAGTAAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.44, C:0.18, G:0.04, T:0.33
Consensus pattern (23 bp):
TGTAATATCCCAAAAATTACTAT
Found at i:538975 original size:23 final size:23
Alignment explanation
Indices: 538926--538975 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
538916 CATAAAGTGT
**
538926 GTAATATCCCAAAAATTACTATT
1 GTAATATCCCAAAAATTACTACA
538949 GTAATA-CCCTAAAAATTACTACA
1 GTAATATCCC-AAAAATTACTACA
538972 GTAA
1 GTAA
538976 GAAAGTAGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 3 0.12
23 21 0.88
ACGTcount: A:0.46, C:0.18, G:0.06, T:0.30
Consensus pattern (23 bp):
GTAATATCCCAAAAATTACTACA
Found at i:550460 original size:27 final size:24
Alignment explanation
Indices: 550430--550478 Score: 62
Period size: 27 Copynumber: 1.9 Consensus size: 24
550420 TTCAAAAAAA
550430 TATAATAATAAATTTAAATATTATATT
1 TATAATAAT-AA-TTAAA-ATTATATT
*
550457 TATATTAATAATTAAAATTATA
1 TATAATAATAATTAAAATTATA
550479 ATAATATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 6 0.29
25 5 0.24
26 2 0.10
27 8 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TATAATAATAATTAAAATTATATT
Found at i:550470 original size:18 final size:18
Alignment explanation
Indices: 550456--550492 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
550446 AATATTATAT
*
550456 TTATATTAATAATTAAAA
1 TTATAATAATAATTAAAA
550474 TTATAATAAT-ATTAAAA
1 TTATAATAATAATTAAAA
550491 TT
1 TT
550493 TCATTTTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTATAATAATAATTAAAA
Found at i:550485 original size:24 final size:24
Alignment explanation
Indices: 550431--550492 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
550421 TCAAAAAAAT
* *
550431 ATAATAATAAATTTAAATATTATA
1 ATAATATTAAAATTAAATATTATA
* *
550455 TTTATATTAATAATTAAA-ATTATA
1 ATAATATTAA-AATTAAATATTATA
550479 ATAATATTAAAATT
1 ATAATATTAAAATT
550493 TCATTTTAGG
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
23 4 0.13
24 21 0.68
25 6 0.19
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
ATAATATTAAAATTAAATATTATA
Found at i:551324 original size:3 final size:3
Alignment explanation
Indices: 551316--551343 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
551306 TCATAGATGA
551316 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
551344 TCATTTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:562806 original size:3 final size:3
Alignment explanation
Indices: 562798--562829 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
562788 CACAATCGAA
562798 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
562830 NNNNNNNNNN
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:566470 original size:15 final size:15
Alignment explanation
Indices: 566450--566478 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
566440 GAATGCCGAA
566450 TAAAACATTTATCTC
1 TAAAACATTTATCTC
566465 TAAAACATTTATCT
1 TAAAACATTTATCT
566479 TTTAAGAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.41
Consensus pattern (15 bp):
TAAAACATTTATCTC
Found at i:568590 original size:22 final size:22
Alignment explanation
Indices: 568557--568617 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
568547 GCCCGACCCG
* *
568557 TTTTTAATTAAAATTAAAATTAT
1 TTTTTAA-TAAAATTAAAACTAA
568580 TTTTTAATAAAATTAAAACTAA
1 TTTTTAATAAAATTAAAACTAA
* *
568602 TTGTTATTAAAATTAA
1 TTTTTAATAAAATTAA
568618 TTGTTAATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 27 0.79
23 7 0.21
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTTTAATAAAATTAAAACTAA
Found at i:568630 original size:16 final size:16
Alignment explanation
Indices: 568593--568632 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
568583 TTAATAAAAT
* *
568593 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAA
568609 TAAAATTAATTGTTAA
1 TAAAATTAATTGTTAA
568625 TAAAATTA
1 TAAAATTA
568633 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAA
Found at i:568710 original size:66 final size:59
Alignment explanation
Indices: 568635--568754 Score: 197
Period size: 59 Copynumber: 2.1 Consensus size: 59
568625 TAAAATTATC
* * *
568635 AAATTAT-TAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTA
1 AAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
*
568693 AATTTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
1 AAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
568752 AAA
1 AAA
568755 CAAACTTGAT
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
58 6 0.11
59 50 0.89
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (59 bp):
AAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
Found at i:568860 original size:22 final size:24
Alignment explanation
Indices: 568820--568863 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
568810 AAATAAACTT
568820 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
568844 AAAATAAAAAA-TA-TATATTT
1 AAAATAAAAAACTATTATATTT
568864 AATATTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:588965 original size:30 final size:30
Alignment explanation
Indices: 588898--588974 Score: 95
Period size: 30 Copynumber: 2.5 Consensus size: 30
588888 TATACTAAAT
* *
588898 TAATATATTACTAATACATAAAATAATATTA
1 TAATATATAACTATTACATAAAAT-ATATTA
588929 TAATATATAACTATTAC-TAAAAT-TATTAA
1 TAATATATAACTATTACATAAAATATATT-A
588958 TACATATATAACTATTA
1 TA-ATATATAACTATTA
588975 TTATAATATA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
28 4 0.10
29 3 0.07
30 20 0.48
31 15 0.36
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (30 bp):
TAATATATAACTATTACATAAAATATATTA
Found at i:589160 original size:14 final size:15
Alignment explanation
Indices: 589136--589164 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
589126 TATTTCAAGC
589136 AATATAATATATAAT
1 AATATAATATATAAT
589151 AATA-AATATATAAT
1 AATATAATATATAAT
589165 GTATTACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AATATAATATATAAT
Found at i:589206 original size:15 final size:15
Alignment explanation
Indices: 589172--589209 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
589162 AATGTATTAC
589172 TATTATATATAAGTAT
1 TATTATATATAAG-AT
589188 TATTATACTATAA-AT
1 TATTATA-TATAAGAT
589203 TATTATA
1 TATTATA
589210 AAAGATGTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 7 0.33
17 5 0.24
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (15 bp):
TATTATATATAAGAT
Found at i:590239 original size:30 final size:30
Alignment explanation
Indices: 590172--590248 Score: 95
Period size: 30 Copynumber: 2.5 Consensus size: 30
590162 TATACTAAAT
* *
590172 TAATATATTACTAATACATAAAATAATATTA
1 TAATATATAACTATTACATAAAAT-ATATTA
590203 TAATATATAACTATTAC-TAAAAT-TATTAA
1 TAATATATAACTATTACATAAAATATATT-A
590232 TACATATATAACTATTA
1 TA-ATATATAACTATTA
590249 TTATAATATA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
28 4 0.10
29 3 0.07
30 20 0.48
31 15 0.36
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (30 bp):
TAATATATAACTATTACATAAAATATATTA
Found at i:590434 original size:14 final size:15
Alignment explanation
Indices: 590410--590438 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
590400 TATTTCAAGC
590410 AATATAATATATAAT
1 AATATAATATATAAT
590425 AATA-AATATATAAT
1 AATATAATATATAAT
590439 GTATTACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AATATAATATATAAT
Found at i:590480 original size:15 final size:15
Alignment explanation
Indices: 590446--590483 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
590436 AATGTATTAC
590446 TATTATATATAAGTAT
1 TATTATATATAAG-AT
590462 TATTATACTATAA-AT
1 TATTATA-TATAAGAT
590477 TATTATA
1 TATTATA
590484 AAAGATGTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 7 0.33
17 5 0.24
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (15 bp):
TATTATATATAAGAT
Found at i:593135 original size:14 final size:16
Alignment explanation
Indices: 593118--593155 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
593108 TTTTTATGTA
593118 ATTTTA-ATT-TTTAT
1 ATTTTATATTATTTAT
593132 ATTTTATATTATTTAT
1 ATTTTATATTATTTAT
*
593148 GTTTTATA
1 ATTTTATA
593156 AAATATTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.29
15 3 0.14
16 12 0.57
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
ATTTTATATTATTTAT
Found at i:594376 original size:57 final size:57
Alignment explanation
Indices: 594272--594384 Score: 174
Period size: 57 Copynumber: 2.0 Consensus size: 57
594262 TATAGATCGA
594272 TACCAAAAAAATTAATTTTAAAATATATTTCAAATTTAAATTATTATTATTTATTTG
1 TACCAAAAAAATTAATTTTAAAATATATTTCAAATTTAAATTATTATTATTTATTTG
* * * *
594329 TACCAAAAAGA-TAATTTTAAAATGTATTTTAAATTTTAAATTTTTATTATTTATTT
1 TACCAAAAAAATTAATTTTAAAATATATTTCAAA-TTTAAATTATTATTATTTATTT
594385 TGAATTTTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
56 20 0.39
57 31 0.61
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.50
Consensus pattern (57 bp):
TACCAAAAAAATTAATTTTAAAATATATTTCAAATTTAAATTATTATTATTTATTTG
Found at i:601434 original size:74 final size:74
Alignment explanation
Indices: 601287--601425 Score: 269
Period size: 74 Copynumber: 1.9 Consensus size: 74
601277 ATTTAAACAA
*
601287 GGGATCCTGCCCAGTAAGTTAGGACACGATTTCTTCTTAATTCCCGAGATCATTTAAAACTTGAG
1 GGGATCATGCCCAGTAAGTTAGGACACGATTTCTTCTTAATTCCCGAGATCATTTAAAACTTGAG
601352 AAAAAAAAG
66 AAAAAAAAG
601361 GGGATCATGCCCAGTAAGTTAGGACACGATTTCTTCTTAATTCCCGAGATCATTTAAAACTTGAG
1 GGGATCATGCCCAGTAAGTTAGGACACGATTTCTTCTTAATTCCCGAGATCATTTAAAACTTGAG
601426 TTTGAAAAGA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
74 64 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.29
Consensus pattern (74 bp):
GGGATCATGCCCAGTAAGTTAGGACACGATTTCTTCTTAATTCCCGAGATCATTTAAAACTTGAG
AAAAAAAAG
Found at i:606243 original size:45 final size:44
Alignment explanation
Indices: 606192--606286 Score: 102
Period size: 44 Copynumber: 2.1 Consensus size: 44
606182 GGTTTGATAT
* **
606192 GATAAGATCTGCTATCTACAGTCTG-CTCCACTACAACTTTAGGGA
1 GATAAGA-CTGATATCTACAACCTGCCT-CACTACAACTTTAGGGA
* * * *
606237 GATAAGACTTATATCTTCAACCTGCCTCACTGCAACTTTAGGGG
1 GATAAGACTGATATCTACAACCTGCCTCACTACAACTTTAGGGA
606281 GATAAG
1 GATAAG
606287 GTTTGTTACT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
44 33 0.79
45 9 0.21
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.28
Consensus pattern (44 bp):
GATAAGACTGATATCTACAACCTGCCTCACTACAACTTTAGGGA
Found at i:606613 original size:44 final size:44
Alignment explanation
Indices: 606213--607345 Score: 496
Period size: 44 Copynumber: 25.7 Consensus size: 44
606203 CTATCTACAG
* * *
606213 TCTGCTCCACTACAACTTTAGGGAGATAAGACTTA-TATCTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTAGTAGCTTCAA
* * * * *
606257 CCTGC-CTCACTGCAACTTTAGGGGGATAAGGTTTGTTA-CTTCAA
1 TCTGCTC-CACTGCAACTTCAGGGAGATAAGATTAG-TAGCTTCAA
* * * * ** * ** *
606301 CCTACTCTACTGCGACTTCATAGAGATAATG-TTTGCGGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAA-GATTAGTAGCTTCAA
* * *
606345 TCTGCTCCGCTGCAAGTTCAGAGG-GATAAGATTAGTGGCTTCAA
1 TCTGCTCCACTGCAACTTCAG-GGAGATAAGATTAGTAGCTTCAA
* * * **
606389 TCTGCTCCATTGTAACTTCAGGGAGATAATATT-GATATTTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTAG-TAGCTTCAA
* * * * * * *
606433 CCTGTTCCCCTGCAACTCCAGGGAGATAAGGTCT-GCTATCTT-TA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TAG-TAGCTTCAA
* * * * * ***
606477 TCTACTCCACTGCAACTTTAGAAAGAGATACGACCT-GTTTTTTCAA
1 TCTGCTCCACTGCAACTTCAG--GGAGATAAGA-TTAGTAGCTTCAA
* * * * ** * * * *
606523 CCTCCTCCACTGCGACTTCAGGGGGAGGAGATTCGTGGTTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCTTCAA
* * *
606567 TCTGCTCCACTGCAACTTCAAGGAGATAGGATTAATAGCTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCTTCAA
* * * * *
606611 TCTTCTCCACTGCAACATCAGGGAGATAAGATTGGTATCTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCTTCAA
* * * * *
606655 CCTGCTCCACTGCAACTTCAGGGAGATAAGGTTGGTTATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTAG-TAGCTTCAA
* *
606700 TCTGCTCCACTGCAACTTCAGGGAGATTAGACTTGTTATGGTAGAATT-AA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA----TTA--GTAG-CTTCAA
* * * * * *
606750 T-TCGAC-CTACTGCAACTTCAGAGG-CATAGGATTCA-TCGTTTTAA
1 TCT-G-CTCCACTGCAACTTCAG-GGAGATAAGATT-AGTAGCTTCAA
* * * *
606794 TCCGCTCAATTGCAACTTCAGGGAGATAGGATTAGTAGCTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCTTCAA
* * * * *
606838 TCTGCTCCGCTGCAACTTTAAGGAGATAAGATT-G--GTTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCTTCAA
* *
606879 TCTGCTCCACTGCAACTTTAGGGAGATAAGATTAGTGGCTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCTTCAA
** *
606923 TCTGCTCCACTGCAACTTCAATGAGATAAGATT-G--G-TTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCTTCAA
* * * *
606963 CCTGCTCCACTGCAACTTCAGGGAGATAAGGTT--T-GATAT-GA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCT-TCAA
* * * *
607004 TTTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTATAGCTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA--T-T-A---GTAGCTTCAA
* * * * * *
607055 TCTGTTCCATTACAACTTCAGGGAAATAAGATTCGCTATCTTC-A
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTAG-TAGCTTCAA
* * * *
607099 ---GCTCCACTGCAAGTTGAGAGAGATAAGACTT-GTATCTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTAGTAGCTTCAA
* * ** * * * *
607140 CCTGCCCCACTATAACTTTAGGGGGATAAGGTTTGTTA-CTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTAG-TAGCTTCAA
* * * * * ** * * * *
607184 CCTACTCTACTGTAACTTTATAGAGATAAGGTTTGTGGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCTTCAA
* * * *
607228 TCTGATCCACTGTAACTTTAGGGAGATAATATTAGT-GACTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTAG-CTTCAA
* * * *
607272 TCTGCTCTAGTGCAACTTCAGGGAGATAAGACTT-GTTGGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTAG-TAGCTTCAA
* * *
607317 TCTGCTCAACTGCAACTTTAAGGAGATAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAA
607346 TATTTGCCAT
Statistics
Matches: 824, Mismatches: 202, Indels: 125
0.72 0.18 0.11
Matches are distributed among these distances:
40 41 0.05
41 88 0.11
42 4 0.00
43 21 0.03
44 484 0.59
45 92 0.11
46 30 0.04
47 1 0.00
48 1 0.00
49 4 0.00
50 25 0.03
51 33 0.04
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.32
Consensus pattern (44 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCTTCAA
Found at i:606892 original size:41 final size:40
Alignment explanation
Indices: 606789--607035 Score: 208
Period size: 41 Copynumber: 5.9 Consensus size: 40
606779 GATTCATCGT
* * * * *
606789 TTTAATCCGCTCAATTGCAACTTCAGGGAGATAGGATTAGTAG
1 TTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATT-G--G
* * *
606832 CTTCAATCTGCTCCGCTGCAACTTTAAGGAGATAAGATTGG
1 -TTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTGG
* *
606873 TTTTAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTAGTGG
1 -TTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGA-T--TGG
* *
606917 CTTCAATCTGCTCCACTGCAACTTCAATGAGATAAGATTGG
1 -TTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTGG
* * * *
606958 TTTAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGA
1 TTTAATCTGCTCCACTGCAACTTCAAGGAGATAA-GATTGG
* * * *
606999 TATGATTTGCTCTACTGCAACTTC-AGAGAGATAAGAT
1 TTTAATCTGCTCCACTGCAACTTCAAG-GAGATAAGAT
607036 CTGTAATTTA
Statistics
Matches: 168, Mismatches: 30, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
40 33 0.20
41 67 0.40
42 1 0.01
43 2 0.01
44 65 0.39
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (40 bp):
TTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTGG
Found at i:607238 original size:88 final size:89
Alignment explanation
Indices: 606807--607345 Score: 244
Period size: 85 Copynumber: 6.2 Consensus size: 89
606797 GCTCAATTGC
* * * * ** *
606807 AACTTCAGGGAGATAGGATTAGT-AGCTTCAATCTGCTCCGCTGCAACTTTA-AGGAGATAAGA-
1 AACTTTAGGGAGATAAGATTAGTGA-CTTCAACCTACTCTACTGCAACTTCAGA-GAGATAAGAC
* * **
606869 ---TTGGTTTTAATCTGCTCCACTGC
64 TTGTTGGCTTTAATCTGATCCACTAT
* * * *
606892 AACTTTAGGGAGATAAGATTAGTGGCTTCAATCTGCTCCACTGCAACTTCA-ATGAGATAAGA--
1 AACTTTAGGGAGATAAGATTAGTGACTTCAACCTACTCTACTGCAACTTCAGA-GAGATAAGACT
* * **
606954 --TTGG-TTTAACCTGCTCCACTGC
65 TGTTGGCTTTAATCTGATCCACTAT
* * * ** *
606976 AACTTCAGGGAGATAAGGTT--TGA-TAT-GATTTGCTCTACTGCAACTTCAGAGAGATAAGATC
1 AACTTTAGGGAGATAAGATTAGTGACT-TCAACCTACTCTACTGCAACTTCAGAGAGATAAGA-C
* * * * * *
607037 TGTAATTTATAGCTTCAATCTGTTCCATTAC
64 --T--TGT-TGGCTTTAATCTGATCCACTAT
* * * * * *
607068 AACTTCAGGGAAATAAGATTCGCT-ATCTTC-AGCT-C-C-ACTGCAAGTTGAGAGAGATAAGAC
1 AACTTTAGGGAGATAAGATTAG-TGA-CTTCAACCTACTCTACTGCAACTTCAGAGAGATAAGAC
* * **
607128 TTGTAT--CTTCAACCTGCCCCACTAT
64 TTGT-TGGCTTTAATCTGATCCACTAT
* * * * * * * **
607153 AACTTTAGGGGGATAAGGTTTGTTACTTCAACCTACTCTACTGTAACTTTATAGAGATAAGGTTT
1 AACTTTAGGGAGATAAGATTAGTGACTTCAACCTACTCTACTGCAACTTCAGAGAGATAAGACTT
*
607218 G-TGGCTTTAATCTGATCCACTGT
66 GTTGGCTTTAATCTGATCCACTAT
* * * * *
607241 AACTTTAGGGAGATAATATTAGTGACTTCAATCTGCTCTAGTGCAACTTCAGGGAGATAAGACTT
1 AACTTTAGGGAGATAAGATTAGTGACTTCAACCTACTCTACTGCAACTTCAGAGAGATAAGACTT
* * **
607306 GTTGGCTTTAATCTGCTCAACTGC
66 GTTGGCTTTAATCTGATCCACTAT
*
607330 AACTTTAAGGAGATAA
1 AACTTTAGGGAGATAA
607346 TATTTGCCAT
Statistics
Matches: 360, Mismatches: 66, Indels: 52
0.75 0.14 0.11
Matches are distributed among these distances:
81 29 0.08
82 4 0.01
84 40 0.11
85 94 0.26
86 2 0.01
87 5 0.01
88 87 0.24
89 35 0.10
90 1 0.00
91 3 0.01
92 52 0.14
93 1 0.00
94 2 0.01
95 4 0.01
96 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (89 bp):
AACTTTAGGGAGATAAGATTAGTGACTTCAACCTACTCTACTGCAACTTCAGAGAGATAAGACTT
GTTGGCTTTAATCTGATCCACTAT
Found at i:607531 original size:51 final size:51
Alignment explanation
Indices: 607399--607531 Score: 126
Period size: 51 Copynumber: 2.6 Consensus size: 51
607389 GACTTACTTT
* * * *
607399 CTTCAACTTCAACGCCAGGGAGATAAGATTCGCTGCCTTTAGCTTTAATCTG
1 CTTC-ACTACAACGCCAAGGAGATAAGATTCGCTACCTTTAGCTTTAACCTG
* * * * *
607451 CTTCGCTGCAATGTC-AGGAAAATAAGATTCGCTACCTTTAGCTTTAACCTG
1 CTTCACTACAACGCCAAGG-AGATAAGATTCGCTACCTTTAGCTTTAACCTG
* *
607502 -TTCCACTATAACGCCAAGGAGATAGGATTC
1 CTT-CACTACAACGCCAAGGAGATAAGATTC
607532 ACCGCCTTCA
Statistics
Matches: 63, Mismatches: 15, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
50 4 0.06
51 52 0.83
52 7 0.11
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (51 bp):
CTTCACTACAACGCCAAGGAGATAAGATTCGCTACCTTTAGCTTTAACCTG
Found at i:607603 original size:72 final size:71
Alignment explanation
Indices: 607477--607622 Score: 157
Period size: 72 Copynumber: 2.0 Consensus size: 71
607467 GGAAAATAAG
* * * * * * *
607477 ATTCGCTACCTTTAGCTTTAACCTGTTCCACTATAACGCCAAGGAGATAGGATTCACCGCCTTCA
1 ATTCGCTACCTTCAGCTTTAACCTATTCCACTACAACGCCAAGGAAACAAGATTCACCACCTTCA
607542 GCTTTA
66 GCTTTA
* * * * * * *
607548 ATTCGCTTCACTTCAGCTTTAATCTATTCCACTACAATGCCAGGGAAACAAGATTCGCTACCTTT
1 ATTCGCTAC-CTTCAGCTTTAACCTATTCCACTACAACGCCAAGGAAACAAGATTCACCACCTTC
607613 AGCTTTA
65 AGCTTTA
607620 ATT
1 ATT
607623 TGTTCTACTG
Statistics
Matches: 60, Mismatches: 14, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
71 8 0.13
72 52 0.87
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.33
Consensus pattern (71 bp):
ATTCGCTACCTTCAGCTTTAACCTATTCCACTACAACGCCAAGGAAACAAGATTCACCACCTTCA
GCTTTA
Found at i:607644 original size:51 final size:52
Alignment explanation
Indices: 607548--607653 Score: 124
Period size: 51 Copynumber: 2.1 Consensus size: 52
607538 TTCAGCTTTA
* *
607548 ATTCGCTTCACTTCAGCTTTAATCTATTCCACTACAATGCCAGGGAAACAAG
1 ATTCGCTACACTTCAGCTTTAATCTATTCCACTACAAAGCCAGGGAAACAAG
* * * * * * *
607600 ATTCGCTAC-CTTTAGCTTTAATTTGTTCTACTGCAAAGCTAGGGAAATAAG
1 ATTCGCTACACTTCAGCTTTAATCTATTCCACTACAAAGCCAGGGAAACAAG
607651 ATT
1 ATT
607654 TGCTGTCTTC
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
51 37 0.82
52 8 0.18
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (52 bp):
ATTCGCTACACTTCAGCTTTAATCTATTCCACTACAAAGCCAGGGAAACAAG
Found at i:607933 original size:88 final size:88
Alignment explanation
Indices: 607820--608006 Score: 250
Period size: 88 Copynumber: 2.1 Consensus size: 88
607810 CTGCTTAGGG
* ** ** * * *
607820 AGACAAGATTTACAATCTTCGACCTACTCCACTGCTGCTCAGGGAGAT-AGGATTGGTGTTTTTG
1 AGACAAGATCTACAATCTTAAACCTACTCCACTAATACTCAGGGAGATAAGG-CTGATGTTTTTG
* * *
607884 ATTTGCTTCACTGTCAGTACAGGA
65 ATCTACTTCACTGCCAGTACAGGA
607908 AGACAAGATCTACAATCTTAAACCTACTCCACTAATACTCAGGGAGATAAGGCTGATGTTTTTGA
1 AGACAAGATCTACAATCTTAAACCTACTCCACTAATACTCAGGGAGATAAGGCTGATGTTTTTGA
607973 TCTACTTCACTGCCAGTACAGGA
66 TCTACTTCACTGCCAGTACAGGA
*
607996 AGACAATATCT
1 AGACAAGATCT
608007 GCTGTTTTCT
Statistics
Matches: 86, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
88 83 0.97
89 3 0.03
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.29
Consensus pattern (88 bp):
AGACAAGATCTACAATCTTAAACCTACTCCACTAATACTCAGGGAGATAAGGCTGATGTTTTTGA
TCTACTTCACTGCCAGTACAGGA
Found at i:609227 original size:40 final size:39
Alignment explanation
Indices: 609166--609243 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
609156 TCATTTTTTA
*
609166 TTTTTTTGGACTCAAAACGCCCTTTGCGGGTTTTCACCC
1 TTTTTTTGAACTCAAAACGCCCTTTGCGGGTTTTCACCC
* * *
609205 TTTTTTTAGAACTCATAGCGCCCTTTGTGGGTTTTCACC
1 TTTTTTT-GAACTCAAAACGCCCTTTGCGGGTTTTCACC
609244 TTGGTTCTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 7 0.21
40 27 0.79
ACGTcount: A:0.15, C:0.26, G:0.18, T:0.41
Consensus pattern (39 bp):
TTTTTTTGAACTCAAAACGCCCTTTGCGGGTTTTCACCC
Found at i:612159 original size:19 final size:20
Alignment explanation
Indices: 612135--612181 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
612125 TGGTAGACTT
* *
612135 TAATGCATATG-ATGTAATG
1 TAATGCAAATGCATGAAATG
612154 TAATGCAAATGCATGAAATG
1 TAATGCAAATGCATGAAATG
612174 -AATGCAAA
1 TAATGCAAA
612182 AAAAGGACGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.45, C:0.09, G:0.19, T:0.28
Consensus pattern (20 bp):
TAATGCAAATGCATGAAATG
Found at i:613810 original size:73 final size:74
Alignment explanation
Indices: 613693--613836 Score: 247
Period size: 73 Copynumber: 2.0 Consensus size: 74
613683 TCTCGAATTT
* *
613693 AAAAAAGAGATCATGCCCAGTAAGTTAGGACACGATCTTTTCTTAATTCCTGAGATCGTTTAAAA
1 AAAAAAGAGATCATGCCCAGTAAGTTAGGACACGATCTTTTCTTAATTCCCGAGATCATTTAAAA
613758 CTTGAGAAA
66 CTTGAGAAA
613767 AAAAAAG-GATCATGCCCAGTAAGTTAGGACACGAT-TTCTTCTTAATTCCCGAGATCATTTAAA
1 AAAAAAGAGATCATGCCCAGTAAGTTAGGACACGATCTT-TTCTTAATTCCCGAGATCATTTAAA
613830 ACTTGAG
65 ACTTGAG
613837 TTTGAAAAGA
Statistics
Matches: 67, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
72 2 0.03
73 58 0.87
74 7 0.10
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.28
Consensus pattern (74 bp):
AAAAAAGAGATCATGCCCAGTAAGTTAGGACACGATCTTTTCTTAATTCCCGAGATCATTTAAAA
CTTGAGAAA
Found at i:615103 original size:19 final size:19
Alignment explanation
Indices: 615079--615117 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
615069 TTTGCGTGTC
615079 TTGCAGGTGACGGCGCAAG
1 TTGCAGGTGACGGCGCAAG
615098 TTGCAGGTGACGGCGCAAG
1 TTGCAGGTGACGGCGCAAG
615117 T
1 T
615118 GGGGGCGGCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.21, G:0.41, T:0.18
Consensus pattern (19 bp):
TTGCAGGTGACGGCGCAAG
Found at i:618523 original size:14 final size:16
Alignment explanation
Indices: 618498--618529 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
618488 CACTCCAACC
618498 AACCCAAAAAAAT-TA
1 AACCCAAAAAAATATA
618513 AACCC-AAAAAATATA
1 AACCCAAAAAAATATA
618528 AA
1 AA
618530 TAACCTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.69, C:0.19, G:0.00, T:0.12
Consensus pattern (16 bp):
AACCCAAAAAAATATA
Found at i:618576 original size:15 final size:16
Alignment explanation
Indices: 618546--618576 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
618536 TAAACTCAGA
618546 TAATTTAAATCCGAAT
1 TAATTTAAATCCGAAT
618562 TAATTTAAA-CCGAAT
1 TAATTTAAATCCGAAT
618577 CAACTCATCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.35
Consensus pattern (16 bp):
TAATTTAAATCCGAAT
Found at i:629158 original size:45 final size:45
Alignment explanation
Indices: 629097--629312 Score: 188
Period size: 45 Copynumber: 4.8 Consensus size: 45
629087 TTGTTGGTTG
* *
629097 AAAAACGAGTAAGACCATAGCTAAAAGACGCTATGGCATCACGAA
1 AAAAACGAGTAAGACCATAGCTGAAAGACGCTATGACATCACGAA
* *
629142 AAAAACGAGTAGGACCATAGTTGAAAGACGCTATGACATCACGAA
1 AAAAACGAGTAAGACCATAGCTGAAAGACGCTATGACATCACGAA
** *
629187 TCAAACGAGTAACACCATAGCTGAAAGACGCTATAGCACTAT-ATC---
1 AAAAACGAGTAAGACCATAGCTGAAAGACGCTAT-G-AC-ATCA-CGAA
* * * * * *
629232 AAAAATGAATAAGACCATAGTTGAAAGACACTATGACAACATGACA
1 AAAAACGAGTAAGACCATAGCTGAAAGACGCTATGACATCACGA-A
* * * * * *
629278 GAAAATGAATATGACCATAGTTGAAAGACACTATG
1 AAAAACGAGTAAGACCATAGCTGAAAGACGCTATG
629313 GCAACATGAC
Statistics
Matches: 142, Mismatches: 20, Indels: 17
0.79 0.11 0.09
Matches are distributed among these distances:
42 1 0.01
43 3 0.02
44 1 0.01
45 97 0.68
46 34 0.24
47 3 0.02
48 3 0.02
ACGTcount: A:0.46, C:0.18, G:0.19, T:0.18
Consensus pattern (45 bp):
AAAAACGAGTAAGACCATAGCTGAAAGACGCTATGACATCACGAA
Found at i:629252 original size:90 final size:90
Alignment explanation
Indices: 629098--629398 Score: 268
Period size: 90 Copynumber: 3.3 Consensus size: 90
629088 TGTTGGTTGA
* * * * * *
629098 AAAACGAGTAAGACCATAGCTAAAAGACGCTATGGCA-TCACGAAAAAAACGAGTAGGACCATAG
1 AAAACGAGTAAGACCATAGCTGAAAGACGCTATGGCACT-A-TACAAAAATGAATAAGACCATAG
* * *
629162 TTGAAAGACGCTATGACATCACGA-AT
64 TTGAAAGACACTATGACAACACGACAG
* * *
629188 CAAACGAGTAACACCATAGCTGAAAGACGCTATAGCACTATATCAAAAATGAATAAGACCATAGT
1 AAAACGAGTAAGACCATAGCTGAAAGACGCTATGGCACTATA-CAAAAATGAATAAGACCATAGT
*
629253 TGAAAGACACTATGACAACATGACAG
65 TGAAAGACACTATGACAACACGACAG
* * * * * *
629279 AAAATGAATATGACCATAGTTGAAAGACACTATGGCAAC-ATGACGGAAAATGAATAAGACCATA
1 AAAACGAGTAAGACCATAGCTGAAAGACGCTATGGC-ACTAT-AC-AAAAATGAATAAGACCATA
* * * *
629343 GTTGAAAGACATTATGGCAATATGAC-G
63 GTTGAAAGACACTATGACAACACGACAG
* * * *
629370 AAAAATGAATAAGATCATAGTTGAAAGAC
1 -AAAACGAGTAAGACCATAGCTGAAAGAC
629399 AATATGACAT
Statistics
Matches: 177, Mismatches: 27, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
89 1 0.01
90 72 0.41
91 34 0.19
92 70 0.40
ACGTcount: A:0.46, C:0.16, G:0.19, T:0.18
Consensus pattern (90 bp):
AAAACGAGTAAGACCATAGCTGAAAGACGCTATGGCACTATACAAAAATGAATAAGACCATAGTT
GAAAGACACTATGACAACACGACAG
Found at i:629294 original size:46 final size:45
Alignment explanation
Indices: 629154--629407 Score: 262
Period size: 46 Copynumber: 5.6 Consensus size: 45
629144 AAACGAGTAG
* * * *** * *
629154 GACCATAGTTGAAAGACGCTATGACATCACGAATCAAACGAGTAA
1 GACCATAGTTGAAAGACACTATGACAACATGACGAAAATGAATAA
* * * *
629199 CACCATAGCTGAAAGACGCTAT-AGC-ACTAT-ATCAAAAATGAATAA
1 GACCATAGTTGAAAGACACTATGA-CAAC-ATGA-CGAAAATGAATAA
*
629244 GACCATAGTTGAAAGACACTATGACAACATGACAGAAAATGAATAT
1 GACCATAGTTGAAAGACACTATGACAACATGAC-GAAAATGAATAA
*
629290 GACCATAGTTGAAAGACACTATGGCAACATGACGGAAAATGAATAA
1 GACCATAGTTGAAAGACACTATGACAACATGAC-GAAAATGAATAA
* * *
629336 GACCATAGTTGAAAGACATTATGGCAATATGACGAAAAATGAATAA
1 GACCATAGTTGAAAGACACTATGACAACATGACG-AAAATGAATAA
* *
629382 GATCATAGTTGAAAGACAATATGACA
1 GACCATAGTTGAAAGACACTATGACA
629408 TTAGGTTGGG
Statistics
Matches: 179, Mismatches: 22, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
44 3 0.02
45 54 0.30
46 122 0.68
ACGTcount: A:0.46, C:0.16, G:0.19, T:0.20
Consensus pattern (45 bp):
GACCATAGTTGAAAGACACTATGACAACATGACGAAAATGAATAA
Found at i:630829 original size:514 final size:514
Alignment explanation
Indices: 629862--630889 Score: 2056
Period size: 514 Copynumber: 2.0 Consensus size: 514
629852 TTGATGTTGG
629862 TTATAAATGGCATGTACTAGAAGCCTTTTTGGTTAATTTATTCATATTGATAATATTTGAATTTT
1 TTATAAATGGCATGTACTAGAAGCCTTTTTGGTTAATTTATTCATATTGATAATATTTGAATTTT
629927 TGTTTGGAAAATCTTGTAGTTATGTAATTATGTTTGGTATATTGGCTTAAAGTTGTGATTATAAA
66 TGTTTGGAAAATCTTGTAGTTATGTAATTATGTTTGGTATATTGGCTTAAAGTTGTGATTATAAA
629992 TGCTTTTGGTCATTTGGTTTATGCCTTATGAAGATAATTTGAAATGTGGTAAAATGTATGTGATG
131 TGCTTTTGGTCATTTGGTTTATGCCTTATGAAGATAATTTGAAATGTGGTAAAATGTATGTGATG
630057 AAATGAAGAATCTGGGTATGTTAAGTACATGTTTAAGGTATTAACTTGTGATTGCAGTGTGTGTG
196 AAATGAAGAATCTGGGTATGTTAAGTACATGTTTAAGGTATTAACTTGTGATTGCAGTGTGTGTG
630122 GTTGTTGGATGTTTAAATTGTGGTACTTGGATGCTTGAACTTAATTGGCAGGTTTTGGTGTGTTT
261 GTTGTTGGATGTTTAAATTGTGGTACTTGGATGCTTGAACTTAATTGGCAGGTTTTGGTGTGTTT
630187 TGAGTCAAGTGGAAGTGGTAATTAGGTGTACATATTGAAAGGTTTGGTTGGAAACTTTGGATTTG
326 TGAGTCAAGTGGAAGTGGTAATTAGGTGTACATATTGAAAGGTTTGGTTGGAAACTTTGGATTTG
630252 GTACCAAATTGTGCATTTTTGCCAAAAACAGAGGCTATGTCTCGATGACCAACCTTCCTCGTCGC
391 GTACCAAATTGTGCATTTTTGCCAAAAACAGAGGCTATGTCTCGATGACCAACCTTCCTCGTCGC
630317 AACGTCGAGTGATAGTGAGTGATGTCACAATGTCAAATGACATGAAGTCGTCACGACGT
456 AACGTCGAGTGATAGTGAGTGATGTCACAATGTCAAATGACATGAAGTCGTCACGACGT
630376 TTATAAATGGCATGTACTAGAAGCCTTTTTGGTTAATTTATTCATATTGATAATATTTGAATTTT
1 TTATAAATGGCATGTACTAGAAGCCTTTTTGGTTAATTTATTCATATTGATAATATTTGAATTTT
630441 TGTTTGGAAAATCTTGTAGTTATGTAATTATGTTTGGTATATTGGCTTAAAGTTGTGATTATAAA
66 TGTTTGGAAAATCTTGTAGTTATGTAATTATGTTTGGTATATTGGCTTAAAGTTGTGATTATAAA
630506 TGCTTTTGGTCATTTGGTTTATGCCTTATGAAGATAATTTGAAATGTGGTAAAATGTATGTGATG
131 TGCTTTTGGTCATTTGGTTTATGCCTTATGAAGATAATTTGAAATGTGGTAAAATGTATGTGATG
630571 AAATGAAGAATCTGGGTATGTTAAGTACATGTTTAAGGTATTAACTTGTGATTGCAGTGTGTGTG
196 AAATGAAGAATCTGGGTATGTTAAGTACATGTTTAAGGTATTAACTTGTGATTGCAGTGTGTGTG
630636 GTTGTTGGATGTTTAAATTGTGGTACTTGGATGCTTGAACTTAATTGGCAGGTTTTGGTGTGTTT
261 GTTGTTGGATGTTTAAATTGTGGTACTTGGATGCTTGAACTTAATTGGCAGGTTTTGGTGTGTTT
630701 TGAGTCAAGTGGAAGTGGTAATTAGGTGTACATATTGAAAGGTTTGGTTGGAAACTTTGGATTTG
326 TGAGTCAAGTGGAAGTGGTAATTAGGTGTACATATTGAAAGGTTTGGTTGGAAACTTTGGATTTG
630766 GTACCAAATTGTGCATTTTTGCCAAAAACAGAGGCTATGTCTCGATGACCAACCTTCCTCGTCGC
391 GTACCAAATTGTGCATTTTTGCCAAAAACAGAGGCTATGTCTCGATGACCAACCTTCCTCGTCGC
630831 AACGTCGAGTGATAGTGAGTGATGTCACAATGTCAAATGACATGAAGTCGTCACGACGT
456 AACGTCGAGTGATAGTGAGTGATGTCACAATGTCAAATGACATGAAGTCGTCACGACGT
630890 GGAAGTGTTG
Statistics
Matches: 514, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
514 514 1.00
ACGTcount: A:0.27, C:0.10, G:0.25, T:0.39
Consensus pattern (514 bp):
TTATAAATGGCATGTACTAGAAGCCTTTTTGGTTAATTTATTCATATTGATAATATTTGAATTTT
TGTTTGGAAAATCTTGTAGTTATGTAATTATGTTTGGTATATTGGCTTAAAGTTGTGATTATAAA
TGCTTTTGGTCATTTGGTTTATGCCTTATGAAGATAATTTGAAATGTGGTAAAATGTATGTGATG
AAATGAAGAATCTGGGTATGTTAAGTACATGTTTAAGGTATTAACTTGTGATTGCAGTGTGTGTG
GTTGTTGGATGTTTAAATTGTGGTACTTGGATGCTTGAACTTAATTGGCAGGTTTTGGTGTGTTT
TGAGTCAAGTGGAAGTGGTAATTAGGTGTACATATTGAAAGGTTTGGTTGGAAACTTTGGATTTG
GTACCAAATTGTGCATTTTTGCCAAAAACAGAGGCTATGTCTCGATGACCAACCTTCCTCGTCGC
AACGTCGAGTGATAGTGAGTGATGTCACAATGTCAAATGACATGAAGTCGTCACGACGT
Found at i:632666 original size:20 final size:21
Alignment explanation
Indices: 632638--632680 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
632628 AAAAAAGACA
*
632638 AAAGCAAAATGA-AACAGAAAG
1 AAAGCAAAAAGAGAA-AGAAAG
632659 AAAG-AAAAAGAGAAAGAAAG
1 AAAGCAAAAAGAGAAAGAAAG
632679 AA
1 AA
632681 GAACCCACGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.72, C:0.05, G:0.21, T:0.02
Consensus pattern (21 bp):
AAAGCAAAAAGAGAAAGAAAG
Found at i:642087 original size:38 final size:38
Alignment explanation
Indices: 642009--642087 Score: 88
Period size: 38 Copynumber: 2.1 Consensus size: 38
641999 AAAAATTATA
* * *
642009 TTTAATACAATAAAATACTCATTATATTTATTTGTTTG
1 TTTAATACAATAAAACACTCATTATATTTATTGGTGTG
* * *
642047 TTTAATATAATAAAACATTTATTATATTTA-TGGTAGTG
1 TTTAATACAATAAAACACTCATTATATTTATTGGT-GTG
642085 TTT
1 TTT
642088 TTGGGTTTAC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
37 3 0.09
38 31 0.91
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.51
Consensus pattern (38 bp):
TTTAATACAATAAAACACTCATTATATTTATTGGTGTG
Found at i:644058 original size:13 final size:12
Alignment explanation
Indices: 644030--644054 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
644020 ACATTCATTT
644030 ATTTTTTTAATA
1 ATTTTTTTAATA
644042 ATTTTTTTAATA
1 ATTTTTTTAATA
644054 A
1 A
644055 ATTTATATAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATTTTTTTAATA
Found at i:644557 original size:31 final size:30
Alignment explanation
Indices: 644514--644578 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 30
644504 ATTTGGCCAG
*
644514 TTTTAGTCTTTATACATTTTAAATTGGTAAA
1 TTTTAGTATTTATACATTTTAAATT-GTAAA
* *
644545 TTTTAGTATTTATACGTTTTAAATTTTAAA
1 TTTTAGTATTTATACATTTTAAATTGTAAA
644575 TTTT
1 TTTT
644579 CAATCCTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 8 0.26
31 23 0.74
ACGTcount: A:0.31, C:0.05, G:0.08, T:0.57
Consensus pattern (30 bp):
TTTTAGTATTTATACATTTTAAATTGTAAA
Found at i:654866 original size:3 final size:3
Alignment explanation
Indices: 654858--654889 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
654848 AATGTTGTAC
654858 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
654890 GCCTACATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:656730 original size:25 final size:25
Alignment explanation
Indices: 656702--656852 Score: 125
Period size: 25 Copynumber: 6.1 Consensus size: 25
656692 AACTCTTCCA
* *
656702 AGCCATATAACAGGAAGCTCATGTG
1 AGCCATATAACGGGAAGCTCATGAG
* **
656727 AGCCATGTAACGGGAAGCTCCGGAG
1 AGCCATATAACGGGAAGCTCATGAG
656752 AGCCAT-TAACGGGAAGCTCAT-ACG
1 AGCCATATAACGGGAAGCTCATGA-G
*
656776 AGCCA-ATATCGGGAAGCTC-TAGAG
1 AGCCATATAACGGGAAGCTCAT-GAG
*
656800 AGCCAT-TAATCGGGAAGCTCCA-GGG
1 AGCCATATAA-CGGGAAGCT-CATGAG
* * * *
656825 AGCCATATATCGAGACGCTCATAAG
1 AGCCATATAACGGGAAGCTCATGAG
656850 AGC
1 AGC
656853 TGTAGTGTGT
Statistics
Matches: 101, Mismatches: 15, Indels: 20
0.74 0.11 0.15
Matches are distributed among these distances:
23 2 0.02
24 41 0.41
25 55 0.54
26 3 0.03
ACGTcount: A:0.32, C:0.23, G:0.28, T:0.17
Consensus pattern (25 bp):
AGCCATATAACGGGAAGCTCATGAG
Found at i:656766 original size:24 final size:24
Alignment explanation
Indices: 656702--656830 Score: 127
Period size: 25 Copynumber: 5.2 Consensus size: 24
656692 AACTCTTCCA
* *
656702 AGCCATATAACAGGAAGCT-CATGTG
1 AGCCAT-TAACGGGAAGCTCCA-GAG
*
656727 AGCCATGTAACGGGAAGCTCCGGAG
1 AGCCAT-TAACGGGAAGCTCCAGAG
*
656752 AGCCATTAACGGGAAGCT-CATACG
1 AGCCATTAACGGGAAGCTCCAGA-G
* * *
656776 AGCCAATATCGGGAAGCTCTAGAG
1 AGCCATTAACGGGAAGCTCCAGAG
*
656800 AGCCATTAATCGGGAAGCTCCAGGG
1 AGCCATTAA-CGGGAAGCTCCAGAG
656825 AGCCAT
1 AGCCAT
656831 ATATCGAGAC
Statistics
Matches: 86, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
23 2 0.02
24 37 0.43
25 46 0.53
26 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.29, T:0.16
Consensus pattern (24 bp):
AGCCATTAACGGGAAGCTCCAGAG
Found at i:656779 original size:49 final size:48
Alignment explanation
Indices: 656702--656819 Score: 146
Period size: 49 Copynumber: 2.4 Consensus size: 48
656692 AACTCTTCCA
* ** * *
656702 AGCCATATAACAGGAAGCTCATGTGAGCCATGTAACGGGAAGCTCCGGAG
1 AGCCAT-TAACGGGAAGCTCATACGAGCCA-ATAACGGGAAGCTCCAGAG
* *
656752 AGCCATTAACGGGAAGCTCATACGAGCCAATATCGGGAAGCTCTAGAG
1 AGCCATTAACGGGAAGCTCATACGAGCCAATAACGGGAAGCTCCAGAG
656800 AGCCATTAATCGGGAAGCTC
1 AGCCATTAA-CGGGAAGCTC
656820 CAGGGAGCCA
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
48 24 0.40
49 30 0.50
50 6 0.10
ACGTcount: A:0.32, C:0.23, G:0.28, T:0.17
Consensus pattern (48 bp):
AGCCATTAACGGGAAGCTCATACGAGCCAATAACGGGAAGCTCCAGAG
Found at i:656946 original size:25 final size:25
Alignment explanation
Indices: 656891--656950 Score: 79
Period size: 24 Copynumber: 2.4 Consensus size: 25
656881 CACAACCAAT
* *
656891 CGGGAAGCTC-CGAAGAGCTATTAA
1 CGGGAAGCTCGCGAAGAACCATTAA
656915 CGGGAAGCTCGC-AAGAACCATATAA
1 CGGGAAGCTCGCGAAGAACCAT-TAA
656940 CGGGAAGCTCG
1 CGGGAAGCTCG
656951 TGACAGCCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
24 17 0.53
25 15 0.47
ACGTcount: A:0.33, C:0.23, G:0.30, T:0.13
Consensus pattern (25 bp):
CGGGAAGCTCGCGAAGAACCATTAA
Found at i:660932 original size:24 final size:25
Alignment explanation
Indices: 660898--660947 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
660888 TGCATATTTA
* *
660898 ACGGCCTCGACCACGTCCACG-CCC
1 ACGGCCACGACCACGACCACGTCCC
*
660922 ACGGCCACGACCCCGACCACGTCCC
1 ACGGCCACGACCACGACCACGTCCC
660947 A
1 A
660948 AAGGCTTCCC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.20, C:0.54, G:0.20, T:0.06
Consensus pattern (25 bp):
ACGGCCACGACCACGACCACGTCCC
Found at i:661590 original size:23 final size:23
Alignment explanation
Indices: 661560--661606 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
661550 GTTCATGAAC
* *
661560 ATATTCATGGACATGTTTGTTTA
1 ATATTCATGAACATGTTCGTTTA
*
661583 ATATTCATGAACTTGTTCGTTTA
1 ATATTCATGAACATGTTCGTTTA
661606 A
1 A
661607 CTTAAATGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.47
Consensus pattern (23 bp):
ATATTCATGAACATGTTCGTTTA
Found at i:663169 original size:20 final size:19
Alignment explanation
Indices: 663144--663194 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
663134 TAAACTTGGA
*
663144 TTCAAGATTTGGGTTCGAGG
1 TTCAAGATTTGAGTTCGA-G
* *
663164 TTCAAGGTTTGAGTTTGAG
1 TTCAAGATTTGAGTTCGAG
*
663183 TTTAAGATTTGA
1 TTCAAGATTTGA
663195 AGTTTTGGGT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.24, C:0.06, G:0.29, T:0.41
Consensus pattern (19 bp):
TTCAAGATTTGAGTTCGAG
Found at i:663655 original size:9 final size:9
Alignment explanation
Indices: 663643--663670 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
663633 ATATAGTTAA
663643 TAATAATAT
1 TAATAATAT
663652 TAATAATAT
1 TAATAATAT
663661 TAATAATAT
1 TAATAATAT
663670 T
1 T
663671 TTAGTAGTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
TAATAATAT
Found at i:663813 original size:27 final size:27
Alignment explanation
Indices: 663748--663822 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 27
663738 CAAAAGGCGT
663748 GTGGTGCCTATCTGATAGGCGGCACCA
1 GTGGTGCCTATCTGATAGGCGGCACCA
** **
663775 GT-GACCCTTATCTGATAGGCGGCACTG
1 GTGGTGCC-TATCTGATAGGCGGCACCA
663802 GTGGTGCCTATCTGATAGGCG
1 GTGGTGCCTATCTGATAGGCG
663823 ACACACCTAG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
26 3 0.08
27 34 0.85
28 3 0.08
ACGTcount: A:0.17, C:0.24, G:0.33, T:0.25
Consensus pattern (27 bp):
GTGGTGCCTATCTGATAGGCGGCACCA
Found at i:667663 original size:12 final size:12
Alignment explanation
Indices: 667646--667681 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
667636 CGACCGTTTG
667646 GGCTCAGGCTCT
1 GGCTCAGGCTCT
*
667658 GGCTCAAGCTCT
1 GGCTCAGGCTCT
*
667670 GGCTCAGCCTCT
1 GGCTCAGGCTCT
667682 ATATCCGGCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.11, C:0.36, G:0.28, T:0.25
Consensus pattern (12 bp):
GGCTCAGGCTCT
Found at i:668339 original size:14 final size:14
Alignment explanation
Indices: 668308--668341 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
668298 AAATTACTTG
*
668308 TTAGAATAGTACCG
1 TTAGAATAGTACCA
*
668322 TTAGAATAGTATCA
1 TTAGAATAGTACCA
668336 TTAGAA
1 TTAGAA
668342 AAAAATGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (14 bp):
TTAGAATAGTACCA
Found at i:669314 original size:18 final size:18
Alignment explanation
Indices: 669282--669331 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 18
669272 CTTTTACCTG
669282 CATAAAATACAAAAAA-AA
1 CATAAAATA-AAAAAATAA
669300 -ATTAAAATAATAAAAATAA
1 CA-TAAAATAA-AAAAATAA
669319 CATAAAATAAAAA
1 CATAAAATAAAAA
669332 TTAAAAACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
17 2 0.07
18 15 0.54
19 10 0.36
20 1 0.04
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (18 bp):
CATAAAATAAAAAAATAA
Found at i:669323 original size:14 final size:15
Alignment explanation
Indices: 669296--669337 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
669286 AAATACAAAA
669296 AAAAATTAAAATAAT
1 AAAAATTAAAATAAT
*
669311 AAAAA-TAACATAAAAT
1 AAAAATTAA-A-ATAAT
669327 AAAAATTAAAA
1 AAAAATTAAAA
669338 ACATAAACTC
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
14 3 0.13
15 7 0.30
16 10 0.43
17 3 0.13
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAAATTAAAATAAT
Found at i:671356 original size:29 final size:29
Alignment explanation
Indices: 671316--671380 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
671306 CTTTTTATTT
* *
671316 TAATTTTATATAATTTAATAACTTTATTTTA
1 TAATATTATAT-ATTTAATAA-TATATTTTA
* *
671347 TAATATTATATATTTTATTATATATTTTA
1 TAATATTATATATTTAATAATATATTTTA
671376 TAATA
1 TAATA
671381 ATACTATTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 13 0.43
30 7 0.23
31 10 0.33
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (29 bp):
TAATATTATATATTTAATAATATATTTTA
Found at i:671367 original size:12 final size:12
Alignment explanation
Indices: 671350--671376 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
671340 TATTTTATAA
671350 TATTATATATTT
1 TATTATATATTT
671362 TATTATATATTT
1 TATTATATATTT
671374 TAT
1 TAT
671377 AATAATACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TATTATATATTT
Found at i:671370 original size:22 final size:21
Alignment explanation
Indices: 671321--671375 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
671311 TATTTTAATT
671321 TTATATAATTTAATAACTTTA
1 TTATATAATTTAATAACTTTA
* *
671342 TTTTATAATATT-ATATATTTTA
1 TTATATAAT-TTAATA-ACTTTA
*
671364 TTATATATTTTA
1 TTATATAATTTA
671376 TAATAATACT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
21 13 0.48
22 14 0.52
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
TTATATAATTTAATAACTTTA
Found at i:680724 original size:28 final size:27
Alignment explanation
Indices: 680686--680784 Score: 144
Period size: 28 Copynumber: 3.6 Consensus size: 27
680676 AAAAATAAAA
680686 ATTTACCAAAATAGTACAACTTTTTTTT
1 ATTTACCAAAATA-TACAACTTTTTTTT
*
680714 ATTTACGAAAATATTACAACTTTTTTTT
1 ATTTACCAAAATA-TACAACTTTTTTTT
* *
680742 ATTTACCAAAATATATAAATTTTTTTTT
1 ATTTACCAAAATATA-CAACTTTTTTTT
680770 ATTTACCAAAATATA
1 ATTTACCAAAATATA
680785 TCAAAAAAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 2 0.03
28 63 0.97
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.47
Consensus pattern (27 bp):
ATTTACCAAAATATACAACTTTTTTTT
Found at i:680878 original size:27 final size:27
Alignment explanation
Indices: 680848--680925 Score: 97
Period size: 27 Copynumber: 2.9 Consensus size: 27
680838 CCCCAATGGT
*
680848 ATTGGCGGCACCAAAGGTGCCAAA-TAA
1 ATTGGCGGCACCAATGGTGCCAAAGT-A
* * *
680875 ATTGGTGGCACCATTGGTGCCAAAGTC
1 ATTGGCGGCACCAATGGTGCCAAAGTA
680902 ATTGGCGGCACC-ATGGTGCCAAAG
1 ATTGGCGGCACCAATGGTGCCAAAG
680926 GGAAAAAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
26 11 0.25
27 32 0.73
28 1 0.02
ACGTcount: A:0.28, C:0.23, G:0.29, T:0.19
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAAAGTA
Found at i:681035 original size:18 final size:19
Alignment explanation
Indices: 680998--681036 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
680988 TCAACTTATT
* *
680998 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACACTA
681017 TTTTAATTTAATAA-ACTA
1 TTTTAATTTAATAACACTA
681035 TT
1 TT
681037 CTCATTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTAATTTAATAACACTA
Found at i:681043 original size:18 final size:19
Alignment explanation
Indices: 681003--681045 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
680993 TTATTTTTTT
* *
681003 ATTTAATAACTCTATTTTA
1 ATTTAATAACACTATTCTA
*
681022 ATTTAATAA-ACTATTCTC
1 ATTTAATAACACTATTCTA
681040 ATTTAA
1 ATTTAA
681046 ATTAAAATAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTAATAACACTATTCTA
Found at i:681081 original size:18 final size:19
Alignment explanation
Indices: 681042--681107 Score: 82
Period size: 19 Copynumber: 3.6 Consensus size: 19
681032 CTATTCTCAT
*
681042 TTAAATTAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
* *
681061 TTAAATGAGAATAG-TTTA
1 TTAAATGAAAATAGAGTTA
*
681079 TTAAATTAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
681098 TTAAAT-AAAA
1 TTAAATGAAAA
681108 AAATTATATG
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
18 19 0.47
19 21 0.52
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.36
Consensus pattern (19 bp):
TTAAATGAAAATAGAGTTA
Found at i:681108 original size:19 final size:19
Alignment explanation
Indices: 681042--681107 Score: 91
Period size: 18 Copynumber: 3.6 Consensus size: 19
681032 CTATTCTCAT
681042 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
* * *
681061 TTAAATGAGAATAG-TTTA
1 TTAAATTAAAATAGAGTTA
681079 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
681098 TTAAA-TAAAA
1 TTAAATTAAAA
681108 AAATTATATG
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
18 20 0.50
19 20 0.50
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.36
Consensus pattern (19 bp):
TTAAATTAAAATAGAGTTA
Found at i:684863 original size:31 final size:30
Alignment explanation
Indices: 684814--684872 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
684804 ATTATACAAA
* *
684814 ATCAAAGTTCATGGATAGCATTGCATATTGG
1 ATCAAAATTCAAGGATAGCATTG-ATATTGG
* *
684845 ATCAAAATTCAAGTATAGCTTTGATATT
1 ATCAAAATTCAAGGATAGCATTGATATT
684873 TATCTCTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 5 0.21
31 19 0.79
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.36
Consensus pattern (30 bp):
ATCAAAATTCAAGGATAGCATTGATATTGG
Found at i:687794 original size:16 final size:16
Alignment explanation
Indices: 687762--687796 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
687752 TCGTTACAGG
* *
687762 AATGGAATAGGGTTGT
1 AATGGAATAGAGCTGT
687778 AATGGAATAGAGCTGT
1 AATGGAATAGAGCTGT
687794 AAT
1 AAT
687797 CAGTAATTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.03, G:0.31, T:0.29
Consensus pattern (16 bp):
AATGGAATAGAGCTGT
Found at i:688082 original size:23 final size:22
Alignment explanation
Indices: 688056--688098 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
688046 CCATGAATAT
688056 TTAATAAATATAGTAATTTTTAA
1 TTAATAAATA-AGTAATTTTTAA
* *
688079 TTAATATATAAGTTATTTTT
1 TTAATAAATAAGTAATTTTT
688099 TCTTTTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (22 bp):
TTAATAAATAAGTAATTTTTAA
Found at i:688765 original size:128 final size:130
Alignment explanation
Indices: 688596--688838 Score: 391
Period size: 128 Copynumber: 1.9 Consensus size: 130
688586 AATGACTGTG
* * *
688596 AATTAACTCAATCAAAGTTTCTCTTCAATTTGTTGCAAGTTTCCCCCTTGGGGATGTGTTGAATG
1 AATTAACTCAATCAAAGTTTCTCTTCAATTTGCTGCAAGTTTCCCCCTTGGAGATATGTTGAATG
*
688661 ATTTTTGTTCTTACCA-TTTTTT-CTTTTCCTTTTTGGTTTGGTTAAAAACATCCATCTATCGTA
66 ATTTTTGTTCTTACCATTTTTTTCCTTTTCCTTTTTGGTTGGGTTAAAAACATCCATCTATCGTA
* *
688724 AATTAACTCAATCAAAGTTTCTCTTTAATTTGCTGCAAGTTTCCCTCTTGGAGATATGTTGAATG
1 AATTAACTCAATCAAAGTTTCTCTTCAATTTGCTGCAAGTTTCCCCCTTGGAGATATGTTGAATG
**
688789 ATTTTTGTTCTTACCATTTTTTTCCCTTTTGGTTTTTGGTTGGGTTAAAA
66 ATTTTTGTTCTTACCATTTTTTT-CCTTTTCCTTTTTGGTTGGGTTAAAA
688839 TGAAAATAAA
Statistics
Matches: 104, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
128 76 0.73
129 6 0.06
131 22 0.21
ACGTcount: A:0.22, C:0.16, G:0.15, T:0.47
Consensus pattern (130 bp):
AATTAACTCAATCAAAGTTTCTCTTCAATTTGCTGCAAGTTTCCCCCTTGGAGATATGTTGAATG
ATTTTTGTTCTTACCATTTTTTTCCTTTTCCTTTTTGGTTGGGTTAAAAACATCCATCTATCGTA
Done.