Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 133 of 135
Found at i:42911657 original size:11 final size:11
Alignment explanation
Indices: 42911625--42911663 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
42911615 TCTATTCCTC
42911625 TCCCC-TCCCT
1 TCCCCTTCCCT
42911635 TCCCCTTCCCCT
1 TCCCCTT-CCCT
42911647 TCCCCTTCCCT
1 TCCCCTTCCCT
*
42911658 TTCCCT
1 TCCCCT
42911664 CCTCCTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 5 0.19
11 10 0.38
12 11 0.42
ACGTcount: A:0.00, C:0.64, G:0.00, T:0.36
Consensus pattern (11 bp):
TCCCCTTCCCT
Found at i:42911663 original size:6 final size:6
Alignment explanation
Indices: 42911631--42911662 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
42911621 CCTCTCCCCT
*
42911631 CCCTTC CCCTTC CCCTTC CCCTTC CCTTTC CC
1 CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC CC
42911663 TCCTCCTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (6 bp):
CCCTTC
Found at i:42925196 original size:16 final size:17
Alignment explanation
Indices: 42925153--42925207 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
42925143 AAAATTATAA
*
42925153 AAAATCATTAAATTTAT
1 AAAATTATTAAATTTAT
* * *
42925170 -AATTTTTTTAATTTAT
1 AAAATTATTAAATTTAT
42925186 AAAATTATTAAATTTTAT
1 AAAATTATTAAA-TTTAT
42925204 AAAA
1 AAAA
42925208 ACAATTTATT
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
16 12 0.41
17 8 0.28
18 9 0.31
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
AAAATTATTAAATTTAT
Found at i:42925419 original size:10 final size:10
Alignment explanation
Indices: 42925373--42925496 Score: 55
Period size: 10 Copynumber: 12.5 Consensus size: 10
42925363 ATTTTTTTGA
*
42925373 AATTTTTTAT
1 AATTTTTAAT
*
42925383 GATTTTTAATT
1 AATTTTTAA-T
*
42925394 AATTTCTAAT
1 AATTTTTAAT
42925404 AATTTTT-AT
1 AATTTTTAAT
42925413 AATTTTT-AT
1 AATTTTTAAT
* *
42925422 GATATTAATGAAT
1 -A-ATT-TTTAAT
* *
42925435 TATTTTTTAT
1 AATTTTTAAT
*
42925445 AA-ATTT-AT
1 AATTTTTAAT
42925453 AAATTTTT-AT
1 -AATTTTTAAT
*
42925463 -GTTTTTAATT
1 AATTTTTAA-T
42925473 AATTTTT-AT
1 AATTTTTAAT
*
42925482 AAATTTTAAT
1 AATTTTTAAT
42925492 AATTT
1 AATTT
42925497 AAATATTTTT
Statistics
Matches: 85, Mismatches: 18, Indels: 22
0.68 0.14 0.18
Matches are distributed among these distances:
8 7 0.08
9 24 0.28
10 32 0.38
11 19 0.22
12 1 0.01
13 2 0.02
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.60
Consensus pattern (10 bp):
AATTTTTAAT
Found at i:42925435 original size:19 final size:19
Alignment explanation
Indices: 42925413--42925481 Score: 50
Period size: 19 Copynumber: 3.5 Consensus size: 19
42925403 TAATTTTTAT
42925413 AATTTTTATGATATTAATGA
1 AATTTTTATGATATTAAT-A
* *
42925433 ATTATTTTTTAT-AAATTTATA
1 A--A-TTTTTATGATATTAATA
* * *
42925454 AATTTTTATGTTTTTAATT
1 AATTTTTATGATATTAATA
42925473 AATTTTTAT
1 AATTTTTAT
42925482 AAATTTTAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
18 7 0.18
19 14 0.37
20 1 0.03
21 2 0.05
22 7 0.18
23 7 0.18
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (19 bp):
AATTTTTATGATATTAATA
Found at i:42925463 original size:41 final size:36
Alignment explanation
Indices: 42925376--42925491 Score: 108
Period size: 37 Copynumber: 3.0 Consensus size: 36
42925366 TTTTTGAAAT
* * *
42925376 TTTTTATGATTTTTAATTAATTTCTAATAATTTTTATAA
1 TTTTTATG-TTTTGAATTAATTT-TTATAA-ATTTATAA
*
42925415 TTTTTATGATATTAATGAATTATTTTTTATAAATTTATAAA
1 TTTTTATG-T-TT--TGAATTAATTTTTATAAATTTAT-AA
*
42925456 TTTTTATGTTTTTAATTAATTTTTATAAATTT-TAA
1 TTTTTATGTTTTGAATTAATTTTTATAAATTTATAA
42925491 T
1 T
42925492 AATTTAAATA
Statistics
Matches: 67, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
35 3 0.04
36 1 0.01
37 19 0.28
39 12 0.18
40 8 0.12
41 15 0.22
42 9 0.13
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.61
Consensus pattern (36 bp):
TTTTTATGTTTTGAATTAATTTTTATAAATTTATAA
Found at i:42925494 original size:19 final size:19
Alignment explanation
Indices: 42925438--42925496 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
42925428 AATGAATTAT
42925438 TTTTTATAAA-TTT-ATAAA
1 TTTTTATAAATTTTAAT-AA
**
42925456 TTTTTAT-GTTTTTAATTAA
1 TTTTTATAAATTTTAA-TAA
42925475 TTTTTATAAATTTTAATAA
1 TTTTTATAAATTTTAATAA
42925494 TTT
1 TTT
42925497 AAATATTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
18 10 0.30
19 16 0.48
20 7 0.21
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTTTATAAATTTTAATAA
Found at i:42931698 original size:12 final size:12
Alignment explanation
Indices: 42931681--42931706 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42931671 TAGTCTTACA
42931681 CAGTCTCAATGT
1 CAGTCTCAATGT
42931693 CAGTCTCAATGT
1 CAGTCTCAATGT
42931705 CA
1 CA
42931707 CAACCCTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (12 bp):
CAGTCTCAATGT
Found at i:42938415 original size:15 final size:15
Alignment explanation
Indices: 42938387--42938435 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
42938377 GAATCTTAGC
*
42938387 AACCTATTGAACCTG
1 AACCTTTTGAACCTG
*
42938402 AACCTTTTGTACCTG
1 AACCTTTTGAACCTG
*
42938417 AACATTTTGAACCTG
1 AACCTTTTGAACCTG
42938432 AACC
1 AACC
42938436 GATTCCCCCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.31, C:0.27, G:0.12, T:0.31
Consensus pattern (15 bp):
AACCTTTTGAACCTG
Found at i:42938451 original size:24 final size:24
Alignment explanation
Indices: 42938424--42938482 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
42938414 CTGAACATTT
42938424 TGAACCTGAACCGATTCCCCCTAC
1 TGAACCTGAACCGATTCCCCCTAC
* *
42938448 TGAACCTGAACCGGTTCCCTCTAC
1 TGAACCTGAACCGATTCCCCCTAC
42938472 TGAACCTGAAC
1 TGAACCTGAAC
42938483 ATATTAGTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.25, C:0.37, G:0.15, T:0.22
Consensus pattern (24 bp):
TGAACCTGAACCGATTCCCCCTAC
Found at i:42942598 original size:25 final size:26
Alignment explanation
Indices: 42942567--42942634 Score: 113
Period size: 25 Copynumber: 2.7 Consensus size: 26
42942557 AATTATCACC
42942567 AACCCAATAACCCAAATTC-TTTAAA
1 AACCCAATAACCCAAATTCTTTTAAA
*
42942592 AATCCAATAACCCAAA-TCTTTTAAA
1 AACCCAATAACCCAAATTCTTTTAAA
42942617 AACCCAATAACCCAAATT
1 AACCCAATAACCCAAATT
42942635 TAACTTAAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
24 2 0.05
25 36 0.92
26 1 0.03
ACGTcount: A:0.49, C:0.28, G:0.00, T:0.24
Consensus pattern (26 bp):
AACCCAATAACCCAAATTCTTTTAAA
Found at i:42942721 original size:21 final size:20
Alignment explanation
Indices: 42942695--42942738 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
42942685 AACCAAGTCA
* *
42942695 GACCGTTGACTGTTGACTGTT
1 GACCGTTGACCG-TGACAGTT
42942716 GACCGTTGACCGTGACAGTT
1 GACCGTTGACCGTGACAGTT
42942736 GAC
1 GAC
42942739 TTTTTCTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.18, C:0.23, G:0.30, T:0.30
Consensus pattern (20 bp):
GACCGTTGACCGTGACAGTT
Found at i:42943842 original size:3 final size:3
Alignment explanation
Indices: 42943792--42943831 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
42943782 CATTATTTTG
42943792 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
42943832 TTGGATTATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:42945170 original size:18 final size:18
Alignment explanation
Indices: 42945147--42945184 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
42945137 TAATATAATT
42945147 TTATTCG-GTTTATTCGAA
1 TTATTCGAG-TTATTCGAA
42945165 TTATTCGAGTTATTCGAA
1 TTATTCGAGTTATTCGAA
42945183 TT
1 TT
42945185 CGAAAATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 18 0.95
19 1 0.05
ACGTcount: A:0.24, C:0.11, G:0.16, T:0.50
Consensus pattern (18 bp):
TTATTCGAGTTATTCGAA
Found at i:42945269 original size:23 final size:24
Alignment explanation
Indices: 42945230--42945276 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
42945220 AAAAAAATTC
**
42945230 AACTCGATTCGTTTAATTC-AAAT
1 AACTCGATTCGAATAATTCGAAAT
42945253 AACTCGATTCGAATAATTCGAAAT
1 AACTCGATTCGAATAATTCGAAAT
42945277 TCGAAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (24 bp):
AACTCGATTCGAATAATTCGAAAT
Found at i:42946379 original size:2 final size:2
Alignment explanation
Indices: 42946361--42946395 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
42946351 GGAATATAAA
* *
42946361 AG AG GG AG AG GG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
42946396 AGAATAGCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (2 bp):
AG
Found at i:42969318 original size:17 final size:17
Alignment explanation
Indices: 42969288--42969320 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
42969278 TGGGTCCTAA
42969288 AAATGCTTCATCTCCTC
1 AAATGCTTCATCTCCTC
42969305 AAAT-CTTCAGTCTCCT
1 AAATGCTTCA-TCTCCT
42969321 ATGTGGCTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.24, C:0.33, G:0.06, T:0.36
Consensus pattern (17 bp):
AAATGCTTCATCTCCTC
Found at i:42970466 original size:47 final size:47
Alignment explanation
Indices: 42970397--42970490 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
42970387 TCTAAATTAT
42970397 AGACACAAACCATCCCCAGTTCATATCCAATACTTAAACCCAAACTC
1 AGACACAAACCATCCCCAGTTCATATCCAATACTTAAACCCAAACTC
42970444 AGACACAAACCATCCCCAGTTCATATCCAATACTTAAACCCAAACTC
1 AGACACAAACCATCCCCAGTTCATATCCAATACTTAAACCCAAACTC
42970491 GCAAGATAAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.40, C:0.36, G:0.04, T:0.19
Consensus pattern (47 bp):
AGACACAAACCATCCCCAGTTCATATCCAATACTTAAACCCAAACTC
Found at i:42976574 original size:30 final size:30
Alignment explanation
Indices: 42976540--42976596 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
42976530 AAAAATATTT
42976540 AAAA-TAGT-AATATAAAATATTATAATTTTC
1 AAAATTAGTAAATA-AAAATATT-TAATTTTC
*
42976570 AAAATTATTAAATAAAAATATTTAATT
1 AAAATTAGTAAATAAAAATATTTAATT
42976597 ATTTATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
30 9 0.38
31 11 0.46
32 4 0.17
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (30 bp):
AAAATTAGTAAATAAAAATATTTAATTTTC
Found at i:42976679 original size:16 final size:16
Alignment explanation
Indices: 42976613--42976679 Score: 57
Period size: 16 Copynumber: 4.2 Consensus size: 16
42976603 ATTTAGTCCT
*
42976613 ATAATAAATAATTAAT-
1 ATAATAAAT-TTTAATA
* *
42976629 ATAATTAATTATT-TTA
1 ATAATAAATT-TTAATA
*
42976645 ATAATAAATTTTAAAA
1 ATAATAAATTTTAATA
*
42976661 ATAATAATTTTTAATA
1 ATAATAAATTTTAATA
42976677 ATA
1 ATA
42976680 TTCTTCACAT
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
15 3 0.08
16 37 0.93
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATAATAAATTTTAATA
Found at i:42976759 original size:15 final size:16
Alignment explanation
Indices: 42976695--42976759 Score: 55
Period size: 15 Copynumber: 4.0 Consensus size: 16
42976685 CACATTGAAA
42976695 ATATTCAAT-ATAAAT
1 ATATTCAATAATAAAT
*
42976710 AT-TTTAATAATAAAAT
1 ATATTCAATAAT-AAAT
*
42976726 ATTTATTACAATTATAAAT
1 A--TATT-CAATAATAAAT
42976745 ATATT-AATAATAAAT
1 ATATTCAATAATAAAT
42976760 GTTTTGTAGT
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
14 5 0.12
15 13 0.32
16 5 0.12
17 4 0.10
18 1 0.03
19 7 0.17
20 5 0.12
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTCAATAATAAAT
Found at i:42982522 original size:6 final size:6
Alignment explanation
Indices: 42982513--42982543 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
42982503 ATTCTCATTG
42982513 CTCAAC CTCAAC CTCAAC CTCAAC CTCAAC C
1 CTCAAC CTCAAC CTCAAC CTCAAC CTCAAC C
42982544 CAAGTAGATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.52, G:0.00, T:0.16
Consensus pattern (6 bp):
CTCAAC
Found at i:42986364 original size:21 final size:20
Alignment explanation
Indices: 42986322--42986358 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
42986312 ATAATGAGAG
*
42986322 TCTATTTTTTAACTATAAAT
1 TCTATTTTTTAAATATAAAT
42986342 TCTATTTTTTAAA-ATAA
1 TCTATTTTTTAAATATAA
42986359 CAATTCCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (20 bp):
TCTATTTTTTAAATATAAAT
Found at i:42987082 original size:31 final size:31
Alignment explanation
Indices: 42987031--42987093 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 31
42987021 ATAAAAAATC
42987031 TAATAAATAAAAAATGTATAAA-ATTATTAAA
1 TAATAAATAAAAAA-GTATAAATATTATTAAA
*
42987062 TAATAAAATAAAATAA-TATAAATATTTTTAAA
1 TAAT-AAATAAAA-AAGTATAAATATTATTAAA
42987094 AAAATTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
31 10 0.36
32 16 0.57
33 2 0.07
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (31 bp):
TAATAAATAAAAAAGTATAAATATTATTAAA
Found at i:42988014 original size:15 final size:16
Alignment explanation
Indices: 42987982--42988017 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
42987972 TTTTGGTACA
*
42987982 AAAATATTTTTGAAAT
1 AAAATATTGTTGAAAT
42987998 AAAATATTGTT-AAAT
1 AAAATATTGTTGAAAT
42988013 AAAAT
1 AAAAT
42988018 GCTTTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.39
Consensus pattern (16 bp):
AAAATATTGTTGAAAT
Found at i:43000454 original size:10 final size:10
Alignment explanation
Indices: 43000439--43000471 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
43000429 ACCCAAGATG
43000439 GAACCAATCC
1 GAACCAATCC
*
43000449 GAACCAATCA
1 GAACCAATCC
43000459 GAACCAATCC
1 GAACCAATCC
43000469 GAA
1 GAA
43000472 TTGCCTAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.45, C:0.33, G:0.12, T:0.09
Consensus pattern (10 bp):
GAACCAATCC
Found at i:43005367 original size:25 final size:24
Alignment explanation
Indices: 43005325--43005386 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
43005315 CGTTGATTTT
* *
43005325 TTATTAAAGT-TATTATTTAATAA
1 TTATTAAAATATAATATTTAATAA
* *
43005348 TTATTTAAAATATAATATTTTATTA
1 TTA-TTAAAATATAATATTTAATAA
*
43005373 TTATTATAATATAA
1 TTATTAAAATATAA
43005387 ATAAAAGAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
23 3 0.09
24 16 0.50
25 13 0.41
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
TTATTAAAATATAATATTTAATAA
Found at i:43005389 original size:25 final size:25
Alignment explanation
Indices: 43005338--43005386 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
43005328 TTAAAGTTAT
43005338 TATTTAATAATTATTTAAAATATAA
1 TATTTAATAATTATTTAAAATATAA
* * *
43005363 TATTTTATTATTA-TTATAATATAA
1 TATTTAATAATTATTTAAAATATAA
43005387 ATAAAAGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
TATTTAATAATTATTTAAAATATAA
Found at i:43023872 original size:48 final size:48
Alignment explanation
Indices: 43023801--43023900 Score: 157
Period size: 48 Copynumber: 2.1 Consensus size: 48
43023791 TTGGGTTTTC
43023801 CTTTAATTCTCTTCATCTTTTATACTT-TCATTTATTATGGTGAAATCT
1 CTTTAATTCTCTTCATCTTTTATA-TTATCATTTATTATGGTGAAATCT
* * *
43023849 CTTTAATTCTCTTCATTTTTTATATTATCTTTTATTATTGTGAAATCT
1 CTTTAATTCTCTTCATCTTTTATATTATCATTTATTATGGTGAAATCT
43023897 CTTT
1 CTTT
43023901 TAACTCGTGA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
47 2 0.04
48 46 0.96
ACGTcount: A:0.22, C:0.15, G:0.05, T:0.58
Consensus pattern (48 bp):
CTTTAATTCTCTTCATCTTTTATATTATCATTTATTATGGTGAAATCT
Found at i:43023916 original size:48 final size:47
Alignment explanation
Indices: 43023801--43023918 Score: 132
Period size: 48 Copynumber: 2.5 Consensus size: 47
43023791 TTGGGTTTTC
* *
43023801 CTTTAATTCTCTTCATCTTTTATACTTTCATTTATTATGGTGAAATCT
1 CTTTAA-TCTCGTCATTTTTTATACTTTCATTTATTATGGTGAAATCT
* * *
43023849 CTTTAATTCTCTTCATTTTTTATA-TTATCTTTTATTATTGTGAAATCT
1 CTTTAA-TCTCGTCATTTTTTATACTT-TCATTTATTATGGTGAAATCT
*
43023897 CTTTTAA-CTCGTGATTTTTTAT
1 C-TTTAATCTCGTCATTTTTTAT
43023919 TTCTTTTAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
47 15 0.24
48 43 0.68
49 5 0.08
ACGTcount: A:0.22, C:0.14, G:0.06, T:0.58
Consensus pattern (47 bp):
CTTTAATCTCGTCATTTTTTATACTTTCATTTATTATGGTGAAATCT
Found at i:43027567 original size:3 final size:3
Alignment explanation
Indices: 43027559--43027583 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
43027549 GCAATTCTAG
43027559 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
43027584 GAAACAGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:43027690 original size:16 final size:17
Alignment explanation
Indices: 43027671--43027702 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
43027661 TTATTAATTA
43027671 ATTT-AGGAAATAGAAT
1 ATTTAAGGAAATAGAAT
43027687 ATTTAAGGAAATAGAA
1 ATTTAAGGAAATAGAA
43027703 AGAGAATTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.53, C:0.00, G:0.19, T:0.28
Consensus pattern (17 bp):
ATTTAAGGAAATAGAAT
Found at i:43031586 original size:3 final size:3
Alignment explanation
Indices: 43031578--43031606 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
43031568 TTACTTCTTA
43031578 ATT ATT ATT ATT ATT ATT ATT ATT -TT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
43031607 TTTTAAACCC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:43038001 original size:90 final size:90
Alignment explanation
Indices: 43037897--43038098 Score: 241
Period size: 91 Copynumber: 2.2 Consensus size: 90
43037887 CTTTTTTTTT
* * *
43037897 ATTCACTTGGGTACTTAAATTTTTAAAATGTATTAAAAAGAT-CTTCAAA-ATATTTC-AAAAAA
1 ATTCAATTGGGTACTTAAACTTTTAAAATGCA-TAAAAA-ATCCTTCAAACAT-TTTCAAAAAAA
*
43037959 AGCAATTAAGCCCCT-ACTTTTATTTTGC
63 AGCAAATAAGCCCCTGA-TTTTATTTTGC
* *
43037987 ATTCAATTGGGTACTTGAACTTTTAAAATGCATAAAAAATGCCTTCAAACCTTTTCAAAAAAAAG
1 ATTCAATTGGGTACTTAAACTTTTAAAATGCATAAAAAAT-CCTTCAAACATTTTCAAAAAAAAG
*
43038052 CAAATAAGCCCCTGATTTTCTTTTGC
65 CAAATAAGCCCCTGATTTTATTTTGC
* * *
43038078 ACTCAATTGAGTACTTGAACT
1 ATTCAATTGGGTACTTAAACT
43038099 GTCAAATACA
Statistics
Matches: 98, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
88 2 0.02
89 6 0.06
90 39 0.40
91 50 0.51
92 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (90 bp):
ATTCAATTGGGTACTTAAACTTTTAAAATGCATAAAAAATCCTTCAAACATTTTCAAAAAAAAGC
AAATAAGCCCCTGATTTTATTTTGC
Found at i:43038115 original size:91 final size:90
Alignment explanation
Indices: 43037949--43038118 Score: 236
Period size: 91 Copynumber: 1.9 Consensus size: 90
43037939 CTTCAAAATA
* * * *
43037949 TTTCAAAAAAAGCAATTAAGCCCCTACTTTTATTTTGCATTCAATTGGGTACTTGAACTTTTAAA
1 TTTCAAAAAAAGCAAATAAGCCCCTACTTTTATTTTGCACTCAATTGAGTACTTGAACTTGTAAA
*
43038014 ATGCATAAAAAATGCCTTCAAACCT
66 ATACATAAAAAATGCCTTCAAACCT
* *
43038039 TTTCAAAAAAAAGCAAATAAGCCCCTGA-TTTTCTTTTGCACTCAATTGAGTACTTGAAC-TGTC
1 TTTC-AAAAAAAGCAAATAAGCCCCT-ACTTTTATTTTGCACTCAATTGAGTACTTGAACTTGTA
*
43038102 AAATACATCAAAAATGC
64 AAATACATAAAAAATGC
43038119 TCTTTGACCG
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
90 21 0.30
91 48 0.69
92 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (90 bp):
TTTCAAAAAAAGCAAATAAGCCCCTACTTTTATTTTGCACTCAATTGAGTACTTGAACTTGTAAA
ATACATAAAAAATGCCTTCAAACCT
Found at i:43038158 original size:20 final size:20
Alignment explanation
Indices: 43038122--43038159 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
43038112 AAAATGCTCT
**
43038122 TTGACCGTTAATTTTAACAG
1 TTGACCGTTAAAGTTAACAG
43038142 TTGACCGTTAAAGTTAAC
1 TTGACCGTTAAAGTTAAC
43038160 TACCCCTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (20 bp):
TTGACCGTTAAAGTTAACAG
Found at i:43038466 original size:15 final size:15
Alignment explanation
Indices: 43038446--43038480 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
43038436 AAATTCTTGA
*
43038446 TTCTTGATTCTTGTT
1 TTCTTGATTCTTATT
*
43038461 TTCTTGCTTCTTATT
1 TTCTTGATTCTTATT
43038476 TTCTT
1 TTCTT
43038481 TCTCAATTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.06, C:0.17, G:0.09, T:0.69
Consensus pattern (15 bp):
TTCTTGATTCTTATT
Found at i:43043079 original size:29 final size:27
Alignment explanation
Indices: 43043047--43043119 Score: 76
Period size: 29 Copynumber: 2.6 Consensus size: 27
43043037 TAATCTTAAC
**
43043047 AATAAAAATTATAAAAATTATTAAATTTT
1 AATAAAAATTATAAAAA--ATTAAAAATT
43043076 AATAAAAGA-TATAAAAAATTAAAAATT
1 AATAAAA-ATTATAAAAAATTAAAAATT
*
43043103 AGAAAAAAATTATAAAA
1 A-ATAAAAATTATAAAA
43043120 TACATAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
27 10 0.26
28 12 0.32
29 15 0.39
30 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (27 bp):
AATAAAAATTATAAAAAATTAAAAATT
Found at i:43043128 original size:19 final size:19
Alignment explanation
Indices: 43043086--43043130 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
43043076 AATAAAAGAT
*
43043086 ATAAAAAATTAAAAATTAG
1 ATAAAAAATTAAAAATTAC
43043105 A-AAAAAATTATAAAA-TAC
1 ATAAAAAATTA-AAAATTAC
43043123 ATAAAAAA
1 ATAAAAAA
43043131 GCCCTTTAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (19 bp):
ATAAAAAATTAAAAATTAC
Found at i:43043405 original size:89 final size:88
Alignment explanation
Indices: 43043244--43043418 Score: 215
Period size: 89 Copynumber: 2.0 Consensus size: 88
43043234 AAAATCAGGG
** * * * * * *
43043244 GCTTAATTGGTTTTTTAAAAATATTTAAGGGCTTTTTGATGCATTTTCAAAGTTCAAGTATCCGA
1 GCTTAATTACTTTTTTAAAAAAATTTAAGAGCTTTTTGACGCATTTTCAAAGCTCAAATATCCAA
*
43043309 TTAAATGCAAAATAAAAATAAGA
66 ATAAATGCAAAATAAAAATAAGA
* * * *
43043332 GCTTAATTACTTTTTTAAAAAAATTTAAAGATCTTTTTGACGTATTTTGAAAGCTCAAATATCTA
1 GCTTAATTACTTTTTTAAAAAAATTT-AAGAGCTTTTTGACGCATTTTCAAAGCTCAAATATCCA
*
43043397 AATGAATGCAAAATAAAAATAA
65 AATAAATGCAAAATAAAAATAA
43043419 AACAGTGATT
Statistics
Matches: 72, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
88 23 0.32
89 49 0.68
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (88 bp):
GCTTAATTACTTTTTTAAAAAAATTTAAGAGCTTTTTGACGCATTTTCAAAGCTCAAATATCCAA
ATAAATGCAAAATAAAAATAAGA
Found at i:43050711 original size:22 final size:20
Alignment explanation
Indices: 43050677--43050727 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
43050667 ATTAATTAAT
43050677 TTTTTTAAATTTTAAAAAAA
1 TTTTTTAAATTTTAAAAAAA
* * *
43050697 TGTTTTTATATTTTTTAAATAA
1 T-TTTTTA-AATTTTAAAAAAA
43050719 TTTTTTAAA
1 TTTTTTAAA
43050728 AAATTCATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 2 0.08
21 12 0.48
22 11 0.44
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
TTTTTTAAATTTTAAAAAAA
Found at i:43051814 original size:13 final size:13
Alignment explanation
Indices: 43051796--43051820 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43051786 TGTGGTGGAA
43051796 AAGTATTTTTGAG
1 AAGTATTTTTGAG
43051809 AAGTATTTTTGA
1 AAGTATTTTTGA
43051821 AAATTTTGGT
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:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (13 bp):
AAGTATTTTTGAG
Found at i:43052610 original size:28 final size:28
Alignment explanation
Indices: 43052570--43052629 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
43052560 CCTTTATGGT
*
43052570 GAGTCTCTGAAAGGAAAGCTCTTGTGGC
1 GAGTCTCTGAAAGGAAAACTCTTGTGGC
* * *
43052598 GAGTCTTTGAAAGGAAAACTTTTGTGGT
1 GAGTCTCTGAAAGGAAAACTCTTGTGGC
43052626 GAGT
1 GAGT
43052630 ACTGAATAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.27, C:0.12, G:0.32, T:0.30
Consensus pattern (28 bp):
GAGTCTCTGAAAGGAAAACTCTTGTGGC
Found at i:43056773 original size:24 final size:24
Alignment explanation
Indices: 43056752--43056797 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
43056742 TTGGTGTTGT
* *
43056752 TTTTGCTATTGTTTTTGTTGTTAA
1 TTTTGCTACTATTTTTGTTGTTAA
*
43056776 TTTTGCTGCTATTTTTGTTGTT
1 TTTTGCTACTATTTTTGTTGTT
43056798 TTTGCTGTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.09, C:0.07, G:0.17, T:0.67
Consensus pattern (24 bp):
TTTTGCTACTATTTTTGTTGTTAA
Found at i:43056804 original size:21 final size:21
Alignment explanation
Indices: 43056746--43056804 Score: 64
Period size: 24 Copynumber: 2.7 Consensus size: 21
43056736 AGTGTTTTGG
** *
43056746 TGTTGTTTTTGCTATTGTTTT
1 TGTTGTTTTTGCTGCTATTTT
43056767 TGTTGTTAATTTTGCTGCTATTTT
1 TGTTG-T--TTTTGCTGCTATTTT
43056791 TGTTGTTTTTGCTG
1 TGTTGTTTTTGCTG
43056805 TTACTTTTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
21 13 0.41
22 1 0.03
23 1 0.03
24 17 0.53
ACGTcount: A:0.07, C:0.07, G:0.20, T:0.66
Consensus pattern (21 bp):
TGTTGTTTTTGCTGCTATTTT
Found at i:43056806 original size:12 final size:12
Alignment explanation
Indices: 43056740--43056806 Score: 50
Period size: 12 Copynumber: 5.8 Consensus size: 12
43056730 GTTCCTAGTG
*
43056740 TTTTGGTGTTGT
1 TTTTGCTGTTGT
*
43056752 TTTTGCTATTGT
1 TTTTGCTGTTGT
* **
43056764 TTTTGTTGTTAA
1 TTTTGCTGTTGT
* *
43056776 TTTTGCTGCT-A
1 TTTTGCTGTTGT
43056787 TTTT--TGTTGT
1 TTTTGCTGTTGT
43056797 TTTTGCTGTT
1 TTTTGCTGTT
43056807 ACTTTTCTTG
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
9 3 0.07
10 4 0.10
11 5 0.12
12 30 0.71
ACGTcount: A:0.06, C:0.06, G:0.21, T:0.67
Consensus pattern (12 bp):
TTTTGCTGTTGT
Found at i:43056812 original size:21 final size:21
Alignment explanation
Indices: 43056746--43056812 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 21
43056736 AGTGTTTTGG
* *
43056746 TGTTGTTTTTGCTATTGTTTT
1 TGTTGTTTTTGCTGTTATTTT
*
43056767 TGTTGTTAATTTTGCTGCTATTTT
1 TGTTG-T--TTTTGCTGTTATTTT
*
43056791 TGTTGTTTTTGCTGTTACTTT
1 TGTTGTTTTTGCTGTTATTTT
43056812 T
1 T
43056813 CTTGCTGTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
21 19 0.50
22 1 0.03
23 1 0.03
24 17 0.45
ACGTcount: A:0.07, C:0.07, G:0.18, T:0.67
Consensus pattern (21 bp):
TGTTGTTTTTGCTGTTATTTT
Found at i:43064797 original size:41 final size:41
Alignment explanation
Indices: 43064728--43064854 Score: 210
Period size: 41 Copynumber: 3.2 Consensus size: 41
43064718 TGTGCATGAT
*
43064728 GTTCTTTGCATTTAT-TATCTGCTTCATGCTTGACTAAATA
1 GTTCTCTGCATTTATATATCTGCTTCATGCTTGACTAAATA
43064768 GTTCTCTGCATTTATATATCTGCTTCATGCTTGACTAAATA
1 GTTCTCTGCATTTATATATCTGCTTCATGCTTGACTAAATA
43064809 GTTCTCTGCA-TT-TATA-CTGCTTCATGCTTGACTAAATA
1 GTTCTCTGCATTTATATATCTGCTTCATGCTTGACTAAATA
43064847 GTT-TCTGC
1 GTTCTCTGC
43064855 TGTTCTTCCA
Statistics
Matches: 85, Mismatches: 1, Indels: 5
0.93 0.01 0.05
Matches are distributed among these distances:
37 5 0.06
38 25 0.29
39 4 0.05
40 16 0.19
41 35 0.41
ACGTcount: A:0.22, C:0.20, G:0.13, T:0.45
Consensus pattern (41 bp):
GTTCTCTGCATTTATATATCTGCTTCATGCTTGACTAAATA
Found at i:43069883 original size:30 final size:30
Alignment explanation
Indices: 43069840--43069933 Score: 116
Period size: 30 Copynumber: 3.1 Consensus size: 30
43069830 TAAACTCTCT
* * *
43069840 AAAACTTAGATTTTGACCCCCAAACTTTTC
1 AAAAATTATATTTTGACCCCTAAACTTTTC
* *
43069870 AAAAATTATATTTTGACCTCTGAACTTTTC
1 AAAAATTATATTTTGACCCCTAAACTTTTC
* * *
43069900 AAAAATTATATTTTAACCCTTAAACTTTCC
1 AAAAATTATATTTTGACCCCTAAACTTTTC
43069930 AAAA
1 AAAA
43069934 CCTTGATTTT
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.38, C:0.20, G:0.04, T:0.37
Consensus pattern (30 bp):
AAAAATTATATTTTGACCCCTAAACTTTTC
Found at i:43076079 original size:112 final size:111
Alignment explanation
Indices: 43075846--43076129 Score: 355
Period size: 112 Copynumber: 2.6 Consensus size: 111
43075836 CATTTTTAAT
*
43075846 TTCATACGAGCTTTGCCTCCAATAAAATTCAATTTTATCCAACTTACAA------CAAGCATTTT
1 TTCACACGAGCTTTGCCTCCAATAAAATTCAATTTTATCCAACTTACAACCTGTTCAAGCATTTT
** * *
43075905 TGTATCGAAATAGCGGTTACTGGACTAATGATTCGTAATCTTTTCA
66 TACATCAAAATAGCGGTTACTGGACCAATGATTCGTAATCTTTTCA
* * * *
43075951 TTCATACGAGCTTTGCCTCCAATAAAATTCAATTTTATCTACCTTACAACCTTGTTCAAGCCTTT
1 TTCACACGAGCTTTGCCTCCAATAAAATTCAATTTTATCCAACTTACAACC-TGTTCAAGCATTT
* * ** *
43076016 TTACATCAAAATAGCTGTTAGTGGACCAATGATTTTTATTCTTTTCA
65 TTACATCAAAATAGCGGTTACTGGACCAATGATTCGTAATCTTTTCA
* * *
43076063 TTCACGCGAGTTTTGCCTCCAATAAAATTCAATTTTATCCATCTTACAACCCTGTTCAAGCATTT
1 TTCACACGAGCTTTGCCTCCAATAAAATTCAATTTTATCCAACTTACAA-CCTGTTCAAGCATTT
43076128 TT
65 TT
43076130 GCATTGAAAT
Statistics
Matches: 153, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
105 47 0.31
112 104 0.68
113 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.38
Consensus pattern (111 bp):
TTCACACGAGCTTTGCCTCCAATAAAATTCAATTTTATCCAACTTACAACCTGTTCAAGCATTTT
TACATCAAAATAGCGGTTACTGGACCAATGATTCGTAATCTTTTCA
Found at i:43076752 original size:50 final size:49
Alignment explanation
Indices: 43076667--43077010 Score: 257
Period size: 49 Copynumber: 7.0 Consensus size: 49
43076657 GACGGATCTA
* * * * *
43076667 GTACCATAG-AGATATGAAGGGAAAGGTTGAGGCCGCAATGGTGAACCCG
1 GTACCTTAGAAGATATG-ATGGAAAGATTGAGGCCGCAACGGCGAACCCG
* **
43076716 GTACCTTAGAAGATGTGATGGAAAAGATTGAGGCCGCAACGGCGAATTCG
1 GTACCTTAGAAGATATGATGG-AAAGATTGAGGCCGCAACGGCGAACCCG
* * ** *
43076766 GTACC--AGGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGTAAACCCA
1 GTACCTTA-GAAGATATG-ATGGAAAGATTGAGGCCGCAACGGCGAACCCG
* * * * * ***
43076815 GTACCTTAAAAGAAATGATAGGAAGGATTGAGGCGGCAACGACGAATATG
1 GTACCTTAGAAGATATGAT-GGAAAGATTGAGGCCGCAACGGCGAACCCG
* * * *
43076865 GTACCAT-GAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCA
1 GTACCTTAGAAGATATG-ATGGAAAGATTGAGGCCGCAACGGCGAACCCG
* * * * * ***
43076914 GTACCTTAAAAGAAATGATAGGAAGGATTGAGGCGGCAACGACGAATATG
1 GTACCTTAGAAGATATGAT-GGAAAGATTGAGGCCGCAACGGCGAACCCG
* * *
43076964 GTACCAT-GAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACC
1 GTACCTTAGAAGATATG-ATGGAAAGATTGAGGCCGCAACGGCGAACC
43077011 TTGTACTTTA
Statistics
Matches: 221, Mismatches: 63, Indels: 22
0.72 0.21 0.07
Matches are distributed among these distances:
48 1 0.00
49 112 0.51
50 107 0.48
51 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (49 bp):
GTACCTTAGAAGATATGATGGAAAGATTGAGGCCGCAACGGCGAACCCG
Found at i:43076770 original size:99 final size:98
Alignment explanation
Indices: 43076587--43077345 Score: 548
Period size: 99 Copynumber: 7.7 Consensus size: 98
43076577 TAGAGTTATA
* * * * * *
43076587 AAGGGAAATGTTAAGGCCGCAACGACGAA-CC--TACCTTAGAAGACGTGATGGGAAAAATCG-A
1 AAGGGAAAGGTTGAGGCCGCAACGGCGAACCCTGTACCTTAGAAGATGTGAT-GGAAAGATTGAA
* * *
43076648 GACTGCAACGACGGA-TCTAGTACCAT-AGAGATATG
65 G-CCGCAACGACGAATTC-GGTACCATGA-AGATATG
* * * *
43076683 AAGGGAAAGGTTGAGGCCGCAATGGTGAACCCGGTACCTTAGAAGATGTGATGGAAAAGATTGAG
1 AAGGGAAAGGTTGAGGCCGCAACGGCGAACCCTGTACCTTAGAAGATGTGATGG-AAAGATTGAA
* *
43076748 GCCGCAACGGCGAATTCGGTACCAGGAAGATATG
65 GCCGCAACGACGAATTCGGTACCATGAAGATATG
** * * ** * *
43076782 AAGGGAAAGGTTGAGGCCGCAACGGTAAACCCAGTACCTTAAAAGAAATGATAGGAAGGATTGAG
1 AAGGGAAAGGTTGAGGCCGCAACGGCGAACCCTGTACCTTAGAAGATGTGAT-GGAAAGATTGAA
*
43076847 GCGGCAACGACGAATAT-GGTACCATGAAGATATG
65 GCCGCAACGACGAAT-TCGGTACCATGAAGATATG
* * ** * *
43076881 AAGGGAAAGGTTGAGGCCGCAACGGCGAACCCAGTACCTTAAAAGAAATGATAGGAAGGATTGAG
1 AAGGGAAAGGTTGAGGCCGCAACGGCGAACCCTGTACCTTAGAAGATGTGAT-GGAAAGATTGAA
*
43076946 GCGGCAACGACGAATAT-GGTACCATGAAGATATG
65 GCCGCAACGACGAAT-TCGGTACCATGAAGATATG
* * ** *
43076980 AAGGGAAAGGTTGAGGCCGCAACGGCGAACCTTGTACTTTAG-AGACT-AAATGGGAACGATTGA
1 AAGGGAAAGGTTGAGGCCGCAACGGCGAACCCTGTACCTTAGAAGA-TGTGAT-GGAAAGATTGA
* * ** ** * *
43077043 AGCCGTAATGGTGAA-TCTTATATCATGGAGATATG
64 AGCCGCAACGACGAATTC-GGTACCATGAAGATATG
* ** * * * * * *
43077078 AAGGGAAAGGTTGAAGCCTTAACGACGAACCTTGTATCTTA-AAAACGTGATGAAAAAGGA-TGA
1 AAGGGAAAGGTTGAGGCCGCAACGGCGAACCCTGTACCTTAGAAGATGTGATG-GAAA-GATTGA
** **
43077141 AGCCGCAACGGTGAA-TCTTATACCATGAAGATAT-
64 AGCCGCAACGACGAATTC-GGTACCATGAAGATATG
* * * * * * * *
43077175 AGAGGAAAAGGTTGAAGCCACAATGGTGAACCTTGTACCTTAG-AGATGTGATGGGAATATTGAA
1 A-AGGGAAAGGTTGAGGCCGCAACGGCGAACCCTGTACCTTAGAAGATGTGATGGAAAGATTGAA
* ** *
43077239 GCTGCAACGACGAAACTTC--TACTGTGGAGATATG
65 GCCGCAACGACG-AA-TTCGGTACCATGAAGATATG
* * * * *
43077273 AAGGGAAAGGTTGAAGCTGCAACGACGAACCTTATACCTTA-AAGATGTGATGGGAAAGATTGAA
1 AAGGGAAAGGTTGAGGCCGCAACGGCGAACCCTGTACCTTAGAAGATGTGAT-GGAAAGATTGAA
43077337 GCCGCAACG
65 GCCGCAACG
43077346 GTGAATCTTA
Statistics
Matches: 549, Mismatches: 89, Indels: 48
0.80 0.13 0.07
Matches are distributed among these distances:
96 26 0.05
97 72 0.13
98 175 0.32
99 267 0.49
100 9 0.02
ACGTcount: A:0.36, C:0.16, G:0.29, T:0.19
Consensus pattern (98 bp):
AAGGGAAAGGTTGAGGCCGCAACGGCGAACCCTGTACCTTAGAAGATGTGATGGAAAGATTGAAG
CCGCAACGACGAATTCGGTACCATGAAGATATG
Found at i:43077292 original size:49 final size:49
Alignment explanation
Indices: 43076774--43077359 Score: 156
Period size: 49 Copynumber: 11.9 Consensus size: 49
43076764 CGGTACCAGG
* * * **
43076774 AAGATATGAAGGGAAAGGTTGAGGCCGCAACG--GTAAACCCAGTACCTTAA
1 AAGATATGAAGGGAAAGATTGAAGCTGCAACGACG-AAACTTA-TACCTT-A
* * * * ** * *
43076824 AAGAAATGATA-GGAAGGATTGAGGCGGCAACGACGAATA-TGGTACCATG
1 AAGATATGA-AGGGAAAGATTGAAGCTGCAACGACGAA-ACTTATACCTTA
* * * * **
43076873 AAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCG-AACCCAGTACCTTAA
1 AAGATATGAAGGGAAAGATTGAAGCTGCAACGACGAAACTTA-TACCTT-A
* * * * ** * *
43076923 AAGAAATGATA-GGAAGGATTGAGGCGGCAACGACGAATA-TGGTACCATG
1 AAGATATGA-AGGGAAAGATTGAAGCTGCAACGACGAA-ACTTATACCTTA
* * * * * * *
43076972 AAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCTTGTACTTTA
1 AAGATATGAAGGGAAAGATTGAAGCTGCAACGACGAAACTTATACCTTA
* * * * * ** * * * *
43077021 GAGACTA--AATGGGAACGATTGAAGCCGTAATGGTGAATCTTATATCATG
1 AAGA-TATGAA-GGGAAAGATTGAAGCTGCAACGACGAAACTTATACCTTA
* * * * * *
43077070 GAGATATGAAGGGAAAGGTTGAAGCCT-TAACGACGAACCTTGTATCTTA
1 AAGATATGAAGGGAAAGATTGAAG-CTGCAACGACGAAACTTATACCTTA
* ** * ** * ** * * *
43077119 AAAACGTGATGAAAAAGGA-TGAAGCCGCAACGGTGAATCTTATACCATG
1 AAGATATGAAGGGAAA-GATTGAAGCTGCAACGACGAAACTTATACCTTA
* * ** * ** * *
43077168 AAGATAT-AGAGGAAAAGGTTGAAGCCACAATGGTGAACCTTGTACCTTA
1 AAGATATGA-AGGGAAAGATTGAAGCTGCAACGACGAAACTTATACCTTA
* * * * * *
43077217 GAGATGTGATGGG-AATATTGAAGCTGCAACGACGAAACTTCTA-CTGTG
1 AAGATATGAAGGGAAAGATTGAAGCTGCAACGACGAAACTTATACCT-TA
* * *
43077265 GAGATATGAAGGGAAAGGTTGAAGCTGCAACGACGAACCTTATACCTTA
1 AAGATATGAAGGGAAAGATTGAAGCTGCAACGACGAAACTTATACCTTA
* * * ** *
43077314 AAGATGTGATGGGAAAGATTGAAGCCGCAACGGTGAATCTTATACC
1 AAGATATGAAGGGAAAGATTGAAGCTGCAACGACGAAACTTATACC
43077360 CTGAGGATAA
Statistics
Matches: 390, Mismatches: 120, Indels: 53
0.69 0.21 0.09
Matches are distributed among these distances:
47 3 0.01
48 43 0.11
49 263 0.67
50 73 0.19
51 5 0.01
52 3 0.01
ACGTcount: A:0.36, C:0.15, G:0.28, T:0.20
Consensus pattern (49 bp):
AAGATATGAAGGGAAAGATTGAAGCTGCAACGACGAAACTTATACCTTA
Found at i:43077924 original size:39 final size:40
Alignment explanation
Indices: 43077584--43078067 Score: 406
Period size: 39 Copynumber: 12.2 Consensus size: 40
43077574 AAGCAAAGCT
* * * *
43077584 ACCATCCAATTTTTTACCCCGATCATGAGGCAAATTGAAG
1 ACCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAG
* * * *
43077624 --CATCCAATCTCTTACCTCGACCATGAGGTAGATTGAA-
1 ACCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAG
* * **
43077661 ACCATTCAATCTTTTACCCTAATCA-GAGGGCAGATTGAAG
1 ACCATCCAATCTCTTACCCCGATCATG-GGGCAGATTGAAG
* ***
43077701 ACACA-CCAATCTTTTACCTTAATCA-GGAGGCAGATTGAAG
1 AC-CATCCAATCTCTTACCCCGATCATGG-GGCAGATTGAAG
** * * *
43077741 --CATATAATCTATTA-CCCTATTCA-GAGGACAGATTGAAG
1 ACCATCCAATCTCTTACCCCGA-TCATG-GGGCAGATTGAAG
* * *
43077779 ACACA-CCAATCTCTTATCCCGATCATGAGGCAGATTGAGG
1 AC-CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAG
*
43077819 ACCATCAAATCTCTTACCCCGATCATGGGGCAGATTGAAG
1 ACCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAG
* *
43077859 ACATCATACAATCTCTTACCCCGATCATGGGGTAGATTGAA-
1 AC--CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAG
* * ** * *
43077900 ACCATCTAATCTCCTACCTTGATCATGAGGCAGATTAAAG
1 ACCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAG
*
43077940 ACATCATCCAATCTCTTACCTCGATCATGGGGCAGATTGAAG
1 AC--CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAG
*
43077982 TCC-TCCAATCTCTTACCCCGATCATGGGGCAGATTGAAG
1 ACCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAG
* *
43078021 ACATCATCCAATCTCTTA-CCCGGTCATGGGG-TGAATTGAAG
1 AC--CATCCAATCTCTTACCCCGATCATGGGGCAG-ATTGAAG
43078062 -CCATCC
1 ACCATCC
43078068 TGTAACATCC
Statistics
Matches: 365, Mismatches: 55, Indels: 50
0.78 0.12 0.11
Matches are distributed among these distances:
37 4 0.01
38 60 0.16
39 96 0.26
40 94 0.26
41 31 0.08
42 80 0.22
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.26
Consensus pattern (40 bp):
ACCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAG
Found at i:43077935 original size:81 final size:80
Alignment explanation
Indices: 43077597--43078051 Score: 441
Period size: 81 Copynumber: 5.7 Consensus size: 80
43077587 ATCCAATTTT
* * * * * *
43077597 TTACCCCGATCATGAGGCAAATTGAAG-CAT--CCAATCTCTTACCTCGACCATGAGGTAGATTG
1 TTACCCTGATCATGAGGCAGATTGAAGACATCACCAATCTCTTACCCCGATCATGGGGCAGATTG
*
43077659 AAACCAT-TCAATCTT
66 AAACCATCT-AATCTC
* * ***
43077674 TTACCCTAATCA-GAGGGCAGATTGAAGACA-CACCAATCTTTTACCTTAATCA-GGAGGCAGAT
1 TTACCCTGATCATGA-GGCAGATTGAAGACATCACCAATCTCTTACCCCGATCATGG-GGCAGAT
* * *
43077736 TG-AAGCATATAATCTA
64 TGAAACCATCTAATCTC
* *
43077752 TTACCCT-ATTCA-GAGGACAGATTGAAGACA-CACCAATCTCTTATCCCGATCATGAGGCAGAT
1 TTACCCTGA-TCATGAGG-CAGATTGAAGACATCACCAATCTCTTACCCCGATCATGGGGCAGAT
* *
43077814 TGAGGACCATCAAATCTC
64 TGA-AACCATCTAATCTC
* * * *
43077832 TTACCCCGATCATGGGGCAGATTGAAGACATCATACAATCTCTTACCCCGATCATGGGGTAGATT
1 TTACCCTGATCATGAGGCAGATTGAAGACATCA-CCAATCTCTTACCCCGATCATGGGGCAGATT
43077897 GAAACCATCTAATCTC
65 GAAACCATCTAATCTC
* * * *
43077913 CTACCTTGATCATGAGGCAGATTAAAGACATCATCCAATCTCTTACCTCGATCATGGGGCAGATT
1 TTACCCTGATCATGAGGCAGATTGAAGACATCA-CCAATCTCTTACCCCGATCATGGGGCAGATT
* *
43077978 GAAGTCC-TCCAATCTC
65 GAA-ACCATCTAATCTC
* * *
43077994 TTACCCCGATCATGGGGCAGATTGAAGACATCATCCAATCTCTTA-CCCGGTCATGGGG
1 TTACCCTGATCATGAGGCAGATTGAAGACATCA-CCAATCTCTTACCCCGATCATGGGG
43078052 TGAATTGAAG
Statistics
Matches: 315, Mismatches: 47, Indels: 29
0.81 0.12 0.07
Matches are distributed among these distances:
76 2 0.01
77 24 0.08
78 64 0.20
79 26 0.08
80 42 0.13
81 126 0.40
82 31 0.10
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (80 bp):
TTACCCTGATCATGAGGCAGATTGAAGACATCACCAATCTCTTACCCCGATCATGGGGCAGATTG
AAACCATCTAATCTC
Found at i:43079893 original size:23 final size:22
Alignment explanation
Indices: 43079863--43079987 Score: 151
Period size: 23 Copynumber: 5.4 Consensus size: 22
43079853 ACACTAGCGC
* *
43079863 GCTCTCTGTTTAGCACGTCTCGT
1 GCTCTCTGATTAGCACGTGT-GT
43079886 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCAC-GTGTGT
*
43079911 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCAC-GTGTGT
*
43079934 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCAC-GTGTGT
43079957 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCAC-GTGTGT
43079980 GCTCTCTG
1 GCTCTCTG
43079988 TTGCCCAGCA
Statistics
Matches: 95, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
23 75 0.79
25 17 0.18
26 3 0.03
ACGTcount: A:0.11, C:0.24, G:0.23, T:0.42
Consensus pattern (22 bp):
GCTCTCTGATTAGCACGTGTGT
Found at i:43079963 original size:46 final size:46
Alignment explanation
Indices: 43079884--43080033 Score: 173
Period size: 46 Copynumber: 3.2 Consensus size: 46
43079874 AGCACGTCTC
*
43079884 GTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTG--ATTAGCACTTTGTGTGCTCTCTGATTAGCACTTTGT
*
43079932 GTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGCACTGTGT
1 GTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGCACTTTGT
* *
43079978 GTGCTCTCTG-TTGCCCAGCAC-TTATGTGCTCTCTG-TTAGTACTTTG-
1 GTGCTCTCTGATT----AGCACTTTGTGTGCTCTCTGATTAGCACTTTGT
*
43080024 GTACTCTCTG
1 GTGCTCTCTG
43080034 CTTGTTCCGT
Statistics
Matches: 92, Mismatches: 6, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
45 2 0.02
46 53 0.58
47 9 0.10
48 23 0.25
49 5 0.05
ACGTcount: A:0.12, C:0.23, G:0.23, T:0.42
Consensus pattern (46 bp):
GTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGCACTTTGT
Found at i:43080031 original size:69 final size:70
Alignment explanation
Indices: 43079887--43080033 Score: 187
Period size: 69 Copynumber: 2.1 Consensus size: 70
43079877 ACGTCTCGTG
*
43079887 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGCACTT
1 CTCTCTG-TATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTATGTGCTCTCTGATTAGCACTT
*
43079952 TGTGTG
65 TGTGTA
*
43079958 CTCTCTG-ATTAGCACTGTGTGTGCTCTCTG-TTGCCCAGCAC-TTATGTGCTCTCTG-TTAGTA
1 CTCTCTGTATTAGCACTGTGTGTGCTCTCTGATT----AGCACTTTATGTGCTCTCTGATTAGCA
43080019 CTTTG-GTA
62 CTTTGTGTA
43080027 CTCTCTG
1 CTCTCTG
43080034 CTTGTTCCGT
Statistics
Matches: 69, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
68 2 0.03
69 32 0.46
70 10 0.14
71 20 0.29
72 5 0.07
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.42
Consensus pattern (70 bp):
CTCTCTGTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTATGTGCTCTCTGATTAGCACTTT
GTGTA
Found at i:43080629 original size:42 final size:42
Alignment explanation
Indices: 43080577--43080698 Score: 163
Period size: 42 Copynumber: 2.8 Consensus size: 42
43080567 TGTTACACAT
43080577 CCAATCTCTTACCTCGATCATGAGGCAGATTGAAGACATCAA
1 CCAATCTCTTACCTCGATCATGAGGCAGATTGAAGACATCAA
* * *
43080619 CCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCAT
1 CCAATCTCTTACCTCGATCATGAGGCAGATTGAAGACATCAA
* * *
43080661 CCAATCTTTTACCTTGAATCAAGAGAGGCAGATTGAAG
1 CCAATCTCTTACCTCG-ATC-A-TGAGGCAGATTGAAG
43080699 CTACCATCGC
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
42 52 0.75
43 3 0.04
44 1 0.01
45 13 0.19
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (42 bp):
CCAATCTCTTACCTCGATCATGAGGCAGATTGAAGACATCAA
Found at i:43082546 original size:30 final size:30
Alignment explanation
Indices: 43082506--43082693 Score: 137
Period size: 30 Copynumber: 6.3 Consensus size: 30
43082496 TTTAACCCTT
* * **
43082506 AAACTCTCCAAAACTTCGATTTTGACCCCC
1 AAACTTTCCAAAAATTATATTTTGACCCCC
**
43082536 AAACTTTCCAAAAATTATATTTTGACCTTC
1 AAACTTTCCAAAAATTATATTTTGACCCCC
* * **
43082566 AAACTTTCTAAAAATTATATTTTAACCCTA
1 AAACTTTCCAAAAATTATATTTTGACCCCC
* * * *
43082596 AAACTTTCCAAAACCTCA-ATTATGACCCCT
1 AAACTTTCCAAAA-ATTATATTTTGACCCCC
* * **
43082626 AAAC-TTCCTAAAAATCACATTTTGACCCTT
1 AAACTTTCC-AAAAATTATATTTTGACCCCC
* ** * *
43082656 GAACTTTTTAAAAATTACATTTTGACCCTC
1 AAACTTTCCAAAAATTATATTTTGACCCCC
43082686 AAACTTTC
1 AAACTTTC
43082694 TAATTTATGT
Statistics
Matches: 127, Mismatches: 27, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
29 7 0.06
30 116 0.91
31 4 0.03
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.35
Consensus pattern (30 bp):
AAACTTTCCAAAAATTATATTTTGACCCCC
Found at i:43082640 original size:90 final size:90
Alignment explanation
Indices: 43082495--43082693 Score: 249
Period size: 90 Copynumber: 2.2 Consensus size: 90
43082485 AGAAATTTTG
* * * * * * *
43082495 TTTTAACCCTTAAACTCTCCAAAACTTCGATTTTGACCCCCAAACTTTCCAAAAATTATATTTTG
1 TTTTAACCCTAAAACTTTCCAAAACCTCAATTATGACCCCCAAACTTTCCAAAAATCACATTTTG
*
43082560 A-CCTTCAAACTTTCTAAAAATTATA
66 ACCCTT-AAACTTTCTAAAAATTACA
*
43082585 TTTTAACCCTAAAACTTTCCAAAACCTCAATTATGACCCCTAAAC-TTCCTAAAAATCACATTTT
1 TTTTAACCCTAAAACTTTCCAAAACCTCAATTATGACCCCCAAACTTTCC-AAAAATCACATTTT
* *
43082649 GACCCTTGAACTTTTTAAAAATTACA
65 GACCCTTAAACTTTCTAAAAATTACA
* *
43082675 TTTTGACCCTCAAACTTTC
1 TTTTAACCCTAAAACTTTC
43082694 TAATTTATGT
Statistics
Matches: 94, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
89 4 0.04
90 86 0.91
91 4 0.04
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.36
Consensus pattern (90 bp):
TTTTAACCCTAAAACTTTCCAAAACCTCAATTATGACCCCCAAACTTTCCAAAAATCACATTTTG
ACCCTTAAACTTTCTAAAAATTACA
Found at i:43085080 original size:44 final size:44
Alignment explanation
Indices: 43084982--43085083 Score: 132
Period size: 44 Copynumber: 2.3 Consensus size: 44
43084972 TTTAGTCTGT
* * *
43084982 CATTTTGGCTTGTACCCACTCGGGCTTGCATTTAGACCGTTCGC
1 CATTTTGGCTTGCACCCACACAGGCTTGCATTTAGACCGTTCGC
* * * **
43085026 CACTTCGGCTTGCACCCACACAGGCTTGTATTTAGACCGTTTTC
1 CATTTTGGCTTGCACCCACACAGGCTTGCATTTAGACCGTTCGC
43085070 CATTTTGGCTTGCA
1 CATTTTGGCTTGCA
43085084 TTTCGACAGG
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.16, C:0.29, G:0.21, T:0.34
Consensus pattern (44 bp):
CATTTTGGCTTGCACCCACACAGGCTTGCATTTAGACCGTTCGC
Found at i:43085239 original size:18 final size:18
Alignment explanation
Indices: 43085201--43085241 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
43085191 CCTTTTCTAA
* **
43085201 AGCTCACACCTTTTGTTG
1 AGCTCACACATTTTGCAG
43085219 AGCTCACACATTTTGCAG
1 AGCTCACACATTTTGCAG
43085237 AGCTC
1 AGCTC
43085242 GCACTTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.22, C:0.29, G:0.17, T:0.32
Consensus pattern (18 bp):
AGCTCACACATTTTGCAG
Found at i:43089017 original size:2 final size:2
Alignment explanation
Indices: 43089006--43089043 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
43088996 CCCTGAAATA
43089006 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
43089044 GAGAGAGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43089048 original size:2 final size:2
Alignment explanation
Indices: 43089043--43089073 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
43089033 ATATATATAT
43089043 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
43089074 TGAATCCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:43091811 original size:27 final size:27
Alignment explanation
Indices: 43091759--43091811 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
43091749 CAATTGAGTA
**
43091759 GTGCCTACCTGACAAGCAACGTCAAAG
1 GTGCCTACCTGACAAGCAACACCAAAG
**
43091786 GTGCCTACCTGACAAGCGGCACCAAA
1 GTGCCTACCTGACAAGCAACACCAAA
43091812 CCTCAATTTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.23, T:0.13
Consensus pattern (27 bp):
GTGCCTACCTGACAAGCAACACCAAAG
Found at i:43095277 original size:24 final size:24
Alignment explanation
Indices: 43095233--43095281 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
43095223 ATTAAACATT
**
43095233 TAATAAATAAAATATTTTATTTTA
1 TAATAAATAAAATATAATATTTTA
43095257 TAATAAATAATAA-ATAATATTTTA
1 TAATAAATAA-AATATAATATTTTA
43095281 T
1 T
43095282 TTTATATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 20 0.91
25 2 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TAATAAATAAAATATAATATTTTA
Found at i:43095958 original size:6 final size:6
Alignment explanation
Indices: 43095947--43095977 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
43095937 AATTAAATAC
*
43095947 AAACAT AAACAT AAGCAT AAACAT AAACAT A
1 AAACAT AAACAT AAACAT AAACAT AAACAT A
43095978 TTTAATTCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.65, C:0.16, G:0.03, T:0.16
Consensus pattern (6 bp):
AAACAT
Found at i:43096393 original size:27 final size:27
Alignment explanation
Indices: 43096352--43096420 Score: 104
Period size: 27 Copynumber: 2.6 Consensus size: 27
43096342 ATACCTATCG
43096352 CCTGACCA-CGATGGAACGTATCCATCA
1 CCTGACCACCG-TGGAACGTATCCATCA
43096379 CCTGACCACCGTGGAACGTATCCATCA
1 CCTGACCACCGTGGAACGTATCCATCA
* *
43096406 CCTGAACACCCTGGA
1 CCTGACCACCGTGGA
43096421 TTATTCGACT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
27 37 0.95
28 2 0.05
ACGTcount: A:0.28, C:0.36, G:0.19, T:0.17
Consensus pattern (27 bp):
CCTGACCACCGTGGAACGTATCCATCA
Found at i:43099344 original size:19 final size:19
Alignment explanation
Indices: 43099309--43099359 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
43099299 ACCATACCCG
*
43099309 TTTTTTTAATA-AATTTAA
1 TTTTTTTAATATTATTTAA
*
43099327 TTTTTTTAATATTTTTTAA
1 TTTTTTTAATATTATTTAA
* *
43099346 ATATTTTAATATTA
1 TTTTTTTAATATTA
43099360 AAAAATTTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 11 0.41
19 16 0.59
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTTTTAATATTATTTAA
Found at i:43100341 original size:4 final size:4
Alignment explanation
Indices: 43100332--43100370 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
43100322 TAGTTTTAAT
*
43100332 GTTA GTTA GTTA GTTA GTTA GTTA GTTA GTAA GTTA GTT
1 GTTA GTTA GTTA GTTA GTTA GTTA GTTA GTTA GTTA GTT
43100371 TTCACTATAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.49
Consensus pattern (4 bp):
GTTA
Found at i:43101449 original size:30 final size:29
Alignment explanation
Indices: 43101415--43101479 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
43101405 TAATTTGTGA
43101415 AAATTAGATC-AAATCAAAAGTTCATGTATG
1 AAATTAGA-CAAAAT-AAAAGTTCATGTATG
* *
43101445 AAATTATACAAAATTAAAGTTCATGTATG
1 AAATTAGACAAAATAAAAGTTCATGTATG
43101474 AAATTA
1 AAATTA
43101480 TACATTAGAC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
29 21 0.66
30 11 0.34
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.32
Consensus pattern (29 bp):
AAATTAGACAAAATAAAAGTTCATGTATG
Found at i:43102000 original size:24 final size:24
Alignment explanation
Indices: 43101950--43102000 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
43101940 TTTTGAGCAA
*
43101950 TTTAATTTTTTTCTTTTATGTTCT
1 TTTAATTTTTTTCTTTTATGTTAT
*
43101974 TTTAATTTTTTTATTTTTAT-TTAT
1 TTTAATTTTTTT-CTTTTATGTTAT
43101998 TTT
1 TTT
43102001 GCATTGTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.78
Consensus pattern (24 bp):
TTTAATTTTTTTCTTTTATGTTAT
Found at i:43110208 original size:24 final size:24
Alignment explanation
Indices: 43110180--43110239 Score: 120
Period size: 24 Copynumber: 2.5 Consensus size: 24
43110170 AGTACTGGAT
43110180 TTTTTGGAGACACAGCTGATGTTG
1 TTTTTGGAGACACAGCTGATGTTG
43110204 TTTTTGGAGACACAGCTGATGTTG
1 TTTTTGGAGACACAGCTGATGTTG
43110228 TTTTTGGAGACA
1 TTTTTGGAGACA
43110240 ACAGGAGGGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.22, C:0.12, G:0.28, T:0.38
Consensus pattern (24 bp):
TTTTTGGAGACACAGCTGATGTTG
Found at i:43114410 original size:111 final size:111
Alignment explanation
Indices: 43114214--43114438 Score: 441
Period size: 111 Copynumber: 2.0 Consensus size: 111
43114204 CACATAATTT
43114214 TACGTAAAATTTTAATAAATATATTCATTACATAAATTATTTTCATCCACGTCATACTATAAATC
1 TACGTAAAATTTTAATAAATATATTCATTACATAAATTATTTTCATCCACGTCATACTATAAATC
43114279 TAATAATTGGTTACAATTTTCGTTTGAAATCTTTTAAGATGATACG
66 TAATAATTGGTTACAATTTTCGTTTGAAATCTTTTAAGATGATACG
43114325 TACGTAAAATTTTAATAAATATATTCATTACATAAATTATTTTCATCCACGTCATACTATAAATC
1 TACGTAAAATTTTAATAAATATATTCATTACATAAATTATTTTCATCCACGTCATACTATAAATC
*
43114390 TAATAATTGGTTACAGTTTTCGTTTGAAATCTTTTAAGATGATACG
66 TAATAATTGGTTACAATTTTCGTTTGAAATCTTTTAAGATGATACG
43114436 TAC
1 TAC
43114439 TCAATATTCA
Statistics
Matches: 113, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
111 113 1.00
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.41
Consensus pattern (111 bp):
TACGTAAAATTTTAATAAATATATTCATTACATAAATTATTTTCATCCACGTCATACTATAAATC
TAATAATTGGTTACAATTTTCGTTTGAAATCTTTTAAGATGATACG
Found at i:43115060 original size:22 final size:22
Alignment explanation
Indices: 43115035--43115094 Score: 61
Period size: 24 Copynumber: 2.7 Consensus size: 22
43115025 AACTTTTTCT
* *
43115035 ATATTTTTTAGAATTTTTTTAA
1 ATATTTTTTAAAATTTTTATAA
*
43115057 ATATAAATTTTAAAATTTTTATAA
1 ATAT--TTTTTAAAATTTTTATAA
43115081 ATA--TTTTAAAATTT
1 ATATTTTTTAAAATTT
43115095 ATTTTTATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 11 0.33
22 4 0.12
24 18 0.55
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
ATATTTTTTAAAATTTTTATAA
Found at i:43122815 original size:18 final size:18
Alignment explanation
Indices: 43122794--43122828 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
43122784 AAAGATATAT
* *
43122794 TAATTAATAATATTATTA
1 TAATAAATAATAATATTA
43122812 TAATAAATAATAATATT
1 TAATAAATAATAATATT
43122829 TTATTATTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TAATAAATAATAATATTA
Found at i:43122841 original size:21 final size:21
Alignment explanation
Indices: 43122792--43122846 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
43122782 CAAAAGATAT
43122792 ATTAATTAATAATATTATTATA
1 ATTAA-TAATAATATTATTATA
*
43122814 ATAAATAATAATATT-TTATTA
1 ATTAATAATAATATTATTA-TA
*
43122835 TTTAAT-ATAATA
1 ATTAATAATAATA
43122847 AAATATAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 9 0.31
21 16 0.55
22 4 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTAATAATAATATTATTATA
Found at i:43130989 original size:55 final size:54
Alignment explanation
Indices: 43130890--43131018 Score: 134
Period size: 55 Copynumber: 2.4 Consensus size: 54
43130880 AAAATATTAT
* * *
43130890 TTCTTTTGGATAGATTATTTTTATGTTTAAATCAATTATCATGTT-AGAATACTTC
1 TTCTTTTGAATTGATTATTTATATGTTTAAATCAATTATCATGTTGA-AAT-CTTC
* * * * * * *
43130945 TTCTTTTGAATTGATTGTTTATATGTTTAAGTCGATTGTTATGTTGAAATGTTG
1 TTCTTTTGAATTGATTATTTATATGTTTAAATCAATTATCATGTTGAAATCTTC
43130999 TTCCTTTTGAATTGATTATT
1 TT-CTTTTGAATTGATTATT
43131019 ATGGTTAAAT
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
54 4 0.07
55 56 0.92
56 1 0.02
ACGTcount: A:0.25, C:0.07, G:0.15, T:0.53
Consensus pattern (54 bp):
TTCTTTTGAATTGATTATTTATATGTTTAAATCAATTATCATGTTGAAATCTTC
Found at i:43133866 original size:30 final size:31
Alignment explanation
Indices: 43133821--43133878 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
43133811 TCATTTTATT
*
43133821 ATATTAATATTA-TTTTGTTGTTATTATTTGA
1 ATATTAATATAATTTTTGTT-TTATTATTTGA
43133852 ATATT-ATATAATTTTTGTTTTATTATT
1 ATATTAATATAATTTTTGTTTTATTATT
43133879 AATTTTGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 13 0.52
31 12 0.48
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (31 bp):
ATATTAATATAATTTTTGTTTTATTATTTGA
Found at i:43133881 original size:18 final size:19
Alignment explanation
Indices: 43133853--43133893 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
43133843 ATTATTTGAA
43133853 TATTATATAATTTTTGTT-T
1 TATTATATAA-TTTTGTTAT
43133872 TATTAT-TAATTTTGTTAT
1 TATTATATAATTTTGTTAT
43133890 TATT
1 TATT
43133894 TTAGAAGCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 7 0.33
18 8 0.38
19 6 0.29
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (19 bp):
TATTATATAATTTTGTTAT
Found at i:43134670 original size:16 final size:16
Alignment explanation
Indices: 43134642--43134685 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
43134632 AAATTATTTG
43134642 TATTATATTATTTTA-A
1 TATT-TATTATTTTATA
43134658 TATTTATTAATTTTATA
1 TATTTATT-ATTTTATA
43134675 TATTT-TTATTT
1 TATTTATTATTT
43134686 ATTGAAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 8 0.31
16 12 0.46
17 6 0.23
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATTTATTATTTTATA
Found at i:43138936 original size:21 final size:21
Alignment explanation
Indices: 43138912--43138953 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
43138902 ATTTTCTTTT
*
43138912 AATGGTCTCGTACATACATTA
1 AATGGTCTCATACATACATTA
*
43138933 AATGGTCTCATCCATACATTA
1 AATGGTCTCATACATACATTA
43138954 CTCAATTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.33
Consensus pattern (21 bp):
AATGGTCTCATACATACATTA
Found at i:43143133 original size:21 final size:21
Alignment explanation
Indices: 43143100--43143142 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
43143090 TTAGGGTTTG
* * *
43143100 AGATTCTAAATTTTAAGTTCA
1 AGATTCGAAATTTAAAATTCA
*
43143121 AGATTCGAGATTTAAAATTCA
1 AGATTCGAAATTTAAAATTCA
43143142 A
1 A
43143143 AGTTTGAAGT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (21 bp):
AGATTCGAAATTTAAAATTCA
Found at i:43145119 original size:32 final size:32
Alignment explanation
Indices: 43145077--43145145 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
43145067 AAAGAAAGAT
43145077 TAAAAAATTCAATTTTTTCATTAAAACTGTTA
1 TAAAAAATTCAATTTTTTCATTAAAACTGTTA
* *
43145109 TAAAACATTCAATTTTTTCATTAAATCTGTTA
1 TAAAAAATTCAATTTTTTCATTAAAACTGTTA
*
43145141 GAAAA
1 TAAAA
43145146 TGCAAATTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.42
Consensus pattern (32 bp):
TAAAAAATTCAATTTTTTCATTAAAACTGTTA
Found at i:43146806 original size:17 final size:17
Alignment explanation
Indices: 43146784--43146817 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
43146774 GAGTTGTTTT
43146784 CTGTTTTTCACCTCCTA
1 CTGTTTTTCACCTCCTA
43146801 CTGTTTTTCACCTCCTA
1 CTGTTTTTCACCTCCTA
43146818 AAACTTCGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.35, G:0.06, T:0.47
Consensus pattern (17 bp):
CTGTTTTTCACCTCCTA
Found at i:43174551 original size:12 final size:12
Alignment explanation
Indices: 43174534--43174558 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43174524 GCTACATGTG
43174534 CATATATATATA
1 CATATATATATA
43174546 CATATATATATA
1 CATATATATATA
43174558 C
1 C
43174559 CGGTGTCTCC
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:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (12 bp):
CATATATATATA
Found at i:43184437 original size:21 final size:21
Alignment explanation
Indices: 43184407--43184446 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
43184397 TTCAGTTTCG
*
43184407 AAATTGATAGGGATTAAATCA
1 AAATTGATAGGAATTAAATCA
*
43184428 AAATTTATAGGAATTAAAT
1 AAATTGATAGGAATTAAAT
43184447 TGTTATAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.15, T:0.33
Consensus pattern (21 bp):
AAATTGATAGGAATTAAATCA
Found at i:43184857 original size:20 final size:22
Alignment explanation
Indices: 43184834--43184876 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
43184824 AGAAATATAT
*
43184834 AAAAATAT-TTAA-ATATTTAA
1 AAAAATATGTTAATAAATTTAA
43184854 AAAAATATGTTAATAAATTTAA
1 AAAAATATGTTAATAAATTTAA
43184876 A
1 A
43184877 TTTAATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 4 0.20
22 8 0.40
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (22 bp):
AAAAATATGTTAATAAATTTAA
Found at i:43184901 original size:24 final size:24
Alignment explanation
Indices: 43184880--43184933 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
43184870 ATTTAAATTT
*
43184880 AATATTTACATTAATATTAAATAA
1 AATAATTACATTAATATTAAATAA
43184904 AATAATTACATTAATATTAAATAA
1 AATAATTACATTAATATTAAATAA
43184928 AATAAT
1 AATAAT
43184934 CTCCTCCACC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (24 bp):
AATAATTACATTAATATTAAATAA
Found at i:43185516 original size:6 final size:5
Alignment explanation
Indices: 43185478--43185514 Score: 56
Period size: 5 Copynumber: 7.0 Consensus size: 5
43185468 AGCTGCCATA
43185478 TTTAT TTTAT TTTAT TTTAT TTTAT ATTTAT ATTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT -TTTAT -TTTAT
43185515 ATAAAATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 20 0.65
6 11 0.35
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTAT
Found at i:43189298 original size:24 final size:24
Alignment explanation
Indices: 43189239--43189299 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
43189229 GAATAATAAA
*
43189239 AGTTTAACTCAAACAAATAAACAG
1 AGTTTAACTGAAACAAATAAACAG
* * * *
43189263 AGTTTAATTGAAATAATTAAATAG
1 AGTTTAACTGAAACAAATAAACAG
43189287 AGTTTAACTGAAA
1 AGTTTAACTGAAA
43189300 GATTATTTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.30
Consensus pattern (24 bp):
AGTTTAACTGAAACAAATAAACAG
Found at i:43189478 original size:3 final size:3
Alignment explanation
Indices: 43189470--43189497 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
43189460 GGGGCACATT
43189470 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
43189498 ATATGGAAAA
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):
TTA
Found at i:43193121 original size:16 final size:16
Alignment explanation
Indices: 43193100--43193132 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
43193090 CAATCACACC
43193100 TAAATTAAAAGATTGG
1 TAAATTAAAAGATTGG
43193116 TAAATTAAAAGATTGG
1 TAAATTAAAAGATTGG
43193132 T
1 T
43193133 GGTGACTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.18, T:0.33
Consensus pattern (16 bp):
TAAATTAAAAGATTGG
Found at i:43193529 original size:56 final size:56
Alignment explanation
Indices: 43193419--43193529 Score: 150
Period size: 56 Copynumber: 2.0 Consensus size: 56
43193409 GGGGTGTTAA
* ** *
43193419 GATATTATTATGCAATATTATATTTTAGTAATTTAATTCCTAATGTGATTTTATAG
1 GATATTATTATGCAATATTATATTTTAGCAATTTAATTCCTAATAAGATATTATAG
** * *
43193475 GATATTATTATGGGATATTATCTTTTAGCAATTTGATTCCTAATAAGATATTATA
1 GATATTATTATGCAATATTATATTTTAGCAATTTAATTCCTAATAAGATATTATA
43193530 CTTTAACAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
56 47 1.00
ACGTcount: A:0.34, C:0.06, G:0.12, T:0.48
Consensus pattern (56 bp):
GATATTATTATGCAATATTATATTTTAGCAATTTAATTCCTAATAAGATATTATAG
Found at i:43193576 original size:2 final size:2
Alignment explanation
Indices: 43193571--43193595 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
43193561 TTATATAAAC
43193571 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
43193596 CCCTTGAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:43196495 original size:30 final size:30
Alignment explanation
Indices: 43196461--43196523 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
43196451 AATATTTATT
*
43196461 AAAAATTAGAAAAAATTTATAAAAATCTTAA
1 AAAAATT-GAAAAAATTTATAAAAATCATAA
* *
43196492 AAAAATTGTAAAATTTTATAAAAATCATAA
1 AAAAATTGAAAAAATTTATAAAAATCATAA
43196522 AA
1 AA
43196524 TATAAAATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 22 0.76
31 7 0.24
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.30
Consensus pattern (30 bp):
AAAAATTGAAAAAATTTATAAAAATCATAA
Found at i:43196808 original size:28 final size:26
Alignment explanation
Indices: 43196776--43196892 Score: 76
Period size: 28 Copynumber: 4.2 Consensus size: 26
43196766 TTTTTTATGC
43196776 ATTTTTATGAAATTTTACAATTTTTTTA
1 ATTTTTAT-AAATTTTA-AATTTTTTTA
*
43196804 ATTTTTA-ATAATATTTAAATATTTTTA
1 ATTTTTATA-AAT-TTTAAATTTTTTTA
* * *
43196831 TATTTTTATTCAAATTTAATAACTTTTATA
1 -ATTTTTA-T-AAATTTTA-AATTTTTTTA
** *
43196861 ATTTTTATTGATTTT-TATTTTTTATA
1 ATTTTTATAAATTTTAAATTTTTT-TA
43196887 ATTTTT
1 ATTTTT
43196893 TGTCACATGT
Statistics
Matches: 70, Mismatches: 11, Indels: 18
0.71 0.11 0.18
Matches are distributed among these distances:
25 5 0.07
26 9 0.13
27 16 0.23
28 19 0.27
29 10 0.14
30 10 0.14
31 1 0.01
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (26 bp):
ATTTTTATAAATTTTAAATTTTTTTA
Found at i:43196866 original size:9 final size:9
Alignment explanation
Indices: 43196776--43196892 Score: 78
Period size: 9 Copynumber: 12.7 Consensus size: 9
43196766 TTTTTTATGC
43196776 ATTTTTATGA
1 ATTTTTAT-A
* *
43196786 AATTTTACA
1 ATTTTTATA
*
43196795 ATTTTTTTA
1 ATTTTTATA
43196804 ATTTTTAATA
1 ATTTTT-ATA
* *
43196814 ATATTTAAA
1 ATTTTTATA
43196823 TATTTTTAT-
1 -ATTTTTATA
43196832 ATTTTTATTCA
1 ATTTTTA-T-A
* *
43196843 AATTTAATA
1 ATTTTTATA
*
43196852 ACTTTTATA
1 ATTTTTATA
*
43196861 ATTTTTATTG
1 ATTTTTA-TA
43196871 ATTTTTAT-
1 ATTTTTATA
43196879 -TTTTTATA
1 ATTTTTATA
43196887 ATTTTT
1 ATTTTT
43196893 TGTCACATGT
Statistics
Matches: 83, Mismatches: 16, Indels: 17
0.72 0.14 0.15
Matches are distributed among these distances:
7 7 0.08
8 7 0.08
9 36 0.43
10 28 0.34
11 5 0.06
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (9 bp):
ATTTTTATA
Found at i:43199483 original size:37 final size:37
Alignment explanation
Indices: 43199433--43199509 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
43199423 TGTTTTATAG
*
43199433 GGAAAGAGGGAATGGAACCTAAGAACGAAAAGACACT
1 GGAAAGAGGGAATGGAACCAAAGAACGAAAAGACACT
*
43199470 GGAAAGAGGGAATGGAACCAAAGAATGAAAAGACACT
1 GGAAAGAGGGAATGGAACCAAAGAACGAAAAGACACT
43199507 GGA
1 GGA
43199510 GAGAACGAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.49, C:0.12, G:0.31, T:0.08
Consensus pattern (37 bp):
GGAAAGAGGGAATGGAACCAAAGAACGAAAAGACACT
Found at i:43205260 original size:24 final size:22
Alignment explanation
Indices: 43205233--43205296 Score: 76
Period size: 24 Copynumber: 2.8 Consensus size: 22
43205223 AAATAATAAA
43205233 TAAATTTTAAATTTAAATTTACTT
1 TAAATTTTAAATTTAAA--TACTT
*
43205257 TAAATTTTTAAATGTTTAATACTT
1 TAAA-TTTTAAAT-TTAAATACTT
43205281 TAAA-TTTAAATTTAAA
1 TAAATTTTAAATTTAAA
43205297 AGAGTCCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
21 4 0.11
22 7 0.19
24 13 0.36
25 8 0.22
26 4 0.11
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.52
Consensus pattern (22 bp):
TAAATTTTAAATTTAAATACTT
Found at i:43206930 original size:30 final size:29
Alignment explanation
Indices: 43206880--43207355 Score: 333
Period size: 30 Copynumber: 16.1 Consensus size: 29
43206870 TAAAAGGACC
* *
43206880 CCCTAAAC-CTTCTCAAAATTATATTTTGA
1 CCCTAAACTTTTCT-AAAATTACATTTTGA
* * *
43206909 CTCCAAAACTTTTCTAAAATTATATTTTAA
1 C-CCTAAACTTTTCTAAAATTACATTTTGA
43206939 CCCTCAAAACTTTT-TAAAATTACATTTTGA
1 CCCT--AAACTTTTCTAAAATTACATTTTGA
* * * *
43206969 CCATTAAAAC-TTCCCAAAATCACATTTTGA
1 CC-CT-AAACTTTTCTAAAATTACATTTTGA
* * ** *
43206999 CCTTTAAACTTTCCTGTAGTTACATTTTGA
1 CC-CTAAACTTTTCTAAAATTACATTTTGA
* * *
43207029 CCCTTAAACATCTT-TAAAATTATATTTTAA
1 CCC-TAAAC-TTTTCTAAAATTACATTTTGA
* * *
43207059 CCCTAAACTTTCCAAAAATTTCATTTTGA
1 CCCTAAACTTTTCTAAAATTACATTTTGA
* *
43207088 CCCCTAAACTTTCCCAAAATTACATTTTGA
1 -CCCTAAACTTTTCTAAAATTACATTTTGA
* *
43207118 CCCTTAAACTTTTC-CAAATTACATTTTAA
1 CCC-TAAACTTTTCTAAAATTACATTTTGA
* * * *
43207147 CACCTAAA-TTTCCCCAAAATTGCATTTTAA
1 C-CCTAAACTTT-TCTAAAATTACATTTTGA
* *
43207177 CCCCTAAACCTTTCTAAAATTGCATTTTGA
1 -CCCTAAACTTTTCTAAAATTACATTTTGA
* * *
43207207 CCCCTAAACCTTTCCAAAATCACATTTTGA
1 -CCCTAAACTTTTCTAAAATTACATTTTGA
* *
43207237 CCC-AAA-TTTTCCCAAAATCACATTTTGA
1 CCCTAAACTTTT-CTAAAATTACATTTTGA
* * *
43207265 CCCTTAAACTTTCCTATAATTACATTTTTA
1 CCC-TAAACTTTTCTAAAATTACATTTTGA
**
43207295 TCCCTAAACTTTTCTAAAATTATGTTTTGA
1 -CCCTAAACTTTTCTAAAATTACATTTTGA
*
43207325 CCCTAAA-TTCTCTGAAAATT-CATTTTCGA
1 CCCTAAACTTTTCT-AAAATTACATTTT-GA
43207354 CC
1 CC
43207356 TTTTTTTTTC
Statistics
Matches: 364, Mismatches: 59, Indels: 48
0.77 0.13 0.10
Matches are distributed among these distances:
27 3 0.01
28 37 0.10
29 68 0.19
30 232 0.64
31 24 0.07
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.38
Consensus pattern (29 bp):
CCCTAAACTTTTCTAAAATTACATTTTGA
Found at i:43207101 original size:89 final size:88
Alignment explanation
Indices: 43206880--43207331 Score: 405
Period size: 89 Copynumber: 5.1 Consensus size: 88
43206870 TAAAAGGACC
* * * * * * * * * *
43206880 CCCTAAACCTTCTCAAAATTATATTTTGACTCCAAAACTTTTCTAAAATTATATTTTAACCCTCA
1 CCCTAAACTTTCCCAAAATCACATTTTGACCCCTAAACTTTCCTAAAATTACATTTTGACCCT-T
*
43206945 AAACTTTTTAAAATTACATTTTGA
65 AAACTCTTTAAAATTACATTTTGA
* ** ** *
43206969 CCATTAAAAC-TTCCCAAAATCACATTTTGACCTTTAAACTTTCCTGTAGTTACATTTTGACCCT
1 CC-CT-AAACTTTCCCAAAATCACATTTTGACCCCTAAACTTTCCTAAAATTACATTTTGACCCT
* *
43207033 TAAACATCTTTAAAATTATATTTTAA
64 TAAAC-TCTTTAAAATTACATTTTGA
* ** *
43207059 CCCTAAACTTTCCAAAAATTTCATTTTGACCCCTAAACTTTCCCAAAATTACATTTTGACCCTTA
1 CCCTAAACTTTCCCAAAATCACATTTTGACCCCTAAACTTTCCTAAAATTACATTTTGACCCTTA
* *
43207124 AACT-TTTCCAAATTACATTTTAA
66 AACTCTTT-AAAATTACATTTTGA
** * *
43207147 CACCTAAA-TTTCCCCAAAATTGCATTTTAACCCCTAAACCTTT-CTAAAATTGCATTTTGACCC
1 C-CCTAAACTTT-CCCAAAATCACATTTTGACCCCTAAA-CTTTCCTAAAATTACATTTTGACCC
* *
43207210 CTAAAC-CTTTCCAAAATCACATTTTGA
63 TTAAACTCTTT--AAAATTACATTTTGA
* * * *
43207237 CCC-AAATTTTCCCAAAATCACATTTTGACCCTTAAACTTTCCTATAATTACATTTTTATCCC-T
1 CCCTAAACTTTCCCAAAATCACATTTTGACCCCTAAACTTTCCTAAAATTACATTTTGA-CCCTT
* **
43207300 AAACTTTTCTAAAATTATGTTTTGA
65 AAACTCTT-TAAAATTACATTTTGA
43207325 CCCTAAA
1 CCCTAAA
43207332 TTCTCTGAAA
Statistics
Matches: 297, Mismatches: 50, Indels: 32
0.78 0.13 0.08
Matches are distributed among these distances:
87 7 0.02
88 81 0.27
89 125 0.42
90 80 0.27
91 4 0.01
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.38
Consensus pattern (88 bp):
CCCTAAACTTTCCCAAAATCACATTTTGACCCCTAAACTTTCCTAAAATTACATTTTGACCCTTA
AACTCTTTAAAATTACATTTTGA
Found at i:43207115 original size:119 final size:117
Alignment explanation
Indices: 43206922--43207331 Score: 379
Period size: 119 Copynumber: 3.5 Consensus size: 117
43206912 CAAAACTTTT
* **
43206922 CTAAAATTATATTTTAACCCTCAAAACTTTTTAAAATTACATTTTGACCATTAAAAC-TTCCCAA
1 CTAAAATTATATTTTAACCCT--AAACTTTCTAAAATTACATTTTGACCCCT-AAACTTTCCCAA
* * * * *
43206986 AATCACATTTTGACCTTTAAAC-TTTCCTGTAGTTACATTTTGAC-CCTTAAACATCT
63 AATCACATTTTGACCCTTAAACTTTTCC--AAATTACATTTTAACACC-TAAACATCC
* * *
43207042 TTAAAATTATATTTTAACCCTAAACTTTCCAAAAATTTCATTTTGACCCCTAAACTTTCCCAAAA
1 CTAAAATTATATTTTAACCCTAAACTTT-CTAAAATTACATTTTGACCCCTAAACTTTCCCAAAA
* **
43207107 TTACATTTTGACCCTTAAACTTTTCCAAATTACATTTTAACACCTAAATTTCC
65 TCACATTTTGACCCTTAAACTTTTCCAAATTACATTTTAACACCTAAACATCC
* ** *
43207160 CCAAAATTGCATTTTAACCCCTAAACCTTTCTAAAATTGCATTTTGACCCCTAAACCTTT-CCAA
1 CTAAAATTATATTTTAA-CCCTAAA-CTTTCTAAAATTACATTTTGACCCCTAAA-CTTTCCCAA
* * * *
43207224 AATCACATTTTGACCC--AAA-TTTTCCCAAAATCACATTTTGAC-CCTTAAACTTTC
63 AATCACATTTTGACCCTTAAACTTTT-CC-AAATTACATTTTAACACC-TAAACATCC
* * * **
43207278 CTATAATTACATTTTTATCCCTAAACTTTTCTAAAATTATGTTTTGA-CCCTAAA
1 CTAAAATTATA-TTTTAACCCTAAAC-TTTCTAAAATTACATTTTGACCCCTAAA
43207332 TTCTCTGAAA
Statistics
Matches: 246, Mismatches: 32, Indels: 27
0.81 0.10 0.09
Matches are distributed among these distances:
116 4 0.02
117 15 0.06
118 94 0.38
119 100 0.41
120 33 0.13
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.38
Consensus pattern (117 bp):
CTAAAATTATATTTTAACCCTAAACTTTCTAAAATTACATTTTGACCCCTAAACTTTCCCAAAAT
CACATTTTGACCCTTAAACTTTTCCAAATTACATTTTAACACCTAAACATCC
Found at i:43207355 original size:29 final size:29
Alignment explanation
Indices: 43207296--43207355 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
43207286 ACATTTTTAT
* *
43207296 CCCTAAACTTTTCTAAAATTATGTTTTGA
1 CCCTAAACTTCTCTAAAATTATGTTTCGA
43207325 CCCTAAA-TTCTCTGAAAATTCAT-TTTCGA
1 CCCTAAACTTCTCT-AAAATT-ATGTTTCGA
43207354 CC
1 CC
43207356 TTTTTTTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 5 0.19
29 20 0.74
30 2 0.07
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (29 bp):
CCCTAAACTTCTCTAAAATTATGTTTCGA
Found at i:43210709 original size:59 final size:59
Alignment explanation
Indices: 43210398--43210711 Score: 452
Period size: 59 Copynumber: 5.3 Consensus size: 59
43210388 TGGATACCCG
* * * * * *
43210398 GGGGGCAAAATGGTAATTTT-AGTGTAATCGGGGTTAAAAATGGAATTTTAAAAGATTC
1 GGGGGTAAAATGGTAATTTTCGGTGAAATCAGGGTTAAAAATGGAATTTTAGAAGCTTC
* * * *
43210456 GGGGGTAAAATGGCAATCTTCGGTGAAATTAGGGTTAAAAATAGAATTTTAGAAGCTTC
1 GGGGGTAAAATGGTAATTTTCGGTGAAATCAGGGTTAAAAATGGAATTTTAGAAGCTTC
* *
43210515 GGGGGTAAAATGGTAATCTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTTC
1 GGGGGTAAAATGGTAATTTTCGGTGAAATCAGGGTTAAAAATGGAATTTTAGAAGCTTC
* * * *
43210574 GAGGGTAAAATGGTAATTTCCGATGAAATTAGGGTTAAAAATGGAATTTTAGAAGCTTC
1 GGGGGTAAAATGGTAATTTTCGGTGAAATCAGGGTTAAAAATGGAATTTTAGAAGCTTC
43210633 GGGGGTAAAATGGTAATTTTCGGTGAAATCAGGGTTAAAAATGGAATTTTAGAAGCTTC
1 GGGGGTAAAATGGTAATTTTCGGTGAAATCAGGGTTAAAAATGGAATTTTAGAAGCTTC
*
43210692 GGGGGTCAAAAT-ATAATTTT
1 GGGGGT-AAAATGGTAATTTT
43210712 GGAAAAGTTT
Statistics
Matches: 229, Mismatches: 25, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
58 17 0.07
59 207 0.90
60 5 0.02
ACGTcount: A:0.35, C:0.07, G:0.28, T:0.30
Consensus pattern (59 bp):
GGGGGTAAAATGGTAATTTTCGGTGAAATCAGGGTTAAAAATGGAATTTTAGAAGCTTC
Found at i:43210729 original size:30 final size:30
Alignment explanation
Indices: 43210693--43210771 Score: 140
Period size: 30 Copynumber: 2.6 Consensus size: 30
43210683 AGAAGCTTCG
43210693 GGGGTCAAAATATAATTTTGGAAAAGTTTT
1 GGGGTCAAAATATAATTTTGGAAAAGTTTT
43210723 GGGGTCAAAATATAATTTTGGAAAAGTTTT
1 GGGGTCAAAATATAATTTTGGAAAAGTTTT
**
43210753 GGGGTTGAAATATAATTTT
1 GGGGTCAAAATATAATTTT
43210772 TAGACAATTT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.38
Consensus pattern (30 bp):
GGGGTCAAAATATAATTTTGGAAAAGTTTT
Found at i:43211104 original size:160 final size:162
Alignment explanation
Indices: 43210868--43211179 Score: 432
Period size: 161 Copynumber: 1.9 Consensus size: 162
43210858 ATTTGAAAAT
* * *
43210868 CTTGAAAAATTTTTGGACCAATTTTGTAATTAAATAAAAGTCGATTTAAGGATTAAATTAAGACA
1 CTTGAAAAATTGTTGGACCAATTTCGTAATTAAATAAAAGTCGATTTAAGGATTAAATTAAAACA
** * * *
43210933 AATTGAAAATAAAAAGGACTAAGTACATAAATAAACCA-AAAAAGACACGTGGCAGTCTCTGGTA
66 AATAAAAAATAAAAAGGACTAAATACATAAATAAACCAGAAAAAGACACGTGGCAGCCTATGGTA
* *
43210997 TAGTCAAAGAGTCAAAGGACTAGTTTATAAAC
131 CAGTCAAACAGTCAAAGGACTAGTTTATAAAC
* * *
43211029 CTTGAAAAATTGTTGGGCCAATTTCGTAATTAAA-ATAAAGTTGATTT-GGGATTAAATTAAAAC
1 CTTGAAAAATTGTTGGACCAATTTCGTAATTAAATA-AAAGTCGATTTAAGGATTAAATTAAAAC
* * **
43211092 AAATAAAAAATAAAAAGGACTAAATGCATAAATAATCCAGAAAGTGACACGTGGCAGCCTATGGT
65 AAATAAAAAATAAAAAGGACTAAATACATAAATAAACCAGAAAAAGACACGTGGCAGCCTATGGT
*
43211157 ACAGTTAAACAGTCAAAGGACTA
130 ACAGTCAAACAGTCAAAGGACTA
43211180 AATTGAAAAG
Statistics
Matches: 131, Mismatches: 18, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
160 49 0.37
161 82 0.63
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.26
Consensus pattern (162 bp):
CTTGAAAAATTGTTGGACCAATTTCGTAATTAAATAAAAGTCGATTTAAGGATTAAATTAAAACA
AATAAAAAATAAAAAGGACTAAATACATAAATAAACCAGAAAAAGACACGTGGCAGCCTATGGTA
CAGTCAAACAGTCAAAGGACTAGTTTATAAAC
Found at i:43212726 original size:20 final size:19
Alignment explanation
Indices: 43212703--43212784 Score: 62
Period size: 20 Copynumber: 4.3 Consensus size: 19
43212693 GACATTGAGC
43212703 TTTAAATTTTTAATGTTAAA
1 TTTAAATTTTTAAT-TTAAA
**
43212723 TTT-AATATTTTAATTTTTA
1 TTTAAAT-TTTTAATTTAAA
* *
43212742 TTTAAA-TTTAAATTCAAA
1 TTTAAATTTTTAATTTAAA
**
43212760 -TTAAATTTAAATATTTAAA
1 TTTAAATTTTTA-ATTTAAA
43212779 TTTAAA
1 TTTAAA
43212785 ATAAATCTAA
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
17 5 0.10
18 12 0.24
19 15 0.31
20 17 0.35
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (19 bp):
TTTAAATTTTTAATTTAAA
Found at i:43212727 original size:6 final size:6
Alignment explanation
Indices: 43212703--43212811 Score: 82
Period size: 6 Copynumber: 18.0 Consensus size: 6
43212693 GACATTGAGC
* * **
43212703 TTTAAA TTTTTAA TGTTAAA TTTAATA TTTTAA TTTTTA TTTAAA TTTAAA
1 TTTAAA -TTTAAA T-TTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA
* * *
43212754 TTCAAA -TTAAA TTTAAATA TTTAAA TTTAAA -ATAAA TCTAAA TTTAAA
1 TTTAAA TTTAAA TTT-AA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
43212802 --TAAA TTTAAA
1 TTTAAA TTTAAA
43212812 ATCAATTTAA
Statistics
Matches: 83, Mismatches: 11, Indels: 17
0.75 0.10 0.15
Matches are distributed among these distances:
4 4 0.05
5 8 0.10
6 48 0.58
7 19 0.23
8 4 0.05
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:43212775 original size:25 final size:25
Alignment explanation
Indices: 43212747--43212796 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
43212737 TTTTATTTAA
* *
43212747 ATTTAAATTCAAATTAAATTTAAAT
1 ATTTAAATTCAAAATAAATCTAAAT
*
43212772 ATTTAAATTTAAAATAAATCTAAAT
1 ATTTAAATTCAAAATAAATCTAAAT
43212797 TTAAATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTTAAATTCAAAATAAATCTAAAT
Found at i:43212775 original size:31 final size:31
Alignment explanation
Indices: 43212740--43212803 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
43212730 TTTTAATTTT
*
43212740 TATTTAAATTTAAATTCAAAT-TAAATTTAAA
1 TATTTAAATTTAAAAT-AAATCTAAATTTAAA
43212771 TATTTAAATTTAAAATAAATCTAAATTTAAA
1 TATTTAAATTTAAAATAAATCTAAATTTAAA
43212802 TA
1 TA
43212804 AATTTAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (31 bp):
TATTTAAATTTAAAATAAATCTAAATTTAAA
Found at i:43212790 original size:42 final size:43
Alignment explanation
Indices: 43212718--43212811 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 43
43212708 ATTTTTAATG
* * ** *
43212718 TTAAATTT-AATATTTTAATTTTTATTTAAATTTAAATTCAAA
1 TTAAATTTAAATATTTTAAATTTAAAATAAATCTAAATTCAAA
*
43212760 TTAAATTTAAATA-TTTAAATTTAAAATAAATCTAAATTTAAA
1 TTAAATTTAAATATTTTAAATTTAAAATAAATCTAAATTCAAA
43212802 -TAAATTTAAA
1 TTAAATTTAAA
43212812 ATCAATTTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
41 10 0.22
42 31 0.69
43 4 0.09
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (43 bp):
TTAAATTTAAATATTTTAAATTTAAAATAAATCTAAATTCAAA
Found at i:43212813 original size:17 final size:16
Alignment explanation
Indices: 43212741--43212811 Score: 85
Period size: 17 Copynumber: 4.4 Consensus size: 16
43212731 TTTAATTTTT
43212741 ATTTAAATTTAAATTCAA
1 ATTTAAATTTAAA-T-AA
43212759 A-TTAAATTTAAAT--
1 ATTTAAATTTAAATAA
43212772 ATTTAAATTTAAAATAA
1 ATTTAAATTT-AAATAA
*
43212789 ATCTAAATTTAAATAA
1 ATTTAAATTTAAATAA
43212805 ATTTAAA
1 ATTTAAA
43212812 ATCAATTTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
13 1 0.02
14 8 0.17
15 4 0.09
16 13 0.28
17 20 0.43
18 1 0.02
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTTAAATTTAAATAA
Found at i:43213428 original size:33 final size:33
Alignment explanation
Indices: 43213364--43213428 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
43213354 ATGTGGTCAT
* *
43213364 TGGCATTTATGTAAGGATTTATAATACACCACA
1 TGGCATATATGTAAGGATTTACAATACACCACA
* * *
43213397 TGGCATATATGTAAGGTTTTACAGTAGACCAC
1 TGGCATATATGTAAGGATTTACAATACACCAC
43213429 GTCATATATG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.32
Consensus pattern (33 bp):
TGGCATATATGTAAGGATTTACAATACACCACA
Found at i:43214600 original size:35 final size:34
Alignment explanation
Indices: 43214555--43214621 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 34
43214545 ACTTTAATTT
43214555 GTTAATTTACCTTTTATTATTTATTTTATTTAATA
1 GTTAATTTACCTTTTATTATTTA-TTTATTTAATA
*
43214590 GTTACTTTACCTTTTATTATTTATTTATTTAA
1 GTTAATTTACCTTTTATTATTTATTTATTTAA
43214622 CAATTAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 9 0.29
35 22 0.71
ACGTcount: A:0.27, C:0.07, G:0.03, T:0.63
Consensus pattern (34 bp):
GTTAATTTACCTTTTATTATTTATTTATTTAATA
Found at i:43216720 original size:43 final size:43
Alignment explanation
Indices: 43216671--43216917 Score: 268
Period size: 43 Copynumber: 5.8 Consensus size: 43
43216661 TCTGTTAATG
* ** *
43216671 TTAGTGGCATTTGTGGGAAAAATGCCGCTAAAGAACATGTTCT
1 TTAGTGGCGTTTGTGGGAAAAGCGCCGCTAAAGAACATGGTCT
* * * *
43216714 ATAGTGGCGTTT-TGGGGAAAGCGTCGCTAAAGATCATGGTCT
1 TTAGTGGCGTTTGTGGGAAAAGCGCCGCTAAAGAACATGGTCT
** **
43216756 TTAGCCGCGTTTGTGGGTGAAGCGCCGCTAAAGAACATGGTCT
1 TTAGTGGCGTTTGTGGGAAAAGCGCCGCTAAAGAACATGGTCT
* * *
43216799 TTAGTGGCGTTTATGGGAAAAGCGCCACTAAAGAACATGATCT
1 TTAGTGGCGTTTGTGGGAAAAGCGCCGCTAAAGAACATGGTCT
* * * *
43216842 TTAGCGGCGTTTGTGGGGAAAA-CACCACTAAAGACCATGG-CTT
1 TTAGTGGCGTTTGT-GGGAAAAGCGCCGCTAAAGAACATGGTC-T
*
43216885 TTAGCGGCGTTTGT-GGAAAAGCGCCGCTAAAGA
1 TTAGTGGCGTTTGTGGGAAAAGCGCCGCTAAAGA
43216918 CCATTGTCGA
Statistics
Matches: 171, Mismatches: 29, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
41 6 0.04
42 44 0.26
43 114 0.67
44 7 0.04
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.26
Consensus pattern (43 bp):
TTAGTGGCGTTTGTGGGAAAAGCGCCGCTAAAGAACATGGTCT
Found at i:43216873 original size:86 final size:85
Alignment explanation
Indices: 43216671--43216917 Score: 284
Period size: 85 Copynumber: 2.9 Consensus size: 85
43216661 TCTGTTAATG
* * * * * * *
43216671 TTAGTGGCATTTGTGGGAAAAATGCCGCTAAAGAACATGTTCTATAGTGGCGTTTTGGGGAAAGC
1 TTAGCGGCGTTTGTGGGGAAAACGCCGCTAAAGAACATGGTCTTTAGTGGCGTTTTGGGAAAAGC
* * *
43216736 GTCGCTAAAGATCATGGTCT
66 GCCGCTAAAGAACATGATCT
* *
43216756 TTAGCCGCGTTTGTGGGTG-AAGCGCCGCTAAAGAACATGGTCTTTAGTGGCGTTTATGGGAAAA
1 TTAGCGGCGTTTGTGGG-GAAAACGCCGCTAAAGAACATGGTCTTTAGTGGCGTTT-TGGGAAAA
*
43216820 GCGCCACTAAAGAACATGATCT
64 GCGCCGCTAAAGAACATGATCT
* * * *
43216842 TTAGCGGCGTTTGTGGGGAAAACACCACTAAAGACCATGG-CTTTTAGCGGCG-TTTGTGGAAAA
1 TTAGCGGCGTTTGTGGGGAAAACGCCGCTAAAGAACATGGTC-TTTAGTGGCGTTTTG-GGAAAA
43216905 GCGCCGCTAAAGA
64 GCGCCGCTAAAGA
43216918 CCATTGTCGA
Statistics
Matches: 137, Mismatches: 20, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
84 2 0.01
85 68 0.50
86 67 0.49
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.26
Consensus pattern (85 bp):
TTAGCGGCGTTTGTGGGGAAAACGCCGCTAAAGAACATGGTCTTTAGTGGCGTTTTGGGAAAAGC
GCCGCTAAAGAACATGATCT
Found at i:43218030 original size:37 final size:37
Alignment explanation
Indices: 43217975--43218052 Score: 129
Period size: 37 Copynumber: 2.1 Consensus size: 37
43217965 AAAATGGAGT
* * *
43217975 TTTTGGAAGTTTGGGGGTAAAAATGTAATTTTTGGAA
1 TTTTGGAAGTTCGAGGGTAAAAATATAATTTTTGGAA
43218012 TTTTGGAAGTTCGAGGGTAAAAATATAATTTTTGGAA
1 TTTTGGAAGTTCGAGGGTAAAAATATAATTTTTGGAA
43218049 TTTT
1 TTTT
43218053 TAGGGTCAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.31, C:0.01, G:0.26, T:0.42
Consensus pattern (37 bp):
TTTTGGAAGTTCGAGGGTAAAAATATAATTTTTGGAA
Found at i:43218044 original size:29 final size:29
Alignment explanation
Indices: 43218012--43218235 Score: 143
Period size: 30 Copynumber: 7.6 Consensus size: 29
43218002 ATTTTTGGAA
*
43218012 TTTTGGAAGTTCGAGGGTAAAAATATAAT
1 TTTTGGAAGTTTGAGGGTAAAAATATAAT
* *
43218041 TTTTGGAATTTTTAGGGTCAAAAATGA-AAT
1 TTTTGGAAGTTTGAGGGT-AAAAAT-ATAAT
43218071 TTTTGGAAGTTTG-GGGATAAAAATATAATT
1 TTTTGGAAGTTTGAGGG-TAAAAATATAA-T
* ** * * **
43218101 TTTTTGATTTTTTG-GGGTTAACATGCAAT
1 TTTTGGA-AGTTTGAGGGTAAAAATATAAT
** *
43218130 TTTCTAAAAGTTTTAGGGTAACAAATATAAT
1 TTT-TGGAAGTTTGAGGGTAA-AAATATAAT
* * *
43218161 TTTTAGAAGTTT-TGGGTAAAAATGTAAT
1 TTTTGGAAGTTTGAGGGTAAAAATATAAT
* ** * *
43218189 TTTGGAGAAGTTCAAGGGTCAAAATACAAT
1 TTTTG-GAAGTTTGAGGGTAAAAATATAAT
43218219 TTTTGGACAGTTT-AGGG
1 TTTTGGA-AGTTTGAGGG
43218236 ACCTTCAGGG
Statistics
Matches: 150, Mismatches: 33, Indels: 24
0.72 0.16 0.12
Matches are distributed among these distances:
28 12 0.08
29 51 0.34
30 70 0.47
31 17 0.11
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.39
Consensus pattern (29 bp):
TTTTGGAAGTTTGAGGGTAAAAATATAAT
Done.