Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 70 of 221
Found at i:20370524 original size:92 final size:91
Alignment explanation
Indices: 20370316--20370582 Score: 275
Period size: 92 Copynumber: 2.8 Consensus size: 91
20370306 AAAAACGCCG
* * * *
20370316 CAAAAAATAAATCAATTTATAAAAAATAAAATAAAAAAATTTTAGCATAGCAAAACGGAGCCATT
1 CAAAAAATAAATCAATTTAT---AAATAATATAAAAAAAATTTAGCATAGCAAAACGGCGTCATT
* *
20370381 TTGTTGAAAATGAAATAGCGGCGTTTTTT
63 TTGTTCAAAATAAAATAGCGGCGTTTTTT
***** *** *
20370410 -ATAAAAACGCCGCAAAAAATAAATCAATATAAAAAAAATTTAGCAGAGCAAAACGGCGTCATTT
1 CA-AAAAATAAATCAATTTATAAAT-AATATAAAAAAAATTTAGCATAGCAAAACGGCGTCATTT
*
20370474 TATTCAAAATAAAATAGCGGCGTTTTTT
64 TGTTCAAAATAAAATAGCGGCGTTTTTT
* * *
20370502 CAAAAAATAAATCAATTTATAAAAAATAAAATAAAAAATTTTTAGAATAGCAAAACGGCGTCATT
1 CAAAAAATAAATCAATTTATAAATAATATAA-AAAAAA--TTTAGCATAGCAAAACGGCGTCATT
20370567 TTGTTCAAAATGAAAA
63 TTGTTCAAAAT-AAAA
20370583 ATTCTTTGCC
Statistics
Matches: 137, Mismatches: 29, Indels: 13
0.77 0.16 0.07
Matches are distributed among these distances:
91 10 0.07
92 78 0.57
93 2 0.01
94 43 0.31
95 4 0.03
ACGTcount: A:0.51, C:0.11, G:0.12, T:0.27
Consensus pattern (91 bp):
CAAAAAATAAATCAATTTATAAATAATATAAAAAAAATTTAGCATAGCAAAACGGCGTCATTTTG
TTCAAAATAAAATAGCGGCGTTTTTT
Found at i:20370939 original size:46 final size:48
Alignment explanation
Indices: 20370872--20370973 Score: 172
Period size: 46 Copynumber: 2.1 Consensus size: 48
20370862 AAAAATGAAA
*
20370872 TAAAAACACTAAAATTTTTAATTTTATCTAATTTTTATAAATATTAC-T
1 TAAAAA-ACTAAAATTTTTAATTTTATCTAATTTTTATAAATATAACTT
20370920 TAAAAAACT-AAATTTTTAATTTTATCTAATTTTTATAAATATAACTT
1 TAAAAAACTAAAATTTTTAATTTTATCTAATTTTTATAAATATAACTT
20370967 TAAAAAA
1 TAAAAAA
20370974 TCTATGTATT
Statistics
Matches: 52, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
46 35 0.67
47 11 0.21
48 6 0.12
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.46
Consensus pattern (48 bp):
TAAAAAACTAAAATTTTTAATTTTATCTAATTTTTATAAATATAACTT
Found at i:20374692 original size:23 final size:22
Alignment explanation
Indices: 20374640--20374692 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
20374630 TCCACGTCTT
*
20374640 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
20374662 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
20374685 TTTCTTTT
1 TTTCTTTT
20374693 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:20379960 original size:3 final size:3
Alignment explanation
Indices: 20379954--20379992 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
20379944 TGAAGAAGAA
* *
20379954 GAT GAT GAT GAT GAT GAT GAT GAT GAA GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
20379993 CCATTTCCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.38, C:0.00, G:0.33, T:0.28
Consensus pattern (3 bp):
GAT
Found at i:20380373 original size:44 final size:43
Alignment explanation
Indices: 20380323--20380422 Score: 121
Period size: 44 Copynumber: 2.3 Consensus size: 43
20380313 ACGGTGTTTT
** *
20380323 TAGCGGCGTTTGTAATCAAAGCG-TCGCTAAAGGTCTTTGATCTA
1 TAGCGGCGTTTGTAAGAAAAGCGCT-GCTAAAGGTC-TTGAGCTA
** *
20380367 TAGCGGCGTTTGTGGGAAAAGTGCTGCTAAAGGTCTTGAGCTA
1 TAGCGGCGTTTGTAAGAAAAGCGCTGCTAAAGGTCTTGAGCTA
20380410 TAGCGGCGTTTGT
1 TAGCGGCGTTTGT
20380423 GTAGAAGTGC
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
43 20 0.41
44 28 0.57
45 1 0.02
ACGTcount: A:0.22, C:0.16, G:0.31, T:0.31
Consensus pattern (43 bp):
TAGCGGCGTTTGTAAGAAAAGCGCTGCTAAAGGTCTTGAGCTA
Found at i:20380453 original size:42 final size:43
Alignment explanation
Indices: 20380347--20380557 Score: 183
Period size: 43 Copynumber: 4.7 Consensus size: 43
20380337 ATCAAAGCGT
*
20380347 CGCTAAAGGTCTTTGATCTATAGCGGCGTTTGTGGGAAAAGTGC
1 CGCTAAAGGTC-CTGATCTATAGCGGCGTTTGTGGGAAAAGTGC
* * * * *
20380391 TGCTAAAGGTCTTGAGCTATAGCGGCGTTTGT-GTAGAAGTGC
1 CGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAAAAGTGC
* *
20380433 CGCTATAGGTCCTGATCTATAGCGGTCTATAGCGGCGTTTGTGGGAAAAGCGC
1 CGCTAAAGGTCCTG------A----TCTATAGCGGCGTTTGTGGGAAAAGTGC
* * * * *
20380486 AGCTAAAGGTCCTAACCTATAGCGGCGTTTGTGGAAAAAGCGC
1 CGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAAAAGTGC
*
20380529 CGCTAAAGGTCATGATCTA-AGCGGCGTTT
1 CGCTAAAGGTCCTGATCTATAGCGGCGTTT
20380558 ATTTATAAAA
Statistics
Matches: 136, Mismatches: 20, Indels: 24
0.76 0.11 0.13
Matches are distributed among these distances:
42 29 0.21
43 61 0.45
44 10 0.07
47 1 0.01
48 1 0.01
52 16 0.12
53 18 0.13
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (43 bp):
CGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAAAAGTGC
Found at i:20380552 original size:95 final size:95
Alignment explanation
Indices: 20380363--20380552 Score: 274
Period size: 95 Copynumber: 2.0 Consensus size: 95
20380353 AGGTCTTTGA
* * * * * * *
20380363 TCTATAGCGGCGTTTGTGGGAAAAGTGCTGCTAAAGGTCTTGAGCTATAGCGGCGTTTGTGTAGA
1 TCTATAGCGGCGTTTGTGGGAAAAGCGCAGCTAAAGGTCCTAACCTATAGCGGCGTTTGTGAAAA
* * *
20380428 AGTGCCGCTATAGGTCCTGATCTATAGCGG
66 AGCGCCGCTAAAGGTCATGATCTATAGCGG
20380458 TCTATAGCGGCGTTTGTGGGAAAAGCGCAGCTAAAGGTCCTAACCTATAGCGGCGTTTGTGGAAA
1 TCTATAGCGGCGTTTGTGGGAAAAGCGCAGCTAAAGGTCCTAACCTATAGCGGCGTTTGT-GAAA
20380523 AAGCGCCGCTAAAGGTCATGATCTA-AGCGG
65 AAGCGCCGCTAAAGGTCATGATCTATAGCGG
20380553 CGTTTATTTA
Statistics
Matches: 84, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
95 60 0.71
96 24 0.29
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (95 bp):
TCTATAGCGGCGTTTGTGGGAAAAGCGCAGCTAAAGGTCCTAACCTATAGCGGCGTTTGTGAAAA
AGCGCCGCTAAAGGTCATGATCTATAGCGG
Found at i:20384316 original size:13 final size:13
Alignment explanation
Indices: 20384298--20384322 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20384288 AGAAGAATGG
20384298 AAAAAAGGAAATA
1 AAAAAAGGAAATA
20384311 AAAAAAGGAAAT
1 AAAAAAGGAAAT
20384323 GAAGTAAAAA
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:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (13 bp):
AAAAAAGGAAATA
Found at i:20385445 original size:24 final size:25
Alignment explanation
Indices: 20385418--20385466 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 25
20385408 TTTTTTTAAT
20385418 TGTTTTTAATTG-TTTCCTTTTTTC
1 TGTTTTTAATTGTTTTCCTTTTTTC
20385442 TGTTTTTAATTGTTTTTCCTTTTTT
1 TGTTTTTAATTG-TTTTCCTTTTTT
20385467 TATTATTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 12 0.52
26 11 0.48
ACGTcount: A:0.08, C:0.10, G:0.08, T:0.73
Consensus pattern (25 bp):
TGTTTTTAATTGTTTTCCTTTTTTC
Found at i:20385486 original size:22 final size:20
Alignment explanation
Indices: 20385454--20385504 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
20385444 TTTTTAATTG
* *
20385454 TTTTTCCTTTTTTTAT-TAT
1 TTTTTTCTTTTTTTTTCTAT
20385473 TTGGTTTTCTTTTTTTTTCTAT
1 TT--TTTTCTTTTTTTTTCTAT
20385495 TTTTTTCTTT
1 TTTTTTCTTT
20385505 ATTATTTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 2 0.07
20 8 0.30
21 12 0.44
22 5 0.19
ACGTcount: A:0.06, C:0.10, G:0.04, T:0.80
Consensus pattern (20 bp):
TTTTTTCTTTTTTTTTCTAT
Found at i:20389495 original size:25 final size:25
Alignment explanation
Indices: 20389440--20389526 Score: 95
Period size: 25 Copynumber: 3.5 Consensus size: 25
20389430 CAGGTCGTAT
* * *
20389440 GAGCTTACCGTTACTCAGCTCGCAT
1 GAGCTTACCGTTATTCAGCTCGGAG
* * *
20389465 GTGCTTACCATTATTTAGCTCGGAG
1 GAGCTTACCGTTATTCAGCTCGGAG
*
20389490 GAGCTTATCGTTATTCAGC-CTGGAG
1 GAGCTTACCGTTATTCAGCTC-GGAG
20389515 GAGCTTACCGTT
1 GAGCTTACCGTT
20389527 TATAGCTCGT
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
24 1 0.02
25 49 0.98
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.32
Consensus pattern (25 bp):
GAGCTTACCGTTATTCAGCTCGGAG
Found at i:20396386 original size:35 final size:35
Alignment explanation
Indices: 20396336--20396411 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 35
20396326 CGCCATTACA
* *
20396336 GAAA-AAAGACAAACAAATAAAAAAATAGAAAAAG
1 GAAATAAAGAAAAACAAATAAAAAAACAGAAAAAG
*
20396370 GAAATAAAGAAAAACAAATAAAAAAACATAAAAAG
1 GAAATAAAGAAAAACAAATAAAAAAACAGAAAAAG
20396405 GACAATA
1 GA-AATA
20396412 GGCAGCAGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
34 4 0.11
35 29 0.78
36 4 0.11
ACGTcount: A:0.75, C:0.07, G:0.11, T:0.08
Consensus pattern (35 bp):
GAAATAAAGAAAAACAAATAAAAAAACAGAAAAAG
Found at i:20398364 original size:23 final size:23
Alignment explanation
Indices: 20398338--20398429 Score: 80
Period size: 23 Copynumber: 3.9 Consensus size: 23
20398328 AGACTCACCA
20398338 CAGCTTGTATGAGCTTACCGTTT
1 CAGCTTGTATGAGCTTACCGTTT
* *
20398361 CAGC-TCTACAGAGCTTACCGTTT
1 CAGCTTGTA-TGAGCTTACCGTTT
* *
20398384 CAGCTCG-ATACAGCTTACCGTTTAT
1 CAGCTTGTAT-GAGCTTACCG-TT-T
*
20398409 CAGCTTGGAATGAGCTTACCG
1 CAGCTT-GTATGAGCTTACCG
20398430 ATCATGGCTC
Statistics
Matches: 54, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
22 3 0.06
23 31 0.57
24 2 0.04
25 6 0.11
26 10 0.19
27 2 0.04
ACGTcount: A:0.22, C:0.26, G:0.21, T:0.32
Consensus pattern (23 bp):
CAGCTTGTATGAGCTTACCGTTT
Found at i:20398413 original size:25 final size:23
Alignment explanation
Indices: 20398349--20398406 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
20398339 AGCTTGTATG
* *
20398349 AGCTTACCGTTTCAGCTCTACAG
1 AGCTTACCGTTTCAGCTCGACAC
*
20398372 AGCTTACCGTTTCAGCTCGATAC
1 AGCTTACCGTTTCAGCTCGACAC
20398395 AGCTTACCGTTT
1 AGCTTACCGTTT
20398407 ATCAGCTTGG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.21, C:0.29, G:0.17, T:0.33
Consensus pattern (23 bp):
AGCTTACCGTTTCAGCTCGACAC
Found at i:20416683 original size:14 final size:15
Alignment explanation
Indices: 20416664--20416707 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
20416654 TGCAACCCAT
20416664 ATTTATTT-ATTTTA
1 ATTTATTTAATTTTA
20416678 ATTTATTTAATTTTGA
1 ATTTATTTAATTTT-A
*
20416694 TTTTAGTTTAATTT
1 ATTTA-TTTAATTT
20416708 ATGTTGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 8 0.31
15 5 0.19
16 5 0.19
17 8 0.31
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (15 bp):
ATTTATTTAATTTTA
Found at i:20416714 original size:21 final size:19
Alignment explanation
Indices: 20416663--20416714 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 19
20416653 ATGCAACCCA
20416663 TATTTATTT-ATTTTAATT
1 TATTTATTTGATTTTAATT
*
20416681 TATTTAATTTTGATTTTAGTT
1 TATTT-A-TTTGATTTTAATT
20416702 TAATTTATGTTGA
1 T-ATTTAT-TTGA
20416715 AAATTAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 1 0.04
20 4 0.14
21 14 0.50
22 4 0.14
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (19 bp):
TATTTATTTGATTTTAATT
Found at i:20417677 original size:41 final size:41
Alignment explanation
Indices: 20417618--20417981 Score: 532
Period size: 41 Copynumber: 8.9 Consensus size: 41
20417608 TGAGTTTTTG
20417618 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
** *
20417659 TAGCCTTTAGCGGCGTTTTTGAATAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
* *
20417700 TGGCCTTTAGCGGCGTTTTTGAATAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
* * *
20417741 GGGCCTTTAGCGGCATTTTTGAAGAAGCGCCACTAGTGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
* *
20417782 GGGCCTTTAGCGGCGTTTTTGAAGAAGCACCGCTAGTGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
20417823 GGGCCTTTAGC-GCGTTTTTGAAGAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
20417863 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
* ** * * *
20417904 AGATCTTTAGCGGTGTTTTTAAAAAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
* * * * *
20417945 TGGCCTTTAGCAGCGTTTTTAAAAAAACGCCGCTAAT
1 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAAT
20417982 AATATTTTTT
Statistics
Matches: 296, Mismatches: 26, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 38 0.13
41 258 0.87
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.29
Consensus pattern (41 bp):
GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
Found at i:20418709 original size:15 final size:16
Alignment explanation
Indices: 20418689--20418720 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
20418679 TTAAGATCAA
20418689 TTATGGATTT-AGGGT
1 TTATGGATTTAAGGGT
20418704 TTATGGATTTAAGGGT
1 TTATGGATTTAAGGGT
20418720 T
1 T
20418721 AGAGGTTAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.47
Consensus pattern (16 bp):
TTATGGATTTAAGGGT
Found at i:20419246 original size:22 final size:22
Alignment explanation
Indices: 20419198--20419248 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
20419188 AGATTTAAGG
* * *
20419198 TTTAGGGGTTAGGAGTTAGGGG
1 TTTAGGGGTTAAGAGCTAGGGA
*
20419220 GTTAGGGGTTAAGAGCTAGGGA
1 TTTAGGGGTTAAGAGCTAGGGA
20419242 TTTAGGG
1 TTTAGGG
20419249 TTTCAAGGGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.02, G:0.47, T:0.29
Consensus pattern (22 bp):
TTTAGGGGTTAAGAGCTAGGGA
Found at i:20419813 original size:13 final size:13
Alignment explanation
Indices: 20419795--20419819 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20419785 ATAGTTTAGG
20419795 TAGTGGCGTTTTT
1 TAGTGGCGTTTTT
20419808 TAGTGGCGTTTT
1 TAGTGGCGTTTT
20419820 CAGCAAAAAC
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:0.08, C:0.08, G:0.32, T:0.52
Consensus pattern (13 bp):
TAGTGGCGTTTTT
Found at i:20422233 original size:252 final size:252
Alignment explanation
Indices: 20421788--20422292 Score: 983
Period size: 252 Copynumber: 2.0 Consensus size: 252
20421778 GAATGGCTGC
20421788 TATGTTATTGGAAACAAAGGAATTTCTCTCCATTTTAGTATGATTTCAATTTATCAAAGCTGTGG
1 TATGTTATTGGAAACAAAGGAATTTCTCTCCATTTTAGTATGATTTCAATTTATCAAAGCTGTGG
20421853 CCTTTTGTATCAAAGTAGATAACTTAGTTCTTCTATTTTCGGTTGAAATGAATTTTGTTGAAGAG
66 CCTTTTGTATCAAAGTAGATAACTTAGTTCTTCTATTTTCGGTTGAAATGAATTTTGTTGAAGAG
20421918 AGTTGAGATGCTGAGAGCTGTGACGAGGTGGTTATGATGGTGGCAATATGTCATGTACATGTTCT
131 AGTTGAGATGCTGAGAGCTGTGACGAGGTGGTTATGATGGTGGCAATATGTCATGTACATGTTCT
20421983 CTAGTGTGCCATACCTTATTCTGTAGGTTGTTAAGTAAAATTATGGGAAACTTGATT
196 CTAGTGTGCCATACCTTATTCTGTAGGTTGTTAAGTAAAATTATGGGAAACTTGATT
20422040 TATGTTATTGGAAACAAAGGAATTTCTCTCCATTTTAGTATGATTTCAATTTATCAAAGCTGTGG
1 TATGTTATTGGAAACAAAGGAATTTCTCTCCATTTTAGTATGATTTCAATTTATCAAAGCTGTGG
*
20422105 CCTTTTGTATCAATGTAGATAACTTAGTTCTTCTATTTTCGGTTGAAATGAATTTTGTTGAAGAG
66 CCTTTTGTATCAAAGTAGATAACTTAGTTCTTCTATTTTCGGTTGAAATGAATTTTGTTGAAGAG
*
20422170 AGTTGAGATGCTGAGAGTTGTGACGAGGTGGTTATGATGGTGGCAATATGTCATGTACATGTTCT
131 AGTTGAGATGCTGAGAGCTGTGACGAGGTGGTTATGATGGTGGCAATATGTCATGTACATGTTCT
*
20422235 CTAGTGTGCCATACCTTATTCTGTAGGTTGTTAAGTAAAATTATGGGCAACTTGATT
196 CTAGTGTGCCATACCTTATTCTGTAGGTTGTTAAGTAAAATTATGGGAAACTTGATT
20422292 T
1 T
20422293 GATTGGTGGT
Statistics
Matches: 250, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
252 250 1.00
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.39
Consensus pattern (252 bp):
TATGTTATTGGAAACAAAGGAATTTCTCTCCATTTTAGTATGATTTCAATTTATCAAAGCTGTGG
CCTTTTGTATCAAAGTAGATAACTTAGTTCTTCTATTTTCGGTTGAAATGAATTTTGTTGAAGAG
AGTTGAGATGCTGAGAGCTGTGACGAGGTGGTTATGATGGTGGCAATATGTCATGTACATGTTCT
CTAGTGTGCCATACCTTATTCTGTAGGTTGTTAAGTAAAATTATGGGAAACTTGATT
Found at i:20423442 original size:28 final size:28
Alignment explanation
Indices: 20423400--20423453 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
20423390 ATTCTTTTCT
20423400 TTTGACAAAGAACTT-GAGGTTGAACTGG
1 TTTGACAAAGAACTTGGA-GTTGAACTGG
* *
20423428 TTTGACTAAGGACTTGGAGTTGAACT
1 TTTGACAAAGAACTTGGAGTTGAACT
20423454 AATTTGATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 21 0.91
29 2 0.09
ACGTcount: A:0.30, C:0.11, G:0.28, T:0.31
Consensus pattern (28 bp):
TTTGACAAAGAACTTGGAGTTGAACTGG
Found at i:20423459 original size:28 final size:28
Alignment explanation
Indices: 20423400--20423460 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
20423390 ATTCTTTTCT
**
20423400 TTTGACAAAGAACTTGAGGTTGAACTGG
1 TTTGACAAAGAACTTGAGGTTGAACTAA
* *
20423428 TTTGACTAAGGACTTG-GAGTTGAACTAA
1 TTTGACAAAGAACTTGAG-GTTGAACTAA
20423456 TTTGA
1 TTTGA
20423461 TTCTTGTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 1 0.04
28 27 0.96
ACGTcount: A:0.31, C:0.10, G:0.26, T:0.33
Consensus pattern (28 bp):
TTTGACAAAGAACTTGAGGTTGAACTAA
Found at i:20425278 original size:42 final size:42
Alignment explanation
Indices: 20425114--20425318 Score: 248
Period size: 43 Copynumber: 4.8 Consensus size: 42
20425104 GTTATATTTT
* * * *
20425114 TAGTGGCGTTTTTGTGAGAAGCGCCGCTAAAGGTATTGAACTA
1 TAGTGGCGTTTGTG-GAAAAGCGCCGCTAAAGGTCTTGAGCTA
* * *
20425157 TAGCGGCGTTTGTGGTAAAAGCGCTGCTAAAGCTCTTGAGCTA
1 TAGTGGCGTTTGTGG-AAAAGCGCCGCTAAAGGTCTTGAGCTA
* * * *
20425200 TAGCGGCGTTTGTGAGAAAAGCGTCGCTAAATGTCTTGGGCTA
1 TAGTGGCGTTTGTG-GAAAAGCGCCGCTAAAGGTCTTGAGCTA
*
20425243 TAGTGGCGTTTGTGGAAAAGTGCCGCTAAAGGTCTTGAGCTA
1 TAGTGGCGTTTGTGGAAAAGCGCCGCTAAAGGTCTTGAGCTA
* * *
20425285 TAGTGGCGTTTTTGGGAAAGTGCCGCTAAAGGTC
1 TAGTGGCGTTTGTGGAAAAGCGCCGCTAAAGGTC
20425319 AATGTCTTTA
Statistics
Matches: 141, Mismatches: 19, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
42 57 0.40
43 83 0.59
44 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.32, T:0.29
Consensus pattern (42 bp):
TAGTGGCGTTTGTGGAAAAGCGCCGCTAAAGGTCTTGAGCTA
Found at i:20425346 original size:85 final size:84
Alignment explanation
Indices: 20425114--20425352 Score: 257
Period size: 85 Copynumber: 2.8 Consensus size: 84
20425104 GTTATATTTT
*
20425114 TAGTGGCGTTTTTGTGAGAAGCGCCGCTAAAGGT-ATTGAACTATAGCGGCGTTTGTGGTAAAAG
1 TAGTGGCGTTTTTGGGA-AAGCGCCGCTAAAGGTCATTG-ACTATAGCGGCGTTTGTGG-AAAAG
*
20425178 CGCTGCTAAAGCTCTTGAGCTA
63 CGCCGCTAAAGCTCTTGAGCTA
* * * * * * * *
20425200 TAGCGGCGTTTGTGAGAAAAGCGTCGCTAAATGTC-TTGGGCTATAGTGGCGTTTGTGGAAAAGT
1 TAGTGGCGTTTTTG-GGAAAGCGCCGCTAAAGGTCATT-GACTATAGCGGCGTTTGTGGAAAAGC
*
20425264 GCCGCTAAAGGTCTTGAGCTA
64 GCCGCTAAAGCTCTTGAGCTA
* * * * * *
20425285 TAGTGGCGTTTTTGGGAAAGTGCCGCTAAAGGTCAATGTCTTTAGCGGCGATTTCTAGAAAAGCG
1 TAGTGGCGTTTTTGGGAAAGCGCCGCTAAAGGTCATTGACTATAGCGGCG-TTTGTGGAAAAGCG
20425350 CCG
65 CCG
20425353 TTATAGCTTA
Statistics
Matches: 124, Mismatches: 24, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
84 26 0.21
85 51 0.41
86 45 0.36
87 2 0.02
ACGTcount: A:0.24, C:0.16, G:0.31, T:0.28
Consensus pattern (84 bp):
TAGTGGCGTTTTTGGGAAAGCGCCGCTAAAGGTCATTGACTATAGCGGCGTTTGTGGAAAAGCGC
CGCTAAAGCTCTTGAGCTA
Found at i:20427881 original size:12 final size:12
Alignment explanation
Indices: 20427864--20427892 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
20427854 GAGTCGTGAG
20427864 CACGACTATTAT
1 CACGACTATTAT
20427876 CACGACTATTAT
1 CACGACTATTAT
20427888 CACGA
1 CACGA
20427893 TAGTAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.34, C:0.28, G:0.10, T:0.28
Consensus pattern (12 bp):
CACGACTATTAT
Found at i:20439557 original size:16 final size:15
Alignment explanation
Indices: 20439535--20439566 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
20439525 ACCCGAAAAC
20439535 CCCAAAAAAAAAGAA
1 CCCAAAAAAAAAGAA
*
20439550 CCCAAAAACAAAGAA
1 CCCAAAAAAAAAGAA
20439565 CC
1 CC
20439567 TTCAAAACGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.28, G:0.06, T:0.00
Consensus pattern (15 bp):
CCCAAAAAAAAAGAA
Found at i:20450248 original size:28 final size:29
Alignment explanation
Indices: 20450208--20450306 Score: 123
Period size: 28 Copynumber: 3.5 Consensus size: 29
20450198 ATAATAAGCC
*
20450208 CGCACACTTAGTGCTTA-ATAGTCGAACT
1 CGCACACTTAGTGCTTACATAATCGAACT
*
20450236 CGCACACTTAGTGC-TATATAATCGAACT
1 CGCACACTTAGTGCTTACATAATCGAACT
* * *
20450264 CGCACACTTAGTGCTATACA-ATTTGAACC
1 CGCACACTTAGTGCT-TACATAATCGAACT
20450293 CGCACACTTAGTGC
1 CGCACACTTAGTGC
20450307 CAATCTCATG
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.03
28 38 0.60
29 20 0.32
30 3 0.05
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCTTACATAATCGAACT
Found at i:20452193 original size:13 final size:13
Alignment explanation
Indices: 20452175--20452200 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20452165 TACAACAAAT
20452175 TTAAGTAGAATCA
1 TTAAGTAGAATCA
20452188 TTAAGTAGAATCA
1 TTAAGTAGAATCA
20452201 ACTTTTGCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (13 bp):
TTAAGTAGAATCA
Found at i:20460430 original size:37 final size:35
Alignment explanation
Indices: 20460384--20460453 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 35
20460374 TTCTAGAAAT
20460384 AATATTATTTTAATAGT-TTAATATTAAATTTAATTG
1 AATATTATTTTAATAGTATT-ATATT-AATTTAATTG
*
20460420 AATATTTATTTTAATAGTATTTTATTAATTTAAT
1 AATA-TTATTTTAATAGTATTATATTAATTTAAT
20460454 ATTAAAGTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 12 0.39
37 17 0.55
38 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (35 bp):
AATATTATTTTAATAGTATTATATTAATTTAATTG
Found at i:20460484 original size:51 final size:48
Alignment explanation
Indices: 20460383--20460485 Score: 118
Period size: 48 Copynumber: 2.1 Consensus size: 48
20460373 ATTCTAGAAA
* * *
20460383 TAATATTATTTTAATAGTTTAATATTAAATTTAATTGAATATTTATTT
1 TAATAGTATTTTAATAATTTAATATTAAATTTAATTGAATATTTAATT
* *
20460431 TAATAGTATTTTATTAATTTAATATTAAAGTGATT-ATCTTAATATTTAATT
1 TAATAGTATTTTAATAATTTAATATTAAA-T--TTAAT-TGAATATTTAATT
20460482 TAAT
1 TAAT
20460486 TTAATGTTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
48 26 0.57
49 1 0.02
50 2 0.04
51 17 0.37
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (48 bp):
TAATAGTATTTTAATAATTTAATATTAAATTTAATTGAATATTTAATT
Found at i:20460560 original size:62 final size:59
Alignment explanation
Indices: 20460469--20460585 Score: 146
Period size: 62 Copynumber: 1.9 Consensus size: 59
20460459 AGTGATTATC
* * * *
20460469 TTAATATTTAATTTAATTTAATGTTTATCTTGTAGATAAATATTCTATTATTTTAATAAGAT
1 TTAATATTTAATTTAATCTAATATTTATC-T-TA-ATAAATATTATATTAATTTAATAAGAT
*
20460531 TTAATA-TTATATTTCATCTAATATTTATCTTAATAAATATTATATTAATTTAATA
1 TTAATATTTA-ATTTAATCTAATATTTATCTTAATAAATATTATATTAATTTAATA
20460586 TTAAAGTGAT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
59 21 0.43
60 2 0.04
61 4 0.08
62 22 0.45
ACGTcount: A:0.39, C:0.04, G:0.03, T:0.53
Consensus pattern (59 bp):
TTAATATTTAATTTAATCTAATATTTATCTTAATAAATATTATATTAATTTAATAAGAT
Found at i:20460804 original size:23 final size:23
Alignment explanation
Indices: 20460757--20460806 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
20460747 TATTTAGAGA
*
20460757 AATTGTAAAATTACTCCACTAGT
1 AATTGTAAAATTACTACACTAGT
* *
20460780 AATTGTAAAATTACTATACTGGT
1 AATTGTAAAATTACTACACTAGT
20460803 AATT
1 AATT
20460807 TTTGTGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (23 bp):
AATTGTAAAATTACTACACTAGT
Found at i:20466806 original size:32 final size:32
Alignment explanation
Indices: 20466770--20466833 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
20466760 AAGCACACCA
*
20466770 ACAACACATGCCAATTCAATTAAACACAATTC
1 ACAACACATACCAATTCAATTAAACACAATTC
*
20466802 ACAACACATACCAGTTCAATTAAACACAATTC
1 ACAACACATACCAATTCAATTAAACACAATTC
20466834 GTTTGAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.47, C:0.28, G:0.03, T:0.22
Consensus pattern (32 bp):
ACAACACATACCAATTCAATTAAACACAATTC
Found at i:20467132 original size:26 final size:26
Alignment explanation
Indices: 20467096--20467159 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 26
20467086 TACATATATA
20467096 CTCACACGAGCTGTGAAAAGAGTATG
1 CTCACACGAGCTGTGAAAAGAGTATG
* * * * *
20467122 CTCACATGAGCTGTTAAATGGGTCTG
1 CTCACACGAGCTGTGAAAAGAGTATG
*
20467148 CTCACACTAGCT
1 CTCACACGAGCT
20467160 ATGAGTCGGA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.25
Consensus pattern (26 bp):
CTCACACGAGCTGTGAAAAGAGTATG
Found at i:20469151 original size:15 final size:15
Alignment explanation
Indices: 20469131--20469162 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
20469121 CATTTCATTA
*
20469131 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
20469146 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
20469161 TT
1 TT
20469163 TGCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:20470786 original size:12 final size:12
Alignment explanation
Indices: 20470752--20470864 Score: 57
Period size: 12 Copynumber: 9.8 Consensus size: 12
20470742 CTTCCAAAAA
*
20470752 TAATA-TTATTT
1 TAATATTTAATT
20470763 TAATAGTTTAATAT
1 TAATA-TTTAAT-T
20470777 T-ATATTTAATT
1 TAATATTTAATT
20470788 TAATATTT-ATCT
1 TAATATTTAAT-T
*
20470800 TAATA-GT-ATT
1 TAATATTTAATT
20470810 T--TA-TTAATT
1 TAATATTTAATT
**
20470819 TAATA-TTAAAG
1 TAATATTTAATT
20470830 TAACTATCTTAATAT
1 TAA-TAT-TTAAT-T
20470845 TAA-ATTTAATT
1 TAATATTTAATT
*
20470856 TAATGTTTA
1 TAATATTTA
20470865 TCTTGTACAT
Statistics
Matches: 81, Mismatches: 8, Indels: 25
0.71 0.07 0.22
Matches are distributed among these distances:
8 3 0.04
9 4 0.05
10 2 0.02
11 25 0.31
12 29 0.36
13 9 0.11
14 6 0.07
15 3 0.04
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.54
Consensus pattern (12 bp):
TAATATTTAATT
Found at i:20470805 original size:37 final size:36
Alignment explanation
Indices: 20470752--20470868 Score: 95
Period size: 37 Copynumber: 3.3 Consensus size: 36
20470742 CTTCCAAAAA
*
20470752 TAATATTATTTTAATAGTTTAATATTATATTTAATT
1 TAATATTATCTTAATAGTTTAATATTATATTTAATT
20470788 TAATATTTATCTTAATAG--T-AT-TT-TA-TTAATT
1 TAATA-TTATCTTAATAGTTTAATATTATATTTAATT
*** *
20470819 TAATATTAAAGTAACTA-TCTTAATATTAAATTTAATT
1 TAATATTATCTTAA-TAGT-TTAATATTATATTTAATT
*
20470856 TAATGTTTATCTT
1 TAAT-ATTATCTT
20470869 GTACATAAAC
Statistics
Matches: 62, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
30 6 0.10
31 13 0.21
32 2 0.03
33 3 0.05
34 4 0.06
35 3 0.05
36 6 0.10
37 21 0.34
38 4 0.06
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.55
Consensus pattern (36 bp):
TAATATTATCTTAATAGTTTAATATTATATTTAATT
Found at i:20480297 original size:21 final size:22
Alignment explanation
Indices: 20480255--20480296 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
20480245 ACAAATTTAA
*
20480255 TTGCACAAAATCTATTAAAAAT
1 TTGCACAAAATCAATTAAAAAT
20480277 TTGCACAAAAAT-AATTAAAA
1 TTGCAC-AAAATCAATTAAAA
20480297 TATGCCAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.55, C:0.12, G:0.05, T:0.29
Consensus pattern (22 bp):
TTGCACAAAATCAATTAAAAAT
Found at i:20488166 original size:25 final size:23
Alignment explanation
Indices: 20488137--20488235 Score: 67
Period size: 25 Copynumber: 4.1 Consensus size: 23
20488127 CCACATAGAA
20488137 ATTTTGATTTTTTATATTTAAAAT
1 ATTTT-ATTTTTTATATTTAAAAT
* * *
20488161 GATTTTTTATTTTTAAATTTTAAAT
1 -ATTTTAT-TTTTTATATTTAAAAT
*
20488186 AATTTT-TCATTTTTATACTTTAAATT
1 -ATTTTAT--TTTTTATA-TTTAAAAT
* *
20488212 TTTTTATGTTTT-TATTTAAAAT
1 ATTTTATTTTTTATATTTAAAAT
20488234 AT
1 AT
20488236 GAAAAATTAA
Statistics
Matches: 59, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
22 8 0.14
23 2 0.03
24 6 0.10
25 36 0.61
26 7 0.12
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (23 bp):
ATTTTATTTTTTATATTTAAAAT
Found at i:20488178 original size:18 final size:19
Alignment explanation
Indices: 20488141--20488177 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
20488131 ATAGAAATTT
20488141 TGATTTTTTATATTTAAAA
1 TGATTTTTTATATTTAAAA
*
20488160 TGATTTTTTATTTTTAAA
1 TGATTTTTTATATTTAAA
20488178 TTTTAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (19 bp):
TGATTTTTTATATTTAAAA
Found at i:20491936 original size:30 final size:31
Alignment explanation
Indices: 20491886--20491947 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
20491876 TTGTACCAAC
*
20491886 ATATACACGTACCAAGATCAAAATTTAGCATT
1 ATATACAC-TACCAAAATCAAAATTTAGCATT
*
20491918 ATATACA-TACCAAAATCAACATTTAGCATT
1 ATATACACTACCAAAATCAAAATTTAGCATT
20491948 CAACCAAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 21 0.75
32 7 0.25
ACGTcount: A:0.45, C:0.19, G:0.06, T:0.29
Consensus pattern (31 bp):
ATATACACTACCAAAATCAAAATTTAGCATT
Found at i:20492075 original size:17 final size:16
Alignment explanation
Indices: 20492049--20492080 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
20492039 TGATAGATCT
20492049 CCGACGAGCTTCCAAA
1 CCGACGAGCTTCCAAA
20492065 CCGATCGAGCTTCCAA
1 CCGA-CGAGCTTCCAA
20492081 TTATCTATAA
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:0.28, C:0.38, G:0.19, T:0.16
Consensus pattern (16 bp):
CCGACGAGCTTCCAAA
Found at i:20495579 original size:34 final size:33
Alignment explanation
Indices: 20495503--20495585 Score: 100
Period size: 34 Copynumber: 2.5 Consensus size: 33
20495493 TGATTCAATA
* *
20495503 ACAGT-TCAGT-TCAGTTGGGTCTTAGCCCATT
1 ACAGTATCAGTATCAGTTGGGCCTCAGCCCATT
20495534 ACAGTATCAGTATCAGTGTGGGCCTCAGCCCATT
1 ACAGTATCAGTATCAGT-TGGGCCTCAGCCCATT
*
20495568 ACAGTGA-CAGTAACAGTT
1 ACAGT-ATCAGTATCAGTT
20495586 TAGACATGCA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
31 5 0.11
32 5 0.11
33 6 0.13
34 28 0.62
35 1 0.02
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (33 bp):
ACAGTATCAGTATCAGTTGGGCCTCAGCCCATT
Found at i:20499448 original size:72 final size:72
Alignment explanation
Indices: 20499331--20499474 Score: 252
Period size: 72 Copynumber: 2.0 Consensus size: 72
20499321 CCTCGCCGTT
*
20499331 ACACCCCATTCGATCTAACTATCTGCAGTGTTAAAAAGGGGTGTGTGAGCTCTTGTAAACTTAGT
1 ACACCCCATTCGATCTAACTATCTGCAGTGTTAAAAAGGGGTGTGTGAGCTCTTGTAAACTCAGT
20499396 GAATATA
66 GAATATA
* * *
20499403 ACACCCCATTCGGTCTAACTATCTGCAGTGTTAAAAATGGGTGTGTGAGCTCTTGTGAACTCAGT
1 ACACCCCATTCGATCTAACTATCTGCAGTGTTAAAAAGGGGTGTGTGAGCTCTTGTAAACTCAGT
20499468 GAATATA
66 GAATATA
20499475 TAGGAAAGAA
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.31
Consensus pattern (72 bp):
ACACCCCATTCGATCTAACTATCTGCAGTGTTAAAAAGGGGTGTGTGAGCTCTTGTAAACTCAGT
GAATATA
Found at i:20515652 original size:3 final size:3
Alignment explanation
Indices: 20515639--20515710 Score: 87
Period size: 3 Copynumber: 24.3 Consensus size: 3
20515629 TTTAGTCTCG
* *
20515639 TTA TT- TTA TTA TTA TTA -AA TTAA TTA GCTA -TA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA -TTA TTA TTA TTA TTA TTA
20515683 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
20515711 GATCATTTAC
Statistics
Matches: 61, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
2 5 0.08
3 51 0.84
4 5 0.08
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:20516014 original size:16 final size:16
Alignment explanation
Indices: 20515995--20516030 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
20515985 ATATTTTATA
*
20515995 ATTTATGTATACATAT
1 ATTTATGTATACATAC
*
20516011 ATTTATGTCTACATAC
1 ATTTATGTATACATAC
20516027 ATTT
1 ATTT
20516031 TTTTAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.06, T:0.50
Consensus pattern (16 bp):
ATTTATGTATACATAC
Found at i:20519300 original size:24 final size:24
Alignment explanation
Indices: 20519268--20519315 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
20519258 TGCCTTTGAA
20519268 TCCTTATGGATGATTAAGTTTAAG
1 TCCTTATGGATGATTAAGTTTAAG
20519292 TCCTTATGGATGATTAAGTTTAAG
1 TCCTTATGGATGATTAAGTTTAAG
20519316 GAAGCTTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.42
Consensus pattern (24 bp):
TCCTTATGGATGATTAAGTTTAAG
Found at i:20521880 original size:24 final size:23
Alignment explanation
Indices: 20521824--20521881 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
20521814 AATAAGAATA
20521824 TTATATTATTTTAAAATATATTTT
1 TTAT-TTATTTTAAAATATATTTT
* **
20521848 TGTAATTATTTTAATTTAATATTTT
1 T-TATTTATTTTAAAAT-ATATTTT
20521873 TTATTTATT
1 TTATTTATT
20521882 ATATTTTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 18 0.64
25 10 0.36
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (23 bp):
TTATTTATTTTAAAATATATTTT
Found at i:20521888 original size:15 final size:15
Alignment explanation
Indices: 20521838--20521893 Score: 57
Period size: 14 Copynumber: 4.0 Consensus size: 15
20521828 ATTATTTTAA
*
20521838 AATATA-TTTT-TGT
1 AATATATTTTTATTT
*
20521851 AAT-TATTTTAATTT
1 AATATATTTTTATTT
20521865 AATAT-TTTTTATTT
1 AATATATTTTTATTT
*
20521879 ATTATATTTTTATTT
1 AATATATTTTTATTT
20521894 GTAGTGATCT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
12 2 0.06
13 6 0.17
14 17 0.49
15 10 0.29
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (15 bp):
AATATATTTTTATTT
Found at i:20524611 original size:21 final size:20
Alignment explanation
Indices: 20524578--20524616 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
20524568 TTTTTATATA
*
20524578 TTTTTAAATATAATAATTAT
1 TTTTTAAATATAAAAATTAT
*
20524598 TTTTTAATTCATAAAAATT
1 TTTTTAAAT-ATAAAAATT
20524617 CAATAACTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTTTAAATATAAAAATTAT
Found at i:20524898 original size:3 final size:3
Alignment explanation
Indices: 20524890--20524920 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
20524880 AAAGGAAAGG
20524890 AGA AGA AGA AGA AGA AGA AGA A-A AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
20524921 GAGGAGGAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:20524992 original size:21 final size:20
Alignment explanation
Indices: 20524959--20524997 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
20524949 TGCCGAAAAA
20524959 AGAAAAGAAAAAGAGAGAACG
1 AGAAAAGAAAAAG-GAGAACG
* *
20524980 AGAATAGAGAAAGGAGAA
1 AGAAAAGAAAAAGGAGAA
20524998 AGAAAGAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.64, C:0.03, G:0.31, T:0.03
Consensus pattern (20 bp):
AGAAAAGAAAAAGGAGAACG
Found at i:20525403 original size:76 final size:79
Alignment explanation
Indices: 20525198--20525429 Score: 235
Period size: 76 Copynumber: 2.9 Consensus size: 79
20525188 GTTTAGTTAT
*
20525198 TAATAATTATTGTTA-CTTAGTATTATTGTTAGTAAAAAACTAATATTATTATTATGGTTAGTTA
1 TAATTATTATTGTTAGC-TAGTATTATTGTTAGTAAAAAACT-ATATTATTATTA-GGTTAGTTA
20525262 TTAGGATTAGTAAAAACCC
63 TT--GATTAGTAAAAACCC
* * *** * *
20525281 TAATTATTATT-TTAGTTAGTATGATTGTTAGTTTTTACACTATATTATTGTTA-GTTA-TTATT
1 TAATTATTATTGTTAGCTAGTATTATTGTTAG-TAAAAAACTATATTATTATTAGGTTAGTTATT
*
20525343 -TTTAGT-AAAACCC
65 GATTAGTAAAAACCC
*
20525356 TAATTATTATTGTTAGCTAGTATTATTTTTAGTAAAAAACTAGTATTATTATT-GTGTTAGTTAT
1 TAATTATTATTGTTAGCTAGTATTATTGTTAGTAAAAAACTA-TATTATTATTAG-GTTAGTTAT
20525420 TAGGATTAGT
64 T--GATTAGT
20525430 GGTTAAATGT
Statistics
Matches: 121, Mismatches: 18, Indels: 22
0.75 0.11 0.14
Matches are distributed among these distances:
75 24 0.20
76 31 0.26
77 4 0.03
78 5 0.04
79 5 0.04
80 4 0.03
81 5 0.04
82 28 0.23
83 15 0.12
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.49
Consensus pattern (79 bp):
TAATTATTATTGTTAGCTAGTATTATTGTTAGTAAAAAACTATATTATTATTAGGTTAGTTATTG
ATTAGTAAAAACCC
Found at i:20527899 original size:5 final size:5
Alignment explanation
Indices: 20527891--20527990 Score: 55
Period size: 5 Copynumber: 20.2 Consensus size: 5
20527881 ATTTAAAATA
* *
20527891 TATAT TATAT TATAT T-TACT TA-AT TA-AT AAGTAT GT-TAT TTTAT
1 TATAT TATAT TATAT TATA-T TATAT TATAT TA-TAT -TATAT TATAT
* * * * * * * *
20527935 TATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
20527985 TATAT T
1 TATAT T
20527991 CTTATATATA
Statistics
Matches: 84, Mismatches: 5, Indels: 12
0.83 0.05 0.12
Matches are distributed among these distances:
4 9 0.11
5 73 0.87
6 2 0.02
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (5 bp):
TATAT
Found at i:20527956 original size:15 final size:15
Alignment explanation
Indices: 20527936--20527989 Score: 90
Period size: 15 Copynumber: 3.6 Consensus size: 15
20527926 TTATTTTATT
20527936 ATATAATATAATATA
1 ATATAATATAATATA
20527951 ATATAATATAATATA
1 ATATAATATAATATA
*
20527966 ATATAATATAATATT
1 ATATAATATAATATA
*
20527981 ATATTATAT
1 ATATAATAT
20527990 TCTTATATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 37 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATATAATATAATATA
Found at i:20529134 original size:27 final size:25
Alignment explanation
Indices: 20529078--20529187 Score: 83
Period size: 22 Copynumber: 4.6 Consensus size: 25
20529068 ACTTTAGCGC
**
20529078 GCTCTCTGATTATTAGCACGTTGGT
1 GCTCTCTGATTATTAGCACGTCAGT
20529103 GCTCTCTGA-TATTTAGCACGTCAGT
1 GCTCTCTGATTA-TTAGCACGTCAGT
* *
20529128 GCTCTCTG--T-TTAGCACATCTGT
1 GCTCTCTGATTATTAGCACGTCAGT
* * *
20529150 GCTCTTTG--TA-TAGCACTTTAGT
1 GCTCTCTGATTATTAGCACGTCAGT
20529172 GCTCTCTG-TTCATTAG
1 GCTCTCTGATT-ATTAG
20529188 TGCATAATAA
Statistics
Matches: 71, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
22 35 0.49
23 1 0.01
24 4 0.06
25 31 0.44
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.41
Consensus pattern (25 bp):
GCTCTCTGATTATTAGCACGTCAGT
Found at i:20529142 original size:22 final size:22
Alignment explanation
Indices: 20529090--20529181 Score: 85
Period size: 22 Copynumber: 4.0 Consensus size: 22
20529080 TCTCTGATTA
**
20529090 TTAGCACGTTGGTGCTCTCTGATAT
1 TTAGCACGTCAGTGCTCTCTG---T
20529115 TTAGCACGTCAGTGCTCTCTGT
1 TTAGCACGTCAGTGCTCTCTGT
* * *
20529137 TTAGCACATCTGTGCTCTTTGT
1 TTAGCACGTCAGTGCTCTCTGT
* * *
20529159 ATAGCACTTTAGTGCTCTCTGT
1 TTAGCACGTCAGTGCTCTCTGT
20529181 T
1 T
20529182 CATTAGTGCA
Statistics
Matches: 56, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
22 37 0.66
25 19 0.34
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.41
Consensus pattern (22 bp):
TTAGCACGTCAGTGCTCTCTGT
Found at i:20531178 original size:41 final size:41
Alignment explanation
Indices: 20531076--20531181 Score: 158
Period size: 41 Copynumber: 2.6 Consensus size: 41
20531066 ACTGGCAATT
* * *
20531076 AGCCTGCTAGACGTAAAGTCCGAAATATTTCACCAGCGTCA
1 AGCCTGCTAGACGTAAAGTCTGAAACATTTCACCAGCATCA
*
20531117 AGCCTGCTAGACGTAAAGTCTGAAACATTTCACCGGCATCA
1 AGCCTGCTAGACGTAAAGTCTGAAACATTTCACCAGCATCA
* *
20531158 AGCCTCCTAGATGTAAAGTCTGAA
1 AGCCTGCTAGACGTAAAGTCTGAA
20531182 TTATCTCATT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (41 bp):
AGCCTGCTAGACGTAAAGTCTGAAACATTTCACCAGCATCA
Found at i:20533007 original size:13 final size:13
Alignment explanation
Indices: 20532989--20533013 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20532979 CAATCAAATG
20532989 CACACAAAATAAA
1 CACACAAAATAAA
20533002 CACACAAAATAA
1 CACACAAAATAA
20533014 TATTAAAATA
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:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:20538899 original size:14 final size:14
Alignment explanation
Indices: 20538882--20538908 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20538872 ACTTACTCTC
20538882 GTTACGGGACTCCT
1 GTTACGGGACTCCT
20538896 GTTACGGGACTCC
1 GTTACGGGACTCC
20538909 CGTCGATTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.26
Consensus pattern (14 bp):
GTTACGGGACTCCT
Found at i:20539441 original size:16 final size:15
Alignment explanation
Indices: 20539420--20539449 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
20539410 TCAAAAAATA
20539420 TATTATTTTCATATTT
1 TATTATTTT-ATATTT
20539436 TATTATTTTATATT
1 TATTATTTTATATT
20539450 ATTTTAGTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTATTTTATATTT
Found at i:20539575 original size:159 final size:159
Alignment explanation
Indices: 20539398--20539912 Score: 831
Period size: 157 Copynumber: 3.3 Consensus size: 159
20539388 GATTTTTCTT
*
20539398 ATTTTATTACTTTCAAAAAATATATTATTTTCATATTTTATTATTTTATATTATTTTAGTACATA
1 ATTTTATTACTTTCAAAAAATATACTATTTTCATATTTTATTATTTTATATTATTTTAGTACATA
* * *
20539463 AAGTTTGAAATGTATTAATTTAGTGTGTTTTTTTATATAAATTTAGTAAAAACCCCTTATTTTGG
66 ATGTTTGAAATGTATTATTTTAGTGTGTTTTTTTATATAAATTTAGTAAAAAACCCTTATTTTGG
*
20539528 CCATTTGTTCGTATTTTTCTTATTTTCAT
131 CCATTTGTTCGTATTTTTCTTATTTTCAG
** *
20539557 ATTTTATTACTTT-AAAAAA-ATGTTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATA
1 ATTTTATTACTTTCAAAAAATATACTATTTTCATATTTTATTATTTTATATTATTTTAGTACATA
* *
20539620 ATGTTTGAAATGCATTATTTTA--GTGTATTTTTATATAAATTTAGTAAAAAACCCTTATTTTGG
66 ATGTTTGAAATGTATTATTTTAGTGTGTTTTTTTATATAAATTTAGTAAAAAACCCTTATTTTGG
* *
20539683 CCATTTGTTCATATTTTTTTTATTTTCAG
131 CCATTTGTTCGTATTTTTCTTATTTTCAG
*
20539712 ATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATA
1 ATTTTATTACTTTCAAAAAATATACTATTTTCATATTTTATTATTTTATATTATTTTAGTACATA
20539777 ATGTTTGAAATGTATTATTTTAGTGTGTTTTTTTATATAAATTTAGTAAAAAACCCTTATTTTGG
66 ATGTTTGAAATGTATTATTTTAGTGTGTTTTTTTATATAAATTTAGTAAAAAACCCTTATTTTGG
* * *
20539842 CCCTTTGTTCGTATTTTTCTTTTTTTCGG
131 CCATTTGTTCGTATTTTTCTTATTTTCAG
** *
20539871 ATTTTATTACTTTCAGTAAATATACTATTTTCATTTTTTATT
1 ATTTTATTACTTTCAAAAAATATACTATTTTCATATTTTATT
20539913 TCTTTTTGTA
Statistics
Matches: 329, Mismatches: 23, Indels: 8
0.91 0.06 0.02
Matches are distributed among these distances:
155 78 0.24
156 6 0.02
157 124 0.38
158 6 0.02
159 115 0.35
ACGTcount: A:0.29, C:0.08, G:0.08, T:0.55
Consensus pattern (159 bp):
ATTTTATTACTTTCAAAAAATATACTATTTTCATATTTTATTATTTTATATTATTTTAGTACATA
ATGTTTGAAATGTATTATTTTAGTGTGTTTTTTTATATAAATTTAGTAAAAAACCCTTATTTTGG
CCATTTGTTCGTATTTTTCTTATTTTCAG
Found at i:20540100 original size:30 final size:29
Alignment explanation
Indices: 20540066--20540211 Score: 122
Period size: 30 Copynumber: 5.4 Consensus size: 29
20540056 AAATTAAATA
20540066 AAATAATAAAACATAGAATGTACATAACAT
1 AAATAATAAAACATA-AATGTACATAACAT
20540096 AAATAATAAAACATAAA--TA-ATAA-AT
1 AAATAATAAAACATAAATGTACATAACAT
*
20540121 AAATAAT--AAC----AT-TA-ATAATA-
1 AAATAATAAAACATAAATGTACATAACAT
* * *
20540141 AAATAATAAGACATATTATGAACATAACAT
1 AAATAATAAAACATA-AATGTACATAACAT
20540171 AAATAATAAAACATAGAATGTACATAACAT
1 AAATAATAAAACATA-AATGTACATAACAT
20540201 AAA-AATTAAAA
1 AAATAA-TAAAA
20540212 TTAAATTATG
Statistics
Matches: 96, Mismatches: 7, Indels: 26
0.74 0.05 0.20
Matches are distributed among these distances:
19 1 0.01
20 13 0.14
21 1 0.01
22 2 0.02
23 3 0.03
25 9 0.09
26 4 0.04
27 4 0.04
28 1 0.01
29 9 0.09
30 49 0.51
ACGTcount: A:0.64, C:0.08, G:0.04, T:0.25
Consensus pattern (29 bp):
AAATAATAAAACATAAATGTACATAACAT
Found at i:20540115 original size:23 final size:22
Alignment explanation
Indices: 20540089--20540155 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 22
20540079 TAGAATGTAC
20540089 ATAACATAAATAATAAAACATAA
1 ATAA-ATAAATAATAAAACATAA
*
20540112 AT-AATAAATAAATAATAACATTA
1 ATAAATAAAT-AATAA-AACATAA
*
20540135 AT-AATAAAATAATAAGACATA
1 ATAAAT-AAATAATAAAACATA
20540156 TTATGAACAT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
21 6 0.16
22 10 0.26
23 18 0.47
24 4 0.11
ACGTcount: A:0.67, C:0.06, G:0.01, T:0.25
Consensus pattern (22 bp):
ATAAATAAATAATAAAACATAA
Found at i:20540176 original size:38 final size:36
Alignment explanation
Indices: 20540062--20540181 Score: 120
Period size: 38 Copynumber: 3.2 Consensus size: 36
20540052 AAATAAATTA
20540062 AATAAAATAATAAAACATAGAATGTACATAACATAAAT
1 AATAAAATAATAAAACATA-AATG-ACATAACATAAAT
*
20540100 AATAAAACATAAATAATAA-ATAAAT-A-ATAACATTAAT
1 AAT-AAA-AT-AATAA-AACATAAATGACATAACATAAAT
* *
20540137 AATAAAATAATAAGACATATTATGAACATAACATAAAT
1 AATAAAATAATAAAACATA-AATG-ACATAACATAAAT
20540175 AATAAAA
1 AATAAAA
20540182 CATAGAATGT
Statistics
Matches: 69, Mismatches: 4, Indels: 18
0.76 0.04 0.20
Matches are distributed among these distances:
33 1 0.01
34 8 0.12
35 4 0.06
36 3 0.04
37 14 0.20
38 21 0.30
39 3 0.04
40 5 0.07
41 8 0.12
42 2 0.03
ACGTcount: A:0.65, C:0.07, G:0.03, T:0.25
Consensus pattern (36 bp):
AATAAAATAATAAAACATAAATGACATAACATAAAT
Found at i:20540479 original size:27 final size:26
Alignment explanation
Indices: 20540448--20540534 Score: 83
Period size: 24 Copynumber: 3.5 Consensus size: 26
20540438 CTTCCCTCCC
20540448 TCTTCTTCTTCTCCTTCTCTTTTTCT
1 TCTTCTTCTTCTCCTTCTCTTTTTCT
**** *
20540474 TCCTTCTAGGCCTCCTTC-C-TCTTCT
1 T-CTTCTTCTTCTCCTTCTCTTTTTCT
*
20540499 TCTTCTTCTTCT-CTTCTCTTTTTAT
1 TCTTCTTCTTCTCCTTCTCTTTTTCT
20540524 T-TTCTTCTTCT
1 TCTTCTTCTTCT
20540535 TTCCTGCAGC
Statistics
Matches: 47, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
23 4 0.09
24 18 0.38
25 11 0.23
26 2 0.04
27 12 0.26
ACGTcount: A:0.02, C:0.34, G:0.02, T:0.61
Consensus pattern (26 bp):
TCTTCTTCTTCTCCTTCTCTTTTTCT
Found at i:20540887 original size:12 final size:12
Alignment explanation
Indices: 20540870--20540894 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20540860 ACCAAAACAG
20540870 GCTTTTAGTGGC
1 GCTTTTAGTGGC
20540882 GCTTTTAGTGGC
1 GCTTTTAGTGGC
20540894 G
1 G
20540895 TTTGGACAAA
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:0.08, C:0.16, G:0.36, T:0.40
Consensus pattern (12 bp):
GCTTTTAGTGGC
Found at i:20541028 original size:40 final size:39
Alignment explanation
Indices: 20540903--20541039 Score: 141
Period size: 40 Copynumber: 3.4 Consensus size: 39
20540893 CGTTTGGACA
* * *
20540903 AAAAACGCCGCTAAAAATCAAGTATTAGCGGCGCTTT-AA
1 AAAAACGCCGCTAAAAAT-GAGCATTAGCGGCGCTTTCAG
*
20540942 ATAAAACGCCGCTAAAGACTGAGCATTAGCGGCGCTTTCAG
1 A-AAAACGCCGCTAAA-AATGAGCATTAGCGGCGCTTTCAG
* * ** **
20540983 GAAAACGCCGCCAAAAATGAGCATTAGCGGCATTTTTTTG
1 AAAAACGCCGCTAAAAATGAGCATTAGCGGC-GCTTTCAG
20541023 AAAAACGCCGCTAAAAA
1 AAAAACGCCGCTAAAAA
20541040 CCTAAGCCCA
Statistics
Matches: 81, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
39 16 0.20
40 62 0.77
41 3 0.04
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (39 bp):
AAAAACGCCGCTAAAAATGAGCATTAGCGGCGCTTTCAG
Found at i:20541587 original size:13 final size:13
Alignment explanation
Indices: 20541547--20541596 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 13
20541537 AGGGTTGTGA
20541547 TTTAGGGGTTAGTGG
1 TTTA-GGGTTAG-GG
20541562 -TTAGGGATTAGGG
1 TTTAGGG-TTAGGG
20541575 ATTT-GGGTTAGGG
1 -TTTAGGGTTAGGG
20541588 TTTAGGGTT
1 TTTAGGGTT
20541597 TAGATTAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
12 3 0.10
13 16 0.52
14 10 0.32
15 2 0.06
ACGTcount: A:0.16, C:0.00, G:0.44, T:0.40
Consensus pattern (13 bp):
TTTAGGGTTAGGG
Found at i:20541666 original size:7 final size:7
Alignment explanation
Indices: 20541656--20541730 Score: 60
Period size: 7 Copynumber: 10.7 Consensus size: 7
20541646 TAGTAGTTAT
20541656 GGGTTTG
1 GGGTTTG
*
20541663 GGGTTTT
1 GGGTTTG
*
20541670 GGGTTTA
1 GGGTTTG
*
20541677 GGGTTTA
1 GGGTTTG
*
20541684 GGGTTAG
1 GGGTTTG
* *
20541691 AGATTTG
1 GGGTTTG
**
20541698 GGGTTAA
1 GGGTTTG
20541705 GGGTTTG
1 GGGTTTG
*
20541712 GGATTTG
1 GGGTTTG
*
20541719 GGGTTAG
1 GGGTTTG
20541726 GGGTT
1 GGGTT
20541731 AGAGGTTAAG
Statistics
Matches: 52, Mismatches: 16, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
7 52 1.00
ACGTcount: A:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (7 bp):
GGGTTTG
Found at i:20541701 original size:21 final size:21
Alignment explanation
Indices: 20541677--20541734 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
20541667 TTTGGGTTTA
20541677 GGGTTTAGGGTTAGAGATTTG
1 GGGTTTAGGGTTAGAGATTTG
* * *
20541698 GGGTTAAGGGTTTGGGATTTG
1 GGGTTTAGGGTTAGAGATTTG
20541719 GGG-TTAGGGGTTAGAG
1 GGGTTTA-GGGTTAGAG
20541735 GTTAAGAGTT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 2 0.07
21 28 0.93
ACGTcount: A:0.17, C:0.00, G:0.48, T:0.34
Consensus pattern (21 bp):
GGGTTTAGGGTTAGAGATTTG
Found at i:20541731 original size:7 final size:7
Alignment explanation
Indices: 20541638--20541738 Score: 51
Period size: 7 Copynumber: 14.4 Consensus size: 7
20541628 TAAATAAGGT
20541638 TTAGGGG
1 TTAGGGG
**
20541645 TTAGTAG
1 TTAGGGG
*
20541652 TTATGGG
1 TTAGGGG
*
20541659 TTTGGGG
1 TTAGGGG
* *
20541666 TTTTGGGT
1 -TTAGGGG
*
20541674 TTAGGGT
1 TTAGGGG
20541681 TTA-GGG
1 TTAGGGG
* *
20541687 TTAGAGA
1 TTAGGGG
*
20541694 TTTGGGG
1 TTAGGGG
*
20541701 TTAAGGG
1 TTAGGGG
* *
20541708 TTTGGGA
1 TTAGGGG
*
20541715 TTTGGGG
1 TTAGGGG
20541722 TTAGGGG
1 TTAGGGG
*
20541729 TTAGAGG
1 TTAGGGG
20541736 TTA
1 TTA
20541739 AGAGTTAGTG
Statistics
Matches: 69, Mismatches: 23, Indels: 4
0.72 0.24 0.04
Matches are distributed among these distances:
6 5 0.07
7 58 0.84
8 6 0.09
ACGTcount: A:0.16, C:0.00, G:0.45, T:0.40
Consensus pattern (7 bp):
TTAGGGG
Found at i:20542367 original size:27 final size:27
Alignment explanation
Indices: 20542335--20542391 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
20542325 TTACATGTTG
20542335 AAATTAATTAAGGGAATGTAAACAAGA
1 AAATTAATTAAGGGAATGTAAACAAGA
20542362 AAATTAATTAAGGGAATGTAAACAAGA
1 AAATTAATTAAGGGAATGTAAACAAGA
20542389 AAA
1 AAA
20542392 AAGAATGCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.58, C:0.04, G:0.18, T:0.21
Consensus pattern (27 bp):
AAATTAATTAAGGGAATGTAAACAAGA
Found at i:20544654 original size:5 final size:5
Alignment explanation
Indices: 20544644--20544790 Score: 159
Period size: 5 Copynumber: 29.4 Consensus size: 5
20544634 AAAACCAATC
*
20544644 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT GATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
* * * * * * * *
20544694 GATAT AATAT GATAT AATAT GATAT GATAT GATAT GATAT GATAT GATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
* * * * * *
20544744 GATAT GATAT GATAT GATAT GATAT GATAT AATAT AATAT AATAT AA
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AA
20544791 AAATAATTAT
Statistics
Matches: 134, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 134 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.39
Consensus pattern (5 bp):
AATAT
Found at i:20544659 original size:10 final size:10
Alignment explanation
Indices: 20544645--20544790 Score: 193
Period size: 10 Copynumber: 14.6 Consensus size: 10
20544635 AAACCAATCA
*
20544645 ATATAATATA
1 ATATAATATG
*
20544655 ATATAATATA
1 ATATAATATG
*
20544665 ATATAATATA
1 ATATAATATG
20544675 ATATAATATG
1 ATATAATATG
20544685 ATATAATATG
1 ATATAATATG
20544695 ATATAATATG
1 ATATAATATG
20544705 ATATAATATG
1 ATATAATATG
*
20544715 ATATGATATG
1 ATATAATATG
*
20544725 ATATGATATG
1 ATATAATATG
*
20544735 ATATGATATG
1 ATATAATATG
*
20544745 ATATGATATG
1 ATATAATATG
*
20544755 ATATGATATG
1 ATATAATATG
* *
20544765 ATATGATATA
1 ATATAATATG
*
20544775 ATATAATATA
1 ATATAATATG
20544785 ATATAA
1 ATATAA
20544791 AAATAATTAT
Statistics
Matches: 132, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
10 132 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (10 bp):
ATATAATATG
Found at i:20545031 original size:22 final size:19
Alignment explanation
Indices: 20544963--20545033 Score: 52
Period size: 21 Copynumber: 3.4 Consensus size: 19
20544953 TAATTATTTT
*
20544963 ATTTTTCTAATTTGTTATTA
1 ATTTTTTTAATTTG-TATTA
* *
20544983 ATTTTTTTTAATTTGGTGTTTG
1 A-TTTTTTTAATTT-GT-ATTA
20545005 ATTTTTTTAATTTAGTACTTA
1 ATTTTTTTAATTT-GTA-TTA
20545026 AGTTTTTT
1 A-TTTTTT
20545034 GGGTTCATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
20 1 0.03
21 29 0.73
22 10 0.25
ACGTcount: A:0.21, C:0.03, G:0.10, T:0.66
Consensus pattern (19 bp):
ATTTTTTTAATTTGTATTA
Found at i:20548654 original size:43 final size:43
Alignment explanation
Indices: 20548589--20548937 Score: 364
Period size: 43 Copynumber: 8.4 Consensus size: 43
20548579 AATAAAAATA
* * * * *
20548589 TGATCTATAGCGGTGTTCGTGAGAGAAGCGTCGCTAAAGGTCT
1 TGATCTATAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCC
* ** * *
20548632 TGATCTATAGCGGCATTTGTGAGAAAAGCGTTGCTAAAAGTCT
1 TGATCTATAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCC
* * * *
20548675 TGATCTATAGTGGCGTTTGTGGGAAAAGTGTCGCTAAAGGTCC
1 TGATCTATAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCC
* * *
20548718 TGATCTATAGCGCCGTTCGTGGGAAAA-----GC-----GT--
1 TGATCTATAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCC
* *
20548749 TGATCTATAGCGGCGTTTGTGGGAAAAGCGCTGCTAAAGGTCC
1 TGATCTATAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCC
* * *
20548792 TGATCTATAGCGGCGTATGTGGGAAAAGCGCCGCTAAAGATCC
1 TGATCTATAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCC
* * * *
20548835 TGATCTATAGCGGCGTTTGTG-GGAAGGCGCCGTTAAAGGTCT
1 TGATCTATAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCC
20548877 TGATCTATAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCC
1 TGATCTATAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCC
*
20548920 TGATCTTTAGCGGCGTTT
1 TGATCTATAGCGGCGTTT
20548938 ATTTCTAAAA
Statistics
Matches: 261, Mismatches: 32, Indels: 26
0.82 0.10 0.08
Matches are distributed among these distances:
31 25 0.10
33 2 0.01
36 2 0.01
38 2 0.01
41 2 0.01
42 37 0.14
43 191 0.73
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.28
Consensus pattern (43 bp):
TGATCTATAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCC
Found at i:20548756 original size:31 final size:31
Alignment explanation
Indices: 20548718--20548778 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
20548708 CTAAAGGTCC
20548718 TGATCTATAGCGCCGTTCGTGGGAAAAGCGT
1 TGATCTATAGCGCCGTTCGTGGGAAAAGCGT
* *
20548749 TGATCTATAGCGGCGTTTGTGGGAAAAGCG
1 TGATCTATAGCGCCGTTCGTGGGAAAAGCG
20548779 CTGCTAAAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.23, C:0.16, G:0.34, T:0.26
Consensus pattern (31 bp):
TGATCTATAGCGCCGTTCGTGGGAAAAGCGT
Found at i:20548788 original size:74 final size:74
Alignment explanation
Indices: 20548674--20548821 Score: 237
Period size: 74 Copynumber: 2.0 Consensus size: 74
20548664 GCTAAAAGTC
* *
20548674 TTGATCTATAGTGGCGTTTGTGGGAAAAGTGTCGCTAAAGGTCCTGATCTATAGCGCCGT-TCGT
1 TTGATCTATAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGGTCCTGATCTATAGCGCCGTAT-GT
20548738 GGGAAAAGCG
65 GGGAAAAGCG
*
20548748 TTGATCTATAGCGGCGTTTGTGGGAAAAGCG-CTGCTAAAGGTCCTGATCTATAGCGGCGTATGT
1 TTGATCTATAGCGGCGTTTGTGGGAAAAGCGTC-GCTAAAGGTCCTGATCTATAGCGCCGTATGT
20548812 GGGAAAAGCG
65 GGGAAAAGCG
20548822 CCGCTAAAGA
Statistics
Matches: 69, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
73 1 0.01
74 67 0.97
75 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.33, T:0.27
Consensus pattern (74 bp):
TTGATCTATAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGGTCCTGATCTATAGCGCCGTATGTG
GGAAAAGCG
Found at i:20548837 original size:117 final size:119
Alignment explanation
Indices: 20548624--20548935 Score: 378
Period size: 117 Copynumber: 2.6 Consensus size: 119
20548614 AAGCGTCGCT
* * * * *
20548624 AAAGGTCTTGATCTATAGCGGCATTTGTGAGAAAAGCGTTGCTAAAAGTCTTGATCTATAGTGGC
1 AAAGG-CTTGATCTATAGCGGCGTTTGTGAGAAAAGCGCTGCTAAAGGTCCTGATCTATAGCGGC
* * * *
20548689 GTTTGTGGGAAAAGTGTCGCTAAAGGTCCTGATCTATAGCGCCGTTCGTGGG-A-
65 GTATGTGGGAAAAGCGCCGCTAAAGATCCTGATCTATAGCGCCGTTCGTGGGAAG
*
20548742 AAA-GCGTTGATCTATAGCGGCGTTTGTGGGAAAAGCGCTGCTAAAGGTCCTGATCTATAGCGGC
1 AAAGGC-TTGATCTATAGCGGCGTTTGTGAGAAAAGCGCTGCTAAAGGTCCTGATCTATAGCGGC
* *
20548806 GTATGTGGGAAAAGCGCCGCTAAAGATCCTGATCTATAGCGGCGTTTGTGGGAAGGCGCCG
65 GTATGTGGGAAAAGCGCCGCTAAAGATCCTGATCTATAGCGCCGTTCGTGGGAA------G
* *
20548867 TTAAAGGTCTTGATCTATAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCCTGATCTTTAGCG
1 --AAAGG-CTTGATCTATAGCGGCGTTTGTGAGAAAAGCGCTGCTAAAGGTCCTGATCTATAGCG
20548932 GCGT
63 GCGT
20548936 TTATTTCTAA
Statistics
Matches: 166, Mismatches: 15, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
116 1 0.01
117 99 0.60
118 4 0.02
127 3 0.02
128 58 0.35
129 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (119 bp):
AAAGGCTTGATCTATAGCGGCGTTTGTGAGAAAAGCGCTGCTAAAGGTCCTGATCTATAGCGGCG
TATGTGGGAAAAGCGCCGCTAAAGATCCTGATCTATAGCGCCGTTCGTGGGAAG
Found at i:20548853 original size:160 final size:159
Alignment explanation
Indices: 20548589--20548906 Score: 415
Period size: 160 Copynumber: 2.0 Consensus size: 159
20548579 AATAAAAATA
* * * *
20548589 TGATCTATAGCGGTGTTCGTGAGAGAAGCGTCGCTAAAGGTCTTGATCTATAGCGGCATTTGTGA
1 TGATCTATAGCGGCGTTCGTGAGAAAAGCGTCGCTAAAGGTCCTGATCTATAGCGGCATATGTGA
** * * * *
20548654 GAAAAGCGTTGCTAAAAGTCTTGATCTATAGTGGCGTTTGTGGGAAAAGTGTCGCTAAAGGTCCT
66 GAAAAGCGCCGCTAAAAGTCCTGATCTATAGCGGCGTTTGTGGG-AAAGCGCCGCTAAAGGTCCT
*
20548719 GATCTATAGCGCCGTTCGTGGGAAAAGCGT
130 GATCTATAGCGCCGTTCGTGAGAAAAGCGT
* * *
20548749 TGATCTATAGCGGCGTTTGTGGGAAAAGCG-CTGCTAAAGGTCCTGATCTATAGCGGCGTATGTG
1 TGATCTATAGCGGCGTTCGTGAGAAAAGCGTC-GCTAAAGGTCCTGATCTATAGCGGCATATGTG
* * * *
20548813 GGAAAAGCGCCGCT-AAAGATCCTGATCTATAGCGGCGTTTGTGGGAAGGCGCCGTTAAAGGTCT
65 AGAAAAGCGCCGCTAAAAG-TCCTGATCTATAGCGGCGTTTGTGGGAAAGCGCCGCTAAAGGTCC
* *
20548877 TGATCTATAGCGGCGTTTGTGAGAAAAGCG
129 TGATCTATAGCGCCGTTCGTGAGAAAAGCG
20548907 CCGCTAAAGG
Statistics
Matches: 136, Mismatches: 20, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
159 46 0.34
160 90 0.66
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.27
Consensus pattern (159 bp):
TGATCTATAGCGGCGTTCGTGAGAAAAGCGTCGCTAAAGGTCCTGATCTATAGCGGCATATGTGA
GAAAAGCGCCGCTAAAAGTCCTGATCTATAGCGGCGTTTGTGGGAAAGCGCCGCTAAAGGTCCTG
ATCTATAGCGCCGTTCGTGAGAAAAGCGT
Found at i:20548903 original size:85 final size:86
Alignment explanation
Indices: 20548749--20548937 Score: 299
Period size: 85 Copynumber: 2.2 Consensus size: 86
20548739 GGAAAAGCGT
* *
20548749 TGATCTATAGCGGCGTTTGTGGGAAAAGCGCTGCTAAAGGTCCTGATCTATAGCGGCGTATGTGG
1 TGATCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTATGTGA
20548814 GAAAAGCGCCGCTAAAGATCC
66 GAAAAGCGCCGCTAAAGATCC
* * * *
20548835 TGATCTATAGCGGCGTTTGTGGG-AAGGCGCCGTTAAAGGTCTTGATCTATAGCGGCGTTTGTGA
1 TGATCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTATGTGA
*
20548899 GAAAAGCGCCGCTAAAGGTCC
66 GAAAAGCGCCGCTAAAGATCC
*
20548920 TGATCTTTAGCGGCGTTT
1 TGATCTATAGCGGCGTTT
20548938 ATTTCTAAAA
Statistics
Matches: 95, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
85 72 0.76
86 23 0.24
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26
Consensus pattern (86 bp):
TGATCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTATGTGA
GAAAAGCGCCGCTAAAGATCC
Found at i:20551680 original size:44 final size:44
Alignment explanation
Indices: 20551618--20551713 Score: 174
Period size: 44 Copynumber: 2.2 Consensus size: 44
20551608 TTTTTGAGGA
* *
20551618 AGGAAAGATATCATAGAAATGATCTCATTTGATGCTTGAATTAG
1 AGGAAAGATATCATAGAAATGATATCATTTGATACTTGAATTAG
20551662 AGGAAAGATATCATAGAAATGATATCATTTGATACTTGAATTAG
1 AGGAAAGATATCATAGAAATGATATCATTTGATACTTGAATTAG
20551706 AGGAAAGA
1 AGGAAAGA
20551714 ATTTCTGAGT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 50 1.00
ACGTcount: A:0.43, C:0.07, G:0.21, T:0.29
Consensus pattern (44 bp):
AGGAAAGATATCATAGAAATGATATCATTTGATACTTGAATTAG
Found at i:20559636 original size:61 final size:59
Alignment explanation
Indices: 20559565--20559711 Score: 183
Period size: 61 Copynumber: 2.5 Consensus size: 59
20559555 TTGTAATAAG
*
20559565 ATTATTATTAAATATAATTTAATAAAAATAAAAATAAATAATTTAATCATATT-TTAACATA
1 ATTATTATTAAATATAATTTAATAAAAAT---AATAAATAATTTAATAATATTCTTAACATA
* * * *
20559626 ATTATCATTAAATACAATTTAAT-AAAATAATATATAATTTAATAATATTCTTAATATA
1 ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATAATATTCTTAACATA
20559684 ATTATTATTAAAATATGAA-TTAATAAAA
1 ATTATTATT-AAATAT-AATTTAATAAAA
20559712 TCATAATATA
Statistics
Matches: 75, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
57 19 0.25
58 15 0.20
59 10 0.13
60 10 0.13
61 21 0.28
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (59 bp):
ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATAATATTCTTAACATA
Found at i:20561960 original size:23 final size:22
Alignment explanation
Indices: 20561899--20561960 Score: 54
Period size: 24 Copynumber: 2.8 Consensus size: 22
20561889 AAAAAAAATT
* *
20561899 AAAAAAAAAGACAG-AAATTTC
1 AAAAAAAAAGAGAGAAAATTGC
* * *
20561920 CAAAAAAAAGTGTTGAAAAGTTGC
1 AAAAAAAAAGAG-AGAAAA-TTGC
20561944 AAAAAAAAAGAGAGAAA
1 AAAAAAAAAGAGAGAAA
20561961 GAATCTGTTT
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
21 9 0.30
22 1 0.03
23 7 0.23
24 13 0.43
ACGTcount: A:0.65, C:0.06, G:0.16, T:0.13
Consensus pattern (22 bp):
AAAAAAAAAGAGAGAAAATTGC
Found at i:20564601 original size:239 final size:239
Alignment explanation
Indices: 20564182--20564897 Score: 1378
Period size: 239 Copynumber: 3.0 Consensus size: 239
20564172 AGATTTATCT
*
20564182 TTTGTAAAACACTTAGATCGTGTTGTGCTTAGTTGTTCCATTTTGCTTGACGATGATCCATCTGT
1 TTTGTAAAACACTTAGATCGTGTTGTGCTTAGTTGTTCCATTTTGCTTGACGATGATCTATCTGT
*
20564247 TTTGGTTGTTGACAATAAGATTATTGTTTCTGATCATTTTTATGATGCATGTGTGAATGAATCTA
66 TTTGGTTGTTGATAATAAGATTATTGTTTCTGATCATTTTTATGATGCATGTGTGAATGAATCTA
20564312 TAGTCAATCGTCTAATGCACGGTATGATTGTGCAACTCCGTGAACCGTGTGAATCCTTTCAAATA
131 TAGTCAATCGTCTAATGCACGGTATGATTGTGCAACTCCGTGAACCGTGTGAATCCTTTCAAATA
20564377 CCTGCTTGTGACGATTATGTCTACCATTTGATTCATTATTCACG
196 CCTGCTTGTGACGATTATGTCTACCATTTGATTCATTATTCACG
20564421 TTTGTAAAACACTTAGATCGTGTTGTGCTTAGTTGTTCCATTTTGCTTGACGATGATCTATCTGT
1 TTTGTAAAACACTTAGATCGTGTTGTGCTTAGTTGTTCCATTTTGCTTGACGATGATCTATCTGT
20564486 TTTGGTTGTTGATAATAAGATTATTGTTTCTGATCATTTTTATGATGCATGTGTGAATGAATCTA
66 TTTGGTTGTTGATAATAAGATTATTGTTTCTGATCATTTTTATGATGCATGTGTGAATGAATCTA
20564551 TAGTCAATCGTCTAATGCACGGTATGATTGTGCAACTCCGTGAACCGTGTGAATCCTTTCAAATA
131 TAGTCAATCGTCTAATGCACGGTATGATTGTGCAACTCCGTGAACCGTGTGAATCCTTTCAAATA
20564616 CCTGCTTGTGACGATTATGTCTACCATTTGATTCATTATTCACG
196 CCTGCTTGTGACGATTATGTCTACCATTTGATTCATTATTCACG
20564660 TTTGTAAAACACTTAGATCGTGTTGTGCTTAGTTGTTCCATTTTGCTTGACGATGATCTATCTGT
1 TTTGTAAAACACTTAGATCGTGTTGTGCTTAGTTGTTCCATTTTGCTTGACGATGATCTATCTGT
20564725 TTTGGTTGTTGATAATAAGATTATTGTTTCTGATCATTTTTATGATGCATGTGTGAATGAATCTA
66 TTTGGTTGTTGATAATAAGATTATTGTTTCTGATCATTTTTATGATGCATGTGTGAATGAATCTA
* * *
20564790 TAATCAATCGTCTAATGCATGGTATGATTGTGCAACTCCGTGAACCTTGTGAATCCTTTCAAATA
131 TAGTCAATCGTCTAATGCACGGTATGATTGTGCAACTCCGTGAACCGTGTGAATCCTTTCAAATA
*
20564855 CCTGCTTTTGACGATTATGTCTACCATTTGATTCATTATTCAC
196 CCTGCTTGTGACGATTATGTCTACCATTTGATTCATTATTCAC
20564898 ATTCTACTTA
Statistics
Matches: 471, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
239 471 1.00
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.41
Consensus pattern (239 bp):
TTTGTAAAACACTTAGATCGTGTTGTGCTTAGTTGTTCCATTTTGCTTGACGATGATCTATCTGT
TTTGGTTGTTGATAATAAGATTATTGTTTCTGATCATTTTTATGATGCATGTGTGAATGAATCTA
TAGTCAATCGTCTAATGCACGGTATGATTGTGCAACTCCGTGAACCGTGTGAATCCTTTCAAATA
CCTGCTTGTGACGATTATGTCTACCATTTGATTCATTATTCACG
Found at i:20580001 original size:25 final size:25
Alignment explanation
Indices: 20579960--20580016 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
20579950 ACAATCCATG
** * *
20579960 TAAATCATGTATTTCATGTAACTTT
1 TAAATCATGTAAATCATATAACATT
20579985 TAAATCATGTAAATCATATAACATT
1 TAAATCATGTAAATCATATAACATT
*
20580010 TATATCA
1 TAAATCA
20580017 ATTCTTTCCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.42
Consensus pattern (25 bp):
TAAATCATGTAAATCATATAACATT
Found at i:20580307 original size:23 final size:23
Alignment explanation
Indices: 20580277--20580345 Score: 104
Period size: 23 Copynumber: 3.0 Consensus size: 23
20580267 CCAAGCTGAT
20580277 AAACGGTAAGCTCTATAGAGCTG
1 AAACGGTAAGCTCTATAGAGCTG
*
20580300 AAACGGTAAGCTTTATAGAGCTG
1 AAACGGTAAGCTCTATAGAGCTG
*
20580323 AAACGATAAGCTC-ATACGAGCTG
1 AAACGGTAAGCTCTATA-GAGCTG
20580346 TGGTGAGTCC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
22 3 0.07
23 39 0.93
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (23 bp):
AAACGGTAAGCTCTATAGAGCTG
Found at i:20585343 original size:7 final size:7
Alignment explanation
Indices: 20585331--20585376 Score: 85
Period size: 7 Copynumber: 6.7 Consensus size: 7
20585321 ACAAAGGAAC
20585331 AAAAAGA
1 AAAAAGA
20585338 AAAAAG-
1 AAAAAGA
20585344 AAAAAGA
1 AAAAAGA
20585351 AAAAAGA
1 AAAAAGA
20585358 AAAAAGA
1 AAAAAGA
20585365 AAAAAGA
1 AAAAAGA
20585372 AAAAA
1 AAAAA
20585377 ACAAACAAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 6 0.16
7 32 0.84
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:20585349 original size:13 final size:13
Alignment explanation
Indices: 20585331--20585394 Score: 85
Period size: 13 Copynumber: 4.8 Consensus size: 13
20585321 ACAAAGGAAC
20585331 AAAAAGAAAAAAG
1 AAAAAGAAAAAAG
20585344 AAAAAGAAAAAAG
1 AAAAAGAAAAAAG
20585357 AAAAAAGAAAAAAG
1 -AAAAAGAAAAAAG
* *
20585371 AAAAA-AACAAAC
1 AAAAAGAAAAAAG
20585383 AAACAAGAAAAA
1 AAA-AAGAAAAA
20585395 TACTAGCTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
12 8 0.18
13 20 0.44
14 17 0.38
ACGTcount: A:0.84, C:0.05, G:0.11, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAAG
Found at i:20585706 original size:27 final size:27
Alignment explanation
Indices: 20585676--20585732 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
20585666 TTTTTGAATA
20585676 TTCTTTAATTTTT-TTTTCAAAATTTTT
1 TTCTTTAATTTTTCTTTTC-AAATTTTT
** *
20585703 TTCTTTTCTTTTTCTTTTCAACTTTTT
1 TTCTTTAATTTTTCTTTTCAAATTTTT
20585730 TTC
1 TTC
20585733 AAAATTTCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 21 0.81
28 5 0.19
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.72
Consensus pattern (27 bp):
TTCTTTAATTTTTCTTTTCAAATTTTT
Found at i:20588561 original size:12 final size:12
Alignment explanation
Indices: 20588533--20588576 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
20588523 CAAACAAAAG
20588533 AAAAATTAAAATGT
1 AAAAA-TAAAAT-T
*
20588547 AAAAATCAAATT
1 AAAAATAAAATT
*
20588559 AAAAATAAAAAT
1 AAAAATAAAATT
20588571 AAAAAT
1 AAAAAT
20588577 GGCTAAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
12 17 0.63
13 5 0.19
14 5 0.19
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (12 bp):
AAAAATAAAATT
Found at i:20588576 original size:19 final size:20
Alignment explanation
Indices: 20588528--20588576 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
20588518 AGAATCAAAC
* *
20588528 AAAAGAAAAATTAAAATGTA
1 AAAATAAAAATTAAAATATA
*
20588548 AAAAT-CAAATTAAAA-ATA
1 AAAATAAAAATTAAAATATA
20588566 AAAATAAAAAT
1 AAAATAAAAAT
20588577 GGCTAAATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 7 0.29
19 13 0.54
20 4 0.17
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.20
Consensus pattern (20 bp):
AAAATAAAAATTAAAATATA
Found at i:20592883 original size:71 final size:72
Alignment explanation
Indices: 20592762--20592917 Score: 244
Period size: 71 Copynumber: 2.2 Consensus size: 72
20592752 TTGTGGATTC
*
20592762 TTCACAGCTCGTG-TAAGCAACATCATGTAAAGTTACCATCCCGACCCACAACTCGTGTGAGCAG
1 TTCACAGCTCGTGTTAAGCAAAATCATGTAAAGTTACCATCCCGACCCACAACTCGTGTGAGCAG
20592826 GCTTATT
66 GCTTATT
* *
20592833 TTCATAGCTCGTGTTAA-CAAAATCATGTAAAGTTACCATCCCGACTCACAACTCGTGTGAGCAG
1 TTCACAGCTCGTGTTAAGCAAAATCATGTAAAGTTACCATCCCGACCCACAACTCGTGTGAGCAG
20592897 GCTTATT
66 GCTTATT
* * *
20592904 CTCAGAACTCGTGT
1 TTCACAGCTCGTGT
20592918 GAGCAACCTT
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
71 75 0.96
72 3 0.04
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (72 bp):
TTCACAGCTCGTGTTAAGCAAAATCATGTAAAGTTACCATCCCGACCCACAACTCGTGTGAGCAG
GCTTATT
Found at i:20592928 original size:27 final size:27
Alignment explanation
Indices: 20592877--20592929 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
20592867 ACCATCCCGA
**
20592877 CTCACAACTCGTGTGAGCAGGCTTATT
1 CTCACAACTCGTGTGAGCAACCTTATT
*
20592904 CTCAGAACTCGTGTGAGCAACCTTAT
1 CTCACAACTCGTGTGAGCAACCTTAT
20592930 CTCGTGTGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (27 bp):
CTCACAACTCGTGTGAGCAACCTTATT
Found at i:20603170 original size:44 final size:44
Alignment explanation
Indices: 20603118--20603233 Score: 214
Period size: 44 Copynumber: 2.6 Consensus size: 44
20603108 GATAGGTAAT
20603118 ATGTGAGAATACTTGTATGTGATATATGATGTACTTATTTTAAG
1 ATGTGAGAATACTTGTATGTGATATATGATGTACTTATTTTAAG
* *
20603162 ATGTGAGAATATTTGTATGTGATATATGATGTACTTATTTTAAT
1 ATGTGAGAATACTTGTATGTGATATATGATGTACTTATTTTAAG
20603206 ATGTGAGAATACTTGTATGTGATATATG
1 ATGTGAGAATACTTGTATGTGATATATG
20603234 TGGTTGGTTA
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 69 1.00
ACGTcount: A:0.32, C:0.03, G:0.21, T:0.44
Consensus pattern (44 bp):
ATGTGAGAATACTTGTATGTGATATATGATGTACTTATTTTAAG
Found at i:20606210 original size:68 final size:68
Alignment explanation
Indices: 20606129--20606280 Score: 205
Period size: 68 Copynumber: 2.2 Consensus size: 68
20606119 TGTCATAGCT
* *
20606129 GAGCTATGGTCTTACACCTTGTAACCCCATGTTTAATGTCCTGGCGGACTCTATTGGTTGCCACA
1 GAGCTATGGTCTTACACCTTGTAACCCCATGTTTAATATCCTGGCAGACTCTATTGGTTGCCACA
20606194 GTC
66 GTC
* * * * * *
20606197 GAGCTATGTTCTTACACTTTGTAACCCCGTGTTTAATATCCTGGTAGACTTTATTGGTTGCCATA
1 GAGCTATGGTCTTACACCTTGTAACCCCATGTTTAATATCCTGGCAGACTCTATTGGTTGCCACA
**
20606262 ACC
66 GTC
*
20606265 AAGCTATGGTCTTACA
1 GAGCTATGGTCTTACA
20606281 TGTTGTACCT
Statistics
Matches: 72, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
68 72 1.00
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.35
Consensus pattern (68 bp):
GAGCTATGGTCTTACACCTTGTAACCCCATGTTTAATATCCTGGCAGACTCTATTGGTTGCCACA
GTC
Found at i:20608978 original size:38 final size:38
Alignment explanation
Indices: 20608927--20609013 Score: 86
Period size: 38 Copynumber: 2.3 Consensus size: 38
20608917 TGGAATTGAA
* * * *
20608927 TATCTACTAGTCCTCCAGGGCGACA-TCGTGACGACTGT
1 TATCTAATGGTCCTCCAGGGCGACACT-ATGACGACGGT
*** *
20608965 TATCTAATGGTCCTTTGGGGTGACACTATGACGACGGT
1 TATCTAATGGTCCTCCAGGGCGACACTATGACGACGGT
20609003 TATCTAATGGT
1 TATCTAATGGT
20609014 TCTTTAGGGT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
38 39 0.98
39 1 0.03
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (38 bp):
TATCTAATGGTCCTCCAGGGCGACACTATGACGACGGT
Found at i:20609044 original size:38 final size:38
Alignment explanation
Indices: 20608964--20609065 Score: 98
Period size: 38 Copynumber: 2.7 Consensus size: 38
20608954 GTGACGACTG
* * * **
20608964 TTATCTAATGGTCCTTTGGGGTGACACTATGACGACGG
1 TTATCTAATGGTTCTTTAGGGTGACACTATGACAACAA
* * *
20609002 TTATCTAATGGTTCTTTAGGGTGATATTGTGACAACAA
1 TTATCTAATGGTTCTTTAGGGTGACACTATGACAACAA
* *
20609040 TTATCTACTGG-TCTTATAGGGCGACA
1 TTATCTAATGGTTCTT-TAGGGTGACA
20609066 TCGTGTAAAC
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
37 4 0.08
38 48 0.92
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.35
Consensus pattern (38 bp):
TTATCTAATGGTTCTTTAGGGTGACACTATGACAACAA
Found at i:20610165 original size:61 final size:58
Alignment explanation
Indices: 20610052--20610167 Score: 137
Period size: 61 Copynumber: 1.9 Consensus size: 58
20610042 ATCAATTTAA
* * *
20610052 TATTAAATTAATATAATACTTATCAAGATAAATATTAGATTAAATTTAATATTAAATC
1 TATTAAATTAATACAATACTTATCAAGATAAATAGTAAATTAAATTTAATATTAAATC
*
20610110 TATTAAATTAATACAATA-TGTATCTAGAAGATAAATAGTAAATTTAATATT-ATATTAA
1 TATTAAATTAATACAATACT-TATC---AAGATAAATAGTAAATTAAAT-TTAATATTAA
20610168 GATAATTCAA
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
57 1 0.02
58 21 0.43
61 25 0.51
62 2 0.04
ACGTcount: A:0.50, C:0.04, G:0.05, T:0.41
Consensus pattern (58 bp):
TATTAAATTAATACAATACTTATCAAGATAAATAGTAAATTAAATTTAATATTAAATC
Found at i:20613474 original size:15 final size:15
Alignment explanation
Indices: 20613456--20613484 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
20613446 TATTGAATCG
20613456 AAAAAATAAA-TTTA
1 AAAAAATAAAGTTTA
20613470 AAAAAATAAAGTTTA
1 AAAAAATAAAGTTTA
20613485 TAGGTTGAGA
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:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (15 bp):
AAAAAATAAAGTTTA
Found at i:20614125 original size:15 final size:15
Alignment explanation
Indices: 20614107--20614137 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
20614097 AAAGAATAAA
*
20614107 TATAAAAACTTAATT
1 TATAAAAAATTAATT
20614122 TATAAAAAATTAATT
1 TATAAAAAATTAATT
20614137 T
1 T
20614138 TTTGGTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (15 bp):
TATAAAAAATTAATT
Found at i:20621991 original size:50 final size:50
Alignment explanation
Indices: 20621854--20622201 Score: 484
Period size: 50 Copynumber: 7.0 Consensus size: 50
20621844 TTTCCTGTAC
* * * ** * *
20621854 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * ** *
20621904 TGCCTATGCCATGT-CCAGACATGGTCTGACGGGGGACCTCTCATCTCAG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
20621953 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
20622003 TGCCAACGCCATGTCCCAGACATGGTCTTACATGTGACCTCTCATCAT-GG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATC-TCGG
* *
20622053 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTAATCTCGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
20622103 TGCCAATGCCATGTCCCAGACATGGTCTAACATGGGACCTCTTATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
20622153 TGCCAACGCTATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
20622202 AGTTTACATG
Statistics
Matches: 264, Mismatches: 31, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
49 39 0.15
50 224 0.85
51 1 0.00
ACGTcount: A:0.22, C:0.31, G:0.21, T:0.26
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:20622812 original size:22 final size:21
Alignment explanation
Indices: 20622772--20622817 Score: 51
Period size: 22 Copynumber: 2.1 Consensus size: 21
20622762 TTTTCTCCCA
20622772 TTCTAGGTCAAAATCTCAT-T
1 TTCTAGGTCAAAATCTCATAT
20622792 TTCTAGGATCTAAAA-CATCATAT
1 TTCTAGG-TC-AAAATC-TCATAT
20622815 TTC
1 TTC
20622818 ACTTATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
20 7 0.32
21 3 0.14
22 8 0.36
23 4 0.18
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.39
Consensus pattern (21 bp):
TTCTAGGTCAAAATCTCATAT
Found at i:20624872 original size:18 final size:19
Alignment explanation
Indices: 20624849--20624887 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
20624839 TACAAATGCA
*
20624849 AACATT-ACATAATTATTT
1 AACATTCACATAATGATTT
*
20624867 AACATTCACATCATGATTT
1 AACATTCACATAATGATTT
20624886 AA
1 AA
20624888 TCTTATCATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.44, C:0.15, G:0.03, T:0.38
Consensus pattern (19 bp):
AACATTCACATAATGATTT
Found at i:20625422 original size:18 final size:18
Alignment explanation
Indices: 20625399--20625454 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
20625389 TTTACAACAT
20625399 AATTCACATTCTATTTTC
1 AATTCACATTCTATTTTC
20625417 AATT--CA--CTATTGTT-
1 AATTCACATTCTATT-TTC
*
20625431 -TTTCACATTCTATTTTC
1 AATTCACATTCTATTTTC
20625448 AATTCAC
1 AATTCAC
20625455 TATCTCATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 14
0.64 0.04 0.31
Matches are distributed among these distances:
13 2 0.07
14 5 0.17
15 4 0.14
16 4 0.14
17 5 0.17
18 9 0.31
ACGTcount: A:0.27, C:0.21, G:0.02, T:0.50
Consensus pattern (18 bp):
AATTCACATTCTATTTTC
Found at i:20625473 original size:6 final size:6
Alignment explanation
Indices: 20625462--20625487 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
20625452 CACTATCTCA
20625462 TATTCT TATTCT TATTCT TATTCT TA
1 TATTCT TATTCT TATTCT TATTCT TA
20625488 GCCCAAAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.15, G:0.00, T:0.65
Consensus pattern (6 bp):
TATTCT
Found at i:20625585 original size:22 final size:22
Alignment explanation
Indices: 20625560--20625625 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
20625550 TGCACTAATG
20625560 AACAGAGAGCACTGAAGTGCTA
1 AACAGAGAGCACTGAAGTGCTA
* *
20625582 AACAGAGAGCACAGATGTGCTA
1 AACAGAGAGCACTGAAGTGCTA
* *
20625604 AACAGAGAGCATTGACGTGCTA
1 AACAGAGAGCACTGAAGTGCTA
20625626 GTGATGCGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.39, C:0.18, G:0.27, T:0.15
Consensus pattern (22 bp):
AACAGAGAGCACTGAAGTGCTA
Found at i:20626679 original size:15 final size:14
Alignment explanation
Indices: 20626658--20626693 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
20626648 ATAATCCTTA
*
20626658 ATAATTATCTTAAT
1 ATAATTATCCTAAT
20626672 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
20626687 ATAATTA
1 ATAATTA
20626694 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:20626991 original size:25 final size:25
Alignment explanation
Indices: 20626963--20627053 Score: 128
Period size: 25 Copynumber: 3.6 Consensus size: 25
20626953 AGTGTTATCA
* * *
20626963 GCTAGTAATCAGAGAACACTGACGT
1 GCTAATAATCAGAGAGCACTGATGT
20626988 GCTAATAATCAGAGAGCACTGATGT
1 GCTAATAATCAGAGAGCACTGATGT
*
20627013 GCTAATAATCAGAGAGCGCTGATGT
1 GCTAATAATCAGAGAGCACTGATGT
* *
20627038 GCTAAGAATTAGAGAG
1 GCTAATAATCAGAGAG
20627054 TGCGCTAAAG
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 60 1.00
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.22
Consensus pattern (25 bp):
GCTAATAATCAGAGAGCACTGATGT
Found at i:20628086 original size:23 final size:23
Alignment explanation
Indices: 20628056--20628102 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
20628046 AATAAGTATG
20628056 TACATATATTAATTACAAATGTA
1 TACATATATTAATTACAAATGTA
* *
20628079 TACATATATTTATTACACATGTA
1 TACATATATTAATTACAAATGTA
20628102 T
1 T
20628103 TTATAATTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.43
Consensus pattern (23 bp):
TACATATATTAATTACAAATGTA
Found at i:20638985 original size:49 final size:49
Alignment explanation
Indices: 20638880--20639405 Score: 892
Period size: 49 Copynumber: 10.9 Consensus size: 49
20638870 TAGTATGGCG
* *
20638880 TAATGGCTGATGTGATGAATGTGAACGTG--TATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
*
20638927 TAATAGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
20638976 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
20639025 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
20639074 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
20639123 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
20639170 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
20639219 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
20639268 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
* *
20639315 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGACAGGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
* * * * *
20639362 GAGTGGCCAACGTGATGGATGTGAAAGTGTATA-A-ATGTGATAAG
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAG
20639406 TCCCGAAGGG
Statistics
Matches: 460, Mismatches: 13, Indels: 12
0.95 0.03 0.02
Matches are distributed among these distances:
47 168 0.37
48 1 0.00
49 291 0.63
ACGTcount: A:0.32, C:0.08, G:0.29, T:0.30
Consensus pattern (49 bp):
TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
Found at i:20639171 original size:145 final size:143
Alignment explanation
Indices: 20638880--20639405 Score: 894
Period size: 145 Copynumber: 3.7 Consensus size: 143
20638870 TAGTATGGCG
* * *
20638880 TAATGGCTGATGTGATGAATGTGAACGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
20638945 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
66 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TAT
20639010 ATATGTGATAAGGCC
129 ATATGTGATAAGGCC
20639025 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGAT
20639090 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
64 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
20639155 ATATGTGATAAGGCC
129 ATATGTGATAAGGCC
20639170 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGAT
20639235 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
64 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
20639300 ATATGTGATAAGGCC
129 ATATGTGATAAGGCC
* * * * * * *
20639315 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGG
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
20639380 ATGTGAAAGTGTATA-A-ATGTGATAAG
66 ATGTGAAAGTGTATATATATGTGATAAG
20639406 TCCCGAAGGG
Statistics
Matches: 369, Mismatches: 10, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
141 10 0.03
142 1 0.00
143 44 0.12
145 219 0.59
147 95 0.26
ACGTcount: A:0.32, C:0.08, G:0.29, T:0.30
Consensus pattern (143 bp):
TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
ATGTGATAAGGCC
Found at i:20652504 original size:21 final size:21
Alignment explanation
Indices: 20652480--20652521 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
20652470 GAAGTTAAAA
20652480 TGTTTTAATTTCTCA-TTAATT
1 TGTTTTAATTTC-CATTTAATT
20652501 TGTTTTAATTTCCATTTAATT
1 TGTTTTAATTTCCATTTAATT
20652522 ACAAAATTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.24, C:0.10, G:0.05, T:0.62
Consensus pattern (21 bp):
TGTTTTAATTTCCATTTAATT
Found at i:20658503 original size:31 final size:29
Alignment explanation
Indices: 20658465--20658527 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
20658455 TCATATCAAA
20658465 ATTTGAAAAAGGTAAAT-TTTTAGTCACTTAT
1 ATTTGAAAAA--T-AATGTTTTAGTCACTTAT
* *
20658496 ATTTGAAATATTATGTTTTAGTCACTTAT
1 ATTTGAAAAATAATGTTTTAGTCACTTAT
20658525 ATT
1 ATT
20658528 AACGTATTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 2 0.07
29 18 0.62
31 9 0.31
ACGTcount: A:0.35, C:0.06, G:0.11, T:0.48
Consensus pattern (29 bp):
ATTTGAAAAATAATGTTTTAGTCACTTAT
Found at i:20658760 original size:20 final size:21
Alignment explanation
Indices: 20658735--20658776 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
20658725 TTTCATTATC
* *
20658735 TTCTA-CTTCTTCATCTGTTT
1 TTCTACCTTCTCCATCTCTTT
20658755 TTCTACCTTCTCCATCTCTTT
1 TTCTACCTTCTCCATCTCTTT
20658776 T
1 T
20658777 AATATAGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.10, C:0.31, G:0.02, T:0.57
Consensus pattern (21 bp):
TTCTACCTTCTCCATCTCTTT
Found at i:20664085 original size:31 final size:29
Alignment explanation
Indices: 20664044--20664117 Score: 71
Period size: 29 Copynumber: 2.5 Consensus size: 29
20664034 TTAACGGTTC
* *
20664044 AGTGAGTAAAATGTTACAACATGTT-AACGTA
1 AGTGACTAAAATGTT--AACAT-TTAAACATA
*
20664075 AGTGACTAAAACG-TAACATTTCAAACATA
1 AGTGACTAAAATGTTAACATTT-AAACATA
20664104 AGTGACTAAAATGT
1 AGTGACTAAAATGT
20664118 AATTTGAGGT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
27 2 0.06
28 5 0.14
29 17 0.47
30 1 0.03
31 11 0.31
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (29 bp):
AGTGACTAAAATGTTAACATTTAAACATA
Found at i:20668682 original size:2 final size:2
Alignment explanation
Indices: 20668675--20668720 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
20668665 TGAGTGGGAA
20668675 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
20668717 TC TC
1 TC TC
20668721 CTTATTTTCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:20674847 original size:21 final size:21
Alignment explanation
Indices: 20674821--20674861 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
20674811 AGACGAGCAA
* *
20674821 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
20674842 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
20674862 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Done.