Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 12 of 185
Found at i:3290728 original size:13 final size:12
Alignment explanation
Indices: 3290700--3290744 Score: 54
Period size: 14 Copynumber: 3.4 Consensus size: 12
3290690 AAGATAATGG
3290700 AAAATAAAGAAA
1 AAAATAAAGAAA
3290712 AAAATAAAGTTAAA
1 AAAATAAAG--AAA
3290726 AAACATAAAAGAAA
1 AAA-AT-AAAGAAA
3290740 AAAAT
1 AAAAT
3290745 TAAATTGCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
12 9 0.31
13 2 0.07
14 12 0.41
15 2 0.07
16 4 0.14
ACGTcount: A:0.78, C:0.02, G:0.07, T:0.13
Consensus pattern (12 bp):
AAAATAAAGAAA
Found at i:3299156 original size:3 final size:3
Alignment explanation
Indices: 3299148--3299172 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3299138 TATATGCATC
3299148 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
3299173 TTTTTCAATT
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:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:3302925 original size:20 final size:20
Alignment explanation
Indices: 3302900--3302940 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
3302890 CAGTTTGCTA
3302900 GTATCTCGCAGAATCAGTGT
1 GTATCTCGCAGAATCAGTGT
3302920 GTATCTCGCAGAATCAGTGT
1 GTATCTCGCAGAATCAGTGT
3302940 G
1 G
3302941 GACTTTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (20 bp):
GTATCTCGCAGAATCAGTGT
Found at i:3306766 original size:24 final size:24
Alignment explanation
Indices: 3306730--3306777 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3306720 AATTTTTCGG
* **
3306730 CAGAGAGAGAGAGCTAAAGAAAAA
1 CAGAGAGAAAGAGAGAAAGAAAAA
3306754 CAGAGAGAAAGAGAGAAAGAAAAA
1 CAGAGAGAAAGAGAGAAAGAAAAA
3306778 AAATCAGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.62, C:0.06, G:0.29, T:0.02
Consensus pattern (24 bp):
CAGAGAGAAAGAGAGAAAGAAAAA
Found at i:3311542 original size:24 final size:24
Alignment explanation
Indices: 3311506--3311553 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3311496 AATTTTTCGG
* **
3311506 CAGAGAGAGAGAGCTAAAGAAAAA
1 CAGAGAGAAAGAGAGAAAGAAAAA
3311530 CAGAGAGAAAGAGAGAAAGAAAAA
1 CAGAGAGAAAGAGAGAAAGAAAAA
3311554 AAAATCAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.62, C:0.06, G:0.29, T:0.02
Consensus pattern (24 bp):
CAGAGAGAAAGAGAGAAAGAAAAA
Found at i:3312009 original size:1 final size:1
Alignment explanation
Indices: 3312003--3312101 Score: 198
Period size: 1 Copynumber: 99.0 Consensus size: 1
3311993 AGAGAACATA
3312003 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3312068 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3312102 GACATATCTT
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 98 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:3328588 original size:15 final size:16
Alignment explanation
Indices: 3328558--3328596 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
3328548 GTTGATGATC
* *
3328558 TTGATTTTGTTTAACA
1 TTGATTGTGTTAAACA
3328574 TT-ATTGTGTTAAACA
1 TTGATTGTGTTAAACA
3328589 TTGATTGT
1 TTGATTGT
3328597 AAATTTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.26, C:0.05, G:0.15, T:0.54
Consensus pattern (16 bp):
TTGATTGTGTTAAACA
Found at i:3343839 original size:30 final size:30
Alignment explanation
Indices: 3343805--3343896 Score: 159
Period size: 30 Copynumber: 3.1 Consensus size: 30
3343795 TCTTAGATAA
3343805 TTTAAAGAGTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTATTAGGATTCAATTACTC
3343835 TTTAAAGAGTTTTATTAGGATTC-ATTACTC
1 TTTAAAGAG-TTTATTAGGATTCAATTACTC
*
3343865 TTGAAAGAGTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTATTAGGATTCAATTACTC
3343895 TT
1 TT
3343897 GTAATTTGCC
Statistics
Matches: 59, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
29 13 0.22
30 33 0.56
31 13 0.22
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.45
Consensus pattern (30 bp):
TTTAAAGAGTTTATTAGGATTCAATTACTC
Found at i:3344450 original size:10 final size:9
Alignment explanation
Indices: 3344428--3344496 Score: 63
Period size: 9 Copynumber: 7.8 Consensus size: 9
3344418 TTATTCTTTA
3344428 AAAAAACAG-
1 AAAAAA-AGC
3344437 AAAAAAAGC
1 AAAAAAAGC
**
3344446 AAAAAGCGC
1 AAAAAAAGC
3344455 -AAAAAAG-
1 AAAAAAAGC
*
3344462 AAAAAACGC
1 AAAAAAAGC
3344471 AAAAAAGAGC
1 AAAAAA-AGC
*
3344481 AAAAAACGC
1 AAAAAAAGC
3344490 AAAAAAA
1 AAAAAAA
3344497 AGTTGCCTAC
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
8 13 0.27
9 27 0.56
10 8 0.17
ACGTcount: A:0.74, C:0.13, G:0.13, T:0.00
Consensus pattern (9 bp):
AAAAAAAGC
Found at i:3344458 original size:16 final size:17
Alignment explanation
Indices: 3344428--3344495 Score: 84
Period size: 17 Copynumber: 3.9 Consensus size: 17
3344418 TTATTCTTTA
*
3344428 AAAAAACAGAAAAAAAGC
1 AAAAAAC-GCAAAAAAGC
*
3344446 AAAAAGCGCAAAAAAG-
1 AAAAAACGCAAAAAAGC
3344462 AAAAAACGCAAAAAAGAGC
1 AAAAAACGC-AAAAA-AGC
3344481 AAAAAACGCAAAAAA
1 AAAAAACGCAAAAAA
3344496 AAGTTGCCTA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
16 8 0.18
17 14 0.32
18 13 0.30
19 9 0.20
ACGTcount: A:0.74, C:0.13, G:0.13, T:0.00
Consensus pattern (17 bp):
AAAAAACGCAAAAAAGC
Found at i:3347644 original size:32 final size:31
Alignment explanation
Indices: 3347599--3347694 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
3347589 CTTAGATAAT
3347599 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
3347630 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
*
3347662 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
3347693 TT
1 TT
3347695 GTAATTTGCC
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:3349540 original size:22 final size:21
Alignment explanation
Indices: 3349512--3349554 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
3349502 AAAGTGGCTT
*
3349512 AATGATAATAATAATAATAATA
1 AATGATAATAA-AATAACAATA
3349534 AATGATAATAAAATAACAATA
1 AATGATAATAAAATAACAATA
3349555 CGATATTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (21 bp):
AATGATAATAAAATAACAATA
Found at i:3351383 original size:10 final size:11
Alignment explanation
Indices: 3351343--3351413 Score: 54
Period size: 12 Copynumber: 6.2 Consensus size: 11
3351333 ACCAAAAAAA
3351343 TTAAAAA-ATT
1 TTAAAAATATT
*
3351353 TAAAAAAGTATT
1 TTAAAAA-TATT
3351365 TTAAAAATATT
1 TTAAAAATATT
* **
3351376 TTAAAATAAAAAA
1 TT-AAA-AATATT
*
3351389 TAAAAAATTATT
1 TTAAAAA-TATT
3351401 TTAAAAATATT
1 TTAAAAATATT
3351412 TT
1 TT
3351414 TTTATTTTTA
Statistics
Matches: 46, Mismatches: 10, Indels: 9
0.71 0.15 0.14
Matches are distributed among these distances:
10 6 0.13
11 14 0.30
12 22 0.48
13 4 0.09
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (11 bp):
TTAAAAATATT
Found at i:3351401 original size:36 final size:38
Alignment explanation
Indices: 3351339--3351413 Score: 118
Period size: 36 Copynumber: 2.0 Consensus size: 38
3351329 AAACACCAAA
3351339 AAAATTAAAAAATTTAAAAAAGTATTTTAAAAATATTTT
1 AAAATTAAAAAA-TTAAAAAAGTATTTTAAAAATATTTT
*
3351378 AAAA-TAAAAAA-TAAAAAATTATTTTAAAAATATTTT
1 AAAATTAAAAAATTAAAAAAGTATTTTAAAAATATTTT
3351414 TTTATTTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
36 24 0.69
38 7 0.20
39 4 0.11
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (38 bp):
AAAATTAAAAAATTAAAAAAGTATTTTAAAAATATTTT
Found at i:3351843 original size:15 final size:17
Alignment explanation
Indices: 3351825--3351862 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
3351815 AAGTTTATAA
3351825 TATTTTATAT-T-ATGT
1 TATTTTATATATGATGT
3351840 TATTTTTATATATGATGT
1 TA-TTTTATATATGATGT
3351858 TATTT
1 TATTT
3351863 AGAGCACATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 2 0.10
16 8 0.40
17 4 0.20
18 6 0.30
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.66
Consensus pattern (17 bp):
TATTTTATATATGATGT
Found at i:3351846 original size:16 final size:18
Alignment explanation
Indices: 3351827--3351862 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3351817 GTTTATAATA
3351827 TTTTATAT-T-ATGTTAT
1 TTTTATATATGATGTTAT
3351843 TTTTATATATGATGTTAT
1 TTTTATATATGATGTTAT
3351861 TT
1 TT
3351863 AGAGCACATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 1 0.06
18 9 0.50
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (18 bp):
TTTTATATATGATGTTAT
Found at i:3352842 original size:4 final size:4
Alignment explanation
Indices: 3352833--3352857 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3352823 TCTTACATAT
3352833 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
3352858 ACCAATCGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:3353308 original size:69 final size:69
Alignment explanation
Indices: 3353195--3353325 Score: 208
Period size: 69 Copynumber: 1.9 Consensus size: 69
3353185 GTGCGGAAGT
* *
3353195 CTCTTTGGGCAAAGGCAAATCTAACTTTTGTCGGAAATCCAAAGCAACATTTGGGCAGCAACTTT
1 CTCTTTGGACAAAGACAAATCTAACTTTTGTCGGAAATCCAAAGCAACATTTGGGCAGCAACTTT
3353260 TAGG
66 TAGG
* ** *
3353264 CTCTTTGGACAAAGACAAATCTACCTTTTGTCGGAAATTTAAAGCAACGTTTGGGCAGCAAC
1 CTCTTTGGACAAAGACAAATCTAACTTTTGTCGGAAATCCAAAGCAACATTTGGGCAGCAAC
3353326 AGCTTAATCT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 56 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (69 bp):
CTCTTTGGACAAAGACAAATCTAACTTTTGTCGGAAATCCAAAGCAACATTTGGGCAGCAACTTT
TAGG
Found at i:3355074 original size:25 final size:26
Alignment explanation
Indices: 3355046--3355096 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
3355036 TATAATATAT
3355046 TATATCAAA-TA-ATATTAAATTTTAA
1 TATATCAAACTATATATT-AATTTTAA
*
3355071 TATATTAAACTATATATTAATTTTAA
1 TATATCAAACTATATATTAATTTTAA
3355097 AACTATGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 8 0.35
26 10 0.43
27 5 0.22
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (26 bp):
TATATCAAACTATATATTAATTTTAA
Found at i:3356399 original size:51 final size:50
Alignment explanation
Indices: 3356331--3356488 Score: 220
Period size: 51 Copynumber: 3.2 Consensus size: 50
3356321 ATCACATTTA
3356331 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTT
1 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTT
* *
3356381 GTCACTTGTCACTGATCAGATAAGTGTTGCTGAAGCTACCAC-T-T-A---
1 -TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTT
* *
3356426 TCACTTGTCACTGATCAGATAAGTTTAGCTAAAGCTACCACTTATCTCTT
1 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTT
3356476 ATCACTTGTCACT
1 -TCACTTGTCACT
3356489 TGTCACTGAC
Statistics
Matches: 94, Mismatches: 6, Indels: 14
0.82 0.05 0.12
Matches are distributed among these distances:
44 38 0.40
45 1 0.01
46 1 0.01
48 1 0.01
49 1 0.01
50 1 0.01
51 51 0.54
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.34
Consensus pattern (50 bp):
TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTT
Found at i:3356424 original size:44 final size:44
Alignment explanation
Indices: 3356328--3356481 Score: 193
Period size: 44 Copynumber: 3.3 Consensus size: 44
3356318 CGGATCACAT
*
3356328 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTGATCAGATAAGTTTAGCTAAAGCTACCAC
*
3356372 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTT-GCTGAAGCTACCAC
1 -T-T-A----TCACTTGTCACTGATCAGATAAGT-TTAGCTAAAGCTACCAC
3356423 TTATCACTTGTCACTGATCAGATAAGTTTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTGATCAGATAAGTTTAGCTAAAGCTACCAC
* *
3356467 TTATCTCTTATCACT
1 TTATCACTTGTCACT
3356482 TGTCACTTGT
Statistics
Matches: 96, Mismatches: 5, Indels: 17
0.81 0.04 0.14
Matches are distributed among these distances:
43 2 0.02
44 50 0.52
45 1 0.01
46 1 0.01
47 1 0.01
48 1 0.01
49 1 0.01
50 1 0.01
51 37 0.39
52 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (44 bp):
TTATCACTTGTCACTGATCAGATAAGTTTAGCTAAAGCTACCAC
Found at i:3358451 original size:3 final size:3
Alignment explanation
Indices: 3358433--3358477 Score: 72
Period size: 3 Copynumber: 14.3 Consensus size: 3
3358423 CTTTTTATCC
3358433 TTA TCTA TTCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA T-TA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3358478 CCTTTAATTC
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 34 0.85
4 6 0.15
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:3358650 original size:36 final size:34
Alignment explanation
Indices: 3358583--3358650 Score: 84
Period size: 36 Copynumber: 1.9 Consensus size: 34
3358573 ATAATATTTA
*
3358583 TATATATTTTTTATTTCATATATATATACATACT
1 TATATATTTTTTATTTCATATATATACACATACT
*
3358617 TATATATTATTTATACTTT-ATATGTATACACATA
1 TATATATT-TTT-TA-TTTCATATATATACACATA
3358651 TATACATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 8 0.28
35 3 0.10
36 15 0.52
37 3 0.10
ACGTcount: A:0.37, C:0.09, G:0.01, T:0.53
Consensus pattern (34 bp):
TATATATTTTTTATTTCATATATATACACATACT
Found at i:3360198 original size:3 final size:3
Alignment explanation
Indices: 3360176--3360217 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
3360166 GAAATAAAAC
* *
3360176 TAA TAA TATA TAA TAG TAA TAA TAA TAA TAA TAA TGA TAA TA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3360218 GAAATTATCA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3361549 original size:6 final size:6
Alignment explanation
Indices: 3361538--3361669 Score: 264
Period size: 6 Copynumber: 22.0 Consensus size: 6
3361528 TACATACTTT
3361538 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
3361586 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
3361634 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
3361670 CCTTTTGTAT
Statistics
Matches: 126, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 126 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
ATATAC
Found at i:3366127 original size:10 final size:10
Alignment explanation
Indices: 3366103--3366189 Score: 61
Period size: 10 Copynumber: 8.5 Consensus size: 10
3366093 AAGAATGTTC
*
3366103 AAAAAACAAAC
1 AAAAAA-AAAG
3366114 AAAAAAAAAG
1 AAAAAAAAAG
* *
3366124 AAAAAATAAC
1 AAAAAAAAAG
3366134 AAAAAATAAA-
1 AAAAAA-AAAG
* *
3366144 AGAAAAGAAG
1 AAAAAAAAAG
3366154 AAAAATAAAAG
1 AAAAA-AAAAG
*
3366165 AAATAAAATA-
1 AAA-AAAAAAG
*
3366175 AAAGAAAAAG
1 AAAAAAAAAG
3366185 AAAAA
1 AAAAA
3366190 GGAGAAGCCA
Statistics
Matches: 59, Mismatches: 12, Indels: 11
0.72 0.15 0.13
Matches are distributed among these distances:
9 6 0.10
10 33 0.56
11 18 0.31
12 2 0.03
ACGTcount: A:0.83, C:0.03, G:0.08, T:0.06
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:3366134 original size:20 final size:19
Alignment explanation
Indices: 3366104--3366189 Score: 75
Period size: 20 Copynumber: 4.3 Consensus size: 19
3366094 AGAATGTTCA
3366104 AAAAACAAACAAAAAAAAAG
1 AAAAA-AAACAAAAAAAAAG
3366124 AAAAAATAACAAAAAATAAAAG
1 AAAAAA-AAC-AAAAA-AAAAG
* *
3366146 AAAAGAAGA-AAAATAAAAG
1 AAAA-AAAACAAAAAAAAAG
* *
3366165 AAATAAAATAAAAGAAAAAG
1 AAAAAAAACAAAA-AAAAAG
3366185 AAAAA
1 AAAAA
3366190 GGAGAAGCCA
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
18 3 0.06
19 13 0.24
20 21 0.39
21 5 0.09
22 10 0.19
23 2 0.04
ACGTcount: A:0.83, C:0.03, G:0.08, T:0.06
Consensus pattern (19 bp):
AAAAAAAACAAAAAAAAAG
Found at i:3366163 original size:14 final size:14
Alignment explanation
Indices: 3366114--3366181 Score: 70
Period size: 14 Copynumber: 4.9 Consensus size: 14
3366104 AAAAACAAAC
*
3366114 AAAAAAAAAG-AA-
1 AAAATAAAAGAAAT
*
3366126 AAAATAACAAAAAAT
1 AAAATAA-AAGAAAT
*
3366141 AAAAGAAAAGAAGA-
1 AAAATAAAAGAA-AT
3366155 AAAATAAAAGAAAT
1 AAAATAAAAGAAAT
3366169 AAAATAAAAGAAA
1 AAAATAAAAGAAA
3366182 AAGAAAAAGG
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
12 6 0.13
13 3 0.07
14 30 0.65
15 7 0.15
ACGTcount: A:0.82, C:0.01, G:0.09, T:0.07
Consensus pattern (14 bp):
AAAATAAAAGAAAT
Found at i:3368028 original size:44 final size:42
Alignment explanation
Indices: 3367964--3368103 Score: 144
Period size: 41 Copynumber: 3.3 Consensus size: 42
3367954 GTGGAGTAGA
* *
3367964 CAGAAAAAACCA-A-TCCTATCTCCCTGAAGTTGCAGTGGAG
1 CAGATAAAACCACAGTCTTATCTCCCTGAAGTTGCAGTGGAG
* * *
3368004 CGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAG
1 CAGA-TAAAACCACAG-TCTTATCTCCCTGAAGTTGCAGTGGAG
* * *
3368048 CAGATCACATC-CAGTCTTATCTCCCTGACA-TTGCAGTGGAG
1 CAGATAAAACCACAGTCTTATCTCCCTGA-AGTTGCAGTGGAG
3368089 CAGACTAAAACCACA
1 CAGA-TAAAACCACA
3368104 AACAACGTCC
Statistics
Matches: 79, Mismatches: 14, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
40 3 0.04
41 34 0.43
42 9 0.11
43 6 0.08
44 27 0.34
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.23
Consensus pattern (42 bp):
CAGATAAAACCACAGTCTTATCTCCCTGAAGTTGCAGTGGAG
Found at i:3373661 original size:35 final size:35
Alignment explanation
Indices: 3373621--3373740 Score: 186
Period size: 35 Copynumber: 3.3 Consensus size: 35
3373611 TGTTCCCGGC
*
3373621 CCCAACCCAAGCAAGTTGAACTCTCCTCTTTCATT
1 CCCAACCCAAGCAAGCTGAACTCTCCTCTTTCATT
3373656 CCCAACCCAAGCAAGCAAGCTGAACTCTCCTCTTTCATT
1 CCCAA-CC---CAAGCAAGCTGAACTCTCCTCTTTCATT
*
3373695 CCCAACCCAAGCAAGCTAAACTCTCCTCTTTCATT
1 CCCAACCCAAGCAAGCTGAACTCTCCTCTTTCATT
3373730 CCCAACCCAAG
1 CCCAACCCAAG
3373741 AAAAAAGGAG
Statistics
Matches: 79, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
35 43 0.54
36 2 0.03
38 2 0.03
39 32 0.41
ACGTcount: A:0.28, C:0.40, G:0.08, T:0.23
Consensus pattern (35 bp):
CCCAACCCAAGCAAGCTGAACTCTCCTCTTTCATT
Found at i:3373671 original size:39 final size:38
Alignment explanation
Indices: 3373628--3373740 Score: 178
Period size: 39 Copynumber: 3.0 Consensus size: 38
3373618 GGCCCCAACC
3373628 CAAGCAAGTTGAACTCTCCTCTTTCATTCCCAACCCAAG
1 CAAGCAAG-TGAACTCTCCTCTTTCATTCCCAACCCAAG
3373667 CAAGCAAGCTGAACTCTCCTCTTTCATTCCCAACCCAAG
1 CAAGCAAG-TGAACTCTCCTCTTTCATTCCCAACCCAAG
*
3373706 CAAGC---TAAACTCTCCTCTTTCATTCCCAACCCAAG
1 CAAGCAAGTGAACTCTCCTCTTTCATTCCCAACCCAAG
3373741 AAAAAAGGAG
Statistics
Matches: 72, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
35 29 0.40
39 43 0.60
ACGTcount: A:0.28, C:0.38, G:0.09, T:0.25
Consensus pattern (38 bp):
CAAGCAAGTGAACTCTCCTCTTTCATTCCCAACCCAAG
Found at i:3374542 original size:1 final size:1
Alignment explanation
Indices: 3374533--3374568 Score: 54
Period size: 1 Copynumber: 36.0 Consensus size: 1
3374523 TTAATTAAAT
* *
3374533 AAAATAAAAATAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3374569 TAAATATTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.94, C:0.00, G:0.00, T:0.06
Consensus pattern (1 bp):
A
Found at i:3375616 original size:35 final size:35
Alignment explanation
Indices: 3375570--3375689 Score: 177
Period size: 35 Copynumber: 3.3 Consensus size: 35
3375560 CTCCTTTTTT
3375570 CTTGGGTTGGGAATGAAAGAGGAGAGTTTAGCTTG
1 CTTGGGTTGGGAATGAAAGAGGAGAGTTTAGCTTG
*
3375605 CTTGGGTTGGGAATGAAAGAGGAGAGTTCAGCTTGCTTG
1 CTTGGGTTGGGAATGAAAGAGGAGAGTT----TAGCTTG
* *
3375644 CTTGGGTTGGGAATGAAAGAGGAGAGTTCAACTTG
1 CTTGGGTTGGGAATGAAAGAGGAGAGTTTAGCTTG
3375679 CTTGGGTTGGG
1 CTTGGGTTGGG
3375690 GCCGGGAACA
Statistics
Matches: 77, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
35 43 0.56
39 34 0.44
ACGTcount: A:0.23, C:0.08, G:0.40, T:0.28
Consensus pattern (35 bp):
CTTGGGTTGGGAATGAAAGAGGAGAGTTTAGCTTG
Found at i:3375654 original size:39 final size:38
Alignment explanation
Indices: 3375570--3375682 Score: 178
Period size: 39 Copynumber: 3.0 Consensus size: 38
3375560 CTCCTTTTTT
*
3375570 CTTGGGTTGGGAATGAAAGAGGAGAGTT---TAGCTTG
1 CTTGGGTTGGGAATGAAAGAGGAGAGTTCACTTGCTTG
3375605 CTTGGGTTGGGAATGAAAGAGGAGAGTTCAGCTTGCTTG
1 CTTGGGTTGGGAATGAAAGAGGAGAGTTCA-CTTGCTTG
3375644 CTTGGGTTGGGAATGAAAGAGGAGAGTTCAACTTGCTTG
1 CTTGGGTTGGGAATGAAAGAGGAGAGTTC-ACTTGCTTG
3375683 GGTTGGGGCC
Statistics
Matches: 72, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
35 28 0.39
39 43 0.60
40 1 0.01
ACGTcount: A:0.25, C:0.09, G:0.38, T:0.28
Consensus pattern (38 bp):
CTTGGGTTGGGAATGAAAGAGGAGAGTTCACTTGCTTG
Found at i:3381293 original size:41 final size:43
Alignment explanation
Indices: 3381226--3381338 Score: 133
Period size: 44 Copynumber: 2.7 Consensus size: 43
3381216 GTGGTTTTAG
*
3381226 TCTGCTCCACTGCAA-TGTCAGGGAGATAAGA-C-TGGATGTGA
1 TCTGCTCCACTGCAACT-TCAGGGAGATAAGATCGTGGATGTAA
* * * *
3381267 TCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATC-GTGGATGTAA
*
3381311 TCCGCTCCACTGCAACTTCAGGGAGATA
1 TCTGCTCCACTGCAACTTCAGGGAGATA
3381339 GGATTGGTTT
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
41 27 0.45
42 2 0.03
44 31 0.52
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (43 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGATCGTGGATGTAA
Found at i:3381327 original size:44 final size:43
Alignment explanation
Indices: 3381215--3381338 Score: 146
Period size: 41 Copynumber: 2.9 Consensus size: 43
3381205 GGACGTTGTT
*
3381215 TGTGGTTTTAGTCTGCTCCACTGCAA-TGTCAGGGAGATAAGAC
1 TGTGGTTTTAATCTGCTCCACTGCAACT-TCAGGGAGATAAGAC
* * * * *
3381258 --TGGATGTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATC
1 TGTGGTTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-C
*
3381300 TGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATA
1 TGTGGTTTTAATCTGCTCCACTGCAACTTCAGGGAGATA
3381339 GGATTGGTTT
Statistics
Matches: 65, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
41 32 0.49
42 2 0.03
44 31 0.48
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (43 bp):
TGTGGTTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAC
Found at i:3382248 original size:24 final size:24
Alignment explanation
Indices: 3382193--3382250 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
3382183 CGGATTGCCC
*
3382193 CCACTGTAATCTTCAAAGTTCAAT
1 CCACTATAATCTTCAAAGTTCAAT
* * *
3382217 CCGCTATAATCTTCAAGGTTCAGT
1 CCACTATAATCTTCAAAGTTCAAT
*
3382241 CCATTATAAT
1 CCACTATAAT
3382251 TTTAGGACAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.34
Consensus pattern (24 bp):
CCACTATAATCTTCAAAGTTCAAT
Found at i:3383155 original size:14 final size:13
Alignment explanation
Indices: 3383134--3383203 Score: 72
Period size: 14 Copynumber: 5.2 Consensus size: 13
3383124 CTCCTTTTTC
3383134 TTTTTCTTTTATT
1 TTTTTCTTTTATT
3383147 TTATTTCTTTTATT
1 TT-TTTCTTTTATT
*
3383161 TTTCTTCTTTTCTT
1 TTT-TTCTTTTATT
*
3383175 TTATTTTTTGTTA-T
1 TT-TTTCTT-TTATT
3383189 TTTTTCTTTT-TT
1 TTTTTCTTTTATT
3383201 TTT
1 TTT
3383204 GTTTGTTTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
12 6 0.12
13 8 0.17
14 31 0.65
15 3 0.06
ACGTcount: A:0.07, C:0.09, G:0.01, T:0.83
Consensus pattern (13 bp):
TTTTTCTTTTATT
Found at i:3383162 original size:19 final size:18
Alignment explanation
Indices: 3383130--3383203 Score: 64
Period size: 19 Copynumber: 3.9 Consensus size: 18
3383120 GCTTCTCCTT
*
3383130 TTTCTTTTTCTTTTATTTTA
1 TTTC-TTTTATTTT-TTTTA
3383150 TTTCTTTTATTTTTCTTCT-
1 TTTCTTTTATTTTT-TT-TA
3383169 TTTCTTTTATTTTTTGTTA
1 TTTCTTTTATTTTTT-TTA
3383188 TTT-TTTCT-TTTTTTTT
1 TTTCTTT-TATTTTTTTT
3383204 GTTTGTTTTT
Statistics
Matches: 48, Mismatches: 1, Indels: 13
0.77 0.02 0.21
Matches are distributed among these distances:
17 2 0.04
18 12 0.25
19 29 0.60
20 5 0.10
ACGTcount: A:0.07, C:0.09, G:0.01, T:0.82
Consensus pattern (18 bp):
TTTCTTTTATTTTTTTTA
Found at i:3383213 original size:20 final size:20
Alignment explanation
Indices: 3383128--3383206 Score: 72
Period size: 20 Copynumber: 3.9 Consensus size: 20
3383118 TGGCTTCTCC
*
3383128 TTTTTCTTTTTCTTTTATT-T
1 TTTTTCTTTTT-TTTTGTTAT
* * *
3383148 TATTTCTTTTATTTTTCTTCT
1 TTTTTCTTTT-TTTTTGTTAT
*
3383169 TTTCTT-TTATTTTTTGTTAT
1 TTT-TTCTTTTTTTTTGTTAT
3383189 TTTTTCTTTTTTTTTGTT
1 TTTTTCTTTTTTTTTGTT
3383207 TGTTTTTTGA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
19 2 0.04
20 37 0.77
21 7 0.15
22 2 0.04
ACGTcount: A:0.06, C:0.09, G:0.03, T:0.82
Consensus pattern (20 bp):
TTTTTCTTTTTTTTTGTTAT
Found at i:3387668 original size:6 final size:6
Alignment explanation
Indices: 3387657--3387782 Score: 252
Period size: 6 Copynumber: 21.0 Consensus size: 6
3387647 ATACAAAAGG
3387657 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
3387705 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
3387753 GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT
3387783 AAAGTATGTA
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 120 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
GTATAT
Found at i:3388710 original size:36 final size:36
Alignment explanation
Indices: 3388658--3388727 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
3388648 ATACTAGTAT
3388658 AAAACGGCGCCGTTTGGCCTTAGGGTTCAGAGACCA
1 AAAACGGCGCCGTTTGGCCTTAGGGTTCAGAGACCA
*
3388694 AAAATGGCGCCGTTTGGCCTTAGGGTTCAGAGAC
1 AAAACGGCGCCGTTTGGCCTTAGGGTTCAGAGAC
3388728 TTTGGTCTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.24, C:0.23, G:0.31, T:0.21
Consensus pattern (36 bp):
AAAACGGCGCCGTTTGGCCTTAGGGTTCAGAGACCA
Found at i:3389118 original size:3 final size:3
Alignment explanation
Indices: 3389103--3389144 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
3389093 TGATAATTTC
* *
3389103 TAT TAT CAT TAT TAT TAT TAT TAT TAC TAT TAT ATAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TA
3389145 GTTTTATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:3390849 original size:3 final size:3
Alignment explanation
Indices: 3390841--3390884 Score: 63
Period size: 3 Copynumber: 14.3 Consensus size: 3
3390831 GAATTAAAGG
3390841 ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ATGA ATA GATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA -ATA A
3390885 GGATAAAAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 2 0.05
3 30 0.79
4 6 0.16
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3390866 original size:17 final size:18
Alignment explanation
Indices: 3390844--3390879 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
3390834 TTAAAGGATA
3390844 ATAATAATAATAAT-AAT
1 ATAATAATAATAATGAAT
3390861 ATAATAATAATAATGAAT
1 ATAATAATAATAATGAAT
3390879 A
1 A
3390880 GATAAGGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (18 bp):
ATAATAATAATAATGAAT
Found at i:3390866 original size:20 final size:21
Alignment explanation
Indices: 3390841--3390879 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
3390831 GAATTAAAGG
3390841 ATAATAATAATAAT-AATAAT
1 ATAATAATAATAATGAATAAT
3390861 ATAATAATAATAATGAATA
1 ATAATAATAATAATGAATA
3390880 GATAAGGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (21 bp):
ATAATAATAATAATGAATAAT
Found at i:3390884 original size:20 final size:20
Alignment explanation
Indices: 3390840--3390884 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
3390830 GGAATTAAAG
3390840 GATAATAATAATAATAATAA
1 GATAATAATAATAATAATAA
*
3390860 TATAATAATAATAATGAAT-A
1 GATAATAATAATAAT-AATAA
3390880 GATAA
1 GATAA
3390885 GGATAAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (20 bp):
GATAATAATAATAATAATAA
Found at i:3392877 original size:51 final size:50
Alignment explanation
Indices: 3392817--3392977 Score: 219
Period size: 51 Copynumber: 3.3 Consensus size: 50
3392807 GTCAGTGACA
3392817 AGTGACAAGTGATAAGAGATAAGTGGTAGCTTTAGCTAAACTTATCTGATC
1 AGTGACAAGTGATAAG-GATAAGTGGTAGCTTTAGCTAAACTTATCTGATC
*
3392868 AGTGACAA--G-T---GATAAGTGGTAGCTTCAGC-AACACTTATCTGATC
1 AGTGACAAGTGATAAGGATAAGTGGTAGCTTTAGCTAA-ACTTATCTGATC
* *
3392912 AGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
1 AGTGACAAGTGATAAG-GATAAGTGGTAGCTTTAGCTAAACTTATCTGATC
3392963 AGTGACAAGTGATAA
1 AGTGACAAGTGATAA
3392978 ATGTGATCCG
Statistics
Matches: 96, Mismatches: 5, Indels: 18
0.81 0.04 0.15
Matches are distributed among these distances:
43 2 0.02
44 38 0.40
46 1 0.01
48 1 0.01
49 1 0.01
51 52 0.54
52 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (50 bp):
AGTGACAAGTGATAAGGATAAGTGGTAGCTTTAGCTAAACTTATCTGATC
Found at i:3392882 original size:44 final size:44
Alignment explanation
Indices: 3392824--3392977 Score: 193
Period size: 44 Copynumber: 3.3 Consensus size: 44
3392814 ACAAGTGACA
* *
3392824 AGTGATAAGAGATAAGTGGTAGCTTTAGCTAAACTTATCTGATC
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTAAACTTATCTGATC
*
3392868 AGTGACAAGTGATAAGTGGTAGCTTCAGC-AACACTTATCTGATCAGTGAC
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTAA-ACTTATCTG---A-T--C
*
3392918 AAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
1 -AGTGACAAGTGATAAGTGGTAGCTTTAGCTAAACTTATCTGATC
3392963 AGTGACAAGTGATAA
1 AGTGACAAGTGATAA
3392978 ATGTGATCCG
Statistics
Matches: 96, Mismatches: 5, Indels: 18
0.81 0.04 0.15
Matches are distributed among these distances:
43 2 0.02
44 50 0.52
45 1 0.01
47 2 0.02
48 2 0.02
50 1 0.01
51 37 0.39
52 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (44 bp):
AGTGACAAGTGATAAGTGGTAGCTTTAGCTAAACTTATCTGATC
Found at i:3396097 original size:69 final size:69
Alignment explanation
Indices: 3395985--3396115 Score: 208
Period size: 69 Copynumber: 1.9 Consensus size: 69
3395975 AGATTAAGCT
* *
3395985 GTTGCTGCCCAAACGTTGCTTTAAATTTCCGACAAAAGGTAGATTTGTCTTTGTCCAAAGAGCCT
1 GTTGCTGCCCAAACGTTGCTTTAAATTTCCGACAAAAGGTAGATTTGCCTTTGCCCAAAGAGCCT
3396050 AAAA
66 AAAA
* ** *
3396054 GTTGCTGCCCAAATGTTGCTTTGGATTTCCGACAAAAGTTAGATTTGCCTTTGCCCAAAGAG
1 GTTGCTGCCCAAACGTTGCTTTAAATTTCCGACAAAAGGTAGATTTGCCTTTGCCCAAAGAG
3396116 ACTTCCGCAC
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 56 1.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (69 bp):
GTTGCTGCCCAAACGTTGCTTTAAATTTCCGACAAAAGGTAGATTTGCCTTTGCCCAAAGAGCCT
AAAA
Found at i:3396462 original size:4 final size:4
Alignment explanation
Indices: 3396453--3396477 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3396443 TGCGATTGGT
3396453 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
3396478 ATATGTAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:3397484 original size:15 final size:18
Alignment explanation
Indices: 3397447--3397482 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3397437 AATGTGCTCT
3397447 AAATAACATCATATATAA
1 AAATAACATCATATATAA
3397465 AAATAACAT-A-ATATAA
1 AAATAACATCATATATAA
3397481 AA
1 AA
3397483 TATTATAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 1 0.06
18 9 0.50
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (18 bp):
AAATAACATCATATATAA
Found at i:3397910 original size:11 final size:11
Alignment explanation
Indices: 3397894--3397964 Score: 61
Period size: 12 Copynumber: 6.2 Consensus size: 11
3397884 TAAAAATAAA
3397894 AAAATATTTTT
1 AAAATATTTTT
3397905 AAAATAATTTTT
1 AAAAT-ATTTTT
* ** *
3397917 TATTTTTATTTT
1 AAAATAT-TTTT
3397929 AAAATATTTTT
1 AAAATATTTTT
3397940 AAAATACTTTTT
1 AAAATA-TTTTT
* *
3397952 TAAATTTTTTT
1 AAAATATTTTT
3397963 AA
1 AA
3397965 TTTTTTTGGT
Statistics
Matches: 46, Mismatches: 11, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
11 22 0.48
12 24 0.52
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (11 bp):
AAAATATTTTT
Found at i:3399781 original size:22 final size:21
Alignment explanation
Indices: 3399746--3399788 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
3399736 ATTAATATCG
*
3399746 TATTGTTATTTTATTATCATT
1 TATTATTATTTTATTATCATT
3399767 TATTATTATTATTATTATCATT
1 TATTATTATT-TTATTATCATT
3399789 AAGCCACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (21 bp):
TATTATTATTTTATTATCATT
Found at i:3401699 original size:31 final size:31
Alignment explanation
Indices: 3401606--3401701 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
3401596 GGCAAATTAC
*
3401606 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
3401637 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
3401669 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
3401700 AA
1 AA
3401702 ATTATCTAAG
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.31
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:3404871 original size:19 final size:19
Alignment explanation
Indices: 3404847--3404908 Score: 99
Period size: 19 Copynumber: 3.3 Consensus size: 19
3404837 TAGGTAACCT
3404847 TTTTTTGCGTTTTTTGCTC
1 TTTTTTGCGTTTTTTGCTC
*
3404866 TTTTTTGCGTTTTTTACTC
1 TTTTTTGCGTTTTTTGCTC
*
3404885 TTTTTTGCGCTTTTTGCT-
1 TTTTTTGCGTTTTTTGCTC
3404903 TTTTTT
1 TTTTTT
3404909 CTATTTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
18 6 0.15
19 34 0.85
ACGTcount: A:0.02, C:0.15, G:0.13, T:0.71
Consensus pattern (19 bp):
TTTTTTGCGTTTTTTGCTC
Found at i:3404908 original size:9 final size:9
Alignment explanation
Indices: 3404845--3404917 Score: 67
Period size: 9 Copynumber: 7.9 Consensus size: 9
3404835 GGTAGGTAAC
3404845 CTTTTTTTG
1 CTTTTTTTG
*
3404854 CGTTTTTTG
1 CTTTTTTTG
3404863 CTCTTTTTTG
1 CT-TTTTTTG
* *
3404873 CGTTTTTTA
1 CTTTTTTTG
3404882 CTCTTTTTTG
1 CT-TTTTTTG
**
3404892 CGCTTTTTG
1 CTTTTTTTG
3404901 CTTTTTTT-
1 CTTTTTTTG
3404909 CTATTTTTT
1 CT-TTTTTT
3404918 TAAAGAATAA
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
8 2 0.04
9 34 0.67
10 15 0.29
ACGTcount: A:0.03, C:0.15, G:0.11, T:0.71
Consensus pattern (9 bp):
CTTTTTTTG
Found at i:3405554 original size:31 final size:31
Alignment explanation
Indices: 3405461--3405556 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
3405451 GGCAAATTAC
*
3405461 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
3405492 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
3405524 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
3405555 AA
1 AA
3405557 ATTATCTAAG
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.31
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:3410915 original size:15 final size:15
Alignment explanation
Indices: 3410860--3410916 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
3410850 TTTGAGTCGT
*
3410860 AAAAAATGAAAATGA
1 AAAAAATAAAAATGA
**
3410875 AATGAA-AAAAAT-A
1 AAAAAATAAAAATGA
*
3410888 GAAAAATAAAAATGA
1 AAAAAATAAAAATGA
3410903 AAAAAATAAAAATG
1 AAAAAATAAAAATG
3410917 GAAAGAGTAA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
13 4 0.12
14 11 0.33
15 18 0.55
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.14
Consensus pattern (15 bp):
AAAAAATAAAAATGA
Found at i:3412877 original size:50 final size:50
Alignment explanation
Indices: 3412809--3412975 Score: 138
Period size: 50 Copynumber: 3.3 Consensus size: 50
3412799 TAGTAGGAAC
* * *
3412809 AGATTAAAGCTACGACGACGGATCTGGTTTCCCCGACATTGCAATTAAAA
1 AGATTAAAGCCACAACGACGGATCTGATTTCCCCGACATTGCAATTAAAA
* * * ** ** * ** *
3412859 AGATTAAAGCCACAACGACGAATCTTACTT-CCTTAGCGGTGCAGTGGAAC
1 AGATTAAAGCCACAACGACGGATCTGATTTCCCCGA-CATTGCAATTAAAA
* * * * *
3412909 AGATTGAAGCTACGACGGCGGATCTGATTTCCCCGATATTGCAATTAAAA
1 AGATTAAAGCCACAACGACGGATCTGATTTCCCCGACATTGCAATTAAAA
*
3412959 AGATTGAAGCCACAACG
1 AGATTAAAGCCACAACG
3412976 GCAAATCTTA
Statistics
Matches: 83, Mismatches: 32, Indels: 4
0.70 0.27 0.03
Matches are distributed among these distances:
49 3 0.04
50 77 0.93
51 3 0.04
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.23
Consensus pattern (50 bp):
AGATTAAAGCCACAACGACGGATCTGATTTCCCCGACATTGCAATTAAAA
Found at i:3412924 original size:100 final size:100
Alignment explanation
Indices: 3412559--3413148 Score: 639
Period size: 100 Copynumber: 5.9 Consensus size: 100
3412549 ACAGTGGAAC
* ** * * *
3412559 AGATTGAAGCCACAACGATGAATCTTGTTTCCCTGGTGGTGTAGTGGAACAGATAGAAGCCACGA
1 AGATTGAAGCCACAACGACGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
* * * *
3412624 TGGTGGATCTGGTTTTCCCAACAATTACAATTAAAA
66 CGGCGGATCTGGTTTCCCCGAC-ATTACAATTAAAA
* * * * * *
3412660 AGATTGAAGCCACAACGGCGAACCTTACTTCCCTGGAGGTATAGTGGAATAGATTGAAGCCACGA
1 AGATTGAAGCCACAACGACGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
* * * *
3412725 CGGTGGATCTGGTTTCTCTGACTTTACAATT--AA
66 CGGCGGATCTGGTTTCCCCGACATTACAATTAAAA
* * * *
3412758 AGATTAAAGCCACAACGACAAATCTTACTTCCTTGGCGGTGTAGTAGGAACAGATTAAAGCTACG
1 AGATTGAAGCCACAACGACGAATCTTACTTCCCTGGCGGTGTAGT-GGAACAGATTGAAGCTACG
* *
3412823 ACGACGGATCTGGTTTCCCCGACATTGCAATTAAAA
65 ACGGCGGATCTGGTTTCCCCGACATTACAATTAAAA
* * * *
3412859 AGATTAAAGCCACAACGACGAATCTTACTTCCTTAGCGGTGCAGTGGAACAGATTGAAGCTACGA
1 AGATTGAAGCCACAACGACGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
* * *
3412924 CGGCGGATCTGATTTCCCCGATATTGCAATTAAAA
66 CGGCGGATCTGGTTTCCCCGACATTACAATTAAAA
* * * ** * * *
3412959 AGATTGAAGCCACAACGGCAAATCTTACTTCCCTAGTAGTGCAGTAGAACAAATTGAAGCTACGA
1 AGATTGAAGCCACAACGACGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
* *
3413024 CGGCGGATCTAGTTTCCCCGATATTACAATTAAAA
66 CGGCGGATCTGGTTTCCCCGACATTACAATTAAAA
* * * ** * *
3413059 A-AGTTGAAGCCACAATGGCGGATCTTACTTCTTTGGCAGTGTAGTGGAATAGATTGAAG-TCAC
1 AGA-TTGAAGCCACAACGACGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCT-AC
* * *
3413122 AACGGCGAATCTTGTTTCCCCGACATT
64 GACGGCGGATCTGGTTTCCCCGACATT
3413149 GTAGTTAAAC
Statistics
Matches: 420, Mismatches: 64, Indels: 11
0.85 0.13 0.02
Matches are distributed among these distances:
98 40 0.10
99 44 0.10
100 219 0.52
101 117 0.28
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (100 bp):
AGATTGAAGCCACAACGACGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
CGGCGGATCTGGTTTCCCCGACATTACAATTAAAA
Found at i:3412991 original size:50 final size:50
Alignment explanation
Indices: 3412837--3413089 Score: 167
Period size: 50 Copynumber: 5.1 Consensus size: 50
3412827 CGGATCTGGT
* * * *
3412837 TTCCCCGACATTGCAATTAAAAAGATTAAAGCCACAACGACGAATCTTAC
1 TTCCCCGATATTGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTAC
** *** * ** * * * * *
3412887 TT-CCTTAGCGGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGAT
1 TTCCCCGA-TATTGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTAC
**
3412937 TTCCCCGATATTGCAATTAAAAAGATTGAAGCCACAACGGCAAATCTTAC
1 TTCCCCGATATTGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTAC
* * * * * *
3412987 TT-CCCTAGTAGTGC-AGTAGAACAA-ATTGAAGCTACGACGGCGGATC-TAGT
1 TTCCCCGA-TATTGCAATTA-AA-AAGATTGAAGCCACAACGGCGGATCTTA-C
* *
3413037 TTCCCCGATATTACAATTAAAAA-AGTTGAAGCCACAATGGCGGATCTTAC
1 TTCCCCGATATTGCAATTAAAAAGA-TTGAAGCCACAACGGCGGATCTTAC
3413087 TTC
1 TTC
3413090 TTTGGCAGTG
Statistics
Matches: 147, Mismatches: 46, Indels: 20
0.69 0.22 0.09
Matches are distributed among these distances:
49 15 0.10
50 118 0.80
51 14 0.10
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.25
Consensus pattern (50 bp):
TTCCCCGATATTGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTAC
Found at i:3414683 original size:22 final size:21
Alignment explanation
Indices: 3414648--3414690 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
3414638 ATTAATATCG
*
3414648 TATTGTTATTTTATTATCATT
1 TATTATTATTTTATTATCATT
3414669 TATTATTATTATTATTATCATT
1 TATTATTATT-TTATTATCATT
3414691 AAGCCACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (21 bp):
TATTATTATTTTATTATCATT
Found at i:3416188 original size:19 final size:21
Alignment explanation
Indices: 3416166--3416205 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
3416156 ACTTCACATT
*
3416166 AATATTTTAA-TCA-TAATAA
1 AATATTTAAACTCACTAATAA
3416185 AATATTTAAACTCACTAATAA
1 AATATTTAAACTCACTAATAA
3416206 TATTATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 3 0.17
21 6 0.33
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.38
Consensus pattern (21 bp):
AATATTTAAACTCACTAATAA
Found at i:3416839 original size:13 final size:13
Alignment explanation
Indices: 3416821--3416862 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
3416811 TAACTCTTCA
3416821 ATATTACATCAAT
1 ATATTACATCAAT
**
3416834 ATATTA-ATGTA-
1 ATATTACATCAAT
3416845 ATATTACATCAAT
1 ATATTACATCAAT
3416858 ATATT
1 ATATT
3416863 CAAACATAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
11 6 0.26
12 6 0.26
13 11 0.48
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (13 bp):
ATATTACATCAAT
Found at i:3418781 original size:77 final size:77
Alignment explanation
Indices: 3418690--3418837 Score: 278
Period size: 77 Copynumber: 1.9 Consensus size: 77
3418680 AAAATGATAG
*
3418690 ATACATATAATTCCTTCCTTTATCTGCTCCAAGAAATTCTAATGCTTATTATGGAAAAGTCTCAA
1 ATACATATAATTCCTTCCTTTATCTGCTCCAAGAAATTCTAATGCTTATCATGGAAAAGTCTCAA
3418755 ACAGTCATAAAT
66 ACAGTCATAAAT
*
3418767 ATACATATAATTCCTTCCTTTATCTGCTCCAAGAAATTCTAATGCTTGTCATGGAAAAGTCTCAA
1 ATACATATAATTCCTTCCTTTATCTGCTCCAAGAAATTCTAATGCTTATCATGGAAAAGTCTCAA
3418832 ACAGTC
66 ACAGTC
3418838 GTTAATTCTT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
77 69 1.00
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.34
Consensus pattern (77 bp):
ATACATATAATTCCTTCCTTTATCTGCTCCAAGAAATTCTAATGCTTATCATGGAAAAGTCTCAA
ACAGTCATAAAT
Found at i:3420322 original size:40 final size:41
Alignment explanation
Indices: 3420181--3420332 Score: 243
Period size: 41 Copynumber: 3.7 Consensus size: 41
3420171 AGATTCATTA
*
3420181 GATGAAAAAGGGGTTGCTAAGTGCAAATTCCCCGAATCACT
1 GATGAAAAAGGGGTTGCTAAGTGCAGATTCCCCGAATCACT
* *
3420222 GATGAAAAAGGAGTTGCTAAGTGCAGATTCCCAGAATCACT
1 GATGAAAAAGGGGTTGCTAAGTGCAGATTCCCCGAATCACT
* * *
3420263 AATGAAAAAGGGGTTGCTAAGTGCAGATTCCCCGAAACTCT
1 GATGAAAAAGGGGTTGCTAAGTGCAGATTCCCCGAATCACT
3420304 GAT-AAAAAGGGGTTGCTAAGTGCAGATTC
1 GATGAAAAAGGGGTTGCTAAGTGCAGATTC
3420333 TCTGAATTAT
Statistics
Matches: 102, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
40 26 0.25
41 76 0.75
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (41 bp):
GATGAAAAAGGGGTTGCTAAGTGCAGATTCCCCGAATCACT
Found at i:3423418 original size:19 final size:21
Alignment explanation
Indices: 3423396--3423435 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
3423386 ACTTTACATT
*
3423396 AATATTTTAA-TCA-TAATAA
1 AATATTTAAACTCACTAATAA
3423415 AATATTTAAACTCACTAATAA
1 AATATTTAAACTCACTAATAA
3423436 TATTGTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 3 0.17
21 6 0.33
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.38
Consensus pattern (21 bp):
AATATTTAAACTCACTAATAA
Found at i:3432756 original size:24 final size:22
Alignment explanation
Indices: 3432729--3432780 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
3432719 AGACACACCA
3432729 TAGCTCGAAAGACAGTCCCGTTAT
1 TAGCTCGAAAG--AGTCCCGTTAT
** *
3432753 TAGCTCTTATGAGTCCCGTTAT
1 TAGCTCGAAAGAGTCCCGTTAT
3432775 TAGCTC
1 TAGCTC
3432781 TTATGAGCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 17 0.68
24 8 0.32
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (22 bp):
TAGCTCGAAAGAGTCCCGTTAT
Found at i:3432769 original size:22 final size:22
Alignment explanation
Indices: 3432742--3432787 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
3432732 CTCGAAAGAC
3432742 AGTCCCGTTATTAGCTCTTATG
1 AGTCCCGTTATTAGCTCTTATG
3432764 AGTCCCGTTATTAGCTCTTATG
1 AGTCCCGTTATTAGCTCTTATG
3432786 AG
1 AG
3432788 CTTTTTGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.39
Consensus pattern (22 bp):
AGTCCCGTTATTAGCTCTTATG
Found at i:3433827 original size:31 final size:31
Alignment explanation
Indices: 3433784--3433843 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
3433774 TAAGACTTAG
*
3433784 TTTTTGGTTGGATTTAAGGGTTATGAATTAA
1 TTTTTGGCTGGATTTAAGGGTTATGAATTAA
3433815 TTTTTGGCTGGATTTAAGGGTTATGAATT
1 TTTTTGGCTGGATTTAAGGGTTATGAATT
3433844 GGCTTGTGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.23, C:0.02, G:0.27, T:0.48
Consensus pattern (31 bp):
TTTTTGGCTGGATTTAAGGGTTATGAATTAA
Found at i:3436296 original size:6 final size:6
Alignment explanation
Indices: 3436285--3436310 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3436275 CTTTTTGAAT
3436285 AACAAA AACAAA AACAAA AACAAA AA
1 AACAAA AACAAA AACAAA AACAAA AA
3436311 AAACCTAATT
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:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (6 bp):
AACAAA
Found at i:3437194 original size:34 final size:33
Alignment explanation
Indices: 3437146--3437262 Score: 128
Period size: 34 Copynumber: 3.5 Consensus size: 33
3437136 TTTTAAAAAA
3437146 TAAATTAGGGTTTAGAGTTTTTTTAAAAATTAAT
1 TAAATTAGGGTTTAGAG-TTTTTTAAAAATTAAT
* * * *
3437180 TAAATTAGGTTTTAGCG-GTATTAAATTAATTAAT
1 TAAATTAGGGTTTAGAGTTTTTTAAA--AATTAAT
* * *
3437214 TAAATTAAGGTTTAAAGTTTTTAAGAAAATTAAT
1 TAAATTAGGGTTTAGAGTTTTTTA-AAAATTAAT
3437248 TAAATTAGGGTTTAG
1 TAAATTAGGGTTTAG
3437263 TTTTAAAAAA
Statistics
Matches: 66, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
32 6 0.09
34 55 0.83
35 3 0.05
36 2 0.03
ACGTcount: A:0.40, C:0.01, G:0.15, T:0.44
Consensus pattern (33 bp):
TAAATTAGGGTTTAGAGTTTTTTAAAAATTAAT
Found at i:3437491 original size:10 final size:10
Alignment explanation
Indices: 3437476--3437501 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
3437466 ATTTTATTAA
3437476 ATAAAACAAT
1 ATAAAACAAT
3437486 ATAAAACAAT
1 ATAAAACAAT
3437496 ATAAAA
1 ATAAAA
3437502 ATAGTTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.73, C:0.08, G:0.00, T:0.19
Consensus pattern (10 bp):
ATAAAACAAT
Found at i:3439825 original size:46 final size:45
Alignment explanation
Indices: 3439758--3439873 Score: 175
Period size: 46 Copynumber: 2.6 Consensus size: 45
3439748 TTTGAGTACT
3439758 TCTGATCAAGTGACAAAGTGATAAGTGGTAG-CATTAACTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGTC--TAACTACACTTA
*
3439804 TCTGATCAAGTGACAAAGTGATAAGTGGTAGTCTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGTCTAACTACACTTA
*
3439849 TCTGATC-AGGGAC-AAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
3439874 ATCATAAGTA
Statistics
Matches: 67, Mismatches: 2, Indels: 5
0.91 0.03 0.07
Matches are distributed among these distances:
43 12 0.18
44 5 0.07
45 18 0.27
46 31 0.46
47 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (45 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGTCTAACTACACTTA
Found at i:3440614 original size:18 final size:18
Alignment explanation
Indices: 3440588--3440627 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
3440578 GACTGGGAAA
*
3440588 AGGAAACATATAAGGGTT
1 AGGAAACATATAAGGGCT
*
3440606 AGGACACATATAAGGGCT
1 AGGAAACATATAAGGGCT
3440624 AGGA
1 AGGA
3440628 TACGCACCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.10, G:0.30, T:0.17
Consensus pattern (18 bp):
AGGAAACATATAAGGGCT
Found at i:3442279 original size:21 final size:21
Alignment explanation
Indices: 3442253--3442308 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
3442243 AACAGCGGTG
*
3442253 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
3442274 GCGGTGAGATTAGATACTGTA
1 GCGGTGAGATTAGATACTGTA
*
3442295 GCAGTGAGATTAGA
1 GCGGTGAGATTAGA
3442309 AACAGCGATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.29, C:0.09, G:0.34, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:3445305 original size:6 final size:6
Alignment explanation
Indices: 3445294--3445331 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
3445284 TTTGCAACCC
*
3445294 AAGGGG AAGGGG AAAGGG AAGGGG AAGGGG AAAGGGG A
1 AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG -AAGGGG A
3445332 GAAGAAGGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (6 bp):
AAGGGG
Found at i:3445317 original size:18 final size:18
Alignment explanation
Indices: 3445294--3445329 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3445284 TTTGCAACCC
3445294 AAGGGGAAGGGGAAAGGG
1 AAGGGGAAGGGGAAAGGG
3445312 AAGGGGAAGGGGAAAGGG
1 AAGGGGAAGGGGAAAGGG
3445330 GAGAAGAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (18 bp):
AAGGGGAAGGGGAAAGGG
Found at i:3445338 original size:18 final size:18
Alignment explanation
Indices: 3445299--3445339 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
3445289 AACCCAAGGG
**
3445299 GAAGGGGAAAGGGAAGGG
1 GAAGGGGAAAGGGAAGAA
*
3445317 GAAGGGGAAAGGGGAGAA
1 GAAGGGGAAAGGGAAGAA
3445335 GAAGG
1 GAAGG
3445340 TAACAGACAT
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:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (18 bp):
GAAGGGGAAAGGGAAGAA
Found at i:3446625 original size:20 final size:20
Alignment explanation
Indices: 3446609--3446647 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3446599 TATTATATTT
3446609 TAATATAATTTGATATAATA
1 TAATATAATTTGATATAATA
* *
3446629 TATTATAGTTTGATATAAT
1 TAATATAATTTGATATAAT
3446648 TAAATTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (20 bp):
TAATATAATTTGATATAATA
Found at i:3448905 original size:16 final size:17
Alignment explanation
Indices: 3448878--3448912 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
3448868 AGGTAAATTT
*
3448878 TAAAACAAAAATGAAAA
1 TAAAACAAAAATCAAAA
3448895 TAAAA-AAAAATCAAAA
1 TAAAACAAAAATCAAAA
3448911 TA
1 TA
3448913 TATGTATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.77, C:0.06, G:0.03, T:0.14
Consensus pattern (17 bp):
TAAAACAAAAATCAAAA
Found at i:3453603 original size:19 final size:19
Alignment explanation
Indices: 3453555--3453603 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
3453545 CCTACCTTTG
3453555 TTAATA-TTTTTT-CAATC
1 TTAATATTTTTTTCCAATC
**
3453572 TT-ATATTCCTTTCCAATC
1 TTAATATTTTTTTCCAATC
3453590 TTAATATTTTTTTC
1 TTAATATTTTTTTC
3453604 GACGTACAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 3 0.12
17 6 0.24
18 7 0.28
19 9 0.36
ACGTcount: A:0.24, C:0.16, G:0.00, T:0.59
Consensus pattern (19 bp):
TTAATATTTTTTTCCAATC
Found at i:3460056 original size:18 final size:19
Alignment explanation
Indices: 3460035--3460083 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 19
3460025 GCAAATATAT
*
3460035 AATAAAAAG-AAATCAACA
1 AATAAAAAGTAAATAAACA
3460053 AAT-AAAAGTAAATAAACA
1 AATAAAAAGTAAATAAACA
*
3460071 AATAAAAATTAAA
1 AATAAAAAGTAAA
3460084 GCACTTAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 5 0.19
18 14 0.52
19 8 0.30
ACGTcount: A:0.73, C:0.06, G:0.04, T:0.16
Consensus pattern (19 bp):
AATAAAAAGTAAATAAACA
Found at i:3464211 original size:28 final size:28
Alignment explanation
Indices: 3464166--3464224 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
3464156 TTTTATTTAT
3464166 TTAGGGTTTAAGAGTTTTAAAAAATAAA
1 TTAGGGTTTAAGAGTTTTAAAAAATAAA
*
3464194 TTAGGGTTTAA-AGTTTTTAAAAAATTAA
1 TTAGGGTTTAAGAG-TTTTAAAAAATAAA
3464222 TTA
1 TTA
3464225 AATTAGGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 2 0.07
28 27 0.93
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (28 bp):
TTAGGGTTTAAGAGTTTTAAAAAATAAA
Found at i:3464237 original size:68 final size:67
Alignment explanation
Indices: 3464182--3464314 Score: 189
Period size: 67 Copynumber: 2.0 Consensus size: 67
3464172 TTTAAGAGTT
*
3464182 TTAA-AAAATAAATTAGGGTTTAAAGTTTTTAA-AAAATTAATTAAATTAGGTTTTAGGGGTTTT
1 TTAATAAAATAAATTAGGGTTTAAAGTTTTTAAGAAAATTAATTAAATTAGGGTTTA-GGGTTTT
3464245 AAA
65 AAA
* * * **
3464248 TTAATTAATTAAATTAGGGTTTAGAGTTTTTAAGAAAATTAATTAAATTAGGGTTTAGTTTTTTA
1 TTAATAAAATAAATTAGGGTTTAAAGTTTTTAAGAAAATTAATTAAATTAGGGTTTAGGGTTTTA
3464313 AA
66 AA
3464315 AATAATTTTG
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
66 4 0.07
67 33 0.56
68 22 0.37
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (67 bp):
TTAATAAAATAAATTAGGGTTTAAAGTTTTTAAGAAAATTAATTAAATTAGGGTTTAGGGTTTTA
AA
Found at i:3464254 original size:34 final size:33
Alignment explanation
Indices: 3464190--3464316 Score: 175
Period size: 34 Copynumber: 3.8 Consensus size: 33
3464180 TTTTAAAAAA
*
3464190 TAAATTAGGGTTTAAAGTTTTTAAAAAATTAAT
1 TAAATTAGGGTTTAGAGTTTTTAAAAAATTAAT
* * * *
3464223 TAAATTAGGTTTTAGGGGTTTTAAATTAATTAAT
1 TAAATTAGGGTTTAGAGTTTTTAAA-AAATTAAT
3464257 TAAATTAGGGTTTAGAGTTTTTAAGAAAATTAAT
1 TAAATTAGGGTTTAGAGTTTTTAA-AAAATTAAT
*
3464291 TAAATTAGGGTTTAG-TTTTTTAAAAA
1 TAAATTAGGGTTTAGAGTTTTTAAAAA
3464317 TAATTTTGTG
Statistics
Matches: 82, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
32 3 0.04
33 28 0.34
34 50 0.61
35 1 0.01
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (33 bp):
TAAATTAGGGTTTAGAGTTTTTAAAAAATTAAT
Found at i:3467179 original size:23 final size:23
Alignment explanation
Indices: 3467140--3467435 Score: 340
Period size: 23 Copynumber: 12.7 Consensus size: 23
3467130 ATTGGGTATA
*
3467140 TATATATGCTGTCCAATTTGGTG
1 TATAAATGCTGTCCAATTTGGTG
* * *
3467163 TATAAATGTTGTTCAATTTAGTG
1 TATAAATGCTGTCCAATTTGGTG
* *
3467186 TATATATGCTTTCCAATTTGGTG
1 TATAAATGCTGTCCAATTTGGTG
*
3467209 TATAAATACTGTCCAATTTGGTG
1 TATAAATGCTGTCCAATTTGGTG
* *
3467232 TATAAATGTTGTCCAATTTAGTG
1 TATAAATGCTGTCCAATTTGGTG
*
3467255 TATATATGCTGTCCAATTTGGTG
1 TATAAATGCTGTCCAATTTGGTG
* *
3467278 TATAAATGCTGTCTAATTTAGTG
1 TATAAATGCTGTCCAATTTGGTG
* *
3467301 TATATATGCTGTCCGATTTGGTG
1 TATAAATGCTGTCCAATTTGGTG
3467324 TATAAATGCTGTCCAATTTGGTG
1 TATAAATGCTGTCCAATTTGGTG
* * * *
3467347 TTTATATGTTGCCCAATTTGGTG
1 TATAAATGCTGTCCAATTTGGTG
* * *
3467370 TATATATATATGTTGTCCAATTGGGTC
1 --TATA-A-ATGCTGTCCAATTTGGTG
* *
3467397 TATAAATGCTGTCCGATTTGATG
1 TATAAATGCTGTCCAATTTGGTG
*
3467420 TATAAAAGCTGTCCAA
1 TATAAATGCTGTCCAA
3467436 ACAAGGTAGA
Statistics
Matches: 226, Mismatches: 43, Indels: 8
0.82 0.16 0.03
Matches are distributed among these distances:
23 203 0.90
24 1 0.00
25 7 0.03
27 15 0.07
ACGTcount: A:0.26, C:0.12, G:0.20, T:0.43
Consensus pattern (23 bp):
TATAAATGCTGTCCAATTTGGTG
Found at i:3467970 original size:18 final size:18
Alignment explanation
Indices: 3467934--3467971 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3467924 GGAAAATGAA
*
3467934 ACATATAAGGGATATGAT
1 ACATATAAGGGATAGGAT
*
3467952 ACATATAAGGGCTAGGAT
1 ACATATAAGGGATAGGAT
3467970 AC
1 AC
3467972 GCACCTAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.11, G:0.24, T:0.24
Consensus pattern (18 bp):
ACATATAAGGGATAGGAT
Found at i:3469440 original size:43 final size:42
Alignment explanation
Indices: 3469374--3469502 Score: 156
Period size: 43 Copynumber: 3.0 Consensus size: 42
3469364 ATAGGATTTC
3469374 CGATATGTGTTATCGTGTAAGACCACGTCTGGGACGTTGGCAT
1 CGATATGTGTTA-CGTGTAAGACCACGTCTGGGACGTTGGCAT
3469417 CGACT-TGTGTTTACGTGTAAGACC-CTGTCTGGGACAG-TGGCAT
1 CGA-TATGTG-TTACGTGTAAGACCAC-GTCTGGGAC-GTTGGCAT
* * *
3469460 TGATATGTGATTACATATAAGACCACGTCTGGGACGTTGGCAT
1 CGATATGTG-TTACGTGTAAGACCACGTCTGGGACGTTGGCAT
3469503 TGTACGAGCT
Statistics
Matches: 75, Mismatches: 4, Indels: 14
0.81 0.04 0.15
Matches are distributed among these distances:
42 3 0.04
43 66 0.88
44 6 0.08
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (42 bp):
CGATATGTGTTACGTGTAAGACCACGTCTGGGACGTTGGCAT
Found at i:3470105 original size:2 final size:2
Alignment explanation
Indices: 3470098--3470151 Score: 67
Period size: 2 Copynumber: 27.5 Consensus size: 2
3470088 TTGGAACAAG
* *
3470098 TA TA TA TA TA TA TA T- TA TG TA TA TA TA TA TA T- TA TG TCA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
3470139 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
3470152 TATGTCATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
1 2 0.04
2 42 0.93
3 1 0.02
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3470122 original size:17 final size:17
Alignment explanation
Indices: 3470100--3470147 Score: 87
Period size: 17 Copynumber: 2.8 Consensus size: 17
3470090 GGAACAAGTA
3470100 TATATATATATATTATG
1 TATATATATATATTATG
3470117 TATATATATATATTATG
1 TATATATATATATTATG
3470134 TCATATATATATAT
1 T-ATATATATATAT
3470148 ATATTATGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 18 0.60
18 12 0.40
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (17 bp):
TATATATATATATTATG
Found at i:3470141 original size:12 final size:12
Alignment explanation
Indices: 3470124--3470162 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
3470114 ATGTATATAT
3470124 ATATATTATGTC
1 ATATATTATGTC
*
3470136 ATATA-TATAT-
1 ATATATTATGTC
3470146 ATATATTATGTC
1 ATATATTATGTC
3470158 ATATA
1 ATATA
3470163 GATAAAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 5 0.22
11 8 0.35
12 10 0.43
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (12 bp):
ATATATTATGTC
Found at i:3470145 original size:22 final size:22
Alignment explanation
Indices: 3470098--3470162 Score: 100
Period size: 22 Copynumber: 3.1 Consensus size: 22
3470088 TTGGAACAAG
*
3470098 TATATATATATA-TAT-T-ATG
1 TATATATATATATTATGTCATA
3470117 TATATATATATATTATGTCATA
1 TATATATATATATTATGTCATA
3470139 TATATATATATATTATGTCATA
1 TATATATATATATTATGTCATA
3470161 TA
1 TA
3470163 GATAAAATGA
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
19 12 0.29
20 3 0.07
21 1 0.02
22 26 0.62
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.51
Consensus pattern (22 bp):
TATATATATATATTATGTCATA
Found at i:3475858 original size:18 final size:18
Alignment explanation
Indices: 3475835--3475927 Score: 159
Period size: 18 Copynumber: 5.2 Consensus size: 18
3475825 CCCAACTACT
*
3475835 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
3475853 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
3475871 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
*
3475889 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
3475907 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
3475925 GTA
1 GTA
3475928 AACGGTCGTA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 70 1.00
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:3475887 original size:36 final size:36
Alignment explanation
Indices: 3475835--3475927 Score: 177
Period size: 36 Copynumber: 2.6 Consensus size: 36
3475825 CCCAACTACT
*
3475835 GTATACGTGAACAGTACCGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
3475871 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
3475907 GTATACGTGAATAGTACCGTA
1 GTATACGTGAATAGTACCGTA
3475928 AACGGTCGTA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 56 1.00
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (36 bp):
GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
Found at i:3484136 original size:20 final size:20
Alignment explanation
Indices: 3484111--3484157 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
3484101 GATATTTTTC
3484111 TTTATATTGATATT-ACTA-TA
1 TTTATATT-ATATTGA-TATTA
3484131 TTTATATTATATTGATATTA
1 TTTATATTATATTGATATTA
3484151 TTTATAT
1 TTTATAT
3484158 CCTTCTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (20 bp):
TTTATATTATATTGATATTA
Found at i:3484246 original size:4 final size:4
Alignment explanation
Indices: 3484237--3484296 Score: 120
Period size: 4 Copynumber: 15.0 Consensus size: 4
3484227 TTATAACTCG
3484237 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
3484285 CATA CATA CATA
1 CATA CATA CATA
3484297 TTTATCTTTG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 56 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:3484479 original size:38 final size:37
Alignment explanation
Indices: 3484437--3484542 Score: 101
Period size: 38 Copynumber: 2.8 Consensus size: 37
3484427 TATTTTGTAA
*
3484437 TTTATATACATATCTATATATATATATACATAT-TTTAT
1 TTTATATTCATAT-TATATATATATATACATATATTT-T
* * * *
3484475 TTTATTTTCATA-AATATATATACATACTTATATTTT
1 TTTATATTCATATTATATATATATATACATATATTTT
*
3484511 TTTATATTTTATAATT-TATATATATATACATA
1 TTTATA-TTCAT-ATTATATATATATATACATA
3484543 CATATATATC
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
36 22 0.41
37 7 0.13
38 25 0.46
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.55
Consensus pattern (37 bp):
TTTATATTCATATTATATATATATATACATATATTTT
Found at i:3484514 original size:36 final size:38
Alignment explanation
Indices: 3484451--3484542 Score: 118
Period size: 36 Copynumber: 2.5 Consensus size: 38
3484441 TATACATATC
3484451 TATATATATATATACATATTTTATTTTAT-TTTCATAA
1 TATATATATATATACATATTTTATTTTATATTTCATAA
* * *
3484488 -ATATATATACATACTTATATTT-TTTTATATTTTATAA
1 TATATATATATATACATAT-TTTATTTTATATTTCATAA
*
3484525 TTTATATATATATACATA
1 TATATATATATATACATA
3484543 CATATATATC
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
36 22 0.48
37 10 0.22
38 14 0.30
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (38 bp):
TATATATATATATACATATTTTATTTTATATTTCATAA
Found at i:3484587 original size:4 final size:4
Alignment explanation
Indices: 3484578--3484603 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
3484568 AATTTTATTC
3484578 TTCT TTCT TTCT TTCT TTCT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT TT
3484604 ATTTATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:3494693 original size:7 final size:7
Alignment explanation
Indices: 3494681--3494745 Score: 69
Period size: 7 Copynumber: 9.0 Consensus size: 7
3494671 AAAATTTAAT
3494681 AAATAAA
1 AAATAAA
3494688 AAATAAA
1 AAATAAA
3494695 AAATAAA
1 AAATAAA
3494702 AAATAAA
1 AAATAAA
**
3494709 AAATATT
1 AAATAAA
*
3494716 AAATATTA
1 AAATA-AA
3494724 AAATAAA
1 AAATAAA
3494731 ATAA-AATA
1 A-AATAA-A
3494739 AAATAAA
1 AAATAAA
3494746 TATTTTTAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
7 38 0.76
8 12 0.24
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (7 bp):
AAATAAA
Found at i:3494702 original size:5 final size:5
Alignment explanation
Indices: 3494687--3494745 Score: 52
Period size: 5 Copynumber: 11.6 Consensus size: 5
3494677 TAATAAATAA
*
3494687 AAAAT AAAA- AATAA- AAAAT AAAA- AATATT AAATATT AAAAT AAAAT
1 AAAAT AAAAT AA-AAT AAAAT AAAAT AA-AAT AAA-A-T AAAAT AAAAT
3494733 AAAAT AAAAT AAA
1 AAAAT AAAAT AAA
3494746 TATTTTTAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
4 6 0.13
5 33 0.72
6 3 0.07
7 4 0.09
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:3494742 original size:37 final size:36
Alignment explanation
Indices: 3494669--3494763 Score: 95
Period size: 37 Copynumber: 2.6 Consensus size: 36
3494659 ATACTATATA
*
3494669 AAAAAAT-TTAATAAATAAAAAATAAAAAATAAAAAAT
1 AAAAAATATTAA-AAAT-TAAAATAAAAAATAAAAAAT
*
3494706 AAAAAATATTAAATATTAAAATAAAATAA-AATAAAAT
1 AAAAAATATTAAAAATTAAAATAAAA-AATAA-AAAAT
* * *
3494743 AAATATTTTTAAAAATTAAAA
1 AAAAAATATTAAAAATTAAAA
3494764 ATAATAATGT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
36 11 0.22
37 34 0.69
38 4 0.08
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (36 bp):
AAAAAATATTAAAAATTAAAATAAAAAATAAAAAAT
Found at i:3499030 original size:8 final size:7
Alignment explanation
Indices: 3499000--3499063 Score: 55
Period size: 7 Copynumber: 9.3 Consensus size: 7
3498990 TTAATATCCA
*
3499000 AATAAGT
1 AATAAAT
3499007 AATAAAT
1 AATAAAT
3499014 AAT-AA-
1 AATAAAT
3499019 AATAAAGT
1 AATAAA-T
3499027 AATAAAT
1 AATAAAT
*
3499034 AAAGTAAAG
1 -AA-TAAAT
3499043 AA-AAAT
1 AATAAAT
3499049 AATAAAT
1 AATAAAT
3499056 AA-AAAT
1 AATAAAT
3499062 AA
1 AA
3499064 AATTTGGGTT
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
5 3 0.06
6 15 0.31
7 16 0.33
8 10 0.21
9 4 0.08
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (7 bp):
AATAAAT
Found at i:3499031 original size:13 final size:12
Alignment explanation
Indices: 3499007--3499066 Score: 58
Period size: 12 Copynumber: 5.2 Consensus size: 12
3498997 CCAAATAAGT
3499007 AATAAATAATAA
1 AATAAATAATAA
3499019 AATAAAGTAAT-A
1 AATAAA-TAATAA
*
3499031 AATAAAGTAA-AG
1 AATAAA-TAATAA
3499043 AA-AAATAAT-A
1 AATAAATAATAA
3499053 AATAAA-AATAA
1 AATAAATAATAA
3499064 AAT
1 AAT
3499067 TTGGGTTGCC
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
10 8 0.20
11 10 0.24
12 19 0.46
13 4 0.10
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (12 bp):
AATAAATAATAA
Found at i:3507501 original size:23 final size:23
Alignment explanation
Indices: 3507475--3507745 Score: 326
Period size: 23 Copynumber: 11.7 Consensus size: 23
3507465 ATTGGGTATA
*
3507475 TATATATGTTGTCCAATTTGGTG
1 TATATATGCTGTCCAATTTGGTG
* * * * *
3507498 TATAAATGTTGTTCAATCTAGTG
1 TATATATGCTGTCCAATTTGGTG
3507521 TATATATGCTGTCCAATTTGGTG
1 TATATATGCTGTCCAATTTGGTG
*
3507544 TATAAATGCTGTCCAATTTGGTG
1 TATATATGCTGTCCAATTTGGTG
* * *
3507567 TATAAATGTTGTCCAATTTAGTG
1 TATATATGCTGTCCAATTTGGTG
3507590 TATATATGCTGTCCAATTTGGTG
1 TATATATGCTGTCCAATTTGGTG
* * *
3507613 TATAAATGCTGTCTAATTTAGTG
1 TATATATGCTGTCCAATTTGGTG
3507636 TATATATGCTGTCCAATTTGGTG
1 TATATATGCTGTCCAATTTGGTG
*
3507659 TATAAATGCTGTCCAATTTGGTG
1 TATATATGCTGTCCAATTTGGTG
* * * *
3507682 TTTATATGTTGCCCAATTTGGTA
1 TATATATGCTGTCCAATTTGGTG
* *
3507705 TATATATCTGCTGTCCGATTTGATG
1 TATATA--TGCTGTCCAATTTGGTG
* *
3507730 TATAAAAGCTGTCCAA
1 TATATATGCTGTCCAA
3507746 ACAAGGTAGA
Statistics
Matches: 210, Mismatches: 36, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
23 193 0.92
25 17 0.08
ACGTcount: A:0.26, C:0.12, G:0.20, T:0.42
Consensus pattern (23 bp):
TATATATGCTGTCCAATTTGGTG
Found at i:3508266 original size:18 final size:18
Alignment explanation
Indices: 3508245--3508280 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3508235 AAAAGGAAAA
*
3508245 ATATAAGGGTTAGGATAC
1 ATATAAGGGCTAGGATAC
3508263 ATATAAGGGCTAGGATAC
1 ATATAAGGGCTAGGATAC
3508281 GCACCTAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.08, G:0.28, T:0.25
Consensus pattern (18 bp):
ATATAAGGGCTAGGATAC
Found at i:3509810 original size:43 final size:42
Alignment explanation
Indices: 3509682--3509811 Score: 165
Period size: 43 Copynumber: 3.0 Consensus size: 42
3509672 CATAGGATTT
* *
3509682 TCGATATGTGTTATCGTGTAAGACCACGTCTGGGACGTTGCCA
1 TCGATATGTGTTA-CGTGTAAGACCATGTCTGGGACGTTGGCA
*
3509725 TCGACT-TGTGTTTACGTGTAAGACCCTGTCTGGGACAG-TGGCA
1 TCGA-TATGTG-TTACGTGTAAGACCATGTCTGGGAC-GTTGGCA
*
3509768 TCGATATGTGATTACGTATAAGACCATGTCTGGGACGTTGGCA
1 TCGATATGTG-TTACGTGTAAGACCATGTCTGGGACGTTGGCA
3509811 T
1 T
3509812 TGTACGAGCT
Statistics
Matches: 76, Mismatches: 6, Indels: 10
0.83 0.07 0.11
Matches are distributed among these distances:
42 2 0.03
43 69 0.91
44 5 0.07
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (42 bp):
TCGATATGTGTTACGTGTAAGACCATGTCTGGGACGTTGGCA
Found at i:3510747 original size:73 final size:72
Alignment explanation
Indices: 3510601--3510772 Score: 227
Period size: 73 Copynumber: 2.4 Consensus size: 72
3510591 AAAATAATCA
* * * *
3510601 TTAGCGGCGTTTTTAAGAAAGCACCGCAAAAAACCTAAGCCGAACGACGTCGTTTCCCGAGCTTT
1 TTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAACATAAACCCAACGACGTCGTTTCCCGAGCTTT
3510666 CGGAGAT
66 CGGAGAT
* ***
3510673 TTAGCGGCGTTTCTAAGAAAGCGCCGCAAAAAAACATAAACCCAACGACGTCGTTTTGTGAGCTT
1 TTAGCGGCGTTTTTAAGAAAGCGCCGC-AAAAAACATAAACCCAACGACGTCGTTTCCCGAGCTT
*
3510738 TCGGGGAT
65 TCGGAGAT
** *
3510746 TTAGAAGCGTTTTTAAGAAAGTGCCGC
1 TTAGCGGCGTTTTTAAGAAAGCGCCGC
3510773 TAATGCTCAG
Statistics
Matches: 86, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
72 25 0.29
73 61 0.71
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (72 bp):
TTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAACATAAACCCAACGACGTCGTTTCCCGAGCTTT
CGGAGAT
Found at i:3510898 original size:113 final size:114
Alignment explanation
Indices: 3510672--3511203 Score: 705
Period size: 114 Copynumber: 4.7 Consensus size: 114
3510662 CTTTCGGAGA
* * * * *
3510672 TTTAGCGGCGTTTCTAAGAAAGCGCCGCAAAAAAACATAAACCCAACGACGTCGTTTTGTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTGTGAGCT
* *
3510737 TTCGGGGATTTAGAAGCGTTTTTAAGAAAGTGCCGCTAATGCTCAGGGC
66 TTCGGGGATTTAGCAGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
*
3510786 TTTAGCGGCGTTTTTGAGAAAGCACCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTGTGAG-T
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTGTGAGCT
* * *
3510850 TTCGGGGATTTAGCAGCGTTTTTAAGGAAGTGCCGCTGATGCTCAGGGC
66 TTCGGGGATTTAGCAGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
* * * * *
3510899 TTCAACAGTGC-TTTCTCA-AAAACGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTGTGAG
1 TTTAGC-G-GCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTGTGAG
* * * * **
3510962 CTTTCAGGGATTTAGCGGCGTTTGTAAGAAAGCGCCGCTAATGGTTTGGGC
64 CTTTCGGGGATTTAGCAGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
* * * *
3511013 TTTAACGGCGTTTTTGGGAAAGCGCCCCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTGTGAGCT
* * *
3511078 TTCGGGGATTTAGCTGCGTTTTTAAGAAAGCGCCACTAATGTTCAGGGC
66 TTCGGGGATTTAGCAGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
* * *
3511127 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAATTA--TAAGCCTAACGACGCCGTTTTTTGAGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAA-AACCTAAGCCCAACGACGCCGTTTTGTGAGC
*
3511190 TTTTGGGGATTTAG
65 TTTCGGGGATTTAG
3511204 AGGCCAAAAA
Statistics
Matches: 367, Mismatches: 45, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
112 2 0.01
113 137 0.37
114 225 0.61
115 3 0.01
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (114 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTGTGAGCT
TTCGGGGATTTAGCAGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
Found at i:3511176 original size:227 final size:225
Alignment explanation
Indices: 3510672--3511204 Score: 703
Period size: 227 Copynumber: 2.3 Consensus size: 225
3510662 CTTTCGGAGA
* *
3510672 TTTAGCGGCGTTTCTAAGAAAGCGCCGCAAAAAAACATAAACCCAACGACGTCGTTTTGTGAGCT
1 TTTAGCGGCGTTTCTAAGAAAGCGCCGC-AAAAAA-ATAAGCCCAACGACGCCGTTTTGTGAGCT
* * *
3510737 TTCGGGGATTTAGAAGCGTTTTTAAGAAAGTGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTG
64 TTCGGGGATTTAGAAGCGTTTGTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAACGGCGTTTTTG
* *
3510802 AGAAAGCACCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTGTGAGTTTCGGGGATTTAGCAGC
129 AGAAAGCACCCCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGTTTCGGGGATTTAGCAGC
* * * *
3510867 GTTTTTAAGGAAGTGCCGCTGATGCTCAGGGC
194 GTTTTTAAGAAAGCGCCACTAATGCTCAGGGC
* *
3510899 TTCAACAGTGC-TTTCTCAA-AAA-CGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTGTGA
1 TTTAGC-G-GCGTTTCT-AAGAAAGCGCCGCAAAAAAA--TAAGCCCAACGACGCCGTTTTGTGA
* ** * **
3510961 GCTTTCAGGGATTTAGCGGCGTTTGTAAGAAAGCGCCGCTAATGGTTTGGGCTTTAACGGCGTTT
61 GCTTTCGGGGATTTAGAAGCGTTTGTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAACGGCGTTT
* *
3511026 TTGGGAAAGCGCCCCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAG
126 TTGAGAAAGCACCCCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAG-TTTCGGGGATTTAG
* *
3511091 CTGCGTTTTTAAGAAAGCGCCACTAATGTTCAGGGC
190 CAGCGTTTTTAAGAAAGCGCCACTAATGCTCAGGGC
* * * * *
3511127 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAATTATAAGCCTAACGACGCCGTTTTTTGAGCTT
1 TTTAGCGGCGTTTCTAAGAAAGCGCCGCAAAAA-AATAAGCCCAACGACGCCGTTTTGTGAGCTT
*
3511192 TTGGGGATTTAGA
65 TCGGGGATTTAGA
3511205 GGCCAAAAAT
Statistics
Matches: 263, Mismatches: 33, Indels: 20
0.83 0.10 0.06
Matches are distributed among these distances:
225 1 0.00
226 9 0.03
227 180 0.68
228 68 0.26
229 5 0.02
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (225 bp):
TTTAGCGGCGTTTCTAAGAAAGCGCCGCAAAAAAATAAGCCCAACGACGCCGTTTTGTGAGCTTT
CGGGGATTTAGAAGCGTTTGTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAACGGCGTTTTTGAG
AAAGCACCCCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGTTTCGGGGATTTAGCAGCGT
TTTTAAGAAAGCGCCACTAATGCTCAGGGC
Found at i:3511541 original size:14 final size:14
Alignment explanation
Indices: 3511522--3511555 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
3511512 AAGTATGGGT
3511522 TTAGGGATTATGGA
1 TTAGGGATTATGGA
3511536 TTAGGGATTATGGA
1 TTAGGGATTATGGA
3511550 TTAGGG
1 TTAGGG
3511556 GTTGGGATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.38, T:0.35
Consensus pattern (14 bp):
TTAGGGATTATGGA
Found at i:3511576 original size:21 final size:21
Alignment explanation
Indices: 3511498--3511579 Score: 60
Period size: 21 Copynumber: 3.8 Consensus size: 21
3511488 GAGTTCATAT
*
3511498 TTTAAGGTTTAGGGAAGTATGGG-
1 TTTAAGGATTAGGG--GT-TGGGA
* * *
3511521 TTTAGGGATTATGGATTAGGGA
1 TTTAAGGATTAGGGGTT-GGGA
*
3511543 -TTATGGATTAGGGGTTGGGA
1 TTTAAGGATTAGGGGTTGGGA
*
3511563 TTTAAGGTTTAGGGGTT
1 TTTAAGGATTAGGGGTT
3511580 AGAGGGTTAG
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
20 5 0.11
21 31 0.66
23 11 0.23
ACGTcount: A:0.23, C:0.00, G:0.39, T:0.38
Consensus pattern (21 bp):
TTTAAGGATTAGGGGTTGGGA
Found at i:3511586 original size:8 final size:7
Alignment explanation
Indices: 3511522--3511604 Score: 51
Period size: 7 Copynumber: 11.6 Consensus size: 7
3511512 AAGTATGGGT
*
3511522 TTAGGGA
1 TTAGGGG
* *
3511529 TTATGGA
1 TTAGGGG
*
3511536 TTAGGGA
1 TTAGGGG
* *
3511543 TTATGGA
1 TTAGGGG
3511550 TTAGGGG
1 TTAGGGG
*
3511557 TT-GGGAT
1 TTAGGG-G
* *
3511564 TTAAGGT
1 TTAGGGG
3511571 TTAGGGG
1 TTAGGGG
3511578 TTAGAGGG
1 TTAG-GGG
3511586 TTAGGGG
1 TTAGGGG
3511593 TTTAGGGG
1 -TTAGGGG
3511601 TTAG
1 TTAG
3511605 ATGTGTTAGG
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
6 3 0.05
7 44 0.70
8 16 0.25
ACGTcount: A:0.22, C:0.00, G:0.43, T:0.35
Consensus pattern (7 bp):
TTAGGGG
Found at i:3511591 original size:15 final size:15
Alignment explanation
Indices: 3511550--3511604 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
3511540 GGATTATGGA
*
3511550 TTAGGGGTT-GGGAT
1 TTAGGGGTTAGGGGT
* *
3511564 TTAAGGTTTAGGGG-
1 TTAGGGGTTAGGGGT
3511578 TTAGAGGGTTAGGGGT
1 TTAG-GGGTTAGGGGT
3511594 TTAGGGGTTAG
1 TTAGGGGTTAG
3511605 ATGTGTTAGG
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
14 10 0.30
15 19 0.58
16 4 0.12
ACGTcount: A:0.18, C:0.00, G:0.47, T:0.35
Consensus pattern (15 bp):
TTAGGGGTTAGGGGT
Found at i:3511598 original size:23 final size:24
Alignment explanation
Indices: 3511568--3511617 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
3511558 TGGGATTTAA
3511568 GGTTTAGGGGTTAGA-GGGTTAGG
1 GGTTTAGGGGTTAGATGGGTTAGG
*
3511591 GGTTTAGGGGTTAGATGTGTTAGG
1 GGTTTAGGGGTTAGATGGGTTAGG
3511615 GGT
1 GGT
3511618 CAAAAGTTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 15 0.60
24 10 0.40
ACGTcount: A:0.16, C:0.00, G:0.50, T:0.34
Consensus pattern (24 bp):
GGTTTAGGGGTTAGATGGGTTAGG
Found at i:3512224 original size:107 final size:103
Alignment explanation
Indices: 3512025--3512224 Score: 312
Period size: 103 Copynumber: 1.9 Consensus size: 103
3512015 AATATATTGA
*
3512025 TTTATAAAAAACGCCGCAAAAAATAAATCAATTTATAAAACAAATAAAAAAAAATTAGTATAGCA
1 TTTATAAAAAACGCCGCAAAAAATAAATCAATTTATAAAACAAATAAAAAAAAATTAGCATAGCA
*
3512090 AAACGGCGTCATTTTGTTGAAAATGAAATAGCGGCGTT
66 AAACGGCGTCATTTTGTTCAAAATGAAATAGCGGCGTT
* *
3512128 TTTATAAAAAACGCCTCAAAAAATTAATCAATTTATAAAA-AAATAAAATAAAAAATTTTTAGCA
1 TTTATAAAAAACGCCGCAAAAAATAAATCAATTTATAAAACAAAT-AAA-AAAAAA---TTAGCA
3512192 TAGCAAAACGGCGTCATTTTGTTCAAAATGAAA
61 TAGCAAAACGGCGTCATTTTGTTCAAAATGAAA
3512225 AAAATTTTGC
Statistics
Matches: 88, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
102 4 0.05
103 41 0.47
104 6 0.07
107 37 0.42
ACGTcount: A:0.51, C:0.12, G:0.11, T:0.27
Consensus pattern (103 bp):
TTTATAAAAAACGCCGCAAAAAATAAATCAATTTATAAAACAAATAAAAAAAAATTAGCATAGCA
AAACGGCGTCATTTTGTTCAAAATGAAATAGCGGCGTT
Found at i:3512417 original size:106 final size:107
Alignment explanation
Indices: 3512269--3512587 Score: 455
Period size: 109 Copynumber: 2.9 Consensus size: 107
3512259 AAAGGTAAGC
* *
3512269 AATAGCGGCGTTTTTATAAAAAAACGCTGCAAAAAATAAATCAATTTATAAAACAAATAAAACAA
1 AATAGCGGCGTTTTTA-AAAAACAC-C-GCAAAAAATAAATCAATTTATAAAACAAATAAAATAA
* *
3512334 AAAAATTTTAGCATAGCAAAACGGCATCATTTTGTTGAAAATG-G
63 AAAATTTTTAGCATAGCAAAACGGCATCATTTTGTTGAAAATGAA
* *
3512378 AATAGCGGCGTTTTTAAAAAACACCGCAAAAAATAAATCAATTTATAAAAAAAATAAAATAAAGA
1 AATAGCGGCGTTTTTAAAAAACACCGCAAAAAATAAATCAATTTATAAAACAAATAAAATAAAAA
* * *
3512443 ATTTTTAGCAGAGCAAAACGGCGTCATTTTGTTCAAAATGAAAA
66 ATTTTTAGCATAGCAAAACGGCATCATTTTGTTGAAAATG--AA
* *
3512487 AATTTTGCGGCG--TTTAAAAAACACCGCAAAAAATAAATCAATTTATAAAACAAATGAAATAAA
1 AA--TAGCGGCGTTTTTAAAAAACACCGCAAAAAATAAATCAATTTATAAAACAAATAAAATAAA
3512550 AAATTTTTAGCATAGCAAAACGGCATCATTTTGTTGAA
64 AAATTTTTAGCATAGCAAAACGGCATCATTTTGTTGAA
3512588 GATGTTACCA
Statistics
Matches: 189, Mismatches: 16, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
106 73 0.39
107 1 0.01
108 7 0.04
109 101 0.53
111 7 0.04
ACGTcount: A:0.49, C:0.12, G:0.13, T:0.26
Consensus pattern (107 bp):
AATAGCGGCGTTTTTAAAAAACACCGCAAAAAATAAATCAATTTATAAAACAAATAAAATAAAAA
ATTTTTAGCATAGCAAAACGGCATCATTTTGTTGAAAATGAA
Found at i:3512551 original size:261 final size:255
Alignment explanation
Indices: 3512030--3512552 Score: 669
Period size: 261 Copynumber: 2.0 Consensus size: 255
3512020 ATTGATTTAT
*
3512030 AAAAAACGCCGCAAAAAATAAATCAATTTATAAAACAAATAAAAAAAAATTAGTATAGCAAAACG
1 AAAAAACGCCGCAAAAAATAAATCAATTTATAAAACAAATAAAAAAAAATTAGCATAGCAAAACG
* * * *
3512095 GCGTCATTTTGTTGAAAATGAAATAGCGGCGTTTTTATAAAAAACGCCTCAAAAAATTAATCAAT
66 GCATCATTTTGTTGAAAATGAAATAGCGGCGTTTTTATAAAAAACACCGCAAAAAATAAATCAAT
*
3512160 TTATAAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAACGGCGTCATTTTGTTCAAAATGAAA
131 TTATAAAAAAATAAAATAAAAAATTTTTAGCAGAGCAAAACGGCGTCATTTTGTTCAAAATGAAA
* * * * ** **** ** ***
3512225 AAAATTTTGCGGCGTTTTTATGAAAATCGCTGCTAAAGGTAAGCAATAGCGGCGTTTTTATA
196 AAAATTTTGCGGCG-TTTTA-GAAAAACACCGCAAAAAATAAGCAATAAAAACAATGAAATA
*
3512287 AAAAAACGCTGCAAAAAATAAATCAATTTATAAAACAAATAAAACAAAAAAATTTTAGCATAGCA
1 AAAAAACGCCGCAAAAAATAAATCAATTTATAAAACAAAT--AA-AAAAAAA--TTAGCATAGCA
*
3512352 AAACGGCATCATTTTGTTGAAAATGGAATAGCGGCG-TTTT-TAAAAAACACCGCAAAAAATAAA
61 AAACGGCATCATTTTGTTGAAAATGAAATAGCGGCGTTTTTATAAAAAACACCGCAAAAAATAAA
*
3512415 TCAATTTATAAAAAAAATAAAATAAAGAATTTTTAGCAGAGCAAAACGGCGTCATTTTGTTCAAA
126 TCAATTTAT-AAAAAAATAAAATAAAAAATTTTTAGCAGAGCAAAACGGCGTCATTTTGTTCAAA
*
3512480 ATG-AAAAAATTTTGCGGCG-TTTA-AAAAACACCGCAAAAAATAAATCAATTTATAAAACAAAT
190 ATGAAAAAAATTTTGCGGCGTTTTAGAAAAACACCGCAAAAAAT-AAGCAA--TA-AAAAC-AAT
3512542 GAAATA
250 GAAATA
3512548 AAAAA
1 AAAAA
3512553 TTTTTAGCAT
Statistics
Matches: 230, Mismatches: 25, Indels: 18
0.84 0.09 0.07
Matches are distributed among these distances:
256 12 0.05
257 44 0.19
258 4 0.02
259 4 0.02
260 53 0.23
261 69 0.30
262 44 0.19
ACGTcount: A:0.50, C:0.12, G:0.13, T:0.26
Consensus pattern (255 bp):
AAAAAACGCCGCAAAAAATAAATCAATTTATAAAACAAATAAAAAAAAATTAGCATAGCAAAACG
GCATCATTTTGTTGAAAATGAAATAGCGGCGTTTTTATAAAAAACACCGCAAAAAATAAATCAAT
TTATAAAAAAATAAAATAAAAAATTTTTAGCAGAGCAAAACGGCGTCATTTTGTTCAAAATGAAA
AAAATTTTGCGGCGTTTTAGAAAAACACCGCAAAAAATAAGCAATAAAAACAATGAAATA
Done.