Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold145
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: 2608604
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 28749 characters in sequence are not A, C, G, or T
File 8 of 15
Found at i:1410547 original size:15 final size:15
Alignment explanation
Indices: 1410527--1410561 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1410517 AGAGAAACTT
1410527 ATTTAATAACATAAC
1 ATTTAATAACATAAC
**
1410542 ATTTAATAAGGTAAC
1 ATTTAATAACATAAC
1410557 ATTTA
1 ATTTA
1410562 GTATAACTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.49, C:0.09, G:0.06, T:0.37
Consensus pattern (15 bp):
ATTTAATAACATAAC
Found at i:1411782 original size:20 final size:20
Alignment explanation
Indices: 1411757--1411794 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1411747 ATATGTTATG
*
1411757 TTATTAAATTAATAATTAAT
1 TTATTAAAATAATAATTAAT
*
1411777 TTATTAAAATATTAATTA
1 TTATTAAAATAATAATTA
1411795 TATATACAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTATTAAAATAATAATTAAT
Found at i:1421356 original size:30 final size:30
Alignment explanation
Indices: 1421291--1421357 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
1421281 TTAAAATATT
* *
1421291 TATTTTATTTAAATTTAAATTTATTAATAA
1 TATTTTATTAAAATTTAAATATATTAATAA
1421321 T-TTTTATTAAATATATTAAA-ATATTAA-AA
1 TATTTTATTAAA-AT-TTAAATATATTAATAA
1421350 TATTTTAT
1 TATTTTAT
1421358 ATTATTTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
29 12 0.38
30 15 0.47
31 5 0.16
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (30 bp):
TATTTTATTAAAATTTAAATATATTAATAA
Found at i:1421526 original size:22 final size:22
Alignment explanation
Indices: 1421495--1421538 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1421485 GATATTTAAA
* *
1421495 AAATAGATTTAGATAAATATAT
1 AAATAGATTTAAAAAAATATAT
*
1421517 AAATATATTTAAAAAAATATAT
1 AAATAGATTTAAAAAAATATAT
1421539 TGAACCTTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (22 bp):
AAATAGATTTAAAAAAATATAT
Found at i:1421806 original size:2 final size:2
Alignment explanation
Indices: 1421765--1421797 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1421755 ATACACACAC
1421765 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1421798 AACTATATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1425369 original size:24 final size:27
Alignment explanation
Indices: 1425342--1425390 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
1425332 TACTTTATTA
1425342 ATTT-TTTTTA-AAA-TATAAATAAGT
1 ATTTATTTTTATAAATTATAAATAAGT
*
1425366 ATTTATTTTTATAAATTATTAATAA
1 ATTTATTTTTATAAATTATAAATAA
1425391 AATAATGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.19
25 6 0.29
26 3 0.14
27 8 0.38
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (27 bp):
ATTTATTTTTATAAATTATAAATAAGT
Found at i:1425804 original size:2 final size:2
Alignment explanation
Indices: 1425797--1425828 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1425787 ATAACTTAGC
1425797 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1425829 GGTGCATTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1426404 original size:20 final size:22
Alignment explanation
Indices: 1426376--1426418 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
1426366 TGTTCTGGAA
1426376 AAGCGTTTAAA-A-AGAGAGAG
1 AAGCGTTTAAACACAGAGAGAG
*
1426396 AAGCTTTTAAACACAGAGAGAG
1 AAGCGTTTAAACACAGAGAGAG
1426418 A
1 A
1426419 GAGAGAGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 1 0.05
22 9 0.45
ACGTcount: A:0.49, C:0.09, G:0.26, T:0.16
Consensus pattern (22 bp):
AAGCGTTTAAACACAGAGAGAG
Found at i:1426415 original size:2 final size:2
Alignment explanation
Indices: 1426410--1426445 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1426400 TTTTAAACAC
*
1426410 AG AG AG AG AG AG AG AG AG AG AG AG CG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1426446 CTATGAGGGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1426972 original size:23 final size:24
Alignment explanation
Indices: 1426945--1426998 Score: 92
Period size: 23 Copynumber: 2.2 Consensus size: 24
1426935 TTTTTTACTT
1426945 TGTAAATTTTAATAAGAA-AAAAA
1 TGTAAATTTTAATAAGAATAAAAA
1426968 TGTAAATTTTAATAAGAATAAAAA
1 TGTAAATTTTAATAAGAATAAAAA
1426992 TAGTAAA
1 T-GTAAA
1426999 AAAATCAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 18 0.62
24 6 0.21
25 5 0.17
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.31
Consensus pattern (24 bp):
TGTAAATTTTAATAAGAATAAAAA
Found at i:1433500 original size:115 final size:113
Alignment explanation
Indices: 1433300--1433531 Score: 342
Period size: 115 Copynumber: 2.0 Consensus size: 113
1433290 TAAATTCACC
* * *
1433300 TCCAGATCATCTTTAGCTATTTGAACTATTTTTTTAAAATACAAATGATCAGAATGGCGATTACG
1 TCCAGATCATCTTTAGCTATTTGAACTATTTTTTTAAAAAAAAAATGATCAGAATGACGATTACG
*
1433365 TACGTCTTCAAATTTCTTCTCTTTATATAGGGTATTACTGGAGTTCCA
66 TACATCTTCAAATTTCTTCTCTTTATATAGGGTATTACTGGAGTTCCA
* *
1433413 TCCAGATCATC-TTAGCTATTTGAACTCTTTTTTTTAAAAAAAAAAAATATATCA-AATGACGAT
1 TCCAGATCATCTTTAGCTATTTGAACT-ATTTTTTT--AAAAAAAAAAT-GATCAGAATGACGAT
* *
1433476 TATGTACATCTTCATATTTCTTCTCTTTATATAGGGTATTACTGGAGTTCCA
62 TACGTACATCTTCAAATTTCTTCTCTTTATATAGGGTATTACTGGAGTTCCA
1433528 TCCA
1 TCCA
1433532 TTCCTGATGG
Statistics
Matches: 107, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
112 15 0.14
113 18 0.17
115 70 0.65
116 4 0.04
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (113 bp):
TCCAGATCATCTTTAGCTATTTGAACTATTTTTTTAAAAAAAAAATGATCAGAATGACGATTACG
TACATCTTCAAATTTCTTCTCTTTATATAGGGTATTACTGGAGTTCCA
Found at i:1434743 original size:18 final size:18
Alignment explanation
Indices: 1434722--1434759 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1434712 ATAATTAATT
* *
1434722 TTTAAAATTTTTTATATA
1 TTTAAAAATTTTAATATA
1434740 TTTAAAAATTTTAATATA
1 TTTAAAAATTTTAATATA
1434758 TT
1 TT
1434760 ATTTTTTAAT
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:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTAAAAATTTTAATATA
Found at i:1434757 original size:20 final size:20
Alignment explanation
Indices: 1434725--1434763 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
1434715 ATTAATTTTT
*
1434725 AAAATTTTTTATA-TATTTA
1 AAAATTTTATATATTATTTA
1434744 AAAATTTTAATATATTATTT
1 AAAATTTT-ATATATTATTT
1434764 TTTAATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 4 0.24
21 5 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
AAAATTTTATATATTATTTA
Found at i:1434786 original size:12 final size:12
Alignment explanation
Indices: 1434734--1434795 Score: 51
Period size: 12 Copynumber: 5.3 Consensus size: 12
1434724 TAAAATTTTT
1434734 TATATATTTAAA
1 TATATATTTAAA
1434746 -A-AT-TTTAATA
1 TATATATTTAA-A
* *
1434756 TATTATTTTTTAA
1 TA-TATATTTAAA
*
1434769 TTTATATTTAAA
1 TATATATTTAAA
1434781 TATATA-TTAAA
1 TATATATTTAAA
1434792 TATA
1 TATA
1434796 AATATCAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
9 5 0.12
10 3 0.08
11 11 0.28
12 13 0.32
13 4 0.10
14 4 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TATATATTTAAA
Found at i:1434805 original size:7 final size:6
Alignment explanation
Indices: 1434777--1434816 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
1434767 AATTTATATT
*
1434777 TAAATA TATAT- TAAATA TAAATA TCAAATA TAAATA TAAA
1 TAAATA TAAATA TAAATA TAAATA T-AAATA TAAATA TAAA
1434817 AATGTTATGC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 4 0.13
6 20 0.67
7 6 0.20
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAATA
Found at i:1434805 original size:13 final size:13
Alignment explanation
Indices: 1434784--1434813 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1434774 ATTTAAATAT
*
1434784 ATATTAAATATAA
1 ATATCAAATATAA
1434797 ATATCAAATATAA
1 ATATCAAATATAA
1434810 ATAT
1 ATAT
1434814 AAAAATGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (13 bp):
ATATCAAATATAA
Found at i:1436244 original size:14 final size:14
Alignment explanation
Indices: 1436225--1436286 Score: 51
Period size: 13 Copynumber: 4.6 Consensus size: 14
1436215 TGATATAATA
1436225 ATAATTTATATTAT
1 ATAATTTATATTAT
* *
1436239 ATAATTT-TTTTTT
1 ATAATTTATATTAT
*
1436252 ATATTTTTATATT-T
1 ATA-ATTTATATTAT
1436266 AT-ATTTAT-TTAT
1 ATAATTTATATTAT
*
1436278 ATTATTTAT
1 ATAATTTAT
1436287 TTTAATTATT
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
11 2 0.05
12 8 0.21
13 13 0.33
14 13 0.33
15 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
ATAATTTATATTAT
Found at i:1436271 original size:26 final size:26
Alignment explanation
Indices: 1436229--1436317 Score: 87
Period size: 24 Copynumber: 3.4 Consensus size: 26
1436219 ATAATAATAA
1436229 TTTATATTATATAATTTTTTTTTATATT
1 TTTATATT-TAT-ATTTTTTTTTATATT
*
1436257 TTTATATTTATA--TTTATTTATATT
1 TTTATATTTATATTTTTTTTTATATT
1436281 ATTTAT-TTTA-ATTATTTTTTTATTATT
1 -TTTATATTTATATT-TTTTTTTA-TATT
*
1436308 TTTATGTTTA
1 TTTATATTTA
1436318 AAATGTTCTT
Statistics
Matches: 53, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
23 1 0.02
24 15 0.28
25 5 0.09
26 13 0.25
27 11 0.21
28 8 0.15
ACGTcount: A:0.27, C:0.00, G:0.01, T:0.72
Consensus pattern (26 bp):
TTTATATTTATATTTTTTTTTATATT
Found at i:1436274 original size:10 final size:10
Alignment explanation
Indices: 1436261--1436308 Score: 50
Period size: 9 Copynumber: 5.1 Consensus size: 10
1436251 TATATTTTTA
1436261 TATTTATATT
1 TATTTATATT
1436271 TATTTATA-T
1 TATTTATATT
1436280 TATTTAT-TT
1 TATTTATATT
*
1436289 TAATTAT-TT
1 TATTTATATT
1436298 T-TTTATTATT
1 TATTTA-TATT
1436308 T
1 T
1436309 TTATGTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
8 3 0.09
9 19 0.58
10 11 0.33
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
TATTTATATT
Found at i:1436312 original size:39 final size:39
Alignment explanation
Indices: 1436229--1436312 Score: 59
Period size: 42 Copynumber: 2.1 Consensus size: 39
1436219 ATAATAATAA
*
1436229 TTTATATTA-T-ATAATTT-TTTTTTATATTTTTATATT
1 TTTATATTATTAATATTTTATTTTTTATATTTTTATATT
* * *
1436265 TATAT-TTATTTATATTATTTATTTTAATTATTTTTTTATTATT
1 TTTATATTATTAATA-T-TTTATTTT--TTATATTTTTA-TATT
1436308 TTTAT
1 TTTAT
1436313 GTTTAAAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
35 3 0.08
36 5 0.14
37 3 0.08
39 3 0.08
40 4 0.11
42 10 0.28
43 8 0.22
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (39 bp):
TTTATATTATTAATATTTTATTTTTTATATTTTTATATT
Found at i:1439866 original size:29 final size:29
Alignment explanation
Indices: 1439828--1439886 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
1439818 TTATATTTAC
*
1439828 TTTAAATTAAATA-TAAAAATATAAAAATA
1 TTTAAATT-AATAGTAAAAAGATAAAAATA
* *
1439857 TTTAACTTAATAGTAAAAAGATTAAAATA
1 TTTAAATTAATAGTAAAAAGATAAAAATA
1439886 T
1 T
1439887 ATTTTTAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 4 0.15
29 22 0.85
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (29 bp):
TTTAAATTAATAGTAAAAAGATAAAAATA
Found at i:1441071 original size:17 final size:18
Alignment explanation
Indices: 1441035--1441071 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
1441025 TCTATTTCAC
1441035 TATTTAAAATAATTAAAT
1 TATTTAAAATAATTAAAT
*
1441053 TATTTAAAA-AATTATAT
1 TATTTAAAATAATTAAAT
1441070 TA
1 TA
1441072 ATATTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TATTTAAAATAATTAAAT
Found at i:1441088 original size:21 final size:21
Alignment explanation
Indices: 1441064--1441103 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1441054 ATTTAAAAAA
*
1441064 TTAT-ATTAATATTTTATAATT
1 TTATAATTAA-ATTTAATAATT
1441085 TTATAATTAAATTTAATAA
1 TTATAATTAAATTTAATAA
1441104 AAAATTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTATAATTAAATTTAATAATT
Found at i:1444467 original size:14 final size:14
Alignment explanation
Indices: 1444450--1444476 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1444440 AAATAATATT
1444450 TTTAAATTTTAATA
1 TTTAAATTTTAATA
1444464 TTTAAATTTTAAT
1 TTTAAATTTTAAT
1444477 TAAATTGAAT
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:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTAAATTTTAATA
Found at i:1458314 original size:3 final size:3
Alignment explanation
Indices: 1458306--1458331 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1458296 TAAACTCCAT
1458306 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
1458332 TTTGCATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1458649 original size:15 final size:15
Alignment explanation
Indices: 1458624--1458740 Score: 64
Period size: 15 Copynumber: 7.9 Consensus size: 15
1458614 GTGTATATAT
*
1458624 ATATATATATATTTA
1 ATATATTTATATTTA
*
1458639 TTATATTTATATTTA
1 ATATATTTATATTTA
*
1458654 AAATATTATATATTT-
1 ATATATT-TATATTTA
**
1458669 -TATATAAAT-TTTA
1 ATATATTTATATTTA
* *
1458682 ATATATTAATA-ATA
1 ATATATTTATATTTA
*
1458696 TATATTATTTAATTTTTA
1 -ATA-TATTT-ATATTTA
* **
1458714 ATATTTTTATATAAA
1 ATATATTTATATTTA
1458729 ATAT-TTTATATT
1 ATATATTTATATT
1458741 ATATTTTAAT
Statistics
Matches: 77, Mismatches: 17, Indels: 17
0.69 0.15 0.15
Matches are distributed among these distances:
12 3 0.04
13 2 0.03
14 21 0.27
15 29 0.38
16 15 0.19
17 5 0.06
18 2 0.03
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATATATTTATATTTA
Found at i:1458672 original size:7 final size:7
Alignment explanation
Indices: 1458617--1458703 Score: 56
Period size: 7 Copynumber: 12.4 Consensus size: 7
1458607 CGTATGTGTG
1458617 TATATAT
1 TATATAT
1458624 ATATATAT
1 -TATATAT
*
1458632 ATATTTAT
1 -TATATAT
1458640 TATAT-T
1 TATATAT
1458646 TATAT-T
1 TATATAT
*
1458652 TAAAATAT
1 T-ATATAT
1458660 TATATAT
1 TATATAT
*
1458667 TTTATA-
1 TATATAT
* *
1458673 TAAATTT
1 TATATAT
1458680 TAATATAT
1 T-ATATAT
*
1458688 TA-ATAA
1 TATATAT
1458694 TATATAT
1 TATATAT
1458701 TAT
1 TAT
1458704 TTAATTTTTA
Statistics
Matches: 62, Mismatches: 12, Indels: 11
0.73 0.14 0.13
Matches are distributed among these distances:
6 16 0.26
7 25 0.40
8 21 0.34
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
TATATAT
Found at i:1458688 original size:52 final size:52
Alignment explanation
Indices: 1458630--1458728 Score: 121
Period size: 52 Copynumber: 1.9 Consensus size: 52
1458620 ATATATATAT
* * *
1458630 ATATATTTATTATATTTA-TATTTAAAATATT-ATATATTTTATATAAATTTTA
1 ATATATTAATAATATATATTATTT-AAATATTAATAT-TTTTATATAAATTTTA
* *
1458682 ATATATTAATAATATATATTATTTAATTTTTAATATTTTTATATAAA
1 ATATATTAATAATATATATTATTTAAATATTAATATTTTTATATAAA
1458729 ATATTTTATA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
52 31 0.77
53 9 0.22
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (52 bp):
ATATATTAATAATATATATTATTTAAATATTAATATTTTTATATAAATTTTA
Found at i:1458697 original size:32 final size:34
Alignment explanation
Indices: 1458656--1458750 Score: 104
Period size: 32 Copynumber: 2.8 Consensus size: 34
1458646 TATATTTAAA
*
1458656 ATATTATATATTTTATATAAATTTTAATA-TATT
1 ATATAATATATTTTATATAAATTTTAATATTATT
* * * *
1458689 A-ATAATATATATTATTTAATTTTTAATATTTTT
1 ATATAATATATTTTATATAAATTTTAATATTATT
* *
1458722 ATATAAAATATTTTATATTATATTTTAAT
1 ATATAATATATTTTATA-TAAATTTTAAT
1458751 TTTTTTATTT
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
32 23 0.47
33 5 0.10
34 12 0.24
35 9 0.18
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (34 bp):
ATATAATATATTTTATATAAATTTTAATATTATT
Found at i:1458732 original size:36 final size:37
Alignment explanation
Indices: 1458623--1458758 Score: 97
Period size: 35 Copynumber: 3.6 Consensus size: 37
1458613 TGTGTATATA
* * *
1458623 TATATATATATATTTATTATATTTATATTTAA-AATATTA
1 TATAT-TATAT-TTTAATATTTTTATA-TTAATAATATTT
* *
1458662 TATATTTTA-TATAA-ATTTTAATATATTAATAATATATAT
1 TATATTATATTTTAATATTTT--TATATTAATAATAT-T-T
1458701 TAT-TTA-ATTTTTAATATTTTTATA-TAA-AATATTT
1 TATATTATA-TTTTAATATTTTTATATTAATAATATTT
*
1458735 TATATTATATTTTAATTTTTTTAT
1 TATATTATATTTTAATATTTTTAT
1458759 TTATCTATTC
Statistics
Matches: 79, Mismatches: 8, Indels: 24
0.71 0.07 0.22
Matches are distributed among these distances:
34 4 0.05
35 22 0.28
36 13 0.16
37 13 0.16
38 10 0.13
39 12 0.15
40 5 0.06
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (37 bp):
TATATTATATTTTAATATTTTTATATTAATAATATTT
Found at i:1459025 original size:2 final size:2
Alignment explanation
Indices: 1459020--1459044 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1459010 ATATATATAG
1459020 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
1459045 AAGTTTCGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1459944 original size:17 final size:17
Alignment explanation
Indices: 1459920--1459960 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
1459910 AAAAGACAAG
*
1459920 TTTTTTATTTTTATT-T
1 TTTTTTATTATTATTAT
1459936 TTATTTTATTATTATTAT
1 TT-TTTTATTATTATTAT
1459954 TTTTTTA
1 TTTTTTA
1459961 CTTGGGGAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 2 0.09
17 17 0.77
18 3 0.14
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTTTTATTATTATTAT
Found at i:1459947 original size:14 final size:13
Alignment explanation
Indices: 1459921--1459958 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
1459911 AAAGACAAGT
1459921 TTTTTA-TTTTTA
1 TTTTTATTTTTTA
1459933 TTTTTATTTTATTA
1 TTTTTATTTT-TTA
*
1459947 TTATTATTTTTT
1 TTTTTATTTTTT
1459959 TACTTGGGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 6 0.26
13 5 0.22
14 12 0.52
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:1459953 original size:20 final size:19
Alignment explanation
Indices: 1459920--1459957 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1459910 AAAAGACAAG
*
1459920 TTTTTTATTTTTATTTTTA
1 TTTTTTATTATTATTTTTA
1459939 TTTTATTATTATTATTTTT
1 TTTT-TTATTATTATTTTT
1459958 TTACTTGGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTTTATTATTATTTTTA
Found at i:1460382 original size:12 final size:10
Alignment explanation
Indices: 1460347--1460382 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
1460337 TTTATTTTAT
*
1460347 TTTTTTTATA
1 TTTTTTAATA
1460357 TTTTTTAATA
1 TTTTTTAATA
1460367 TTTTTTAATA
1 TTTTTTAATA
1460377 TGTTTT
1 T-TTTT
1460383 GAGGATTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 20 0.83
11 4 0.17
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (10 bp):
TTTTTTAATA
Found at i:1463194 original size:3 final size:3
Alignment explanation
Indices: 1463186--1463218 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
1463176 GACCTCTATG
*
1463186 ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1463219 TTTTTTTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1464792 original size:20 final size:20
Alignment explanation
Indices: 1464724--1464792 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
1464714 ACTTAAAATG
1464724 AAAATATTAATAATT-TATTT
1 AAAATATT-ATAATTATATTT
**
1464744 ATTTATATTAT-ATTATATTT
1 A-AAATATTATAATTATATTT
1464764 -AAA-ATTATAATTATATTT
1 AAAATATTATAATTATATTT
1464782 AAAATATTATA
1 AAAATATTATA
1464793 TTTTTAAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
17 5 0.12
18 10 0.25
19 6 0.15
20 14 0.35
21 5 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
AAAATATTATAATTATATTT
Found at i:1464810 original size:33 final size:33
Alignment explanation
Indices: 1464753--1464833 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
1464743 TATTTATATT
*
1464753 ATATTATA-TTTAAAATTATAATTATATTTAAA
1 ATATTATATTTTTAAATTATAATTATATTTAAA
*
1464785 ATATTATATTTTTAAATTATGATTATATTTAAA
1 ATATTATATTTTTAAATTATAATTATATTTAAA
* *
1464818 ATATCATATATTTAAA
1 ATATTATATTTTTAAA
1464834 AAAATTATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
32 8 0.18
33 36 0.82
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (33 bp):
ATATTATATTTTTAAATTATAATTATATTTAAA
Found at i:1464829 original size:16 final size:17
Alignment explanation
Indices: 1464755--1464845 Score: 93
Period size: 16 Copynumber: 5.6 Consensus size: 17
1464745 TTTATATTAT
1464755 ATTATATTTAAAATTATA
1 ATTATATTTAAAA-TATA
*
1464773 ATTATATTTAAAATATT
1 ATTATATTTAAAATATA
* * *
1464790 A-TATTTTTAAATTATG
1 ATTATATTTAAAATATA
*
1464806 ATTATATTTAAAATATC
1 ATTATATTTAAAATATA
1464823 A-TATATTTAAAA-A-A
1 ATTATATTTAAAATATA
1464837 ATTAT-TTTA
1 ATTATATTTA
1464846 TTAATAATTT
Statistics
Matches: 63, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
14 5 0.08
15 4 0.06
16 24 0.38
17 17 0.27
18 13 0.21
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (17 bp):
ATTATATTTAAAATATA
Found at i:1465071 original size:5 final size:5
Alignment explanation
Indices: 1465056--1465194 Score: 58
Period size: 5 Copynumber: 28.0 Consensus size: 5
1465046 TAACAACTCG
* * * * *
1465056 TATATT TATAT TATAT CATAT T-TAA TATAT AATAA TAT-T TATAT AATTAT
1 TATA-T TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TA-TAT
* * * * *
1465106 TATA- TAAAT TTTAA TATAT T-T-T TAT-T TTTA- TATTAT TATTT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TA-TAT TATAT TATAT
* * *
1465152 TATAT TATAT TTTATT TTTAT TATATT TATAA TATAAT TATAT
1 TATAT TATAT TATA-T TATAT TATA-T TATAT TAT-AT TATAT
1465195 CGTATTTAAA
Statistics
Matches: 98, Mismatches: 24, Indels: 23
0.68 0.17 0.16
Matches are distributed among these distances:
3 2 0.02
4 15 0.15
5 57 0.58
6 24 0.24
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:1465078 original size:16 final size:18
Alignment explanation
Indices: 1465057--1465100 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 18
1465047 AACAACTCGT
*
1465057 ATATTTATAT-TAT-ATC
1 ATATTTATATATATAATA
1465073 ATATTTA-ATATATAATA
1 ATATTTATATATATAATA
1465090 ATATTTATATA
1 ATATTTATATA
1465101 ATTATTATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 2 0.08
16 10 0.42
17 9 0.38
18 3 0.12
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
ATATTTATATATATAATA
Found at i:1465138 original size:16 final size:17
Alignment explanation
Indices: 1465113--1465172 Score: 61
Period size: 18 Copynumber: 3.5 Consensus size: 17
1465103 TATTATATAA
*
1465113 ATTTTAATA-TATTTTT
1 ATTTTTATATTATTTTT
1465129 ATTTTTATATTATTATTT
1 ATTTTTATATTATT-TTT
*
1465147 -TATATTATATTATATTTT
1 AT-TTTTATATTAT-TTTT
1465165 ATTTTTAT
1 ATTTTTAT
1465173 TATATTTATA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
16 8 0.22
17 5 0.14
18 21 0.58
19 2 0.06
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
ATTTTTATATTATTTTT
Found at i:1465165 original size:36 final size:39
Alignment explanation
Indices: 1465093--1465193 Score: 111
Period size: 37 Copynumber: 2.7 Consensus size: 39
1465083 TATAATAATA
*
1465093 TTTATATAATTATTATATAAATTTTAATATATTTTTATT
1 TTTATATAATTATTATATAAATTATAATATATTTTTATT
* * *
1465132 TTTATATTATTATT-T-TATATTATATTATA-TTTTATT
1 TTTATATAATTATTATATAAATTATAATATATTTTTATT
* *
1465168 TTTATTATATTTATAATAT-AATTATA
1 TTTA-TATAATTATTATATAAATTATA
1465194 TCGTATTTAA
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
36 11 0.22
37 18 0.35
38 8 0.16
39 14 0.27
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (39 bp):
TTTATATAATTATTATATAAATTATAATATATTTTTATT
Found at i:1465175 original size:16 final size:16
Alignment explanation
Indices: 1465114--1465179 Score: 69
Period size: 16 Copynumber: 3.8 Consensus size: 16
1465104 ATTATATAAA
*
1465114 TTTTAATATATTTTTATT
1 TTTTATTATA-TTTTA-T
1465132 TTTATATTATTATTTTAT
1 TTT-TATTA-TATTTTAT
*
1465150 ATTATATTATATTTTAT
1 -TTTTATTATATTTTAT
1465167 TTTTATTATATTT
1 TTTTATTATATTT
1465180 ATAATATAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
16 12 0.29
17 8 0.19
18 9 0.21
19 11 0.26
20 2 0.05
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTATTATATTTTAT
Found at i:1465186 original size:25 final size:25
Alignment explanation
Indices: 1465103--1465186 Score: 65
Period size: 25 Copynumber: 3.5 Consensus size: 25
1465093 TTTATATAAT
1465103 TATTATATAA-ATTTTAATATATTTT-
1 TATTATATAATATTTT-AT-TATTTTA
*
1465128 TATT-T-T--TATATTATTATTTTA
1 TATTATATAATATTTTATTATTTTA
* *
1465149 TATTATATTATATTTTATTTTTATTA
1 TATTATATAATATTTTATTATT-TTA
1465175 TATT-TATAATAT
1 TATTATATAATAT
1465187 AATTATATCG
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
20 6 0.12
21 6 0.12
22 5 0.10
23 2 0.04
24 1 0.02
25 21 0.44
26 7 0.15
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (25 bp):
TATTATATAATATTTTATTATTTTA
Found at i:1465201 original size:33 final size:31
Alignment explanation
Indices: 1465138--1465201 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 31
1465128 TATTTTTATA
* **
1465138 TTATTATTTTATATTATATTATATTTTATTT
1 TTATTATTTTATAATATATTATATCGTATTT
1465169 TTATTATATTTATAATATAATTATATCGTATTT
1 TTATTAT-TTTATAATAT-ATTATATCGTATTT
1465202 AAAATTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 7 0.25
32 9 0.32
33 12 0.43
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (31 bp):
TTATTATTTTATAATATATTATATCGTATTT
Found at i:1465459 original size:23 final size:24
Alignment explanation
Indices: 1465433--1465479 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
1465423 TATTTTCCCA
*
1465433 TTAATTATATA-ATTATAT-ATTTT
1 TTAAATATATACA-TATATGATTTT
1465456 TTAAATATATACATATATGATTTT
1 TTAAATATATACATATATGATTTT
1465480 ATTTTTTGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (24 bp):
TTAAATATATACATATATGATTTT
Found at i:1467396 original size:3 final size:3
Alignment explanation
Indices: 1467388--1467428 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1467378 AATTTTCATA
1467388 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1467429 AGCTTTGCTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1469788 original size:17 final size:17
Alignment explanation
Indices: 1469766--1469800 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1469756 TAAATATATG
1469766 TAATTAATTATAAATTT
1 TAATTAATTATAAATTT
*
1469783 TAATTAATTTTAAATTT
1 TAATTAATTATAAATTT
1469800 T
1 T
1469801 CACTTAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TAATTAATTATAAATTT
Found at i:1475159 original size:14 final size:14
Alignment explanation
Indices: 1475140--1475166 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1475130 TAACATAAAA
1475140 TATTATTTATATTC
1 TATTATTTATATTC
1475154 TATTATTTATATT
1 TATTATTTATATT
1475167 TAAAATAGAG
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:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTATTTATATTC
Found at i:1478300 original size:33 final size:35
Alignment explanation
Indices: 1478257--1478322 Score: 93
Period size: 33 Copynumber: 1.9 Consensus size: 35
1478247 TGTTTACATT
*
1478257 AATTTTAATATAT-TA-ATA-ATTTATAATTTTATA
1 AATTTAAATATATGTATATATATTTAT-ATTTTATA
1478290 AATTTAAATATATGTATATATATTTATATTTTA
1 AATTTAAATATATGTATATATATTTATATTTTA
1478323 ATTATATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 12 0.41
34 2 0.07
35 9 0.31
36 6 0.21
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (35 bp):
AATTTAAATATATGTATATATATTTATATTTTATA
Found at i:1479550 original size:22 final size:22
Alignment explanation
Indices: 1479525--1479567 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1479515 TATAATTACT
*
1479525 TTTAAAAATGATATTTAATATA
1 TTTAAAAATGAAATTTAATATA
* *
1479547 TTTAAAATTTAAATTTAATAT
1 TTTAAAAATGAAATTTAATAT
1479568 GCAATGTCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TTTAAAAATGAAATTTAATATA
Found at i:1481146 original size:17 final size:18
Alignment explanation
Indices: 1481107--1481143 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1481097 TTTATTTTAA
1481107 TTTAATTATAAAATATAT
1 TTTAATTATAAAATATAT
*
1481125 ATTAA-TATAAAA-ATAT
1 TTTAATTATAAAATATAT
1481141 TTT
1 TTT
1481144 TAAATTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 2
0.81 0.10 0.10
Matches are distributed among these distances:
16 6 0.35
17 7 0.41
18 4 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTAATTATAAAATATAT
Found at i:1481170 original size:12 final size:12
Alignment explanation
Indices: 1481153--1481184 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1481143 TTAAATTATT
1481153 ATAAATTTTTAA
1 ATAAATTTTTAA
1481165 ATAAATTTTTAA
1 ATAAATTTTTAA
*
1481177 ATTAATTT
1 ATAAATTT
1481185 AATTTTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
ATAAATTTTTAA
Found at i:1481502 original size:2 final size:2
Alignment explanation
Indices: 1481489--1481530 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1481479 GAGCCGACGG
*
1481489 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1481531 GTAAATTTAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1482144 original size:2 final size:2
Alignment explanation
Indices: 1482137--1482164 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1482127 TTTAAATGCT
1482137 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1482165 AAATAAAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1482615 original size:118 final size:113
Alignment explanation
Indices: 1482331--1482647 Score: 372
Period size: 116 Copynumber: 2.7 Consensus size: 113
1482321 TATAAGAGAA
* *
1482331 AAAACT-AGCCAATAGGTTGGCCTTGGCTCTGATAGGTATGAAACTTTTCTTCCTTTTATAAGCT
1 AAAACTAAG-CAATGGGTTGGCCTTGGCTTTGATAGGTATGAAACTTTTCTTCCTTTTATAAGCT
*
1482395 AACCCAATTAATGAATATT-AATTTTAACAATTATTTCGTCTTTTATAAG
65 AACCCAATTAGTGAATATTGAATTTTAACAATTATTTCG-CTTTTATAAG
* * * * *
1482444 AAATCTAAGCAATGGGTTGGTCTTGGCTTTTTCATAGGTATGAAAGTTTTCTTCCCTTTTTTAAG
1 AAAACTAAGCAATGGGTTGGCCTTGGC--TTTGATAGGTATGAAACTTTTCTT-CCTTTTATAAG
*** *
1482509 CTAACCCAAATTAGTGAATATTGGACAATTATT-ATTTTTTTTTC-CTTTTATAAG
63 CTAACCC-AATTAGTGAATATT-G--AATT-TTAACAATTATTTCGCTTTTATAAG
*
1482563 AATAACTAAGCAATGGGTTGGCCTTGGCTTTGATAGGTATGAAACTTTTCTTCCTTTCATAAGCT
1 AA-AACTAAGCAATGGGTTGGCCTTGGCTTTGATAGGTATGAAACTTTTCTTCCTTTTATAAGCT
**
1482628 AACCCTGTTAGTGAATATTG
65 AACCCAATTAGTGAATATTG
1482648 CTTGAATTTA
Statistics
Matches: 173, Mismatches: 20, Indels: 20
0.81 0.09 0.09
Matches are distributed among these distances:
113 21 0.12
114 2 0.01
115 22 0.13
116 29 0.17
117 29 0.17
118 22 0.13
119 12 0.07
120 23 0.13
121 11 0.06
122 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (113 bp):
AAAACTAAGCAATGGGTTGGCCTTGGCTTTGATAGGTATGAAACTTTTCTTCCTTTTATAAGCTA
ACCCAATTAGTGAATATTGAATTTTAACAATTATTTCGCTTTTATAAG
Found at i:1483820 original size:2 final size:2
Alignment explanation
Indices: 1483813--1483843 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1483803 AGGTCAAAGT
1483813 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1483844 TCATTGTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1497700 original size:27 final size:27
Alignment explanation
Indices: 1497665--1497734 Score: 70
Period size: 30 Copynumber: 2.4 Consensus size: 27
1497655 ATTTGATATA
* *
1497665 TATTAAAATATAAATA-TAAAATATAAT
1 TATTTAAATATAAAAATTAAAA-ATAAT
1497692 TATTTAAATATATAAAAAATTAAAAATAAT
1 TATTT-AA-ATAT-AAAAATTAAAAATAAT
1497722 TATATTAAATATA
1 TAT-TTAAATATA
1497735 TATCTATAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
27 4 0.11
28 3 0.08
29 8 0.22
30 14 0.39
31 7 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (27 bp):
TATTTAAATATAAAAATTAAAAATAAT
Found at i:1497730 original size:31 final size:31
Alignment explanation
Indices: 1497663--1497736 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
1497653 AAATTTGATA
*
1497663 TATATTAAA-ATAT-AAATATAAAATATAAT
1 TATATTAAATATATAAAAAATAAAATATAAT
1497692 TAT-TTAAATATATAAAAAATTAAAA-ATAAT
1 TATATTAAATATATAAAAAA-TAAAATATAAT
1497722 TATATTAAATATATA
1 TATATTAAATATATA
1497737 TCTATAAACA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
28 5 0.12
29 7 0.17
30 12 0.30
31 16 0.40
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (31 bp):
TATATTAAATATATAAAAAATAAAATATAAT
Found at i:1499279 original size:15 final size:14
Alignment explanation
Indices: 1499256--1499304 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
1499246 TTTATATTAT
*
1499256 ATTTGGATTTAAATA
1 ATTTTGATTT-AATA
1499271 ATTTTGATTTAATCA
1 ATTTTGATTTAAT-A
* *
1499286 GTTTTGAATTAATA
1 ATTTTGATTTAATA
1499300 ATTTT
1 ATTTT
1499305 TATGTCAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
14 8 0.28
15 21 0.72
ACGTcount: A:0.35, C:0.02, G:0.10, T:0.53
Consensus pattern (14 bp):
ATTTTGATTTAATA
Found at i:1504865 original size:13 final size:13
Alignment explanation
Indices: 1504847--1504872 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1504837 GCTATGTTAC
1504847 TTAGATTCAGACA
1 TTAGATTCAGACA
1504860 TTAGATTCAGACA
1 TTAGATTCAGACA
1504873 CGTGAATGTT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TTAGATTCAGACA
Found at i:1512197 original size:22 final size:21
Alignment explanation
Indices: 1512175--1512219 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
1512165 AATTTTTTTA
*
1512175 TATATCTTATT-TTTTAAAAT
1 TATATTTTATTATTTTAAAAT
1512195 TAT-TTTTATTATTTTAAAA-
1 TATATTTTATTATTTTAAAAT
1512214 TATATT
1 TATATT
1512220 ATAAAATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
TATATTTTATTATTTTAAAAT
Found at i:1512203 original size:19 final size:21
Alignment explanation
Indices: 1512181--1512219 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1512171 TTTATATATC
1512181 TTATT-TTTTAAAAT-TATTT
1 TTATTATTTTAAAATATATTT
1512200 TTATTATTTTAAAATATATT
1 TTATTATTTTAAAATATATT
1512220 ATAAAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 9 0.50
21 4 0.22
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TTATTATTTTAAAATATATTT
Found at i:1513958 original size:16 final size:17
Alignment explanation
Indices: 1513922--1513958 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
1513912 TTATGACAAT
1513922 ATTATTTAAGAAAAACG
1 ATTATTTAAGAAAAACG
1513939 -TTATTTAAGAAAAA-G
1 ATTATTTAAGAAAAACG
1513954 ATTAT
1 ATTAT
1513959 CTAATTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 1 0.05
16 18 0.95
ACGTcount: A:0.51, C:0.03, G:0.11, T:0.35
Consensus pattern (17 bp):
ATTATTTAAGAAAAACG
Found at i:1515999 original size:16 final size:15
Alignment explanation
Indices: 1515981--1516061 Score: 56
Period size: 16 Copynumber: 5.1 Consensus size: 15
1515971 TATACATAAA
1515981 ATAAAATAAAATATT
1 ATAAAATAAAATATT
* *
1515996 AATATATTAAAAATATGT
1 -ATAAAAT-AAAATAT-T
*
1516014 A-AAAATATAATATT
1 ATAAAATAAAATATT
* *
1516028 TTAAATATAAAAAATT
1 ATAAA-ATAAAATATT
1516044 ATAAATATAAATATATT
1 ATAAA-ATAAA-ATATT
1516061 A
1 A
1516062 AATTTTTTTT
Statistics
Matches: 50, Mismatches: 10, Indels: 9
0.72 0.14 0.13
Matches are distributed among these distances:
14 1 0.02
15 9 0.18
16 26 0.52
17 13 0.26
18 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (15 bp):
ATAAAATAAAATATT
Found at i:1516038 original size:48 final size:49
Alignment explanation
Indices: 1515943--1516059 Score: 127
Period size: 48 Copynumber: 2.5 Consensus size: 49
1515933 AATTTATAGT
1515943 TATTAATAAAATAATAAATATATAAAAATATACATAAAATAAAATAAAA
1 TATTAATAAAATAATAAATATATAAAAATATACATAAAATAAAATAAAA
* * * ***
1515992 TATTAATATATTAA-AAATATGTAAAAATATA-ATATTTTAAATATAAAA
1 TATTAATAAAATAATAAATATATAAAAATATACATAAAATAAA-ATAAAA
*
1516040 AATT-AT-AAAT-ATAAATATAT
1 TATTAATAAAATAATAAATATAT
1516060 TAAATTTTTT
Statistics
Matches: 56, Mismatches: 10, Indels: 7
0.77 0.14 0.10
Matches are distributed among these distances:
45 1 0.02
46 9 0.16
47 9 0.16
48 25 0.45
49 12 0.21
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (49 bp):
TATTAATAAAATAATAAATATATAAAAATATACATAAAATAAAATAAAA
Found at i:1516041 original size:24 final size:26
Alignment explanation
Indices: 1515978--1516059 Score: 66
Period size: 24 Copynumber: 3.3 Consensus size: 26
1515968 AAATATACAT
1515978 AAAATA-AAATAAAATATTAATATATTA
1 AAAATATAAA-AAAATA-TAATATATTA
**
1516005 AAAATATGTAAAAATATAATAT-TT-
1 AAAATATAAAAAAATATAATATATTA
* *
1516029 TAAATATAAAAAATTATAA-ATA-TA
1 AAAATATAAAAAAATATAATATATTA
*
1516053 AATATAT
1 AAAATAT
1516060 TAAATTTTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
23 3 0.07
24 20 0.45
25 2 0.05
26 6 0.14
27 12 0.27
28 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (26 bp):
AAAATATAAAAAAATATAATATATTA
Found at i:1516289 original size:16 final size:16
Alignment explanation
Indices: 1516268--1516307 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
1516258 ATATATATTT
*
1516268 ATTTAAATTTAAATTA
1 ATTTAAAATTAAATTA
* *
1516284 ATTTAAAATTAACTTG
1 ATTTAAAATTAAATTA
1516300 ATTTAAAA
1 ATTTAAAA
1516308 ATATTTATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (16 bp):
ATTTAAAATTAAATTA
Found at i:1521438 original size:11 final size:11
Alignment explanation
Indices: 1521419--1521452 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1521409 CATGCTCATA
1521419 TTATATAATTT
1 TTATATAATTT
*
1521430 TTATTTAATTT
1 TTATATAATTT
1521441 TTATA-AATTT
1 TTATATAATTT
1521451 TT
1 TT
1521453 TTAAAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 7 0.33
11 14 0.67
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTATATAATTT
Found at i:1521593 original size:20 final size:20
Alignment explanation
Indices: 1521546--1521593 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1521536 TTACATTATA
* *
1521546 ATATTATATATTTATTTTTT
1 ATATGATATATTTATTCTTT
* *
1521566 ACAAGATATATTTATTCTTT
1 ATATGATATATTTATTCTTT
1521586 ATATGATA
1 ATATGATA
1521594 AAAATTATAT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.56
Consensus pattern (20 bp):
ATATGATATATTTATTCTTT
Found at i:1521710 original size:18 final size:18
Alignment explanation
Indices: 1521687--1521733 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
1521677 TAAAATTCAA
1521687 TTATTTTTTAAAT-AAAT
1 TTATTTTTTAAATCAAAT
*
1521704 TTAATTTTTT-ATTCAAAT
1 TT-ATTTTTTAAATCAAAT
1521722 TTATTTTTTAAA
1 TTATTTTTTAAA
1521734 CTTAATATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATTTTTTAAATCAAAT
Found at i:1522354 original size:20 final size:20
Alignment explanation
Indices: 1522319--1522356 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1522309 TTTTTTTTAA
*
1522319 TTTAATTTTGAGATTTTACC
1 TTTAATTTTGAAATTTTACC
*
1522339 TTTAATTTTTAAATTTTA
1 TTTAATTTTGAAATTTTA
1522357 AATTATTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61
Consensus pattern (20 bp):
TTTAATTTTGAAATTTTACC
Found at i:1526762 original size:3 final size:3
Alignment explanation
Indices: 1526756--1526784 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1526746 AAAAAAAAAA
1526756 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1526785 AAAGGTTTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1528755 original size:2 final size:2
Alignment explanation
Indices: 1528748--1528773 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1528738 TATCTTTTCA
1528748 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
1528774 GCCACCTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1530008 original size:3 final size:3
Alignment explanation
Indices: 1530000--1530033 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
1529990 GGTGATGGCA
*
1530000 GTG GTG GTG GCG GTG GTG GTG GTG GTG GTG GTG G
1 GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG G
1530034 AGGACTGGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.03, G:0.68, T:0.29
Consensus pattern (3 bp):
GTG
Found at i:1530010 original size:12 final size:12
Alignment explanation
Indices: 1529990--1530033 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
1529980 TGCTTCTGGG
* *
1529990 GGTGATGGCAGT
1 GGTGGTGGCGGT
1530002 GGTGGTGGCGGT
1 GGTGGTGGCGGT
*
1530014 GGTGGTGGTGGT
1 GGTGGTGGCGGT
1530026 GGTGGTGG
1 GGTGGTGG
1530034 AGGACTGGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.05, C:0.05, G:0.64, T:0.27
Consensus pattern (12 bp):
GGTGGTGGCGGT
Found at i:1532709 original size:29 final size:29
Alignment explanation
Indices: 1532621--1532710 Score: 85
Period size: 29 Copynumber: 3.1 Consensus size: 29
1532611 CAAATGAAAG
* * *
1532621 ATTAAAATATTTATTTATGTATAGATTAAAG
1 ATTAAAA-ATTTATTTATATGTA-ATTAAAA
* **
1532652 ATT-AAAGTTTATTTGGATGTGAATTAAAA
1 ATTAAAAATTTATTTATATGT-AATTAAAA
1532681 ATTAAAAATTTATTTATATGTAA-TAAAA
1 ATTAAAAATTTATTTATATGTAATTAAAA
1532709 AT
1 AT
1532711 ACAAAAACTT
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
28 7 0.15
29 20 0.42
30 18 0.38
31 3 0.06
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.43
Consensus pattern (29 bp):
ATTAAAAATTTATTTATATGTAATTAAAA
Found at i:1533607 original size:1 final size:1
Alignment explanation
Indices: 1533601--1533633 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
1533591 GGCTTTAAGC
1533601 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1533634 CTGGGCTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1533926 original size:47 final size:45
Alignment explanation
Indices: 1533851--1534018 Score: 191
Period size: 47 Copynumber: 3.7 Consensus size: 45
1533841 ATTTAAATTT
*
1533851 TAATAATTAAATTGATTTTATTTTATTTTTATTAAATTTAATTTGAA
1 TAATAATTAAA-T-ATTTTATTTGATTTTTATTAAATTTAATTTGAA
* * *
1533898 TAATAATTAAATATTTTCAATTTGATTTTTATT---TATAAGTTAAA
1 TAATAATTAAATATTTT--ATTTGATTTTTATTAAATTTAATTTGAA
* * *
1533942 AAATAATT-ATTATTTTATTTTATTTTTATTAAATTTAATTTGAA
1 TAATAATTAAATATTTTATTTGATTTTTATTAAATTTAATTTGAA
1533986 TAATAATTAAATATTTTCAATTTGATTTTTATT
1 TAATAATTAAATATTTT--ATTTGATTTTTATT
1534019 TATAAGTTAA
Statistics
Matches: 100, Mismatches: 13, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
41 13 0.13
43 7 0.07
44 30 0.30
45 12 0.12
46 1 0.01
47 37 0.37
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.57
Consensus pattern (45 bp):
TAATAATTAAATATTTTATTTGATTTTTATTAAATTTAATTTGAA
Found at i:1533963 original size:88 final size:88
Alignment explanation
Indices: 1533865--1534046 Score: 364
Period size: 88 Copynumber: 2.1 Consensus size: 88
1533855 AATTAAATTG
1533865 ATTTTATTTTATTTTTATTAAATTTAATTTGAATAATAATTAAATATTTTCAATTTGATTTTTAT
1 ATTTTATTTTATTTTTATTAAATTTAATTTGAATAATAATTAAATATTTTCAATTTGATTTTTAT
1533930 TTATAAGTTAAAAAATAATTATT
66 TTATAAGTTAAAAAATAATTATT
1533953 ATTTTATTTTATTTTTATTAAATTTAATTTGAATAATAATTAAATATTTTCAATTTGATTTTTAT
1 ATTTTATTTTATTTTTATTAAATTTAATTTGAATAATAATTAAATATTTTCAATTTGATTTTTAT
1534018 TTATAAGTTAAAAAATAATTATT
66 TTATAAGTTAAAAAATAATTATT
1534041 ATTTTA
1 ATTTTA
1534047 ATATATCTAA
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 94 1.00
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (88 bp):
ATTTTATTTTATTTTTATTAAATTTAATTTGAATAATAATTAAATATTTTCAATTTGATTTTTAT
TTATAAGTTAAAAAATAATTATT
Found at i:1534035 original size:44 final size:44
Alignment explanation
Indices: 1533899--1534038 Score: 178
Period size: 44 Copynumber: 3.2 Consensus size: 44
1533889 TAATTTGAAT
1533899 AATAATTAAATATTTTCAATTTGATTTTTATTTATAAGTTAAAA
1 AATAATTAAATATTTTCAATTTGATTTTTATTTATAAGTTAAAA
* * * * * *
1533943 AATAATT-ATTATTTT--ATTTTATTTTTATTAAATTTAATTTGAAT
1 AATAATTAAATATTTTCAATTTGATTTTTATT---TATAAGTTAAAA
1533987 AATAATTAAATATTTTCAATTTGATTTTTATTTATAAGTTAAAA
1 AATAATTAAATATTTTCAATTTGATTTTTATTTATAAGTTAAAA
1534031 AATAATTA
1 AATAATTA
1534039 TTATTTTAAT
Statistics
Matches: 78, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
41 13 0.17
43 7 0.09
44 38 0.49
45 7 0.09
47 13 0.17
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (44 bp):
AATAATTAAATATTTTCAATTTGATTTTTATTTATAAGTTAAAA
Found at i:1534035 original size:47 final size:47
Alignment explanation
Indices: 1533896--1534041 Score: 164
Period size: 47 Copynumber: 3.2 Consensus size: 47
1533886 ATTTAATTTG
1533896 AATAATAATTAAATATTTTCAATTTGATTTTTATTTATAAGTT--AA
1 AATAATAATTAAATATTTTCAATTTGATTTTTATTTATAAGTTAAAA
* * * **
1533941 AA-AATAATT-ATTATTTT--ATTTTATTTTTA-TTA-AATTTAATTTG
1 AATAATAATTAAATATTTTCAATTTGATTTTTATTTATAAGTTAA--AA
1533984 AATAATAATTAAATATTTTCAATTTGATTTTTATTTATAAGTTAAAA
1 AATAATAATTAAATATTTTCAATTTGATTTTTATTTATAAGTTAAAA
*
1534031 AATAATTATTA
1 AATAATAATTA
1534042 TTTTAATATA
Statistics
Matches: 80, Mismatches: 11, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
39 4 0.05
40 3 0.04
41 11 0.14
43 9 0.11
44 14 0.17
45 9 0.11
47 21 0.26
48 3 0.04
49 6 0.08
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.53
Consensus pattern (47 bp):
AATAATAATTAAATATTTTCAATTTGATTTTTATTTATAAGTTAAAA
Found at i:1536680 original size:41 final size:39
Alignment explanation
Indices: 1536613--1536689 Score: 118
Period size: 41 Copynumber: 1.9 Consensus size: 39
1536603 ATAAATTTGG
* *
1536613 AAACAAAAATACTGTGTGCCATAAATTTGGAAGATCCTC
1 AAACAAAAATACTGAGTGCCATAAATTTCGAAGATCCTC
1536652 AAACAAAAATACCATGAGTGCCATAAATTTCGAAGATC
1 AAACAAAAATA-C-TGAGTGCCATAAATTTCGAAGATC
1536690 AACAAAACTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
39 11 0.32
40 1 0.03
41 22 0.65
ACGTcount: A:0.44, C:0.18, G:0.14, T:0.23
Consensus pattern (39 bp):
AAACAAAAATACTGAGTGCCATAAATTTCGAAGATCCTC
Found at i:1540414 original size:47 final size:48
Alignment explanation
Indices: 1540323--1540415 Score: 125
Period size: 47 Copynumber: 2.0 Consensus size: 48
1540313 ATATTAAAGG
* *
1540323 ATAGATTTTTACAGTACCCAAGCTCCATTTATCTCTCAGGAAGCTAGA
1 ATAGATTTTTACAGTAACCAAGCTCCATTTATCTCTCAGAAAGCTAGA
* * * *
1540371 ATAGA-TTTTACAGTAACCATGTTCCATTTATCTTTTAGAAAGCTA
1 ATAGATTTTTACAGTAACCAAGCTCCATTTATCTCTCAGAAAGCTA
1540416 AATTTTAGAT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
47 34 0.87
48 5 0.13
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.35
Consensus pattern (48 bp):
ATAGATTTTTACAGTAACCAAGCTCCATTTATCTCTCAGAAAGCTAGA
Found at i:1541965 original size:2 final size:2
Alignment explanation
Indices: 1541918--1541957 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1541908 TTTGTAACCC
1541918 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1541958 TTTATATAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1542686 original size:21 final size:21
Alignment explanation
Indices: 1542660--1542700 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1542650 AACAAACTCC
1542660 CACTTCAAGAATCAATAAAAA
1 CACTTCAAGAATCAATAAAAA
*
1542681 CACTTCAAGAATCCATAAAA
1 CACTTCAAGAATCAATAAAA
1542701 CGAACATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.54, C:0.22, G:0.05, T:0.20
Consensus pattern (21 bp):
CACTTCAAGAATCAATAAAAA
Found at i:1543178 original size:31 final size:33
Alignment explanation
Indices: 1543109--1543182 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 33
1543099 AAATAATATT
* * *
1543109 ATAATATTAAA-ATAATTTTATATTTTTATAATT
1 ATAAT-TTAAATAAAATTTTATATTATTATAATA
1543142 A-AATTTAAATAAAATTTT-TATTATTA-AATA
1 ATAATTTAAATAAAATTTTATATTATTATAATA
1543172 ATAATTTAAAT
1 ATAATTTAAAT
1543183 TGTTATTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
30 4 0.11
31 21 0.58
32 10 0.28
33 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (33 bp):
ATAATTTAAATAAAATTTTATATTATTATAATA
Found at i:1543182 original size:26 final size:26
Alignment explanation
Indices: 1543119--1543189 Score: 72
Period size: 25 Copynumber: 2.7 Consensus size: 26
1543109 ATAATATTAA
* *
1543119 AATAATTTTATATTTTTATAATTAAAT
1 AATAA-TTTAAATTTTTATTATTAAAT
* * *
1543146 -TTAAATAAAATTTTTATTATTAAAT
1 AATAATTTAAATTTTTATTATTAAAT
*
1543171 AATAATTTAAATTGTTATT
1 AATAATTTAAATTTTTATT
1543190 TAAATTTGTA
Statistics
Matches: 34, Mismatches: 9, Indels: 3
0.74 0.20 0.07
Matches are distributed among these distances:
25 17 0.50
26 17 0.50
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (26 bp):
AATAATTTAAATTTTTATTATTAAAT
Found at i:1547663 original size:25 final size:25
Alignment explanation
Indices: 1547635--1547688 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 25
1547625 AGAACTGCAC
*
1547635 ATTT-CAGCAAGCTTTAGTATCCAAA
1 ATTTCCAGCAAGCTTTAGGAT-CAAA
*
1547660 ATTTCCAGGAAGCTTTAGGATCAAA
1 ATTTCCAGCAAGCTTTAGGATCAAA
1547685 ATTT
1 ATTT
1547689 TCGAAATTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 12 0.46
26 14 0.54
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (25 bp):
ATTTCCAGCAAGCTTTAGGATCAAA
Found at i:1551647 original size:2 final size:2
Alignment explanation
Indices: 1551642--1551675 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1551632 AGACTAAATG
* *
1551642 CA CA CA CA CA CA CA GA CA CA CA AA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1551676 TATATATACA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.44, G:0.03, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1551686 original size:10 final size:10
Alignment explanation
Indices: 1551673--1551714 Score: 59
Period size: 10 Copynumber: 4.3 Consensus size: 10
1551663 AAACACACAC
1551673 ACATATATAT
1 ACATATATAT
1551683 ACATATATAT
1 ACATATATAT
* *
1551693 ATATATATAC
1 ACATATATAT
1551703 ACATATAT-T
1 ACATATATAT
1551712 ACA
1 ACA
1551715 AGATCAAAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
9 3 0.11
10 25 0.89
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (10 bp):
ACATATATAT
Found at i:1559471 original size:24 final size:24
Alignment explanation
Indices: 1559439--1559484 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1559429 AATTTAAGTA
*
1559439 ATTTAATTTTAATTTTAATATTTG
1 ATTTAATTTTAATTTGAATATTTG
*
1559463 ATTTGATTTTAATTTGAATATT
1 ATTTAATTTTAATTTGAATATT
1559485 ATTGAATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.61
Consensus pattern (24 bp):
ATTTAATTTTAATTTGAATATTTG
Found at i:1561932 original size:19 final size:21
Alignment explanation
Indices: 1561903--1561948 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
1561893 AACGACGAAT
*
1561903 AATTT-ATTTGATTTG-AT-A
1 AATTTAATTTGAATTGAATAA
1561921 AATTTAATTTGAATTGAATAA
1 AATTTAATTTGAATTGAATAA
1561942 AATTTAA
1 AATTTAA
1561949 GCATGAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 5 0.21
19 9 0.38
20 2 0.08
21 8 0.33
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (21 bp):
AATTTAATTTGAATTGAATAA
Found at i:1562491 original size:24 final size:23
Alignment explanation
Indices: 1562459--1562516 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 23
1562449 AATACAATAC
* *
1562459 TTATATTAAACATATTATATTAA
1 TTATATTAAAAATATAATATTAA
1562482 TTATATTTAAAAATATAATATTAAA
1 TTATA-TTAAAAATATAATATT-AA
*
1562507 TTTTATTAAA
1 TTATATTAAA
1562517 TGTTTTATGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.17
24 19 0.63
25 6 0.20
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TTATATTAAAAATATAATATTAA
Found at i:1562912 original size:2 final size:2
Alignment explanation
Indices: 1562905--1562936 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1562895 ATTGACGACA
1562905 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1562937 CATTACCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1563779 original size:3 final size:3
Alignment explanation
Indices: 1563771--1563811 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
1563761 TTGACCTCAC
* *
1563771 AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AAC AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1563812 CATGCTAACA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:1566164 original size:5 final size:5
Alignment explanation
Indices: 1566154--1566210 Score: 78
Period size: 5 Copynumber: 11.2 Consensus size: 5
1566144 GTCTTTTTAC
* * *
1566154 TAATA TAATA TAATA TAATA TAATA TAATA TATATA TTATA TCATA TAAAA
1 TAATA TAATA TAATA TAATA TAATA TAATA TA-ATA TAATA TAATA TAATA
1566205 TAATA T
1 TAATA T
1566211 TATAGTACTA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
5 42 0.91
6 4 0.09
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
TAATA
Found at i:1566788 original size:16 final size:16
Alignment explanation
Indices: 1566769--1566802 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1566759 CAGATTATAG
1566769 ATTTATATATTATTAT
1 ATTTATATATTATTAT
*
1566785 ATTTATATATTTTTAT
1 ATTTATATATTATTAT
1566801 AT
1 AT
1566803 ATAATAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTTATATATTATTAT
Found at i:1566793 original size:26 final size:26
Alignment explanation
Indices: 1566736--1566804 Score: 65
Period size: 26 Copynumber: 2.7 Consensus size: 26
1566726 CTTTTGTTAG
1566736 ATTTATAT-ATTTA-ATATTATTATC
1 ATTTATATAATTTATATATTATTATC
* *
1566760 AGATTATA-GATTTATATATTATTAT-
1 A-TTTATATAATTTATATATTATTATC
*
1566785 ATTTATATATTTTTATATAT
1 ATTTATATA-ATTTATATAT
1566805 AATAATTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
24 6 0.17
25 11 0.31
26 19 0.53
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (26 bp):
ATTTATATAATTTATATATTATTATC
Found at i:1566883 original size:8 final size:8
Alignment explanation
Indices: 1566870--1566921 Score: 58
Period size: 8 Copynumber: 6.8 Consensus size: 8
1566860 TATATTTATC
1566870 TATATATT
1 TATATATT
1566878 TATATATAT
1 TATATAT-T
1566887 TATAT-TT
1 TATATATT
1566894 TA-AT-TT
1 TATATATT
1566900 TATGATA-T
1 TAT-ATATT
1566908 TATATATT
1 TATATATT
1566916 TATATA
1 TATATA
1566922 AATTTAAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
6 6 0.15
7 6 0.15
8 21 0.54
9 6 0.15
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (8 bp):
TATATATT
Found at i:1566899 original size:21 final size:22
Alignment explanation
Indices: 1566844--1566917 Score: 75
Period size: 21 Copynumber: 3.4 Consensus size: 22
1566834 ATAAATTAAA
1566844 ATATATATTAATTTA-ATATATT
1 ATATAT-TTAATTTATATATATT
* *
1566866 -TATCTATATATTTATATATATT
1 ATATATTTA-ATTTATATATATT
1566888 ATAT-TTTAATTT-TATGATATT
1 ATATATTTAATTTATAT-ATATT
1566909 ATATATTTA
1 ATATATTTA
1566918 TATAAATTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
20 5 0.11
21 22 0.50
22 14 0.32
23 3 0.07
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (22 bp):
ATATATTTAATTTATATATATT
Found at i:1566917 original size:16 final size:15
Alignment explanation
Indices: 1566845--1566921 Score: 58
Period size: 13 Copynumber: 5.4 Consensus size: 15
1566835 TAAATTAAAA
1566845 TATATATTA-AT-TT
1 TATATATTATATATT
* * *
1566858 AATATATT-TATCTA
1 TATATATTATATATT
1566872 TATAT-TTATATATAT
1 TATATATTATATAT-T
*
1566887 TATATTTTA-AT-TT
1 TATATATTATATATT
1566900 TATGATATTATATATT
1 TAT-ATATTATATATT
1566916 TATATA
1 TATATA
1566922 AATTTAAATA
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
13 15 0.30
14 15 0.30
15 12 0.24
16 8 0.16
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (15 bp):
TATATATTATATATT
Found at i:1567192 original size:24 final size:24
Alignment explanation
Indices: 1567129--1567202 Score: 62
Period size: 24 Copynumber: 3.0 Consensus size: 24
1567119 TTATTTTTTA
* * *
1567129 TTTAAATATGTATAAAATTAATTT
1 TTTAAAAATATATATAATTAATTT
*
1567153 TATTCAAAAA-CT-TATAATTAATTT
1 T-TT-AAAAATATATATAATTAATTT
*
1567177 TTTAAAAATATATATACATAAATTT
1 TTTAAAAATATATATA-ATTAATTT
1567202 T
1 T
1567203 AATTTTTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
22 5 0.12
23 3 0.08
24 17 0.43
25 11 0.28
26 4 0.10
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (24 bp):
TTTAAAAATATATATAATTAATTT
Found at i:1567739 original size:2 final size:2
Alignment explanation
Indices: 1567723--1567782 Score: 86
Period size: 2 Copynumber: 30.5 Consensus size: 2
1567713 TTGAGTTCTT
*
1567723 TC TC TT TC T- 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
* *
1567764 TC TT TC TC TG TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC T
1567783 TTTTAGGTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.00, C:0.43, G:0.02, T:0.55
Consensus pattern (2 bp):
TC
Found at i:1573268 original size:2 final size:2
Alignment explanation
Indices: 1573261--1573292 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1573251 TCATCTTCTT
*
1573261 TC TC TC TC TC TC TC TC TC TC TC TC GC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1573293 GGTTCTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.03, T:0.47
Consensus pattern (2 bp):
TC
Found at i:1574601 original size:83 final size:80
Alignment explanation
Indices: 1574433--1574602 Score: 189
Period size: 80 Copynumber: 2.1 Consensus size: 80
1574423 GTTGTGTTTT
* * * * * *
1574433 TTATATGATATTGTATTAATAATTCGTATTATATAGATTTCGATACATTTTTATGTGTCTGTTAT
1 TTATATTATATTGTATTAATAATTCATATTATATAAATTTCAAAACATTTTTATGTGTATGTTAT
* *
1574498 TTTTTTCGTATCATC
66 TTTTTTAGTATCATA
* * *
1574513 TTATATTAT-TTGATATTAATAATTCATATTATATAAATTTTAAAATATTATTATATGTGCTATT
1 TTATATTATATTG-TATTAATAATTCATATTATATAAATTTCAAAACATT-TT-TATGTG-TATG
*
1574577 TTATTTTTTTAGTATCGTA
62 TTATTTTTTTAGTATCATA
1574596 TTATATT
1 TTATATT
1574603 TTGTTTCGTG
Statistics
Matches: 74, Mismatches: 12, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
79 3 0.04
80 38 0.51
81 2 0.03
82 6 0.08
83 25 0.34
ACGTcount: A:0.31, C:0.06, G:0.08, T:0.55
Consensus pattern (80 bp):
TTATATTATATTGTATTAATAATTCATATTATATAAATTTCAAAACATTTTTATGTGTATGTTAT
TTTTTTAGTATCATA
Found at i:1577065 original size:2 final size:2
Alignment explanation
Indices: 1577058--1577095 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1577048 AACTATGTAT
1577058 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1577096 GAAAGGAGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1577431 original size:22 final size:22
Alignment explanation
Indices: 1577404--1577451 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1577394 TAAAATAAAA
1577404 AATATA-GAAATATTAAAATTTT
1 AATATATGAAATATT-AAATTTT
* *
1577426 AATATATTAAATATTAATTTTT
1 AATATATGAAATATTAAATTTT
1577448 AATA
1 AATA
1577452 ATTAATTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
AATATATGAAATATTAAATTTT
Found at i:1577437 original size:23 final size:21
Alignment explanation
Indices: 1577411--1577456 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
1577401 AAAAATATAG
1577411 AAATATTAAAATTTTAATATATT
1 AAATATT-AAATTTTAATA-ATT
*
1577434 AAATATTAATTTTTAATAATT
1 AAATATTAAATTTTAATAATT
1577455 AA
1 AA
1577457 TTCAACTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.23
22 10 0.45
23 7 0.32
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
AAATATTAAATTTTAATAATT
Found at i:1578010 original size:2 final size:2
Alignment explanation
Indices: 1578003--1578031 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1577993 CACTTTTTAC
1578003 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1578032 ACCTTGGGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1581184 original size:31 final size:32
Alignment explanation
Indices: 1581149--1581209 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
1581139 TTTATTTTAT
* * *
1581149 TATTTAAAATTATA-TTAAATGATAATATTAA
1 TATTTAAAATTAAATTTAAATAAAAATATTAA
1581180 TATTTAAAATTAAATTTAAATAAAAATATT
1 TATTTAAAATTAAATTTAAATAAAAATATT
1581210 TTTAATTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 13 0.50
32 13 0.50
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (32 bp):
TATTTAAAATTAAATTTAAATAAAAATATTAA
Found at i:1582089 original size:60 final size:60
Alignment explanation
Indices: 1582015--1582128 Score: 192
Period size: 60 Copynumber: 1.9 Consensus size: 60
1582005 TTTTTCATCA
* * * *
1582015 TCGTCGTCATCATCATCATCTTTCCTCGAGGCCACACCTTCTTCGTTTTCATCGTCGTCG
1 TCGTCGACAACATCATCACCTTTCCTCGAGGCCACACCTTCTTCGTCTTCATCGTCGTCG
1582075 TCGTCGACAACATCATCACCTTTCCTCGAGGCCACACCTTCTTCGTCTTCATCG
1 TCGTCGACAACATCATCACCTTTCCTCGAGGCCACACCTTCTTCGTCTTCATCG
1582129 CCATCATCAT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 50 1.00
ACGTcount: A:0.16, C:0.37, G:0.14, T:0.33
Consensus pattern (60 bp):
TCGTCGACAACATCATCACCTTTCCTCGAGGCCACACCTTCTTCGTCTTCATCGTCGTCG
Found at i:1582165 original size:3 final size:3
Alignment explanation
Indices: 1582157--1582187 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1582147 GATGCCACAC
1582157 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1582188 AGGCTTTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:1583424 original size:18 final size:19
Alignment explanation
Indices: 1583396--1583435 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
1583386 TAAATATAAA
*
1583396 AAAATTAAATAAAATTATT
1 AAAATTAAATAAAATAATT
*
1583415 AAAA-TAAATATAATAATT
1 AAAATTAAATAAAATAATT
1583433 AAA
1 AAA
1583436 TTTTTTTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATTAAATAAAATAATT
Found at i:1584081 original size:16 final size:16
Alignment explanation
Indices: 1584060--1584123 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 16
1584050 TAAATATATT
1584060 AAAATTTATATAATAA
1 AAAATTTATATAATAA
1584076 AAAA-TTAT-TAATATA
1 AAAATTTATATAATA-A
*
1584091 TTAAAATATATA-AATAA
1 --AAAATTTATATAATAA
*
1584108 ATAATATTATATAATA
1 AAAAT-TTATATAATA
1584124 TTATTAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 13
0.70 0.06 0.24
Matches are distributed among these distances:
14 5 0.13
15 9 0.24
16 8 0.21
17 9 0.24
18 7 0.18
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AAAATTTATATAATAA
Found at i:1584087 original size:14 final size:15
Alignment explanation
Indices: 1584060--1584123 Score: 51
Period size: 17 Copynumber: 4.0 Consensus size: 15
1584050 TAAATATATT
*
1584060 AAAATTTATATAATA
1 AAAAATTATATAATA
1584075 AAAAATTAT-TAATA
1 AAAAATTATATAATA
1584089 TATTAAAA-TATATAAATA
1 -A--AAAATTATAT-AATA
1584107 AATAATATTATATAATA
1 AA-AA-ATTATATAATA
1584124 TTATTAAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
14 5 0.12
15 10 0.25
16 5 0.12
17 11 0.28
18 9 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAAAATTATATAATA
Found at i:1584088 original size:75 final size:70
Alignment explanation
Indices: 1583972--1584163 Score: 180
Period size: 70 Copynumber: 2.7 Consensus size: 70
1583962 TATGTCAATT
*
1583972 TTATAAATAT-TTAAAATTTATATAAAAAATTAAAATATAATATAAAATATGATAAAAATA-AAA
1 TTATAAATATATTAAAATTTATATAATAAA-TAAAATATAATAT---AT-T-A-AAAAATATAAA
*
1584035 TAAATATTATTA
59 TAAATAATATTA
* *
1584047 TTATAAATATATTAAAATTTATATAATAAA-AAATTATTAATATATTAAAATATATAAATAAATA
1 TTATAAATATATTAAAATTTATATAATAAATAAAATA-TAATATATTAAAAAATATAAATAAATA
1584111 ATATTA
65 ATATTA
* * *
1584117 -TAT-AATATTATTAAAATATATATATATAATATAACATA-AATAAATTA
1 TTATAAATA-TATTAAAATTTATATA-ATAA-ATAAAATATAATATATTA
1584164 TTAAATTTAA
Statistics
Matches: 102, Mismatches: 8, Indels: 19
0.79 0.06 0.15
Matches are distributed among these distances:
68 4 0.04
69 24 0.24
70 27 0.26
71 2 0.02
72 6 0.06
74 5 0.05
75 16 0.16
76 18 0.18
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.40
Consensus pattern (70 bp):
TTATAAATATATTAAAATTTATATAATAAATAAAATATAATATATTAAAAAATATAAATAAATAA
TATTA
Found at i:1584089 original size:33 final size:35
Alignment explanation
Indices: 1584045--1584150 Score: 137
Period size: 33 Copynumber: 3.0 Consensus size: 35
1584035 TAAATATTAT
* *
1584045 TATTATAAATATATTAAAATTTATATAATAAA-AA
1 TATTATTAATATATTAAAATATATATAATAAATAA
1584079 -ATTATTAATATATTAAAATATATA-AATAAATAA
1 TATTATTAATATATTAAAATATATATAATAAATAA
1584112 TATTATATAATATTATTAAAATATATATATATAATATAA
1 TATTAT-TAATA-TATTAAAATATATATA-ATAA-ATAA
1584151 CATAAATAAA
Statistics
Matches: 63, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
32 6 0.10
33 24 0.38
34 5 0.08
35 5 0.08
36 14 0.22
37 1 0.02
38 4 0.06
39 4 0.06
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (35 bp):
TATTATTAATATATTAAAATATATATAATAAATAA
Found at i:1584160 original size:29 final size:28
Alignment explanation
Indices: 1584102--1584160 Score: 64
Period size: 29 Copynumber: 2.1 Consensus size: 28
1584092 TAAAATATAT
* * * *
1584102 AAATAAATAATATTATATAATATTATTA
1 AAATAAATAATATAATATAACATAAATA
*
1584130 AAATATATATATATAATATAACATAAATA
1 AAATAAATA-ATATAATATAACATAAATA
1584159 AA
1 AA
1584161 TTATTAAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 8 0.32
29 17 0.68
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (28 bp):
AAATAAATAATATAATATAACATAAATA
Done.