Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold11
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: 5230303
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 140504 characters in sequence are not A, C, G, or T
File 11 of 29
Found at i:1488717 original size:64 final size:64
Alignment explanation
Indices: 1488631--1488759 Score: 186
Period size: 64 Copynumber: 2.0 Consensus size: 64
1488621 TGATATCATG
* * * * *
1488631 AATTTAGTGATACAAAATAGATTAAAATTATTATAATAAATGTGAAATAACTTTATTTTAAATA
1 AATTTAGGGATACAAAATAGATTAAAAATATTATAATAAATGTAAAATAAATTCATTTTAAATA
** *
1488695 AATTTAGGGATATTAAATAGATTAAAAATATTATAATAAATTTAAAATAAATTCATTTTAAATA
1 AATTTAGGGATACAAAATAGATTAAAAATATTATAATAAATGTAAAATAAATTCATTTTAAATA
1488759 A
1 A
1488760 GTTAAAGATA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
64 57 1.00
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (64 bp):
AATTTAGGGATACAAAATAGATTAAAAATATTATAATAAATGTAAAATAAATTCATTTTAAATA
Found at i:1488741 original size:20 final size:18
Alignment explanation
Indices: 1488704--1488743 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
1488694 AAATTTAGGG
*
1488704 ATATTAAATAGATTAAAA
1 ATATTAAATAAATTAAAA
*
1488722 ATATTATAATAAATTTAAA
1 ATATTA-AATAAATTAAAA
1488741 ATA
1 ATA
1488744 AATTCATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (18 bp):
ATATTAAATAAATTAAAA
Found at i:1488787 original size:64 final size:64
Alignment explanation
Indices: 1488645--1488788 Score: 166
Period size: 64 Copynumber: 2.2 Consensus size: 64
1488635 TAGTGATACA
* * * * * * **
1488645 AAATAGATTAAAATTATTATAATAAATGTGAAATAACTTTATTTTAAATAAATTTAGGGATATT
1 AAATAGAATAAAAATATTATAATAAATGTAAAATAAATTCATTTTAAATAAAGTTAAAGATATT
* *
1488709 AAATAGATTAAAAATATTATAATAAATTTAAAATAAATTCATTTTAAAT-AAGTTAAAGATATT
1 AAATAGAATAAAAATATTATAATAAATGTAAAATAAATTCATTTTAAATAAAGTTAAAGATATT
1488772 ATAATA-AATACAAAATA
1 A-AATAGAATA-AAAATA
1488789 AAAGATATTT
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
63 15 0.22
64 54 0.78
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (64 bp):
AAATAGAATAAAAATATTATAATAAATGTAAAATAAATTCATTTTAAATAAAGTTAAAGATATT
Found at i:1489259 original size:15 final size:15
Alignment explanation
Indices: 1489217--1489260 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
1489207 ATAATGTTTT
1489217 TTAAAATT-TAATTA
1 TTAAAATTATAATTA
1489231 -TAAAATATATAATTA
1 TTAAAAT-TATAATTA
*
1489246 TTAAAATTAAAATTA
1 TTAAAATTATAATTA
1489261 AATTTTAGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 6 0.23
14 1 0.04
15 13 0.50
16 6 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TTAAAATTATAATTA
Found at i:1496195 original size:17 final size:17
Alignment explanation
Indices: 1496173--1496206 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1496163 ATAAATTAAA
1496173 AATAAATAATTATTTTT
1 AATAAATAATTATTTTT
1496190 AATAAATAATTATTTTT
1 AATAAATAATTATTTTT
1496207 TAAAATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AATAAATAATTATTTTT
Found at i:1496541 original size:24 final size:22
Alignment explanation
Indices: 1496505--1496554 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 22
1496495 AATAAACACT
1496505 TTTAATTATATTTTATACTATAAA
1 TTTAATTATATTTTATA--ATAAA
*
1496529 TTTAATT-TAATTTTTTAATAAA
1 TTTAATTAT-ATTTTATAATAAA
1496551 TTTA
1 TTTA
1496555 CCAAATGTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 9 0.38
23 1 0.04
24 14 0.58
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTAATTATATTTTATAATAAA
Found at i:1497566 original size:15 final size:13
Alignment explanation
Indices: 1497536--1497586 Score: 50
Period size: 15 Copynumber: 3.7 Consensus size: 13
1497526 CAAATAAAAA
1497536 ATATTTATATTA-
1 ATATTTATATTAT
1497548 ATATTATATATATAT
1 ATATT-TATAT-TAT
*
1497563 ATATGATATATTTAT
1 ATAT-TTATA-TTAT
1497578 ATATTTATA
1 ATATTTATA
1497587 AAATAAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
12 5 0.16
13 5 0.16
14 6 0.19
15 15 0.47
16 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (13 bp):
ATATTTATATTAT
Found at i:1502225 original size:47 final size:47
Alignment explanation
Indices: 1502158--1502256 Score: 123
Period size: 46 Copynumber: 2.1 Consensus size: 47
1502148 TAAATTTATT
* * *
1502158 TTTTTTAATTTGAGTTTTATT-TAAATTATTATTTATTAATT-AAAATAA
1 TTTTTTAATTTAAATTTTATTATAAA--A-TATATATTAATTAAAAATAA
1502206 TTTTTT-ATTTAAATTTTATTATAAAATATATATTAATTAAAAATAA
1 TTTTTTAATTTAAATTTTATTATAAAATATATATTAATTAAAAATAA
1502252 TTTTT
1 TTTTT
1502257 AATCTTTTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
45 11 0.24
46 13 0.28
47 12 0.26
48 10 0.22
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (47 bp):
TTTTTTAATTTAAATTTTATTATAAAATATATATTAATTAAAAATAA
Found at i:1505552 original size:23 final size:21
Alignment explanation
Indices: 1505508--1505552 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
1505498 TCAAATCTGA
*
1505508 TTTAATATTTAAAAATTTTAT
1 TTTAATATTTAAAAATTATAT
*
1505529 TTTATTATTTATAAAATATATAT
1 TTTAATATTTA-AAAAT-TATAT
1505552 T
1 T
1505553 AAAATATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 10 0.50
22 5 0.25
23 5 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTAATATTTAAAAATTATAT
Found at i:1505592 original size:21 final size:21
Alignment explanation
Indices: 1505563--1505612 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1505553 AAAATATATT
* *
1505563 TTTAT-ATTAATTTTATATAA
1 TTTATAATTAAATTTAAATAA
1505583 TTTATAATTAAATTTAAATAA
1 TTTATAATTAAATTTAAATAA
* *
1505604 ATAATAATT
1 TTTATAATT
1505613 TTTATTAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 5 0.20
21 20 0.80
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTATAATTAAATTTAAATAA
Found at i:1505620 original size:21 final size:20
Alignment explanation
Indices: 1505594--1505642 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
1505584 TTATAATTAA
1505594 ATTTAAATAAATAATAATTT
1 ATTTAAATAAATAATAATTT
* * *
1505614 TTATTAATTAAATAGTAATTT
1 AT-TTAAATAAATAATAATTT
1505635 ATTTAAAT
1 ATTTAAAT
1505643 CTATTTAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
ATTTAAATAAATAATAATTT
Found at i:1505689 original size:16 final size:15
Alignment explanation
Indices: 1505670--1505703 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
1505660 ATTTTATTTT
*
1505670 AAATTTAATCTAATTC
1 AAATTTAAT-TAAATC
1505686 AAATTTAATTAAATC
1 AAATTTAATTAAATC
1505701 AAA
1 AAA
1505704 CTAACAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (15 bp):
AAATTTAATTAAATC
Found at i:1506061 original size:23 final size:24
Alignment explanation
Indices: 1506034--1506126 Score: 73
Period size: 27 Copynumber: 3.7 Consensus size: 24
1506024 TCGATCAGTT
1506034 AAATTGATTTAATTAAA-AATTAA
1 AAATTGATTTAATTAAATAATTAA
* * *
1506057 AAATTTATTTGATTAGAAGTTATATAA
1 AAATTGATTTAATTA-AA-TAAT-TAA
1506084 AAATTGAATTTTAATTAAACTAACTT-A
1 AAATTG-A-TTTAATTAAA-TAA-TTAA
*
1506111 AAATTGATTCAATTAA
1 AAATTGATTTAATTAA
1506127 TAAAAAAATC
Statistics
Matches: 55, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
23 13 0.24
24 2 0.04
25 8 0.15
26 3 0.05
27 15 0.27
28 6 0.11
29 8 0.15
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.41
Consensus pattern (24 bp):
AAATTGATTTAATTAAATAATTAA
Found at i:1506814 original size:7 final size:7
Alignment explanation
Indices: 1506804--1506830 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1506794 AATGTTTAAT
1506804 AAATTTA
1 AAATTTA
1506811 AAATTTA
1 AAATTTA
1506818 AAATTTA
1 AAATTTA
1506825 AAATTT
1 AAATTT
1506831 TTATTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
AAATTTA
Found at i:1508743 original size:54 final size:53
Alignment explanation
Indices: 1508649--1508770 Score: 166
Period size: 52 Copynumber: 2.4 Consensus size: 53
1508639 GGTATTATAA
* *
1508649 ATATATATATAT-TATGAGTACTTGTAATTTTTATTAATATGAGTACTCATAT
1 ATATATATATATATATGAGTACTTGTAATATATATTAATATGAGTACTCATAT
1508701 ATATATATATATATATGAGTACTTGTAA-ATATATATATATATGAGTACTCATAT
1 ATATATATATATATATGAGTACTTGTAATATATAT-TA-ATATGAGTACTCATAT
1508755 AT-T-TAT-TA-ATATGAGT
1 ATATATATATATATATGAGT
1508771 GAGAAAAATG
Statistics
Matches: 65, Mismatches: 2, Indels: 8
0.87 0.03 0.11
Matches are distributed among these distances:
50 8 0.12
51 2 0.03
52 19 0.29
53 18 0.28
54 18 0.28
ACGTcount: A:0.39, C:0.05, G:0.10, T:0.46
Consensus pattern (53 bp):
ATATATATATATATATGAGTACTTGTAATATATATTAATATGAGTACTCATAT
Found at i:1508766 original size:26 final size:27
Alignment explanation
Indices: 1508649--1508766 Score: 106
Period size: 26 Copynumber: 4.6 Consensus size: 27
1508639 GGTATTATAA
**
1508649 ATATATA-TATAT-TATGAGTACTTGT
1 ATATATATTATATATATGAGTACTCAT
*
1508674 A-AT-TTTTAT-TAATATGAGTACTCAT
1 ATATATATTATAT-ATATGAGTACTCAT
**
1508699 ATATATATATATATATATGAGTACTTGT
1 ATATATAT-TATATATATGAGTACTCAT
*
1508727 AAATATA-TATATATATGAGTACTCAT
1 ATATATATTATATATATGAGTACTCAT
*
1508753 ATATTTATTA-ATAT
1 ATATATATTATATAT
1508767 GAGTGAGAAA
Statistics
Matches: 74, Mismatches: 11, Indels: 15
0.74 0.11 0.15
Matches are distributed among these distances:
23 2 0.03
24 5 0.07
25 13 0.18
26 28 0.38
27 4 0.05
28 21 0.28
29 1 0.01
ACGTcount: A:0.40, C:0.05, G:0.08, T:0.47
Consensus pattern (27 bp):
ATATATATTATATATATGAGTACTCAT
Found at i:1508932 original size:16 final size:17
Alignment explanation
Indices: 1508913--1508949 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1508903 ATTCATTCGA
*
1508913 TAAATTTAATTTTA-AT
1 TAAATTTAATTTAATAT
1508929 TAAA-TTAATTTAATAT
1 TAAATTTAATTTAATAT
1508945 TAAAT
1 TAAAT
1508950 ATATTAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TAAATTTAATTTAATAT
Found at i:1508940 original size:20 final size:20
Alignment explanation
Indices: 1508915--1508957 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1508905 TCATTCGATA
* *
1508915 AATTTAATTTTAATTAAATT
1 AATTTAATATTAAATAAATT
*
1508935 AATTTAATATTAAATATATT
1 AATTTAATATTAAATAAATT
1508955 AAT
1 AAT
1508958 AAATAAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AATTTAATATTAAATAAATT
Found at i:1509484 original size:2 final size:2
Alignment explanation
Indices: 1509456--1509508 Score: 72
Period size: 2 Copynumber: 27.0 Consensus size: 2
1509446 AATTTAAATA
* * *
1509456 AT AT A- AT AT AT AA AT AC AT AT AG 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
1509497 AT AT AT AT AT AT
1 AT AT AT AT AT AT
1509509 TAAGAACATT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (2 bp):
AT
Found at i:1509668 original size:27 final size:27
Alignment explanation
Indices: 1509621--1509684 Score: 87
Period size: 27 Copynumber: 2.3 Consensus size: 27
1509611 TACATATTTT
1509621 TATATGTTATAATTATTTTAAAATATTA
1 TATAT-TTATAATTATTTTAAAATATTA
1509649 TATATTTA-AATATATTTTAAAATATTA
1 TATATTTATAAT-TATTTTAAAATATTA
1509676 -ATAATTTAT
1 TAT-ATTTAT
1509685 GAAGTATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
26 5 0.15
27 23 0.70
28 5 0.15
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (27 bp):
TATATTTATAATTATTTTAAAATATTA
Found at i:1509740 original size:24 final size:24
Alignment explanation
Indices: 1509713--1509774 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
1509703 TATTTTTATA
*
1509713 TTTATATTTTATTTATATTATTTT
1 TTTATATTTTATTTATATTACTTT
*
1509737 TTTA-ATATATATTTATATTACTTT
1 TTTATAT-TTTATTTATATTACTTT
*
1509761 TTTATTATATTATT
1 TTTA-TATTTTATT
1509775 GTGACTTGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
23 2 0.06
24 23 0.74
25 4 0.13
26 2 0.06
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTATATTTTATTTATATTACTTT
Found at i:1509745 original size:41 final size:40
Alignment explanation
Indices: 1509695--1509774 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 40
1509685 GAAGTATAAA
*
1509695 TTTTAATATATTTTTATATTTA-TATTTTATTTATATTATTT
1 TTTTAATATATATTTATA-TTACTATTTTA-TTATATTATTT
*
1509736 TTTTAATATATATTTATATTACTTTTTTATTATATTATT
1 TTTTAATATATATTTATATTACTATTTTATTATATTATT
1509775 GTGACTTGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
40 13 0.36
41 23 0.64
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (40 bp):
TTTTAATATATATTTATATTACTATTTTATTATATTATTT
Found at i:1510269 original size:12 final size:12
Alignment explanation
Indices: 1510219--1510268 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
1510209 TTTATTTTTT
1510219 AATATAATATAA
1 AATATAATATAA
*
1510231 ATTAT-ATGATATA
1 AATATAAT-ATA-A
*
1510244 TATATAATATAA
1 AATATAATATAA
1510256 AATATAAT-TAA
1 AATATAATATAA
1510267 AA
1 AA
1510269 AACAGGTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
11 7 0.23
12 15 0.48
13 7 0.23
14 2 0.06
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (12 bp):
AATATAATATAA
Found at i:1512655 original size:2 final size:2
Alignment explanation
Indices: 1512648--1512675 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1512638 TCTATATTTC
1512648 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
1512676 AGAATTAATT
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:1513038 original size:6 final size:6
Alignment explanation
Indices: 1513029--1513053 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1513019 TGTTTTTGGT
1513029 TTAATG TTAATG TTAATG TTAATG T
1 TTAATG TTAATG TTAATG TTAATG T
1513054 AATATTATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (6 bp):
TTAATG
Found at i:1513850 original size:15 final size:14
Alignment explanation
Indices: 1513807--1513850 Score: 61
Period size: 15 Copynumber: 3.0 Consensus size: 14
1513797 CAGAACATAG
1513807 AATATAAATATGAAA
1 AATATAAATAT-AAA
*
1513822 AATATAAATTTAAA
1 AATATAAATATAAA
1513836 AATTATAAATATAAA
1 AA-TATAAATATAAA
1513851 CGTACATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 5 0.19
15 21 0.81
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (14 bp):
AATATAAATATAAA
Found at i:1515052 original size:29 final size:28
Alignment explanation
Indices: 1515001--1515085 Score: 102
Period size: 28 Copynumber: 3.0 Consensus size: 28
1514991 TTAAAGTTTA
*
1515001 TTATTTTATTTAAATAAATTTTATATTT
1 TTATTATATTTAAATAAATTTTATATTT
* **
1515029 TTATTATATTTTAATAAATGTTTAT-GCT
1 TTATTATATTTAAATAAAT-TTTATATTT
1515057 TTATTTATATTTAAATAAATTTT-TATTT
1 TTA-TTATATTTAAATAAATTTTATATTT
1515085 T
1 T
1515086 AAATGAAAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
27 1 0.02
28 26 0.55
29 20 0.43
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.62
Consensus pattern (28 bp):
TTATTATATTTAAATAAATTTTATATTT
Found at i:1515107 original size:57 final size:56
Alignment explanation
Indices: 1515001--1515109 Score: 130
Period size: 57 Copynumber: 1.9 Consensus size: 56
1514991 TTAAAGTTTA
* * * * *
1515001 TTATTTTATTTAAATAAATTTTATATTTTTATTATATTTTAATAAATGTTTATGCT
1 TTATTTTATTTAAATAAATTTTATATTTTAATGAAAATTCAATAAATGTTTATGCT
**
1515057 TTATTTATATTTAAATAAATTTT-TATTTTAAATGAAAATTCAATTTATGTTTA
1 TTATTT-TATTTAAATAAATTTTATATTTT-AATGAAAATTCAATAAATGTTTA
1515110 ATTAATCCCA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
56 12 0.27
57 32 0.73
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.58
Consensus pattern (56 bp):
TTATTTTATTTAAATAAATTTTATATTTTAATGAAAATTCAATAAATGTTTATGCT
Found at i:1515766 original size:8 final size:8
Alignment explanation
Indices: 1515734--1515758 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1515724 TTAATTCGAG
1515734 TAATTTTT
1 TAATTTTT
1515742 TAATTTTT
1 TAATTTTT
1515750 TAATTTTT
1 TAATTTTT
1515758 T
1 T
1515759 TTATTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TAATTTTT
Found at i:1515831 original size:26 final size:24
Alignment explanation
Indices: 1515800--1515883 Score: 82
Period size: 26 Copynumber: 3.3 Consensus size: 24
1515790 TAATAATATT
*
1515800 ATAATTTAATTTAAATTTTAATATAA
1 ATAATTTAATTTAAA--TTAATTTAA
1515826 ATAA-TTAAGTTTAAAATTATATTTAA
1 ATAATTTAA-TTT-AAATTA-ATTTAA
*
1515852 ATATATTTAA-TTAAACTAATTTAA
1 ATA-ATTTAATTTAAATTAATTTAA
1515876 ATAATTTA
1 ATAATTTA
1515884 GTTTTTTTCT
Statistics
Matches: 51, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
23 5 0.10
24 9 0.18
25 12 0.24
26 17 0.33
27 4 0.08
28 4 0.08
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (24 bp):
ATAATTTAATTTAAATTAATTTAA
Found at i:1521235 original size:25 final size:24
Alignment explanation
Indices: 1521206--1521262 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 24
1521196 TAATAAAAAA
1521206 ATTATTTATTTAAAATTTAATTTG
1 ATTATTTATTTAAAATTTAATTTG
* * *
1521230 ATTTATTGATTTAAAATTTTATTTT
1 A-TTATTTATTTAAAATTTAATTTG
1521255 ATTATTTA
1 ATTATTTA
1521263 AAATAATATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 7 0.25
25 21 0.75
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (24 bp):
ATTATTTATTTAAAATTTAATTTG
Found at i:1521253 original size:20 final size:20
Alignment explanation
Indices: 1521224--1521266 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
1521214 TTTAAAATTT
1521224 AATTTGA-TTTATTGATTTAA
1 AATTTGATTTTATT-ATTTAA
*
1521244 AATTTTATTTTATTATTTAA
1 AATTTGATTTTATTATTTAA
1521264 AAT
1 AAT
1521267 AATATTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (20 bp):
AATTTGATTTTATTATTTAA
Found at i:1521272 original size:20 final size:21
Alignment explanation
Indices: 1521231--1521273 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
1521221 TTTAATTTGA
**
1521231 TTTATTGATTTAAAATTTTAT
1 TTTATTGATTTAAAATAATAT
1521252 TTTATT-ATTTAAAATAATAT
1 TTTATTGATTTAAAATAATAT
1521272 TT
1 TT
1521274 AAAATATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TTTATTGATTTAAAATAATAT
Found at i:1521298 original size:23 final size:24
Alignment explanation
Indices: 1521262--1521316 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
1521252 TTTATTATTT
1521262 AAAATAATATTTAAAATATTAAA-A
1 AAAATAATATTTAAAAT-TTAAATA
* *
1521286 AAAATTATA-TTAATATTTAAATA
1 AAAATAATATTTAAAATTTAAATA
1521309 AAAATAAT
1 AAAATAAT
1521317 TTTTTATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.19
23 14 0.52
24 8 0.30
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATAATATTTAAAATTTAAATA
Found at i:1525951 original size:17 final size:17
Alignment explanation
Indices: 1525929--1525962 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1525919 AAATTGAAGG
1525929 CATACTCATATTAGATA
1 CATACTCATATTAGATA
* *
1525946 CATACTTATATTCGATA
1 CATACTCATATTAGATA
1525963 TTTAGTCTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.18, G:0.06, T:0.38
Consensus pattern (17 bp):
CATACTCATATTAGATA
Found at i:1532856 original size:14 final size:15
Alignment explanation
Indices: 1532839--1532879 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
1532829 ATTAATATTT
1532839 ATATATTTTTAA-AA
1 ATATATTTTTAATAA
*
1532853 ATATA-TTTAAATAA
1 ATATATTTTTAATAA
*
1532867 AAATATTTTTAAT
1 ATATATTTTTAAT
1532880 TATTAAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
13 5 0.23
14 11 0.50
15 6 0.27
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATATATTTTTAATAA
Found at i:1532867 original size:16 final size:16
Alignment explanation
Indices: 1532848--1532878 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1532838 TATATATTTT
1532848 TAAAAATATATTTAAA
1 TAAAAATATATTTAAA
*
1532864 TAAAAATATTTTTAA
1 TAAAAATATATTTAA
1532879 TTATTAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAAAATATATTTAAA
Found at i:1532932 original size:20 final size:20
Alignment explanation
Indices: 1532896--1532933 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1532886 ATAATTATTT
*
1532896 ATATTAAATTAAATTATAAC
1 ATATTAAATAAAATTATAAC
1532916 ATATTAAA-AAAAGTTATA
1 ATATTAAATAAAA-TTATA
1532934 TTTAAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (20 bp):
ATATTAAATAAAATTATAAC
Found at i:1535645 original size:23 final size:23
Alignment explanation
Indices: 1535590--1535649 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
1535580 ATTAATTAAT
*
1535590 TTTTTA-ATTAATTAATTATATTA
1 TTTTTATATT-ATTATTTATATTA
*
1535613 -TTTTATTATTATTATTTTTATTA
1 TTTTTA-TATTATTATTTATATTA
1535636 TTTTTATATT-TTAT
1 TTTTTATATTATTAT
1535650 GAAAGGATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
22 9 0.28
23 15 0.47
24 8 0.25
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (23 bp):
TTTTTATATTATTATTTATATTA
Found at i:1536694 original size:17 final size:19
Alignment explanation
Indices: 1536653--1536706 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
1536643 CTTGACTAAT
*
1536653 TTTTTAAAC-AAATTGTATA
1 TTTTTAATCAAAATT-TATA
1536672 TTTTT-ATCAAAATTTAT-
1 TTTTTAATCAAAATTTATA
*
1536689 TTTTTAATCAATATTTAT
1 TTTTTAATCAAAATTTAT
1536707 GTATAAATCC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 5 0.16
18 16 0.52
19 10 0.32
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.56
Consensus pattern (19 bp):
TTTTTAATCAAAATTTATA
Found at i:1536881 original size:30 final size:30
Alignment explanation
Indices: 1536847--1536932 Score: 111
Period size: 30 Copynumber: 2.8 Consensus size: 30
1536837 AAGTGCCAGT
1536847 AATTAAGAGTTTATTTGAGTATAAATTAAA
1 AATTAAGAGTTTATTTGAGTATAAATTAAA
* * *
1536877 AATTAA-ATGTTTATTTAAGTTTAAGTTAAA
1 AATTAAGA-GTTTATTTGAGTATAAATTAAA
*
1536907 ATGTTAAGAGTTTATTTGAGTATAAA
1 A-ATTAAGAGTTTATTTGAGTATAAA
1536933 AAAATTCAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
29 1 0.02
30 26 0.57
31 18 0.39
32 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (30 bp):
AATTAAGAGTTTATTTGAGTATAAATTAAA
Found at i:1543640 original size:13 final size:13
Alignment explanation
Indices: 1543610--1543694 Score: 55
Period size: 13 Copynumber: 6.2 Consensus size: 13
1543600 ATTTTTCCTC
* *
1543610 AAATATTCAAATT
1 AAATATTTATATT
*
1543623 TAATATTTATATT
1 AAATATTTATATT
1543636 AAATATTTAT-TT
1 AAATATTTATATT
*
1543648 AAATATAAATATATT
1 AAATAT--TTATATT
1543663 AAACACATATTTATATT
1 --A-A-ATATTTATATT
* *
1543680 TAATATTTATCTT
1 AAATATTTATATT
1543693 AA
1 AA
1543695 TTTTATTAAT
Statistics
Matches: 56, Mismatches: 9, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
12 8 0.14
13 30 0.54
14 4 0.07
15 2 0.04
17 7 0.12
18 1 0.02
19 4 0.07
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (13 bp):
AAATATTTATATT
Found at i:1543649 original size:12 final size:12
Alignment explanation
Indices: 1543620--1543653 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
1543610 AAATATTCAA
1543620 ATTT-AATATTT
1 ATTTAAATATTT
1543631 ATATTAAATATTT
1 AT-TTAAATATTT
1543644 ATTTAAATAT
1 ATTTAAATAT
1543654 AAATATATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 2 0.10
12 10 0.48
13 9 0.43
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTTAAATATTT
Found at i:1543990 original size:21 final size:23
Alignment explanation
Indices: 1543936--1543990 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
1543926 AATTGATCAA
*
1543936 ATTTATATTATATTTTTTTAAGT
1 ATTTATATTTTATTTTTTTAAGT
* *
1543959 ATATATAATTTTTTTTTTTTAA-T
1 ATTTAT-ATTTTATTTTTTTAAGT
1543982 -TTTATATTT
1 ATTTATATTT
1543991 AATATATATT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
21 4 0.15
22 4 0.15
23 6 0.22
24 13 0.48
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (23 bp):
ATTTATATTTTATTTTTTTAAGT
Found at i:1544435 original size:24 final size:23
Alignment explanation
Indices: 1544382--1544429 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 23
1544372 GATTTTTAAA
1544382 ATATTTATTTTTTTATTTTATAT
1 ATATTTATTTTTTTATTTTATAT
1544405 GATATTTAATTTTGTTTATTGTTAT
1 -ATATTT-ATTTT-TTTATT-TTAT
1544430 TTATTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 6 0.29
25 5 0.24
26 6 0.29
27 4 0.19
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (23 bp):
ATATTTATTTTTTTATTTTATAT
Found at i:1545457 original size:14 final size:14
Alignment explanation
Indices: 1545438--1545466 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1545428 AATTTTTAAA
1545438 AATATATAAATATT
1 AATATATAAATATT
1545452 AATATATAAATATT
1 AATATATAAATATT
1545466 A
1 A
1545467 TTTTTATTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AATATATAAATATT
Found at i:1545596 original size:13 final size:14
Alignment explanation
Indices: 1545559--1545596 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
1545549 TAAATCACAG
1545559 TTTAATTTATAATA
1 TTTAATTTATAATA
*
1545573 TTTTTATTTATAATA
1 -TTTAATTTATAATA
1545588 -TTAATTTAT
1 TTTAATTTAT
1545597 GATTATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 8 0.38
15 13 0.62
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTAATTTATAATA
Found at i:1549055 original size:19 final size:19
Alignment explanation
Indices: 1549033--1549071 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1549023 TTTGCACACA
1549033 CGAATCTTGTTTCCACATC
1 CGAATCTTGTTTCCACATC
1549052 CGAATCTTGTTTCCACATC
1 CGAATCTTGTTTCCACATC
1549071 C
1 C
1549072 AGTTGGCACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.33, G:0.10, T:0.36
Consensus pattern (19 bp):
CGAATCTTGTTTCCACATC
Found at i:1550120 original size:11 final size:11
Alignment explanation
Indices: 1550104--1550140 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
1550094 AATATTACGA
1550104 ATTTATATTAT
1 ATTTATATTAT
1550115 ATTTATATTA-
1 ATTTATATTAT
1550125 ATTT-T-TTAT
1 ATTTATATTAT
1550134 ATTTATA
1 ATTTATA
1550141 AAATTTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
8 3 0.13
9 5 0.22
10 5 0.22
11 10 0.43
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
ATTTATATTAT
Found at i:1550139 original size:30 final size:30
Alignment explanation
Indices: 1550104--1550223 Score: 84
Period size: 30 Copynumber: 3.9 Consensus size: 30
1550094 AATATTACGA
*
1550104 ATTTATATTATATTTATATTAATTTTTTAT
1 ATTTATATTATATTTATATTAATTTTATAT
** *
1550134 ATTTATAAAATTTTATATATTTAAATTTTGATAT
1 ATTTATATTATATT-TATA-TT-AATTTT-ATAT
* *
1550168 ATTAATAATT-TATTT-TATATAATTTAATAT
1 ATTTAT-ATTATATTTATAT-TAATTTTATAT
* *
1550198 ATTTAT-TTATAATATATGTTAATTTT
1 ATTTATATTAT-ATTTATATTAATTTT
1550224 TTTTATATTT
Statistics
Matches: 68, Mismatches: 13, Indels: 18
0.69 0.13 0.18
Matches are distributed among these distances:
28 2 0.03
29 1 0.01
30 29 0.43
31 12 0.18
32 5 0.07
33 7 0.10
34 11 0.16
35 1 0.01
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (30 bp):
ATTTATATTATATTTATATTAATTTTATAT
Found at i:1550149 original size:16 final size:16
Alignment explanation
Indices: 1550128--1550203 Score: 54
Period size: 16 Copynumber: 4.8 Consensus size: 16
1550118 TATATTAATT
1550128 TTTTATATTTATAAAA
1 TTTTATATTTATAAAA
1550144 TTTTATATATT-T-AAA
1 TTTTATAT-TTATAAAA
*
1550159 TTTTGATATATTA-ATAA
1 TTTT-ATAT-TTATAAAA
*
1550176 -TTTAT-TTTATATAA
1 TTTTATATTTATAAAA
1550190 TTTAATATATTTAT
1 TTT--TATATTTAT
1550204 TTATAATATA
Statistics
Matches: 50, Mismatches: 1, Indels: 16
0.75 0.01 0.24
Matches are distributed among these distances:
13 3 0.06
14 5 0.10
15 11 0.22
16 19 0.38
17 7 0.14
18 5 0.10
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (16 bp):
TTTTATATTTATAAAA
Found at i:1550202 original size:18 final size:18
Alignment explanation
Indices: 1550112--1550203 Score: 76
Period size: 18 Copynumber: 5.5 Consensus size: 18
1550102 GAATTTATAT
*
1550112 TATATTTATATTAATTTTT
1 TATATTTATA-TAATTTTA
*
1550131 TATATTTATAAAATTTTA
1 TATATTTATATAATTTTA
1550149 TATA-TT-TA-AATTTTGA
1 TATATTTATATAATTTT-A
1550165 TATA-TTA-ATAA--TT-
1 TATATTTATATAATTTTA
*
1550178 TAT-TTTATATAATTTAA
1 TATATTTATATAATTTTA
1550195 TATATTTAT
1 TATATTTAT
1550204 TTATAATATA
Statistics
Matches: 61, Mismatches: 3, Indels: 19
0.73 0.04 0.23
Matches are distributed among these distances:
13 6 0.10
14 4 0.07
15 8 0.13
16 11 0.18
17 7 0.11
18 15 0.25
19 10 0.16
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (18 bp):
TATATTTATATAATTTTA
Found at i:1550208 original size:10 final size:10
Alignment explanation
Indices: 1550104--1550208 Score: 50
Period size: 9 Copynumber: 11.1 Consensus size: 10
1550094 AATATTACGA
1550104 ATTTATATTAT
1 ATTTATA-TAT
1550115 ATTTATAT-T
1 ATTTATATAT
*
1550124 AATTT-TTTAT
1 -ATTTATATAT
*
1550134 ATTTATA-AA
1 ATTTATATAT
1550143 ATTT-TATAT
1 ATTTATATAT
1550152 ATTTA-A-AT
1 ATTTATATAT
*
1550160 -TTT-GATAT
1 ATTTATATAT
* *
1550168 ATTAATAATTT
1 ATTTAT-ATAT
1550179 ATTT-TATAT
1 ATTTATATAT
1550188 AATTTA-ATAT
1 -ATTTATATAT
*
1550198 ATTTATTTAT
1 ATTTATATAT
1550208 A
1 A
1550209 ATATATGTTA
Statistics
Matches: 71, Mismatches: 10, Indels: 27
0.66 0.09 0.25
Matches are distributed among these distances:
7 4 0.06
8 6 0.08
9 28 0.39
10 20 0.28
11 13 0.18
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (10 bp):
ATTTATATAT
Found at i:1550230 original size:17 final size:18
Alignment explanation
Indices: 1550210--1550251 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
1550200 TTATTTATAA
1550210 TATATGTTAATTT-TTTT-
1 TATAT-TTAATTTGTTTTG
*
1550227 TATATTTTATTTGTTTTG
1 TATATTTAATTTGTTTTG
1550245 TATATTT
1 TATATTT
1550252 TTTAAATTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 6 0.27
17 9 0.41
18 7 0.32
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.71
Consensus pattern (18 bp):
TATATTTAATTTGTTTTG
Found at i:1550248 original size:18 final size:16
Alignment explanation
Indices: 1550219--1550252 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
1550209 ATATATGTTA
1550219 ATTTTTTTTATATTTT
1 ATTTTTTTTATATTTT
1550235 ATTTGTTTTGTATATTTT
1 ATTT-TTTT-TATATTTT
1550253 TTAAATTGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 4 0.25
18 8 0.50
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (16 bp):
ATTTTTTTTATATTTT
Found at i:1550679 original size:2 final size:2
Alignment explanation
Indices: 1550662--1550703 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
1550652 AAATTAAGCA
*
1550662 AT AT -T AT AT AG A- 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
1550702 AT
1 AT
1550704 GTTTTGATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1553970 original size:3 final size:3
Alignment explanation
Indices: 1553927--1553951 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1553917 TTACACAAGT
1553927 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
1553952 TTATGAAAAT
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1555073 original size:35 final size:40
Alignment explanation
Indices: 1555034--1555116 Score: 106
Period size: 41 Copynumber: 2.2 Consensus size: 40
1555024 TGAATAAATA
1555034 TAAATATG-ATATAA-AT-TATTAAA-AT-ATTTA-AATTT
1 TAAATATGAATATAATATATATTAAATATAATTTATAA-TT
1555069 TAAATATGAATATAATATATATTAAATATAATTTATTAATT
1 TAAATATGAATATAATATATATTAAATATAATTTA-TAATT
1555110 TAAATAT
1 TAAATAT
1555117 ATTATATTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
35 8 0.20
36 6 0.15
37 2 0.05
38 7 0.17
39 2 0.05
40 5 0.12
41 9 0.22
42 2 0.05
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (40 bp):
TAAATATGAATATAATATATATTAAATATAATTTATAATT
Found at i:1555107 original size:14 final size:16
Alignment explanation
Indices: 1555077--1555120 Score: 51
Period size: 14 Copynumber: 3.0 Consensus size: 16
1555067 TTTAAATATG
1555077 AATATAATATATATTA
1 AATATAATATATATTA
1555093 AATATAAT-T-TATT-
1 AATATAATATATATTA
*
1555106 AATTTAA-ATATATTA
1 AATATAATATATATTA
1555121 TATTGTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
13 7 0.29
14 8 0.33
15 1 0.04
16 8 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATATAATATATATTA
Found at i:1555114 original size:19 final size:20
Alignment explanation
Indices: 1555067--1555122 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
1555057 ATATTTAAAT
1555067 TTTAAATATGAATATAATATA
1 TTTAAATAT-AATATAATATA
* *
1555088 TATTAAATATAATTTATTA-A
1 T-TTAAATATAATATAATATA
*
1555108 TTTAAATATATTATA
1 TTTAAATATAATATA
1555123 TTGTATTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 12 0.40
20 2 0.07
21 8 0.27
22 8 0.27
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
TTTAAATATAATATAATATA
Found at i:1562026 original size:2 final size:2
Alignment explanation
Indices: 1562019--1562065 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1562009 AATGGATAGC
1562019 TA TA 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 TA TA
1562061 TA TA T
1 TA TA T
1562066 TGTGATGCAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1562734 original size:2 final size:2
Alignment explanation
Indices: 1562727--1562760 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1562717 GAAGTTGTTC
1562727 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
1562761 TACATTTATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1563047 original size:29 final size:30
Alignment explanation
Indices: 1562984--1563039 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1562974 TAAGAAAAAA
1562984 ATTTA-TAAATACTAAAGTTTAAATATGAG
1 ATTTATTAAATACTAAAGTTTAAATATGAG
*
1563013 ATTTATTAAATA-TTAAGTTTTAAATAT
1 ATTTATTAAATACTAAAG-TTTAAATAT
1563040 AATTTTATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
29 9 0.38
30 15 0.62
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.45
Consensus pattern (30 bp):
ATTTATTAAATACTAAAGTTTAAATATGAG
Found at i:1563153 original size:16 final size:16
Alignment explanation
Indices: 1563113--1563157 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 16
1563103 AAATAAATAA
*
1563113 AAATTTA-TAAATATC
1 AAATTTATTAAATATT
1563128 AAA--T-TTAAATATT
1 AAATTTATTAAATATT
1563141 AAATTTATTAAATATT
1 AAATTTATTAAATATT
1563157 A
1 A
1563158 TTTTTTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
13 11 0.44
15 4 0.16
16 10 0.40
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
AAATTTATTAAATATT
Found at i:1563970 original size:30 final size:29
Alignment explanation
Indices: 1563911--1563978 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
1563901 AATTTTTATA
* *
1563911 TAAATTATAAAATTTTAATTTTATCAAAT
1 TAAATCATTAAATTTTAATTTTATCAAAT
* *
1563940 TATATCATTAAATTTTTATTATTAAT-AAAT
1 TAAATCATTAAATTTTAATT-TT-ATCAAAT
1563970 TAAATCATT
1 TAAATCATT
1563979 TATACTAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
29 16 0.50
30 14 0.44
31 2 0.06
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (29 bp):
TAAATCATTAAATTTTAATTTTATCAAAT
Found at i:1564466 original size:53 final size:49
Alignment explanation
Indices: 1564373--1564472 Score: 119
Period size: 52 Copynumber: 2.0 Consensus size: 49
1564363 TTATTTAAAC
*
1564373 TTAATTTTAAAAATATATAAATATTTATATAAAATAATTTTTAAATTTTA
1 TTAATTTTAAAAATATATAAATATTTAAATAAAATAA-TTTTAAATTTTA
* * * *
1564423 TTAATTTATAAATAATTTTTAAAGTATTTAAATTAAATCATTTTAAATTT
1 TTAATTT-TAAA-AATATATAAA-TATTTAAATAAAATAATTTTAAATTT
1564473 ATATAAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
50 7 0.17
51 4 0.10
52 18 0.43
53 13 0.31
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (49 bp):
TTAATTTTAAAAATATATAAATATTTAAATAAAATAATTTTAAATTTTA
Found at i:1565306 original size:19 final size:17
Alignment explanation
Indices: 1565279--1565313 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 17
1565269 TATTTGCTTT
1565279 TTTTATTTTATAATTTTG
1 TTTTATTTTAT-ATTTTG
1565297 TTTTATTTTTATATTTT
1 TTTTA-TTTTATATTTT
1565314 TATTAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (17 bp):
TTTTATTTTATATTTTG
Found at i:1566351 original size:20 final size:20
Alignment explanation
Indices: 1566326--1566363 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1566316 AATTTTACTT
*
1566326 TTATTATAACTTAAATTTTA
1 TTATTATAAATTAAATTTTA
1566346 TTATTATAAATTAAATTT
1 TTATTATAAATTAAATTT
1566364 AACTTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (20 bp):
TTATTATAAATTAAATTTTA
Found at i:1566483 original size:19 final size:19
Alignment explanation
Indices: 1566442--1566485 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1566432 ATATAATATA
1566442 ATATAT-TATAATTTAAAT
1 ATATATCTATAATTTAAAT
1566460 ATATATCTAT-ATTTATAAT
1 ATATATCTATAATTTA-AAT
*
1566479 CTATATC
1 ATATATC
1566486 GAATGTGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (19 bp):
ATATATCTATAATTTAAAT
Found at i:1566546 original size:22 final size:23
Alignment explanation
Indices: 1566512--1566559 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
1566502 TTATTTTTGT
* *
1566512 TAATTTGTTTATTTTTAAATAAA
1 TAATTTGTATATTTTAAAATAAA
1566535 TAATTT-TATATTTTAAAATAAA
1 TAATTTGTATATTTTAAAATAAA
1566557 TAA
1 TAA
1566560 AATAAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TAATTTGTATATTTTAAAATAAA
Found at i:1566562 original size:9 final size:9
Alignment explanation
Indices: 1566548--1566572 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1566538 TTTTATATTT
1566548 TAAAATAAA
1 TAAAATAAA
1566557 TAAAATAAA
1 TAAAATAAA
1566566 TAAAATA
1 TAAAATA
1566573 TATATTTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
TAAAATAAA
Found at i:1566861 original size:16 final size:16
Alignment explanation
Indices: 1566832--1566866 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1566822 ATCAATTAGG
1566832 TAAATTTTATTAATAA
1 TAAATTTTATTAATAA
1566848 TAAATATTTA-TAATAA
1 TAAAT-TTTATTAATAA
1566864 TAA
1 TAA
1566867 TTTAGAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TAAATTTTATTAATAA
Found at i:1566933 original size:14 final size:14
Alignment explanation
Indices: 1566914--1566941 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1566904 AGTTTAAAAG
1566914 ATTATTCATGCTTT
1 ATTATTCATGCTTT
1566928 ATTATTCATGCTTT
1 ATTATTCATGCTTT
1566942 TATATATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.57
Consensus pattern (14 bp):
ATTATTCATGCTTT
Found at i:1567509 original size:4 final size:4
Alignment explanation
Indices: 1567500--1567538 Score: 55
Period size: 4 Copynumber: 10.0 Consensus size: 4
1567490 CAGTTATATT
1567500 TTAA TTAA TTAA TTAA TTTAA TT-A TTAA -TAA TTAA TTAA
1 TTAA TTAA TTAA TTAA -TTAA TTAA TTAA TTAA TTAA TTAA
1567539 GCGATTAGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
3 6 0.19
4 22 0.69
5 4 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (4 bp):
TTAA
Found at i:1568546 original size:10 final size:10
Alignment explanation
Indices: 1568531--1568646 Score: 61
Period size: 10 Copynumber: 11.9 Consensus size: 10
1568521 TTTAAAATAT
1568531 TATATATTTA
1 TATATATTTA
1568541 TATATATTTA
1 TATATATTTA
* *
1568551 AATATA-TAA
1 TATATATTTA
*
1568560 TAATTTATATTA
1 T-ATATAT-TTA
*
1568572 TATAAATTTA
1 TATATATTTA
*
1568582 -ATA-AATT-
1 TATATATTTA
1568589 TATATATTTA
1 TATATATTTA
1568599 TATTATATTTA
1 TA-TATATTTA
*
1568610 TCT-TATTT-
1 TATATATTTA
1568618 TATTCATATGTTA
1 TA-T-ATAT-TTA
1568631 T-TATATTT-
1 TATATATTTA
1568639 TAT-TATTT
1 TATATATTT
1568647 TTTTTATATT
Statistics
Matches: 82, Mismatches: 11, Indels: 28
0.68 0.09 0.23
Matches are distributed among these distances:
8 13 0.16
9 17 0.21
10 29 0.35
11 17 0.21
12 5 0.06
13 1 0.01
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.59
Consensus pattern (10 bp):
TATATATTTA
Found at i:1568546 original size:26 final size:25
Alignment explanation
Indices: 1568517--1568595 Score: 83
Period size: 26 Copynumber: 3.1 Consensus size: 25
1568507 TTATAATAAT
1568517 TATATTTAAAATATTATATATTTATA
1 TATATTTAAAATATTATA-ATTTATA
*
1568543 TATATTTAAATATATAATAATTTATA
1 TATATTTAAA-ATATTATAATTTATA
*
1568569 T-TATAT-AAAT-TTAATAAATTTATA
1 TATATTTAAAATATT-AT-AATTTATA
1568593 TAT
1 TAT
1568596 TTATATTATA
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
22 1 0.02
23 4 0.09
24 11 0.24
25 5 0.11
26 18 0.39
27 7 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
TATATTTAAAATATTATAATTTATA
Found at i:1568596 original size:26 final size:27
Alignment explanation
Indices: 1568523--1568601 Score: 71
Period size: 27 Copynumber: 3.0 Consensus size: 27
1568513 TAATTATATT
* *
1568523 TAAA-ATATTATATATTTATATA-TATT
1 TAAATATATAATA-ATTTATATATTATA
1568549 TAAATATATAATAA-TT-TATATTATA
1 TAAATATATAATAATTTATATATTATA
1568574 TAAAT-T-TAATAAATTTATATATTTATA
1 TAAATATATAAT-AATTTATATA-TTATA
1568601 T
1 T
1568602 TATATTTATC
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
23 4 0.09
24 7 0.16
25 12 0.27
26 9 0.20
27 13 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
TAAATATATAATAATTTATATATTATA
Found at i:1568598 original size:32 final size:30
Alignment explanation
Indices: 1568526--1568606 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 30
1568516 TTATATTTAA
* *
1568526 AATATTATATATTTATATATATTTAAATATAT
1 AATATT-TATA-TTATATAAATTTAAAAATAT
*
1568558 AATAATTTATATTATATAAATTTAATAAATTT
1 AAT-ATTTATATTATATAAATTTAA-AAATAT
1568590 ATATATTTATATTATAT
1 A-ATATTTATATTATAT
1568607 TTATCTTATT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
31 13 0.30
32 25 0.58
33 5 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (30 bp):
AATATTTATATTATATAAATTTAAAAATAT
Found at i:1568631 original size:21 final size:19
Alignment explanation
Indices: 1568586--1568657 Score: 76
Period size: 19 Copynumber: 3.7 Consensus size: 19
1568576 AATTTAATAA
1568586 ATTTA-TATATTTATATTAT
1 ATTTATTATATTT-TATTAT
1568605 ATTTATCT-TATTTTATTCAT
1 ATTTAT-TATATTTTATT-AT
1568625 ATGTTATTATATTTTATTAT
1 AT-TTATTATATTTTATTAT
* *
1568645 TTTTTTTATATTT
1 ATTTATTATATTT
1568658 AAAATTAATA
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
19 19 0.41
20 13 0.28
21 14 0.30
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (19 bp):
ATTTATTATATTTTATTAT
Found at i:1568649 original size:10 final size:10
Alignment explanation
Indices: 1568587--1568657 Score: 69
Period size: 10 Copynumber: 7.2 Consensus size: 10
1568577 ATTTAATAAA
1568587 TTTA-TATAT
1 TTTATTATAT
1568596 TTATATTATA-
1 TT-TATTATAT
1568606 TTTATCT-TAT
1 TTTAT-TATAT
1568616 TTTATTCATAT
1 TTTATT-ATAT
*
1568627 GTTATTATAT
1 TTTATTATAT
1568637 TTTATTAT-T
1 TTTATTATAT
*
1568646 TTTTTTATAT
1 TTTATTATAT
1568656 TT
1 TT
1568658 AAAATTAATA
Statistics
Matches: 52, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
9 16 0.31
10 24 0.46
11 12 0.23
ACGTcount: A:0.27, C:0.03, G:0.01, T:0.69
Consensus pattern (10 bp):
TTTATTATAT
Found at i:1581077 original size:22 final size:22
Alignment explanation
Indices: 1581033--1581077 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1581023 CACGTTAGTT
* ** *
1581033 ATTTAAATTTTTTTATTTTTTA
1 ATTTAAAATTTTTTAAATGTTA
1581055 ATTTAAAATTTTTTAAATGTTA
1 ATTTAAAATTTTTTAAATGTTA
1581077 A
1 A
1581078 CATTATTTCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
ATTTAAAATTTTTTAAATGTTA
Found at i:1582024 original size:13 final size:13
Alignment explanation
Indices: 1582006--1582044 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
1581996 AAATTTAACT
1582006 TAATTAATATATA
1 TAATTAATATATA
* *
1582019 TAATTAATTTTTA
1 TAATTAATATATA
*
1582032 AAATTAATATATA
1 TAATTAATATATA
1582045 ATTATTTTTA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TAATTAATATATA
Found at i:1582066 original size:23 final size:25
Alignment explanation
Indices: 1582007--1582066 Score: 90
Period size: 23 Copynumber: 2.5 Consensus size: 25
1581997 AATTTAACTT
1582007 AATTAATATATATAATTAATTTTTAA
1 AATT-ATATATATAATTAATTTTTAA
1582033 AATTA-ATATATAATT-ATTTTTAA
1 AATTATATATATAATTAATTTTTAA
1582056 AATTATA-ATAT
1 AATTATATATAT
1582067 TTAATGTGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
23 17 0.52
24 11 0.33
25 1 0.03
26 4 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
AATTATATATATAATTAATTTTTAA
Found at i:1582384 original size:14 final size:14
Alignment explanation
Indices: 1582365--1582406 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
1582355 AAATCTGAAG
1582365 ATAATATAATAAAT
1 ATAATATAATAAAT
* *
1582379 ATAATAAAATATAT
1 ATAATATAATAAAT
*
1582393 TTAATAT-ATAAAT
1 ATAATATAATAAAT
1582406 A
1 A
1582407 ATATTTATAT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
ATAATATAATAAAT
Found at i:1582410 original size:18 final size:19
Alignment explanation
Indices: 1582376--1582413 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
1582366 TAATATAATA
1582376 AATATAATAAAATATATTT
1 AATATAATAAAATATATTT
1582395 AATAT-AT-AAATAATATTT
1 AATATAATAAAAT-ATATTT
1582413 A
1 A
1582414 TATTTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.22
18 9 0.50
19 5 0.28
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AATATAATAAAATATATTT
Found at i:1582416 original size:17 final size:17
Alignment explanation
Indices: 1582385--1582433 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
1582375 AAATATAATA
1582385 AAATATATTTAATATAT
1 AAATATATTTAATATAT
*
1582402 AAATAATATTT-ATATTT
1 AAAT-ATATTTAATATAT
*
1582419 AAA-AT-TTTGATATAT
1 AAATATATTTAATATAT
1582434 TTAATAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
14 3 0.11
15 7 0.25
17 12 0.43
18 6 0.21
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (17 bp):
AAATATATTTAATATAT
Found at i:1582453 original size:19 final size:19
Alignment explanation
Indices: 1582411--1582461 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 19
1582401 TAAATAATAT
1582411 TTATATTTAA-AATTTTGA
1 TTATATTTAATAATTTTGA
1582429 -TATATTTAATAATTTAT-A
1 TTATATTTAATAATTT-TGA
1582447 TTATATTTATATAAT
1 TTATATTTA-ATAAT
1582462 AAAAAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
17 9 0.31
18 6 0.21
19 9 0.31
20 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
TTATATTTAATAATTTTGA
Found at i:1582614 original size:32 final size:33
Alignment explanation
Indices: 1582577--1582638 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
1582567 ATATATATGA
1582577 ATAAATTTTAACAAATTTAT-TATTTATATTTT
1 ATAAATTTTAACAAATTTATATATTTATATTTT
* * *
1582609 ATAAATTTTGATATATTTATATATTTATAT
1 ATAAATTTTAACAAATTTATATATTTATAT
1582639 CGTATTAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 17 0.65
33 9 0.35
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (33 bp):
ATAAATTTTAACAAATTTATATATTTATATTTT
Found at i:1582632 original size:8 final size:8
Alignment explanation
Indices: 1582591--1582638 Score: 55
Period size: 8 Copynumber: 6.0 Consensus size: 8
1582581 ATTTTAACAA
1582591 ATTTAT-T
1 ATTTATAT
1582598 ATTTATAT
1 ATTTATAT
*
1582606 -TTTATAA
1 ATTTATAT
1582613 ATTTTGATAT
1 A-TTT-ATAT
1582623 ATTTATAT
1 ATTTATAT
1582631 ATTTATAT
1 ATTTATAT
1582639 CGTATTAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
7 12 0.34
8 13 0.37
9 6 0.17
10 4 0.11
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (8 bp):
ATTTATAT
Found at i:1587331 original size:21 final size:20
Alignment explanation
Indices: 1587294--1587332 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1587284 TATTTTTATT
* *
1587294 TAAATTTGATTATAAATATA
1 TAAATTTAATTAAAAATATA
1587314 TAAATATTAATTAAAAATA
1 TAAAT-TTAATTAAAAATA
1587333 ATTTTTTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (20 bp):
TAAATTTAATTAAAAATATA
Found at i:1587871 original size:2 final size:2
Alignment explanation
Indices: 1587866--1587914 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1587856 ACACACACAC
1587866 AT 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 AT
1587908 AT AT AT A
1 AT AT AT A
1587915 CATAAGTATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1588108 original size:22 final size:23
Alignment explanation
Indices: 1588065--1588108 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
1588055 GTAAAATAAA
*
1588065 AAATAATTAATAAATTATAAGTT
1 AAATAATTAATAAATTAAAAGTT
1588088 AAAT-ATTAATATAA-TAAAAGT
1 AAATAATTAATA-AATTAAAAGT
1588109 ATGTATGTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (23 bp):
AAATAATTAATAAATTAAAAGTT
Found at i:1588184 original size:21 final size:21
Alignment explanation
Indices: 1588138--1588188 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1588128 TATATTTATT
*
1588138 TTTTAAAAAATTACTTTTTGC
1 TTTTAAAAAATTACTATTTGC
*
1588159 -CTTAAAAAATTATCTATTT-C
1 TTTTAAAAAATTA-CTATTTGC
1588179 TTTTAAAAAA
1 TTTTAAAAAA
1588189 CCTTCTCGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.47
Consensus pattern (21 bp):
TTTTAAAAAATTACTATTTGC
Found at i:1589163 original size:12 final size:12
Alignment explanation
Indices: 1589147--1589180 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1589137 TTTAAAGAAA
1589147 AAATTAAATAAT
1 AAATTAAATAAT
*
1589159 TAATTAAATAAT
1 AAATTAAATAAT
*
1589171 AAATAAAATA
1 AAATTAAATA
1589181 TATGACAGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAATTAAATAAT
Found at i:1589241 original size:17 final size:17
Alignment explanation
Indices: 1589219--1589251 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1589209 AAAAAAAGCT
1589219 ATACTTATTAAATATAA
1 ATACTTATTAAATATAA
*
1589236 ATACTTTTTAAATATA
1 ATACTTATTAAATATA
1589252 CCCTAAAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (17 bp):
ATACTTATTAAATATAA
Found at i:1589744 original size:19 final size:19
Alignment explanation
Indices: 1589720--1589756 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1589710 TGTTTCATTT
*
1589720 TTTAATTATTTTTTAAAAC
1 TTTAATAATTTTTTAAAAC
1589739 TTTAATAATTTTTTAAAA
1 TTTAATAATTTTTTAAAA
1589757 ATATGGGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTAATAATTTTTTAAAAC
Found at i:1590265 original size:11 final size:11
Alignment explanation
Indices: 1590228--1590278 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
1590218 GTATTCCTAT
1590228 TTTA-TTTATA
1 TTTATTTTATA
* *
1590238 TATAGTTTATA
1 TTTATTTTATA
1590249 TATTATTTTATA
1 T-TTATTTTATA
* *
1590261 TTTATATTATT
1 TTTATTTTATA
1590272 TTTATTT
1 TTTATTT
1590279 ATTAAATTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
10 3 0.09
11 21 0.64
12 9 0.27
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (11 bp):
TTTATTTTATA
Found at i:1590268 original size:16 final size:16
Alignment explanation
Indices: 1590247--1590326 Score: 78
Period size: 16 Copynumber: 5.1 Consensus size: 16
1590237 ATATAGTTTA
1590247 TATATTATTTTATATT
1 TATATTATTTTATATT
1590263 TATATTATTTT-TATT
1 TATATTATTTTATATT
*
1590278 TAT-TAAATTTTA-ATT
1 TATAT-TATTTTATATT
* *
1590293 TCT-TATATTTTATAAT
1 TATAT-TATTTTATATT
*
1590309 TATATTATATTATATT
1 TATATTATTTTATATT
1590325 TA
1 TA
1590327 AAATTTTAAT
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
14 1 0.02
15 25 0.47
16 26 0.49
17 1 0.02
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (16 bp):
TATATTATTTTATATT
Found at i:1593162 original size:2 final size:2
Alignment explanation
Indices: 1593155--1593179 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1593145 TATATTAGCT
1593155 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1593180 TAACATTAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1593241 original size:2 final size:2
Alignment explanation
Indices: 1593234--1593267 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1593224 ATCGACTTGC
1593234 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
1593268 TAAGAAGCAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1595652 original size:13 final size:14
Alignment explanation
Indices: 1595612--1595646 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
1595602 TTACATCTAA
*
1595612 TAAATTTAAATA-T
1 TAAATTTTAATATT
1595625 TAAATTTTAATATT
1 TAAATTTTAATATT
1595639 TAAATTTT
1 TAAATTTT
1595647 TTATTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TAAATTTTAATATT
Found at i:1595846 original size:24 final size:24
Alignment explanation
Indices: 1595815--1595860 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1595805 AATTAAATTT
*
1595815 AAAATTTAATATTTAA-TATTTAC
1 AAAATTTAATATATAATTATTTAC
1595838 AAAATTTTAATATATAATTATTT
1 AAAA-TTTAATATATAATTATTT
1595861 TTATTTACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 11 0.55
25 5 0.25
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
AAAATTTAATATATAATTATTTAC
Found at i:1596042 original size:4 final size:5
Alignment explanation
Indices: 1596031--1596062 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
1596021 GATTTTAGAC
1596031 TAAAA T-AAA T-AAA TAAAA TAAAA TAAAA TAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
1596063 CAAAAAGCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 8 0.31
5 18 0.69
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
TAAAA
Found at i:1596665 original size:15 final size:14
Alignment explanation
Indices: 1596640--1596674 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
1596630 AGTAATTAAT
*
1596640 AAATATTTTTAAAA
1 AAATTTTTTTAAAA
1596654 ATAATTTTTTTAAAA
1 A-AATTTTTTTAAAA
1596669 AAATTT
1 AAATTT
1596675 CAAAGACGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
AAATTTTTTTAAAA
Found at i:1596724 original size:14 final size:13
Alignment explanation
Indices: 1596707--1596742 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
1596697 AGTTATTCTC
*
1596707 AAAAATTATCCCT
1 AAAAATTATCACT
1596720 AAAAAATTATCACT
1 -AAAAATTATCACT
1596734 AAAAATTAT
1 AAAAATTAT
1596743 TTTTTAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.56, C:0.14, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAAATTATCACT
Found at i:1596751 original size:13 final size:15
Alignment explanation
Indices: 1596735--1596766 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
1596725 ATTATCACTA
1596735 AAAATTAT-TTTTT-
1 AAAATTATATTTTTG
1596748 AAAATTATATTTTTG
1 AAAATTATATTTTTG
1596763 AAAA
1 AAAA
1596767 AATTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 5 0.29
15 4 0.24
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
AAAATTATATTTTTG
Found at i:1597263 original size:20 final size:20
Alignment explanation
Indices: 1597235--1597360 Score: 73
Period size: 20 Copynumber: 6.2 Consensus size: 20
1597225 TAAAATAAAA
1597235 TTATAATATTATATTAAATT
1 TTATAATATTATATTAAATT
*
1597255 TTATCATATTAATCATATTTAAA-T
1 TTAT-A-A-T-ATTATA-TTAAATT
* *
1597279 TTAAACATATTATATTATA-T
1 TTATA-ATATTATATTAAATT
*
1597299 TTATAATATTAATATTATA-T
1 TTATAATATT-ATATTAAATT
*
1597319 TTATTAA-A-TATATTATATT
1 TTA-TAATATTATATTAAATT
* * *
1597338 TAATATTATTAAATTAAATT
1 TTATAATATTATATTAAATT
1597358 TTA
1 TTA
1597361 AAAAAATTGC
Statistics
Matches: 85, Mismatches: 11, Indels: 20
0.73 0.09 0.17
Matches are distributed among these distances:
18 10 0.12
19 10 0.12
20 37 0.44
21 9 0.11
22 2 0.02
23 3 0.04
24 9 0.11
25 5 0.06
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (20 bp):
TTATAATATTATATTAAATT
Found at i:1597277 original size:25 final size:26
Alignment explanation
Indices: 1597240--1597310 Score: 74
Period size: 25 Copynumber: 2.7 Consensus size: 26
1597230 TAAAATTATA
* * *
1597240 ATATTATA-TTAAATTTTATCATATT
1 ATATCATATTTAAATTTAAACATATT
1597265 A-ATCATATTTAAATTTAAACATATT
1 ATATCATATTTAAATTTAAACATATT
*
1597290 ATATTATATTTATAATATTAA
1 ATATCATATTTA-AAT-TTAA
1597311 TATTATATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
24 5 0.13
25 17 0.45
26 9 0.24
27 3 0.08
28 4 0.11
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (26 bp):
ATATCATATTTAAATTTAAACATATT
Found at i:1597295 original size:5 final size:5
Alignment explanation
Indices: 1597285--1597521 Score: 64
Period size: 5 Copynumber: 46.8 Consensus size: 5
1597275 AAATTTAAAC
* *
1597285 ATATT ATATT ATATT -TATA ATATT AATATT ATATT -TATT A-AAT ATATT
1 ATATT ATATT ATATT ATATT ATATT -ATATT ATATT ATATT ATATT ATATT
* * * * ** * * *
1597333 ATATT -TAAT ATTATT AAATT AAATT TTAAAA AAATT GCTCATT ACTTTT
1 ATATT ATATT A-TATT ATATT ATATT AT-ATT ATATT -AT-ATT A-TATT
** * *
1597382 ATGCT ATTATT AATATTT ATATT TTATT ATATT ATATA ATATT -TATAT
1 ATATT AT-ATT -ATAT-T ATATT ATATT ATATT ATATT ATATT ATAT-T
* * * * *
1597430 ATTTT ATATT -TATAT AAATT TTAAT A-ATT ATATT TTA-T ATATT -T-TT
1 ATATT ATATT ATAT-T ATATT ATATT ATATT ATATT ATATT ATATT ATATT
* * *
1597476 A-AAT ATATT ATATT ATATT TTAATT ATTTTT ATATT ATATTT ATAT
1 ATATT ATATT ATATT ATATT AT-ATT A-TATT ATATT ATA-TT ATAT
1597522 AATCAGCACT
Statistics
Matches: 164, Mismatches: 43, Indels: 50
0.64 0.17 0.19
Matches are distributed among these distances:
3 2 0.01
4 28 0.17
5 91 0.55
6 35 0.21
7 8 0.05
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (5 bp):
ATATT
Found at i:1597323 original size:9 final size:9
Alignment explanation
Indices: 1597285--1597339 Score: 56
Period size: 9 Copynumber: 5.8 Consensus size: 9
1597275 AAATTTAAAC
1597285 ATATTATATT
1 ATATT-TATT
*
1597295 ATATTTATA
1 ATATTTATT
1597304 ATATTAATATT
1 ATATT--TATT
1597315 ATATTTATT
1 ATATTTATT
* *
1597324 AAATATATT
1 ATATTTATT
1597333 ATATTTA
1 ATATTTA
1597340 ATATTATTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
9 24 0.65
10 5 0.14
11 8 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
ATATTTATT
Found at i:1597479 original size:31 final size:31
Alignment explanation
Indices: 1597389--1597521 Score: 93
Period size: 31 Copynumber: 4.3 Consensus size: 31
1597379 TTTATGCTAT
* *
1597389 TATTAATATTTATATTTTAT-TA-TATTATATAA
1 TATT-ATA-TTATATTTTATATATTTTTAAAT-A
*
1597421 TATT-TA-TATATTTTATAT-TTATATAAAT-
1 TATTATATTATATTTTATATATT-TTTAAATA
1597449 T-TTAATAATTATATTTTATATATTTTTAAATA
1 TATT-AT-ATTATATTTTATATATTTTTAAATA
*
1597481 TATTATATTATATTTTA-ATTATTTTTATATTA
1 TATTATATTATATTTTATA-TATTTTTA-AATA
1597513 TATTTATAT
1 TA-TTATAT
1597522 AATCAGCACT
Statistics
Matches: 83, Mismatches: 5, Indels: 25
0.73 0.04 0.22
Matches are distributed among these distances:
27 2 0.02
28 11 0.13
29 3 0.04
30 8 0.10
31 37 0.45
32 14 0.17
33 8 0.10
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (31 bp):
TATTATATTATATTTTATATATTTTTAAATA
Found at i:1597518 original size:21 final size:21
Alignment explanation
Indices: 1597454--1597518 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
1597444 TAAATTTTAA
*
1597454 TAATTATATTTTATA-TATTTT
1 TAATTAT-TTTTATATTATATT
* *
1597475 TAAATA-TATTATATTATATTT
1 TAATTATTTTTATATTATA-TT
1597496 TAATTATTTTTATATTATATT
1 TAATTATTTTTATATTATATT
1597517 TA
1 TA
1597519 TATAATCAGC
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
19 6 0.17
20 3 0.08
21 16 0.44
22 11 0.31
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TAATTATTTTTATATTATATT
Found at i:1599084 original size:21 final size:19
Alignment explanation
Indices: 1599039--1599085 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
1599029 AAAAAATAAA
*
1599039 ATATTAAA-ATTTATTTTT
1 ATATTAAATATTTATATTT
1599057 ATA-TAAATATTTTATATTT
1 ATATTAAATA-TTTATATTT
1599076 ATAATTAAAT
1 AT-ATTAAAT
1599086 TAAATAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 4 0.17
18 4 0.17
19 10 0.42
20 1 0.04
21 5 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATATTAAATATTTATATTT
Found at i:1601784 original size:18 final size:18
Alignment explanation
Indices: 1601763--1601797 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1601753 TAATCTTATT
*
1601763 TATTTCATATTTAAAAAA
1 TATTTCATATATAAAAAA
*
1601781 TATTTTATATATAAAAA
1 TATTTCATATATAAAAA
1601798 TTAAAAATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
TATTTCATATATAAAAAA
Found at i:1607533 original size:4 final size:4
Alignment explanation
Indices: 1607524--1607554 Score: 53
Period size: 4 Copynumber: 7.5 Consensus size: 4
1607514 GTGCATAACT
1607524 TTTA TTTA TTTA TTTA TTTA TTTCA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTT-A TTTA TT
1607555 AGTGGAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 22 0.85
5 4 0.15
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:1607686 original size:22 final size:22
Alignment explanation
Indices: 1607658--1607706 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
1607648 TTATATATAA
*
1607658 ATATAAAATATA-ATATTTAAAT
1 ATATAAAAAATATATA-TTAAAT
*
1607680 ATATAAAAAATTTATATTAAAT
1 ATATAAAAAATATATATTAAAT
1607702 ATATA
1 ATATA
1607707 TTTATATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
ATATAAAAAATATATATTAAAT
Found at i:1607709 original size:17 final size:16
Alignment explanation
Indices: 1607689--1607725 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
1607679 TATATAAAAA
1607689 ATTTATATTAAATATAT
1 ATTTATATT-AATATAT
*
1607706 ATTTATATTAATATTT
1 ATTTATATTAATATAT
1607722 ATTT
1 ATTT
1607726 CGAATTCCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTTATATTAATATAT
Found at i:1611731 original size:16 final size:16
Alignment explanation
Indices: 1611689--1611731 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
1611679 ATTTATGTAA
* *
1611689 AATATTTTATAATTTT
1 AATATTTTTTAATTTG
1611705 AAT-TTTATTTAATTTG
1 AATATTT-TTTAATTTG
1611721 AATATTTTTTA
1 AATATTTTTTA
1611732 TAAAATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 3 0.13
16 17 0.74
17 3 0.13
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (16 bp):
AATATTTTTTAATTTG
Found at i:1612988 original size:23 final size:24
Alignment explanation
Indices: 1612943--1612990 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
1612933 ATGAACCAAT
1612943 ATATCATAATGAATAAATATTTAA
1 ATATCATAATGAATAAATATTTAA
* * *
1612967 ATATCA-AATTAATAATTTTTTAA
1 ATATCATAATGAATAAATATTTAA
1612990 A
1 A
1612991 GTTTCAAACT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (24 bp):
ATATCATAATGAATAAATATTTAA
Found at i:1613592 original size:20 final size:20
Alignment explanation
Indices: 1613567--1613617 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
1613557 TACTATATAT
1613567 AATATTTATTTAATAT-TAAA
1 AATATTTATTTAATATGT-AA
*
1613587 AATATTT-TTAAATATGTAA
1 AATATTTATTTAATATGTAA
1613606 AA-ATTTATTTAA
1 AATATTTATTTAA
1613618 ATAAACCAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 4 0.15
19 15 0.56
20 8 0.30
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
AATATTTATTTAATATGTAA
Done.