Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold477
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: 400253
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
File 1 of 3
Found at i:2109 original size:19 final size:19
Alignment explanation
Indices: 2070--2110 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
2060 AATAACTTTT
**
2070 ATTTTAATTTAAAATTTAA
1 ATTTTAATTTAAAATAAAA
2089 ATTTTAATTTAAAATAAAA
1 ATTTTAATTTAAAATAAAA
2108 ATT
1 ATT
2111 AAATCACTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTTAATTTAAAATAAAA
Found at i:2856 original size:27 final size:27
Alignment explanation
Indices: 2804--2854 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
2794 TTTTTTAATT
* *
2804 AATTATTAACATCATTAATATGAAATA
1 AATTATAAACATCATTAATATAAAATA
*
2831 AATTATAAATATCATT-ATATAAAA
1 AATTATAAACATCATTAATATAAAA
2855 ATTATATTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 7 0.33
27 14 0.67
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.37
Consensus pattern (27 bp):
AATTATAAACATCATTAATATAAAATA
Found at i:3437 original size:20 final size:22
Alignment explanation
Indices: 3401--3441 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
3391 TTTTATAATC
3401 AAATAAATTATTAATAAATAAA
1 AAATAAATTATTAATAAATAAA
3423 AAATAAA-TA-TAATAAATAA
1 AAATAAATTATTAATAAATAA
3442 TATAAGTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
21 2 0.11
22 7 0.37
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (22 bp):
AAATAAATTATTAATAAATAAA
Found at i:3642 original size:13 final size:13
Alignment explanation
Indices: 3626--3652 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3616 AAATTTTATA
3626 AAAATTTAAATTT
1 AAAATTTAAATTT
3639 AAAATTTAAATTT
1 AAAATTTAAATTT
3652 A
1 A
3653 TTAAATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAAATTTAAATTT
Found at i:3660 original size:15 final size:15
Alignment explanation
Indices: 3627--3671 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
3617 AATTTTATAA
3627 AAATTTAAATTTA--
1 AAATTTAAATTTATT
3640 AAATTTAAATTTATT
1 AAATTTAAATTTATT
* *
3655 AAATTTTAATTCATT
1 AAATTTAAATTTATT
3670 AA
1 AA
3672 TAATTTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 13 0.46
15 15 0.54
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
AAATTTAAATTTATT
Found at i:4049 original size:8 final size:9
Alignment explanation
Indices: 4032--4177 Score: 70
Period size: 9 Copynumber: 15.4 Consensus size: 9
4022 AGATCTAATA
4032 ATTTATT-T
1 ATTTATTAT
4040 ATTTTATTAT
1 A-TTTATTAT
4050 ATTTA-TAT
1 ATTTATTAT
4058 ATTTATTAT
1 ATTTATTAT
4067 ATTATAATTAT
1 ATT-T-ATTAT
**
4078 AATTTAAAAT
1 -ATTTATTAT
4088 A-TT-TTAT
1 ATTTATTAT
*
4095 ATTTATATAAA
1 ATTTAT-T-AT
*
4106 ATTTAATAT
1 ATTTATTAT
4115 ATTAATATT-T
1 ATT--TATTAT
*
4125 ATATTATATAA
1 AT-TTAT-TAT
**
4136 ATTTTAAAAT
1 A-TTTATTAT
4146 ATTTA-TAT
1 ATTTATTAT
4154 ATTTATATTAT
1 A-TT-TATTAT
4165 ATTTATTAT
1 ATTTATTAT
4174 ATTT
1 ATTT
4178 TATAATTATA
Statistics
Matches: 106, Mismatches: 13, Indels: 37
0.68 0.08 0.24
Matches are distributed among these distances:
7 3 0.03
8 16 0.15
9 41 0.39
10 18 0.17
11 24 0.23
12 4 0.04
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
ATTTATTAT
Found at i:4063 original size:22 final size:22
Alignment explanation
Indices: 4035--4190 Score: 73
Period size: 22 Copynumber: 7.1 Consensus size: 22
4025 TCTAATAATT
* *
4035 TATTTATTTTATTATATTTATA
1 TATTTATTATATTATAATTATA
4057 TATTTATTATATTATAATTATA
1 TATTTATTATATTATAATTATA
* * *
4079 -ATTTAAAATATTTTATATTTATA
1 TATTT--ATTATATTATAATTATA
*
4102 TAAAATTTAATATATTA-ATATT-TA
1 T---ATTTATTATATTATA-ATTATA
* *
4126 TA-TTATATAAATTTTAA--A-A
1 TATTTAT-TATATTATAATTATA
4145 TATTTA-TATATT-T-A-TATTA
1 TATTTATTATATTATAATTA-TA
4164 TATTTATTATATTTTATAATTATA
1 TATTTATTATA--TTATAATTATA
4188 TAT
1 TAT
4191 GTCCAATATT
Statistics
Matches: 103, Mismatches: 11, Indels: 38
0.68 0.07 0.25
Matches are distributed among these distances:
16 1 0.01
17 2 0.02
18 5 0.05
19 10 0.10
20 10 0.10
21 11 0.11
22 23 0.22
23 15 0.15
24 10 0.10
25 12 0.12
27 4 0.04
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TATTTATTATATTATAATTATA
Found at i:4104 original size:31 final size:28
Alignment explanation
Indices: 4056--4190 Score: 100
Period size: 31 Copynumber: 4.6 Consensus size: 28
4046 TTATATTTAT
4056 ATATTTATTATATTATA-ATTATAATTTAAA
1 ATATTTA-TAT-TTATATA-TATAATTTAAA
*
4086 ATATTTTATATTTATATA-A-AATTTAAT
1 ATA-TTTATATTTATATATATAATTTAAA
*
4113 ATATTAATATTTATATTATATAAATTTTAAA
1 ATATTTATATTTATA-TATAT-AA-TTTAAA
**
4144 ATATTTATATATT-TATAT-TATATTTATT
1 ATATTTATAT-TTATATATATA-ATTTAAA
*
4172 ATATTTTATAATTATATAT
1 ATA-TTTATATTTATATAT
4191 GTCCAATATT
Statistics
Matches: 87, Mismatches: 7, Indels: 23
0.74 0.06 0.20
Matches are distributed among these distances:
26 11 0.13
27 12 0.14
28 12 0.14
29 18 0.21
30 12 0.14
31 20 0.23
32 2 0.02
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
ATATTTATATTTATATATATAATTTAAA
Found at i:4129 original size:39 final size:38
Alignment explanation
Indices: 4086--4182 Score: 110
Period size: 39 Copynumber: 2.5 Consensus size: 38
4076 ATAATTTAAA
4086 ATATT-TTATATTTATATAAA-ATTTAATATATTAATATTT
1 ATATTATTATATTT-TATAAATATTT-ATATATTAATA-TT
* *
4125 ATATTATATAAATTTTA-AAATATTTATATATTTATATT
1 ATATTAT-TATATTTTATAAATATTTATATATTAATATT
4163 ATATTTATTATATTTTATAA
1 ATA-TTATTATATTTTATAA
4183 TTATATATGT
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
38 13 0.26
39 24 0.48
40 7 0.14
41 6 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (38 bp):
ATATTATTATATTTTATAAATATTTATATATTAATATT
Found at i:4147 original size:33 final size:30
Alignment explanation
Indices: 4085--4166 Score: 101
Period size: 33 Copynumber: 2.5 Consensus size: 30
4075 TATAATTTAA
4085 AATATTTTATATTTATATAAAATTTAATATATT
1 AATA-TTTATA-TTATATAAAATTTAATAT-TT
*
4118 AATATTTATATTATATAAATTTTAAAATATTT
1 AATATTTATATTATATAAAATTT--AATATTT
4150 ATATATTTATATTATAT
1 A-ATATTTATATTATAT
4167 TTATTATATT
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
31 12 0.27
32 9 0.20
33 24 0.53
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (30 bp):
AATATTTATATTATATAAAATTTAATATTT
Found at i:4169 original size:59 final size:58
Alignment explanation
Indices: 4032--4177 Score: 178
Period size: 59 Copynumber: 2.6 Consensus size: 58
4022 AGATCTAATA
*
4032 ATTTATTTATTT-TATTATATTT-ATATATTTATTATATTATAATTATAATTTAAAAT
1 ATTTATATATTTATATTATATTTAATATATTTATTATATTATAATTATAATTTAAAAT
* *
4088 ATTT-TATATTTATATAAAATTTAATATATTAATATTTATATTAT-A-TA-AATTTTAAAAT
1 ATTTATATATTTATATTATATTTAATATATT--TA-TTATATTATAATTATAA-TTTAAAAT
*
4146 ATTTATATATTTATATTATATTTATTATATTT
1 ATTTATATATTTATATTATATTTAATATATTT
4178 TATAATTATA
Statistics
Matches: 77, Mismatches: 6, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
55 6 0.08
56 12 0.16
57 10 0.13
58 14 0.18
59 26 0.34
60 9 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (58 bp):
ATTTATATATTTATATTATATTTAATATATTTATTATATTATAATTATAATTTAAAAT
Found at i:4453 original size:12 final size:12
Alignment explanation
Indices: 4436--4501 Score: 77
Period size: 12 Copynumber: 5.8 Consensus size: 12
4426 AAATGGCGTG
4436 AATATAATATAA
1 AATATAATATAA
4448 AATATAATAT--
1 AATATAATATAA
4458 AATATAA-A-AA
1 AATATAATATAA
*
4468 TAATATAAAATAA
1 -AATATAATATAA
*
4481 AAAATAATATAA
1 AATATAATATAA
4493 AATATAATA
1 AATATAATA
4502 ATAATTTATA
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
9 1 0.02
10 7 0.15
11 7 0.15
12 29 0.63
13 2 0.04
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AATATAATATAA
Found at i:4458 original size:17 final size:17
Alignment explanation
Indices: 4436--4575 Score: 92
Period size: 17 Copynumber: 8.0 Consensus size: 17
4426 AAATGGCGTG
4436 AATATAATATAAAATAT
1 AATATAATATAAAATAT
4453 AATATAATATAAAA-AT
1 AATATAATATAAAATAT
* *
4469 AATATAAAATAAAAAAT
1 AATATAATATAAAATAT
* *
4486 AATATAAAATATAATAAT
1 AATATAATATAAAAT-AT
4504 AATTTATAAATATATTAAA-ATT
1 AA--TAT-AATATA--AAATA-T
* *
4526 TATATAATATAAATTATT
1 AATATAATATAAAATA-T
4544 AATAT-AT-TAAAAT-T
1 AATATAATATAAAATAT
* *
4558 TATATAAATATATAATAT
1 AATAT-AATATAAAATAT
4576 TAAAAAATAA
Statistics
Matches: 99, Mismatches: 11, Indels: 25
0.73 0.08 0.19
Matches are distributed among these distances:
14 5 0.05
16 22 0.22
17 38 0.38
18 12 0.12
19 6 0.06
20 6 0.06
21 6 0.06
22 2 0.02
23 2 0.02
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AATATAATATAAAATAT
Found at i:4497 original size:35 final size:33
Alignment explanation
Indices: 4436--4538 Score: 98
Period size: 33 Copynumber: 2.9 Consensus size: 33
4426 AAATGGCGTG
* *
4436 AATATAATATAAAATATAATATAATATAAAAAT
1 AATATAAAATAAAAAATAATATAATATAAAAAT
*
4469 AATATAAAATAAAAAATAATATAAAATATAATAAT
1 AATATAAAATAAAAAATAATAT--AATATAAAAAT
* *
4504 AATTTATAAATATATTAAAATTTATATAATATAAA
1 AA--TATAAA-ATA--AAAAATAATATAATATAAA
4539 TTATTAATAT
Statistics
Matches: 57, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
33 20 0.35
35 12 0.21
37 6 0.11
38 10 0.18
40 9 0.16
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (33 bp):
AATATAAAATAAAAAATAATATAATATAAAAAT
Found at i:4530 original size:14 final size:14
Alignment explanation
Indices: 4513--4563 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
4503 TAATTTATAA
4513 ATATATTAAAATTT
1 ATATATTAAAATTT
*
4527 ATATAATATAAATTATTA
1 ATAT-AT-TAAA--ATTT
4545 ATATATTAAAATTT
1 ATATATTAAAATTT
4559 ATATA
1 ATATA
4564 AATATATAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
14 12 0.39
15 2 0.06
16 8 0.26
17 2 0.06
18 7 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
ATATATTAAAATTT
Found at i:4533 original size:45 final size:46
Alignment explanation
Indices: 4436--4547 Score: 131
Period size: 45 Copynumber: 2.5 Consensus size: 46
4426 AAATGGCGTG
4436 AATATAATATAAAATATAAT-ATAATATAAAAATAATATAAAATAA
1 AATATAATATAAAATATAATAATAATATAAAAATAATATAAAATAA
* * * *
4481 AAAATAATATAAAATATAATAATAATTTATAAAT-ATATTAAAAT-T
1 AATATAATATAAAATATAATAATAATATAAAAATAATA-TAAAATAA
* *
4526 TATATAATATAAATTATTAATA
1 AATATAATATAAAATA-TAATA
4548 TATTAAAATT
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
45 35 0.61
46 22 0.39
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (46 bp):
AATATAATATAAAATATAATAATAATATAAAAATAATATAAAATAA
Found at i:4551 original size:32 final size:32
Alignment explanation
Indices: 4494--4578 Score: 118
Period size: 32 Copynumber: 2.6 Consensus size: 32
4484 ATAATATAAA
* *
4494 ATATAATAATAATTTATAAATATATTAAAATTT
1 ATATAAT-ATAAATTATTAATATATTAAAATTT
4527 ATATAATATAAATTATTAATATATTAAAATTT
1 ATATAATATAAATTATTAATATATTAAAATTT
4559 ATATAAATATATAA-TATTAA
1 ATAT-AATATA-AATTATTAA
4579 AAAATAAAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
32 27 0.56
33 19 0.40
34 2 0.04
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (32 bp):
ATATAATATAAATTATTAATATATTAAAATTT
Found at i:4568 original size:18 final size:19
Alignment explanation
Indices: 4488--4570 Score: 81
Period size: 18 Copynumber: 4.6 Consensus size: 19
4478 TAAAAAATAA
* *
4488 TATAAAATATAATAATAATT
1 TATATAATATATTAA-AATT
4508 TATA-AATATATTAAAATT
1 TATATAATATATTAAAATT
4526 TATAT-A-ATA-T-AAA-T
1 TATATAATATATTAAAATT
4540 TAT-TAATATATTAAAATT
1 TATATAATATATTAAAATT
4558 TATATAAATATAT
1 TATAT-AATATAT
4571 AATATTAAAA
Statistics
Matches: 54, Mismatches: 1, Indels: 16
0.76 0.01 0.23
Matches are distributed among these distances:
13 1 0.02
14 5 0.09
15 6 0.11
16 2 0.04
17 6 0.11
18 13 0.24
19 10 0.19
20 11 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TATATAATATATTAAAATT
Found at i:4569 original size:38 final size:37
Alignment explanation
Indices: 4436--4574 Score: 100
Period size: 32 Copynumber: 3.8 Consensus size: 37
4426 AAATGGCGTG
*
4436 AATATAATATAAAATATAATATAATATAAAAAT-AA-TATA
1 AATAT-AT-TAAAATAT-ATA-AATATAATAATAAATTATA
* *
4475 AA-ATA-AAAAATAATATAAAATATAATAATAATTTATA
1 AATATATTAAAAT-ATAT-AAATATAATAATAAATTATA
*
4512 AATATATTAAAAT-T-T--ATATAAT-ATAAATTATT
1 AATATATTAAAATATATAAATATAATAATAAATTATA
4544 AATATATTAAAATTTATATAAATAT-ATAATA
1 AATATATTAAAA--TATATAAATATAATAATA
4575 TTAAAAAATA
Statistics
Matches: 81, Mismatches: 6, Indels: 27
0.71 0.05 0.24
Matches are distributed among these distances:
32 20 0.25
33 7 0.09
34 1 0.01
35 18 0.22
36 6 0.07
37 10 0.12
38 12 0.15
39 7 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (37 bp):
AATATATTAAAATATATAAATATAATAATAAATTATA
Found at i:4587 original size:32 final size:32
Alignment explanation
Indices: 4494--4588 Score: 95
Period size: 32 Copynumber: 2.9 Consensus size: 32
4484 ATAATATAAA
* * * *
4494 ATATAATAATAATTTATAAATATATTAAAATTT
1 ATATAAT-ATAAATTATTAATAAAATAAAATTT
* *
4527 ATATAATATAAATTATTAATATATTAAAATTT
1 ATATAATATAAATTATTAATAAAATAAAATTT
4559 ATATAAATATATAA-TATTAA-AAAATAAAAT
1 ATAT-AATATA-AATTATTAATAAAATAAAAT
4589 AAATAAGACT
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
32 35 0.62
33 19 0.34
34 2 0.04
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (32 bp):
ATATAATATAAATTATTAATAAAATAAAATTT
Found at i:4604 original size:11 final size:11
Alignment explanation
Indices: 4588--4624 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
4578 AAAAATAAAA
4588 TAAATAAGACT
1 TAAATAAGACT
*
4599 TAAATAA-A-A
1 TAAATAAGACT
4608 TAAATAAGACT
1 TAAATAAGACT
4619 TAAATA
1 TAAATA
4625 TAAAAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 7 0.32
10 2 0.09
11 13 0.59
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.27
Consensus pattern (11 bp):
TAAATAAGACT
Found at i:4605 original size:20 final size:20
Alignment explanation
Indices: 4580--4624 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
4570 TAATATTAAA
4580 AAATAAAATAAATAAGACTT
1 AAATAAAATAAATAAGACTT
4600 AAATAAAATAAATAAGACTT
1 AAATAAAATAAATAAGACTT
4620 AAATA
1 AAATA
4625 TAAAAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.24
Consensus pattern (20 bp):
AAATAAAATAAATAAGACTT
Found at i:5700 original size:20 final size:21
Alignment explanation
Indices: 5663--5702 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5653 TTTTTAATTC
*
5663 AAAATTATGAAGTAATATTAA
1 AAAAATATGAAGTAATATTAA
*
5684 AAAAATATGTAGT-ATATTA
1 AAAAATATGAAGTAATATTA
5703 GTTTTTACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (21 bp):
AAAAATATGAAGTAATATTAA
Found at i:5796 original size:14 final size:15
Alignment explanation
Indices: 5768--5799 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
5758 TTAAAAATAA
5768 AAAATTATAAATATT
1 AAAATTATAAATATT
5783 AAAATT-TAAATATT
1 AAAATTATAAATATT
5797 AAA
1 AAA
5800 TATATTTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAATTATAAATATT
Found at i:6069 original size:42 final size:41
Alignment explanation
Indices: 6022--6113 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 41
6012 AAAATTAATA
* *
6022 TTAATTTTTATATACTTT-TATAATTTAATTTAAATAAAATTT
1 TTAATTTTTA-ATA-TTTATATAAATTAAATTAAATAAAATTT
* * *
6064 TTAATTATTTAATATTTATTTAAATTAAATTAAATTAATTTT
1 TTAATT-TTTAATATTTATATAAATTAAATTAAATAAAATTT
6106 TTAATTTT
1 TTAATTTT
6114 ATTTATGTAC
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
41 5 0.12
42 34 0.79
43 4 0.09
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (41 bp):
TTAATTTTTAATATTTATATAAATTAAATTAAATAAAATTT
Found at i:6092 original size:37 final size:33
Alignment explanation
Indices: 6044--6118 Score: 87
Period size: 37 Copynumber: 2.2 Consensus size: 33
6034 TACTTTTATA
*
6044 ATTTAATTTAAATAAAATTTTTAATTATTTAATATTT
1 ATTTAAATTAAATAAAA---TTAATTATTTAAT-TTT
* *
6081 ATTTAAATTAAATTAAATTAATTTTTTAATTTT
1 ATTTAAATTAAATAAAATTAATTATTTAATTTT
6114 ATTTA
1 ATTTA
6119 TGTACAGGTC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
33 8 0.23
34 12 0.34
37 15 0.43
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (33 bp):
ATTTAAATTAAATAAAATTAATTATTTAATTTT
Found at i:6556 original size:21 final size:21
Alignment explanation
Indices: 6530--6576 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
6520 AAAGTTTAAA
6530 AAATA-TATTATAATAATATTT
1 AAATATTATTATAATAA-ATTT
*
6551 AAATATTTTTATAATAAATTT
1 AAATATTATTATAATAAATTT
6572 AAATA
1 AAATA
6577 AAATTTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AAATATTATTATAATAAATTT
Found at i:6593 original size:25 final size:26
Alignment explanation
Indices: 6550--6599 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
6540 TAATAATATT
6550 TAAATATTTTTATAATAAAT-TTAAA
1 TAAATATTTTTATAATAAATATTAAA
*
6575 TAAA-ATTTTTATTATTAAATATTAA
1 TAAATATTTTTA-TAATAAATATTAA
6600 TTCAGATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 7 0.32
25 11 0.50
26 4 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
TAAATATTTTTATAATAAATATTAAA
Found at i:7745 original size:19 final size:21
Alignment explanation
Indices: 7723--7765 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
7713 TACATATTAT
*
7723 AATTAAAAATTAA-T-ATAAA
1 AATTAAAAATGAATTCATAAA
*
7742 AATTTAAAATGAATTCATAAA
1 AATTAAAAATGAATTCATAAA
7763 AAT
1 AAT
7766 AAATTACACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 11 0.55
20 1 0.05
21 8 0.40
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (21 bp):
AATTAAAAATGAATTCATAAA
Found at i:8519 original size:30 final size:29
Alignment explanation
Indices: 8483--8541 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
8473 AGATTTTACT
*
8483 TTTTTATATAAATTTATTTTTAACTAAATA
1 TTTTTATATAAATTT-TTTTAAACTAAATA
* *
8513 TTTTTATTTAAATTTTTTTAAATTAAATA
1 TTTTTATATAAATTTTTTTAAACTAAATA
8542 AATTTTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 12 0.46
30 14 0.54
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (29 bp):
TTTTTATATAAATTTTTTTAAACTAAATA
Found at i:8545 original size:19 final size:19
Alignment explanation
Indices: 8521--8564 Score: 81
Period size: 18 Copynumber: 2.4 Consensus size: 19
8511 TATTTTTATT
8521 TAAATTTTTTTAAATTAAA
1 TAAATTTTTTTAAATTAAA
8540 TAAA-TTTTTTAAATTAAA
1 TAAATTTTTTTAAATTAAA
8558 TAAATTT
1 TAAATTT
8565 AAATTTGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TAAATTTTTTTAAATTAAA
Found at i:8792 original size:24 final size:22
Alignment explanation
Indices: 8731--8799 Score: 77
Period size: 24 Copynumber: 3.0 Consensus size: 22
8721 TTTAGGCTGC
8731 TTTATTTAATT-TAAATTTTTA
1 TTTATTTAATTATAAATTTTTA
*
8752 TTTATTTAATAAAATAAATTTTTA
1 TTTATTTAAT--TATAAATTTTTA
*
8776 TTTCAATTTAATTATAAATATTTA
1 TTT--ATTTAATTATAAATTTTTA
8800 AATTTTTAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
21 10 0.25
24 23 0.57
26 7 0.17
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTATTTAATTATAAATTTTTA
Found at i:8832 original size:48 final size:47
Alignment explanation
Indices: 8734--8835 Score: 111
Period size: 48 Copynumber: 2.1 Consensus size: 47
8724 AGGCTGCTTT
* * * *
8734 ATTTAATTTAAATTTTTATTTATTTAATAAAATAAATTTTTATTTCA
1 ATTTAATTTAAATTTTAAATTATTTAATAAAAAAAATTTTTATATCA
8781 ATTTAATTATAAATATTTAAATT-TTTAATATAAAAATAATTTTTA-AT-A
1 ATTTAATT-TAAAT-TTTAAATTATTTAATA-AAAAA-AATTTTTATATCA
8829 ATTTAAT
1 ATTTAAT
8836 ATTTTTTATA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
47 8 0.17
48 20 0.43
49 11 0.23
50 8 0.17
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (47 bp):
ATTTAATTTAAATTTTAAATTATTTAATAAAAAAAATTTTTATATCA
Found at i:8898 original size:17 final size:17
Alignment explanation
Indices: 8876--8909 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
8866 AAACTGAACC
8876 AAATTTAAACTTAAATA
1 AAATTTAAACTTAAATA
*
8893 AAATTTAAATTTAAATA
1 AAATTTAAACTTAAATA
8910 TTTTTAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATTTAAACTTAAATA
Found at i:9128 original size:22 final size:22
Alignment explanation
Indices: 9079--9128 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
9069 ATTGAAGCTA
* *
9079 ATATTTAATTTTAAATTTAGTT
1 ATATTTAAATTTAAATTTAATT
9101 ATATTTAAATTTAAATTTAAATT
1 ATATTTAAATTTAAATTT-AATT
9124 A-ATTT
1 ATATTT
9129 TTAATACTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
ATATTTAAATTTAAATTTAATT
Found at i:9365 original size:158 final size:155
Alignment explanation
Indices: 9080--9368 Score: 481
Period size: 158 Copynumber: 1.8 Consensus size: 155
9070 TTGAAGCTAA
* *
9080 TATTTAATTTTAAATTTAGTTATATTTAAATTTAAATTTAAATTAATTTTTAATACTAATTAAAA
1 TATTTAATTATAAACTTAGTTATATTTAAATTTAAATTTAAATTAATTTTTAATACTAATTAAAA
*
9145 TATATATATTAATAATAAAAAAATTTAATTAAACTTACAAAATATTTAATTTAAATATTAAAATA
66 TATATATATTAATAATAAAAAAATTTAATTAAAATTACAAAATATTTAATTTAAATATTAAAATA
9210 TACAATTTTAGATTATTTAATAGCT
131 TACAATTTTAGATTATTTAATAGCT
* * *
9235 TATTTAATTATAAACTTAGTTATATTTTAATTTGAATTTAAATTAACTTTTTTTAATATTAATTT
1 TATTTAATTATAAACTTAGTTATATTTAAATTTAAATTTAAATTAA---TTTTTAATACTAA-TT
9300 AAAA-ATATATATTAATAATAAAAAAATTTAATTAAAATTACAAAATATTTAATTTAAATATTAA
62 AAAATATATATATTAATAATAAAAAAATTTAATTAAAATTACAAAATATTTAATTTAAATATTAA
9364 AATAT
127 AATAT
9369 TTAAATTTAA
Statistics
Matches: 124, Mismatches: 6, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
155 42 0.34
158 76 0.61
159 6 0.05
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.47
Consensus pattern (155 bp):
TATTTAATTATAAACTTAGTTATATTTAAATTTAAATTTAAATTAATTTTTAATACTAATTAAAA
TATATATATTAATAATAAAAAAATTTAATTAAAATTACAAAATATTTAATTTAAATATTAAAATA
TACAATTTTAGATTATTTAATAGCT
Found at i:9389 original size:22 final size:21
Alignment explanation
Indices: 9320--9378 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
9310 ATTAATAATA
*
9320 AAAAAATTTAA-TTAAA-ATT
1 AAAATATTTAATTTAAATATT
9339 ACAAAATATTTAATTTAAATATT
1 --AAAATATTTAATTTAAATATT
9362 AAAATATTTAAATTTAA
1 AAAATATTT-AATTTAA
9379 CTTATTTAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
21 19 0.56
22 12 0.35
23 3 0.09
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
AAAATATTTAATTTAAATATT
Found at i:20977 original size:75 final size:74
Alignment explanation
Indices: 20897--21268 Score: 365
Period size: 75 Copynumber: 5.0 Consensus size: 74
20887 TTGTCAAAGA
* * * * * *
20897 TTTATTTTTCTGGCGAGCAGGATTTAAATGATGAGCACAGGTTTGACAGCCAGAGTGAGTGTTGT
1 TTTATTTTTCTGGCGACCAAGATTT-AATGACGAGCACAGGTCTGGCAGCCAGAGTGAGTGTTGG
*
20962 CTATCAGGAT
65 CTACCAGGAT
* * * * *
20972 TTTATTTTT-TGGCGACTAAGATTT-ATGTAGCGAGTACAAGTCTGGCAGCTAGAGTGAATGTTG
1 TTTATTTTTCTGGCGACCAAGATTTAATG-A-CGAGCACAGGTCTGGCAGCCAGAGTGAGTGTTG
*
21035 GCTACCAAGAT
64 GCTACCAGGAT
* * *
21046 TTTGTCTTTT-TGGCGACCAGGATTTATGTGACGAGCACAGGTCTGGCAGCCAGAGTGAGTGTTG
1 TTTAT-TTTTCTGGCGACCAAGATTTA-ATGACGAGCACAGGTCTGGCAGCCAGAGTGAGTGTTG
*
21110 GCTACTAGGAT
64 GCTACCAGGAT
*** * * * *
21121 TACGTCTTTCTGGCGACCAAGATTTATGTGGCGAGCACAGGTCTGGCAGCCAGAATGAGTGTTGG
1 TTTATTTTTCTGGCGACCAAGATTTA-ATGACGAGCACAGGTCTGGCAGCCAGAGTGAGTGTTGG
21186 CTACCAGGAT
65 CTACCAGGAT
** * * * * *
21196 TCCATCTTTCTGACGACCAAGATTT-ATGTAGCGAGCACAGGTTTGACAGACAGAGTGAGTGTTG
1 TTTATTTTTCTGGCGACCAAGATTTAATG-A-CGAGCACAGGTCTGGCAGCCAGAGTGAGTGTTG
21260 GCTACCAGG
64 GCTACCAGG
21269 GTTGGCTACC
Statistics
Matches: 250, Mismatches: 39, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
72 3 0.01
73 3 0.01
74 53 0.21
75 188 0.75
76 1 0.00
77 2 0.01
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (74 bp):
TTTATTTTTCTGGCGACCAAGATTTAATGACGAGCACAGGTCTGGCAGCCAGAGTGAGTGTTGGC
TACCAGGAT
Found at i:21204 original size:150 final size:150
Alignment explanation
Indices: 20902--21268 Score: 445
Period size: 150 Copynumber: 2.5 Consensus size: 150
20892 AAAGATTTAT
* ** * *
20902 TTTTCTGGCGAGCAGGATTTAAATGATGAGCACAGGTTTGACAGCCAGAGTGAGTGTTGTCTA-T
1 TTTT-TGGCGACCAGGATTTATGTGACGAGCACAGGTTTGACAGCCAGAGTGAGTGTTGGCTACT
** * * * * *
20966 CAGGATTTTATTTTTTGGCGACTAAGATTTATGTAGCGAGTACAAGTCTGGCAGCTAGAGTGAAT
65 CAGGATTACATTTTCTGGCGACCAAGATTTATGTAGCGAGCACAAGTCTGGCAGCCAGAATGAAT
***
21031 GTTGGCTACCAAGATTTTGTC
130 GTTGGCTACCAAGATTCCATC
* *
21052 TTTTTGGCGACCAGGATTTATGTGACGAGCACAGGTCTGGCAGCCAGAGTGAGTGTTGGCTACT-
1 TTTTTGGCGACCAGGATTTATGTGACGAGCACAGGTTTGACAGCCAGAGTGAGTGTTGGCTACTC
* * * *
21116 AGGATTACGTCTTTCTGGCGACCAAGATTTATGTGGCGAGCACAGGTCTGGCAGCCAGAATGAGT
66 AGGATTACAT-TTTCTGGCGACCAAGATTTATGTAGCGAGCACAAGTCTGGCAGCCAGAATGAAT
*
21181 GTTGGCTACCAGGATTCCATC
130 GTTGGCTACCAAGATTCCATC
* * * *
21202 TTTCTGACGACCAAGATTTATGT-AGCGAGCACAGGTTTGACAGACAGAGTGAGTGTTGGCTAC-
1 TTTTTGGCGACCAGGATTTATGTGA-CGAGCACAGGTTTGACAGCCAGAGTGAGTGTTGGCTACT
21265 CAGG
65 CAGG
21269 GTTGGCTACC
Statistics
Matches: 185, Mismatches: 28, Indels: 8
0.84 0.13 0.04
Matches are distributed among these distances:
149 59 0.32
150 126 0.68
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.29
Consensus pattern (150 bp):
TTTTTGGCGACCAGGATTTATGTGACGAGCACAGGTTTGACAGCCAGAGTGAGTGTTGGCTACTC
AGGATTACATTTTCTGGCGACCAAGATTTATGTAGCGAGCACAAGTCTGGCAGCCAGAATGAATG
TTGGCTACCAAGATTCCATC
Found at i:21274 original size:13 final size:13
Alignment explanation
Indices: 21256--21281 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21246 CAGAGTGAGT
21256 GTTGGCTACCAGG
1 GTTGGCTACCAGG
21269 GTTGGCTACCAGG
1 GTTGGCTACCAGG
21282 ATTCCATCCT
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:0.15, C:0.23, G:0.38, T:0.23
Consensus pattern (13 bp):
GTTGGCTACCAGG
Found at i:21331 original size:88 final size:88
Alignment explanation
Indices: 21181--21358 Score: 257
Period size: 88 Copynumber: 2.0 Consensus size: 88
21171 CAGAATGAGT
* * *
21181 GTTGGCTACCAGGATTCCATCTTTCTGACGACCAAGATTTATGTAGCGAGCACAGGTTTGACAGA
1 GTTGGCTACCAGGATTCCATCCTTCTGACGACCAAGATTTATGTAGCGAGCACAAGTCTGACAGA
* * *
21246 CAGAGTGAGTGTTGGCTACCAGG
66 CAGAATAAGTGTTGGCGACCAGG
* * * *
21269 GTTGGCTACCAGGATTCCATCCTTCTGACGACTAAGATTTATGTGGCGAGTACAAGTCTGACAGC
1 GTTGGCTACCAGGATTCCATCCTTCTGACGACCAAGATTTATGTAGCGAGCACAAGTCTGACAGA
*
21334 CAGAATAAGTGTTGGCGATCAGG
66 CAGAATAAGTGTTGGCGACCAGG
21357 GT
1 GT
21359 ATAACAATTG
Statistics
Matches: 79, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
88 79 1.00
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.26
Consensus pattern (88 bp):
GTTGGCTACCAGGATTCCATCCTTCTGACGACCAAGATTTATGTAGCGAGCACAAGTCTGACAGA
CAGAATAAGTGTTGGCGACCAGG
Found at i:21865 original size:78 final size:78
Alignment explanation
Indices: 21736--22292 Score: 578
Period size: 78 Copynumber: 7.2 Consensus size: 78
21726 GGGCAAAATT
* * * * * * *
21736 GGAGTGACTTAGTGTCAGTGATAATATTAATGCCGTGGTGGCGATTAGGATCGTGGTGCTATGGT
1 GGAGTGACTTGGTGTCACTGATAGTATTGATGCCGTGGTGGCGATCAGGATCGTAGTGCCATGGT
*
21801 GGCGAGCAGGATC
66 GGCTAGCAGGATC
* * * * *
21814 GGAGTGACTTGGTGCCACTGACAGTATTGATGCTGTGGTGGTGATCAGGATCGTAGTGCTATGGT
1 GGAGTGACTTGGTGTCACTGATAGTATTGATGCCGTGGTGGCGATCAGGATCGTAGTGCCATGGT
*
21879 GGCTAGCAAGATC
66 GGCTAGCAGGATC
* * * * * * * * ** *
21892 GGAGTGCCATGGTGTCATTGATAATATTGATGCCATGGTAGTGATCAGGGTTATAGTGACATGGT
1 GGAGTGACTTGGTGTCACTGATAGTATTGATGCCGTGGTGGCGATCAGGATCGTAGTGCCATGGT
21957 GGCTAGCAGGATC
66 GGCTAGCAGGATC
* * * * * * * * **
21970 GAAATGCCATGGTGTCACTGACAGTATTGATGCCATGGTGACAATCAGGATCGGGGTGCCATGGT
1 GGAGTGACTTGGTGTCACTGATAGTATTGATGCCGTGGTGGCGATCAGGATCGTAGTGCCATGGT
* * *
22035 GCCGAGCAAGATC
66 GGCTAGCAGGATC
* * ** * *
22048 GAATTGACTTGGTGTCACTGATAGTA-CAATGCCGTGGTGGCGATCAGGATCATAGTGACATGGT
1 GGAGTGACTTGGTGTCACTGATAGTATTGATGCCGTGGTGGCGATCAGGATCGTAGTGCCATGGT
22112 GGCTAGCAGGATC
66 GGCTAGCAGGATC
* * ** *
22125 AGAGTGACTTGGTGCCACTGACCGTATTGATGCCGTGGTGGTGATCAGGATCGTAGTGCCATGGT
1 GGAGTGACTTGGTGTCACTGATAGTATTGATGCCGTGGTGGCGATCAGGATCGTAGTGCCATGGT
*
22190 GGCTAGCAGGATT
66 GGCTAGCAGGATC
* * * * *
22203 GGAGTGCCATGGTGTCACTGATAGTAGTGATGCCATGGTGGCGATCAGGATCAT-GATGCCATGG
1 GGAGTGACTTGGTGTCACTGATAGTATTGATGCCGTGGTGGCGATCAGGATCGTAG-TGCCATGG
*
22267 TGGCGAGCAGGATC
65 TGGCTAGCAGGATC
*
22281 AGAGTGACTTGG
1 GGAGTGACTTGG
22293 AATCGAGACC
Statistics
Matches: 389, Mismatches: 88, Indels: 4
0.81 0.18 0.01
Matches are distributed among these distances:
77 60 0.15
78 329 0.85
ACGTcount: A:0.23, C:0.16, G:0.35, T:0.26
Consensus pattern (78 bp):
GGAGTGACTTGGTGTCACTGATAGTATTGATGCCGTGGTGGCGATCAGGATCGTAGTGCCATGGT
GGCTAGCAGGATC
Found at i:22121 original size:26 final size:26
Alignment explanation
Indices: 22082--22288 Score: 81
Period size: 26 Copynumber: 8.0 Consensus size: 26
22072 TACAATGCCG
* *
22082 TGGTGGCGATCAGGATCATAGTGACA
1 TGGTGGCGAGCAGGATCAGAGTGACA
* *
22108 TGGTGGCTAGCAGGATCAGAGTGACT
1 TGGTGGCGAGCAGGATCAGAGTGACA
* * * * * *
22134 TGGT-GCCACTGACCGTAT-TGA-TGCCG
1 TGGTGGCGA--G-CAGGATCAGAGTGACA
* * *
22160 TGGTGGTGATCAGGATC-GTAGTGCCA
1 TGGTGGCGAGCAGGATCAG-AGTGACA
* ** *
22186 TGGTGGCTAGCAGGATTGGAGTGCCA
1 TGGTGGCGAGCAGGATCAGAGTGACA
* *
22212 TGGTGTC-A-C-TGAT-AGTAGTGATGCCA
1 TGGTGGCGAGCAGGATCAG-AGTGA---CA
* *
22238 TGGTGGCGATCAGGATCATGA-TGCCA
1 TGGTGGCGAGCAGGATCA-GAGTGACA
22264 TGGTGGCGAGCAGGATCAGAGTGAC
1 TGGTGGCGAGCAGGATCAGAGTGAC
22289 TTGGAATCGA
Statistics
Matches: 134, Mismatches: 29, Indels: 36
0.67 0.15 0.18
Matches are distributed among these distances:
22 1 0.01
23 7 0.05
24 6 0.04
25 7 0.05
26 93 0.69
27 7 0.05
28 5 0.04
29 5 0.04
30 2 0.01
31 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.37, T:0.24
Consensus pattern (26 bp):
TGGTGGCGAGCAGGATCAGAGTGACA
Found at i:23908 original size:75 final size:75
Alignment explanation
Indices: 23657--23931 Score: 250
Period size: 75 Copynumber: 3.7 Consensus size: 75
23647 TTGGCAATCG
* * * * * * * *
23657 AGATTTATGTAGCGAGTACAAGTTTGGCAGCTAGAGTGACTGTT-AGCCACCAATATTCCGTCCT
1 AGATTTATGTAGCGAGCACAGGTCTGACAACTAGAGTGAGTGTTGA-CTACCAAGATTCCGTCCT
*
23721 TCTGATGACCA
65 TCTGGTGACCA
* ** * * * *
23732 AGATTTATGTGGCGAGCACAGGTCTGGTAGCCAGAGTGAGTGTTGGCTACC-AGAATTCCGTCAT
1 AGATTTATGTAGCGAGCACAGGTCTGACAACTAGAGTGAGTGTTGACTACCAAG-ATTCCGTCCT
* * *
23796 TCTCGTAATCA
65 TCTGGTGACCA
* * *
23807 GGATTTATGTAACGAGCACAGGTCTGACAACTAGAGTGAGTGTTGACTACCAAGATTCCATCCTT
1 AGATTTATGTAGCGAGCACAGGTCTGACAACTAGAGTGAGTGTTGACTACCAAGATTCCGTCCTT
*
23872 CTGGCGACCA
66 CTGGTGACCA
* * * * *
23882 ATATTTATGTGGCGAGTACAGCTCTGACAA-TCAGAGTTAGTGTTGACTAC
1 AGATTTATGTAGCGAGCACAGGTCTGACAACT-AGAGTGAGTGTTGACTAC
23932 TAAGGTTGGC
Statistics
Matches: 160, Mismatches: 36, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
74 2 0.01
75 156 0.98
76 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (75 bp):
AGATTTATGTAGCGAGCACAGGTCTGACAACTAGAGTGAGTGTTGACTACCAAGATTCCGTCCTT
CTGGTGACCA
Found at i:23917 original size:150 final size:150
Alignment explanation
Indices: 23658--23931 Score: 343
Period size: 150 Copynumber: 1.8 Consensus size: 150
23648 TGGCAATCGA
* * * * * * *
23658 GATTTATGTAGCGAGTACAAGTTTGGCAGCTAGAGTGACTGTTAGCCACCAATATTCCGTCCTTC
1 GATTTATGTAACGAGCACAAGTCTGACAACTAGAGTGACTGTTAGCCACCAAGATTCCATCCTTC
* * ** * *
23723 TGATGACCAAGATTTATGTGGCGAGCACAGGTCTGGTAGCCAGAGTGAGTGTTGGCTACCAGAAT
66 TGACGACCAAGATTTATGTGGCGAGCACAGCTCTGACAACCAGAGTGAGTGTTGACTACCAGAAT
23788 TCCGTCATTCTCGTAATCAG
131 TCCGTCATTCTCGTAATCAG
* * *
23808 GATTTATGTAACGAGCACAGGTCTGACAACTAGAGTGAGTGTT-GACTACCAAGATTCCATCCTT
1 GATTTATGTAACGAGCACAAGTCTGACAACTAGAGTGACTGTTAG-CCACCAAGATTCCATCCTT
* * * * *
23872 CTGGCGACCAATATTTATGTGGCGAGTACAGCTCTGACAATCAGAGTTAGTGTTGACTAC
65 CTGACGACCAAGATTTATGTGGCGAGCACAGCTCTGACAACCAGAGTGAGTGTTGACTAC
23932 TAAGGTTGGC
Statistics
Matches: 102, Mismatches: 21, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
149 1 0.01
150 101 0.99
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.28
Consensus pattern (150 bp):
GATTTATGTAACGAGCACAAGTCTGACAACTAGAGTGACTGTTAGCCACCAAGATTCCATCCTTC
TGACGACCAAGATTTATGTGGCGAGCACAGCTCTGACAACCAGAGTGAGTGTTGACTACCAGAAT
TCCGTCATTCTCGTAATCAG
Found at i:25278 original size:11 final size:11
Alignment explanation
Indices: 25262--25286 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
25252 AAATATACTT
25262 TTTATTAATTA
1 TTTATTAATTA
25273 TTTATTAATTA
1 TTTATTAATTA
25284 TTT
1 TTT
25287 TTTTTATCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTATTAATTA
Found at i:27115 original size:15 final size:15
Alignment explanation
Indices: 27095--27123 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
27085 ATTGTGTTCG
27095 AAGTAAATAAAAAAA
1 AAGTAAATAAAAAAA
27110 AAGTAAATAAAAAA
1 AAGTAAATAAAAAA
27124 TTTTTAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (15 bp):
AAGTAAATAAAAAAA
Found at i:27479 original size:5 final size:5
Alignment explanation
Indices: 27463--27518 Score: 71
Period size: 5 Copynumber: 11.0 Consensus size: 5
27453 ATTATTTATA
27463 TAAAT T-AAT TAAAT TAAATT TAAAT TAAAT T-AAT TAAAT TAAATT CTAAAT
1 TAAAT TAAAT TAAAT TAAA-T TAAAT TAAAT TAAAT TAAAT TAAA-T -TAAAT
27514 TAAAT
1 TAAAT
27519 AAAAAAAATC
Statistics
Matches: 46, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
4 8 0.17
5 27 0.59
6 7 0.15
7 4 0.09
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (5 bp):
TAAAT
Found at i:27496 original size:25 final size:26
Alignment explanation
Indices: 27463--27518 Score: 105
Period size: 25 Copynumber: 2.2 Consensus size: 26
27453 ATTATTTATA
27463 TAAATTAATTAAATTAAATT-TAAAT
1 TAAATTAATTAAATTAAATTCTAAAT
27488 TAAATTAATTAAATTAAATTCTAAAT
1 TAAATTAATTAAATTAAATTCTAAAT
27514 TAAAT
1 TAAAT
27519 AAAAAAAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 20 0.67
26 10 0.33
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
TAAATTAATTAAATTAAATTCTAAAT
Found at i:27521 original size:21 final size:20
Alignment explanation
Indices: 27463--27521 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 20
27453 ATTATTTATA
27463 TAAATT-AATTAAATTAAATT
1 TAAATTAAATTAAA-TAAATT
*
27483 TAAATTAAATTAATTAAA-T
1 TAAATTAAATTAAATAAATT
27502 TAAATTCTAAATTAAATAAA
1 TAAA-T-TAAATTAAATAAA
27522 AAAAATCTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 5 0.15
20 11 0.32
21 18 0.53
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAATTAAATTAAATAAATT
Found at i:27527 original size:21 final size:21
Alignment explanation
Indices: 27488--27527 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
27478 AAATTTAAAT
* **
27488 TAAATTAATTAAATTAAATTC
1 TAAATTAAATAAAAAAAATTC
27509 TAAATTAAATAAAAAAAAT
1 TAAATTAAATAAAAAAAAT
27528 CTTTGAATAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAATTAAATAAAAAAAATTC
Found at i:27527 original size:26 final size:25
Alignment explanation
Indices: 27473--27527 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 25
27463 TAAATTAATT
* **
27473 AAATTAAATTTAAATTAAATTAATT
1 AAATTAAATTTAAATTAAATAAAAA
27498 AAATTAAATTCTAAATTAAATAAAAA
1 AAATTAAATT-TAAATTAAATAAAAA
27524 AAAT
1 AAAT
27528 CTTTGAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 10 0.38
26 16 0.62
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (25 bp):
AAATTAAATTTAAATTAAATAAAAA
Found at i:28657 original size:21 final size:21
Alignment explanation
Indices: 28629--28695 Score: 84
Period size: 21 Copynumber: 3.2 Consensus size: 21
28619 TTTAAATATA
28629 TATT-TTATTAATTTTAATTT
1 TATTATTATTAATTTTAATTT
* **
28649 TATTATTATGAAAATTAATTT
1 TATTATTATTAATTTTAATTT
28670 TATTATTATT-ATTATTAATTT
1 TATTATTATTAATT-TTAATTT
28691 TATTA
1 TATTA
28696 AAATTAATGT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
20 5 0.13
21 34 0.87
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (21 bp):
TATTATTATTAATTTTAATTT
Found at i:28672 original size:36 final size:37
Alignment explanation
Indices: 28630--28715 Score: 99
Period size: 36 Copynumber: 2.4 Consensus size: 37
28620 TTAAATATAT
28630 ATTTTATTAATT-TTAATT-TT-ATTATTATGAAAATTA
1 ATTTTATTAATTATT-ATTATTAATT-TTATGAAAATTA
*
28666 ATTTTATT-ATTATTATTATTAATTTTATTAAAATTA
1 ATTTTATTAATTATTATTATTAATTTTATGAAAATTA
* *
28702 ATGTTATTATTTAT
1 ATTTTATTAATTAT
28716 CTAAATAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
35 6 0.14
36 30 0.70
37 7 0.16
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (37 bp):
ATTTTATTAATTATTATTATTAATTTTATGAAAATTA
Found at i:28701 original size:21 final size:21
Alignment explanation
Indices: 28662--28701 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28652 TATTATGAAA
**
28662 ATTAATTTTATTATTATTATT
1 ATTAATTTTATTAAAATTATT
28683 ATTAATTTTATTAAAATTA
1 ATTAATTTTATTAAAATTA
28702 ATGTTATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTAATTTTATTAAAATTATT
Found at i:29056 original size:20 final size:21
Alignment explanation
Indices: 29033--29072 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
29023 TTTATTAATT
29033 ATAAA-AATTTAAATTTTTAG
1 ATAAATAATTTAAATTTTTAG
* *
29053 ATAAATATTTTTAATTTTTA
1 ATAAATAATTTAAATTTTTA
29073 AATTTAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (21 bp):
ATAAATAATTTAAATTTTTAG
Found at i:35487 original size:7 final size:8
Alignment explanation
Indices: 35465--35494 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
35455 TATCTGTAAA
35465 AAAACAAAG
1 AAAA-AAAG
35474 AAAAAAAG
1 AAAAAAAG
35482 AAAAAAAG
1 AAAAAAAG
35490 AAAAA
1 AAAAA
35495 GAGGTGGAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 17 0.81
9 4 0.19
ACGTcount: A:0.87, C:0.03, G:0.10, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:36333 original size:30 final size:28
Alignment explanation
Indices: 36268--36336 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 28
36258 TTTCTTGCTC
36268 AATAAATTTAA--ATATAATATTTAAAA
1 AATAAATTTAATTATATAATATTTAAAA
36294 AAT-AATTTAATTATGATAA-ATTATAAAA
1 AATAAATTTAATTAT-ATAATATT-TAAAA
36322 ATATAAATTTAATTA
1 A-ATAAATTTAATTA
36337 GAATATAATG
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
25 7 0.19
26 3 0.08
27 5 0.14
28 10 0.27
29 2 0.05
30 10 0.27
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (28 bp):
AATAAATTTAATTATATAATATTTAAAA
Found at i:36351 original size:30 final size:28
Alignment explanation
Indices: 36268--36351 Score: 70
Period size: 30 Copynumber: 3.0 Consensus size: 28
36258 TTTCTTGCTC
* *
36268 AATAAATTTAAATATAATAT--TTAAAA
1 AATAAATTTAATTAGAATATAATTAAAA
36294 AAT-AATTTAATTATG-ATA-AATTATAAAA
1 AATAAATTTAATTA-GAATATAA-T-TAAAA
36322 ATATAAATTTAATTAGAATATAATGTAAAA
1 A-ATAAATTTAATTAGAATATAAT-TAAAA
36352 TAATCTTAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
25 12 0.26
26 3 0.07
27 1 0.02
28 6 0.13
29 3 0.07
30 19 0.41
31 2 0.04
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (28 bp):
AATAAATTTAATTAGAATATAATTAAAA
Found at i:36384 original size:22 final size:21
Alignment explanation
Indices: 36341--36394 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
36331 TAATTAGAAT
* *
36341 ATAATGTAAAATAATCTTAAAA
1 ATAAT-TAAAATAATATAAAAA
36363 ATAATTAAAATAAATATAAAAA
1 ATAATTAAAAT-AATATAAAAA
*
36385 GTGAATTAAA
1 AT-AATTAAA
36395 TATGACACAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 6 0.22
22 14 0.52
23 7 0.26
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.30
Consensus pattern (21 bp):
ATAATTAAAATAATATAAAAA
Found at i:36586 original size:18 final size:18
Alignment explanation
Indices: 36565--36615 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
36555 TATTAAAAAT
36565 AAAATAATATAAAATAAA
1 AAAATAATATAAAATAAA
*
36583 AAAATTAA-ATAAATTTAAA
1 AAAA-TAATATAAA-ATAAA
36602 AATAATAAT-TAAAA
1 AA-AATAATATAAAA
36616 CATAACACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
18 9 0.33
19 16 0.59
20 2 0.07
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (18 bp):
AAAATAATATAAAATAAA
Found at i:36775 original size:20 final size:19
Alignment explanation
Indices: 36739--36797 Score: 79
Period size: 20 Copynumber: 3.2 Consensus size: 19
36729 TAACAATTTT
*
36739 TTTCT-TTCCTTTCTTCCC
1 TTTCTCTTCCTTTTTTCCC
36757 TTTCTCTTCCATTTTTTCCC
1 TTTCTCTTCC-TTTTTTCCC
36777 TTTCTCTT--TTTTTTCCC
1 TTTCTCTTCCTTTTTTCCC
36794 TTTC
1 TTTC
36798 CCGTTCGTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
17 13 0.34
18 5 0.13
19 4 0.11
20 16 0.42
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTCTCTTCCTTTTTTCCC
Found at i:36951 original size:20 final size:19
Alignment explanation
Indices: 36900--36953 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
36890 CTTTTGTCCC
36900 TTTATTTTATATATTAAAA
1 TTTATTTTATATATTAAAA
**
36919 TAAATTTTAATATATTAATAA
1 TTTATTTT-ATATATTAA-AA
*
36940 TTTATATTATATAT
1 TTTATTTTATATAT
36954 ATTTTAATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 6 0.21
20 15 0.54
21 7 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTATTTTATATATTAAAA
Found at i:36969 original size:20 final size:19
Alignment explanation
Indices: 36902--36974 Score: 67
Period size: 18 Copynumber: 3.7 Consensus size: 19
36892 TTTGTCCCTT
*
36902 TATTTTATATATTAAAATA
1 TATTTTATATATTATAATA
*
36921 AATTTTAATATATTAATAATTTA
1 TATTTT-ATATATT-ATAA--TA
* *
36944 TATTATATATATTTTAATA
1 TATTTTATATATTATAATA
36963 TA-TTTATATATT
1 TATTTTATATATT
36975 TCCATTATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
18 9 0.20
19 9 0.20
20 7 0.16
21 6 0.14
22 7 0.16
23 6 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TATTTTATATATTATAATA
Found at i:36975 original size:8 final size:8
Alignment explanation
Indices: 36928--36996 Score: 54
Period size: 8 Copynumber: 8.5 Consensus size: 8
36918 ATAAATTTTA
*
36928 ATATATTA
1 ATATATTT
36936 ATA-ATTT
1 ATATATTT
*
36943 ATAT-TAT
1 ATATATTT
36950 ATATATTTT
1 ATATA-TTT
36959 AATATATTT
1 -ATATATTT
36968 ATATATTT
1 ATATATTT
36976 CCAT-TATTT
1 --ATATATTT
*
36985 ATATTTTT
1 ATATATTT
36993 ATAT
1 ATAT
36997 CTTATTTTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
7 14 0.28
8 19 0.38
9 10 0.20
10 7 0.14
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (8 bp):
ATATATTT
Found at i:36985 original size:17 final size:18
Alignment explanation
Indices: 36942--36988 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
36932 ATTAATAATT
*
36942 TATATTATATATATTTTAA
1 TATATT-TATATATTTCAA
*
36961 TATATTTATATATTTCCA
1 TATATTTATATATTTCAA
36979 T-TATTTATAT
1 TATATTTATAT
36989 TTTTATATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 9 0.35
18 11 0.42
19 6 0.23
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (18 bp):
TATATTTATATATTTCAA
Found at i:36988 original size:33 final size:32
Alignment explanation
Indices: 36922--36996 Score: 96
Period size: 33 Copynumber: 2.3 Consensus size: 32
36912 ATTAAAATAA
*
36922 ATTTTAATATATTAATAATTTATATTATATAT
1 ATTTTAATATATTAATAATTTACATTATATAT
* * *
36954 ATTTTAATATATTTATATATTTCCATTATTTAT
1 ATTTTAATATATTAATA-ATTTACATTATATAT
*
36987 ATTTTTATAT
1 ATTTTAATAT
36997 CTTATTTTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
32 16 0.43
33 21 0.57
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (32 bp):
ATTTTAATATATTAATAATTTACATTATATAT
Found at i:37014 original size:12 final size:12
Alignment explanation
Indices: 36989--37043 Score: 58
Period size: 12 Copynumber: 4.7 Consensus size: 12
36979 TTATTTATAT
**
36989 TTTTATATCTTA
1 TTTTATATAATA
37001 TTTTATATAATA
1 TTTTATATAATA
* *
37013 TTTTA-ATTATT
1 TTTTATATAATA
*
37024 TTTTAAATAATA
1 TTTTATATAATA
37036 TTTTATAT
1 TTTTATAT
37044 TTATATAATA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
11 9 0.26
12 26 0.74
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (12 bp):
TTTTATATAATA
Found at i:37056 original size:23 final size:23
Alignment explanation
Indices: 36989--37057 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
36979 TTATTTATAT
*
36989 TTTTATATCTTATTTTATATAATA
1 TTTTATAT-TTATTTAATATAATA
37013 TTTTAATTATTT-TTTAA-ATAATA
1 TTTT-A-TATTTATTTAATATAATA
*
37036 TTTTATATTTATATAATATAAT
1 TTTTATATTTATTTAATATAAT
37058 TATAGTTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
21 5 0.13
22 5 0.13
23 15 0.38
24 8 0.21
25 3 0.08
26 3 0.08
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (23 bp):
TTTTATATTTATTTAATATAATA
Found at i:37596 original size:28 final size:29
Alignment explanation
Indices: 37547--37601 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
37537 ATTTCAAATT
*
37547 ATTTAAAATTTTAACTTAAAATAATTTCA
1 ATTTAAAATTTTAAATTAAAATAATTTCA
*
37576 ATTT-AAATTTTAAATTTAAATAATTT
1 ATTTAAAATTTTAAATTAAAATAATTT
37602 AAAAATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 20 0.83
29 4 0.17
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (29 bp):
ATTTAAAATTTTAAATTAAAATAATTTCA
Found at i:37600 original size:22 final size:22
Alignment explanation
Indices: 37575--37629 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
37565 AAATAATTTC
37575 AATTTAAATTTTAAATTTAAAT
1 AATTTAAATTTTAAATTTAAAT
** * *
37597 AATTTAAAAATTAAATTTGATT
1 AATTTAAATTTTAAATTTAAAT
*
37619 GATTTAAATTT
1 AATTTAAATTT
37630 AATAATTAGA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (22 bp):
AATTTAAATTTTAAATTTAAAT
Found at i:37840 original size:22 final size:22
Alignment explanation
Indices: 37804--37845 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
37794 AACACTTTTG
*
37804 TATTAAATGAGTTAATACAAAAA
1 TATTAAATCAGTTAAT-CAAAAA
37827 TATT-AATCAGTTAATCAAA
1 TATTAAATCAGTTAATCAAA
37846 TCCTTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 10 0.56
23 4 0.22
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.33
Consensus pattern (22 bp):
TATTAAATCAGTTAATCAAAAA
Found at i:38899 original size:6 final size:6
Alignment explanation
Indices: 38890--38927 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
38880 TTTTTTTTAT
*
38890 TTTAAA TTTAAA TTTAAA TTTAAT TTTAACA TTTAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA T
38928 CTCATTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 24 0.83
7 5 0.17
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:38934 original size:19 final size:18
Alignment explanation
Indices: 38896--38939 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
38886 TTATTTTAAA
*
38896 TTTAAATTTAAATTTAAT
1 TTTAAATTTAAATCTAAT
*
38914 TTTAACATTTAAATCTCAT
1 TTTAA-ATTTAAATCTAAT
*
38933 TTAAAAT
1 TTTAAAT
38940 CAAATCGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTAAATTTAAATCTAAT
Found at i:42115 original size:13 final size:13
Alignment explanation
Indices: 42097--42137 Score: 57
Period size: 13 Copynumber: 3.1 Consensus size: 13
42087 TCAGATTATT
42097 TTTTAATTATTTA
1 TTTTAATTATTTA
42110 TTTTAA-TATTTA
1 TTTTAATTATTTA
42122 TATTTAATATATTTA
1 T-TTTAAT-TATTTA
42137 T
1 T
42138 ATACAAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 7 0.28
13 11 0.44
15 7 0.28
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TTTTAATTATTTA
Found at i:42138 original size:15 final size:15
Alignment explanation
Indices: 42098--42139 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
42088 CAGATTATTT
42098 TTTAAT-TATTTAT-
1 TTTAATATATTTATA
42111 TTT-A-ATATTTATA
1 TTTAATATATTTATA
42124 TTTAATATATTTATA
1 TTTAATATATTTATA
42139 T
1 T
42140 ACAAATTGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 8 0.32
13 6 0.24
14 1 0.04
15 10 0.40
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTAATATATTTATA
Found at i:42762 original size:20 final size:20
Alignment explanation
Indices: 42720--42763 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
42710 ATAAAATATT
* *
42720 TATATTTAATATTTATATCA
1 TATATATAATATTTAGATCA
42740 TATATATAATATTTAAGAT-A
1 TATATATAATATTT-AGATCA
42760 TATA
1 TATA
42764 AAATAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (20 bp):
TATATATAATATTTAGATCA
Found at i:44290 original size:24 final size:23
Alignment explanation
Indices: 44248--44299 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
44238 TTAATTGTTT
* *
44248 TTTATAAATATTATTTTAACTAA
1 TTTATAAATATTATATTAACAAA
44271 TATTATCAAATATTA-ATTAACAAA
1 T-TTAT-AAATATTATATTAACAAA
44295 TTTAT
1 TTTAT
44300 GCAGATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
23 5 0.20
24 12 0.48
25 8 0.32
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (23 bp):
TTTATAAATATTATATTAACAAA
Found at i:46329 original size:124 final size:125
Alignment explanation
Indices: 46195--46433 Score: 347
Period size: 124 Copynumber: 1.9 Consensus size: 125
46185 AGGTTATTAT
* * * * * *
46195 TTATATTTTATATTTTATATGTGATTAATTGAATTAATGTTTTAAGTTAAGTGATATTAATTAAA
1 TTATATTTTATACTTTATACGTGATTAATTGAATTAATATTGTAAGTTAAATAATATTAATTAAA
* * *
46260 TTAAATTAATTAAATTTTAAATTATAAT-AAAAGATAAAATATAAGATATTATTTATTTAA
66 TTAAAATAATTAAAATTTAAATTATAATAAAAAG-TAAAACATAAGATATTATTTATTTAA
* *
46320 TTATA-TTTATACTTTATACGTGATTAATTGAGTTAATATTGTAAGTTAAATAATATTAATTTAA
1 TTATATTTTATACTTTATACGTGATTAATTGAATTAATATTGTAAGTTAAATAATATTAATTAAA
*
46384 TTAAAATAATTAAAATTTAAATTATAATAAAAAGTAAAACATAGGATATT
66 TTAAAATAATTAAAATTTAAATTATAATAAAAAGTAAAACATAAGATATT
46434 TTGAATATTT
Statistics
Matches: 101, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
124 91 0.90
125 10 0.10
ACGTcount: A:0.46, C:0.01, G:0.08, T:0.45
Consensus pattern (125 bp):
TTATATTTTATACTTTATACGTGATTAATTGAATTAATATTGTAAGTTAAATAATATTAATTAAA
TTAAAATAATTAAAATTTAAATTATAATAAAAAGTAAAACATAAGATATTATTTATTTAA
Found at i:46974 original size:25 final size:24
Alignment explanation
Indices: 46930--46979 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
46920 TTTTAATTTA
*
46930 TTATTTTTTAAAATATAATA-ATT
1 TTATTTTTTAAAATAAAATATATT
46953 TTATTTTTTAAAAAATAAAATATATT
1 TTATTTTTT--AAAATAAAATATATT
46979 T
1 T
46980 ATCCCTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 9 0.39
25 10 0.43
26 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TTATTTTTTAAAATAAAATATATT
Found at i:46980 original size:25 final size:23
Alignment explanation
Indices: 46930--46981 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
46920 TTTTAATTTA
* *
46930 TTATTTTTTAAAATATAATAATT
1 TTATTTTTTAAAAAATAAAAATT
46953 TTATTTTTTAAAAAATAAAATATAT
1 TTATTTTTTAAAAAATAAAA-AT-T
46978 TTAT
1 TTAT
46982 CCCTAAATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 18 0.72
24 2 0.08
25 5 0.20
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TTATTTTTTAAAAAATAAAAATT
Found at i:48758 original size:62 final size:62
Alignment explanation
Indices: 48689--48810 Score: 169
Period size: 62 Copynumber: 2.0 Consensus size: 62
48679 TATTTAAATT
**
48689 GTTATAATTTTAGATTAATTCCTA-CTT-ACTTAGT-ATGACATTTATATACTAATTAAATTAGA
1 GTTATAATTTTAGATTAATT-CTACCTTAAC-TAGTAAT-ACAGCTATATACTAATTAAATTAGA
*
48751 GTTATAATTTTAGATTAATTCTACCTTAACTAGTAATAGAGCTATATACTAATTAAATTA
1 GTTATAATTTTAGATTAATTCTACCTTAACTAGTAATACAGCTATATACTAATTAAATTA
48811 AGAATTTCTG
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
61 3 0.06
62 47 0.87
63 4 0.07
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.43
Consensus pattern (62 bp):
GTTATAATTTTAGATTAATTCTACCTTAACTAGTAATACAGCTATATACTAATTAAATTAGA
Found at i:48926 original size:28 final size:26
Alignment explanation
Indices: 48874--48926 Score: 61
Period size: 28 Copynumber: 2.0 Consensus size: 26
48864 ATGTTGTTGA
*
48874 TTTACATTTTTTTAATATTCTTCTTC
1 TTTACATTTTTTTAATATTCATCTTC
* *
48900 TTTACCTTTATTTTATATATTGATCTT
1 TTTACATTT-TTTTA-ATATTCATCTT
48927 TTTTTTATGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 8 0.36
27 5 0.23
28 9 0.41
ACGTcount: A:0.21, C:0.13, G:0.02, T:0.64
Consensus pattern (26 bp):
TTTACATTTTTTTAATATTCATCTTC
Found at i:49147 original size:14 final size:13
Alignment explanation
Indices: 49116--49175 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
49106 GATATTTAAA
*
49116 TTTTAATAATTAACT
1 TTTTAAT-ATT-ATT
*
49131 TTTTAATCTCTATT
1 TTTTAATAT-TATT
*
49145 TTTTAAAATTATT
1 TTTTAATATTATT
*
49158 TTTTAATA-AATT
1 TTTTAATATTATT
49170 TTTTAA
1 TTTTAA
49176 ATTTCACGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
12 9 0.24
13 11 0.29
14 10 0.26
15 8 0.21
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTTAATATTATT
Found at i:49573 original size:12 final size:12
Alignment explanation
Indices: 49556--49580 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
49546 GTAAATTGCT
49556 TTTTTTTTTTTA
1 TTTTTTTTTTTA
49568 TTTTTTTTTTTA
1 TTTTTTTTTTTA
49580 T
1 T
49581 CTTTGTAGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTTTTTTTTTA
Found at i:50766 original size:29 final size:30
Alignment explanation
Indices: 50719--50818 Score: 91
Period size: 29 Copynumber: 3.3 Consensus size: 30
50709 TGTTATCATC
*
50719 TTATATTATGTTT-TTATATTTGTAA-TATAT
1 TTATATTAT-TTTATTATA-TTATAATTATAT
50749 TTATA-TATTTTATTATATTATAATTATAT
1 TTATATTATTTTATTATATTATAATTATAT
* *
50778 TTAAATTATTTTATATTTAATTAATAATTCATA-
1 TTATATTATTTTAT-TAT-ATT-ATAATT-ATAT
50811 TTATATTA
1 TTATATTA
50819 ATAAATATAA
Statistics
Matches: 59, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
28 8 0.14
29 17 0.29
30 13 0.22
31 2 0.03
32 3 0.05
33 13 0.22
34 3 0.05
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.60
Consensus pattern (30 bp):
TTATATTATTTTATTATATTATAATTATAT
Found at i:50776 original size:11 final size:11
Alignment explanation
Indices: 50760--50815 Score: 53
Period size: 11 Copynumber: 5.0 Consensus size: 11
50750 TATATATTTT
50760 ATTATATTATA
1 ATTATATTATA
50771 ATTATATT-TAA
1 ATTATATTAT-A
*
50782 ATTATTTTATA
1 ATTATATTATA
*
50793 TTTA-ATTAATA
1 ATTATATT-ATA
50804 ATTCATATTATA
1 ATT-ATATTATA
50816 TTAATAAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
10 3 0.08
11 25 0.69
12 5 0.14
13 3 0.08
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (11 bp):
ATTATATTATA
Found at i:50778 original size:21 final size:20
Alignment explanation
Indices: 50732--50779 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 20
50722 TATTATGTTT
50732 TTATATTTGTAATATATTTA
1 TTATATTTGTAATATATTTA
*
50752 -TATATTT-TATTATATTATAA
1 TTATATTTGTAATATATT-T-A
50772 TTATATTT
1 TTATATTT
50780 AAATTATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 8 0.33
19 8 0.33
20 1 0.04
21 7 0.29
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
TTATATTTGTAATATATTTA
Found at i:50791 original size:22 final size:21
Alignment explanation
Indices: 50752--50815 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 21
50742 AATATATTTA
*
50752 TATATTTTATTATATTATAAT
1 TATATTTAATTATATTATAAT
* *
50773 TATATTTAAATTATTTTATATT
1 TATATTT-AATTATATTATAAT
50795 TA-ATTAATAATTCATATTATA
1 TATATT--TAATT-ATATTATA
50816 TTAATAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
21 10 0.29
22 17 0.49
23 8 0.23
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
TATATTTAATTATATTATAAT
Found at i:51983 original size:21 final size:22
Alignment explanation
Indices: 51959--52004 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
51949 AAATATGATT
51959 TTTTAAAAAAT-ATTATTATTA
1 TTTTAAAAAATAATTATTATTA
* *
51980 TTTTAATAAATAATTATTTTTA
1 TTTTAAAAAATAATTATTATTA
52002 TTT
1 TTT
52005 AATTTTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTTAAAAAATAATTATTATTA
Found at i:51983 original size:22 final size:23
Alignment explanation
Indices: 51958--52004 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
51948 TAAATATGAT
51958 TTTTTAAAAAAT-ATTATTATTA
1 TTTTTAAAAAATAATTATTATTA
* *
51980 -TTTTAATAAATAATTATTTTTA
1 TTTTTAAAAAATAATTATTATTA
52002 TTT
1 TTT
52005 AATTTTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
21 10 0.48
22 9 0.43
23 2 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTTTAAAAAATAATTATTATTA
Found at i:54272 original size:17 final size:16
Alignment explanation
Indices: 54233--54272 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
54223 TTTTAAATAT
54233 ATTATTTAAAAATAAA
1 ATTATTTAAAAATAAA
*
54249 ATAATTTATAAAATAAA
1 ATTATTTA-AAAATAAA
*
54266 TTTATTT
1 ATTATTT
54273 TTTTAAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTATTTAAAAATAAA
Found at i:57911 original size:2 final size:2
Alignment explanation
Indices: 57904--57940 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
57894 TCTAAAGGTG
57904 TA TA TA 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 TA TA TA T
57941 GTATTTTGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:73916 original size:2 final size:2
Alignment explanation
Indices: 73911--73968 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
73901 CTCTATTTTC
73911 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
73953 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
73969 AAGAAGGAGG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:79669 original size:38 final size:40
Alignment explanation
Indices: 79616--79692 Score: 97
Period size: 38 Copynumber: 2.0 Consensus size: 40
79606 AAATGTATAT
* * *
79616 TATAATATAATTTTTT-TAATTTTAATCAAATATTAAATTA
1 TATAATATAATTTTTTAT-ATTATAATAAAATAATAAATTA
79656 TATAAT-TAA-TTTTTATATTATAATAAAATAATAAATT
1 TATAATATAATTTTTTATATTATAATAAAATAATAAATT
79693 TAATCTTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
38 23 0.70
39 4 0.12
40 6 0.18
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (40 bp):
TATAATATAATTTTTTATATTATAATAAAATAATAAATTA
Found at i:80149 original size:6 final size:6
Alignment explanation
Indices: 80138--80167 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
80128 GCTTATTCGA
80138 TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC
1 TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC
80168 ATCTGCAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (6 bp):
TCTTCC
Found at i:83974 original size:16 final size:17
Alignment explanation
Indices: 83943--83987 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
83933 GTTTTCAATG
*
83943 AATTTATAAAATATAAAT
1 AATTTA-AAAAAATAAAT
83961 -ATTTAAAAAAATAAAT
1 AATTTAAAAAAATAAAT
*
83977 AATATAAAAAA
1 AATTTAAAAAA
83988 CATAGCATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 10 0.42
17 14 0.58
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AATTTAAAAAAATAAAT
Found at i:85974 original size:3 final size:3
Alignment explanation
Indices: 85966--85995 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
85956 TATATGTGTC
85966 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
85996 GTTAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:92068 original size:20 final size:20
Alignment explanation
Indices: 92043--92094 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
92033 ATATGAAATG
92043 AATATAAAATATAATTTTAA
1 AATATAAAATATAATTTTAA
*
92063 AATATATAAA-AAAATTTTAA
1 AATATA-AAATATAATTTTAA
*
92083 AA-ATCAAATATA
1 AATATAAAATATA
92095 GTGTATATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 3 0.11
19 4 0.15
20 17 0.63
21 3 0.11
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (20 bp):
AATATAAAATATAATTTTAA
Found at i:93119 original size:1 final size:1
Alignment explanation
Indices: 93115--93148 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
93105 GGGTTTTGCG
* *
93115 CCCCCTCCCCCCCCCCCCCACCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
93149 TTTTTTTTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.03, C:0.94, G:0.00, T:0.03
Consensus pattern (1 bp):
C
Found at i:93138 original size:14 final size:14
Alignment explanation
Indices: 93115--93147 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
93105 GGGTTTTGCG
*
93115 CCCCCTCCCCCCCC
1 CCCCCACCCCCCCC
93129 CCCCCACCCCCCCC
1 CCCCCACCCCCCCC
93143 CCCCC
1 CCCCC
93148 CTTTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.03, C:0.94, G:0.00, T:0.03
Consensus pattern (14 bp):
CCCCCACCCCCCCC
Found at i:99697 original size:30 final size:30
Alignment explanation
Indices: 99631--99704 Score: 107
Period size: 29 Copynumber: 2.5 Consensus size: 30
99621 ATAACTTTAT
*
99631 TTAAATAAGTTTTTATATTTTTATTATACA
1 TTAAATAAATTTTTATATTTTTATTATACA
*
99661 -TAAATAAATTTTTAT-TTTTTATTCTACA
1 TTAAATAAATTTTTATATTTTTATTATACA
99689 CTTAAATAAATTTTTA
1 -TTAAATAAATTTTTA
99705 ACTTTTAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 12 0.30
29 14 0.35
30 14 0.35
ACGTcount: A:0.38, C:0.05, G:0.01, T:0.55
Consensus pattern (30 bp):
TTAAATAAATTTTTATATTTTTATTATACA
Found at i:99711 original size:30 final size:29
Alignment explanation
Indices: 99631--99711 Score: 101
Period size: 30 Copynumber: 2.8 Consensus size: 29
99621 ATAACTTTAT
*
99631 TTAAATAAGTTTTTATATTTTTATTATACA
1 TTAAATAAATTTTTA-ATTTTTATTATACA
* *
99661 -TAAATAAATTTTTATTTTTTATTCTACA
1 TTAAATAAATTTTTAATTTTTATTATACA
*
99689 CTTAAATAAATTTTTAACTTTTA
1 -TTAAATAAATTTTTAATTTTTA
99712 ATTTTTATTC
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
28 12 0.27
29 13 0.30
30 19 0.43
ACGTcount: A:0.37, C:0.06, G:0.01, T:0.56
Consensus pattern (29 bp):
TTAAATAAATTTTTAATTTTTATTATACA
Found at i:101446 original size:17 final size:17
Alignment explanation
Indices: 101424--101480 Score: 69
Period size: 17 Copynumber: 3.2 Consensus size: 17
101414 ATTATTTAAA
101424 AAATTTAAATAAAAAAT
1 AAATTTAAATAAAAAAT
101441 AAATTTAAATAAAAAAATT
1 AAATTTAAAT-AAAAAA-T
** *
101460 AAATTTATTTATAAAAT
1 AAATTTAAATAAAAAAT
101477 AAAT
1 AAAT
101481 CTGATTTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
17 15 0.43
18 11 0.31
19 9 0.26
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AAATTTAAATAAAAAAT
Found at i:101475 original size:19 final size:19
Alignment explanation
Indices: 101424--101466 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
101414 ATTATTTAAA
101424 AAATTT-AA-ATAAAAAAT
1 AAATTTAAATATAAAAAAT
101441 AAATTTAAATA-AAAAAATT
1 AAATTTAAATATAAAAAA-T
101460 AAATTTA
1 AAATTTA
101467 TTTATAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 6 0.26
18 8 0.35
19 9 0.39
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATTTAAATATAAAAAAT
Found at i:102359 original size:20 final size:20
Alignment explanation
Indices: 102334--102408 Score: 73
Period size: 20 Copynumber: 3.6 Consensus size: 20
102324 TTAAAATATT
102334 ATATATTTTTATAATTTTTA
1 ATATATTTTTATAATTTTTA
* *
102354 ATATATTTATATTAATTATT-
1 ATATATTTTTA-TAATTTTTA
*
102374 ATTTATTTTTATATTATATTTTA
1 ATATATTTTTATA--AT-TTTTA
102397 A-ATATTTTTATA
1 ATATATTTTTATA
102409 TTATTTATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
19 2 0.05
20 19 0.43
21 9 0.20
22 13 0.30
23 1 0.02
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
ATATATTTTTATAATTTTTA
Found at i:102385 original size:10 final size:10
Alignment explanation
Indices: 102332--102414 Score: 51
Period size: 10 Copynumber: 8.0 Consensus size: 10
102322 ATTTAAAATA
*
102332 TTATATATTT
1 TTATTTATTT
*
102342 TTA-TAATTT
1 TTATTTATTT
*
102351 TTAATATATTT
1 TT-ATTTATTT
* * *
102362 ATATTAATTA
1 TTATTTATTT
102372 TTATTTATTT
1 TTATTTATTT
102382 TTATATTATATT
1 TTAT-TTAT-TT
**
102394 TTAAATATTT
1 TTATTTATTT
102404 TTATATTATTT
1 TTAT-TTATTT
102415 ATATGATGTA
Statistics
Matches: 53, Mismatches: 15, Indels: 9
0.69 0.19 0.12
Matches are distributed among these distances:
9 6 0.11
10 25 0.47
11 17 0.32
12 5 0.09
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
TTATTTATTT
Found at i:102385 original size:22 final size:22
Alignment explanation
Indices: 102330--102416 Score: 76
Period size: 22 Copynumber: 4.1 Consensus size: 22
102320 AAATTTAAAA
*
102330 TATTATATA-TTTT-TA-TAAT
1 TATTAAATATTTTTATATTAAT
* *
102349 T-TTTAATATATTTATATTAAT
1 TATTAAATATTTTTATATTAAT
**
102370 TATTATTTATTTTTATATTATAT
1 TATTAAATATTTTTATATTA-AT
*
102393 T-TTAAATATTTTTATATTATT
1 TATTAAATATTTTTATATTAAT
102414 TAT
1 TAT
102417 ATGATGTAAT
Statistics
Matches: 52, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
18 5 0.10
19 4 0.08
20 2 0.04
21 7 0.13
22 31 0.60
23 3 0.06
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
TATTAAATATTTTTATATTAAT
Found at i:102733 original size:18 final size:18
Alignment explanation
Indices: 102696--102764 Score: 67
Period size: 18 Copynumber: 4.1 Consensus size: 18
102686 TATTTTTATT
102696 AATTATATAAATATAATAA
1 AATTAT-TAAATATAATAA
* *
102715 AATTATTAAATTTATTAA
1 AATTATTAAATATAATAA
102733 AATTA-TAAA-AT-A-AA
1 AATTATTAAATATAATAA
*
102747 AATGA-TAAATATAATAA
1 AATTATTAAATATAATAA
102764 A
1 A
102765 CATATTTTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
14 10 0.24
15 2 0.05
16 2 0.05
17 7 0.17
18 15 0.36
19 6 0.14
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (18 bp):
AATTATTAAATATAATAA
Found at i:102799 original size:11 final size:11
Alignment explanation
Indices: 102769--102826 Score: 53
Period size: 12 Copynumber: 5.0 Consensus size: 11
102759 AATAAACATA
*
102769 TTTTATAATAT
1 TTTTATATTAT
102780 TTATTATATTAT
1 TT-TTATATTAT
102792 TTTTATATTTAT
1 TTTTATA-TTAT
**
102804 TAAATATATTAT
1 T-TTTATATTAT
*
102816 ATTTATATTAT
1 TTTTATATTAT
102827 AATTTTATGT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
11 15 0.39
12 19 0.50
13 4 0.11
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TTTTATATTAT
Found at i:103222 original size:17 final size:17
Alignment explanation
Indices: 103202--103247 Score: 67
Period size: 17 Copynumber: 2.7 Consensus size: 17
103192 TTTGAAAATT
103202 AAAAATTTTAATTTATA
1 AAAAATTTTAATTTATA
103219 AAAATATTTTAA-TTATA
1 AAAA-ATTTTAATTTATA
*
103236 AAATATTTTAAT
1 AAAAATTTTAAT
103248 ATTAAGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 7 0.27
17 12 0.46
18 7 0.27
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AAAAATTTTAATTTATA
Found at i:103229 original size:18 final size:17
Alignment explanation
Indices: 103201--103247 Score: 71
Period size: 16 Copynumber: 2.8 Consensus size: 17
103191 TTTTGAAAAT
103201 TAAAA-ATTTTAATTTA
1 TAAAATATTTTAATTTA
103217 TAAAAATATTTTAA-TTA
1 T-AAAATATTTTAATTTA
103234 TAAAATATTTTAAT
1 TAAAATATTTTAAT
103248 ATTAAGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 13 0.46
17 8 0.29
18 7 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAAAATATTTTAATTTA
Found at i:104268 original size:19 final size:19
Alignment explanation
Indices: 104244--104302 Score: 72
Period size: 17 Copynumber: 3.3 Consensus size: 19
104234 TATGTAATTA
104244 TTAATTAAATAATATTATT
1 TTAATTAAATAATATTATT
*
104263 TTAATTAAATAA-A-AATT
1 TTAATTAAATAATATTATT
*
104280 TTCA--AAATAATATTATT
1 TTAATTAAATAATATTATT
104297 TTAATT
1 TTAATT
104303 TTATAAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
15 6 0.19
16 1 0.03
17 12 0.38
18 1 0.03
19 12 0.38
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
TTAATTAAATAATATTATT
Found at i:104326 original size:34 final size:35
Alignment explanation
Indices: 104239--104326 Score: 101
Period size: 34 Copynumber: 2.5 Consensus size: 35
104229 AAATATATGT
104239 AATTATTAATTAAATAATATTATTTTAATTAAATAAA
1 AATTATTAATT--ATAATATTATTTTAATTAAATAAA
* **
104276 AATT-TTCAA-AATAATATTATTTTAATTTTATAAA
1 AATTATT-AATTATAATATTATTTTAATTAAATAAA
104310 AATTATTAATTA-AATAT
1 AATTATTAATTATAATAT
104327 AAAATTTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
34 33 0.75
35 3 0.07
36 2 0.05
37 6 0.14
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (35 bp):
AATTATTAATTATAATATTATTTTAATTAAATAAA
Found at i:106568 original size:10 final size:11
Alignment explanation
Indices: 106516--106569 Score: 58
Period size: 10 Copynumber: 4.9 Consensus size: 11
106506 AGATTATTTA
106516 TTTAATTTAAT
1 TTTAATTTAAT
*
106527 TTTGA-TTAAT
1 TTTAATTTAAT
*
106537 TTTAATATAAAT
1 TTTAAT-TTAAT
106549 TTTAAATTTAA-
1 TTT-AATTTAAT
106560 TTTAATTTAA
1 TTTAATTTAA
106570 AATATTATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
10 16 0.44
11 7 0.19
12 10 0.28
13 3 0.08
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (11 bp):
TTTAATTTAAT
Found at i:106936 original size:19 final size:20
Alignment explanation
Indices: 106912--106956 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 20
106902 TTAAATAATT
106912 TATATTTTATAAATTT-TAA
1 TATATTTTATAAATTTATAA
*
106931 TATA-TTTATATATTTATAA
1 TATATTTTATAAATTTATAA
*
106950 TTTATTT
1 TATATTT
106957 ATATTATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 10 0.45
19 10 0.45
20 2 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TATATTTTATAAATTTATAA
Found at i:106937 original size:25 final size:26
Alignment explanation
Indices: 106900--106949 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
106890 TCTTTTTTAC
106900 TTTTAAATAATTTATAT-TTTATAAA
1 TTTTAAATAATTTATATATTTATAAA
106925 TTTT-AATATATTTATATATTTATAA
1 TTTTAAATA-ATTTATATATTTATAA
106950 TTTATTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 4 0.17
25 12 0.52
26 7 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
TTTTAAATAATTTATATATTTATAAA
Found at i:106957 original size:19 final size:18
Alignment explanation
Indices: 106912--106998 Score: 70
Period size: 19 Copynumber: 4.6 Consensus size: 18
106902 TTAAATAATT
*
106912 TATATTTTATAAATTTTAA
1 TATA-TTTATATATTTTAA
106931 TATATTTATATATTTATAA
1 TATATTTATATATTT-TAA
* **
106950 TTTATTTATATTATTTTTT
1 TATATTTATA-TATTTTAA
106969 TAATATTATATTATATTTTAA
1 T-ATATT-TA-TATATTTTAA
106990 T-T-TTTATAT
1 TATATTTATAT
106999 TATATTTATC
Statistics
Matches: 56, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
16 3 0.05
17 2 0.04
18 12 0.21
19 19 0.34
20 9 0.16
21 9 0.16
22 2 0.04
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TATATTTATATATTTTAA
Found at i:106959 original size:25 final size:25
Alignment explanation
Indices: 106909--106986 Score: 83
Period size: 25 Copynumber: 3.2 Consensus size: 25
106899 CTTTTAAATA
*
106909 ATTTATATTTTATAAATTT-TAATAT
1 ATTTATATTTTAT-AATTTATATTAT
106934 ATTTATATATTTATAATTTAT-TTAT
1 ATTTATAT-TTTATAATTTATATTAT
*
106959 A-TTAT-TTTTTTAATATTATATTAT
1 ATTTATATTTTATAAT-TTATATTAT
106983 ATTT
1 ATTT
106987 TAATTTTTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
22 7 0.15
23 5 0.11
24 9 0.20
25 19 0.41
26 6 0.13
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (25 bp):
ATTTATATTTTATAATTTATATTAT
Found at i:106963 original size:24 final size:24
Alignment explanation
Indices: 106931--107007 Score: 70
Period size: 25 Copynumber: 3.1 Consensus size: 24
106921 TAAATTTTAA
*
106931 TATATTTATATATTTATAATTTATT
1 TATA-TTATATATTTTTAATTTATT
106956 TATATTAT-T-TTTTTAATATTATAT
1 TATATTATATATTTTTAAT-TTAT-T
*
106980 TATATTTTA-ATTTTTATATTATATT
1 TATATTATATATTTTTA-ATT-TATT
107005 TAT
1 TAT
107008 CTCGTATTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
22 7 0.16
23 5 0.11
24 12 0.27
25 15 0.34
26 5 0.11
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (24 bp):
TATATTATATATTTTTAATTTATT
Done.