Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1110
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: 30442
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:2649 original size:18 final size:18
Alignment explanation
Indices: 2626--2690 Score: 77
Period size: 20 Copynumber: 3.8 Consensus size: 18
2616 GTAGCTTAAA
2626 TTGTATCGATACAACACT
1 TTGTATCGATACAACACT
2644 TTGTATCGAT---ACA--
1 TTGTATCGATACAACACT
2657 TTGTATCGATACAACACTT
1 TTGTATCGATACAACAC-T
2676 TATGTATCGATACAA
1 T-TGTATCGATACAA
2691 ATCGTTGAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
13 10 0.25
15 3 0.08
16 3 0.08
18 10 0.25
19 1 0.03
20 13 0.32
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.35
Consensus pattern (18 bp):
TTGTATCGATACAACACT
Found at i:2662 original size:13 final size:13
Alignment explanation
Indices: 2644--2669 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2634 ATACAACACT
2644 TTGTATCGATACA
1 TTGTATCGATACA
2657 TTGTATCGATACA
1 TTGTATCGATACA
2670 ACACTTTATG
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2663 original size:31 final size:33
Alignment explanation
Indices: 2625--2689 Score: 116
Period size: 31 Copynumber: 2.0 Consensus size: 33
2615 AGTAGCTTAA
2625 ATTGTATCGATACAACAC-TT-TGTATCGATAC
1 ATTGTATCGATACAACACTTTATGTATCGATAC
2656 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACACTTTATGTATCGATAC
2689 A
1 A
2690 AATCGTTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 18 0.56
32 2 0.06
33 12 0.38
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.35
Consensus pattern (33 bp):
ATTGTATCGATACAACACTTTATGTATCGATAC
Found at i:4621 original size:8 final size:7
Alignment explanation
Indices: 4606--4673 Score: 54
Period size: 7 Copynumber: 9.7 Consensus size: 7
4596 CATGAATAAT
4606 TTATATA
1 TTATATA
4613 TTCATATA
1 TT-ATATA
*
4621 TTTTTATA
1 -TTATATA
4629 TTATATA
1 TTATATA
4636 -TATAT-
1 TTATATA
4641 TTATATCA
1 TTATAT-A
4649 -TATTATA
1 TTA-TATA
*
4656 TTATATT
1 TTATATA
4663 TTATAT-
1 TTATATA
4669 TTATA
1 TTATA
4674 AAATTTTTAA
Statistics
Matches: 51, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
6 15 0.29
7 20 0.39
8 14 0.27
9 2 0.04
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (7 bp):
TTATATA
Found at i:4634 original size:5 final size:5
Alignment explanation
Indices: 4624--4729 Score: 67
Period size: 5 Copynumber: 20.8 Consensus size: 5
4614 TCATATATTT
*
4624 TTATA TTATA TATATA TTTATA TCATA TTATA TTATA TTTTATA TT-TA
1 TTATA TTATA T-TATA -TTATA TTATA TTATA TTATA --TTATA TTATA
* * * * * *
4672 TAAAA TT-T- TTAAA TATATA TTATA TTATA TTACA TCATA TTTTTA TTAT-
1 TTATA TTATA TTATA T-TATA TTATA TTATA TTATA TTATA -TTATA TTATA
4721 TTATA TTAT
1 TTATA TTAT
4730 TTTAATATAA
Statistics
Matches: 77, Mismatches: 14, Indels: 20
0.69 0.13 0.18
Matches are distributed among these distances:
3 2 0.03
4 7 0.09
5 47 0.61
6 15 0.19
7 6 0.08
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (5 bp):
TTATA
Found at i:4638 original size:17 final size:17
Alignment explanation
Indices: 4616--4737 Score: 74
Period size: 17 Copynumber: 6.8 Consensus size: 17
4606 TTATATATTC
4616 ATATATTTTTATATTAT
1 ATATATTTTTATATTAT
*
4633 ATATATATTTATATCATATT
1 ATATATTTTTATAT--TA-T
4653 ATATTATATTTTATATT-T
1 ATA-TAT-TTTTATATTAT
*
4671 ATAAAATTTTTA-A--AT
1 AT-ATATTTTTATATTAT
*
4686 ATATATTATATTATATTAC
1 ATATATT-T-TTATATTAT
4705 ATCATATTTTTATTATT-T
1 AT-ATATTTTTA-TATTAT
*
4723 ATATTATTTTAATAT
1 ATA-TATTTTTATAT
4738 AACTATATCT
Statistics
Matches: 83, Mismatches: 7, Indels: 30
0.69 0.06 0.25
Matches are distributed among these distances:
14 4 0.05
15 4 0.05
16 4 0.05
17 23 0.28
18 17 0.20
19 11 0.13
20 10 0.12
21 3 0.04
22 7 0.08
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (17 bp):
ATATATTTTTATATTAT
Found at i:4663 original size:40 final size:40
Alignment explanation
Indices: 4617--4702 Score: 106
Period size: 40 Copynumber: 2.1 Consensus size: 40
4607 TATATATTCA
*
4617 TATATTTTTATA-TTATATATATATTT-ATATCATATTATAT
1 TATATTTTTATATTTATA-AAATATTTAATAT-ATATTATAT
*
4657 TATA-TTTTATATTTATAAAATTTTTAAATATATATTATAT
1 TATATTTTTATATTTATAAAATATTT-AATATATATTATAT
4697 TATATT
1 TATATT
4703 ACATCATATT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
39 13 0.32
40 22 0.55
41 5 0.12
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (40 bp):
TATATTTTTATATTTATAAAATATTTAATATATATTATAT
Found at i:4673 original size:45 final size:48
Alignment explanation
Indices: 4619--4729 Score: 113
Period size: 50 Copynumber: 2.3 Consensus size: 48
4609 TATATTCATA
* * *
4619 TATT-TTTATATTATATATATAT-TTATATCATATTATATTATA-TTT
1 TATTATTTATATTATAAATATATATTATATCATATTACATCATATTTT
* *
4664 TA-TATTTATAAAATTTTTAAATATATATTATATTATATTACATCATATTTT
1 TATTATTTAT---A-TTATAAATATATATTATATCATATTACATCATATTTT
4715 TATTATTTATATTAT
1 TATTATTTATATTAT
4730 TTTAATATAA
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
44 1 0.02
45 7 0.13
48 4 0.08
49 11 0.21
50 17 0.33
51 5 0.10
52 7 0.13
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (48 bp):
TATTATTTATATTATAAATATATATTATATCATATTACATCATATTTT
Found at i:5085 original size:16 final size:16
Alignment explanation
Indices: 5061--5105 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
5051 ATTATTTTAT
*
5061 TAAAT-TTTTTAATTA
1 TAAATATTTTTAAATA
5076 TAAATATTTTTAAATA
1 TAAATATTTTTAAATA
*
5092 TAAGTATTTTTAAA
1 TAAATATTTTTAAA
5106 AAAAAGTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 5 0.19
16 22 0.81
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
TAAATATTTTTAAATA
Found at i:5241 original size:20 final size:21
Alignment explanation
Indices: 5199--5242 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
5189 GTGATTAAGA
5199 AAAAATATAAATAATATTCTTT
1 AAAAATATAAAT-ATATTCTTT
* *
5221 AAAAATATTAAT-TATTTTTT
1 AAAAATATAAATATATTCTTT
5241 AA
1 AA
5243 TACAAAATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 9 0.45
22 11 0.55
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
AAAAATATAAATATATTCTTT
Found at i:5574 original size:23 final size:23
Alignment explanation
Indices: 5544--5589 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
5534 ATTTTAAATT
*
5544 AAAAAATAATAAT-TATTTATAA
1 AAAAAATAATAATAAATTTATAA
*
5566 AAAATAATATTAATAAATTTATAA
1 AAAA-AATAATAATAAATTTATAA
5590 TTAAATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 8 0.40
24 8 0.40
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
AAAAAATAATAATAAATTTATAA
Found at i:6298 original size:23 final size:23
Alignment explanation
Indices: 6241--6308 Score: 88
Period size: 23 Copynumber: 3.0 Consensus size: 23
6231 ATAAAATTTT
* *
6241 AATTTTTAA-TAAATT-ATTCAA
1 AATTTTAAAGTAAATTAATTTAA
6262 AA-TTTAAAGTTAAATTAATTTAA
1 AATTTTAAAG-TAAATTAATTTAA
6285 AATTTTAAAGTAAATTAATTTAA
1 AATTTTAAAGTAAATTAATTTAA
6308 A
1 A
6309 TTTAGCCTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
20 5 0.12
21 2 0.05
22 6 0.15
23 21 0.51
24 7 0.17
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.44
Consensus pattern (23 bp):
AATTTTAAAGTAAATTAATTTAA
Found at i:6370 original size:23 final size:23
Alignment explanation
Indices: 6338--6384 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
6328 TTTTACCTCC
6338 ATTTAATCTCCTCCATGATTTTA
1 ATTTAATCTCCTCCATGATTTTA
*
6361 ATTTAGTCTCCTCCATGATTTTA
1 ATTTAATCTCCTCCATGATTTTA
6384 A
1 A
6385 CACTATCTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.21, G:0.06, T:0.47
Consensus pattern (23 bp):
ATTTAATCTCCTCCATGATTTTA
Found at i:7372 original size:2 final size:2
Alignment explanation
Indices: 7365--7390 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
7355 CCAAAAGAAA
7365 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
7391 TTGAGGAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8850 original size:18 final size:19
Alignment explanation
Indices: 8827--8862 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
8817 TTAAAAAATT
8827 TAAATTAAT-TTTGATTAC
1 TAAATTAATATTTGATTAC
*
8845 TAAATTGATATTTGATTA
1 TAAATTAATATTTGATTA
8863 ATTTCAAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (19 bp):
TAAATTAATATTTGATTAC
Found at i:9655 original size:39 final size:39
Alignment explanation
Indices: 9610--9685 Score: 93
Period size: 39 Copynumber: 1.9 Consensus size: 39
9600 AAATAATAAA
*
9610 TTAAAA-TATGTATAT-TTAAAATAAATAATTATAAAATAT
1 TTAAAATTATATATATGTT-AAAT-AATAATTATAAAATAT
* *
9649 TTAAAATTATATTTATGTTAAATAATAATTATTAAAT
1 TTAAAATTATATATATGTTAAATAATAATTATAAAAT
9686 TTATATTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 19 0.59
40 11 0.34
41 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (39 bp):
TTAAAATTATATATATGTTAAATAATAATTATAAAATAT
Found at i:9684 original size:31 final size:31
Alignment explanation
Indices: 9640--9718 Score: 108
Period size: 31 Copynumber: 2.5 Consensus size: 31
9630 ATAAATAATT
9640 ATAAAA-TATTTAAAATTATATTTATGTT-AA
1 ATAAAATTA-TTAAAATTATATTTATGTTAAA
*
9670 ATAATAATTATTAAATTTATATTTATGTTAAA
1 ATAA-AATTATTAAAATTATATTTATGTTAAA
*
9702 ATAAAATTAATAAAATT
1 ATAAAATTATTAAAATT
9719 TTTATTTTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
30 4 0.09
31 31 0.72
32 8 0.19
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.46
Consensus pattern (31 bp):
ATAAAATTATTAAAATTATATTTATGTTAAA
Found at i:9718 original size:32 final size:31
Alignment explanation
Indices: 9650--9725 Score: 102
Period size: 32 Copynumber: 2.5 Consensus size: 31
9640 ATAAAATATT
9650 TAAAA-TTATATTTATGTTAAATAATAATTA
1 TAAAATTTATATTTATGTTAAATAATAATTA
*
9680 TTAAATTTATATTTATGTTAAAATAA-AATTAA
1 TAAAATTTATATTTATGTT-AAATAATAATT-A
*
9712 TAAAATTTTTATTT
1 TAAAATTTATATTT
9726 TATATTATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
30 4 0.10
31 17 0.43
32 19 0.47
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (31 bp):
TAAAATTTATATTTATGTTAAATAATAATTA
Found at i:11802 original size:67 final size:67
Alignment explanation
Indices: 11637--11827 Score: 215
Period size: 67 Copynumber: 2.8 Consensus size: 67
11627 TTTTTTTTTT
* *
11637 TTTTTCTTTTTAAATTGAACTCAATCTTTTTCTAAGGTGAGTTAAGCTTAAGGATTGCTGTCTAG
1 TTTTTCTTTTT-AATCGAACTCAATCTTTTTCTAAGGTGAGTCAAGCTTAAGGATTGCTGTCTAG
11702 ATC
65 ATC
* * * * * * *
11705 TTTTTCTTATTTAGTCAAACTCAATTTTTTTTTAAAGG-GAGTCGAGCTTAA-GATTGTTGTTTA
1 TTTTTCTT-TTTAATCGAACTCAATCTTTTTCT-AAGGTGAGTCAAGCTTAAGGATTGCTGTCTA
*
11768 GGTC
64 GATC
* * *
11772 TTTTTCTTTTTCAATCGAACTTAGTCTTTTTCTAAGGTGAGTCAAGCTTACGGATT
1 TTTTTCTTTTT-AATCGAACTCAATCTTTTTCTAAGGTGAGTCAAGCTTAAGGATT
11828 TCCTTTCAGT
Statistics
Matches: 100, Mismatches: 18, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
66 7 0.07
67 47 0.47
68 39 0.39
69 7 0.07
ACGTcount: A:0.24, C:0.13, G:0.17, T:0.47
Consensus pattern (67 bp):
TTTTTCTTTTTAATCGAACTCAATCTTTTTCTAAGGTGAGTCAAGCTTAAGGATTGCTGTCTAGA
TC
Found at i:17353 original size:12 final size:14
Alignment explanation
Indices: 17336--17469 Score: 63
Period size: 12 Copynumber: 9.9 Consensus size: 14
17326 TATTAGAATT
17336 ATATAA-ATA-AAA
1 ATATAATATATAAA
*
17348 ATATAATATATAAT
1 ATATAATATATAAA
*
17362 ATATAATATAT--T
1 ATATAATATATAAA
17374 ATATAATATA-AAA
1 ATATAATATATAAA
* *
17387 TATATTATAAATAAA
1 -ATATAATATATAAA
* *
17402 AAATATATAAATAAA
1 ATATA-ATATATAAA
*
17417 TTATTAA-AT-TAAA
1 ATA-TAATATATAAA
* *
17430 CTAT-ATAT-TAAT
1 ATATAATATATAAA
17442 ATAT-ATATAATAGAA
1 ATATAATAT-ATA-AA
*
17457 ATAGAATATATAA
1 ATATAATATATAA
17470 TAGAATTAAT
Statistics
Matches: 95, Mismatches: 14, Indels: 24
0.71 0.11 0.18
Matches are distributed among these distances:
11 1 0.01
12 30 0.32
13 9 0.09
14 28 0.29
15 21 0.22
16 6 0.06
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (14 bp):
ATATAATATATAAA
Found at i:17359 original size:19 final size:20
Alignment explanation
Indices: 17335--17417 Score: 88
Period size: 19 Copynumber: 4.5 Consensus size: 20
17325 GTATTAGAAT
17335 TATATAAATA-AAAATATAA
1 TATATAAATATAAAATATAA
* *
17354 TATAT-AATATATAATATAT
1 TATATAAATATAAAATATAA
17373 TATAT-AATATAAAATAT-A
1 TATATAAATATAAAATATAA
*
17391 T-TATAAATAAAAAATAT-A
1 TATATAAATATAAAATATAA
*
17409 TAAATAAAT
1 TATATAAAT
17418 TATTAAATTA
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
17 3 0.05
18 18 0.33
19 34 0.62
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
TATATAAATATAAAATATAA
Found at i:17360 original size:7 final size:7
Alignment explanation
Indices: 17335--17471 Score: 72
Period size: 7 Copynumber: 21.3 Consensus size: 7
17325 GTATTAGAAT
17335 TATATAA
1 TATATAA
17342 -ATA-AA
1 TATATAA
*
17347 AATATAA
1 TATATAA
17354 TATATAA
1 TATATAA
17361 TATATAA
1 TATATAA
17368 TATAT--
1 TATATAA
17373 TATATAA
1 TATATAA
17380 TATA-AA
1 TATATAA
*
17386 -ATATAT
1 TATATAA
17392 TATA-AA
1 TATATAA
* *
17398 TAAAAAA
1 TATATAA
17405 TATATAA
1 TATATAA
17412 -ATA-AA
1 TATATAA
17417 T-TATTAA
1 TATA-TAA
17424 -AT-TAA
1 TATATAA
17429 -ACTAT-A
1 TA-TATAA
17435 TAT-TAA
1 TATATAA
17441 TATAT-A
1 TATATAA
17447 TATAATAGA
1 TAT-ATA-A
* *
17456 AATAGAA
1 TATATAA
17463 TATATAA
1 TATATAA
17470 TA
1 TA
17472 GAATTAATAT
Statistics
Matches: 101, Mismatches: 10, Indels: 38
0.68 0.07 0.26
Matches are distributed among these distances:
5 19 0.19
6 27 0.27
7 50 0.50
8 2 0.02
9 3 0.03
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (7 bp):
TATATAA
Found at i:17366 original size:26 final size:26
Alignment explanation
Indices: 17335--17471 Score: 79
Period size: 27 Copynumber: 5.1 Consensus size: 26
17325 GTATTAGAAT
17335 TATATAAATAAAAATATAATATATAA
1 TATATAAATAAAAATATAATATATAA
*
17361 TATATAATATATTATATAATATAAAATAT-A
1 TATATAA-ATA--A-A-AATATAATATATAA
*
17391 T-TATAAATAAAAA-ATATATAAATAA
1 TATATAAATAAAAATATA-ATATATAA
* *
17416 -ATTATTAAATTAAACTAT-ATAT-TAATA
1 TA-TA-TAAATAAAAATATAATATAT-A-A
* *
17443 TATATATAATAGAAATAGAATATATAA
1 TATATA-AATAAAAATATAATATATAA
17470 TA
1 TA
17472 GAATTAATAT
Statistics
Matches: 84, Mismatches: 10, Indels: 33
0.66 0.08 0.26
Matches are distributed among these distances:
23 3 0.04
24 6 0.07
25 3 0.04
26 16 0.19
27 24 0.29
28 11 0.13
29 7 0.08
30 3 0.04
31 11 0.13
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (26 bp):
TATATAAATAAAAATATAATATATAA
Found at i:17531 original size:24 final size:23
Alignment explanation
Indices: 17499--17547 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
17489 TTAATTATAC
*
17499 AATATAATTAAATAATAAGAAAT
1 AATATAATTAAATAACAAGAAAT
*
17522 AATATAAATTCAATAACAAGAAAT
1 AATAT-AATTAAATAACAAGAAAT
17546 AA
1 AA
17548 GGAATTCACT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (23 bp):
AATATAATTAAATAACAAGAAAT
Found at i:17755 original size:52 final size:49
Alignment explanation
Indices: 17578--17939 Score: 288
Period size: 52 Copynumber: 7.1 Consensus size: 49
17568 ATATATGTTG
*
17578 TATATGTAAATCCTGAATTAC-TTTTAAAATAATAAAAATTAAAAATATTTT
1 TATAT-TAAAT-CTGAATTACTTTTTAAAATAATAAAAATAAAAAATA-TTT
* * * *
17629 TATATTAAATCTAAATCACTATTT-AAATAATAAAAATTAAAAATATTT
1 TATATTAAATCTGAATTACTTTTTAAAATAATAAAAATAAAAAATATTT
* *
17677 T-TATTAAATTTTTAATTA-TTATTTAAAA-AATTAAAAAACTAAAAAATATTT
1 TATATTAAA-TCTGAATTACTT-TTTAAAATAA-T-AAAAA-TAAAAAATATTT
* * *
17728 TCTATCAAATACTGAATTACTTTTTAAAA-AATGTAAAATTAAAAAATATTT
1 TATATTAAAT-CTGAATTACTTTTTAAAATAA--TAAAAATAAAAAATATTT
* * *
17779 TATAATAAATC-GTAATTACTATTTAAAATAATAAAAAATTAAAAATATTT
1 TATATTAAATCTG-AATTACTTTTTAAAATAAT-AAAAATAAAAAATATTT
* * *
17829 TATATTAAATCTTGAACTATTTTTTTAAAACAATAAAAAATAAAAAAATATTT
1 TATATTAAATC-TGAATTA-CTTTTTAAAATAAT-AAAAAT-AAAAAATATTT
* * * * * *
17882 TATATTAAATTTTAAAGTACTATTTAAAATAGTAAAAACTTTCAAAAATATTT
1 TATATTAAA-TCTGAATTACTTTTTAAAATAATAAAAA---TAAAAAATATTT
17935 TATAT
1 TATAT
17940 ATGTACTGGG
Statistics
Matches: 256, Mismatches: 33, Indels: 42
0.77 0.10 0.13
Matches are distributed among these distances:
47 8 0.03
48 15 0.06
49 34 0.13
50 53 0.21
51 48 0.19
52 54 0.21
53 42 0.16
54 2 0.01
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (49 bp):
TATATTAAATCTGAATTACTTTTTAAAATAATAAAAATAAAAAATATTT
Found at i:17757 original size:51 final size:49
Alignment explanation
Indices: 17578--17891 Score: 289
Period size: 50 Copynumber: 6.2 Consensus size: 49
17568 ATATATGTTG
*
17578 TATATGTAAATCCTGAATTAC-TTTTAAAATAAT-AAAAATTAAAAATATTTT
1 TATAT-TAAAT-CTGAATTACTTTTTAAAA-AATAAAAAATAAAAAATA-TTT
* * * * *
17629 TATATTAAATCTAAATCACTATTTAAATAAT-AAAAATTAAAAATATTT
1 TATATTAAATCTGAATTACTTTTTAAAAAATAAAAAATAAAAAATATTT
* *
17677 T-TATTAAATTTTTAATTA-TTATTTAAAAAATTAAAAAACTAAAAAATATTT
1 TATATTAAA-TCTGAATTACTT-TTTAAAAAA-TAAAAAA-TAAAAAATATTT
* * * *
17728 TCTATCAAATACTGAATTACTTTTTAAAAAATGTAAAATTAAAAAATATTT
1 TATATTAAAT-CTGAATTACTTTTTAAAAAAT-AAAAAATAAAAAATATTT
* * *
17779 TATAATAAATC-GTAATTACTATTTAAAATAATAAAAAATTAAAAATATTT
1 TATATTAAATCTG-AATTACTTTTTAAAA-AATAAAAAATAAAAAATATTT
* *
17829 TATATTAAATCTTGAACTATTTTTTTAAAACAATAAAAAATAAAAAAATATTT
1 TATATTAAATC-TGAATTA-CTTTTTAAAA-AATAAAAAAT-AAAAAATATTT
17882 TATATTAAAT
1 TATATTAAAT
17892 TTTAAAGTAC
Statistics
Matches: 219, Mismatches: 28, Indels: 30
0.79 0.10 0.11
Matches are distributed among these distances:
47 8 0.04
48 18 0.08
49 26 0.12
50 56 0.26
51 45 0.21
52 44 0.20
53 22 0.10
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (49 bp):
TATATTAAATCTGAATTACTTTTTAAAAAATAAAAAATAAAAAATATTT
Found at i:18183 original size:22 final size:23
Alignment explanation
Indices: 18132--18205 Score: 102
Period size: 22 Copynumber: 3.4 Consensus size: 23
18122 TCTCGATAAA
18132 AAGTCATATGTATATTT-GTTA-
1 AAGTCATATGTATATTTAGTTAT
18153 AAGTCATATGTATATTTAGTTAT
1 AAGTCATATGTATATTTAGTTAT
* *
18176 AA-TTATATGTACATTTAGTTAT
1 AAGTCATATGTATATTTAGTTAT
18198 -AGTCATAT
1 AAGTCATAT
18206 ATATCAATTT
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
21 18 0.38
22 27 0.57
23 2 0.04
ACGTcount: A:0.35, C:0.05, G:0.12, T:0.47
Consensus pattern (23 bp):
AAGTCATATGTATATTTAGTTAT
Found at i:18304 original size:22 final size:22
Alignment explanation
Indices: 18279--18335 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
18269 TAATTTTTTG
18279 TCATATATACATTTAATAAAAA
1 TCATATATACATTTAATAAAAA
* * * *
18301 TCATATAT-CTATTTAGTTATAG
1 TCATATATAC-ATTTAATAAAAA
18323 TCATATATACATT
1 TCATATATACATT
18336 CAATTTTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 1 0.03
22 27 0.93
23 1 0.03
ACGTcount: A:0.42, C:0.11, G:0.04, T:0.44
Consensus pattern (22 bp):
TCATATATACATTTAATAAAAA
Found at i:18496 original size:22 final size:20
Alignment explanation
Indices: 18471--18513 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
18461 TTAGTTAAAG
18471 TCATATGTACATCTATTTATAA
1 TCATATGTACAT-TATTT-TAA
*
18493 TCATATGTATATTATTTTAA
1 TCATATGTACATTATTTTAA
18513 T
1 T
18514 GAACTGACCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 4 0.20
21 5 0.25
22 11 0.55
ACGTcount: A:0.35, C:0.09, G:0.05, T:0.51
Consensus pattern (20 bp):
TCATATGTACATTATTTTAA
Found at i:18654 original size:54 final size:53
Alignment explanation
Indices: 18597--18901 Score: 190
Period size: 43 Copynumber: 6.3 Consensus size: 53
18587 ATGATTAATT
18597 TTTTTAAATAGTAATTCATGATTTAATATAAAATATTTTCAAATATTTTATTA
1 TTTTTAAATAGTAATTCATGATTTAATATAAAATATTTTCAAATATTTTATTA
* * * *
18650 TTTTTTAAATAATAATT-TTGGGTTTAATATAAAATATGTT---AT-TTTT-TTA
1 -TTTTTAAATAGTAATTCAT-GATTTAATATAAAATATTTTCAAATATTTTATTA
* * *
18699 TTTTTAAAAACTAATTCAAGATTTAAT-TAAAATA-TTTCTAAA-ACTTTTATTA
1 TTTTTAAATAGTAATTCATGATTTAATATAAAATATTTTC-AAATA-TTTTATTA
* *
18751 CTTTT-AATAGTAATTCAGGATTTAATAT-AAATATTTT----TA----ATT-
1 TTTTTAAATAGTAATTCATGATTTAATATAAAATATTTTCAAATATTTTATTA
* * * * *
18793 TTTTAAAATAATAATTTAAGATTTAATAT-GAA-A---T---AT-TTTTATTA
1 TTTTTAAATAGTAATTCATGATTTAATATAAAATATTTTCAAATATTTTATTA
* *
18837 TTTTTAAATAGTAATT-AAGATTTAATATAAAATATTTT--TAT-TTTTATTA
1 TTTTTAAATAGTAATTCATGATTTAATATAAAATATTTTCAAATATTTTATTA
*
18886 TTTTTAAATAGGAATT
1 TTTTTAAATAGTAATT
18902 TATAAAATAT
Statistics
Matches: 202, Mismatches: 24, Indels: 55
0.72 0.09 0.20
Matches are distributed among these distances:
39 1 0.00
40 1 0.00
42 4 0.02
43 40 0.20
44 16 0.08
45 1 0.00
46 2 0.01
47 7 0.03
48 23 0.11
49 28 0.14
50 5 0.02
51 29 0.14
52 11 0.05
53 1 0.00
54 33 0.16
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (53 bp):
TTTTTAAATAGTAATTCATGATTTAATATAAAATATTTTCAAATATTTTATTA
Found at i:18773 original size:51 final size:51
Alignment explanation
Indices: 18597--19274 Score: 251
Period size: 52 Copynumber: 13.9 Consensus size: 51
18587 ATGATTAATT
*
18597 TTTTTAAATAGTAATTCATGATTTAATATAAAATATTTTCAAATATTTTATTA
1 TTTTTAAATAGTAATTCAGGATTTAATATAAAATATTTT-AAA-ATTTTATTA
* ** * * *
18650 TTTTTTAAATAATAATTTTGGGTTTAATATAAAATATGTT---ATTTTTTTA
1 -TTTTTAAATAGTAATTCAGGATTTAATATAAAATATTTTAAAATTTTATTA
* * *
18699 TTTTTAAAAACTAATTCAAGATTTAAT-TAAAATATTTCTAAAACTTTTATTA
1 TTTTTAAATAGTAATTCAGGATTTAATATAAAATATTT-TAAAA-TTTTATTA
* *
18751 CTTTT-AATAGTAATTCAGGATTTAATAT-AAATATTTT-TAATTTT-TTA
1 TTTTTAAATAGTAATTCAGGATTTAATATAAAATATTTTAAAATTTTATTA
* * * *
18798 -----AAATAATAATTTAAGATTTAATATGAAATA---T----TTTTATTA
1 TTTTTAAATAGTAATTCAGGATTTAATATAAAATATTTTAAAATTTTATTA
* * *
18837 TTTTTAAATAGTAATT-AAGATTTAATATAAAATATTTT-TATTTTTATTA
1 TTTTTAAATAGTAATTCAGGATTTAATATAAAATATTTTAAAATTTTATTA
* * *
18886 -TTTT---TA--AA-T-AGGAATT--TATAAAATATTTTTAATTTTTATTA
1 TTTTTAAATAGTAATTCAGGATTTAATATAAAATATTTTAAAATTTTATTA
* * * **
18927 TATTTTAAATAATAATT-TGAGATTTAAT-TATAAT-TTTTACTATTTTA--A
1 T-TTTTAAATAGTAATTCAG-GATTTAATATAAAATATTTTAAAATTTTATTA
* ** ** * * **
18975 ATAGT-AATTTTAGATTTA--ATATAA-AT--AA-ATTTT-ATTTTTTATCT-
1 TTTTTAAATAGTA-ATTCAGGATTTAATATAAAATATTTTAAAATTTTAT-TA
* * * * *
19019 TTTTTAG-TAGTAATT-TGACATTTAATATAAAATACTTCTT-CAGTTTTATTA
1 TTTTTAAATAGTAATTCAG-GATTTAATATAAAATA-TT-TTAAAATTTTATTA
* * * *
19070 TTTTTAAATAGAAAATT-TGGATTTAATATAAAATATATTTTTACATTTTTATTAA
1 TTTTTAAATAG-TAATTCAGGATTTAATAT-AAA-ATA-TTTTAAAATTTTATT-A
* * * * *
19125 TTTTTAAATAGCAATTC-GCTATTCAATGTAACATATTTTAAAATTTTTATTA
1 TTTTTAAATAGTAATTCAG-GATTTAATATAAAATATTTTAAAA-TTTTATTA
* * * *
19177 TTTTAAAATAATAATT-TGAGATTTAATATAAAATATATTT--AATTAT-TTA
1 TTTTTAAATAGTAATTCAG-GATTTAATATAAAATAT-TTTAAAATTTTATTA
** *
19226 TTATTTAAATTTTAATTCAAGATTTAATATAAAATATTTTTAAAATTTT
1 TT-TTTAAATAGTAATTCAGGATTTAATATAAAATA-TTTTAAAATTTT
19275 TTTGAATACT
Statistics
Matches: 476, Mismatches: 82, Indels: 134
0.69 0.12 0.19
Matches are distributed among these distances:
38 4 0.01
39 3 0.01
40 13 0.03
41 11 0.02
42 12 0.03
43 52 0.11
44 20 0.04
45 13 0.03
46 10 0.02
47 17 0.04
48 35 0.07
49 26 0.05
50 50 0.11
51 49 0.10
52 64 0.13
53 24 0.05
54 54 0.11
55 19 0.04
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (51 bp):
TTTTTAAATAGTAATTCAGGATTTAATATAAAATATTTTAAAATTTTATTA
Found at i:18797 original size:23 final size:23
Alignment explanation
Indices: 18771--18843 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 23
18761 TAATTCAGGA
18771 TTTAATATAAATATTTTTAATTT
1 TTTAATATAAATATTTTTAATTT
* * **
18794 TTTAAAAT-AATA-ATTTAA-GA
1 TTTAATATAAATATTTTTAATTT
*
18814 TTTAATATGAAATATTTTTATTATT
1 TTTAATAT-AAATATTTTTAAT-TT
18839 TTTAA
1 TTTAA
18844 ATAGTAATTA
Statistics
Matches: 36, Mismatches: 9, Indels: 8
0.68 0.17 0.15
Matches are distributed among these distances:
20 7 0.19
21 5 0.14
22 8 0.22
23 11 0.31
25 5 0.14
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (23 bp):
TTTAATATAAATATTTTTAATTT
Found at i:18892 original size:135 final size:134
Alignment explanation
Indices: 18637--19033 Score: 360
Period size: 135 Copynumber: 2.9 Consensus size: 134
18627 AAATATTTTC
** * *
18637 AAATATTTTATTATTTTTTAAATAATAATTTTGGGTTTAATATAAAATATGTTATTTTTTTATTT
1 AAATATTTTATTATTTTTTAAATAATAATTTAAGATTTAATAT-AAATA---T-TTTTATTATTT
* * * * *
18702 TTAAAAACTAATTCAAGATTTAAT-TAAAATATTTCTAAAACTTTTATTACTTTTAATAGTAATT
61 TTAAATAGTAATT-AAGATTTAATATAAAATATTT-T--TATTTTTATTATTTTTAATAGTAATT
* **
18766 CAGGATTTAATAT
122 CAGAAAATAATAT
*
18779 AAATATTTT-TAATTTTTTAAAATAATAATTTAAGATTTAATATGAAATATTTTTATTATTTTTA
1 AAATATTTTATTATTTTTT-AAATAATAATTTAAGATTTAATAT-AAATATTTTTATTATTTTTA
* * *
18843 AATAGTAATTAAGATTTAATATAAAATATTTTTATTTTTATTATTTTTAAATAGGAATTTATAAA
64 AATAGTAATTAAGATTTAATATAAAATATTTTTATTTTTATTATTTTT-AATAGTAATTCAGAAA
* *
18908 ATATTTT
128 ATAATAT
* * * * *
18915 TAAT-TTTTATTATATTTTAAATAATAATTTGAGATTTAAT-TATA-ATTTTTACTA-TTTTAAA
1 AAATATTTTATTATTTTTTAAATAATAATTTAAGATTTAATATAAATATTTTTATTATTTTTAAA
* * *
18976 TAGTAATTTTAGATTTAATAT-AAATAAATTTTATTTTTTATCT-TTTTTAGTAGTAATT
66 TAGTAA-TTAAGATTTAATATAAAAT-ATTTTTA-TTTTTAT-TATTTTTAATAGTAATT
19034 TGACATTTAA
Statistics
Matches: 218, Mismatches: 29, Indels: 26
0.80 0.11 0.10
Matches are distributed among these distances:
131 17 0.08
132 36 0.17
133 14 0.06
134 2 0.01
135 38 0.17
136 25 0.11
137 11 0.05
138 31 0.14
139 1 0.00
141 8 0.04
142 35 0.16
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (134 bp):
AAATATTTTATTATTTTTTAAATAATAATTTAAGATTTAATATAAATATTTTTATTATTTTTAAA
TAGTAATTAAGATTTAATATAAAATATTTTTATTTTTATTATTTTTAATAGTAATTCAGAAAATA
ATAT
Found at i:18903 original size:43 final size:42
Alignment explanation
Indices: 18809--18938 Score: 140
Period size: 43 Copynumber: 3.1 Consensus size: 42
18799 AATAATAATT
* * ** *
18809 TAAGATTTAATATGAAATATTTTTATTATTT-TTAAATAGTAAT
1 TAAGATTTAATATAAAATATTTTTATT-TTTATT-ATTTTTAAA
18852 TAAGATTTAATATAAAATATTTTTATTTTTATTATTTTTAAA
1 TAAGATTTAATATAAAATATTTTTATTTTTATTATTTTTAAA
* *
18894 TAGGAATT--TATAAAATATTTTTAATTTTTATTATATTTTAAA
1 TAAGATTTAATATAAAATATTTTT-ATTTTTATTAT-TTTTAAA
18936 TAA
1 TAA
18939 TAATTTGAGA
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
40 14 0.18
41 11 0.14
42 23 0.30
43 28 0.37
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.54
Consensus pattern (42 bp):
TAAGATTTAATATAAAATATTTTTATTTTTATTATTTTTAAA
Found at i:18986 original size:21 final size:19
Alignment explanation
Indices: 18924--18991 Score: 57
Period size: 21 Copynumber: 3.4 Consensus size: 19
18914 TTAATTTTTA
18924 TTATATTTTAAATAATAATT
1 TTATATTTTAAAT-ATAATT
* * *
18944 TGAGA-TTTAATTATAATTT
1 TTATATTTTAAATATAA-TT
18963 TTACTATTTTAAATAGTAATT
1 TTA-TATTTTAAATA-TAATT
*
18984 TTAGATTT
1 TTATATTT
18992 AATATAAATA
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
18 4 0.11
19 10 0.27
20 8 0.22
21 12 0.32
22 3 0.08
ACGTcount: A:0.38, C:0.01, G:0.06, T:0.54
Consensus pattern (19 bp):
TTATATTTTAAATATAATT
Found at i:19012 original size:40 final size:39
Alignment explanation
Indices: 18924--18998 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 39
18914 TTAATTTTTA
*
18924 TTATATTTTAAATAATAATTTGAGATTTAATTATAATTT
1 TTATATTTTAAATAATAATTTGAGATTTAATTATAATAT
* *
18963 TTACTATTTTAAATAGTAATTTTAGATTTAA-TATAA
1 TTA-TATTTTAAATAATAATTTGAGATTTAATTATAA
18999 ATAAATTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
39 8 0.24
40 25 0.76
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.52
Consensus pattern (39 bp):
TTATATTTTAAATAATAATTTGAGATTTAATTATAATAT
Found at i:19226 original size:52 final size:50
Alignment explanation
Indices: 18957--19268 Score: 240
Period size: 50 Copynumber: 6.1 Consensus size: 50
18947 GATTTAATTA
* * *
18957 TAATTTTTACTATTTTAAATAGTAATTTTAGATTTAATAT-AAATAAATTT
1 TAATTTTTATTATTTTAAATAGTAATTTGAGATTTAATATAAAATATA-TT
* * * *
19007 TATTTTTTATCT-TTTTTAGTAGTAATTTGACATTTAATATAAAATACT-TCT
1 TAATTTTTAT-TATTTTAAATAGTAATTTGAGATTTAATATAAAATA-TAT-T
* * *
19058 TCAGTTTTATTATTTTTAAATAGAAAATTTG-GATTTAATATAAAATATATTTT
1 TAATTTTTATTA-TTTTAAATAG-TAATTTGAGATTTAATATAAAATATA--TT
* * ** * * *
19111 TACATTTTTATTAATTTTTAAATAGCAATTCGCTATTCAATGTAACATAT-TT
1 TA-ATTTTTATT-A-TTTTAAATAGTAATTTGAGATTTAATATAAAATATATT
*
19163 TAAAATTTTTATTATTTTAAAATAATAATTTGAGATTTAATATAAAATATATT
1 T--AATTTTTATTATTTT-AAATAGTAATTTGAGATTTAATATAAAATATATT
** ** *
19216 TAATTATTTATTA-TTTAAATTTTAATTCAAGATTTAATATAAAATATTTT
1 TAATT-TTTATTATTTTAAATAGTAATTTGAGATTTAATATAAAATATATT
19266 TAA
1 TAA
19269 AATTTTTTTG
Statistics
Matches: 209, Mismatches: 35, Indels: 36
0.75 0.12 0.13
Matches are distributed among these distances:
50 66 0.32
51 26 0.12
52 57 0.27
53 20 0.10
54 15 0.07
55 25 0.12
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.51
Consensus pattern (50 bp):
TAATTTTTATTATTTTAAATAGTAATTTGAGATTTAATATAAAATATATT
Found at i:19519 original size:2 final size:2
Alignment explanation
Indices: 19507--19552 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
19497 CCTCTAATCA
* *
19507 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19549 AT AT
1 AT AT
19553 GTATGTGTAG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19522 original size:10 final size:10
Alignment explanation
Indices: 19507--19556 Score: 82
Period size: 10 Copynumber: 5.0 Consensus size: 10
19497 CCTCTAATCA
19507 ATATATGTAT
1 ATATATGTAT
*
19517 ATATATATAT
1 ATATATGTAT
*
19527 ATATATATAT
1 ATATATGTAT
19537 ATATATGTAT
1 ATATATGTAT
19547 ATATATGTAT
1 ATATATGTAT
19557 GTGTAGACAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 38 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (10 bp):
ATATATGTAT
Found at i:19785 original size:20 final size:20
Alignment explanation
Indices: 19757--19831 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
19747 TCATACCCTG
19757 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
19777 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
19797 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
19817 ATGTATCGATACATT
1 ATGTATCGATACATT
19832 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:19824 original size:40 final size:39
Alignment explanation
Indices: 19757--19834 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
19747 TCATACCCTG
* *
19757 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
19797 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
19835 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:20767 original size:22 final size:23
Alignment explanation
Indices: 20741--20793 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 23
20731 AGCCCTTGAC
20741 CATGCATTTTTTTTATTATG-TT
1 CATGCATTTTTTTTATTATGTTT
20763 CATGC---TTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
20783 CATGCATTTTT
1 CATGCATTTTT
20794 AACATGTCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 12 0.44
20 7 0.26
22 5 0.19
23 3 0.11
ACGTcount: A:0.17, C:0.11, G:0.09, T:0.62
Consensus pattern (23 bp):
CATGCATTTTTTTTATTATGTTT
Found at i:20773 original size:19 final size:20
Alignment explanation
Indices: 20749--20794 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
20739 ACCATGCATT
20749 TTTTTTATTATG-TTCATGC
1 TTTTTTATTATGTTTCATGC
20768 TTTTTTATTATGTTTCATGC
1 TTTTTTATTATGTTTCATGC
*
20788 ATTTTTA
1 TTTTTTA
20795 ACATGTCCAG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.17, C:0.09, G:0.09, T:0.65
Consensus pattern (20 bp):
TTTTTTATTATGTTTCATGC
Found at i:20800 original size:20 final size:20
Alignment explanation
Indices: 20761--20800 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
20751 TTTTATTATG
* **
20761 TTCATGCTTTTTTATTATGT
1 TTCATGCATTTTTAACATGT
20781 TTCATGCATTTTTAACATGT
1 TTCATGCATTTTTAACATGT
20801 CCAGCATCTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.20, C:0.12, G:0.10, T:0.57
Consensus pattern (20 bp):
TTCATGCATTTTTAACATGT
Found at i:26965 original size:15 final size:17
Alignment explanation
Indices: 26929--26972 Score: 58
Period size: 15 Copynumber: 2.8 Consensus size: 17
26919 AAAGTCAAAA
*
26929 GCAAAAGCACAAAAGAT
1 GCAAAAGCAAAAAAGAT
26946 G-AAAAG-AAAAAAG-T
1 GCAAAAGCAAAAAAGAT
26960 GCAAAAGCAAAAA
1 GCAAAAGCAAAAA
26973 TAAAAAAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 2 0.08
15 11 0.46
16 10 0.42
17 1 0.04
ACGTcount: A:0.66, C:0.11, G:0.18, T:0.05
Consensus pattern (17 bp):
GCAAAAGCAAAAAAGAT
Found at i:28321 original size:27 final size:27
Alignment explanation
Indices: 28280--29812 Score: 1928
Period size: 27 Copynumber: 57.0 Consensus size: 27
28270 TAATGTGACT
* *
28280 CTTTAAAGCCCACAACTCCGTGGCAACC
1 CTTTTAAGTCCACAACTCCGTGGC-ACC
28308 C-TTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
28334 CTTTTAAGTCCACAACTCCGT-GCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
28360 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* *
28388 C-TTTAAGTCCACAACTTCGT-GCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
**
28413 CTTTTAAAGTCCACAACTCCGTGGCATT
1 CTTTT-AAGTCCACAACTCCGTGGCACC
28441 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
28468 GTTTTAAGTCCACAACTCCGTGGCA-C
1 CTTTTAAGTCCACAACTCCGTGGCACC
28494 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
28522 CTTTTAAGACCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
28549 CTTTTAAGTCCATAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
28576 CTTTTAAGTCCATAACTCCGTGGCACT
1 CTTTTAAGTCCACAACTCCGTGGCACC
28603 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
28630 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* * *
28657 CTTTTAAGTCCATAACTTCGCGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
28684 CTTTTAAGTCCACAACTCC-TGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
28711 C-TTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
28737 CTTTAAAGCCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
28764 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
28792 TTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
28819 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* *
28847 CTTTTAAGTCCACAACTTCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* **
28874 CTTTAAAGTCCACAACTCCGTGGCATT
1 CTTTTAAGTCCACAACTCCGTGGCACC
28901 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
28928 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
28955 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
28983 CTTTTAAGACCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
29010 CTTTTAAGTCCACAACTCCGTGGCA-C
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
29036 CTTTTAAGTCCATAACTCCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
29064 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
29091 CTTTTTAAGTCCACAACTCCGTGGCACC
1 C-TTTTAAGTCCACAACTCCGTGGCACC
29119 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* * *
29146 CTTTTAAGTCCATAACTTCGCGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
29173 CTTTTAAGTCC-CAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
29200 CTTTTAAGACCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
29227 CTTTTAAGTCTACAACTCCGTGACACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
** * *
29254 CTTTTAAGTCACACAACT-TTTAAGTCCACAA
1 CTTTTAAGTC-CACAACTCCGT--G-GCAC-C
* * * * ** * *
29285 C-TCT--GTGGCATATCT-TTTAAGTCCACAA
1 CTTTTAAGT-CCACAACTCCGT--G-GCAC-C
* * ** *** *
29313 C-TCT--GTGGCAC--C-CTTTTAAAGTC
1 CTTTTAAGT-CCACAACTCCGTGGCA-CC
** * * *
29336 C--ACAACT-C-C--GT--G-GCCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
29354 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
29381 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
29408 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* *
29436 CTTTTAAGTCCACAACTTCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
29463 CTTTTAAGTCCACAAC-CCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
29489 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
29516 CTTTTAAGT-CACAACTCCGCGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
29542 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* *
29570 CTTTTAAGACCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
29597 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
29624 CTTTTAAGTCTACAACTCCGTGGCA-C
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
29650 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
29677 CTTTTAAGACCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* * *
29704 CTTTTAAGTCCATAACTCCGTGGTA-T
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
29730 CTCTTTAAGTCCACAACTCTGTGGC-CC
1 CT-TTTAAGTCCACAACTCCGTGGCACC
* *
29757 CTTTTAAAGTCCACAACTCTGTGGTACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
29785 CTTTTAGAATCCACAACTCTGTGGCACC
1 CTTTTA-AGTCCACAACTCCGTGGCACC
29813 TATTTCAAAG
Statistics
Matches: 1349, Mismatches: 107, Indels: 98
0.87 0.07 0.06
Matches are distributed among these distances:
18 2 0.00
19 1 0.00
20 3 0.00
21 2 0.00
22 2 0.00
23 2 0.00
24 2 0.00
25 2 0.00
26 203 0.15
27 830 0.62
28 293 0.22
29 1 0.00
30 5 0.00
31 1 0.00
ACGTcount: A:0.23, C:0.35, G:0.14, T:0.28
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:28390 original size:54 final size:54
Alignment explanation
Indices: 28280--29812 Score: 2252
Period size: 54 Copynumber: 28.5 Consensus size: 54
28270 TAATGTGACT
* *
28280 CTTTAAAGCCCACAACTCCGTGGCAACCC-TTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGC-ACCCTTTTAAGTCCACAACTCCGTGGCACC
28334 CTTTTAAGTCCACAACTCCGT-GCACCCTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CC
* * **
28388 C-TTTAAGTCCACAACTTCGT-GCATCCTTTTAAAGTCCACAACTCCGTGGCATT
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACC
*
28441 CTTTTAAGTCCACAACTCCGTGGCACCGTTTTAAGTCCACAACTCCGTGGCA-C
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
*
28494 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGACCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACC
* * *
28549 CTTTTAAGTCCATAACTCCGTGGCACCCTTTTAAGTCCATAACTCCGTGGCACT
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
28603 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
* * *
28657 CTTTTAAGTCCATAACTTCGCGGCACCCTTTTAAGTCCACAACTCC-TGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CC
* *
28711 C-TTTAAGTCCACAACTCCGTGGCACCCTTTAAAGCCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
*
28764 CTTTTAAGTCCACAACTCCGTGGCATCCTTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACC
* *
28819 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTTCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACC
* **
28874 CTTTAAAGTCCACAACTCCGTGGCATTCTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
28928 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CC
*
28983 CTTTTAAGACCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-C
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
* *
29036 CTTTTAAGTCCATAACTCCGTGGCATCTCTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACC
29091 CTTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
1 C-TTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
* * *
29146 CTTTTAAGTCCATAACTTCGCGGCACCCTTTTAAGTCC-CAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CC
* * *
29200 CTTTTAAGACCACAACTCCGTGGCACCCTTTTAAGTCTACAACTCCGTGACACC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
* * **
29254 CTTTTAAGT-CAC-A--------CA-ACTTTTAAGTCCACAACTCTGTGGCATAT
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CC
*
29298 CTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCCACC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGG-CACC
29354 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
* *
29408 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTTCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACC
29463 CTTTTAAGTCCACAAC-CCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
*
29516 CTTTTAAGT-CACAACTCCGCGGCACCCTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CC
* *
29570 CTTTTAAGACCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
* *
29624 CTTTTAAGTCTACAACTCCGTGGCA-CCTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
* * * *
29677 CTTTTAAGACCACAACTCCGTGGCACCCTTTTAAGTCCATAACTCCGTGGTA-T
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
* * *
29730 CTCTTTAAGTCCACAACTCTGTGGC-CCCTTTTAAAGTCCACAACTCTGTGGTACC
1 CT-TTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACC
* *
29785 CTTTTAGAATCCACAACTCTGTGGCACC
1 CTTTTA-AGTCCACAACTCCGTGGCACC
29813 TATTTCAAAG
Statistics
Matches: 1346, Mismatches: 92, Indels: 80
0.89 0.06 0.05
Matches are distributed among these distances:
43 22 0.02
44 11 0.01
45 3 0.00
46 1 0.00
52 11 0.01
53 294 0.22
54 573 0.43
55 356 0.26
56 73 0.05
57 2 0.00
ACGTcount: A:0.23, C:0.35, G:0.14, T:0.28
Consensus pattern (54 bp):
CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
Found at i:28479 original size:81 final size:81
Alignment explanation
Indices: 28280--29812 Score: 2252
Period size: 81 Copynumber: 19.0 Consensus size: 81
28270 TAATGTGACT
* *
28280 CTTTAAAGCCCACAACTCCGTGGCAACCC-TTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGC-ACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
28344 CACAACTCCGT-GCACC
65 CACAACTCCGTGGCACC
* *
28360 CTTTTAAGTCCACAACTCCGTGGCATCCC-TTTAAGTCCACAACTTCGT-GCATCCTTTTAAAGT
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGT
**
28423 CCACAACTCCGTGGCATT
64 CCACAACTCCGTGGCACC
*
28441 CTTTTAAGTCCACAACTCCGTGGCACCGTTTTAAGTCCACAACTCCGTGGCA-CCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
28505 ACAACTCCGTGGCATCC
66 ACAACTCCGTGGCA-CC
* *
28522 CTTTTAAGACCACAACTCCGTGGCACCCTTTTAAGTCCATAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
* *
28587 ATAACTCCGTGGCACT
66 ACAACTCCGTGGCACC
28603 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
* * *
28668 ATAACTTCGCGGCACC
66 ACAACTCCGTGGCACC
* *
28684 CTTTTAAGTCCACAACTCC-TGGCATCCC-TTTAAGTCCACAACTCCGTGGCACCCTTTAAAGCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
28747 CACAACTCCGTGGCACC
65 CACAACTCCGTGGCACC
*
28764 CTTTTAAGTCCACAACTCCGTGGCATCCTTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
28829 CACAACTCCGTGGCATCC
65 CACAACTCCGTGGCA-CC
* * * **
28847 CTTTTAAGTCCACAACTTCGTGGCATCCTTTAAAGTCCACAACTCCGTGGCATTCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
28912 ACAACTCCGTGGCACC
66 ACAACTCCGTGGCACC
*
28928 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGAC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTC
28993 CACAACTCCGTGGCACC
65 CACAACTCCGTGGCACC
* *
29010 CTTTTAAGTCCACAACTCCGTGGCA-CCTTTTAAGTCCATAACTCCGTGGCATCTCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTC
29074 CACAACTCCGTGGCACC
65 CACAACTCCGTGGCACC
29091 CTTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1 C-TTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
* * *
29156 CATAACTTCGCGGCACC
65 CACAACTCCGTGGCACC
*
29173 CTTTTAAGTCC-CAACTCCGTGGCATCCCTTTTAAGACCACAACTCCGTGGCACCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
* *
29237 TACAACTCCGTGACACC
65 CACAACTCCGTGGCACC
* * **
29254 CTTTTAAGT-CAC-A--------CA-ACTTTTAAGTCCACAACTCTGTGGCATATCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTC
*
29308 CACAACTCTGTGGCACC
65 CACAACTCCGTGGCACC
29325 CTTTTAAAGTCCACAACTCCGTGGCCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGT
1 CTTTT-AAGTCCACAACTCCGTGG-CACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGT
29390 CCACAACTCCGTGGCACC
64 CCACAACTCCGTGGCACC
* *
29408 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTTCGTGGCATCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
29473 CACAAC-CCGTGGCACC
65 CACAACTCCGTGGCACC
*
29489 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGT-CACAACTCCGCGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
29553 ACAACTCCGTGGCATCC
66 ACAACTCCGTGGCA-CC
* * *
29570 CTTTTAAGACCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCT
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
29635 ACAACTCCGTGGCA-C
66 ACAACTCCGTGGCACC
* *
29650 CTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGACCACAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
* * *
29715 ATAACTCCGTGGTA-T
66 ACAACTCCGTGGCACC
* * * *
29730 CTCTTTAAGTCCACAACTCTGTGGC-CCCTTTTAAAGTCCACAACTCTGTGGTACCCTTTTAGAA
1 CT-TTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTA-AG
*
29794 TCCACAACTCTGTGGCACC
63 TCCACAACTCCGTGGCACC
29813 TATTTCAAAG
Statistics
Matches: 1325, Mismatches: 90, Indels: 73
0.89 0.06 0.05
Matches are distributed among these distances:
70 23 0.02
71 29 0.02
72 6 0.00
73 3 0.00
74 1 0.00
79 40 0.03
80 270 0.20
81 503 0.38
82 342 0.26
83 84 0.06
84 24 0.02
ACGTcount: A:0.23, C:0.35, G:0.14, T:0.28
Consensus pattern (81 bp):
CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
ACAACTCCGTGGCACC
Found at i:29283 original size:15 final size:16
Alignment explanation
Indices: 29254--29286 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
29244 CCGTGACACC
29254 CTTTTAAGTCACACAA
1 CTTTTAAGTCACACAA
29270 CTTTTAAGTC-CACAA
1 CTTTTAAGTCACACAA
29285 CT
1 CT
29287 CTGTGGCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.33
Consensus pattern (16 bp):
CTTTTAAGTCACACAA
Found at i:29312 original size:43 final size:43
Alignment explanation
Indices: 29227--29314 Score: 115
Period size: 43 Copynumber: 2.0 Consensus size: 43
29217 CCGTGGCACC
* *
29227 CTTTTAAGTCTACAACTCCGTGACACCCTTTTAAGTCACACAA
1 CTTTTAAGTCCACAACTCCGTGACAACCTTTTAAGTCACACAA
* * *
29270 CTTTTAAGTCCACAACTCTGTGGCATATCTTTTAAGTC-CACAA
1 CTTTTAAGTCCACAACTCCGTGACA-ACCTTTTAAGTCACACAA
29313 CT
1 CT
29315 CTGTGGCACC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
43 29 0.74
44 10 0.26
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.33
Consensus pattern (43 bp):
CTTTTAAGTCCACAACTCCGTGACAACCTTTTAAGTCACACAA
Found at i:29326 original size:71 final size:70
Alignment explanation
Indices: 29200--29342 Score: 198
Period size: 71 Copynumber: 2.0 Consensus size: 70
29190 CGTGGCATCC
* *
29200 CTTTTAAGACCACAACTCCGTGGCACCCTTTTAAGTCTACAACTCCGTGACACCCTTTT-AAGTC
1 CTTTTAAGACCACAACTCCGTGGCAACCTTTTAAGTCCACAACTCCGTGACACCCTTTTAAAGTC
29264 ACACAA
66 -CACAA
* * * * *
29270 CTTTTAAGTCCACAACTCTGTGGCATATCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGT
1 CTTTTAAGACCACAACTCCGTGGCA-ACCTTTTAAGTCCACAACTCCGTGACACCCTTTTAAAGT
29335 CCACAA
65 CCACAA
29341 CT
1 CT
29343 CCGTGGCCAC
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
70 23 0.36
71 36 0.56
72 5 0.08
ACGTcount: A:0.27, C:0.31, G:0.12, T:0.30
Consensus pattern (70 bp):
CTTTTAAGACCACAACTCCGTGGCAACCTTTTAAGTCCACAACTCCGTGACACCCTTTTAAAGTC
CACAA
Found at i:29879 original size:32 final size:32
Alignment explanation
Indices: 29796--30346 Score: 856
Period size: 32 Copynumber: 17.2 Consensus size: 32
29786 TTTTAGAATC
* * *
29796 CACAACTCTGTGGC-ACCTATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
29827 CACAAGTCGGTGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTC---GGTGGCAACCCATTTCAAAGCCCA
*
29862 CAGAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
29894 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
29926 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
29958 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
29990 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
30022 CACAAGTCGGTGGCAACCCTTTTCAAAG-CCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
30053 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
30085 CACAAGTTGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
30117 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
30149 CACAAGTCGGTGGCAACCCATTCCAAAGCCC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
30180 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
30212 CACAAGTCAGTGGCAACCCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
30244 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
30276 CATAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* ** * *
30308 CACGAGTCGGTGGCAATTCTTTTCAAGGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
30340 CATAAGT
1 CACAAGT
30347 TAGTGGCACC
Statistics
Matches: 486, Mismatches: 28, Indels: 11
0.93 0.05 0.02
Matches are distributed among these distances:
31 69 0.14
32 389 0.80
34 5 0.01
35 23 0.05
ACGTcount: A:0.29, C:0.33, G:0.19, T:0.18
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
Found at i:30358 original size:127 final size:128
Alignment explanation
Indices: 29796--30359 Score: 848
Period size: 127 Copynumber: 4.4 Consensus size: 128
29786 TTTTAGAATC
* * * * *
29796 CACAACTCTGTGGC-ACCTATTTCAAAGCCCACACAAGTCGGTGGTGGCAACCCATTTCAAAGCC
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTC---AGTGGCAACCCTTTTCAAAGCC
* *
29860 CACAGAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCC
63 CACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCC
29925 A
128 A
*
29926 CACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCAC
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCAGTGGCAACCCTTTTCAAAGCCCAC
* *
29991 ACAAGTCGGTGGCAACCCTTTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAG-CCA
66 ACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* ** *
30053 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCCAC
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCAGTGGCAACCCTTTTCAAAGCCCAC
* *
30118 ACAAGTCGGTGGCAACCCTTTTCAAAGCCCACACAAGTCGGTGGCAACCCATTCCAAAGCCC-
66 ACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
30180 CACAAGTCGGTGGCAACCCATTCCAAAGCCCACACAAGTCAGTGGCAACCCTTTTCAAAGCCCAC
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCAGTGGCAACCCTTTTCAAAGCCCAC
*
30245 ACAAGTCGGTGGCAACCCATTTCAAAGCCCACATAAGTCGGTGGCAACCCATTTCAAAGCCCA
66 ACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* ** * * * *
30308 CACGAGTCGGTGGCAATTCTTTTCAAGGCCCACATAAGTTAGTGGC-ACCCTT
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCAGTGGCAACCCTT
30360 CTTTTTTTAA
Statistics
Matches: 404, Mismatches: 27, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
127 247 0.61
128 121 0.30
130 12 0.03
131 24 0.06
ACGTcount: A:0.29, C:0.33, G:0.19, T:0.18
Consensus pattern (128 bp):
CACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCAGTGGCAACCCTTTTCAAAGCCCAC
ACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCA
Done.