Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1020
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: 40130
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Found at i:624 original size:4 final size:4
Alignment explanation
Indices: 615--660 Score: 58
Period size: 4 Copynumber: 11.8 Consensus size: 4
605 ACCACTATGC
* * *
615 AATA AATA AATA AATA AAT- AATA TATA TATA TATA AATA AATA AAT
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AAT
661 GCTGCTTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
3 3 0.08
4 36 0.92
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (4 bp):
AATA
Found at i:2260 original size:19 final size:21
Alignment explanation
Indices: 2236--2276 Score: 68
Period size: 19 Copynumber: 2.0 Consensus size: 21
2226 ATAATAAATA
2236 TTAATTTGT-TAAAT-TTTAT
1 TTAATTTGTGTAAATATTTAT
2255 TTAATTTGTGTAAATATTTAT
1 TTAATTTGTGTAAATATTTAT
2276 T
1 T
2277 ATGAATTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 9 0.45
20 5 0.25
21 6 0.30
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (21 bp):
TTAATTTGTGTAAATATTTAT
Found at i:2291 original size:18 final size:17
Alignment explanation
Indices: 2268--2301 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2258 ATTTGTGTAA
2268 ATATTTATTATGAATTAT
1 ATATTTATTAT-AATTAT
*
2286 ATATTTTTTATAATTA
1 ATATTTATTATAATTA
2302 AAAAATTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
ATATTTATTATAATTAT
Found at i:2447 original size:2 final size:2
Alignment explanation
Indices: 2440--2474 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2430 GAGACGGCTA
2440 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2475 AGTTTGTGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3580 original size:20 final size:21
Alignment explanation
Indices: 3542--3580 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
3532 TAAATTTATT
*
3542 TAAATAATTAATTACAATTAA
1 TAAATAATTAATAACAATTAA
*
3563 TAAA-AATTAATAATAATT
1 TAAATAATTAATAACAATT
3581 TTATATTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAATAATTAATAACAATTAA
Found at i:4128 original size:22 final size:22
Alignment explanation
Indices: 4087--4128 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
4077 CAAATTACGT
4087 AATTAAATTTTTATTATTAACA
1 AATTAAATTTTTATTATTAACA
4109 AATTAAATTATTTA-TATTAA
1 AATTAAATT-TTTATTATTAA
4129 TTTTGTCAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
AATTAAATTTTTATTATTAACA
Found at i:4387 original size:16 final size:16
Alignment explanation
Indices: 4360--4392 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
4350 AAAGTTGATG
4360 ATAAATTTATTAATAAA
1 ATAAATTTATT-ATAAA
4377 ATAAA-TTATTATAAA
1 ATAAATTTATTATAAA
4392 A
1 A
4393 GCCCCTCCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 5 0.31
17 5 0.31
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATAAATTTATTATAAA
Found at i:4623 original size:14 final size:14
Alignment explanation
Indices: 4604--4647 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
4594 AATTAATTGT
4604 TTAAATTTTTAATA
1 TTAAATTTTTAATA
* *
4618 TTAAATTTATAAGCA
1 TTAAATTTTTAA-TA
4633 TTAAATTTTTAATA
1 TTAAATTTTTAATA
4647 T
1 T
4648 AAAAATTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (14 bp):
TTAAATTTTTAATA
Found at i:5026 original size:4 final size:4
Alignment explanation
Indices: 5017--5053 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
5007 TTTTATCATT
*
5017 TTTC TTTC TTTC TTTC TTTC TTT- TTT- TTTT TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
5054 TGGAAGGATG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
3 6 0.19
4 25 0.81
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (4 bp):
TTTC
Found at i:9566 original size:13 final size:12
Alignment explanation
Indices: 9546--9586 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 12
9536 TTGAATATGA
9546 AAAATTATTTTT
1 AAAATTATTTTT
9558 AACAATTATTCTTT
1 AA-AATTATT-TTT
9572 AAAATTATTTTT
1 AAAATTATTTTT
9584 AAA
1 AAA
9587 CAGTATAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 8 0.30
13 14 0.52
14 5 0.19
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (12 bp):
AAAATTATTTTT
Found at i:9642 original size:33 final size:33
Alignment explanation
Indices: 9600--9666 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
9590 TATAGAGAAC
** *
9600 AATATTTATTTTTAATATTTTTAAATTTAAAAT
1 AATATTTATTTTTAATATAATTAAAATTAAAAT
9633 AATATTTATTTTTAATATAATTAAAATTAAAAT
1 AATATTTATTTTTAATATAATTAAAATTAAAAT
9666 A
1 A
9667 GAGAGAATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (33 bp):
AATATTTATTTTTAATATAATTAAAATTAAAAT
Found at i:9646 original size:18 final size:18
Alignment explanation
Indices: 9600--9653 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 18
9590 TATAGAGAAC
9600 AATATTTATTTTT--AAT
1 AATATTTATTTTTAAAAT
* **
9616 -ATTTTTAAATTTAAAAT
1 AATATTTATTTTTAAAAT
*
9633 AATATTTATTTTTAATAT
1 AATATTTATTTTTAAAAT
9651 AAT
1 AAT
9654 TAAAATTAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
15 9 0.32
17 3 0.11
18 16 0.57
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
AATATTTATTTTTAAAAT
Found at i:9873 original size:3 final size:3
Alignment explanation
Indices: 9865--9896 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
9855 ATAGAGTCGC
9865 ATT ATT ATT ATT -TT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
9897 TTGAAGAACC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:10025 original size:2 final size:2
Alignment explanation
Indices: 10012--10041 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
10002 GTTACTATGA
*
10012 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10042 TTCAAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:10376 original size:19 final size:18
Alignment explanation
Indices: 10352--10402 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
10342 CTTGTAAATA
10352 TAAATATGATATAAATTAT
1 TAAATATGATATAAATT-T
10371 TAAATAT-AT-TAAAATTT
1 TAAATATGATAT-AAATTT
10388 TAAATATGAATATAA
1 TAAATATG-ATATAA
10403 TACATGTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
17 9 0.32
18 7 0.25
19 11 0.39
20 1 0.04
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (18 bp):
TAAATATGATATAAATTT
Found at i:10383 original size:17 final size:19
Alignment explanation
Indices: 10352--10402 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 19
10342 CTTGTAAATA
10352 TAAATATGATAT-AAATTAT
1 TAAATATGATATAAAATT-T
10371 TAAATAT-AT-TAAAATTT
1 TAAATATGATATAAAATTT
10388 TAAATATGAATATAA
1 TAAATATG-ATATAA
10403 TACATGTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
17 9 0.32
18 7 0.25
19 9 0.32
20 3 0.11
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (19 bp):
TAAATATGATATAAAATTT
Found at i:10440 original size:24 final size:22
Alignment explanation
Indices: 10412--10491 Score: 69
Period size: 24 Copynumber: 3.6 Consensus size: 22
10402 ATACATGTTC
* *
10412 AAATATATTGTATTACTCATATCT
1 AAATATATTATATTAATC-TAT-T
10436 AAATATATTATATTAATCTATT
1 AAATATATTATATTAATCTATT
*
10458 AAAT-TATT-T-TTATATTTA-T
1 AAATATATTATATTA-ATCTATT
10477 AACATATATTATATT
1 AA-ATATATTATATT
10492 TTATATCGTA
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
19 6 0.12
20 7 0.15
21 8 0.17
22 6 0.12
23 5 0.10
24 16 0.33
ACGTcount: A:0.41, C:0.06, G:0.01, T:0.51
Consensus pattern (22 bp):
AAATATATTATATTAATCTATT
Found at i:11081 original size:2 final size:2
Alignment explanation
Indices: 11074--11107 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
11064 ATAAAAACTA
* *
11074 AT AT AT AT GT AT AT GT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11108 TTATTTATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12239 original size:19 final size:19
Alignment explanation
Indices: 12217--12255 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
12207 ATTTGTATTT
12217 ATATTAT-TTTTTATATAAA
1 ATATTATATTTTTATA-AAA
12236 ATATTATATTTTTATAAAA
1 ATATTATATTTTTATAAAA
12255 A
1 A
12256 AATTTACATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATATTATATTTTTATAAAA
Found at i:12258 original size:21 final size:19
Alignment explanation
Indices: 12217--12256 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
12207 ATTTGTATTT
*
12217 ATATTATTTTTTATATAAA
1 ATATTATTTTTTATAAAAA
12236 ATATTATATTTTTATAAAAA
1 ATATTAT-TTTTTATAAAAA
12256 A
1 A
12257 ATTTACATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATATTATTTTTTATAAAAA
Found at i:13740 original size:18 final size:19
Alignment explanation
Indices: 13717--13765 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
13707 TATTATTTAA
* *
13717 TAAAATTTATT-TTATAAT
1 TAAAATTTATTATAATAAC
13735 TAAAATTTTATTAATAATAAC
1 TAAAA-TTTATT-ATAATAAC
13756 TAAAATTTAT
1 TAAAATTTAT
13766 AAAATAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 5 0.19
19 6 0.23
20 5 0.19
21 10 0.38
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
TAAAATTTATTATAATAAC
Found at i:13771 original size:21 final size:20
Alignment explanation
Indices: 13730--13780 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
13720 AATTTATTTT
*
13730 ATAATTAAAATTTTATTAATA
1 ATAA-TAAAATTTTATAAATA
13751 ATAACTAAAA-TTTATAAAATA
1 ATAA-TAAAATTTTAT-AAATA
*
13772 ACAATAAAA
1 ATAATAAAA
13781 ATCCCAACAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (20 bp):
ATAATAAAATTTTATAAATA
Found at i:14575 original size:23 final size:23
Alignment explanation
Indices: 14532--14575 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
14522 TTTAAAGTTA
* *
14532 TTTTATTTTAAGGTATGATTTAT
1 TTTTATTTTAAGATATAATTTAT
14555 TTTTATTTATAAGAT-TAATTT
1 TTTTATTT-TAAGATATAATTT
14576 GTTTAGAGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 13 0.72
24 5 0.28
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (23 bp):
TTTTATTTTAAGATATAATTTAT
Found at i:14861 original size:19 final size:18
Alignment explanation
Indices: 14832--14898 Score: 75
Period size: 18 Copynumber: 3.7 Consensus size: 18
14822 GTGAATTTCG
14832 AAAAAGAAAGGAAAGAAATA
1 AAAAAG-AAGGAAAGAAA-A
*
14852 AAAAAGAAGGAAAGAAGA
1 AAAAAGAAGGAAAGAAAA
14870 AAAAAG-AGGAAA-AAAA
1 AAAAAGAAGGAAAGAAAA
*
14886 AGAAAAAAAGGAA
1 A-AAAAGAAGGAA
14899 GAGCTGTTGC
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
16 4 0.10
17 10 0.24
18 12 0.29
19 10 0.24
20 6 0.14
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.01
Consensus pattern (18 bp):
AAAAAGAAGGAAAGAAAA
Found at i:18012 original size:11 final size:12
Alignment explanation
Indices: 17996--18028 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
17986 TATATCCGTT
17996 AAAATAAAA-TA
1 AAAATAAAAGTA
18007 AAAATAAAAGTA
1 AAAATAAAAGTA
18019 AAAGATAAAA
1 AAA-ATAAAA
18029 ACCATAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 5 0.25
13 6 0.30
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (12 bp):
AAAATAAAAGTA
Found at i:19409 original size:12 final size:12
Alignment explanation
Indices: 19374--19413 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
19364 AATTTTTAAA
19374 ATAAAATATCAAT
1 ATAAAATAT-AAT
19387 AT-AAA-ATAAT
1 ATAAAATATAAT
19397 ATAAAATATAAT
1 ATAAAATATAAT
19409 ATAAA
1 ATAAA
19414 TACATAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 5 0.20
11 5 0.20
12 13 0.52
13 2 0.08
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (12 bp):
ATAAAATATAAT
Found at i:19499 original size:18 final size:18
Alignment explanation
Indices: 19478--19517 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
19468 ATAGAAAATT
19478 TTAATCATTTAGATT-ATA
1 TTAAT-ATTTAGATTCATA
*
19496 TTAATATTTATATTCATA
1 TTAATATTTAGATTCATA
19514 TTAA
1 TTAA
19518 GAAATAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.53
Consensus pattern (18 bp):
TTAATATTTAGATTCATA
Found at i:19610 original size:25 final size:25
Alignment explanation
Indices: 19574--19637 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
19564 GAACATCATT
*
19574 TAACATATTTTTTACTATTTAACCA
1 TAACATAATTTTTACTATTTAACCA
*
19599 TAACATAATTTTTACTATTTAATCA
1 TAACATAATTTTTACTATTTAACCA
*
19624 TCAAAAT-ATTTTTA
1 T-AACATAATTTTTA
19638 TTTAACACCT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
25 31 0.89
26 4 0.11
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.48
Consensus pattern (25 bp):
TAACATAATTTTTACTATTTAACCA
Found at i:20109 original size:14 final size:14
Alignment explanation
Indices: 20090--20116 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20080 GACATGAATC
20090 AGTATAAAATTTAT
1 AGTATAAAATTTAT
20104 AGTATAAAATTTA
1 AGTATAAAATTTA
20117 GAAGAATTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (14 bp):
AGTATAAAATTTAT
Found at i:20867 original size:22 final size:22
Alignment explanation
Indices: 20833--20877 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
20823 TGATGGAGGA
20833 ATATCATTTTTTTAATTGATGC
1 ATATCATTTTTTTAATTGATGC
*
20855 ATATC-TTTCTTTTTATTGATGC
1 ATATCATTT-TTTTAATTGATGC
20877 A
1 A
20878 CTTGCCTACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.24, C:0.11, G:0.09, T:0.56
Consensus pattern (22 bp):
ATATCATTTTTTTAATTGATGC
Found at i:23655 original size:17 final size:17
Alignment explanation
Indices: 23635--23670 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
23625 AAGGAAGATG
* *
23635 AAGAAGAAAGAAAGAAA
1 AAGAAAAAAAAAAGAAA
23652 AAGAAAAAAAAAAGAAA
1 AAGAAAAAAAAAAGAAA
23669 AA
1 AA
23671 ATATGAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAGAAAAAAAAAAGAAA
Found at i:24047 original size:2 final size:2
Alignment explanation
Indices: 24034--24068 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
24024 TTATTTTATT
*
24034 TA TA TG 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 T
24069 TTTGAAAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:30139 original size:36 final size:35
Alignment explanation
Indices: 30059--30139 Score: 85
Period size: 36 Copynumber: 2.3 Consensus size: 35
30049 CAAAATGACA
* *
30059 AAAAAAAAAAGTCAAAAGCAAAAGCACAAAAAATG
1 AAAACAAAAAGTCAAAAGCAAAAGCACAAAAAAGG
* *
30094 AAAAGAAAAAGTGCAAAAGCAAAA-TA-AAAAAAGGG
1 AAAACAAAAAGT-CAAAAGCAAAAGCACAAAAAA-GG
30129 AACAACAAAAA
1 AA-AACAAAAA
30140 TAAAAAAAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
34 6 0.15
35 15 0.38
36 18 0.46
ACGTcount: A:0.72, C:0.10, G:0.14, T:0.05
Consensus pattern (35 bp):
AAAACAAAAAGTCAAAAGCAAAAGCACAAAAAAGG
Found at i:30413 original size:13 final size:13
Alignment explanation
Indices: 30397--30422 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30387 CCTAAAAAAA
30397 AAAAAAAAAAACC
1 AAAAAAAAAAACC
30410 AAAAAAAAAAACC
1 AAAAAAAAAAACC
30423 TTTTCACCCT
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:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAACC
Found at i:31483 original size:30 final size:31
Alignment explanation
Indices: 31443--31551 Score: 92
Period size: 26 Copynumber: 3.8 Consensus size: 31
31433 GTACTGTGAC
*
31443 CTTTTCAAAGTCCACGACTCAGTGGCATTTT
1 CTTTTCAAAGTCCACAACTCAGTGGCATTTT
*
31474 CTTTT-AAAGTCCACAACTCTGTGGCA---T
1 CTTTTCAAAGTCCACAACTCAGTGGCATTTT
* * **
31501 CCTTT--AAGTCCACAACTCTGTGGCA--CC
1 CTTTTCAAAGTCCACAACTCAGTGGCATTTT
*
31528 CTTTT-AAAGTCCACAACTCCGTGG
1 CTTTTCAAAGTCCACAACTCAGTGG
31552 TACCCTTTTA
Statistics
Matches: 70, Mismatches: 6, Indels: 7
0.84 0.07 0.08
Matches are distributed among these distances:
26 20 0.29
27 9 0.13
28 17 0.24
30 19 0.27
31 5 0.07
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31
Consensus pattern (31 bp):
CTTTTCAAAGTCCACAACTCAGTGGCATTTT
Found at i:31533 original size:27 final size:27
Alignment explanation
Indices: 31474--32073 Score: 907
Period size: 27 Copynumber: 22.0 Consensus size: 27
31464 GTGGCATTTT
*
31474 CTTTTAAAGTCCACAACTCTGTGGCATC
1 CTTTT-AAGTCCACAACTCTGTGGCACC
31502 C-TTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCTGTGGCACC
* *
31528 CTTTTAAAGTCCACAACTCCGTGGTACC
1 CTTTT-AAGTCCACAACTCTGTGGCACC
31556 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCTGTGGCACC
* * *
31583 CTTTTAAAATCCACAACTCCGTGGTACC
1 CTTTT-AAGTCCACAACTCTGTGGCACC
*
31611 CTTTTTAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCTGTGGCACC
31638 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCTGTGGCACC
31665 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCTGTGGCACC
*
31692 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCTGTGGCACC
* *
31719 CTTTTAAGTCCATAACTCTGTGGCATCT
1 CTTTTAAGTCCACAACTCTGTGGCA-CC
*
31747 TTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCTGTGGCACC
*
31774 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCTGTGGCACC
*
31802 CTTTTTAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCTGTGGCACC
*
31829 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCTGTGGCACC
31856 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCTGTGGCACC
*
31883 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCTGTGGCA-CC
* * *
31911 CTTTTAAGTCCACAACTCCGCGGCATCT
1 CTTTTAAGTCCACAACTCTGTGGCA-CC
*
31939 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCTGTGGCACC
31966 C-TTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCTGTGGCACC
*
31992 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCTGTGGCACC
* **
32019 CTTTTAAGTCCACAACTCCGTGGCGTC
1 CTTTTAAGTCCACAACTCTGTGGCACC
*
32046 CTTTTAAATCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCTGTGGCACC
32073 C
1 C
32074 ATTTCAAAGC
Statistics
Matches: 525, Mismatches: 40, Indels: 15
0.91 0.07 0.03
Matches are distributed among these distances:
26 47 0.09
27 326 0.62
28 152 0.29
ACGTcount: A:0.23, C:0.34, G:0.14, T:0.29
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCTGTGGCACC
Found at i:32088 original size:136 final size:135
Alignment explanation
Indices: 31474--32073 Score: 907
Period size: 136 Copynumber: 4.4 Consensus size: 135
31464 GTGGCATTTT
31474 CTTTTAAAGTCCACAACTCTGTGGCATCC-TTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGT
1 CTTTT-AAGTCCACAACTCTGTGGCATCCTTTTAAGTCCACAACTCTGTGGCACCCTTTT-AAGT
* * *
31538 CCACAACTCCGTGGTACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAATCCACAACTCC
64 CCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCC
*
31603 GTGGTACC
128 GTGGCACC
* *
31611 CTTTTTAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCTGTGGCATCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCC
* * *
31676 ACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCATAACTCTGTG
66 ACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTG
*
31741 GCATCT
131 GCA-CC
* * * *
31747 TTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTTAGTC
1 CTTTTAAGTCCACAACTCTGTGGCATCCTTTT-AAGTCCACAACTCTGTGGCACCCTTTTAAGTC
* *
31812 CACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGT
65 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGT
31877 GGCACC
130 GGCACC
* * * *
31883 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGCGGCATCTCTTTTAAGT
1 CTTTTAAGTCCACAACTCTGTGGCAT-CCTTTTAAGTCCACAACTCTGTGGCA-CCCTTTTAAGT
*
31948 CCACAACTCCGTGGCACCC-TTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCG
64 CCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCG
32012 TGGCACC
129 TGGCACC
* * *
32019 CTTTTAAGTCCACAACTCCGTGGCGTCCTTTTAAATCCACAACTCTGTGGCACCC
1 CTTTTAAGTCCACAACTCTGTGGCATCCTTTTAAGTCCACAACTCTGTGGCACCC
32074 ATTTCAAAGC
Statistics
Matches: 428, Mismatches: 30, Indels: 13
0.91 0.06 0.03
Matches are distributed among these distances:
134 2 0.00
135 39 0.09
136 221 0.52
137 166 0.39
ACGTcount: A:0.23, C:0.34, G:0.14, T:0.29
Consensus pattern (135 bp):
CTTTTAAGTCCACAACTCTGTGGCATCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCC
ACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTG
GCACC
Found at i:32114 original size:32 final size:32
Alignment explanation
Indices: 32056--32559 Score: 795
Period size: 32 Copynumber: 15.8 Consensus size: 32
32046 CTTTTAAATC
* *
32056 CACAACTCTGTGGC-ACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
32087 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
32119 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
32151 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
32183 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
32215 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
32247 CACAAGTCGGTGGCAACCCATTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCA-TTTCAAAGCCCA
32280 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
32312 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
32344 CACAAGTCGGTGGCAACCCATTTCAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTC-AAAGCCCA
*
32377 CACAGGTCGGTGGC-ACCCA-TTCTAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTC-AAAGCCCA
*
32408 CACAAGTAGG-GGCAA-CCA-TTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
** *
32437 CACAAGTCGGTGGCAACCTTTTTCAAAGCCCC
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * *
32469 CAGAAGTTGGTGGCAACCCATTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
32501 CGCAAGTCGGTGGCAACCCATTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * *
32533 CGCAAGTCAGTGGCAACCCTTTTCAAA
1 CACAAGTCGGTGGCAACCCATTTCAAA
32560 TCACCATTTT
Statistics
Matches: 442, Mismatches: 24, Indels: 13
0.92 0.05 0.03
Matches are distributed among these distances:
29 17 0.04
30 14 0.03
31 33 0.07
32 325 0.74
33 53 0.12
ACGTcount: A:0.31, C:0.34, G:0.19, T:0.16
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
Found at i:33844 original size:12 final size:12
Alignment explanation
Indices: 33816--33851 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 12
33806 GAAGATGAAG
33816 AAGAAAGAAAGAAA
1 AAGAAA-AAA-AAA
33830 AAGAAAAAAAAA
1 AAGAAAAAAAAA
33842 AAGAAAAAAA
1 AAGAAAAAAA
33852 TATGAAATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 13 0.59
13 3 0.14
14 6 0.27
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
AAGAAAAAAAAA
Found at i:34227 original size:2 final size:2
Alignment explanation
Indices: 34214--34248 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
34204 TTATTTTATT
*
34214 TA TA TG 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 T
34249 TTTGAAAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Done.