Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1509
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: 73235
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Found at i:537 original size:4 final size:4
Alignment explanation
Indices: 528--573 Score: 58
Period size: 4 Copynumber: 11.8 Consensus size: 4
518 ACCACTATGC
* * *
528 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
574 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:2162 original size:19 final size:21
Alignment explanation
Indices: 2138--2178 Score: 68
Period size: 19 Copynumber: 2.0 Consensus size: 21
2128 ATAATAAATA
2138 TTAATTTGT-TAAAT-TTTAT
1 TTAATTTGTGTAAATATTTAT
2157 TTAATTTGTGTAAATATTTAT
1 TTAATTTGTGTAAATATTTAT
2178 T
1 T
2179 ATGAATTATT
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:2349 original size:2 final size:2
Alignment explanation
Indices: 2342--2376 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2332 GAGACGGCTA
2342 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
2377 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:3060 original size:7 final size:7
Alignment explanation
Indices: 3050--3095 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
3040 TAATATAATT
3050 TTAAAAA
1 TTAAAAA
3057 TTAAATAA
1 TTAAA-AA
3065 TTTAAAAA
1 -TTAAAAA
*
3073 -TAAATA
1 TTAAAAA
3079 TTAAAAA
1 TTAAAAA
3086 TT-AAAA
1 TTAAAAA
3092 TTAA
1 TTAA
3096 GATATTTGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
6 11 0.33
7 13 0.39
8 4 0.12
9 5 0.15
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (7 bp):
TTAAAAA
Found at i:3092 original size:15 final size:16
Alignment explanation
Indices: 3034--3090 Score: 66
Period size: 16 Copynumber: 3.6 Consensus size: 16
3024 TAGATAAAAT
3034 AAAATATAATATAATTTTA
1 AAAAT-TAA-ATAA-TTTA
3053 AAAATTAAATAATTTA
1 AAAATTAAATAATTTA
3069 AAAA-TAAAT-A-TTA
1 AAAATTAAATAATTTA
3082 AAAATTAAA
1 AAAATTAAA
3091 ATTAAGATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
13 7 0.19
14 5 0.14
15 5 0.14
16 8 0.22
17 4 0.11
18 3 0.08
19 5 0.14
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAATTAAATAATTTA
Found at i:3100 original size:21 final size:22
Alignment explanation
Indices: 3051--3101 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
3041 AATATAATTT
*
3051 TAAAAATTAAATAATTTAAAAA
1 TAAATATTAAATAATTTAAAAA
*
3073 TAAATATTAAA-AA-TTAAAAT
1 TAAATATTAAATAATTTAAAAA
3093 TAAGATATT
1 TAA-ATATT
3102 TGTTATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 9 0.35
21 7 0.27
22 10 0.38
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
TAAATATTAAATAATTTAAAAA
Found at i:3467 original size:10 final size:10
Alignment explanation
Indices: 3451--3487 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
3441 AAATTATTTA
3451 AATAATTAAT
1 AATAATTAAT
*
3461 TATAATTAAT
1 AATAATTAAT
*
3471 AAAAATTAAT
1 AATAATTAAT
3481 AATAATT
1 AATAATT
3488 TTATATTTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
AATAATTAAT
Found at i:3479 original size:20 final size:21
Alignment explanation
Indices: 3449--3487 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
3439 AAAAATTATT
*
3449 TAAATAATTAATTATAATTAA
1 TAAATAATTAATAATAATTAA
3470 TAAA-AATTAATAATAATT
1 TAAATAATTAATAATAATT
3488 TTATATTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAATAATTAATAATAATTAA
Found at i:3485 original size:30 final size:30
Alignment explanation
Indices: 3429--3494 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
3419 TAAATTTACG
*
3429 ATTATATTAAAAAAATTATTTAAATAATTA
1 ATTATATTAAAAAAATTATATAAATAATTA
3459 ATTATAATTAATAAAAATTA-AT-AATAATT-
1 ATTAT-ATTAA-AAAAATTATATAAATAATTA
3488 -TTATATT
1 ATTATATT
3495 TGTATATAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
27 3 0.09
28 4 0.12
30 12 0.36
31 6 0.18
32 8 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
ATTATATTAAAAAAATTATATAAATAATTA
Found at i:4218 original size:34 final size:35
Alignment explanation
Indices: 4152--4218 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 35
4142 TTTTATCAAA
*
4152 ATTACATAATAAAATTAATATAAATCACTTAATTT
1 ATTACATAATAAAATTAATATAAATAACTTAATTT
* *
4187 ATTA-ATAATAAAAGTTTA-ATAAATAATTTAAT
1 ATTACATAATAAAA-TTAATATAAATAACTTAAT
4219 GAAATTAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 21 0.75
35 7 0.25
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (35 bp):
ATTACATAATAAAATTAATATAAATAACTTAATTT
Found at i:4282 original size:16 final size:16
Alignment explanation
Indices: 4255--4287 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
4245 AAAGTTGATG
4255 ATAAATTTATTAATAAA
1 ATAAATTTATT-ATAAA
4272 ATAAA-TTATTATAAA
1 ATAAATTTATTATAAA
4287 A
1 A
4288 GCCCCCTCCC
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:4516 original size:14 final size:14
Alignment explanation
Indices: 4497--4540 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
4487 AATTAATTGT
4497 TTAAATTTTTAATA
1 TTAAATTTTTAATA
* *
4511 TTAAATTTATAAGCA
1 TTAAATTTTTAA-TA
4526 TTAAATTTTTAATA
1 TTAAATTTTTAATA
4540 T
1 T
4541 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:4919 original size:4 final size:4
Alignment explanation
Indices: 4910--4948 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
4900 TTTTATCATT
* *
4910 TTTC TTTC TTTC TTTC TTTC TTTT TTTC TTTT TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
4949 TGGAAGGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (4 bp):
TTTC
Found at i:9479 original size:13 final size:13
Alignment explanation
Indices: 9436--9481 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
9426 TTGAAGATTG
9436 AAAAATTATTTTT
1 AAAAATTATTTTT
* *
9449 AACAATCATTTTT
1 AAAAATTATTTTT
* *
9462 TAAAATTATTTTA
1 AAAAATTATTTTT
9475 AAAAATT
1 AAAAATT
9482 TTAGAAATAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
AAAAATTATTTTT
Found at i:9527 original size:33 final size:33
Alignment explanation
Indices: 9488--9551 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
9478 AATTTTAGAA
* ** *
9488 ATATTTATTTTTAATATTTTTAAATTTAAAACG
1 ATATTTATCTTTAATATAATTAAAATTAAAACG
9521 ATATTTATCTTTAATATAATTAAAATTAAAA
1 ATATTTATCTTTAATATAATTAAAATTAAAA
9552 TAAAAAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (33 bp):
ATATTTATCTTTAATATAATTAAAATTAAAACG
Found at i:9757 original size:3 final size:3
Alignment explanation
Indices: 9749--9780 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
9739 ATAGAGTCGC
9749 ATT ATT ATT ATT -TT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
9781 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:9909 original size:2 final size:2
Alignment explanation
Indices: 9896--9933 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
9886 GTTACTATGA
*
9896 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9934 TTCAAAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:10275 original size:17 final size:19
Alignment explanation
Indices: 10244--10294 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 19
10234 CTTATAAATA
10244 TAAATATGATAT-AAATTAT
1 TAAATATGATATAAAATT-T
10263 TAAATAT-AT-TAAAATTT
1 TAAATATGATATAAAATTT
10280 TAAATATGAATATAA
1 TAAATATG-ATATAA
10295 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:12129 original size:19 final size:19
Alignment explanation
Indices: 12107--12145 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
12097 ATTTGTATTT
12107 ATATTAT-TTTTTATATAAA
1 ATATTATATTTTTATA-AAA
12126 ATATTATATTTTTATAAAA
1 ATATTATATTTTTATAAAA
12145 A
1 A
12146 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:12148 original size:21 final size:19
Alignment explanation
Indices: 12107--12146 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
12097 ATTTGTATTT
*
12107 ATATTATTTTTTATATAAA
1 ATATTATTTTTTATAAAAA
12126 ATATTATATTTTTATAAAAA
1 ATATTAT-TTTTTATAAAAA
12146 A
1 A
12147 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:14455 original size:23 final size:23
Alignment explanation
Indices: 14412--14455 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
14402 TTTAAAGTTA
* *
14412 TTTTATTTTAAGGTATGATTTAT
1 TTTTATTTTAAGATATAATTTAT
14435 TTTTATTTATAAGAT-TAATTT
1 TTTTATTT-TAAGATATAATTT
14456 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:14731 original size:9 final size:9
Alignment explanation
Indices: 14720--14779 Score: 52
Period size: 9 Copynumber: 6.8 Consensus size: 9
14710 TTCGAAGAAG
*
14720 AAAGGAAAG
1 AAAGGAAAA
**
14729 AAATAAAAA
1 AAAGGAAAA
14738 AGAAGG-AAA
1 A-AAGGAAAA
*
14747 GAA-GAAAA
1 AAAGGAAAA
14755 AAAGGAAAA
1 AAAGGAAAA
*
14764 AAAAGAAAA
1 AAAGGAAAA
14773 AAAGGAA
1 AAAGGAA
14780 GAGCTGTTGC
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
7 1 0.03
8 7 0.18
9 29 0.74
10 2 0.05
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.02
Consensus pattern (9 bp):
AAAGGAAAA
Found at i:14745 original size:19 final size:19
Alignment explanation
Indices: 14721--14776 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
14711 TCGAAGAAGA
14721 AAGGAAAGAA-ATAAAAAAG
1 AAGGAAAGAAGA-AAAAAAG
14740 AAGGAAAGAAGAAAAAAAGG
1 AAGGAAAGAAGAAAAAAA-G
*
14760 AA--AAAAAAGAAAAAAAG
1 AAGGAAAGAAGAAAAAAAG
14777 GAAGAGCTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
17 1 0.03
18 13 0.38
19 16 0.47
20 4 0.12
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (19 bp):
AAGGAAAGAAGAAAAAAAG
Found at i:17899 original size:11 final size:12
Alignment explanation
Indices: 17883--17915 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
17873 TATATCCGTT
17883 AAAATAAAA-TA
1 AAAATAAAAGTA
17894 AAAATAAAAGTA
1 AAAATAAAAGTA
17906 AAAGATAAAA
1 AAA-ATAAAA
17916 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:19296 original size:12 final size:12
Alignment explanation
Indices: 19261--19300 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
19251 AATTTTTAAA
19261 ATAAAATATCAAT
1 ATAAAATAT-AAT
19274 AT-AAA-ATAAT
1 ATAAAATATAAT
19284 ATAAAATATAAT
1 ATAAAATATAAT
19296 ATAAA
1 ATAAA
19301 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:19386 original size:18 final size:18
Alignment explanation
Indices: 19365--19404 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
19355 ATAGAAAATT
19365 TTAATCATTTAGATT-ATA
1 TTAAT-ATTTAGATTCATA
*
19383 TTAATATTTATATTCATA
1 TTAATATTTAGATTCATA
19401 TTAA
1 TTAA
19405 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:19497 original size:25 final size:25
Alignment explanation
Indices: 19461--19524 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
19451 GAACATCATT
*
19461 TAACATATTTTTTACTATTTAACCA
1 TAACATAATTTTTACTATTTAACCA
*
19486 TAACATAATTTTTACTATTTAATCA
1 TAACATAATTTTTACTATTTAACCA
*
19511 TCAAAAT-ATTTTTA
1 T-AACATAATTTTTA
19525 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:19991 original size:14 final size:14
Alignment explanation
Indices: 19972--19998 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19962 GACATGAATC
19972 AGTATAAAATTTAT
1 AGTATAAAATTTAT
19986 AGTATAAAATTTA
1 AGTATAAAATTTA
19999 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:20751 original size:22 final size:22
Alignment explanation
Indices: 20717--20761 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
20707 TGATGGAGGA
20717 ATATCATTTTTTTAATTGATGC
1 ATATCATTTTTTTAATTGATGC
*
20739 ATAT-ATTTCTTTTTATTGATGC
1 ATATCATTT-TTTTAATTGATGC
20761 A
1 A
20762 CTTGCCTACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.27, C:0.09, G:0.09, T:0.56
Consensus pattern (22 bp):
ATATCATTTTTTTAATTGATGC
Found at i:26915 original size:18 final size:18
Alignment explanation
Indices: 26894--26928 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
26884 TTTTAATAAA
26894 TTTT-AAATAGACAAATTT
1 TTTTAAAATA-ACAAATTT
26912 TTTTAAAATAACAAATT
1 TTTTAAAATAACAAATT
26929 AAAAATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (18 bp):
TTTTAAAATAACAAATTT
Found at i:29429 original size:2 final size:2
Alignment explanation
Indices: 29422--29468 Score: 60
Period size: 2 Copynumber: 23.0 Consensus size: 2
29412 CATAATCGAG
*
29422 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA GTT TA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA -TA TA
29465 TA TA
1 TA TA
29469 CCCGAAAACA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
1 1 0.03
2 36 0.90
3 3 0.08
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:32325 original size:26 final size:23
Alignment explanation
Indices: 32281--32327 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 23
32271 CATTTATTTG
*
32281 TTATTAAAATAATATTATATAAT
1 TTATTAAAATAATAATATATAAT
32304 TTATTAATAATATATAAATATATA
1 TTATTAA-AATA-AT-AATATATA
32328 TACATATATC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 7 0.35
24 4 0.20
25 2 0.10
26 7 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TTATTAAAATAATAATATATAAT
Found at i:32773 original size:2 final size:2
Alignment explanation
Indices: 32766--32800 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
32756 TTTAGAATTT
32766 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 T
32801 TGAAAGAAAC
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:33399 original size:23 final size:23
Alignment explanation
Indices: 33373--33429 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 23
33363 ATACATTAAA
33373 AATATTAAAAATATTTTTAT-ATT
1 AATATT-AAAATATTTTTATAATT
*
33396 AATATTAACATATTTTTATAATT
1 AATATTAAAATATTTTTATAATT
*
33419 AA-ATTTAAATA
1 AATATTAAAATA
33430 AAATATAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 19 0.63
23 11 0.37
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
AATATTAAAATATTTTTATAATT
Found at i:33523 original size:114 final size:113
Alignment explanation
Indices: 33369--33574 Score: 333
Period size: 114 Copynumber: 1.8 Consensus size: 113
33359 TAAAATACAT
* * *
33369 TAAAAATATTAAAAATATTTTTATATTAATATTAACATATTTTTATAATTAAATTT-AAATAAAA
1 TAAAAATATTAAAAATATTTTTACACTAATATTAACATATTTTCATAATTAAATTTAAAATAAAA
33433 TATAATTTTATCATTTAAATAATACTTTTAAAAGCTCATTTTATTATC
66 TATAATTTTATCATTTAAATAATACTTTTAAAAGCTCATTTTATTATC
* *
33481 TAAAATATATTAAAAATTATTTTTACACTAATATTTATATATTTTCATAATTAAATTTAAAATAA
1 TAAAA-ATATTAAAAA-TATTTTTACACTAATATTAACATATTTTCATAATTAAATTTAAAATAA
*
33546 AATATAATTTTATTATTTAAATAATACTT
64 AATATAATTTTATCATTTAAATAATACTT
33575 CAAGTGGACA
Statistics
Matches: 85, Mismatches: 6, Indels: 3
0.90 0.06 0.03
Matches are distributed among these distances:
112 5 0.06
113 10 0.12
114 36 0.42
115 34 0.40
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (113 bp):
TAAAAATATTAAAAATATTTTTACACTAATATTAACATATTTTCATAATTAAATTTAAAATAAAA
TATAATTTTATCATTTAAATAATACTTTTAAAAGCTCATTTTATTATC
Found at i:33769 original size:2 final size:2
Alignment explanation
Indices: 33762--33786 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
33752 CTTCCTTTAC
33762 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
33787 ATAATCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35364 original size:23 final size:23
Alignment explanation
Indices: 35316--35365 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
35306 GAAATTGGTT
*
35316 AAAGAAAAATAAAAAATACGGAA
1 AAAGAAAAATAAAAAATACAGAA
* *
35339 AAAGAAGAATAAAAATATATAGAA
1 AAAGAAAAATAAAAA-ATACAGAA
35363 AAA
1 AAA
35366 TATTTTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.74, C:0.02, G:0.12, T:0.12
Consensus pattern (23 bp):
AAAGAAAAATAAAAAATACAGAA
Found at i:35531 original size:25 final size:27
Alignment explanation
Indices: 35489--35542 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
35479 ATCTTTAAAC
** *
35489 TTTTTAAAATAATGATAAT-TAATTTA
1 TTTTTAAAATAAAAATAATATAATATA
35515 TTTTT-AAATAAAAATAATATAATATA
1 TTTTTAAAATAAAAATAATATAATATA
35541 TT
1 TT
35543 AATATCAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 11 0.46
26 13 0.54
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (27 bp):
TTTTTAAAATAAAAATAATATAATATA
Found at i:35981 original size:3 final size:3
Alignment explanation
Indices: 35973--36022 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
35963 TTTTAAAACT
*
35973 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
36021 AT
1 AT
36023 TCCTGTTTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:36256 original size:22 final size:22
Alignment explanation
Indices: 36231--36280 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 22
36221 TTTAAAAAAA
*
36231 TTAAAAATAATTAATAATTA-TT
1 TTAAAAATAA-TAAAAATTATTT
36253 TT-AAAA-AATAAAAATTATTT
1 TTAAAAATAATAAAAATTATTT
36273 TTAAAAAT
1 TTAAAAAT
36281 TTTAAGGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
19 8 0.33
20 6 0.25
21 8 0.33
22 2 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TTAAAAATAATAAAAATTATTT
Found at i:36282 original size:29 final size:30
Alignment explanation
Indices: 36206--36285 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 30
36196 AAGTTTGAAC
*
36206 AAAAAT-ATT-AT-AAAATTTAAAAAAATT
1 AAAAATAATTAATAAAAATTTTAAAAAATT
**
36233 AAAAATAATTAATAATTATTTTAAAAAA-T
1 AAAAATAATTAATAAAAATTTTAAAAAATT
* **
36262 AAAAATTATTTTTAAAAATTTTAA
1 AAAAATAATTAATAAAAATTTTAA
36286 GGATAAAAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
27 6 0.14
28 3 0.07
29 22 0.52
30 11 0.26
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (30 bp):
AAAAATAATTAATAAAAATTTTAAAAAATT
Found at i:36970 original size:2 final size:2
Alignment explanation
Indices: 36963--37004 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
36953 TAAAAAGACA
36963 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
37005 TATTGAAGAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37165 original size:32 final size:32
Alignment explanation
Indices: 37109--37186 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 32
37099 TTATAAAGTT
* * *
37109 TTTGGGTTATTTTCGGCTTCGGGTCATTTTGGG
1 TTTGGATTA-TTTCGGCTTCGGGTCACTTTGGA
* *
37142 TTTGGATTATTTCGGGTTGGGGTCACTTTGGA
1 TTTGGATTATTTCGGCTTCGGGTCACTTTGGA
* *
37174 TTCGGATCATTTC
1 TTTGGATTATTTC
37187 AGATTCAGGT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
32 30 0.79
33 8 0.21
ACGTcount: A:0.10, C:0.13, G:0.31, T:0.46
Consensus pattern (32 bp):
TTTGGATTATTTCGGCTTCGGGTCACTTTGGA
Found at i:37199 original size:16 final size:16
Alignment explanation
Indices: 37172--37246 Score: 80
Period size: 16 Copynumber: 4.7 Consensus size: 16
37162 GGTCACTTTG
*
37172 GATTCGGATCATTTCA
1 GATTCGGGTCATTTCA
*
37188 GATTCAGGTCATTTCA
1 GATTCGGGTCATTTCA
**
37204 -AGTTCGGGTTGTTTCA
1 GA-TTCGGGTCATTTCA
*
37220 GATTCGAGTCATTTCA
1 GATTCGGGTCATTTCA
*
37236 GGTTCGGGTCA
1 GATTCGGGTCA
37247 ATCAGGTTTA
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
15 1 0.02
16 45 0.96
17 1 0.02
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.37
Consensus pattern (16 bp):
GATTCGGGTCATTTCA
Found at i:37243 original size:32 final size:32
Alignment explanation
Indices: 37183--37244 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 32
37173 ATTCGGATCA
37183 TTTCAGATTCAGGTCATTTCAAGTTCGGGTTG
1 TTTCAGATTCAGGTCATTTCAAGTTCGGGTTG
*
37215 TTTCAGATTC-GAGTCATTTCAGGTTCGGGT
1 TTTCAGATTCAG-GTCATTTCAAGTTCGGGT
37245 CAATCAGGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 1 0.04
32 27 0.96
ACGTcount: A:0.18, C:0.16, G:0.26, T:0.40
Consensus pattern (32 bp):
TTTCAGATTCAGGTCATTTCAAGTTCGGGTTG
Found at i:37286 original size:53 final size:53
Alignment explanation
Indices: 37217--37340 Score: 126
Period size: 53 Copynumber: 2.3 Consensus size: 53
37207 TCGGGTTGTT
* *
37217 TCAGATTCGAGTCATTTCAG-GTTCGGGTCAATCAGGTTTAACA-CTCGGGTTAA
1 TCAGATTCGAGTCATTT-AGAATTCGAGTCAATCAGGTTTAACATC-CGGGTTAA
* * * *
37270 TCAGGTTCGGGTCATTTTGAATTCGAGTTAATCAGGTTTAACATCCGGGTTAAA
1 TCAGATTCGAGTCATTTAGAATTCGAGTCAATCAGGTTTAACATCCGGGTT-AA
* * *
37324 TTATATTCAAGTCATTT
1 TCAGATTCGAGTCATTT
37341 TAAGATTTAG
Statistics
Matches: 57, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
52 1 0.02
53 41 0.72
54 15 0.26
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (53 bp):
TCAGATTCGAGTCATTTAGAATTCGAGTCAATCAGGTTTAACATCCGGGTTAA
Found at i:38333 original size:16 final size:16
Alignment explanation
Indices: 38314--38357 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
38304 GGTTCGGCTA
*
38314 ATTTCGAATTTGGGTT
1 ATTTCGGATTTGGGTT
* *
38330 ATTTCGGGTTCGGGTT
1 ATTTCGGATTTGGGTT
38346 ATTTCGGATTTG
1 ATTTCGGATTTG
38358 AGTCACTTTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.14, C:0.09, G:0.30, T:0.48
Consensus pattern (16 bp):
ATTTCGGATTTGGGTT
Found at i:38334 original size:32 final size:32
Alignment explanation
Indices: 38293--38362 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
38283 TTAATTATTC
38293 GGGTCATTTCAGGTTCGGCTAATTTCGAATTT
1 GGGTCATTTCAGGTTCGGCTAATTTCGAATTT
* * * * *
38325 GGGTTATTTCGGGTTCGGGTTATTTCGGATTT
1 GGGTCATTTCAGGTTCGGCTAATTTCGAATTT
*
38357 GAGTCA
1 GGGTCA
38363 CTTTGGATTC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.16, C:0.13, G:0.30, T:0.41
Consensus pattern (32 bp):
GGGTCATTTCAGGTTCGGCTAATTTCGAATTT
Found at i:38925 original size:29 final size:30
Alignment explanation
Indices: 38861--38926 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
38851 ACTTTATTTG
* *
38861 ATATAAAAACTTATTTAGATATAAATTAAA
1 ATATAAAAACTTATTTAAATATAAATAAAA
* *
38891 AGATAAAAATTTATTTAAATAT-AATAAAA
1 ATATAAAAACTTATTTAAATATAAATAAAA
38920 ATATAAA
1 ATATAAA
38927 GGCTTCTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
29 12 0.39
30 19 0.61
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.35
Consensus pattern (30 bp):
ATATAAAAACTTATTTAAATATAAATAAAA
Found at i:39720 original size:22 final size:22
Alignment explanation
Indices: 39695--39736 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
39685 AATTAAAAAA
* * *
39695 TTATATTTATATTTATATAATT
1 TTATAATTAAATTTAAATAATT
39717 TTATAATTAAATTTAAATAA
1 TTATAATTAAATTTAAATAA
39737 AATATTATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTATAATTAAATTTAAATAATT
Found at i:40243 original size:22 final size:22
Alignment explanation
Indices: 40208--40249 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
40198 TTTTATTATT
40208 TAAATTTAATTATAAAAATATA
1 TAAATTTAATTATAAAAATATA
40230 TAAATATTAA-TATAAAAATA
1 TAAAT-TTAATTATAAAAATA
40250 AATTTTAAAT
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATTTAATTATAAAAATATA
Found at i:42341 original size:21 final size:22
Alignment explanation
Indices: 42297--42341 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
42287 TGATCTGAAT
42297 TATTATTTAAGTAATAAAATTA
1 TATTATTTAAGTAATAAAATTA
*
42319 TATT-TTTAATTAA-AAAATATA
1 TATTATTTAAGTAATAAAAT-TA
42340 TA
1 TA
42342 AATATTAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 5 0.24
21 12 0.57
22 4 0.19
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
TATTATTTAAGTAATAAAATTA
Found at i:43562 original size:22 final size:22
Alignment explanation
Indices: 43519--43563 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
43509 AAAAAAATTC
*
43519 ATTTTTATGTTAACATTAATAT
1 ATTTTTATATTAACATTAATAT
*
43541 ATTTTTATAATTAA-ATTTATAT
1 ATTTTTAT-ATTAACATTAATAT
43563 A
1 A
43564 AAAATATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (22 bp):
ATTTTTATATTAACATTAATAT
Found at i:46309 original size:20 final size:20
Alignment explanation
Indices: 46281--46355 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
46271 TCATACCCTG
46281 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
46301 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
46321 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
46341 ATGTATCGATACATT
1 ATGTATCGATACATT
46356 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:46348 original size:40 final size:39
Alignment explanation
Indices: 46281--46358 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
46271 TCATACCCTG
* *
46281 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
46321 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
46359 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:50354 original size:34 final size:33
Alignment explanation
Indices: 50306--50526 Score: 257
Period size: 34 Copynumber: 6.5 Consensus size: 33
50296 TGGTAAAAAC
*
50306 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
50339 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
50373 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
50407 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
50441 CTCCCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
* *
50475 CACCCATTTAATCAATAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
50509 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
50527 TCTCCCACTT
Statistics
Matches: 160, Mismatches: 19, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
33 22 0.14
34 132 0.82
35 6 0.04
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:50422 original size:68 final size:67
Alignment explanation
Indices: 50308--50526 Score: 287
Period size: 68 Copynumber: 3.2 Consensus size: 67
50298 GTAAAAACCA
* * *
50308 CCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAAT
50373 CAC
65 CAC
* * * *
50376 CCATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAAT
*
50441 CTC
65 CAC
* * * * *
50444 CCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAATAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTA-CCATTTAATCAACAATGGTAAGCTACCAAAT
50509 CA-
65 CAC
50511 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
50527 TCTCCCACTT
Statistics
Matches: 131, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
67 17 0.13
68 113 0.86
69 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.26
Consensus pattern (67 bp):
CCATTTAATCAACAATGGCAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATC
AC
Found at i:50450 original size:102 final size:101
Alignment explanation
Indices: 50306--50526 Score: 361
Period size: 102 Copynumber: 2.2 Consensus size: 101
50296 TGGTAAAAAC
* *
50306 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
*
50371 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAATAATGGTAAACTACCAAAT
** * * *
50407 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCA
50472 AATCACCCATTTAATCAATAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAATAATGGTAAACTACCAAAT
50509 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
50527 TCTCCCACTT
Statistics
Matches: 109, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 16 0.15
102 93 0.85
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAATAATGGTAAACTACCAAAT
Found at i:54983 original size:34 final size:33
Alignment explanation
Indices: 54935--55153 Score: 253
Period size: 34 Copynumber: 6.5 Consensus size: 33
54925 TGGTAAAAAC
*
54935 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
54968 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
55002 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
55036 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
55070 CTCCCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
* *
55104 CACCCATTTAATCAATAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
55138 CACCATTTAATCAACA
1 CACCATTTAATCAACA
55154 CATATCTTAT
Statistics
Matches: 158, Mismatches: 19, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
33 20 0.13
34 132 0.84
35 6 0.04
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:55051 original size:68 final size:67
Alignment explanation
Indices: 54937--55153 Score: 283
Period size: 68 Copynumber: 3.2 Consensus size: 67
54927 GTAAAAACCA
* * *
54937 CCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAAT
55002 CAC
65 CAC
* * * *
55005 CCATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAAT
*
55070 CTC
65 CAC
* * * * *
55073 CCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAATAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTA-CCATTTAATCAACAATGGTAAGCTACCAAAT
55138 CA-
65 CAC
55140 CCATTTAATCAACA
1 CCATTTAATCAACA
55154 CATATCTTAT
Statistics
Matches: 129, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
67 15 0.12
68 113 0.88
69 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (67 bp):
CCATTTAATCAACAATGGCAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATC
AC
Found at i:55114 original size:102 final size:101
Alignment explanation
Indices: 54935--55153 Score: 357
Period size: 102 Copynumber: 2.2 Consensus size: 101
54925 TGGTAAAAAC
* *
54935 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
*
55000 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAATAATGGTAAACTACCAAAT
** * * *
55036 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCA
55101 AATCACCCATTTAATCAATAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAATAATGGTAAACTACCAAAT
55138 CACCATTTAATCAACA
1 CACCATTTAATCAACA
55154 CATATCTTAT
Statistics
Matches: 107, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 14 0.13
102 93 0.87
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAATAATGGTAAACTACCAAAT
Found at i:55296 original size:29 final size:28
Alignment explanation
Indices: 55246--55300 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
55236 TGTATATAAA
* *
55246 TAATTATTTAATTTTAAAGTAAATTAAT
1 TAATTATTAAATTATAAAGTAAATTAAT
*
55274 TAATTATATAAATTATAAGGTAAATTA
1 TAATTAT-TAAATTATAAAGTAAATTA
55301 TTTGATTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 7 0.30
29 16 0.70
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.45
Consensus pattern (28 bp):
TAATTATTAAATTATAAAGTAAATTAAT
Found at i:57517 original size:18 final size:18
Alignment explanation
Indices: 57483--57520 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
57473 TTCTTAATTT
*
57483 TTAATTTTTATATAAAAA
1 TTAATTTTAATATAAAAA
57501 TTAATTTTAACTA-AAAAA
1 TTAATTTTAA-TATAAAAA
57519 TT
1 TT
57521 TTATACTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTTTAATATAAAAA
Found at i:58071 original size:18 final size:18
Alignment explanation
Indices: 58044--58080 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
58034 ATACTCTTTT
*
58044 AAATATATTTAAAAAATA
1 AAATAAATTTAAAAAATA
58062 AAATAAATTTAAAAAATA
1 AAATAAATTTAAAAAATA
58080 A
1 A
58081 TATATGTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
AAATAAATTTAAAAAATA
Found at i:60809 original size:100 final size:102
Alignment explanation
Indices: 60667--60857 Score: 287
Period size: 100 Copynumber: 1.9 Consensus size: 102
60657 TGTAAGTTGA
* *
60667 TTGTGAATATTATTGTGTTGATTATGAAATCATATAAATTCATGTTTTTGTTTGTGAATATTGTT
1 TTGTGAATATTATTGTGTTCATTATGAAATCATATAAATTCATGTTTTTATTTGTGAATATTGTT
60732 GTATTGATTATGAGATCATATAAATTGATGTTTTTAT
66 GTATTGATTATGAGATCATATAAATTGATGTTTTTAT
* * * * *
60769 TTGTGAAT-TT-TTTTGTTCATTATGAGATCATGTAACTTCATGTTTTTATTTGTGAATGTTGTT
1 TTGTGAATATTATTGTGTTCATTATGAAATCATATAAATTCATGTTTTTATTTGTGAATATTGTT
* *
60832 GTGTTGATTGTGAGATCATATAAATT
66 GTATTGATTATGAGATCATATAAATT
60858 CATTTTATAA
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
100 70 0.88
101 2 0.03
102 8 0.10
ACGTcount: A:0.27, C:0.04, G:0.18, T:0.51
Consensus pattern (102 bp):
TTGTGAATATTATTGTGTTCATTATGAAATCATATAAATTCATGTTTTTATTTGTGAATATTGTT
GTATTGATTATGAGATCATATAAATTGATGTTTTTAT
Found at i:60812 original size:49 final size:51
Alignment explanation
Indices: 60667--60860 Score: 275
Period size: 51 Copynumber: 3.8 Consensus size: 51
60657 TGTAAGTTGA
* * *
60667 TTGTGAATATTATTGTGTTGATTATGAAATCATATAAATTCATGTTTTTGT
1 TTGTGAATATTGTTGTGTTGATTATGAGATCATATAAATTCATGTTTTTAT
* *
60718 TTGTGAATATTGTTGTATTGATTATGAGATCATATAAATTGATGTTTTTAT
1 TTGTGAATATTGTTGTGTTGATTATGAGATCATATAAATTCATGTTTTTAT
* * * *
60769 TTGTGAAT-TT-TTTTGTTCATTATGAGATCATGTAACTTCATGTTTTTAT
1 TTGTGAATATTGTTGTGTTGATTATGAGATCATATAAATTCATGTTTTTAT
* *
60818 TTGTGAATGTTGTTGTGTTGATTGTGAGATCATATAAATTCAT
1 TTGTGAATATTGTTGTGTTGATTATGAGATCATATAAATTCAT
60861 TTTATAAAAT
Statistics
Matches: 125, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
49 41 0.33
50 4 0.03
51 80 0.64
ACGTcount: A:0.27, C:0.05, G:0.18, T:0.51
Consensus pattern (51 bp):
TTGTGAATATTGTTGTGTTGATTATGAGATCATATAAATTCATGTTTTTAT
Found at i:68290 original size:22 final size:22
Alignment explanation
Indices: 68265--68306 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
68255 ATTAAAATAT
68265 TATTTATAT-ATTAATATTTATA
1 TATTTATATAATTAA-ATTTATA
*
68287 TATTTTTATAATTAAATTTA
1 TATTTATATAATTAAATTTA
68307 AATAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TATTTATATAATTAAATTTATA
Found at i:68637 original size:18 final size:19
Alignment explanation
Indices: 68594--68638 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
68584 ATTAATTTTT
* *
68594 TAAAAATATCAAACATATA
1 TAAAATTATCAAAAATATA
68613 TAAAATTAT-AAAAATATA
1 TAAAATTATCAAAAATATA
68631 TAAAATTA
1 TAAAATTA
68639 ATTAATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (19 bp):
TAAAATTATCAAAAATATA
Found at i:69146 original size:20 final size:20
Alignment explanation
Indices: 69123--69176 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
69113 TTTACACATG
* *
69123 ATAATTTTAA-ATACAATTAA
1 ATAATTATAATATAC-ATAAA
*
69143 ATAAATATAATATACATAAA
1 ATAATTATAATATACATAAA
*
69163 ATAATTAAAATATA
1 ATAATTATAATATA
69177 ATATAATACG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 24 0.86
21 4 0.14
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (20 bp):
ATAATTATAATATACATAAA
Found at i:69149 original size:14 final size:14
Alignment explanation
Indices: 69130--69183 Score: 56
Period size: 14 Copynumber: 3.7 Consensus size: 14
69120 ATGATAATTT
*
69130 TAAATACAATTAAA
1 TAAATATAATTAAA
*
69144 TAAATATAATATACA
1 TAAATATAAT-TAAA
69159 TAAA-ATAATTAAAA
1 TAAATATAATT-AAA
69173 TATAATATAAT
1 TA-AATATAAT
69184 ACGATACAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 1 0.03
14 18 0.55
15 9 0.27
16 5 0.15
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (14 bp):
TAAATATAATTAAA
Found at i:71687 original size:36 final size:36
Alignment explanation
Indices: 71621--71689 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
71611 AAAATTACGG
* **
71621 ATATTAAAATTAAATTATAAATTTATTAAATATCAT
1 ATATTAAAAATAAATTATAAATCGATTAAATATCAT
*
71657 ATATTAAAAATAATTATATAAATCGA-TAAATAT
1 ATATTAAAAATAAAT-TATAAATCGATTAAATAT
71690 AAAATTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
36 20 0.71
37 8 0.29
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (36 bp):
ATATTAAAAATAAATTATAAATCGATTAAATATCAT
Done.