Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold430
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: 426104
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
File 4 of 4
Found at i:401797 original size:16 final size:18
Alignment explanation
Indices: 401768--401804 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
401758 ATTTTTATAA
*
401768 ATTTTTATATAATT-ATT
1 ATTTTAATATAATTAATT
401785 ATTTTAATA-AATTAATT
1 ATTTTAATATAATTAATT
401802 ATT
1 ATT
401805 ATATTTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTTTAATATAATTAATT
Found at i:401813 original size:21 final size:20
Alignment explanation
Indices: 401774--401824 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 20
401764 ATAAATTTTT
401774 ATATAATTATTATTTTAATA
1 ATATAATTATTATTTTAATA
401794 A-ATTAATTATTATATTTAATA
1 ATA-TAATTATTAT-TTTAATA
401815 ATATAATTAT
1 ATATAATTAT
401825 ACTCATCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 1 0.04
20 11 0.39
21 15 0.54
22 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATAATTATTATTTTAATA
Found at i:402513 original size:24 final size:24
Alignment explanation
Indices: 402486--402543 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 24
402476 TGTATTTGAT
*
402486 ATATATTTAAATAAGTATATAAAA
1 ATATATTTAAATAAATATATAAAA
**
402510 ATATTATTT-TTTAAATATATAAAA
1 ATA-TATTTAAATAAATATATAAAA
*
402534 AAAT-TTTAAA
1 ATATATTTAAA
402544 AATTAAAATC
Statistics
Matches: 26, Mismatches: 6, Indels: 5
0.70 0.16 0.14
Matches are distributed among these distances:
22 3 0.12
23 1 0.04
24 17 0.65
25 5 0.19
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
ATATATTTAAATAAATATATAAAA
Found at i:403333 original size:20 final size:20
Alignment explanation
Indices: 403296--403347 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
403286 TAAATTAAAT
*
403296 AAATATTATCAATTTAA-TAA
1 AAATATTAT-AATATAATTAA
*
403316 AAATATTATAATAATAATTTA
1 AAATATTATAAT-ATAATTAA
*
403337 AAATATAATAA
1 AAATATTATAA
403348 ATGATAATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 3 0.11
20 12 0.44
21 12 0.44
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATATTATAATATAATTAA
Found at i:403559 original size:14 final size:15
Alignment explanation
Indices: 403532--403574 Score: 58
Period size: 13 Copynumber: 3.1 Consensus size: 15
403522 AATAAATAAT
403532 AAAATATA-AT-TTA
1 AAAATATATATATTA
403545 AAAATA-ATATATT-
1 AAAATATATATATTA
403558 AAAATATATATATTA
1 AAAATATATATATTA
403573 AA
1 AA
403575 GTGTATACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 1 0.04
13 14 0.54
14 9 0.35
15 2 0.08
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAAATATATATATTA
Found at i:403560 original size:26 final size:27
Alignment explanation
Indices: 403522--403574 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
403512 TAACATATTT
403522 AATAAATAATAAAATATA-AT-TTAAA
1 AATAAATAATAAAATATATATATTAAA
*
403547 AATAATATATTAAAATATATATATTAAA
1 AATAA-ATAATAAAATATATATATTAAA
403575 GTGTATACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 5 0.21
26 12 0.50
27 2 0.08
28 5 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (27 bp):
AATAAATAATAAAATATATATATTAAA
Found at i:403581 original size:14 final size:14
Alignment explanation
Indices: 403531--403574 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
403521 TAATAAATAA
403531 TAAAATATA-AT-T
1 TAAAATATATATAT
403543 TAAAA-ATAATATAT
1 TAAAATAT-ATATAT
403557 TAAAATATATATAT
1 TAAAATATATATAT
403571 TAAA
1 TAAA
403575 GTGTATACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 2 0.07
12 6 0.21
13 2 0.07
14 16 0.57
15 2 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TAAAATATATATAT
Found at i:403823 original size:4 final size:4
Alignment explanation
Indices: 403814--403840 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
403804 CGTCTTACTT
403814 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
403841 TGCGTGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:404080 original size:19 final size:20
Alignment explanation
Indices: 404057--404105 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
404047 TAAAAAATTT
404057 TAAAAATAAAAA-TTAGAAAA
1 TAAAAATAAAAATTTA-AAAA
*
404077 -AAAATTAAAAATTTAAAAA
1 TAAAAATAAAAATTTAAAAA
404096 TAAAAATAAA
1 TAAAAATAAA
404106 TAATATAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (20 bp):
TAAAAATAAAAATTTAAAAA
Found at i:404508 original size:20 final size:21
Alignment explanation
Indices: 404473--404512 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
404463 CTACTTTTAT
*
404473 AAATAAAGTTTAAACTATTAA
1 AAATAAAGTCTAAACTATTAA
404494 AAATAAA-TCTAAACTATTA
1 AAATAAAGTCTAAACTATTA
404513 TGTTATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (21 bp):
AAATAAAGTCTAAACTATTAA
Found at i:405235 original size:17 final size:17
Alignment explanation
Indices: 405193--405235 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
405183 TTAAAAATAA
*
405193 AAAAAAATTAATTTTGT
1 AAAAAATTTAATTTTGT
*
405210 -AAAAGTTTAATTTTGT
1 AAAAAATTTAATTTTGT
405226 AAAAAATTTA
1 AAAAAATTTA
405236 TTTATATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (17 bp):
AAAAAATTTAATTTTGT
Found at i:406156 original size:4 final size:4
Alignment explanation
Indices: 406142--406183 Score: 59
Period size: 4 Copynumber: 10.8 Consensus size: 4
406132 ACCACTATGC
* *
406142 AATA AAT- AATA AATA AATA AATA TATA TATA AATA AATA AAT
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AAT
406184 GCTGCTTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 3 0.09
4 32 0.91
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (4 bp):
AATA
Found at i:406491 original size:17 final size:18
Alignment explanation
Indices: 406465--406506 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
406455 AGTTCGATTT
* *
406465 TTTATTTTTTTTAA-ATA
1 TTTATATTTTATAATATA
406482 TTTATATTTTATAATATA
1 TTTATATTTTATAATATA
*
406500 TTCATAT
1 TTTATAT
406507 ACGTATATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTATATTTTATAATATA
Found at i:407790 original size:19 final size:21
Alignment explanation
Indices: 407766--407806 Score: 68
Period size: 19 Copynumber: 2.0 Consensus size: 21
407756 ATAATAAATA
407766 TTAATTTGT-TAAAT-TTTAT
1 TTAATTTGTGTAAATATTTAT
407785 TTAATTTGTGTAAATATTTAT
1 TTAATTTGTGTAAATATTTAT
407806 T
1 T
407807 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:407978 original size:2 final size:2
Alignment explanation
Indices: 407971--408007 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
407961 GAGACGGCTA
407971 AG 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 AG A
408008 AGTTTGTGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:408708 original size:19 final size:20
Alignment explanation
Indices: 408668--408708 Score: 68
Period size: 18 Copynumber: 2.1 Consensus size: 20
408658 TAGATAAAAT
408668 AAAATATAATATAATTTTAA
1 AAAATATAATATAATTTTAA
408688 AAAAT-TAA-ATAATTTTAA
1 AAAATATAATATAATTTTAA
408706 AAA
1 AAA
408709 TAAATATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 13 0.62
19 3 0.14
20 5 0.24
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAATATAATATAATTTTAA
Found at i:409102 original size:10 final size:10
Alignment explanation
Indices: 409086--409122 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
409076 AAATTATTTA
409086 AATAATTAAT
1 AATAATTAAT
*
409096 TATAATTAAT
1 AATAATTAAT
*
409106 AAAAATTAAT
1 AATAATTAAT
409116 AATAATT
1 AATAATT
409123 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:409114 original size:20 final size:21
Alignment explanation
Indices: 409084--409122 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
409074 AAAAATTATT
*
409084 TAAATAATTAATTATAATTAA
1 TAAATAATTAATAATAATTAA
409105 TAAA-AATTAATAATAATT
1 TAAATAATTAATAATAATT
409123 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:409120 original size:30 final size:30
Alignment explanation
Indices: 409064--409129 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
409054 TAAATTTACG
*
409064 ATTATATTAAAAAAATTATTTAAATAATTA
1 ATTATATTAAAAAAATTATATAAATAATTA
409094 ATTATAATTAATAAAAATTA-AT-AATAATT-
1 ATTAT-ATTAA-AAAAATTATATAAATAATTA
409123 -TTATATT
1 ATTATATT
409130 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:409643 original size:22 final size:21
Alignment explanation
Indices: 409618--409665 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
409608 AATTTATCAA
409618 ATTACATAATTAAATT-TTTATT
1 ATTACA-AATTAAATTATTTA-T
409640 ATTAACAAATTAAATTATTTAT
1 ATT-ACAAATTAAATTATTTAT
409662 ATTA
1 ATTA
409666 ATTTTGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 1 0.04
22 16 0.67
23 7 0.29
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTACAAATTAAATTATTTAT
Found at i:409666 original size:22 final size:22
Alignment explanation
Indices: 409625--409666 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
409615 CAAATTACAT
409625 AATTAAATTTTTATTATTAACA
1 AATTAAATTTTTATTATTAACA
409647 AATTAAATTATTTA-TATTAA
1 AATTAAATT-TTTATTATTAA
409667 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:409925 original size:16 final size:16
Alignment explanation
Indices: 409898--409930 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
409888 AAAGTTGATG
409898 ATAAATTTATTAATAAA
1 ATAAATTTATT-ATAAA
409915 ATAAA-TTATTATAAA
1 ATAAATTTATTATAAA
409930 A
1 A
409931 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:410161 original size:14 final size:14
Alignment explanation
Indices: 410142--410185 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
410132 AATTAATTGT
410142 TTAAATTTTTAATA
1 TTAAATTTTTAATA
* *
410156 TTAAATTTATAAGCA
1 TTAAATTTTTAA-TA
410171 TTAAATTTTTAATA
1 TTAAATTTTTAATA
410185 T
1 T
410186 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:410563 original size:4 final size:4
Alignment explanation
Indices: 410554--410591 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
410544 TTTTATCATT
*
410554 TTTC TTTC TTTC TTTC TTTC TTT- TTTC TTTT TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
410592 TGGAAGGATG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 3 0.10
4 28 0.90
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (4 bp):
TTTC
Found at i:415121 original size:13 final size:13
Alignment explanation
Indices: 415078--415121 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
415068 TTGAAGATTG
415078 AAAAATTATTTTT
1 AAAAATTATTTTT
* *
415091 AACAATCATTTTT
1 AAAAATTATTTTT
*
415104 TAAAATTATTTTT
1 AAAAATTATTTTT
415117 AAAAA
1 AAAAA
415122 ATTTTAGAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (13 bp):
AAAAATTATTTTT
Found at i:415177 original size:33 final size:33
Alignment explanation
Indices: 415131--415194 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
415121 AATTTTAGAA
* ** *
415131 ATATTTATTTTTAATATTTTTAAATTTAAAACG
1 ATATTTATCTTTAATATAATTAAAATTAAAACG
415164 ATATTTATCTTTAATATAATTAAAATTAAAA
1 ATATTTATCTTTAATATAATTAAAATTAAAA
415195 TAAAAAAATA
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:415401 original size:3 final size:3
Alignment explanation
Indices: 415393--415423 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
415383 ATAGAGTCGC
415393 ATT ATT ATT ATTT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT
415424 TTGAAGAACC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:415552 original size:2 final size:2
Alignment explanation
Indices: 415539--415576 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
415529 GTTACTATGA
*
415539 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
415577 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:415918 original size:17 final size:19
Alignment explanation
Indices: 415887--415937 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 19
415877 CTTATAAATA
415887 TAAATATGATAT-AAATTAT
1 TAAATATGATATAAAATT-T
415906 TAAATAT-AT-TAAAATTT
1 TAAATATGATATAAAATTT
415923 TAAATATGAATATAA
1 TAAATATG-ATATAA
415938 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:417763 original size:19 final size:19
Alignment explanation
Indices: 417741--417779 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
417731 ATTTGTATTT
417741 ATATTAT-TTTTTATATAAA
1 ATATTATATTTTTATA-AAA
417760 ATATTATATTTTTATAAAA
1 ATATTATATTTTTATAAAA
417779 A
1 A
417780 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:417782 original size:21 final size:19
Alignment explanation
Indices: 417741--417780 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
417731 ATTTGTATTT
*
417741 ATATTATTTTTTATATAAA
1 ATATTATTTTTTATAAAAA
417760 ATATTATATTTTTATAAAAA
1 ATATTAT-TTTTTATAAAAA
417780 A
1 A
417781 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:418143 original size:28 final size:30
Alignment explanation
Indices: 418092--418149 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 30
418082 GGGGTTTTAA
* *
418092 TATTTATAAAATTTTTAATTAAATAAATTT
1 TATTTATAAAATATTTAATCAAATAAATTT
418122 TATTTA-AAAATATTTAA-CAAATAAATTT
1 TATTTATAAAATATTTAATCAAATAAATTT
418150 AAAGTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 10 0.38
29 10 0.38
30 6 0.23
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (30 bp):
TATTTATAAAATATTTAATCAAATAAATTT
Found at i:419247 original size:17 final size:19
Alignment explanation
Indices: 419230--419277 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
419220 TATTATTTAA
* *
419230 TAAAATTTATT-TTATAAT
1 TAAAATTTATTATAATAAC
*
419248 TAAATTTTATTAATAATAAC
1 TAAAATTTATT-ATAATAAC
419268 TAAAATTTAT
1 TAAAATTTAT
419278 AAAATAACAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 10 0.42
20 14 0.58
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
TAAAATTTATTATAATAAC
Found at i:419271 original size:20 final size:18
Alignment explanation
Indices: 419243--419285 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
419233 AATTTATTTT
* *
419243 ATAATTAAATTTTATTAATA
1 ATAACTAAAATTTA-TAA-A
419263 ATAACTAAAATTTATAAA
1 ATAACTAAAATTTATAAA
419281 ATAAC
1 ATAAC
419286 AATAAAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 6 0.29
19 3 0.14
20 12 0.57
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (18 bp):
ATAACTAAAATTTATAAA
Found at i:420084 original size:23 final size:23
Alignment explanation
Indices: 420041--420089 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
420031 TTTAAAGTTA
* *
420041 TTTTATTTTAAGGTATGATTTAT
1 TTTTATTTTAAGATATAATTTAT
*
420064 TTTTATTTATAAGAT-TAATTTGT
1 TTTTATTT-TAAGATATAATTTAT
420087 TTT
1 TTT
420090 AGAGGTATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (23 bp):
TTTTATTTTAAGATATAATTTAT
Found at i:420365 original size:19 final size:18
Alignment explanation
Indices: 420341--420405 Score: 82
Period size: 19 Copynumber: 3.7 Consensus size: 18
420331 GTGAATTTCG
420341 AAAAAGAAGGAAAGAAATA
1 AAAAAGAAGGAAAGAAA-A
*
420360 AAAAAGAAGGAAAGAAGA
1 AAAAAGAAGGAAAGAAAA
420378 AAAAAG-AGGAAA-AAAA
1 AAAAAGAAGGAAAGAAAA
420394 AGAAAA-AAGGAA
1 A-AAAAGAAGGAA
420406 GAGCTGTTGC
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
16 4 0.10
17 15 0.36
18 7 0.17
19 16 0.38
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (18 bp):
AAAAAGAAGGAAAGAAAA
Found at i:420389 original size:10 final size:10
Alignment explanation
Indices: 420341--420407 Score: 52
Period size: 10 Copynumber: 7.0 Consensus size: 10
420331 GTGAATTTCG
*
420341 AAAAAGAAGG
1 AAAAAGAAGA
* *
420351 AAAGA-AATA
1 AAAAAGAAGA
420360 AAAAAGAAG-
1 AAAAAGAAGA
*
420369 -GAAAGAAGA
1 AAAAAGAAGA
*
420378 AAAAAGAGGA
1 AAAAAGAAGA
420388 AAAAA-AAGA
1 AAAAAGAAGA
420397 AAAAAGGAAGA
1 AAAAA-GAAGA
420408 GCTGTTGCGT
Statistics
Matches: 43, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
8 7 0.16
9 14 0.33
10 18 0.42
11 4 0.09
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.01
Consensus pattern (10 bp):
AAAAAGAAGA
Found at i:423514 original size:11 final size:12
Alignment explanation
Indices: 423498--423530 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
423488 TATATCCGTT
423498 AAAATAAAA-TA
1 AAAATAAAAGTA
423509 AAAATAAAAGTA
1 AAAATAAAAGTA
423521 AAAGATAAAA
1 AAA-ATAAAA
423531 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:424889 original size:17 final size:18
Alignment explanation
Indices: 424867--424911 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
424857 AAGTAATTTT
*
424867 TAAAATAAATAT-CAATA
1 TAAAATAAATATAAAATA
424884 TAAAAT-AATATAAAATA
1 TAAAATAAATATAAAATA
*
424901 TAATATAAATA
1 TAAAATAAATA
424912 CATAAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 5 0.21
17 15 0.62
18 4 0.17
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAAATAAATATAAAATA
Found at i:424903 original size:12 final size:12
Alignment explanation
Indices: 424873--424909 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
424863 TTTTTAAAAT
424873 AAATATCAATAT-
1 AAATAT-AATATA
424885 AAA-ATAATATA
1 AAATATAATATA
424896 AAATATAATATA
1 AAATATAATATA
424908 AA
1 AA
424910 TACATAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 5 0.22
11 5 0.22
12 13 0.57
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATATAATATA
Found at i:424995 original size:18 final size:18
Alignment explanation
Indices: 424974--425013 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
424964 ATAGAAAATT
424974 TTAATCATTTAGATT-ATA
1 TTAAT-ATTTAGATTCATA
*
424992 TTAATATTTATATTCATA
1 TTAATATTTAGATTCATA
425010 TTAA
1 TTAA
425014 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:425105 original size:25 final size:25
Alignment explanation
Indices: 425069--425132 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
425059 GAACATCATT
*
425069 TAACATATTTTTTACTATTTAACCA
1 TAACATAATTTTTACTATTTAACCA
*
425094 TAACATAATTTTTACTATTTAATCA
1 TAACATAATTTTTACTATTTAACCA
*
425119 TCAAAAT-ATTTTTA
1 T-AACATAATTTTTA
425133 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
Done.