Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold65
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: 3097370
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.31
Warning! 315397 characters in sequence are not A, C, G, or T
File 5 of 17
Found at i:1105545 original size:14 final size:12
Alignment explanation
Indices: 1105519--1105547 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
1105509 ATTCATTCAT
1105519 TTATATAATTTA
1 TTATATAATTTA
1105531 TTATATAA-TTA
1 TTATATAATTTA
1105542 TTATAT
1 TTATAT
1105548 TTAAAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TTATATAATTTA
Found at i:1105549 original size:20 final size:18
Alignment explanation
Indices: 1105526--1105609 Score: 63
Period size: 17 Copynumber: 4.8 Consensus size: 18
1105516 CATTTATATA
1105526 ATTTATTATATAATTATTAT
1 ATTTA-TATATAATT-TTAT
* *
1105546 ATTTA-AAATATTTTTAT
1 ATTTATATATAATTTTAT
1105563 ATTTATATA-AATTTTA-
1 ATTTATATATAATTTTAT
*
1105579 ATATAT-TAATAA-TTTAT
1 ATTTATAT-ATAATTTTAT
*
1105596 A-TTATATAAAATTT
1 ATTTATATATAATTT
1105610 AAAAATTTTA
Statistics
Matches: 51, Mismatches: 7, Indels: 15
0.70 0.10 0.21
Matches are distributed among these distances:
15 1 0.02
16 16 0.31
17 21 0.41
18 8 0.16
20 5 0.10
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTATATATAATTTTAT
Found at i:1105582 original size:18 final size:18
Alignment explanation
Indices: 1105531--1105638 Score: 58
Period size: 18 Copynumber: 6.3 Consensus size: 18
1105521 ATATAATTTA
1105531 TTATAT-AATTATT-ATAT
1 TTATATAAATT-TTAATAT
*
1105548 TTA-A-AATATTTTTATAT
1 TTATATAA-ATTTTAATAT
1105565 TTATATAAATTTTAATAT
1 TTATATAAATTTTAATAT
1105583 ATTA-AT-AA-TTT-ATA-
1 -TTATATAAATTTTAATAT
* *
1105597 TTATATAAAATTTAAAAAT
1 TTATAT-AAATTTTAATAT
*
1105616 TT-TAATTAATTTTAATA-
1 TTAT-ATAAATTTTAATAT
1105633 TTATAT
1 TTATAT
1105639 TTGTATATTT
Statistics
Matches: 71, Mismatches: 6, Indels: 28
0.68 0.06 0.27
Matches are distributed among these distances:
13 3 0.04
14 2 0.03
15 3 0.04
16 9 0.13
17 21 0.30
18 24 0.34
19 9 0.13
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTATATAAATTTTAATAT
Found at i:1105608 original size:16 final size:16
Alignment explanation
Indices: 1105558--1105610 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
1105548 TTAAAATATT
1105558 TTTATATT-TATATAAA
1 TTTATATTATATA-AAA
*
1105574 TTT-TAATATATTAATAA
1 TTTATATTATA-TAA-AA
1105591 TTTATATTATATAAAA
1 TTTATATTATATAAAA
1105607 TTTA
1 TTTA
1105611 AAAATTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
15 3 0.10
16 12 0.39
17 10 0.32
18 6 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTATATTATATAAAA
Found at i:1105608 original size:33 final size:36
Alignment explanation
Indices: 1105557--1105638 Score: 100
Period size: 33 Copynumber: 2.4 Consensus size: 36
1105547 TTTAAAATAT
* *
1105557 TTTTATATT-TATATAAATTTTAATATATTAA-TAA
1 TTTTATATTATATATAAATTTAAAAATATTAATTAA
*
1105591 -TTTATATTATATA-AAATTTAAAAATTTTAATTAA
1 TTTTATATTATATATAAATTTAAAAATATTAATTAA
1105625 TTTTAATATTATAT
1 TTTT-ATATTATAT
1105639 TTGTATATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
33 22 0.54
34 7 0.17
35 3 0.07
36 9 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (36 bp):
TTTTATATTATATATAAATTTAAAAATATTAATTAA
Found at i:1107357 original size:44 final size:44
Alignment explanation
Indices: 1107294--1107382 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
1107284 TCGGTCAGTT
1107294 AGTTTATTAAAAGTTGGAGCTCTTCAGACAAGCAATTAGCGAGA
1 AGTTTATTAAAAGTTGGAGCTCTTCAGACAAGCAATTAGCGAGA
1107338 AGTTTATTAAAAGTTGGAGCTCTTCAGACAAGCAATTAGCGAGA
1 AGTTTATTAAAAGTTGGAGCTCTTCAGACAAGCAATTAGCGAGA
1107382 A
1 A
1107383 ATTACTGCTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.27
Consensus pattern (44 bp):
AGTTTATTAAAAGTTGGAGCTCTTCAGACAAGCAATTAGCGAGA
Found at i:1107721 original size:21 final size:21
Alignment explanation
Indices: 1107696--1107824 Score: 122
Period size: 21 Copynumber: 6.1 Consensus size: 21
1107686 TGGCCAAACA
*
1107696 TGAAAAAGCAGTGGACCAAAG
1 TGAAAAAGCAGTGAACCAAAG
* *
1107717 TGAAAAGGCAGTGAATCGAAA-
1 TGAAAAAGCAGTGAA-CCAAAG
*
1107738 TGAAAAGGCAGTGAACCGAAA-
1 TGAAAAAGCAGTGAACC-AAAG
*
1107759 TGAAAAAGCGGTGAACC-AAG
1 TGAAAAAGCAGTGAACCAAAG
*
1107779 ATG-AAAAGCCGGTGAACCAAAG
1 -TGAAAAAG-CAGTGAACCAAAG
* *
1107801 CGAAAAGGCAGTGAACCAAAG
1 TGAAAAAGCAGTGAACCAAAG
1107822 TGA
1 TGA
1107825 GGAAGCATTT
Statistics
Matches: 91, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
19 2 0.02
20 6 0.07
21 72 0.79
22 11 0.12
ACGTcount: A:0.47, C:0.15, G:0.29, T:0.10
Consensus pattern (21 bp):
TGAAAAAGCAGTGAACCAAAG
Found at i:1107763 original size:42 final size:42
Alignment explanation
Indices: 1107695--1107819 Score: 146
Period size: 42 Copynumber: 3.0 Consensus size: 42
1107685 TTGGCCAAAC
* * *
1107695 ATGAAAAAGCAGTGGACCAAAGTGAAAAGGCAGTGAATCGAA-
1 ATGAAAAGGCAGTGAACCAAAGTGAAAAGGCAGTGAA-CCAAG
* *
1107737 ATGAAAAGGCAGTGAACCGAAA-TGAAAAAGCGGTGAACCAAG
1 ATGAAAAGGCAGTGAACC-AAAGTGAAAAGGCAGTGAACCAAG
* * *
1107779 ATGAAAAGCCGGTGAACCAAAGCGAAAAGGCAGTGAACCAA
1 ATGAAAAGGCAGTGAACCAAAGTGAAAAGGCAGTGAACCAA
1107820 AGTGAGGAAG
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 6 0.09
42 61 0.87
43 3 0.04
ACGTcount: A:0.47, C:0.15, G:0.28, T:0.10
Consensus pattern (42 bp):
ATGAAAAGGCAGTGAACCAAAGTGAAAAGGCAGTGAACCAAG
Found at i:1107794 original size:63 final size:63
Alignment explanation
Indices: 1107695--1107817 Score: 160
Period size: 63 Copynumber: 2.0 Consensus size: 63
1107685 TTGGCCAAAC
* * * *
1107695 ATGAAAAAGCAGTGGACCAAAGTGAAAAGGCAGTGAATCGAAA-TGAAAAGGCAGTGAACCGAA
1 ATGAAAAAGCAGTGAACCAAAGTGAAAAGCCAGTGAA-CCAAAGCGAAAAGGCAGTGAACCGAA
* *
1107758 ATGAAAAAGCGGTGAACC-AAGATGAAAAGCCGGTGAACCAAAGCGAAAAGGCAGTGAACC
1 ATGAAAAAGCAGTGAACCAAAG-TGAAAAGCCAGTGAACCAAAGCGAAAAGGCAGTGAACC
1107818 AAAGTGAGGA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
62 7 0.13
63 45 0.87
ACGTcount: A:0.46, C:0.15, G:0.28, T:0.10
Consensus pattern (63 bp):
ATGAAAAAGCAGTGAACCAAAGTGAAAAGCCAGTGAACCAAAGCGAAAAGGCAGTGAACCGAA
Found at i:1133692 original size:25 final size:25
Alignment explanation
Indices: 1133659--1133708 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1133649 TTAACAATGC
1133659 ATAAATTTATGTCTTATTAGTGAGT
1 ATAAATTTATGTCTTATTAGTGAGT
1133684 ATAAATTTATGTCTTATTAGTGAGT
1 ATAAATTTATGTCTTATTAGTGAGT
1133709 TAGATGATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.04, G:0.16, T:0.48
Consensus pattern (25 bp):
ATAAATTTATGTCTTATTAGTGAGT
Found at i:1134759 original size:17 final size:17
Alignment explanation
Indices: 1134718--1134753 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 17
1134708 AATACACTTT
1134718 AAATGAAAAAATAATAAA
1 AAAT-AAAAAATAATAAA
1134736 AAATAAAAAATTAATAAA
1 AAATAAAAAA-TAATAAA
1134754 TATAAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (17 bp):
AAATAAAAAATAATAAA
Found at i:1140123 original size:11 final size:11
Alignment explanation
Indices: 1140107--1140132 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1140097 CTTCCACTTG
1140107 AAAAGAAAAGA
1 AAAAGAAAAGA
1140118 AAAAGAAAAGA
1 AAAAGAAAAGA
1140129 AAAA
1 AAAA
1140133 TCCATGACCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAGA
Found at i:1141184 original size:16 final size:16
Alignment explanation
Indices: 1141160--1141191 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1141150 AGCAAAAAGA
*
1141160 AGGATTAAATAAGAAG
1 AGGAATAAATAAGAAG
1141176 AGGAATAAATAAGAAG
1 AGGAATAAATAAGAAG
1141192 CAATAGTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.25, T:0.16
Consensus pattern (16 bp):
AGGAATAAATAAGAAG
Found at i:1159135 original size:105 final size:104
Alignment explanation
Indices: 1159001--1159209 Score: 337
Period size: 105 Copynumber: 2.0 Consensus size: 104
1158991 TCTTAAACGG
* * ** *
1159001 ACTACTTTGTGGGAAAAAACATAGAAGCCAAATATTTTGATAAGAATAGCATTGAACAAACAATG
1 ACTACTTTGCGGAAAAAAACATAGAAGCCAAATATACTGATAAGAATAGCATTGAACAAACAATA
1159066 AACTATAACCTGTTGGAAAGAGAGAACATCAGACCTGAA
66 AACTATAACCTGTTGGAAAGAGAGAACATCAGACCTGAA
*
1159105 ACTACTTTGCGAGAAAAAAACATGGAAGCCAAATATACTGATAAGAATAGCATTGAACAAACAAT
1 ACTACTTTGCG-GAAAAAAACATAGAAGCCAAATATACTGATAAGAATAGCATTGAACAAACAAT
* *
1159170 AAACTATTACCTGTTGGAAGGAGAGAACATCAGACCTGAA
65 AAACTATAACCTGTTGGAAAGAGAGAACATCAGACCTGAA
1159210 TCGTGTGCGC
Statistics
Matches: 96, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
104 10 0.10
105 86 0.90
ACGTcount: A:0.45, C:0.15, G:0.18, T:0.21
Consensus pattern (104 bp):
ACTACTTTGCGGAAAAAAACATAGAAGCCAAATATACTGATAAGAATAGCATTGAACAAACAATA
AACTATAACCTGTTGGAAAGAGAGAACATCAGACCTGAA
Found at i:1160441 original size:4 final size:4
Alignment explanation
Indices: 1160432--1160458 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1160422 CTGCATTATT
1160432 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1160459 TAACTTAATC
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:1160631 original size:26 final size:28
Alignment explanation
Indices: 1160600--1160670 Score: 76
Period size: 26 Copynumber: 2.6 Consensus size: 28
1160590 AAACATTTTT
1160600 TATTTTTATTAATTAATATTTTT-A-AA
1 TATTTTTATTAATTAATATTTTTAATAA
* *
1160626 TATTTTT-TAAATATATTATTTTTAATAA
1 TATTTTTATTAAT-TAATATTTTTAATAA
*
1160654 TATTATTATTATATTAA
1 TATTTTTATTA-ATTAA
1160671 ATAAAATAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
25 4 0.11
26 16 0.46
27 1 0.03
28 8 0.23
29 4 0.11
30 2 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (28 bp):
TATTTTTATTAATTAATATTTTTAATAA
Found at i:1160649 original size:15 final size:15
Alignment explanation
Indices: 1160599--1160660 Score: 60
Period size: 13 Copynumber: 4.3 Consensus size: 15
1160589 TAAACATTTT
*
1160599 TTATTTTTATTAATTA
1 TTATTTTTAATAA-TA
*
1160615 ATATTTTT-A-AATA
1 TTATTTTTAATAATA
*
1160628 TT-TTTTAAAT-ATA
1 TTATTTTTAATAATA
1160641 TTATTTTTAATAATA
1 TTATTTTTAATAATA
1160656 TTATT
1 TTATT
1160661 ATTATATTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
12 4 0.11
13 9 0.24
14 9 0.24
15 8 0.22
16 7 0.19
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTATTTTTAATAATA
Found at i:1160769 original size:16 final size:17
Alignment explanation
Indices: 1160747--1160780 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1160737 TTTTTAAAAA
1160747 ATATATAAAATTATTTTT
1 ATATAT-AAATTATTTTT
*
1160765 ATATATAATTTATTTT
1 ATATATAAATTATTTT
1160781 ATAAATGGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATATATAAATTATTTTT
Found at i:1161202 original size:18 final size:18
Alignment explanation
Indices: 1161156--1161216 Score: 51
Period size: 17 Copynumber: 3.6 Consensus size: 18
1161146 TAGTTTTTTT
*
1161156 ATTT-AAATATT-TTATT
1 ATTTAAAATATTATTATC
*
1161172 TTTTAAAA-A-TATTTAT-
1 ATTTAAAATATTA-TTATC
1161188 ATTTAAAATATTATTATC
1 ATTTAAAATATTATTATC
*
1161206 AATTAAAATAT
1 ATTTAAAATAT
1161217 AATATAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
15 1 0.03
16 11 0.31
17 12 0.33
18 12 0.33
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
ATTTAAAATATTATTATC
Found at i:1161204 original size:17 final size:17
Alignment explanation
Indices: 1161155--1161216 Score: 51
Period size: 16 Copynumber: 3.7 Consensus size: 17
1161145 TTAGTTTTTT
1161155 TATTT-AAATATT-TTA
1 TATTTAAAATATTATTA
*
1161170 TTTTTTAAAA-A-TATTTA
1 -TATTTAAAATATTA-TTA
1161187 TATTTAAAATATTATTA
1 TATTTAAAATATTATTA
*
1161204 TCAATTAAAATAT
1 T-ATTTAAAATAT
1161217 AATATAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
15 1 0.03
16 13 0.35
17 11 0.30
18 12 0.32
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (17 bp):
TATTTAAAATATTATTA
Found at i:1163496 original size:8 final size:8
Alignment explanation
Indices: 1163485--1163514 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1163475 AAAGGATGTG
1163485 TTGATAAC
1 TTGATAAC
*
1163493 TTGATATC
1 TTGATAAC
1163501 TTGATAAC
1 TTGATAAC
1163509 TTGATA
1 TTGATA
1163515 TCTATAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.43
Consensus pattern (8 bp):
TTGATAAC
Found at i:1163506 original size:16 final size:16
Alignment explanation
Indices: 1163485--1163517 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1163475 AAAGGATGTG
1163485 TTGATAACTTGATATC
1 TTGATAACTTGATATC
1163501 TTGATAACTTGATATC
1 TTGATAACTTGATATC
1163517 T
1 T
1163518 ATAAAAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.45
Consensus pattern (16 bp):
TTGATAACTTGATATC
Found at i:1168847 original size:2 final size:2
Alignment explanation
Indices: 1168840--1168878 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1168830 GGATCATCTT
1168840 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1168879 GTATTGAGAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1170838 original size:2 final size:2
Alignment explanation
Indices: 1170831--1170856 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1170821 ACATCATTAA
1170831 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
1170857 GTTTTTAAAA
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:1172217 original size:24 final size:24
Alignment explanation
Indices: 1172188--1172234 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1172178 GTATATTAAC
*
1172188 ATATAT-TAA-ATATATAAAATAA
1 ATATATATAATATATAAAAAATAA
*
1172210 ATATATATAATATTTAAAAAATAA
1 ATATATATAATATATAAAAAATAA
1172234 A
1 A
1172235 GTGAACAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 6 0.29
23 3 0.14
24 12 0.57
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (24 bp):
ATATATATAATATATAAAAAATAA
Found at i:1172376 original size:17 final size:17
Alignment explanation
Indices: 1172356--1172407 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
1172346 TTTTGAGCAA
1172356 AATTATTAAATATTAAT
1 AATTATTAAATATTAAT
*
1172373 AATTTTTAAAATATGT--T
1 AATTATT-AAATAT-TAAT
1172390 AATTATTAAATATTAAT
1 AATTATTAAATATTAAT
1172407 A
1 A
1172408 TTTTTTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 1 0.03
16 6 0.21
17 15 0.52
18 6 0.21
19 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (17 bp):
AATTATTAAATATTAAT
Found at i:1172415 original size:17 final size:17
Alignment explanation
Indices: 1172361--1172416 Score: 53
Period size: 16 Copynumber: 3.3 Consensus size: 17
1172351 AGCAAAATTA
1172361 TTAAATATTAATAATTTT
1 TTAAATATTAAT-ATTTT
* * *
1172379 TAAAATATGT--TAATTA
1 TTAAATAT-TAATATTTT
1172395 TTAAATATTAATATTTT
1 TTAAATATTAATATTTT
1172412 TTAAA
1 TTAAA
1172417 ATTTTAAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 7
0.69 0.14 0.17
Matches are distributed among these distances:
15 1 0.03
16 10 0.34
17 10 0.34
18 7 0.24
19 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
TTAAATATTAATATTTT
Found at i:1174240 original size:20 final size:21
Alignment explanation
Indices: 1174176--1174242 Score: 55
Period size: 26 Copynumber: 2.9 Consensus size: 21
1174166 GCGATTGTAA
1174176 TTTTTTCTGTTAATTAATAAGT
1 TTTTTTCTGTTAATTAAT-AGT
*
1174198 TTTTATTACTTTATTAAATTTAATA-T
1 TTTT-TT-C--TGTT-AA-TTAATAGT
1174224 TTTTTTCTGTTAATTAATA
1 TTTTTTCTGTTAATTAATA
1174243 AGCTCTTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
20 6 0.16
21 2 0.05
22 7 0.19
23 2 0.05
24 2 0.05
25 2 0.05
26 8 0.22
27 3 0.08
28 5 0.14
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.61
Consensus pattern (21 bp):
TTTTTTCTGTTAATTAATAGT
Found at i:1176175 original size:2 final size:2
Alignment explanation
Indices: 1176168--1176200 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1176158 ATTTCCATGT
1176168 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1176201 TTTTTGGTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1177577 original size:43 final size:43
Alignment explanation
Indices: 1177530--1177617 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
1177520 GCAAGTTGTC
1177530 GATAAGGTTCTAAAGTAATATATCACAAATATGTTCCGATGAT
1 GATAAGGTTCTAAAGTAATATATCACAAATATGTTCCGATGAT
1177573 GATAAGGTTCTAAAGTAATATATCACAAATATGTTCCGATGAT
1 GATAAGGTTCTAAAGTAATATATCACAAATATGTTCCGATGAT
1177616 GA
1 GA
1177618 CTGCCGAGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (43 bp):
GATAAGGTTCTAAAGTAATATATCACAAATATGTTCCGATGAT
Found at i:1186864 original size:3 final size:3
Alignment explanation
Indices: 1186856--1186904 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
1186846 CAATAATTTA
1186856 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1186904 A
1 A
1186905 ATCATTGAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1187137 original size:2 final size:2
Alignment explanation
Indices: 1187130--1187154 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1187120 GCAAAAACTA
1187130 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
1187155 ATTTCTTAAA
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:1187378 original size:19 final size:18
Alignment explanation
Indices: 1187336--1187415 Score: 67
Period size: 19 Copynumber: 4.4 Consensus size: 18
1187326 ATTATAATTA
*
1187336 AATTTAAATAAAAATATT
1 AATTTAAATAAAAATAAT
* *
1187354 ATTTTAATTAATAAATAAT
1 AATTTAAATAA-AAATAAT
1187373 AATTTAAAT-AAAATCGAAT
1 AATTTAAATAAAAAT--AAT
*
1187392 CGATTTAAATAAAAA-AAT
1 -AATTTAAATAAAAATAAT
1187410 -ATTTAA
1 AATTTAA
1187416 TTTATATTTA
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
16 6 0.12
17 4 0.08
18 13 0.25
19 16 0.31
20 8 0.16
21 4 0.08
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (18 bp):
AATTTAAATAAAAATAAT
Found at i:1187448 original size:17 final size:17
Alignment explanation
Indices: 1187422--1187457 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1187412 TTAATTTATA
*
1187422 TTTAATTTATCTAATTT
1 TTTAAATTATCTAATTT
*
1187439 TTTAAATTATTTAATTT
1 TTTAAATTATCTAATTT
1187456 TT
1 TT
1187458 GAATCTATCA
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:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTAAATTATCTAATTT
Found at i:1188513 original size:21 final size:21
Alignment explanation
Indices: 1188472--1188519 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
1188462 GAATAAAGCA
* *
1188472 TTAAATTTTTAGTTTTGATATT
1 TTAAATTTTAAATTTTGATA-T
1188494 TTAAATTTTAAATTTT-ATAT
1 TTAAATTTTAAATTTTGATAT
1188514 TTAAAT
1 TTAAAT
1188520 CTCATCATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 7 0.29
21 3 0.12
22 14 0.58
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.60
Consensus pattern (21 bp):
TTAAATTTTAAATTTTGATAT
Found at i:1189239 original size:23 final size:23
Alignment explanation
Indices: 1189196--1189239 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
1189186 AATAATTTGA
*
1189196 ATCATAAACTTGTGGTTAAGAAG
1 ATCATAAACTTGTGGTCAAGAAG
*
1189219 ATCATAATCGTTG-GGTCAAGA
1 ATCATAAAC-TTGTGGTCAAGA
1189240 TTGAGTTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 15 0.83
24 3 0.17
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (23 bp):
ATCATAAACTTGTGGTCAAGAAG
Found at i:1189271 original size:2 final size:2
Alignment explanation
Indices: 1189264--1189297 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1189254 TGAAAAATAC
1189264 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
1189298 CCCTCTACCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1190681 original size:61 final size:60
Alignment explanation
Indices: 1190563--1190684 Score: 199
Period size: 61 Copynumber: 2.0 Consensus size: 60
1190553 CTGTAGGTGA
* *
1190563 ATTAATAAGCACTGTGGCACTGTCACTTTTTTCATCAAAAACGGTTAGCACACGTTTTTC
1 ATTAATAAGCACTGTGGCACTGCCACTTTTTTCATCAAAAACGGTTAGCACAAGTTTTTC
* *
1190623 ATTAATAAGCATTGTGGCACTGCCATTTTTTTTCATCAAAAACGGTTAGCACAAGTTTTTC
1 ATTAATAAGCACTGTGGCACTGCCA-CTTTTTTCATCAAAAACGGTTAGCACAAGTTTTTC
1190684 A
1 A
1190685 CTTATTTCGA
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
60 23 0.40
61 34 0.60
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.36
Consensus pattern (60 bp):
ATTAATAAGCACTGTGGCACTGCCACTTTTTTCATCAAAAACGGTTAGCACAAGTTTTTC
Found at i:1196560 original size:15 final size:15
Alignment explanation
Indices: 1196523--1196560 Score: 62
Period size: 13 Copynumber: 2.7 Consensus size: 15
1196513 AATAAAAAAT
1196523 TATTCACTGACTAGC
1 TATTCACTGACTAGC
1196538 TATT--CTGACTAGC
1 TATTCACTGACTAGC
1196551 TATTCACTGA
1 TATTCACTGA
1196561 GGACATAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 13 0.62
15 8 0.38
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (15 bp):
TATTCACTGACTAGC
Found at i:1201890 original size:2 final size:2
Alignment explanation
Indices: 1201883--1201918 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1201873 TTATTATTAT
*
1201883 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1201919 CACACACCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1202149 original size:9 final size:9
Alignment explanation
Indices: 1202135--1202165 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1202125 TAAATGCATG
*
1202135 AAAAGGTCA
1 AAAAGGTGA
1202144 AAAAGGTGA
1 AAAAGGTGA
1202153 AAAAGGTGA
1 AAAAGGTGA
1202162 AAAA
1 AAAA
1202166 ATGTGAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.61, C:0.03, G:0.26, T:0.10
Consensus pattern (9 bp):
AAAAGGTGA
Found at i:1202439 original size:2 final size:2
Alignment explanation
Indices: 1202429--1202463 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1202419 TTTTTTTCTT
*
1202429 TA TA CA 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
1202464 GGATGGATTG
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:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1205457 original size:2 final size:2
Alignment explanation
Indices: 1205450--1205474 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1205440 ACATACATAC
1205450 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
1205475 CTTGTAATGG
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:1208104 original size:11 final size:11
Alignment explanation
Indices: 1208088--1208121 Score: 50
Period size: 11 Copynumber: 2.9 Consensus size: 11
1208078 TTCCATCTTC
1208088 TTTTATTTATA
1 TTTTATTTATA
1208099 TTTTATTTATTA
1 TTTTATTTA-TA
1208111 TTTCTATTTAT
1 TTT-TATTTAT
1208122 TTTCAATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 9 0.43
12 6 0.29
13 6 0.29
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTATTTATA
Found at i:1208113 original size:18 final size:17
Alignment explanation
Indices: 1208090--1208123 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1208080 CCATCTTCTT
1208090 TTATTTATATTTTATTTA
1 TTATTTATA-TTTATTTA
*
1208108 TTATTTCTATTTATTT
1 TTATTTATATTTATTT
1208124 TCAATTATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (17 bp):
TTATTTATATTTATTTA
Found at i:1209193 original size:15 final size:13
Alignment explanation
Indices: 1209164--1209188 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1209154 AATTAATTAA
1209164 AATATTATTTTTT
1 AATATTATTTTTT
1209177 AATATTATTTTT
1 AATATTATTTTT
1209189 ATTAAATGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
AATATTATTTTTT
Found at i:1209494 original size:17 final size:17
Alignment explanation
Indices: 1209467--1209512 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
1209457 AATTATTATT
1209467 AATAA-AAATTTAATTA
1 AATAATAAATTTAATTA
*
1209483 TAA-AATAAATTTTATTA
1 -AATAATAAATTTAATTA
*
1209500 AATAATAATTTTA
1 AATAATAAATTTA
1209513 TATTTTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 4 0.17
17 20 0.83
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AATAATAAATTTAATTA
Found at i:1209523 original size:13 final size:13
Alignment explanation
Indices: 1209505--1209530 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1209495 TATTAAATAA
1209505 TAATTTTATATTT
1 TAATTTTATATTT
1209518 TAATTTTATATTT
1 TAATTTTATATTT
1209531 AAAATTTAAA
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:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TAATTTTATATTT
Found at i:1210105 original size:20 final size:20
Alignment explanation
Indices: 1210044--1210105 Score: 62
Period size: 18 Copynumber: 3.3 Consensus size: 20
1210034 GTATTATTTT
*
1210044 TTATGTGTCAA-AATTATTA
1 TTATATGTCAATAATTATTA
*
1210063 TTA-AT-TTATATAATT-TT-
1 TTATATGTCA-ATAATTATTA
1210080 TTATATGTCAATAATTATTA
1 TTATATGTCAATAATTATTA
1210100 TTATAT
1 TTATAT
1210106 ATTTTGATAG
Statistics
Matches: 34, Mismatches: 3, Indels: 11
0.71 0.06 0.23
Matches are distributed among these distances:
17 5 0.15
18 12 0.35
19 11 0.32
20 6 0.18
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (20 bp):
TTATATGTCAATAATTATTA
Found at i:1210658 original size:16 final size:17
Alignment explanation
Indices: 1210631--1210671 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
1210621 TTTTTCAAAT
1210631 AAATTTTA-TTAATT-A
1 AAATTTTATTTAATTAA
*
1210646 TAATTTTATTTAATTAA
1 AAATTTTATTTAATTAA
1210663 AAATTTTAT
1 AAATTTTAT
1210672 AAATATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 7 0.32
16 6 0.27
17 9 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AAATTTTATTTAATTAA
Found at i:1211066 original size:11 final size:11
Alignment explanation
Indices: 1211050--1211074 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1211040 TCTTTCTTTC
1211050 TCTCATTTTTT
1 TCTCATTTTTT
1211061 TCTCATTTTTT
1 TCTCATTTTTT
1211072 TCT
1 TCT
1211075 TTTTCTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.20, G:0.00, T:0.72
Consensus pattern (11 bp):
TCTCATTTTTT
Found at i:1211573 original size:23 final size:23
Alignment explanation
Indices: 1211547--1211604 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
1211537 AATACAAAAT
*
1211547 TAAAAATTAATTAAAACATAATA
1 TAAAAATTAAATAAAACATAATA
* *
1211570 TAAAAAATAAATATAACATAATA
1 TAAAAATTAAATAAAACATAATA
*
1211593 TACAAATATAAA
1 TAAAAAT-TAAA
1211605 AAATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 25 0.86
24 4 0.14
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAAAATTAAATAAAACATAATA
Found at i:1211616 original size:31 final size:30
Alignment explanation
Indices: 1211566--1211669 Score: 90
Period size: 31 Copynumber: 3.5 Consensus size: 30
1211556 ATTAAAACAT
**
1211566 AATATAAAAAATAAATATAACATAATATACA
1 AATATAAAAAATATTTATAA-ATAATATACA
* *
1211597 AATATAAAAAATATTTATAAATATTATATA
1 AATATAAAAAATATTTATAAATAATATACA
* *
1211627 AAT-T-TATAATATTT-TAAATAATA-ACA
1 AATATAAAAAATATTTATAAATAATATACA
1211653 AATTAAATAAAAAATAT
1 AA-T--ATAAAAAATAT
1211670 AAACCCTTAA
Statistics
Matches: 58, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
26 4 0.07
27 9 0.16
28 8 0.14
29 1 0.02
30 12 0.21
31 24 0.41
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (30 bp):
AATATAAAAAATATTTATAAATAATATACA
Found at i:1211722 original size:26 final size:26
Alignment explanation
Indices: 1211689--1211755 Score: 82
Period size: 26 Copynumber: 2.5 Consensus size: 26
1211679 AATTTTTTTT
*
1211689 ATATATAAAATAATAAATACATTA-AA
1 ATATATAAAA-AATAAATAAATTATAA
* *
1211715 ATATATAAAAAACAAAATAAATTATTA
1 ATATATAAAAAA-TAAATAAATTATAA
1211742 ATATATAAAAAATA
1 ATATATAAAAAATA
1211756 TACAAAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
25 2 0.06
26 20 0.57
27 13 0.37
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (26 bp):
ATATATAAAAAATAAATAAATTATAA
Found at i:1212240 original size:24 final size:24
Alignment explanation
Indices: 1212187--1212240 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
1212177 GTAAAATATA
1212187 ATTTTAAAATAATAAATAATAAAT
1 ATTTTAAAATAATAAATAATAAAT
* * **
1212211 AATTT-AAATATATTAATAATTCAT
1 ATTTTAAAATA-ATAAATAATAAAT
1212235 ATTTTA
1 ATTTTA
1212241 TATTATAATC
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
ATTTTAAAATAATAAATAATAAAT
Found at i:1212254 original size:18 final size:20
Alignment explanation
Indices: 1212219--1212255 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
1212209 ATAATTTAAA
1212219 TATATTAATAATTCATATTT
1 TATATTAATAATTCATATTT
1212239 TATATT-ATAA-TCATATT
1 TATATTAATAATTCATATT
1212256 ATTTTTATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 4 0.24
20 6 0.35
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (20 bp):
TATATTAATAATTCATATTT
Found at i:1212339 original size:33 final size:33
Alignment explanation
Indices: 1212297--1212360 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
1212287 ATTATTTATA
1212297 ATAAATTTAAATATATT-AAACATTTATATTTT
1 ATAAATTTAAATATATTCAAACATTTATATTTT
* *
1212329 ATAAATTTTAAATATATTCATATATTTATATT
1 ATAAA-TTTAAATATATTCAAACATTTATATT
1212361 ATTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 5 0.18
33 12 0.43
34 11 0.39
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (33 bp):
ATAAATTTAAATATATTCAAACATTTATATTTT
Found at i:1212400 original size:13 final size:13
Alignment explanation
Indices: 1212358--1212401 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
1212348 ATATATTTAT
1212358 ATTATTTTTTAAA
1 ATTATTTTTTAAA
* *
1212371 ATTATATATTT-AT
1 ATTAT-TTTTTAAA
1212384 ATTATTTTTTAAA
1 ATTATTTTTTAAA
1212397 ATTAT
1 ATTAT
1212402 CTCATATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 4 0.16
13 17 0.68
14 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
ATTATTTTTTAAA
Found at i:1212418 original size:29 final size:29
Alignment explanation
Indices: 1212334--1212423 Score: 109
Period size: 26 Copynumber: 3.2 Consensus size: 29
1212324 ATTTTATAAA
1212334 TTTT-AAATATATTCATATATTTATATTATT
1 TTTTAAAAT-TATTCATAT-TTTATATTATT
1212364 TTTTAAAATTA-T-ATA-TTTATATTATT
1 TTTTAAAATTATTCATATTTTATATTATT
*
1212390 TTTTAAAATTATCTCATATTTTA-AATATT
1 TTTTAAAATTAT-TCATATTTTATATTATT
1212419 TTTTA
1 TTTTA
1212424 TATAATTAAA
Statistics
Matches: 54, Mismatches: 1, Indels: 11
0.82 0.02 0.17
Matches are distributed among these distances:
26 22 0.41
28 4 0.07
29 14 0.26
30 10 0.19
31 4 0.07
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (29 bp):
TTTTAAAATTATTCATATTTTATATTATT
Found at i:1212577 original size:114 final size:114
Alignment explanation
Indices: 1212416--1212634 Score: 413
Period size: 114 Copynumber: 1.9 Consensus size: 114
1212406 TATTTTAAAT
1212416 ATTTTTTATATAATTAAAAAATTATCAAATAATCTGATTGGATGATGAAAAATAATTTCTTAATT
1 ATTTTTTATATAATTAAAAAATTATCAAATAATCTGATTGGATGATGAAAAATAATTTCTTAATT
*
1212481 TTTCAT-AAAAATTTAAATTCGAACATGCAACCGACACATGAGACAACA
66 TTTCATAAAAAATTTAAATTCAAACATGCAACCGACACATGAGACAACA
1212529 ATTTTTTATATAATTAAAAAAATTATCAAATAATCTGATTGGATGATGAAAAATAATTTCTTAAT
1 ATTTTTTATATAATT-AAAAAATTATCAAATAATCTGATTGGATGATGAAAAATAATTTCTTAAT
1212594 TTTTCATAAAAAATTTAAATTCAAACATGCAACCGACACAT
65 TTTTCATAAAAAATTTAAATTCAAACATGCAACCGACACAT
1212635 TAAATAAAAA
Statistics
Matches: 103, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
113 15 0.15
114 56 0.54
115 32 0.31
ACGTcount: A:0.46, C:0.11, G:0.08, T:0.36
Consensus pattern (114 bp):
ATTTTTTATATAATTAAAAAATTATCAAATAATCTGATTGGATGATGAAAAATAATTTCTTAATT
TTTCATAAAAAATTTAAATTCAAACATGCAACCGACACATGAGACAACA
Found at i:1213127 original size:14 final size:15
Alignment explanation
Indices: 1213108--1213141 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
1213098 ACTTACGTAA
1213108 AAAAATTTAAAA-AT
1 AAAAATTTAAAAGAT
1213122 AAAAA-TTAAAAGAT
1 AAAAATTTAAAAGAT
1213136 AAAAAT
1 AAAAAT
1213142 ATTTTTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (15 bp):
AAAAATTTAAAAGAT
Found at i:1214692 original size:12 final size:12
Alignment explanation
Indices: 1214677--1214730 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
1214667 TAATTATCTC
1214677 TAATTTTATATT
1 TAATTTTATATT
* *
1214689 TAATTTTGTGTAT
1 TAATTTTATAT-T
1214702 T-ATTTTATA-T
1 TAATTTTATATT
1214712 T--TTTTATATT
1 TAATTTTATATT
1214722 TAATTTTAT
1 TAATTTTAT
1214731 TAAAATATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
9 7 0.21
10 4 0.12
12 21 0.62
13 2 0.06
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.69
Consensus pattern (12 bp):
TAATTTTATATT
Found at i:1214718 original size:14 final size:14
Alignment explanation
Indices: 1214680--1214728 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 14
1214670 TTATCTCTAA
1214680 TTTTATATTTAATT
1 TTTTATATTTAATT
1214694 TTGTGTATTATTTTATATT
1 TT-T-TA-TA-TTTA-ATT
1214713 TTTTATATTTAATT
1 TTTTATATTTAATT
1214727 TT
1 TT
1214729 ATTAAAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
14 7 0.23
15 5 0.17
16 4 0.13
17 4 0.13
18 5 0.17
19 5 0.17
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.71
Consensus pattern (14 bp):
TTTTATATTTAATT
Found at i:1215193 original size:28 final size:28
Alignment explanation
Indices: 1215138--1215212 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 28
1215128 GACTATTATA
* *
1215138 AATATTT-TTATTATTA-TAATAATCATT
1 AATATTTATTA-TATTATTAACAACCATT
1215165 AATATTTATTATATTATTAACAACCATT
1 AATATTTATTATATTATTAACAACCATT
* * *
1215193 AAAATTATATTTTATCATTA
1 AATATT-TATTATATTATTA
1215213 TATTATATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
27 12 0.30
28 17 0.43
29 11 0.28
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.51
Consensus pattern (28 bp):
AATATTTATTATATTATTAACAACCATT
Found at i:1215206 original size:59 final size:58
Alignment explanation
Indices: 1215096--1215214 Score: 136
Period size: 59 Copynumber: 2.0 Consensus size: 58
1215086 AACTAACAAA
* * * *
1215096 AATAGTCATTATTATTTATTATATTTTGAAATGACTATTATAAATATTTTTATTATTAT
1 AATAATCATTAATATTTATTATATTTTGAAA-GACCATTATAAATATTTTTATCATTAT
1215155 AATAATCATTAATATTTATTATATTATT-AACA-ACCATTA-AAATTATATTTTATCATTAT
1 AATAATCATTAATATTTATTATATT-TTGAA-AGACCATTATAAA-TAT-TTTTATCATTAT
1215214 A
1 A
1215215 TTATATATAT
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
57 3 0.06
58 9 0.17
59 37 0.71
60 3 0.06
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.50
Consensus pattern (58 bp):
AATAATCATTAATATTTATTATATTTTGAAAGACCATTATAAATATTTTTATCATTAT
Found at i:1216081 original size:2 final size:2
Alignment explanation
Indices: 1216074--1216098 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1216064 ATACCCTCAT
1216074 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 T
1216099 TGGGGGTGGA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1216772 original size:2 final size:2
Alignment explanation
Indices: 1216765--1216790 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1216755 TAATATTATG
1216765 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
1216791 GCAGGGATGA
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:1217982 original size:2 final size:2
Alignment explanation
Indices: 1217975--1218004 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1217965 TTAATTATCC
*
1217975 TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1218005 CATACACACA
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):
TA
Found at i:1219383 original size:48 final size:48
Alignment explanation
Indices: 1219317--1219425 Score: 137
Period size: 48 Copynumber: 2.3 Consensus size: 48
1219307 ATAAAGCTGA
* * * * ** *
1219317 GAGTGGAATGTAATATTATCGGTTTCTGATTGATGTTATAAAAACTGC
1 GAGTGAAATGGAACATTATCCGTTTCTGATAAATGCTATAAAAACTGC
*
1219365 GGGTGAAATGGAACATTATCCGTTTCTGATAAATGCTATAAAAACTGC
1 GAGTGAAATGGAACATTATCCGTTTCTGATAAATGCTATAAAAACTGC
*
1219413 GAGTGGAATGGAA
1 GAGTGAAATGGAA
1219426 TGCTATCATT
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.34, C:0.10, G:0.25, T:0.31
Consensus pattern (48 bp):
GAGTGAAATGGAACATTATCCGTTTCTGATAAATGCTATAAAAACTGC
Found at i:1219439 original size:48 final size:48
Alignment explanation
Indices: 1219333--1219447 Score: 122
Period size: 48 Copynumber: 2.4 Consensus size: 48
1219323 AATGTAATAT
* ** * * *
1219333 TATCGGTTTCTGATTGATGTTATAAAAACTGCGGGTGAAATGGAACAT
1 TATCAGTTTCTGATAAATGCTATAAAAACTGCGAGTGAAATGGAACAC
* * **
1219381 TATCCGTTTCTGATAAATGCTATAAAAACTGCGAGTGGAATGGAATGC
1 TATCAGTTTCTGATAAATGCTATAAAAACTGCGAGTGAAATGGAACAC
* *
1219429 TATCATTTTCTAATAAATG
1 TATCAGTTTCTGATAAATG
1219448 TGTGGGAGTT
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 55 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.34
Consensus pattern (48 bp):
TATCAGTTTCTGATAAATGCTATAAAAACTGCGAGTGAAATGGAACAC
Found at i:1220768 original size:31 final size:31
Alignment explanation
Indices: 1220732--1220794 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 31
1220722 AAAGGACATA
*
1220732 TTTATATAA-ATTTTGATATATTTT-TTTATAT
1 TTTATATAATATTTTAAT-TATTTTATTT-TAT
1220763 TTTATATAATATTTTAATTATTTTATTTTAT
1 TTTATATAATATTTTAATTATTTTATTTTAT
1220794 T
1 T
1220795 ATATTTTCGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 19 0.66
32 10 0.34
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (31 bp):
TTTATATAATATTTTAATTATTTTATTTTAT
Found at i:1220774 original size:12 final size:11
Alignment explanation
Indices: 1220732--1220788 Score: 52
Period size: 12 Copynumber: 5.5 Consensus size: 11
1220722 AAAGGACATA
*
1220732 TTTATATAAAT
1 TTTATATATAT
1220743 TTTGATATAT-T
1 TTT-ATATATAT
1220754 TTT-T-TATAT
1 TTTATATATAT
1220763 TTTATATAATAT
1 TTTATAT-ATAT
1220775 TTTA-AT-TAT
1 TTTATATATAT
1220784 TTTAT
1 TTTAT
1220789 TTTATTATAT
Statistics
Matches: 39, Mismatches: 1, Indels: 13
0.74 0.02 0.25
Matches are distributed among these distances:
8 3 0.08
9 12 0.31
10 1 0.03
11 10 0.26
12 13 0.33
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (11 bp):
TTTATATATAT
Found at i:1223160 original size:28 final size:28
Alignment explanation
Indices: 1223117--1223181 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
1223107 TTATATTGTT
*
1223117 AATA-TTTAAATTTATTA-TAAAATATA
1 AATATTTTAAATATATTATTAAAATATA
*
1223143 AATATTTTGAAATATATTATTAAAATATT
1 AATATTTT-AAATATATTATTAAAATATA
1223172 AAT-TTTTAAA
1 AATATTTTAAA
1223182 GTAAATATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 4 0.12
27 6 0.18
28 13 0.38
29 11 0.32
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (28 bp):
AATATTTTAAATATATTATTAAAATATA
Found at i:1223486 original size:20 final size:21
Alignment explanation
Indices: 1223439--1223487 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
1223429 ACATAATTTT
* *
1223439 AAATTACTTATTTATTATATT
1 AAATTATTTATTTATTATATA
*
1223460 TAA-TATTTATTTATTAT-TA
1 AAATTATTTATTTATTATATA
1223479 AAATTATTT
1 AAATTATTT
1223488 TAAATATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 3 0.13
20 18 0.78
21 2 0.09
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
AAATTATTTATTTATTATATA
Found at i:1223787 original size:22 final size:22
Alignment explanation
Indices: 1223761--1223813 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
1223751 TTAATAATAA
1223761 AATTTTAAAATTATTTTAT-ATT
1 AATTTTAAAA-TATTTTATAATT
* *
1223783 AATTTTTATATATTTTATAATT
1 AATTTTAAAATATTTTATAATT
*
1223805 AAATTTAAA
1 AATTTTAAA
1223814 TACAAATATT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 8 0.32
22 17 0.68
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
AATTTTAAAATATTTTATAATT
Found at i:1223811 original size:21 final size:21
Alignment explanation
Indices: 1223772--1223811 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1223762 ATTTTAAAAT
*
1223772 TATTTTATATTAATTTTTATA
1 TATTTTATATTAATATTTATA
1223793 TATTTTATAATTAA-ATTTA
1 TATTTTAT-ATTAATATTTA
1223812 AATACAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTTTATATTAATATTTATA
Found at i:1223997 original size:2 final size:2
Alignment explanation
Indices: 1223990--1224021 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1223980 CATCACCATT
*
1223990 TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1224022 ATTCATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1224595 original size:2 final size:2
Alignment explanation
Indices: 1224588--1224618 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1224578 ATTAGAATAC
1224588 AT AT AT 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 AT AT AT A
1224619 CACACACATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1227255 original size:44 final size:44
Alignment explanation
Indices: 1227191--1227285 Score: 172
Period size: 44 Copynumber: 2.1 Consensus size: 44
1227181 CGGTATAGAA
*
1227191 ATTTAATCTTCATATTTTAATTCCATCCATATTTGGCAACTGGAT
1 ATTT-ATCTTCATATTTTAATTCCATCCATATTTGGCAACGGGAT
1227236 ATTTATCTTCATATTTTAATTCCATCCATATTTGGCAACGGGAT
1 ATTTATCTTCATATTTTAATTCCATCCATATTTGGCAACGGGAT
1227280 ATTTAT
1 ATTTAT
1227286 ATATGTGTGT
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 45 0.92
45 4 0.08
ACGTcount: A:0.28, C:0.17, G:0.09, T:0.45
Consensus pattern (44 bp):
ATTTATCTTCATATTTTAATTCCATCCATATTTGGCAACGGGAT
Found at i:1227602 original size:33 final size:34
Alignment explanation
Indices: 1227531--1227635 Score: 92
Period size: 33 Copynumber: 3.1 Consensus size: 34
1227521 TTATATATTA
* * **
1227531 ATATTATATTAATATTTTTTTA-TTATATCATAATT
1 ATATT-TAATAATATTTTTTTATTTAAATTTTAA-T
1227566 ATATTTAA-AATATTTTTTTATTTAAATTTTAAT
1 ATATTTAATAATATTTTTTTATTTAAATTTTAAT
* * *
1227599 ATA-TTAATAAT-TTATTTTATATAAATTTATAAA
1 ATATTTAATAATATTTTTTTATTTAAATTT-TAAT
1227632 ATAT
1 ATAT
1227636 ATATTTACAT
Statistics
Matches: 59, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
32 19 0.32
33 25 0.42
34 10 0.17
35 5 0.08
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (34 bp):
ATATTTAATAATATTTTTTTATTTAAATTTTAAT
Found at i:1240339 original size:13 final size:14
Alignment explanation
Indices: 1240321--1240353 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1240311 TATAAAAATT
*
1240321 AAAATT-TTTTTAA
1 AAAATTATTTATAA
1240334 AAAATTATTTATAA
1 AAAATTATTTATAA
1240348 AAAATT
1 AAAATT
1240354 CTCACAACAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AAAATTATTTATAA
Found at i:1240726 original size:12 final size:12
Alignment explanation
Indices: 1240711--1240765 Score: 58
Period size: 12 Copynumber: 4.6 Consensus size: 12
1240701 ATAAATTTTG
*
1240711 ATATATTATATT
1 ATATTTTATATT
*
1240723 ATATTTTATATA
1 ATATTTTATATT
1240735 ATATTTTA-ATT
1 ATATTTTATATT
*
1240746 ATTTTTTTATATT
1 A-TATTTTATATT
*
1240759 TTATTTT
1 ATATTTT
1240766 TTTATGTCTA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
11 3 0.09
12 29 0.83
13 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTTTATATT
Found at i:1240733 original size:31 final size:31
Alignment explanation
Indices: 1240658--1240762 Score: 115
Period size: 31 Copynumber: 3.3 Consensus size: 31
1240648 GTTAAAAGTG
*
1240658 ATATATTTATATAAATTTTAATAAATTAATAATT
1 ATAT-TTTATATAAATTTTAATATATT-AT-ATT
*
1240692 -TATTTTTATATAAATTTTGATATATTATATT
1 ATA-TTTTATATAAATTTTAATATATTATATT
* *
1240723 ATATTTTATATAATATTTTAAT-TATTTTTTT
1 ATATTTTATATAA-ATTTTAATATATTATATT
1240754 ATATTTTAT
1 ATATTTTAT
1240763 TTTTTTATGT
Statistics
Matches: 63, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
31 29 0.46
32 11 0.17
33 22 0.35
34 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (31 bp):
ATATTTTATATAAATTTTAATATATTATATT
Found at i:1240780 original size:18 final size:17
Alignment explanation
Indices: 1240740--1240781 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 17
1240730 ATATAATATT
1240740 TTAATTATTTTTTTATA
1 TTAATTATTTTTTTATA
*
1240757 TT--TTATTTTTTTATG
1 TTAATTATTTTTTTATA
1240772 TCTAATTATT
1 T-TAATTATT
1240782 GCATCTAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
15 13 0.62
16 1 0.05
17 2 0.10
18 5 0.24
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (17 bp):
TTAATTATTTTTTTATA
Found at i:1240914 original size:28 final size:26
Alignment explanation
Indices: 1240882--1240950 Score: 66
Period size: 28 Copynumber: 2.5 Consensus size: 26
1240872 AATTGAATAA
1240882 TTTATATGTTTATAGTATATTCAAAATT
1 TTTATAT-TTTATAGTATATTCAAAA-T
* * *
1240910 TTTATATATTATAATTATATTTAAAAT
1 TTTATATTTTAT-AGTATATTCAAAAT
*
1240937 ATTATATATTTATA
1 TTTATAT-TTTATA
1240951 TAAATTTCGA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
27 12 0.35
28 22 0.65
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (26 bp):
TTTATATTTTATAGTATATTCAAAAT
Found at i:1240954 original size:20 final size:20
Alignment explanation
Indices: 1240915--1240954 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1240905 AAATTTTTAT
*
1240915 ATATTATAATTATATTTAAA
1 ATATTATAATTATATATAAA
1240935 ATATTATATATT-TATATAAA
1 ATATTATA-ATTATATATAAA
1240955 TTTCGATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATTATAATTATATATAAA
Found at i:1241045 original size:12 final size:11
Alignment explanation
Indices: 1241001--1241046 Score: 51
Period size: 12 Copynumber: 4.2 Consensus size: 11
1240991 AACATAATTA
*
1241001 TATATTTATAT
1 TATATTTATTT
1241012 TAT-TTTATTT
1 TATATTTATTT
1241022 T-TATTATATTT
1 TATATT-TATTT
1241033 TATATCTTATTT
1 TATAT-TTATTT
1241045 TA
1 TA
1241047 ATTATTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
9 1 0.03
10 9 0.30
11 9 0.30
12 10 0.33
13 1 0.03
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (11 bp):
TATATTTATTT
Found at i:1241045 original size:23 final size:24
Alignment explanation
Indices: 1241001--1241057 Score: 71
Period size: 23 Copynumber: 2.3 Consensus size: 24
1240991 AACATAATTA
* *
1241001 TATATTTATATTATTTTATTTTTAT
1 TATATTT-TATTATCTTATTTTAAT
1241026 TATATTTTA-TATCTTATTTTAAT
1 TATATTTTATTATCTTATTTTAAT
1241049 TATTATTTT
1 TA-TATTTT
1241058 TTTGTTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 14 0.48
24 8 0.28
25 7 0.24
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (24 bp):
TATATTTTATTATCTTATTTTAAT
Found at i:1243044 original size:29 final size:28
Alignment explanation
Indices: 1242994--1243049 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
1242984 GTTAATATTT
*
1242994 AAATATATTATTAAAATGTTATTATTTTG
1 AAATATATTATTAAAATATTATT-TTTTG
*
1243023 AAATATATTATTAAATTATTATTTTTT
1 AAATATATTATTAAAATATTATTTTTT
1243050 AAAAGTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (28 bp):
AAATATATTATTAAAATATTATTTTTTG
Found at i:1243766 original size:21 final size:21
Alignment explanation
Indices: 1243740--1243790 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1243730 AATTAATAAA
1243740 AAATTTAAAAAATTTAT-ATT
1 AAATTTAAAAAATTTATAATT
* * *
1243760 AATATTTATATATTTTATAATT
1 AA-ATTTAAAAAATTTATAATT
1243782 AAATTTAAA
1 AAATTTAAA
1243791 TAAAAATATT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 2 0.08
21 18 0.72
22 5 0.20
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AAATTTAAAAAATTTATAATT
Found at i:1245028 original size:2 final size:2
Alignment explanation
Indices: 1245021--1245046 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1245011 AGCTGCTTTA
1245021 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
1245047 TGCACTTGAT
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:1245104 original size:2 final size:2
Alignment explanation
Indices: 1245097--1245138 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1245087 TATTATGATA
1245097 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1245139 CAGGGATGAC
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1247384 original size:2 final size:2
Alignment explanation
Indices: 1247379--1247410 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1247369 TATATATATA
1247379 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1247411 AAAATGATAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1247683 original size:20 final size:20
Alignment explanation
Indices: 1247660--1247699 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1247650 TTTTTTTATT
1247660 ATATTATAATTATATTTAAA
1 ATATTATAATTATATTTAAA
* * *
1247680 ATATTTTATTTTTATTTAAA
1 ATATTATAATTATATTTAAA
1247700 TTTTAATAAA
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:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATATTATAATTATATTTAAA
Found at i:1247758 original size:15 final size:15
Alignment explanation
Indices: 1247716--1247759 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
1247706 TAAATTAATA
* *
1247716 ATTTATATTATATAA
1 ATTTATATAATATAT
*
1247731 ATTT-TAAAATATAT
1 ATTTATATAATATAT
1247745 ATTTATATAATATAT
1 ATTTATATAATATAT
1247760 TAATTAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATTTATATAATATAT
Found at i:1251504 original size:3 final size:3
Alignment explanation
Indices: 1251498--1251525 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1251488 CTAATGGTGC
1251498 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1251526 AACATTAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1255329 original size:16 final size:16
Alignment explanation
Indices: 1255308--1255341 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1255298 AATTAAAACT
1255308 ATATAAACAAAATGAA
1 ATATAAACAAAATGAA
1255324 ATATAAACAAAATGAA
1 ATATAAACAAAATGAA
1255340 AT
1 AT
1255342 TAAGGTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.21
Consensus pattern (16 bp):
ATATAAACAAAATGAA
Found at i:1256437 original size:2 final size:2
Alignment explanation
Indices: 1256430--1256462 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1256420 CTTTTCTTTC
1256430 AT AT AT AT 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 AT AT AT AT A
1256463 GACAGATCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1264149 original size:29 final size:29
Alignment explanation
Indices: 1264116--1264177 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
1264106 TCGGATCAAT
1264116 TGAACAACTTGTTTTAGTTGATCAGAAGA
1 TGAACAACTTGTTTTAGTTGATCAGAAGA
1264145 TGAACAACTTGTTTTAGTTGATCAGAAGA
1 TGAACAACTTGTTTTAGTTGATCAGAAGA
1264174 TGAA
1 TGAA
1264178 GACCCAGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.35, C:0.10, G:0.21, T:0.34
Consensus pattern (29 bp):
TGAACAACTTGTTTTAGTTGATCAGAAGA
Found at i:1266943 original size:45 final size:45
Alignment explanation
Indices: 1266879--1267022 Score: 216
Period size: 45 Copynumber: 3.0 Consensus size: 45
1266869 TTATGGACAA
1266879 GAGTTGGCACAATGGTTTCGTCTGTTAAATGTTAATAGTTGCATT
1 GAGTTGGCACAATGGTTTCGTCTGTTAAATGTTAATAGTTGCATT
*
1266924 GAGTTGGCACAATGGTTTCGTCTGTTAAATGTTAAATGTTAATAGTTGCATG
1 GAGTTGGCACAATGGTTTCGTC-------TGTTAAATGTTAATAGTTGCATT
1266976 GAGTTGGCACAATGGTTTCGTCTGTTAAATGTTAATAGTTGCATT
1 GAGTTGGCACAATGGTTTCGTCTGTTAAATGTTAATAGTTGCATT
1267021 GA
1 GA
1267023 CTTACTGCCT
Statistics
Matches: 90, Mismatches: 2, Indels: 14
0.85 0.02 0.13
Matches are distributed among these distances:
45 46 0.51
52 44 0.49
ACGTcount: A:0.26, C:0.10, G:0.25, T:0.39
Consensus pattern (45 bp):
GAGTTGGCACAATGGTTTCGTCTGTTAAATGTTAATAGTTGCATT
Found at i:1266980 original size:52 final size:52
Alignment explanation
Indices: 1266901--1267010 Score: 211
Period size: 52 Copynumber: 2.1 Consensus size: 52
1266891 TGGTTTCGTC
*
1266901 TGTTAAATGTTAATAGTTGCATTGAGTTGGCACAATGGTTTCGTCTGTTAAA
1 TGTTAAATGTTAATAGTTGCATGGAGTTGGCACAATGGTTTCGTCTGTTAAA
1266953 TGTTAAATGTTAATAGTTGCATGGAGTTGGCACAATGGTTTCGTCTGTTAAA
1 TGTTAAATGTTAATAGTTGCATGGAGTTGGCACAATGGTTTCGTCTGTTAAA
1267005 TGTTAA
1 TGTTAA
1267011 TAGTTGCATT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 57 1.00
ACGTcount: A:0.27, C:0.09, G:0.24, T:0.40
Consensus pattern (52 bp):
TGTTAAATGTTAATAGTTGCATGGAGTTGGCACAATGGTTTCGTCTGTTAAA
Found at i:1267498 original size:13 final size:14
Alignment explanation
Indices: 1267461--1267507 Score: 55
Period size: 13 Copynumber: 3.5 Consensus size: 14
1267451 TTTTATTAAA
1267461 ATATTTATAA-ATTT
1 ATATTT-TAATATTT
*
1267475 ATA-TTTGATATTT
1 ATATTTTAATATTT
1267488 A-ATTTTAATATTT
1 ATATTTTAATATTT
1267501 ATATTTT
1 ATATTTT
1267508 TTAAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
12 3 0.11
13 17 0.61
14 8 0.29
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (14 bp):
ATATTTTAATATTT
Found at i:1267713 original size:2 final size:2
Alignment explanation
Indices: 1267706--1267748 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1267696 TAAGTGCTTT
1267706 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1267748 T
1 T
1267749 TATGACAGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1270002 original size:24 final size:24
Alignment explanation
Indices: 1269970--1270018 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
1269960 ATTAAATTTG
*
1269970 TGTTTTCCCTTTCCGTCTTCCTCC
1 TGTTTTCCCTTTCCATCTTCCTCC
1269994 TGTTTTCCCTTTCCATCTTCCTCC
1 TGTTTTCCCTTTCCATCTTCCTCC
1270018 T
1 T
1270019 ATTGAAGTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.02, C:0.41, G:0.06, T:0.51
Consensus pattern (24 bp):
TGTTTTCCCTTTCCATCTTCCTCC
Found at i:1270402 original size:53 final size:53
Alignment explanation
Indices: 1270330--1270434 Score: 201
Period size: 53 Copynumber: 2.0 Consensus size: 53
1270320 AACTTCAGAA
*
1270330 GATTGAGAGAAAGCAGGCAATGAATGAAAACTCAAACCATACGACAAACTGAT
1 GATTGAGAGAAAGCAGGCAATGAACGAAAACTCAAACCATACGACAAACTGAT
1270383 GATTGAGAGAAAGCAGGCAATGAACGAAAACTCAAACCATACGACAAACTGA
1 GATTGAGAGAAAGCAGGCAATGAACGAAAACTCAAACCATACGACAAACTGA
1270435 AGTGATTTCT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.48, C:0.18, G:0.21, T:0.13
Consensus pattern (53 bp):
GATTGAGAGAAAGCAGGCAATGAACGAAAACTCAAACCATACGACAAACTGAT
Found at i:1274308 original size:22 final size:19
Alignment explanation
Indices: 1274288--1274334 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
1274278 CATATAAAAT
1274288 AAATATAT-TAATATATTA
1 AAATATATATAATATATTA
*
1274306 AAATTTATATAATATATTA
1 AAATATATATAATATATTA
*
1274325 TAAATTTATA
1 -AAATATATA
1274335 AAAAAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 7 0.27
19 10 0.38
20 9 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AAATATATATAATATATTA
Found at i:1274318 original size:19 final size:21
Alignment explanation
Indices: 1274291--1274334 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 21
1274281 ATAAAATAAA
1274291 TATATTAATATATTA-AAATT
1 TATATTAATATATTATAAATT
1274311 TATA-TAATATATTATAAATT
1 TATATTAATATATTATAAATT
1274331 TATA
1 TATA
1274335 AAAAAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TATATTAATATATTATAAATT
Found at i:1277245 original size:2 final size:2
Alignment explanation
Indices: 1277238--1277272 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1277228 AAAGCATGTT
1277238 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
1277273 TTTAAGGCGA
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:1277520 original size:23 final size:25
Alignment explanation
Indices: 1277481--1277534 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
1277471 TTTATTAATT
* *
1277481 TTTTTA-TTATATAATA-TATATTA
1 TTTTTATTTATATAATATTACATAA
*
1277504 TTTTTATTTTTAT-ATATTACATAA
1 TTTTTATTTATATAATATTACATAA
1277528 TTTTTAT
1 TTTTTAT
1277535 CATATAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 9 0.35
24 17 0.65
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (25 bp):
TTTTTATTTATATAATATTACATAA
Found at i:1277598 original size:21 final size:20
Alignment explanation
Indices: 1277539--1277598 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
1277529 TTTTATCATA
*
1277539 TAAAAAATAAATATATAATAT
1 TAAAAAATAAATATA-AAAAT
* * *
1277560 TATAATATAAATTTTAAAAAT
1 TAAAAAATAAA-TATAAAAAT
1277581 TAAAAAATATAATATAAA
1 TAAAAAATA-AATATAAA
1277599 TAAATTCAAT
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
21 25 0.83
22 5 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
TAAAAAATAAATATAAAAAT
Found at i:1277688 original size:16 final size:15
Alignment explanation
Indices: 1277625--1277689 Score: 51
Period size: 16 Copynumber: 4.1 Consensus size: 15
1277615 TAAAATATTT
1277625 ATTTAAAT-ATATAAA
1 ATTTAAATAATAT-AA
* *
1277640 ATATATATATATATAA
1 ATTTAAATA-ATATAA
* *
1277656 TTTTAAATTATATTAA
1 ATTTAAATAATA-TAA
1277672 ATTTAAATAACTATAA
1 ATTTAAATAA-TATAA
1277688 AT
1 AT
1277690 AATATTAATA
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
15 9 0.24
16 23 0.61
17 6 0.16
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTTAAATAATATAA
Found at i:1278271 original size:39 final size:39
Alignment explanation
Indices: 1278243--1278321 Score: 97
Period size: 39 Copynumber: 1.9 Consensus size: 39
1278233 TTTTTATATT
1278243 AATATTAATATTTA-TATATTTTATAATTAATTTTAAATAA
1 AATATT-AT-TTTATTATATTTTATAATTAATTTTAAATAA
* *
1278283 AATATTATTTTATTTTATTTTATAAATAATAATTTAAAT
1 AATATTATTTTATTATATTTTATAATTAAT--TTTAAAT
1278322 TGTGAATCGT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
38 4 0.12
39 17 0.50
40 6 0.18
41 7 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (39 bp):
AATATTATTTTATTATATTTTATAATTAATTTTAAATAA
Found at i:1279317 original size:17 final size:18
Alignment explanation
Indices: 1279285--1279319 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1279275 TTAATATAAT
*
1279285 ATATTTAATTTTTTAAAA
1 ATATTTAATATTTTAAAA
1279303 ATATTT-ATATTTTAAAA
1 ATATTTAATATTTTAAAA
1279320 GGTTGTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATATTTAATATTTTAAAA
Found at i:1279364 original size:17 final size:17
Alignment explanation
Indices: 1279342--1279391 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 17
1279332 TAAATTTATT
1279342 TAAATATATTTTAAATA
1 TAAATATATTTTAAATA
* *
1279359 TAAATATTTTTTAAAAA
1 TAAATATATTTTAAATA
1279376 TAAA-A-ATTTTAAATA
1 TAAATATATTTTAAATA
1279391 T
1 T
1279392 TATATGATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
15 9 0.31
16 1 0.03
17 19 0.66
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAATATATTTTAAATA
Found at i:1279921 original size:13 final size:13
Alignment explanation
Indices: 1279905--1279934 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1279895 TATCTTCAAT
*
1279905 AATTATTATGATA
1 AATTATTATGAAA
1279918 AATTATTATGAAA
1 AATTATTATGAAA
1279931 AATT
1 AATT
1279935 TTAATTAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (13 bp):
AATTATTATGAAA
Found at i:1280153 original size:5 final size:5
Alignment explanation
Indices: 1280145--1280172 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1280135 ATATTATATT
1280145 ATAAA ATAAA ATAAA ATAAA ATAAA ATA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATA
1280173 TATTTATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
ATAAA
Found at i:1280187 original size:18 final size:17
Alignment explanation
Indices: 1280143--1280201 Score: 59
Period size: 18 Copynumber: 3.5 Consensus size: 17
1280133 TAATATTATA
1280143 TTATAAAATAAAATAA-
1 TTATAAAATAAAATAAT
*
1280159 -AATAAAATAAAATATAT
1 TTATAAAATAAAATA-AT
* *
1280176 TTATAAATTAAATTAAT
1 TTATAAAATAAAATAAT
1280193 TTATTAAAA
1 TTA-TAAAA
1280202 ATAAGTTTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
15 13 0.38
16 1 0.03
17 5 0.15
18 15 0.44
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
TTATAAAATAAAATAAT
Found at i:1286754 original size:38 final size:38
Alignment explanation
Indices: 1286643--1286762 Score: 103
Period size: 38 Copynumber: 3.2 Consensus size: 38
1286633 TTTAATAATA
* *
1286643 AAAATAATATTTTTATTTAAATATAATTATAAAA-TTAAA-
1 AAAAT-ATAATTTAATTT-AATATAATT-TAAAATTTAAAT
*
1286682 AAAATAT--TTTAA--TAATATAA--AAAAATTATAAAAT
1 AAAATATAATTTAATTTAATATAATTTAAAATT-T-AAAT
1286716 AAAATATAATTTAATTTAATATAATTTAAAATTTAAAT
1 AAAATATAATTTAATTTAATATAATTTAAAATTTAAAT
*
1286754 AAAAAATAA
1 AAAATATAA
1286763 AAAATTTTAA
Statistics
Matches: 67, Mismatches: 4, Indels: 21
0.73 0.04 0.23
Matches are distributed among these distances:
30 4 0.06
31 1 0.01
32 1 0.01
33 10 0.15
34 8 0.12
36 9 0.13
38 22 0.33
39 6 0.09
40 6 0.09
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (38 bp):
AAAATATAATTTAATTTAATATAATTTAAAATTTAAAT
Found at i:1287193 original size:14 final size:14
Alignment explanation
Indices: 1287176--1287212 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1287166 TTTGTAAAAA
*
1287176 AAAAATTTAATTTT
1 AAAAATTAAATTTT
*
1287190 AAAAATAAAATTTT
1 AAAAATTAAATTTT
1287204 AAAAATTAA
1 AAAAATTAA
1287213 TATATGACTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AAAAATTAAATTTT
Found at i:1287194 original size:19 final size:20
Alignment explanation
Indices: 1287164--1287202 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1287154 GAAGGGTTAA
1287164 AATTTGTAAAAAAAAAATTT
1 AATTTGTAAAAAAAAAATTT
*
1287184 AATTT-TAAAAATAAAATTT
1 AATTTGTAAAAAAAAAATTT
1287203 TAAAAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (20 bp):
AATTTGTAAAAAAAAAATTT
Done.