Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 129432109
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: 129432109
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 392 of 425
Found at i:120360348 original size:21 final size:21
Alignment explanation
Indices: 120360324--120360368 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
120360314 AAAATAAACT
120360324 TAAAATGATTCAAATCTTAAG
1 TAAAATGATTCAAATCTTAAG
120360345 TAAAATGATTCAAATCTTAAG
1 TAAAATGATTCAAATCTTAAG
120360366 TAA
1 TAA
120360369 TGTGTTGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (21 bp):
TAAAATGATTCAAATCTTAAG
Found at i:120360945 original size:6 final size:6
Alignment explanation
Indices: 120360934--120360961 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
120360924 TAGTTTACAT
120360934 AAAATA AAAATA AAAATA AAAATA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAA
120360962 GAGAATTAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAATA
Found at i:120362509 original size:14 final size:15
Alignment explanation
Indices: 120362477--120362510 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
120362467 CTTCTTTAAT
120362477 TTATAAATAATAAAA
1 TTATAAATAATAAAA
*
120362492 TTATAAAT-ATACAA
1 TTATAAATAATAAAA
120362506 TTATA
1 TTATA
120362511 TAAATTACAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (15 bp):
TTATAAATAATAAAA
Found at i:120378729 original size:18 final size:18
Alignment explanation
Indices: 120378702--120378737 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
120378692 ATTAAATTAA
*
120378702 ATAAATTATTAAAAATTT
1 ATAAAATATTAAAAATTT
120378720 ATAAAATATTAAAAATTT
1 ATAAAATATTAAAAATTT
120378738 GGTTTGTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATAAAATATTAAAAATTT
Found at i:120380708 original size:2 final size:2
Alignment explanation
Indices: 120380696--120380731 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
120380686 TTCACATGCA
*
120380696 TG TG CG 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
120380732 AATGGCTATT
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:0.00, C:0.03, G:0.50, T:0.47
Consensus pattern (2 bp):
TG
Found at i:120386547 original size:11 final size:11
Alignment explanation
Indices: 120386528--120386591 Score: 69
Period size: 11 Copynumber: 5.9 Consensus size: 11
120386518 TATTTTGATG
120386528 CTATT-TTTTA
1 CTATTATTTTA
*
120386538 TTATTATTTT-
1 CTATTATTTTA
*
120386548 CTCACTATTTTA
1 CT-ATTATTTTA
120386560 CTATTATTTTA
1 CTATTATTTTA
*
120386571 CTATTATGTTA
1 CTATTATTTTA
*
120386582 CTACTATTTT
1 CTATTATTTT
120386592 GTTGTTATTG
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
10 5 0.11
11 37 0.84
12 2 0.05
ACGTcount: A:0.23, C:0.12, G:0.02, T:0.62
Consensus pattern (11 bp):
CTATTATTTTA
Found at i:120386576 original size:33 final size:32
Alignment explanation
Indices: 120386528--120386591 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 32
120386518 TATTTTGATG
* *
120386528 CTATTTTTTATTATTAT-TTTCTCACTATTTTA
1 CTATTTTTTACTATTATGTTACT-ACTATTTTA
120386560 CTATTATTTTACTATTATGTTACTACTATTTT
1 CTATT-TTTTACTATTATGTTACTACTATTTT
120386592 GTTGTTATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 5 0.18
33 19 0.68
34 4 0.14
ACGTcount: A:0.23, C:0.12, G:0.02, T:0.62
Consensus pattern (32 bp):
CTATTTTTTACTATTATGTTACTACTATTTTA
Found at i:120387040 original size:23 final size:23
Alignment explanation
Indices: 120387014--120387057 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
120387004 AAAACTATAA
120387014 TATTTTTA-AATGAATAAGTATGT
1 TATTTTTATAATGAA-AAGTATGT
*
120387037 TATTTTTATAATGTAAAGTAT
1 TATTTTTATAATGAAAAGTAT
120387058 AGACACGTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (23 bp):
TATTTTTATAATGAAAAGTATGT
Found at i:120387799 original size:81 final size:80
Alignment explanation
Indices: 120387648--120387799 Score: 191
Period size: 80 Copynumber: 1.9 Consensus size: 80
120387638 GGCTTCAATG
* * * *
120387648 TTCAATTTGATAAATGAGTTTTTTTTTCTCAATTTGGTACTTGAGTTTAGCTTTAATATTTACTT
1 TTCAATTTGATAAATGAGTTTTTTTTTCTCAATTTAGTACTTAAGTTCAGCTTTAATATTTAATT
120387713 TGGTACTCGAGCTTT
66 TGGTACTCGAGCTTT
** * *
120387728 TTCAATTTGATATTTGAGTTTTTTTTGT-TCAGTTTAAGTA-TCTAAGTTCAGCTTTAATGTTTA
1 TTCAATTTGATAAATGAGTTTTTTTT-TCTCAATTT-AGTACT-TAAGTTCAGCTTTAATATTTA
120387791 ATTTGGTAC
63 ATTTGGTAC
120387800 ATGAGTCTTT
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
80 31 0.51
81 30 0.49
ACGTcount: A:0.23, C:0.10, G:0.15, T:0.52
Consensus pattern (80 bp):
TTCAATTTGATAAATGAGTTTTTTTTTCTCAATTTAGTACTTAAGTTCAGCTTTAATATTTAATT
TGGTACTCGAGCTTT
Found at i:120390024 original size:98 final size:98
Alignment explanation
Indices: 120389855--120390054 Score: 400
Period size: 98 Copynumber: 2.0 Consensus size: 98
120389845 ATTAAAAAAA
120389855 AGTCAATGAAGCTTTAACAAAGTTGGCAAAGATAGGGTAGAGGTGTGTATGGGCCGGGCCGGGCT
1 AGTCAATGAAGCTTTAACAAAGTTGGCAAAGATAGGGTAGAGGTGTGTATGGGCCGGGCCGGGCT
120389920 CAACTAAAATTTTAGGTCCGTTTGCTAGGCCCG
66 CAACTAAAATTTTAGGTCCGTTTGCTAGGCCCG
120389953 AGTCAATGAAGCTTTAACAAAGTTGGCAAAGATAGGGTAGAGGTGTGTATGGGCCGGGCCGGGCT
1 AGTCAATGAAGCTTTAACAAAGTTGGCAAAGATAGGGTAGAGGTGTGTATGGGCCGGGCCGGGCT
120390018 CAACTAAAATTTTAGGTCCGTTTGCTAGGCCCG
66 CAACTAAAATTTTAGGTCCGTTTGCTAGGCCCG
120390051 AGTC
1 AGTC
120390055 TGGCCCAAAA
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 102 1.00
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (98 bp):
AGTCAATGAAGCTTTAACAAAGTTGGCAAAGATAGGGTAGAGGTGTGTATGGGCCGGGCCGGGCT
CAACTAAAATTTTAGGTCCGTTTGCTAGGCCCG
Found at i:120390154 original size:12 final size:12
Alignment explanation
Indices: 120390137--120390169 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
120390127 CGGCCCGCCC
120390137 ATATTAATTTTT
1 ATATTAATTTTT
120390149 ATATT-ATTTTT
1 ATATTAATTTTT
120390160 ATA-TAATTTT
1 ATATTAATTTT
120390170 AAAAAAACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:120390760 original size:57 final size:57
Alignment explanation
Indices: 120390699--120390811 Score: 226
Period size: 57 Copynumber: 2.0 Consensus size: 57
120390689 AAACATATAT
120390699 TTGTATTTGTCTTATACTTTTCTTGTATTGTATTCTAGTGAAACTTAAAAAAAAAAA
1 TTGTATTTGTCTTATACTTTTCTTGTATTGTATTCTAGTGAAACTTAAAAAAAAAAA
120390756 TTGTATTTGTCTTATACTTTTCTTGTATTGTATTCTAGTGAAACTTAAAAAAAAAA
1 TTGTATTTGTCTTATACTTTTCTTGTATTGTATTCTAGTGAAACTTAAAAAAAAAA
120390812 GTAAAAAATT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.46
Consensus pattern (57 bp):
TTGTATTTGTCTTATACTTTTCTTGTATTGTATTCTAGTGAAACTTAAAAAAAAAAA
Found at i:120398560 original size:15 final size:14
Alignment explanation
Indices: 120398524--120398567 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
120398514 TTTCTTTTCT
*
120398524 AATTTACAATATTTA
1 AATTTAAAAT-TTTA
*
120398539 AATTTAAATTTTTA
1 AATTTAAAATTTTA
120398553 AATATTAAAATTTTA
1 AAT-TTAAAATTTTA
120398568 TCACTTAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 7 0.28
15 18 0.72
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (14 bp):
AATTTAAAATTTTA
Found at i:120403091 original size:26 final size:24
Alignment explanation
Indices: 120403060--120403119 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 24
120403050 ATTTTGAAAC
120403060 ATATATTTGAAATATTTTATTAATAT
1 ATATATTTGAAATATTTTA--AATAT
*
120403086 ATATATTT-TAA-ATTTTAAATAT
1 ATATATTTGAAATATTTTAAATAT
120403108 ATAT-TTTGAAAT
1 ATATATTTGAAAT
120403120 TACTTTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
21 3 0.10
22 11 0.37
24 6 0.20
25 2 0.07
26 8 0.27
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (24 bp):
ATATATTTGAAATATTTTAAATAT
Found at i:120403109 original size:20 final size:22
Alignment explanation
Indices: 120403079--120403120 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
120403069 AAATATTTTA
120403079 TTAATATATATATTTT-AAATT
1 TTAATATATATATTTTGAAATT
120403100 TTAA-ATATATATTTTGAAATT
1 TTAATATATATATTTTGAAATT
120403121 ACTTTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TTAATATATATATTTTGAAATT
Found at i:120403134 original size:21 final size:23
Alignment explanation
Indices: 120403108--120403164 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
120403098 TTTTAAATAT
*
120403108 ATATTTTGAA-ATTACTTTTTAA
1 ATATTTTAAATATTACTTTTTAA
*
120403130 A-ATTTTAAATATTATTTTTTAA
1 ATATTTTAAATATTACTTTTTAA
120403152 ATA-TTTAAATATT
1 ATATTTTAAATATT
120403165 TTAAACTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 7 0.23
22 23 0.74
23 1 0.03
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (23 bp):
ATATTTTAAATATTACTTTTTAA
Found at i:120403255 original size:34 final size:33
Alignment explanation
Indices: 120403097--120403285 Score: 121
Period size: 34 Copynumber: 5.7 Consensus size: 33
120403087 TATATTTTAA
* *
120403097 ATTTTAAATATATATTTTGAAATTACTTTT-TAAA
1 ATTTTAAAT-TATATTTTTAAATTA-TTTTATAAT
120403131 ATTTTAAA-TATTATTTTTTAAA-TA-TTTA-AAT
1 ATTTTAAATTA-TA-TTTTTAAATTATTTTATAAT
*
120403162 ATTTTAAACTTTCAAATTTGTT--ATTAGTTTTATAAT
1 ATTTTAAA--TT-ATATTT-TTAAATTA-TTTTATAAT
* * *
120403198 AATTTAAA-TAT-TATTTAATTTATTTTATAAT
1 ATTTTAAATTATATTTTTAAATTATTTTATAAT
*
120403229 ATTTTAAATTATGATTTTTAAATTATTTT-TAAAG
1 ATTTTAAATTAT-ATTTTTAAATTATTTTAT-AAT
*
120403263 ATATTCAAATTAT-TTTTTAAATT
1 AT-TTTAAATTATATTTTTAAATT
120403286 CTATTTAAAA
Statistics
Matches: 124, Mismatches: 12, Indels: 39
0.71 0.07 0.22
Matches are distributed among these distances:
30 2 0.02
31 31 0.25
32 10 0.08
33 21 0.17
34 36 0.29
35 14 0.11
36 10 0.08
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (33 bp):
ATTTTAAATTATATTTTTAAATTATTTTATAAT
Found at i:120403282 original size:67 final size:66
Alignment explanation
Indices: 120403072--120403291 Score: 163
Period size: 66 Copynumber: 3.3 Consensus size: 66
120403062 ATATTTGAAA
* *
120403072 TATTTTATTAATATATATATTT-TAA-ATTTTAAATATATATTTTGAAATTACTTTTTAAAATTT
1 TATTTT-TTAAT-TATAT-TTTATAATATTTTAAAT-TATATTTTTAAATTA-TTTTTAAAATAT
120403135 TAAATAT
61 TAAA-AT
* * *
120403142 TATTTTTTAA--ATA-TTTA-AATATTTTAAACTTTCAAATTTGTT--ATTAGTTTTATAATAAT
1 TATTTTTTAATTATATTTTATAATATTTTAAA--TT-ATATTT-TTAAATTATTTTTAAAAT-AT
*
120403201 TTAAA-
61 TAAAAT
* *
120403206 TATTATTTAATT-TATTTTATAATATTTTAAATTATGATTTTTAAATTATTTTTAAAGATATTCA
1 TATTTTTTAATTATATTTTATAATATTTTAAATTAT-ATTTTTAAATTATTTTTAAA-ATATTAA
120403270 AAT
64 AAT
*
120403273 TATTTTTTAAATTCTATTT
1 TATTTTTT-AATTATATTT
120403292 AAAAGTTAAA
Statistics
Matches: 120, Mismatches: 12, Indels: 37
0.71 0.07 0.22
Matches are distributed among these distances:
64 17 0.14
65 25 0.21
66 32 0.27
67 26 0.22
68 5 0.04
69 9 0.08
70 6 0.05
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (66 bp):
TATTTTTTAATTATATTTTATAATATTTTAAATTATATTTTTAAATTATTTTTAAAATATTAAAA
T
Found at i:120403518 original size:18 final size:20
Alignment explanation
Indices: 120403481--120403524 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
120403471 TTTCACTTTT
120403481 TTTTTACTTATTTATTATTA
1 TTTTTACTTATTTATTATTA
*
120403501 TTTTTAGTT-TTT-TTATTA
1 TTTTTACTTATTTATTATTA
120403519 TCTTTT
1 T-TTTT
120403525 GTCTTTTTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 7 0.32
19 7 0.32
20 8 0.36
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.75
Consensus pattern (20 bp):
TTTTTACTTATTTATTATTA
Found at i:120403531 original size:18 final size:18
Alignment explanation
Indices: 120403495--120403532 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
120403485 TACTTATTTA
*
120403495 TTATTATTTTTAGTTTTT
1 TTATTATTTTTAGTCTTT
120403513 TTATTATCTTTT-GTCTTT
1 TTATTAT-TTTTAGTCTTT
120403531 TT
1 TT
120403533 CCTTAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.13, C:0.05, G:0.05, T:0.76
Consensus pattern (18 bp):
TTATTATTTTTAGTCTTT
Found at i:120403641 original size:25 final size:24
Alignment explanation
Indices: 120403591--120403647 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
120403581 TTTTAAAAAA
*
120403591 TTTAAA-ATGTATATTTGAAATGT
1 TTTAAATATATATATTTGAAATGT
*
120403614 TTTATAATATATATATTTTTAAAT-T
1 TTTA-AATATATATA-TTTGAAATGT
120403639 TTTAAATAT
1 TTTAAATAT
120403648 TATTTTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
23 4 0.14
24 7 0.24
25 11 0.38
26 7 0.24
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.54
Consensus pattern (24 bp):
TTTAAATATATATATTTGAAATGT
Found at i:120403698 original size:21 final size:21
Alignment explanation
Indices: 120403656--120403707 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
120403646 ATTATTTTAA
* ** *
120403656 ATTAGTTTTTAAATTTTGAAT
1 ATTATTTTTTAAACATTAAAT
120403677 ATTATTTTTTAAACATTAAAT
1 ATTATTTTTTAAACATTAAAT
120403698 ATATATTTTT
1 AT-TATTTTT
120403708 AAAATTTGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 19 0.73
22 7 0.27
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.58
Consensus pattern (21 bp):
ATTATTTTTTAAACATTAAAT
Found at i:120403767 original size:27 final size:25
Alignment explanation
Indices: 120403727--120403791 Score: 67
Period size: 25 Copynumber: 2.4 Consensus size: 25
120403717 TTTTTTTTAC
*
120403727 TTTTTTTAACTTTTGTCATTTCTCTGACA
1 TTTTTTT-A-TTTTGTC-TTTATCTGA-A
*
120403756 TTTTTTTATTTTGTCTTTATCTTAA
1 TTTTTTTATTTTGTCTTTATCTGAA
*
120403781 TTTATTTATTT
1 TTTTTTTATTT
120403792 ATTTTTATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 11 0.33
26 7 0.21
27 7 0.21
28 1 0.03
29 7 0.21
ACGTcount: A:0.17, C:0.11, G:0.05, T:0.68
Consensus pattern (25 bp):
TTTTTTTATTTTGTCTTTATCTGAA
Found at i:120403788 original size:25 final size:27
Alignment explanation
Indices: 120403737--120403791 Score: 69
Period size: 25 Copynumber: 2.1 Consensus size: 27
120403727 TTTTTTTAAC
* *
120403737 TTTTGTCATTTCTCTGACATTTTTTTA
1 TTTTGTCATTTATCTGACATTTATTTA
*
120403764 TTTTGTC-TTTATCTTA-ATTTATTTA
1 TTTTGTCATTTATCTGACATTTATTTA
120403789 TTT
1 TTT
120403792 ATTTTTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 11 0.44
26 7 0.28
27 7 0.28
ACGTcount: A:0.16, C:0.11, G:0.05, T:0.67
Consensus pattern (27 bp):
TTTTGTCATTTATCTGACATTTATTTA
Found at i:120403807 original size:24 final size:24
Alignment explanation
Indices: 120403771--120403831 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
120403761 TTATTTTGTC
*
120403771 TTTATCTTAA-TTTATTTATTTATT
1 TTTATTTTAATTTTATTT-TTTATT
*
120403795 TTTATTTTTATTTTATTTTTTATT
1 TTTATTTTAATTTTATTTTTTATT
*
120403819 ATTA--TTAATTTTA
1 TTTATTTTAATTTTA
120403832 AAAAAATTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 8 0.25
24 17 0.53
25 7 0.22
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.74
Consensus pattern (24 bp):
TTTATTTTAATTTTATTTTTTATT
Found at i:120403811 original size:21 final size:22
Alignment explanation
Indices: 120403780--120403831 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
120403770 CTTTATCTTA
120403780 ATTTA-TTTATTTATTT-TTATT
1 ATTTATTTTATTT-TTTATTATT
120403801 -TTTATTTTATTTTTTATTATT
1 ATTTATTTTATTTTTTATTATT
*
120403822 ATTAATTTTA
1 ATTTATTTTA
120403832 AAAAAATTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 7 0.26
21 12 0.44
22 8 0.30
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (22 bp):
ATTTATTTTATTTTTTATTATT
Found at i:120403875 original size:22 final size:20
Alignment explanation
Indices: 120403835--120403897 Score: 63
Period size: 22 Copynumber: 3.0 Consensus size: 20
120403825 AATTTTAAAA
* *
120403835 AAATTTGAAATGTATATTTG
1 AAATTTTAAATATATATTTG
*
120403855 AAATGTTTATAATATATATTTTTT
1 AAAT-TTTA-AATATATA--TTTG
120403879 AAATTTTAAATATATATTT
1 AAATTTTAAATATATATTT
120403898 TTTAAATTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
20 7 0.19
21 3 0.08
22 15 0.42
23 4 0.11
24 7 0.19
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.52
Consensus pattern (20 bp):
AAATTTTAAATATATATTTG
Found at i:120403898 original size:22 final size:23
Alignment explanation
Indices: 120403855--120403905 Score: 86
Period size: 22 Copynumber: 2.2 Consensus size: 23
120403845 TGTATATTTG
120403855 AAATGTTTATAATATATATTTTTT
1 AAAT-TTTATAATATATATTTTTT
120403879 AAATTTTA-AATATATATTTTTT
1 AAATTTTATAATATATATTTTTT
120403901 AAATT
1 AAATT
120403906 GTTTTTCTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 19 0.70
23 4 0.15
24 4 0.15
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
AAATTTTATAATATATATTTTTT
Found at i:120403931 original size:34 final size:33
Alignment explanation
Indices: 120403872--120403971 Score: 130
Period size: 33 Copynumber: 3.0 Consensus size: 33
120403862 TATAATATAT
*
120403872 ATTTTTTAAATTTTAAATATATATTTTTTAAATT
1 ATTTTTTAAATTTTAAATAT-TATTTTTTAAATC
*
120403906 GTTTTTCTAAATTTTAAATATTA-TTTTTAAATC
1 ATTTTT-TAAATTTTAAATATTATTTTTTAAATC
* *
120403939 ATTGTTTAAAAATTTAAATATTATTTTTTAAAT
1 ATT-TTTTAAATTTTAAATATTATTTTTTAAAT
120403972 ATTAAATATA
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
33 25 0.43
34 19 0.33
35 14 0.24
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (33 bp):
ATTTTTTAAATTTTAAATATTATTTTTTAAATC
Found at i:120403998 original size:21 final size:21
Alignment explanation
Indices: 120403948--120403986 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
120403938 CATTGTTTAA
120403948 AAAT-TTAAATATTATTTTTT
1 AAATATTAAATATTATTTTTT
120403968 AAATATTAAATA-TATTTTT
1 AAATATTAAATATTATTTTT
120403987 AATTAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
AAATATTAAATATTATTTTTT
Found at i:120404126 original size:24 final size:24
Alignment explanation
Indices: 120404075--120404151 Score: 77
Period size: 25 Copynumber: 3.2 Consensus size: 24
120404065 ATTTTAATTT
*
120404075 TTTTTATAATT-TTTTTAATTATGAA
1 TTTTTA-AATTATTTTAAATTATG-A
120404100 TTTTTAAATTATTTTAAATTATGA
1 TTTTTAAATTATTTTAAATTATGA
* * *
120404124 -TTTGAAATTATTTAAAATATATTA
1 TTTTTAAATTATTTTAAAT-TATGA
120404148 TTTT
1 TTTT
120404152 AAAGATATGA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
23 16 0.36
24 9 0.20
25 20 0.44
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (24 bp):
TTTTTAAATTATTTTAAATTATGA
Found at i:120404135 original size:23 final size:23
Alignment explanation
Indices: 120404082--120404150 Score: 68
Period size: 23 Copynumber: 2.9 Consensus size: 23
120404072 TTTTTTTTAT
* *
120404082 AATT-TTTTTAATTATGAATTTTTA
1 AATTATTTTAAATTATG-A-TTTGA
120404106 AATTATTTTAAATTATGATTTGA
1 AATTATTTTAAATTATGATTTGA
* *
120404129 AATTATTTAAAATATATTATTT
1 AATTATTTTAAAT-TATGATTT
120404151 TAAAGATATG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.41
24 12 0.31
25 11 0.28
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (23 bp):
AATTATTTTAAATTATGATTTGA
Found at i:120404352 original size:22 final size:23
Alignment explanation
Indices: 120404314--120404365 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
120404304 ATTGTAAGAA
*
120404314 TTAATATTTAAAAAAATATATAT
1 TTAAAATTTAAAAAAATATATAT
120404337 TTAAAATTT-AAAAAATATATAT
1 TTAAAATTTAAAAAAATATATAT
120404359 TATAAAA
1 T-TAAAA
120404366 CATTTCAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 14 0.52
23 13 0.48
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
TTAAAATTTAAAAAAATATATAT
Found at i:120404423 original size:14 final size:14
Alignment explanation
Indices: 120404400--120404448 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
120404390 TTTTAAAATT
120404400 AATAATAAAAAATAA
1 AATAA-AAAAAATAA
*
120404415 AATAAAAAAAAAAA
1 AATAAAAAAAATAA
*
120404429 AAT-AAATAAATAA
1 AATAAAAAAAATAA
120404442 AGATAAA
1 A-ATAAA
120404449 GACAAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 9 0.31
14 13 0.45
15 7 0.24
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (14 bp):
AATAAAAAAAATAA
Found at i:120404431 original size:33 final size:34
Alignment explanation
Indices: 120404394--120404459 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 34
120404384 CAAGTTTTTT
* *
120404394 AAAATTAAT-AATAAAAAATAAA-ATAAAAAAAAA
1 AAAATAAATAAAT-AAAAATAAAGACAAAAAAAAA
*
120404427 AAAATAAATAAATAAAGATAAAGACAAAAAAAA
1 AAAATAAATAAATAAAAATAAAGACAAAAAAAA
120404460 TGTCAGAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 16 0.57
34 12 0.43
ACGTcount: A:0.80, C:0.02, G:0.03, T:0.15
Consensus pattern (34 bp):
AAAATAAATAAATAAAAATAAAGACAAAAAAAAA
Found at i:120404494 original size:10 final size:11
Alignment explanation
Indices: 120404475--120404508 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
120404465 GAGAAATGAC
120404475 AAAAGTTAAAA
1 AAAAGTTAAAA
*
120404486 AAAAGTAAAAA
1 AAAAGTTAAAA
*
120404497 AAAATTTAAAA
1 AAAAGTTAAAA
120404508 A
1 A
120404509 TATATATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (11 bp):
AAAAGTTAAAA
Found at i:120404554 original size:21 final size:20
Alignment explanation
Indices: 120404496--120404562 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 20
120404486 AAAAGTAAAA
*
120404496 AAAAATTTAAAAATATATATT
1 AAAATTTTAAAAATA-ATATT
* *
120404517 TAATTTTTAAAAAATAATATT
1 AAAATTTT-AAAAATAATATT
120404538 CAAAATTTTAAAAATAAT-TT
1 -AAAATTTTAAAAATAATATT
120404558 AAAAT
1 AAAAT
120404563 AATATTTAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
19 5 0.13
20 2 0.05
21 19 0.49
22 13 0.33
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAATTTTAAAAATAATATT
Found at i:120404740 original size:19 final size:19
Alignment explanation
Indices: 120404718--120404756 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
120404708 AAGACAGAAT
120404718 ATAATAAAAAACTAAAAAA
1 ATAATAAAAAACTAAAAAA
* *
120404737 ATAATAAATAAGTAAAAAA
1 ATAATAAAAAACTAAAAAA
120404756 A
1 A
120404757 AAAGTGAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.18
Consensus pattern (19 bp):
ATAATAAAAAACTAAAAAA
Found at i:120405107 original size:21 final size:22
Alignment explanation
Indices: 120405070--120405124 Score: 78
Period size: 21 Copynumber: 2.5 Consensus size: 22
120405060 GAAAGTTTAA
120405070 AATATTTAAATATTTAAAAAA-T
1 AATATTTAAA-ATTTAAAAAAGT
120405092 AATATTTAAAATTTAAAAAAGT
1 AATATTTAAAATTTAAAAAAGT
*
120405114 AAT-TTCAAAAT
1 AATATTTAAAAT
120405125 ATATATTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
21 17 0.55
22 14 0.45
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (22 bp):
AATATTTAAAATTTAAAAAAGT
Found at i:120405221 original size:14 final size:14
Alignment explanation
Indices: 120405204--120405257 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
120405194 TAATAATAAT
120405204 AAATAAATAAAAGA
1 AAATAAATAAAAGA
120405218 AAATAAAT-AAAGA
1 AAATAAATAAAAGA
* *
120405231 AAAAAAGACAAAAGA
1 AAATAA-ATAAAAGA
120405246 AAAGTAAA-AAAA
1 AAA-TAAATAAAA
120405258 AAACAAGAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 10 0.29
14 13 0.38
15 9 0.26
16 2 0.06
ACGTcount: A:0.80, C:0.02, G:0.09, T:0.09
Consensus pattern (14 bp):
AAATAAATAAAAGA
Found at i:120405243 original size:28 final size:27
Alignment explanation
Indices: 120405212--120405265 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
120405202 ATAAATAAAT
120405212 AAAAGAAAA-TAAATAAAGAAAAAAAGAC
1 AAAAGAAAAGTAAA-AAA-AAAAAAAGAC
*
120405240 AAAAGAAAAGTAAAAAAAAAACAAGA
1 AAAAGAAAAGTAAAAAAAAAAAAAGA
120405266 ACTGACATGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 8 0.33
28 12 0.50
29 4 0.17
ACGTcount: A:0.80, C:0.04, G:0.11, T:0.06
Consensus pattern (27 bp):
AAAAGAAAAGTAAAAAAAAAAAAAGAC
Found at i:120405655 original size:23 final size:22
Alignment explanation
Indices: 120405615--120405657 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
120405605 TAAAGAAAGA
120405615 AAAAATAACTTATATATTAATT
1 AAAAATAACTTATATATTAATT
* *
120405637 AAAAATTACTATATTTATTAA
1 AAAAATAACT-TATATATTAA
120405658 ATATTTTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (22 bp):
AAAAATAACTTATATATTAATT
Found at i:120406953 original size:20 final size:21
Alignment explanation
Indices: 120406916--120406959 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
120406906 AACCATTTTC
** *
120406916 AAATCGAGTTTTGGAAAATGG
1 AAATCGAGTTTTAAAAAACGG
120406937 AAATCGA-TTTTAAAAAACGG
1 AAATCGAGTTTTAAAAAACGG
120406957 AAA
1 AAA
120406960 CGGGAGTCGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.48, C:0.07, G:0.20, T:0.25
Consensus pattern (21 bp):
AAATCGAGTTTTAAAAAACGG
Found at i:120407761 original size:2 final size:2
Alignment explanation
Indices: 120407754--120407794 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
120407744 CTTCACATAA
120407754 AT AT AT AT 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 AT AT AT AT A
120407795 AAGAAATGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:120408125 original size:49 final size:48
Alignment explanation
Indices: 120408072--120408168 Score: 133
Period size: 48 Copynumber: 2.0 Consensus size: 48
120408062 TAATATAGGG
* * *
120408072 TTTAAAATAAATAATATATAAAATAGTTT-AACTACATAATGTATATAAA
1 TTTAAAATAAATAATATAT-AAA-AGTTTAAAATAAATAACGTATATAAA
*
120408121 TTTAAAATAAATAATATGTAAAAGTTTAAAATAAATAACGTATATAAA
1 TTTAAAATAAATAATATATAAAAGTTTAAAATAAATAACGTATATAAA
120408169 AAGAAAATCA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
47 5 0.12
48 20 0.47
49 18 0.42
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (48 bp):
TTTAAAATAAATAATATATAAAAGTTTAAAATAAATAACGTATATAAA
Found at i:120408148 original size:24 final size:24
Alignment explanation
Indices: 120408071--120408169 Score: 103
Period size: 24 Copynumber: 4.0 Consensus size: 24
120408061 CTAATATAGG
120408071 GTTTAAAATAAATAATATATAAAATA
1 GTTTAAAATAAATAATATAT-AAA-A
* * *
120408097 GTTT-AACTACATAATGTATATAAA
1 GTTTAAAATAAATAATATATA-AAA
*
120408121 -TTTAAAATAAATAATATGTAAAA
1 GTTTAAAATAAATAATATATAAAA
120408144 GTTTAAAATAAATAACGTATATAAAA
1 GTTTAAAATAAATAA--TATATAAAA
120408170 AGAAAATCAT
Statistics
Matches: 60, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
23 6 0.10
24 28 0.47
25 14 0.23
26 12 0.20
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.34
Consensus pattern (24 bp):
GTTTAAAATAAATAATATATAAAA
Found at i:120409984 original size:44 final size:44
Alignment explanation
Indices: 120409921--120410327 Score: 286
Period size: 44 Copynumber: 9.3 Consensus size: 44
120409911 CAGCTCGTTA
120409921 CCCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTGTTT
1 CCCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTGTTT
* ** * * *
120409965 CCCTACTGCTTGGGGGGTTAA-GATC-T-GTAAATTC-AGCCTGTTA
1 CCCTACTGCTTAGGGGGTTAAGGCCCTTCGT--CTTCGA-TCTGTTT
*
120410008 CCCTACTGCTTAGGGGGTTAAGGCCCTTCGCCTTCGATCTGTTT
1 CCCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTGTTT
* * ** ** * * *
120410052 CCCTACTGTTTAGAGGGTTAA-GATCTGTAAAT-TTAG-CCTGTTA
1 CCCTACTGCTTAGGGGGTTAAGGCCCT-T-CGTCTTCGATCTGTTT
* *
120410095 CCCTACTGCTTAAGGGGTTAAGGCCCTTCGTCTTCGATCTATTT
1 CCCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTGTTT
* ** ** * * *
120410139 CCCTATTGCTTAGGGGGTTAA-GATCTATAAAT-TTAG-CCTGTTA
1 CCCTACTGCTTAGGGGGTTAAGGCCCT-T-CGTCTTCGATCTGTTT
*
120410182 CCCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTTGATCTGTTT
1 CCCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTGTTT
** * * *
120410226 CCCTACTGCTTAGGGGGTTAA-GATC-T-GTAAATTC-AGCCTGTTA
1 CCCTACTGCTTAGGGGGTTAAGGCCCTTCGT--CTTCGA-TCTGTTT
* * **
120410269 CCCTATTGCTTAGGGGGTTAAGGTCCTTCGTCTTCGATCT-ACT
1 CCCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTGTTT
120410312 CCACTACTGCTTAGGG
1 CC-CTACTGCTTAGGG
120410328 AGATAAGATC
Statistics
Matches: 271, Mismatches: 67, Indels: 50
0.70 0.17 0.13
Matches are distributed among these distances:
41 4 0.01
42 6 0.02
43 122 0.45
44 131 0.48
45 5 0.02
46 3 0.01
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (44 bp):
CCCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTGTTT
Found at i:120409985 original size:87 final size:87
Alignment explanation
Indices: 120409873--120410482 Score: 809
Period size: 87 Copynumber: 7.0 Consensus size: 87
120409863 ATTTCCAGCT
* *
120409873 TGTTACCCTACTACTTAGGGGGTTAAGATCTGTAAATTCAG-CTCGTTACCCTACTGCTTAGGGG
1 TGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCT-GTTACCCTACTGCTTAGGGG
120409937 GTTAAGGCCCTTCGTCTTCGATC
65 GTTAAGGCCCTTCGTCTTCGATC
*
120409960 TGTTTCCCTACTGCTTGGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGG
1 TGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGG
*
120410025 TTAAGGCCCTTCGCCTTCGATC
66 TTAAGGCCCTTCGTCTTCGATC
* * * *
120410047 TGTTTCCCTACTGTTTAGAGGGTTAAGATCTGTAAATTTAGCCTGTTACCCTACTGCTTAAGGGG
1 TGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGG
120410112 TTAAGGCCCTTCGTCTTCGATC
66 TTAAGGCCCTTCGTCTTCGATC
* * * *
120410134 TATTTCCCTATTGCTTAGGGGGTTAAGATCTATAAATTTAGCCTGTTACCCTACTGCTTAGGGGG
1 TGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGG
*
120410199 TTAAGGCCCTTCGTCTTTGATC
66 TTAAGGCCCTTCGTCTTCGATC
*
120410221 TGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTATTGCTTAGGGGG
1 TGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGG
*
120410286 TTAAGGTCCTTCGTCTTCGATC
66 TTAAGGCCCTTCGTCTTCGATC
** * * * *
120410308 T-ACTCCACTACTGCTTAGGGAGATAAGATCTG-CAATTCAACCTGTTACCCTACTGCTTA-GGG
1 TGTTTCC-CTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGG
* ** * *
120410370 TTTAAGGTTCTTCGTATTTGATC
65 GTTAAGGCCCTTCGTCTTCGATC
** * * * * * * *
120410393 T-ACTCCACTTCTGCTTAGGGAGATAAGATCTG-CAATTCGGTCTGTTACCCTACTGCTTAAGGG
1 TGTTTCC-CTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGG
* * *
120410456 TTTAAGACCCTTTGTCTTCGATC
65 GTTAAGGCCCTTCGTCTTCGATC
120410479 TGTT
1 TGTT
120410483 ACACCATTCT
Statistics
Matches: 472, Mismatches: 47, Indels: 8
0.90 0.09 0.02
Matches are distributed among these distances:
85 77 0.16
86 48 0.10
87 345 0.73
88 2 0.00
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (87 bp):
TGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGG
TTAAGGCCCTTCGTCTTCGATC
Found at i:120418563 original size:19 final size:20
Alignment explanation
Indices: 120418535--120418576 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
120418525 GTCTTTTCGC
* *
120418535 GAAATTTAATGCACATG-AT
1 GAAATGTAATGCAAATGAAT
120418554 GAAATGTAATGCAAATGAAT
1 GAAATGTAATGCAAATGAAT
120418574 GAA
1 GAA
120418577 TGCAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.48, C:0.07, G:0.19, T:0.26
Consensus pattern (20 bp):
GAAATGTAATGCAAATGAAT
Found at i:120422279 original size:2 final size:2
Alignment explanation
Indices: 120422272--120422320 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
120422262 AGAACTTCAC
120422272 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
120422314 AT AT AT A
1 AT AT AT A
120422321 AAGAAATGTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:120422652 original size:49 final size:48
Alignment explanation
Indices: 120422599--120422695 Score: 133
Period size: 48 Copynumber: 2.0 Consensus size: 48
120422589 TAATATAGGG
* * *
120422599 TTTAAAATAAATAATATATAAAATAGTTT-AACTACATAATGTATATAAA
1 TTTAAAATAAATAATATAT-AAA-AGTTTAAAATAAATAACGTATATAAA
*
120422648 TTTAAAATAAATAATATGTAAAAGTTTAAAATAAATAACGTATATAAA
1 TTTAAAATAAATAATATATAAAAGTTTAAAATAAATAACGTATATAAA
120422696 AAGAAAATCA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
47 5 0.12
48 20 0.47
49 18 0.42
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (48 bp):
TTTAAAATAAATAATATATAAAAGTTTAAAATAAATAACGTATATAAA
Found at i:120422675 original size:24 final size:24
Alignment explanation
Indices: 120422598--120422696 Score: 103
Period size: 24 Copynumber: 4.0 Consensus size: 24
120422588 CTAATATAGG
120422598 GTTTAAAATAAATAATATATAAAATA
1 GTTTAAAATAAATAATATAT-AAA-A
* * *
120422624 GTTT-AACTACATAATGTATATAAA
1 GTTTAAAATAAATAATATATA-AAA
*
120422648 -TTTAAAATAAATAATATGTAAAA
1 GTTTAAAATAAATAATATATAAAA
120422671 GTTTAAAATAAATAACGTATATAAAA
1 GTTTAAAATAAATAA--TATATAAAA
120422697 AGAAAATCAT
Statistics
Matches: 60, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
23 6 0.10
24 28 0.47
25 14 0.23
26 12 0.20
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.34
Consensus pattern (24 bp):
GTTTAAAATAAATAATATATAAAA
Found at i:120424279 original size:2 final size:2
Alignment explanation
Indices: 120424272--120424299 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
120424262 AATGTTATGG
120424272 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
120424300 GAAAATGGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:120428327 original size:9 final size:9
Alignment explanation
Indices: 120428308--120428338 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
120428298 TTATGTGTTC
120428308 TTTATTTTTA
1 TTTA-TTTTA
120428318 TTTATTTTA
1 TTTATTTTA
120428327 TTTATTTTA
1 TTTATTTTA
120428336 TTT
1 TTT
120428339 TTCACAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 17 0.81
10 4 0.19
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:120432781 original size:5 final size:5
Alignment explanation
Indices: 120432761--120432793 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
120432751 TTATGTGTTC
120432761 TTTAT TTT-T ATTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT -TTTAT TTTAT TTTAT TTTAT TTT
120432794 TCACTATGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 1 0.04
5 24 0.92
6 1 0.04
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:120432998 original size:32 final size:32
Alignment explanation
Indices: 120432952--120433012 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
120432942 TAATTAGTCT
* * * *
120432952 GAGTTTTTATATTAAATTAATTAATTTATCAC
1 GAGTTATTAAATTAAAGTAATCAATTTATCAC
120432984 GAGTTATTAAATTAAAGTAATCAATTTAT
1 GAGTTATTAAATTAAAGTAATCAATTTAT
120433013 ATATTTATGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (32 bp):
GAGTTATTAAATTAAAGTAATCAATTTATCAC
Found at i:120434034 original size:3 final size:3
Alignment explanation
Indices: 120434026--120434058 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
120434016 AATTCCAAAG
120434026 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
120434059 GCGGAGAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:120434808 original size:19 final size:19
Alignment explanation
Indices: 120434773--120434810 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
120434763 TATGCTTTAG
* *
120434773 TTTATATTATTTTATGATA
1 TTTATATTATATAATGATA
120434792 TTTATATTATATAATGATA
1 TTTATATTATATAATGATA
120434811 GCATCTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (19 bp):
TTTATATTATATAATGATA
Found at i:120442068 original size:23 final size:25
Alignment explanation
Indices: 120442014--120442070 Score: 64
Period size: 23 Copynumber: 2.3 Consensus size: 25
120442004 ATTATTCAAA
120442014 AAAATAATTAATTAACATAATTAATT
1 AAAAT-ATTAATTAACATAATTAATT
** *
120442040 CTAATATTAATTAA-GTAA-TAATT
1 AAAATATTAATTAACATAATTAATT
120442063 AAAATATT
1 AAAATATT
120442071 TAAAATTTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 11 0.42
24 3 0.12
25 9 0.35
26 3 0.12
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (25 bp):
AAAATATTAATTAACATAATTAATT
Found at i:120447372 original size:24 final size:25
Alignment explanation
Indices: 120447339--120447388 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
120447329 GGGAAGCCTT
* *
120447339 TGGGACGTGGTCGGGGTCGTGGCCG
1 TGGGACGTGGACGGGGTCGAGGCCG
*
120447364 TGGG-CGTGGACGTGGTCGAGGCCG
1 TGGGACGTGGACGGGGTCGAGGCCG
120447388 T
1 T
120447389 TAAATATGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.06, C:0.20, G:0.54, T:0.20
Consensus pattern (25 bp):
TGGGACGTGGACGGGGTCGAGGCCG
Found at i:120451390 original size:24 final size:24
Alignment explanation
Indices: 120451358--120451420 Score: 72
Period size: 25 Copynumber: 2.6 Consensus size: 24
120451348 CAACTCGAAA
* *
120451358 GAGCGTCCCGTTATTAGCTCTTAT
1 GAGCATCCCGTTATTAGCTCTCAT
*
120451382 GAGCATCCCGATACTTAGCTCTCAT
1 GAGCATCCCGTTA-TTAGCTCTCAT
**
120451407 GAGTTTCCCGTTAT
1 GAGCATCCCGTTAT
120451421 ATGGTTCTTG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
24 12 0.38
25 20 0.62
ACGTcount: A:0.19, C:0.27, G:0.19, T:0.35
Consensus pattern (24 bp):
GAGCATCCCGTTATTAGCTCTCAT
Found at i:120453848 original size:3 final size:3
Alignment explanation
Indices: 120453797--120453836 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
120453787 AACGTGCACC
120453797 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
120453837 AAGCTTAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:120456587 original size:5 final size:5
Alignment explanation
Indices: 120456577--120456619 Score: 77
Period size: 5 Copynumber: 8.6 Consensus size: 5
120456567 TTGTGTGTTC
*
120456577 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTGT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
120456620 TCACAAATTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.16, C:0.00, G:0.02, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:120461016 original size:5 final size:5
Alignment explanation
Indices: 120461006--120461037 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
120460996 TTGTGTGTTC
120461006 TTTAT TTTA- TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
120461038 TCACAATATG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:120461020 original size:9 final size:9
Alignment explanation
Indices: 120461006--120461036 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
120460996 TTGTGTGTTC
120461006 TTTATTTTA
1 TTTATTTTA
120461015 TTTATTTTA
1 TTTATTTTA
120461024 TTTTATTTTA
1 -TTTATTTTA
120461034 TTT
1 TTT
120461037 TTCACAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:120464420 original size:31 final size:28
Alignment explanation
Indices: 120464382--120464440 Score: 73
Period size: 31 Copynumber: 2.0 Consensus size: 28
120464372 TGTGGATTGT
*
120464382 TTTGAATGAATATGAGCTTCAATAAGTTAAA
1 TTTGAATGAATAT-AG-ATCAATAA-TTAAA
*
120464413 TTTGAATGTATATAGATCAATAATTAAA
1 TTTGAATGAATATAGATCAATAATTAAA
120464441 GAAAACAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 5 0.19
29 7 0.27
30 2 0.08
31 12 0.46
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.37
Consensus pattern (28 bp):
TTTGAATGAATATAGATCAATAATTAAA
Found at i:120464784 original size:44 final size:42
Alignment explanation
Indices: 120464710--120464876 Score: 133
Period size: 43 Copynumber: 3.9 Consensus size: 42
120464700 TGATATGTGT
* * *
120464710 TTTCGTGTAAGACCACGTCTGGGACGTTGGCATTG-ACTTATGA
1 TTTCGTGTAAGACCACGTCTGAGACATTGGCATCGTA-TT-TGA
*
120464753 TTTACGTGTAAGACCATGTCTGAGACATTGGCATCGTATTTGA
1 TTT-CGTGTAAGACCACGTCTGAGACATTGGCATCGTATTTGA
* * * *
120464796 TTTCGTGTAAGACC-CTGT-TTAGGACAGTGGCGTCAATATTTGA
1 TTTCGTGTAAGACCAC-GTCTGA-GACATTGGCATC-GTATTTGA
* * * * * *
120464839 TTACATGTAAGACCATGTCTGGGACGTTGGCATTGTAT
1 TTTCGTGTAAGACCACGTCTGAGACATTGGCATCGTAT
120464877 GTGCTTTCCG
Statistics
Matches: 98, Mismatches: 19, Indels: 15
0.74 0.14 0.11
Matches are distributed among these distances:
41 2 0.02
42 26 0.27
43 38 0.39
44 31 0.32
45 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (42 bp):
TTTCGTGTAAGACCACGTCTGAGACATTGGCATCGTATTTGA
Found at i:120467663 original size:46 final size:46
Alignment explanation
Indices: 120467604--120467818 Score: 224
Period size: 46 Copynumber: 4.7 Consensus size: 46
120467594 AACCTAATGT
*
120467604 CATAGTGTCTTTCAACTATGGCCTTATTCATTTTCCGTCATGTTGC
1 CATAGTGTCTTTCAACTATGGTCTTATTCATTTTCCGTCATGTTGC
* *
120467650 CATAGTGTCTTTCAACTATGGTCTTATTCATTTTCTGTCATGTTGT
1 CATAGTGTCTTTCAACTATGGTCTTATTCATTTTCCGTCATGTTGC
* ***
120467696 CATAATGTCTTTCAACTATGGTCTTATTCATTTT-CAAAATAG-TGC
1 CATAGTGTCTTTCAACTATGGTCTTATTCATTTTCCGTCAT-GTTGC
* * * * * * * *
120467741 TACAGCGTATTTCAACTATGGTGTTACTCATTTGATTCGTGATG-T--
1 CATAGTGTCTTTCAACTATGGTCTTATTCATTT--TCCGTCATGTTGC
*
120467786 CATAGTGTCTTTCAACTATGGTTTTATTCATTT
1 CATAGTGTCTTTCAACTATGGTCTTATTCATTT
120467819 AATTCGTGAT
Statistics
Matches: 140, Mismatches: 25, Indels: 9
0.80 0.14 0.05
Matches are distributed among these distances:
45 57 0.41
46 77 0.55
47 3 0.02
48 3 0.02
ACGTcount: A:0.21, C:0.18, G:0.15, T:0.46
Consensus pattern (46 bp):
CATAGTGTCTTTCAACTATGGTCTTATTCATTTTCCGTCATGTTGC
Found at i:120467684 original size:22 final size:22
Alignment explanation
Indices: 120467659--120467732 Score: 55
Period size: 22 Copynumber: 3.3 Consensus size: 22
120467649 CCATAGTGTC
120467659 TTTCAACTATGGTCTTATTCAT
1 TTTCAACTATGGTCTTATTCAT
** *
120467681 TTTC-TGTCATGTTGTCATAATGTC-T
1 TTTCAACT-ATG--GTC-TTAT-TCAT
120467706 -TTCAACTATGGTCTTATTCAT
1 TTTCAACTATGGTCTTATTCAT
120467727 TTTCAA
1 TTTCAA
120467733 AATAGTGCTA
Statistics
Matches: 38, Mismatches: 6, Indels: 16
0.63 0.10 0.27
Matches are distributed among these distances:
20 2 0.05
21 5 0.13
22 15 0.39
24 9 0.24
25 5 0.13
26 2 0.05
ACGTcount: A:0.22, C:0.18, G:0.11, T:0.50
Consensus pattern (22 bp):
TTTCAACTATGGTCTTATTCAT
Found at i:120467799 original size:45 final size:43
Alignment explanation
Indices: 120467600--120467866 Score: 221
Period size: 45 Copynumber: 5.9 Consensus size: 43
120467590 TCCCAACCTA
* * *
120467600 ATGTCATAGTGTCTTTCAACTATGGCCTTATTCATTTTCCGTC
1 ATGTCATAGTGTCTTTCAACTATGGTCTTATTCATTTTTCGTG
*
120467643 ATGTTGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTTCTGTCATG
1 ATG-T--CATAGTGTCTTTCAACTATGGTCTTATTCA-TTT-T-TCGTG
* * ***
120467692 TTGTCATAATGTCTTTCAACTATGGTCTTATTCA-TTTTCAAA
1 ATGTCATAGTGTCTTTCAACTATGGTCTTATTCATTTTTCGTG
* * * * *
120467734 ATAGTGCTACAGCGTATTTCAACTATGGTGTTACTCATTTGATTCGTG
1 AT-GT-C-ATAGTGTCTTTCAACTATGGTCTTATTCATTT--TTCGTG
*
120467782 ATGTCATAGTGTCTTTCAACTATGGTTTTATTCATTTAATTCGTG
1 ATGTCATAGTGTCTTTCAACTATGGTCTTATTCATTT--TTCGTG
* * ** * *
120467827 ATGCCATAGCGTCTTTCAGTTATGGTCTTACTCGTTTTTC
1 ATGTCATAGTGTCTTTCAACTATGGTCTTATTCATTTTTC
120467867 AACCAACAAA
Statistics
Matches: 181, Mismatches: 31, Indels: 24
0.77 0.13 0.10
Matches are distributed among these distances:
42 4 0.02
43 9 0.05
44 4 0.02
45 87 0.48
46 61 0.34
47 5 0.03
48 7 0.04
49 4 0.02
ACGTcount: A:0.21, C:0.18, G:0.16, T:0.45
Consensus pattern (43 bp):
ATGTCATAGTGTCTTTCAACTATGGTCTTATTCATTTTTCGTG
Found at i:120467838 original size:90 final size:91
Alignment explanation
Indices: 120467600--120467859 Score: 276
Period size: 90 Copynumber: 2.9 Consensus size: 91
120467590 TCCCAACCTA
* ** * *
120467600 ATGTCATAGTGTCTTTCAACTATGGCCTTATTCATTTTCCGTCATGTTGCCATAGTGTCTTTCAA
1 ATGTCATAGTGTCTTTCAACTATGGTCTTATTCATTTT-AATCATGATGCCATAGCGTCTTTCAA
* **
120467665 CTATGGTCTTATTCATTTTCTGTCATG
65 CTATGGTCTTACTCATTTGATGTCATG
* * * * * *
120467692 TTGTCATAATGTCTTTCAACTATGGTCTTATTCATTTTCAA-AAT-AGTGCTACAGCGTATTTCA
1 ATGTCATAGTGTCTTTCAACTATGGTCTTATTCATTTT-AATCATGA-TGCCATAGCGTCTTTCA
* *
120467755 ACTATGGTGTTACTCATTTGAT-TCGTG
64 ACTATGGTCTTACTCATTTGATGTCATG
* * *
120467782 ATGTCATAGTGTCTTTCAACTATGGTTTTATTCA-TTTAATTCGTGATGCCATAGCGTCTTTCAG
1 ATGTCATAGTGTCTTTCAACTATGGTCTTATTCATTTTAA-TCATGATGCCATAGCGTCTTTCAA
*
120467846 TTATGGTCTTACTC
65 CTATGGTCTTACTC
120467860 GTTTTTCAAC
Statistics
Matches: 137, Mismatches: 27, Indels: 10
0.79 0.16 0.06
Matches are distributed among these distances:
88 2 0.01
89 3 0.02
90 62 0.45
91 34 0.25
92 36 0.26
ACGTcount: A:0.21, C:0.18, G:0.16, T:0.45
Consensus pattern (91 bp):
ATGTCATAGTGTCTTTCAACTATGGTCTTATTCATTTTAATCATGATGCCATAGCGTCTTTCAAC
TATGGTCTTACTCATTTGATGTCATG
Found at i:120471953 original size:14 final size:13
Alignment explanation
Indices: 120471936--120471969 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
120471926 GTGAATGTGG
120471936 AAAAGAAAAAGAAA
1 AAAAGAAAAA-AAA
*
120471950 AAAAGAAAAAATA
1 AAAAGAAAAAAAA
120471963 AAAAGAA
1 AAAAGAA
120471970 TATAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (13 bp):
AAAAGAAAAAAAA
Found at i:120475882 original size:50 final size:50
Alignment explanation
Indices: 120475799--120475895 Score: 149
Period size: 50 Copynumber: 1.9 Consensus size: 50
120475789 TTGATTTTAT
*
120475799 AAATAAAAGATTTATTAATTAAAAAGATGAATTAAAAATAAAAAAATTGA
1 AAATAAAAGATTTATTAATTAAAAACATGAATTAAAAATAAAAAAATTGA
* * * *
120475849 AAATAATATATTTATTAATTAAAAACATTAATTAAAAGTAAAAAAAT
1 AAATAAAAGATTTATTAATTAAAAACATGAATTAAAAATAAAAAAAT
120475896 ATTGAAATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.63, C:0.01, G:0.05, T:0.31
Consensus pattern (50 bp):
AAATAAAAGATTTATTAATTAAAAACATGAATTAAAAATAAAAAAATTGA
Found at i:120484583 original size:9 final size:10
Alignment explanation
Indices: 120484559--120484586 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
120484549 TTCGGTGACT
120484559 ATTTTTTATA
1 ATTTTTTATA
120484569 ATTTTTTATA
1 ATTTTTTATA
120484579 ATTTTTTA
1 ATTTTTTA
120484587 AAGTTAAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
ATTTTTTATA
Found at i:120487089 original size:15 final size:16
Alignment explanation
Indices: 120487059--120487092 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
120487049 GTTCTTTCAT
*
120487059 AATAATGAAATTATAA
1 AATAATGAAATGATAA
120487075 AATAAT-AAATGATAA
1 AATAATGAAATGATAA
120487090 AAT
1 AAT
120487093 TATATTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (16 bp):
AATAATGAAATGATAA
Found at i:120490519 original size:26 final size:26
Alignment explanation
Indices: 120490440--120490528 Score: 69
Period size: 26 Copynumber: 3.5 Consensus size: 26
120490430 ATAAAAATTT
* *
120490440 AAATTTAAATTTGAAATAT-CTTTAA
1 AAATTTAATTTTGAAATATATTTTAA
* * **
120490465 AATTATTT-ATTTTACAAATAAATAATAA
1 AA--ATTTAATTTT-GAAATATATTTTAA
120490493 AAATTTAATTTTGAAATATATTTT-A
1 AAATTTAATTTTGAAATATATTTTAA
120490518 AAA-TTAATTTT
1 AAATTTAATTTT
120490529 CGTGGTATTG
Statistics
Matches: 49, Mismatches: 10, Indels: 11
0.70 0.14 0.16
Matches are distributed among these distances:
24 8 0.16
25 6 0.12
26 16 0.33
27 14 0.29
28 5 0.10
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.47
Consensus pattern (26 bp):
AAATTTAATTTTGAAATATATTTTAA
Found at i:120492397 original size:16 final size:16
Alignment explanation
Indices: 120492376--120492414 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
120492366 TCAAGTATTT
*
120492376 TATAAAATATAAATAA
1 TATAAAATATAAAAAA
120492392 TATAAAATATAAAAAA
1 TATAAAATATAAAAAA
120492408 T-TAAAAT
1 TATAAAAT
120492415 TACATAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
TATAAAATATAAAAAA
Found at i:120494655 original size:28 final size:30
Alignment explanation
Indices: 120494596--120494667 Score: 112
Period size: 28 Copynumber: 2.5 Consensus size: 30
120494586 AATTTTAAAA
*
120494596 AATAATAATTTATGCATACATTAAATTTTT
1 AATAATATTTTATGCATACATTAAATTTTT
*
120494626 AATAATATTTTATG-A-ATATTAAATTTTT
1 AATAATATTTTATGCATACATTAAATTTTT
120494654 AATAATATTTTATG
1 AATAATATTTTATG
120494668 TATTGTTAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
28 26 0.65
29 1 0.03
30 13 0.32
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (30 bp):
AATAATATTTTATGCATACATTAAATTTTT
Found at i:120500225 original size:16 final size:17
Alignment explanation
Indices: 120500196--120500229 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
120500186 TATTACGATC
120500196 TATATTATAATAATAGT
1 TATATTATAATAATAGT
*
120500213 TATA-TATATTAATAGT
1 TATATTATAATAATAGT
120500229 T
1 T
120500230 TTAGTAATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (17 bp):
TATATTATAATAATAGT
Found at i:120506259 original size:20 final size:20
Alignment explanation
Indices: 120506227--120506264 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
120506217 TATTTCTACT
120506227 TTTCAGATTTTAAAATTTAA
1 TTTCAGATTTTAAAATTTAA
*
120506247 TTTCA-ATTGTTAATATTT
1 TTTCAGATT-TTAAAATTT
120506265 GCTAAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.55
Consensus pattern (20 bp):
TTTCAGATTTTAAAATTTAA
Found at i:120508548 original size:18 final size:18
Alignment explanation
Indices: 120508510--120508547 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
120508500 ATATTGTATA
120508510 TTAATATTTATTAAAATT
1 TTAATATTTATTAAAATT
120508528 TTAA-ATTTACTTCAAAATT
1 TTAATATTTA-TT-AAAATT
120508547 T
1 T
120508548 AGATGCATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.28
18 6 0.33
19 7 0.39
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (18 bp):
TTAATATTTATTAAAATT
Found at i:120510671 original size:26 final size:26
Alignment explanation
Indices: 120510609--120510662 Score: 83
Period size: 27 Copynumber: 2.1 Consensus size: 26
120510599 CGTTTAGGTC
*
120510609 AAAATTGAAACTTTAAATACTTTTAAA
1 AAAATTGAAACTTTAAATA-TTTGAAA
120510636 AAAATTGAAACTTTAAAT-TTTGAAA
1 AAAATTGAAACTTTAAATATTTGAAA
120510661 AA
1 AA
120510663 TACATGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 8 0.31
27 18 0.69
ACGTcount: A:0.54, C:0.06, G:0.06, T:0.35
Consensus pattern (26 bp):
AAAATTGAAACTTTAAATATTTGAAA
Found at i:120510894 original size:22 final size:23
Alignment explanation
Indices: 120510852--120510895 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
120510842 ACGTCTACTT
*
120510852 CATAAAATATTTTAAAAGAAAAA
1 CATAAAATAGTTTAAAAGAAAAA
*
120510875 CATAAAA-AGTTTAAACGAAAA
1 CATAAAATAGTTTAAAAGAAAA
120510896 GTTCATTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.23
Consensus pattern (23 bp):
CATAAAATAGTTTAAAAGAAAAA
Found at i:120512461 original size:14 final size:14
Alignment explanation
Indices: 120512442--120512471 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
120512432 TATAGTTGTT
120512442 TTTCAATCTATAAA
1 TTTCAATCTATAAA
120512456 TTTCAATCTATAAA
1 TTTCAATCTATAAA
120512470 TT
1 TT
120512472 AGAAAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (14 bp):
TTTCAATCTATAAA
Found at i:120516529 original size:14 final size:14
Alignment explanation
Indices: 120516512--120516541 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
120516502 TAAATTAGTC
120516512 TATATATATTAGAT
1 TATATATATTAGAT
120516526 TATATATATTAGAT
1 TATATATATTAGAT
120516540 TA
1 TA
120516542 AAGAGTATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
TATATATATTAGAT
Found at i:120534597 original size:18 final size:17
Alignment explanation
Indices: 120534570--120534604 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
120534560 ATGTTGAATG
120534570 GAATTTTAATATTTTAT
1 GAATTTTAATATTTTAT
*
120534587 GAATATTTAATGTTTTAT
1 GAAT-TTTAATATTTTAT
120534605 TTAATTAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (17 bp):
GAATTTTAATATTTTAT
Found at i:120535690 original size:18 final size:18
Alignment explanation
Indices: 120535663--120535697 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
120535653 GAAAATTTAA
* *
120535663 TATTATTATAATTATAAT
1 TATTAATATAAATATAAT
120535681 TATTAATATAAATATAA
1 TATTAATATAAATATAA
120535698 ATATAAAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TATTAATATAAATATAAT
Found at i:120535710 original size:24 final size:24
Alignment explanation
Indices: 120535654--120535710 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
120535644 TCCTAGAATG
* * *
120535654 AAAATTTAATATTATTATAATTAT
1 AAAATTTAATATAAATATAAATAT
*
120535678 -AATTATTAATATAAATATAAATAT
1 AAAAT-TTAATATAAATATAAATAT
120535702 AAAATTTAA
1 AAAATTTAA
120535711 ATTTAAATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
23 3 0.12
24 20 0.77
25 3 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
AAAATTTAATATAAATATAAATAT
Found at i:120544676 original size:8 final size:8
Alignment explanation
Indices: 120544660--120544703 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
120544650 GAAATTTTAA
*
120544660 TATATTTT
1 TATAATTT
120544668 TATAATTT
1 TATAATTT
*
120544676 TATAATTA
1 TATAATTT
120544684 TAT-ATTT
1 TATAATTT
*
120544691 TAGAATTT
1 TATAATTT
120544699 TATAA
1 TATAA
120544704 AAATATTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
7 5 0.17
8 25 0.83
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (8 bp):
TATAATTT
Found at i:120544709 original size:23 final size:23
Alignment explanation
Indices: 120544658--120544714 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
120544648 TTGAAATTTT
* *
120544658 AATATATTTTTATAATTTTATAAT
1 AATATA-TTTTAGAATTTTATAAA
*
120544682 TATATATTTTAGAATTTTATAAA
1 AATATATTTTAGAATTTTATAAA
120544705 AATAT-TTTTA
1 AATATATTTTA
120544715 AACAATTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 5 0.17
23 19 0.66
24 5 0.17
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
AATATATTTTAGAATTTTATAAA
Found at i:120544733 original size:20 final size:20
Alignment explanation
Indices: 120544704--120544748 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 20
120544694 AATTTTATAA
120544704 AAATATTTTTAAACAATTTTAC
1 AAAT-TTTTTAAA-AATTTTAC
*
120544726 AAATTTTTTAAAATTTTTAC
1 AAATTTTTTAAAAATTTTAC
120544746 AAA
1 AAA
120544749 ACTTTACATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.45
21 8 0.36
22 4 0.18
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATTTTTTAAAAATTTTAC
Found at i:120545307 original size:13 final size:13
Alignment explanation
Indices: 120545289--120545313 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
120545279 TTCATGGCGG
120545289 AACCCAAAAATTA
1 AACCCAAAAATTA
120545302 AACCCAAAAATT
1 AACCCAAAAATT
120545314 TCCCCCAAAA
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:0.60, C:0.24, G:0.00, T:0.16
Consensus pattern (13 bp):
AACCCAAAAATTA
Found at i:120545743 original size:8 final size:8
Alignment explanation
Indices: 120545731--120545762 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
120545721 TAAGACTGAG
*
120545731 TTGAATCG
1 TTGAATCA
120545739 TTGAATCA
1 TTGAATCA
120545747 TTGAATCA
1 TTGAATCA
120545755 TTGAATCA
1 TTGAATCA
120545763 GTGGAAAGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (8 bp):
TTGAATCA
Found at i:120549203 original size:5 final size:5
Alignment explanation
Indices: 120549193--120549218 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
120549183 TATGATCTAA
120549193 TATTT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT T
120549219 GTAAAATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:120549439 original size:20 final size:20
Alignment explanation
Indices: 120549416--120549453 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
120549406 TATAATTTTT
120549416 ATTA-TTAATATCTAATTATG
1 ATTACTTAATAT-TAATTATG
*
120549436 ATTACTTATTATTAATTA
1 ATTACTTAATATTAATTA
120549454 AATGACATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (20 bp):
ATTACTTAATATTAATTATG
Found at i:120550214 original size:20 final size:20
Alignment explanation
Indices: 120550191--120550260 Score: 61
Period size: 25 Copynumber: 3.2 Consensus size: 20
120550181 TAAAATTTAT
120550191 TTAAATTTAATTAAAAAATA
1 TTAAATTTAATTAAAAAATA
*
120550211 TT-AATATTAATATAAAATTATTTA
1 TTAAAT-TTAAT-TAAAA--A-ATA
120550235 TTTAAATTTAATTATAAAAATA
1 -TTAAATTTAATTA-AAAAATA
120550257 TTAA
1 TTAA
120550261 TATTAATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 15
0.70 0.04 0.26
Matches are distributed among these distances:
19 3 0.08
20 7 0.17
21 9 0.22
22 2 0.05
23 2 0.05
24 4 0.10
25 10 0.25
26 3 0.08
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTAAATTTAATTAAAAAATA
Found at i:120550268 original size:46 final size:45
Alignment explanation
Indices: 120550185--120550271 Score: 165
Period size: 46 Copynumber: 1.9 Consensus size: 45
120550175 TAATAATAAA
120550185 ATTTATTTAAATTTAATTAAAAAATATTAATATTAATATAAAATT
1 ATTTATTTAAATTTAATTAAAAAATATTAATATTAATATAAAATT
120550230 ATTTATTTAAATTTAATTATAAAAATATTAATATTAATATAA
1 ATTTATTTAAATTTAATTA-AAAAATATTAATATTAATATAA
120550272 TTTTATATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 19 0.46
46 22 0.54
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (45 bp):
ATTTATTTAAATTTAATTAAAAAATATTAATATTAATATAAAATT
Found at i:120550295 original size:46 final size:45
Alignment explanation
Indices: 120550185--120550287 Score: 158
Period size: 46 Copynumber: 2.3 Consensus size: 45
120550175 TAATAATAAA
120550185 ATTTATTTAAATTTAATTA-AAAAATATTAATATTAATATAAAATT
1 ATTTATTTAAATTTAATTATAAAAATATTAATATTAATAT-AAATT
120550230 ATTTATTTAAATTTAATTATAAAAATATTAATATTAATAT-AATT
1 ATTTATTTAAATTTAATTATAAAAATATTAATATTAATATAAATT
*
120550274 -TTATATTTATATTT
1 ATT-TATTTAAATTT
120550288 TAAATTATTT
Statistics
Matches: 55, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
43 2 0.04
44 14 0.25
45 19 0.35
46 20 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (45 bp):
ATTTATTTAAATTTAATTATAAAAATATTAATATTAATATAAATT
Found at i:120560961 original size:2 final size:2
Alignment explanation
Indices: 120560954--120561003 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
120560944 GGCCACCCAA
120560954 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
120560996 AT AT AT AT
1 AT AT AT AT
120561004 TTAATTGTTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:120569372 original size:19 final size:19
Alignment explanation
Indices: 120569339--120569399 Score: 52
Period size: 21 Copynumber: 3.0 Consensus size: 19
120569329 AAAAAACTAA
*
120569339 AGCTTTTTTTCTATTCTTTTT
1 AGCTATTTTT-TATT-TTTTT
*
120569360 A-CTGTTTTTTATTATTTTGT
1 AGCTATTTTTTATT-TTTT-T
120569380 AGCTATTTTCTTATTTTTTT
1 AGCTATTTT-TTATTTTTTT
120569400 CCACTATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 8 0.24
20 10 0.29
21 11 0.32
22 5 0.15
ACGTcount: A:0.13, C:0.10, G:0.07, T:0.70
Consensus pattern (19 bp):
AGCTATTTTTTATTTTTTT
Found at i:120570911 original size:3 final size:3
Alignment explanation
Indices: 120570903--120570951 Score: 53
Period size: 3 Copynumber: 16.3 Consensus size: 3
120570893 GTAGTCGTTT
* * * * *
120570903 TTG TTG TTG TTG TTG TTG TTA TTG TTA TTG TTA TTT TTG TTG TGG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
120570951 T
1 T
120570952 GGTTAATGTA
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.06, C:0.00, G:0.27, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:120576099 original size:20 final size:20
Alignment explanation
Indices: 120576050--120576089 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
120576040 TTTTAATTAT
120576050 TGTTACTAATAATCTTTTTA
1 TGTTACTAATAATCTTTTTA
120576070 TGTTACTAATAATCTTTTTA
1 TGTTACTAATAATCTTTTTA
120576090 GTTTCATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.10, G:0.05, T:0.55
Consensus pattern (20 bp):
TGTTACTAATAATCTTTTTA
Found at i:120576790 original size:19 final size:20
Alignment explanation
Indices: 120576753--120576792 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
120576743 TTTTTAATAT
**
120576753 ATATATTATTATTGCCTTTA
1 ATATATTATTATTAACTTTA
120576773 ATATA-TATTATTAACTTTA
1 ATATATTATTATTAACTTTA
120576792 A
1 A
120576793 GGTTAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (20 bp):
ATATATTATTATTAACTTTA
Found at i:120579124 original size:26 final size:26
Alignment explanation
Indices: 120579086--120579193 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
120579076 TGATAGAAAT
*
120579086 TGATAATGGGTTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
120579112 TGATAATGAGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
120579138 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
120579164 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
120579190 TGAT
1 TGAT
120579194 TGGAATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.06, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:120580709 original size:26 final size:26
Alignment explanation
Indices: 120580680--120580732 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
120580670 TTTACAGTTT
120580680 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* *
120580706 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
120580732 T
1 T
120580733 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:120582427 original size:32 final size:32
Alignment explanation
Indices: 120582390--120582462 Score: 146
Period size: 32 Copynumber: 2.3 Consensus size: 32
120582380 TTTTTAAAAT
120582390 ATAATTGTTATACAACAATTTATATTTTTATA
1 ATAATTGTTATACAACAATTTATATTTTTATA
120582422 ATAATTGTTATACAACAATTTATATTTTTATA
1 ATAATTGTTATACAACAATTTATATTTTTATA
120582454 ATAATTGTT
1 ATAATTGTT
120582463 GAACTTAATG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.40, C:0.05, G:0.04, T:0.51
Consensus pattern (32 bp):
ATAATTGTTATACAACAATTTATATTTTTATA
Found at i:120583014 original size:145 final size:145
Alignment explanation
Indices: 120582569--120583433 Score: 1259
Period size: 145 Copynumber: 6.0 Consensus size: 145
120582559 ATAAGTAAAA
* * * * *
120582569 TATTTTCGTATATTA-TT-TTTATATTATTTTAGTAAAAAATGTTTCAAATGTATTATGTAAGTA
1 TATTTTCGTATTTTATTTCTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTG
* *
120582632 TTTTTTTATATTAATTTAATAAATAACCCTGATTTT-GACATTTTCTTCGTATTTTTTTCGTATC
66 TTTTTTTATATT--TTTAATAAATAACCCTGATTTTAG-CACTTTATTCGTATTTTTTTCGTATC
120582696 TTATTTTTTAAAATATAT
128 TTATTTTTTAAAATATAT
*
120582714 TATTTTCGTATTTTATTTCTTCATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAA--G
1 TATTTTCGTATTTTATTTCTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTG
* *
120582777 TATTTTTATATTTTTCAATAAATAACCCTGATTTTAGCACTTTATTTGTATTTTTTTCGTATCTT
66 TTTTTTTATATTTTT-AATAAATAACCCTGATTTTAGCACTTTATTCGTATTTTTTTCGTATCTT
120582842 ATTTTTTAAAATATAT
130 ATTTTTTAAAATATAT
* *
120582858 TATTTTTGTATTTTATTTCTTTATATTATTTTAGTACATAATGGTTCAAATGTATTATTTAAGTG
1 TATTTTCGTATTTTATTTCTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTG
* *
120582923 TTTTTTTATATTTTTAATAAATAACCCTGATTTTAGCACTTTATTCGTATTTTTTTCTTATATTA
66 TTTTTTTATATTTTTAATAAATAACCCTGATTTTAGCACTTTATTCGTATTTTTTTCGTATCTTA
120582988 TTTTTTAAAATATAT
131 TTTTTTAAAATATAT
* * * * *
120583003 TATTTTCGTATTTTATTTTTTTATATTATTTTAGCAAAAAATGTTTCAAATGTATTATGTAAGTG
1 TATTTTCGTATTTTATTTCTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTG
* * *
120583068 -TTTTTTATATTAATTTAATAAATAACCCTAATTTT-GACACTTTCTTCATA-TTTTTTCGTATC
66 TTTTTTTATATT--TTTAATAAATAACCCTGATTTTAG-CACTTTATTCGTATTTTTTTCGTATC
120583130 TTATTTTTTAAAATATAT
128 TTATTTTTTAAAATATAT
*
120583148 TATTTTCGTATTTTATTTCTTCATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGT-
1 TATTTTCGTATTTTATTTCTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTG
* *
120583212 ATTTTTTATATTTTTTCAATAAATAACCCTGATTTTAGCACTTTATTCGTA-TTTTTT-GTTTCT
66 TTTTTTTATA-TTTTT-AATAAATAACCCTGATTTTAGCACTTTATTCGTATTTTTTTCGTATCT
120583275 TATTTTTTAAAATATAT
129 TATTTTTTAAAATATAT
*
120583292 TATTTTCGTATTTTATTTCTTTATATTATTTTAGTACATAATATTTCAAATGTATTATTTAAGTG
1 TATTTTCGTATTTTATTTCTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTG
* * * *
120583357 TTTTTATAT-TTTTTAATAAATAACCTTGATTTTAGCACTTTATTCATATTTTTATTTTCGTATA
66 TTTTTTTATATTTTTAATAAATAACCCTGATTTTAGCACTTTATTCGTA--TTT-TTTTCGTATC
120583421 TTATTTTATTAAA
128 TTATTTT-TTAAA
120583434 TTAATATAAT
Statistics
Matches: 653, Mismatches: 47, Indels: 37
0.89 0.06 0.05
Matches are distributed among these distances:
142 32 0.05
143 8 0.01
144 217 0.33
145 286 0.44
146 56 0.09
147 49 0.08
148 5 0.01
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.56
Consensus pattern (145 bp):
TATTTTCGTATTTTATTTCTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTG
TTTTTTTATATTTTTAATAAATAACCCTGATTTTAGCACTTTATTCGTATTTTTTTCGTATCTTA
TTTTTTAAAATATAT
Found at i:120583204 original size:55 final size:55
Alignment explanation
Indices: 120583108--120583216 Score: 130
Period size: 55 Copynumber: 2.0 Consensus size: 55
120583098 ATTTTGACAC
* * * * **
120583108 TTTCTTCATATTTTTTCGTATCTTATTTTTTAAAATATATTATTTTCGTATTTTA
1 TTTCTTCATATTTTTTAGTATCATAATGTTTAAAATATATTATTTAAGTATTTTA
* *
120583163 TTTCTTCATATTATTTTAGTA-CATAATGTTTCAAATGTATTATTTAAGTATTTT
1 TTTCTTCATATT-TTTTAGTATCATAATGTTTAAAATATATTATTTAAGTATTTT
120583217 TTATATTTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
55 38 0.84
56 7 0.16
ACGTcount: A:0.27, C:0.08, G:0.06, T:0.60
Consensus pattern (55 bp):
TTTCTTCATATTTTTTAGTATCATAATGTTTAAAATATATTATTTAAGTATTTTA
Found at i:120599268 original size:2 final size:2
Alignment explanation
Indices: 120599240--120599304 Score: 78
Period size: 2 Copynumber: 32.0 Consensus size: 2
120599230 TAATTTAAAA
* *
120599240 AT AT TT AT AT AT -T AT TT AT AGT CAT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T -AT AT AT AT AT AT AT AT AT AT
*
120599283 AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
120599305 GCATATTTGA
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
1 1 0.02
2 50 0.93
3 2 0.04
4 1 0.02
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (2 bp):
AT
Found at i:120599732 original size:93 final size:93
Alignment explanation
Indices: 120599567--120599737 Score: 229
Period size: 93 Copynumber: 1.8 Consensus size: 93
120599557 ATGCTCAGAC
* *
120599567 TTATCCTATAAATAAGTGTCAATTTTTTCACTATTTTCAATAAAAGTTAATTTTAATCTCACATT
1 TTATCCTATAAATAAATGTAAATTTTTTCACTATTTTCAATAAAAGTTAATTTTAATCTCACATT
**
120599632 GTTTAGAGAATACTAATATATAGCACAT
66 GACTAGAGAATACTAATATATAGCACAT
* ** * *
120599660 TTATCTTATAAATAAATG-AAATTTTTTCACTATTTTCGTTAAAAATTTAATTTTAATC-CTATA
1 TTATCCTATAAATAAATGTAAATTTTTTCACTATTTTCAAT-AAAAGTTAATTTTAATCTC-ACA
120599723 TTGACTAGAGAATAC
64 TTGACTAGAGAATAC
120599738 CTTCATAGCT
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
92 20 0.30
93 47 0.70
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (93 bp):
TTATCCTATAAATAAATGTAAATTTTTTCACTATTTTCAATAAAAGTTAATTTTAATCTCACATT
GACTAGAGAATACTAATATATAGCACAT
Found at i:120607168 original size:29 final size:30
Alignment explanation
Indices: 120607134--120607205 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 30
120607124 CAAAAAGTTG
* *
120607134 AAATACCAACTT-AAAAAAATGTCAAATTT
1 AAATACCAAATTAAAAAAAATATCAAATTT
*
120607163 AAATACCAAATTAAAAAAAAATATCAAGTTT
1 AAATACCAAATT-AAAAAAAATATCAAATTT
120607194 AAATACCAAATT
1 AAATACCAAATT
120607206 GAGCTAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 11 0.29
31 27 0.71
ACGTcount: A:0.58, C:0.12, G:0.03, T:0.26
Consensus pattern (30 bp):
AAATACCAAATTAAAAAAAATATCAAATTT
Found at i:120612234 original size:13 final size:12
Alignment explanation
Indices: 120612216--120612263 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 12
120612206 AAACTTTATT
120612216 TATTTTTATATA
1 TATTTTTATATA
*
120612228 GTATTTTTATAAA
1 -TATTTTTATATA
*
120612241 TATATTTTACATA
1 TAT-TTTTATATA
120612254 T-TTTTTATAT
1 TATTTTTATAT
120612264 TATAAAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
11 7 0.23
12 4 0.13
13 19 0.63
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (12 bp):
TATTTTTATATA
Found at i:120612267 original size:23 final size:25
Alignment explanation
Indices: 120612210--120612267 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 25
120612200 CAATTAAAAC
*
120612210 TTTAT-TTAT-TTTTATATAGTATT
1 TTTATATTATATTTTACATAGTATT
*
120612233 TTTATAAATATATTTTACATA-T-TT
1 TTTAT-ATTATATTTTACATAGTATT
120612257 TTTATATTATA
1 TTTATATTATA
120612268 AAATATATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
23 10 0.34
24 7 0.24
25 4 0.14
26 8 0.28
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (25 bp):
TTTATATTATATTTTACATAGTATT
Found at i:120614124 original size:16 final size:16
Alignment explanation
Indices: 120614103--120614139 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
120614093 AATTAAAAAA
* *
120614103 ATTAAAAATCATATAT
1 ATTAAAAATAATAAAT
120614119 ATTAAAAATAATAAAT
1 ATTAAAAATAATAAAT
120614135 ATTAA
1 ATTAA
120614140 TATAATTATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (16 bp):
ATTAAAAATAATAAAT
Found at i:120615238 original size:108 final size:108
Alignment explanation
Indices: 120615068--120615302 Score: 348
Period size: 108 Copynumber: 2.2 Consensus size: 108
120615058 TTTTTTTTAG
* *
120615068 TTTTTAATAATAAAATGACTTAATTAATATAACATCAATAGTTTAGAGTTGTAATTAGAATATTT
1 TTTTTAATAATAAAAGGACTTAATTAATATAACATCAATAGTTTAGAGTTGTAATTAAAATATTT
*
120615133 TGAAGTTTAAACTTATATTTTCTTCTTATTCTAATTATTAAAAA
66 TGAAATTTAAACTTATATTTTCTTCTTATT-TAATTATTAAAAA
* * *
120615177 TTTTTAATAATGAAAGGACTTAATTAATA-AATATTAATAGTTTAGAGTTGTAATTAAAATATTT
1 TTTTTAATAATAAAAGGACTTAATTAATATAACATCAATAGTTTAGAGTTGTAATTAAAATATTT
* *
120615241 TGAAATTTAAATTTATATTTTCTTCTTATTTTATTATTAAAAA
66 TGAAATTTAAACTTATATTTTCTTCTTATTTAATTATTAAAAA
* *
120615284 GTCTTAAT-ATAAAAAGGAC
1 TTTTTAATAAT-AAAAGGAC
120615303 AAGTTAACAC
Statistics
Matches: 114, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
106 2 0.02
107 25 0.22
108 60 0.53
109 27 0.24
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (108 bp):
TTTTTAATAATAAAAGGACTTAATTAATATAACATCAATAGTTTAGAGTTGTAATTAAAATATTT
TGAAATTTAAACTTATATTTTCTTCTTATTTAATTATTAAAAA
Found at i:120627482 original size:32 final size:32
Alignment explanation
Indices: 120627441--120627505 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
120627431 GTTGCTGACC
120627441 TACTCTTCTTCCTCCTCTTCTACGGTTCAAGT
1 TACTCTTCTTCCTCCTCTTCTACGGTTCAAGT
120627473 TACTCTTCTTCCTCCTCTTCTACGGTTCAAGT
1 TACTCTTCTTCCTCCTCTTCTACGGTTCAAGT
120627505 T
1 T
120627506 TTTCCTATAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.12, C:0.34, G:0.09, T:0.45
Consensus pattern (32 bp):
TACTCTTCTTCCTCCTCTTCTACGGTTCAAGT
Found at i:120636811 original size:42 final size:42
Alignment explanation
Indices: 120636748--120636845 Score: 117
Period size: 42 Copynumber: 2.3 Consensus size: 42
120636738 GGCTAGATTC
* * * *
120636748 TTGTAATAATATATCAATTATTGAGCTATCTGAATTCAATTA
1 TTGTAATAATAGATTAGTTATTAAGCTATCTGAATTCAATTA
* * *
120636790 TCT-TAATATTAGATTAGTTATTAAGTTATTTGAATTCAATTA
1 T-TGTAATAATAGATTAGTTATTAAGCTATCTGAATTCAATTA
120636832 TTGTAATAATAGAT
1 TTGTAATAATAGAT
120636846 CAATTCAGGC
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
41 1 0.02
42 44 0.96
43 1 0.02
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46
Consensus pattern (42 bp):
TTGTAATAATAGATTAGTTATTAAGCTATCTGAATTCAATTA
Found at i:120636832 original size:22 final size:21
Alignment explanation
Indices: 120636761--120636833 Score: 53
Period size: 22 Copynumber: 3.4 Consensus size: 21
120636751 TAATAATATA
* *
120636761 TCAATTATTGAGCTATCTGAAT
1 TCAATTATTAAG-TATTTGAAT
*
120636783 TCAATTATCTTAA-TATTAG-AT
1 TCAATTA--TTAAGTATTTGAAT
*
120636804 T-AGTTATTAAGTTATTTGAAT
1 TCAATTATTAAG-TATTTGAAT
120636825 TCAATTATT
1 TCAATTATT
120636834 GTAATAATAG
Statistics
Matches: 39, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
18 4 0.10
20 9 0.23
21 6 0.15
22 17 0.44
24 3 0.08
ACGTcount: A:0.34, C:0.08, G:0.10, T:0.48
Consensus pattern (21 bp):
TCAATTATTAAGTATTTGAAT
Found at i:120636931 original size:30 final size:28
Alignment explanation
Indices: 120636895--120636963 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 28
120636885 TATTGACATT
120636895 GAATTTTAAGGGATCTAATCAAAATTTTTA
1 GAATTTTAA--GATCTAATCAAAATTTTTA
* *
120636925 GAATTTTTGAAGATTTAATTAAAATTTTTA
1 GAA-TTTT-AAGATCTAATCAAAATTTTTA
120636955 GAAATTTTA
1 G-AATTTTA
120636964 GAAGGGTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
29 1 0.03
30 25 0.74
31 6 0.18
32 2 0.06
ACGTcount: A:0.41, C:0.03, G:0.12, T:0.45
Consensus pattern (28 bp):
GAATTTTAAGATCTAATCAAAATTTTTA
Found at i:120636974 original size:31 final size:30
Alignment explanation
Indices: 120636910--120636985 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 30
120636900 TTAAGGGATC
* *
120636910 TAATCAAAATTTTTAGAATTTTTGAAGATT
1 TAATCAAAATTTTTAGAATTTTAGAAGAGT
* *
120636940 TAATTAAAATTTTTAGAAATTTTAGAAGGGT
1 TAATCAAAATTTTTAG-AATTTTAGAAGAGT
* *
120636971 TAATGAGAATTTTTA
1 TAATCAAAATTTTTA
120636986 AAAAATAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
30 15 0.38
31 24 0.62
ACGTcount: A:0.41, C:0.01, G:0.13, T:0.45
Consensus pattern (30 bp):
TAATCAAAATTTTTAGAATTTTAGAAGAGT
Done.