Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167860.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_13, whole genome shotgun sequence
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: 22724830
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82000 characters in sequence are not A, C, G, or T
File 10 of 109
Found at i:1671884 original size:24 final size:24
Alignment explanation
Indices: 1671838--1671890 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1671828 TAAAGAAAGC
1671838 TAAATCTAAATTAAAATTAAAATT
1 TAAATCTAAATTAAAATTAAAATT
* *
1671862 TAAATC-AAATTCAATATTGAAATT
1 TAAATCTAAATT-AAAATTAAAATT
*
1671886 GAAAT
1 TAAAT
1671891 TGAAATCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.36
Consensus pattern (24 bp):
TAAATCTAAATTAAAATTAAAATT
Found at i:1671915 original size:30 final size:30
Alignment explanation
Indices: 1671850--1671919 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
1671840 AATCTAAATT
* *
1671850 AAAATTAAAATTTAAATCAAATTCAATATT
1 AAAATTAAAATTGAAATCAAATTCAATATC
* * *
1671880 GAAATTGAAATTGAAATCAAATTACAA-CTC
1 AAAATTAAAATTGAAATCAAATT-CAATATC
1671910 AAAATTAAAA
1 AAAATTAAAA
1671920 ATTTTGAAGC
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
30 29 0.91
31 3 0.09
ACGTcount: A:0.57, C:0.09, G:0.04, T:0.30
Consensus pattern (30 bp):
AAAATTAAAATTGAAATCAAATTCAATATC
Found at i:1672359 original size:15 final size:16
Alignment explanation
Indices: 1672339--1672373 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
1672329 TTTGGAAGGT
1672339 AAATTT-AAAAAAAAA
1 AAATTTCAAAAAAAAA
1672354 AAATTTGCAAAAAAAAA
1 AAATTT-CAAAAAAAAA
1672371 AAA
1 AAA
1672374 AAAACCCCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
17 12 0.67
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.17
Consensus pattern (16 bp):
AAATTTCAAAAAAAAA
Found at i:1674980 original size:34 final size:31
Alignment explanation
Indices: 1674941--1675008 Score: 82
Period size: 34 Copynumber: 2.1 Consensus size: 31
1674931 TAATATATTT
*
1674941 AAAAATTAAAAATAATACAATGATTATTTATAAA
1 AAAAATTAAAAATAATA-AAT-AATATTT-TAAA
* *
1674975 AAAAATTAAAGATATTAAATAATATTTTAAA
1 AAAAATTAAAAATAATAAATAATATTTTAAA
1675006 AAA
1 AAA
1675009 TTATGATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 7 0.23
32 6 0.19
33 3 0.10
34 15 0.48
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.32
Consensus pattern (31 bp):
AAAAATTAAAAATAATAAATAATATTTTAAA
Found at i:1675397 original size:25 final size:25
Alignment explanation
Indices: 1675369--1675421 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
1675359 TATTTATCTA
1675369 TTTATTTACTTAT-TTATTTTTCTTT
1 TTTATTTACTTATCTT-TTTTTCTTT
* *
1675394 TTTATTTTCTTGTCTTTTTTTCTTT
1 TTTATTTACTTATCTTTTTTTCTTT
1675419 TTT
1 TTT
1675422 TTTTCTAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 23 0.92
26 2 0.08
ACGTcount: A:0.09, C:0.09, G:0.02, T:0.79
Consensus pattern (25 bp):
TTTATTTACTTATCTTTTTTTCTTT
Found at i:1675401 original size:12 final size:12
Alignment explanation
Indices: 1675356--1675427 Score: 60
Period size: 12 Copynumber: 5.9 Consensus size: 12
1675346 GTTGATACCA
1675356 TTTTATTTATC-T
1 TTTTATTT-TCTT
* *
1675368 ATTTATTTACTT
1 TTTTATTTTCTT
*
1675380 ATTTATTTTTCTT
1 TTTTA-TTTTCTT
1675393 TTTTATTTTCTT
1 TTTTATTTTCTT
1675405 GTCTTT-TTTTCTT
1 -T-TTTATTTTCTT
1675418 TTTT-TTTTCT
1 TTTTATTTTCT
1675428 AGTAGCAGCT
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
11 10 0.19
12 21 0.40
13 18 0.35
14 3 0.06
ACGTcount: A:0.11, C:0.10, G:0.01, T:0.78
Consensus pattern (12 bp):
TTTTATTTTCTT
Found at i:1677363 original size:21 final size:21
Alignment explanation
Indices: 1677324--1677363 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1677314 ATTTTTTTGA
*
1677324 AAATTTTTTATATATTATTTT
1 AAATTTTTTATATAGTATTTT
1677345 AAATTTTATTATA-AGTATT
1 AAATTTT-TTATATAGTATT
1677364 CATGCATATT
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:0.03, T:0.60
Consensus pattern (21 bp):
AAATTTTTTATATAGTATTTT
Found at i:1684579 original size:24 final size:24
Alignment explanation
Indices: 1684523--1684582 Score: 86
Period size: 23 Copynumber: 2.5 Consensus size: 24
1684513 AGAGCTTAAA
1684523 ATAATTTATTTAAAAAAATAGAAC
1 ATAATTTATTTAAAAAAATAGAAC
* * *
1684547 ATAA-ATATTTGATAAAATAGAAC
1 ATAATTTATTTAAAAAAATAGAAC
1684570 ATAATTTATTTAA
1 ATAATTTATTTAA
1684583 TCTTGATGGG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 20 0.67
24 10 0.33
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (24 bp):
ATAATTTATTTAAAAAAATAGAAC
Found at i:1685385 original size:6 final size:6
Alignment explanation
Indices: 1685376--1685427 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
1685366 AGTTAAATCT
* * * * * *
1685376 AAATTA AAATTA AAATTA AAATCA AATTTA ATATTG AAATTG AAATTG
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
1685424 AAAT
1 AAAT
1685428 CAAATTACAA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.35
Consensus pattern (6 bp):
AAATTA
Found at i:1685406 original size:24 final size:24
Alignment explanation
Indices: 1685343--1685421 Score: 69
Period size: 24 Copynumber: 3.5 Consensus size: 24
1685333 CCACAAACTA
*
1685343 AAAATTAAAA-CTAAATT-AAA-G
1 AAAATTAAAATCTAAATTAAAATT
*
1685364 AAAGTT-AAATCTAAATTAAAATT
1 AAAATTAAAATCTAAATTAAAATT
*
1685387 AAAATTAAAATC-AAATTTAATATT
1 AAAATTAAAATCTAAA-TTAAAATT
* *
1685411 GAAATTGAAAT
1 AAAATTAAAAT
1685422 TGAAATCAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
20 3 0.06
21 12 0.26
22 3 0.06
23 8 0.17
24 21 0.45
ACGTcount: A:0.59, C:0.04, G:0.05, T:0.32
Consensus pattern (24 bp):
AAAATTAAAATCTAAATTAAAATT
Found at i:1687606 original size:18 final size:17
Alignment explanation
Indices: 1687585--1687629 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
1687575 ATCAAGCTAG
*
1687585 ATAATTTTATTTAAATCC
1 ATAATTTTATTTAAAT-A
* *
1687603 ATAAATATATTTAAATA
1 ATAATTTTATTTAAATA
1687620 ATAATTTTAT
1 ATAATTTTAT
1687630 CTATTTAATT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (17 bp):
ATAATTTTATTTAAATA
Found at i:1687658 original size:19 final size:18
Alignment explanation
Indices: 1687608--1687658 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
1687598 AATCCATAAA
* *
1687608 TATATTTAAATAATAATT
1 TATATTTAATTAATTATT
* *
1687626 T-TATCTATTTAATTATCT
1 TATATTTAATTAATTAT-T
1687644 TATATTTAATTAATT
1 TATATTTAATTAATT
1687659 TTTCATTTAA
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
17 11 0.44
18 3 0.12
19 11 0.44
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (18 bp):
TATATTTAATTAATTATT
Found at i:1688492 original size:30 final size:29
Alignment explanation
Indices: 1688448--1688521 Score: 73
Period size: 30 Copynumber: 2.5 Consensus size: 29
1688438 TATCTCTAAC
1688448 AATATATTT-AAAATA-AAA-ATAATACAAT
1 AATAT-TTTAAAAATATAAAGATAATA-AAT
*
1688476 AATTATTTATAAAAATATTAAAGATATTAAAT
1 AA-TATTT-TAAAAATA-TAAAGATAATAAAT
1688508 AATATTTTAAAAAT
1 AATATTTTAAAAAT
1688522 TATGATAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
28 4 0.10
29 4 0.10
30 13 0.33
31 5 0.13
32 8 0.21
33 5 0.13
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (29 bp):
AATATTTTAAAAATATAAAGATAATAAAT
Found at i:1688867 original size:4 final size:4
Alignment explanation
Indices: 1688860--1688894 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
1688850 TTGACACCAT
* *
1688860 TTTA TTTA TCTA TTTA TTTA TTTA CTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1688895 TTCTTTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:1689798 original size:21 final size:22
Alignment explanation
Indices: 1689754--1689798 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
1689744 AAAAAATTTT
* * *
1689754 TTTTAAATTTTTTTGTATATTA
1 TTTTAAATTTTATTATATAATA
1689776 TTTTAAATTTTATTAT-TAATA
1 TTTTAAATTTTATTATATAATA
1689797 TT
1 TT
1689799 CATGCATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTTAAATTTTATTATATAATA
Found at i:1691355 original size:2 final size:2
Alignment explanation
Indices: 1691331--1691421 Score: 136
Period size: 2 Copynumber: 47.5 Consensus size: 2
1691321 TTCTGCATTT
*
1691331 TA TA -A TA TA -A TA TA -A TA -A TA TA TA TA AA 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
*
1691369 TA TA TA TA TA TA TA TA TA TA TA TA TA AA 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
1691411 TA TA TA TA TA T
1 TA TA TA TA TA T
1691422 GATTTGATGC
Statistics
Matches: 81, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
1 4 0.05
2 77 0.95
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1694008 original size:2 final size:2
Alignment explanation
Indices: 1694001--1694025 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1693991 AAATAAATAA
1694001 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
1694026 ATAATGATGT
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:1694900 original size:20 final size:20
Alignment explanation
Indices: 1694853--1694900 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
1694843 TATAAAATGT
*
1694853 AATTTTTTGATTTTATTAAA
1 AATTTTATGATTTTATTAAA
*
1694873 CATATTTATGATTTT-TTAAAA
1 AAT-TTTATGATTTTATT-AAA
1694894 AATTTTA
1 AATTTTA
1694901 AGTCCGTGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
AATTTTATGATTTTATTAAA
Found at i:1697109 original size:24 final size:24
Alignment explanation
Indices: 1697053--1697112 Score: 86
Period size: 23 Copynumber: 2.5 Consensus size: 24
1697043 AGAGCTTAAA
1697053 ATAATTTATTTAAAAAAATAGAAC
1 ATAATTTATTTAAAAAAATAGAAC
* * *
1697077 ATAA-ATATTTGATAAAATAGAAC
1 ATAATTTATTTAAAAAAATAGAAC
1697100 ATAATTTATTTAA
1 ATAATTTATTTAA
1697113 TCTTGATGGG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 20 0.67
24 10 0.33
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (24 bp):
ATAATTTATTTAAAAAAATAGAAC
Found at i:1697674 original size:11 final size:11
Alignment explanation
Indices: 1697658--1697687 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1697648 TTCACTAAAT
1697658 TTGTGATTTTA
1 TTGTGATTTTA
1697669 TTGTGATTTTA
1 TTGTGATTTTA
1697680 TT-TGATTT
1 TTGTGATTT
1697688 GATTTTTCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.32
11 13 0.68
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.67
Consensus pattern (11 bp):
TTGTGATTTTA
Found at i:1697950 original size:24 final size:24
Alignment explanation
Indices: 1697887--1697965 Score: 69
Period size: 24 Copynumber: 3.5 Consensus size: 24
1697877 CCACAAACTA
*
1697887 AAAATTAAAA-CTAAATT-AAA-G
1 AAAATTAAAATCTAAATTAAAATT
*
1697908 AAAGTT-AAATCTAAATTAAAATT
1 AAAATTAAAATCTAAATTAAAATT
*
1697931 AAAATTAAAATC-AAATTTAATATT
1 AAAATTAAAATCTAAA-TTAAAATT
* *
1697955 GAAATTGAAAT
1 AAAATTAAAAT
1697966 TGCAATCAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
20 3 0.06
21 12 0.26
22 3 0.06
23 8 0.17
24 21 0.45
ACGTcount: A:0.59, C:0.04, G:0.05, T:0.32
Consensus pattern (24 bp):
AAAATTAAAATCTAAATTAAAATT
Found at i:1699237 original size:19 final size:19
Alignment explanation
Indices: 1699213--1699250 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1699203 GGTTGTTACG
1699213 TGTAAGGAACTTTGAAGAA
1 TGTAAGGAACTTTGAAGAA
1699232 TGTAAGGAACTTTGAAGAA
1 TGTAAGGAACTTTGAAGAA
1699251 CTATTATACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.05, G:0.26, T:0.26
Consensus pattern (19 bp):
TGTAAGGAACTTTGAAGAA
Found at i:1701071 original size:33 final size:32
Alignment explanation
Indices: 1701015--1701082 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
1701005 CAATATATTT
1701015 AAAAATTAAAAATAATACAATAATTATTTATAA
1 AAAAATTAAAAATAATACAATAA-TATTTATAA
* * *
1701048 AAAATATTAAAGATATTA-AATAATATTTTTAA
1 AAAA-ATTAAAAATAATACAATAATATTTATAA
1701080 AAA
1 AAA
1701083 TTATGATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 11 0.35
33 9 0.29
34 11 0.35
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (32 bp):
AAAAATTAAAAATAATACAATAATATTTATAA
Found at i:1701440 original size:4 final size:4
Alignment explanation
Indices: 1701433--1701496 Score: 55
Period size: 4 Copynumber: 16.8 Consensus size: 4
1701423 TTGACACCAT
* * *
1701433 TTTA TTTA TCTA TTTA TTTA TTTA CTTA TTTA -TT- TTTA TTT- TTATT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT-TA
*
1701479 TTTA TTT- TTTT TTTA TTT
1 TTTA TTTA TTTA TTTA TTT
1701497 CCTTTTCTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
3 9 0.18
4 38 0.78
5 2 0.04
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:1701508 original size:6 final size:6
Alignment explanation
Indices: 1701461--1701496 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
1701451 TATTTACTTA
1701461 TTTATT TTTATT TTTATT TTTATT TTT-TT TTTATT T
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT T
1701497 CCTTTTCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTATT
Found at i:1702390 original size:21 final size:23
Alignment explanation
Indices: 1702345--1702390 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
1702335 AAAATTTTTT
* *
1702345 TTTTGAAATTTTTTTATATATTA
1 TTTTGAAATTTTATTATATAATA
1702368 TTTT-AAATTTTATTAT-TAATA
1 TTTTGAAATTTTATTATATAATA
1702389 TT
1 TT
1702391 CATGCATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.29
22 11 0.52
23 4 0.19
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (23 bp):
TTTTGAAATTTTATTATATAATA
Found at i:1710968 original size:20 final size:20
Alignment explanation
Indices: 1710943--1710989 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1710933 AATATGTGTA
* *
1710943 TTGATTTTGTTGATGTGACG
1 TTGATTTTGTTGACGTAACG
*
1710963 TTGATTTTGTTGACGTAATG
1 TTGATTTTGTTGACGTAACG
1710983 TTGATTT
1 TTGATTT
1710990 GCTGAGGTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.17, C:0.04, G:0.26, T:0.53
Consensus pattern (20 bp):
TTGATTTTGTTGACGTAACG
Found at i:1711138 original size:31 final size:32
Alignment explanation
Indices: 1711103--1711163 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
1711093 AAATGATCTT
* *
1711103 TATACTCGCATAAAATTT-GAAATTTAGTCTC
1 TATACTCACATAAAATTTAAAAATTTAGTCTC
* *
1711134 TATACTTACATGAAATTTAAAAATTTAGTC
1 TATACTCACATAAAATTTAAAAATTTAGTC
1711164 CTTGTATTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 15 0.60
32 10 0.40
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.39
Consensus pattern (32 bp):
TATACTCACATAAAATTTAAAAATTTAGTCTC
Found at i:1712045 original size:15 final size:14
Alignment explanation
Indices: 1712017--1712072 Score: 51
Period size: 15 Copynumber: 3.9 Consensus size: 14
1712007 TTAAAATAAT
**
1712017 ATTAATTTTGATTAG
1 ATTAATTTAAATT-G
1712032 ATTAATTTAAATT-
1 ATTAATTTAAATTG
1712045 ATTAATATTATAATTG
1 ATTAAT-TTA-AATTG
*
1712061 ATTAATATAAAT
1 ATTAATTTAAAT
1712073 GATAATAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
13 6 0.17
14 6 0.17
15 17 0.49
16 6 0.17
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (14 bp):
ATTAATTTAAATTG
Found at i:1712066 original size:16 final size:15
Alignment explanation
Indices: 1712031--1712072 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
1712021 ATTTTGATTA
1712031 GATTAAT-TTAAATT
1 GATTAATATTAAATT
1712045 -ATTAATATTATAATT
1 GATTAATATTA-AATT
1712060 GATTAATA-TAAAT
1 GATTAATATTAAAT
1712073 GATAATAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 6 0.24
14 6 0.24
15 6 0.24
16 7 0.28
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (15 bp):
GATTAATATTAAATT
Found at i:1714169 original size:21 final size:21
Alignment explanation
Indices: 1714130--1714169 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1714120 ATTTTTTTGA
*
1714130 AAATTTTTTATATATTATTTT
1 AAATTTTTTATATAATATTTT
1714151 AAATTTTATTAT-TAATATT
1 AAATTTT-TTATATAATATT
1714170 CATGCATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
AAATTTTTTATATAATATTTT
Found at i:1721415 original size:24 final size:24
Alignment explanation
Indices: 1721359--1721418 Score: 77
Period size: 23 Copynumber: 2.5 Consensus size: 24
1721349 AGAGCTTAAA
*
1721359 ATAATTTATTTAAAAAAATAGATC
1 ATAATTTATTTAAAAAAATAGAAC
* * *
1721383 ATAA-ATATTTGATAAAATAGAAC
1 ATAATTTATTTAAAAAAATAGAAC
1721406 ATAATTTATTTAA
1 ATAATTTATTTAA
1721419 TCTTGATGGG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
23 19 0.66
24 10 0.34
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.38
Consensus pattern (24 bp):
ATAATTTATTTAAAAAAATAGAAC
Found at i:1722268 original size:24 final size:24
Alignment explanation
Indices: 1722222--1722274 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1722212 TAAAGAAAGC
1722222 TAAATCTAAATTAAAATTAAAATT
1 TAAATCTAAATTAAAATTAAAATT
* *
1722246 TAAATC-AAATTCAATATTGAAATT
1 TAAATCTAAATT-AAAATTAAAATT
*
1722270 GAAAT
1 TAAAT
1722275 TGAAATCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.36
Consensus pattern (24 bp):
TAAATCTAAATTAAAATTAAAATT
Found at i:1722299 original size:30 final size:30
Alignment explanation
Indices: 1722234--1722303 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
1722224 AATCTAAATT
* *
1722234 AAAATTAAAATTTAAATCAAATTCAATATT
1 AAAATTAAAATTGAAATCAAATTCAATATC
* * *
1722264 GAAATTGAAATTGAAATCAAATTACAA-CTC
1 AAAATTAAAATTGAAATCAAATT-CAATATC
1722294 AAAATTAAAA
1 AAAATTAAAA
1722304 ATTTTGAGCT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
30 29 0.91
31 3 0.09
ACGTcount: A:0.57, C:0.09, G:0.04, T:0.30
Consensus pattern (30 bp):
AAAATTAAAATTGAAATCAAATTCAATATC
Found at i:1725766 original size:4 final size:4
Alignment explanation
Indices: 1725749--1725783 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
1725739 TTGATACCAT
* *
1725749 TTTA TTTA TCTA TTTA TTTA TTTA CTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1725784 TTCTTTTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:1725817 original size:25 final size:23
Alignment explanation
Indices: 1725781--1725839 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
1725771 TACTTATTTA
*
1725781 TTTTTCTTTTTTCCTTTCTTGT-CT
1 TTTTTTTTTTTTCCTTT-TT-TCCT
*
1725805 TTTTTTTTCTTTTTCTTTTTTCCT
1 TTTTTTTT-TTTTCCTTTTTTCCT
1725829 TTTTTTTTTTT
1 TTTTTTTTTTT
1725840 AGTAGCAGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 4 0.13
24 19 0.61
25 8 0.26
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (23 bp):
TTTTTTTTTTTTCCTTTTTTCCT
Found at i:1725825 original size:13 final size:13
Alignment explanation
Indices: 1725804--1725838 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
1725794 CTTTCTTGTC
1725804 TTTTTTTTT-CTT
1 TTTTTTTTTCCTT
1725816 TTTCTTTTTTCCTT
1 TTT-TTTTTTCCTT
1725830 TTTTTTTTT
1 TTTTTTTTT
1725839 TAGTAGCAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 3 0.14
13 12 0.57
14 6 0.29
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (13 bp):
TTTTTTTTTCCTT
Found at i:1725825 original size:14 final size:13
Alignment explanation
Indices: 1725781--1725839 Score: 57
Period size: 14 Copynumber: 4.4 Consensus size: 13
1725771 TACTTATTTA
1725781 TTTTTC-TTTTTT
1 TTTTTCTTTTTTT
**
1725793 CCTTTCTTGTCTTTT
1 TTTTTCTT-T-TTTT
1725808 TTTTTCTTTTTCTT
1 TTTTTCTTTTT-TT
*
1725822 TTTTCCTTTTTTT
1 TTTTTCTTTTTTT
1725835 TTTTT
1 TTTTT
1725840 AGTAGCAGCT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
12 4 0.11
13 9 0.24
14 14 0.38
15 10 0.27
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (13 bp):
TTTTTCTTTTTTT
Found at i:1727228 original size:219 final size:218
Alignment explanation
Indices: 1726889--1727291 Score: 496
Period size: 219 Copynumber: 1.8 Consensus size: 218
1726879 TCTTATAAAT
* *
1726889 TAATAAAAAAATAAGAAAATAAAATTTTTATCCGATGATGAGATTCAAAGGTATTCTGAGTAGTG
1 TAATAAAAAAATAAGAAAATAAAA-TTTTATCCAATGATGAGATTCAAAAGTATTCTGAGTAGTG
* * * *
1726954 ATACCTATGAAATCTTTAGGCGAGAAGATTTTTTTAAATACTACCAGTATATTAGAGTATTTATA
65 ATACCTACGAAATCCTTAGGCGAGAAGATTTTTTTAAATACTACCAGTATATTAGAATATTTAGA
** *
1727019 -AAAAGTTTTTAATATAATAAAA-ATTTTCTTTTTCTATTAATAATAAATAAAATTAACTAATTT
130 GAAAA-ACTTCAATATAATAAAATATTTTCTTTTT-TATTAA-AATAAA-AAAATTAACTAATTT
1727082 ATTGAAAAATAAAGTGATAAAGGAATAG
191 ATTGAAAAATAAAGTGATAAAGGAATAG
*
1727110 TAAT-AAAAAATAAGAAAA-AAAA-TTTATCCAATGATGGGATTCTAAAAGTATTCTGAGTAGTG
1 TAATAAAAAAATAAGAAAATAAAATTTTATCCAATGATGAGATTC-AAAAGTATTCTGAGTAGTG
*** * * * *
1727172 ATTTTTTACGAAATCCTTAGGTGA-AA-ATGTTTCTTTAAATATTATCAGTGTATTAGAATATTT
65 A-TACCTACGAAATCCTTAGGCGAGAAGAT-TTT-TTTAAATACTACCAGTATATTAGAATATTT
* * *
1727235 AGAGAAAAACTTCAATATAATAAAATTTTTTCTTTTTTTTTAAAATAAAAATATTAA
127 AGAGAAAAACTTCAATATAATAAAATATTTTCTTTTTTATTAAAATAAAAAAATTAA
1727292 TAAAACAATT
Statistics
Matches: 156, Mismatches: 20, Indels: 16
0.81 0.10 0.08
Matches are distributed among these distances:
217 27 0.17
218 30 0.19
219 67 0.43
220 28 0.18
221 4 0.03
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.37
Consensus pattern (218 bp):
TAATAAAAAAATAAGAAAATAAAATTTTATCCAATGATGAGATTCAAAAGTATTCTGAGTAGTGA
TACCTACGAAATCCTTAGGCGAGAAGATTTTTTTAAATACTACCAGTATATTAGAATATTTAGAG
AAAAACTTCAATATAATAAAATATTTTCTTTTTTATTAAAATAAAAAAATTAACTAATTTATTGA
AAAATAAAGTGATAAAGGAATAG
Found at i:1728312 original size:2 final size:2
Alignment explanation
Indices: 1728291--1728343 Score: 58
Period size: 2 Copynumber: 28.0 Consensus size: 2
1728281 GCATTTTGCA
*
1728291 AT AT A- AT AT A- AT AT -T AT AT AT AT AT AT AT AT AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
1728330 AC AT TT AT AT AT AT
1 AT AT AT AT AT AT AT
1728344 GATTTGATGC
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
1 3 0.07
2 41 0.93
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1735519 original size:31 final size:31
Alignment explanation
Indices: 1735484--1735543 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
1735474 AAGTGACCTT
** *
1735484 TATACTCGTATAAAATTTGAAATTTAGTCTC
1 TATACTCACATAAAATTTAAAATTTAGTCTC
* *
1735515 TATACTTACATGAAATTTAAAATTTAGTC
1 TATACTCACATAAAATTTAAAATTTAGTC
1735544 CTTGTATTCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (31 bp):
TATACTCACATAAAATTTAAAATTTAGTCTC
Found at i:1735805 original size:25 final size:25
Alignment explanation
Indices: 1735775--1735826 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
1735765 CCAAATCTAT
1735775 TAAAAATCTATCACAAAATTTTCAA
1 TAAAAATCTATCACAAAATTTTCAA
* *
1735800 TAAAAATCTATCATAAAATTTTTAA
1 TAAAAATCTATCACAAAATTTTCAA
1735825 TA
1 TA
1735827 TATGATACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.37
Consensus pattern (25 bp):
TAAAAATCTATCACAAAATTTTCAA
Found at i:1736408 original size:29 final size:29
Alignment explanation
Indices: 1736374--1736455 Score: 76
Period size: 33 Copynumber: 2.7 Consensus size: 29
1736364 GAAATATTTA
*
1736374 AATTAATTAAAATAATATTA-ATTTGATT
1 AATTAATTAAAATAATATTATAATTGATT
1736402 AGATTAATTTAAATTATTAATATTATAATTGATT
1 A-ATTAA-TTAAA--A-TAATATTATAATTGATT
* *
1736436 AATTAAATGATAATAATATT
1 AATT-AATTAAAATAATATT
1736456 TTTATTAATA
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
28 1 0.02
29 5 0.11
30 12 0.27
31 1 0.02
32 1 0.02
33 14 0.32
34 10 0.23
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (29 bp):
AATTAATTAAAATAATATTATAATTGATT
Found at i:1736438 original size:16 final size:14
Alignment explanation
Indices: 1736390--1736443 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
1736380 TTAAAATAAT
*
1736390 ATTAATTT-GATTAG
1 ATTAATTTAAATT-G
1736404 ATTAATTTAAATT-
1 ATTAATTTAAATTG
1736417 ATTAATATTATAATTG
1 ATTAAT-TTA-AATTG
1736433 ATTAA-TTAAAT
1 ATTAATTTAAAT
1736444 GATAATAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
13 9 0.26
14 14 0.40
15 7 0.20
16 5 0.14
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (14 bp):
ATTAATTTAAATTG
Found at i:1738527 original size:23 final size:25
Alignment explanation
Indices: 1738492--1738538 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
1738482 TTTTTCAATA
1738492 AAAATATATTAATTT-TAATTATTTT
1 AAAATATATTAATTTAT-ATTATTTT
1738517 AAAATA-A-TAATTTATATTATTT
1 AAAATATATTAATTTATATTATTT
1738539 AATAAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 13 0.62
24 2 0.10
25 6 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
AAAATATATTAATTTATATTATTTT
Found at i:1738553 original size:17 final size:20
Alignment explanation
Indices: 1738518--1738559 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 20
1738508 AATTATTTTA
1738518 AAATAATAATTTATATTATT
1 AAATAATAATTTATATTATT
*
1738538 TAATAA-AATTT-T-TTATT
1 AAATAATAATTTATATTATT
1738555 AAATA
1 AAATA
1738560 TATATGTAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 9 0.45
18 1 0.05
19 5 0.25
20 5 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AAATAATAATTTATATTATT
Found at i:1741519 original size:2 final size:2
Alignment explanation
Indices: 1741508--1741540 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1741498 AGTGATCATT
1741508 TA TA -A 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
1741541 AATTGATGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1743437 original size:2 final size:2
Alignment explanation
Indices: 1743432--1743460 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1743422 AAAGAAATCC
1743432 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 T
1743461 TTCTATCCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1744011 original size:23 final size:23
Alignment explanation
Indices: 1743985--1744053 Score: 111
Period size: 23 Copynumber: 3.0 Consensus size: 23
1743975 CTCGGCACCC
* *
1743985 TTAAAAAATTGAAAATTTTAATT
1 TTAAATAATTAAAAATTTTAATT
1744008 TTAAATAATTAAAAATTTTAATT
1 TTAAATAATTAAAAATTTTAATT
1744031 TTAAATAATTAAAAATGTTTAAT
1 TTAAATAATTAAAAAT-TTTAAT
1744054 CTTTCTCTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
23 37 0.86
24 6 0.14
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (23 bp):
TTAAATAATTAAAAATTTTAATT
Found at i:1744579 original size:48 final size:43
Alignment explanation
Indices: 1744501--1744594 Score: 116
Period size: 48 Copynumber: 2.1 Consensus size: 43
1744491 ATTTCTTAAA
* **
1744501 TTTTTTTTATAAATTTTTAACTTTTGATTTTCTTTTATTAATG
1 TTTTTTTTATAAATTTTTAACTTTTAATTTTCTAATATTAATG
1744544 TTTTTTTTATTATAATTTATTGAAACTTTTAATTTTCTAATATTAATG
1 TTTTTTTTA-TA-AATTT-TT--AACTTTTAATTTTCTAATATTAATG
1744592 TTT
1 TTT
1744595 GACTATTGAT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
43 9 0.21
44 2 0.05
45 5 0.12
46 2 0.05
48 25 0.58
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (43 bp):
TTTTTTTTATAAATTTTTAACTTTTAATTTTCTAATATTAATG
Found at i:1744702 original size:21 final size:22
Alignment explanation
Indices: 1744656--1744712 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 22
1744646 TTGCTAACTT
1744656 TTTTTTG-AATAAA-ATTCAAA
1 TTTTTTGTAATAAATATTCAAA
* *
1744676 TCTTTTGTAATAAATA-TCAAG
1 TTTTTTGTAATAAATATTCAAA
*
1744697 TTTTTTTTACATAAAT
1 TTTTTTGTA-ATAAAT
1744713 TTTAAACTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 6 0.20
21 17 0.57
22 7 0.23
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.49
Consensus pattern (22 bp):
TTTTTTGTAATAAATATTCAAA
Found at i:1745130 original size:162 final size:160
Alignment explanation
Indices: 1744783--1745249 Score: 598
Period size: 162 Copynumber: 2.9 Consensus size: 160
1744773 TTTTTTAATG
* *
1744783 AATTTTTTACTTTTGATTTTCTACTATTTATATTTTTTAAAACCATTATTTGTTAAAATTTATTG
1 AATTTTTTACTTTTGATTTTCTTCTATTTATA-TTTTTAAAATCATTATTTGTTAAAATTTATTG
* * * *
1744848 AAACTTTTAGTTTTCTAATATTAATATTTTTTACTATTGATTTTTTGTAATTTATAATTTTTCAT
65 AAACTTTTAGTTTTCTAATATTAATGTTTTTTACTATTGATTTTTTGTGACTTATGATTTTTCAT
* * * **
1744913 CACAATAG-ATTT-TTGGATGCCTATTTTTTTATG
130 --C--TTGTTTTTATTGGATGCCTATATTTTTACA
*
1744946 GATTTTTTACTTTTGATTTTCTTCTATTTATATTCTTTAAAATCATTATTTGTTAAAATTTATTG
1 AATTTTTTACTTTTGATTTTCTTCTATTTATATT-TTTAAAATCATTATTTGTTAAAATTTATTG
* *
1745011 AAACTTTTAGTTTT-TAATATTAATGTTTTTTACTATTGATTTTCTTATGACTTATGATTTTTTA
65 AAACTTTTAGTTTTCTAATATTAATGTTTTTTACTATTGATTTT-TTGTGACTTATGATTTTTCA
*
1745075 TCTTGTTTTTATTCGGATGCTTATATTTTTACA
129 TCTTGTTTTTATT-GGATGCCTATATTTTTACA
* *
1745108 AATTTTTTACTTTTGATTTTCTTTTATTTATACTTTTTAAAATCGTTATTTGTTAAAATTTATTG
1 AATTTTTTACTTTTGATTTTCTTCTATTTATA-TTTTTAAAATCATTATTTGTTAAAATTTATTG
* * * * * *
1745173 AAAATTTTAGTTTTCTAATATTAATGTTATTGATTTTTTTATTTTGTTGTGACTTATGATTTTTC
65 AAACTTTTAGTTTTCTAATATTAATGTTTTTTA-CTATTGATTTT-TTGTGACTTATGATTTTTC
*
1745238 ATCTTTTTTTTA
128 ATCTTGTTTTTA
1745250 GGAGTGGGAG
Statistics
Matches: 268, Mismatches: 28, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
159 2 0.01
160 3 0.01
161 3 0.01
162 117 0.44
163 107 0.40
164 36 0.13
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.59
Consensus pattern (160 bp):
AATTTTTTACTTTTGATTTTCTTCTATTTATATTTTTAAAATCATTATTTGTTAAAATTTATTGA
AACTTTTAGTTTTCTAATATTAATGTTTTTTACTATTGATTTTTTGTGACTTATGATTTTTCATC
TTGTTTTTATTGGATGCCTATATTTTTACA
Found at i:1753442 original size:14 final size:16
Alignment explanation
Indices: 1753423--1753458 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
1753413 TAAAAAGATT
1753423 AATAAAAG-TAAA-AA
1 AATAAAAGATAAAGAA
1753437 AAT-AAAGATAAAGAA
1 AATAAAAGATAAAGAA
1753452 AATAAAA
1 AATAAAA
1753459 AAAATAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 4 0.21
14 7 0.37
15 5 0.26
16 3 0.16
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.14
Consensus pattern (16 bp):
AATAAAAGATAAAGAA
Found at i:1753816 original size:55 final size:53
Alignment explanation
Indices: 1753724--1753828 Score: 165
Period size: 55 Copynumber: 1.9 Consensus size: 53
1753714 ATATAGATAG
* * *
1753724 AAGTGGTAGCTATAGAATAAAAATGATTGAATTAAGGAAGACAGCTAATTTGA
1 AAGTGGCAGCTATAGAAAAAAAATGATTGAATAAAGGAAGACAGCTAATTTGA
1753777 AAGTGGCAGCTATCAGATAAAAAAATGATTGAATAAAGGAAGACAGCTAATT
1 AAGTGGCAGCTAT-AGA-AAAAAAATGATTGAATAAAGGAAGACAGCTAATT
1753829 GGAAGAGCAA
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
53 12 0.26
54 3 0.06
55 32 0.68
ACGTcount: A:0.47, C:0.08, G:0.22, T:0.24
Consensus pattern (53 bp):
AAGTGGCAGCTATAGAAAAAAAATGATTGAATAAAGGAAGACAGCTAATTTGA
Found at i:1755476 original size:22 final size:22
Alignment explanation
Indices: 1755445--1755489 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1755435 TTTCATTTTT
* *
1755445 TTTTATTTTTTCCTCTTTTTAA
1 TTTTAATTTTTCATCTTTTTAA
*
1755467 TTTTAATTTTTCATTTTTTTAA
1 TTTTAATTTTTCATCTTTTTAA
1755489 T
1 T
1755490 CACCATACCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTTAATTTTTCATCTTTTTAA
Found at i:1757798 original size:1 final size:1
Alignment explanation
Indices: 1757792--1757816 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1757782 CACTCATCTT
1757792 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
1757817 CTTGCATGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1758532 original size:3 final size:3
Alignment explanation
Indices: 1758518--1758549 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1758508 CTTGCTTCCG
*
1758518 TTA TTA TGA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1758550 TTGCAAACAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1769705 original size:16 final size:18
Alignment explanation
Indices: 1769684--1769720 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1769674 AAATTATTTT
1769684 TTTAAA-AATT-ATATAA
1 TTTAAATAATTGATATAA
*
1769700 TTTAAATTATTGATATAA
1 TTTAAATAATTGATATAA
1769718 TTT
1 TTT
1769721 TTAAAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 6 0.33
17 3 0.17
18 9 0.50
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
TTTAAATAATTGATATAA
Found at i:1772122 original size:22 final size:22
Alignment explanation
Indices: 1772096--1772139 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1772086 TGTATATTTA
*
1772096 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
1772118 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
1772140 GAAGATTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:1772338 original size:25 final size:23
Alignment explanation
Indices: 1772286--1772344 Score: 82
Period size: 25 Copynumber: 2.5 Consensus size: 23
1772276 AAAATTTTCA
* *
1772286 GCCTTCATTGCTGACTTTTTTAG
1 GCCTTCATTGCTGACCTGTTTAG
1772309 GCCTTCATTGCTGAATCCTGTTTAG
1 GCCTTCATTGCTG-A-CCTGTTTAG
1772334 GCCTTCATTGC
1 GCCTTCATTGC
1772345 CGAACCCTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 13 0.41
24 1 0.03
25 18 0.56
ACGTcount: A:0.14, C:0.25, G:0.19, T:0.42
Consensus pattern (23 bp):
GCCTTCATTGCTGACCTGTTTAG
Found at i:1772542 original size:18 final size:18
Alignment explanation
Indices: 1772519--1772553 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1772509 ATGTTCTTTG
*
1772519 GGTAAAGTTTCTAGTTCA
1 GGTAAAGCTTCTAGTTCA
*
1772537 GGTAAAGCTTCTGGTTC
1 GGTAAAGCTTCTAGTTC
1772554 TCATGGATTA
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:0.23, C:0.14, G:0.26, T:0.37
Consensus pattern (18 bp):
GGTAAAGCTTCTAGTTCA
Found at i:1776022 original size:22 final size:22
Alignment explanation
Indices: 1775996--1776039 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1775986 TGTATATTTA
1775996 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCTCTAGAATTAAG
1776018 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCTCTAGAATTAAG
1776040 GAAGATTTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (22 bp):
TATTTGTATCTCTAGAATTAAG
Found at i:1776460 original size:22 final size:21
Alignment explanation
Indices: 1776435--1776500 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 21
1776425 TGTATATTCA
1776435 TATTTGTATATCTAGAATTAAG
1 TATTTGTAT-TCTAGAATTAAG
*
1776457 TATTTGTATCCCTAGAATTAAG
1 TATTTGTAT-TCTAGAATTAAG
*
1776479 TATTTGCATTCTTAGAATTAAG
1 TATTTGTATTC-TAGAATTAAG
1776501 GACAGAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 1 0.03
22 38 0.97
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (21 bp):
TATTTGTATTCTAGAATTAAG
Found at i:1783043 original size:31 final size:31
Alignment explanation
Indices: 1783005--1783067 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
1782995 TTGTACCAGA
1783005 TAGTATTTCTCCTGAGATATATAATTTAACC
1 TAGTATTTCTCCTGAGATATATAATTTAACC
1783036 TAGTATTTCTCCTGAGATATATAATTTAACC
1 TAGTATTTCTCCTGAGATATATAATTTAACC
1783067 T
1 T
1783068 CAGTGGGAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.43
Consensus pattern (31 bp):
TAGTATTTCTCCTGAGATATATAATTTAACC
Found at i:1792600 original size:21 final size:21
Alignment explanation
Indices: 1792563--1792603 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1792553 ATTTTAAAAT
*
1792563 TAAAAAATATATTATTTTTAA
1 TAAAAAATATATCATTTTTAA
1792584 TAAAATAAT-TATCATTTTTA
1 TAAAA-AATATATCATTTTTA
1792604 GCGCAATCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
TAAAAAATATATCATTTTTAA
Found at i:1792967 original size:2 final size:2
Alignment explanation
Indices: 1792962--1792997 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1792952 GTATATAAAC
*
1792962 AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1792998 CCTAAAAACA
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:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1803016 original size:13 final size:12
Alignment explanation
Indices: 1802990--1803023 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1802980 AGCTTTATCC
*
1802990 TTTTTCTTGGTT
1 TTTTTTTTGGTT
1803002 TTTTTTTTGGTT
1 TTTTTTTTGGTT
1803014 TTTGTTTTTG
1 TTT-TTTTTG
1803024 CATGTGATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 14 0.70
13 6 0.30
ACGTcount: A:0.00, C:0.03, G:0.18, T:0.79
Consensus pattern (12 bp):
TTTTTTTTGGTT
Found at i:1805407 original size:3 final size:3
Alignment explanation
Indices: 1805399--1805430 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1805389 TCAAGTATAC
1805399 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1805431 TGTTTTCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1817566 original size:22 final size:22
Alignment explanation
Indices: 1817541--1817591 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
1817531 CAGACCAGAT
1817541 CGAACTGTTCCCTAAACCCGAC
1 CGAACTGTTCCCTAAACCCGAC
1817563 CGAACTGTTCCCTAAACCCGAC
1 CGAACTGTTCCCTAAACCCGAC
1817585 CGAACTG
1 CGAACTG
1817592 CTCTTCAGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.27, C:0.39, G:0.16, T:0.18
Consensus pattern (22 bp):
CGAACTGTTCCCTAAACCCGAC
Found at i:1818248 original size:14 final size:14
Alignment explanation
Indices: 1818177--1818379 Score: 88
Period size: 14 Copynumber: 13.8 Consensus size: 14
1818167 TCAAATTTCA
1818177 AAACCCTAAAACCTCC
1 AAACCCTAAAA--TCC
* * *
1818193 TAACCTTTAAATCC
1 AAACCCTAAAATCC
* *
1818207 AAACCCCAAAACCC
1 AAACCCTAAAATCC
1818221 AAAATCCCTAAAATCC
1 -AAA-CCCTAAAATCC
* *
1818237 AAACCCTTAAATCA
1 AAACCCTAAAATCC
*
1818251 AAACCCT-AAACCTC
1 AAACCCTAAAATC-C
***
1818265 AAATTTTAAAA-CC
1 AAACCCTAAAATCC
1818278 AAAACCCTAAAATCTCC
1 -AAACCCTAAAA--TCC
* *
1818295 AAACTCTAAAATCA
1 AAACCCTAAAATCC
* *
1818309 AAATCCTAAACCTTCC
1 AAACCCTAAA--ATCC
*
1818325 ATACCCTAAAATCC
1 AAACCCTAAAATCC
* * *
1818339 AAACCTTAAGACCCTCT
1 AAACCCTAA-A--ATCC
*
1818356 AAACCTTAAAAT-C
1 AAACCCTAAAATCC
1818369 AAACCCTAAAA
1 AAACCCTAAAA
1818380 CCCTCAAAAC
Statistics
Matches: 138, Mismatches: 36, Indels: 29
0.68 0.18 0.14
Matches are distributed among these distances:
13 15 0.11
14 62 0.45
15 10 0.07
16 38 0.28
17 13 0.09
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (14 bp):
AAACCCTAAAATCC
Found at i:1818311 original size:30 final size:30
Alignment explanation
Indices: 1818204--1818381 Score: 134
Period size: 30 Copynumber: 6.0 Consensus size: 30
1818194 AACCTTTAAA
* *
1818204 TCCAAACCCCAAAACCCAAAATCCCTAAAA--
1 TCCAAACCCTAAAA-TCAAAA-CCCTAAAACC
*
1818234 TCCAAACCCTTAAATCAAAACCCT-AAACC
1 TCCAAACCCTAAAATCAAAACCCTAAAACC
*** * *
1818263 T-CAAATTTTAAAACCAAAACCCTAAAATC
1 TCCAAACCCTAAAATCAAAACCCTAAAACC
* *
1818292 TCCAAACTCTAAAATCAAAATCCT-AAACC
1 TCCAAACCCTAAAATCAAAACCCTAAAACC
* * * *
1818321 TTCCATACCCTAAAATCCAAACCTTAAGACCC
1 -TCCAAACCCTAAAATCAAAACCCTAA-AACC
* *
1818353 TCTAAACCTTAAAATC-AAACCCTAAAACC
1 TCCAAACCCTAAAATCAAAACCCTAAAACC
1818382 CTCAAAACTC
Statistics
Matches: 116, Mismatches: 25, Indels: 15
0.74 0.16 0.10
Matches are distributed among these distances:
27 3 0.03
28 21 0.18
29 18 0.16
30 57 0.49
31 14 0.12
32 3 0.03
ACGTcount: A:0.47, C:0.34, G:0.01, T:0.19
Consensus pattern (30 bp):
TCCAAACCCTAAAATCAAAACCCTAAAACC
Found at i:1818446 original size:23 final size:23
Alignment explanation
Indices: 1818397--1818446 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
1818387 AACTCAACCG
* *
1818397 AAAATCTTAAAATCCGAATCTTC
1 AAAATCTTAAAACCCGAACCTTC
* * *
1818420 AAAATCTTGAAACCCTAACCTTT
1 AAAATCTTAAAACCCGAACCTTC
1818443 AAAA
1 AAAA
1818447 CCTCTACTCA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (23 bp):
AAAATCTTAAAACCCGAACCTTC
Found at i:1818871 original size:23 final size:25
Alignment explanation
Indices: 1818817--1818862 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1818807 CTGTTTGATG
*
1818817 ATAAAATATTTTATAATAAAAAAGA
1 ATAATATATTTTATAATAAAAAAGA
1818842 ATAATATATTTT-TAA-AAAAAA
1 ATAATATATTTTATAATAAAAAA
1818863 TTATGATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 3 0.15
25 11 0.55
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (25 bp):
ATAATATATTTTATAATAAAAAAGA
Found at i:1818877 original size:20 final size:20
Alignment explanation
Indices: 1818832--1818886 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
1818822 ATATTTTATA
1818832 ATAAAAAAGAATAATATATTT
1 ATAAAAAA-AATAATATATTT
* *
1818853 TTAAAAAAAATTATGATA-TT
1 ATAAAAAAAATAAT-ATATTT
1818873 ATAAAATAAAATAA
1 ATAAAA-AAAATAA
1818887 AAATAACATT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.33
Consensus pattern (20 bp):
ATAAAAAAAATAATATATTT
Found at i:1820969 original size:170 final size:165
Alignment explanation
Indices: 1820637--1821115 Score: 404
Period size: 172 Copynumber: 2.8 Consensus size: 165
1820627 ATAATATGAC
* * * * * * *
1820637 AATTATTTTTCTTGAAATTTCATTTAAATT-CTTTCACCCTTTGGGACAAATTTAAAGAAATTTC
1 AATTA-TTTTATTAAAATTTCATCTAAATTACTTT-ACCATTGGGGACAAATTTAGAGAAATTTT
* * * * *
1820701 TCATATAGAGATTTCCTAATAATTTATCA-TTCGAAATTTCTAAGAATCTCATTC-TTGGATAAT
64 TCATATAGAGATTTCTTAAAAATTTACCATTTC-AAATTTTTAAGAATTTCA-TCATTGGATAAT
1820764 TGTCAAATATTTTCAACTAAAATTTTTTATTTGAAAA-AAATA-T
127 T-T---ATA-TTT-AACTAAAATTTTTTATTTGAAAATAAATATT
*
1820807 AATTACTTTTATTAAAATTTCATCTAAATTACTTTACCATTGGGGACCAATTTAGAGAAATTTTT
1 AATTA-TTTTATTAAAATTTCATCTAAATTACTTTACCATTGGGGACAAATTTAGAGAAATTTTT
*
1820872 CATTTAGAGATTTCTTAAGAAATTTACCATTTCAAATTTTTAAGAATTTCATCATTGGATAATTT
65 CATATAGAGATTTCTTAA-AAATTTACCATTTCAAATTTTTAAGAATTTCATCATTGGATAATTT
* *
1820937 ATATTTAACTCCAAATTTTTTTTTTGTTTGAAAATAAATATT
129 ATATTTAACT--AAA---ATTTTTTATTTGAAAATAAATATT
* * * * *
1820979 AATTATTGTTATTGAAACTTT-ATCTAAATTATTTTACCA-TGTGGAACAAACTTAGAAAAAAGT
1 AATTATT-TTATT-AAAATTTCATCTAAATTACTTTACCATTG-GGGACAAATTTAG-AGAAA-T
** ** * *
1821042 TTTT-ACCTAG-GAACT-TTACACAAATTTACCATTTGAAATTTTTATA-AATTTCATCATTAGA
61 TTTTCATATAGAGATTTCTTA-A-AAATTTACCATTTCAAATTTTTA-AGAATTTCATCATTGGA
*
1821103 TAATTAATATTTA
123 TAATTTATATTTA
1821116 TTTTCATAAA
Statistics
Matches: 260, Mismatches: 31, Indels: 34
0.80 0.10 0.10
Matches are distributed among these distances:
165 4 0.02
166 3 0.01
167 6 0.02
170 84 0.32
171 50 0.19
172 93 0.36
173 15 0.06
174 5 0.02
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44
Consensus pattern (165 bp):
AATTATTTTATTAAAATTTCATCTAAATTACTTTACCATTGGGGACAAATTTAGAGAAATTTTTC
ATATAGAGATTTCTTAAAAATTTACCATTTCAAATTTTTAAGAATTTCATCATTGGATAATTTAT
ATTTAACTAAAATTTTTTATTTGAAAATAAATATT
Found at i:1821961 original size:10 final size:9
Alignment explanation
Indices: 1821946--1821988 Score: 54
Period size: 8 Copynumber: 4.9 Consensus size: 9
1821936 TTCAACCAAT
1821946 TATTTTTTC
1 TATTTTTTC
1821955 TA-TTTTTC
1 TATTTTTTC
*
1821963 TCAATTTTTC
1 T-ATTTTTTC
1821973 TATTTTTT-
1 TATTTTTTC
1821981 TATTTTTT
1 TATTTTTT
1821989 TGTTAACAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
8 15 0.48
9 9 0.29
10 7 0.23
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (9 bp):
TATTTTTTC
Found at i:1821989 original size:18 final size:18
Alignment explanation
Indices: 1821947--1821988 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1821937 TCAACCAATT
1821947 ATTTTTTCTATTTTTCTC
1 ATTTTTTCTATTTTTCTC
* *
1821965 AATTTTTCTATTTTT-TT
1 ATTTTTTCTATTTTTCTC
1821982 ATTTTTT
1 ATTTTTT
1821989 TGTTAACAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (18 bp):
ATTTTTTCTATTTTTCTC
Found at i:1822714 original size:13 final size:14
Alignment explanation
Indices: 1822696--1822724 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1822686 AGATGTTTAT
1822696 TATTTAAT-TATAA
1 TATTTAATATATAA
1822709 TATTTAATATATAA
1 TATTTAATATATAA
1822723 TA
1 TA
1822725 AATAATTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TATTTAATATATAA
Found at i:1827500 original size:18 final size:17
Alignment explanation
Indices: 1827474--1827507 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1827464 TTAGTGGAGG
1827474 TAAAAATATATATAATAC
1 TAAAAATATATA-AATAC
*
1827492 TAAATATATATAAATA
1 TAAAAATATATAAATA
1827508 AATTAAAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAAAATATATAAATAC
Found at i:1833138 original size:17 final size:18
Alignment explanation
Indices: 1833111--1833150 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
1833101 CACAAAAGAT
1833111 AACTATATGAACCAACTA
1 AACTATATGAACCAACTA
*
1833129 AACT-TATGAACCAATTA
1 AACTATATGAACCAACTA
1833146 AACTA
1 AACTA
1833151 AGTTCTGAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.50, C:0.20, G:0.05, T:0.25
Consensus pattern (18 bp):
AACTATATGAACCAACTA
Found at i:1837890 original size:63 final size:63
Alignment explanation
Indices: 1837805--1837976 Score: 195
Period size: 63 Copynumber: 2.7 Consensus size: 63
1837795 TAGTTAAGGC
* * * *
1837805 TGCTTAAGTACAGGGATCTATTTGAATAAATGATTTGAAAGAAACCAAATTTTGTACTTT-AGAT
1 TGCTTAAGTA-GGGGATCTATTTGAATAAATGATTTGAAAGAAACCAAATCTAGTA-TTTAAAAT
* *
1837869 TGCTTAAGTAGGGGATCTATTTGAATAAATGATCTGAAA-AAATCTAAATCTAGTATTTAAAAT
1 TGCTTAAGTAGGGGATCTATTTGAATAAATGATTTGAAAGAAA-CCAAATCTAGTATTTAAAAT
* * * * *
1837932 TGTTTAAGTCGACGGATGTAGTTGAATAAATGATTTGAAAGAAAC
1 TGCTTAAGTAG-GGGATCTATTTGAATAAATGATTTGAAAGAAAC
1837977 TAAGCAGAGG
Statistics
Matches: 92, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
62 6 0.07
63 48 0.52
64 35 0.38
65 3 0.03
ACGTcount: A:0.39, C:0.08, G:0.19, T:0.34
Consensus pattern (63 bp):
TGCTTAAGTAGGGGATCTATTTGAATAAATGATTTGAAAGAAACCAAATCTAGTATTTAAAAT
Found at i:1838945 original size:60 final size:60
Alignment explanation
Indices: 1838841--1839078 Score: 279
Period size: 60 Copynumber: 4.0 Consensus size: 60
1838831 TTTATATATA
** * **
1838841 TTTTAAGAAAAATTGATACTTTTAACTTTTCCTTAAAAGGTTTTTCTTGATAATTTTTAT
1 TTTTAAGAAAAATTGATACTTCCAACTTTTCCTCAAAATATTTTTCTTGATAATTTTTAT
* * *
1838901 TTTTAAGAAAAATTGATACTTCCAATTTTTTCTCAAAATATTTTTC-TGA-AA-TTTTAA
1 TTTTAAGAAAAATTGATACTTCCAACTTTTCCTCAAAATATTTTTCTTGATAATTTTTAT
* * ** *
1838958 TTTCAAGGAAAATTGATACTTTTAACTTTTCCTCAAAATATTTTTCTTAATAATTTTTAT
1 TTTTAAGAAAAATTGATACTTCCAACTTTTCCTCAAAATATTTTTCTTGATAATTTTTAT
* * * * *
1839018 TTTTAAGGAAAATTGATACTTCCAATTTTTTCTCAAAAT-GTTTT-TTGAAAATTTTTAT
1 TTTTAAGAAAAATTGATACTTCCAACTTTTCCTCAAAATATTTTTCTTGATAATTTTTAT
1839076 TTT
1 TTT
1839079 AGAAATTTTA
Statistics
Matches: 151, Mismatches: 24, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
57 45 0.30
58 19 0.13
59 9 0.06
60 78 0.52
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (60 bp):
TTTTAAGAAAAATTGATACTTCCAACTTTTCCTCAAAATATTTTTCTTGATAATTTTTAT
Found at i:1839002 original size:117 final size:117
Alignment explanation
Indices: 1838840--1839077 Score: 379
Period size: 117 Copynumber: 2.0 Consensus size: 117
1838830 TTTTATATAT
* * * *
1838840 ATTTTAAGAAAAATTGATACTTTTAACTTTTCCTTAAAAGGTTTTTCTTGATAATTTTTATTTTT
1 ATTTCAAGAAAAATTGATACTTTTAACTTTTCCTCAAAAGATTTTTCTTAATAATTTTTATTTTT
1838905 AAGAAAAATTGATACTTCCAATTTTTTCTCAAAATATTTTTCTG-AAATTTTA
66 AAGAAAAATTGATACTTCCAATTTTTTCTCAAAATATTTTT-TGAAAATTTTA
* *
1838957 ATTTCAAGGAAAATTGATACTTTTAACTTTTCCTCAAAATATTTTTCTTAATAATTTTTATTTTT
1 ATTTCAAGAAAAATTGATACTTTTAACTTTTCCTCAAAAGATTTTTCTTAATAATTTTTATTTTT
* * *
1839022 AAGGAAAATTGATACTTCCAATTTTTTCTCAAAATGTTTTTTGAAAATTTTT
66 AAGAAAAATTGATACTTCCAATTTTTTCTCAAAATATTTTTTGAAAATTTTA
1839074 ATTT
1 ATTT
1839078 TAGAAATTTT
Statistics
Matches: 111, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
116 2 0.02
117 109 0.98
ACGTcount: A:0.34, C:0.10, G:0.07, T:0.50
Consensus pattern (117 bp):
ATTTCAAGAAAAATTGATACTTTTAACTTTTCCTCAAAAGATTTTTCTTAATAATTTTTATTTTT
AAGAAAAATTGATACTTCCAATTTTTTCTCAAAATATTTTTTGAAAATTTTA
Found at i:1839004 original size:71 final size:67
Alignment explanation
Indices: 1838927--1839140 Score: 169
Period size: 60 Copynumber: 3.2 Consensus size: 67
1838917 TACTTCCAAT
1838927 TTTTTCTCAAAATATTTTTCTGAAATTTTAATTTCAAGGAAAATTGATACTTTTAACTTTTCCTC
1 TTTTTCT-AAAATATTTTT-TGAAATTTT-ATTT-AAGGAAAATTGATACTTTTAACTTTTCCTC
1838992 AAAATA
62 AAAATA
* * ** * *
1838998 TTTTTCT-TAATAATTTTT---A--TT-TTTAAGGAAAATTGATACTTCCAATTTTTTCTCAAAA
1 TTTTTCTAAAATATTTTTTGAAATTTTATTTAAGGAAAATTGATACTTTTAACTTTTCCTCAAAA
*
1839056 TG
66 TA
* * *
1839058 TTTTT-TGAAAATTTTTATTTTAGAAATTTTATTTTAAGAAAAATTGATA-TTTTCAACATTTCC
1 TTTTTCT-AAAA-TATT-TTTT-GAAATTTTA-TTTAAGGAAAATTGATACTTTT-AACTTTTCC
1839121 TCAAAAATA
60 TC-AAAATA
1839130 TTTTT-TAAAAT
1 TTTTTCTAAAAT
1839141 TTTATTTTCA
Statistics
Matches: 112, Mismatches: 17, Indels: 29
0.71 0.11 0.18
Matches are distributed among these distances:
59 1 0.01
60 36 0.32
61 5 0.04
62 2 0.02
63 6 0.05
65 1 0.01
67 1 0.01
68 1 0.01
69 10 0.09
70 3 0.03
71 35 0.31
72 11 0.10
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.50
Consensus pattern (67 bp):
TTTTTCTAAAATATTTTTTGAAATTTTATTTAAGGAAAATTGATACTTTTAACTTTTCCTCAAAA
TA
Found at i:1839089 original size:14 final size:15
Alignment explanation
Indices: 1839070--1839098 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1839060 TTTTGAAAAT
1839070 TTTTATTTT-AGAAA
1 TTTTATTTTAAGAAA
1839084 TTTTATTTTAAGAAA
1 TTTTATTTTAAGAAA
1839099 AATTGATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (15 bp):
TTTTATTTTAAGAAA
Found at i:1839141 original size:71 final size:71
Alignment explanation
Indices: 1839012--1839148 Score: 179
Period size: 71 Copynumber: 1.9 Consensus size: 71
1839002 TCTTAATAAT
* ** * *
1839012 TTTTATTTTTAAGGAAAATTGATACTTCCAATTTTTTCTCAAAATGTTTTTTGAAAATTTTTATT
1 TTTTATTTTTAAGAAAAATTGATACTTCCAACATTTCCTCAAAATATTTTTTGAAAA-TTTTATT
1839077 TTAGAAA
65 TTAGAAA
* *
1839084 TTTTA-TTTTAAGAAAAATTGATATTTTCAACATTTCCTCAAAAATATTTTTT-AAAATTTTATT
1 TTTTATTTTTAAGAAAAATTGATACTTCCAACATTTCCTC-AAAATATTTTTTGAAAATTTTATT
1839147 TT
65 TT
1839149 CAAGGAAAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
70 9 0.16
71 32 0.56
72 16 0.28
ACGTcount: A:0.35, C:0.07, G:0.06, T:0.52
Consensus pattern (71 bp):
TTTTATTTTTAAGAAAAATTGATACTTCCAACATTTCCTCAAAATATTTTTTGAAAATTTTATTT
TAGAAA
Found at i:1839158 original size:30 final size:31
Alignment explanation
Indices: 1839123--1839190 Score: 102
Period size: 32 Copynumber: 2.2 Consensus size: 31
1839113 ACATTTCCTC
*
1839123 AAAAATATTTTTT-AAAATTTTATTTTCAAG
1 AAAAATATTTTTTAAAAATTTGATTTTCAAG
*
1839153 GAAAATATTTTTTAAAAAATTTGATTTTCAAG
1 AAAAATATTTTTT-AAAAATTTGATTTTCAAG
1839185 AAAAAT
1 AAAAAT
1839191 TGTTACTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 12 0.36
32 21 0.64
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (31 bp):
AAAAATATTTTTTAAAAATTTGATTTTCAAG
Found at i:1839963 original size:18 final size:17
Alignment explanation
Indices: 1839930--1839963 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1839920 AAACTTTTAA
*
1839930 TATTTTTTTTTGCTTTC
1 TATTTTTTTGTGCTTTC
1839947 TATTTTTTTGTGACTTT
1 TATTTTTTTGTG-CTTT
1839964 GAGATTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.09, C:0.09, G:0.09, T:0.74
Consensus pattern (17 bp):
TATTTTTTTGTGCTTTC
Found at i:1840276 original size:5 final size:5
Alignment explanation
Indices: 1840268--1840298 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
1840258 AAAGAAAAAA
1840268 AAATT AAATT AAATT -AATT AAATT AAATT AA
1 AAATT AAATT AAATT AAATT AAATT AAATT AA
1840299 TAGAGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
AAATT
Found at i:1840288 original size:14 final size:14
Alignment explanation
Indices: 1840269--1840299 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1840259 AAGAAAAAAA
1840269 AATTAAATTAAATT
1 AATTAAATTAAATT
1840283 AATTAAATTAAATT
1 AATTAAATTAAATT
1840297 AAT
1 AAT
1840300 AGAGAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AATTAAATTAAATT
Found at i:1840321 original size:3 final size:3
Alignment explanation
Indices: 1840308--1840337 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
1840298 ATAGAGAAAA
1840308 AAT AGAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AA
1840338 AGTCCACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1841699 original size:7 final size:8
Alignment explanation
Indices: 1841689--1841735 Score: 58
Period size: 8 Copynumber: 5.6 Consensus size: 8
1841679 TCTTTTTCTC
1841689 TTTTTATTT
1 TTTTTA-TT
1841698 TTTTTATT
1 TTTTTATT
1841706 TTTTTATT
1 TTTTTATT
*
1841714 TTTTCTCTT
1 TTTT-TATT
*
1841723 TTTTCATT
1 TTTTTATT
1841731 TTTTT
1 TTTTT
1841736 CATCCATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
8 20 0.61
9 13 0.39
ACGTcount: A:0.09, C:0.06, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTTTATT
Found at i:1841709 original size:17 final size:17
Alignment explanation
Indices: 1841689--1841735 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
1841679 TCTTTTTCTC
1841689 TTTTTATTTTTTTTATT
1 TTTTTATTTTTTTTATT
* *
1841706 TTTTTATTTTTTCTCTT
1 TTTTTATTTTTTTTATT
*
1841723 TTTTCATTTTTTT
1 TTTTTATTTTTTT
1841736 CATCCATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.09, C:0.06, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTTATTTTTTTTATT
Found at i:1841736 original size:9 final size:9
Alignment explanation
Indices: 1841689--1841738 Score: 54
Period size: 9 Copynumber: 5.9 Consensus size: 9
1841679 TCTTTTTCTC
1841689 TTTTT-ATT
1 TTTTTCATT
*
1841697 TTTTTTATT
1 TTTTTCATT
1841706 TTTTT-A-T
1 TTTTTCATT
1841713 TTTTTC-TCT
1 TTTTTCAT-T
1841722 TTTTTCATT
1 TTTTTCATT
1841731 TTTTTCAT
1 TTTTTCAT
1841739 CCATTTTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
7 6 0.16
8 6 0.16
9 24 0.65
10 1 0.03
ACGTcount: A:0.10, C:0.08, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTCATT
Found at i:1842129 original size:11 final size:10
Alignment explanation
Indices: 1842112--1842145 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
1842102 TGGCATTCAT
1842112 TTTTTTTTTC
1 TTTTTTTTTC
*
1842122 TCTTTTTTTC
1 TTTTTTTTTC
1842132 TTTTATTTTTC
1 TTTT-TTTTTC
1842143 TTT
1 TTT
1842146 CTCTTTCCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:1842152 original size:21 final size:21
Alignment explanation
Indices: 1842111--1842152 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1842101 GTGGCATTCA
* *
1842111 TTTTTTTTTTCTCTTTTTTTC
1 TTTTATTTTTCTCTTTCTTTC
1842132 TTTTATTTTTCT-TTCTCTTTC
1 TTTTATTTTTCTCTT-TCTTTC
1842153 CATCTTTGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (21 bp):
TTTTATTTTTCTCTTTCTTTC
Found at i:1842158 original size:25 final size:25
Alignment explanation
Indices: 1842112--1842159 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
1842102 TGGCATTCAT
* ***
1842112 TTTTTTTTTCTCTTTTTTTCTTTTA
1 TTTTTCTTTCTCTTTCCATCTTTTA
1842137 TTTTTCTTTCTCTTTCCATCTTT
1 TTTTTCTTTCTCTTTCCATCTTT
1842160 GAGATCTTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (25 bp):
TTTTTCTTTCTCTTTCCATCTTTTA
Found at i:1847902 original size:60 final size:58
Alignment explanation
Indices: 1847830--1847942 Score: 172
Period size: 60 Copynumber: 1.9 Consensus size: 58
1847820 TTATACAAGA
* *
1847830 AAAATTGATACTTTCAACTTTTCCTTAAAAGTTTTTTCTTGATAATTTTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTTAAAA-TGTTTT-TTGAAAATTTTTATTTTTAAGG
* *
1847890 AAAATTGGTACTTTCAACTTTTTCTTAAAATGTTTTTTGAAAATTTTTATTTT
1 AAAATTGATACTTTCAACTTTTCCTTAAAATGTTTTTTGAAAATTTTTATTTT
1847943 AGAAATTTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
58 16 0.33
59 5 0.10
60 28 0.57
ACGTcount: A:0.30, C:0.09, G:0.08, T:0.53
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTCCTTAAAATGTTTTTTGAAAATTTTTATTTTTAAGG
Found at i:1847953 original size:14 final size:15
Alignment explanation
Indices: 1847934--1847962 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1847924 TTTTGAAAAT
1847934 TTTTATTTT-AGAAA
1 TTTTATTTTAAGAAA
1847948 TTTTATTTTAAGAAA
1 TTTTATTTTAAGAAA
1847963 AATTAATACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (15 bp):
TTTTATTTTAAGAAA
Found at i:1847965 original size:71 final size:71
Alignment explanation
Indices: 1847876--1848012 Score: 188
Period size: 71 Copynumber: 1.9 Consensus size: 71
1847866 TCTTGATAAT
* ** * * *
1847876 TTTTATTTTTAAGGAAAATTGGTACTTTCAACTTTTTCT-TAAAATGTTTTTTGAAAATTTTTAT
1 TTTTATTTTTAAGAAAAATTAATACTTTCAACTTTTCCTCAAAAATATTTTTT-AAAA-TTTTAT
1847940 TTTAGAAA
64 TTTAGAAA
1847948 TTTTA-TTTTAAGAAAAATTAATACTTTCAACTTTTCCTCAAAAATATTTTTTAAAATTTTATTT
1 TTTTATTTTTAAGAAAAATTAATACTTTCAACTTTTCCTCAAAAATATTTTTTAAAATTTTATTT
1848012 T
66 T
1848013 CAAGGAAAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
70 9 0.16
71 33 0.57
72 16 0.28
ACGTcount: A:0.34, C:0.07, G:0.06, T:0.53
Consensus pattern (71 bp):
TTTTATTTTTAAGAAAAATTAATACTTTCAACTTTTCCTCAAAAATATTTTTTAAAATTTTATTT
TAGAAA
Found at i:1848035 original size:71 final size:70
Alignment explanation
Indices: 1847898--1848037 Score: 160
Period size: 71 Copynumber: 2.0 Consensus size: 70
1847888 GGAAAATTGG
* * * * *
1847898 TACTTTCAACTTTTTCTTAAAATGTTTTTTGAAAATTTTTATTTTAGAAATTTTATTTTAAGAAA
1 TACTTTCAACTTTTCCTAAAAATATTTTTTGAAAATTTTTATTTTAGAAAATATATTTT-AGAAA
1847963 AATTAA
65 AATTAA
*
1847969 TACTTTCAACTTTTCCTCAAAAATATTTTTT-AAAA-TTTTATTTTCAAGGAAAATATATTTT-T
1 TACTTTCAACTTTTCCT-AAAAATATTTTTTGAAAATTTTTATTTT--A-GAAAATATATTTTAG
1848031 AAAAATT
62 AAAAATT
1848038 TGATTTTCAA
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
70 9 0.15
71 27 0.46
72 12 0.20
73 11 0.19
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (70 bp):
TACTTTCAACTTTTCCTAAAAATATTTTTTGAAAATTTTTATTTTAGAAAATATATTTTAGAAAA
ATTAA
Found at i:1848036 original size:32 final size:32
Alignment explanation
Indices: 1847987--1848054 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 32
1847977 ACTTTTCCTC
*
1847987 AAAAATAT-TTTTT-AAAATTTTATTTTCAAG
1 AAAAATATATTTTTAAAAATTTGATTTTCAAG
*
1848017 GAAAATATATTTTTAAAAATTTGATTTTCAAG
1 AAAAATATATTTTTAAAAATTTGATTTTCAAG
1848049 AAAAAT
1 AAAAAT
1848055 TGATACTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 7 0.21
31 5 0.15
32 21 0.64
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (32 bp):
AAAAATATATTTTTAAAAATTTGATTTTCAAG
Found at i:1848907 original size:19 final size:20
Alignment explanation
Indices: 1848871--1848909 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1848861 TTTGTTTCTA
1848871 ATTTCTCTGTGTTCTTTTTT
1 ATTTCTCTGTGTTCTTTTTT
1848891 ATTT-TCTGTAGTT-TTTTTT
1 ATTTCTCTGT-GTTCTTTTTT
1848910 CATTCCCCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.08, C:0.10, G:0.10, T:0.72
Consensus pattern (20 bp):
ATTTCTCTGTGTTCTTTTTT
Found at i:1849163 original size:3 final size:3
Alignment explanation
Indices: 1849152--1849200 Score: 89
Period size: 3 Copynumber: 16.0 Consensus size: 3
1849142 TAAAGAAAAA
1849152 AAT AGAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1849198 AAT
1 AAT
1849201 TAAAGTCTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1849726 original size:18 final size:18
Alignment explanation
Indices: 1849690--1849726 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1849680 ATAATTAGAA
*
1849690 AATCAACTGAATTGAATT
1 AATCAACTGAATAGAATT
*
1849708 AATCAACTGAATAGGATT
1 AATCAACTGAATAGAATT
1849726 A
1 A
1849727 CGTTCTTACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.30
Consensus pattern (18 bp):
AATCAACTGAATAGAATT
Found at i:1856119 original size:14 final size:16
Alignment explanation
Indices: 1856088--1856121 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
1856078 AATATAGTAA
1856088 AAAAATAATTATTATT
1 AAAAATAATTATTATT
1856104 AAAAAT-ATTA-TATT
1 AAAAATAATTATTATT
1856118 AAAA
1 AAAA
1856122 TTTATAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 4 0.22
16 6 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAAATAATTATTATT
Found at i:1856197 original size:23 final size:23
Alignment explanation
Indices: 1856154--1856197 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
1856144 ATATCATTTG
* *
1856154 TTAATTAATAATATATCAAATAA
1 TTAATTAAAAATATATAAAATAA
1856177 TTAATTAAAAAT-TAATAAAAT
1 TTAATTAAAAATAT-ATAAAAT
1856198 CGTAATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 1 0.06
23 17 0.94
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
TTAATTAAAAATATATAAAATAA
Found at i:1856478 original size:19 final size:19
Alignment explanation
Indices: 1856456--1856494 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1856446 TTTTTTTATT
*
1856456 ATTTTAAATTAATAAAATA
1 ATTTGAAATTAATAAAATA
* *
1856475 ATTTGAAATTTATTAAATA
1 ATTTGAAATTAATAAAATA
1856494 A
1 A
1856495 AATATCAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (19 bp):
ATTTGAAATTAATAAAATA
Found at i:1865496 original size:17 final size:19
Alignment explanation
Indices: 1865469--1865506 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
1865459 TTCACGAATA
*
1865469 AAAAAATTTATTAAT-TAT
1 AAAAAATTTATAAATATAT
1865487 AAAAAA-TTATAAATATAT
1 AAAAAATTTATAAATATAT
1865505 AA
1 AA
1865507 TCAAATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAAAATTTATAAATATAT
Found at i:1866402 original size:30 final size:30
Alignment explanation
Indices: 1866336--1866404 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
1866326 TTATTTAAAA
*
1866336 TCAATTTAATCTTTAAATATTTATTTTTAC
1 TCAATTAAATCTTTAAATATTTATTTTTAC
*
1866366 TTAATTAAAT-TTTAAAATATTTATTTTTA-
1 TCAATTAAATCTTT-AAATATTTATTTTTAC
1866395 TCCAATTAAA
1 T-CAATTAAA
1866405 CTACCAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 4 0.12
30 30 0.88
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (30 bp):
TCAATTAAATCTTTAAATATTTATTTTTAC
Found at i:1866493 original size:21 final size:21
Alignment explanation
Indices: 1866452--1866490 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1866442 ATTTTCATTT
1866452 AATAAAAATTTAATTGATTAA
1 AATAAAAATTTAATTGATTAA
*
1866473 AATAAATATTTAA-TGATT
1 AATAAAAATTTAATTGATT
1866491 TAATTAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (21 bp):
AATAAAAATTTAATTGATTAA
Found at i:1869542 original size:30 final size:30
Alignment explanation
Indices: 1869485--1869542 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
1869475 GCTAAAACGA
* * *
1869485 GTTTTTCTCATGAGCTGCACACTGAGTTTG
1 GTTTTGCTCAGGAGCTGCACACAGAGTTTG
1869515 GTTTTGCTCAGGAGCTGCTA-ACAGAGTT
1 GTTTTGCTCAGGAGCTGC-ACACAGAGTT
1869543 CCGTTCATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 23 0.96
31 1 0.04
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (30 bp):
GTTTTGCTCAGGAGCTGCACACAGAGTTTG
Found at i:1874573 original size:31 final size:31
Alignment explanation
Indices: 1874538--1874599 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
1874528 TCTGGTCACT
* * *
1874538 TGTTATAGACAAGATC-ACATTTAGATAACCA
1 TGTTATAAACAAGA-CAACACTCAGATAACCA
1874569 TGTTATAAACAAGACAACACTCAGATAACCA
1 TGTTATAAACAAGACAACACTCAGATAACCA
1874600 CAGTTCCCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 1 0.04
31 26 0.96
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.24
Consensus pattern (31 bp):
TGTTATAAACAAGACAACACTCAGATAACCA
Found at i:1887928 original size:15 final size:15
Alignment explanation
Indices: 1887905--1887942 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1887895 ATGGGAAGCG
*
1887905 AGAGGAAGGAAAAGA
1 AGAGCAAGGAAAAGA
*
1887920 AGAGCAAGGAAAGGA
1 AGAGCAAGGAAAAGA
1887935 AGAGCAAG
1 AGAGCAAG
1887943 AAGAGATCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.55, C:0.05, G:0.39, T:0.00
Consensus pattern (15 bp):
AGAGCAAGGAAAAGA
Found at i:1888353 original size:5 final size:5
Alignment explanation
Indices: 1888343--1888371 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
1888333 AAGTTCAAAT
1888343 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1888372 GGTTTTTGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:1896654 original size:14 final size:15
Alignment explanation
Indices: 1896621--1896655 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
1896611 TAGTTTCATT
1896621 ATTTTGGTTGCTTAA
1 ATTTTGGTTGCTTAA
*
1896636 ATTTTGGTT-CTTTA
1 ATTTTGGTTGCTTAA
1896650 ATTTTG
1 ATTTTG
1896656 AAAGCTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.17, C:0.06, G:0.17, T:0.60
Consensus pattern (15 bp):
ATTTTGGTTGCTTAA
Found at i:1901013 original size:2 final size:2
Alignment explanation
Indices: 1901006--1901050 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
1900996 ACGACTCTAT
* * *
1901006 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC GC AC GC AC GC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1901048 AC A
1 AC A
1901051 TACATAATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.44, C:0.49, G:0.07, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1906064 original size:41 final size:42
Alignment explanation
Indices: 1906005--1906092 Score: 133
Period size: 41 Copynumber: 2.1 Consensus size: 42
1905995 TGTGTTCAGA
* * *
1906005 TAAATTTTAGTTATAATACATTGACTACTA-TTATTTTAAGT
1 TAAAATTTAGGTATAATACATTGACTACTATTTATTATAAGT
1906046 TAAAATTTAGGTATAATACATTGACTACTATTTTATTATAAGT
1 TAAAATTTAGGTATAATACATTGACTACTA-TTTATTATAAGT
1906089 TAAA
1 TAAA
1906093 TCATGCTGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
41 28 0.67
43 14 0.33
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (42 bp):
TAAAATTTAGGTATAATACATTGACTACTATTTATTATAAGT
Found at i:1910660 original size:23 final size:25
Alignment explanation
Indices: 1910633--1910686 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 25
1910623 TATTTTTTAA
*
1910633 TATTTTATATATAATA-A-TACTTT
1 TATTTTAAATATAATAGATTACTTT
* *
1910656 TATTTTAAATTTAATAGATTAGTTT
1 TATTTTAAATATAATAGATTACTTT
1910681 TATTTT
1 TATTTT
1910687 CTAATTCAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 14 0.54
24 1 0.04
25 11 0.42
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (25 bp):
TATTTTAAATATAATAGATTACTTT
Found at i:1911986 original size:25 final size:28
Alignment explanation
Indices: 1911958--1912020 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 28
1911948 CATGTTTAAT
*
1911958 AAAAATATTTAT-TAATT-ATTT-TTTA
1 AAAAATATTTATATAATTAATTTATCTA
*
1911983 AAAAA-ATTTATATATTTAATTTATCTA
1 AAAAATATTTATATAATTAATTTATCTA
1912010 ATAAAATATTT
1 A-AAAATATTT
1912021 TAATTTATCA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
24 6 0.19
25 9 0.29
26 4 0.13
27 4 0.13
28 4 0.13
29 4 0.13
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (28 bp):
AAAAATATTTATATAATTAATTTATCTA
Done.