Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr8
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: 70076365
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3341059 characters in sequence are not A, C, G, or T
File 178 of 210
Found at i:59221729 original size:42 final size:42
Alignment explanation
Indices: 59221552--59221851 Score: 250
Period size: 42 Copynumber: 7.2 Consensus size: 42
59221542 TAGAAAAAAA
* * * ** *
59221552 CGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTA-GAAAAAA
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTATTATTAAG
** * * ** *
59221593 CGCCGCTAAAGTCCATGTTCTTTAGCGGCGCTTAATAAAAAA
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTATTATTAAG
* * * * * * *
59221635 CGCCGCTAAAGACCTTGTTCTTTAGAGGCGCTTAGCTA-AAAA
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTA-TTATTAAG
* * *
59221677 CGCTGTTAAAGATCATGTTCTTTAGCGGCGTTTATTATTAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTATTATTAAG
* * * *
59221719 TGCCGCTAAAGAACATGGTATTTAGCGGCGTTTTTTATTAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTATTATTAAG
* **
59221761 CGTCGCTAAAGAACATGGACTTTAGCGGCGTTT-TT-TCTAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTATTAT-TAAG
* *
59221802 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTT-TTTTCTAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTATTAT-TAAG
59221844 CGCCGCTA
1 CGCCGCTA
59221852 CTAAGAGCCG
Statistics
Matches: 226, Mismatches: 28, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
40 1 0.00
41 74 0.33
42 149 0.66
43 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.30
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTATTATTAAG
Found at i:59221730 original size:84 final size:83
Alignment explanation
Indices: 59221532--59221706 Score: 264
Period size: 83 Copynumber: 2.1 Consensus size: 83
59221522 CGGCTCTTAG
*
59221532 TAGCGGCGCTTAGA-AAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAACGC
1 TAGCGGCGCTTA-ATAAAAAACGCCGCTAAAGACCATGTTCTTTAGAGGCGCTTAGAAAAAACGC
59221596 CGCTAAAGTCCATGTTCTT
65 CGCTAAAGTCCATGTTCTT
* *
59221615 TAGCGGCGCTTAATAAAAAACGCCGCTAAAGACCTTGTTCTTTAGAGGCGCTTAGCTAAAAACGC
1 TAGCGGCGCTTAATAAAAAACGCCGCTAAAGACCATGTTCTTTAGAGGCGCTTAG-AAAAAACGC
* *
59221680 TGTTAAAGAT-CATGTTCTT
65 CGCTAAAG-TCCATGTTCTT
59221699 TAGCGGCG
1 TAGCGGCG
59221707 TTTATTATTA
Statistics
Matches: 84, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
82 1 0.01
83 51 0.61
84 31 0.37
85 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.25
Consensus pattern (83 bp):
TAGCGGCGCTTAATAAAAAACGCCGCTAAAGACCATGTTCTTTAGAGGCGCTTAGAAAAAACGCC
GCTAAAGTCCATGTTCTT
Found at i:59221827 original size:83 final size:84
Alignment explanation
Indices: 59221696--59221851 Score: 246
Period size: 83 Copynumber: 1.9 Consensus size: 84
59221686 AGATCATGTT
*
59221696 CTTTAGCGGCGTTTATTATTAAGTGCCGCTAAAGAACATGGTATTTAGCGGCGTTTTTTAT-TAA
1 CTTTAGCGGCGTTTATTATTAAGCGCCGCTAAAGAACATGGTATTTAGCGGCGTTTTTT-TCTAA
*
59221760 GCGTCGCTAAAGAACATGGA
65 GCGCCGCTAAAGAACATGGA
*
59221780 CTTTAGCGGCGTTT-TT-TCTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAA
1 CTTTAGCGGCGTTTATTAT-TAAGCGCCGCTAAAGAACATGGTATTTAGCGGCGTTTTTTTCTAA
59221843 GCGCCGCTA
65 GCGCCGCTA
59221852 CTAAGAGCCG
Statistics
Matches: 67, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
82 2 0.03
83 51 0.76
84 14 0.21
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (84 bp):
CTTTAGCGGCGTTTATTATTAAGCGCCGCTAAAGAACATGGTATTTAGCGGCGTTTTTTTCTAAG
CGCCGCTAAAGAACATGGA
Found at i:59223348 original size:15 final size:15
Alignment explanation
Indices: 59223328--59223357 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
59223318 TTTTTACAAA
59223328 TATTTATAAATACAT
1 TATTTATAAATACAT
59223343 TATTTATAAATACAT
1 TATTTATAAATACAT
59223358 AGGCAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (15 bp):
TATTTATAAATACAT
Found at i:59226444 original size:42 final size:42
Alignment explanation
Indices: 59226389--59226468 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 42
59226379 ATTTTTGGTT
* * *
59226389 AAAAATTACCCGAATTACACGCATTACCCGAATTGAATCACA
1 AAAAATTAACCGAATTACACGAATTAACCGAATTGAATCACA
*
59226431 AAAAATTAACCGAATTACCCGAATTAACCGAATTGAAT
1 AAAAATTAACCGAATTACACGAATTAACCGAATTGAAT
59226469 TACTACATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.45, C:0.23, G:0.10, T:0.23
Consensus pattern (42 bp):
AAAAATTAACCGAATTACACGAATTAACCGAATTGAATCACA
Found at i:59226452 original size:9 final size:9
Alignment explanation
Indices: 59226434--59226464 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
59226424 AATCACAAAA
59226434 AATTAACCG
1 AATTAACCG
*
59226443 AATTACCCG
1 AATTAACCG
59226452 AATTAACCG
1 AATTAACCG
59226461 AATT
1 AATT
59226465 GAATTACTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:59232648 original size:14 final size:14
Alignment explanation
Indices: 59232629--59232665 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
59232619 GCATCATTGG
59232629 ATATACTGAAGGAA
1 ATATACTGAAGGAA
*
59232643 ATATACTTAAGGAA
1 ATATACTGAAGGAA
*
59232657 AGATACTGA
1 ATATACTGA
59232666 CACATATAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.08, G:0.19, T:0.24
Consensus pattern (14 bp):
ATATACTGAAGGAA
Found at i:59242742 original size:15 final size:15
Alignment explanation
Indices: 59242724--59242753 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
59242714 TTCTGTTGCC
59242724 GTTGTTGGTGTTGGT
1 GTTGTTGGTGTTGGT
*
59242739 GTTGTTGTTGTTGGT
1 GTTGTTGGTGTTGGT
59242754 TTTGAAGATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.43, T:0.57
Consensus pattern (15 bp):
GTTGTTGGTGTTGGT
Found at i:59248619 original size:36 final size:35
Alignment explanation
Indices: 59248579--59248658 Score: 124
Period size: 36 Copynumber: 2.3 Consensus size: 35
59248569 TTTGATATTG
* *
59248579 ATTAGAATAAGGTGTTTCAATCTTACTATATATTCT
1 ATTAGAATAAGGTGTTTAAATCTTACTATA-ATCCT
*
59248615 ATTAGAATAAGGTGTTTAAATCTTACTATACTCCT
1 ATTAGAATAAGGTGTTTAAATCTTACTATAATCCT
59248650 ATTAGAATA
1 ATTAGAATA
59248659 TGATTTTACA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 12 0.29
36 29 0.71
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.41
Consensus pattern (35 bp):
ATTAGAATAAGGTGTTTAAATCTTACTATAATCCT
Found at i:59255823 original size:59 final size:60
Alignment explanation
Indices: 59255727--59255842 Score: 155
Period size: 59 Copynumber: 1.9 Consensus size: 60
59255717 TTTTGGGGCT
* * *
59255727 TGAACTTAGCAATTCTTCCCACATTGGAGCCTGAACTTTTTTTT-GTTCAAATTAGGTTC
1 TGAACTTAGCAATTCTTCACACATTGGAGCCTAAACTTTTTTTTAGTCCAAATTAGGTTC
* * *
59255786 TGAACTT-GACAATTGTTCACACATTGGGGTCTAAACTTTTTTTTAGTCCAAATTAGG
1 TGAACTTAG-CAATTCTTCACACATTGGAGCCTAAACTTTTTTTTAGTCCAAATTAGG
59255843 CCCTAAATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
58 1 0.02
59 37 0.76
60 11 0.22
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (60 bp):
TGAACTTAGCAATTCTTCACACATTGGAGCCTAAACTTTTTTTTAGTCCAAATTAGGTTC
Found at i:59256019 original size:30 final size:30
Alignment explanation
Indices: 59255983--59256055 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
59255973 AAAAGTCCCC
*
59255983 AATATGAAAAAATTGCCAAATTTAAA-CTCT
1 AATATGAAAAAATTACCAAATTTAAATCT-T
* *
59256013 AATATGAGAAAAATTATCAAATTTAGATCTT
1 AATATGA-AAAAATTACCAAATTTAAATCTT
*
59256044 AATCTGAAAAAA
1 AATATGAAAAAA
59256056 AAAATCAAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
30 12 0.32
31 23 0.62
32 2 0.05
ACGTcount: A:0.52, C:0.10, G:0.08, T:0.30
Consensus pattern (30 bp):
AATATGAAAAAATTACCAAATTTAAATCTT
Found at i:59270563 original size:5 final size:5
Alignment explanation
Indices: 59270553--59270577 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
59270543 AAAATAGTTA
59270553 AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT
59270578 TAACAACTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:59275390 original size:2 final size:2
Alignment explanation
Indices: 59275383--59275407 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
59275373 TTGTTTAACA
59275383 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
59275408 TATTGTGAAT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:59278001 original size:2 final size:2
Alignment explanation
Indices: 59277994--59278018 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
59277984 TTGTTTAACA
59277994 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
59278019 TATTGTGAAT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:59309185 original size:100 final size:99
Alignment explanation
Indices: 59309009--59309202 Score: 289
Period size: 100 Copynumber: 1.9 Consensus size: 99
59308999 AGTAATGACG
* * * * * * *
59309009 CATGGTATTGAATAATTTAATAAATGTTTTCACAAACAGACATTAAGCAAATGGTTTTTAGCAGA
1 CATGGTATTGAATAATTTAAGAAATATATTCACAAACAAACATAAACCAAAGGGTTTTTAGCAGA
*
59309074 TAAAGCTTGGCACCCAAGGAATAAGATGATGGAA
66 TAAAGCATGGCACCCAAGGAATAAGATGATGGAA
*
59309108 CATGGTATTGAATAATTTTAAGAAATATATTCTCAAACAAACATAAACCAAAGGGTTTTTAGCAG
1 CATGGTATTGAATAA-TTTAAGAAATATATTCACAAACAAACATAAACCAAAGGGTTTTTAGCAG
*
59309173 ATAAAGCATGGCACCCGAGGAATAAGATGA
65 ATAAAGCATGGCACCCAAGGAATAAGATGA
59309203 CTCCAGACGA
Statistics
Matches: 84, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
99 15 0.18
100 69 0.82
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.27
Consensus pattern (99 bp):
CATGGTATTGAATAATTTAAGAAATATATTCACAAACAAACATAAACCAAAGGGTTTTTAGCAGA
TAAAGCATGGCACCCAAGGAATAAGATGATGGAA
Found at i:59323751 original size:21 final size:23
Alignment explanation
Indices: 59323725--59323770 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
59323715 CATAAGATTT
59323725 GCATGTAAT-AAC-TTAGGGTTC
1 GCATGTAATAAACATTAGGGTTC
*
59323746 GCATGTCATAAACAATTAGGGTTC
1 GCATGTAATAAAC-ATTAGGGTTC
59323770 G
1 G
59323771 TGTAACATCG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 8 0.38
22 3 0.14
24 10 0.48
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.30
Consensus pattern (23 bp):
GCATGTAATAAACATTAGGGTTC
Found at i:59326542 original size:42 final size:42
Alignment explanation
Indices: 59326514--59326671 Score: 228
Period size: 42 Copynumber: 3.8 Consensus size: 42
59326504 TTATTGCCAG
*
59326514 TGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCGA
1 TGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATACCGA
* * * *
59326556 TGAAATAATTTTAGACTTTACGTCTAGCAGGCTTAATACCGG
1 TGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATACCGA
*
59326598 TGAAACAATATCAGACTTTACATCTAGCAGGCTTAATACCGA
1 TGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATACCGA
* * *
59326640 TGAAAC-ATTTCAGACTATATGTCTAGCAGGCT
1 TGAAACAATATCAGACTTTACGTCTAGCAGGCT
59326672 AAGTGCCGGT
Statistics
Matches: 102, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
41 22 0.22
42 80 0.78
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.29
Consensus pattern (42 bp):
TGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATACCGA
Found at i:59326640 original size:84 final size:83
Alignment explanation
Indices: 59326495--59326671 Score: 255
Period size: 84 Copynumber: 2.1 Consensus size: 83
59326485 GGCTTAGTGC
* * * * *
59326495 CTAGCAGACTTATTGCCAGTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCGATGAA
1 CTAGCAGGCTTAATACCAGTGAAACAATATCAGACTTTACATCTAGCAGGCTTAATACCGATGAA
* *
59326560 ATAATTTTAGACTTTACGT
66 A-AATTTCAGACTATACGT
*
59326579 CTAGCAGGCTTAATACCGGTGAAACAATATCAGACTTTACATCTAGCAGGCTTAATACCGATGAA
1 CTAGCAGGCTTAATACCAGTGAAACAATATCAGACTTTACATCTAGCAGGCTTAATACCGATGAA
* *
59326644 ACATTTCAGACTATATGT
66 AAATTTCAGACTATACGT
59326662 CTAGCAGGCT
1 CTAGCAGGCT
59326672 AAGTGCCGGT
Statistics
Matches: 83, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
83 23 0.28
84 60 0.72
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (83 bp):
CTAGCAGGCTTAATACCAGTGAAACAATATCAGACTTTACATCTAGCAGGCTTAATACCGATGAA
AAATTTCAGACTATACGT
Found at i:59333183 original size:89 final size:89
Alignment explanation
Indices: 59333003--59333182 Score: 249
Period size: 88 Copynumber: 2.0 Consensus size: 89
59332993 ATTAAGCCTC
* * *** * *
59333003 AAAGCTCTCAAAGTTTTTCAAAAAATGCAATTAAGCCTCTATTTTTTTTTGCATTCATTTGGATA
1 AAAGCCCTCAAACTTTTTCAAAAAAAAAAATTAAGCCTCTATTTTTTTTTGCACTCAATTGGATA
*
59333068 CTTAAACTTTCAAAATGTATCAAA
66 CTTAAACTTTCAAAATGCATCAAA
59333092 AAAGCCCTCAAACTTTTTCAAAAAAAAAAATTAAGTCC-CTA-TTTTTTTTGCACTCAATT-GAG
1 AAAGCCCTCAAACTTTTTCAAAAAAAAAAATTAAG-CCTCTATTTTTTTTTGCACTCAATTGGA-
59333154 TACTTAAACTTTCAAAATGCATCAAA
64 TACTTAAACTTTCAAAATGCATCAAA
59333180 AAA
1 AAA
59333183 AATTTTAAGC
Statistics
Matches: 81, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
87 2 0.02
88 44 0.54
89 33 0.41
90 2 0.02
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (89 bp):
AAAGCCCTCAAACTTTTTCAAAAAAAAAAATTAAGCCTCTATTTTTTTTTGCACTCAATTGGATA
CTTAAACTTTCAAAATGCATCAAA
Found at i:59333425 original size:59 final size:59
Alignment explanation
Indices: 59333311--59333440 Score: 167
Period size: 59 Copynumber: 2.2 Consensus size: 59
59333301 TAAAGTTGTA
*
59333311 AAAGAAATAT-AAAAAATTGTAACATTTTATAAAAATCGTAAAAAAAATTATAAAATAT
1 AAAGAAATATAAAAAAATTGTAAAATTTTATAAAAATCGTAAAAAAAATTATAAAATAT
* * ** *
59333369 ATAGAAATATAAAAAAATTGTAAAATTTTAT-AAAGTCGT-AAGGAAATTATACAAAATGT
1 AAAGAAATATAAAAAAATTGTAAAATTTTATAAAAATCGTAAAAAAAATTAT--AAAATAT
59333428 AAAGAAATATAAA
1 AAAGAAATATAAA
59333441 TTTTGTGAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
57 9 0.15
58 16 0.26
59 37 0.60
ACGTcount: A:0.60, C:0.03, G:0.08, T:0.28
Consensus pattern (59 bp):
AAAGAAATATAAAAAAATTGTAAAATTTTATAAAAATCGTAAAAAAAATTATAAAATAT
Found at i:59339516 original size:15 final size:15
Alignment explanation
Indices: 59339493--59339527 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
59339483 AGTATTAAGC
*
59339493 AAATGAAATAAAAAA
1 AAATTAAATAAAAAA
*
59339508 AAATTAAATAAAACA
1 AAATTAAATAAAAAA
59339523 AAATT
1 AAATT
59339528 GGCTCTGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.20
Consensus pattern (15 bp):
AAATTAAATAAAAAA
Found at i:59345165 original size:20 final size:20
Alignment explanation
Indices: 59345140--59345180 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
59345130 GTTCATCTAC
59345140 TGGTTGTTGCGTGTGAATAT
1 TGGTTGTTGCGTGTGAATAT
59345160 TGGTTGTTGCGTGTGAATAT
1 TGGTTGTTGCGTGTGAATAT
59345180 T
1 T
59345181 CTAGTTATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.15, C:0.05, G:0.34, T:0.46
Consensus pattern (20 bp):
TGGTTGTTGCGTGTGAATAT
Found at i:59350175 original size:3 final size:3
Alignment explanation
Indices: 59350167--59350191 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
59350157 CTTTCTCTGT
59350167 ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC A
59350192 ATGGGTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:59355406 original size:32 final size:33
Alignment explanation
Indices: 59355370--59355434 Score: 123
Period size: 32 Copynumber: 2.0 Consensus size: 33
59355360 ACATTTCGAC
59355370 AACAAGAAGAAAAAAA-CACCAGCAAACAAGGT
1 AACAAGAAGAAAAAAAGCACCAGCAAACAAGGT
59355402 AACAAGAAGAAAAAAAGCACCAGCAAACAAGGT
1 AACAAGAAGAAAAAAAGCACCAGCAAACAAGGT
59355435 TTTTCATCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 16 0.50
33 16 0.50
ACGTcount: A:0.62, C:0.18, G:0.17, T:0.03
Consensus pattern (33 bp):
AACAAGAAGAAAAAAAGCACCAGCAAACAAGGT
Found at i:59356453 original size:39 final size:39
Alignment explanation
Indices: 59356410--59356488 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
59356400 AGGTGATGGT
59356410 AAATATATCTGCAAGAAATTAACAAATTACTTACTTGGA
1 AAATATATCTGCAAGAAATTAACAAATTACTTACTTGGA
59356449 AAATATATCTGCAAGAAATTAACAAATTACTTACTTGGA
1 AAATATATCTGCAAGAAATTAACAAATTACTTACTTGGA
59356488 A
1 A
59356489 GGGACAAAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.47, C:0.13, G:0.10, T:0.30
Consensus pattern (39 bp):
AAATATATCTGCAAGAAATTAACAAATTACTTACTTGGA
Found at i:59369461 original size:19 final size:19
Alignment explanation
Indices: 59369437--59369490 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
59369427 TGAATCAGCT
* *
59369437 CTTACGAGCTTCTGTTTAG
1 CTTACGAGCTTCTGTTCAA
*
59369456 CTTACGAGCTTCTGCTCAA
1 CTTACGAGCTTCTGTTCAA
*
59369475 CTTTCGAGCTTCTGTT
1 CTTACGAGCTTCTGTT
59369491 GGCGTATTCG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.15, C:0.26, G:0.19, T:0.41
Consensus pattern (19 bp):
CTTACGAGCTTCTGTTCAA
Found at i:59369696 original size:21 final size:20
Alignment explanation
Indices: 59369669--59369717 Score: 80
Period size: 21 Copynumber: 2.4 Consensus size: 20
59369659 AATAGAAGTT
59369669 ATGAATGACAGGAAATTGAC
1 ATGAATGACAGGAAATTGAC
*
59369689 AGTGAATGACAGGGAATTGAC
1 A-TGAATGACAGGAAATTGAC
59369710 ATGAATGA
1 ATGAATGA
59369718 TTTTATTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 8 0.30
21 19 0.70
ACGTcount: A:0.43, C:0.08, G:0.29, T:0.20
Consensus pattern (20 bp):
ATGAATGACAGGAAATTGAC
Found at i:59387601 original size:94 final size:94
Alignment explanation
Indices: 59387340--59387762 Score: 602
Period size: 94 Copynumber: 4.4 Consensus size: 94
59387330 AACGCTAAAC
* *
59387340 CCCAAACCCTAATTTATTTGATTTTTTCTTAAAAATCCTAAACACTAAACCCTAATCTAATTTTT
1 CCCAAACCCTAATTTATTTGATTTTTCCTTAAAAACCCTAAACACTAAACCCTAATCTAA--TTT
59387405 TTTAAAATTTATAATTAATTTACTCAAGTAA
64 TTTAAAATTTATAATTAATTTACTCAAGTAA
*
59387436 CCCCAAACCTTAATTTATTTGATTTTTCCTTAAAAACCCTAAAC-CTTAAACCCTAATCTAAATT
1 -CCCAAACCCTAATTTATTTGATTTTTCCTTAAAAACCCTAAACAC-TAAACCCTAATCT-AATT
59387500 TTTTAAAA-TTATAATTAATTTACTCAAGTAA
63 TTTTAAAATTTATAATTAATTTACTCAAGTAA
*
59387531 CCCAAACCCTAATTTATTTGATTTTATCCTTAAGAACCCTAAACACTAAACCCTAATCTAATTTT
1 CCCAAACCCTAATTTATTTGATTTT-TCCTTAAAAACCCTAAACACTAAACCCTAATCTAATTTT
59387596 TTAAAATTTATAATTAATTTACTCAAGTAA
65 TTAAAATTTATAATTAATTTACTCAAGTAA
* * *
59387626 CCTTAAACCCTAATTTATTT-ATTTTTCCTTAAAAACCATAAACAGTAAACCCTAATCTAATTTT
1 CC-CAAACCCTAATTTATTTGATTTTTCCTTAAAAACCCTAAACACTAAACCCTAATCTAATTTT
* * **
59387690 TTAAAATTTATAATTAATTTAATTAAAAAA
65 TTAAAATTTATAATTAATTTACTCAAGTAA
* * * *
59387720 CCCTAGACCCTTATTTATTTAATTTTTTTCTT-AAAACCCTAAA
1 CCC-AAACCCTAATTTATTTGA-TTTTTCCTTAAAAACCCTAAA
59387763 ATCTAAAAAC
Statistics
Matches: 299, Mismatches: 18, Indels: 20
0.89 0.05 0.06
Matches are distributed among these distances:
94 114 0.38
95 94 0.31
96 36 0.12
97 53 0.18
98 2 0.01
ACGTcount: A:0.39, C:0.19, G:0.02, T:0.40
Consensus pattern (94 bp):
CCCAAACCCTAATTTATTTGATTTTTCCTTAAAAACCCTAAACACTAAACCCTAATCTAATTTTT
TAAAATTTATAATTAATTTACTCAAGTAA
Found at i:59387614 original size:190 final size:188
Alignment explanation
Indices: 59387340--59387762 Score: 625
Period size: 190 Copynumber: 2.2 Consensus size: 188
59387330 AACGCTAAAC
*
59387340 CCCAAACCCTAATTTATTTGATTTTTTCTTAAAAATCCTAAACACTAAACCCTAATCTAATTTTT
1 CCCAAACCCTAATTTATTTGATTTTTTCTT-AAAACCCTAAACACTAAACCCTAATCTAA-TTTT
*
59387405 TTTAAAATTTATAATTAATTTACTCAAGTAACCCCAAACCTTAATTTATTTGATTTTTCCTTAAA
64 TTTAAAATTTATAATTAATTTACTCAAGTAACCCCAAACCCTAATTTATTT-ATTTTTCCTTAAA
* ** * **
59387470 AACCCTAAACCTTAAACCCTAATCTAAATTTTTTAAAA-TTATAATTAATTTACTCAAGTAA
128 AACCATAAACAGTAAACCCTAATCT-AATTTTTTAAAATTTATAATTAATTTAATCAAAAAA
*
59387531 CCCAAACCCTAATTTATTTGATTTTATCCTTAAGAACCCTAAACACTAAACCCTAATCTAA-TTT
1 CCCAAACCCTAATTTATTTGATTTT-TTCTTAA-AACCCTAAACACTAAACCCTAATCTAATTTT
**
59387595 TTTAAAATTTATAATTAATTTACTCAAGTAACCTTAAACCCTAATTTATTTATTTTTCCTTAAAA
64 TTTAAAATTTATAATTAATTTACTCAAGTAACCCCAAACCCTAATTTATTTATTTTTCCTTAAAA
*
59387660 ACCATAAACAGTAAACCCTAATCTAATTTTTTAAAATTTATAATTAATTTAATTAAAAAA
129 ACCATAAACAGTAAACCCTAATCTAATTTTTTAAAATTTATAATTAATTTAATCAAAAAA
* * *
59387720 CCCTAGACCCTTATTTATTTAATTTTTTTCTTAAAACCCTAAA
1 CCC-AAACCCTAATTTATTTGA-TTTTTTCTTAAAACCCTAAA
59387763 ATCTAAAAAC
Statistics
Matches: 211, Mismatches: 16, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
188 12 0.06
189 66 0.31
190 72 0.34
191 31 0.15
192 30 0.14
ACGTcount: A:0.39, C:0.19, G:0.02, T:0.40
Consensus pattern (188 bp):
CCCAAACCCTAATTTATTTGATTTTTTCTTAAAACCCTAAACACTAAACCCTAATCTAATTTTTT
TAAAATTTATAATTAATTTACTCAAGTAACCCCAAACCCTAATTTATTTATTTTTCCTTAAAAAC
CATAAACAGTAAACCCTAATCTAATTTTTTAAAATTTATAATTAATTTAATCAAAAAA
Found at i:59387913 original size:40 final size:41
Alignment explanation
Indices: 59387844--59387937 Score: 104
Period size: 40 Copynumber: 2.3 Consensus size: 41
59387834 GTGATTCCTT
*
59387844 AAGGAAGCG-CTT-TGTCCACGTGAACACAAAGCGCACCCTC
1 AAGGAAGCGTTTTCTGTCCACGTG-ACACAAAGCGCACCCTC
* ** *
59387884 AAGGAAGCGTTTTCTGTCCACGTG-GACAAAGCGCTTCCTT
1 AAGGAAGCGTTTTCTGTCCACGTGACACAAAGCGCACCCTC
*
59387924 GAGGAAGCGTTTTC
1 AAGGAAGCGTTTTC
59387938 CTGCTTTATC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
40 34 0.74
41 2 0.04
42 10 0.22
ACGTcount: A:0.26, C:0.27, G:0.26, T:0.22
Consensus pattern (41 bp):
AAGGAAGCGTTTTCTGTCCACGTGACACAAAGCGCACCCTC
Found at i:59388351 original size:11 final size:10
Alignment explanation
Indices: 59388323--59388349 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
59388313 ATCAAAAAAC
59388323 AAAAAAACAA
1 AAAAAAACAA
59388333 AAAAAAACAA
1 AAAAAAACAA
59388343 AAAAAAA
1 AAAAAAA
59388350 ACCTGAACTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:59388421 original size:27 final size:27
Alignment explanation
Indices: 59388391--59388457 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
59388381 AGGGAAGCAG
*
59388391 GTTGGCGGCACCAATGGAGGGATCCGT
1 GTTGGCGGCACCAATGGAGGGATCCCT
*
59388418 GTTGGCGGCACCAGTGGAGGGATCCCT
1 GTTGGCGGCACCAATGGAGGGATCCCT
59388445 GTTGGCGGCACCA
1 GTTGGCGGCACCA
59388458 CCCTTGAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.16, C:0.25, G:0.40, T:0.18
Consensus pattern (27 bp):
GTTGGCGGCACCAATGGAGGGATCCCT
Found at i:59388537 original size:10 final size:10
Alignment explanation
Indices: 59388506--59388577 Score: 54
Period size: 10 Copynumber: 6.6 Consensus size: 10
59388496 AGGAGAGGGG
*
59388506 AAGAAGAAGA
1 AAGAAAAAGA
59388516 AAGAAAGGAAGA
1 AAGAAA--AAGA
59388528 AAGAAAAAGA
1 AAGAAAAAGA
* *
59388538 AGGAAAAGGA
1 AAGAAAAAGA
59388548 AAGGAGAGGAAAGA
1 AA-GA-A--AAAGA
59388562 AAGAAAAAGA
1 AAGAAAAAGA
*
59388572 AGGAAA
1 AAGAAA
59388578 GAAAAGGAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
10 28 0.56
11 2 0.04
12 12 0.24
13 2 0.04
14 6 0.12
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (10 bp):
AAGAAAAAGA
Found at i:59388537 original size:22 final size:23
Alignment explanation
Indices: 59388506--59388607 Score: 73
Period size: 24 Copynumber: 4.3 Consensus size: 23
59388496 AGGAGAGGGG
*
59388506 AAGAAGAAGAAAG-AAAGGAAGA
1 AAGAAAAAGAAAGAAAAGGAAGA
*
59388528 AAGAAAAAGAAGGAAAAGGAA-A
1 AAGAAAAAGAAAGAAAAGGAAGA
* * *
59388550 GGAGAGGAAAGAAAGAAAAAGAAGGA
1 -AAGA-AAAAGAAAGAAAAGGAA-GA
* ***
59388576 AAGAAAAGGAAAGGGGAGGAAAGA
1 AAGAAAAAGAAAGAAAAGG-AAGA
59388600 AAGAAAAA
1 AAGAAAAA
59388608 TAAGGAAAGA
Statistics
Matches: 60, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
22 12 0.20
23 10 0.17
24 32 0.53
25 5 0.08
26 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (23 bp):
AAGAAAAAGAAAGAAAAGGAAGA
Found at i:59388543 original size:14 final size:14
Alignment explanation
Indices: 59388509--59388634 Score: 73
Period size: 14 Copynumber: 9.1 Consensus size: 14
59388499 AGAGGGGAAG
59388509 AAGAA-GAAAG-AA
1 AAGAAGGAAAGAAA
*
59388521 AGGAA-GAAAGAAA
1 AAGAAGGAAAGAAA
*
59388534 AAGAAGGAAAAGGAA
1 AAGAAGG-AAAGAAA
*
59388549 AGGAGAGGAAAGAAA
1 AAGA-AGGAAAGAAA
* *
59388564 GAA-AAAGAAGGAAA
1 -AAGAAGGAAAGAAA
***
59388578 GAA-AAGGAAAGGGG
1 -AAGAAGGAAAGAAA
* *
59388592 AGGAAAGAAAGAAA
1 AAGAAGGAAAGAAA
*
59388606 AATAAGGAAAGAAA
1 AAGAAGGAAAGAAA
*
59388620 AATAAGGAAAGAAA
1 AAGAAGGAAAGAAA
59388634 A
1 A
59388635 GGAAAGGAGA
Statistics
Matches: 87, Mismatches: 21, Indels: 10
0.74 0.18 0.08
Matches are distributed among these distances:
12 9 0.10
13 7 0.08
14 51 0.59
15 16 0.18
16 4 0.05
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (14 bp):
AAGAAGGAAAGAAA
Found at i:59388564 original size:28 final size:28
Alignment explanation
Indices: 59388509--59388640 Score: 89
Period size: 28 Copynumber: 4.8 Consensus size: 28
59388499 AGAGGGGAAG
59388509 AAGAA-GAAAG-AAAGG-AAGAAAGAAA
1 AAGAAGGAAAGAAAAGGAAAGAAAGAAA
59388534 AAGAAGGAAAAGGAAAGGAGAGGAAAGAAAGAAA
1 AAGAAGG-AAA-G-AA--A-AGGAAAGAAAGAAA
**
59388568 AAGAAGGAAAGAAAAGGAAAG---G-GG
1 AAGAAGGAAAGAAAAGGAAAGAAAGAAA
* * ** *
59388592 AGGAAAGAAAGAAAAATAAGGAAAGAAA
1 AAGAAGGAAAGAAAAGGAAAGAAAGAAA
*
59388620 AATAAGGAAAGAAAAGGAAAG
1 AAGAAGGAAAGAAAAGGAAAG
59388641 GAGAAGAGAA
Statistics
Matches: 79, Mismatches: 15, Indels: 23
0.68 0.13 0.20
Matches are distributed among these distances:
24 16 0.20
25 6 0.08
26 1 0.01
27 4 0.05
28 23 0.29
29 1 0.01
30 1 0.01
31 2 0.03
32 2 0.03
33 6 0.08
34 17 0.22
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.02
Consensus pattern (28 bp):
AAGAAGGAAAGAAAAGGAAAGAAAGAAA
Found at i:59388582 original size:38 final size:38
Alignment explanation
Indices: 59388524--59388620 Score: 148
Period size: 38 Copynumber: 2.7 Consensus size: 38
59388514 GAAAGAAAGG
59388524 AAGAAAGAAAAAGAA-G---GAAAAGGAAAGGAGAGGA
1 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAGGA
*
59388558 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGGGAGGA
1 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAGGA
*
59388596 AAGAAAGAAAAATAAGGAAAGAAAA
1 AAGAAAGAAAAAGAAGGAAAGAAAA
59388621 ATAAGGAAAG
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
34 15 0.26
35 1 0.02
38 41 0.72
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.01
Consensus pattern (38 bp):
AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAGGA
Found at i:59388584 original size:10 final size:10
Alignment explanation
Indices: 59388526--59388640 Score: 71
Period size: 10 Copynumber: 11.5 Consensus size: 10
59388516 AAGAAAGGAA
*
59388526 GAAAGAAAAA
1 GAAAGAAAAG
*
59388536 GAAGGAAAAG
1 GAAAGAAAAG
* *
59388546 GAAAGGAGAG
1 GAAAGAAAAG
59388556 GAAAG-AAA-
1 GAAAGAAAAG
59388564 GAAA-AAGAAG
1 GAAAGAA-AAG
59388574 GAAAGAAAAG
1 GAAAGAAAAG
***
59388584 GAAAGGGGAG
1 GAAAGAAAAG
59388594 GAAAG-AAA-
1 GAAAGAAAAG
59388602 GAAA-AATAAG
1 GAAAGAA-AAG
59388612 GAAAGAAAAATAAG
1 GAAAG---AA-AAG
59388626 GAAAGAAAAG
1 GAAAGAAAAG
59388636 GAAAG
1 GAAAG
59388641 GAGAAGAGAA
Statistics
Matches: 83, Mismatches: 11, Indels: 22
0.72 0.09 0.19
Matches are distributed among these distances:
8 10 0.12
9 7 0.08
10 51 0.61
11 4 0.05
14 11 0.13
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (10 bp):
GAAAGAAAAG
Found at i:59388633 original size:18 final size:18
Alignment explanation
Indices: 59388509--59388619 Score: 95
Period size: 18 Copynumber: 6.1 Consensus size: 18
59388499 AGAGGGGAAG
59388509 AAGAAGAAAGAAAGG-AAGA
1 AAGAA-AAAG-AAGGAAAGA
59388528 AAGAAAAAGAAGG--A-A
1 AAGAAAAAGAAGGAAAGA
* *
59388543 AAGGAAAGGAGAGGAAAGA
1 AAGAAAAAGA-AGGAAAGA
59388562 AAGAAAAAGAAGGAAAGAA
1 AAGAAAAAGAAGGAAAG-A
** *
59388581 AAGGAAAGGGGAGGAAAGA
1 AA-GAAAAAGAAGGAAAGA
*
59388600 AAGAAAAATAAGGAAAGA
1 AAGAAAAAGAAGGAAAGA
59388618 AA
1 AA
59388620 AATAAGGAAA
Statistics
Matches: 75, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
15 9 0.12
16 4 0.05
17 4 0.05
18 26 0.35
19 20 0.27
20 12 0.16
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.01
Consensus pattern (18 bp):
AAGAAAAAGAAGGAAAGA
Found at i:59389338 original size:19 final size:19
Alignment explanation
Indices: 59389314--59389354 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
59389304 TAATATTTGG
*
59389314 TATTTTTTTAATATTTTAT
1 TATTTTTGTAATATTTTAT
*
59389333 TATTTTTGTAATGTTTTAT
1 TATTTTTGTAATATTTTAT
59389352 TAT
1 TAT
59389355 GGGTTTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (19 bp):
TATTTTTGTAATATTTTAT
Found at i:59389439 original size:28 final size:29
Alignment explanation
Indices: 59389390--59389460 Score: 110
Period size: 28 Copynumber: 2.5 Consensus size: 29
59389380 AATAAAAAAA
59389390 TTACCAAAATAT-TATAACTTTTTCTTAT
1 TTACCAAAATATATATAACTTTTTCTTAT
* *
59389418 TTACCAAAAAATATATAA-TTTTTTTTAT
1 TTACCAAAATATATATAACTTTTTCTTAT
59389446 TTACCAAAATATATA
1 TTACCAAAATATATA
59389461 AAAAAAGTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
28 34 0.87
29 5 0.13
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.46
Consensus pattern (29 bp):
TTACCAAAATATATATAACTTTTTCTTAT
Found at i:59389481 original size:18 final size:19
Alignment explanation
Indices: 59389460--59389503 Score: 65
Period size: 17 Copynumber: 2.4 Consensus size: 19
59389450 CAAAATATAT
*
59389460 AAAAAAAGT-AAAAAACA-
1 AAAAAAAATAAAAAAACAG
59389477 AAAAAAAATAAAAAAACAG
1 AAAAAAAATAAAAAAACAG
59389496 AAAAAAAA
1 AAAAAAAA
59389504 CACACTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 8 0.33
18 8 0.33
19 8 0.33
ACGTcount: A:0.86, C:0.05, G:0.05, T:0.05
Consensus pattern (19 bp):
AAAAAAAATAAAAAAACAG
Found at i:59390733 original size:17 final size:17
Alignment explanation
Indices: 59390711--59390747 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
59390701 ATGGGGTAAG
59390711 ATGCTATTCTAATATTC
1 ATGCTATTCTAATATTC
*
59390728 ATGCTATTTTAATATTC
1 ATGCTATTCTAATATTC
59390745 ATG
1 ATG
59390748 ACATCTTACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.30, C:0.14, G:0.08, T:0.49
Consensus pattern (17 bp):
ATGCTATTCTAATATTC
Found at i:59393474 original size:15 final size:14
Alignment explanation
Indices: 59393434--59393462 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
59393424 TTTTTGTATC
59393434 AATTTAATTATTCT
1 AATTTAATTATTCT
59393448 AATTTAATTATTCT
1 AATTTAATTATTCT
59393462 A
1 A
59393463 GTTTTAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTTAATTATTCT
Found at i:59393764 original size:61 final size:62
Alignment explanation
Indices: 59393653--59393770 Score: 161
Period size: 61 Copynumber: 1.9 Consensus size: 62
59393643 CCACTAATCC
* *
59393653 TAATAACTAACACAATAATAATATTAATAATTTTATATACAAAATAATACTAACTAAAATTAT
1 TAATAACTAACACAAAAATAATACTAAT-ATTTTATATACAAAATAATACTAACTAAAATTAT
*
59393716 TAATAACTAACTACAAAAATAATACTAAT-TTTT-TACTA-ACAATAATACTAACTAA
1 TAATAACTAAC-ACAAAAATAATACTAATATTTTATA-TACAAAATAATACTAACTAA
59393771 CATCTTAATA
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
61 18 0.36
62 6 0.12
63 11 0.22
64 15 0.30
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (62 bp):
TAATAACTAACACAAAAATAATACTAATATTTTATATACAAAATAATACTAACTAAAATTAT
Found at i:59393784 original size:3 final size:3
Alignment explanation
Indices: 59393776--59393801 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
59393766 ACTAACATCT
59393776 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
59393802 CTATAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:59394164 original size:27 final size:27
Alignment explanation
Indices: 59394114--59394196 Score: 94
Period size: 27 Copynumber: 3.1 Consensus size: 27
59394104 GGTTGGCAGG
** **
59394114 ACTGGTGCCGCCAACAGGGATCCCTCC
1 ACTGGTGCCGCCAACCTGCTTCCCTCC
**
59394141 ACTGGTGCCGCCAACCTGCTTCCCTTG
1 ACTGGTGCCGCCAACCTGCTTCCCTCC
**
59394168 TTTGGTGCCGCCAACCTGCTTCCCTCC
1 ACTGGTGCCGCCAACCTGCTTCCCTCC
59394195 AC
1 AC
59394197 CCAGGGAGTT
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.13, C:0.42, G:0.22, T:0.23
Consensus pattern (27 bp):
ACTGGTGCCGCCAACCTGCTTCCCTCC
Found at i:59394253 original size:23 final size:22
Alignment explanation
Indices: 59394222--59394265 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
59394212 ATCAGTTCAG
59394222 TTTTTTTTTTCGGTTTTTTATT
1 TTTTTTTTTTCGGTTTTTTATT
**
59394244 TTTTTATTTTTTTGTTTTTTAT
1 TTTTT-TTTTTCGGTTTTTTAT
59394266 ATATTTTGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.07, C:0.02, G:0.07, T:0.84
Consensus pattern (22 bp):
TTTTTTTTTTCGGTTTTTTATT
Found at i:59394291 original size:23 final size:23
Alignment explanation
Indices: 59394263--59394308 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
59394253 TTTTGTTTTT
59394263 TATATATTTTGGTAAATAAAAAA
1 TATATATTTTGGTAAATAAAAAA
59394286 TATATATTTTGGTAAATAAAAAA
1 TATATATTTTGGTAAATAAAAAA
59394309 AAGTTATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (23 bp):
TATATATTTTGGTAAATAAAAAA
Found at i:59398211 original size:29 final size:29
Alignment explanation
Indices: 59398146--59398212 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
59398136 GGATTTTGAG
*
59398146 AGTTTTCAGACCTAATTGAAATTTTATTT
1 AGTTTTAAGACCTAATTGAAATTTTATTT
* *
59398175 AATCTTAAGA-CTAAATT-AAATTTTGATTT
1 AGTTTTAAGACCT-AATTGAAATTTT-ATTT
59398204 AGTTTTAAG
1 AGTTTTAAG
59398213 GTTAATTTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
28 9 0.29
29 22 0.71
ACGTcount: A:0.36, C:0.07, G:0.10, T:0.46
Consensus pattern (29 bp):
AGTTTTAAGACCTAATTGAAATTTTATTT
Found at i:59416409 original size:44 final size:43
Alignment explanation
Indices: 59416127--59416940 Score: 295
Period size: 44 Copynumber: 18.8 Consensus size: 43
59416117 TCGGTGGCCG
* * * *
59416127 ATAATCTTATCTCTCTAAAGTTACAGTGGAGCAGATTAGAACC
1 ATAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCC
* * * * * * *
59416170 GATAATCCTATCTCCCTAAAGTTACAGTGGAGCGGATGAAAACC
1 -ATAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCC
* * * * * *** *
59416214 TTGGATCTTATCTCACTGAAGTTACAG-AGAGCAGATCCCA-TC
1 AT-AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCC
* * * * * *
59416256 -TAGTCTTATCTCCCTGAAGTTACAGTAGAGCAGACTAAGTGGGC
1 ATAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAG-AGCC
* * * *
59416300 A-AGTCTTATC-CTCCTGAAGTTGTAGT-GAGGCAGACTGAAGATG-G
1 ATAATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-T-TAGA-GCC
* *
59416344 AAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAGAGCC
1 ATAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCC
* * * * *
59416387 GATAATCCTATCTCCCTGAAGTTGTAGTGAAGCAGATTAAAACC
1 -ATAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCC
* * * *** *
59416431 -TCAGATCTTATCTCTCTGAAGTTACAG-AGAGCAGATCCCA-TC
1 AT-A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCC
* *
59416473 -TAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAG-C
1 ATAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAG--AGCC
* * * *
59416517 A-AGTCTTATC-CTCCTGAAGATGCAGT-GAGGCAGACTGAAGATGGC
1 ATAATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-T-TAGA-GCC
** * * *
59416562 A-AATCTTATCTCTTTAAAGTTGCAGTAGAGCAGATTAAAGCC
1 ATAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCC
* * * *
59416604 GATAATCCTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAACC
1 -ATAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCC
* * * * *
59416648 -TCAGATCTTATCTCTCTGAAGTTGAAG-AGAGCAGA-TCGCA-TC
1 AT-A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAG-AGCC
* * *
59416690 -TAGTCTTATCTCCCTGAAGTTGCGGTGGAGCAGACTAAGTAAG-C
1 ATAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAG--AGCC
* * * *
59416734 A-AGTCTTATC-CTCCTGAAGATGCAGT-GAGGCAGACTGAAGATGGC
1 ATAATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-T-TAGA-GCC
* * *
59416779 A-AATCTTATCTCCTTGAAGTTGTAGTGGAGCAGATTAAAGCC
1 ATAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCC
* * ** * *
59416821 GACAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACTTC
1 -ATAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGC--C
* ** * * *
59416867 A-GATCTTATCTCTATGAAGTTGCAG-AGAGCAGA-TCGCA-TC
1 ATAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAG-AGCC
* *
59416907 -TAGTCTTATCTTCCTGAAGTTGCAGTGGAGCAGA
1 ATAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
59416941 CTGGCAGATC
Statistics
Matches: 595, Mismatches: 120, Indels: 113
0.72 0.14 0.14
Matches are distributed among these distances:
40 80 0.13
41 32 0.05
42 16 0.03
43 53 0.09
44 317 0.53
45 87 0.15
46 10 0.02
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.27
Consensus pattern (43 bp):
ATAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCC
Found at i:59416506 original size:217 final size:217
Alignment explanation
Indices: 59416129--59416942 Score: 1272
Period size: 217 Copynumber: 3.8 Consensus size: 217
59416119 GGTGGCCGAT
* * *
59416129 AATCTTATCTCTCTAAAGTTACAGTGGAGCAGATTAGAA-CCGATAATCCTATCTCCCTAAAGTT
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTA-AAGCCGATAATCCTATCTCCCTGAAGTT
* * * * ** *
59416193 ACAGTGGAGCGGATGAAAACCTTGGATCTTATCTCACTGAAGTTACAGAGAGCAGATCCCATCTA
65 GCAGTGAAGCAGATTAAAACCTCAGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCCCATCTA
* * ** * *
59416258 GTCTTATCTCCCTGAAGTTACAGTAGAGCAGACTAAGTGGGCAAGTCTTATCCTCCTGAAGTTGT
130 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGATGC
*
59416323 AGTGAGGCAGACTGAAGATGGAA
195 AGTGAGGCAGACTGAAGATGGCA
*
59416346 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAGAGCCGATAATCCTATCTCCCTGAAGTTG
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTG
*
59416411 TAGTGAAGCAGATTAAAACCTCAGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCCCATCTAG
66 CAGTGAAGCAGATTAAAACCTCAGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCCCATCTAG
59416476 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGATGCA
131 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGATGCA
59416541 GTGAGGCAGACTGAAGATGGCA
196 GTGAGGCAGACTGAAGATGGCA
** *
59416563 AATCTTATCTCTTTAAAGTTGCAGTAGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTG
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTG
*
59416628 CAGTGAAGCAGATTAAAACCTCAGATCTTATCTCTCTGAAGTTGA-AGAGAGCAGATCGCATCTA
66 CAGTGAAGCAGATTAAAACCTCAGATCTTATCTCTCTGAAGTT-ACAGAGAGCAGATCCCATCTA
*
59416692 GTCTTATCTCCCTGAAGTTGCGGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGATGC
130 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGATGC
59416757 AGTGAGGCAGACTGAAGATGGCA
195 AGTGAGGCAGACTGAAGATGGCA
* * * *
59416780 AATCTTATCTCCTTGAAGTTGTAGTGGAGCAGATTAAAGCCGACAATCCTATCTCCCTGAAGTTG
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTG
* ** * * * *
59416845 CAGTGGAGTGGATTAAAACTTCAGATCTTATCTCTATGAAGTTGCAGAGAGCAGATCGCATCTAG
66 CAGTGAAGCAGATTAAAACCTCAGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCCCATCTAG
*
59416910 TCTTATCTTCCTGAAGTTGCAGTGGAGCAGACT
131 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT
59416943 GGCAGATCAA
Statistics
Matches: 555, Mismatches: 39, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
216 1 0.00
217 553 1.00
218 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (217 bp):
AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTG
CAGTGAAGCAGATTAAAACCTCAGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCCCATCTAG
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGATGCA
GTGAGGCAGACTGAAGATGGCA
Found at i:59417219 original size:17 final size:17
Alignment explanation
Indices: 59417197--59417238 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
59417187 GACCCGAGGT
* *
59417197 GGCCCAAACCCAACTGA
1 GGCCCAAACCAAACAGA
59417214 GGCCCAAACCAAACAGA
1 GGCCCAAACCAAACAGA
*
59417231 AGCCCAAA
1 GGCCCAAA
59417239 GTAGATTTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.43, C:0.38, G:0.17, T:0.02
Consensus pattern (17 bp):
GGCCCAAACCAAACAGA
Found at i:59420200 original size:3 final size:3
Alignment explanation
Indices: 59420192--59420723 Score: 1064
Period size: 3 Copynumber: 177.3 Consensus size: 3
59420182 ACACTCATCT
59420192 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
59420240 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
59420288 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
59420336 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
59420384 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
59420432 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
59420480 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
59420528 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
59420576 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
59420624 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
59420672 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
59420720 TAA T
1 TAA T
59420724 CATTCAATTA
Statistics
Matches: 529, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 529 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:59421036 original size:16 final size:17
Alignment explanation
Indices: 59421006--59421038 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
59420996 TTGTTTATTA
*
59421006 TTTAATAAATGTAATAT
1 TTTAATAAATATAATAT
59421023 TTTAAT-AATATAATAT
1 TTTAATAAATATAATAT
59421039 AATAATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TTTAATAAATATAATAT
Found at i:59421166 original size:5 final size:5
Alignment explanation
Indices: 59421158--59421196 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
59421148 TTATTTATTT
*
59421158 TATAA TATAA TATAA TATAA TAATAA TAATAA TTTAA TA
1 TATAA TATAA TATAA TATAA T-ATAA T-ATAA TATAA TA
59421197 ACATATTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 20 0.65
6 11 0.35
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:59434169 original size:244 final size:244
Alignment explanation
Indices: 59433740--59434227 Score: 976
Period size: 244 Copynumber: 2.0 Consensus size: 244
59433730 CATAATCCTA
59433740 TCAGAGTATTGCTTGACAGTTTCTTCTTCCTTCATCTTCAAATTCTCGAAATCTCTTCTCAAGTT
1 TCAGAGTATTGCTTGACAGTTTCTTCTTCCTTCATCTTCAAATTCTCGAAATCTCTTCTCAAGTT
59433805 CAACAACTGTTGCTGCCTTGTCCTTTCTGTCCCTTGAAACTCTTCCTGCAACTTGTCCCAGGCCT
66 CAACAACTGTTGCTGCCTTGTCCTTTCTGTCCCTTGAAACTCTTCCTGCAACTTGTCCCAGGCCT
59433870 GTTTTGGTAATTCACAGGCCATAATCCTTGTGAAGATCACATCAGACACTGAGTTCTGAATACAA
131 GTTTTGGTAATTCACAGGCCATAATCCTTGTGAAGATCACATCAGACACTGAGTTCTGAATACAA
59433935 GACATAGCCGTGTGCCTCTTGGTCCTCTCATCAGCATGCTGCCTAATCT
196 GACATAGCCGTGTGCCTCTTGGTCCTCTCATCAGCATGCTGCCTAATCT
59433984 TCAGAGTATTGCTTGACAGTTTCTTCTTCCTTCATCTTCAAATTCTCGAAATCTCTTCTCAAGTT
1 TCAGAGTATTGCTTGACAGTTTCTTCTTCCTTCATCTTCAAATTCTCGAAATCTCTTCTCAAGTT
59434049 CAACAACTGTTGCTGCCTTGTCCTTTCTGTCCCTTGAAACTCTTCCTGCAACTTGTCCCAGGCCT
66 CAACAACTGTTGCTGCCTTGTCCTTTCTGTCCCTTGAAACTCTTCCTGCAACTTGTCCCAGGCCT
59434114 GTTTTGGTAATTCACAGGCCATAATCCTTGTGAAGATCACATCAGACACTGAGTTCTGAATACAA
131 GTTTTGGTAATTCACAGGCCATAATCCTTGTGAAGATCACATCAGACACTGAGTTCTGAATACAA
59434179 GACATAGCCGTGTGCCTCTTGGTCCTCTCATCAGCATGCTGCCTAATCT
196 GACATAGCCGTGTGCCTCTTGGTCCTCTCATCAGCATGCTGCCTAATCT
59434228 GAGCCACTGT
Statistics
Matches: 244, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
244 244 1.00
ACGTcount: A:0.22, C:0.28, G:0.16, T:0.34
Consensus pattern (244 bp):
TCAGAGTATTGCTTGACAGTTTCTTCTTCCTTCATCTTCAAATTCTCGAAATCTCTTCTCAAGTT
CAACAACTGTTGCTGCCTTGTCCTTTCTGTCCCTTGAAACTCTTCCTGCAACTTGTCCCAGGCCT
GTTTTGGTAATTCACAGGCCATAATCCTTGTGAAGATCACATCAGACACTGAGTTCTGAATACAA
GACATAGCCGTGTGCCTCTTGGTCCTCTCATCAGCATGCTGCCTAATCT
Found at i:59437532 original size:17 final size:16
Alignment explanation
Indices: 59437505--59437552 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
59437495 TTCAAAACTA
59437505 TATATGAATTTTGATT
1 TATATGAATTTTGATT
* *
59437521 TAATATGCA-TTTG-TA
1 T-ATATGAATTTTGATT
59437536 TATATGAATTTTGATT
1 TATATGAATTTTGATT
59437552 T
1 T
59437553 TGTGCAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
14 6 0.24
15 6 0.24
16 7 0.28
17 6 0.24
ACGTcount: A:0.31, C:0.02, G:0.12, T:0.54
Consensus pattern (16 bp):
TATATGAATTTTGATT
Found at i:59437538 original size:31 final size:31
Alignment explanation
Indices: 59437503--59437585 Score: 109
Period size: 31 Copynumber: 2.7 Consensus size: 31
59437493 ATTTCAAAAC
59437503 TATATATGAATTTTGATTTAATATGC-ATTT
1 TATATATGAATTTTGATTTAATATGCAATTT
*
59437533 GTATATATGAATTTTGATTT--TGTGCAATTT
1 -TATATATGAATTTTGATTTAATATGCAATTT
*
59437563 TATATAAGAAATTTTGATTTAAT
1 TATATATG-AATTTTGATTTAAT
59437586 CAAATTCTCA
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
29 11 0.24
30 15 0.33
31 19 0.41
32 1 0.02
ACGTcount: A:0.34, C:0.02, G:0.12, T:0.52
Consensus pattern (31 bp):
TATATATGAATTTTGATTTAATATGCAATTT
Found at i:59438810 original size:26 final size:26
Alignment explanation
Indices: 59438745--59438798 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
59438735 AAATCAGAGA
*
59438745 AAAAAAGAGAAAAATAAGAAAAATGT
1 AAAAAAGAGAAAAATAAGAAAAAAGT
59438771 AAAAAAGAGAAAAATAAGAAAAAAGT
1 AAAAAAGAGAAAAATAAGAAAAAAGT
59438797 AA
1 AA
59438799 TTAATTGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (26 bp):
AAAAAAGAGAAAAATAAGAAAAAAGT
Found at i:59466340 original size:13 final size:13
Alignment explanation
Indices: 59466322--59466346 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59466312 TCTCCATTTT
59466322 TCATTTTTCATTC
1 TCATTTTTCATTC
59466335 TCATTTTTCATT
1 TCATTTTTCATT
59466347 TTTTATTTTT
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:0.16, C:0.20, G:0.00, T:0.64
Consensus pattern (13 bp):
TCATTTTTCATTC
Found at i:59466374 original size:8 final size:7
Alignment explanation
Indices: 59466316--59466356 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
59466306 TTAGCCTCTC
59466316 CATTTTT
1 CATTTTT
59466323 CATTTTT
1 CATTTTT
*
59466330 CA-TTCT
1 CATTTTT
59466336 CATTTTT
1 CATTTTT
59466343 CATTTTT
1 CATTTTT
*
59466350 TATTTTT
1 CATTTTT
59466357 TTATTTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
6 5 0.17
7 25 0.83
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.71
Consensus pattern (7 bp):
CATTTTT
Found at i:59468335 original size:17 final size:18
Alignment explanation
Indices: 59468303--59468339 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
59468293 TCTGCACAGT
59468303 ATGATTATGAATGAAAGA
1 ATGATTATGAATGAAAGA
*
59468321 ATGATT-TGGATGAAAGA
1 ATGATTATGAATGAAAGA
59468338 AT
1 AT
59468340 AAAAGAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.30
Consensus pattern (18 bp):
ATGATTATGAATGAAAGA
Found at i:59472558 original size:139 final size:140
Alignment explanation
Indices: 59472308--59472586 Score: 542
Period size: 139 Copynumber: 2.0 Consensus size: 140
59472298 CTCTCGTAAA
59472308 AAAAGGAACCCCTTACAATTCGTTTGAATGGCCTTTATATAGTAATTTTTACACAATTTATTTTT
1 AAAAGGAACCCCTTACAATTCGTTTGAATGGCCTTTATATAGTAATTTTTACACAATTTATTTTT
59472373 TTTTCTACTGTTTTGTCCTTCTTTGCTTGCGTGTTCTCCTTTGTTTTGCAGGTGGAGCAGGTGG-
66 TTTTCTACTGTTTTGTCCTTCTTTGCTTGCGTGTTCTCCTTTGTTTTGCAGGTGGAGCAGGTGGT
59472437 GCAAGTGGGC
131 GCAAGTGGGC
*
59472447 AAAAGGAACCCCTTACAATTCGTTTGAATGGCCTTTATATAGTCATTTTTACACAATTTATTTTT
1 AAAAGGAACCCCTTACAATTCGTTTGAATGGCCTTTATATAGTAATTTTTACACAATTTATTTTT
59472512 TTTTCTACTGTTTTGTCCTTCTTTGCTTGCGTGTTCTCCTTTGTTTTGCAGGTGGAGCAGGTGGT
66 TTTTCTACTGTTTTGTCCTTCTTTGCTTGCGTGTTCTCCTTTGTTTTGCAGGTGGAGCAGGTGGT
59472577 GCAAGTGGGC
131 GCAAGTGGGC
59472587 GAAGCAGTGG
Statistics
Matches: 138, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
139 128 0.93
140 10 0.07
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.43
Consensus pattern (140 bp):
AAAAGGAACCCCTTACAATTCGTTTGAATGGCCTTTATATAGTAATTTTTACACAATTTATTTTT
TTTTCTACTGTTTTGTCCTTCTTTGCTTGCGTGTTCTCCTTTGTTTTGCAGGTGGAGCAGGTGGT
GCAAGTGGGC
Found at i:59477180 original size:13 final size:13
Alignment explanation
Indices: 59477162--59477191 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
59477152 AAGGGAAGAT
59477162 AAATTTGGTGGTC
1 AAATTTGGTGGTC
59477175 AAATTTGGTGGTC
1 AAATTTGGTGGTC
59477188 AAAT
1 AAAT
59477192 CTACAAGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.37
Consensus pattern (13 bp):
AAATTTGGTGGTC
Found at i:59481742 original size:6 final size:6
Alignment explanation
Indices: 59481731--59481760 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
59481721 TCATGTCCGG
59481731 GTGTAA GTGTAA GTGTAA GTGTAA GTGTAA
1 GTGTAA GTGTAA GTGTAA GTGTAA GTGTAA
59481761 ATTATATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (6 bp):
GTGTAA
Found at i:59485144 original size:173 final size:172
Alignment explanation
Indices: 59484815--59485128 Score: 399
Period size: 167 Copynumber: 1.8 Consensus size: 172
59484805 CTCCATAAAT
* * *
59484815 ATTACCTCTAAGCACATTTACACAGCATACAAACATACTCTTTGAAAAATATAACAAAGTGCTCG
1 ATTACCTCTAAGCACATTTACACAGCATACAAACAAACTCTTTCAAAAATATAACAAAGTGCACG
** *
59484880 TTAAAGCCATACGACAAGAAAGGAACTTAACATAAAGAATCATGGGGACGATTCATTTCTGCATG
66 GCAAAGCCA-ACGACAAGAAAGGAACTTAACACAAAGAATCATGGGGACGATTCATTTCTGCATG
* * *
59484945 CACAATGTATGTCCCTATATGACAGCTTCAGTTTGGAGTAACA
130 CACAATGCATGTCCCTAAACGACAGCTTCAGTTTGGAGTAACA
* * * * *
59484988 ATTACCTCTAAGCACATTTACACAGCA-ACCAACAAACTC-TTCAGAAATGTAACAAATTGCAGG
1 ATTACCTCTAAGCACATTTACACAGCATACAAACAAACTCTTTCAAAAATATAACAAAGTGCACG
* *
59485051 GCAAAGCC-AC-ACAA-CAAGGAA-TTAATC-CAAAGAATCATGGGGATGATTCATTTTCTGCAT
66 GCAAAGCCAACGACAAGAAAGGAACTTAA-CACAAAGAATCATGGGGACGATTCA-TTTCTGCAT
*
59485111 GCATAATGCATGTCCCTA
129 GCACAATGCATGTCCCTA
59485129 GAAGAAAACG
Statistics
Matches: 124, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
166 25 0.20
167 32 0.26
168 4 0.03
169 2 0.02
171 24 0.19
172 10 0.08
173 27 0.22
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.25
Consensus pattern (172 bp):
ATTACCTCTAAGCACATTTACACAGCATACAAACAAACTCTTTCAAAAATATAACAAAGTGCACG
GCAAAGCCAACGACAAGAAAGGAACTTAACACAAAGAATCATGGGGACGATTCATTTCTGCATGC
ACAATGCATGTCCCTAAACGACAGCTTCAGTTTGGAGTAACA
Found at i:59492170 original size:14 final size:14
Alignment explanation
Indices: 59492159--59492196 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
59492149 CTTTAAACTC
59492159 AAACCATAAAACAT
1 AAACCATAAAACAT
*
59492173 AAACC-CAAAACAT
1 AAACCATAAAACAT
59492186 GAAACCATAAA
1 -AAACCATAAA
59492197 TCTTAACCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
13 7 0.35
14 10 0.50
15 3 0.15
ACGTcount: A:0.63, C:0.24, G:0.03, T:0.11
Consensus pattern (14 bp):
AAACCATAAAACAT
Found at i:59492175 original size:20 final size:21
Alignment explanation
Indices: 59492152--59492196 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
59492142 CCCAAAACTT
* *
59492152 TAAACTCAAACCAT-AAAACA
1 TAAACCCAAAACATGAAAACA
*
59492172 TAAACCCAAAACATGAAACCA
1 TAAACCCAAAACATGAAAACA
59492193 TAAA
1 TAAA
59492197 TCTTAACCTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.60, C:0.24, G:0.02, T:0.13
Consensus pattern (21 bp):
TAAACCCAAAACATGAAAACA
Found at i:59492252 original size:19 final size:19
Alignment explanation
Indices: 59492228--59492268 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
59492218 CCTTAAACTT
59492228 TAAACACTATCA-AAATCCA
1 TAAACACTATCATAAA-CCA
59492247 TAAACACTATCATAAACCA
1 TAAACACTATCATAAACCA
59492266 TAA
1 TAA
59492269 TTTTGATACC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.54, C:0.24, G:0.00, T:0.22
Consensus pattern (19 bp):
TAAACACTATCATAAACCA
Found at i:59492766 original size:28 final size:28
Alignment explanation
Indices: 59492703--59492766 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 28
59492693 AAACACATGA
* *
59492703 ACCCTAAACTTTAAACCTTAAACACTAC
1 ACCCTAAACTTAAAACATTAAACACTAC
* * *
59492731 ACCTTAAACTTAAAATATTAAAGACTA-
1 ACCCTAAACTTAAAACATTAAACACTAC
59492758 AGCCCTAAA
1 A-CCCTAAA
59492767 GCCAAAAGCT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
27 1 0.03
28 28 0.97
ACGTcount: A:0.47, C:0.25, G:0.03, T:0.25
Consensus pattern (28 bp):
ACCCTAAACTTAAAACATTAAACACTAC
Found at i:59492857 original size:21 final size:20
Alignment explanation
Indices: 59492833--59492885 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
59492823 TAATAAACCT
59492833 TAAACCTTAAATAC-AAGAACA
1 TAAACC-TAAAT-CTAAGAACA
*
59492854 TAAATCCTAAATCTAAGATCA
1 TAAA-CCTAAATCTAAGAACA
59492875 TAAACCATAAA
1 TAAACC-TAAA
59492886 CCCTAATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
20 3 0.11
21 23 0.82
22 2 0.07
ACGTcount: A:0.55, C:0.19, G:0.04, T:0.23
Consensus pattern (20 bp):
TAAACCTAAATCTAAGAACA
Found at i:59494880 original size:9 final size:9
Alignment explanation
Indices: 59494866--59494900 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
59494856 TTGTTTTTCG
*
59494866 TATTATTCT
1 TATTATTTT
59494875 TATTATTTT
1 TATTATTTT
*
59494884 TATCATTTT
1 TATTATTTT
59494893 TATTATTT
1 TATTATTT
59494901 ATTTTTCCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (9 bp):
TATTATTTT
Found at i:59502122 original size:45 final size:45
Alignment explanation
Indices: 59502015--59502867 Score: 535
Period size: 44 Copynumber: 18.6 Consensus size: 45
59502005 TCATCGTGGT
* * * * * **
59502015 AAATCTTATATCCCTGAAGTTACAGTGGAGTAGATTAAAGCCA-C
1 AAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAGATAGC
* *
59502059 AAATCTTATCGT-TCTGAAGTTGCAGTGGAGCAAATTGAATATAGC
1 AAATCTTATC-TCTCTGAAGTTGCAGTGGAGCAGATTGAAGATAGC
* * * *
59502104 AAATCTTATCTCTATGAAGTTGCAGTAGAGCAGATTGAAGCTA-T
1 AAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAGATAGC
* * *
59502148 AAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGATAGT
1 AAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAGATAGC
* * * * *
59502193 GAATCTTATCTCTCTGAAGTTGCAGTAGAGTAAATTGAAGCTA-C
1 AAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAGATAGC
* *
59502237 AAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAATG-TAG-
1 AAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAA-GATAGC
* * * * * *
59502281 AGAATCTGATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAGCTA-C
1 A-AATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAGATAGC
*
59502326 AAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAGATAGT
1 AAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAGATAGC
* * * *
59502371 GAATCTTATCTCTCTAAAGTTGCAGTGGAGTAGATTAAAGATAGC
1 AAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAGATAGC
* * * * * *
59502416 AAATCTTAT-TTTCCTAAAGTTACAGTGGAACAGATTAAAGCTACAAGTTAC
1 AAATCTTATCTCT-CTGAAGTTGCAGTGGAGCAGATTGAAG--A-TAG---C
* * *
59502467 AAA-CATTATCTCCCTGAAGTTGTAGTGGAGTAGATTGAAGAT-GC
1 AAATC-TTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAGATAGC
* * * * * * *
59502511 GAATCTTATTTCCCTAAAGTTGCAGTGGAACATATTAAAGCTACAAATTA-C
1 AAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATT---G--A-AGA-TAGC
* *
59502562 AAATCTTATATC-CTTGAAGTTGCAGTGGAGCAAATTGAAGATA-C
1 AAATCTTATCTCTC-TGAAGTTGCAGTGGAGCAGATTGAAGATAGC
* * * * * *
59502606 AACTCTTAT-TTTCCTAAAATTGCAGTGGAACAGATTACGACTA-AAAGTTAC
1 AAATCTTATCTCT-CTGAAGTTGCAGTGGAGCAGATT--GA--AGATAG---C
* * *
59502657 AAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAATAT-GC
1 AAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAGATAGC
* * * * *
59502701 GAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATT-AAAACTACAAGTTAC
1 AAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAGA-T---AG---C
* * * * *
59502752 AAATCTTATTTC-CTTGAAGCTGCAATGGAGCATATTGAAGCTA-C
1 AAATCTTATCTCTC-TGAAGTTGCAGTGGAGCAGATTGAAGATAGC
* * * *
59502796 TAATATTATCTCTCTGAAGTTGCAGTGGAGTAGATTGTAGCA-A-C
1 AAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAG-ATAGC
*
59502840 AAATCCTATAC-CTCTGAAGTTGCAGTGG
1 AAATCTTAT-CTCTCTGAAGTTGCAGTGG
59502868 GTTGGAATGA
Statistics
Matches: 640, Mismatches: 115, Indels: 108
0.74 0.13 0.13
Matches are distributed among these distances:
43 4 0.01
44 293 0.46
45 192 0.30
46 3 0.00
47 7 0.01
48 7 0.01
49 4 0.01
50 5 0.01
51 121 0.19
52 4 0.01
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.31
Consensus pattern (45 bp):
AAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAGATAGC
Found at i:59502139 original size:89 final size:89
Alignment explanation
Indices: 59502013--59502865 Score: 583
Period size: 89 Copynumber: 9.3 Consensus size: 89
59502003 AGTCATCGTG
* * * * * * *
59502013 GTAAATCTTATATCCCTGAAGTTACAGTGGAGTAGATTAAAGCCACAAATCTTATCGT-TCTGAA
1 GTAAATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATTGAAGCTACAAATCTTATC-TCCCTGAA
* *
59502077 GTTGCAGTGGAGCAAATTGAATATA
65 GTTGCAGTGGAGCAGATTGAAGATA
* * * *
59502102 GCAAATCTTATCTCTATGAAGTTGCAGTAGAGCAGATTGAAGCTATAAATCTTATCTCCCTGAAG
1 GTAAATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATTGAAGCTACAAATCTTATCTCCCTGAAG
*
59502167 TTGCAGTGGAGTAGATTGAAGATA
66 TTGCAGTGGAGCAGATTGAAGATA
* *
59502191 GTGAATCTTATCTCTCTGAAGTTGCAGTAGAGTAAATTGAAGCTACAAATCTTATCTCCCTGAAG
1 GTAAATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATTGAAGCTACAAATCTTATCTCCCTGAAG
*
59502256 TTGTAGTGGAGCAGATTGAATG-TA
66 TTGCAGTGGAGCAGATTGAA-GATA
* * * *
59502280 G-AGAATCTGATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAGCTACAAATCTTATCTCTCTGAA
1 GTA-AATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATTGAAGCTACAAATCTTATCTCCCTGAA
59502344 GTTGCAGTGGAGCAGATTGAAGATA
65 GTTGCAGTGGAGCAGATTGAAGATA
* * * * * * * *
59502369 GTGAATCTTATCTCTCTAAAGTTGCAGTGGAGTAGATTAAAGATAGCAAATCTTATTTTCCTAAA
1 GTAAATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATTGAAGCTA-CAAATCTTATCTCCCTGAA
* * * *
59502434 GTTACAGTGGAACAGATTAAAGCTACAA
65 GTTGCAGTGGAGCAGATTGAAG--A-TA
* * * * * * * * *
59502462 GTTACAAACATTATCTCCCTGAAGTTGTAGTGGAGTAGATTGAAGATGCGAATCTTATTTCCCTA
1 G-TA-AATC-TTATCTCTCTGAAGTTGCAGTAGAGTAGATTGAAGCTACAAATCTTATCTCCCTG
* * * *
59502527 AAGTTGCAGTGGAACATATTAAAGCTACAAA
63 AAGTTGCAGTGGAGCAGATTGAAG----ATA
* * * * * * * * * *
59502558 TTACAAATCTTATATC-CTTGAAGTTGCAGTGGAGCAAATTGAAGATACAACTCTTATTTTCCTA
1 GT--AAATCTTATCTCTC-TGAAGTTGCAGTAGAGTAGATTGAAGCTACAAATCTTATCTCCCTG
* * *
59502622 AAATTGCAGTGGAACAGATTACGACTA-AAA
63 AAGTTGCAGTGGAGCAGATT--GA--AGATA
* * * * ** * * *
59502652 GTTACAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAATATGCGAATCTTATTTCCCTG
1 G-T--AAATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATTGAAGCTACAAATCTTATCTCCCTG
* *
59502717 AAGTTGCAGTGGAACAGATT-AAAACTACAA
63 AAGTTGCAGTGGAGCAGATTGAAGA-T---A
* * * * * * * * *
59502747 GTTACAAATCTTATTTC-CTTGAAGCTGCAATGGAGCATATTGAAGCTACTAATATTATCTCTCT
1 G-T--AAATCTTATCTCTC-TGAAGTTGCAGTAGAGTAGATTGAAGCTACAAATCTTATCTCCCT
* *
59502811 GAAGTTGCAGTGGAGTAGATTGTAGCA-A
62 GAAGTTGCAGTGGAGCAGATTGAAG-ATA
* *
59502839 -CAAATCCTATAC-CTCTGAAGTTGCAGT
1 GTAAATCTTAT-CTCTCTGAAGTTGCAGT
59502866 GGGTTGGAAT
Statistics
Matches: 629, Mismatches: 102, Indels: 67
0.79 0.13 0.08
Matches are distributed among these distances:
88 21 0.03
89 270 0.43
90 36 0.06
91 1 0.00
92 3 0.00
93 2 0.00
94 6 0.01
95 245 0.39
96 40 0.06
97 4 0.01
99 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.31
Consensus pattern (89 bp):
GTAAATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATTGAAGCTACAAATCTTATCTCCCTGAAG
TTGCAGTGGAGCAGATTGAAGATA
Found at i:59502588 original size:51 final size:49
Alignment explanation
Indices: 59502415--59502764 Score: 237
Period size: 51 Copynumber: 7.3 Consensus size: 49
59502405 TTAAAGATAG
* * *
59502415 CAAATCTTATTTTCCTAAAGTTACAGTGGAACAGATTAAAGCTACAAGTTA
1 CAAATCTTATTTCCCTAAAGTTGCAGTGGAACAGATT-AAGCTA-AAATTA
* * * ** * *
59502466 CAAA-CATTATCTCCCTGAAGTTGTAGTGGAGTAGATT--G--AAGA-TG
1 CAAATC-TTATTTCCCTAAAGTTGCAGTGGAACAGATTAAGCTAAAATTA
* *
59502510 CGAATCTTATTTCCCTAAAGTTGCAGTGGAACATATTAAAGCTACAAATTA
1 CAAATCTTATTTCCCTAAAGTTGCAGTGGAACAGATT-AAGCTA-AAATTA
* * * * * *
59502561 CAAATCTTATATCCTTGAAGTTGCAGTGGAGCAAATT--G--AAGA-TA
1 CAAATCTTATTTCCCTAAAGTTGCAGTGGAACAGATTAAGCTAAAATTA
* * * *
59502605 CAACTCTTATTTTCCTAAAATTGCAGTGGAACAGATTACGACTAAAAGTTA
1 CAAATCTTATTTCCCTAAAGTTGCAGTGGAACAGATTAAG-CTAAAA-TTA
* * * *
59502656 CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATT--G--AATA-TG
1 CAAATCTTATTTCCCTAAAGTTGCAGTGGAACAGATTAAGCTAAAATTA
* * * *
59502700 CGAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAAACTACAAGTTA
1 CAAATCTTATTTCCCTAAAGTTGCAGTGGAACAGATT-AAGCTA-AAATTA
59502751 CAAATCTTATTTCC
1 CAAATCTTATTTCC
59502765 TTGAAGCTGC
Statistics
Matches: 225, Mismatches: 51, Indels: 46
0.70 0.16 0.14
Matches are distributed among these distances:
44 94 0.42
45 4 0.02
46 6 0.03
47 1 0.00
48 2 0.01
49 6 0.03
50 4 0.02
51 108 0.48
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (49 bp):
CAAATCTTATTTCCCTAAAGTTGCAGTGGAACAGATTAAGCTAAAATTA
Found at i:59502831 original size:95 final size:95
Alignment explanation
Indices: 59502103--59502824 Score: 572
Period size: 95 Copynumber: 7.8 Consensus size: 95
59502093 TTGAATATAG
** * * ** * *
59502103 CAAATCTTATCTCTATGAAGTTGCAGTAGAGCAGATTGAAGCTATAAATCTTATCTCCCTGAAGT
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACGAATCTTATTTCCCTAAAGT
** *
59502168 TGCAGTGGAGTAGATTGAAGA-T---AG-T-
66 TGCAGTGGAACAGATT-AAAACTACAAGTTA
* * * * * * * * *
59502193 -GAATCTTATCTCTCTGAAGTTGCAGTAGAGTAAATTGAAGCTACAAATCTTATCTCCCTGAAGT
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACGAATCTTATTTCCCTAAAGT
* * *
59502257 TGTAGTGGAGCAGATT-GAA-T----G-TA
66 TGCAGTGGAACAGATTAAAACTACAAGTTA
* * * * * * * * * *
59502280 GAGAATCTGATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAGCTACAAATCTTATCTCTCTGAAG
1 CA-AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACGAATCTTATTTCCCTAAAG
* *
59502345 TTGCAGTGGAGCAGATTGAAGA-T---AG-T-
65 TTGCAGTGGAACAGATT-AAAACTACAAGTTA
* * * * * * *
59502371 -GAATCTTATCTCTCTAAAGTTGCAGTGGAGTAGATTAAAGATAGCAAATCTTATTTTCCTAAAG
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA-CGAATCTTATTTCCCTAAAG
* *
59502435 TTACAGTGGAACAGATTAAAGCTACAAGTTA
65 TTGCAGTGGAACAGATTAAAACTACAAGTTA
* * *
59502466 CAAA-CATTATCTCCCTGAAGTTGTAGTGGAGTAGATTGAAGATGCGAATCTTATTTCCCTAAAG
1 CAAATC-TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACGAATCTTATTTCCCTAAAG
* * *
59502530 TTGCAGTGGAACATATTAAAGCTACAAATTA
65 TTGCAGTGGAACAGATTAAAACTACAAGTTA
* * * * *
59502561 CAAATCTTATATCCTTGAAGTTGCAGTGGAGCAAATTGAAGATAC-AACTCTTATTTTCCTAAAA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACGAA-TCTTATTTCCCTAAAG
** *
59502625 TTGCAGTGGAACAGATTACGACTAAAAGTTA
65 TTGCAGTGGAACAGATTAAAACTACAAGTTA
* * * *
59502656 CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAATATGCGAATCTTATTTCCCTGAAGT
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACGAATCTTATTTCCCTAAAGT
59502721 TGCAGTGGAACAGATTAAAACTACAAGTTA
66 TGCAGTGGAACAGATTAAAACTACAAGTTA
* * * * * * * * * * *
59502751 CAAATCTTATTTCCTTGAAGCTGCAATGGAGCATATTGAAGCTACTAATATTATCTCTCTGAAGT
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACGAATCTTATTTCCCTAAAGT
59502816 TGCAGTGGA
66 TGCAGTGGA
59502825 GTAGATTGTA
Statistics
Matches: 532, Mismatches: 82, Indels: 31
0.82 0.13 0.05
Matches are distributed among these distances:
86 2 0.00
87 2 0.00
89 185 0.35
90 32 0.06
91 2 0.00
92 2 0.00
93 2 0.00
94 3 0.01
95 264 0.50
96 38 0.07
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.31
Consensus pattern (95 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACGAATCTTATTTCCCTAAAGT
TGCAGTGGAACAGATTAAAACTACAAGTTA
Found at i:59503042 original size:13 final size:13
Alignment explanation
Indices: 59503024--59503049 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
59503014 TCGTCCGAGC
59503024 CCAAACAAAAAAA
1 CCAAACAAAAAAA
59503037 CCAAACAAAAAAA
1 CCAAACAAAAAAA
59503050 GCAGAAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (13 bp):
CCAAACAAAAAAA
Found at i:59512264 original size:59 final size:60
Alignment explanation
Indices: 59512145--59512266 Score: 165
Period size: 59 Copynumber: 2.0 Consensus size: 60
59512135 AGCTTGAAGT
* ** *
59512145 TGTAATTAGAATATTTTGAAGCTTGGGGGCCAGTTTAGAATGAGAATCATAATTTGGGGA
1 TGTAATTAGAACATTTTGAAGCTTGGGAACCAGTTTAGAATGAAAATCATAATTTGGGGA
* * * *
59512205 TGTAATTAGAACATTTTGAAG-TTTGGAACCGGTTTAGAATGAAAATTATAGTTTGGGGA
1 TGTAATTAGAACATTTTGAAGCTTGGGAACCAGTTTAGAATGAAAATCATAATTTGGGGA
59512264 TGT
1 TGT
59512267 CACGTGCAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
59 34 0.63
60 20 0.37
ACGTcount: A:0.32, C:0.06, G:0.27, T:0.35
Consensus pattern (60 bp):
TGTAATTAGAACATTTTGAAGCTTGGGAACCAGTTTAGAATGAAAATCATAATTTGGGGA
Found at i:59516130 original size:25 final size:25
Alignment explanation
Indices: 59516056--59516162 Score: 83
Period size: 25 Copynumber: 4.3 Consensus size: 25
59516046 ACCACGACTT
* * * *
59516056 GTATGAGTTTCCCGATTTACAGCTT
1 GTATGAGATTACCGATTCACAGCTC
* * **
59516081 GTAAGAGCTTACCGATTCTTAGCTC
1 GTATGAGATTACCGATTCACAGCTC
59516106 GTATGAGATTACCGATTCACAGCTC
1 GTATGAGATTACCGATTCACAGCTC
* * *
59516131 -T-TGAGAGCATATCGATTCATAGCTC
1 GTATGAGA--TTACCGATTCACAGCTC
59516156 GTATGAG
1 GTATGAG
59516163 CATACATGTC
Statistics
Matches: 64, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
23 5 0.08
24 1 0.02
25 53 0.83
26 1 0.02
27 4 0.06
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (25 bp):
GTATGAGATTACCGATTCACAGCTC
Found at i:59516138 original size:50 final size:50
Alignment explanation
Indices: 59516056--59516162 Score: 135
Period size: 50 Copynumber: 2.1 Consensus size: 50
59516046 ACCACGACTT
* * * * *
59516056 GTATGAGTTTCCCGATTTACAGCTTGTAAGAGCTTACCGATTCTTAGCTC
1 GTATGAGATTACCGATTCACAGCTTGTAAGAGCATACCGATTCATAGCTC
* *
59516106 GTATGAGATTACCGATTCACAGCTCT-TGAGAGCATATCGATTCATAGCTC
1 GTATGAGATTACCGATTCACAGCT-TGTAAGAGCATACCGATTCATAGCTC
59516156 GTATGAG
1 GTATGAG
59516163 CATACATGTC
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
50 48 0.98
51 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (50 bp):
GTATGAGATTACCGATTCACAGCTTGTAAGAGCATACCGATTCATAGCTC
Found at i:59516163 original size:25 final size:25
Alignment explanation
Indices: 59516067--59516167 Score: 89
Period size: 25 Copynumber: 4.0 Consensus size: 25
59516057 TATGAGTTTC
* * * * *
59516067 CCGATTTACAGCTTGTAAGAGCTTA
1 CCGATTCATAGCTCGTATGAGCATA
*
59516092 CCGATTCTTAGCTCGTATGAG-ATTA
1 CCGATTCATAGCTCGTATGAGCA-TA
* *
59516117 CCGATTCACAGCTCTTGA-GAGCATA
1 CCGATTCATAGCTCGT-ATGAGCATA
*
59516142 TCGATTCATAGCTCGTATGAGCATA
1 CCGATTCATAGCTCGTATGAGCATA
59516167 C
1 C
59516168 ATGTCTATGA
Statistics
Matches: 59, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
24 1 0.02
25 56 0.95
26 2 0.03
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.31
Consensus pattern (25 bp):
CCGATTCATAGCTCGTATGAGCATA
Found at i:59527991 original size:15 final size:15
Alignment explanation
Indices: 59527962--59527990 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
59527952 ACATCTACAA
59527962 AATAAAATATATTTT
1 AATAAAATATATTTT
59527977 AATAAAATAT-TTTT
1 AATAAAATATATTTT
59527991 TTTAAAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AATAAAATATATTTT
Found at i:59528104 original size:10 final size:10
Alignment explanation
Indices: 59528086--59528140 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 10
59528076 AAATACTTTT
59528086 AAAATTATTA
1 AAAATTATTA
*
59528096 AAAAATATTA
1 AAAATTATTA
*
59528106 ATAATTATTA
1 AAAATTATTA
*
59528116 AAAGATT-CTA
1 AAA-ATTATTA
59528126 AAATATTA-TA
1 AAA-ATTATTA
59528136 AAAAT
1 AAAAT
59528141 AAAATATGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
9 2 0.05
10 32 0.86
11 3 0.08
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (10 bp):
AAAATTATTA
Found at i:59528304 original size:18 final size:19
Alignment explanation
Indices: 59528274--59528320 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
59528264 ATAAATAAAT
*
59528274 AAAA-ATTAGAAA-TTATA
1 AAAATATTAAAAATTTATA
59528291 AAAATATTAAAAATTTATA
1 AAAATATTAAAAATTTATA
59528310 AAAAT-TTAAAA
1 AAAATATTAAAA
59528321 TGTCAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 4 0.15
18 13 0.48
19 10 0.37
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (19 bp):
AAAATATTAAAAATTTATA
Found at i:59541780 original size:18 final size:17
Alignment explanation
Indices: 59541752--59541786 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
59541742 NNNNNNNNNA
*
59541752 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
59541769 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
59541787 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:59542037 original size:16 final size:16
Alignment explanation
Indices: 59542016--59542051 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
59542006 GATTTGCTAT
59542016 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
59542032 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
59542048 TACA
1 TACA
59542052 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:59553443 original size:6 final size:6
Alignment explanation
Indices: 59553432--59553461 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
59553422 CAGAATGAGA
59553432 TTAATT TTAATT TTAATT TTAATT TTAATT
1 TTAATT TTAATT TTAATT TTAATT TTAATT
59553462 CCGATTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TTAATT
Found at i:59554551 original size:9 final size:9
Alignment explanation
Indices: 59554537--59554573 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
59554527 TATAGTTTGA
59554537 TATTCGAAT
1 TATTCGAAT
59554546 TATTCGAAT
1 TATTCGAAT
*
59554555 TATTCGAGT
1 TATTCGAAT
59554564 TATTCGAAT
1 TATTCGAAT
59554573 T
1 T
59554574 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:59556253 original size:2 final size:2
Alignment explanation
Indices: 59556246--59556272 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
59556236 TAACTTGTTT
59556246 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 T
59556273 TTAAAATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:59556301 original size:18 final size:19
Alignment explanation
Indices: 59556278--59556314 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
59556268 TATATTTAAA
59556278 ATATAAAT-TTTGGAATTT
1 ATATAAATATTTGGAATTT
*
59556296 ATATAAATATTTTGAATTT
1 ATATAAATATTTGGAATTT
59556315 TAAAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (19 bp):
ATATAAATATTTGGAATTT
Found at i:59556309 original size:20 final size:20
Alignment explanation
Indices: 59556284--59556328 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
59556274 TAAAATATAA
*
59556284 ATTTTGGAATTTATATAAA-T
1 ATTTTGGAATTT-TAAAAATT
59556304 ATTTT-GAATTTTAAAAATT
1 ATTTTGGAATTTTAAAAATT
59556323 ATTTTG
1 ATTTTG
59556329 ATTTATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 5 0.23
19 12 0.55
20 5 0.23
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (20 bp):
ATTTTGGAATTTTAAAAATT
Found at i:59556314 original size:19 final size:19
Alignment explanation
Indices: 59556278--59556334 Score: 66
Period size: 18 Copynumber: 3.1 Consensus size: 19
59556268 TATATTTAAA
*
59556278 ATATAAAT-TTTGGAATTT
1 ATATAAATATTTTGAATTT
59556296 ATATAAATATTTTGAATTT
1 ATATAAATATTTTGAATTT
*
59556315 -TAAAAATTATTTTG-ATTT
1 ATATAAA-TATTTTGAATTT
59556333 AT
1 AT
59556335 TTTGTACTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 17 0.50
19 17 0.50
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (19 bp):
ATATAAATATTTTGAATTT
Found at i:59560073 original size:457 final size:458
Alignment explanation
Indices: 59559213--59560123 Score: 1414
Period size: 457 Copynumber: 2.0 Consensus size: 458
59559203 TTTAGAGGTA
* *
59559213 TTTTAGGGATTTTAGCCTTAGAGTGTTCGAAATTTTGAGACATGGAATACCGGTAATATTTTTTA
1 TTTTAGGGATTTTAGCCTTAAAGTGTTCGAAATTTTGAGACATGGAATACCGATAATATTTTTTA
* * *
59559278 TTATGGTTTTTAGAAAATTAAATCAATTTTTGAAAATGAGTTTTAAAGACCTTCAATTTTGAAAA
66 CTATGGTTTTTAAAAAATTAAATCAATTTTTGAAAAAGAGTTTTAAAGACCTTCAATTTTGAAAA
* *
59559343 TTGGACTGATTTGTAAAAGAGTCAAAATTATGAGTTTTTAAGAGGCAATTAGATCAGATTTTAAA
131 TTGGACTGATTTGTAAAAGAATCAAAATTATGAGTTTTTAAGAAGCAATTAGATCAGATTTTAAA
* * * **
59559408 ATCCAACCTAATAACCCCTATTTATAGTTTTATTTTCACGTTAGTCTTCTTCTTTTCTCATACTT
196 ATCCAACCTAAAAACCCCCATTTATAGTTTTATTTTCACATTAGTCTTCTTCTCCTCTCATACTT
* * *
59559473 GTGCCATCCATAGTTCTCCCAACTCTCCCAATCGATTTTGAATTCTAACTCCTAATTCCTTTTGA
261 GTGCCATCCATAATTCTCCCAACTCTCCCAATCGATTTTGAATTCCAAATCCTAATTCCTTTTGA
* * *
59559538 TTTCTATCATCTCTTAAGTTATAAGTCTCCATAGAAGTTAAGAAAAACACCTAAAAACACCATTG
326 TTTCTATCATCTCTTAAGTTATAAATCTCCATAGAAATTAAGAAAAACACCCAAAAACACCATTG
* ** * * *
59559603 ATTTCTTCATTGTCAAGCTTGTGAGTTTTTCGGGTTTTCGATCAAATGTTTAATTTTTCGTCAAA
391 ATTTCTCCATTGTCAAGCTTGTGAGTTTTTCAAGTTTTCGATCAAACGTTCAATTTTTCATCAAA
59559668 GAG
456 GAG
* * * * *
59559671 TTTTAGGGATTTTAGCCTTAAAGTGTTTGGAATTTTGTGACATGGTATACCGATAATGTTTTTTA
1 TTTTAGGGATTTTAGCCTTAAAGTGTTCGAAATTTTGAGACATGGAATACCGATAATATTTTTTA
59559736 CTATGGTTTTTAAAAAATTAAATCAATTTTTGAAAAAGAGTTTTAAAGACCTTCAATTTTGAAAA
66 CTATGGTTTTTAAAAAATTAAATCAATTTTTGAAAAAGAGTTTTAAAGACCTTCAATTTTGAAAA
*
59559801 TTGGACTGATTTGTAAAA-AATACAAAATTGTGAGTTTTTAA-AAGCAATTAGA-CTAGATTTTA
131 TTGGACTGATTTGTAAAAGAAT-CAAAATTATGAGTTTTTAAGAAGCAATTAGATC-AGATTTTA
* *
59559863 TAATCCAACTTAAAAACCCCCATTTATAGTTTTATTTTCACATTAGTCTTCTTCTCCTCTCATAC
194 AAATCCAACCTAAAAACCCCCATTTATAGTTTTATTTTCACATTAGTCTTCTTCTCCTCTCATAC
* * * * * *
59559928 TTGTGTCGTCCATAATTCTCCTAACTCTCCCAATTGGTTTTGAATTCCAAATCCTAGTTCCTTTT
259 TTGTGCCATCCATAATTCTCCCAACTCTCCCAATCGATTTTGAATTCCAAATCCTAATTCCTTTT
* *
59559993 GATTTTTATCATCTCTTAAGTTATAAATCTCCATAGAAATTAAGAAAAACACCCAAAAGCACCAT
324 GATTTCTATCATCTCTTAAGTTATAAATCTCCATAGAAATTAAGAAAAACACCCAAAAACACCAT
*
59560058 TGATTTCTCCATTGTCAAGCTTGTGAGTTTTTCAAGTTTTTGATCAAACGTTCAATTTTTCATCA
389 TGATTTCTCCATTGTCAAGCTTGTGAGTTTTTCAAGTTTTCGATCAAACGTTCAATTTTTCATCA
59560123 A
454 A
59560124 CTAAGGAACG
Statistics
Matches: 410, Mismatches: 41, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
456 1 0.00
457 253 0.62
458 156 0.38
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (458 bp):
TTTTAGGGATTTTAGCCTTAAAGTGTTCGAAATTTTGAGACATGGAATACCGATAATATTTTTTA
CTATGGTTTTTAAAAAATTAAATCAATTTTTGAAAAAGAGTTTTAAAGACCTTCAATTTTGAAAA
TTGGACTGATTTGTAAAAGAATCAAAATTATGAGTTTTTAAGAAGCAATTAGATCAGATTTTAAA
ATCCAACCTAAAAACCCCCATTTATAGTTTTATTTTCACATTAGTCTTCTTCTCCTCTCATACTT
GTGCCATCCATAATTCTCCCAACTCTCCCAATCGATTTTGAATTCCAAATCCTAATTCCTTTTGA
TTTCTATCATCTCTTAAGTTATAAATCTCCATAGAAATTAAGAAAAACACCCAAAAACACCATTG
ATTTCTCCATTGTCAAGCTTGTGAGTTTTTCAAGTTTTCGATCAAACGTTCAATTTTTCATCAAA
GAG
Found at i:59564398 original size:107 final size:108
Alignment explanation
Indices: 59564212--59564426 Score: 423
Period size: 107 Copynumber: 2.0 Consensus size: 108
59564202 GGGCTATTAC
59564212 ATGACCATTATGCAATTTGTCTATAAAGATGTTTTTGAGTATGTTAATATATGCTTGAATGTTAT
1 ATGACCATTATGCAATTTGTCTATAAAGATGTTTTTGAGTATGTTAATATATGCTTGAATGTTAT
59564277 GTGATTATATGTGTATTGTGATATATGC-TAAATGTTGTGTGA
66 GTGATTATATGTGTATTGTGATATATGCTTAAATGTTGTGTGA
59564319 ATGACCATTATGCAATTTGTCTATAAAGATGTTTTTGAGTATGTTAATATATGCTTGAATGTTAT
1 ATGACCATTATGCAATTTGTCTATAAAGATGTTTTTGAGTATGTTAATATATGCTTGAATGTTAT
59564384 GTGATTATATGTGTATTGTGATATATGCTTAAATGTTGTGTGA
66 GTGATTATATGTGTATTGTGATATATGCTTAAATGTTGTGTGA
59564427 TTATACGTGT
Statistics
Matches: 107, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
107 93 0.87
108 14 0.13
ACGTcount: A:0.29, C:0.06, G:0.20, T:0.45
Consensus pattern (108 bp):
ATGACCATTATGCAATTTGTCTATAAAGATGTTTTTGAGTATGTTAATATATGCTTGAATGTTAT
GTGATTATATGTGTATTGTGATATATGCTTAAATGTTGTGTGA
Found at i:59564408 original size:39 final size:39
Alignment explanation
Indices: 59564365--59564455 Score: 146
Period size: 39 Copynumber: 2.3 Consensus size: 39
59564355 GAGTATGTTA
* * *
59564365 ATATATGCTTGAATGTTATGTGATTATATGTGTATTGTG
1 ATATATGCTTAAATGTTATGTGATTATACGTGTAATGTG
*
59564404 ATATATGCTTAAATGTTGTGTGATTATACGTGTAATGTG
1 ATATATGCTTAAATGTTATGTGATTATACGTGTAATGTG
59564443 ATATATGCTTAAA
1 ATATATGCTTAAA
59564456 AGTGAATATG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.30, C:0.04, G:0.21, T:0.45
Consensus pattern (39 bp):
ATATATGCTTAAATGTTATGTGATTATACGTGTAATGTG
Found at i:59567526 original size:24 final size:25
Alignment explanation
Indices: 59567473--59567545 Score: 62
Period size: 24 Copynumber: 3.0 Consensus size: 25
59567463 GGAAGCTTAT
* *
59567473 AAGAGCC-ATAATCGGGAAACTCATG
1 AAGAGCCAATAATCGGGAAGCTC-CG
* * *
59567498 -CGAGCTAATAA-CGGGTAGCTCCG
1 AAGAGCCAATAATCGGGAAGCTCCG
*
59567521 AAGAGCCATTAATCGGGAAGCTCCG
1 AAGAGCCAATAATCGGGAAGCTCCG
59567546 GATAGCCATA
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
23 1 0.03
24 20 0.56
25 15 0.42
ACGTcount: A:0.33, C:0.23, G:0.27, T:0.16
Consensus pattern (25 bp):
AAGAGCCAATAATCGGGAAGCTCCG
Found at i:59568213 original size:13 final size:13
Alignment explanation
Indices: 59568195--59568222 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
59568185 TTTTATTTTA
59568195 TTATTTATCATCT
1 TTATTTATCATCT
59568208 TTATTTATCATCT
1 TTATTTATCATCT
59568221 TT
1 TT
59568223 CCAATTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATTTATCATCT
Found at i:59580190 original size:32 final size:31
Alignment explanation
Indices: 59580153--59580218 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
59580143 TTACTTAAGA
59580153 AATAAATATATAATAAATTATGTTTAT-TACAT
1 AATAAATATATAA-AAATTATGTTTATGTA-AT
* *
59580185 AATAAATATATAAAATTTATTTTTATGTAAT
1 AATAAATATATAAAAATTATGTTTATGTAAT
59580216 AAT
1 AAT
59580219 TAGACACGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
31 16 0.52
32 15 0.48
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (31 bp):
AATAAATATATAAAAATTATGTTTATGTAAT
Found at i:59592366 original size:6 final size:6
Alignment explanation
Indices: 59592355--59592388 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
59592345 AGGATTTGTT
*
59592355 GCTGCC GCTGCC GCTGCC GCTGCC GCCGCC GCTG
1 GCTGCC GCTGCC GCTGCC GCTGCC GCTGCC GCTG
59592389 GAATCGGTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.35, T:0.15
Consensus pattern (6 bp):
GCTGCC
Found at i:59595968 original size:20 final size:21
Alignment explanation
Indices: 59595943--59595981 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
59595933 AGGGTTATTT
59595943 TAATTTTTA-CTATTTTTCTA
1 TAATTTTTATCTATTTTTCTA
*
59595963 TAATTTTTATTTATTTTTC
1 TAATTTTTATCTATTTTTC
59595982 ACCCACAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (21 bp):
TAATTTTTATCTATTTTTCTA
Found at i:59598171 original size:3 final size:3
Alignment explanation
Indices: 59598163--59598194 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
59598153 TTCCCCTGTT
*
59598163 TTA TTA TTA TGA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
59598195 TATAATTTGA
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:59599812 original size:18 final size:16
Alignment explanation
Indices: 59599780--59599814 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
59599770 GGCTTGGGAA
59599780 AAAATTAGGCTGGTTT
1 AAAATTAGGCTGGTTT
59599796 AAAATATAGGCTAGGTTT
1 AAAAT-TAGGCT-GGTTT
59599814 A
1 A
59599815 GGCTTAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 6 0.35
18 6 0.35
ACGTcount: A:0.37, C:0.06, G:0.23, T:0.34
Consensus pattern (16 bp):
AAAATTAGGCTGGTTT
Found at i:59607612 original size:42 final size:43
Alignment explanation
Indices: 59607561--59607702 Score: 157
Period size: 42 Copynumber: 3.4 Consensus size: 43
59607551 TGGAAACCTG
* **
59607561 TAAGGGTTAAACGGAAGCTC-TTAGCAGCTGAA-TAGAAACCCA
1 TAAGGGTTAAACTGAAGCTCAAAAG-AGCTGAACTAGAAACCCA
* * * *
59607603 TAAGGGTTAATCTAAAGCTCAGAAGAGCTAAACTA-AAACCCA
1 TAAGGGTTAAACTGAAGCTCAAAAGAGCTGAACTAGAAACCCA
* *
59607645 TTAGGGTTAAACTGAAGCTCAAAAGAGCTGAACT-GAAACCTA
1 TAAGGGTTAAACTGAAGCTCAAAAGAGCTGAACTAGAAACCCA
*
59607687 GAAGGGTTAAACTGAA
1 TAAGGGTTAAACTGAA
59607703 ACTTATATGA
Statistics
Matches: 83, Mismatches: 14, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
42 79 0.95
43 4 0.05
ACGTcount: A:0.42, C:0.17, G:0.22, T:0.20
Consensus pattern (43 bp):
TAAGGGTTAAACTGAAGCTCAAAAGAGCTGAACTAGAAACCCA
Found at i:59611619 original size:15 final size:14
Alignment explanation
Indices: 59611585--59611627 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
59611575 TGTCCTCGTT
59611585 TTTTATTTATGTTAA
1 TTTTATTTAT-TTAA
*
59611600 TTTTATTTATTTAT
1 TTTTATTTATTTAA
59611614 TGTTTATATTATTT
1 T-TTTAT-TTATTT
59611628 CTATACAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 4 0.16
15 15 0.60
16 6 0.24
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (14 bp):
TTTTATTTATTTAA
Found at i:59611625 original size:20 final size:19
Alignment explanation
Indices: 59611586--59611627 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
59611576 GTCCTCGTTT
*
59611586 TTTATTTATGTTAATTTTA
1 TTTATTTATGTTAATATTA
*
59611605 TTTATTTATTGTTTATATTA
1 TTTATTTA-TGTTAATATTA
59611625 TTT
1 TTT
59611628 CTATACAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (19 bp):
TTTATTTATGTTAATATTA
Found at i:59615237 original size:25 final size:24
Alignment explanation
Indices: 59615191--59615239 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
59615181 ATTGTCTTCT
**
59615191 TTCTCTCAACTTTCTACGTCTCTC
1 TTCTCTCAACTTTCTAAATCTCTC
*
59615215 TTCTCTCATCTTTGCTAAATCTCTC
1 TTCTCTCAACTTT-CTAAATCTCTC
59615240 ACTCACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.14, C:0.35, G:0.04, T:0.47
Consensus pattern (24 bp):
TTCTCTCAACTTTCTAAATCTCTC
Found at i:59620893 original size:25 final size:27
Alignment explanation
Indices: 59620854--59620909 Score: 80
Period size: 25 Copynumber: 2.1 Consensus size: 27
59620844 TTTCATAATT
59620854 TTTTAAAAAAATTATAAGTTT-TTTTA
1 TTTTAAAAAAATTATAAGTTTATTTTA
* *
59620880 TTTT-AAAAATTTATAATTTTATTTTA
1 TTTTAAAAAAATTATAAGTTTATTTTA
59620906 TTTT
1 TTTT
59620910 TTTAAAATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 14 0.52
26 13 0.48
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (27 bp):
TTTTAAAAAAATTATAAGTTTATTTTA
Found at i:59621147 original size:7 final size:7
Alignment explanation
Indices: 59621135--59621161 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
59621125 TGTTTCAAAA
59621135 TTAAATT
1 TTAAATT
59621142 TTAAATT
1 TTAAATT
59621149 TTAAATT
1 TTAAATT
59621156 TTAAAT
1 TTAAAT
59621162 AATGAAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TTAAATT
Found at i:59631214 original size:55 final size:54
Alignment explanation
Indices: 59631040--59631233 Score: 157
Period size: 54 Copynumber: 3.6 Consensus size: 54
59631030 ATCCTCTTAC
* * * ** *
59631040 TTTCCTCCCAAACCC-CCAAAA-ATTATTCATTTTACTTTTTCTTCCAAACTTTTA
1 TTTCCT-CCAAACCCTCCAAAATTTTTTTCCTTTT-CTTTCCCTCCCAAACTTTTA
** * *
59631094 CTTTCC-CCAAA-CCTCCAATTTTTTTTTCCTTTTTTTTCCCTCCCAAAACTTCTA
1 -TTTCCTCCAAACCCTCCAAAATTTTTTTCCTTTTCTTTCCCTCCC-AAACTTTTA
* * *
59631148 CTTCCTCCAAACCCTTCAAAATTTTTTTCCTTTTGCTTTCCC-CTCAAACTTTTA
1 TTTCCTCCAAACCCTCCAAAATTTTTTTCCTTTT-CTTTCCCTCCCAAACTTTTA
59631202 TTTCCTCTCAAACCC-CCAAAAACTTTTTTTCC
1 TTTCCTC-CAAACCCTCC-AAAA-TTTTTTTCC
59631234 AAATTTATGT
Statistics
Matches: 111, Mismatches: 19, Indels: 17
0.76 0.13 0.12
Matches are distributed among these distances:
52 2 0.02
53 20 0.18
54 37 0.33
55 37 0.33
56 15 0.14
ACGTcount: A:0.23, C:0.34, G:0.01, T:0.43
Consensus pattern (54 bp):
TTTCCTCCAAACCCTCCAAAATTTTTTTCCTTTTCTTTCCCTCCCAAACTTTTA
Found at i:59638612 original size:22 final size:22
Alignment explanation
Indices: 59638587--59638630 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
59638577 CAATTACATG
59638587 CATAACATTATTTACAAACAAA
1 CATAACATTATTTACAAACAAA
*
59638609 CATAACATTATTTGCAAACAAA
1 CATAACATTATTTACAAACAAA
59638631 ATTGGAACTA
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:0.52, C:0.18, G:0.02, T:0.27
Consensus pattern (22 bp):
CATAACATTATTTACAAACAAA
Found at i:59641865 original size:20 final size:20
Alignment explanation
Indices: 59641801--59641866 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
59641791 AGGCATCGTA
* *
59641801 ATGCAAATAGGAGCATGAAT
1 ATGCTAATAGGAGCACGAAT
* *
59641821 ATTCTATTAGGAGCACCG--T
1 ATGCTAATAGGAGCA-CGAAT
59641840 ACTGCTAATAGGAGCACGAAT
1 A-TGCTAATAGGAGCACGAAT
*
59641861 GTGCTA
1 ATGCTA
59641867 TCAGGAACTG
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
19 4 0.11
20 29 0.83
21 2 0.06
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (20 bp):
ATGCTAATAGGAGCACGAAT
Found at i:59645067 original size:29 final size:30
Alignment explanation
Indices: 59645004--59645070 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 30
59644994 AGTTTTTTAA
* * * *
59645004 ATTATACAAAAGTTAAAAATTTTATAGAAT
1 ATTATAAAAAAATTAAAAATTTTATAAAAC
*
59645034 A-TATAAAAAAATT-AAAATTTTGTAAAAC
1 ATTATAAAAAAATTAAAAATTTTATAAAAC
59645062 ATTATAAAA
1 ATTATAAAA
59645071 TTATACAGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 13 0.42
29 17 0.55
30 1 0.03
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.34
Consensus pattern (30 bp):
ATTATAAAAAAATTAAAAATTTTATAAAAC
Found at i:59645070 original size:28 final size:29
Alignment explanation
Indices: 59645004--59645070 Score: 66
Period size: 28 Copynumber: 2.3 Consensus size: 29
59644994 AGTTTTTTAA
* * *
59645004 ATTATACAAAAGTTAAAAATTTTATAGAAT
1 ATTATA-AAAAATTAAAAATTTTATAAAAC
*
59645034 A-TATAAAAAAATT-AAAATTTTGTAAAAC
1 ATTAT-AAAAAATTAAAAATTTTATAAAAC
59645062 ATTATAAAA
1 ATTATAAAA
59645071 TTATACAGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
28 17 0.55
29 12 0.39
30 2 0.06
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.34
Consensus pattern (29 bp):
ATTATAAAAAATTAAAAATTTTATAAAAC
Found at i:59648947 original size:3 final size:3
Alignment explanation
Indices: 59648939--59648990 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
59648929 CAGTTATGGT
59648939 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
59648987 TTA T
1 TTA T
59648991 GCTTTGATAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:59651467 original size:13 final size:13
Alignment explanation
Indices: 59651449--59651473 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59651439 ATCATGCACG
59651449 TAAATATCATATA
1 TAAATATCATATA
59651462 TAAATATCATAT
1 TAAATATCATAT
59651474 TTCAAAAAAG
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:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (13 bp):
TAAATATCATATA
Found at i:59651693 original size:109 final size:109
Alignment explanation
Indices: 59651499--59651879 Score: 611
Period size: 109 Copynumber: 3.5 Consensus size: 109
59651489 TATTTCTAAT
* ** *
59651499 TAAGGCAATATTTAGTATTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGAGTGTCGTTTTTT
1 TAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGTTTTTT
* *
59651564 CTTGTTCAACCAAATAGCTTAATATCCTTTTAAAAATTTTAAAA
66 CTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTTAAAA
59651608 TAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGTTTTTT
1 TAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGTTTTTT
59651673 CTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTTAAAA
66 CTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTTAAAA
* * * * *
59651717 TATGCCAATGTTTTGCGTTTGGAAATTTGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTT
1 TAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGTTTTTT
*
59651782 CTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTCAAAA
66 CTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTTAAAA
* * * *
59651826 TAAGGCAATGTTTTGCGTTTGGAAATTCGA-AGAACGTGCCCTAATGTGCTGGGT
1 TAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGT
59651880 TTCGATTTCT
Statistics
Matches: 254, Mismatches: 18, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
108 21 0.08
109 233 0.92
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.35
Consensus pattern (109 bp):
TAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGTTTTTT
CTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTTAAAA
Found at i:59653278 original size:29 final size:31
Alignment explanation
Indices: 59653246--59653310 Score: 100
Period size: 29 Copynumber: 2.2 Consensus size: 31
59653236 TTACAAATTT
59653246 AGAATTTAGTCTATGTA-TTTTTAT-TTTCA
1 AGAATTTAGTCTATGTACTTTTTATATTTCA
*
59653275 AGAATTTAGTCTATTTACTTTTTATATTTCA
1 AGAATTTAGTCTATGTACTTTTTATATTTCA
59653306 A-AATT
1 AGAATT
59653311 CAAGTCCAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 16 0.48
30 11 0.33
31 6 0.18
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (31 bp):
AGAATTTAGTCTATGTACTTTTTATATTTCA
Found at i:59654651 original size:38 final size:38
Alignment explanation
Indices: 59654600--59654676 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
59654590 ACCAAGATAG
*
59654600 TTTGCGTAGTTTGACCTCTATCTATGTTTGTGGGTCCT
1 TTTGCGTAGTTTGACCTCTATCTATATTTGTGGGTCCT
*
59654638 TTTGCGTAGTTTGACCTCTATTTATATTTGTGGGTCCT
1 TTTGCGTAGTTTGACCTCTATCTATATTTGTGGGTCCT
59654676 T
1 T
59654677 GCCTAAATCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.49
Consensus pattern (38 bp):
TTTGCGTAGTTTGACCTCTATCTATATTTGTGGGTCCT
Found at i:59662956 original size:23 final size:23
Alignment explanation
Indices: 59662925--59662975 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
59662915 ACCTACTTTC
* *
59662925 TTACTGTAGTAATTTTCAGGG-TA
1 TTACAGTAGAAATTTTC-GGGATA
59662948 TTACAGTAGAAATTTTCGGGATA
1 TTACAGTAGAAATTTTCGGGATA
59662971 TTACA
1 TTACA
59662976 TTTCTCTCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 3 0.12
23 22 0.88
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (23 bp):
TTACAGTAGAAATTTTCGGGATA
Done.