Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168381.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_6, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 26551601
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 64000 characters in sequence are not A, C, G, or T
File 2 of 130
Found at i:287892 original size:16 final size:16
Alignment explanation
Indices: 287871--287902 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
287861 AATTATTCAT
*
287871 CAAAATATTCAATTAA
1 CAAAATATTAAATTAA
287887 CAAAATATTAAATTAA
1 CAAAATATTAAATTAA
287903 AAACTCTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.31
Consensus pattern (16 bp):
CAAAATATTAAATTAA
Found at i:288708 original size:30 final size:29
Alignment explanation
Indices: 288674--288738 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 29
288664 CACGTGATAT
288674 AATTAATGATTTAATTGAGTTAAAATAAAA
1 AATTAATGATTTAATTGA-TTAAAATAAAA
*
288704 AATTAATGATTTAATTGATTATAATAAAA
1 AATTAATGATTTAATTGATTAAAATAAAA
*
288733 TATTAA
1 AATTAA
288739 AAACTTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
29 15 0.45
30 18 0.55
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (29 bp):
AATTAATGATTTAATTGATTAAAATAAAA
Found at i:288746 original size:29 final size:29
Alignment explanation
Indices: 288684--288754 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
288674 AATTAATGAT
* ** *
288684 TTAATTGAGTTAAAATAAAAAATTAATGAT
1 TTAATTGA-TTATAATAAAAAATTAAAAAC
*
288714 TTAATTGATTATAATAAAATATTAAAAAC
1 TTAATTGATTATAATAAAAAATTAAAAAC
288743 TTAAATT-ATTAT
1 TT-AATTGATTAT
288755 TAATCTATGA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 23 0.66
30 12 0.34
ACGTcount: A:0.52, C:0.01, G:0.06, T:0.41
Consensus pattern (29 bp):
TTAATTGATTATAATAAAAAATTAAAAAC
Found at i:297698 original size:80 final size:80
Alignment explanation
Indices: 297565--297716 Score: 270
Period size: 80 Copynumber: 1.9 Consensus size: 80
297555 TGACATAATT
*
297565 AATTTTGGGATGGGAATTTCATTTTAATGCTTACTAGCTCCAGTAAAAGCTAGATTCACTTTGAT
1 AATTTTGGGATGGGAATTTCATTTTAATGCTTACTAGCTCCAATAAAAGCTAGATTCACTTTGAT
*
297630 GGAAGGCACATGATA
66 GAAAGGCACATGATA
297645 AATTTTGGGATGGGAATTT-ATTTTTAATGCTTACTAGCTCCAATAAAAGCTAGATTCACTTTGA
1 AATTTTGGGATGGGAATTTCA-TTTTAATGCTTACTAGCTCCAATAAAAGCTAGATTCACTTTGA
297709 TGAAAGGC
65 TGAAAGGC
297717 CTTGTTATAA
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
79 1 0.01
80 68 0.99
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35
Consensus pattern (80 bp):
AATTTTGGGATGGGAATTTCATTTTAATGCTTACTAGCTCCAATAAAAGCTAGATTCACTTTGAT
GAAAGGCACATGATA
Found at i:302558 original size:2 final size:2
Alignment explanation
Indices: 302551--302587 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
302541 GCCCCTTCTA
*
302551 TC TC TC TC TC TC TC TC TC TC TC AC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
302588 TTTCTTTTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.03, C:0.49, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:309738 original size:32 final size:32
Alignment explanation
Indices: 309697--309761 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
309687 TCTCTATTTA
309697 CTAAACTAATACTCTGGGAGAAATCACGTGTC
1 CTAAACTAATACTCTGGGAGAAATCACGTGTC
309729 CTAAACTAATACTCTGGGAGAAATCACGTGTC
1 CTAAACTAATACTCTGGGAGAAATCACGTGTC
309761 C
1 C
309762 AGAAGAATGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (32 bp):
CTAAACTAATACTCTGGGAGAAATCACGTGTC
Found at i:313276 original size:11 final size:12
Alignment explanation
Indices: 313245--313280 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
313235 ATAATCACAT
313245 AATCAATATCTA
1 AATCAATATCTA
*
313257 AATCTATATC-A
1 AATCAATATCTA
313268 AATCAATATCTA
1 AATCAATATCTA
313280 A
1 A
313281 TATTCTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (12 bp):
AATCAATATCTA
Found at i:313327 original size:11 final size:11
Alignment explanation
Indices: 313309--313369 Score: 56
Period size: 11 Copynumber: 5.8 Consensus size: 11
313299 CAAATCAATC
313309 TAGAATATTAT
1 TAGAATATTAT
*
313320 TGGAATATTAT
1 TAGAATATTAT
*
313331 TAGAATAATAT
1 TAGAATATTAT
* **
313342 CATCA-A-T-T
1 TAGAATATTAT
313350 TAGAATATTAT
1 TAGAATATTAT
313361 TAGAATATT
1 TAGAATATT
313370 GGTGACATCC
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
8 3 0.08
9 2 0.05
10 2 0.05
11 31 0.82
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (11 bp):
TAGAATATTAT
Found at i:318080 original size:30 final size:30
Alignment explanation
Indices: 318021--318076 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
318011 AGTTATTCAA
*
318021 CTTTAATTTTTATACTAATAGATCTTTATC
1 CTTTAATTTGTATACTAATAGATCTTTATC
318051 CTTTAATTTGTAT-CTAAATA-ATCTTT
1 CTTTAATTTGTATACT-AATAGATCTTT
318077 TATCATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.30, C:0.12, G:0.04, T:0.54
Consensus pattern (30 bp):
CTTTAATTTGTATACTAATAGATCTTTATC
Found at i:323291 original size:2 final size:2
Alignment explanation
Indices: 323284--323311 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
323274 TAATTATTTA
323284 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
323312 GTGTGTGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:324429 original size:17 final size:19
Alignment explanation
Indices: 324396--324432 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
324386 TTATAAGTTT
324396 TATATATATTGTAATATAA
1 TATATATATTGTAATATAA
324415 TATATATATT-T-ATATAA
1 TATATATATTGTAATATAA
324432 T
1 T
324433 TGATTTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 1 0.06
19 10 0.56
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (19 bp):
TATATATATTGTAATATAA
Found at i:324800 original size:2 final size:2
Alignment explanation
Indices: 324793--324829 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
324783 AACGATGAGA
324793 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
324830 ACAAATTAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:329877 original size:29 final size:29
Alignment explanation
Indices: 329838--329901 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
329828 TATTTAATTA
*
329838 TATTTTAATTT-ATTCATTAATA-AATTATT
1 TATTATAATTTGATT-A-TAATATAATTATT
329867 TATTATAATTTGATTATAATATAATTATT
1 TATTATAATTTGATTATAATATAATTATT
*
329896 GATTAT
1 TATTAT
329902 TCAGTTGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 5 0.16
29 23 0.74
30 3 0.10
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (29 bp):
TATTATAATTTGATTATAATATAATTATT
Found at i:329912 original size:30 final size:28
Alignment explanation
Indices: 329855--329919 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 28
329845 ATTTATTCAT
* *
329855 TAATAAATTATTTATTATAATTTGATTA
1 TAATAAATTATTGATTATAAGTTGATTA
*
329883 TAATATAATTATTGATTATTCAGTTGATTA
1 TAATA-AATTATTGATTA-TAAGTTGATTA
329913 T-ATAAAT
1 TAATAAAT
329920 ACGTAATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 8 0.25
29 14 0.44
30 10 0.31
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.51
Consensus pattern (28 bp):
TAATAAATTATTGATTATAAGTTGATTA
Found at i:337846 original size:3 final size:3
Alignment explanation
Indices: 337838--337900 Score: 117
Period size: 3 Copynumber: 21.0 Consensus size: 3
337828 TATATATATG
*
337838 ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
337886 ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA
337901 CGAAAAATAA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:344176 original size:18 final size:18
Alignment explanation
Indices: 344153--344206 Score: 81
Period size: 18 Copynumber: 3.0 Consensus size: 18
344143 ATGAGGGGGG
*
344153 TACCCTCCAGCAGGTGGA
1 TACCCTCCAGGAGGTGGA
*
344171 TACCCTCCAGGGGGTGGA
1 TACCCTCCAGGAGGTGGA
*
344189 TACCCCCCAGGAGGTGGA
1 TACCCTCCAGGAGGTGGA
344207 GGGTATGCAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.20, C:0.31, G:0.33, T:0.15
Consensus pattern (18 bp):
TACCCTCCAGGAGGTGGA
Found at i:344242 original size:6 final size:6
Alignment explanation
Indices: 344231--344259 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
344221 TGGGTATCCT
344231 CCATGA CCATGA CCATGA CCATGA CCATG
1 CCATGA CCATGA CCATGA CCATGA CCATG
344260 GTGTGAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.34, G:0.17, T:0.17
Consensus pattern (6 bp):
CCATGA
Found at i:345689 original size:13 final size:13
Alignment explanation
Indices: 345673--345698 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
345663 AGTAATATGA
345673 TAAACTAAATTGT
1 TAAACTAAATTGT
345686 TAAACTAAATTGT
1 TAAACTAAATTGT
345699 CTCAGTTATC
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:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
TAAACTAAATTGT
Found at i:346735 original size:2 final size:2
Alignment explanation
Indices: 346728--346758 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
346718 TCACCTTCAC
346728 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
346759 AGAAAACAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:355272 original size:7 final size:7
Alignment explanation
Indices: 355260--355285 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
355250 TGTCTCAAGG
355260 CCTGACT
1 CCTGACT
355267 CCTGACT
1 CCTGACT
355274 CCTGACT
1 CCTGACT
355281 CCTGA
1 CCTGA
355286 GCAGGGGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.42, G:0.15, T:0.27
Consensus pattern (7 bp):
CCTGACT
Found at i:363875 original size:15 final size:17
Alignment explanation
Indices: 363843--363875 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
363833 TTTTCAGTTG
363843 ATGATTAAGAGAGAGAA
1 ATGATTAAGAGAGAGAA
363860 ATGATTAA-AG-GAGAA
1 ATGATTAAGAGAGAGAA
363875 A
1 A
363876 CTTCACCTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 2 0.12
17 8 0.50
ACGTcount: A:0.55, C:0.00, G:0.27, T:0.18
Consensus pattern (17 bp):
ATGATTAAGAGAGAGAA
Found at i:364449 original size:3 final size:3
Alignment explanation
Indices: 364441--364487 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
364431 AGATGACAAC
364441 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
364488 ATGAGAGTAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:365150 original size:15 final size:15
Alignment explanation
Indices: 365115--365156 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
365105 TTTTTGCATT
* *
365115 TTTAAAATTTTTATA
1 TTTAAAATTATTAAA
365130 -TTAAAATTATTAAA
1 TTTAAAATTATTAAA
*
365144 TTTAAAAATATTA
1 TTTAAAATTATTA
365157 TTTAATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTAAAATTATTAAA
Found at i:365254 original size:2 final size:2
Alignment explanation
Indices: 365247--365286 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
365237 ACTCTTCTTT
365247 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
365287 GCAAATTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:367085 original size:11 final size:11
Alignment explanation
Indices: 367069--367098 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
367059 TTGACCTTCC
367069 TTTTCTTCCTT
1 TTTTCTTCCTT
*
367080 TTTTCTTTCTT
1 TTTTCTTCCTT
367091 TTTTCTTC
1 TTTTCTTC
367099 TTAATCAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTCTTCCTT
Found at i:371483 original size:2 final size:2
Alignment explanation
Indices: 371471--371531 Score: 70
Period size: 2 Copynumber: 31.0 Consensus size: 2
371461 GTAGATTTAT
* * *
371471 TA TA TA AA TA TA TA TA TA TA TA AA TA TA TA T- TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
371512 TA TT TA TA TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
371532 ACGATAATGA
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:371510 original size:23 final size:23
Alignment explanation
Indices: 371479--371525 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
371469 ATTATATAAA
*
371479 TATATATATATATAAATATATAT
1 TATAAATATATATAAATATATAT
**
371502 TATAAATATATATTTATATATAT
1 TATAAATATATATAAATATATAT
371525 T
1 T
371526 TATATAACGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TATAAATATATATAAATATATAT
Found at i:387793 original size:10 final size:10
Alignment explanation
Indices: 387778--387824 Score: 58
Period size: 10 Copynumber: 4.5 Consensus size: 10
387768 AAAGTGGCTC
387778 ATATAAATAT
1 ATATAAATAT
387788 ATATAAATAAAT
1 ATATAAAT--AT
*
387800 AAATAAATAT
1 ATATAAATAT
*
387810 ATATATATAT
1 ATATAAATAT
387820 ATATA
1 ATATA
387825 TTCAGAGTCC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
10 23 0.72
12 9 0.28
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
ATATAAATAT
Found at i:387813 original size:4 final size:4
Alignment explanation
Indices: 387778--387825 Score: 51
Period size: 4 Copynumber: 12.0 Consensus size: 4
387768 AAAGTGGCTC
* * * * *
387778 ATAT AAAT ATAT ATAA ATAA ATAA ATAA ATAT ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
387826 TCAGAGTCCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (4 bp):
ATAT
Found at i:388538 original size:5 final size:5
Alignment explanation
Indices: 388530--388580 Score: 59
Period size: 5 Copynumber: 9.8 Consensus size: 5
388520 TAAAATAAAA
*
388530 TTATT TTATT TTATT TTATT TTATT TATAATAT TT-TC TTATT TTATT
1 TTATT TTATT TTATT TTATT TTATT T-T-AT-T TTATT TTATT TTATT
388577 TTAT
1 TTAT
388581 CATATACCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
4 2 0.05
5 32 0.80
6 1 0.03
7 3 0.08
8 2 0.05
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.75
Consensus pattern (5 bp):
TTATT
Found at i:389544 original size:19 final size:18
Alignment explanation
Indices: 389516--389575 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
389506 TTTTAATTAA
*
389516 AAAATCATAAAATTAATT
1 AAAATAATAAAATTAATT
* *
389534 ATAAATAAT-AAATAAACT
1 A-AAATAATAAAATTAATT
*
389552 AAAATAAAAAATATTAATT
1 AAAATAATAAA-ATTAATT
389571 AAAAT
1 AAAAT
389576 TTAAAATGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
17 6 0.18
18 11 0.33
19 16 0.48
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAATAATAAAATTAATT
Found at i:389587 original size:20 final size:19
Alignment explanation
Indices: 389559--389601 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
389549 ACTAAAATAA
*
389559 AAAATATTAATTAAA-ATTT
1 AAAATATT-ATCAAATATTT
389578 AAAATGATTATCAAATATTT
1 AAAAT-ATTATCAAATATTT
389598 AAAA
1 AAAA
389602 ATCTCAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (19 bp):
AAAATATTATCAAATATTT
Found at i:391398 original size:15 final size:15
Alignment explanation
Indices: 391378--391456 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
391368 TAATTTATTA
*
391378 ATATTAATAAATCAT
1 ATATTAATAAATAAT
391393 ATATTAATAAATAAT
1 ATATTAATAAATAAT
* *
391408 ATATTAATGTATTAAT
1 ATATTAAT-AAATAAT
* *
391424 A-AATAATATTATAAT
1 ATATTAATA-AATAAT
*
391439 GTATTAATAAATAAT
1 ATATTAATAAATAAT
391454 ATA
1 ATA
391457 CTATTAATAA
Statistics
Matches: 50, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
15 38 0.76
16 12 0.24
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (15 bp):
ATATTAATAAATAAT
Found at i:391420 original size:8 final size:8
Alignment explanation
Indices: 391363--391456 Score: 58
Period size: 8 Copynumber: 12.5 Consensus size: 8
391353 TAAATAATAT
391363 TATATTAA
1 TATATTAA
*
391371 TTTATT-A
1 TATATTAA
391378 -ATATTAA
1 TATATTAA
* *
391385 TA-AATCA
1 TATATTAA
391392 TATATTAA
1 TATATTAA
*
391400 TA-AATAA
1 TATATTAA
391407 TATATTAA
1 TATATTAA
*
391415 TGTATTAA
1 TATATTAA
*
391423 TA-AATAA
1 TATATTAA
391430 TAT-TATAA
1 TATAT-TAA
*
391438 TGTATTAA
1 TATATTAA
*
391446 TA-AATAA
1 TATATTAA
391453 TATA
1 TATA
391457 CTATTAATAA
Statistics
Matches: 63, Mismatches: 15, Indels: 16
0.67 0.16 0.17
Matches are distributed among these distances:
6 4 0.06
7 25 0.40
8 33 0.52
9 1 0.02
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (8 bp):
TATATTAA
Found at i:391438 original size:23 final size:24
Alignment explanation
Indices: 391394--391464 Score: 110
Period size: 23 Copynumber: 3.0 Consensus size: 24
391384 ATAAATCATA
391394 TATTAATAAATAATA-TATTAATG
1 TATTAATAAATAATATTATTAATG
391417 TATTAATAAATAATATTA-TAATG
1 TATTAATAAATAATATTATTAATG
391440 TATTAATAAATAATATACTATTAAT
1 TATTAATAAATAATAT--TATTAAT
391465 AAAGAATAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
23 36 0.82
24 2 0.05
25 2 0.05
26 4 0.09
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (24 bp):
TATTAATAAATAATATTATTAATG
Found at i:391730 original size:26 final size:27
Alignment explanation
Indices: 391681--391732 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
391671 TATTAACTCA
391681 TCAAAATAATAAAAAATTTCTTTCAAT
1 TCAAAATAATAAAAAATTTCTTTCAAT
*
391708 TCAAAA-AATATAAATATTT-TTTCAA
1 TCAAAATAATA-AAAAATTTCTTTCAA
391733 AATAATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (27 bp):
TCAAAATAATAAAAAATTTCTTTCAAT
Found at i:395423 original size:24 final size:23
Alignment explanation
Indices: 395379--395432 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
395369 TAATTCCTTG
*
395379 ATTAAAAATAATTAATAAAAAAT
1 ATTAAAAATAATTAATAAAAAAA
*
395402 ATTAAAACATAAATT-ATTAAAAAA
1 ATTAAAA-AT-AATTAATAAAAAAA
395426 ATTAAAA
1 ATTAAAA
395433 TTATCTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 7 0.26
24 16 0.59
25 4 0.15
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (23 bp):
ATTAAAAATAATTAATAAAAAAA
Found at i:395613 original size:19 final size:19
Alignment explanation
Indices: 395589--395631 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
395579 TTATTTTCTA
395589 TTTATTGATATT-ATATATT
1 TTTATTGATATTAAT-TATT
**
395608 TTTATTTTTATTAATTATT
1 TTTATTGATATTAATTATT
395627 TTTAT
1 TTTAT
395632 CATAATAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (19 bp):
TTTATTGATATTAATTATT
Found at i:403489 original size:17 final size:18
Alignment explanation
Indices: 403456--403506 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
403446 CGAGCCAAAG
*
403456 GTTTT-TTTTTTTCATTTA
1 GTTTTATTTATTT-ATTTA
403474 GTTTTA-TTATTTATTTA
1 GTTTTATTTATTTATTTA
*
403491 TTTTTATTTATTTATT
1 GTTTTATTTATTTATT
403507 GACTAAATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 10 0.34
18 19 0.66
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.76
Consensus pattern (18 bp):
GTTTTATTTATTTATTTA
Found at i:403497 original size:14 final size:14
Alignment explanation
Indices: 403480--403506 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
403470 TTTAGTTTTA
403480 TTATTTATTTATTT
1 TTATTTATTTATTT
403494 TTATTTATTTATT
1 TTATTTATTTATT
403507 GACTAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (14 bp):
TTATTTATTTATTT
Found at i:403503 original size:18 final size:18
Alignment explanation
Indices: 403457--403506 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 18
403447 GAGCCAAAGG
403457 TTTTT-TTT-TTTCATTTA
1 TTTTTATTTATTT-ATTTA
*
403474 GTTTTA-TTATTTATTTA
1 TTTTTATTTATTTATTTA
403491 TTTTTATTTATTTATT
1 TTTTTATTTATTTATT
403507 GACTAAATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 16 0.57
18 12 0.43
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (18 bp):
TTTTTATTTATTTATTTA
Found at i:403663 original size:56 final size:56
Alignment explanation
Indices: 403563--403751 Score: 190
Period size: 56 Copynumber: 3.3 Consensus size: 56
403553 TTCAATGATC
*
403563 TATTTAAAATAAAAATTTGAAAAAAAATATTTTTGAAGGAAAGTTGAATA-TATCAATT
1 TATTTAAAATAAAAA-TT-AAAAAAAATATTTTAGAAGGAAAGTTGAA-AGTATCAATT
*
403621 TCATTTAAACATAAAAATT-AAAAAAATA-TTTAGAGGGAAAGTTGAAAGTATCAATT
1 T-ATTTAAA-ATAAAAATTAAAAAAAATATTTTAGAAGGAAAGTTGAAAGTATCAATT
* ***
403677 TTTCTTAAAATAAAAATTTTTTAAAAATATTTTTAAGAA--AAAGTTGAAAGTATCAATTT
1 TAT-TTAAAATAAAAA-TTAAAAAAAATA-TTTT-AGAAGGAAAGTTGAAAGTATCAA-TT
403736 TATTTGAAAATAAAAA
1 TATTT-AAAATAAAAA
403752 AAAAAGATTT
Statistics
Matches: 113, Mismatches: 7, Indels: 21
0.80 0.05 0.15
Matches are distributed among these distances:
55 9 0.08
56 32 0.28
57 16 0.14
58 20 0.18
59 26 0.23
60 10 0.09
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.36
Consensus pattern (56 bp):
TATTTAAAATAAAAATTAAAAAAAATATTTTAGAAGGAAAGTTGAAAGTATCAATT
Found at i:403724 original size:58 final size:57
Alignment explanation
Indices: 403565--403944 Score: 179
Period size: 59 Copynumber: 6.4 Consensus size: 57
403555 CAATGATCTA
** * *
403565 TTTAAAATAAAAATTTGAAAAAAAATATTTTTGAAG-GAAAGTTGAATA-TATCAATTTCA
1 TTTAAAATAAAAATTT-TTAAAAAATATTTTT-AAGAAAAAGTTGAA-AGTATCAATTT-T
* **
403624 TTTAAACATAAAAA---TTAAAAAA-ATATTTAGAGGGAAAGTTGAAAGTATCAATTTT
1 TTTAAA-ATAAAAATTTTTAAAAAATATTTTTA-AGAAAAAGTTGAAAGTATCAATTTT
*
403679 TCTTAAAATAAAAATTTTTTAAAAATATTTTTAAGAAAAAGTTGAAAGTATCAATTTT
1 T-TTAAAATAAAAATTTTTAAAAAATATTTTTAAGAAAAAGTTGAAAGTATCAATTTT
* * * ** ** * *
403737 ATTTGAAAATAAAAAAAAAAGATTTT-AAGAAAAGATTT-TTAAAGAAAAGTTGAAATTATCAAA
1 -TTT-AAAAT-----AAAAA-TTTTTAAAAAATATTTTTAAGAAA---AAGTTGAAAGTATCAAT
403800 TTT
55 TTT
* * *
403803 TCTTAAAA-ATAAAATTTTCAAAAAATATTTATTGAGGAAAAA-TGGAAAGTATCAATTTT
1 T-TTAAAATA-AAAATTTTTAAAAAATATTT-TT-AAGAAAAAGTTGAAAGTATCAATTTT
* * * * * * * *
403862 TTAAAAAAATAAAATTATCAAGAAAAGTATTTTTAAGGAAACGTTGAAAATATAAATTTT
1 TTTAAAATA-AAAATTTTTAA-AAAA-TATTTTTAAGAAAAAGTTGAAAGTATCAATTTT
*
403922 TCTTGAAAATAAAAA-CTTTAAAA
1 T-TT-AAAATAAAAATTTTTAAAA
403945 TACTTAAAAA
Statistics
Matches: 248, Mismatches: 41, Indels: 64
0.70 0.12 0.18
Matches are distributed among these distances:
54 1 0.00
55 16 0.06
56 30 0.12
58 37 0.15
59 56 0.23
60 43 0.17
61 12 0.05
62 5 0.02
63 6 0.02
64 13 0.05
65 9 0.04
66 20 0.08
ACGTcount: A:0.52, C:0.04, G:0.10, T:0.35
Consensus pattern (57 bp):
TTTAAAATAAAAATTTTTAAAAAATATTTTTAAGAAAAAGTTGAAAGTATCAATTTT
Found at i:403771 original size:13 final size:15
Alignment explanation
Indices: 403753--403785 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
403743 AAATAAAAAA
403753 AAAAGA-TTTT-AAG
1 AAAAGATTTTTAAAG
403766 AAAAGATTTTTAAAG
1 AAAAGATTTTTAAAG
403781 AAAAG
1 AAAAG
403786 TTGAAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.33
14 4 0.22
15 8 0.44
ACGTcount: A:0.58, C:0.00, G:0.15, T:0.27
Consensus pattern (15 bp):
AAAAGATTTTTAAAG
Found at i:403828 original size:16 final size:17
Alignment explanation
Indices: 403797--403829 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
403787 TGAAATTATC
*
403797 AAATTTTCTTAAAAATA
1 AAATTTTCTAAAAAATA
403814 AAATTTTC-AAAAAATA
1 AAATTTTCTAAAAAATA
403830 TTTATTGAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATTTTCTAAAAAATA
Found at i:403843 original size:59 final size:60
Alignment explanation
Indices: 403763--403935 Score: 187
Period size: 59 Copynumber: 2.9 Consensus size: 60
403753 AAAAGATTTT
* * *
403763 AAGAAAAG-ATTTTTAAAGAAAAGTTGAAATTATCAAATTTTCTTAAAAATAAAATTTTC
1 AAGAAAAGTATTTTTAAGGAAAAGTTGAAAATATCAAATTTTCTTAAAAATAAAATTATC
* * * *
403822 AA-AAAA-TATTTATTGAGGAAAAATGGAAAGTATC-AATTTT-TTAAAAAAATAAAATTATC
1 AAGAAAAGTATTT-TTAAGGAAAAGTTGAAAATATCAAATTTTCTT--AAAAATAAAATTATC
* *
403881 AAGAAAAGTATTTTTAAGGAAACGTTGAAAATAT-AAATTTTTCTTGAAAATAAAA
1 AAGAAAAGTATTTTTAAGGAAAAGTTGAAAATATCAAA-TTTTCTTAAAAATAAAA
403936 ACTTTAAAAT
Statistics
Matches: 93, Mismatches: 12, Indels: 17
0.76 0.10 0.14
Matches are distributed among these distances:
57 2 0.02
58 14 0.15
59 35 0.38
60 31 0.33
61 9 0.10
62 2 0.02
ACGTcount: A:0.52, C:0.04, G:0.10, T:0.34
Consensus pattern (60 bp):
AAGAAAAGTATTTTTAAGGAAAAGTTGAAAATATCAAATTTTCTTAAAAATAAAATTATC
Found at i:404942 original size:23 final size:23
Alignment explanation
Indices: 404894--404944 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
404884 TAATTAAAAA
*
404894 AATAATATAATATAAGTATATAT
1 AATAATATAATATAAGTATACAT
* * *
404917 AATAATATGATATAGGTATACCT
1 AATAATATAATATAAGTATACAT
404940 AATAA
1 AATAA
404945 AGAAAACAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.53, C:0.04, G:0.08, T:0.35
Consensus pattern (23 bp):
AATAATATAATATAAGTATACAT
Found at i:414866 original size:15 final size:16
Alignment explanation
Indices: 414836--414868 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
414826 ATAATTTCAT
*
414836 TATATTAATTTTTAAA
1 TATATTAATATTTAAA
414852 TATATTAA-ATTTAAA
1 TATATTAATATTTAAA
414867 TA
1 TA
414869 AAAAATTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TATATTAATATTTAAA
Found at i:423449 original size:58 final size:58
Alignment explanation
Indices: 423359--423475 Score: 216
Period size: 58 Copynumber: 2.0 Consensus size: 58
423349 TCAGGAGCTG
423359 GTTCTAGGCTTGTGGTTTCTGCAATTAATTAAAATCTCCTATTTATCAAATTTCATTT
1 GTTCTAGGCTTGTGGTTTCTGCAATTAATTAAAATCTCCTATTTATCAAATTTCATTT
* *
423417 GTTCTAGGCTTGTGGTTTCTGCAATTAGTTAAAATCTCCTATTTATTAAATTTCATTT
1 GTTCTAGGCTTGTGGTTTCTGCAATTAATTAAAATCTCCTATTTATCAAATTTCATTT
423475 G
1 G
423476 CAAAAAGAGG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.47
Consensus pattern (58 bp):
GTTCTAGGCTTGTGGTTTCTGCAATTAATTAAAATCTCCTATTTATCAAATTTCATTT
Found at i:425527 original size:7 final size:7
Alignment explanation
Indices: 425515--425539 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
425505 TAGTGAGATG
425515 AAAAAAT
1 AAAAAAT
425522 AAAAAAT
1 AAAAAAT
425529 AAAAAAT
1 AAAAAAT
425536 AAAA
1 AAAA
425540 TATTAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:429968 original size:38 final size:38
Alignment explanation
Indices: 429917--429992 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
429907 CTCTTTTCCT
429917 TTGTTTTAGTGAAAGTTGGTAGGTACAATTACAATACC
1 TTGTTTTAGTGAAAGTTGGTAGGTACAATTACAATACC
*
429955 TTGTTTTAGTGAAATTTGGTAGGTACAATTACAATACC
1 TTGTTTTAGTGAAAGTTGGTAGGTACAATTACAATACC
429993 AAGAAGTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.38
Consensus pattern (38 bp):
TTGTTTTAGTGAAAGTTGGTAGGTACAATTACAATACC
Found at i:434402 original size:25 final size:25
Alignment explanation
Indices: 434373--434422 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
434363 TAACATAGTC
434373 TTGTTGTTATCTATGTACATATGCT
1 TTGTTGTTATCTATGTACATATGCT
*
434398 TTGTTGTTGTCTATGTACATATGCT
1 TTGTTGTTATCTATGTACATATGCT
434423 AAACTAGTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.52
Consensus pattern (25 bp):
TTGTTGTTATCTATGTACATATGCT
Found at i:442624 original size:18 final size:18
Alignment explanation
Indices: 442597--442638 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
442587 CAATTATAGG
*
442597 TTTTTATATAAAAAAATA
1 TTTTTTTATAAAAAAATA
442615 TTTTTTTATAAAAAAATA
1 TTTTTTTATAAAAAAATA
442633 TTTTTT
1 TTTTTT
442639 ATATTATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTTTTTTATAAAAAAATA
Found at i:443190 original size:76 final size:76
Alignment explanation
Indices: 443063--443212 Score: 264
Period size: 76 Copynumber: 2.0 Consensus size: 76
443053 AGAAAACTCA
*
443063 ATGTAATAATAAGCCACAGACTAGACTCGAAAGGGATGTCGGGGTTGACCGCCTGCTCATACACA
1 ATGTAATAATAAGCCACAGACTAGACTCGAAAGGGATGTCGGGGTTAACCGCCTGCTCATACACA
443128 ATCCATCCTCC
66 ATCCATCCTCC
* * *
443139 ATGTAATAATAAGCCATAGACTAGACTCTAAAGGGGTGTCGGGGTTAACCGCCTGCTCATACACA
1 ATGTAATAATAAGCCACAGACTAGACTCGAAAGGGATGTCGGGGTTAACCGCCTGCTCATACACA
443204 ATCCATCCT
66 ATCCATCCT
443213 TAGCTGTGAG
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 70 1.00
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.23
Consensus pattern (76 bp):
ATGTAATAATAAGCCACAGACTAGACTCGAAAGGGATGTCGGGGTTAACCGCCTGCTCATACACA
ATCCATCCTCC
Found at i:443687 original size:27 final size:29
Alignment explanation
Indices: 443641--443695 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
443631 ATTTTATATT
*
443641 TATATAAAAATATTATTTAAGAT-ATTTTG
1 TATATAAAAATATTACTTAA-ATAATTTTG
443670 TATATAAAAATA-T-CTTAAATAATTTT
1 TATATAAAAATATTACTTAAATAATTTT
443696 TTTATAGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 2 0.08
27 9 0.38
28 1 0.04
29 12 0.50
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (29 bp):
TATATAAAAATATTACTTAAATAATTTTG
Found at i:444076 original size:22 final size:22
Alignment explanation
Indices: 444030--444077 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
444020 AAAATAAAAT
* *
444030 AAAAAATTATTATCATATATCA
1 AAAAAATTATAATAATATATCA
444052 AAAAAATTATAATAATGATAT-A
1 AAAAAATTATAATAAT-ATATCA
444074 AAAA
1 AAAA
444078 TTAATATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (22 bp):
AAAAAATTATAATAATATATCA
Found at i:449461 original size:40 final size:40
Alignment explanation
Indices: 449417--449496 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
449407 AGTTTACTAA
449417 TGTTATTGGATGTAGAGTGCATGATCTTTCACTTTTGATT
1 TGTTATTGGATGTAGAGTGCATGATCTTTCACTTTTGATT
449457 TGTTATTGGATGTAGAGTGCATGATCTTTCACTTTTGATT
1 TGTTATTGGATGTAGAGTGCATGATCTTTCACTTTTGATT
449497 GAGTGTTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.20, C:0.10, G:0.23, T:0.47
Consensus pattern (40 bp):
TGTTATTGGATGTAGAGTGCATGATCTTTCACTTTTGATT
Found at i:479170 original size:3 final size:3
Alignment explanation
Indices: 479162--479206 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
479152 CTAAAGTTTG
479162 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
479207 TTAGAGAGAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:481593 original size:18 final size:18
Alignment explanation
Indices: 481570--481604 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
481560 CTTGCTCGTC
*
481570 TCTTTCTCCTTTTTTTTT
1 TCTTTCTACTTTTTTTTT
481588 TCTTTCTACTTTTTTTT
1 TCTTTCTACTTTTTTTT
481605 GTTGCCGTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (18 bp):
TCTTTCTACTTTTTTTTT
Found at i:492581 original size:51 final size:51
Alignment explanation
Indices: 492507--492618 Score: 170
Period size: 51 Copynumber: 2.2 Consensus size: 51
492497 AGTGGTGGCT
* * *
492507 GTCCCGGTGGCCCACCTGGAAAGCCGAAGGCCCCAAGCCCAGGAGGTGGTG
1 GTCCAGGTGGCCCACCTGAAAAGCCGAAGGCCCCAAGCCCAGGAGGGGGTG
* * *
492558 GTCCTGGTGGCCTACTTGAAAAGCCGAAGGCCCCAAGCCCAGGAGGGGGTG
1 GTCCAGGTGGCCCACCTGAAAAGCCGAAGGCCCCAAGCCCAGGAGGGGGTG
492609 GTCCAGGTGG
1 GTCCAGGTGG
492619 TGGGCCATGT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.20, C:0.29, G:0.38, T:0.12
Consensus pattern (51 bp):
GTCCAGGTGGCCCACCTGAAAAGCCGAAGGCCCCAAGCCCAGGAGGGGGTG
Found at i:493754 original size:31 final size:29
Alignment explanation
Indices: 493716--493783 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 29
493706 ATATATGATA
493716 ATTTATATTATCATATTATATAAAATATTAT
1 ATTTATATTAT-ATATTATATAAAA-ATTAT
*
493747 ATTTATATTATATTTTATATAAAAATTAT
1 ATTTATATTATATATTATATAAAAATTAT
493776 ATATTATA
1 AT-TTATA
493784 ATTTATAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
29 7 0.20
30 17 0.49
31 11 0.31
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (29 bp):
ATTTATATTATATATTATATAAAAATTAT
Found at i:493764 original size:18 final size:18
Alignment explanation
Indices: 493719--493790 Score: 63
Period size: 18 Copynumber: 3.8 Consensus size: 18
493709 TATGATAATT
*
493719 TATATTATCATATTATATAA
1 TATATTAT-AT-TTATATTA
*
493739 AATATTATATTTATATTA
1 TATATTATATTTATATTA
* ** *
493757 TATTTTATATAAAAATTA
1 TATATTATATTTATATTA
493775 TATATTATAATTTATA
1 TATATTAT-ATTTATA
493791 ATGATAAAAA
Statistics
Matches: 40, Mismatches: 11, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
18 27 0.68
19 6 0.15
20 7 0.17
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (18 bp):
TATATTATATTTATATTA
Found at i:493856 original size:20 final size:21
Alignment explanation
Indices: 493818--493856 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
493808 TATAATTTTT
**
493818 TAATTTTATTTAATTTATTTA
1 TAATTTTATTTAAAATATTTA
493839 TAATTTT-TTTAAAATATT
1 TAATTTTATTTAAAATATT
493857 AAATTATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TAATTTTATTTAAAATATTTA
Found at i:506795 original size:2 final size:2
Alignment explanation
Indices: 506750--506782 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
506740 ATCTGAACCA
506750 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
506783 AAGACGGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:509989 original size:1 final size:1
Alignment explanation
Indices: 509983--510007 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
509973 TCAGACCCAT
509983 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
510008 CAGCAACCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:515198 original size:19 final size:20
Alignment explanation
Indices: 515166--515203 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
515156 TTTTTAACCT
*
515166 AAAATAATTAAATAAAAATA
1 AAAATAAATAAATAAAAATA
515186 AAAATAAAT-AATAAAAAT
1 AAAATAAATAAATAAAAAT
515204 TGATAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAATAAATAAATAAAAATA
Found at i:515209 original size:13 final size:13
Alignment explanation
Indices: 515175--515203 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
515165 TAAAATAATT
515175 AAATAAA-AATAA
1 AAATAAATAATAA
515187 AAATAAATAATAA
1 AAATAAATAATAA
515200 AAAT
1 AAAT
515204 TGATAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AAATAAATAATAA
Found at i:517846 original size:20 final size:19
Alignment explanation
Indices: 517821--517864 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
517811 CCCCTAGATT
*
517821 TAATAATATAAAATTTAATA
1 TAATAATATAAAA-TGAATA
*
517841 TAATAATATAATATGAATA
1 TAATAATATAAAATGAATA
517860 TAATA
1 TAATA
517865 TAAATATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
TAATAATATAAAATGAATA
Found at i:517861 original size:11 final size:11
Alignment explanation
Indices: 517823--517887 Score: 58
Period size: 13 Copynumber: 5.5 Consensus size: 11
517813 CCTAGATTTA
517823 ATAATATAAAAT
1 ATAATAT-AAAT
*
517835 TTAATATAATAAT
1 ATAATAT-A-AAT
*
517848 ATAATATGAAT
1 ATAATATAAAT
517859 ATAATATAAAT
1 ATAATATAAAT
*
517870 ATAAAATATAAAA
1 AT--AATATAAAT
517883 ATAAT
1 ATAAT
517888 TTAATTTAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
11 18 0.40
12 8 0.18
13 19 0.42
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:517877 original size:24 final size:24
Alignment explanation
Indices: 517825--517892 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
517815 TAGATTTAAT
* *
517825 AATATAAAATTTAATATAATAATAT
1 AATATAAAA-ATAATATAATAATAA
* *
517850 AATATGAATATAATATAA-ATATAA
1 AATATAAAAATAATATAATA-ATAA
*
517874 AATATAAAAATAATTTAAT
1 AATATAAAAATAATATAAT
517893 TTAAAATTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
23 1 0.03
24 26 0.76
25 7 0.21
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (24 bp):
AATATAAAAATAATATAATAATAA
Found at i:517934 original size:35 final size:35
Alignment explanation
Indices: 517885--517951 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
517875 ATATAAAAAT
**
517885 AATTTAATTTAAAAT-TTTAATAATTATTATATTTA
1 AATTTAATAAAAAATATTTAAT-ATTATTATATTTA
* *
517920 AATTTAATAAAAAATATTTTATATTTTTATAT
1 AATTTAATAAAAAATATTTAATATTATTATAT
517952 AAATATAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 22 0.81
36 5 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (35 bp):
AATTTAATAAAAAATATTTAATATTATTATATTTA
Found at i:518005 original size:37 final size:38
Alignment explanation
Indices: 517935--518007 Score: 98
Period size: 37 Copynumber: 1.9 Consensus size: 38
517925 AATAAAAAAT
517935 ATTTTATATTTTTATATAAATATAATATAAATATATTA
1 ATTTTATATTTTTATATAAATATAATATAAATATATTA
*
517973 ATTTTA-ATATTTTATAT-GATATAA-ATACAATATAT
1 ATTTTATAT-TTTTATATAAATATAATATA-AATATAT
518008 ATTTTTCCCT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
36 3 0.09
37 15 0.47
38 14 0.44
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (38 bp):
ATTTTATATTTTTATATAAATATAATATAAATATATTA
Found at i:518008 original size:39 final size:38
Alignment explanation
Indices: 517935--518010 Score: 93
Period size: 38 Copynumber: 2.0 Consensus size: 38
517925 AATAAAAAAT
*
517935 ATTTTATATTTTTATATAAATATAATATAAATATATTA
1 ATTTTATATTTTTATATAAATATAATACAAATATATTA
*
517973 ATTTTA-ATATTTTATAT-GATATAAATACAATATATATT
1 ATTTTATAT-TTTTATATAAATAT-AATACAA-ATATATT
518011 TTTCCCTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
37 6 0.18
38 20 0.61
39 7 0.21
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (38 bp):
ATTTTATATTTTTATATAAATATAATACAAATATATTA
Found at i:518801 original size:13 final size:13
Alignment explanation
Indices: 518775--518803 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
518765 ACATGAACCC
518775 AACACGAAACAAA
1 AACACGAAACAAA
518788 AACAC-AAACAAA
1 AACACGAAACAAA
518800 AACA
1 AACA
518804 ATTCCCCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.72, C:0.24, G:0.03, T:0.00
Consensus pattern (13 bp):
AACACGAAACAAA
Found at i:524788 original size:39 final size:39
Alignment explanation
Indices: 524740--524819 Score: 133
Period size: 39 Copynumber: 2.1 Consensus size: 39
524730 AAAAAATTAA
* *
524740 TTCTCAAGAGAGAAAAATTTACTAATATTTGTAAGATGC
1 TTCTCAAGAGAGAAAAATTGACTAATATTTGTAAAATGC
*
524779 TTCTCAAGAGAGAAAAGTTGACTAATATTTGTAAAATGC
1 TTCTCAAGAGAGAAAAATTGACTAATATTTGTAAAATGC
524818 TT
1 TT
524820 TCGCAGATCT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (39 bp):
TTCTCAAGAGAGAAAAATTGACTAATATTTGTAAAATGC
Found at i:528915 original size:149 final size:149
Alignment explanation
Indices: 528642--528934 Score: 507
Period size: 149 Copynumber: 2.0 Consensus size: 149
528632 CATAAGCATG
* * *
528642 GACAATTACTGTTCTTTTCCAAGAATCAGATACTGTGAACAAAAGGGCCTTGACAATCACATAAC
1 GACAATTACTGTTCTCTTCCAAGAATCAGATACTGTGAACAAAAAGGCCTTGACAATCACAAAAC
528707 ACTGTTGCTTCCAAATGTAAAATAGAAGATATGTGACAATTGGAACCTTCCTTTGAAGGTTTTTC
66 ACTGTTGCTTCCAAATGTAAAATAGAAGATATGTGACAATTGGAACCTTCCTTTGAAGGTTTTTC
**
528772 TATTTATTTATTTTGGGTA
131 TACATATTTATTTTGGGTA
*
528791 GACAATTACTGTTCTCTTCCAAGAATCAGATACTGTGAACAAAAATGCCTTGACAATCACAAAAC
1 GACAATTACTGTTCTCTTCCAAGAATCAGATACTGTGAACAAAAAGGCCTTGACAATCACAAAAC
*
528856 ACTGTTGCTTCCAAATGTAAAATAGAAGATATGTGACACTTGGAACCTTCCTCTT-AAGGTTTTT
66 ACTGTTGCTTCCAAATGTAAAATAGAAGATATGTGACAATTGGAACCTTCCT-TTGAAGGTTTTT
528920 CTACATATTTATTTT
130 CTACATATTTATTTT
528935 TAGTAGATAG
Statistics
Matches: 136, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
149 134 0.99
150 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (149 bp):
GACAATTACTGTTCTCTTCCAAGAATCAGATACTGTGAACAAAAAGGCCTTGACAATCACAAAAC
ACTGTTGCTTCCAAATGTAAAATAGAAGATATGTGACAATTGGAACCTTCCTTTGAAGGTTTTTC
TACATATTTATTTTGGGTA
Found at i:543759 original size:16 final size:16
Alignment explanation
Indices: 543738--543790 Score: 61
Period size: 16 Copynumber: 3.0 Consensus size: 16
543728 TAAATAAGTG
543738 ATTTATTTAAAATTTT
1 ATTTATTTAAAATTTT
543754 ATTTATTTAAAATATAAATT
1 ATTTATTTAAAAT-T---TT
543774 ATTTATTTAATAATTTT
1 ATTTATTTAA-AATTTT
543791 GTTAAATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
16 13 0.41
17 3 0.09
20 13 0.41
21 3 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTATTTAAAATTTT
Found at i:543813 original size:25 final size:25
Alignment explanation
Indices: 543768--543815 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
543758 ATTTAAAATA
** *
543768 TAAATTATTTATTTAATAATTTTGT
1 TAAATTATTTAAGTAAAAATTTTGT
543793 TAAATTATTTAAGTAAAAATTTT
1 TAAATTATTTAAGTAAAAATTTT
543816 AAGTTTTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (25 bp):
TAAATTATTTAAGTAAAAATTTTGT
Found at i:543870 original size:20 final size:19
Alignment explanation
Indices: 543830--543885 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
543820 TTTATTGTAA
* *
543830 ATATGTAATAGTAAGTTTT
1 ATATGTAATAATAAATTTT
543849 ATATGTAATAATAAAATTTT
1 ATATGTAATAAT-AAATTTT
*
543869 AT-TATAAT-ATAAATTTT
1 ATATGTAATAATAAATTTT
543886 TTCATATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 7 0.21
18 2 0.06
19 16 0.48
20 8 0.24
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (19 bp):
ATATGTAATAATAAATTTT
Found at i:543933 original size:22 final size:22
Alignment explanation
Indices: 543908--543981 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
543898 ATAAATATTG
*
543908 AATTTTTAATCTTAAAAATGTC
1 AATTTTTTATCTTAAAAATGTC
* * *
543930 AATTTTATTTTTTATTAAAAATATC
1 AA--TT-TTTTATCTTAAAAATGTC
*
543955 AAGTTTTTATCTTAAAAATGTC
1 AATTTTTTATCTTAAAAATGTC
543977 -ATTTT
1 AATTTT
543982 GTTTAATTCT
Statistics
Matches: 40, Mismatches: 9, Indels: 7
0.71 0.16 0.12
Matches are distributed among these distances:
21 4 0.10
22 17 0.43
23 1 0.03
24 2 0.05
25 16 0.40
ACGTcount: A:0.38, C:0.07, G:0.04, T:0.51
Consensus pattern (22 bp):
AATTTTTTATCTTAAAAATGTC
Found at i:543997 original size:47 final size:48
Alignment explanation
Indices: 543910--544000 Score: 123
Period size: 47 Copynumber: 1.9 Consensus size: 48
543900 AAATATTGAA
* *
543910 TTTTTAATCTTAAAAATGTCAATTTTATTTTTTATTAAAAATATCAAG
1 TTTTTAATCTTAAAAATGTCAATTTTATTTATTATAAAAAATATCAAG
* *
543958 TTTTT-ATCTTAAAAATGTC-ATTTTGTTTAATTCTAAAAAATAT
1 TTTTTAATCTTAAAAATGTCAATTTTATTT-ATTATAAAAAATAT
544001 TTTTTTTATA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
46 8 0.21
47 25 0.66
48 5 0.13
ACGTcount: A:0.38, C:0.07, G:0.04, T:0.51
Consensus pattern (48 bp):
TTTTTAATCTTAAAAATGTCAATTTTATTTATTATAAAAAATATCAAG
Found at i:556421 original size:35 final size:37
Alignment explanation
Indices: 556375--556454 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
556365 CATTGTATAT
556375 TTGTAAATAATTGTAAAAAT-A-GTCACTTGAGCTTG
1 TTGTAAATAATTGTAAAAATAATGTCACTTGAGCTTG
* *
556410 TTGTAAATAATTGTAAAAATAATTTTCATTTGAGCTTG
1 TTGTAAATAATTGTAAAAATAA-TGTCACTTGAGCTTG
556448 TTGTAAA
1 TTGTAAA
556455 AATAGTTTCT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
35 20 0.50
36 1 0.03
38 19 0.47
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.41
Consensus pattern (37 bp):
TTGTAAATAATTGTAAAAATAATGTCACTTGAGCTTG
Found at i:572960 original size:13 final size:13
Alignment explanation
Indices: 572942--572966 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
572932 GAAATCGGCG
572942 GTTCTCTGGGAGA
1 GTTCTCTGGGAGA
572955 GTTCTCTGGGAG
1 GTTCTCTGGGAG
572967 GCGAGTAACT
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:0.12, C:0.16, G:0.40, T:0.32
Consensus pattern (13 bp):
GTTCTCTGGGAGA
Found at i:577278 original size:14 final size:15
Alignment explanation
Indices: 577224--577305 Score: 55
Period size: 14 Copynumber: 5.6 Consensus size: 15
577214 TAACAAATGA
577224 AAAAAAAAGTGAAAG
1 AAAAAAAAGTGAAAG
*
577239 AATAAAAAG-GAAAG
1 AAAAAAAAGTGAAAG
***
577253 TTTAAAAA-TGAAA-
1 AAAAAAAAGTGAAAG
577266 AAAAAAAAGTGAAGAAG
1 AAAAAAAAGTG-A-AAG
* *
577283 AAATAAAAG-AAAAG
1 AAAAAAAAGTGAAAG
*
577297 AAAATAAAG
1 AAAAAAAAG
577306 AATGTATAAG
Statistics
Matches: 52, Mismatches: 10, Indels: 11
0.71 0.14 0.15
Matches are distributed among these distances:
13 5 0.10
14 27 0.52
15 10 0.19
16 2 0.04
17 8 0.15
ACGTcount: A:0.72, C:0.00, G:0.17, T:0.11
Consensus pattern (15 bp):
AAAAAAAAGTGAAAG
Found at i:577344 original size:15 final size:13
Alignment explanation
Indices: 577323--577362 Score: 55
Period size: 15 Copynumber: 3.0 Consensus size: 13
577313 AAGAAAGAAC
577323 AAAAAGATAAATT
1 AAAAAGATAAATT
577336 GAGAAAAGATAAATT
1 -A-AAAAGATAAATT
577351 AAAAAGA-AAATT
1 AAAAAGATAAATT
577363 TGACTTGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.20
13 6 0.24
14 2 0.08
15 12 0.48
ACGTcount: A:0.68, C:0.00, G:0.12, T:0.20
Consensus pattern (13 bp):
AAAAAGATAAATT
Found at i:577632 original size:30 final size:30
Alignment explanation
Indices: 577596--577673 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 30
577586 ATTAATTTAT
577596 ATTAAGGACTTATTTAAGAAT-AAATTAAAG
1 ATTAAGGACTTATTT-AGAATAAAATTAAAG
*
577626 ATTAAGGATTTATTT-GAATACAAATTAAAG
1 ATTAAGGACTTATTTAGAATA-AAATTAAAG
* * *
577656 TTTGAGAACTTATTTAGA
1 ATTAAGGACTTATTTAGA
577674 CCAAAGTAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
28 4 0.10
30 34 0.85
31 2 0.05
ACGTcount: A:0.45, C:0.04, G:0.14, T:0.37
Consensus pattern (30 bp):
ATTAAGGACTTATTTAGAATAAAATTAAAG
Found at i:578236 original size:2 final size:2
Alignment explanation
Indices: 578229--578255 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
578219 TTCATTGAGT
578229 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
578256 GTTTTCATAT
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:578864 original size:40 final size:39
Alignment explanation
Indices: 578819--578896 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 39
578809 TATCATTGTC
*
578819 TTTTTTTTTTTTGTATATTTCATC-TTATTTAATATTTTTCG
1 TTTTTATTTTTT-TATATTTC-TCTTTA-TTAATATTTTTCG
578860 TTTTTACTTTTTTTATATTTCTCTTTATTAATATTTT
1 TTTTTA-TTTTTTTATATTTCTCTTTATTAATATTTT
578897 AAAATTGACT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
40 12 0.35
41 16 0.47
42 6 0.18
ACGTcount: A:0.18, C:0.08, G:0.03, T:0.72
Consensus pattern (39 bp):
TTTTTATTTTTTTATATTTCTCTTTATTAATATTTTTCG
Found at i:579955 original size:2 final size:2
Alignment explanation
Indices: 579950--579976 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
579940 TATATAAGTG
579950 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
579977 GTACACGCAC
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:580065 original size:94 final size:94
Alignment explanation
Indices: 579962--580152 Score: 382
Period size: 94 Copynumber: 2.0 Consensus size: 94
579952 TATATATATA
579962 TATATATATATATATGTACACGCACCACACTACATATATATCAAATGTCCAAAGAAAGAAAGCAA
1 TATATATATATATATGTACACGCACCACACTACATATATATCAAATGTCCAAAGAAAGAAAGCAA
580027 ATATAAAAATAAAATTAATGAATTTTGAG
66 ATATAAAAATAAAATTAATGAATTTTGAG
580056 TATATATATATATATGTACACGCACCACACTACATATATATCAAATGTCCAAAGAAAGAAAGCAA
1 TATATATATATATATGTACACGCACCACACTACATATATATCAAATGTCCAAAGAAAGAAAGCAA
580121 ATATAAAAATAAAATTAATGAATTTTGAG
66 ATATAAAAATAAAATTAATGAATTTTGAG
580150 TAT
1 TAT
580153 TGAGATAGTA
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 97 1.00
ACGTcount: A:0.50, C:0.13, G:0.09, T:0.28
Consensus pattern (94 bp):
TATATATATATATATGTACACGCACCACACTACATATATATCAAATGTCCAAAGAAAGAAAGCAA
ATATAAAAATAAAATTAATGAATTTTGAG
Found at i:581763 original size:36 final size:36
Alignment explanation
Indices: 581716--581817 Score: 132
Period size: 36 Copynumber: 2.8 Consensus size: 36
581706 ACTTTGTATG
* *
581716 TGAATCTGGAGATGGTGTTGAGCTTTCCCCTGCATC
1 TGAATCTGGAGATGGTGTTGACCTTTCCCCTGCACC
* * *
581752 TGAATTTGGAGACGGTGTTGACCTTTCCCCTGTACC
1 TGAATCTGGAGATGGTGTTGACCTTTCCCCTGCACC
* * *
581788 TGAAACTGGAGATGGTGTTAACATTTCCCC
1 TGAATCTGGAGATGGTGTTGACCTTTCCCC
581818 ATCCCACCAA
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 56 1.00
ACGTcount: A:0.20, C:0.23, G:0.25, T:0.32
Consensus pattern (36 bp):
TGAATCTGGAGATGGTGTTGACCTTTCCCCTGCACC
Found at i:585071 original size:14 final size:16
Alignment explanation
Indices: 585042--585076 Score: 56
Period size: 14 Copynumber: 2.3 Consensus size: 16
585032 TACTCTTAAA
585042 ATTATAATTATTTTAT
1 ATTATAATTATTTTAT
585058 ATTATAA-T-TTTTAT
1 ATTATAATTATTTTAT
585072 ATTAT
1 ATTAT
585077 CAAATTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.58
15 1 0.05
16 7 0.37
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
ATTATAATTATTTTAT
Found at i:585777 original size:2 final size:2
Alignment explanation
Indices: 585770--585813 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
585760 CGCACAATAA
*
585770 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT A- AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
585810 AT AT
1 AT AT
585814 GTGTCTTGAC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:587066 original size:22 final size:22
Alignment explanation
Indices: 587032--587094 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
587022 AAAAGTAACT
* *
587032 TAATATTTAATATTTATTTTTA
1 TAATTTTTTATATTTATTTTTA
*
587054 TAATTTTTTATATTTATATTTA
1 TAATTTTTTATATTTATTTTTA
* * *
587076 TCATTATTATATCTTTATT
1 TAATT-TTTTATATTTATT
587095 GTTTTATTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
22 23 0.70
23 10 0.30
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (22 bp):
TAATTTTTTATATTTATTTTTA
Found at i:587092 original size:29 final size:29
Alignment explanation
Indices: 587034--587093 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 29
587024 AAGTAACTTA
** *
587034 ATATTTAATATTTATTTTTATAATTTTTT
1 ATATTTAATATTTATCATTATAATTCTTT
*
587063 ATATTT-ATATTTATCATTATTATATCTTT
1 ATATTTAATATTTATCATTATAAT-TCTTT
587092 AT
1 AT
587094 TGTTTTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 14 0.54
29 12 0.46
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (29 bp):
ATATTTAATATTTATCATTATAATTCTTT
Found at i:587734 original size:6 final size:6
Alignment explanation
Indices: 587723--587758 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
587713 TAGAAAAATA
*
587723 TATATT TATATT TATATT TACATT TATATT T-TATT T
1 TATATT TATATT TATATT TATATT TATATT TATATT T
587759 TACCAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (6 bp):
TATATT
Found at i:588150 original size:27 final size:27
Alignment explanation
Indices: 588099--588151 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
588089 CAATAAATTA
* *
588099 AAAAATACAAAAAATGAAAATAAAAAT
1 AAAAATACAAAAAAAGAAAAGAAAAAT
588126 AAAAATACAAAAAAA-AGAAAGAAAAA
1 AAAAATACAAAAAAAGA-AAAGAAAAA
588152 AATCGATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 1 0.04
27 22 0.96
ACGTcount: A:0.81, C:0.04, G:0.06, T:0.09
Consensus pattern (27 bp):
AAAAATACAAAAAAAGAAAAGAAAAAT
Found at i:593640 original size:8 final size:8
Alignment explanation
Indices: 593621--593699 Score: 126
Period size: 8 Copynumber: 10.0 Consensus size: 8
593611 ATACTATGCT
593621 TGAAAAAA
1 TGAAAAAA
593629 -GAAAAAA
1 TGAAAAAA
593636 TGAAAAAA
1 TGAAAAAA
593644 TGAAAAAA
1 TGAAAAAA
593652 TGAAAAAA
1 TGAAAAAA
593660 TGAAAAAA
1 TGAAAAAA
593668 TG-AAAAA
1 TGAAAAAA
593675 TGAAAAAA
1 TGAAAAAA
*
593683 TGAAAATGA
1 TGAAAA-AA
593692 TGAAAAAA
1 TGAAAAAA
593700 GGTGAACAAG
Statistics
Matches: 66, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
7 14 0.21
8 45 0.68
9 7 0.11
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.13
Consensus pattern (8 bp):
TGAAAAAA
Found at i:593650 original size:24 final size:24
Alignment explanation
Indices: 593621--593699 Score: 126
Period size: 23 Copynumber: 3.3 Consensus size: 24
593611 ATACTATGCT
593621 TGAAAAAA-GAAAAAATGAAAAAA
1 TGAAAAAATGAAAAAATGAAAAAA
593644 TGAAAAAATGAAAAAATGAAAAAA
1 TGAAAAAATGAAAAAATGAAAAAA
*
593668 TG-AAAAATGAAAAAATGAAAATGA
1 TGAAAAAATGAAAAAATGAAAA-AA
593692 TGAAAAAA
1 TGAAAAAA
593700 GGTGAACAAG
Statistics
Matches: 52, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
23 27 0.52
24 20 0.38
25 5 0.10
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.13
Consensus pattern (24 bp):
TGAAAAAATGAAAAAATGAAAAAA
Found at i:594839 original size:41 final size:41
Alignment explanation
Indices: 594720--595086 Score: 554
Period size: 41 Copynumber: 8.9 Consensus size: 41
594710 GTCTAGGAGT
594720 ATTTAC-TTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
594760 ATTTAC-TTTTCAAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTTC-AAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
594802 ATTTACTTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
*
594843 ATTTA-TTTTTCAAAGTTCCGTTGCCTCTGTTTAGTGGAGCA
1 ATTTACTTTTTCAAAGTT-CGTTGCCTCTGTTTAGAGGAGCA
594884 ATTTA-TTTTTCAAAGTTTCGTTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTTCAAAG-TTCGTTGCCTCTGTTTAGAGGAGCA
594925 ATTTACTTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
594966 ATTTA-TTTTTCAAAGTTCCGTTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTTCAAAGTT-CGTTGCCTCTGTTTAGAGGAGCA
*
595007 ATTTAC-TTTTCAAAG-TCGTGGTGCCTCTGTTGAGAGGAGCA
1 ATTTACTTTTTCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
*
595048 ATTTATTTTTTCAAAG-TCGTGGTGCCTCTGTTTAGAGGA
1 ATTTACTTTTTCAAAGTTCGT--TGCCTCTGTTTAGAGGA
595087 ACTTCGGCAA
Statistics
Matches: 309, Mismatches: 5, Indels: 24
0.91 0.01 0.07
Matches are distributed among these distances:
39 3 0.01
40 40 0.13
41 184 0.60
42 73 0.24
43 9 0.03
ACGTcount: A:0.22, C:0.16, G:0.21, T:0.41
Consensus pattern (41 bp):
ATTTACTTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
Found at i:595137 original size:30 final size:30
Alignment explanation
Indices: 595096--595180 Score: 136
Period size: 30 Copynumber: 2.8 Consensus size: 30
595086 AACTTCGGCA
*
595096 AAAAAAAAAAAAAAAAAAACAAAAAAAAAC
1 AAAAAAAAAAAACAAAAAACAAAAAAAAAC
595126 AAAACAAAAAAAACAAAAAA-AAAAAAAAAC
1 AAAA-AAAAAAAACAAAAAACAAAAAAAAAC
595156 AAAAAACAAAAAACAAAAAACAAAA
1 AAAAAA-AAAAAACAAAAAACAAAA
595181 TTTTTTTTAA
Statistics
Matches: 51, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
29 2 0.04
30 31 0.61
31 18 0.35
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (30 bp):
AAAAAAAAAAAACAAAAAACAAAAAAAAAC
Found at i:595145 original size:37 final size:37
Alignment explanation
Indices: 595094--595180 Score: 135
Period size: 37 Copynumber: 2.4 Consensus size: 37
595084 GGAACTTCGG
595094 CAAAAAAAA-AAAAAAAAAAAACAAA-AAAAAACAAAA
1 CAAAAAAAACAAAAAAAAAAAA-AAACAAAAAACAAAA
595130 CAAAAAAAACAAAAAAAAAAAAAAACAAAAAACAAAA
1 CAAAAAAAACAAAAAAAAAAAAAAACAAAAAACAAAA
595167 -AACAAAAAACAAAA
1 CAA-AAAAAACAAAA
595181 TTTTTTTTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
36 14 0.29
37 34 0.71
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (37 bp):
CAAAAAAAACAAAAAAAAAAAAAAACAAAAAACAAAA
Found at i:595198 original size:1 final size:1
Alignment explanation
Indices: 595095--595180 Score: 100
Period size: 1 Copynumber: 86.0 Consensus size: 1
595085 GAACTTCGGC
* * * * *
595095 AAAAAAAAAAAAAAAAAAAACAAAAAAAAACAAAACAAAAAAAACAAAAAAAAAAAAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
595160 AACAAAAAACAAAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAA
595181 TTTTTTTTAA
Statistics
Matches: 69, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 69 1.00
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:596137 original size:19 final size:20
Alignment explanation
Indices: 596113--596156 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
596103 TCCGGCCAAC
596113 TTCCGACG-AAATTTCCAGA
1 TTCCGACGAAAATTTCCAGA
596132 TTCCGACGAAAATTTCCAGA
1 TTCCGACGAAAATTTCCAGA
*
596152 ATCCG
1 TTCCG
596157 GCACCGGTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (20 bp):
TTCCGACGAAAATTTCCAGA
Found at i:596244 original size:23 final size:23
Alignment explanation
Indices: 596218--596263 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
596208 GAGAGAGAGG
596218 GGGAGGAGTGTTCTGCCGAAAAA
1 GGGAGGAGTGTTCTGCCGAAAAA
596241 GGGAGGAGTGTTCTGCCGAAAAA
1 GGGAGGAGTGTTCTGCCGAAAAA
596264 CAGAGGAAGG
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:0.30, C:0.13, G:0.39, T:0.17
Consensus pattern (23 bp):
GGGAGGAGTGTTCTGCCGAAAAA
Found at i:596269 original size:23 final size:23
Alignment explanation
Indices: 596220--596270 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
596210 GAGAGAGGGG
**
596220 GAGGAGTGTTCTGCCGAAAAAGG
1 GAGGAGTGTTCTGCCGAAAAACA
596243 GAGGAGTGTTCTGCCGAAAAACA
1 GAGGAGTGTTCTGCCGAAAAACA
596266 GAGGA
1 GAGGA
596271 AGGTGCCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.33, C:0.14, G:0.37, T:0.16
Consensus pattern (23 bp):
GAGGAGTGTTCTGCCGAAAAACA
Found at i:596543 original size:12 final size:13
Alignment explanation
Indices: 596507--596547 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
596497 GTTTTTTTTT
596507 TTTTATTTCTTT-
1 TTTTATTTCTTTA
* *
596519 GTTTATTTGTTTA
1 TTTTATTTCTTTA
596532 TTTTATTT-TTTA
1 TTTTATTTCTTTA
596544 TTTT
1 TTTT
596548 TTAGATTAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 18 0.72
13 7 0.28
ACGTcount: A:0.12, C:0.02, G:0.05, T:0.80
Consensus pattern (13 bp):
TTTTATTTCTTTA
Found at i:596931 original size:57 final size:57
Alignment explanation
Indices: 596628--597378 Score: 1080
Period size: 59 Copynumber: 12.7 Consensus size: 57
596618 AAAATTCTAA
*
596628 AAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTCA
1 AAAAA-ATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAA-TTTCC
*
596687 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAATAAATTTCC
1 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT---AG--AAATAAATTTCC
596749 AAAATAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
1 --AA-AAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
* * *
596809 AAAAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTCCTCATAAATAAATTTCAAA
1 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTC--C
596867 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
1 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
* * *
596924 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTCAAA
1 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTC--C
596983 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
1 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
*
597040 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
1 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
597097 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTA-AGAATAAATTTCC
1 --AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGA-AATAAATTTCC
597156 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAATAAATTTCC
1 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT---AG--AAATAAATTTCC
* *
597218 AAAAAAAGTATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
1 -AAAAAA-TATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
597277 AAAAAA-AGGGTTTTT-GAGGAAAAGTTGAAAGTATCAATTTTCCTT-GAAAATCGAAATTTCC
1 AAAAAATA---TTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTAG-AAAT--AAATTTCC
*
597338 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
597379 CTAAAAAAAA
Statistics
Matches: 639, Mismatches: 20, Indels: 66
0.88 0.03 0.09
Matches are distributed among these distances:
56 41 0.06
57 164 0.26
58 61 0.10
59 232 0.36
60 14 0.02
61 17 0.03
62 18 0.03
63 14 0.02
64 38 0.06
65 40 0.06
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.34
Consensus pattern (57 bp):
AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
Found at i:596973 original size:116 final size:117
Alignment explanation
Indices: 596626--597378 Score: 1146
Period size: 116 Copynumber: 6.4 Consensus size: 117
596616 AAAAAATTCT
* *
596626 AAAAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTCAAAAA
1 AAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAA-TTTCCAAAA
596691 AATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAATAAATTTCC
65 AATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC-T--AAG-AAAATAAATTT-C
*
596749 AAAATAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAAAA
1 AAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAAAA
* *
596814 ATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTCCTCA-TAAATAAATTTC
66 ATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTAAGAAAATAAATTTC
596864 AAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAAAA
1 AAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAAAA
*
596929 ATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAG-AAATAAATTTC
66 ATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTAAGAAAATAAATTTC
596980 AAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAAAA
1 AAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAAAA
*
597045 ATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAG-AAATAAATTTC
66 ATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTAAGAAAATAAATTTC
*
597096 CAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTA-AGAATAAATTTCCAAAA
1 AAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGA-AATAAATTTCCAAAA
*
597160 AATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAATAAATTTC
65 AATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC-T--AAG-AAAATAAATTTC
* * * *
597217 CAAAAAAAGTATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTCAAAAA
1 AAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAAAA
* *
597282 A-AGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT-TGAAAATCGAAATTTC
66 ATA---TTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTAAGAAAAT--AAATTTC
* *
597337 --CAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
597379 CTAAAAAAAA
Statistics
Matches: 598, Mismatches: 18, Indels: 33
0.92 0.03 0.05
Matches are distributed among these distances:
115 74 0.12
116 263 0.44
117 1 0.00
118 46 0.08
119 3 0.01
120 9 0.02
121 99 0.17
122 19 0.03
123 84 0.14
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (117 bp):
AAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAAAA
ATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTAAGAAAATAAATTTC
Found at i:597136 original size:27 final size:27
Alignment explanation
Indices: 597106--597194 Score: 65
Period size: 27 Copynumber: 3.2 Consensus size: 27
597096 CAAAAAAAAT
597106 ATTTTTAGGGAAAAGTTGAAAGTATCA
1 ATTTTTAGGGAAAAGTTGAAAGTATCA
* * * * **
597133 ATTTTCCTTAAGAATAAATTTCCAAAAAAT--
1 A-TTT--TTAGGGA-AAAGTT-GAAAGTATCA
597163 ATTTTTAGGGAAAAGTTGAAAGTATCA
1 ATTTTTAGGGAAAAGTTGAAAGTATCA
597190 ATTTT
1 ATTTT
597195 CCTTAAAAGA
Statistics
Matches: 43, Mismatches: 12, Indels: 14
0.62 0.17 0.20
Matches are distributed among these distances:
25 5 0.12
26 5 0.12
27 11 0.26
28 3 0.07
29 3 0.07
30 6 0.14
31 5 0.12
32 5 0.12
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.37
Consensus pattern (27 bp):
ATTTTTAGGGAAAAGTTGAAAGTATCA
Found at i:597921 original size:20 final size:20
Alignment explanation
Indices: 597870--597913 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
597860 ATATAAATAG
* *
597870 TTTTTTAATTATTTATTTAA
1 TTTTATAATTATTTATATAA
597890 TTTTATAATTATTTATATATA
1 TTTTATAATTATTTATATA-A
597911 TTT
1 TTT
597914 ATATTTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTATAATTATTTATATAA
Found at i:598163 original size:11 final size:11
Alignment explanation
Indices: 598147--598180 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
598137 AATTTGGGTT
598147 GTTCGTCGAAA
1 GTTCGTCGAAA
598158 GTTCGTCGAAAA
1 GTTCGTCG-AAA
*
598170 GTTCATCGAAA
1 GTTCGTCGAAA
598181 AATTCATCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (11 bp):
GTTCGTCGAAA
Found at i:598172 original size:12 final size:12
Alignment explanation
Indices: 598147--598181 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
598137 AATTTGGGTT
598147 GTTCGTCG-AAA
1 GTTCGTCGAAAA
598158 GTTCGTCGAAAA
1 GTTCGTCGAAAA
*
598170 GTTCATCGAAAA
1 GTTCGTCGAAAA
598182 ATTCATCGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 8 0.36
12 14 0.64
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (12 bp):
GTTCGTCGAAAA
Found at i:599161 original size:130 final size:126
Alignment explanation
Indices: 598996--599274 Score: 339
Period size: 125 Copynumber: 2.2 Consensus size: 126
598986 ATAAATATCT
* * * *
598996 AAATTATAAAAAAATTAATTTTAAATGACAAAAAGATATGTATTTAAGTTATATATATCTAAATT
1 AAATTATTAAAAAATTAATTTTAAAAGACAAAAAGATATATATTTAA---ATA-ATATATAAATT
** *
599061 ATTAGAAAATCAAT-TTAGGATAACTAATAAATTTTT-AATACTTTTATTTTTTTTATAAACACC
62 ATTA-AAAATCAATATT-GGATAACTAAT-AATTTTTAAATACTTTTATTCATTTGATAAACACC
599124 AT-
124 ATA
** *
599126 AAATTATTAGTAAATTAATTTTAAAAGATAAAAAGATATATATTTAAATAATATATAAATTATTA
1 AAATTATTAAAAAATTAATTTTAAAAGACAAAAAGATATATATTTAAATAATATATAAATTATTA
* * * * *
599191 AAAATTAATATTGGATAACTTATAATTTTTAAATATTTTTGTTCATTTGATAAATACCATA
66 AAAATCAATATTGGATAACTAATAATTTTTAAATACTTTTATTCATTTGATAAACACCATA
599252 AAATTATTAAAAAATTAATTTTA
1 AAATTATTAAAAAATTAATTTTA
599275 TGCGATAAAT
Statistics
Matches: 129, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
124 7 0.05
125 41 0.32
126 37 0.29
127 3 0.02
130 41 0.32
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.42
Consensus pattern (126 bp):
AAATTATTAAAAAATTAATTTTAAAAGACAAAAAGATATATATTTAAATAATATATAAATTATTA
AAAATCAATATTGGATAACTAATAATTTTTAAATACTTTTATTCATTTGATAAACACCATA
Found at i:599283 original size:126 final size:128
Alignment explanation
Indices: 598995--599274 Score: 345
Period size: 130 Copynumber: 2.2 Consensus size: 128
598985 GATAAATATC
* * * * *
598995 TAAATTATAAAAAAATTAATTTTAAATGACAAAAAGATATGTATTTAAGTTATATATATCTAAAT
1 TAAATTATTAAAAAATTAATTTTAAAAGATAAAAAGATATATATTTAA--TATATATATATAAAT
** *
599060 TATTAGAAAATCAATTTAGGATAACTAATAAATTTTTAATACTTTTATTTTTTTTATAAACACCA
64 TATTAGAAAATCAATTTAGGATAACTAATAAATTTTTAATACTTTTATTCATTTGATAAACACCA
**
599125 TAAATTATTAGTAAATTAATTTTAAAAGATAAAAAGATATATATTTAA-ATA-ATATATAAATTA
1 TAAATTATTAAAAAATTAATTTTAAAAGATAAAAAGATATATATTTAATATATATATATAAATTA
* * * * *
599188 TTA-AAAATTAATATT-GGATAACTTAT-AATTTTTAAATATTTTTGTTCATTTGATAAATACCA
66 TTAGAAAATCAAT-TTAGGATAACTAATAAATTTTT-AATACTTTTATTCATTTGATAAACACCA
599250 TAAAATTATTAAAAAATTAATTTTA
1 T-AAATTATTAAAAAATTAATTTTA
599275 TGCGATAAAT
Statistics
Matches: 130, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
124 7 0.05
125 41 0.32
126 37 0.28
127 3 0.02
130 42 0.32
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.42
Consensus pattern (128 bp):
TAAATTATTAAAAAATTAATTTTAAAAGATAAAAAGATATATATTTAATATATATATATAAATTA
TTAGAAAATCAATTTAGGATAACTAATAAATTTTTAATACTTTTATTCATTTGATAAACACCA
Found at i:599334 original size:21 final size:20
Alignment explanation
Indices: 599287--599325 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
599277 CGATAAATAA
*
599287 TATAAATTTGTTTTATTTAT
1 TATAAATATGTTTTATTTAT
599307 T-TAAATAT-TTTTATTTAT
1 TATAAATATGTTTTATTTAT
599325 T
1 T
599326 TGATAAATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 11 0.61
19 6 0.33
20 1 0.06
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (20 bp):
TATAAATATGTTTTATTTAT
Found at i:599360 original size:40 final size:38
Alignment explanation
Indices: 599316--599393 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 38
599306 TTTAAATATT
*
599316 TTTATTTATTTGATAAATACCACGTAAAATTATTAGAAAA
1 TTTATTTATTTGATAAATACCA--TAAAATTATTAAAAAA
*
599356 TTTATTTATTTGATAAATATCATAAAATTATTAAAAAA
1 TTTATTTATTTGATAAATACCATAAAATTATTAAAAAA
599394 AACTTTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 15 0.42
40 21 0.58
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (38 bp):
TTTATTTATTTGATAAATACCATAAAATTATTAAAAAA
Found at i:600427 original size:14 final size:14
Alignment explanation
Indices: 600393--600436 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
600383 GATTAAGGGG
*
600393 AGAAATAGATATAT
1 AGAAATATATATAT
* *
600407 TGAAAATATGTATAT
1 AG-AAATATATATAT
600422 AGAAATATATATAT
1 AGAAATATATATAT
600436 A
1 A
600437 TATATTATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (14 bp):
AGAAATATATATAT
Found at i:602498 original size:34 final size:33
Alignment explanation
Indices: 602460--602537 Score: 111
Period size: 33 Copynumber: 2.3 Consensus size: 33
602450 GAAAAAACAT
*
602460 AAAATTTTATAAACCCTTAAAATTAAATATATA
1 AAAATTTTATAAACCCTTAAAAATAAATATATA
* * *
602493 AAAAATTTACAAATCCTTAAAAATAAATATATA
1 AAAATTTTATAAACCCTTAAAAATAAATATATA
602526 AAAATTTATATA
1 AAAATTT-TATA
602538 CCACAAGTGC
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
33 35 0.92
34 3 0.08
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.35
Consensus pattern (33 bp):
AAAATTTTATAAACCCTTAAAAATAAATATATA
Found at i:606785 original size:30 final size:30
Alignment explanation
Indices: 606749--607296 Score: 272
Period size: 30 Copynumber: 17.3 Consensus size: 30
606739 TCAAAAATGA
* *
606749 AAGTGCAGACCAGGAGTTCAGCAAACAAGG
1 AAGTGCAGACCACGAGTTCAGCAGACAAGG
* * *
606779 AAGTGCAGACCACGATTTCCGCAGACCAGG
1 AAGTGCAGACCACGAGTTCAGCAGACAAGG
* *
606809 AAGGGCTAGCGCAGACCATGAGTTCAGCAAACAAGG
1 AA--G-T---GCAGACCACGAGTTCAGCAGACAAGG
* * *
606845 AAGTGCAGACCACTAGCTCCGCAGACAAGG
1 AAGTGCAGACCACGAGTTCAGCAGACAAGG
* * * *
606875 AAGTACAAACCACGAGTACTGCAGACAAGG
1 AAGTGCAGACCACGAGTTCAGCAGACAAGG
* * ** *
606905 AAGTACAAACGGCAAGTTCCA-CAGACAAGG
1 AAGTGCAGACCACGAGTT-CAGCAGACAAGG
* * *
606935 AAGCGCAGGCACAGACAACTAGTTCTGCAGACAAGG
1 AAGTGCA-G-AC---C-ACGAGTTCAGCAGACAAGG
*
606971 AAGTGCAGACCACGAGTTCCGCAGA-ACAGG
1 AAGTGCAGACCACGAGTTCAGCAGACA-AGG
* * *
607001 AAGTGCTAGCGCAGACCATGAGTTCAACAAACAAGG
1 AA--G-T---GCAGACCACGAGTTCAGCAGACAAGG
* *
607037 AAGTGCAGACCACTAGTTCCGCAGACAAGG
1 AAGTGCAGACCACGAGTTCAGCAGACAAGG
* * *
607067 AAGTACAAACCACGAGTTCTGCAGACAAGG
1 AAGTGCAGACCACGAGTTCAGCAGACAAGG
* * * * *
607097 AAGTACAAACCGCAAGTTCCGCAGACAAGG
1 AAGTGCAGACCACGAGTTCAGCAGACAAGG
* * * * *
607127 AAGCGCAAGCACAAACAACTAGTCCTGCGGACAAGG
1 AAGTGC-AG-AC---C-ACGAGTTCAGCAGACAAGG
* *
607163 AAGTGCAGGCGCAGGCCATGAGTTCAGCAAACAAGG
1 AAGTGCA---G-A--CCACGAGTTCAGCAGACAAGG
* * *
607199 AAGTGCAGACCGCAAGTTCCGCAGACAAGG
1 AAGTGCAGACCACGAGTTCAGCAGACAAGG
* * * * * * *
607229 TAGTACAAACCGCAAGTTCCGCAGACAAAG
1 AAGTGCAGACCACGAGTTCAGCAGACAAGG
* * * *
607259 AAGTACAAACCACAAGTTCCGCAGACAAGG
1 AAGTGCAGACCACGAGTTCAGCAGACAAGG
*
607289 AAGCGCAG
1 AAGTGCAG
607297 GCACAGACAA
Statistics
Matches: 403, Mismatches: 82, Indels: 66
0.73 0.15 0.12
Matches are distributed among these distances:
29 1 0.00
30 269 0.67
31 3 0.01
32 7 0.02
33 5 0.01
34 4 0.01
35 4 0.01
36 104 0.26
37 2 0.00
38 3 0.01
40 1 0.00
ACGTcount: A:0.37, C:0.25, G:0.26, T:0.11
Consensus pattern (30 bp):
AAGTGCAGACCACGAGTTCAGCAGACAAGG
Done.