Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015131.1 Kokia drynarioides strain JFW-HI SEQ_130175, 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: 745397
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 719 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:589 original size:18 final size:19
Alignment explanation
Indices: 560--595 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
550 TTAGAATATG
560 AAATTGTAAATTTATTTAA
1 AAATTGTAAATTTATTTAA
579 AAATT-TAAATTTATTTA
1 AAATTGTAAATTTATTTA
596 TCATTTACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
AAATTGTAAATTTATTTAA
Found at i:5961 original size:8 final size:8
Alignment explanation
Indices: 5944--5974 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
5934 CCTTTTACTA
*
5944 TATATTTG
1 TATATATG
5952 TATATATG
1 TATATATG
5960 TATATATG
1 TATATATG
5968 TATATAT
1 TATATAT
5975 AGCAAACCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (8 bp):
TATATATG
Found at i:11187 original size:40 final size:41
Alignment explanation
Indices: 11130--11211 Score: 139
Period size: 40 Copynumber: 2.0 Consensus size: 41
11120 CGGACTTAAC
11130 CTATAAGCAAAAAATTAAACAAGTTAAGAACCAATATATGAT
1 CTATAAG-AAAAAATTAAACAAGTTAAGAACCAATATATGAT
*
11172 CTATAAG-AAAAATTAACCAAGTTAAGAACCAATATATGAT
1 CTATAAGAAAAAATTAAACAAGTTAAGAACCAATATATGAT
11212 TTATGCCTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
40 32 0.82
42 7 0.18
ACGTcount: A:0.54, C:0.12, G:0.10, T:0.24
Consensus pattern (41 bp):
CTATAAGAAAAAATTAAACAAGTTAAGAACCAATATATGAT
Found at i:11409 original size:17 final size:17
Alignment explanation
Indices: 11355--11447 Score: 91
Period size: 17 Copynumber: 5.4 Consensus size: 17
11345 ATAGCACATC
11355 TGCGAGCTCACCCAAAGA
1 TGCGAGCTCA-CCAAAGA
* *
11373 TGCCAGCTCAGCAAAGA
1 TGCGAGCTCACCAAAGA
11390 TGCGAGCTCACCAACA-A
1 TGCGAGCTCACCAA-AGA
* *
11407 TGCGAGCTCGCCAAAGT
1 TGCGAGCTCACCAAAGA
* *
11424 TGCGAAG-TAACCAAAGG
1 TGCG-AGCTCACCAAAGA
11441 TGCGAGC
1 TGCGAGC
11448 ACTGTTAGAC
Statistics
Matches: 62, Mismatches: 9, Indels: 9
0.77 0.11 0.11
Matches are distributed among these distances:
16 3 0.05
17 47 0.76
18 12 0.19
ACGTcount: A:0.32, C:0.29, G:0.26, T:0.13
Consensus pattern (17 bp):
TGCGAGCTCACCAAAGA
Found at i:19847 original size:3 final size:3
Alignment explanation
Indices: 19839--19868 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
19829 GGATTCGTAT
*
19839 TCA TCA TCA TCA TCA TCA TCT TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
19869 AAAGAAGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.37
Consensus pattern (3 bp):
TCA
Found at i:25465 original size:24 final size:24
Alignment explanation
Indices: 25437--25495 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
25427 TAGACTAATA
*
25437 AGAGTTTGACTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
* *
25461 AGAGTTTAATTGAAACAATTAAAC
1 AGAGTTTAACTGAAACAAATAAAC
*
25485 AAAGTTTAACT
1 AGAGTTTAACT
25496 AAAAGATTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.27
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:29857 original size:24 final size:24
Alignment explanation
Indices: 29792--29858 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
29782 AATCTAGACT
* *
29792 AATAAGAGTTTGACTCAAACAAATA
1 AATAA-AGTTTAACTGAAACAAATA
* * *
29817 AACAAAGTTTAATTGAAACAATTA
1 AATAAAGTTTAACTGAAACAAATA
29841 AATAAAGTTTAACTGAAA
1 AATAAAGTTTAACTGAAA
29859 GATTATTTCT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
24 31 0.89
25 4 0.11
ACGTcount: A:0.54, C:0.09, G:0.10, T:0.27
Consensus pattern (24 bp):
AATAAAGTTTAACTGAAACAAATA
Found at i:30918 original size:16 final size:16
Alignment explanation
Indices: 30899--30957 Score: 50
Period size: 16 Copynumber: 3.6 Consensus size: 16
30889 TTATTTTTTA
30899 ATTTTTTTATTTTAAT
1 ATTTTTTTATTTTAAT
** *
30915 ATTTAATAATTTT-AT
1 ATTTTTTTATTTTAAT
30930 ATATTTTTTATTTATTAA-
1 AT-TTTTTTA-TT-TTAAT
30948 ATTTTTTTAT
1 ATTTTTTTAT
30958 ATAGTCATAT
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
15 4 0.12
16 15 0.45
17 9 0.27
18 4 0.12
19 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
ATTTTTTTATTTTAAT
Found at i:30924 original size:24 final size:23
Alignment explanation
Indices: 30897--30957 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 23
30887 TATTATTTTT
30897 TAATTTTTTTATTTTAATATTTAA
1 TAATTTTTTTATTTT-ATATTTAA
* * *
30921 TAATTTTATATATTTTTTATTTAT
1 TAATTTT-TTTATTTTATATTTAA
30945 TAAATTTTTTTAT
1 T-AATTTTTTTAT
30958 ATAGTCATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
24 18 0.58
25 13 0.42
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (23 bp):
TAATTTTTTTATTTTATATTTAA
Found at i:35543 original size:9 final size:9
Alignment explanation
Indices: 35509--35535 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
35499 TTGCTTTATC
35509 TCACATTTG
1 TCACATTTG
35518 TCACATTTG
1 TCACATTTG
35527 TCACATTTG
1 TCACATTTG
35536 GTCCATTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.44
Consensus pattern (9 bp):
TCACATTTG
Found at i:46696 original size:8 final size:8
Alignment explanation
Indices: 46672--46740 Score: 50
Period size: 9 Copynumber: 7.9 Consensus size: 8
46662 TTAAAATTGA
*
46672 TATAAACT
1 TATAAAAT
46680 TACTAAAAT
1 TA-TAAAAT
46689 TATAAAATAT
1 TAT-AAA-AT
*
46699 TATAAAAA
1 TATAAAAT
46707 TATAATAAT
1 TATAA-AAT
46716 GTA-ATAAAT
1 -TATA-AAAT
46725 TATAAAAT
1 TATAAAAT
46733 TAATAAAA
1 T-ATAAAA
46741 ACTTATTCAA
Statistics
Matches: 50, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
8 16 0.32
9 26 0.52
10 8 0.16
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (8 bp):
TATAAAAT
Found at i:46738 original size:16 final size:17
Alignment explanation
Indices: 46685--46739 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 17
46675 AAACTTACTA
*
46685 AAATTATAAAATATTAT
1 AAATTATAAAATATAAT
* *
46702 AAAAATATAATAATGTAAT
1 -AAATTATAA-AATATAAT
46721 AAATTATAAAAT-TAAT
1 AAATTATAAAATATAAT
46737 AAA
1 AAA
46740 AACTTATTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 7 0.22
17 3 0.09
18 16 0.50
19 6 0.19
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (17 bp):
AAATTATAAAATATAAT
Found at i:46836 original size:10 final size:9
Alignment explanation
Indices: 46803--46854 Score: 52
Period size: 9 Copynumber: 5.6 Consensus size: 9
46793 TAAAACTTGT
46803 TAAAAATTA
1 TAAAAATTA
*
46812 TAAAAAAATA
1 T-AAAAATTA
46822 TTAAAAA-TA
1 -TAAAAATTA
*
46831 TATAAATTTA
1 TA-AAAATTA
46841 TAAAAATTA
1 TAAAAATTA
46850 TAAAA
1 TAAAA
46855 GAAAAAGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
8 2 0.06
9 17 0.47
10 16 0.44
11 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
TAAAAATTA
Found at i:47261 original size:10 final size:10
Alignment explanation
Indices: 47246--47388 Score: 56
Period size: 10 Copynumber: 15.3 Consensus size: 10
47236 CCAATTCAAG
*
47246 TTTTTATGAT
1 TTTTTATAAT
47256 TTTTTAT--T
1 TTTTTATAAT
* *
47264 GTTTTATAAA
1 TTTTTATAAT
*
47274 TTTATATAAT
1 TTTTTATAAT
* *
47284 TTTTAAT-AC
1 TTTTTATAAT
*
47293 TTTTTATGAT
1 TTTTTATAAT
47303 TTTTATATAA-
1 TTTT-TATAAT
47313 --TTT-TAAT
1 TTTTTATAAT
**
47320 ACTTTATAAT
1 TTTTTATAAT
*
47330 TTTTTATACT
1 TTTTTATAAT
* *
47340 TTATTAGAA-
1 TTTTTATAAT
*
47349 TTTTTAT-GT
1 TTTTTATAAT
*
47358 TTTTAATAA-
1 TTTTTATAAT
*
47367 TATTTATAA-
1 TTTTTATAAT
*
47376 TATTTATAAT
1 TTTTTATAAT
47386 TTT
1 TTT
47389 ATAAAATTAT
Statistics
Matches: 97, Mismatches: 25, Indels: 22
0.67 0.17 0.15
Matches are distributed among these distances:
6 3 0.03
7 1 0.01
8 9 0.09
9 37 0.38
10 43 0.44
11 4 0.04
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.63
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:47287 original size:19 final size:20
Alignment explanation
Indices: 47265--47315 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
47255 TTTTTTATTG
47265 TTTTATA-AATTTATATAAT
1 TTTTATATAATTTATATAAT
* * *
47284 TTTTA-ATACTTTTTATGAT
1 TTTTATATAATTTATATAAT
47303 TTTTATATAATTT
1 TTTTATATAATTT
47316 TAATACTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 1 0.04
19 19 0.73
20 6 0.23
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTTATATAATTTATATAAT
Found at i:47298 original size:29 final size:29
Alignment explanation
Indices: 47265--47324 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
47255 TTTTTTATTG
47265 TTTTAT-AAATTTATATAATTTTTAATACT
1 TTTTATGAAATTTATATAA-TTTTAATACT
**
47294 TTTTATGATTTTTATATAATTTTAATACT
1 TTTTATGAAATTTATATAATTTTAATACT
47323 TT
1 TT
47325 ATAATTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 18 0.64
30 10 0.36
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (29 bp):
TTTTATGAAATTTATATAATTTTAATACT
Found at i:47299 original size:47 final size:47
Alignment explanation
Indices: 47246--47374 Score: 131
Period size: 46 Copynumber: 2.7 Consensus size: 47
47236 CCAATTCAAG
47246 TTTTTATGATTTTTTATTGTTTTATAAATTTATATAATTTTTAATAC
1 TTTTTATGATTTTTTATTGTTTTATAAATTTATATAATTTTTAATAC
** * * *
47293 TTTTTATGATTTTTATATAATTTTA-ATACTT-TATAATTTTTTATAC
1 TTTTTATGATTTTT-TATTGTTTTATAAATTTATATAATTTTTAATAC
*
47339 TTTATTA-GAATTTTTA-TGTTTTTAATAATATTTATA
1 TTT-TTATGATTTTTTATTG-TTTT-ATAA-ATTTATA
47375 ATATTTATAA
Statistics
Matches: 65, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
45 6 0.09
46 24 0.37
47 22 0.34
48 11 0.17
49 2 0.03
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (47 bp):
TTTTTATGATTTTTTATTGTTTTATAAATTTATATAATTTTTAATAC
Found at i:47316 original size:19 final size:19
Alignment explanation
Indices: 47265--47446 Score: 61
Period size: 18 Copynumber: 9.9 Consensus size: 19
47255 TTTTTTATTG
47265 TTTTATA-AATTTATATAAT
1 TTTTATATAATTT-TATAAT
* *
47284 TTTTA-ATACTTTTTATGAT
1 TTTTATATA-ATTTTATAAT
*
47303 TTTTATATAATTTTAATACT
1 TTTTATATAATTTT-ATAAT
* * *
47323 TTATA-AT-TTTTTATACT
1 TTTTATATAATTTTATAAT
* * *
47340 TTAT-TAGAATTTT-TATGT
1 TTTTATATAATTTTATA-AT
47358 TTTTA-ATAATATTTATAA-
1 TTTTATATAAT-TTTATAAT
*
47376 TATT-TATAATTTTATAA-
1 TTTTATATAATTTTATAAT
**
47393 AATTATATCAATTTTCAT-AT
1 TTTTATAT-AATTTT-ATAAT
*
47413 TTTT-TCAT-ATTTAATAAT
1 TTTTAT-ATAATTTTATAAT
*
47431 ATTTATAT--TTTTATAA
1 TTTTATATAATTTTATAA
47447 AGATTTTCTA
Statistics
Matches: 125, Mismatches: 20, Indels: 38
0.68 0.11 0.21
Matches are distributed among these distances:
17 31 0.25
18 39 0.31
19 34 0.27
20 21 0.17
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (19 bp):
TTTTATATAATTTTATAAT
Found at i:47329 original size:16 final size:17
Alignment explanation
Indices: 47308--47343 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
47298 ATGATTTTTA
47308 TATAA-TTTTAATACTT
1 TATAATTTTTAATACTT
*
47324 TATAATTTTTTATACTT
1 TATAATTTTTAATACTT
47341 TAT
1 TAT
47344 TAGAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (17 bp):
TATAATTTTTAATACTT
Found at i:47334 original size:29 final size:30
Alignment explanation
Indices: 47274--47337 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
47264 GTTTTATAAA
*
47274 TTTATATAATTTTTAATACTTTTTATGATT
1 TTTATATAATTTTTAATACTTTTAATGATT
47304 TTTATATAA-TTTTAATACTTTATAAT--TT
1 TTTATATAATTTTTAATACTTT-TAATGATT
47332 TTTATA
1 TTTATA
47338 CTTTATTAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 8 0.25
29 12 0.38
30 12 0.38
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (30 bp):
TTTATATAATTTTTAATACTTTTAATGATT
Found at i:47375 original size:9 final size:9
Alignment explanation
Indices: 47363--47446 Score: 61
Period size: 9 Copynumber: 9.4 Consensus size: 9
47353 TATGTTTTTA
47363 ATAATATTT
1 ATAATATTT
47372 ATAATATTT
1 ATAATATTT
47381 ATAAT-TTT
1 ATAATATTT
*
47389 ATAAAATTAT
1 ATAATATT-T
47399 ATCAAT-TTT
1 AT-AATATTT
47408 CAT-AT-TTT
1 -ATAATATTT
* *
47416 TTCATATTT
1 ATAATATTT
47425 AATAATATTT
1 -ATAATATTT
*
47435 AT-ATTTTT
1 ATAATATTT
47443 ATAA
1 ATAA
47447 AGATTTTCTA
Statistics
Matches: 61, Mismatches: 6, Indels: 16
0.73 0.07 0.19
Matches are distributed among these distances:
7 1 0.02
8 21 0.34
9 23 0.38
10 14 0.23
11 2 0.03
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (9 bp):
ATAATATTT
Found at i:47654 original size:22 final size:23
Alignment explanation
Indices: 47620--47664 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
47610 TGATAAGAGA
47620 TTTAATTGATTTT-TTTACATTT
1 TTTAATTGATTTTCTTTACATTT
*
47642 TTTAATT-ACTTTTCTTTATATTT
1 TTTAATTGA-TTTTCTTTACATTT
47665 AAGCCATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 1 0.05
22 11 0.55
23 8 0.40
ACGTcount: A:0.22, C:0.07, G:0.02, T:0.69
Consensus pattern (23 bp):
TTTAATTGATTTTCTTTACATTT
Found at i:47682 original size:7 final size:7
Alignment explanation
Indices: 47670--47694 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
47660 TATTTAAGCC
47670 ATTGGAA
1 ATTGGAA
47677 ATTGGAA
1 ATTGGAA
47684 ATTGGAA
1 ATTGGAA
47691 ATTG
1 ATTG
47695 TCATTAATTT
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:0.40, C:0.00, G:0.28, T:0.32
Consensus pattern (7 bp):
ATTGGAA
Found at i:56137 original size:24 final size:24
Alignment explanation
Indices: 56098--56160 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
56088 TAGACTAATA
* * *
56098 AGAATTTGACTCAAACAACTAAAC
1 AGAATTTAACTGAAACAAATAAAC
*
56122 AGAATTTAATTGAAACAAATAAAC
1 AGAATTTAACTGAAACAAATAAAC
*
56146 AGAGTTTAACTGAAA
1 AGAATTTAACTGAAA
56161 AATTATTTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.52, C:0.13, G:0.11, T:0.24
Consensus pattern (24 bp):
AGAATTTAACTGAAACAAATAAAC
Found at i:58173 original size:24 final size:24
Alignment explanation
Indices: 58146--58219 Score: 103
Period size: 24 Copynumber: 3.1 Consensus size: 24
58136 ATTTGACTCG
*
58146 AACAACTAAACAGAATTTAATTGA
1 AACAAATAAACAGAATTTAATTGA
* *
58170 AACAAATAAATAGAGTTTAATTGA
1 AACAAATAAACAGAATTTAATTGA
* *
58194 AACAAATAAACAAAATTTAACTGA
1 AACAAATAAACAGAATTTAATTGA
58218 AA
1 AA
58220 GATTATTTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.58, C:0.09, G:0.08, T:0.24
Consensus pattern (24 bp):
AACAAATAAACAGAATTTAATTGA
Found at i:62287 original size:23 final size:22
Alignment explanation
Indices: 62268--62308 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
62258 AAAGGTTTGC
62268 CAAAT-CAATAAAAATGGG-TT
1 CAAATACAATAAAAATGGGTTT
62288 CAAATAACAATAAAAATGGGT
1 CAAAT-ACAATAAAAATGGGT
62309 AAATTACTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
22 13 0.72
ACGTcount: A:0.54, C:0.10, G:0.15, T:0.22
Consensus pattern (22 bp):
CAAATACAATAAAAATGGGTTT
Found at i:62621 original size:16 final size:16
Alignment explanation
Indices: 62600--62633 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
62590 TAGAGATCAA
62600 ATCAAAAGAAGTGCAT
1 ATCAAAAGAAGTGCAT
62616 ATCAAAAGAAGTGCAT
1 ATCAAAAGAAGTGCAT
62632 AT
1 AT
62634 AAATGGGGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.18, T:0.21
Consensus pattern (16 bp):
ATCAAAAGAAGTGCAT
Found at i:71141 original size:4 final size:4
Alignment explanation
Indices: 71116--71208 Score: 96
Period size: 4 Copynumber: 23.2 Consensus size: 4
71106 TGCAAGTAAA
* * * * * *
71116 ACAT AGAT AAAT ACAG ACAT ACAT ACAT GCAT ACAT AAAT ACAT GCAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * *
71164 GCAT GCAT GCAT GCAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
71209 TATTCAAAGA
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 78 1.00
ACGTcount: A:0.46, C:0.22, G:0.09, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:77265 original size:75 final size:74
Alignment explanation
Indices: 77143--77291 Score: 208
Period size: 75 Copynumber: 2.0 Consensus size: 74
77133 CGAGCCTGTC
* ** *
77143 TGGCGAACTCCACTGTAAGACCTGCATGCATCCTACTAGTAAGATCCAACCAGGTCGTAGGTAGA
1 TGGCGAACCCCACTGTAAGACCCACATGCATCCTACTAATAAGATCCAACCAGGTCGTAGGTAGA
77208 CAATCCGAA
66 CAATCCGAA
* * * *
77217 TGGCGAACCCCCACTGTAAGACCCACATGTATCTTACTAATAGGATCCAATCAGGTCGTAGGTAG
1 TGGCGAA-CCCCACTGTAAGACCCACATGCATCCTACTAATAAGATCCAACCAGGTCGTAGGTAG
*
77282 ACGATCCGAA
65 ACAATCCGAA
77292 ATATACCCAG
Statistics
Matches: 65, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
74 7 0.11
75 58 0.89
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.21
Consensus pattern (74 bp):
TGGCGAACCCCACTGTAAGACCCACATGCATCCTACTAATAAGATCCAACCAGGTCGTAGGTAGA
CAATCCGAA
Found at i:78163 original size:30 final size:30
Alignment explanation
Indices: 78119--78199 Score: 76
Period size: 30 Copynumber: 2.7 Consensus size: 30
78109 AAATTTTAAA
* * * *
78119 TTAATAATAGTAAAATTATACTTT-AATTCT
1 TTAAAAATAATAAAATTATAATTTAAACT-T
78149 TTAAAAATAATAAAAATT-TAATTTAAACTT
1 TTAAAAATAAT-AAAATTATAATTTAAACTT
* *
78179 TTAAAAATTATAAAAATATAA
1 TTAAAAATAATAAAATTATAA
78200 ATAATTAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
29 5 0.12
30 28 0.67
31 9 0.21
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (30 bp):
TTAAAAATAATAAAATTATAATTTAAACTT
Found at i:86128 original size:22 final size:21
Alignment explanation
Indices: 86093--86139 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
86083 CGATCTAAGG
86093 AAAAATAAAATAAACAAAATT
1 AAAAATAAAATAAACAAAATT
* *
86114 AAAAATAAAAGTAAATAGAATT
1 AAAAATAAAA-TAAACAAAATT
86136 AAAA
1 AAAA
86140 GAAATAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.19
Consensus pattern (21 bp):
AAAAATAAAATAAACAAAATT
Found at i:86146 original size:15 final size:16
Alignment explanation
Indices: 86119--86148 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
86109 AAATTAAAAA
86119 TAAAAGTAAATAGAAT
1 TAAAAGTAAATAGAAT
86135 TAAAAG-AAATAGAA
1 TAAAAGTAAATAGAA
86149 AATAAGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.67, C:0.00, G:0.13, T:0.20
Consensus pattern (16 bp):
TAAAAGTAAATAGAAT
Found at i:88624 original size:14 final size:14
Alignment explanation
Indices: 88605--88633 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
88595 TTCTTGTTTC
88605 TTTCTTGATAGGTT
1 TTTCTTGATAGGTT
88619 TTTCTTGATAGGTT
1 TTTCTTGATAGGTT
88633 T
1 T
88634 AACATAGCTT
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:0.14, C:0.07, G:0.21, T:0.59
Consensus pattern (14 bp):
TTTCTTGATAGGTT
Found at i:91404 original size:19 final size:21
Alignment explanation
Indices: 91361--91404 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
91351 AAAATTAATA
*
91361 ATTTTATTTAATTGATTCATG
1 ATTTTATTAAATTGATTCATG
91382 -TTTTATTAAATT-ATT-ATG
1 ATTTTATTAAATTGATTCATG
91400 ATTTT
1 ATTTT
91405 TTAGCAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 3 0.14
19 7 0.33
20 11 0.52
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.61
Consensus pattern (21 bp):
ATTTTATTAAATTGATTCATG
Found at i:102663 original size:153 final size:153
Alignment explanation
Indices: 102308--102762 Score: 864
Period size: 153 Copynumber: 3.0 Consensus size: 153
102298 TTTTGAATGC
*
102308 TAGCTCTTATAATTTGTGCTGATGC-AAATAAAATTAAATTAAATCATTATGGTTTTATTATGTC
1 TAGCTCTTATAATTTGTGCTGATACAAAATAAAATTAAATTAAATCATTATGGTTTTATTATGTC
102372 CTTAACATAATGGTTAACATGGAACAATTTGGTTTAGCAGCATGGAAATCCTAATCCTGCAAAG-
66 CTTAACATAATGGTTAACATGGAACAATTTGGTTTAGCAGCATGGAAATCCTAATCCTGCAAAGT
102436 --TGTATCTACATCAACATCTCA
131 ACTGTATCTACATCAACATCTCA
*
102457 TAGCTCTTATAATTTGTGCTGATACAAAATAAAATTAAATTAAATCATTATGGTTTTGTTATGTC
1 TAGCTCTTATAATTTGTGCTGATACAAAATAAAATTAAATTAAATCATTATGGTTTTATTATGTC
102522 CTTAACATAATGGTTAACATGGAACAATTTGGTTTAGCAGCATGGAAATCCTAATCCTGCAAAGT
66 CTTAACATAATGGTTAACATGGAACAATTTGGTTTAGCAGCATGGAAATCCTAATCCTGCAAAGT
102587 ACTGTATCTACATCAACATCTCA
131 ACTGTATCTACATCAACATCTCA
102610 TAGCTCTTATAATTTGTGCTGATACAAAATAAAATTAAATTAAATCATTATGGTTTTATTATGTC
1 TAGCTCTTATAATTTGTGCTGATACAAAATAAAATTAAATTAAATCATTATGGTTTTATTATGTC
102675 CTTAACATAATGGTTAACATGGAACAATTTGGTTTAGCAGCATGGAAATCCTAATCCTGCAAAGT
66 CTTAACATAATGGTTAACATGGAACAATTTGGTTTAGCAGCATGGAAATCCTAATCCTGCAAAGT
102740 ACTGTATCTACATCAACATCTCA
131 ACTGTATCTACATCAACATCTCA
102763 CCGACACAAT
Statistics
Matches: 299, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
149 24 0.08
150 102 0.34
153 173 0.58
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (153 bp):
TAGCTCTTATAATTTGTGCTGATACAAAATAAAATTAAATTAAATCATTATGGTTTTATTATGTC
CTTAACATAATGGTTAACATGGAACAATTTGGTTTAGCAGCATGGAAATCCTAATCCTGCAAAGT
ACTGTATCTACATCAACATCTCA
Found at i:109193 original size:16 final size:14
Alignment explanation
Indices: 109166--109203 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
109156 CACTAGTCGG
109166 TAAAAAAATTATAT
1 TAAAAAAATTATAT
109180 TAAAAAATATT-TA-
1 TAAAAAA-ATTATAT
109193 TAAAAAAATTA
1 TAAAAAAATTA
109204 CAAAGCAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 3 0.14
13 7 0.32
14 9 0.41
15 3 0.14
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
TAAAAAAATTATAT
Found at i:110364 original size:21 final size:22
Alignment explanation
Indices: 110339--110388 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
110329 CCAAATCATG
* *
110339 TTTATTTATTATTTT-TGAATT
1 TTTATATAATATTTTATGAATT
*
110360 TTTATATAATATTTTATGAAGTA
1 TTTATATAATATTTTATGAA-TT
110383 TTTATA
1 TTTATA
110389 CATTCATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 13 0.54
22 4 0.17
23 7 0.29
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (22 bp):
TTTATATAATATTTTATGAATT
Found at i:114619 original size:31 final size:32
Alignment explanation
Indices: 114579--114638 Score: 97
Period size: 31 Copynumber: 1.9 Consensus size: 32
114569 GATAAAAGTG
114579 AAACAACATAATAAAAAAA-TATTAGAAAAAAA
1 AAACAACATAATAAAAAAATTATTA-AAAAAAA
114611 AAAC-ACATAATAAAAAAATTATTAAAAA
1 AAACAACATAATAAAAAAATTATTAAAAA
114639 TCTAAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
31 18 0.67
32 9 0.33
ACGTcount: A:0.73, C:0.07, G:0.02, T:0.18
Consensus pattern (32 bp):
AAACAACATAATAAAAAAATTATTAAAAAAAA
Found at i:114685 original size:13 final size:13
Alignment explanation
Indices: 114667--114692 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
114657 AATTCACTTT
114667 TATTATTTTTTAA
1 TATTATTTTTTAA
114680 TATTATTTTTTAA
1 TATTATTTTTTAA
114693 AATTTTTATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TATTATTTTTTAA
Found at i:114983 original size:15 final size:15
Alignment explanation
Indices: 114963--114999 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
114953 CTTTATTTAT
114963 ATTTCAAAAATCATC
1 ATTTCAAAAATCATC
114978 ATTTCAAAAATCATC
1 ATTTCAAAAATCATC
114993 ATTTCAA
1 ATTTCAA
115000 TTCGGATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (15 bp):
ATTTCAAAAATCATC
Found at i:115140 original size:24 final size:25
Alignment explanation
Indices: 115113--115161 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
115103 GATTTTAGAA
115113 ATTTT-TTTTTTATAAA-ATAATTTT
1 ATTTTATTTTTT-TAAATATAATTTT
*
115137 ATTTTATTTTTTTAAATATATTTTT
1 ATTTTATTTTTTTAAATATAATTTT
115162 TAAATTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (25 bp):
ATTTTATTTTTTTAAATATAATTTT
Found at i:115168 original size:28 final size:27
Alignment explanation
Indices: 115091--115168 Score: 65
Period size: 28 Copynumber: 2.9 Consensus size: 27
115081 ATTTGGTTCA
* **
115091 TTTTTTAAATTTGATTTTAGAAATTTTT
1 TTTTTTAAATAT-ATTTTTTAAATTTTT
*
115119 TTTTTATAAA-ATA-ATTTT--ATTTTAT
1 TTTTT-TAAATATATTTTTTAAATTTT-T
115144 TTTTTTAAATATATTTTTTAAATTT
1 TTTTTTAAATATATTTTTTAAATTT
115169 ATATGAATAC
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
24 9 0.23
25 9 0.23
26 6 0.15
27 1 0.03
28 10 0.26
29 4 0.10
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (27 bp):
TTTTTTAAATATATTTTTTAAATTTTT
Found at i:119704 original size:28 final size:26
Alignment explanation
Indices: 119660--119718 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
119650 ATATTTATAT
119660 TATATTATTTTAATATTTAATAATTTTA
1 TATATTATTTTAATA-TTAA-AATTTTA
* *
119688 TATATT-TTTTATTTATTAAAATTTTT
1 TATATTATTTTA-ATATTAAAATTTTA
119714 TATAT
1 TATAT
119719 AGTTATCTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 11 0.39
27 9 0.32
28 8 0.29
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (26 bp):
TATATTATTTTAATATTAAAATTTTA
Found at i:119823 original size:18 final size:17
Alignment explanation
Indices: 119797--119831 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
119787 AATGCGTTCT
*
119797 AAATTACATAATATATAA
1 AAATAACATAATA-ATAA
119815 AAATAACATAATAATAA
1 AAATAACATAATAATAA
119832 GTTATGATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
AAATAACATAATAATAA
Found at i:127801 original size:16 final size:18
Alignment explanation
Indices: 127777--127813 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
127767 AATTTTATCA
*
127777 TTATTAATT-TAAAAT-T
1 TTATAAATTATAAAATAT
127793 TTATAAATTATAAAATAT
1 TTATAAATTATAAAATAT
127811 TTA
1 TTA
127814 AATGAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 8 0.44
17 6 0.33
18 4 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTATAAATTATAAAATAT
Found at i:130548 original size:126 final size:126
Alignment explanation
Indices: 130386--130914 Score: 611
Period size: 126 Copynumber: 4.2 Consensus size: 126
130376 GAGAGATAGT
* * * * * *** *
130386 GATGGTGATGGTGAAATGCTTGATGAAAATAGATCTACTGGTTCTCATAGTGAGGAGCAAAATCA
1 GATGGTGATGGTGATATGGTTGATGAAAGTAGATCTACTGATTCTCATAGCGAGGAGCACGGTGA
* * * * ** * * *
130451 GCACTTATCGGTAGAAGGGCGACGTAATGGTTGCTATGAGAAGGAACAAAATGCATCCAGA
66 GAACTTATCGGTAGAAGGCCAACATAATGGACGCTATGAGAAAGATCAAAATACATCCAGA
* * * ** * *
130512 GATAGTGATGGCGATATGCTTGATGAACA-TAGATCTACTGATTCTTGTAGCAAGGAGCACGCTG
1 GATGGTGATGGTGATATGGTTGATGAA-AGTAGATCTACTGATTCTCATAGCGAGGAGCACGGTG
* *
130576 AGAACCTATCGGTAGAAGGCCAACATAATGGACGCTATGAGAAAGATCAAAATACTTCCAGA
65 AGAACTTATCGGTAGAAGGCCAACATAATGGACGCTATGAGAAAGATCAAAATACATCCAGA
* *
130638 GATGGTGATGGTGATATGGTTGATGAAAGTAGGTCTATTGATTCTCATAGCGAGGAGCACGGTGA
1 GATGGTGATGGTGATATGGTTGATGAAAGTAGATCTACTGATTCTCATAGCGAGGAGCACGGTGA
* * *
130703 GAACTTATCGGCT-GAAGGCCAACGTAATGGACGCTATGAGAAACATCAAAATACTTCCAGA
66 GAACTTATCGG-TAGAAGGCCAACATAATGGACGCTATGAGAAAGATCAAAATACATCCAGA
* * *
130764 GATGGTGATGGTGATATGGTTGATGAAAGTAGGTCTATTGATTCTCATAGTGAGGAGCACGGTGA
1 GATGGTGATGGTGATATGGTTGATGAAAGTAGATCTACTGATTCTCATAGCGAGGAGCACGGTGA
* * * ** * *
130829 GGACTTATCGGTAGAAGG---ACATAATGGTA-GCAAAGAGGCAGATCAAATTGCATCCAGA
66 GAACTTATCGGTAGAAGGCCAACATAATGG-ACGCTATGAGAAAGATCAAAATACATCCAGA
130887 GATGGTGATGGTGATATGGTTGATGAAA
1 GATGGTGATGGTGATATGGTTGATGAAA
130915 ATGGACCAAA
Statistics
Matches: 352, Mismatches: 46, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
123 57 0.16
124 1 0.00
125 2 0.01
126 290 0.82
127 2 0.01
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.25
Consensus pattern (126 bp):
GATGGTGATGGTGATATGGTTGATGAAAGTAGATCTACTGATTCTCATAGCGAGGAGCACGGTGA
GAACTTATCGGTAGAAGGCCAACATAATGGACGCTATGAGAAAGATCAAAATACATCCAGA
Found at i:139815 original size:45 final size:45
Alignment explanation
Indices: 139765--139855 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
139755 CTTTATTAGC
139765 ATCCTCAATACCATATCTAATTGTCCATTCACCACCAAAGCATCA
1 ATCCTCAATACCATATCTAATTGTCCATTCACCACCAAAGCATCA
139810 ATCCTCAATACCATATCTAATTGTCCATTCACCACCAAAGCATCA
1 ATCCTCAATACCATATCTAATTGTCCATTCACCACCAAAGCATCA
139855 A
1 A
139856 CTTACCCTCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.36, C:0.33, G:0.04, T:0.26
Consensus pattern (45 bp):
ATCCTCAATACCATATCTAATTGTCCATTCACCACCAAAGCATCA
Found at i:144394 original size:21 final size:20
Alignment explanation
Indices: 144370--144408 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
144360 GAAACTGAGT
*
144370 CATTAGAGTTGAAATTGAAAC
1 CATTAGA-TTGAAAATGAAAC
*
144391 CATTATATTGAAAATGAA
1 CATTAGATTGAAAATGAA
144409 TCTCCAATCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (20 bp):
CATTAGATTGAAAATGAAAC
Found at i:145135 original size:19 final size:19
Alignment explanation
Indices: 145111--145151 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
145101 CTATTAAGGA
*
145111 AATAATATCTCTTAAATAG
1 AATAATATCTCCTAAATAG
*
145130 AATAATATCTCCTAATTAG
1 AATAATATCTCCTAAATAG
145149 AAT
1 AAT
145152 CTCTAAAAAT
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:0.46, C:0.12, G:0.05, T:0.37
Consensus pattern (19 bp):
AATAATATCTCCTAAATAG
Found at i:152496 original size:31 final size:31
Alignment explanation
Indices: 152455--152543 Score: 106
Period size: 31 Copynumber: 2.9 Consensus size: 31
152445 GGGCATCAGT
* * *
152455 CATTTATATTTGCATATCCATACCTTGTAAT
1 CATTCATATTTGCATATTCATACCTTGTAAA
* * *
152486 CATTCGTATTTGCATATTCATACCCTATAAA
1 CATTCATATTTGCATATTCATACCTTGTAAA
* *
152517 CATTCATATTTACATATTCATATCTTG
1 CATTCATATTTGCATATTCATACCTTG
152544 CACAATCACA
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.30, C:0.20, G:0.06, T:0.44
Consensus pattern (31 bp):
CATTCATATTTGCATATTCATACCTTGTAAA
Found at i:164438 original size:217 final size:219
Alignment explanation
Indices: 164042--164460 Score: 540
Period size: 217 Copynumber: 1.9 Consensus size: 219
164032 TGTTTACGGG
* * ** *
164042 GGAATAAACCAGATACATCAAATGCAATTCTAGTTAAACCAAATGTGGATATTTTCATAGTTTTA
1 GGAATAAACCAGATACATCAAATGCAATTATAGTAAAACCAAATGCAGATA--TT-ATAGCTTTA
* *
164107 TAAATCCTGATGAGAAATTTCTGACTGATTAGTTTTGTATCTTGAAAGCTATAAACAATAAAGTT
63 GAAATCCTGATGAGAAATTTCTGACCGATTAGTTTTGTATCTTGAAAGCTATAAACAATAAAGTT
* * * *
164172 GAGCTTGAAGAGAGTTGCATCCATAACTTACAGTAGGTTTGCGTAATCTTCTTTTTAAATAGAAT
128 GAACTTGAAGAGAGTTGCATCCATAACTTACAGTAGATTTGCATAATCTTCTTTTTAAATAGAAA
164237 CAGATTTTACTTGCAAATTGGGCTGGA
193 CAGATTTTACTTGCAAATTGGGCTGGA
* *
164264 GGAATAAACCAGATACATCAAATGTAATTATAGTAAAACCGAATGCAGATA-T-T-GCTTTAGAA
1 GGAATAAACCAGATACATCAAATGCAATTATAGTAAAACCAAATGCAGATATTATAGCTTTAGAA
* * *
164326 ATCCTGATGAGAAATTTCTGACCGATTACTTTTTGTATTTTGACAGCTATAAA-AGATAAAGTTG
66 ATCCTGATGAGAAATTTCTGACCGATTA-GTTTTGTATCTTGAAAGCTATAAACA-ATAAAGTTG
* * ** * * * * *
164390 AACTTGAGGAGAGTTGCGTCCATAACTTATGGTCGATTTGTATAATCTTTTTTTTGAATGGAAAC
129 AACTTGAAGAGAGTTGCATCCATAACTTACAGTAGATTTGCATAATCTTCTTTTTAAATAGAAAC
164455 AGATTT
194 AGATTT
164461 GCTATTGCAA
Statistics
Matches: 170, Mismatches: 25, Indels: 9
0.83 0.12 0.04
Matches are distributed among these distances:
216 35 0.21
217 89 0.52
219 1 0.01
222 45 0.26
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.35
Consensus pattern (219 bp):
GGAATAAACCAGATACATCAAATGCAATTATAGTAAAACCAAATGCAGATATTATAGCTTTAGAA
ATCCTGATGAGAAATTTCTGACCGATTAGTTTTGTATCTTGAAAGCTATAAACAATAAAGTTGAA
CTTGAAGAGAGTTGCATCCATAACTTACAGTAGATTTGCATAATCTTCTTTTTAAATAGAAACAG
ATTTTACTTGCAAATTGGGCTGGA
Found at i:171275 original size:20 final size:20
Alignment explanation
Indices: 171223--171302 Score: 56
Period size: 20 Copynumber: 3.9 Consensus size: 20
171213 TAAAATTACA
* *
171223 AAAAAATAAAACTAATTTTT
1 AAAAATTAAAAATAATTTTT
**
171243 AAAAATTTTAAATAATTTTT
1 AAAAATTAAAAATAATTTTT
*
171263 -AAAATTCAAAAATTTTATTTTT
1 AAAAATT-AAAAA--TAATTTTT
*
171285 AAAAAATTATAAA-AATTT
1 -AAAAATTAAAAATAATTT
171303 CAAATATATA
Statistics
Matches: 46, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
19 6 0.13
20 23 0.50
22 7 0.15
23 4 0.09
24 6 0.13
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
AAAAATTAAAAATAATTTTT
Found at i:182624 original size:31 final size:32
Alignment explanation
Indices: 182589--182669 Score: 119
Period size: 32 Copynumber: 2.6 Consensus size: 32
182579 CTTAATATAA
* * **
182589 AATTTAGTACTTGAACTTGTCAC-TTTTTCCT
1 AATTTAGTACCTAAACTTAACACTTTTTTCCT
182620 AATTTAGTACCTAAACTTAACACTTTTTTCCT
1 AATTTAGTACCTAAACTTAACACTTTTTTCCT
182652 AATTTAGTACCTAAACTT
1 AATTTAGTACCTAAACTT
182670 TTTTGGACCC
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
31 19 0.42
32 26 0.58
ACGTcount: A:0.30, C:0.20, G:0.06, T:0.44
Consensus pattern (32 bp):
AATTTAGTACCTAAACTTAACACTTTTTTCCT
Found at i:182936 original size:31 final size:31
Alignment explanation
Indices: 182899--182975 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
182889 CTCAAAAAGT
*
182899 TTTAAGTACCAACTTTA-AAAAA-ATTGTCAAG
1 TTTAAGTACCAA-ATTAGAAAAACA-TGTCAAG
*
182930 TTTAAGTACTAAATTAGAAAAACATGTCAAG
1 TTTAAGTACCAAATTAGAAAAACATGTCAAG
182961 TTTGAA-TACCAAATT
1 TTT-AAGTACCAAATT
182976 GAACAAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
30 3 0.08
31 34 0.85
32 3 0.08
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.32
Consensus pattern (31 bp):
TTTAAGTACCAAATTAGAAAAACATGTCAAG
Found at i:182951 original size:32 final size:30
Alignment explanation
Indices: 182895--182984 Score: 83
Period size: 31 Copynumber: 2.9 Consensus size: 30
182885 AGACCTCAAA
* * *
182895 AAGTTTTAAGTACCAACTTTAAAAAAATTGTC
1 AAGTTTGAA-TACCAAATTGAAAAAAA-TGTC
* *
182927 AAGTTT-AAGTACTAAATTAGAAAAACATGTC
1 AAGTTTGAA-TACCAAATT-GAAAAAAATGTC
182958 AAGTTTGAATACCAAATTGAACAAAAA
1 AAGTTTGAATACCAAATTGAA-AAAAA
182985 AAAAGGGTAC
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
30 3 0.06
31 32 0.65
32 14 0.29
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.29
Consensus pattern (30 bp):
AAGTTTGAATACCAAATTGAAAAAAATGTC
Found at i:184919 original size:29 final size:30
Alignment explanation
Indices: 184908--185256 Score: 274
Period size: 29 Copynumber: 11.8 Consensus size: 30
184898 TTTGACCCCA
* *
184908 AAACTTCCAAAAATTACATATTTAACCTC-
1 AAACTTCCAAAAATTCCATTTTTAACCTCG
184937 AAACTTCCAAAAATTCCATTTTTAACCTCG
1 AAACTTCCAAAAATTCCATTTTTAACCTCG
* * * *
184967 AAACTTCCAAAAATTACA-TTTTCACCCCT
1 AAACTTCCAAAAATTCCATTTTTAACCTCG
* * * *
184996 AAACTACCAAAAATTCAAATTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTTAACCTCG
*
185026 AAACTTCCAAAAAATT-CATTTTTACCCTCG
1 AAACTTCC-AAAAATTCCATTTTTAACCTCG
*
185056 -AACTTCCAAAAATTCCATTTTTTACCTCG
1 AAACTTCCAAAAATTCCATTTTTAACCTCG
*
185085 AAACTTCCAAAAATTACATTTTT-ACCTCCG
1 AAACTTCCAAAAATTCCATTTTTAACCT-CG
* * * * *
185115 -AACTTTCAAAAATCTCGA-TTTTGACCCCT
1 AAACTTCCAAAAAT-TCCATTTTTAACCTCG
* *
185144 AAAC-TCCAAAAAAATACCA-TTTTACCCTC-
1 AAACTTCC--AAAAATTCCATTTTTAACCTCG
* * *
185173 AAA-TGTCCAAAAATTCCATTTTTAGCCCCT
1 AAACT-TCCAAAAATTCCATTTTTAACCTCG
* * * *
185203 AAACTTTCAAAAATTACC-CTTTTACCCTTG
1 AAACTTCCAAAAATT-CCATTTTTAACCTCG
** *
185233 AATGTT-CAAAAATTCTATTTTTAA
1 AAACTTCCAAAAATTCCATTTTTAA
185257 TCCCGATTTT
Statistics
Matches: 257, Mismatches: 45, Indels: 36
0.76 0.13 0.11
Matches are distributed among these distances:
28 17 0.07
29 116 0.45
30 108 0.42
31 16 0.06
ACGTcount: A:0.38, C:0.26, G:0.03, T:0.33
Consensus pattern (30 bp):
AAACTTCCAAAAATTCCATTTTTAACCTCG
Found at i:184971 original size:59 final size:58
Alignment explanation
Indices: 184876--185219 Score: 329
Period size: 59 Copynumber: 5.8 Consensus size: 58
184866 TAAAGGTCCC
* ** *
184876 CAAACTTCTCCAAAATTGTATTTTTGACCCCAAAACTTCCAAAAATTACATATTTAACCT
1 CAAACTTC-CAAAAATTCCATTTTTGACCCCGAAACTTCCAAAAATTACAT-TTTAACCT
* * * *
184936 CAAACTTCCAAAAATTCCATTTTTAACCTCGAAACTTCCAAAAATTACATTTTCACCC
1 CAAACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCCAAAAATTACATTTTAACCT
* * * * *
184994 CTAAACTACCAAAAATTCAAATTTTGACCTCGAAACTTCCAAAAAATT-CATTTTTACCCT
1 C-AAACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCC-AAAAATTACA-TTTTAACCT
* * * *
185054 CGAACTTCCAAAAATTCCATTTTTTACCTCGAAACTTCCAAAAATTACATTTTTACCT
1 CAAACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCCAAAAATTACATTTTAACCT
* * * * * *
185112 CCGAACTTTCAAAAATCTCGA-TTTTGACCCCTAAAC-TCCAAAAAAATACCATTTTACCCT
1 -CAAACTTCCAAAAAT-TCCATTTTTGACCCCGAAACTTCC-AAAAATTA-CATTTTAACCT
* *
185172 CAAA-TGTCCAAAAATTCCATTTTT-AGCCCCTAAACTTTCAAAAATTAC
1 CAAACT-TCCAAAAATTCCATTTTTGA-CCCCGAAACTTCCAAAAATTAC
185220 CCTTTTACCC
Statistics
Matches: 237, Mismatches: 35, Indels: 26
0.80 0.12 0.09
Matches are distributed among these distances:
58 30 0.13
59 171 0.72
60 36 0.15
ACGTcount: A:0.38, C:0.27, G:0.03, T:0.32
Consensus pattern (58 bp):
CAAACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCCAAAAATTACATTTTAACCT
Found at i:185086 original size:118 final size:117
Alignment explanation
Indices: 184897--185219 Score: 379
Period size: 118 Copynumber: 2.7 Consensus size: 117
184887 AAAATTGTAT
* * *
184897 TTTTGACCCCAAAACTTCC-AAAAATTACATATTTAACCTCAAACTTCCAAAAATTCCATTTTTA
1 TTTTGACCCCAAAACTTCCAAAAAATT-CATTTTTACCCTC-AACTTCCAAAAATTCCATTTTTT
184961 ACCTCGAAACTTCCAAAAATTACATTTTCACC-CCTAAACTACCAAAAAT-TCAAA
64 ACCTCGAAACTTCCAAAAATTACATTTTCACCTCC-AAACTACCAAAAATCTC-AA
* *
185015 TTTTGACCTCGAAACTTCCAAAAAATTCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTTA
1 TTTTGACCCCAAAACTTCCAAAAAATTCATTTTTACCCTC-AACTTCCAAAAATTCCATTTTTTA
* * ** *
185080 CCTCGAAACTTCCAAAAATTACATTTTTACCTCCGAACTTTCAAAAATCTCGA
65 CCTCGAAACTTCCAAAAATTACATTTTCACCTCCAAACTACCAAAAATCTCAA
* * *
185133 TTTTGACCCCTAAAC-TCCAAAAAAATACCA-TTTTACCCTCAAATGTCCAAAAATTCCA-TTTT
1 TTTTGACCCCAAAACTTCC-AAAAAAT-TCATTTTTACCCTCAACT-TCCAAAAATTCCATTTTT
* * *
185195 TAGCCCCTAAACTTTCAAAAATTAC
63 TA-CCTCGAAACTTCCAAAAATTAC
185220 CCTTTTACCC
Statistics
Matches: 180, Mismatches: 18, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
117 12 0.07
118 155 0.86
119 13 0.07
ACGTcount: A:0.38, C:0.27, G:0.03, T:0.32
Consensus pattern (117 bp):
TTTTGACCCCAAAACTTCCAAAAAATTCATTTTTACCCTCAACTTCCAAAAATTCCATTTTTTAC
CTCGAAACTTCCAAAAATTACATTTTCACCTCCAAACTACCAAAAATCTCAA
Found at i:185275 original size:59 final size:58
Alignment explanation
Indices: 185153--185379 Score: 156
Period size: 59 Copynumber: 3.9 Consensus size: 58
185143 TAAACTCCAA
* ** * * ** * ** **
185153 AAAAATACCATTTTACCCTCAAATGTCCAAAAATTCCATTTTTAGCCCCTAAACTTTCA
1 AAAATTACCATTTTACCCTTGAATGTTCAAAAATTCTATTTTTAATCCC-GATTTTTTT
*
185212 AAAATTACCCTTTTACCCTTGAATGTTCAAAAATTCTATTTTTAATCCCGATTTTCTTT
1 AAAATTACCATTTTACCCTTGAATGTTCAAAAATTCTATTTTTAATCCCGATTTT-TTT
* * * * * * *
185271 AAAATTACCATTTTACCCTTGGATGTCCCAAAATT-TCGTTTTTGATCTCAATTTTTTT
1 AAAATTACCATTTTACCCTTGAATGTTCAAAAATTCT-ATTTTTAATCCCGATTTTTTT
* * * *
185329 AAAAGTTACCGTTTTATCCC--GAGTG-TCTAAAAATTCAATTTTTAACCCCGA
1 AAAA-TTACCATTTTA-CCCTTGAATGTTC-AAAAATTCTATTTTTAATCCCGA
185380 ACTTTCCCAA
Statistics
Matches: 130, Mismatches: 32, Indels: 13
0.74 0.18 0.07
Matches are distributed among these distances:
57 1 0.01
58 29 0.22
59 97 0.75
60 3 0.02
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (58 bp):
AAAATTACCATTTTACCCTTGAATGTTCAAAAATTCTATTTTTAATCCCGATTTTTTT
Found at i:188856 original size:104 final size:104
Alignment explanation
Indices: 188676--188883 Score: 371
Period size: 104 Copynumber: 2.0 Consensus size: 104
188666 ATTAGACCAT
* *
188676 CTTGAAGACATCACTCTATCCTAAGAGCTCATCGGTAGTATTTACATCACTCGGTTATATGGCAT
1 CTTGAAGACATCACTCTATCCCAAGAGCTCATCGGTAGTATATACATCACTCGGTTATATGGCAT
188741 GTACTAGGATGAAATGACTTATTCTACTTGTATAGATGA
66 GTACTAGGATGAAATGACTTATTCTACTTGTATAGATGA
* **
188780 CTTGAAGACATCACTCTATCCCGAGAGCTTGTCGGTAGTATATACATCACTCGGTTATATGGCAT
1 CTTGAAGACATCACTCTATCCCAAGAGCTCATCGGTAGTATATACATCACTCGGTTATATGGCAT
188845 GTACTAGGATGAAATGACTTATTCTACTTGTATAGATGA
66 GTACTAGGATGAAATGACTTATTCTACTTGTATAGATGA
188884 ATGAATCTTT
Statistics
Matches: 99, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
104 99 1.00
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.33
Consensus pattern (104 bp):
CTTGAAGACATCACTCTATCCCAAGAGCTCATCGGTAGTATATACATCACTCGGTTATATGGCAT
GTACTAGGATGAAATGACTTATTCTACTTGTATAGATGA
Found at i:192773 original size:17 final size:17
Alignment explanation
Indices: 192751--192789 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
192741 ATGAATGCAG
192751 GCCTTCCAGATTCTGTA
1 GCCTTCCAGATTCTGTA
192768 GCCTTCCAGATTCTGTA
1 GCCTTCCAGATTCTGTA
192785 GCCTT
1 GCCTT
192790 TTACAGAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.15, C:0.31, G:0.18, T:0.36
Consensus pattern (17 bp):
GCCTTCCAGATTCTGTA
Found at i:194515 original size:14 final size:14
Alignment explanation
Indices: 194496--194525 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
194486 TTAATTGATT
194496 TTTAATTAAATAAA
1 TTTAATTAAATAAA
*
194510 TTTAATTAATTAAA
1 TTTAATTAAATAAA
194524 TT
1 TT
194526 GTCTACATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTAATTAAATAAA
Found at i:200545 original size:22 final size:22
Alignment explanation
Indices: 200518--200569 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
200508 CAAAAGAACG
*
200518 GAGAGCACCAAGGTGCTAAACA
1 GAGAGCACAAAGGTGCTAAACA
*
200540 GAGAGCACAAATGTGCTAAACA
1 GAGAGCACAAAGGTGCTAAACA
200562 GAGAGCAC
1 GAGAGCAC
200570 TTTACGTGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.42, C:0.21, G:0.27, T:0.10
Consensus pattern (22 bp):
GAGAGCACAAAGGTGCTAAACA
Found at i:201506 original size:23 final size:23
Alignment explanation
Indices: 201480--201524 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
201470 AATTTTGAAT
**
201480 TTCAAATTATTCGAATCGAGTTA
1 TTCAAATTAAACGAATCGAGTTA
*
201503 TTCAAGTTAAACGAATCGAGTT
1 TTCAAATTAAACGAATCGAGTT
201525 GAATTTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.36
Consensus pattern (23 bp):
TTCAAATTAAACGAATCGAGTTA
Found at i:204091 original size:41 final size:41
Alignment explanation
Indices: 204034--204129 Score: 147
Period size: 41 Copynumber: 2.3 Consensus size: 41
204024 GAATTTTATT
*
204034 TTAACAAGAATTCTAGTCACCAAATTCTAACAATCTCCACC
1 TTAACAAGAATTCTAGTCACCAAATTCTAACAATCTCCACA
* * *
204075 TTAACAAGAATTCTAGTCTCCCAATTCTAATAATCTCCACA
1 TTAACAAGAATTCTAGTCACCAAATTCTAACAATCTCCACA
*
204116 TTGACAAGAATTCT
1 TTAACAAGAATTCT
204130 TTGCGAACAA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.38, C:0.26, G:0.06, T:0.30
Consensus pattern (41 bp):
TTAACAAGAATTCTAGTCACCAAATTCTAACAATCTCCACA
Found at i:220444 original size:12 final size:12
Alignment explanation
Indices: 220427--220451 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
220417 TTTGCCTTTT
220427 GCTTTTATTACG
1 GCTTTTATTACG
220439 GCTTTTATTACG
1 GCTTTTATTACG
220451 G
1 G
220452 TCATCTCATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.16, G:0.20, T:0.48
Consensus pattern (12 bp):
GCTTTTATTACG
Found at i:221914 original size:1 final size:1
Alignment explanation
Indices: 221869--221894 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
221859 TCATAAATAC
221869 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
221895 NNNNNNNNNN
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:229611 original size:76 final size:77
Alignment explanation
Indices: 229469--229611 Score: 189
Period size: 76 Copynumber: 1.9 Consensus size: 77
229459 GTAACCATAT
** * * * *
229469 AACAAATGTTTCTTAATACAAAATCCTCATATTTTGTGTCAGATACTTCTCTTTTATACAACACT
1 AACAAATACTTCTCAATACAAAATCCTCATATTCTGTGTCAAATACTTCTCATTTATACAACACT
229534 TTCTTACCATGA
66 TTCTTACCATGA
* * * *
229546 AACAAATACTTCTCAATACAAAATTCTCA-ATTCTGTGTCAAATACTTTTCATTTATGCAATACT
1 AACAAATACTTCTCAATACAAAATCCTCATATTCTGTGTCAAATACTTCTCATTTATACAACACT
229610 TT
66 TT
229612 ATGGATATCT
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
76 31 0.55
77 25 0.45
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.40
Consensus pattern (77 bp):
AACAAATACTTCTCAATACAAAATCCTCATATTCTGTGTCAAATACTTCTCATTTATACAACACT
TTCTTACCATGA
Found at i:235344 original size:37 final size:37
Alignment explanation
Indices: 235287--235411 Score: 187
Period size: 37 Copynumber: 3.4 Consensus size: 37
235277 CATCTACAAA
* * * *
235287 TTCAGGCTTTATGCCCAGTAGGTTTCGTGCTGGTGTT
1 TTCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGGTGTT
*
235324 TTCAAGCTTTGTGCCTAGTAGGCTTCGTGCCGGTGTT
1 TTCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGGTGTT
*
235361 TTCAGGCTTTGTGTCTAGTAGGCTTCGTGCCGGTGTT
1 TTCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGGTGTT
*
235398 TTTAGGCTTTGTGC
1 TTCAGGCTTTGTGC
235412 TGGTGTTTTC
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 79 1.00
ACGTcount: A:0.10, C:0.19, G:0.30, T:0.41
Consensus pattern (37 bp):
TTCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGGTGTT
Found at i:235369 original size:21 final size:21
Alignment explanation
Indices: 235343--235469 Score: 82
Period size: 21 Copynumber: 6.5 Consensus size: 21
235333 TGTGCCTAGT
235343 AGGCTTCGTGCCGGTGTTTTC
1 AGGCTTCGTGCCGGTGTTTTC
* *
235364 AGGCTTTGTGTC--TAG---T-
1 AGGCTTCGTGCCGGT-GTTTTC
*
235380 AGGCTTCGTGCCGGTGTTTTT
1 AGGCTTCGTGCCGGTGTTTTC
* *
235401 AGGCTTTGTGCTGGTGTTTTC
1 AGGCTTCGTGCCGGTGTTTTC
235422 AGGCTGT-GTGCC--TAG----C
1 AGGCT-TCGTGCCGGT-GTTTTC
235438 AGGCTTCGTGCCGGTGTTTTC
1 AGGCTTCGTGCCGGTGTTTTC
*
235459 AGGCTGCGTGC
1 AGGCTTCGTGC
235470 TTAGCAGGCT
Statistics
Matches: 81, Mismatches: 9, Indels: 32
0.66 0.07 0.26
Matches are distributed among these distances:
15 1 0.01
16 21 0.26
17 3 0.04
18 2 0.02
19 2 0.02
20 3 0.04
21 48 0.59
22 1 0.01
ACGTcount: A:0.07, C:0.20, G:0.35, T:0.38
Consensus pattern (21 bp):
AGGCTTCGTGCCGGTGTTTTC
Found at i:235442 original size:37 final size:37
Alignment explanation
Indices: 235401--235489 Score: 142
Period size: 37 Copynumber: 2.4 Consensus size: 37
235391 CGGTGTTTTT
* * *
235401 AGGCTTTGTGCTGGTGTTTTCAGGCTGTGTGCCTAGC
1 AGGCTTCGTGCCGGTGTTTTCAGGCTGCGTGCCTAGC
*
235438 AGGCTTCGTGCCGGTGTTTTCAGGCTGCGTGCTTAGC
1 AGGCTTCGTGCCGGTGTTTTCAGGCTGCGTGCCTAGC
235475 AGGCTTCGTGCCGGT
1 AGGCTTCGTGCCGGT
235490 ATTCGGGCTA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.08, C:0.22, G:0.36, T:0.34
Consensus pattern (37 bp):
AGGCTTCGTGCCGGTGTTTTCAGGCTGCGTGCCTAGC
Found at i:235470 original size:58 final size:58
Alignment explanation
Indices: 235343--235470 Score: 193
Period size: 58 Copynumber: 2.2 Consensus size: 58
235333 TGTGCCTAGT
* * * * *
235343 AGGCTTCGTGCCGGTGTTTTCAGGCTTTGTGTCTAGTAGGCTTCGTGCCGGTGTTTTT
1 AGGCTTCGTGCTGGTGTTTTCAGGCTGTGTGCCTAGCAGGCTTCGTGCCGGTGTTTTC
*
235401 AGGCTTTGTGCTGGTGTTTTCAGGCTGTGTGCCTAGCAGGCTTCGTGCCGGTGTTTTC
1 AGGCTTCGTGCTGGTGTTTTCAGGCTGTGTGCCTAGCAGGCTTCGTGCCGGTGTTTTC
*
235459 AGGCTGCGTGCT
1 AGGCTTCGTGCT
235471 TAGCAGGCTT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
58 62 1.00
ACGTcount: A:0.07, C:0.20, G:0.34, T:0.38
Consensus pattern (58 bp):
AGGCTTCGTGCTGGTGTTTTCAGGCTGTGTGCCTAGCAGGCTTCGTGCCGGTGTTTTC
Found at i:235479 original size:95 final size:95
Alignment explanation
Indices: 235305--235489 Score: 284
Period size: 95 Copynumber: 1.9 Consensus size: 95
235295 TTATGCCCAG
* * *
235305 TAGGTTTCGTGCTGGTGTTTTCAAGCTTTGTGCCTAGTAGGCTTCGTGCCGGTGTTTTCAGGCTT
1 TAGGTTTCGTGCTGGTGTTTTCAAGCTGTGTGCCTAGCAGGCTTCGTGCCGGTGTTTTCAGGCTG
* *
235370 TGTGTCTAGTAGGCTTCGTGCCGGTGTTTT
66 CGTGTCTAGCAGGCTTCGTGCCGGTGTTTT
*
235400 TAGGCTTT-GTGCTGGTGTTTTCAGGCTGTGTGCCTAGCAGGCTTCGTGCCGGTGTTTTCAGGCT
1 TAGG-TTTCGTGCTGGTGTTTTCAAGCTGTGTGCCTAGCAGGCTTCGTGCCGGTGTTTTCAGGCT
235464 GCGTG-CTTAGCAGGCTTCGTGCCGGT
65 GCGTGTC-TAGCAGGCTTCGTGCCGGT
235490 ATTCGGGCTA
Statistics
Matches: 82, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
94 1 0.01
95 78 0.95
96 3 0.04
ACGTcount: A:0.08, C:0.20, G:0.34, T:0.38
Consensus pattern (95 bp):
TAGGTTTCGTGCTGGTGTTTTCAAGCTGTGTGCCTAGCAGGCTTCGTGCCGGTGTTTTCAGGCTG
CGTGTCTAGCAGGCTTCGTGCCGGTGTTTT
Found at i:251756 original size:21 final size:21
Alignment explanation
Indices: 251731--251776 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
251721 AATTACTTTA
251731 AATCTCGAATCTTAAATTTTG
1 AATCTCGAATCTTAAATTTTG
251752 AATCTCGAATCTTAAATTTTG
1 AATCTCGAATCTTAAATTTTG
251773 AATC
1 AATC
251777 ATGAGCCTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (21 bp):
AATCTCGAATCTTAAATTTTG
Found at i:251949 original size:18 final size:18
Alignment explanation
Indices: 251926--251970 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
251916 TTCAAGATTT
*
251926 GAGTTTGGATTCGGGTTC
1 GAGTTTGGATTCGGGGTC
* *
251944 GAGTTTAGGTTTGGGGGTC
1 GAGTTT-GGATTCGGGGTC
251963 GAGTTTGG
1 GAGTTTGG
251971 GGTTCAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.11, C:0.07, G:0.44, T:0.38
Consensus pattern (18 bp):
GAGTTTGGATTCGGGGTC
Found at i:252034 original size:20 final size:19
Alignment explanation
Indices: 251991--252042 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
251981 CAAGGTTTAA
*
251991 AGTTCAAGATTCATGTTGG
1 AGTTCAAGATTCATGTTCG
*
252010 AGTTCAAGCTTCATAGTTCG
1 AGTTCAAGATTCAT-GTTCG
*
252030 AGTTCAAGGTTCA
1 AGTTCAAGATTCA
252043 GGCTTTAGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (19 bp):
AGTTCAAGATTCATGTTCG
Found at i:252602 original size:15 final size:16
Alignment explanation
Indices: 252582--252636 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 16
252572 TATTTAAAAT
252582 AAAAAATTAAA-ATTA
1 AAAAAATTAAATATTA
*
252597 AAAAAAGTACAATATT-
1 AAAAAATTA-AATATTA
* *
252613 AAATATTTAAATATTA
1 AAAAAATTAAATATTA
252629 AAAAAATT
1 AAAAAATT
252637 GACTTTGATC
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
15 14 0.45
16 14 0.45
17 3 0.10
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (16 bp):
AAAAAATTAAATATTA
Found at i:252836 original size:15 final size:15
Alignment explanation
Indices: 252800--252828 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
252790 TAAATTTTTT
252800 TATAAAATTTTAAAA
1 TATAAAATTTTAAAA
252815 TATAAAATTTTAAA
1 TATAAAATTTTAAA
252829 TTTTAAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TATAAAATTTTAAAA
Found at i:254202 original size:19 final size:17
Alignment explanation
Indices: 254162--254206 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 17
254152 ACAGGTAGAT
254162 TTTCAATAATATTTAAAA
1 TTTCAA-AATATTTAAAA
254180 -TTCAAAATATTTATAAAA
1 TTTCAAAATA-TT-TAAAA
254198 TTTCAAAAT
1 TTTCAAAAT
254207 TTATGTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 4 0.17
17 7 0.29
18 5 0.21
19 8 0.33
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTCAAAATATTTAAAA
Found at i:254243 original size:19 final size:19
Alignment explanation
Indices: 254212--254249 Score: 60
Period size: 18 Copynumber: 2.0 Consensus size: 19
254202 AAAATTTATG
254212 TTTTAAAAAATATA-AAAA
1 TTTTAAAAAATATATAAAA
254230 TTTTAAAAAGATATATAAAA
1 TTTTAAAAA-ATATATAAAA
254250 AAAGTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.50
19 5 0.28
20 4 0.22
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (19 bp):
TTTTAAAAAATATATAAAA
Found at i:255530 original size:18 final size:19
Alignment explanation
Indices: 255507--255551 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
255497 AATAAAGTTT
255507 TATTTTAATATTT-TTAT-A
1 TATTTTAAT-TTTATTATCA
255525 TATTTTAATTTTATTATGCA
1 TATTTTAATTTTATTAT-CA
255545 TATTTTA
1 TATTTTA
255552 TTATCTCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 3 0.12
18 13 0.54
20 8 0.33
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (19 bp):
TATTTTAATTTTATTATCA
Found at i:256113 original size:24 final size:25
Alignment explanation
Indices: 256079--256134 Score: 80
Period size: 24 Copynumber: 2.3 Consensus size: 25
256069 ATATATAATT
*
256079 TAAAAATAATTTTAAA-TTTATAAAA
1 TAAAAATAATTTAAAATTTTA-AAAA
256104 TAAAAA-AATTTAAAATTTTAAAAA
1 TAAAAATAATTTAAAATTTTAAAAA
256128 TAAAAAT
1 TAAAAAT
256135 TGAAAAACTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 18 0.64
25 10 0.36
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (25 bp):
TAAAAATAATTTAAAATTTTAAAAA
Found at i:258924 original size:39 final size:39
Alignment explanation
Indices: 258870--258948 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
258860 TTATAGAATT
258870 TTAAATTTAAGGTTTTGCTAGAAGCATCTAAATGAATCA
1 TTAAATTTAAGGTTTTGCTAGAAGCATCTAAATGAATCA
*
258909 TTAAATTTAAGGTTTTGCTAGAAGCATCTAAATGGATCA
1 TTAAATTTAAGGTTTTGCTAGAAGCATCTAAATGAATCA
258948 T
1 T
258949 GACATCTGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (39 bp):
TTAAATTTAAGGTTTTGCTAGAAGCATCTAAATGAATCA
Found at i:259364 original size:30 final size:31
Alignment explanation
Indices: 259291--259367 Score: 83
Period size: 30 Copynumber: 2.6 Consensus size: 31
259281 CTCAAGTTTT
*
259291 AAAAGTTTTCATTTT-GAGCATCGGAAAATA
1 AAAATTTTTCATTTTAGAGCATCGGAAAATA
*
259321 AAAATTTTT-ATTTTAG-GCA-C-GAACATA
1 AAAATTTTTCATTTTAGAGCATCGGAAAATA
259348 AAAATCATTTTCATTTTAGA
1 AAAAT--TTTTCATTTTAGA
259368 CATTGCCTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
27 11 0.28
28 1 0.03
29 12 0.30
30 16 0.40
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (31 bp):
AAAATTTTTCATTTTAGAGCATCGGAAAATA
Found at i:270272 original size:11 final size:11
Alignment explanation
Indices: 270258--270355 Score: 52
Period size: 11 Copynumber: 8.5 Consensus size: 11
270248 CAAATTCCTT
*
270258 TAAAATAGTAA
1 TAAAATAATAA
270269 TAAAATTAATAA
1 TAAAA-TAATAA
*
270281 TAAAATAAAAAA
1 TAAAAT-AATAA
* * *
270293 TTATATAATATC
1 TAAAATAATA-A
*
270305 TAAACAATAACAA
1 T-AA-AATAATAA
*
270318 TAAAATAATAG
1 TAAAATAATAA
*
270329 TAACATAATAA
1 TAAAATAATAA
* * *
270340 TGAAATGATAG
1 TAAAATAATAA
270351 TAAAA
1 TAAAA
270356 CTGTAAAAAA
Statistics
Matches: 63, Mismatches: 19, Indels: 10
0.68 0.21 0.11
Matches are distributed among these distances:
11 35 0.56
12 21 0.33
13 2 0.03
14 5 0.08
ACGTcount: A:0.63, C:0.04, G:0.05, T:0.28
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:270336 original size:22 final size:22
Alignment explanation
Indices: 270311--270353 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
270301 TATCTAAACA
270311 ATAACAATAAAATAATAGTAAC
1 ATAACAATAAAATAATAGTAAC
* * *
270333 ATAATAATGAAATGATAGTAA
1 ATAACAATAAAATAATAGTAA
270354 AACTGTAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.05, G:0.09, T:0.26
Consensus pattern (22 bp):
ATAACAATAAAATAATAGTAAC
Found at i:270677 original size:36 final size:36
Alignment explanation
Indices: 270630--270701 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
270620 AAACAACAAT
270630 TCCCATTAAATTGATTCGGATTTATATTAAGAATTG
1 TCCCATTAAATTGATTCGGATTTATATTAAGAATTG
*
270666 TCCCATTAAATTGATTTGGATTTATATTAAGAATTG
1 TCCCATTAAATTGATTCGGATTTATATTAAGAATTG
270702 AATAAATTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (36 bp):
TCCCATTAAATTGATTCGGATTTATATTAAGAATTG
Found at i:280836 original size:40 final size:40
Alignment explanation
Indices: 280781--280887 Score: 169
Period size: 40 Copynumber: 2.7 Consensus size: 40
280771 GACAGAAAAC
* *
280781 GCCGCAAAAGGTAAAGTAATGGCGGCGCTTTTACATAAAT
1 GCCGCAAAAGGTAAAGCAATAGCGGCGCTTTTACATAAAT
*
280821 GCCGCAAAAGGTAAAGCAATAGCGGCGTTTTTACATAAAT
1 GCCGCAAAAGGTAAAGCAATAGCGGCGCTTTTACATAAAT
* *
280861 GCCACAAAAGGTAAAGCAATAGTGGCG
1 GCCGCAAAAGGTAAAGCAATAGCGGCG
280888 TTTGTAGGAA
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 62 1.00
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.20
Consensus pattern (40 bp):
GCCGCAAAAGGTAAAGCAATAGCGGCGCTTTTACATAAAT
Found at i:280942 original size:41 final size:41
Alignment explanation
Indices: 280774--281036 Score: 198
Period size: 41 Copynumber: 6.5 Consensus size: 41
280764 AAGTTTGGAC
* * * *
280774 AGAAAACGCCGCAAAAGGT-AAAGTAATGGCGGCGCTTT-T-
1 AGAAAACGCCGCTAAAGGTCAAAGCATTAGCGGCG-TTTATG
* * * * *
280813 ACATAAATGCCGCAAAAGGT-AAAGCAATAGCGGCGTTT-TT
1 AGA-AAACGCCGCTAAAGGTCAAAGCATTAGCGGCGTTTATG
* * * * * * *
280853 ACATAAATGCCACAAAAGGT-AAAGCAATAGTGGCGTTTGT-
1 AGA-AAACGCCGCTAAAGGTCAAAGCATTAGCGGCGTTTATG
* *
280893 AGGAAAAACGCTGCTAAAGGTCAAAGCATTAGCGGCGTTTACG
1 A-G-AAAACGCCGCTAAAGGTCAAAGCATTAGCGGCGTTTATG
* * *
280936 AGAAAACGCCACTAAAGGTCAGAGCATTAGCGGTGTTTATG
1 AGAAAACGCCGCTAAAGGTCAAAGCATTAGCGGCGTTTATG
* * * * *
280977 AGAAAATGTCGCTAAAGGTTAGAGCATTAGCAGCGTTTATG
1 AGAAAACGCCGCTAAAGGTCAAAGCATTAGCGGCGTTTATG
281018 AGAAAACGCCGCTAAAGGT
1 AGAAAACGCCGCTAAAGGT
281037 AAGAGAACGC
Statistics
Matches: 189, Mismatches: 28, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
39 6 0.03
40 65 0.34
41 99 0.52
42 18 0.10
43 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.21
Consensus pattern (41 bp):
AGAAAACGCCGCTAAAGGTCAAAGCATTAGCGGCGTTTATG
Found at i:281047 original size:20 final size:20
Alignment explanation
Indices: 281022--281061 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
281012 TTTATGAGAA
281022 AACGCCGCTAAAGGTAAGAG
1 AACGCCGCTAAAGGTAAGAG
281042 AACGCCGCTAAAGGTAAGAG
1 AACGCCGCTAAAGGTAAGAG
281062 CATTAGCGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.30, T:0.10
Consensus pattern (20 bp):
AACGCCGCTAAAGGTAAGAG
Found at i:281566 original size:18 final size:20
Alignment explanation
Indices: 281529--281567 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
281519 ATTTATATCT
*
281529 ATTTATATTTTTCATTTTAA
1 ATTTATATTTTTCATATTAA
281549 ATTTAT-TTTTTCA-ATTAA
1 ATTTATATTTTTCATATTAA
281567 A
1 A
281568 AATTTTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 7 0.39
20 6 0.33
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTATATTTTTCATATTAA
Found at i:281570 original size:20 final size:20
Alignment explanation
Indices: 281529--281572 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
281519 ATTTATATCT
**
281529 ATTTATATTTTTCATTTTAA
1 ATTTATATTTTTCATTAAAA
281549 ATTTAT-TTTTTCAATTAAAA
1 ATTTATATTTTTC-ATTAAAA
281569 ATTT
1 ATTT
281573 TATAATACTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTTATATTTTTCATTAAAA
Found at i:285295 original size:29 final size:29
Alignment explanation
Indices: 285258--285336 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 29
285248 TGAATGCCCA
* *
285258 AGGGTAAAATGGTAATTTTTGACACTTTG
1 AGGGCAAAATGGTAATTTTTGACACTTCG
*
285287 -GAGGCAAAATGGTAATTTTAGACACTTCG
1 AG-GGCAAAATGGTAATTTTTGACACTTCG
* *
285316 AGGGTAAAATCGTAATTTTTG
1 AGGGCAAAATGGTAATTTTTG
285337 GATGTTCGGG
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
28 1 0.02
29 40 0.95
30 1 0.02
ACGTcount: A:0.33, C:0.09, G:0.24, T:0.34
Consensus pattern (29 bp):
AGGGCAAAATGGTAATTTTTGACACTTCG
Found at i:285344 original size:29 final size:28
Alignment explanation
Indices: 285312--285382 Score: 88
Period size: 28 Copynumber: 2.4 Consensus size: 28
285302 TTTTAGACAC
285312 TTCGAGGGTAAAATCGTAATTTTTGGATG
1 TTCG-GGGTAAAATCGTAATTTTTGGATG
* * *
285341 TTCGGGGTAAAATGGTGATTTTTGGAAAG
1 TTCGGGGTAAAATCGTAATTTTTGG-ATG
285370 TTCGGGGTCAAAA
1 TTCGGGGT-AAAA
285383 ATATATTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 19 0.51
29 14 0.38
30 4 0.11
ACGTcount: A:0.28, C:0.07, G:0.31, T:0.34
Consensus pattern (28 bp):
TTCGGGGTAAAATCGTAATTTTTGGATG
Found at i:285361 original size:28 final size:29
Alignment explanation
Indices: 285259--285382 Score: 92
Period size: 29 Copynumber: 4.3 Consensus size: 29
285249 GAATGCCCAA
* * * *
285259 GGGTAAAATGGTAATTTTT-GACACTTTG
1 GGGTAAAATCGTAATTTTTGGAAAGTTCG
* * * * *
285287 GAGGCAAAATGGTAA-TTTTAGACACTTCG
1 G-GGTAAAATCGTAATTTTTGGAAAGTTCG
*
285316 AGGGTAAAATCGTAATTTTTGG-ATGTTCG
1 -GGGTAAAATCGTAATTTTTGGAAAGTTCG
* *
285345 GGGTAAAATGGTGATTTTTGGAAAGTTCG
1 GGGTAAAATCGTAATTTTTGGAAAGTTCG
285374 GGGTCAAAA
1 GGGT-AAAA
285383 ATATATTTTT
Statistics
Matches: 79, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
28 24 0.30
29 45 0.57
30 10 0.13
ACGTcount: A:0.31, C:0.08, G:0.28, T:0.33
Consensus pattern (29 bp):
GGGTAAAATCGTAATTTTTGGAAAGTTCG
Found at i:285421 original size:59 final size:58
Alignment explanation
Indices: 285350--285511 Score: 166
Period size: 58 Copynumber: 2.8 Consensus size: 58
285340 GTTCGGGGTA
* * *
285350 AAATGGTGATTTTTGGAAAGTTCGGGGTCAAAAATATATTTTTTGGACATTCAAGGGT
1 AAATGGTAATTTTTGGAAAGTTCGGGGTCAAAAATATATTTTTTGGACATCCAAGGCT
* * * * * * *
285408 AAGTTGGTAA-TTTTGGAAAGTTTGGAGTAAAAAAAAGTGATTTTATGGACATCCGAGGCT
1 AA-ATGGTAATTTTTGGAAAGTTCGGGGTCAAAAATA-T-ATTTTTTGGACATCCAAGGCT
* *
285468 AAAT-GTAATTTTTGGAAAGTTCGAGGTCAAAAATGAAATTTTTT
1 AAATGGTAATTTTTGGAAAGTTCGGGGTCAAAAAT-ATATTTTTT
285512 AGGCATATGG
Statistics
Matches: 81, Mismatches: 18, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
58 34 0.42
59 27 0.33
60 20 0.25
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35
Consensus pattern (58 bp):
AAATGGTAATTTTTGGAAAGTTCGGGGTCAAAAATATATTTTTTGGACATCCAAGGCT
Found at i:285508 original size:30 final size:29
Alignment explanation
Indices: 285468--285676 Score: 133
Period size: 30 Copynumber: 7.1 Consensus size: 29
285458 ATCCGAGGCT
285468 AAATGTAATTTTTGGAAAGTTCGAGGTCAA
1 AAATGTAATTTTTGG-AAGTTCGAGGTCAA
* * * *
285498 AAATGAAATTTTTTAGGCA-TATGGGGGT--A
1 AAATGTAA-TTTTT-GGAAGT-TCGAGGTCAA
* *
285527 AAATAGTAATTTTTGGAAGTTTG-GGGCAA
1 AAAT-GTAATTTTTGGAAGTTCGAGGTCAA
* * * * *
285556 AAATGTGATTTTTGAAAAGTACAAGGTTAA
1 AAATGTAATTTTTG-GAAGTTCGAGGTCAA
*
285586 AAATGTAATTTTTAGAAGTTCGAGGGTC-A
1 AAATGTAATTTTTGGAAGTTCGA-GGTCAA
** * *
285615 AAATACAAATTTTGGAAGTTTGAGGGGTC-A
1 AAATGTAATTTTTGGAAGTTCGA--GGTCAA
*
285645 AAATGTAATTTTTGGAAGTTTAGAGGTCAA
1 AAATGTAATTTTTGGAAG-TTCGAGGTCAA
285675 AA
1 AA
285677 TATGATTTTT
Statistics
Matches: 136, Mismatches: 30, Indels: 26
0.71 0.16 0.14
Matches are distributed among these distances:
27 2 0.01
28 14 0.10
29 49 0.36
30 54 0.40
31 15 0.11
32 2 0.01
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.33
Consensus pattern (29 bp):
AAATGTAATTTTTGGAAGTTCGAGGTCAA
Found at i:285551 original size:29 final size:30
Alignment explanation
Indices: 285519--285687 Score: 111
Period size: 29 Copynumber: 5.8 Consensus size: 30
285509 TTTAGGCATA
285519 TGGGGGT-AAAATAGTAATTTTTGGAAGTT
1 TGGGGGTCAAAATAGTAATTTTTGGAAGTT
* * *
285548 T-GGGG-CAAAA-ATGTGATTTTTGAAAAGTA
1 TGGGGGTCAAAATA-GTAATTTTTG-GAAGTT
*** * * *
285577 CAAGGTTAAAAAT-GTAATTTTTAGAAGTT
1 TGGGGGTCAAAATAGTAATTTTTGGAAGTT
* * * *
285606 CGAGGGTCAAAATA-CAAATTTTGGAAGTT
1 TGGGGGTCAAAATAGTAATTTTTGGAAGTT
285635 TGAGGGGTCAAAAT-GTAATTTTTGGAAGTT
1 TG-GGGGTCAAAATAGTAATTTTTGGAAGTT
* * *
285665 TAGAGGTCAAAATA-TGATTTTTG
1 TGGGGGTCAAAATAGTAATTTTTG
285688 AAAAGTTCAA
Statistics
Matches: 106, Mismatches: 24, Indels: 20
0.71 0.16 0.13
Matches are distributed among these distances:
27 1 0.01
28 17 0.16
29 50 0.47
30 34 0.32
31 4 0.04
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.35
Consensus pattern (30 bp):
TGGGGGTCAAAATAGTAATTTTTGGAAGTT
Found at i:285687 original size:59 final size:57
Alignment explanation
Indices: 285522--285747 Score: 165
Period size: 59 Copynumber: 3.9 Consensus size: 57
285512 AGGCATATGG
* * * *
285522 GGGTAAAATAGTAATTTTTGGAAGTTT-G-GGGCAAAAATGTGATTTTTGAAAAGTACAA
1 GGGTAAAAT-GTAATTTTTGGAAGTTTAGAGGTC-AAAATATGATTTTTG-GAAGTTCAA
* * * ** * * *
285580 GGTTAAAAATGTAATTTTTAGAAG-TTCGAGGGTCAAAATACAAATTTTGGAAGTTTGAG
1 GGGT-AAAATGTAATTTTTGGAAGTTTAGA-GGTCAAAATATGATTTTTGGAAG-TTCAA
*
285639 GGGTCAAAATGTAATTTTTGGAAGTTTAGAGGTCAAAATATGATTTTTGAAAAGTTCAA
1 GGGT-AAAATGTAATTTTTGGAAGTTTAGAGGTCAAAATATGATTTTTG-GAAGTTCAA
* * ** *
285698 GGGTTAAAATATAATTTTTAGAAAGTACAG-GGT-AAAATATGATTGTTGGA
1 GGG-TAAAATGTAATTTTT-GGAAGTTTAGAGGTCAAAATATGATTTTTGGA
285748 TGGATTAGGA
Statistics
Matches: 132, Mismatches: 27, Indels: 19
0.74 0.15 0.11
Matches are distributed among these distances:
57 3 0.02
58 34 0.26
59 77 0.58
60 18 0.14
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.34
Consensus pattern (57 bp):
GGGTAAAATGTAATTTTTGGAAGTTTAGAGGTCAAAATATGATTTTTGGAAGTTCAA
Found at i:285694 original size:30 final size:30
Alignment explanation
Indices: 285563--285737 Score: 107
Period size: 30 Copynumber: 6.0 Consensus size: 30
285553 CAAAAATGTG
* * *
285563 ATTTTTGAAAAGTACA-AGGTTAAAAATGTA
1 ATTTTTGAAAAGTTCAGAGG-TCAAAATATA
* *
285593 ATTTTT-AGAAGTTC-GAGGGTCAAAATACA
1 ATTTTTGAAAAGTTCAGA-GGTCAAAATATA
* * * * *
285622 AATTTTG-GAAGTTTGAGGGGTCAAAATGTA
1 ATTTTTGAAAAG-TTCAGAGGTCAAAATATA
* * *
285652 ATTTTTG-GAAGTTTAGAGGTCAAAATATG
1 ATTTTTGAAAAGTTCAGAGGTCAAAATATA
*
285681 ATTTTTGAAAAGTTCA-AGGGTTAAAATATA
1 ATTTTTGAAAAGTTCAGA-GGTCAAAATATA
*
285711 ATTTTT-AGAAAGTACAG-GGT-AAAATAT
1 ATTTTTGA-AAAGTTCAGAGGTCAAAATAT
285738 GATTGTTGGA
Statistics
Matches: 116, Mismatches: 20, Indels: 20
0.74 0.13 0.13
Matches are distributed among these distances:
28 7 0.06
29 49 0.42
30 59 0.51
31 1 0.01
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.34
Consensus pattern (30 bp):
ATTTTTGAAAAGTTCAGAGGTCAAAATATA
Found at i:285715 original size:29 final size:29
Alignment explanation
Indices: 285565--285737 Score: 95
Period size: 29 Copynumber: 5.9 Consensus size: 29
285555 AAAATGTGAT
* * * *
285565 TTTTGAAAAGTACAAGGTTAAAAATGTAA
1 TTTTGAAAAGTTCAAGGGTCAAAATATAA
* * * *
285594 TTTTTAGAAGTTCGAGGGTCAAAATACAAA
1 TTTTGAAAAGTTCAAGGGTCAAAATA-TAA
* * * *
285624 TTTTG-GAAGTTTGAGGGGTCAAAATGTAA
1 TTTTGAAAAG-TTCAAGGGTCAAAATATAA
* * *
285653 TTTTTG-GAAGTT-TAGAGGTCAAAATATGAT
1 -TTTTGAAAAGTTCAAG-GGTCAAAATAT-AA
*
285683 TTTTGAAAAGTTCAAGGGTTAAAATATAA
1 TTTTGAAAAGTTCAAGGGTCAAAATATAA
* *
285712 TTTTTAGAAAGTAC-AGGGT-AAAATAT
1 TTTTGA-AAAGTTCAAGGGTCAAAATAT
285738 GATTGTTGGA
Statistics
Matches: 112, Mismatches: 24, Indels: 17
0.73 0.16 0.11
Matches are distributed among these distances:
28 8 0.07
29 53 0.47
30 49 0.44
31 2 0.02
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.34
Consensus pattern (29 bp):
TTTTGAAAAGTTCAAGGGTCAAAATATAA
Found at i:289239 original size:16 final size:16
Alignment explanation
Indices: 289218--289249 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
289208 AGAAATATTT
*
289218 ATGTTAAAGGACTAAA
1 ATGTTAAAGGAATAAA
289234 ATGTTAAAGGAATAAA
1 ATGTTAAAGGAATAAA
289250 TTTGTAAGGA
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:0.53, C:0.03, G:0.19, T:0.25
Consensus pattern (16 bp):
ATGTTAAAGGAATAAA
Found at i:290124 original size:193 final size:194
Alignment explanation
Indices: 289740--290164 Score: 473
Period size: 193 Copynumber: 2.2 Consensus size: 194
289730 GTATCACATG
* *
289740 TGTTACGAATCCTCGACAGCTCGTGTGAGCAGCATCGTGAGTCAGGAAATGAGTAAAGAATCCAA
1 TGTTACGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGAGTCA-GAAAAGAGTAAAGAATCCAA
* * ** *
289805 GAATGGATTACAAGCCCTACGATGGTTGAGATTTATGCATAAATGTATATTCTCGACAACTCGTG
65 GAATGGATTACAAGCCCTACGATGGTTGAGACTTATGCATAAATGCATACACTCGACAACTAGTG
** * * * *
289870 TGAGCATTATCGTTAAGGAACAGTTATATGCACAAATATCGTATCGATGATTGAGGTACCGCATG
130 TGAGCAGCATCGTTAAGGAACAGTTATATGCACAAACATCGTACCGATGATGGAGGTACCGCATA
* ** * * * **
289935 TGTTGCGAGTTTTCGATAGCTTGTGTGAGCAGCATCGTGAGTC-GAAAAGAG-ATATGAATCTTA
1 TGTTACGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGAGTCAGAAAAGAGTA-AAGAATCCAA
* * * * * * *
289998 GGATGGATTATAGGCCCTGCGATGGTTGGGACTTATGCATAAGTGCATACACTTGACAACTAGTG
65 GAATGGATTACAAGCCCTACGATGGTTGAGACTTATGCATAAATGCATACACTCGACAACTAGTG
* * *
290063 TGAGCAGCATCGTT-AGGAGATAGTTATATAG-ATAAACATCGTACCGATGGCTGGA-GTACCGC
130 TGAGCAGCATCGTTAAGGA-ACAGTTATAT-GCACAAACATCGTACCGAT-GATGGAGGTACCGC
290125 ATA
192 ATA
* *
290128 TGTTATGAGTCCTCGACGGCTCGTGTGAGCAGCATCG
1 TGTTACGAGTCCTCGACAGCTCGTGTGAGCAGCATCG
290165 AATACTGGTA
Statistics
Matches: 188, Mismatches: 38, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
192 5 0.03
193 141 0.75
194 5 0.03
195 37 0.20
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (194 bp):
TGTTACGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGAGTCAGAAAAGAGTAAAGAATCCAAG
AATGGATTACAAGCCCTACGATGGTTGAGACTTATGCATAAATGCATACACTCGACAACTAGTGT
GAGCAGCATCGTTAAGGAACAGTTATATGCACAAACATCGTACCGATGATGGAGGTACCGCATA
Found at i:295052 original size:43 final size:43
Alignment explanation
Indices: 294979--295377 Score: 327
Period size: 43 Copynumber: 9.1 Consensus size: 43
294969 TCTGTTACTA
* * ** *
294979 TTAGCGGCATTTGT-AGAAAAATGCCGTTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
* * * * * *
295021 TTAGCGGTGTTTGTGGGAAAAGTGTCGTTAAACACTATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
* * ** * *
295064 TTAGCGGCTTTACCGACGTTTGTGGGAAAAGAGTCAATAAAAACCCTGTTCT
1 TTAGC-G-------G-CGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
*
295116 TTAGCGGCGTTTGTGGGAAAAGCGCCACTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
* * * *
295159 TTA-CTGGCGTTTGAGTGAAAAGCGCCGCTAAAGATCATGGTCT
1 TTAGC-GGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
** *
295202 TTAGCGGCGTTTGTGGGAAAAGCATCGCTAAAGATCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
* * * *
295245 TTAGTGGCGTTTGTGGGAAAAGCGCCGCTAAAAACTATGTTAT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
* * * *
295288 TTAACGGCGTTTGTGAGAAAAGCGCCGCTAAAAACCATGTTAT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
* * ** * *
295331 TTAGCGACATTT-TTTGTAAAGCGCTGCTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
*
295373 ATAGC
1 TTAGC
295378 AGTGTTTTTC
Statistics
Matches: 295, Mismatches: 50, Indels: 24
0.80 0.14 0.07
Matches are distributed among these distances:
42 41 0.14
43 215 0.73
44 3 0.01
51 2 0.01
52 34 0.12
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (43 bp):
TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
Found at i:299439 original size:29 final size:29
Alignment explanation
Indices: 299406--299471 Score: 123
Period size: 29 Copynumber: 2.3 Consensus size: 29
299396 CAGAATATGA
299406 AATAATTTATTCAATTTAAAATCAATAAG
1 AATAATTTATTCAATTTAAAATCAATAAG
*
299435 AATAATTTATTCAATTTAAAATCAATCAG
1 AATAATTTATTCAATTTAAAATCAATAAG
299464 AATAATTT
1 AATAATTT
299472 TAGGGATTGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.39
Consensus pattern (29 bp):
AATAATTTATTCAATTTAAAATCAATAAG
Found at i:303996 original size:50 final size:50
Alignment explanation
Indices: 303918--304019 Score: 168
Period size: 50 Copynumber: 2.0 Consensus size: 50
303908 TTGGTCACTT
* *
303918 GTTTCGGTAGAAGTTGCAGGATAGGACTTCTTAGCTCTCTAGAGTTTTTA
1 GTTTCGGTAGAAGTTGCAGGATAAGACTTCTTAGCTCTATAGAGTTTTTA
* *
303968 GTTTCGGTAGAAGTTGCAGGGTAAGACTTCTTAGCTCTATGGAGTTTTTA
1 GTTTCGGTAGAAGTTGCAGGATAAGACTTCTTAGCTCTATAGAGTTTTTA
304018 GT
1 GT
304020 GTTAGTAGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.22, C:0.13, G:0.27, T:0.38
Consensus pattern (50 bp):
GTTTCGGTAGAAGTTGCAGGATAAGACTTCTTAGCTCTATAGAGTTTTTA
Found at i:307294 original size:29 final size:29
Alignment explanation
Indices: 307261--307356 Score: 140
Period size: 29 Copynumber: 3.3 Consensus size: 29
307251 GCAAGATATG
*
307261 AAATAATTTATTCT-ATTTAAAATCAATCA
1 AAATAATTTATT-TAATTTAAAATAAATCA
307290 AAATAATTTATTTAATTTAAAATAAATCA
1 AAATAATTTATTTAATTTAAAATAAATCA
* *
307319 AAATAATTTATTTAATTTAAAATTAATTA
1 AAATAATTTATTTAATTTAAAATAAATCA
*
307348 GAATAATTT
1 AAATAATTT
307357 TAGAGATTAA
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
28 1 0.02
29 61 0.98
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (29 bp):
AAATAATTTATTTAATTTAAAATAAATCA
Found at i:310825 original size:17 final size:16
Alignment explanation
Indices: 310803--310873 Score: 70
Period size: 17 Copynumber: 4.2 Consensus size: 16
310793 TTTGGACATT
*
310803 ATTTAAATGAATTTTAA
1 ATTTAAAT-AAATTTAA
** *
310820 ATTTAAATTTATAATAA
1 ATTTAAATAAAT-TTAA
*
310837 ATTAAAATAAATTTAA
1 ATTTAAATAAATTTAA
310853 ATTTAAAATAAATTTAA
1 ATTT-AAATAAATTTAA
310870 ATTT
1 ATTT
310874 GTTGGGCCCA
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
16 7 0.16
17 36 0.84
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (16 bp):
ATTTAAATAAATTTAA
Found at i:310826 original size:6 final size:6
Alignment explanation
Indices: 310815--310873 Score: 56
Period size: 6 Copynumber: 10.5 Consensus size: 6
310805 TTAAATGAAT
*
310815 TTTAAA TTTAAA TTTATAA --TAAA -TTAAA -ATAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
310860 -ATAAA TTTAAA TTT
1 TTTAAA TTTAAA TTT
310874 GTTGGGCCCA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
4 2 0.04
5 14 0.31
6 27 0.60
7 2 0.04
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:310847 original size:27 final size:27
Alignment explanation
Indices: 310817--310871 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
310807 AAATGAATTT
*
310817 TAAATTTAAATTTATAATAAATTAAAA
1 TAAATTTAAATTTAAAATAAATTAAAA
*
310844 TAAATTTAAATTTAAAATAAATTTAAA
1 TAAATTTAAATTTAAAATAAATTAAAA
310871 T
1 T
310872 TTGTTGGGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
TAAATTTAAATTTAAAATAAATTAAAA
Found at i:312180 original size:27 final size:28
Alignment explanation
Indices: 312150--312210 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
312140 TCAAGAATTC
*
312150 TATTAAAAA-GAGGATCAAAGGAAACAA
1 TATTAAAAACAAGGATCAAAGGAAACAA
312177 TATTAAAAACAAGGATCAAAGGAAACAA
1 TATTAAAAACAAGGATCAAAGGAAACAA
312205 TCATTA
1 T-ATTA
312211 GTTGGAGATT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 9 0.29
28 18 0.58
29 4 0.13
ACGTcount: A:0.57, C:0.10, G:0.15, T:0.18
Consensus pattern (28 bp):
TATTAAAAACAAGGATCAAAGGAAACAA
Found at i:323395 original size:16 final size:16
Alignment explanation
Indices: 323376--323408 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
323366 TGTTGATGAG
323376 AAAGAAGAATGATGCA
1 AAAGAAGAATGATGCA
323392 AAAGAAGAATGATGCA
1 AAAGAAGAATGATGCA
323408 A
1 A
323409 TCGGAGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.06, G:0.24, T:0.12
Consensus pattern (16 bp):
AAAGAAGAATGATGCA
Found at i:323548 original size:29 final size:29
Alignment explanation
Indices: 323514--324026 Score: 349
Period size: 29 Copynumber: 17.4 Consensus size: 29
323504 AAAAGGGTAC
**
323514 TTTTGGAATTTCGGGGCCAAAAATGGGAT
1 TTTTGGAATTTCGGGGTTAAAAATGGGAT
* * *
323543 CTTTGGAACTTCAGGGG-T-AAAATGGAAT
1 TTTTGGAATTTC-GGGGTTAAAAATGGGAT
*
323571 TTTTGGACATTTTGGGGTT-AAAATGGGAT
1 TTTTGGA-ATTTCGGGGTTAAAAATGGGAT
* * * *
323600 TTTTGGAAGTTCGGGGGTAAAATTGGAAT
1 TTTTGGAATTTCGGGGTTAAAAATGGGAT
* *
323629 TTTTGGAAGTTTTGGGGTCAAAAATGGGAT
1 TTTTGGAA-TTTCGGGGTTAAAAATGGGAT
* * *
323659 TTTTAGAAGTTCAGAGGG-T-AAAATAGGAT
1 TTTTGGAATTTC-G-GGGTTAAAAATGGGAT
** * *
323688 TTTTGGAAGTTTTAGGGTGAAAAATGAGAT
1 TTTTGGAA-TTTCGGGGTTAAAAATGGGAT
* * **
323718 TTTTGGAAGTTCGGGGGTAAAAATGAAAT
1 TTTTGGAATTTCGGGGTTAAAAATGGGAT
* * * *
323747 TTTTAGAAGTTTCGAGGTAAAAAATGAGAT
1 TTTTGGAA-TTTCGGGGTTAAAAATGGGAT
* * * *
323777 TTTTGGAAGTTCGGGGGTAAAAATAGAAT
1 TTTTGGAATTTCGGGGTTAAAAATGGGAT
* * *
323806 TTTTAGAAATTTCGAGGTCAAAAATGGGAT
1 TTTT-GGAATTTCGGGGTTAAAAATGGGAT
* *
323836 TTTTGGAAGTTTAGGGG-TAAAAATGGAAT
1 TTTTGGAA-TTTCGGGGTTAAAAATGGGAT
* * * *
323865 TTTTGGAAGTTTTGAGGTCAAAAAAGGGAT
1 TTTTGGAA-TTTCGGGGTTAAAAATGGGAT
* * *
323895 TTTT-TAAGTTTCGGTGTCAAAAATGGGAAT
1 TTTTGGAA-TTTCGGGGTTAAAAATGGG-AT
* * * *
323925 TTTTGGAAGTTT-GGGGGTAGAAACGGAAT
1 TTTTGGAA-TTTCGGGGTTAAAAATGGGAT
* *
323954 TTTTGGAAATTTCGGGGTCAAAAATGAGAT
1 TTTTGG-AATTTCGGGGTTAAAAATGGGAT
* * * * *
323984 TTTTAGAAGTTCGAGGCTAAAAAGGGGAT
1 TTTTGGAATTTCGGGGTTAAAAATGGGAT
324013 TTTTGGAAGTTTCG
1 TTTTGGAA-TTTCG
324027 AGACCTTCAA
Statistics
Matches: 370, Mismatches: 95, Indels: 37
0.74 0.19 0.07
Matches are distributed among these distances:
28 30 0.08
29 185 0.50
30 146 0.39
31 9 0.02
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.34
Consensus pattern (29 bp):
TTTTGGAATTTCGGGGTTAAAAATGGGAT
Found at i:324026 original size:59 final size:59
Alignment explanation
Indices: 323514--324023 Score: 467
Period size: 59 Copynumber: 8.7 Consensus size: 59
323504 AAAAGGGTAC
* * * * *
323514 TTTTGGAA-TTTCGGGGCCAAAAATGGGATCTTTGGAACTTCAGGGGT-AAAATG-GAAT
1 TTTTGGAAGTTT-GAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGAGAAT
* * * *
323571 TTTTGGACATTTTGGGGT-TAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATTG-GAAT
1 TTTTGGA-AGTTTGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGAGAAT
* * * *
323629 TTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTAGAAGTTCAGAGGGT-AAAAT-AGGAT
1 TTTTGGAAG-TTTGAGGTCAAAAATGGGATTTTTGGAAGTTC-GGGGGTAAAAATGAGAAT
* * *
323688 TTTTGGAAGTTTTAGGGTGAAAAATGAGATTTTTGGAAGTTCGGGGGTAAAAATGA-AAT
1 TTTTGGAAGTTTGA-GGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGAGAAT
* * *
323747 TTTTAGAAGTTTCGAGGTAAAAAATGAGATTTTTGGAAGTTCGGGGGTAAAAAT-AGAAT
1 TTTTGGAAGTTT-GAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGAGAAT
* * **
323806 TTTTAGAAATTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTAGGGGTAAAAATG-GAAT
1 TTTTGGAAGTTT-GAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGAGAAT
* * * *
323865 TTTTGGAAGTTTTGAGGTCAAAAAAGGGATTTTT-TAAGTTTC-GGTGTCAAAAATGGGAAT
1 TTTTGGAAG-TTTGAGGTCAAAAATGGGATTTTTGGAAG-TTCGGGGGT-AAAAATGAGAAT
* * * * *
323925 TTTTGGAAGTTTGGGGGT-AGAAACGGAATTTTTGGAAATTTC-GGGGTCAAAAATGAG-AT
1 TTTTGGAAGTTT-GAGGTCAAAAATGGGATTTTTGG-AAGTTCGGGGGT-AAAAATGAGAAT
* * *
323984 TTTTAGAAGTTCGAGG-CTAAAAAGGGGATTTTTGGAAGTT
1 TTTTGGAAGTTTGAGGTC-AAAAATGGGATTTTTGGAAGTT
324024 TCGAGACCTT
Statistics
Matches: 383, Mismatches: 48, Indels: 43
0.81 0.10 0.09
Matches are distributed among these distances:
57 33 0.09
58 52 0.14
59 253 0.66
60 43 0.11
61 2 0.01
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.34
Consensus pattern (59 bp):
TTTTGGAAGTTTGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGAGAAT
Found at i:324558 original size:16 final size:16
Alignment explanation
Indices: 324537--324595 Score: 82
Period size: 16 Copynumber: 3.7 Consensus size: 16
324527 CATCCTCCAT
*
324537 GTCGGCCACCGACTCA
1 GTCGACCACCGACTCA
* *
324553 GTCGGCCACCAACTCA
1 GTCGACCACCGACTCA
*
324569 GTCGACCATCGACTCA
1 GTCGACCACCGACTCA
324585 GTCGACCACCG
1 GTCGACCACCG
324596 TGAGCGATTG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.22, C:0.42, G:0.22, T:0.14
Consensus pattern (16 bp):
GTCGACCACCGACTCA
Found at i:325785 original size:17 final size:16
Alignment explanation
Indices: 325763--325850 Score: 68
Period size: 17 Copynumber: 5.2 Consensus size: 16
325753 TTTGGACATT
325763 ATTTAAATGAATTTTAA
1 ATTTAAAT-AATTTTAA
* **
325780 ATTTAAATTTATAATAA
1 ATTTAAA-TAATTTTAA
*
325797 ATTTAAATAAATTTAA
1 ATTTAAATAATTTTAA
**
325813 ATTTAAAATAAACTTAA
1 ATTT-AAATAATTTTAA
* *
325830 TTTTAAAATAAATTTAA
1 ATTT-AAATAATTTTAA
325847 ATTT
1 ATTT
325851 GTTGGGCCCA
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
16 9 0.16
17 48 0.83
18 1 0.02
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (16 bp):
ATTTAAATAATTTTAA
Found at i:325786 original size:6 final size:6
Alignment explanation
Indices: 325775--325850 Score: 65
Period size: 6 Copynumber: 13.5 Consensus size: 6
325765 TTAAATGAAT
325775 TTTAAA TTTAAA TTTATAA --TAAA TTTAAA --TAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * *
325820 -ATAAA CTTAAT TTTAAA -ATAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
325851 GTTGGGCCCA
Statistics
Matches: 56, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
4 6 0.11
5 10 0.18
6 38 0.68
7 2 0.04
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:325807 original size:10 final size:10
Alignment explanation
Indices: 325763--325814 Score: 59
Period size: 11 Copynumber: 4.8 Consensus size: 10
325753 TTTGGACATT
325763 ATTTAAATGAA
1 ATTTAAAT-AA
*
325774 TTTTAAATTTAA
1 ATTTAAA--TAA
325786 ATTTATAATAA
1 ATTTA-AATAA
325797 ATTTAAATAA
1 ATTTAAATAA
325807 ATTTAAAT
1 ATTTAAAT
325815 TTAAAATAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
10 13 0.36
11 14 0.39
12 6 0.17
13 3 0.08
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (10 bp):
ATTTAAATAA
Found at i:325807 original size:27 final size:27
Alignment explanation
Indices: 325777--325829 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
325767 AAATGAATTT
* *
325777 TAAATTTAAATTTATAATAAATTTAAA
1 TAAATTTAAATTTAAAATAAACTTAAA
325804 TAAATTTAAATTTAAAATAAACTTAA
1 TAAATTTAAATTTAAAATAAACTTAA
325830 TTTTAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (27 bp):
TAAATTTAAATTTAAAATAAACTTAAA
Found at i:325845 original size:11 final size:11
Alignment explanation
Indices: 325783--325847 Score: 53
Period size: 11 Copynumber: 5.9 Consensus size: 11
325773 ATTTTAAATT
*
325783 TAAATTTATAA
1 TAAATTTAAAA
325794 TAAATTT-AAA
1 TAAATTTAAAA
*
325804 TAAATTTAAATT
1 TAAATTTAAA-A
* *
325816 TAAA-ATAAACT
1 TAAATTTAAA-A
*
325827 TAATTTTAAAA
1 TAAATTTAAAA
325838 TAAATTTAAA
1 TAAATTTAAA
325848 TTTGTTGGGC
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
10 9 0.21
11 26 0.60
12 8 0.19
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (11 bp):
TAAATTTAAAA
Done.