Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013795.1 Kokia drynarioides strain JFW-HI SEQ_128823, 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: 203481
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 121 characters in sequence are not A, C, G, or T
Found at i:7475 original size:2 final size:2
Alignment explanation
Indices: 7468--7501 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
7458 GCTTACACAA
7468 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7502 GGAGATGAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9942 original size:24 final size:24
Alignment explanation
Indices: 9889--9943 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
9879 ATAATTTTTC
* * *
9889 AGTTAAATTCTGTTTATTTATTTT
1 AGTTAAATTATATTTATTTATTTG
*
9913 AATTAAATTATATTTATTTATTTG
1 AGTTAAATTATATTTATTTATTTG
9937 AGTTAAA
1 AGTTAAA
9944 CTTTTATTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.56
Consensus pattern (24 bp):
AGTTAAATTATATTTATTTATTTG
Found at i:11792 original size:23 final size:23
Alignment explanation
Indices: 11766--11817 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
11756 GGGACCTTAG
11766 TGTGCTATCCGATTAGCACTGTA
1 TGTGCTATCCGATTAGCACTGTA
* * *
11789 TGTGCTTTTCGATTAGCACTGTG
1 TGTGCTATCCGATTAGCACTGTA
11812 TGTGCT
1 TGTGCT
11818 CTCTGTTTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.15, C:0.19, G:0.25, T:0.40
Consensus pattern (23 bp):
TGTGCTATCCGATTAGCACTGTA
Found at i:11898 original size:23 final size:23
Alignment explanation
Indices: 11801--11951 Score: 101
Period size: 23 Copynumber: 6.4 Consensus size: 23
11791 TGCTTTTCGA
*
11801 TTAGCACTGTGTGTGCTCTCTGT
1 TTAGCACTTTGTGTGCTCTCTGT
* ** *
11824 TTACCACATTT-CATGCTCTCCGTT
1 TTAGCAC-TTTGTGTGCTCTCTG-T
* **
11848 ATTAGCACTTCGTGTGCTCTCTAA
1 -TTAGCACTTTGTGTGCTCTCTGT
*
11872 TTAGCACTTTGTGTACTCTCTGT
1 TTAGCACTTTGTGTGCTCTCTGT
*
11895 TTAGCA-TTGTATGTGCTCTCTGT
1 TTAGCACTT-TGTGTGCTCTCTGT
* *
11918 TGCTCAGCAC-TTATGTGCTCTTTGT
1 T--T-AGCACTTTGTGTGCTCTCTGT
*
11943 TTAGTACTT
1 TTAGCACTT
11952 CGGTACTCTC
Statistics
Matches: 98, Mismatches: 20, Indels: 20
0.71 0.14 0.14
Matches are distributed among these distances:
22 6 0.06
23 54 0.55
24 5 0.05
25 28 0.29
26 5 0.05
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (23 bp):
TTAGCACTTTGTGTGCTCTCTGT
Found at i:20173 original size:2 final size:2
Alignment explanation
Indices: 20166--20191 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20156 TAAAACATCG
20166 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
20192 TATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:20243 original size:2 final size:2
Alignment explanation
Indices: 20191--20232 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
20181 ACACACACAC
20191 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20233 CAGCAATATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26332 original size:31 final size:31
Alignment explanation
Indices: 26275--26334 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
26265 AGTTAGATCC
* **
26275 TGAACTTGACAATTGTTCTCGTATTAAAATT
1 TGAAATTGACAATTGTTCTCACATTAAAATT
26306 TGAAATTGACAATT-TCTCTCACATTAAAA
1 TGAAATTGACAATTGT-TCTCACATTAAAA
26335 CCTAAATTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 1 0.04
31 24 0.96
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (31 bp):
TGAAATTGACAATTGTTCTCACATTAAAATT
Found at i:31019 original size:4 final size:4
Alignment explanation
Indices: 31010--31036 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
31000 TCACAAACTT
31010 AAAC AAAC AAAC AAAC AAAC AAAC AAA
1 AAAC AAAC AAAC AAAC AAAC AAAC AAA
31037 AATTAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:33566 original size:3 final size:3
Alignment explanation
Indices: 33558--33592 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
33548 CACCAACTCT
33558 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
33593 CCTGAACAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:34183 original size:16 final size:17
Alignment explanation
Indices: 34162--34194 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
34152 TGTCAATAGG
34162 AATATTTATT-TAATTT
1 AATATTTATTATAATTT
*
34178 AATATTTTTTATAATTT
1 AATATTTATTATAATTT
34195 CCCCAATAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
AATATTTATTATAATTT
Found at i:34878 original size:13 final size:15
Alignment explanation
Indices: 34860--34891 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
34850 ATTTTATTTG
34860 ATATAA-AAATA-TA
1 ATATAATAAATAGTA
34873 ATATAATAAATAGTA
1 ATATAATAAATAGTA
34888 ATAT
1 ATAT
34892 TAATTATCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.35
14 5 0.29
15 6 0.35
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (15 bp):
ATATAATAAATAGTA
Found at i:39210 original size:29 final size:27
Alignment explanation
Indices: 39166--39224 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
39156 TTTATCTTGA
*
39166 TTAAAAATACACTTTA-ATTTTTAATTT
1 TTAAAAATACACTTTATAATTTT-ATTT
39193 TTAAAAATACACTTTTTATAATTTTATTT
1 TTAAAAATACAC--TTTATAATTTTATTT
39222 TTA
1 TTA
39225 TTTACTAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 12 0.43
29 11 0.39
30 5 0.18
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (27 bp):
TTAAAAATACACTTTATAATTTTATTT
Found at i:55407 original size:17 final size:17
Alignment explanation
Indices: 55385--55420 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
55375 CACAGTATAA
55385 CTGGTCTTTGTTATTTC
1 CTGGTCTTTGTTATTTC
55402 CTGGTCTTTGTTATTTC
1 CTGGTCTTTGTTATTTC
55419 CT
1 CT
55421 CATTGTACCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.06, C:0.19, G:0.17, T:0.58
Consensus pattern (17 bp):
CTGGTCTTTGTTATTTC
Found at i:60831 original size:17 final size:17
Alignment explanation
Indices: 60784--60831 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 17
60774 ATAATTAAAG
60784 TTTATTTAATATTTTTA
1 TTTATTTAATATTTTTA
*
60801 ---ATTTAATATATTTA
1 TTTATTTAATATTTTTA
*
60815 TTTATTTAAAATTTTTA
1 TTTATTTAATATTTTTA
60832 CTCATAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
14 13 0.52
17 12 0.48
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTATTTAATATTTTTA
Found at i:61660 original size:21 final size:20
Alignment explanation
Indices: 61635--61682 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 20
61625 GATTTGAATA
61635 AAAAAATTTAAATATCAAATT
1 AAAAAATTTAAATATCAAA-T
* *
61656 AAAAAACTTAAATATTAAAT
1 AAAAAATTTAAATATCAAAT
61676 AAAAAAT
1 AAAAAAT
61683 AAAAAATTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAAAATTTAAATATCAAAT
Found at i:82522 original size:41 final size:41
Alignment explanation
Indices: 82423--82523 Score: 157
Period size: 41 Copynumber: 2.5 Consensus size: 41
82413 TATGAAAAAT
* * *
82423 GCCGCTAAAGGTCAGAGAATTAGCGGCGCTTATGGGAAAGC
1 GCCGCTAAAGGTCAGAGCATTAGCGGCGCTGATGGAAAAGC
* *
82464 GCCGCTAAAGGTTAGAGCATTAGCGGTGCTGATGGAAAAGC
1 GCCGCTAAAGGTCAGAGCATTAGCGGCGCTGATGGAAAAGC
82505 GCCGCTAAAGGTCAGAGCA
1 GCCGCTAAAGGTCAGAGCA
82524 AGCGCTGCTA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.30, C:0.20, G:0.34, T:0.17
Consensus pattern (41 bp):
GCCGCTAAAGGTCAGAGCATTAGCGGCGCTGATGGAAAAGC
Found at i:82533 original size:22 final size:22
Alignment explanation
Indices: 82501--82545 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
82491 GCTGATGGAA
82501 AAGCGCCGCTAAAGGTCAGAGC
1 AAGCGCCGCTAAAGGTCAGAGC
*
82523 AAGCGCTGCTAAAGGTCAGAGC
1 AAGCGCCGCTAAAGGTCAGAGC
82545 A
1 A
82546 TTAGCGGCGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.33, C:0.24, G:0.31, T:0.11
Consensus pattern (22 bp):
AAGCGCCGCTAAAGGTCAGAGC
Found at i:82567 original size:63 final size:63
Alignment explanation
Indices: 82460--82586 Score: 175
Period size: 63 Copynumber: 2.0 Consensus size: 63
82450 GCTTATGGGA
* * * *
82460 AAGCGCCGCTAAAGGTTAGAGCATTAGCGGTGCTGATGGAAAAGCGCCGCTAAAGGTCAGAGC
1 AAGCGCCGCTAAAGGTCAGAGCATTAGCGGCGCTGATGGAAAAGCGCCGCGAAAGATCAGAGC
* * *
82523 AAGCGCTGCTAAAGGTCAGAGCATTAGCGGCGCTTAT-GAGAAAGCGCTGCGAAAGATCAGAGC
1 AAGCGCCGCTAAAGGTCAGAGCATTAGCGGCGCTGATGGA-AAAGCGCCGCGAAAGATCAGAGC
82586 A
1 A
82587 TTAGCGGCGC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
62 2 0.04
63 54 0.96
ACGTcount: A:0.31, C:0.20, G:0.32, T:0.16
Consensus pattern (63 bp):
AAGCGCCGCTAAAGGTCAGAGCATTAGCGGCGCTGATGGAAAAGCGCCGCGAAAGATCAGAGC
Found at i:82583 original size:41 final size:41
Alignment explanation
Indices: 82523--82639 Score: 162
Period size: 41 Copynumber: 2.9 Consensus size: 41
82513 AGGTCAGAGC
*
82523 AAGCGCTGCTAAAGGTCAGAGCATTAGCGGCGCTTATGAGA
1 AAGCGCTGCTAAAGGTCAGAGCATTAGCGGCGCTTATGAAA
* * *
82564 AAGCGCTGCGAAAGATCAGAGCATTAGCGGCGCTGATGAAA
1 AAGCGCTGCTAAAGGTCAGAGCATTAGCGGCGCTTATGAAA
* * * *
82605 AAACGCCGCTAAAGGTTAGTGCATTAGCGGCGCTT
1 AAGCGCTGCTAAAGGTCAGAGCATTAGCGGCGCTT
82640 TCTCATAAAC
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 65 1.00
ACGTcount: A:0.30, C:0.21, G:0.31, T:0.19
Consensus pattern (41 bp):
AAGCGCTGCTAAAGGTCAGAGCATTAGCGGCGCTTATGAAA
Found at i:82585 original size:104 final size:104
Alignment explanation
Indices: 82426--82620 Score: 309
Period size: 104 Copynumber: 1.9 Consensus size: 104
82416 GAAAAATGCC
* * * * *
82426 GCTAAAGGTCAGAGAATTAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTTAGAGCATTAGCGGT
1 GCTAAAGGTCAGAGAATTAGCGGCGCTTATGAGAAAGCGCCGCGAAAGATCAGAGCATTAGCGGC
* *
82491 GCTGATGGAAAAGCGCCGCTAAAGGTCAGAGCAAGCGCT
66 GCTGATGAAAAAACGCCGCTAAAGGTCAGAGCAAGCGCT
* *
82530 GCTAAAGGTCAGAGCATTAGCGGCGCTTATGAGAAAGCGCTGCGAAAGATCAGAGCATTAGCGGC
1 GCTAAAGGTCAGAGAATTAGCGGCGCTTATGAGAAAGCGCCGCGAAAGATCAGAGCATTAGCGGC
82595 GCTGATGAAAAAACGCCGCTAAAGGT
66 GCTGATGAAAAAACGCCGCTAAAGGT
82621 TAGTGCATTA
Statistics
Matches: 82, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
104 82 1.00
ACGTcount: A:0.31, C:0.19, G:0.32, T:0.17
Consensus pattern (104 bp):
GCTAAAGGTCAGAGAATTAGCGGCGCTTATGAGAAAGCGCCGCGAAAGATCAGAGCATTAGCGGC
GCTGATGAAAAAACGCCGCTAAAGGTCAGAGCAAGCGCT
Found at i:91347 original size:19 final size:18
Alignment explanation
Indices: 91325--91363 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
91315 AGTAAAATTT
91325 TATCACGATTAAAAAATAA
1 TATCA-GATTAAAAAATAA
* *
91344 TATCATATTTAAAAATAA
1 TATCAGATTAAAAAATAA
91362 TA
1 TA
91364 ATCTAAAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.56, C:0.08, G:0.03, T:0.33
Consensus pattern (18 bp):
TATCAGATTAAAAAATAA
Found at i:101396 original size:7 final size:7
Alignment explanation
Indices: 101384--101409 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
101374 TGAAAGGCTC
101384 GAGAGTT
1 GAGAGTT
101391 GAGAGTT
1 GAGAGTT
101398 GAGAGTT
1 GAGAGTT
101405 GAGAG
1 GAGAG
101410 AGAGAGAGCT
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:0.31, C:0.00, G:0.46, T:0.23
Consensus pattern (7 bp):
GAGAGTT
Found at i:105373 original size:7 final size:7
Alignment explanation
Indices: 105328--105369 Score: 66
Period size: 7 Copynumber: 6.0 Consensus size: 7
105318 TTATAGCAAA
105328 AGAACAG
1 AGAACAG
105335 AGAACAG
1 AGAACAG
*
105342 AGAACGG
1 AGAACAG
105349 AGAACAG
1 AGAACAG
105356 AGAACAG
1 AGAACAG
*
105363 TGAACAG
1 AGAACAG
105370 TGAAGAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.52, C:0.14, G:0.31, T:0.02
Consensus pattern (7 bp):
AGAACAG
Found at i:106372 original size:17 final size:18
Alignment explanation
Indices: 106334--106374 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
106324 CTAGAGCATA
*
106334 CAGATGCACAATCAGAAT
1 CAGATGCACAACCAGAAT
*
106352 -AGATGCACAACCTG-AT
1 CAGATGCACAACCAGAAT
106368 CAGATGC
1 CAGATGC
106375 TGAAGCAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 2 0.10
17 18 0.90
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (18 bp):
CAGATGCACAACCAGAAT
Found at i:110136 original size:15 final size:15
Alignment explanation
Indices: 110102--110150 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 15
110092 ATATACTAAA
110102 TTAAATAA-ATTTCCTT
1 TTAAATAATATTT--TT
110118 TTAAATAATATTTTT
1 TTAAATAATATTTTT
110133 TTAAA-AATATATTTT
1 TTAAATAATAT-TTTT
110148 TTA
1 TTA
110151 TTTATTCTCG
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
14 5 0.16
15 14 0.45
16 8 0.26
17 4 0.13
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (15 bp):
TTAAATAATATTTTT
Found at i:110144 original size:16 final size:15
Alignment explanation
Indices: 110116--110149 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
110106 ATAAATTTCC
*
110116 TTTTAAATAATATTT
1 TTTTAAAAAATATTT
110131 TTTTAAAAATATATTT
1 TTTTAAAAA-ATATTT
110147 TTT
1 TTT
110150 ATTTATTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTAAAAAATATTT
Found at i:110176 original size:2 final size:2
Alignment explanation
Indices: 110166--110195 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
110156 TCTCGAAAAA
*
110166 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
110196 TTAATGTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:117623 original size:28 final size:29
Alignment explanation
Indices: 117592--117648 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 29
117582 TTACTCAATC
117592 CTAATTCCTAACTCATATTT-AAAATATT
1 CTAATTCCTAACTCATATTTAAAAATATT
*
117620 CTAATTCCTAACTCATGTTTAAAAATATT
1 CTAATTCCTAACTCATATTTAAAAATATT
117649 AAAATTTTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 19 0.70
29 8 0.30
ACGTcount: A:0.39, C:0.18, G:0.02, T:0.42
Consensus pattern (29 bp):
CTAATTCCTAACTCATATTTAAAAATATT
Found at i:117883 original size:17 final size:18
Alignment explanation
Indices: 117861--117902 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
117851 CAATTGTTAT
117861 ATAATATAT-AAATAATA
1 ATAATATATAAAATAATA
*
117878 ATAATA-ATAAAATAGTA
1 ATAATATATAAAATAATA
*
117895 ACAATATA
1 ATAATATA
117903 ATAACGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 2 0.10
17 18 0.86
18 1 0.05
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (18 bp):
ATAATATATAAAATAATA
Found at i:127008 original size:11 final size:9
Alignment explanation
Indices: 126969--127002 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
126959 TATGGAATTC
126969 CTTTTTTTT
1 CTTTTTTTT
*
126978 TTTTTTTTT
1 CTTTTTTTT
126987 CTTTTTTTT
1 CTTTTTTTT
126996 CTTTTTT
1 CTTTTTT
127003 GGTTCTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:127008 original size:20 final size:18
Alignment explanation
Indices: 126969--127008 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
126959 TATGGAATTC
*
126969 CTTTTTTTTTTTTTTTTT
1 CTTTTTTTTTTTTTTGTT
126987 CTTTTTTTTCTTTTTTGGTT
1 CTTTTTTTT-TTTTTT-GTT
127007 CT
1 CT
127009 AAAATTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
19 6 0.32
20 4 0.21
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.85
Consensus pattern (18 bp):
CTTTTTTTTTTTTTTGTT
Found at i:130990 original size:1 final size:1
Alignment explanation
Indices: 130984--131009 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
130974 NNNNNNNNNN
130984 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
131010 GAGTTGTTAC
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:136009 original size:20 final size:21
Alignment explanation
Indices: 135978--136024 Score: 78
Period size: 20 Copynumber: 2.3 Consensus size: 21
135968 ACAAAAAATA
135978 CAAAATAATCAAAATAATTTT
1 CAAAATAATCAAAATAATTTT
135999 CAAAA-AATCAAAATAATTTT
1 CAAAATAATCAAAATAATTTT
*
136019 TAAAAT
1 CAAAAT
136025 TAAAAATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.32
Consensus pattern (21 bp):
CAAAATAATCAAAATAATTTT
Found at i:136030 original size:19 final size:20
Alignment explanation
Indices: 135978--136032 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
135968 ACAAAAAATA
*
135978 CAAAATAATCAAAATAATTTT
1 CAAAA-AATAAAAATAATTTT
*
135999 CAAAAAATCAAAATAATTTT
1 CAAAAAATAAAAATAATTTT
* *
136019 -TAAAATTAAAAATA
1 CAAAAAATAAAAATA
136033 TTTGAAACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 11 0.35
20 15 0.48
21 5 0.16
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (20 bp):
CAAAAAATAAAAATAATTTT
Found at i:139400 original size:23 final size:24
Alignment explanation
Indices: 139356--139408 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
139346 TTCAGCCTGT
*
139356 GTGTGCCCTCTGTTATTAGCACTTC
1 GTGTGCCCCCTG-TATTAGCACTTC
*
139381 GTGTGCCCCCTG-ATTAGCACTTT
1 GTGTGCCCCCTGTATTAGCACTTC
139404 GTGTG
1 GTGTG
139409 TCGTCTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 15 0.58
25 11 0.42
ACGTcount: A:0.11, C:0.26, G:0.25, T:0.38
Consensus pattern (24 bp):
GTGTGCCCCCTGTATTAGCACTTC
Found at i:139409 original size:25 final size:25
Alignment explanation
Indices: 139353--139409 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
139343 CTGTTCAGCC
*
139353 TGTGTGTGCCCTCTGTTATTAGCACT
1 TGTGTGTGCCCCCTG-TATTAGCACT
*
139379 T-CGTGTGCCCCCTG-ATTAGCACTT
1 TGTGTGTGCCCCCTGTATTAGCAC-T
139403 TGTGTGT
1 TGTGTGT
139410 CGTCTATTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
23 8 0.31
24 2 0.08
25 15 0.58
26 1 0.04
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.40
Consensus pattern (25 bp):
TGTGTGTGCCCCCTGTATTAGCACT
Found at i:160260 original size:20 final size:21
Alignment explanation
Indices: 160222--160260 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
160212 GTGTTTTCAC
160222 TACACAACGATTGTGCAAGCA
1 TACACAACGATTGTGCAAGCA
160243 TACAC-ACG-TTGATGCAAG
1 TACACAACGATTG-TGCAAG
160261 TATAGTTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.18
20 9 0.53
21 5 0.29
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.21
Consensus pattern (21 bp):
TACACAACGATTGTGCAAGCA
Found at i:163016 original size:22 final size:24
Alignment explanation
Indices: 162976--163019 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
162966 TGATAAAGTA
162976 TTTTGATATAATAAATTAAAATGT
1 TTTTGATATAATAAATTAAAATGT
*
163000 TTTTGA-AT-ATAAGTTAAAAT
1 TTTTGATATAATAAATTAAAAT
163020 TGATAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
23 2 0.11
24 6 0.32
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (24 bp):
TTTTGATATAATAAATTAAAATGT
Found at i:163158 original size:20 final size:19
Alignment explanation
Indices: 163117--163180 Score: 58
Period size: 20 Copynumber: 3.3 Consensus size: 19
163107 AAATCAAGTT
*
163117 AAAATGAATTT-AAAAATGTC
1 AAAAT-AATTTGAACAAT-TC
163137 AAAATAATTTGAACTAATTC
1 AAAATAATTTGAAC-AATTC
* * *
163157 AAAATCATTTTAACACTTC
1 AAAATAATTTGAACAATTC
163176 AAAAT
1 AAAAT
163181 GGTTTTCAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
19 14 0.37
20 21 0.55
21 3 0.08
ACGTcount: A:0.52, C:0.11, G:0.05, T:0.33
Consensus pattern (19 bp):
AAAATAATTTGAACAATTC
Found at i:163273 original size:18 final size:19
Alignment explanation
Indices: 163241--163282 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
163231 TTTGGCCAAG
*
163241 TATCGATAATTCTTG-AAA
1 TATCGATAATCCTTGTAAA
*
163259 TATCGATACTCCTTGTAAA
1 TATCGATAATCCTTGTAAA
163278 -ATCGA
1 TATCGA
163283 GATCAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.36
Consensus pattern (19 bp):
TATCGATAATCCTTGTAAA
Found at i:165134 original size:14 final size:14
Alignment explanation
Indices: 165117--165160 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
165107 CAGGTCAACT
165117 GGTCAAATTCAATG
1 GGTCAAATTCAATG
* *
165131 GGTC-GA-TAAATG
1 GGTCAAATTCAATG
165143 GGTCAAATTCAATG
1 GGTCAAATTCAATG
165157 GGTC
1 GGTC
165161 GATCAACGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
12 9 0.38
13 2 0.08
14 13 0.54
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.27
Consensus pattern (14 bp):
GGTCAAATTCAATG
Found at i:166375 original size:28 final size:28
Alignment explanation
Indices: 166328--166591 Score: 157
Period size: 28 Copynumber: 10.0 Consensus size: 28
166318 CATTTTTATA
* *
166328 CATATGTATAAGTTGGCGAGCGTAAACG
1 CATATGTATAAGCTGACGAGCGTAAACG
* *
166356 CATATGTATAAGCTGACGAGCATAAATG
1 CATATGTATAAGCTGACGAGCGTAAACG
*
166384 CGTATGTATAAGCTGACGAGCGTAAACG
1 CATATGTATAAGCTGACGAGCGTAAACG
** * * * *
166412 ----TGTGCAAGTTGGCAAGCGTAAATG
1 CATATGTATAAGCTGACGAGCGTAAACG
* *
166436 CGTATGTATAAGCTGACGAGC--ATA--
1 CATATGTATAAGCTGACGAGCGTAAACG
* ** * *
166460 -A-ATG--TAAGTTGGTGAGTGTAAATG
1 CATATGTATAAGCTGACGAGCGTAAACG
* *
166484 CATATGTATAAGCTGGCGAGCGTAAATG
1 CATATGTATAAGCTGACGAGCGTAAACG
*
166512 CATATGTATAAGCTGACGAGCATAAACG
1 CATATGTATAAGCTGACGAGCGTAAACG
** *
166540 ----TGTGCAAGCTGGA-GAGCATAAACG
1 CATATGTATAAGCT-GACGAGCGTAAACG
* * *
166564 CATAAGCATAAGCTGATGAGCGTAAACG
1 CATATGTATAAGCTGACGAGCGTAAACG
166592 TGTGCAAGCT
Statistics
Matches: 180, Mismatches: 38, Indels: 36
0.71 0.15 0.14
Matches are distributed among these distances:
20 9 0.05
22 5 0.03
24 37 0.21
25 3 0.02
26 5 0.03
27 2 0.01
28 119 0.66
ACGTcount: A:0.34, C:0.14, G:0.28, T:0.23
Consensus pattern (28 bp):
CATATGTATAAGCTGACGAGCGTAAACG
Found at i:166490 original size:48 final size:49
Alignment explanation
Indices: 166378--166511 Score: 180
Period size: 48 Copynumber: 2.7 Consensus size: 49
166368 CTGACGAGCA
166378 TAAATGCGTATGTATAAGCTGACGAGCGTAAACGTGTGCAAGTTGGCAAGCG
1 TAAATGCGTATGTATAAGCTGACGAGCGTAAA--TGT-CAAGTTGGCAAGCG
* ** *
166430 TAAATGCGTATGTATAAGCTGACGAGCATAAATGT-AAGTTGGTGAGTG
1 TAAATGCGTATGTATAAGCTGACGAGCGTAAATGTCAAGTTGGCAAGCG
* *
166478 TAAATGCATATGTATAAGCTGGCGAGCGTAAATG
1 TAAATGCGTATGTATAAGCTGACGAGCGTAAATG
166512 CATATGTATA
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
48 41 0.55
50 3 0.04
52 31 0.41
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.26
Consensus pattern (49 bp):
TAAATGCGTATGTATAAGCTGACGAGCGTAAATGTCAAGTTGGCAAGCG
Found at i:166556 original size:24 final size:24
Alignment explanation
Indices: 166521--166602 Score: 76
Period size: 24 Copynumber: 3.2 Consensus size: 24
166511 GCATATGTAT
166521 AAGCTGACGAGCATAAACGTGTGC
1 AAGCTGACGAGCATAAACGTGTGC
**
166545 AAGCTGGA-GAGCATAAACGCATAAGC
1 AAGCT-GACGAGCATAAACG--TGTGC
* *
166571 ATAAGCTGATGAGCGTAAACGTGTGC
1 --AAGCTGACGAGCATAAACGTGTGC
166597 AAGCTG
1 AAGCTG
166603 GCCAGCGTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
24 22 0.47
25 2 0.04
26 6 0.13
27 2 0.04
28 15 0.32
ACGTcount: A:0.35, C:0.18, G:0.29, T:0.17
Consensus pattern (24 bp):
AAGCTGACGAGCATAAACGTGTGC
Found at i:166575 original size:128 final size:128
Alignment explanation
Indices: 166336--166625 Score: 357
Period size: 128 Copynumber: 2.2 Consensus size: 128
166326 TACATATGTA
*
166336 TAAGTTGGCGAGCGTAAACGCATATGTATAAGCTGACGAGCATAAATGCGTATGTATAAGCTGAC
1 TAAGTTGGCGAGCGTAAACGCATATGTATAAGCTGACGAGCATAAATGCATATGTATAAGCTGAC
* * * * * * *
166401 GAGCGTAAACGTGTGCAAGTTGGCAAGCGTAAATGCGTATGTATAAGCTGACGAGCATAAATG
66 GAGCATAAACGTGTGCAAGCTGGCAAGCATAAACGCATAAGCATAAGCTGACGAGCATAAATG
* * * * *
166464 TAAGTTGGTGAGTGTAAATGCATATGTATAAGCTGGCGAGCGTAAATGCATATGTATAAGCTGAC
1 TAAGTTGGCGAGCGTAAACGCATATGTATAAGCTGACGAGCATAAATGCATATGTATAAGCTGAC
* *
166529 GAGCATAAACGTGTGCAAGCTGG-AGAGCATAAACGCATAAGCATAAGCTGATGAGCGTAAACGT
66 GAGCATAAACGTGTGCAAGCTGGCA-AGCATAAACGCATAAGCATAAGCTGACGAGCATAAA--T
166593 G
128 G
* * * *
166594 TGCAAGCTGGCCAGCGTAAATGCATATTTATA
1 T--AAGTTGGCGAGCGTAAACGCATATGTATA
166626 CATATTTACA
Statistics
Matches: 137, Mismatches: 20, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
127 1 0.01
128 109 0.80
130 3 0.02
132 24 0.18
ACGTcount: A:0.34, C:0.15, G:0.28, T:0.24
Consensus pattern (128 bp):
TAAGTTGGCGAGCGTAAACGCATATGTATAAGCTGACGAGCATAAATGCATATGTATAAGCTGAC
GAGCATAAACGTGTGCAAGCTGGCAAGCATAAACGCATAAGCATAAGCTGACGAGCATAAATG
Found at i:166619 original size:52 final size:52
Alignment explanation
Indices: 166493--166619 Score: 182
Period size: 52 Copynumber: 2.4 Consensus size: 52
166483 GCATATGTAT
* *
166493 AAGCTGGCGAGCGTAAATGCATATGTATAAGCTGACGAGCATAAACGTGTGC
1 AAGCTGGCGAGCGTAAATGCATAAGCATAAGCTGACGAGCATAAACGTGTGC
* * * * *
166545 AAGCTGGAGAGCATAAACGCATAAGCATAAGCTGATGAGCGTAAACGTGTGC
1 AAGCTGGCGAGCGTAAATGCATAAGCATAAGCTGACGAGCATAAACGTGTGC
*
166597 AAGCTGGCCAGCGTAAATGCATA
1 AAGCTGGCGAGCGTAAATGCATA
166620 TTTATACATA
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 64 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (52 bp):
AAGCTGGCGAGCGTAAATGCATAAGCATAAGCTGACGAGCATAAACGTGTGC
Found at i:170093 original size:12 final size:11
Alignment explanation
Indices: 170072--170115 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
170062 AATAACTTAA
170072 TAATAAAATAT
1 TAATAAAATAT
*
170083 TACTAAAAATAT
1 TAAT-AAAATAT
170095 TAATAAAATAT
1 TAATAAAATAT
*
170106 TAATTAAATA
1 TAATAAAATA
170116 ACTTTTTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 19 0.66
12 10 0.34
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (11 bp):
TAATAAAATAT
Found at i:171064 original size:2 final size:2
Alignment explanation
Indices: 171057--171081 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
171047 ATCTACTTTA
171057 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
171082 ATTTATAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:173813 original size:24 final size:24
Alignment explanation
Indices: 173784--174149 Score: 166
Period size: 24 Copynumber: 15.2 Consensus size: 24
173774 ATCAAAGTAA
173784 AGTAAACGTATATAAGCTGACGAG
1 AGTAAACGTATATAAGCTGACGAG
* * * *
173808 AGTAAACCTGTGTCAGCTGACGAG
1 AGTAAACGTATATAAGCTGACGAG
* * *
173832 CGTAAAAGTATATAAGCTGATGAG
1 AGTAAACGTATATAAGCTGACGAG
* * * * *
173856 CA-TAAATGTGTACAAGATGATGAG
1 -AGTAAACGTATATAAGCTGACGAG
*
173880 CA-TAAACGTATATGAGCTGACGAG
1 -AGTAAACGTATATAAGCTGACGAG
* ** * *
173904 CA-TAAACGTGTGCAAGTTAACGAG
1 -AGTAAACGTATATAAGCTGACGAG
* * *
173928 TGTAAATGTATATGAGCTGACGAG
1 AGTAAACGTATATAAGCTGACGAG
* * * * ** *
173952 TGTAATCATGTGCAAGCTAACGAG
1 AGTAAACGTATATAAGCTGACGAG
*
173976 CA-TAAACGTATATGAGCTGACGAG
1 -AGTAAACGTATATAAGCTGACGAG
* * * *
174000 CGTAAATGTATATGAGCTGACAAG
1 AGTAAACGTATATAAGCTGACGAG
* * * *
174024 CGTAAATGTATATAAGCTAACAAG
1 AGTAAACGTATATAAGCTGACGAG
* * ** *
174048 CA-TAAACATGTGCAAGTTGACGAG
1 -AGTAAACGTATATAAGCTGACGAG
* * *
174072 CGTAAACATGTATAAGCTGACGAG
1 AGTAAACGTATATAAGCTGACGAG
* * * **
174096 CGTAAATGTGTGCAAGCTGACGAG
1 AGTAAACGTATATAAGCTGACGAG
* * *
174120 CGTAAACGTAAATAAGCTGGCGAG
1 AGTAAACGTATATAAGCTGACGAG
*
174144 CGTAAA
1 AGTAAA
174150 ATGTAATAAA
Statistics
Matches: 256, Mismatches: 80, Indels: 12
0.74 0.23 0.03
Matches are distributed among these distances:
24 256 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.22
Consensus pattern (24 bp):
AGTAAACGTATATAAGCTGACGAG
Found at i:173843 original size:48 final size:48
Alignment explanation
Indices: 173785--174149 Score: 293
Period size: 48 Copynumber: 7.6 Consensus size: 48
173775 TCAAAGTAAA
173785 GTAAACGTATATAAGCTGACGAGAGTAAACCTGTGTC-AGCTGACGAGC
1 GTAAACGTATATAAGCTGACGAGAGTAAA-CTGTGTCAAGCTGACGAGC
* * * *
173833 GTAAAAGTATATAAGCTGATGAGCA-TAAA-TGTGTACAAGATGATGAGC
1 GTAAACGTATATAAGCTGACGAG-AGTAAACTGTGT-CAAGCTGACGAGC
* * * * *
173881 ATAAACGTATATGAGCTGACGAGCA-TAAAC-GTGTGCAAGTTAACGAGT
1 GTAAACGTATATAAGCTGACGAG-AGTAAACTGTGT-CAAGCTGACGAGC
* * * * *
173929 GTAAATGTATATGAGCTGACGAGTGTAATCATGTG-CAAGCTAACGAGC
1 GTAAACGTATATAAGCTGACGAGAGTAAAC-TGTGTCAAGCTGACGAGC
* * * * *
173977 ATAAACGTATATGAGCTGACGAGCGTAAA-TGTAT-ATGAGCTGACAAGC
1 GTAAACGTATATAAGCTGACGAGAGTAAACTGTGTCA--AGCTGACGAGC
* * * *
174025 GTAAATGTATATAAGCTAACAAGCA-TAAACATGTG-CAAGTTGACGAGC
1 GTAAACGTATATAAGCTGACGAG-AGTAAAC-TGTGTCAAGCTGACGAGC
* * *
174073 GTAAACATGTATAAGCTGACGAGCGTAAA-TGTGTGCAAGCTGACGAGC
1 GTAAACGTATATAAGCTGACGAGAGTAAACTGTGT-CAAGCTGACGAGC
* * *
174121 GTAAACGTAAATAAGCTGGCGAGCGTAAA
1 GTAAACGTATATAAGCTGACGAGAGTAAA
174150 ATGTAATAAA
Statistics
Matches: 254, Mismatches: 46, Indels: 34
0.76 0.14 0.10
Matches are distributed among these distances:
46 13 0.05
47 1 0.00
48 232 0.91
49 1 0.00
50 7 0.03
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (48 bp):
GTAAACGTATATAAGCTGACGAGAGTAAACTGTGTCAAGCTGACGAGC
Found at i:173977 original size:96 final size:95
Alignment explanation
Indices: 173786--174153 Score: 355
Period size: 96 Copynumber: 3.8 Consensus size: 95
173776 CAAAGTAAAG
* *
173786 TAAACGTATATAAGCTGACGAG-AGTAAACCTGTGTC-AGCTGACGAGCGTAAAAGTATATAAGC
1 TAAACGTATATAAGCTGACGAGCA-TAAACGTGTG-CAAGCTGACGAGCGTAAATGTATATAAGC
* *
173849 TGATGAGCATAA-ATGTGTACAAGATGATGAGCA
64 TGACGAGCATAACATGTG--CAAGATGACGAGCA
* * * * *
173882 TAAACGTATATGAGCTGACGAGCATAAACGTGTGCAAGTTAACGAGTGTAAATGTATATGAGCTG
1 TAAACGTATATAAGCTGACGAGCATAAACGTGTGCAAGCTGACGAGCGTAAATGTATATAAGCTG
** * *
173947 ACGAGTGTAATCATGTGCAAGCTAACGAGCA
66 ACGAGCATAA-CATGTGCAAGATGACGAGCA
* * * * *** * *
173978 TAAACGTATATGAGCTGACGAGCGTAAATGTATATGAGCTGACAAGCGTAAATGTATATAAGCTA
1 TAAACGTATATAAGCTGACGAGCATAAACGTGTGCAAGCTGACGAGCGTAAATGTATATAAGCTG
* * *
174043 ACAAGCATAAACATGTGCAAGTTGACGAGCG
66 ACGAGCAT-AACATGTGCAAGATGACGAGCA
* * * * * *
174074 TAAACATGTATAAGCTGACGAGCGTAAATGTGTGCAAGCTGACGAGCGTAAACGTAAATAAGCTG
1 TAAACGTATATAAGCTGACGAGCATAAACGTGTGCAAGCTGACGAGCGTAAATGTATATAAGCTG
* * *
174139 GCGAGCGTAAAATGT
66 ACGAGCATAACATGT
174154 AATAAATATG
Statistics
Matches: 221, Mismatches: 46, Indels: 11
0.79 0.17 0.04
Matches are distributed among these distances:
95 7 0.03
96 206 0.93
97 3 0.01
98 5 0.02
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (95 bp):
TAAACGTATATAAGCTGACGAGCATAAACGTGTGCAAGCTGACGAGCGTAAATGTATATAAGCTG
ACGAGCATAACATGTGCAAGATGACGAGCA
Found at i:173999 original size:72 final size:72
Alignment explanation
Indices: 173923--174154 Score: 226
Period size: 72 Copynumber: 3.2 Consensus size: 72
173913 GTGCAAGTTA
* *
173923 ACGAGTGT-AAATGTATATGAGCTGACGAGTGTAATCATGTGCAAGCTAACGAGCATAAACGTAT
1 ACGAGCGTAAAATGTATATGAGCTGACGAGCGTAAT-ATGTGCAAGCTAACGAGCATAAACGTAT
173987 ATGAGCTG
65 ATGAGCTG
* ** *
173995 ACGAGCGT-AAATGTATATGAGCTGACAAGCGTAA-ATGTATATAAGCTAACAAGCATAAAC--A
1 ACGAGCGTAAAATGTATATGAGCTGACGAGCGTAATATG--TGCAAGCTAACGAGCATAAACGTA
* *
174056 TGTGCAAGTTG
64 TATG--AGCTG
* * *
174067 ACGAGCGTAAACATGTATA--AGCTGACGAGCGTAAATGTGTGCAAGCTGACGAGCGTAAACGTA
1 ACGAGCGTAAA-ATGTATATGAGCTGACGAGCGT-AATATGTGCAAGCTAACGAGCATAAACGTA
* *
174130 AATAAGCTG
64 TATGAGCTG
*
174139 GCGAGCGTAAAATGTA
1 ACGAGCGTAAAATGTA
174155 ATAAATATGG
Statistics
Matches: 130, Mismatches: 20, Indels: 21
0.76 0.12 0.12
Matches are distributed among these distances:
70 7 0.05
71 5 0.04
72 103 0.79
73 4 0.03
74 11 0.08
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (72 bp):
ACGAGCGTAAAATGTATATGAGCTGACGAGCGTAATATGTGCAAGCTAACGAGCATAAACGTATA
TGAGCTG
Found at i:174739 original size:52 final size:52
Alignment explanation
Indices: 174635--174739 Score: 147
Period size: 52 Copynumber: 2.0 Consensus size: 52
174625 TTGGAATAAC
* *
174635 TCAACAAAGTATTGGTAGAAGTTTAGAGGAAAGGATACCTTGGCTACAGACT
1 TCAACAAAGTATTGGTAGAAGTTCAGAGGAAAGGATACATTGGCTACAGACT
* * * * *
174687 TCAACAATGTATTGGTAGAAGTTCAGAGGACAGGATATATTGGTTACTGACT
1 TCAACAAAGTATTGGTAGAAGTTCAGAGGAAAGGATACATTGGCTACAGACT
174739 T
1 T
174740 GAGTTGTTTC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (52 bp):
TCAACAAAGTATTGGTAGAAGTTCAGAGGAAAGGATACATTGGCTACAGACT
Found at i:180733 original size:30 final size:30
Alignment explanation
Indices: 180697--180774 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 30
180687 ATTTTAACCC
* *
180697 AAGGATTAAATTGGAATTTTTGTGAAATTT
1 AAGGATTAAATTGGAATTTTTATGAAACTT
* * *
180727 AAGGATTAATTTGTAA-ATTTATGAAACTT
1 AAGGATTAAATTGGAATTTTTATGAAACTT
*
180756 AAGGACTAAATT-GAATTTT
1 AAGGATTAAATTGGAATTTT
180775 AATTAAATTT
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
28 2 0.05
29 22 0.58
30 14 0.37
ACGTcount: A:0.40, C:0.03, G:0.17, T:0.41
Consensus pattern (30 bp):
AAGGATTAAATTGGAATTTTTATGAAACTT
Found at i:182711 original size:270 final size:270
Alignment explanation
Indices: 182260--182789 Score: 961
Period size: 270 Copynumber: 2.0 Consensus size: 270
182250 ATTGGAACAT
182260 CATACCATTGTATGTACATGGGTTGGGTTGTATGGTAGAAAACGTGGTAATCACCCCTTCAAACG
1 CATACCATTGTATGTACATGGGTTGGGTTGTATGGTAGAAAACGTGGTAATCACCCCTTCAAACG
* * *
182325 GCTGGTAGTAAAACCACTGCGATTTGTGACAATTGGATGAGGAGGGGTTCTAGGGAACCTCTCCA
66 GCTGGTAGTAAAACCACAGCGATTAGTGACAATTGGATGAGGAGGGGTTCTACGGAACCTCTCCA
*
182390 CTGTGTTGGTGCGCTAGAGATTGGGTGCATTGCATTGTGATTGTGAATTTATTGCATTTGTGTGA
131 CTGTGTTGGTGCGCTAGAGATTAGGTGCATTGCATTGTGATTGTGAATTTATTGCATTTGTGTGA
*
182455 TATGTTGTATGCTTCTTTAAAATGTTTTGAGAAAACTTCTGTGATATTGTGTTGTGTTTGTATGC
196 TATGTTGTATGCTTCTTTAAAATGTTTTGAGAAAACTTCTGTGATATTGTGTTATGTTTGTATGC
182520 TTCTTTATTA
261 TTCTTTATTA
* *
182530 CATACCATTGTATGTACATGGGTTGGGTTGTATGGTGGAAGACGTGGTAATCACCCCTTCAAACG
1 CATACCATTGTATGTACATGGGTTGGGTTGTATGGTAGAAAACGTGGTAATCACCCCTTCAAACG
*
182595 GCTGGTAGTAAAACCACAGTGATTAGTGACAATTGGATGAGGAGGGGTTCTACGGAACCTCTCCA
66 GCTGGTAGTAAAACCACAGCGATTAGTGACAATTGGATGAGGAGGGGTTCTACGGAACCTCTCCA
* * *
182660 TTGTGTTGGTGCGCTGGAGATTAGGTGCATTGCATTGTGCTTGTGAATTTATTGCATTTGTGTGA
131 CTGTGTTGGTGCGCTAGAGATTAGGTGCATTGCATTGTGATTGTGAATTTATTGCATTTGTGTGA
182725 TATGTTGTATGCTTCTTTAAAATGTTTTGAGAAAACTTCTGTGATATTGTGTTATGTTTGTATGC
196 TATGTTGTATGCTTCTTTAAAATGTTTTGAGAAAACTTCTGTGATATTGTGTTATGTTTGTATGC
182790 AATTTAGAGA
Statistics
Matches: 249, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
270 249 1.00
ACGTcount: A:0.23, C:0.13, G:0.27, T:0.37
Consensus pattern (270 bp):
CATACCATTGTATGTACATGGGTTGGGTTGTATGGTAGAAAACGTGGTAATCACCCCTTCAAACG
GCTGGTAGTAAAACCACAGCGATTAGTGACAATTGGATGAGGAGGGGTTCTACGGAACCTCTCCA
CTGTGTTGGTGCGCTAGAGATTAGGTGCATTGCATTGTGATTGTGAATTTATTGCATTTGTGTGA
TATGTTGTATGCTTCTTTAAAATGTTTTGAGAAAACTTCTGTGATATTGTGTTATGTTTGTATGC
TTCTTTATTA
Found at i:183980 original size:29 final size:29
Alignment explanation
Indices: 183917--183981 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
183907 AAAAAAACTT
*
183917 TTTTTCCAATTTTGACTTTTCTCCCCTAAA
1 TTTTT-CAATTTTGACTTTTCTCCCCCAAA
*
183947 ATTTTCAATTTTGACTTTT-TCCTCCCAAA
1 TTTTTCAATTTTGACTTTTCTCC-CCCAAA
183976 TTTTTC
1 TTTTTC
183982 TGTCGTTTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 3 0.10
29 24 0.77
30 4 0.13
ACGTcount: A:0.20, C:0.25, G:0.03, T:0.52
Consensus pattern (29 bp):
TTTTTCAATTTTGACTTTTCTCCCCCAAA
Found at i:183996 original size:3 final size:3
Alignment explanation
Indices: 183988--184125 Score: 276
Period size: 3 Copynumber: 46.0 Consensus size: 3
183978 TTTCTGTCGT
183988 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
184036 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
184084 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
184126 ACAACCGAGT
Statistics
Matches: 135, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 135 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:185356 original size:13 final size:12
Alignment explanation
Indices: 185329--185373 Score: 72
Period size: 12 Copynumber: 3.7 Consensus size: 12
185319 ATTTTAATAG
185329 TAACTTAAATTT
1 TAACTTAAATTT
*
185341 TAACTTAAGTTTT
1 TAACTTAA-ATTT
185354 TAACTTAAATTT
1 TAACTTAAATTT
185366 TAACTTAA
1 TAACTTAA
185374 GAACGGGACA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 19 0.63
13 11 0.37
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (12 bp):
TAACTTAAATTT
Found at i:187665 original size:15 final size:15
Alignment explanation
Indices: 187645--187694 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
187635 ACAAAACGAT
187645 AACGTAAGTGATTAA
1 AACGTAAGTGATTAA
* *
187660 AACGTAA--CATTTA
1 AACGTAAGTGATTAA
*
187673 AACATAAGTGATTAA
1 AACGTAAGTGATTAA
*
187688 AATGTAA
1 AACGTAA
187695 TTTGAAATAA
Statistics
Matches: 26, Mismatches: 7, Indels: 4
0.70 0.19 0.11
Matches are distributed among these distances:
13 10 0.38
15 16 0.62
ACGTcount: A:0.50, C:0.08, G:0.14, T:0.28
Consensus pattern (15 bp):
AACGTAAGTGATTAA
Found at i:191875 original size:163 final size:163
Alignment explanation
Indices: 191580--191903 Score: 513
Period size: 163 Copynumber: 2.0 Consensus size: 163
191570 CTTGAAAACT
* * * * *
191580 GAGCAGTTGATTGATTTGATTTCTGAACCTTAAGTCCACTCCTTTTGAAAAGAAAATGTTACTTT
1 GAGCAATTGACTGATGTAATTTCTGAACCTCAAGTCCACTCCTTTTGAAAAGAAAATGTTACTTT
* * *
191645 TCCTTGAGCTAACCTTATGTCCTGAAATACCACATAAAAGCTTTAAAATATCAGTTAATAGTTAT
66 TCCTTGAGCTAACCTTATGTCCTGAAATACCACAGAAAAGCTTCAAAATATCAGTTAATAATTAT
191710 GCTTGATTTAGCTCCGCTTTGCAAAATAAAATC
131 GCTTGATTTAGCTCCGCTTTGCAAAATAAAATC
* * *
191743 GAGCAATTGACTGATGTAATTTTTGAACCTCGAGTCTACTCCTTTTGAAAAGAAAATGTTACTTT
1 GAGCAATTGACTGATGTAATTTCTGAACCTCAAGTCCACTCCTTTTGAAAAGAAAATGTTACTTT
* * *
191808 TCCTTGAGCTAACCTTGTGTCTTGAAATACCACAGAAAAGCTTCAGAATATCAGTTAATAATTAT
66 TCCTTGAGCTAACCTTATGTCCTGAAATACCACAGAAAAGCTTCAAAATATCAGTTAATAATTAT
*
191873 GCTTGATTTAGCTCCGTTTTGCAAAATAAAA
131 GCTTGATTTAGCTCCGCTTTGCAAAATAAAA
191904 CCAGATCTTC
Statistics
Matches: 146, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
163 146 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (163 bp):
GAGCAATTGACTGATGTAATTTCTGAACCTCAAGTCCACTCCTTTTGAAAAGAAAATGTTACTTT
TCCTTGAGCTAACCTTATGTCCTGAAATACCACAGAAAAGCTTCAAAATATCAGTTAATAATTAT
GCTTGATTTAGCTCCGCTTTGCAAAATAAAATC
Found at i:194596 original size:2 final size:2
Alignment explanation
Indices: 194589--194615 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
194579 ATCTACCATA
194589 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 A
194616 ATTTGAACTG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:194810 original size:17 final size:18
Alignment explanation
Indices: 194768--194813 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
194758 TTTTAATTAA
*
194768 ATAAATATAATTTTATCT
1 ATAAATATGATTTTATCT
*
194786 ACAAATATGATTTTAT-T
1 ATAAATATGATTTTATCT
*
194803 TTAAATATGAT
1 ATAAATATGAT
194814 AATAATTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.48
Consensus pattern (18 bp):
ATAAATATGATTTTATCT
Found at i:195378 original size:40 final size:42
Alignment explanation
Indices: 195312--195402 Score: 125
Period size: 40 Copynumber: 2.2 Consensus size: 42
195302 TTAAAAATAT
* *
195312 TTATATT-AAAAAACACTAACTTTAAATATAATAAATTTTTTA
1 TTATATTAAAAAAACACTAAC-GTAAATATAATAAATATTTTA
195354 TTATATTAAAAAAACAC-AA-GTAAATATAATAAATATTTTA
1 TTATATTAAAAAAACACTAACGTAAATATAATAAATATTTTA
*
195394 TTGTATTAA
1 TTATATTAA
195403 GTATTATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
40 27 0.60
42 9 0.20
43 9 0.20
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (42 bp):
TTATATTAAAAAAACACTAACGTAAATATAATAAATATTTTA
Found at i:195544 original size:20 final size:19
Alignment explanation
Indices: 195519--195591 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 19
195509 TATTGGATTA
195519 ATAATTTAATATAAATATAT
1 ATAA-TTAATATAAATATAT
* * *
195539 ATAATTATTATTTAACATAT
1 ATAATTAATA-TAAATATAT
* *
195559 ATAATTAATATAACATTTTT
1 ATAATTAATATAA-ATATAT
195579 ATAATATAATATA
1 ATAAT-TAATATA
195592 TTCGGGTTGG
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
19 7 0.17
20 28 0.67
21 7 0.17
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.47
Consensus pattern (19 bp):
ATAATTAATATAAATATAT
Found at i:197217 original size:18 final size:17
Alignment explanation
Indices: 197184--197220 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
197174 ATGAGATGAG
*
197184 AATAAATTTTTTAATTA
1 AATAAATTTATTAATTA
197201 AATAAATTTAATTAATTA
1 AATAAATTT-ATTAATTA
197219 AA
1 AA
197221 AATTTTAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AATAAATTTATTAATTA
Found at i:199408 original size:18 final size:19
Alignment explanation
Indices: 199370--199409 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
199360 CCCCAAAGTT
199370 CATAAACAAGACAATAATG
1 CATAAACAAGACAATAATG
* *
199389 CATAAACATGACCA-AATG
1 CATAAACAAGACAATAATG
199407 CAT
1 CAT
199410 GAGGGTATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.53, C:0.20, G:0.10, T:0.17
Consensus pattern (19 bp):
CATAAACAAGACAATAATG
Found at i:203433 original size:2 final size:2
Alignment explanation
Indices: 203426--203451 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
203416 AGAACACAAA
203426 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
203452 TTTTGAGTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.