Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000426.1 Hibiscus syriacus cultivar Beakdansim tig00000778_pilon, 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: 3165331
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 15
Found at i:1828099 original size:17 final size:17
Alignment explanation
Indices: 1828067--1828098 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1828057 GTTAAGGTTG
1828067 GAGATTTGAGATTTTTA
1 GAGATTTGAGATTTTTA
1828084 GAGATTTGAG-TTTTT
1 GAGATTTGAGATTTTT
1828099 TTTAATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (17 bp):
GAGATTTGAGATTTTTA
Found at i:1830505 original size:15 final size:14
Alignment explanation
Indices: 1830485--1830519 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
1830475 GAAAATCAAG
*
1830485 AATAAAGATTAAGA
1 AATAAAGACTAAGA
1830499 CAATAAAGACTAAGA
1 -AATAAAGACTAAGA
1830514 AATAAA
1 AATAAA
1830520 AATAAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.66, C:0.06, G:0.11, T:0.17
Consensus pattern (14 bp):
AATAAAGACTAAGA
Found at i:1830641 original size:16 final size:16
Alignment explanation
Indices: 1830620--1830651 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1830610 AGATGGTGGC
1830620 GTGGATGATATTGATA
1 GTGGATGATATTGATA
1830636 GTGGATGATATTGATA
1 GTGGATGATATTGATA
1830652 ATGAAGATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.31, T:0.38
Consensus pattern (16 bp):
GTGGATGATATTGATA
Found at i:1831398 original size:26 final size:27
Alignment explanation
Indices: 1831369--1831420 Score: 79
Period size: 26 Copynumber: 1.9 Consensus size: 27
1831359 GTCTATAGAC
*
1831369 AAATTTTTAATTT-AATTAATTTTTAA
1 AAATTATTAATTTAAATTAATTTTTAA
1831395 AAATTATTAATTTAAAATTAATTTTT
1 AAATTATTAATTT-AAATTAATTTTT
1831421 GGTTTCATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 12 0.52
28 11 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
AAATTATTAATTTAAATTAATTTTTAA
Found at i:1842202 original size:19 final size:19
Alignment explanation
Indices: 1842180--1842219 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1842170 TTAAAGAGGA
1842180 TAAGGGAAGTTGAAGAACT
1 TAAGGGAAGTTGAAGAACT
1842199 TAAGGGAAGTTGAAGAACT
1 TAAGGGAAGTTGAAGAACT
1842218 TA
1 TA
1842220 TTCAACAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.05, G:0.30, T:0.23
Consensus pattern (19 bp):
TAAGGGAAGTTGAAGAACT
Found at i:1846771 original size:21 final size:21
Alignment explanation
Indices: 1846746--1846789 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1846736 GAGCCTGTGG
1846746 GGGAAACCTTTTGAGGTGTTT
1 GGGAAACCTTTTGAGGTGTTT
1846767 GGGAAACCTTTTGAGGTGTTT
1 GGGAAACCTTTTGAGGTGTTT
1846788 GG
1 GG
1846790 TAGGAACGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.18, C:0.09, G:0.36, T:0.36
Consensus pattern (21 bp):
GGGAAACCTTTTGAGGTGTTT
Found at i:1854379 original size:21 final size:20
Alignment explanation
Indices: 1854355--1854393 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1854345 TATAAAAACA
*
1854355 ATAAAAAATTCTTGATAATTT
1 ATAAAAAATTATT-ATAATTT
*
1854376 ATAAATAATTATTATAAT
1 ATAAAAAATTATTATAAT
1854394 CCTAAACCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (20 bp):
ATAAAAAATTATTATAATTT
Found at i:1857439 original size:39 final size:39
Alignment explanation
Indices: 1857396--1857503 Score: 128
Period size: 39 Copynumber: 2.8 Consensus size: 39
1857386 ATAGTTATTT
* * *
1857396 AATTATTTCACCATAACATTTTAAATTCTTAATTTCA-GA
1 AATTATTTCACCATAACATTGTAAATTATTAATAT-ATGA
* * *
1857435 AATTATTTTACTATAACATTGTAAATTATTAATATATTA
1 AATTATTTCACCATAACATTGTAAATTATTAATATATGA
* *
1857474 AATTATTTCACCATAACATTCTAAGTTATT
1 AATTATTTCACCATAACATTGTAAATTATT
1857504 TCTCTTAACT
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
38 1 0.02
39 57 0.98
ACGTcount: A:0.40, C:0.12, G:0.03, T:0.45
Consensus pattern (39 bp):
AATTATTTCACCATAACATTGTAAATTATTAATATATGA
Found at i:1857607 original size:24 final size:24
Alignment explanation
Indices: 1857577--1857624 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1857567 TATCTTTTGA
* *
1857577 TTATGTAATT-TAAATTTTTAAATT
1 TTATGT-ATTATAAAATTTCAAATT
1857601 TTATGTATTATAAAATTTCAAATT
1 TTATGTATTATAAAATTTCAAATT
1857625 CTATATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (24 bp):
TTATGTATTATAAAATTTCAAATT
Found at i:1866498 original size:2 final size:2
Alignment explanation
Indices: 1866493--1866517 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1866483 AGGTGAAATA
1866493 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
1866518 AAAGATATTG
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:1870192 original size:24 final size:24
Alignment explanation
Indices: 1870165--1870214 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
1870155 CAGCTCGTAT
*
1870165 AAATTGCACCGAAGTACCGCATAG
1 AAATTGCACCGAAGTACCACATAG
*
1870189 AAATTGCACCGAAGTGCCACATAG
1 AAATTGCACCGAAGTACCACATAG
1870213 AA
1 AA
1870215 TGTCCCAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.40, C:0.24, G:0.20, T:0.16
Consensus pattern (24 bp):
AAATTGCACCGAAGTACCACATAG
Found at i:1872080 original size:14 final size:16
Alignment explanation
Indices: 1872056--1872088 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1872046 AAAGTTAAAT
1872056 TTTTTATTTGT-TTTA
1 TTTTTATTTGTGTTTA
1872071 TTTTTA-TTGTGTTTA
1 TTTTTATTTGTGTTTA
1872086 TTT
1 TTT
1872089 CATTTAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.79
Consensus pattern (16 bp):
TTTTTATTTGTGTTTA
Found at i:1875830 original size:34 final size:34
Alignment explanation
Indices: 1875784--1875856 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 34
1875774 TCCACACCTG
*
1875784 CCCACGCGGATACAATCTCAAATCTATC-TCCACA
1 CCCACGCGGATACAATCTCAAATCCATCAT-CACA
* * *
1875818 CCCATGCGGATACATTTTCAAATCCATCATCACA
1 CCCACGCGGATACAATCTCAAATCCATCATCACA
1875852 CCCAC
1 CCCAC
1875857 TACCTAACTG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
34 32 0.97
35 1 0.03
ACGTcount: A:0.32, C:0.38, G:0.08, T:0.22
Consensus pattern (34 bp):
CCCACGCGGATACAATCTCAAATCCATCATCACA
Found at i:1877371 original size:22 final size:22
Alignment explanation
Indices: 1877345--1877407 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
1877335 TTATTATATA
1877345 TATTAAATATTTATATATTTTT
1 TATTAAATATTTATATATTTTT
* *
1877367 TATTAAAAATTTGTATCATTTTT
1 TATTAAATATTTATAT-ATTTTT
* *
1877390 T-TAAAAT-TTTATAAATTT
1 TATTAAATATTTATATATTT
1877408 AAACTTATGA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
20 4 0.12
21 5 0.15
22 18 0.53
23 7 0.21
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (22 bp):
TATTAAATATTTATATATTTTT
Found at i:1880848 original size:2 final size:2
Alignment explanation
Indices: 1880841--1880868 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1880831 AAAATCGGTT
1880841 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1880869 GTATGGTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1880921 original size:32 final size:32
Alignment explanation
Indices: 1880880--1880941 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
1880870 TATGGTTTTG
*
1880880 AAAATACGTTTTTGAAAAAGTATAATATATTA
1 AAAACACGTTTTTGAAAAAGTATAATATATTA
*
1880912 AAAACACGTTTTTGAAAACGTATAATATAT
1 AAAACACGTTTTTGAAAAAGTATAATATAT
1880942 ATAGTTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.35
Consensus pattern (32 bp):
AAAACACGTTTTTGAAAAAGTATAATATATTA
Found at i:1880984 original size:37 final size:39
Alignment explanation
Indices: 1880909--1881014 Score: 137
Period size: 37 Copynumber: 2.8 Consensus size: 39
1880899 GTATAATATA
*
1880909 TTAAAAACACGTTTTTGAAAACGTATA-ATATATATAGTT
1 TTAAAAACA-TTTTTTGAAAACGTATATATATATATAGTT
*
1880948 TTAAAAATATTTTTTGAAAACGTATATA-ATAT-TAGTT
1 TTAAAAACATTTTTTGAAAACGTATATATATATATAGTT
* * *
1880985 TTGAAAACATATTTTGAAAACATATATATA
1 TTAAAAACATTTTTTGAAAACGTATATATA
1881015 GTTTTTTAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
37 29 0.49
38 21 0.36
39 9 0.15
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (39 bp):
TTAAAAACATTTTTTGAAAACGTATATATATATATAGTT
Found at i:1881001 original size:13 final size:13
Alignment explanation
Indices: 1880983--1881009 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1880973 ATAATATTAG
1880983 TTTTGAAAACATA
1 TTTTGAAAACATA
1880996 TTTTGAAAACATA
1 TTTTGAAAACATA
1881009 T
1 T
1881010 ATATAGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (13 bp):
TTTTGAAAACATA
Found at i:1883063 original size:26 final size:28
Alignment explanation
Indices: 1883021--1883072 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
1883011 ATTTAGTTTC
* *
1883021 AAATTCAACTTATAAACTC-TTTTCTAA
1 AAATTCAACTTAAAAACCCATTTTCTAA
1883048 AAATTC-ACTTAAAAACCCATTTTCT
1 AAATTCAACTTAAAAACCCATTTTCT
1883073 TTAATCTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.40, C:0.21, G:0.00, T:0.38
Consensus pattern (28 bp):
AAATTCAACTTAAAAACCCATTTTCTAA
Found at i:1883505 original size:10 final size:10
Alignment explanation
Indices: 1883474--1883530 Score: 57
Period size: 10 Copynumber: 5.8 Consensus size: 10
1883464 TTACATATAA
1883474 TATATATTAT
1 TATATATTAT
*
1883484 ATAGTTTATTAT
1 -TA-TATATTAT
1883496 TATATATTAT
1 TATATATTAT
*
1883506 TATTTATTAT
1 TATATATTAT
1883516 T-TAT-TTAT
1 TATATATTAT
1883524 T-TATATT
1 TATATATT
1883531 TTAAAAAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
8 8 0.20
9 4 0.10
10 17 0.43
11 4 0.10
12 7 0.17
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (10 bp):
TATATATTAT
Found at i:1883525 original size:15 final size:16
Alignment explanation
Indices: 1883478--1883527 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 16
1883468 ATATAATATA
1883478 TATTATATAGTTTA-T
1 TATTATATAGTTTATT
*
1883493 TATTATATATTATTATT
1 TATTATATAGT-TTATT
*
1883510 TATTATTTA-TTTATT
1 TATTATATAGTTTATT
1883525 TAT
1 TAT
1883528 ATTTTAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 18 0.58
16 4 0.13
17 9 0.29
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (16 bp):
TATTATATAGTTTATT
Found at i:1883533 original size:15 final size:14
Alignment explanation
Indices: 1883478--1883533 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 14
1883468 ATATAATATA
*
1883478 TATTATATAGTTTAT
1 TATT-TATATTTTAT
*
1883493 TA-TTATATATTAT
1 TATTTATATTTTAT
1883506 TATTTAT-TATTTATT
1 TATTTATAT-TTTA-T
1883521 TATTTATATTTTA
1 TATTTATATTTTA
1883534 AAAAATAGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
13 11 0.32
14 8 0.24
15 14 0.41
16 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (14 bp):
TATTTATATTTTAT
Found at i:1886810 original size:13 final size:13
Alignment explanation
Indices: 1886791--1886851 Score: 59
Period size: 13 Copynumber: 4.3 Consensus size: 13
1886781 GTCATGATCC
1886791 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
1886804 TACCCGACTCGTT
1 GACCCGACCCGTT
1886817 GACCCGACCAGACATGTT
1 GACCCGACC---C--GTT
1886835 GACCCGACCCGTT
1 GACCCGACCCGTT
1886848 GACC
1 GACC
1886852 GGCGTTGACC
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
13 25 0.64
15 1 0.03
16 1 0.03
18 12 0.31
ACGTcount: A:0.20, C:0.41, G:0.21, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1889426 original size:24 final size:24
Alignment explanation
Indices: 1889308--1889423 Score: 164
Period size: 24 Copynumber: 4.8 Consensus size: 24
1889298 TTCGATTTGA
1889308 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
*
1889332 ATTCTGATCTGATA-TCTGACATAG
1 ATTCTGATCTGATACT-TGACATGG
*
1889356 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
*
1889380 ATTCTGATCTGATACTTGACCTGG
1 ATTCTGATCTGATACTTGACATGG
*
1889404 AGTT-TGATATGATACTTGAC
1 A-TTCTGATCTGATACTTGAC
1889424 CTGATTTATG
Statistics
Matches: 84, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
23 1 0.01
24 80 0.95
25 3 0.04
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:1894115 original size:13 final size:13
Alignment explanation
Indices: 1894097--1894123 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1894087 CATAGTTGAA
1894097 CAGTCTTCATATG
1 CAGTCTTCATATG
1894110 CAGTCTTCATATG
1 CAGTCTTCATATG
1894123 C
1 C
1894124 GCGTCTGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:1898523 original size:12 final size:13
Alignment explanation
Indices: 1898478--1898522 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
1898468 ATCCCCGATT
1898478 ACCCGATTACCCG
1 ACCCGATTACCCG
*
1898491 CCCCGATTACCCG
1 ACCCGATTACCCG
*
1898504 ACCCGA-TACCTG
1 ACCCGATTACCCG
1898516 ACCCGAT
1 ACCCGAT
1898523 AAATATTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 11 0.39
13 17 0.61
ACGTcount: A:0.22, C:0.47, G:0.16, T:0.16
Consensus pattern (13 bp):
ACCCGATTACCCG
Found at i:1898580 original size:36 final size:35
Alignment explanation
Indices: 1898524--1898595 Score: 83
Period size: 36 Copynumber: 2.0 Consensus size: 35
1898514 TGACCCGATA
* * *
1898524 AATATTAAAAATAATTATTTATATATATATATATAT
1 AATATTAAAAAT-ATTATTTAAATAAAAATATATAT
1898560 AATATTAATAAAT-TTAATTTAAATAAAAATATATAT
1 AATATTAA-AAATATT-ATTTAAATAAAAATATATAT
1898596 TTAATATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
35 2 0.06
36 25 0.81
37 4 0.13
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (35 bp):
AATATTAAAAATATTATTTAAATAAAAATATATAT
Found at i:1898601 original size:17 final size:18
Alignment explanation
Indices: 1898576--1898614 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
1898566 AATAAATTTA
1898576 ATTTAAATAAAAATATAT
1 ATTTAAATAAAAATATAT
*
1898594 ATTTAATATAAATATATAT
1 ATTTAA-ATAAAAATATAT
1898613 AT
1 AT
1898615 ATATACCCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTTAAATAAAAATATAT
Found at i:1898605 original size:23 final size:23
Alignment explanation
Indices: 1898571--1898618 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1898561 ATATTAATAA
*
1898571 ATTTAATTTAAATAAAAATATAT
1 ATTTAATATAAATAAAAATATAT
* *
1898594 ATTTAATATAAATATATATATAT
1 ATTTAATATAAATAAAAATATAT
1898617 AT
1 AT
1898619 ACCCAGCCCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTAATATAAATAAAAATATAT
Found at i:1898661 original size:12 final size:12
Alignment explanation
Indices: 1898637--1898682 Score: 76
Period size: 12 Copynumber: 3.9 Consensus size: 12
1898627 CGATTCTCGG
1898637 CCCAATA-CCGA
1 CCCAATACCCGA
1898648 CCCAATACCCGA
1 CCCAATACCCGA
*
1898660 CCCAATACCCGG
1 CCCAATACCCGA
1898672 CCCAATACCCG
1 CCCAATACCCG
1898683 TTTAAATAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
11 7 0.21
12 26 0.79
ACGTcount: A:0.30, C:0.50, G:0.11, T:0.09
Consensus pattern (12 bp):
CCCAATACCCGA
Found at i:1900527 original size:21 final size:22
Alignment explanation
Indices: 1900477--1900527 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
1900467 CTATATGGCG
*
1900477 CGTTTTCATCTGCCTTTATGGCA
1 CGTTTTCATCTG-CTTTATGACA
* *
1900500 TGTTTTCATCTG-TTTGTGACA
1 CGTTTTCATCTGCTTTATGACA
1900521 CGTTTTC
1 CGTTTTC
1900528 TTTTGTCTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 13 0.54
23 11 0.46
ACGTcount: A:0.12, C:0.22, G:0.18, T:0.49
Consensus pattern (22 bp):
CGTTTTCATCTGCTTTATGACA
Found at i:1901628 original size:18 final size:17
Alignment explanation
Indices: 1901595--1901649 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 17
1901585 TTAACATTTT
1901595 AATTTTTATATTATTAA
1 AATTTTTATATTATTAA
1901612 AATTTATTATTTAATTATTAA
1 AATTT-TTA--T-ATTATTAA
*
1901633 AA--TGTATATTATTAA
1 AATTTTTATATTATTAA
1901648 AA
1 AA
1901650 ATATATTAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
15 10 0.30
16 1 0.03
17 5 0.15
18 5 0.15
19 1 0.03
20 1 0.03
21 10 0.30
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
AATTTTTATATTATTAA
Found at i:1901630 original size:21 final size:24
Alignment explanation
Indices: 1901599--1901645 Score: 73
Period size: 21 Copynumber: 2.1 Consensus size: 24
1901589 CATTTTAATT
1901599 TTTATATTATTAAAAT-T-TATTA
1 TTTATATTATTAAAATGTATATTA
1901621 TTTA-ATTATTAAAATGTATATTA
1 TTTATATTATTAAAATGTATATTA
1901644 TT
1 TT
1901646 AAAAATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 11 0.48
22 5 0.22
23 7 0.30
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
TTTATATTATTAAAATGTATATTA
Found at i:1901656 original size:14 final size:15
Alignment explanation
Indices: 1901625--1901657 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1901615 TTATTATTTA
*
1901625 ATTATTAAAATGTAT
1 ATTATTAAAATATAT
1901640 ATTATTAAAA-ATAT
1 ATTATTAAAATATAT
1901654 ATTA
1 ATTA
1901658 ACCTAACCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (15 bp):
ATTATTAAAATATAT
Found at i:1901933 original size:2 final size:2
Alignment explanation
Indices: 1901926--1901951 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1901916 TATTTCAAAA
1901926 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
1901952 GGTTAACTAA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1903672 original size:21 final size:21
Alignment explanation
Indices: 1903648--1903698 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
1903638 GGCTTCACCG
1903648 CCGACCACCGCATCGTCGCCT
1 CCGACCACCGCATCGTCGCCT
*
1903669 CCGACCATCGCATCGTCGCCT
1 CCGACCACCGCATCGTCGCCT
1903690 CCGACCACC
1 CCGACCACC
1903699 ACGTCAACCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.16, C:0.53, G:0.18, T:0.14
Consensus pattern (21 bp):
CCGACCACCGCATCGTCGCCT
Found at i:1904767 original size:19 final size:19
Alignment explanation
Indices: 1904740--1904778 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1904730 AGTTTTTTGG
*
1904740 AACCAGTCCAATCGAACCA
1 AACCAGTCCAATCAAACCA
* *
1904759 AACCGGTCCAGTCAAACCA
1 AACCAGTCCAATCAAACCA
1904778 A
1 A
1904779 TCTGAGCTGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.36, G:0.13, T:0.10
Consensus pattern (19 bp):
AACCAGTCCAATCAAACCA
Found at i:1904865 original size:22 final size:22
Alignment explanation
Indices: 1904837--1904885 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
1904827 GACTTGATCG
1904837 TTGACTTTAACTAG-AGTTGACT
1 TTGACTTTAACTAGCA-TTGACT
**
1904859 TTGACTTTGTCTAGCATTGACT
1 TTGACTTTAACTAGCATTGACT
1904881 TTGAC
1 TTGAC
1904886 CAAACAATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.43
Consensus pattern (22 bp):
TTGACTTTAACTAGCATTGACT
Found at i:1910126 original size:41 final size:40
Alignment explanation
Indices: 1910055--1910132 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 40
1910045 GTAAAATTTA
*
1910055 AAATTTAATGATATTTTATAATACTATTTTTATAATTTTGT
1 AAATTTAATGAAATTTTATAATACTATTTTT-TAATTTTGT
*
1910096 AAATTTCAATGAAATTTTA-AATA-TATTTTTTTATTTT
1 AAATTT-AATGAAATTTTATAATACTATTTTTTAATTTT
1910133 TGTATTGTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 6 0.18
40 7 0.21
41 10 0.29
42 11 0.32
ACGTcount: A:0.37, C:0.03, G:0.04, T:0.56
Consensus pattern (40 bp):
AAATTTAATGAAATTTTATAATACTATTTTTTAATTTTGT
Found at i:1910134 original size:40 final size:41
Alignment explanation
Indices: 1910055--1910136 Score: 114
Period size: 40 Copynumber: 2.0 Consensus size: 41
1910045 GTAAAATTTA
*
1910055 AAATTTAATGATATTTTATAATACTATTTTTATAATTTTGT
1 AAATTTAATGAAATTTTATAATACTATTTTTATAATTTTGT
* *
1910096 AAATTTCAATGAAATTTTA-AATA-TATTTTTTTATTTTTGT
1 AAATTT-AATGAAATTTTATAATACTATTTTTATAATTTTGT
1910136 A
1 A
1910137 TTGTATTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
40 16 0.43
41 10 0.27
42 11 0.30
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (41 bp):
AAATTTAATGAAATTTTATAATACTATTTTTATAATTTTGT
Found at i:1910765 original size:16 final size:17
Alignment explanation
Indices: 1910746--1910789 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
1910736 TATCCTAATA
*
1910746 TTTATATT-TATATATT
1 TTTATATTATAAATATT
1910762 TTTATAGTTATAAATATT
1 TTTATA-TTATAAATATT
*
1910780 TTTCTATTAT
1 TTTATATTAT
1910790 TATAACTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 6 0.25
17 6 0.25
18 12 0.50
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (17 bp):
TTTATATTATAAATATT
Found at i:1911505 original size:27 final size:26
Alignment explanation
Indices: 1911445--1911501 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
1911435 ATCAGAATCT
* *
1911445 TTTATAAATTAAAAGAATTTAAATTA
1 TTTATAAATTAAAAGAATTAAAATTC
1911471 TATTATAAGATTAAAA-AATTAAAATTC
1 T-TTATAA-ATTAAAAGAATTAAAATTC
1911498 TTTA
1 TTTA
1911502 ATAATTAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 4 0.15
27 16 0.59
28 7 0.26
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.42
Consensus pattern (26 bp):
TTTATAAATTAAAAGAATTAAAATTC
Found at i:1912748 original size:2 final size:2
Alignment explanation
Indices: 1912741--1912825 Score: 161
Period size: 2 Copynumber: 42.5 Consensus size: 2
1912731 TTATCCCAGG
*
1912741 TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1912783 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1912825 T
1 T
1912826 TGAAGTCTAA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1915592 original size:17 final size:17
Alignment explanation
Indices: 1915572--1915609 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
1915562 TTAGTATCAC
1915572 TATATTATTATAATTAA
1 TATATTATTATAATTAA
*
1915589 TATATTATTATTATTAA
1 TATATTATTATAATTAA
1915606 -ATAT
1 TATAT
1915610 CTACACCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TATATTATTATAATTAA
Found at i:1918308 original size:22 final size:22
Alignment explanation
Indices: 1918280--1918322 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1918270 AACGGTCAAC
1918280 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
1918302 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
1918323 AGACCGGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:1918343 original size:19 final size:19
Alignment explanation
Indices: 1918321--1918398 Score: 79
Period size: 19 Copynumber: 4.1 Consensus size: 19
1918311 TCGGGTCGGG
1918321 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
1918340 TCAGACCGGTCAAATCGGT
1 TCAGACCGGTCAAACCGGT
*
1918359 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
* *
1918378 TCAAACCGATCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
1918398 T
1 T
1918399 TCCAGCAGCC
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
18 3 0.06
19 37 0.77
20 8 0.17
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:1923140 original size:27 final size:27
Alignment explanation
Indices: 1923102--1923156 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
1923092 CTTTATTATA
1923102 AAGTTAAAATCAATTAAATTAAATTTG
1 AAGTTAAAATCAATTAAATTAAATTTG
1923129 AAGTTAAAATCAATTAAATTAAATTTG
1 AAGTTAAAATCAATTAAATTAAATTTG
1923156 A
1 A
1923157 CTAAATTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.53, C:0.04, G:0.07, T:0.36
Consensus pattern (27 bp):
AAGTTAAAATCAATTAAATTAAATTTG
Found at i:1924315 original size:15 final size:15
Alignment explanation
Indices: 1924295--1924324 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1924285 ATAGCCTTCG
*
1924295 TAATCATCATCATCA
1 TAATCATCAGCATCA
1924310 TAATCATCAGCATCA
1 TAATCATCAGCATCA
1924325 GCATCGTCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.27, G:0.03, T:0.30
Consensus pattern (15 bp):
TAATCATCAGCATCA
Found at i:1927656 original size:205 final size:205
Alignment explanation
Indices: 1927304--1927724 Score: 797
Period size: 205 Copynumber: 2.1 Consensus size: 205
1927294 GAACCAGTTT
*
1927304 TTTACTTTAACCTTTAGTAAGCGGATATACTAGATTCTTCTCTGACTTTAATAATCCTTTTAAGG
1 TTTACTTTAACCTTTAATAAGCGGATATACTAGATTCTTCTCTGACTTTAATAATCCTTTTAAGG
*
1927369 CACCCTACATTACTAAATTTTAAGATATAAATAAATCCTTAAGTGTCTTAGATAAAGTGTAAACA
66 CACCCTACATTACTAAATTTTAAGATATAAATAAATCCTTAAGTGTCTTAAATAAAGTGTAAACA
*
1927434 AATTTTCTTGTACATTTACTCATTCATACTCATTCATTCTTGAGTAAAGTTCGTTATTAGTTTTA
131 AATTTTCTTGTACATTTACTCATTCATACTCATTCATACTTGAGTAAAGTTCGTTATTAGTTTTA
*
1927499 ACCACAAAAC
196 AACACAAAAC
1927509 TTTACTTTAACCTTTAATAAGCGGATATACTAGATTCTTCTCTGACTTTAATAATCCTTTTAAGG
1 TTTACTTTAACCTTTAATAAGCGGATATACTAGATTCTTCTCTGACTTTAATAATCCTTTTAAGG
1927574 CACCCTACATTACTAAATTTTAAGATATAAATAAATCCTTAAGTGTCTTAAATAAAGTGTAAACA
66 CACCCTACATTACTAAATTTTAAGATATAAATAAATCCTTAAGTGTCTTAAATAAAGTGTAAACA
1927639 AATTTTCTTGTACATTTACTCATTCATACTCATTCATACTTGAGTAAAGTTCGTTATTAGTTTTA
131 AATTTTCTTGTACATTTACTCATTCATACTCATTCATACTTGAGTAAAGTTCGTTATTAGTTTTA
1927704 AACACAAAAC
196 AACACAAAAC
*
1927714 TATACTTTAAC
1 TTTACTTTAAC
1927725 AAACCAGAGC
Statistics
Matches: 211, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
205 211 1.00
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (205 bp):
TTTACTTTAACCTTTAATAAGCGGATATACTAGATTCTTCTCTGACTTTAATAATCCTTTTAAGG
CACCCTACATTACTAAATTTTAAGATATAAATAAATCCTTAAGTGTCTTAAATAAAGTGTAAACA
AATTTTCTTGTACATTTACTCATTCATACTCATTCATACTTGAGTAAAGTTCGTTATTAGTTTTA
AACACAAAAC
Found at i:1928382 original size:110 final size:110
Alignment explanation
Indices: 1928210--1928720 Score: 772
Period size: 110 Copynumber: 4.7 Consensus size: 110
1928200 ATTCTTCGTC
* * * *
1928210 GTGAAGTTGAAATTGACTC----TGAAACTGGAAAGTTGTTTGTTGATAGTCAATCTCCCCTTCG
1 GTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCGCCCCTTCG
*
1928271 CTGTAAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCGCT
66 CTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCGCT
* *
1928316 GTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTCTGTTGACAGTCAGTCGCCCATTCG
1 GTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCGCCCCTTCG
* * *
1928381 CTATGAAGTTGAGCTTGTGTTGTCTCGAGT-CATATATTCTTCGTT
66 CTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCA-ATATCCTTCGCT
* *
1928426 GTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTTAGTCACCCCTTCG
1 GTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCGCCCCTTCG
1928491 CTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCGCT
66 CTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCGCT
* * *
1928536 GCGAAATTGAAATTGATTCTGAATG--A---AAAAGTTGTTTGTTGACAGTCAGTCGCCCCTTCG
1 GTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCGCCCCTTCG
*
1928596 CTGTGAAGTTGAGCTTGTGTTGTCTCGAGTTCAATATCCTTCGCT
66 CTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCGCT
*
1928641 GTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTTGTTTGTTGACCGTCAGTCGCCCCTTC
1 GTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAG-TTGTTTGTTGACAGTCAGTCGCCCCTTC
*
1928706 GTTGTGAAGTTGAGC
65 GCTGTGAAGTTGAGC
1928721 AACCACCATC
Statistics
Matches: 365, Mismatches: 28, Indels: 19
0.89 0.07 0.05
Matches are distributed among these distances:
105 98 0.27
106 19 0.05
107 1 0.00
108 1 0.00
109 2 0.01
110 201 0.55
111 43 0.12
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.35
Consensus pattern (110 bp):
GTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCGCCCCTTCG
CTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCGCT
Found at i:1928676 original size:215 final size:217
Alignment explanation
Indices: 1928210--1928720 Score: 775
Period size: 215 Copynumber: 2.4 Consensus size: 217
1928200 ATTCTTCGTC
* * * *
1928210 GTGAAGTTGAAATTGACTC----TGAAACTGGAAAGTTGTTTGTTGATAGTCAATCTCCCCTTCG
1 GTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCACCCCTTCG
* * *
1928271 CTGTAAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCT
66 CTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGCGAAATTGAAATTGACTCT
1928336 GAATGAAACTGAAAAGTTGTCTGTTGACAGTCAGTCGCCCATTCGCTATGAAGTTGAGCTTGTGT
131 GAATG-AAC--AAAAGTTGTCTGTTGACAGTCAGTCGCCCATTCGCTATGAAGTTGAGCTTGTGT
* *
1928401 TGTCTCGAGTCATATATTCTTCGTT
193 TGTCTCGAGTCATATATCCTTCGCT
*
1928426 GTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTTAGTCACCCCTTCG
1 GTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCACCCCTTCG
*
1928491 CTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGCGAAATTGAAATTGATTCT
66 CTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGCGAAATTGAAATTGACTCT
* * *
1928556 GAATG-A-AAAAGTTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGT
131 GAATGAACAAAAGTTGTCTGTTGACAGTCAGTCGCCCATTCGCTATGAAGTTGAGCTTGTGTTGT
1928619 CTCGAGTTCA-ATATCCTTCGCT
196 CTCGAG-TCATATATCCTTCGCT
* *
1928641 GTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTTGTTTGTTGACCGTCAGTCGCCCCTTC
1 GTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAG-TTGTTTGTTGACAGTCAGTCACCCCTTC
*
1928706 GTTGTGAAGTTGAGC
65 GCTGTGAAGTTGAGC
1928721 AACCACCATC
Statistics
Matches: 271, Mismatches: 18, Indels: 12
0.90 0.06 0.04
Matches are distributed among these distances:
215 106 0.39
216 61 0.23
218 1 0.00
220 103 0.38
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.35
Consensus pattern (217 bp):
GTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCACCCCTTCG
CTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGCGAAATTGAAATTGACTCT
GAATGAACAAAAGTTGTCTGTTGACAGTCAGTCGCCCATTCGCTATGAAGTTGAGCTTGTGTTGT
CTCGAGTCATATATCCTTCGCT
Found at i:1932873 original size:34 final size:34
Alignment explanation
Indices: 1932835--1932921 Score: 108
Period size: 33 Copynumber: 2.6 Consensus size: 34
1932825 AGTCATACTT
* *
1932835 GGACTCAAAATGC-TTCGGTTTTAGTGTTTCAATA
1 GGACTCAAAATACGTT-GGTTTTAGTGTTTCAACA
1932869 GGACTC-AAATACGTTGGTTTTAGTGTTTCAACA
1 GGACTCAAAATACGTTGGTTTTAGTGTTTCAACA
* *
1932902 AGACTC-AAATATGTTGGTTT
1 GGACTCAAAATACGTTGGTTT
1932922 ATTTTCCGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
33 40 0.83
34 8 0.17
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.38
Consensus pattern (34 bp):
GGACTCAAAATACGTTGGTTTTAGTGTTTCAACA
Found at i:1932892 original size:33 final size:33
Alignment explanation
Indices: 1932851--1932921 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1932841 AAAATGCTTC
* *
1932851 GGTTTTAGTGTTTCAATAGGACTCAAATACGTT
1 GGTTTTAGTGTTTCAACAAGACTCAAATACGTT
*
1932884 GGTTTTAGTGTTTCAACAAGACTCAAATATGTT
1 GGTTTTAGTGTTTCAACAAGACTCAAATACGTT
1932917 GGTTT
1 GGTTT
1932922 ATTTTCCGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.27, C:0.11, G:0.21, T:0.41
Consensus pattern (33 bp):
GGTTTTAGTGTTTCAACAAGACTCAAATACGTT
Found at i:1933028 original size:25 final size:23
Alignment explanation
Indices: 1932972--1933029 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 23
1932962 TGCATGCAAA
1932972 AATAATAAAAT-AAAAATATATT
1 AATAATAAAATAAAAAATATATT
1932994 AATAAT-AAATAAATAAATATA-T
1 AATAATAAAATAAA-AAATATATT
1933016 AATATAGTAAAATA
1 AATA-A-TAAAATA
1933030 TTTTTATAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
21 4 0.13
22 13 0.42
23 8 0.26
24 1 0.03
25 5 0.16
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (23 bp):
AATAATAAAATAAAAAATATATT
Found at i:1943962 original size:29 final size:29
Alignment explanation
Indices: 1943920--1943976 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
1943910 AGTGTTGGTC
1943920 GTAGGTCGCCATGCACTCCGGGCGACCTT
1 GTAGGTCGCCATGCACTCCGGGCGACCTT
1943949 GTAGGTCGCCATGCACTCCGGGCGACCT
1 GTAGGTCGCCATGCACTCCGGGCGACCT
1943977 ACCCTCGCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.14, C:0.35, G:0.32, T:0.19
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCCGGGCGACCTT
Found at i:1944021 original size:33 final size:33
Alignment explanation
Indices: 1943980--1944065 Score: 111
Period size: 33 Copynumber: 2.6 Consensus size: 33
1943970 GCGACCTACC
* *
1943980 CTCGCTCGGCTT-CCCTCGGATTCCCTCGTATAG
1 CTCGCTCGG-TTGCCCTCGGATGCCCTCGCATAG
1944013 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
1 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
* * *
1944046 CTCGTTCGGATGGCCTCGGA
1 CTCGCTCGGTTGCCCTCGGA
1944066 CAGATGGCCT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 2 0.04
33 45 0.96
ACGTcount: A:0.09, C:0.37, G:0.27, T:0.27
Consensus pattern (33 bp):
CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
Found at i:1944036 original size:10 final size:10
Alignment explanation
Indices: 1943992--1944117 Score: 56
Period size: 10 Copynumber: 11.6 Consensus size: 10
1943982 CGCTCGGCTT
*
1943992 CCCTCGGATT
1 CCCTCGGATG
*
1944002 CCCTCGTATAG
1 CCCTCGGAT-G
*
1944013 CTCGCTCGGTTG
1 C-C-CTCGGATG
1944025 CCCTCGGATG
1 CCCTCGGATG
*
1944035 CCCTCGCATAG
1 CCCTCGGAT-G
*
1944046 CTCGTTCGGATG
1 C-C-CTCGGATG
*
1944058 GCCTCGGACAGATG
1 CCCTC-G---GATG
*
1944072 GCCTCGGATG
1 CCCTCGGATG
*
1944082 GCCTCGGATG
1 CCCTCGGATG
*
1944092 CTCTCGGATAG
1 CCCTCGGAT-G
1944103 -CCTCGGATG
1 CCCTCGGATG
*
1944112 CTCTCG
1 CCCTCG
1944118 AATAGCCTCG
Statistics
Matches: 90, Mismatches: 14, Indels: 24
0.70 0.11 0.19
Matches are distributed among these distances:
9 1 0.01
10 57 0.63
11 7 0.08
12 5 0.06
13 11 0.12
14 9 0.10
ACGTcount: A:0.12, C:0.34, G:0.29, T:0.25
Consensus pattern (10 bp):
CCCTCGGATG
Found at i:1944097 original size:20 final size:20
Alignment explanation
Indices: 1944074--1944128 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
1944064 GACAGATGGC
*
1944074 CTCGGATGGCCTCGGATGCT
1 CTCGGATAGCCTCGGATGCT
1944094 CTCGGATAGCCTCGGATGCT
1 CTCGGATAGCCTCGGATGCT
*
1944114 CTCGAATAGCCTCGG
1 CTCGGATAGCCTCGG
1944129 TAGGATGGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.15, C:0.31, G:0.31, T:0.24
Consensus pattern (20 bp):
CTCGGATAGCCTCGGATGCT
Found at i:1944127 original size:10 final size:9
Alignment explanation
Indices: 1944072--1944128 Score: 60
Period size: 10 Copynumber: 5.8 Consensus size: 9
1944062 CGGACAGATG
1944072 GCCTCGGAT
1 GCCTCGGAT
1944081 GGCCTCGGAT
1 -GCCTCGGAT
1944091 GCTCTCGGAT
1 GC-CTCGGAT
1944101 AGCCTCGGAT
1 -GCCTCGGAT
*
1944111 GCTCTCGAAT
1 GC-CTCGGAT
1944121 AGCCTCGG
1 -GCCTCGG
1944129 TAGGATGGCC
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
9 4 0.10
10 33 0.80
11 4 0.10
ACGTcount: A:0.14, C:0.32, G:0.32, T:0.23
Consensus pattern (9 bp):
GCCTCGGAT
Found at i:1944141 original size:14 final size:14
Alignment explanation
Indices: 1944122--1944156 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
1944112 CTCTCGAATA
1944122 GCCTCGGTAGGATG
1 GCCTCGGTAGGATG
*
1944136 GCCTCGGTCGGATG
1 GCCTCGGTAGGATG
1944150 GCCTCGG
1 GCCTCGG
1944157 ATGCCCAGCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.09, C:0.29, G:0.43, T:0.20
Consensus pattern (14 bp):
GCCTCGGTAGGATG
Found at i:1948418 original size:29 final size:27
Alignment explanation
Indices: 1948385--1948478 Score: 84
Period size: 27 Copynumber: 3.4 Consensus size: 27
1948375 AAGTTAATAT
1948385 ATTTTTAAATGAAAATAAAAATTAGTCAC
1 ATTTTTAAATGAAAATAAAAATTA-T-AC
* *
1948414 ATTTTT-AAT-AAATTAAAATAAATTATAT
1 ATTTTTAAATGAAA--ATAA-AAATTATAC
* * *
1948442 ATTTTTAAATGAATATAAAAATAAAAC
1 ATTTTTAAATGAAAATAAAAATTATAC
1948469 ATTTTTAAAT
1 ATTTTTAAAT
1948479 TAAGTTAATA
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
27 19 0.36
28 13 0.25
29 13 0.25
30 8 0.15
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.40
Consensus pattern (27 bp):
ATTTTTAAATGAAAATAAAAATTATAC
Found at i:1948491 original size:27 final size:25
Alignment explanation
Indices: 1948442--1948532 Score: 80
Period size: 27 Copynumber: 3.5 Consensus size: 25
1948432 TAAATTATAT
*
1948442 ATTTTTAAATGAA-TATAAAAATAAAA
1 ATTTTTAAATTAAGT-T-AAAATAAAA
1948468 CATTTTTAAATTAAGTTAATAATAAAA
1 -ATTTTTAAATTAAGTTAA-AATAAAA
* *
1948495 TATATTT-AA-TAAGTTGAAATAAAA
1 -ATTTTTAAATTAAGTTAAAATAAAA
1948519 ATATTTTAAATTAA
1 AT-TTTTAAATTAA
1948533 TATATATAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
23 2 0.04
24 10 0.19
25 9 0.17
26 7 0.13
27 25 0.46
28 1 0.02
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.40
Consensus pattern (25 bp):
ATTTTTAAATTAAGTTAAAATAAAA
Found at i:1949347 original size:31 final size:31
Alignment explanation
Indices: 1949279--1949353 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
1949269 GTTAACTCGG
* * ** *
1949279 TGACCAAAACTTAATTAAATAAAAACGTAAG
1 TGACCATATCTTAATTAAATAAAAACAAAAA
* *
1949310 TAACCATATCTTAATTAAATAAAAATAAAAA
1 TGACCATATCTTAATTAAATAAAAACAAAAA
1949341 TGACCATATCTTA
1 TGACCATATCTTA
1949354 TGTTTTTTTG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.53, C:0.13, G:0.05, T:0.28
Consensus pattern (31 bp):
TGACCATATCTTAATTAAATAAAAACAAAAA
Found at i:1952252 original size:9 final size:9
Alignment explanation
Indices: 1952238--1952266 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
1952228 TCTATTAAAG
1952238 CTTAATTCA
1 CTTAATTCA
1952247 CTTAATTCA
1 CTTAATTCA
1952256 CTTAATTCA
1 CTTAATTCA
1952265 CT
1 CT
1952267 AGTCCTCCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.24, G:0.00, T:0.45
Consensus pattern (9 bp):
CTTAATTCA
Found at i:1954137 original size:5 final size:5
Alignment explanation
Indices: 1954027--1954136 Score: 175
Period size: 5 Copynumber: 22.0 Consensus size: 5
1954017 TACAATACAA
* *
1954027 GCAAT GCAAT GCAAT GCAAT GCAAT GCAGT GCAAT GCAGT GCAAT GCAAT
1 GCAAT GCAAT GCAAT GCAAT GCAAT GCAAT GCAAT GCAAT GCAAT GCAAT
*
1954077 GCAGT GCAAT GCAAT GCAAT GCAAT GCAAT GCAAT GCAAT GCAAT GCAAT
1 GCAAT GCAAT GCAAT GCAAT GCAAT GCAAT GCAAT GCAAT GCAAT GCAAT
* *
1954127 ACAAT ACAAT
1 GCAAT GCAAT
1954137 ATATATAGCC
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 98 1.00
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.20
Consensus pattern (5 bp):
GCAAT
Found at i:1965640 original size:19 final size:19
Alignment explanation
Indices: 1965616--1965657 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
1965606 CAGTTCGAGA
1965616 AAATGCTTGAACAAGTATG
1 AAATGCTTGAACAAGTATG
1965635 AAATGCTTGAACAAGTATG
1 AAATGCTTGAACAAGTATG
1965654 AAAT
1 AAAT
1965658 TGTCGGGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.45, C:0.10, G:0.19, T:0.26
Consensus pattern (19 bp):
AAATGCTTGAACAAGTATG
Found at i:1967650 original size:15 final size:15
Alignment explanation
Indices: 1967630--1967662 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1967620 TAATATCACC
1967630 GTTTGAGATTTTAAG
1 GTTTGAGATTTTAAG
*
1967645 GTTTGATATTTTAAG
1 GTTTGAGATTTTAAG
1967660 GTT
1 GTT
1967663 GTAGAGTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (15 bp):
GTTTGAGATTTTAAG
Found at i:1972276 original size:26 final size:26
Alignment explanation
Indices: 1972240--1972291 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
1972230 ATTGGCAAAT
1972240 CCCAGTCTCAGTTTTACAGATAGAAA
1 CCCAGTCTCAGTTTTACAGATAGAAA
1972266 CCCAGTCTCAGTTTTACAGATAGAAA
1 CCCAGTCTCAGTTTTACAGATAGAAA
1972292 ATCATATAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (26 bp):
CCCAGTCTCAGTTTTACAGATAGAAA
Found at i:1977073 original size:22 final size:22
Alignment explanation
Indices: 1977033--1977075 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1977023 TAATCTATGC
*
1977033 TGTTTAGATATTTTGTTTTTGG
1 TGTTTAGATATTATGTTTTTGG
1977055 TGTTTAGATAATTAT-TTTTTG
1 TGTTTAGAT-ATTATGTTTTTG
1977076 TTATTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.63
Consensus pattern (22 bp):
TGTTTAGATATTATGTTTTTGG
Found at i:1981655 original size:41 final size:41
Alignment explanation
Indices: 1981610--1981694 Score: 116
Period size: 41 Copynumber: 2.1 Consensus size: 41
1981600 GTATCTTAAG
* * * * *
1981610 GGTACAATAGATTGGAAGCTTGAGTTTATTGGCTATCATGT
1 GGTACAATAGATTGAAAACTTGAGTATATTGGATATCATAT
*
1981651 GGTACAATATATTGAAAACTTGAGTATATTGGATATCATAT
1 GGTACAATAGATTGAAAACTTGAGTATATTGGATATCATAT
1981692 GGT
1 GGT
1981695 TTCAGAAGGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (41 bp):
GGTACAATAGATTGAAAACTTGAGTATATTGGATATCATAT
Found at i:1985483 original size:2 final size:2
Alignment explanation
Indices: 1985478--1985516 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1985468 TTATATACCT
1985478 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1985517 GTGAAAGGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1993145 original size:20 final size:20
Alignment explanation
Indices: 1993107--1993146 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1993097 CTTCAAAATC
* *
1993107 ATTTTTCAAAATTTCATTTT
1 ATTTTTCAAAATCTAATTTT
1993127 ATTTTTCAAAATCTAATTTT
1 ATTTTTCAAAATCTAATTTT
1993147 TCTTTCAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTTTTCAAAATCTAATTTT
Found at i:1993154 original size:19 final size:20
Alignment explanation
Indices: 1993110--1993154 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1993100 CAAAATCATT
* * *
1993110 TTTCAAAATTTCATTTTATT
1 TTTCAAAATCTAATTTTATC
1993130 TTTCAAAATCTAATTTT-TC
1 TTTCAAAATCTAATTTTATC
1993149 TTTCAA
1 TTTCAA
1993155 GATAAAATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.31, C:0.13, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTCAAAATCTAATTTTATC
Found at i:1999137 original size:23 final size:23
Alignment explanation
Indices: 1999111--1999232 Score: 129
Period size: 23 Copynumber: 5.3 Consensus size: 23
1999101 GAGTCAAGGG
* * * *
1999111 TTCTATGCGGTCCTTTGAGACAA
1 TTCTATGCGGTCATTCGGGACAT
* *
1999134 TTCTACGTGGTCATTCGGGACAT
1 TTCTATGCGGTCATTCGGGACAT
*
1999157 TTCTATGTGGTCATTCGGGACAT
1 TTCTATGCGGTCATTCGGGACAT
*
1999180 TTCTATGCGGTCCTTCGGGACAT
1 TTCTATGCGGTCATTCGGGACAT
* * *
1999203 ATCTATGTTGTTC-TTCGGGACAT
1 TTCTATG-CGGTCATTCGGGACAT
1999226 TTCTATG
1 TTCTATG
1999233 TGGCACTTTG
Statistics
Matches: 85, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
23 82 0.96
24 3 0.04
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (23 bp):
TTCTATGCGGTCATTCGGGACAT
Found at i:2002679 original size:2 final size:2
Alignment explanation
Indices: 2002672--2002704 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2002662 CTTAACTTTC
2002672 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2002705 ATCAGATCGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2004484 original size:29 final size:29
Alignment explanation
Indices: 2004451--2004507 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
2004441 ATAAATTAAT
*
2004451 TTGATGTCATTGCTTATATCAATTTAGTA
1 TTGATGTCATTGCTTACATCAATTTAGTA
2004480 TTGATGTCATTGCTTACATCAATTTAGT
1 TTGATGTCATTGCTTACATCAATTTAGT
2004508 TAGGTGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.47
Consensus pattern (29 bp):
TTGATGTCATTGCTTACATCAATTTAGTA
Found at i:2009113 original size:29 final size:29
Alignment explanation
Indices: 2009080--2009136 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
2009070 CTAAATTAAT
2009080 TTGATGTCATTGCTTACATCAATTTAGTA
1 TTGATGTCATTGCTTACATCAATTTAGTA
2009109 TTGATGTCATTGCTTACATCAATTTAGT
1 TTGATGTCATTGCTTACATCAATTTAGT
2009137 TAGGTGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.46
Consensus pattern (29 bp):
TTGATGTCATTGCTTACATCAATTTAGTA
Found at i:2011375 original size:12 final size:12
Alignment explanation
Indices: 2011358--2011387 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
2011348 AGTGTAGGAA
2011358 AGTGAGGAAAAG
1 AGTGAGGAAAAG
2011370 AGTGAGGAAAAG
1 AGTGAGGAAAAG
2011382 AGTGAG
1 AGTGAG
2011388 TAACGAGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.43, T:0.10
Consensus pattern (12 bp):
AGTGAGGAAAAG
Found at i:2023830 original size:20 final size:20
Alignment explanation
Indices: 2023807--2023913 Score: 101
Period size: 20 Copynumber: 5.3 Consensus size: 20
2023797 AATTTGTAAA
2023807 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
2023827 TCGCAACGC-GATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
* *
2023847 TCACAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
* * *
2023867 TCGCAACGCGGAATTTCAAAT
1 TCGCAACACAGAA-GTCAAAT
** *
2023888 TCGCAACTGA-AATTCAAAT
1 TCGCAACACAGAAGTCAAAT
2023907 TCGCAAC
1 TCGCAAC
2023914 TAGATTTTCG
Statistics
Matches: 72, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
19 16 0.22
20 42 0.58
21 14 0.19
ACGTcount: A:0.41, C:0.25, G:0.14, T:0.20
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:2023830 original size:40 final size:40
Alignment explanation
Indices: 2023786--2023913 Score: 138
Period size: 40 Copynumber: 3.2 Consensus size: 40
2023776 AGTTTCCAAT
2023786 TTCGCAACGCGAATTTGTAAA-TCGCAACACAGAAGTCAAA
1 TTCGCAACGCGAATTTGTAAATTCGCAACACA-AAGTCAAA
* *
2023826 TTCGCAACGCG-A-TAGTCAAATTCACAACACAAAAGTCAAA
1 TTCGCAACGCGAATTTGT-AAATTCGCAACAC-AAAGTCAAA
* ** *
2023866 TTCGCAACGCGGAATTT-CAAATTCGCAACTGAAATTCAAA
1 TTCGCAACGC-GAATTTGTAAATTCGCAACACAAAGTCAAA
2023906 TTCGCAAC
1 TTCGCAAC
2023914 TAGATTTTCG
Statistics
Matches: 74, Mismatches: 8, Indels: 12
0.79 0.09 0.13
Matches are distributed among these distances:
38 3 0.04
39 4 0.05
40 53 0.72
41 12 0.16
42 1 0.01
43 1 0.01
ACGTcount: A:0.40, C:0.24, G:0.15, T:0.21
Consensus pattern (40 bp):
TTCGCAACGCGAATTTGTAAATTCGCAACACAAAGTCAAA
Found at i:2023929 original size:20 final size:19
Alignment explanation
Indices: 2023861--2023933 Score: 83
Period size: 19 Copynumber: 3.7 Consensus size: 19
2023851 AACACAAAAG
*
2023861 TCAAATTCGCAACGCGGAATT
1 TCAAATTCGCAA--CTGAATT
*
2023882 TCAAATTCGCAACTGAAAT
1 TCAAATTCGCAACTGAATT
*
2023901 TCAAATTCGCAACTAGATTT
1 TCAAATTCGCAACT-GAATT
*
2023921 TCGAATTCGCAAC
1 TCAAATTCGCAAC
2023934 ACGAATTTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
19 19 0.41
20 15 0.33
21 12 0.26
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:2024760 original size:12 final size:12
Alignment explanation
Indices: 2024739--2024772 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2024729 ACCACATTTC
*
2024739 CAATACCAAACA
1 CAATATCAAACA
2024751 CAATATCAAACA
1 CAATATCAAACA
*
2024763 CAATCTCAAA
1 CAATATCAAA
2024773 ACTCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:2027232 original size:18 final size:18
Alignment explanation
Indices: 2027209--2027244 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2027199 AAGCAAAAGG
2027209 AAATCAAAATCGCAATCA
1 AAATCAAAATCGCAATCA
*
2027227 AAATCAAAATCTCAATCA
1 AAATCAAAATCGCAATCA
2027245 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCGCAATCA
Found at i:2027601 original size:20 final size:20
Alignment explanation
Indices: 2027578--2027642 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 20
2027568 GCGGATTTGA
2027578 CTTTCGCGTTGCGAATTTAC
1 CTTTCGCGTTGCGAATTTAC
**
2027598 CTTTCGCGTTGTAAATTTGA-
1 CTTTCGCGTTGCGAATTT-AC
*
2027618 CTTTTGCGTTGCGAAAATTTAC
1 CTTTCGCGTTGCG--AATTTAC
2027640 CTT
1 CTT
2027643 CAACATGTCT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
20 26 0.72
21 2 0.06
22 8 0.22
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.43
Consensus pattern (20 bp):
CTTTCGCGTTGCGAATTTAC
Found at i:2029122 original size:6 final size:6
Alignment explanation
Indices: 2029111--2029155 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
2029101 AAGCAAAAGG
* * *
2029111 AAATCA AAATCA CAATCA AAATCA AAATCA AAATCC CAATCA AAA
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAA
2029156 CCGGCTTCAC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.62, C:0.22, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATCA
Found at i:2029129 original size:12 final size:12
Alignment explanation
Indices: 2029112--2029155 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
2029102 AGCAAAAGGA
2029112 AATCAAAATCAC
1 AATCAAAATCAC
*
2029124 AATCAAAATCAA
1 AATCAAAATCAC
*
2029136 AATCAAAATCCC
1 AATCAAAATCAC
2029148 AATCAAAA
1 AATCAAAA
2029156 CCGGCTTCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.61, C:0.23, G:0.00, T:0.16
Consensus pattern (12 bp):
AATCAAAATCAC
Found at i:2029701 original size:28 final size:28
Alignment explanation
Indices: 2029669--2029722 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
2029659 ATAATTCTTA
*
2029669 TTTACACATCAAATTAAACAAATCAACT
1 TTTACAAATCAAATTAAACAAATCAACT
* **
2029697 TTTACAAATCAACTTTTACAAATCAA
1 TTTACAAATCAAATTAAACAAATCAA
2029723 TTAAACAAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.31
Consensus pattern (28 bp):
TTTACAAATCAAATTAAACAAATCAACT
Found at i:2029703 original size:14 final size:14
Alignment explanation
Indices: 2029686--2029722 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
2029676 ATCAAATTAA
2029686 ACAAATCAACTTTT
1 ACAAATCAACTTTT
2029700 ACAAATCAACTTTT
1 ACAAATCAACTTTT
2029714 ACAAATCAA
1 ACAAATCAA
2029723 TTAAACAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2031035 original size:21 final size:21
Alignment explanation
Indices: 2030995--2031092 Score: 90
Period size: 21 Copynumber: 4.7 Consensus size: 21
2030985 GCCAGCAGGA
* **
2030995 CCTCTTGAACTATGATAGGGG
1 CCTCTTGAACGATGGGAGGGG
*
2031016 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAACGATGGGAGGGG
* * *
2031037 ACTCTTTG-ATGATGAGAGGGG
1 CCTC-TTGAACGATGGGAGGGG
* *
2031058 CCTCTTGAACGATAGGAGGTG
1 CCTCTTGAACGATGGGAGGGG
*
2031079 CCTCTTGAATGATG
1 CCTCTTGAACGATG
2031093 ATAGGTGCAT
Statistics
Matches: 60, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
20 3 0.05
21 54 0.90
22 3 0.05
ACGTcount: A:0.21, C:0.17, G:0.35, T:0.27
Consensus pattern (21 bp):
CCTCTTGAACGATGGGAGGGG
Found at i:2031042 original size:42 final size:42
Alignment explanation
Indices: 2030996--2031097 Score: 127
Period size: 42 Copynumber: 2.4 Consensus size: 42
2030986 CCAGCAGGAC
* *
2030996 CTCTTGAACT-ATGATAGGGGCCTCTTGAACGGTGGGAGGGGA
1 CTCTTGAA-TGATGATAGGGGCCTCTTGAACGATAGGAGGGGA
* * *
2031038 CTCTTTG-ATGATGAGAGGGGCCTCTTGAACGATAGGAGGTGC
1 CTC-TTGAATGATGATAGGGGCCTCTTGAACGATAGGAGGGGA
2031080 CTCTTGAATGATGATAGG
1 CTCTTGAATGATGATAGG
2031098 TGCATCAGGC
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
41 4 0.08
42 44 0.86
43 3 0.06
ACGTcount: A:0.23, C:0.16, G:0.35, T:0.26
Consensus pattern (42 bp):
CTCTTGAATGATGATAGGGGCCTCTTGAACGATAGGAGGGGA
Found at i:2033312 original size:20 final size:20
Alignment explanation
Indices: 2033287--2033333 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
2033277 ATTGCAACGA
2033287 GAAAATCGCAACGCGAAAAT
1 GAAAATCGCAACGCGAAAAT
* *
2033307 GAAAATTGCAACGCGAAACT
1 GAAAATCGCAACGCGAAAAT
2033327 -AAAATCG
1 GAAAATCG
2033334 TGTTGCGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.49, C:0.19, G:0.19, T:0.13
Consensus pattern (20 bp):
GAAAATCGCAACGCGAAAAT
Found at i:2033324 original size:14 final size:14
Alignment explanation
Indices: 2033259--2033306 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
2033249 ACACGAAAAT
*
2033259 GAAAATCGCAACAC
1 GAAAATCGCAACGC
* * *
2033273 CAAAATTGCAACGA
1 GAAAATCGCAACGC
2033287 GAAAATCGCAACGC
1 GAAAATCGCAACGC
2033301 GAAAAT
1 GAAAAT
2033307 GAAAATTGCA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.50, C:0.23, G:0.17, T:0.10
Consensus pattern (14 bp):
GAAAATCGCAACGC
Found at i:2033734 original size:22 final size:22
Alignment explanation
Indices: 2033707--2033753 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
2033697 GATGGAGATA
*
2033707 GACGGATTTCGCCGGAGATGTG
1 GACGGATTTCGCCGGAGATGGG
*
2033729 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
2033751 GAC
1 GAC
2033754 AAATGTCTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.19, C:0.17, G:0.43, T:0.21
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:2033894 original size:20 final size:20
Alignment explanation
Indices: 2033869--2033986 Score: 71
Period size: 20 Copynumber: 5.8 Consensus size: 20
2033859 ATATTGTGTT
2033869 TCGCGTTGCGAATTTGATTA
1 TCGCGTTGCGAATTTGATTA
* *
2033889 TCGCGTTGTGAATTTAACTT-
1 TCGCGTTGCGAATTTGA-TTA
* *
2033909 TTGTGTTGCGAATTTGACTT-
1 TCGCGTTGCGAATTTGA-TTA
* * **
2033929 TTGTGTTGCGAATTT-AAAA
1 TCGCGTTGCGAATTTGATTA
* *
2033948 TTCAGTGTTGCGAATTTGACTA
1 -TC-GCGTTGCGAATTTGATTA
* *
2033970 TCGCATTGTGAATTTGA
1 TCGCGTTGCGAATTTGA
2033987 CTTCTGTGTT
Statistics
Matches: 79, Mismatches: 14, Indels: 10
0.77 0.14 0.10
Matches are distributed among these distances:
19 1 0.01
20 59 0.75
21 17 0.22
22 2 0.03
ACGTcount: A:0.22, C:0.12, G:0.23, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGATTA
Found at i:2033917 original size:40 final size:40
Alignment explanation
Indices: 2033873--2034000 Score: 150
Period size: 40 Copynumber: 3.2 Consensus size: 40
2033863 TGTGTTTCGC
*
2033873 GTTGCGAATTTGATTATCGCGTTGTGAATTTAACTTTTGT
1 GTTGCGAATTTGATTATCGCGTTGTGAATTTAACTTCTGT
* * * * *
2033913 GTTGCGAATTTGACTT-TTGTGTTGCGAATTTAAAATTCAGT
1 GTTGCGAATTTGA-TTATCGCGTTGTGAATTT-AACTTCTGT
* * *
2033954 GTTGCGAATTTGACTATCGCATTGTGAATTTGACTTCTGT
1 GTTGCGAATTTGATTATCGCGTTGTGAATTTAACTTCTGT
2033994 GTTGCGA
1 GTTGCGA
2034001 TTTACAAATT
Statistics
Matches: 71, Mismatches: 14, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
40 39 0.55
41 32 0.45
ACGTcount: A:0.21, C:0.12, G:0.23, T:0.44
Consensus pattern (40 bp):
GTTGCGAATTTGATTATCGCGTTGTGAATTTAACTTCTGT
Found at i:2035361 original size:2 final size:2
Alignment explanation
Indices: 2035356--2035427 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
2035346 AAAAAACCAA
2035356 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
2035398 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
2035428 TAGAGTCGAC
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2037569 original size:6 final size:6
Alignment explanation
Indices: 2037560--2037584 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2037550 GATAGATGTA
2037560 TTTATT TTTATT TTTATT TTTATT T
1 TTTATT TTTATT TTTATT TTTATT T
2037585 CTTTAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTATT
Found at i:2044137 original size:2 final size:2
Alignment explanation
Indices: 2044130--2044182 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
2044120 TCTACCCGAT
2044130 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2044172 TA TA TA TA TA T
1 TA TA TA TA TA T
2044183 TTTAAATATT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2044606 original size:31 final size:30
Alignment explanation
Indices: 2044542--2044603 Score: 99
Period size: 31 Copynumber: 2.1 Consensus size: 30
2044532 AATTTTTTTT
2044542 AATAATTTAGATACTTATTTTGACTAAAAA
1 AATAATTTAGATACTTATTTTGACTAAAAA
*
2044572 AATAACTTTAGATATTTATTTTGA-TAAAAA
1 AATAA-TTTAGATACTTATTTTGACTAAAAA
2044602 AA
1 AA
2044604 ATACTAAATG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 13 0.43
31 17 0.57
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.40
Consensus pattern (30 bp):
AATAATTTAGATACTTATTTTGACTAAAAA
Found at i:2049211 original size:27 final size:27
Alignment explanation
Indices: 2049129--2049211 Score: 62
Period size: 27 Copynumber: 3.1 Consensus size: 27
2049119 TATTTTTAAT
*
2049129 TTTTAATTTAATTATCTATTATTAAAA
1 TTTTAATTTAATTATCTATTGTTAAAA
*** * * **
2049156 GAATAATATTAA-TATGT-TACGTTTTAA
1 TTTTAAT-TTAATTATCTAT-TGTTAAAA
2049183 TTTTAATTTAATTATCTATTGTTAAAA
1 TTTTAATTTAATTATCTATTGTTAAAA
2049210 TT
1 TT
2049212 AATAATAATA
Statistics
Matches: 37, Mismatches: 15, Indels: 8
0.62 0.25 0.13
Matches are distributed among these distances:
26 5 0.14
27 27 0.73
28 5 0.14
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.53
Consensus pattern (27 bp):
TTTTAATTTAATTATCTATTGTTAAAA
Found at i:2050224 original size:14 final size:15
Alignment explanation
Indices: 2050199--2050227 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2050189 TAATATTATA
2050199 ATATATTATTGTAAC
1 ATATATTATTGTAAC
2050214 ATATA-TATTGTAAC
1 ATATATTATTGTAAC
2050228 GTCTGCAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (15 bp):
ATATATTATTGTAAC
Found at i:2051057 original size:30 final size:28
Alignment explanation
Indices: 2051023--2051096 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 28
2051013 GAAAATTGAA
* *
2051023 TTAAACGGAGACGGGAAAAAATTGTTTATG
1 TTAAATGG-GACGGG-AAAAATCGTTTATG
**
2051053 TTAAATGGGATAAGGAAAAATCGTTTATG
1 TTAAATGGGA-CGGGAAAAATCGTTTATG
2051082 TTAAATGGGGACGGG
1 TTAAAT-GGGACGGG
2051097 TTTATTAATC
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
29 23 0.64
30 13 0.36
ACGTcount: A:0.38, C:0.05, G:0.30, T:0.27
Consensus pattern (28 bp):
TTAAATGGGACGGGAAAAATCGTTTATG
Found at i:2051222 original size:15 final size:15
Alignment explanation
Indices: 2051137--2051241 Score: 50
Period size: 13 Copynumber: 7.5 Consensus size: 15
2051127 CGATAAATAT
*
2051137 TATAAATAA-TTAT-
1 TATATATAATTTATA
*
2051150 TATATAT-ATATATA
1 TATATATAATTTATA
2051164 TATATAATAATATTA-A
1 TATAT-ATAAT-TTATA
* * *
2051180 TAAATTTAATTTAAA
1 TATATATAATTTATA
* *
2051195 T-TA-AAAATATATA
1 TATATATAATTTATA
2051208 TATA-AT-ATTTATA
1 TATATATAATTTATA
*
2051221 TAT-T-TAATTTAAA
1 TATATATAATTTATA
2051234 TATATATA
1 TATATATA
2051242 CCCGGCCCGA
Statistics
Matches: 68, Mismatches: 13, Indels: 20
0.67 0.13 0.20
Matches are distributed among these distances:
12 2 0.03
13 34 0.50
14 13 0.19
15 10 0.15
16 7 0.10
17 2 0.03
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATATATAATTTATA
Found at i:2058079 original size:27 final size:27
Alignment explanation
Indices: 2058049--2058102 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
2058039 GTATCATTTC
2058049 GATCACTTGTGTAATCGACATTACAGG
1 GATCACTTGTGTAATCGACATTACAGG
2058076 GATCACTTGTGTAATCGACATTACAGG
1 GATCACTTGTGTAATCGACATTACAGG
2058103 TAAATCAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (27 bp):
GATCACTTGTGTAATCGACATTACAGG
Found at i:2060151 original size:31 final size:31
Alignment explanation
Indices: 2060113--2060212 Score: 182
Period size: 31 Copynumber: 3.2 Consensus size: 31
2060103 TATTACTGAA
*
2060113 CTCGACTTGACTCAAAAAGTTCAAAGTTGAG
1 CTCGACTTGACTCAAAAAGTTCAAAATTGAG
2060144 CTCGACTTGACTCAAAAAGTTCAAAATTGAG
1 CTCGACTTGACTCAAAAAGTTCAAAATTGAG
2060175 CTCGACTTGACTCAAAAAGTTCAAAATTGAG
1 CTCGACTTGACTCAAAAAGTTCAAAATTGAG
*
2060206 TTCGACT
1 CTCGACT
2060213 CGAAAACGCG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 67 1.00
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (31 bp):
CTCGACTTGACTCAAAAAGTTCAAAATTGAG
Found at i:2062778 original size:63 final size:63
Alignment explanation
Indices: 2062625--2062784 Score: 178
Period size: 63 Copynumber: 2.5 Consensus size: 63
2062615 ATTGTTCAGT
* * * *
2062625 GTGTATCGATGCACAGGAAGTGCATCGATGCACCCATTCAAAATGGAAACATCGAATACAATTA
1 GTGTATCGATGCA-TGGTAGTGCATCGATGCACCCATTCAAAATGAAAACATCGAAGACAATTA
* ** * * ***
2062689 GTGCATCGATGCATAATGAGTACATCGATGCACCCCTT-AAAATGAAAACATCGAAGGTGATTA
1 GTGTATCGATGCATGGT-AGTGCATCGATGCACCCATTCAAAATGAAAACATCGAAGACAATTA
2062752 GTGTATCGATGCATGGGTAGTGCATCGATGCAC
1 GTGTATCGATGCAT-GGTAGTGCATCGATGCAC
2062785 ATGTTAAATA
Statistics
Matches: 78, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
63 47 0.60
64 31 0.40
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (63 bp):
GTGTATCGATGCATGGTAGTGCATCGATGCACCCATTCAAAATGAAAACATCGAAGACAATTA
Found at i:2063454 original size:21 final size:21
Alignment explanation
Indices: 2063430--2063499 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
2063420 TATGAACATG
2063430 TGAATTATATGAAAAGTGATA
1 TGAATTATATGAAAAGTGATA
* * *
2063451 TGAATTACATGAAAAGAAGCTA
1 TGAATTATATGAAAAG-TGATA
* *
2063473 TGAGCTTATATGAACATGTGATA
1 TGA-ATTATATGAA-AAGTGATA
2063496 TGAA
1 TGAA
2063500 AGTGTATATG
Statistics
Matches: 37, Mismatches: 9, Indels: 5
0.73 0.18 0.10
Matches are distributed among these distances:
21 15 0.41
22 6 0.16
23 14 0.38
24 2 0.05
ACGTcount: A:0.44, C:0.06, G:0.20, T:0.30
Consensus pattern (21 bp):
TGAATTATATGAAAAGTGATA
Found at i:2066993 original size:63 final size:64
Alignment explanation
Indices: 2066855--2067013 Score: 203
Period size: 63 Copynumber: 2.5 Consensus size: 64
2066845 ATTGTTCAGT
* * *
2066855 GTGTATCGATGCACATGAAGTGCATCGATGCACCCATTAAAAATGGAAACATCGAATGCAATTA
1 GTGTATCGATGCATATGAAGTGCATCGATGCACCCATTAAAAATGAAAACATCGAAGGCAATTA
* * * * **
2066919 GTGCATCGATGCATAAGGAGTGCATCGATGCACCC-TTTAAAATGAAAACATCGAAGGTGATTA
1 GTGTATCGATGCATATGAAGTGCATCGATGCACCCATTAAAAATGAAAACATCGAAGGCAATTA
* * *
2066982 GTGTATCGATGCATGTGTAGTGTATCGATGCA
1 GTGTATCGATGCATATGAAGTGCATCGATGCA
2067014 TGGGTAGTGC
Statistics
Matches: 81, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
63 50 0.62
64 31 0.38
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (64 bp):
GTGTATCGATGCATATGAAGTGCATCGATGCACCCATTAAAAATGAAAACATCGAAGGCAATTA
Found at i:2067004 original size:19 final size:19
Alignment explanation
Indices: 2066980--2067032 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
2066970 CGAAGGTGAT
*
2066980 TAGTGTATCGATGCATGTG
1 TAGTGTATCGATGCATGGG
2066999 TAGTGTATCGATGCATGGG
1 TAGTGTATCGATGCATGGG
*
2067018 TAGTGCATCGATGCA
1 TAGTGTATCGATGCA
2067033 CATGTTAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.23, C:0.13, G:0.32, T:0.32
Consensus pattern (19 bp):
TAGTGTATCGATGCATGGG
Found at i:2067066 original size:20 final size:22
Alignment explanation
Indices: 2067021--2067078 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
2067011 GCATGGGTAG
2067021 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
2067045 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
2067065 TGCATCGATGCACT
1 TGCATCGATGCACT
2067079 TCAAGGGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 18 0.53
22 1 0.03
23 2 0.06
24 13 0.38
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:2067704 original size:21 final size:21
Alignment explanation
Indices: 2067679--2067748 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
2067669 TGTGAACATG
2067679 TGAATTATATGAAAAGTGATA
1 TGAATTATATGAAAAGTGATA
* * *
2067700 TGAATTACATGAAAAGAAGCTA
1 TGAATTATATGAAAAG-TGATA
* *
2067722 TGAGCTTATATGAACATGTGATA
1 TGA-ATTATATGAA-AAGTGATA
2067745 TGAA
1 TGAA
2067749 AGTGTATATG
Statistics
Matches: 37, Mismatches: 9, Indels: 5
0.73 0.18 0.10
Matches are distributed among these distances:
21 15 0.41
22 6 0.16
23 14 0.38
24 2 0.05
ACGTcount: A:0.44, C:0.06, G:0.20, T:0.30
Consensus pattern (21 bp):
TGAATTATATGAAAAGTGATA
Found at i:2070325 original size:35 final size:35
Alignment explanation
Indices: 2070284--2070358 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
2070274 TTCATGTTCA
2070284 AAATTCCAAAACACTTCAATTACATTCTAAACCTC
1 AAATTCCAAAACACTTCAATTACATTCTAAACCTC
* * * *
2070319 AAATTCCAAAATACTTTAATTATATTCTAAACCTT
1 AAATTCCAAAACACTTCAATTACATTCTAAACCTC
2070354 AAATT
1 AAATT
2070359 GAAGTATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (35 bp):
AAATTCCAAAACACTTCAATTACATTCTAAACCTC
Found at i:2070402 original size:35 final size:35
Alignment explanation
Indices: 2070354--2070429 Score: 107
Period size: 35 Copynumber: 2.2 Consensus size: 35
2070344 TCTAAACCTT
2070354 AAATTGAAGTATTTTAGAATTTAGGATTTAAAATA
1 AAATTGAAGTATTTTAGAATTTAGGATTTAAAATA
* * * * *
2070389 TAATTGAATTATTTTGGAATTTAGGGTTTAGAATA
1 AAATTGAAGTATTTTAGAATTTAGGATTTAAAATA
2070424 AAATTG
1 AAATTG
2070430 GGAAATGTGT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.41, C:0.00, G:0.17, T:0.42
Consensus pattern (35 bp):
AAATTGAAGTATTTTAGAATTTAGGATTTAAAATA
Found at i:2071199 original size:13 final size:14
Alignment explanation
Indices: 2071176--2071205 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
2071166 TTCTCATTAC
2071176 AGACGTGCATATGA
1 AGACGTGCATATGA
2071190 AGAC-TGCATATGA
1 AGACGTGCATATGA
2071203 AGA
1 AGA
2071206 TTGTCCAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.40, C:0.13, G:0.27, T:0.20
Consensus pattern (14 bp):
AGACGTGCATATGA
Found at i:2086299 original size:16 final size:16
Alignment explanation
Indices: 2086278--2086327 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
2086268 GAAACATACG
2086278 CACATATATATATATA
1 CACATATATATATATA
**
2086294 CACATACCTATATATA
1 CACATATATATATATA
* * *
2086310 TACATATGTATACATA
1 CACATATATATATATA
2086326 CA
1 CA
2086328 TGTATGTATG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.46, C:0.18, G:0.02, T:0.34
Consensus pattern (16 bp):
CACATATATATATATA
Found at i:2086487 original size:16 final size:17
Alignment explanation
Indices: 2086466--2086498 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
2086456 ATATACATTA
2086466 TTTTATTAT-ATAATAT
1 TTTTATTATCATAATAT
2086482 TTTTATTATCATAATAT
1 TTTTATTATCATAATAT
2086499 ATAATATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTATTATCATAATAT
Found at i:2086668 original size:23 final size:24
Alignment explanation
Indices: 2086624--2086675 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
2086614 AATAAAAATA
* *
2086624 TTTAAAAATATATTTATTAATAATT
1 TTTAAAAATATATGTATCAAT-ATT
2086649 TTTAAAAATATA-GTA-CAATATT
1 TTTAAAAATATATGTATCAATATT
2086671 TTTAA
1 TTTAA
2086676 TTTAATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 8 0.32
23 3 0.12
24 2 0.08
25 12 0.48
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (24 bp):
TTTAAAAATATATGTATCAATATT
Found at i:2088691 original size:30 final size:31
Alignment explanation
Indices: 2088657--2088728 Score: 76
Period size: 30 Copynumber: 2.3 Consensus size: 31
2088647 ACTAAAGTTT
*
2088657 AATTAATTTTAATTTAATTACT-TAAC-TTTA
1 AATT-ATTTTAATTTAATCACTCTAACTTTTA
* *
2088687 AATTATTCTTAGTTTAATCATTCTAACTTTTA
1 AATTATT-TTAATTTAATCACTCTAACTTTTA
2088719 AATTTATTTT
1 AA-TTATTTT
2088729 TTAATTATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
29 3 0.09
30 15 0.43
31 4 0.11
32 8 0.23
33 5 0.14
ACGTcount: A:0.35, C:0.08, G:0.01, T:0.56
Consensus pattern (31 bp):
AATTATTTTAATTTAATCACTCTAACTTTTA
Found at i:2089353 original size:2 final size:2
Alignment explanation
Indices: 2089346--2089370 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2089336 ATCTGACGAC
2089346 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2089371 TACTTGAGAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2090945 original size:15 final size:15
Alignment explanation
Indices: 2090921--2090950 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2090911 TTGATAGAAA
*
2090921 ATTTTCAAATTTTAT
1 ATTTTAAAATTTTAT
2090936 ATTTTAAAATTTTAT
1 ATTTTAAAATTTTAT
2090951 TTATGTATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTTAAAATTTTAT
Done.