Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold66
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: 4623749
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 850 characters in sequence are not A, C, G, or T
File 11 of 26
Found at i:1827291 original size:6 final size:6
Alignment explanation
Indices: 1827280--1827304 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1827270 AACTGTGAAA
1827280 AAAAAG AAAAAG AAAAAG AAAAAG A
1 AAAAAG AAAAAG AAAAAG AAAAAG A
1827305 TATTCAAAAG
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:1833489 original size:2 final size:2
Alignment explanation
Indices: 1833482--1833509 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1833472 TTTCATTTGG
1833482 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
1833510 TTCGGTGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1834581 original size:15 final size:14
Alignment explanation
Indices: 1834539--1834586 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
1834529 TTATATGATG
*
1834539 TTTAAAATTTTTTAT
1 TTTAAAA-TTTATAT
*
1834554 ATTAAATATTTATAAT
1 TTTAAA-ATTTAT-AT
1834570 TTTAAAATTTATAT
1 TTTAAAATTTATAT
1834584 TTT
1 TTT
1834587 CATTATAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 5 0.18
15 15 0.54
16 8 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTAAAATTTATAT
Found at i:1835456 original size:27 final size:28
Alignment explanation
Indices: 1835426--1835484 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
1835416 ATAAATTATT
*
1835426 AATATACTAAAAT-TAA-TATAATTAAAA
1 AATAT-CTAAAATATAATTATAATAAAAA
* *
1835453 AATATTTTAAATATAATTATAATAAAAA
1 AATATCTAAAATATAATTATAATAAAAA
1835481 AATA
1 AATA
1835485 CACAATTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 5 0.19
27 8 0.30
28 14 0.52
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.36
Consensus pattern (28 bp):
AATATCTAAAATATAATTATAATAAAAA
Found at i:1837122 original size:33 final size:33
Alignment explanation
Indices: 1837079--1837174 Score: 158
Period size: 33 Copynumber: 2.9 Consensus size: 33
1837069 TACGAAATTT
* *
1837079 GATCAAAGTTAACCCAAAGTGTATAATATCTAA
1 GATCAGAGTTAATCCAAAGTGTATAATATCTAA
1837112 GATCAGAGTTAATCCAAAGTGTATAATATCTAA
1 GATCAGAGTTAATCCAAAGTGTATAATATCTAA
*
1837145 GATCAGAGTTAATCAAAAGTGTATAA-ATCT
1 GATCAGAGTTAATCCAAAGTGTATAATATCT
1837175 GTGATCAAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
32 4 0.07
33 56 0.93
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (33 bp):
GATCAGAGTTAATCCAAAGTGTATAATATCTAA
Found at i:1839137 original size:21 final size:20
Alignment explanation
Indices: 1839113--1839152 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
1839103 TGATAAGATC
1839113 AATTTTAACAATAAAATTAAA
1 AATTTTAACAA-AAAATTAAA
*
1839134 AATTTTAACAAAATATTAA
1 AATTTTAACAAAAAATTAA
1839153 CTAATATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (20 bp):
AATTTTAACAAAAAATTAAA
Found at i:1845782 original size:18 final size:18
Alignment explanation
Indices: 1845756--1845790 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1845746 TGAATATTGA
* *
1845756 ATACGAATATATTTCAAC
1 ATACAAATATATATCAAC
1845774 ATACAAATATATATCAA
1 ATACAAATATATATCAA
1845791 TTATATAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.14, G:0.03, T:0.31
Consensus pattern (18 bp):
ATACAAATATATATCAAC
Found at i:1846003 original size:2 final size:2
Alignment explanation
Indices: 1845990--1846021 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1845980 TTTTGTCTCC
*
1845990 AT AT AC 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
1846022 CTCTTTTACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1847163 original size:13 final size:13
Alignment explanation
Indices: 1847137--1847178 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
1847127 ATATTTATTT
1847137 TTAAATAT--ATA
1 TTAAATATGAATA
1847148 TTAAATATGAATA
1 TTAAATATGAATA
1847161 TTAAATATGAATA
1 TTAAATATGAATA
*
1847174 CTAAA
1 TTAAA
1847179 AAAATAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
11 8 0.29
13 20 0.71
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (13 bp):
TTAAATATGAATA
Found at i:1848131 original size:2 final size:2
Alignment explanation
Indices: 1848124--1848155 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1848114 AGAATATACT
1848124 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
1848156 GCCTAGCTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1848479 original size:2 final size:2
Alignment explanation
Indices: 1848472--1848497 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1848462 TACCTCAAAC
1848472 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
1848498 TATTAATCAT
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:1848744 original size:2 final size:2
Alignment explanation
Indices: 1848737--1848778 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1848727 TATCTTTGAG
1848737 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
1848779 TCTCTTTGTT
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:1849378 original size:2 final size:2
Alignment explanation
Indices: 1849366--1849400 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1849356 GCTATATTGC
* *
1849366 TA TA CA TA TA TA TA TA CA 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 T
1849401 GTAAAAGAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1849381 original size:12 final size:12
Alignment explanation
Indices: 1849366--1849400 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
1849356 GCTATATTGC
1849366 TATACATATATA
1 TATACATATATA
1849378 TATACATATATA
1 TATACATATATA
*
1849390 TATATATATAT
1 TATACATATAT
1849401 GTAAAAGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (12 bp):
TATACATATATA
Found at i:1851726 original size:16 final size:16
Alignment explanation
Indices: 1851707--1851737 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1851697 AAAGTAAGTG
*
1851707 AAATAAAAAATATAAA
1 AAATAAAAAAGATAAA
1851723 AAATAAAAAAGATAA
1 AAATAAAAAAGATAA
1851738 GAGAAAAAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (16 bp):
AAATAAAAAAGATAAA
Found at i:1859075 original size:21 final size:20
Alignment explanation
Indices: 1859045--1859086 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1859035 TTTAAAAAAA
* *
1859045 ATATTTTTATATTAATATTT
1 ATATTTTTATAATAAAATTT
1859065 ATATATTTTATAATAAAATTT
1 ATAT-TTTTATAATAAAATTT
1859086 A
1 A
1859087 AATAAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATATTTTTATAATAAAATTT
Found at i:1859120 original size:48 final size:47
Alignment explanation
Indices: 1859000--1859122 Score: 133
Period size: 48 Copynumber: 2.5 Consensus size: 47
1858990 TTCATTTAAA
1859000 TTATATATATTTATTATTTATAATTAATAAAAAAATTTAAAAAAAATATTT
1 TTATAT-TATTTA-TATTTAT--TTAATAAAAAAATTTAAAAAAAATATTT
* * *
1859051 TTATATTAATATT-TATATATTTTATAATAAAATTTAAATAAAAATATTT
1 TTATATT-AT-TTATATTTATTTAATAAAAAAATTTAAA-AAAAATATTT
1859100 TTA-ATTATTTAATATTTATTTAA
1 TTATATTATTT-ATATTTATTTAA
1859123 ATCAAATTAA
Statistics
Matches: 62, Mismatches: 5, Indels: 13
0.77 0.06 0.16
Matches are distributed among these distances:
46 2 0.03
47 2 0.03
48 28 0.45
49 13 0.21
50 7 0.11
51 8 0.13
52 2 0.03
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (47 bp):
TTATATTATTTATATTTATTTAATAAAAAAATTTAAAAAAAATATTT
Found at i:1859439 original size:7 final size:7
Alignment explanation
Indices: 1859427--1859452 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1859417 GATAAAACAG
1859427 ATTTTAT
1 ATTTTAT
1859434 ATTTTAT
1 ATTTTAT
1859441 ATTTTAT
1 ATTTTAT
1859448 ATTTT
1 ATTTT
1859453 TTTAAATATT
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:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
ATTTTAT
Found at i:1859575 original size:18 final size:18
Alignment explanation
Indices: 1859535--1859593 Score: 82
Period size: 18 Copynumber: 3.1 Consensus size: 18
1859525 AATTAAATTC
1859535 TTATTTTTAATAATTATAAA
1 TTATTTTTAAT-ATTA-AAA
*
1859555 TTATATTTAATATTAAAA
1 TTATTTTTAATATTAAAA
1859573 TTATTTTTAATATATAAAA
1 TTATTTTTAATAT-TAAAA
1859592 TT
1 TT
1859594 TTAAAAATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
18 15 0.42
19 11 0.31
20 10 0.28
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTATTTTTAATATTAAAA
Found at i:1862270 original size:21 final size:21
Alignment explanation
Indices: 1862238--1862289 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1862228 GTTCCTCCAC
* *
1862238 CACCACCGCCACCTCC-CTCAA
1 CACCACCACCACCGCCAC-CAA
*
1862259 CTCCACCACCACCGCCACCAA
1 CACCACCACCACCGCCACCAA
1862280 CACCACCACC
1 CACCACCACC
1862290 TCCATCTCCT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 25 0.96
22 1 0.04
ACGTcount: A:0.27, C:0.63, G:0.04, T:0.06
Consensus pattern (21 bp):
CACCACCACCACCGCCACCAA
Found at i:1867904 original size:42 final size:42
Alignment explanation
Indices: 1867843--1867997 Score: 159
Period size: 42 Copynumber: 3.6 Consensus size: 42
1867833 GTTGTTCATA
* ** *
1867843 AGAACAAATCATATGGTGGAGTTCAATCT-CCCGGGCTCCTGG
1 AGAACAAATCAGACAGTGGAGTTCAAT-TGCCCAGGCTCCTGG
* * *
1867885 AGAACAAATCAGACAGTGGAGTTCTATTGCACAGTCTCCTCCCGG
1 AGAACAAATCAGACAGTGGAGTTCAATTGCCCAGGCTCCT---GG
**
1867930 AGAACAAATCAGACAGTGGAGTTCAATTGCCCAGGCTCCCAG
1 AGAACAAATCAGACAGTGGAGTTCAATTGCCCAGGCTCCTGG
* * *
1867972 AGGACAAATCAGATAATGGAGTTCAA
1 AGAACAAATCAGACAGTGGAGTTCAA
1867998 CCCCCCTGGC
Statistics
Matches: 94, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
41 1 0.01
42 55 0.59
45 38 0.40
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.21
Consensus pattern (42 bp):
AGAACAAATCAGACAGTGGAGTTCAATTGCCCAGGCTCCTGG
Found at i:1867941 original size:45 final size:45
Alignment explanation
Indices: 1867878--1867997 Score: 147
Period size: 45 Copynumber: 2.7 Consensus size: 45
1867868 ATCTCCCGGG
* * *
1867878 CTCCTGGAGAACAAATCAGACAGTGGAGTTCTATTGCACAGTCTC
1 CTCCCGGAGAACAAATCAGACAGTGGAGTTCAATTGCACAGGCTC
*
1867923 CTCCCGGAGAACAAATCAGACAGTGGAGTTCAATTGCCCAGG---
1 CTCCCGGAGAACAAATCAGACAGTGGAGTTCAATTGCACAGGCTC
* * * *
1867965 CTCCCAGAGGACAAATCAGATAATGGAGTTCAA
1 CTCCCGGAGAACAAATCAGACAGTGGAGTTCAA
1867998 CCCCCCTGGC
Statistics
Matches: 67, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
42 29 0.43
45 38 0.57
ACGTcount: A:0.33, C:0.24, G:0.23, T:0.20
Consensus pattern (45 bp):
CTCCCGGAGAACAAATCAGACAGTGGAGTTCAATTGCACAGGCTC
Found at i:1868695 original size:3 final size:3
Alignment explanation
Indices: 1868687--1868720 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1868677 TAACTCTTGG
1868687 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
1868721 TTGAGAGTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:1869769 original size:22 final size:24
Alignment explanation
Indices: 1869744--1869791 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
1869734 AAATTGATTT
1869744 AAATTA-TT-ATTTAATAATAAAA
1 AAATTATTTAATTTAATAATAAAA
*
1869766 AAATTATTTAAATTTAATTATAAAA
1 AAATTATTT-AATTTAATAATAAAA
1869791 A
1 A
1869792 TATATTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 6 0.27
23 2 0.09
25 14 0.64
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
AAATTATTTAATTTAATAATAAAA
Found at i:1869804 original size:25 final size:25
Alignment explanation
Indices: 1869752--1869801 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
1869742 TTAAATTATT
*
1869752 ATTTAATAATAAAAAAATTATTTAA
1 ATTTAATAATAAAAAAATTATTAAA
* *
1869777 ATTTAATTATAAAAATA-TATTAAA
1 ATTTAATAATAAAAAAATTATTAAA
1869801 A
1 A
1869802 ATTATATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
ATTTAATAATAAAAAAATTATTAAA
Found at i:1871723 original size:34 final size:34
Alignment explanation
Indices: 1871680--1871748 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
1871670 TAGTGATAAG
1871680 TCCAAAATGAATAATTATGAAGTTAAAGAACAAA
1 TCCAAAATGAATAATTATGAAGTTAAAGAACAAA
*
1871714 TCCAAAATGAATAATTATGGAGTTAAAGAACAAA
1 TCCAAAATGAATAATTATGAAGTTAAAGAACAAA
1871748 T
1 T
1871749 AGATACTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.54, C:0.09, G:0.13, T:0.25
Consensus pattern (34 bp):
TCCAAAATGAATAATTATGAAGTTAAAGAACAAA
Found at i:1872440 original size:2 final size:2
Alignment explanation
Indices: 1872433--1872470 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1872423 TAGATTTGTG
*
1872433 AT AT AT AT AT AT AT AT GT 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
1872471 GGCTGTAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1874049 original size:31 final size:32
Alignment explanation
Indices: 1874011--1874075 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 32
1874001 TTAATTTAAA
*
1874011 AAATTATT-TTTTTAT-TTAA-AATTAT-ATT
1 AAATTTTTATTTTTATATTAATAATTATAATT
*
1874039 AAATTTTTATTTTTATATTAATATTTATAATT
1 AAATTTTTATTTTTATATTAATAATTATAATT
1874071 AAATT
1 AAATT
1874076 AATAAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 7 0.23
29 7 0.23
30 4 0.13
31 5 0.16
32 8 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (32 bp):
AAATTTTTATTTTTATATTAATAATTATAATT
Found at i:1874076 original size:18 final size:18
Alignment explanation
Indices: 1874023--1874079 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
1874013 ATTATTTTTT
*
1874023 TATTTAAAATTATATTAAA
1 TATTTATAATTATATT-AA
* **
1874042 TTTTTATTTTTATATTAA
1 TATTTATAATTATATTAA
*
1874060 TATTTATAATTAAATTAA
1 TATTTATAATTATATTAA
1874078 TA
1 TA
1874080 AAAATATTTT
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
18 18 0.60
19 12 0.40
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTTATAATTATATTAA
Found at i:1877204 original size:2 final size:2
Alignment explanation
Indices: 1877197--1877231 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
1877187 TCTGTGAATA
*
1877197 AT AT AT AT AT AT AT AT AT AT AT AT A- AG AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1877232 TTCTATGCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1881683 original size:30 final size:30
Alignment explanation
Indices: 1881649--1881709 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
1881639 TGCTGAAAGA
1881649 TAGTTTTGCACGCAAAAGCACATAAAACAT
1 TAGTTTTGCACGCAAAAGCACATAAAACAT
*
1881679 TAGTTTTGCACGCAAAAGCACATATAACAT
1 TAGTTTTGCACGCAAAAGCACATAAAACAT
1881709 T
1 T
1881710 TTGTGCTCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (30 bp):
TAGTTTTGCACGCAAAAGCACATAAAACAT
Found at i:1883399 original size:13 final size:13
Alignment explanation
Indices: 1883381--1883411 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1883371 ATTTTATACG
1883381 TATTTATATTTAA
1 TATTTATATTTAA
1883394 TATTTATATTTAA
1 TATTTATATTTAA
1883407 -ATTTA
1 TATTTA
1883412 AATAAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TATTTATATTTAA
Found at i:1884845 original size:25 final size:25
Alignment explanation
Indices: 1884806--1884854 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1884796 TTTTATATTT
*
1884806 TTATTTAAATTTAAATT-ATTTGAA
1 TTATTTAAATGTAAATTAATTTGAA
1884830 TTATATTAAATGTAAATTAATTTGA
1 TTAT-TTAAATGTAAATTAATTTGA
1884855 CAACTTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.18
25 12 0.55
26 6 0.27
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (25 bp):
TTATTTAAATGTAAATTAATTTGAA
Found at i:1885178 original size:2 final size:2
Alignment explanation
Indices: 1885171--1885197 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1885161 TCATTTCCAC
1885171 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
1885198 ATCCAGGAGA
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:1885855 original size:24 final size:25
Alignment explanation
Indices: 1885828--1885875 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
1885818 AATGACTTAA
1885828 TTTCTTCTT-TTATGTTGTTTTTTT
1 TTTCTTCTTCTTATGTTGTTTTTTT
* *
1885852 TTTCTTTTTCCTTATTTTGTTTTT
1 TTTCTTCTT-CTTATGTTGTTTTT
1885876 CCATCTAACG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
26 12 0.60
ACGTcount: A:0.04, C:0.10, G:0.06, T:0.79
Consensus pattern (25 bp):
TTTCTTCTTCTTATGTTGTTTTTTT
Found at i:1888962 original size:27 final size:26
Alignment explanation
Indices: 1888932--1889011 Score: 72
Period size: 33 Copynumber: 2.8 Consensus size: 26
1888922 TCTTAATTAT
1888932 ATTTTAAATATTTTATATTTATATAAA
1 ATTTTAAATATTTTATATTTATAT-AA
1888959 ATTTGATATATTAATATTTTATA-TTATATAA
1 A-TT--T-TA--AATATTTTATATTTATATAA
1888990 ATTTTAAAATATTTTTATATTT
1 ATTTT-AAATA-TTTTATATTT
1889012 TTATCATATT
Statistics
Matches: 44, Mismatches: 0, Indels: 17
0.72 0.00 0.28
Matches are distributed among these distances:
26 4 0.09
27 9 0.20
28 6 0.14
30 3 0.07
31 5 0.11
32 6 0.14
33 11 0.25
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (26 bp):
ATTTTAAATATTTTATATTTATATAA
Found at i:1888995 original size:16 final size:17
Alignment explanation
Indices: 1888928--1888995 Score: 72
Period size: 16 Copynumber: 4.2 Consensus size: 17
1888918 TATATCTTAA
*
1888928 TTATATTTTA-AATATT
1 TTATATTATATAATATT
*
1888944 TTATATTTATATAAAATT
1 TTATA-TTATATAATATT
*
1888962 TGATA-TAT-TAATATT
1 TTATATTATATAATATT
1888977 TTATATTATATAA-ATT
1 TTATATTATATAATATT
1888993 TTA
1 TTA
1888996 AAATATTTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
15 10 0.23
16 17 0.40
17 7 0.16
18 9 0.21
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (17 bp):
TTATATTATATAATATT
Found at i:1889002 original size:32 final size:33
Alignment explanation
Indices: 1888938--1889002 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
1888928 TTATATTTTA
* *
1888938 AATATTTTATATTTATATAAAATTTGATATATT
1 AATATTTTATATTTATATAAAATTTAAAATATT
*
1888971 AATATTTTATA-TTATATAAATTTTAAAATATT
1 AATATTTTATATTTATATAAAATTTAAAATATT
1889003 TTTATATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (33 bp):
AATATTTTATATTTATATAAAATTTAAAATATT
Found at i:1889020 original size:19 final size:19
Alignment explanation
Indices: 1888998--1889055 Score: 55
Period size: 22 Copynumber: 2.9 Consensus size: 19
1888988 AAATTTTAAA
1888998 ATATTTTTATATTTTTATC
1 ATATTTTTATATTTTTATC
*
1889017 ATATTTATTTTACATTTTATATC
1 ATA--T-TTTTATATTTT-TATC
*
1889040 ATATTTTAAT-TTTTTA
1 ATATTTTTATATTTTTA
1889056 AATATTATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
18 2 0.06
19 7 0.22
20 4 0.12
21 2 0.06
22 10 0.31
23 7 0.22
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (19 bp):
ATATTTTTATATTTTTATC
Found at i:1889027 original size:22 final size:23
Alignment explanation
Indices: 1889002--1889045 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
1888992 TTTAAAATAT
*
1889002 TTTTATATTTT-TATCATATTTA
1 TTTTACATTTTATATCATATTTA
1889024 TTTTACATTTTATATCATATTT
1 TTTTACATTTTATATCATATTT
1889046 TAATTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTTACATTTTATATCATATTTA
Found at i:1890740 original size:2 final size:2
Alignment explanation
Indices: 1890731--1890760 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1890721 TTATATATTT
1890731 AC AC -C AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1890761 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1892362 original size:17 final size:17
Alignment explanation
Indices: 1892310--1892363 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
1892300 AAATACATCT
1892310 TAAAATTTATAT-AATA
1 TAAAATTTATATAAATA
*
1892326 T-GAA-TTA-ATAATATA
1 TAAAATTTATATAA-ATA
1892341 TTAAAATTTATATAAATA
1 -TAAAATTTATATAAATA
1892359 TAAAA
1 TAAAA
1892364 CACTTTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 11
0.70 0.05 0.26
Matches are distributed among these distances:
13 2 0.07
14 4 0.13
15 5 0.17
16 2 0.07
17 7 0.23
18 6 0.20
19 4 0.13
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:1893904 original size:8 final size:8
Alignment explanation
Indices: 1893863--1893920 Score: 59
Period size: 8 Copynumber: 7.5 Consensus size: 8
1893853 TCGTATTGTA
*
1893863 ATTTAAAG
1 ATTTAAAT
* *
1893871 ATTAAAAA
1 ATTTAAAT
1893879 ATTATAAAT
1 ATT-TAAAT
1893888 A-TT-AAT
1 ATTTAAAT
1893894 ATTTAAAT
1 ATTTAAAT
1893902 A-TTAAAT
1 ATTTAAAT
1893909 ATTTAAAT
1 ATTTAAAT
1893917 ATTT
1 ATTT
1893921 TTTAATTATA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
6 4 0.10
7 10 0.24
8 24 0.57
9 4 0.10
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (8 bp):
ATTTAAAT
Found at i:1893911 original size:15 final size:15
Alignment explanation
Indices: 1893863--1893919 Score: 71
Period size: 15 Copynumber: 3.7 Consensus size: 15
1893853 TCGTATTGTA
* *
1893863 ATTTAAAGATTAAAAA
1 ATTTAAATATT-AAAT
1893879 ATTATAAATATT-AAT
1 ATT-TAAATATTAAAT
1893894 ATTTAAATATTAAAT
1 ATTTAAATATTAAAT
1893909 ATTTAAATATT
1 ATTTAAATATT
1893920 TTTTAATTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
14 8 0.22
15 19 0.51
16 3 0.08
17 7 0.19
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (15 bp):
ATTTAAATATTAAAT
Found at i:1895998 original size:19 final size:19
Alignment explanation
Indices: 1895970--1896013 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
1895960 ATATAAATAT
*
1895970 ATTT-AATATTTTAAAAAA
1 ATTTAAATATTTAAAAAAA
*
1895988 TTTTAAATATTTAAAAAAA
1 ATTTAAATATTTAAAAAAA
1896007 ATTTAAA
1 ATTTAAA
1896014 AAAATTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
ATTTAAATATTTAAAAAAA
Found at i:1896050 original size:18 final size:17
Alignment explanation
Indices: 1896027--1896061 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1896017 ATTATATTTT
*
1896027 TATATTAATATTTAAATA
1 TATATTAA-ATATAAATA
1896045 TATATTAAATATAAATA
1 TATATTAAATATAAATA
1896062 AAAATAACGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TATATTAAATATAAATA
Found at i:1896782 original size:25 final size:26
Alignment explanation
Indices: 1896754--1896807 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
1896744 TGGATTTCAA
**
1896754 TATTCAATGTTTTAAATTTTT-TATT
1 TATTCAAAATTTTAAATTTTTATATT
* *
1896779 TATTTAAAATTTTATATTTTTATATT
1 TATTCAAAATTTTAAATTTTTATATT
1896805 TAT
1 TAT
1896808 ATTTAAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 17 0.71
26 7 0.29
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (26 bp):
TATTCAAAATTTTAAATTTTTATATT
Found at i:1897114 original size:17 final size:17
Alignment explanation
Indices: 1897092--1897147 Score: 69
Period size: 17 Copynumber: 3.2 Consensus size: 17
1897082 TAAATTATCT
1897092 ATTTAAATTTAAAATTA
1 ATTTAAATTTAAAATTA
1897109 ATTTAATATTTAAAA-TA
1 ATTTAA-ATTTAAAATTA
**
1897126 ATTTAAATAAAAATATTA
1 ATTTAAATTTAAA-ATTA
1897144 ATTT
1 ATTT
1897148 CATTAAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
16 5 0.15
17 15 0.44
18 14 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATTTAAATTTAAAATTA
Found at i:1897145 original size:18 final size:18
Alignment explanation
Indices: 1897124--1897158 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1897114 ATATTTAAAA
1897124 TAATTTAAATAAAAATAT
1 TAATTTAAATAAAAATAT
* *
1897142 TAATTTCATTAAAAATA
1 TAATTTAAATAAAAATA
1897159 AACTTAGATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (18 bp):
TAATTTAAATAAAAATAT
Found at i:1897157 original size:33 final size:33
Alignment explanation
Indices: 1897116--1897193 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 33
1897106 TTAATTTAAT
* *
1897116 ATTT-AAAATAATTTAAATAAAAATATTAATTTC
1 ATTTAAAAATAACTTAAAT-AAAATATTAAATTC
* *
1897149 A-TTAAAAATAAACTTAGATAAATTATTAAATTC
1 ATTTAAAAAT-AACTTAAATAAAATATTAAATTC
1897182 ATTTAAAAATAA
1 ATTTAAAAATAA
1897194 ATAAATTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
32 2 0.05
33 21 0.55
34 15 0.39
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.38
Consensus pattern (33 bp):
ATTTAAAAATAACTTAAATAAAATATTAAATTC
Found at i:1897289 original size:24 final size:23
Alignment explanation
Indices: 1897239--1897290 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 23
1897229 ACTTGATCTG
1897239 TTTTTAATTATATACTATATTAA
1 TTTTTAATTATATACTATATTAA
* *
1897262 TTTTATATTTATATATTATA-TAA
1 TTTT-TAATTATATACTATATTAA
1897285 TTTTTA
1 TTTTTA
1897291 GTATATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 2 0.08
23 11 0.42
24 13 0.50
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTTTAATTATATACTATATTAA
Found at i:1897491 original size:10 final size:10
Alignment explanation
Indices: 1897476--1897500 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1897466 TTATTTATTT
1897476 ATAAATATAA
1 ATAAATATAA
1897486 ATAAATATAA
1 ATAAATATAA
1897496 ATAAA
1 ATAAA
1897501 AATTAAGACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
ATAAATATAA
Found at i:1899342 original size:9 final size:9
Alignment explanation
Indices: 1899318--1899351 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
1899308 ATTAAATAAT
*
1899318 AAATTAAATT
1 AAATTAAA-A
1899328 AAATTAAAA
1 AAATTAAAA
1899337 AAATTAAAA
1 AAATTAAAA
1899346 AAATTA
1 AAATTA
1899352 TATATTCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (9 bp):
AAATTAAAA
Found at i:1899995 original size:26 final size:26
Alignment explanation
Indices: 1899961--1900019 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
1899951 ATACGAATAT
* *
1899961 ATTAAATTTTTTTATATAT-TTATAAA
1 ATTATATTTTTATATATATATTA-AAA
*
1899987 ATTATATTTTTATATTTATATTAAAA
1 ATTATATTTTTATATATATATTAAAA
1900013 A-TATATT
1 ATTATATT
1900020 AAATACGAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 6 0.21
26 20 0.69
27 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
ATTATATTTTTATATATATATTAAAA
Found at i:1899996 original size:24 final size:25
Alignment explanation
Indices: 1899969--1900019 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
1899959 ATATTAAATT
*
1899969 TTTTTATATATT-TA-TAAAATTATA
1 TTTTTATAT-TTATATTAAAAATATA
1899993 TTTTTATATTTATATTAAAAATATA
1 TTTTTATATTTATATTAAAAATATA
1900018 TT
1 TT
1900020 AAATACGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 2 0.08
24 11 0.46
25 11 0.46
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
TTTTTATATTTATATTAAAAATATA
Found at i:1902928 original size:15 final size:15
Alignment explanation
Indices: 1902889--1902933 Score: 72
Period size: 17 Copynumber: 2.9 Consensus size: 15
1902879 ATTAAAATTT
1902889 AATTTATTTTTTAAA
1 AATTTATTTTTTAAA
1902904 AAGTTATATTTTTTAAA
1 AA-TT-TATTTTTTAAA
1902921 AATTTATTTTTTA
1 AATTTATTTTTTA
1902934 TTTATATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 11 0.39
16 4 0.14
17 13 0.46
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (15 bp):
AATTTATTTTTTAAA
Found at i:1904393 original size:23 final size:23
Alignment explanation
Indices: 1904367--1904412 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1904357 AATAGATGAT
* *
1904367 AAAATTAATTTTAGTAAAATTAA
1 AAAAATAATTATAGTAAAATTAA
*
1904390 AAAAATAATTATAGTGAAATTAA
1 AAAAATAATTATAGTAAAATTAA
1904413 TTAATATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.35
Consensus pattern (23 bp):
AAAAATAATTATAGTAAAATTAA
Found at i:1915421 original size:27 final size:26
Alignment explanation
Indices: 1915391--1915448 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
1915381 AATTTCAAAC
*
1915391 ATAATACAATTATATAACACAATAAAA
1 ATAATACAA-AATATAACACAATAAAA
* *
1915418 ATAAT-CAAAATATGACACAATACAA
1 ATAATACAAAATATAACACAATAAAA
1915443 ATAATA
1 ATAATA
1915449 AACACAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 19 0.70
26 3 0.11
27 5 0.19
ACGTcount: A:0.62, C:0.12, G:0.02, T:0.24
Consensus pattern (26 bp):
ATAATACAAAATATAACACAATAAAA
Found at i:1916149 original size:10 final size:10
Alignment explanation
Indices: 1916134--1916159 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1916124 TCACAAAATT
1916134 AAAAAAAGAA
1 AAAAAAAGAA
1916144 AAAAAAAGAA
1 AAAAAAAGAA
1916154 AAAAAA
1 AAAAAA
1916160 TGTCAAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:1916314 original size:26 final size:27
Alignment explanation
Indices: 1916285--1916344 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 27
1916275 TAGAAATGTT
* *
1916285 TTAATATTTATAAATATTTAA-TTAAA
1 TTAATATTGATAAAAATTTAAGTTAAA
*
1916311 TTAATAATGATAAAAATTTAAGTTAAA
1 TTAATATTGATAAAAATTTAAGTTAAA
1916338 TT-ATATT
1 TTAATATT
1916345 AAATAATAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 22 0.76
27 7 0.24
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (27 bp):
TTAATATTGATAAAAATTTAAGTTAAA
Found at i:1916587 original size:20 final size:20
Alignment explanation
Indices: 1916564--1916610 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
1916554 ATAAAATAAA
*
1916564 ATATTAATATGTAAAATTTT
1 ATATAAATATGTAAAATTTT
* *
1916584 ATATAAATTTGTAATATTTT
1 ATATAAATATGTAAAATTTT
*
1916604 AAATAAA
1 ATATAAA
1916611 CAAAAAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (20 bp):
ATATAAATATGTAAAATTTT
Found at i:1916839 original size:21 final size:22
Alignment explanation
Indices: 1916807--1916851 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
1916797 TAACAACATA
1916807 ACATAGAAAAAATTAAAAT-ATT
1 ACATAGAAAAAA-TAAAATAATT
1916829 ACATA-AAAAAATAAAATAATT
1 ACATAGAAAAAATAAAATAATT
1916850 AC
1 AC
1916852 GATACAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.27
21 11 0.50
22 5 0.23
ACGTcount: A:0.67, C:0.07, G:0.02, T:0.24
Consensus pattern (22 bp):
ACATAGAAAAAATAAAATAATT
Found at i:1919910 original size:2 final size:2
Alignment explanation
Indices: 1919903--1919937 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1919893 GCCTAACTAG
1919903 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1919938 GGTAGGATTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1920371 original size:32 final size:32
Alignment explanation
Indices: 1920307--1920390 Score: 95
Period size: 32 Copynumber: 2.7 Consensus size: 32
1920297 TATAATATTA
* * *
1920307 TATAAAAATATTTAAATTTATATAATGTAAAT
1 TATAAATATATTAAAATTTATATAATGAAAAT
*
1920339 TATTAATATATTAAAATTTATATAAAT-AAAAT
1 TATAAATATATTAAAATTTATAT-AATGAAAAT
1920371 TATAAAT-TA-TAAAA-TTATAT
1 TATAAATATATTAAAATTTATAT
1920391 GGATATAATA
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 6 0.13
30 5 0.11
31 2 0.04
32 30 0.65
33 3 0.07
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (32 bp):
TATAAATATATTAAAATTTATATAATGAAAAT
Found at i:1920953 original size:18 final size:19
Alignment explanation
Indices: 1920913--1920954 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
1920903 GATATTTTAA
*
1920913 ATTT-TAAATTTTTTATTT
1 ATTTATAAATATTTTATTT
1920931 A-TTATAAATATTTT-TTT
1 ATTTATAAATATTTTATTT
1920948 ATTTATA
1 ATTTATA
1920955 TTTGATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
ATTTATAAATATTTTATTT
Found at i:1921151 original size:27 final size:26
Alignment explanation
Indices: 1921083--1921151 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 26
1921073 TTATCTTATA
1921083 ATTTAATTTAATTAATAATTTAAAATT
1 ATTTAA-TTAATTAATAATTTAAAATT
* **
1921110 AATTAATTAATTTAATAATATTTTAATT
1 ATTTAATTAA-TTAATAAT-TTAAAATT
*
1921138 ATTTAATCAATTAA
1 ATTTAATTAATTAA
1921152 ATTAATCAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
26 4 0.11
27 17 0.49
28 14 0.40
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (26 bp):
ATTTAATTAATTAATAATTTAAAATT
Found at i:1921535 original size:16 final size:16
Alignment explanation
Indices: 1921514--1921547 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1921504 GGAAGATTAC
1921514 AATTAAAAAAATTAAA
1 AATTAAAAAAATTAAA
1921530 AATTAAAAAAATTAAA
1 AATTAAAAAAATTAAA
1921546 AA
1 AA
1921548 AAAAAAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AATTAAAAAAATTAAA
Found at i:1921550 original size:10 final size:9
Alignment explanation
Indices: 1921514--1921549 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
1921504 GGAAGATTAC
1921514 AATTAAAAA
1 AATTAAAAA
1921523 AATT--AAA
1 AATTAAAAA
1921530 AATTAAAAA
1 AATTAAAAA
1921539 AATTAAAAA
1 AATTAAAAA
1921548 AA
1 AA
1921550 AAAAAAAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 7 0.28
9 18 0.72
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (9 bp):
AATTAAAAA
Found at i:1921553 original size:16 final size:16
Alignment explanation
Indices: 1921518--1921556 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1921508 GATTACAATT
**
1921518 AAAAAAATTAAAAATT
1 AAAAAAATTAAAAAAA
1921534 AAAAAAATTAAAAAAA
1 AAAAAAATTAAAAAAA
1921550 AAAAAAA
1 AAAAAAA
1921557 GAGAGGAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (16 bp):
AAAAAAATTAAAAAAA
Found at i:1922237 original size:2 final size:2
Alignment explanation
Indices: 1922230--1922265 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1922220 TATATCAATT
1922230 TA TA TA TA -A 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 T
1922266 TACTTTTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1925121 original size:2 final size:2
Alignment explanation
Indices: 1925114--1925145 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1925104 TTATACGAAG
1925114 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
1925146 TCATTAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1927417 original size:15 final size:17
Alignment explanation
Indices: 1927397--1927429 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
1927387 TGATTAAGAT
1927397 TGTTAA-AATTT-TTTG
1 TGTTAATAATTTCTTTG
1927412 TGTTAATAATTTCTTTG
1 TGTTAATAATTTCTTTG
1927429 T
1 T
1927430 TTTTGTCGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 5 0.31
17 5 0.31
ACGTcount: A:0.24, C:0.03, G:0.12, T:0.61
Consensus pattern (17 bp):
TGTTAATAATTTCTTTG
Found at i:1931754 original size:18 final size:18
Alignment explanation
Indices: 1931731--1931765 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1931721 TACATCGGCA
*
1931731 CTTCAGAGATAGTGAGTG
1 CTTCAGAGATACTGAGTG
1931749 CTTCAGAGATACTGAGT
1 CTTCAGAGATACTGAGT
1931766 TTCTAACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (18 bp):
CTTCAGAGATACTGAGTG
Found at i:1936232 original size:69 final size:69
Alignment explanation
Indices: 1936116--1936253 Score: 213
Period size: 69 Copynumber: 2.0 Consensus size: 69
1936106 CCTAAGATTG
* * * *
1936116 TTTATTCTGGGGGCTGTTGGATATGGTATTGGCGACCTCTTTACAAAATTAGATGGTGGCCTCGA
1 TTTACTCTGGGAGCTGTTGGATATGCTATGGGCGACCTCTTTACAAAATTAGATGGTGGCCTCGA
1936181 TAAA
66 TAAA
* * *
1936185 TTTACTCTGGGAGTTGTTGGGTATGCTATGGGCGACCTCTTTACAAAATTAGATGGTGGCCTTGA
1 TTTACTCTGGGAGCTGTTGGATATGCTATGGGCGACCTCTTTACAAAATTAGATGGTGGCCTCGA
1936250 TAAA
66 TAAA
1936254 ATGAAATCCT
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 62 1.00
ACGTcount: A:0.23, C:0.14, G:0.28, T:0.35
Consensus pattern (69 bp):
TTTACTCTGGGAGCTGTTGGATATGCTATGGGCGACCTCTTTACAAAATTAGATGGTGGCCTCGA
TAAA
Found at i:1938401 original size:97 final size:98
Alignment explanation
Indices: 1938246--1938443 Score: 362
Period size: 97 Copynumber: 2.0 Consensus size: 98
1938236 ATTTTAAGTA
1938246 AGTTAATTCTATCATTAATTATGATGATGCTGTAGTAGATGAAGTCTTGGCTCAAAGCTTGTA-T
1 AGTTAATTCTATCATTAATTATGATGATGCTGTAGTAGATGAAGTCTTGGCTCAAAGCTTGTATT
*
1938310 TTTTTTTTAAGCAATTAGTGGGGATTTAGAGGG
66 TTTTTTTTAAGCAACTAGTGGGGATTTAGAGGG
1938343 AGTTAATTCTATCATTAATTATGATGATGCTGTAGTAGATGAAGTCTTGGCTCAAAGCTTGTATT
1 AGTTAATTCTATCATTAATTATGATGATGCTGTAGTAGATGAAGTCTTGGCTCAAAGCTTGTA-T
*
1938408 TTTTTTTTTAAGCAACTCGTGGGGATTTAGAGGG
65 TTTTTTTTTAAGCAACTAGTGGGGATTTAGAGGG
1938442 AG
1 AG
1938444 CGAGGAGGAT
Statistics
Matches: 97, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
97 63 0.65
99 34 0.35
ACGTcount: A:0.27, C:0.09, G:0.24, T:0.40
Consensus pattern (98 bp):
AGTTAATTCTATCATTAATTATGATGATGCTGTAGTAGATGAAGTCTTGGCTCAAAGCTTGTATT
TTTTTTTTAAGCAACTAGTGGGGATTTAGAGGG
Found at i:1938605 original size:6 final size:6
Alignment explanation
Indices: 1938594--1938631 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
1938584 TTAACTGAAC
1938594 TTTTAT TTTTAT TTTTA- TTTTAT TTTGATAT TTTTAT T
1 TTTTAT TTTTAT TTTTAT TTTTAT TTT--TAT TTTTAT T
1938632 AAATTATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.17
6 18 0.62
8 6 0.21
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:1938614 original size:11 final size:12
Alignment explanation
Indices: 1938594--1938631 Score: 51
Period size: 11 Copynumber: 3.1 Consensus size: 12
1938584 TTAACTGAAC
1938594 TTTTATTTTTAT
1 TTTTATTTTTAT
1938606 TTTTA-TTTTAT
1 TTTTATTTTTAT
1938617 TTTGATATTTTTAT
1 TTT--TATTTTTAT
1938631 T
1 T
1938632 AAATTATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 9 0.39
12 5 0.22
13 2 0.09
14 7 0.30
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (12 bp):
TTTTATTTTTAT
Found at i:1938616 original size:17 final size:18
Alignment explanation
Indices: 1938594--1938631 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
1938584 TTAACTGAAC
1938594 TTTTATTTT-TATTTTTA
1 TTTTATTTTATATTTTTA
1938611 TTTTATTTTGATATTTTTA
1 TTTTATTTT-ATATTTTTA
1938630 TT
1 TT
1938632 AAATTATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.47
19 10 0.53
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (18 bp):
TTTTATTTTATATTTTTA
Found at i:1944298 original size:15 final size:15
Alignment explanation
Indices: 1944278--1944317 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
1944268 TAATCATGTC
*
1944278 CATCCACCACCCGTG
1 CATCCACCACCCATG
*
1944293 CATCCACAACCCATG
1 CATCCACCACCCATG
1944308 CATCCACCAC
1 CATCCACCAC
1944318 TTGTTTACCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.28, C:0.53, G:0.07, T:0.12
Consensus pattern (15 bp):
CATCCACCACCCATG
Found at i:1944904 original size:75 final size:75
Alignment explanation
Indices: 1944776--1945019 Score: 353
Period size: 75 Copynumber: 3.3 Consensus size: 75
1944766 ATGTGAAATA
* * * *
1944776 TGCAAATTATTTCGGATTAGTTGTTGATAGTAGTAATGTGAAATATACAGAAACATTTGTTAATT
1 TGCAGATTATCTCAGATTAGTTGTTGATAGTAGTAATGTGAAATATGCAGAAACATTTGTTAATT
1944841 GTAATTATCG
66 GTAATTATCG
* * *
1944851 TGCAGATTATCTCAGATTAGTTATTGATAGTAGCAATGTGAAATATGCAGAAACATTTCTTAATT
1 TGCAGATTATCTCAGATTAGTTGTTGATAGTAGTAATGTGAAATATGCAGAAACATTTGTTAATT
*
1944916 GTAGTTATCG
66 GTAATTATCG
* * *
1944926 TGCAGATTATCTCGGATTAGTTGTTGATAGTAGTATTGTGAAATATGCTGAAACATTTGTTAATT
1 TGCAGATTATCTCAGATTAGTTGTTGATAGTAGTAATGTGAAATATGCAGAAACATTTGTTAATT
*
1944991 GTAATTATCA
66 GTAATTATCG
* * *
1945001 TACATATTATCTAAGATTA
1 TGCAGATTATCTCAGATTA
1945020 TCGTTTCATC
Statistics
Matches: 149, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
75 149 1.00
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.40
Consensus pattern (75 bp):
TGCAGATTATCTCAGATTAGTTGTTGATAGTAGTAATGTGAAATATGCAGAAACATTTGTTAATT
GTAATTATCG
Found at i:1946084 original size:105 final size:105
Alignment explanation
Indices: 1945902--1946218 Score: 580
Period size: 105 Copynumber: 3.0 Consensus size: 105
1945892 TGATAGCAGG
1945902 TTATACCCGAGGTTGGTCAGTCTGATGGAGCTATCAGATTACTCCAAAAAATGGAGAGCGAAGGT
1 TTATACCCGAGGTTGGTCAGTCTGATGGAGCTATCAGATTACTCCAAAAAATGGAGAGCGAAGGT
*
1945967 GTTAGGCTAGATGTAGTCGCTATCACAATTCACAGCTATA
66 GTTAGGCTAGATGTAGTTGCTATCACAATTCACAGCTATA
* * *
1946007 TTATACCCAAGGTTGATCAGTCTGATGGAGCTATCAGATTACTCCAAAAAATGGAGAGCAAAGGT
1 TTATACCCGAGGTTGGTCAGTCTGATGGAGCTATCAGATTACTCCAAAAAATGGAGAGCGAAGGT
1946072 GTTAGGCTAGATGTAGTTGCTATCACAATTCACAGCTATA
66 GTTAGGCTAGATGTAGTTGCTATCACAATTCACAGCTATA
* *
1946112 TTATACCCGAGGTTGGTCAGTCTGATGGCGCTATCAGATTACTCCAAAAAATGGAGAGTGAAGGT
1 TTATACCCGAGGTTGGTCAGTCTGATGGAGCTATCAGATTACTCCAAAAAATGGAGAGCGAAGGT
1946177 GTTAGGCTAGATGTAGTTGCTATCACAATTCACAGCTATA
66 GTTAGGCTAGATGTAGTTGCTATCACAATTCACAGCTATA
1946217 TT
1 TT
1946219 GCTCAGACTC
Statistics
Matches: 203, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
105 203 1.00
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (105 bp):
TTATACCCGAGGTTGGTCAGTCTGATGGAGCTATCAGATTACTCCAAAAAATGGAGAGCGAAGGT
GTTAGGCTAGATGTAGTTGCTATCACAATTCACAGCTATA
Found at i:1951178 original size:6 final size:6
Alignment explanation
Indices: 1951169--1951211 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
1951159 AATATTAAAA
*
1951169 TTTAAT TTTAAAT TTTAA- TTTAAT TTTAAT TTTAAT TTAAAT T
1 TTTAAT TTT-AAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT T
1951212 AAATAAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
5 5 0.15
6 23 0.68
7 6 0.18
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
TTTAAT
Found at i:1951195 original size:11 final size:12
Alignment explanation
Indices: 1951104--1951211 Score: 62
Period size: 13 Copynumber: 8.9 Consensus size: 12
1951094 TATATTTAAA
1951104 TAATTTATAATTT
1 TAATTT-TAATTT
* *
1951117 TAATTATGATTTT
1 TAATT-TTAATTT
* * *
1951130 TATTTTTTATGTA
1 TAATTTTAAT-TT
*
1951143 TAAATTT-ATTT
1 TAATTTTAATTT
1951154 TAA--TTAATATT
1 TAATTTTAAT-TT
* *
1951165 AAAATTTAATTT
1 TAATTTTAATTT
1951177 TAAATTTTAA-TT
1 T-AATTTTAATTT
1951189 TAATTTTAATTT
1 TAATTTTAATTT
*
1951201 TAATTTAAATT
1 TAATTTTAATT
1951212 AAATAAATTT
Statistics
Matches: 73, Mismatches: 14, Indels: 17
0.70 0.13 0.16
Matches are distributed among these distances:
9 2 0.03
10 2 0.03
11 16 0.22
12 21 0.29
13 31 0.42
14 1 0.01
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (12 bp):
TAATTTTAATTT
Found at i:1951211 original size:18 final size:18
Alignment explanation
Indices: 1951167--1951208 Score: 77
Period size: 17 Copynumber: 2.4 Consensus size: 18
1951157 TTAATATTAA
1951167 AATTTAATTTTAAATTTT
1 AATTTAATTTTAAATTTT
1951185 AATTTAATTTT-AATTTT
1 AATTTAATTTTAAATTTT
1951202 AATTTAA
1 AATTTAA
1951209 ATTAAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
AATTTAATTTTAAATTTT
Found at i:1951253 original size:39 final size:35
Alignment explanation
Indices: 1951176--1951292 Score: 106
Period size: 33 Copynumber: 3.5 Consensus size: 35
1951166 AAATTTAATT
** **
1951176 TTAAATTTTAATTTAATTTTAATTTTAAT-TTAAA
1 TTAAATTAAAATTTAAAATTAATTTTAATCTTAAA
1951210 TTAAA-T-AAATTTAATAATTAATTTT-ATCTTAAA
1 TTAAATTAAAATTTAA-AATTAATTTTAATCTTAAA
*
1951243 TTAAATTTAAAATTTAAAATTAA--TTAA--TAAATA
1 TTAAA-TTAAAATTTAAAATTAATTTTAATCTTAA-A
1951276 TTAAATTAAAATTTAAA
1 TTAAATTAAAATTTAAA
1951293 CCGTAAATTT
Statistics
Matches: 72, Mismatches: 4, Indels: 16
0.78 0.04 0.17
Matches are distributed among these distances:
32 24 0.33
33 27 0.38
34 6 0.08
35 7 0.10
36 8 0.11
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (35 bp):
TTAAATTAAAATTTAAAATTAATTTTAATCTTAAA
Found at i:1951264 original size:19 final size:19
Alignment explanation
Indices: 1951238--1951292 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 19
1951228 TAATTTTATC
1951238 TTAAATTAAATTTAAAAT-
1 TTAAATTAAATTTAAAATA
*
1951256 TTAAAATT-AATTAATAAATA
1 TT-AAATTAAATTTA-AAATA
1951276 TTAAATTAAAATTTAAA
1 TTAAATT-AAATTTAAA
1951293 CCGTAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
18 7 0.23
19 14 0.47
20 4 0.13
21 5 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TTAAATTAAATTTAAAATA
Found at i:1953447 original size:34 final size:34
Alignment explanation
Indices: 1953390--1953570 Score: 220
Period size: 34 Copynumber: 5.4 Consensus size: 34
1953380 AAAATTACTA
** *
1953390 TTAATCAACAATGACAACCTACCAAATCTCCCAT
1 TTAATCAACAATGGTAAACTACCAAATCTCCCAT
* ** * *
1953424 TTAGTCAACAATGGTAAGTTACCAAATTTTCCAT
1 TTAATCAACAATGGTAAACTACCAAATCTCCCAT
* *
1953458 TTAATCAACAATGGTAAGCTACCAAATCTTCCAT
1 TTAATCAACAATGGTAAACTACCAAATCTCCCAT
* * * *
1953492 TTAGTCAACAATGGCAAACCACCAAATCACCCAT
1 TTAATCAACAATGGTAAACTACCAAATCTCCCAT
*
1953526 TTAATCAACAATGGTAAACTACCAAATC-ACCAT
1 TTAATCAACAATGGTAAACTACCAAATCTCCCAT
1953559 TTAATCAACAAT
1 TTAATCAACAAT
1953571 TCTCCCACTT
Statistics
Matches: 127, Mismatches: 20, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
33 16 0.13
34 111 0.87
ACGTcount: A:0.41, C:0.25, G:0.07, T:0.27
Consensus pattern (34 bp):
TTAATCAACAATGGTAAACTACCAAATCTCCCAT
Found at i:1957768 original size:34 final size:34
Alignment explanation
Indices: 1957722--1957906 Score: 169
Period size: 34 Copynumber: 5.5 Consensus size: 34
1957712 GTAAAAACTA
**
1957722 TCATTTAATCAACAATGACAACCTACCAAATCTC
1 TCATTTAATCAACAATGGTAACCTACCAAATCTC
* * * *
1957756 TCATTTAGTCAACAATGGTAAGCTATCAAAAT-TT
1 TCATTTAATCAACAATGGTAACCTA-CCAAATCTC
** *
1957790 TCATTTAATCAACAATGGTAAGTTACTAAATCTC
1 TCATTTAATCAACAATGGTAACCTACCAAATCTC
* ** *
1957824 TCATTTAATTAACAATGACAAACC-ACCAAATCAC
1 TCATTTAATCAACAATG-GTAACCTACCAAATCTC
* * * * *
1957858 CCATTTAATCAATAATGGTAAACTACTAAATCAC
1 TCATTTAATCAACAATGGTAACCTACCAAATCTC
1957892 T-ATTTAATCAACAAT
1 TCATTTAATCAACAAT
1957907 TAAGACAAAA
Statistics
Matches: 121, Mismatches: 26, Indels: 9
0.78 0.17 0.06
Matches are distributed among these distances:
33 21 0.17
34 93 0.77
35 7 0.06
ACGTcount: A:0.42, C:0.21, G:0.06, T:0.31
Consensus pattern (34 bp):
TCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:1958527 original size:23 final size:23
Alignment explanation
Indices: 1958472--1958543 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
1958462 TATTTCTAGA
* *
1958472 TTATTAATTTTTAA-ATTTATAT
1 TTATTAATTTTTAATATATAAAT
**
1958494 TTAATGCATTTTTAATATATAAAT
1 TT-ATTAATTTTTAATATATAAAT
* *
1958518 TTATTAATTTATAATTTAT-AAT
1 TTATTAATTTTTAATATATAAAT
1958540 TTAT
1 TTAT
1958544 ATATTATTAT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
22 9 0.22
23 23 0.57
24 8 0.20
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (23 bp):
TTATTAATTTTTAATATATAAAT
Found at i:1958530 original size:18 final size:16
Alignment explanation
Indices: 1958501--1958566 Score: 59
Period size: 15 Copynumber: 4.1 Consensus size: 16
1958491 TATTTAATGC
1958501 ATTT-TTAA-TATATAA
1 ATTTATTAATTATAT-A
1958516 ATTTATTAATT-TATA
1 ATTTATTAATTATATA
1958531 ATTTA-TAATTTATATA
1 ATTTATTAA-TTATATA
*
1958547 TTATTATTAAATTATATA
1 AT-TTATT-AATTATATA
1958565 AT
1 AT
1958567 ATTACTTATT
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
14 3 0.07
15 12 0.29
16 12 0.29
17 4 0.10
18 9 0.21
19 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTTATTAATTATATA
Found at i:1958534 original size:7 final size:7
Alignment explanation
Indices: 1958501--1958544 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
1958491 TATTTAATGC
*
1958501 ATTTTTA
1 ATTTATA
*
1958508 ATATATAA
1 ATTTAT-A
1958516 ATTTATTA
1 ATTTA-TA
1958524 ATTTATA
1 ATTTATA
1958531 ATTTATA
1 ATTTATA
1958538 ATTTATA
1 ATTTATA
1958545 TATTATTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
7 20 0.62
8 11 0.34
9 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
ATTTATA
Found at i:1958569 original size:18 final size:18
Alignment explanation
Indices: 1958509--1958570 Score: 62
Period size: 18 Copynumber: 3.7 Consensus size: 18
1958499 GCATTTTTAA
1958509 TATATAA-ATTTATT-AAT
1 TATATAATA-TTATTAAAT
*
1958526 T-TATAAT-TTA-TAATT
1 TATATAATATTATTAAAT
*
1958541 TATATATTATTATTAAAT
1 TATATAATATTATTAAAT
1958559 TATATAATATTA
1 TATATAATATTA
1958571 CTTATTAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
14 1 0.03
15 6 0.17
16 10 0.28
17 4 0.11
18 15 0.42
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TATATAATATTATTAAAT
Found at i:1958578 original size:22 final size:19
Alignment explanation
Indices: 1958537--1958578 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
1958527 TATAATTTAT
1958537 AATTTATATATTATTATTA
1 AATTTATATATTATTATTA
1958556 AATTATATAATATTACTTATTA
1 AATT-TAT-ATATTA-TTATTA
1958578 A
1 A
1958579 TAAATAGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 4 0.20
20 3 0.15
21 6 0.30
22 7 0.35
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
AATTTATATATTATTATTA
Found at i:1963028 original size:15 final size:15
Alignment explanation
Indices: 1963008--1963047 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
1962998 TAATCATGTC
*
1963008 CATCCACCACCCGTG
1 CATCCACCACCCATG
*
1963023 CATCCACAACCCATG
1 CATCCACCACCCATG
1963038 CATCCACCAC
1 CATCCACCAC
1963048 TTGTTTACCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.28, C:0.53, G:0.07, T:0.12
Consensus pattern (15 bp):
CATCCACCACCCATG
Found at i:1963634 original size:75 final size:75
Alignment explanation
Indices: 1963506--1963749 Score: 353
Period size: 75 Copynumber: 3.3 Consensus size: 75
1963496 ATGTGAAATA
* * * *
1963506 TGCAAATTATTTCGGATTAGTTGTTGATAGTAGTAATGTGAAATATACAGAAACATTTGTTAATT
1 TGCAGATTATCTCAGATTAGTTGTTGATAGTAGTAATGTGAAATATGCAGAAACATTTGTTAATT
1963571 GTAATTATCG
66 GTAATTATCG
* * *
1963581 TGCAGATTATCTCAGATTAGTTATTGATAGTAGCAATGTGAAATATGCAGAAACATTTCTTAATT
1 TGCAGATTATCTCAGATTAGTTGTTGATAGTAGTAATGTGAAATATGCAGAAACATTTGTTAATT
*
1963646 GTAGTTATCG
66 GTAATTATCG
* * *
1963656 TGCAGATTATCTCGGATTAGTTGTTGATAGTAGTATTGTGAAATATGCTGAAACATTTGTTAATT
1 TGCAGATTATCTCAGATTAGTTGTTGATAGTAGTAATGTGAAATATGCAGAAACATTTGTTAATT
*
1963721 GTAATTATCA
66 GTAATTATCG
* * *
1963731 TACATATTATCTAAGATTA
1 TGCAGATTATCTCAGATTA
1963750 TCGTTTCATC
Statistics
Matches: 149, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
75 149 1.00
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.40
Consensus pattern (75 bp):
TGCAGATTATCTCAGATTAGTTGTTGATAGTAGTAATGTGAAATATGCAGAAACATTTGTTAATT
GTAATTATCG
Found at i:1964813 original size:105 final size:105
Alignment explanation
Indices: 1964631--1965052 Score: 772
Period size: 105 Copynumber: 4.0 Consensus size: 105
1964621 TGATAGCAGG
*
1964631 TTATACCCGAGGTTGGTCAGTCTGATGGAGCTATCAGATTACTCCAAAAAATGGAGAGCGAAGGT
1 TTATACCCGAGGTTGGTCAGTCTGATGGAGCTATCAGATTACTCCAAAAAATGGAGAGCAAAGGT
*
1964696 GTTAGGCTAGATGTAGTCGCTATCACAATTCACAGCTATA
66 GTTAGGCTAGATGTAGTTGCTATCACAATTCACAGCTATA
* *
1964736 TTATACCCAAGGTTGATCAGTCTGATGGAGCTATCAGATTACTCCAAAAAATGGAGAGCAAAGGT
1 TTATACCCGAGGTTGGTCAGTCTGATGGAGCTATCAGATTACTCCAAAAAATGGAGAGCAAAGGT
1964801 GTTAGGCTAGATGTAGTTGCTATCACAATTCACAGCTATA
66 GTTAGGCTAGATGTAGTTGCTATCACAATTCACAGCTATA
*
1964841 TTATACCCGAGGTTGGTCAGTCTGATGGCGCTATCAGATTACTCCAAAAAATGGAGAGCAAAGGT
1 TTATACCCGAGGTTGGTCAGTCTGATGGAGCTATCAGATTACTCCAAAAAATGGAGAGCAAAGGT
1964906 GTTAGGCTAGATGTAGTTGCTATCACAATTCACAGCTATA
66 GTTAGGCTAGATGTAGTTGCTATCACAATTCACAGCTATA
* **
1964946 TTATACCCGAGGTTGGTCAGTCTGATGGCGCTATCAGATTACTCCAAAAAATGGAGAGTGAAGGT
1 TTATACCCGAGGTTGGTCAGTCTGATGGAGCTATCAGATTACTCCAAAAAATGGAGAGCAAAGGT
1965011 GTTAGGCTAGATGTAGTTGCTATCACAATTCACAGCTATA
66 GTTAGGCTAGATGTAGTTGCTATCACAATTCACAGCTATA
1965051 TT
1 TT
1965053 GCTCAGACTC
Statistics
Matches: 308, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
105 308 1.00
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.28
Consensus pattern (105 bp):
TTATACCCGAGGTTGGTCAGTCTGATGGAGCTATCAGATTACTCCAAAAAATGGAGAGCAAAGGT
GTTAGGCTAGATGTAGTTGCTATCACAATTCACAGCTATA
Found at i:1969991 original size:6 final size:6
Alignment explanation
Indices: 1969941--1970067 Score: 89
Period size: 6 Copynumber: 20.5 Consensus size: 6
1969931 TATATTTAAA
* *
1969941 TAATTT ATAATTT TAATTA TAATTT TTATTT T--TTAT GT-ATATT TAATTT
1 TAATTT -TAATTT TAATTT TAATTT TAATTT TAATT-T -TAAT-TT TAATTT
* *
1969990 TAAATTT TAATTT TAATTT AAATTT TAATTT TAATTT AAATAATT TAATTT
1 T-AATTT TAATTT TAATTT TAATTT TAATTT TAATTT TAAT--TT TAATTT
* * * * *
1970041 TTATCT TAAATT AAATTT AAATTT TAA
1 TAATTT TAATTT TAATTT TAATTT TAA
1970068 AAATTAATTA
Statistics
Matches: 97, Mismatches: 15, Indels: 17
0.75 0.12 0.13
Matches are distributed among these distances:
4 2 0.02
5 1 0.01
6 72 0.74
7 16 0.16
8 6 0.06
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.60
Consensus pattern (6 bp):
TAATTT
Found at i:1969996 original size:43 final size:44
Alignment explanation
Indices: 1969921--1970008 Score: 119
Period size: 43 Copynumber: 2.0 Consensus size: 44
1969911 TTAAATTAAA
1969921 TTATTTTTTATATATTTAAATAATTTATAATTTTAATTATAATTT
1 TTATTTTTTATATATTTAAAT-ATTTATAATTTTAATTATAATTT
*
1969966 TTATTTTTTATGTATATTT-AAT-TTTA-AATTTTAATTTTAATTT
1 TTATTTTTTA--TATATTTAAATATTTATAATTTTAATTATAATTT
1970009 AAATTTTAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
43 16 0.40
44 4 0.10
45 10 0.25
46 3 0.08
47 7 0.17
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (44 bp):
TTATTTTTTATATATTTAAATATTTATAATTTTAATTATAATTT
Found at i:1970015 original size:43 final size:46
Alignment explanation
Indices: 1969911--1970058 Score: 121
Period size: 44 Copynumber: 3.3 Consensus size: 46
1969901 TTAAATTAAA
* *
1969911 TTAAATTAAATTATTTTTTATATATTTAAATAATTTATAATTTTAATT
1 TTAATTTAAATT-TTTTATATATATTTAAAT-ATTTATAATTTTAATT
* ** *
1969959 ATAATTTTTATTTTTTATGTATATTT-AAT-TTTA-AATTTTAATT
1 TTAATTTAAATTTTTTATATATATTTAAATATTTATAATTTTAATT
* * *
1970002 TTAATTTAAATTTTAATT-T-TA-ATTTAAATAATT-TAATTTTTATC
1 TTAATTTAAATTTT--TTATATATATTTAAATATTTATAATTTTAATT
*
1970046 TTAAATTAAATTT
1 TTAATTTAAATTT
1970059 AAATTTTAAA
Statistics
Matches: 82, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
42 4 0.05
43 26 0.32
44 27 0.33
45 2 0.02
46 3 0.04
47 12 0.15
48 8 0.10
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.60
Consensus pattern (46 bp):
TTAATTTAAATTTTTTATATATATTTAAATATTTATAATTTTAATT
Found at i:1970068 original size:18 final size:18
Alignment explanation
Indices: 1969983--1970101 Score: 68
Period size: 18 Copynumber: 6.6 Consensus size: 18
1969973 TTATGTATAT
* *
1969983 TTAATTTTAAATTTTAAT
1 TTAAATTTAAATTTTAAA
* *
1970001 TTTAATTTAAATTTTAAT
1 TTAAATTTAAATTTTAAA
*
1970019 TTTAATTTAAA---T-AA
1 TTAAATTTAAATTTTAAA
* ** *
1970033 TTTAATTTTTATCTTAAA
1 TTAAATTTAAATTTTAAA
1970051 TTAAATTTAAATTTTAAAAA
1 TTAAATTTAAATTTT--AAA
*
1970071 TT-AATTAATAAATATTAAA
1 TTAAATT--TAAATTTTAAA
1970090 TTAAAATTTAAA
1 TT-AAATTTAAA
1970102 CCGTAAATTT
Statistics
Matches: 81, Mismatches: 10, Indels: 19
0.74 0.09 0.17
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
17 1 0.01
18 40 0.49
19 13 0.16
20 5 0.06
21 11 0.14
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (18 bp):
TTAAATTTAAATTTTAAA
Found at i:1972249 original size:34 final size:34
Alignment explanation
Indices: 1972205--1972387 Score: 217
Period size: 34 Copynumber: 5.4 Consensus size: 34
1972195 AAAAATTACT
**
1972205 ATTTAATCAACAATGACAACCTACCAAATCTCCC
1 ATTTAATCAACAATGGTAACCTACCAAATCTCCC
* ** * *
1972239 ATTTAGTCAACAATGGTAAGTTACCAAATTTTCC
1 ATTTAATCAACAATGGTAACCTACCAAATCTCCC
* *
1972273 ATTTAATCAACAATGGTAAGCTACCAAATCTTCC
1 ATTTAATCAACAATGGTAACCTACCAAATCTCCC
* * *
1972307 ATTTAGTCAACAATGGCAAACC-ACCAAATCACCC
1 ATTTAATCAACAATGG-TAACCTACCAAATCTCCC
* *
1972341 ATTTAATCAACAATGGTAAACTACCAAATC-ACC
1 ATTTAATCAACAATGGTAACCTACCAAATCTCCC
1972374 ATTTAATCAACAAT
1 ATTTAATCAACAAT
1972388 TCTCCCACTT
Statistics
Matches: 128, Mismatches: 19, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
33 19 0.15
34 106 0.83
35 3 0.02
ACGTcount: A:0.41, C:0.25, G:0.07, T:0.27
Consensus pattern (34 bp):
ATTTAATCAACAATGGTAACCTACCAAATCTCCC
Found at i:1972342 original size:102 final size:101
Alignment explanation
Indices: 1972205--1972387 Score: 269
Period size: 102 Copynumber: 1.8 Consensus size: 101
1972195 AAAAATTACT
* * ** *
1972205 ATTTAATCAACAATGACAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGTTACCAAATTT
1 ATTTAATCAACAATGACAACCTACCAAATCACCCATTTAATCAACAATGGTAAACTACCAAA-TC
*
1972270 TCCATTTAATCAACAATGGTAAGCTACCAAATCTTCC
65 ACCATTTAATCAACAATGGTAAGCTACCAAATCTTCC
* *
1972307 ATTTAGTCAACAATGGCAAACC-ACCAAATCACCCATTTAATCAACAATGGTAAACTACCAAATC
1 ATTTAATCAACAATGAC-AACCTACCAAATCACCCATTTAATCAACAATGGTAAACTACCAAATC
1972371 ACCATTTAATCAACAAT
65 ACCATTTAATCAACAAT
1972388 TCTCCCACTT
Statistics
Matches: 72, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
101 17 0.24
102 51 0.71
103 4 0.06
ACGTcount: A:0.41, C:0.25, G:0.07, T:0.27
Consensus pattern (101 bp):
ATTTAATCAACAATGACAACCTACCAAATCACCCATTTAATCAACAATGGTAAACTACCAAATCA
CCATTTAATCAACAATGGTAAGCTACCAAATCTTCC
Found at i:1976581 original size:34 final size:34
Alignment explanation
Indices: 1976535--1976719 Score: 176
Period size: 34 Copynumber: 5.5 Consensus size: 34
1976525 GTAAAAACTA
**
1976535 TCATTTAATCAACAATGACAACCTACCAAATCTC
1 TCATTTAATCAACAATGGTAACCTACCAAATCTC
* * * * *
1976569 TCATTTAGTCAACAATGGTAAGCTATCAAATTTT
1 TCATTTAATCAACAATGGTAACCTACCAAATCTC
** *
1976603 TCATTTAATCAACAATGGTAAGTTACTAAATCTC
1 TCATTTAATCAACAATGGTAACCTACCAAATCTC
* ** *
1976637 TCATTTAATTAACAATGACAAACC-ACCAAATCAC
1 TCATTTAATCAACAATG-GTAACCTACCAAATCTC
* * * * *
1976671 CCATTTAATCAATAATGGTAAACTACTAAATCAC
1 TCATTTAATCAACAATGGTAACCTACCAAATCTC
1976705 T-ATTTAATCAACAAT
1 TCATTTAATCAACAAT
1976720 TAAGACAAAA
Statistics
Matches: 120, Mismatches: 29, Indels: 5
0.78 0.19 0.03
Matches are distributed among these distances:
33 16 0.13
34 102 0.85
35 2 0.02
ACGTcount: A:0.42, C:0.21, G:0.06, T:0.31
Consensus pattern (34 bp):
TCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:1977344 original size:23 final size:23
Alignment explanation
Indices: 1977289--1977360 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
1977279 TATTTCTAGA
* *
1977289 TTATTAATTTTTAA-ATTTATAT
1 TTATTAATTTTTAATATATAAAT
**
1977311 TTAATGCATTTTTAATATATAAAT
1 TT-ATTAATTTTTAATATATAAAT
* *
1977335 TTATTAATTTATAATTTAT-AAT
1 TTATTAATTTTTAATATATAAAT
1977357 TTAT
1 TTAT
1977361 ATATTATTAT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
22 9 0.22
23 23 0.57
24 8 0.20
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (23 bp):
TTATTAATTTTTAATATATAAAT
Found at i:1977347 original size:18 final size:16
Alignment explanation
Indices: 1977318--1977383 Score: 59
Period size: 15 Copynumber: 4.1 Consensus size: 16
1977308 TATTTAATGC
1977318 ATTT-TTAA-TATATAA
1 ATTTATTAATTATAT-A
1977333 ATTTATTAATT-TATA
1 ATTTATTAATTATATA
1977348 ATTTA-TAATTTATATA
1 ATTTATTAA-TTATATA
*
1977364 TTATTATTAAATTATATA
1 AT-TTATT-AATTATATA
1977382 AT
1 AT
1977384 ATTACTTATT
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
14 3 0.07
15 12 0.29
16 12 0.29
17 4 0.10
18 9 0.21
19 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTTATTAATTATATA
Found at i:1977351 original size:7 final size:7
Alignment explanation
Indices: 1977318--1977361 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
1977308 TATTTAATGC
*
1977318 ATTTTTA
1 ATTTATA
*
1977325 ATATATAA
1 ATTTAT-A
1977333 ATTTATTA
1 ATTTA-TA
1977341 ATTTATA
1 ATTTATA
1977348 ATTTATA
1 ATTTATA
1977355 ATTTATA
1 ATTTATA
1977362 TATTATTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
7 20 0.62
8 11 0.34
9 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
ATTTATA
Found at i:1977386 original size:18 final size:18
Alignment explanation
Indices: 1977326--1977387 Score: 62
Period size: 18 Copynumber: 3.7 Consensus size: 18
1977316 GCATTTTTAA
1977326 TATATAA-ATTTATT-AAT
1 TATATAATA-TTATTAAAT
*
1977343 T-TATAAT-TTA-TAATT
1 TATATAATATTATTAAAT
*
1977358 TATATATTATTATTAAAT
1 TATATAATATTATTAAAT
1977376 TATATAATATTA
1 TATATAATATTA
1977388 CTTATTAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
14 1 0.03
15 6 0.17
16 10 0.28
17 4 0.11
18 15 0.42
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TATATAATATTATTAAAT
Found at i:1977395 original size:22 final size:19
Alignment explanation
Indices: 1977354--1977395 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
1977344 TATAATTTAT
1977354 AATTTATATATTATTATTA
1 AATTTATATATTATTATTA
1977373 AATTATATAATATTACTTATTA
1 AATT-TAT-ATATTA-TTATTA
1977395 A
1 A
1977396 TAAATAGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 4 0.20
20 3 0.15
21 6 0.30
22 7 0.35
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
AATTTATATATTATTATTA
Found at i:1978779 original size:24 final size:24
Alignment explanation
Indices: 1978752--1978821 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
1978742 ACACTATATT
1978752 TATTATAATTATAAATATAATAAA
1 TATTATAATTATAAATATAATAAA
*
1978776 TATTAT--TTAATTAATTATAATAAA
1 TATTATAATT-A-TAAATATAATAAA
1978800 TA-T-TAATTATAAATATTAATAA
1 TATTATAATTATAAATA-TAATAA
1978822 TAAAAAAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
22 8 0.21
23 9 0.23
24 22 0.56
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TATTATAATTATAAATATAATAAA
Found at i:1980078 original size:3 final size:3
Alignment explanation
Indices: 1980070--1980096 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1980060 GTTTTGATGG
1980070 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1980097 CTGGACCGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:1981294 original size:15 final size:17
Alignment explanation
Indices: 1981261--1981295 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1981251 TAGAAAAATT
*
1981261 TATATATTTGTATTATA
1 TATATATTTATATTATA
1981278 TATATATTTATATTATA
1 TATATATTTATATTATA
1981295 T
1 T
1981296 CTCAATTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (17 bp):
TATATATTTATATTATA
Found at i:1981462 original size:28 final size:28
Alignment explanation
Indices: 1981401--1981463 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
1981391 TTTAAATATT
* *
1981401 ATAAATTTATATAAACTTTTTTATCTAA
1 ATAATTTTATATAAACTTTTATATCTAA
* * * *
1981429 AAAATTTTATATAAGCTTTTATATGTTA
1 ATAATTTTATATAAACTTTTATATCTAA
1981457 ATAATTT
1 ATAATTT
1981464 ATTTTGTATA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (28 bp):
ATAATTTTATATAAACTTTTATATCTAA
Found at i:1981895 original size:14 final size:14
Alignment explanation
Indices: 1981876--1981907 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1981866 TTAAAATAAT
1981876 TATTTTTATATTAA
1 TATTTTTATATTAA
1981890 TATTTTTATATTAA
1 TATTTTTATATTAA
1981904 -ATTT
1 TATTT
1981908 AAATAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TATTTTTATATTAA
Found at i:1982853 original size:66 final size:64
Alignment explanation
Indices: 1982730--1982858 Score: 172
Period size: 66 Copynumber: 2.0 Consensus size: 64
1982720 AGACGGGGTT
* *
1982730 AACAATGATTTTCCCTTCATTTTCAGACAAGGATGTCAGACAATTTGAGAAATTTTTTTAGTCGG
1 AACAATGATTTTCCCTTCATTTTCAGACAAAGACGTCAGACAATTTGAGAAA-TTTTTTAGTCGG
* *
1982795 AACAATGGGTTTTCCCTTCATTTTCAGACAAAGACGTGAGACAATTTG-GCATAA-TTTTTAGTC
1 AACAAT-GATTTTCCCTTCATTTTCAGACAAAGACGTCAGACAATTTGAG-A-AATTTTTTAGTC
1982858 G
63 G
1982859 AAACTTCCCG
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
65 17 0.30
66 38 0.67
67 2 0.04
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (64 bp):
AACAATGATTTTCCCTTCATTTTCAGACAAAGACGTCAGACAATTTGAGAAATTTTTTAGTCGG
Found at i:1983049 original size:14 final size:15
Alignment explanation
Indices: 1983030--1983058 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1983020 ATTTTTTATT
1983030 TTTATTTT-ATTTAA
1 TTTATTTTAATTTAA
1983044 TTTATTTTAATTTAA
1 TTTATTTTAATTTAA
1983059 ATAATAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTATTTTAATTTAA
Found at i:1983055 original size:45 final size:46
Alignment explanation
Indices: 1983025--1983124 Score: 125
Period size: 48 Copynumber: 2.2 Consensus size: 46
1983015 TGGTTATTTT
*
1983025 TTAT-TTTTATTTTATTTAATTTATTTTAATTTAAATAATAATTAA
1 TTATATTTTATTTGATTTAATTTATTTTAATTTAAATAATAATTAA
* *
1983070 TTATATTTTATTTGATTTAATTTTTATTTATAAATTAAA-AATAATTAT
1 TTATATTTTATTTGATTTAA--TTTATTT-TAATTTAAATAATAATTAA
1983118 TTA-ATTT
1 TTATATTT
1983125 GATCATTTGC
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
45 4 0.08
46 14 0.29
47 4 0.08
48 18 0.38
49 8 0.17
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (46 bp):
TTATATTTTATTTGATTTAATTTATTTTAATTTAAATAATAATTAA
Found at i:1988901 original size:17 final size:18
Alignment explanation
Indices: 1988879--1988912 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1988869 TTAAAGATGC
1988879 AATTATATT-TTTATTTT
1 AATTATATTATTTATTTT
1988896 AATTATATTATTTATTT
1 AATTATATTATTTATTT
1988913 ATTTATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
AATTATATTATTTATTTT
Found at i:1988913 original size:17 final size:17
Alignment explanation
Indices: 1988879--1988930 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
1988869 TTAAAGATGC
1988879 AATTATATT-TTTATTTT
1 AATTATATTATTTA-TTT
1988896 AATTATATTATTTATTT
1 AATTATATTATTTATTT
*
1988913 -ATT-TATTA-ATATTT
1 AATTATATTATTTATTT
1988927 AATT
1 AATT
1988931 CGAAATATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 5 0.16
15 8 0.25
16 3 0.09
17 12 0.38
18 4 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
AATTATATTATTTATTT
Found at i:1989638 original size:17 final size:17
Alignment explanation
Indices: 1989616--1989652 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
1989606 AAAAAATTTA
*
1989616 ATATATTTATATAGAAT
1 ATATATTTATATAAAAT
1989633 ATATATTTATATAAAAT
1 ATATATTTATATAAAAT
1989650 ATA
1 ATA
1989653 GATTCCGAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (17 bp):
ATATATTTATATAAAAT
Found at i:1990657 original size:4 final size:4
Alignment explanation
Indices: 1990648--1990717 Score: 77
Period size: 4 Copynumber: 17.5 Consensus size: 4
1990638 ATTGAAAAGG
* * * * * * *
1990648 ATAT ATAT ATAT ATAT ATAG ATAG ATAG GTAT AGAT AGAT AAAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
1990696 ATAT ATAT ATAT ATAT ATAT AT
1 ATAT ATAT ATAT ATAT ATAT AT
1990718 TTGATTTCCT
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 59 1.00
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (4 bp):
ATAT
Done.