Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold220
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: 3999181
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 12171 characters in sequence are not A, C, G, or T
File 9 of 19
Found at i:1905014 original size:2 final size:2
Alignment explanation
Indices: 1905009--1905070 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
1904999 TGTGTGTGTG
1905009 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
1905051 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
1905071 ATCACTTAAC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1906373 original size:93 final size:93
Alignment explanation
Indices: 1906230--1906400 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
1906220 TAATAATAAT
* *
1906230 AAAAAAAACAGACATTCACATTTGACCATTTGCGCTTATAACTAAGTAAATCCAAGCTAAACTGA
1 AAAAAAAAAAGACATACACATTTGACCATTTGCGCTTATAACTAAGTAAATCCAAGCTAAACTGA
1906295 CATGGTAGCTAATAATACACAAAAAAAA
66 CATGGTAGCTAATAATACACAAAAAAAA
* * *
1906323 AAAAAAAAAAGACATACACTTTTGACCATTTGCGCTTATAACTAATTAAATCCAAGCTAAACTGC
1 AAAAAAAAAAGACATACACATTTGACCATTTGCGCTTATAACTAAGTAAATCCAAGCTAAACTGA
1906388 CATGGTAGCTAAT
66 CATGGTAGCTAAT
1906401 TAAGAGTAAC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.46, C:0.19, G:0.11, T:0.25
Consensus pattern (93 bp):
AAAAAAAAAAGACATACACATTTGACCATTTGCGCTTATAACTAAGTAAATCCAAGCTAAACTGA
CATGGTAGCTAATAATACACAAAAAAAA
Found at i:1911191 original size:2 final size:2
Alignment explanation
Indices: 1911179--1911213 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1911169 GCAAAACATC
* *
1911179 CT CT CT GT CT CT CC CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1911214 ACGCACACAT
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:0.00, C:0.51, G:0.03, T:0.46
Consensus pattern (2 bp):
CT
Found at i:1913083 original size:33 final size:32
Alignment explanation
Indices: 1913033--1913104 Score: 85
Period size: 33 Copynumber: 2.3 Consensus size: 32
1913023 ATAAAATAAA
* *
1913033 ATAAATA--AATATGTTAAATTTTATATAATAT
1 ATAAATATTAATATGTTAAAATTTATA-AAAAT
* *
1913064 ATAATTATTAATATTTTAAAATTTATAAAAAT
1 ATAAATATTAATATGTTAAAATTTATAAAAAT
1913096 ATAAATATT
1 ATAAATATT
1913105 TTAAATATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
31 6 0.18
32 12 0.35
33 16 0.47
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (32 bp):
ATAAATATTAATATGTTAAAATTTATAAAAAT
Found at i:1915787 original size:29 final size:29
Alignment explanation
Indices: 1915750--1915814 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
1915740 ATATTGATAA
* *
1915750 TTTATATATTCGT-ATTATG-TTAATATAT
1 TTTATATATT-ATAATTATGTTTAAAATAT
1915778 TTTATTATATTATAATTATGTTTAAAATAT
1 TTTA-TATATTATAATTATGTTTAAAATAT
1915808 TTT-TATA
1 TTTATATA
1915815 ATTTATATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
28 9 0.28
29 12 0.38
30 11 0.34
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (29 bp):
TTTATATATTATAATTATGTTTAAAATAT
Found at i:1915821 original size:30 final size:29
Alignment explanation
Indices: 1915763--1915821 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
1915753 ATATATTCGT
* *
1915763 ATTATGTTAATATATTTTATTATATTATA
1 ATTATGTTAAAATATTTTATAATATTATA
1915792 ATTATGTTTAAAATATTTTTATAAT-TTATA
1 ATTATG-TTAAAATA-TTTTATAATATTATA
1915822 TAATTTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 6 0.23
30 12 0.46
31 8 0.31
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (29 bp):
ATTATGTTAAAATATTTTATAATATTATA
Found at i:1915897 original size:22 final size:21
Alignment explanation
Indices: 1915824--1915899 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 21
1915814 AATTTATATA
1915824 ATTTTGATAT-ATTAATAATTT
1 ATTTT-ATATAATTAATAATTT
* *
1915845 ATTTTATATAAATTTTAAAAATAT
1 ATTTTATAT-AA--TTAATAATTT
1915869 A-TTTATATAATTAATAATTT
1 ATTTTATATAATTAATAATTT
1915889 ATTTGTATATA
1 ATTT-TATATA
1915900 TTCGTATAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
20 13 0.29
21 7 0.16
22 9 0.20
23 7 0.16
24 9 0.20
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (21 bp):
ATTTTATATAATTAATAATTT
Found at i:1916572 original size:2 final size:2
Alignment explanation
Indices: 1916565--1916589 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1916555 ATTTGCCCAC
1916565 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
1916590 ACTGCGGGCT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1916802 original size:29 final size:28
Alignment explanation
Indices: 1916739--1916802 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 28
1916729 TAATTCGATT
* *
1916739 TTAAATTTTTTTAAATTAATTAAATTAA
1 TTAAATATTTTAAAATTAATTAAATTAA
*
1916767 TAAAAATATTTTAAAATTAAATT-AATTGAA
1 T-TAAATATTTTAAAATT-AATTAAATT-AA
1916797 TTAAAT
1 TTAAAT
1916803 TTAAATTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
28 1 0.03
29 21 0.72
30 7 0.24
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (28 bp):
TTAAATATTTTAAAATTAATTAAATTAA
Found at i:1916820 original size:20 final size:20
Alignment explanation
Indices: 1916776--1916823 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
1916766 ATAAAAATAT
*
1916776 TTTAAAATTAAATTAATTGA
1 TTTAAATTTAAATTAATTGA
* *
1916796 ATTAAATTTAAATTAATTGG
1 TTTAAATTTAAATTAATTGA
1916816 TTTAAATT
1 TTTAAATT
1916824 GATTTTAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (20 bp):
TTTAAATTTAAATTAATTGA
Found at i:1917055 original size:16 final size:17
Alignment explanation
Indices: 1917020--1917057 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1917010 CTGAATCAAT
* *
1917020 AAATAAATTAATTTTTA
1 AAATTAATTAATTTTAA
1917037 AAATTAATTAA-TTTAA
1 AAATTAATTAATTTTAA
1917053 AAATT
1 AAATT
1917058 GAATAAATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATTAATTAATTTTAA
Found at i:1921904 original size:3 final size:3
Alignment explanation
Indices: 1921896--1921929 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1921886 ATTGGCTGCC
1921896 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1921930 TGTTGTTGTT
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:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:1922456 original size:25 final size:26
Alignment explanation
Indices: 1922399--1922457 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
1922389 TTAGTTAATA
* *
1922399 TATAAATAAATATAATTATATATTTT
1 TATAAATAAATATAATTACATAATTT
*
1922425 TAAAAATAAAT-T-ATTAACATAATTT
1 TATAAATAAATATAATT-ACATAATTT
1922450 TATAAATA
1 TATAAATA
1922458 TATTTTTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
24 3 0.11
25 15 0.54
26 10 0.36
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (26 bp):
TATAAATAAATATAATTACATAATTT
Found at i:1928292 original size:25 final size:25
Alignment explanation
Indices: 1928264--1928311 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
1928254 ATGATTAAAA
1928264 AATAAAAA-ATAATATTAATTTAATT
1 AATAAAAATATAAT-TTAATTTAATT
*
1928289 AATAAAAATTTAATTTAATTTAA
1 AATAAAAATATAATTTAATTTAA
1928312 ACTTAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
AATAAAAATATAATTTAATTTAATT
Found at i:1929791 original size:14 final size:13
Alignment explanation
Indices: 1929717--1929784 Score: 56
Period size: 12 Copynumber: 5.5 Consensus size: 13
1929707 ATACATATAC
1929717 ATATATAAAA-AT
1 ATATATAAAATAT
1929729 ATATATAAAATA-
1 ATATATAAAATAT
**
1929741 A-A-ATAACTTATT
1 ATATATAAAATA-T
*
1929753 AATATAAAAAATAT
1 -ATATATAAAATAT
1929767 ATATATAAAATAT
1 ATATATAAAATAT
1929780 A-ATAT
1 ATATAT
1929785 TTTAAATGCG
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
10 6 0.14
11 1 0.02
12 15 0.34
13 15 0.34
14 2 0.05
15 5 0.11
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.35
Consensus pattern (13 bp):
ATATATAAAATAT
Found at i:1929904 original size:14 final size:14
Alignment explanation
Indices: 1929873--1929901 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1929863 ATTAAATAAT
1929873 AATTTATATATTTA
1 AATTTATATATTTA
1929887 AATTT-TATATTTA
1 AATTTATATATTTA
1929900 AA
1 AA
1929902 ATTAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTTATATATTTA
Found at i:1930279 original size:13 final size:12
Alignment explanation
Indices: 1930243--1930281 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
1930233 AAATATGACT
1930243 TAAAAAATAAT-
1 TAAAAAATAATA
*
1930254 TAAAATATAATA
1 TAAAAAATAATA
1930266 TAAAAAATAGATA
1 TAAAAAATA-ATA
1930279 TAA
1 TAA
1930282 CATGAATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 10 0.42
12 8 0.33
13 6 0.25
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (12 bp):
TAAAAAATAATA
Found at i:1930506 original size:17 final size:17
Alignment explanation
Indices: 1930486--1930520 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1930476 AAAAAATTTA
1930486 AAATATAATATAAAAAT
1 AAATATAATATAAAAAT
* *
1930503 AAATATATTATATAAAT
1 AAATATAATATAAAAAT
1930520 A
1 A
1930521 CGTATATGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAATATAATATAAAAAT
Found at i:1930642 original size:10 final size:10
Alignment explanation
Indices: 1930627--1930675 Score: 62
Period size: 10 Copynumber: 4.6 Consensus size: 10
1930617 ATTTAAAGTT
*
1930627 AAAAAAGTAG
1 AAAAAAGAAG
1930637 AAAAAAGAAG
1 AAAAAAGAAG
1930647 AAAAAAAAAGAAG
1 ---AAAAAAGAAG
1930660 AAAAAAGAAG
1 AAAAAAGAAG
1930670 AAAAAA
1 AAAAAA
1930676 ATAGATATGT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
10 25 0.71
13 10 0.29
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (10 bp):
AAAAAAGAAG
Found at i:1930655 original size:13 final size:13
Alignment explanation
Indices: 1930637--1930676 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
1930627 AAAAAAGTAG
1930637 AAAAAAGAAGAAA
1 AAAAAAGAAGAAA
1930650 AAAAAAGAAGAAA
1 AAAAAAGAAGAAA
*
1930663 AAAGAAGAA-AAA
1 AAAAAAGAAGAAA
1930675 AA
1 AA
1930677 TAGATATGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 5 0.19
13 21 0.81
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAGAAA
Found at i:1930655 original size:23 final size:23
Alignment explanation
Indices: 1930627--1930676 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
1930617 ATTTAAAGTT
*
1930627 AAAAAAGTAGAAAAAAGAAGAAA
1 AAAAAAGAAGAAAAAAGAAGAAA
1930650 AAAAAAGAAGAAAAAAGAAGAAA
1 AAAAAAGAAGAAAAAAGAAGAAA
1930673 AAAA
1 AAAA
1930677 TAGATATGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (23 bp):
AAAAAAGAAGAAAAAAGAAGAAA
Found at i:1930721 original size:30 final size:30
Alignment explanation
Indices: 1930661--1930728 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 30
1930651 AAAAAGAAGA
*
1930661 AAAAAGAAGAAAAAAATAGATATGTATAATTT
1 AAAAATAAGAAAAAAATAGATA-GTATAA-TT
*
1930693 AAAAATAAGAAGAAAATAGATA-TATAATT
1 AAAAATAAGAAAAAAATAGATAGTATAATT
1930722 AAAAATA
1 AAAAATA
1930729 GATATATGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 9 0.26
30 5 0.15
32 20 0.59
ACGTcount: A:0.66, C:0.00, G:0.10, T:0.24
Consensus pattern (30 bp):
AAAAATAAGAAAAAAATAGATAGTATAATT
Found at i:1931187 original size:17 final size:17
Alignment explanation
Indices: 1931167--1931214 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 17
1931157 TCACTTAATC
1931167 AAATATATATTTTTATT-
1 AAATATATATTTTT-TTA
*
1931184 AAATATTTATTATTTTTA
1 AAATATATATT-TTTTTA
1931202 AAATTATATATTT
1 AAA-TATATATTT
1931215 AATATTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 12 0.46
18 7 0.27
19 7 0.27
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
AAATATATATTTTTTTA
Found at i:1931210 original size:21 final size:21
Alignment explanation
Indices: 1931198--1931240 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1931188 ATTTATTATT
1931198 TTTAAAATTATATATTTAATA
1 TTTAAAATTATATATTTAATA
*
1931219 TTTAAAATTGT-TATTTTAATA
1 TTTAAAATTATATA-TTTAATA
1931240 T
1 T
1931241 AATTGATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
TTTAAAATTATATATTTAATA
Found at i:1931699 original size:10 final size:10
Alignment explanation
Indices: 1931684--1931733 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
1931674 TTATTTTATT
*
1931684 TTTTAAAATA
1 TTTTAATATA
1931694 TTTTAATATAA
1 TTTTAATAT-A
*
1931705 TTTTTATATA
1 TTTTAATATA
*
1931715 TTTTTA-ATA
1 TTTTAATATA
1931724 -TTTAATATA
1 TTTTAATATA
1931733 T
1 T
1931734 ATTAGGTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
8 4 0.12
9 6 0.18
10 15 0.44
11 9 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TTTTAATATA
Found at i:1931708 original size:22 final size:22
Alignment explanation
Indices: 1931683--1931724 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1931673 ATTATTTTAT
1931683 TTTTTAAA-ATATTTTAATATAA
1 TTTTTAAATAT-TTTTAATATAA
*
1931705 TTTTTATATATTTTTAATAT
1 TTTTTAAATATTTTTAATAT
1931725 TTAATATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTTTAAATATTTTTAATATAA
Found at i:1931711 original size:29 final size:29
Alignment explanation
Indices: 1931677--1931732 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
1931667 AAAATTATTA
1931677 TTTTAT-T-TTTTAAAATATTTTAATATAAT
1 TTTTATATATTTT-AAATA-TTTAATATAAT
*
1931706 TTTTATATATTTTTAATATTTAATATA
1 TTTTATATATTTTAAATATTTAATATA
1931733 TATTAGGTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
29 15 0.62
30 5 0.21
31 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (29 bp):
TTTTATATATTTTAAATATTTAATATAAT
Found at i:1931771 original size:28 final size:27
Alignment explanation
Indices: 1931740--1931792 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
1931730 ATATATTAGG
1931740 TATATACACTAAAATTATATATTATATA
1 TATATACACTAAAATTATAT-TTATATA
* *
1931768 TATATATATTAAAATTATATTTATA
1 TATATACACTAAAATTATATTTATA
1931793 AATAAATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (27 bp):
TATATACACTAAAATTATATTTATATA
Found at i:1931795 original size:13 final size:14
Alignment explanation
Indices: 1931751--1931795 Score: 58
Period size: 13 Copynumber: 3.3 Consensus size: 14
1931741 ATATACACTA
1931751 AAATTATATATTAT
1 AAATTATATATTAT
*
1931765 ATATATATATATTA-
1 AAAT-TATATATTAT
1931779 AAATTATAT-TTAT
1 AAATTATATATTAT
1931792 AAAT
1 AAAT
1931796 AAATTATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 3 0.11
13 9 0.33
14 6 0.22
15 9 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
AAATTATATATTAT
Found at i:1933601 original size:5 final size:5
Alignment explanation
Indices: 1933586--1933622 Score: 56
Period size: 5 Copynumber: 7.2 Consensus size: 5
1933576 CATACCCTAT
*
1933586 AAAGAA AAAGA AAAGA AAAGA AAAGA AGAGA AAAGA A
1 AAAG-A AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA A
1933623 GGATTTCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 25 0.86
6 4 0.14
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:1934188 original size:2 final size:2
Alignment explanation
Indices: 1934181--1934217 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1934171 TTCTTCATAA
1934181 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1934218 TTTTAACTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1934655 original size:19 final size:20
Alignment explanation
Indices: 1934614--1934665 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
1934604 TATCATTTCA
*
1934614 TTTTTGTTTTTGTTAGGCTTC
1 TTTTT-TTTTTGTTAGGCCTC
*
1934635 TTTTTTTTTT-TTTGGCCTC
1 TTTTTTTTTTGTTAGGCCTC
1934654 TTGATTTTTTTT
1 TT--TTTTTTTT
1934666 CAGACGTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 9 0.33
20 5 0.19
21 13 0.48
ACGTcount: A:0.04, C:0.10, G:0.13, T:0.73
Consensus pattern (20 bp):
TTTTTTTTTTGTTAGGCCTC
Found at i:1934721 original size:2 final size:2
Alignment explanation
Indices: 1934714--1934743 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1934704 ACTGAAAAGA
1934714 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
1934744 GCAAAAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1935294 original size:16 final size:18
Alignment explanation
Indices: 1935248--1935293 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
1935238 ATTCTCAATA
*
1935248 AATAA-ATAAATTTTATT
1 AATAACATATATTTTATT
1935265 AATAATCATATATTTTATT
1 AATAA-CATATATTTTATT
*
1935284 AATAAAATAT
1 AATAACATAT
1935294 TAAAATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 5 0.20
18 4 0.16
19 16 0.64
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (18 bp):
AATAACATATATTTTATT
Found at i:1935309 original size:28 final size:27
Alignment explanation
Indices: 1935276--1935331 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 27
1935266 ATAATCATAT
*
1935276 ATTTTATTAA-TAAAATATTAAAATTTTA
1 ATTTTAATAATTAAAA-ATT-AAATTTTA
1935304 ATTTTAATAATTAAAAATTAAATTTTA
1 ATTTTAATAATTAAAAATTAAATTTTA
1935331 A
1 A
1935332 CAACTTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 9 0.35
28 12 0.46
29 5 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
ATTTTAATAATTAAAAATTAAATTTTA
Found at i:1935318 original size:21 final size:21
Alignment explanation
Indices: 1935292--1935331 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1935282 TTAATAAAAT
* *
1935292 ATTAAAATTTTAATTTTAATA
1 ATTAAAAATTAAATTTTAATA
1935313 ATTAAAAATTAAATTTTAA
1 ATTAAAAATTAAATTTTAA
1935332 CAACTTTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTAAAAATTAAATTTTAATA
Found at i:1936575 original size:2 final size:2
Alignment explanation
Indices: 1936568--1936599 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1936558 TCAGGAATTA
1936568 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
1936600 GACAAGAAAC
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:1938592 original size:19 final size:20
Alignment explanation
Indices: 1938546--1938593 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
1938536 TTTATTTAAA
1938546 TTTAATTATAAAATATATAAT
1 TTTAA-TATAAAATATATAAT
* *
1938567 ATTAATATAAAATA-ATTAT
1 TTTAATATAAAATATATAAT
1938586 TTTAATAT
1 TTTAATAT
1938594 TTTTTAAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 11 0.46
20 9 0.38
21 4 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TTTAATATAAAATATATAAT
Found at i:1941645 original size:28 final size:28
Alignment explanation
Indices: 1941605--1941660 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
1941595 CACACTATGA
1941605 GGTCCCATTTCATGTTTGAAATCTTGAC
1 GGTCCCATTTCATGTTTGAAATCTTGAC
1941633 GGTCCCATTTCATGTTTGAAATCTTGAC
1 GGTCCCATTTCATGTTTGAAATCTTGAC
1941661 CCCAAAAGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.39
Consensus pattern (28 bp):
GGTCCCATTTCATGTTTGAAATCTTGAC
Found at i:1943890 original size:2 final size:2
Alignment explanation
Indices: 1943883--1943911 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1943873 CTCTTTAAAA
1943883 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 A
1943912 CTCTTTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1944081 original size:2 final size:2
Alignment explanation
Indices: 1944076--1944107 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1944066 TGTGTGTATG
1944076 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
1944108 CTTCTTAATC
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:1944558 original size:2 final size:2
Alignment explanation
Indices: 1944551--1944589 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1944541 CATATTCATC
1944551 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
1944590 GTATGTATAA
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:1952351 original size:2 final size:2
Alignment explanation
Indices: 1952344--1952369 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1952334 TGTCATTAAC
1952344 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
1952370 GAAGTTTCAA
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:1958968 original size:7 final size:7
Alignment explanation
Indices: 1958956--1958995 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
1958946 AACACAATTA
*
1958956 TTTTTTC
1 TTTTTGC
*
1958963 TTTTTTC
1 TTTTTGC
1958970 TTTTTGC
1 TTTTTGC
1958977 TTTTTGC
1 TTTTTGC
*
1958984 TTTTTCC
1 TTTTTGC
1958991 TTTTT
1 TTTTT
1958996 CCGCAGTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (7 bp):
TTTTTGC
Found at i:1958986 original size:21 final size:21
Alignment explanation
Indices: 1958956--1958995 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1958946 AACACAATTA
* *
1958956 TTTTTTCTTTTTTCTTTTTGC
1 TTTTTGCTTTTTCCTTTTTGC
1958977 TTTTTGCTTTTTCCTTTTT
1 TTTTTGCTTTTTCCTTTTT
1958996 CCGCAGTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (21 bp):
TTTTTGCTTTTTCCTTTTTGC
Found at i:1965168 original size:4 final size:4
Alignment explanation
Indices: 1965159--1965189 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
1965149 CTTTATGAAG
1965159 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCT
1965190 ATTATTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
TCTT
Found at i:1965197 original size:3 final size:3
Alignment explanation
Indices: 1965189--1965213 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1965179 TCTTTCTTTC
1965189 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
1965214 TCTGTTTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1966701 original size:19 final size:20
Alignment explanation
Indices: 1966674--1966715 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1966664 AATATATAAT
*
1966674 ATAAATATAATATTA-AAAA
1 ATAAATATAATATGATAAAA
*
1966693 ATAATTATAATATGATAAAA
1 ATAAATATAATATGATAAAA
1966713 ATA
1 ATA
1966716 TGTAAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
ATAAATATAATATGATAAAA
Found at i:1967428 original size:17 final size:18
Alignment explanation
Indices: 1967384--1967434 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 18
1967374 TATTTTTATT
*
1967384 AATTATTTTTATATATAA
1 AATTATTTTAATATATAA
*
1967402 TATT-TATTTAATAT-TAA
1 AATTAT-TTTAATATATAA
1967419 AATTATTTTAATATAT
1 AATTATTTTAATATAT
1967435 TATTATCTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
17 15 0.56
18 12 0.44
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
AATTATTTTAATATATAA
Found at i:1967439 original size:16 final size:16
Alignment explanation
Indices: 1967385--1967440 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 16
1967375 ATTTTTATTA
1967385 ATTATTTTTATATATAAT
1 ATTA-TTTTA-ATATAAT
*
1967403 ATT-TATTTAATATTAAA
1 ATTAT-TTTAATA-TAAT
*
1967420 ATTATTTTAATATATT
1 ATTATTTTAATATAAT
1967436 ATTAT
1 ATTAT
1967441 CTAATTAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
16 11 0.34
17 17 0.53
18 4 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTATTTTAATATAAT
Found at i:1968198 original size:13 final size:15
Alignment explanation
Indices: 1968180--1968211 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
1968170 AATTATTTAA
1968180 ATTTAATAT-AAT-T
1 ATTTAATATGAATAT
1968193 ATTTAATATGAATAT
1 ATTTAATATGAATAT
1968208 ATTT
1 ATTT
1968212 TATTTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 3 0.18
15 5 0.29
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
ATTTAATATGAATAT
Found at i:1968206 original size:19 final size:19
Alignment explanation
Indices: 1968170--1968208 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1968160 ATTAAAATTA
*
1968170 AATTATTTAAATTTAATAT
1 AATTATTTAAATTGAATAT
1968189 AATTATTT-AATATGAATAT
1 AATTATTTAAAT-TGAATAT
1968208 A
1 A
1968209 TTTTATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (19 bp):
AATTATTTAAATTGAATAT
Found at i:1970130 original size:45 final size:46
Alignment explanation
Indices: 1970059--1970192 Score: 125
Period size: 43 Copynumber: 2.9 Consensus size: 46
1970049 GAGTTAATTG
* *
1970059 AATAATTTATATGTTTATGTCATTTTTATAAATTTTATTATATTATAAT
1 AATAATTTATAT-TATAT-T-ATTTTTAAAAATTTTATTATATTATAAT
* * *
1970108 AAT-ATTTA-ATATATTTTATTTTTAAAAAATTT-TTA-A-TATATT
1 AATAATTTATAT-TATATTATTTTTAAAAATTTTATTATATTATAAT
*
1970150 AATAATTTATATTATATTAATTTTAAAATATTTATATTATATT
1 AATAATTTATATTATATTATTTTTAAAA-ATTT-TATTATATT
1970193 TACGTCGTAC
Statistics
Matches: 69, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
42 8 0.12
43 20 0.29
44 8 0.12
45 14 0.20
46 4 0.06
47 6 0.09
48 6 0.09
49 3 0.04
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (46 bp):
AATAATTTATATTATATTATTTTTAAAAATTTTATTATATTATAAT
Found at i:1970142 original size:27 final size:30
Alignment explanation
Indices: 1970103--1970192 Score: 62
Period size: 27 Copynumber: 3.0 Consensus size: 30
1970093 TTATTATATT
* *
1970103 ATAATAATATTTAATATATTTTATT-T-TT
1 ATAAAAATTTTTAATATATTTTATTATATT
*
1970131 A-AAAAATTTTTAATATATTAATAATTTATATT
1 ATAAAAATTTTTAATATATT--TTA-TTATATT
** *
1970163 ATATTAA-TTTTAAAATATTTATATTATATT
1 ATAAAAATTTTTAATATATTT-TATTATATT
1970193 TACGTCGTAC
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
27 16 0.33
28 1 0.02
29 2 0.04
30 10 0.21
31 2 0.04
32 14 0.29
33 3 0.06
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
ATAAAAATTTTTAATATATTTTATTATATT
Found at i:1971367 original size:19 final size:19
Alignment explanation
Indices: 1971335--1971372 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
1971325 TATTCCTGGA
*
1971335 ACAGCGTATCACAAATGTTT
1 ACAGCGTATAAC-AATGTTT
1971355 ACAG-GTATAACAATGTTT
1 ACAGCGTATAACAATGTTT
1971373 TTTTCATACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 6 0.35
20 4 0.24
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (19 bp):
ACAGCGTATAACAATGTTT
Found at i:1975343 original size:90 final size:91
Alignment explanation
Indices: 1975179--1975351 Score: 285
Period size: 90 Copynumber: 1.9 Consensus size: 91
1975169 AAAAAAACAT
* *
1975179 ATATAAGTAACGAATATTCAATGAAATTTTTGAAGTTTTTCAAAATCAAATAAGTCAAATAATCA
1 ATATAAGTAACGAATATTCAATGAAATTTTTGAAGTTTTTCAAAATAAAATAAGTAAAATAATCA
1975244 AAAAGTTATTTCATAATGCAGCACAA
66 AAAAGTTATTTCATAATGCAGCACAA
* *
1975270 ATATAAGTAACGAATATTCAATGAAA-TTTTGAAGTTTTTCAAAATAAAATCAGTAAAATCATCA
1 ATATAAGTAACGAATATTCAATGAAATTTTTGAAGTTTTTCAAAATAAAATAAGTAAAATAATCA
* *
1975334 ACAGGTTATTTCATAATG
66 AAAAGTTATTTCATAATG
1975352 TAGCGCATAT
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
90 50 0.66
91 26 0.34
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.33
Consensus pattern (91 bp):
ATATAAGTAACGAATATTCAATGAAATTTTTGAAGTTTTTCAAAATAAAATAAGTAAAATAATCA
AAAAGTTATTTCATAATGCAGCACAA
Found at i:1978085 original size:35 final size:35
Alignment explanation
Indices: 1978039--1978111 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
1978029 ACAGGCGGAA
*
1978039 TCCATTACGTCTGCACCTTGTTCGTCGAATTCTCC
1 TCCATAACGTCTGCACCTTGTTCGTCGAATTCTCC
1978074 TCCATAACGTCTGCACCTTGTTCGTCGAATTCTCC
1 TCCATAACGTCTGCACCTTGTTCGTCGAATTCTCC
1978109 TCC
1 TCC
1978112 GCCTCCACTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.15, C:0.36, G:0.14, T:0.36
Consensus pattern (35 bp):
TCCATAACGTCTGCACCTTGTTCGTCGAATTCTCC
Found at i:1978520 original size:20 final size:20
Alignment explanation
Indices: 1978495--1978540 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1978485 AAGAATTGAA
*
1978495 GAGGGATACGAGAGAGGGAT
1 GAGGGATACGAGAGAGGGAG
* **
1978515 GAGGGATGCTTGAGAGGGAG
1 GAGGGATACGAGAGAGGGAG
1978535 GAGGGA
1 GAGGGA
1978541 GCCTCTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.04, G:0.54, T:0.11
Consensus pattern (20 bp):
GAGGGATACGAGAGAGGGAG
Found at i:1978690 original size:24 final size:27
Alignment explanation
Indices: 1978617--1978687 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
1978607 AAACAAGCCT
* *
1978617 CCATATTTGACAAATACAAAGGA-AACCA
1 CCATTTTTGACAAACACAAA--ATAACCA
1978645 CCATTTTTGACAAACACAAAATAACCA
1 CCATTTTTGACAAACACAAAATAACCA
1978672 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
1978688 AATGGGTGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.23
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAATAACCA
Found at i:1983253 original size:28 final size:27
Alignment explanation
Indices: 1983196--1983259 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 27
1983186 AGTCTCCATA
1983196 TTTGACAAATACAAAGGAAACCATCATT
1 TTTGACAAATACAAA-GAAACCATCATT
1983224 TTTGACAAATACAAA-ATAACCA-CAATT
1 TTTGACAAATACAAAGA-AACCATC-ATT
*
1983251 TTTTACAAA
1 TTTGACAAA
1983260 CAAATGGGTG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
26 2 0.06
27 16 0.48
28 15 0.45
ACGTcount: A:0.48, C:0.17, G:0.06, T:0.28
Consensus pattern (27 bp):
TTTGACAAATACAAAGAAACCATCATT
Found at i:1987971 original size:2 final size:2
Alignment explanation
Indices: 1987964--1987995 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1987954 AACATATGTA
1987964 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
1987996 TTTTTTTTTT
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:1988746 original size:23 final size:23
Alignment explanation
Indices: 1988720--1988763 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
1988710 CACTTAAAAA
*
1988720 ATTTTAAATTATATTTTTATTAT
1 ATTTTAAATTATATTTATATTAT
1988743 ATTTTAAATTATATTTATATT
1 ATTTTAAATTATATTTATATT
1988764 TTTTAAATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
ATTTTAAATTATATTTATATTAT
Found at i:1988753 original size:12 final size:12
Alignment explanation
Indices: 1988720--1988758 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
1988710 CACTTAAAAA
1988720 ATTTTAAATTAT
1 ATTTTAAATTAT
*
1988732 ATTTT-TATTAT
1 ATTTTAAATTAT
1988743 ATTTTAAATTAT
1 ATTTTAAATTAT
1988755 ATTT
1 ATTT
1988759 ATATTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 10 0.42
12 14 0.58
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATTTTAAATTAT
Found at i:1992151 original size:3 final size:3
Alignment explanation
Indices: 1992143--1992178 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1992133 TGCTTTGTTA
1992143 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1992179 TGATTTTGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2000601 original size:6 final size:7
Alignment explanation
Indices: 2000583--2000610 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
2000573 GAAATTCATG
2000583 TAAAAAA
1 TAAAAAA
2000590 TAAAAAA
1 TAAAAAA
2000597 TAAAAAA
1 TAAAAAA
2000604 TAAAAAA
1 TAAAAAA
2000611 GTTCAAATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
TAAAAAA
Found at i:2005554 original size:2 final size:2
Alignment explanation
Indices: 2005547--2005572 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2005537 ATCTCATTTA
2005547 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
2005573 TTATGCGGAT
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:2008195 original size:23 final size:22
Alignment explanation
Indices: 2008097--2008196 Score: 57
Period size: 23 Copynumber: 4.4 Consensus size: 22
2008087 TAAATTTAAT
2008097 TATAAA-AATAT-T-AATATTAA
1 TATAAATAATATATAAATATT-A
*
2008117 TATAAAAATAATATTTAAATAATTTTA
1 TAT--AAATAATATATAAAT-A--TTA
*
2008144 AATAAA-AATATATAAATATTA
1 TATAAATAATATATAAATATTA
*
2008165 TATAAAATAATATAT-TATCATTA
1 TAT-AAATAATATATAAAT-ATTA
2008188 TTATAAATA
1 -TATAAATA
2008197 CTAAAAAAAT
Statistics
Matches: 64, Mismatches: 4, Indels: 21
0.72 0.04 0.24
Matches are distributed among these distances:
20 3 0.05
21 5 0.08
22 8 0.12
23 22 0.34
24 14 0.22
25 6 0.09
26 1 0.02
27 3 0.05
28 2 0.03
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (22 bp):
TATAAATAATATATAAATATTA
Found at i:2008195 original size:49 final size:47
Alignment explanation
Indices: 2008098--2008196 Score: 121
Period size: 47 Copynumber: 2.1 Consensus size: 47
2008088 AAATTTAATT
*
2008098 ATAAAAATATTAATATTAATATAAAAATAATATTTAAATAATTTTAA
1 ATAAAAATATTAATATTAATATAAAAATAATATTTAAATAATTATAA
* *
2008145 ATAAAAATATATAAATATT-ATAT-AAAATAATATATTATCATTATTATAA
1 ATAAAAATAT-T-AATATTAATATAAAAATAATAT-TTA-AATAATTATAA
2008194 ATA
1 ATA
2008197 CTAAAAAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
47 20 0.44
48 8 0.18
49 17 0.38
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (47 bp):
ATAAAAATATTAATATTAATATAAAAATAATATTTAAATAATTATAA
Found at i:2009741 original size:2 final size:2
Alignment explanation
Indices: 2009734--2009767 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2009724 CTGTTTTCCT
2009734 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
2009768 CATTCCTATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2023233 original size:22 final size:25
Alignment explanation
Indices: 2023184--2023234 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
2023174 AAAATACAAG
2023184 AAAATAAATAAAATAATTATTTAATA
1 AAAATAAATAAAATAATTATTT-ATA
*
2023210 AAAATAAA-AAATTAA-TATTT-TA
1 AAAATAAATAAAATAATTATTTATA
2023232 AAA
1 AAA
2023235 TTTTAGTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 5 0.21
24 5 0.21
25 6 0.25
26 8 0.33
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (25 bp):
AAAATAAATAAAATAATTATTTATA
Found at i:2023562 original size:12 final size:12
Alignment explanation
Indices: 2023535--2023570 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
2023525 AAGAATTTAA
2023535 TAATAATAATAAT
1 TAATAAT-ATAAT
*
2023548 TAATAATATACT
1 TAATAATATAAT
2023560 TAATAATATAA
1 TAATAATATAA
2023571 ATAAATATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 14 0.67
13 7 0.33
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (12 bp):
TAATAATATAAT
Found at i:2023758 original size:31 final size:31
Alignment explanation
Indices: 2023723--2023935 Score: 117
Period size: 31 Copynumber: 6.9 Consensus size: 31
2023713 ATAACATATG
* *
2023723 TAATAATATTTAATAATATATTAGAATATCT
1 TAATAATATTTAATAATATATTAAAATAACT
* *
2023754 TAATAATTTTTCATAATATATTAAAATAACT
1 TAATAATATTTAATAATATATTAAAATAACT
2023785 TAATAATATATTAA-AAT-TATGT-AAATAA-T
1 TAATAATAT-TTAATAATATAT-TAAAATAACT
* * *
2023814 TATATTTAAATTTTTAATGATATATT-ACATAACATT
1 TA-A--T-AATATTTAATAATATATTAAAATAAC--T
* * * **
2023850 TAATAATATATATTAAAATATTTTAATAAC-
1 TAATAATATTTAATAATATATTAAAATAACT
*
2023880 -AAT-AT-TTTAATAATAT-TTATAATATA-T
1 TAATAATATTTAATAATATATTAAAATA-ACT
*
2023907 TAAAAATATTTTAATAATAT-TTAATAATA
1 TAATAATA-TTTAATAATATATTAA-AATA
2023936 TATTTATATT
Statistics
Matches: 141, Mismatches: 22, Indels: 37
0.70 0.11 0.19
Matches are distributed among these distances:
26 7 0.05
27 9 0.06
28 4 0.03
29 8 0.06
30 10 0.07
31 53 0.38
32 25 0.18
33 18 0.13
34 3 0.02
35 1 0.01
36 3 0.02
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (31 bp):
TAATAATATTTAATAATATATTAAAATAACT
Found at i:2023771 original size:21 final size:20
Alignment explanation
Indices: 2023540--2024481 Score: 209
Period size: 21 Copynumber: 45.9 Consensus size: 20
2023530 TTTAATAATA
*
2023540 ATAATAATTAATAATATACTT
1 ATAATATTTAATAATATA-TT
*
2023561 AATAATA-TAAATAA-ATATT
1 -ATAATATTTAATAATATATT
*
2023580 CATAATAATTAA-AA-ATA-T
1 -ATAATATTTAATAATATATT
* *
2023598 ATAA-ATCTAATAATATTTT
1 ATAATATTTAATAATATATT
* *
2023617 ATTAATATTTAATAAAATACT
1 A-TAATATTTAATAATATATT
* * * **
2023638 ACTATTA-GTAATATATTACAAAC
1 A-TAATATTTAATA-A-TA-TATT
* * *
2023661 AAAAAATTTAATAATATATA
1 ATAATATTTAATAATATATT
*
2023681 AAAATATTTAA-AATTAATATT
1 ATAATATTTAATAA-T-ATATT
* ** *
2023702 AAAAATATAAAATAACATATGT
1 -ATAATATTTAATAATATAT-T
2023724 AATAATATTTAATAATATATT
1 -ATAATATTTAATAATATATT
* *
2023745 AGAATATCTTAATAAT-TTTT
1 ATAATAT-TTAATAATATATT
2023765 CATAATATATTAA-AATA-ACTT
1 -ATAATAT-TTAATAATATA-TT
2023786 AATAATATATTAA-AAT-TA-T
1 -ATAATAT-TTAATAATATATT
* *
2023805 GTAA-A--TAATTATAT-TT
1 ATAATATTTAATAATATATT
* *
2023821 A-AATTTTTAATGATATATT
1 ATAATATTTAATAATATATT
*
2023840 ACATAACATTTAATAATATATATT
1 --ATAATATTTAAT-A-ATATATT
* **
2023864 AAAATATTT--TAATA-ACA
1 ATAATATTTAATAATATATT
2023881 AT-AT-TTTAATAATAT-TT
1 ATAATATTTAATAATATATT
* *
2023898 ATAATATATTAAAAATATTTT
1 ATAATAT-TTAATAATATATT
2023919 AATAATATTTAATAATATATT
1 -ATAATATTTAATAATATATT
* *
2023940 -T-ATATTTTATAAT-TAATA
1 ATAATATTTAATAATAT-ATT
* *
2023958 ATTAATATTTTAATAGTATTTT
1 A-TAATA-TTTAATAATATATT
* * *
2023980 AATGATAGTTAATTAATATGTT
1 -ATAATATTTAA-TAATATATT
* *
2024002 ATAATTAATTATTAA-AAGATTTT
1 ATAA-T-A-T-TTAATAATATATT
*
2024025 AATAATTATTTTATAATAT-TT
1 -ATAA-TATTTAATAATATATT
* *
2024046 -TAATGTATTCAATAATATTTT
1 ATAA--TATTTAATAATATATT
*
2024067 AAAATATATATTAA-AATATATT
1 -ATA-ATAT-TTAATAATATATT
* *
2024089 ATAATATTTTAAAAATATTTT
1 ATAATA-TTTAATAATATATT
* *
2024110 AAAATATTTATATAATATATA
1 ATAATATTTA-ATAATATATT
2024131 ATAATAATTTAATAATAAATATAT
1 ATAAT-ATTTAATAAT--ATAT-T
2024155 ATTGAAATATTTAATAATAAATATT
1 A-T--AATATTTAATAAT--ATATT
* * *
2024180 -T-AT-TTTATTGATAGT-TA
1 ATAATATTTAATAATA-TATT
*
2024197 ATTAATATTTTATAATTAATTATT
1 A-TAATATTTAATAA-T-A-TATT
* *
2024221 AAAATATTTTAATAATATTTT
1 ATAATA-TTTAATAATATATT
* *
2024242 GTAATATTT--TAATGTATGT
1 ATAATATTTAATAATATAT-T
* *
2024261 AATAACATTTTA-AATAT-TT
1 -ATAATATTTAATAATATATT
*
2024280 ATATGATATATAATAATAT-TT
1 ATA--ATATTTAATAATATATT
* * *
2024301 AGAAAATATTTAAGAATATTTT
1 --ATAATATTTAATAATATATT
* *
2024323 AAAATATAGTAATAATATATT
1 ATAATAT-TTAATAATATATT
* * * * *
2024344 TTTATAATAAAT-ATATCTT
1 ATAATATTTAATAATATATT
*
2024363 AAAATATTCTAATAATATATTTT
1 ATAATATT-TAATAATATA--TT
2024386 ATAATATTTGAATAATA-A-T
1 ATAATATTT-AATAATATATT
2024405 -T-ATA-TTAATAACTATTATT
1 ATAATATTTAATAA-TA-TATT
* *
2024424 TTAATATATTAAAAAATATATT
1 ATAATAT-TT-AATAATATATT
2024446 -TAAATATTTAATAATATA-T
1 AT-AATATTTAATAATATATT
*
2024465 AAAATATTTAATAATAT
1 ATAATATTTAATAATAT
2024482 GTTTAATAAA
Statistics
Matches: 683, Mismatches: 131, Indels: 215
0.66 0.13 0.21
Matches are distributed among these distances:
14 3 0.00
15 12 0.02
16 12 0.02
17 22 0.03
18 44 0.06
19 64 0.09
20 113 0.17
21 190 0.28
22 113 0.17
23 57 0.08
24 28 0.04
25 6 0.01
26 16 0.02
27 3 0.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (20 bp):
ATAATATTTAATAATATATT
Found at i:2023885 original size:14 final size:14
Alignment explanation
Indices: 2023866--2023892 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2023856 TATATATTAA
2023866 AATATTTTAATAAC
1 AATATTTTAATAAC
2023880 AATATTTTAATAA
1 AATATTTTAATAA
2023893 TATTTATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (14 bp):
AATATTTTAATAAC
Found at i:2023903 original size:9 final size:10
Alignment explanation
Indices: 2023666--2024481 Score: 224
Period size: 10 Copynumber: 78.2 Consensus size: 10
2023656 CAAACAAAAA
2023666 ATTTAATAAT
1 ATTTAATAAT
* *
2023676 ATATAAAAAT
1 ATTTAATAAT
2023686 ATTTAA-AATT
1 ATTTAATAA-T
*
2023696 AATATTAAAAAT
1 -AT-TTAATAAT
**
2023708 ATAAAATAACAT
1 ATTTAAT-A-AT
*
2023720 ATGTAATAAT
1 ATTTAATAAT
2023730 ATTTAATAAT
1 ATTTAATAAT
*
2023740 ATATT-AGAAT
1 AT-TTAATAAT
2023750 ATCTTAATAAT
1 AT-TTAATAAT
* *
2023761 TTTTCATAAT
1 ATTTAATAAT
2023771 ATATTAA-AAT
1 AT-TTAATAAT
*
2023781 AACTTAATAAT
1 -ATTTAATAAT
2023792 ATATTAA-AATT
1 AT-TTAATAA-T
*
2023803 ATGTAAATAATT
1 AT-TTAATAA-T
*
2023815 ATATTTA-AAT
1 AT-TTAATAAT
* *
2023825 TTTTAATGAT
1 ATTTAATAAT
*
2023835 ATATTACATAAC
1 AT-TTA-ATAAT
2023847 ATTTAATAATAT
1 ATTTAAT-A-AT
2023859 ATATTAA-AAT
1 AT-TTAATAAT
2023869 ATTTTAATAACAAT
1 A-TTTAAT---AAT
2023883 ATTTTAATAAT
1 A-TTTAATAAT
2023894 ATTT-ATAAT
1 ATTTAATAAT
*
2023903 ATATTAAAAAT
1 AT-TTAATAAT
2023914 ATTTTAATAAT
1 A-TTTAATAAT
2023925 ATTTAATAAT
1 ATTTAATAAT
*
2023935 ATATTTAT-AT
1 AT-TTAATAAT
*
2023945 TTTATAATTAAT
1 ATT-TAA-TAAT
*
2023957 AATTAAT-AT
1 ATTTAATAAT
*
2023966 -TTTAATAGT
1 ATTTAATAAT
*
2023975 ATTTTAATGAT
1 A-TTTAATAAT
*
2023986 AGTTAATTAAT
1 ATTTAA-TAAT
2023997 ATGTT-ATAATT
1 AT-TTAATAA-T
*
2024008 AATTATTAA-AAG
1 -A-T-TTAATAAT
2024020 ATTTTAATAATT
1 A-TTTAATAA-T
*
2024032 ATTTTATAAT
1 ATTTAATAAT
*
2024042 ATTTTAAT-GT
1 A-TTTAATAAT
*
2024052 ATTCAATAAT
1 ATTTAATAAT
*
2024062 ATTTTAAAATAT
1 A-TTTAATA-AT
2024074 ATATTAA-AAT
1 AT-TTAATAAT
2024084 ATATT-ATAAT
1 AT-TTAATAAT
*
2024094 ATTTTAAAAAT
1 A-TTTAATAAT
2024105 ATTTTAA-AAT
1 A-TTTAATAAT
2024115 ATTTATATAAT
1 ATTTA-ATAAT
*
2024126 ATATAATAAT
1 ATTTAATAAT
2024136 AATTTAATAAT
1 -ATTTAATAAT
2024147 A---AAT-AT
1 ATTTAATAAT
*
2024153 ATATTGA-AAT
1 AT-TTAATAAT
2024163 ATTTAATAAT
1 ATTTAATAAT
** * *
2024173 AAATATTTAT
1 ATTTAATAAT
* *
2024183 -TTTATTGAT
1 ATTTAATAAT
*
2024192 AGTTAATTAAT
1 ATTTAA-TAAT
*
2024203 ATTTTATAATT
1 ATTTAATAA-T
2024214 AATTATTAA-AAT
1 -A-T-TTAATAAT
2024226 ATTTTAATAAT
1 A-TTTAATAAT
**
2024237 ATTTTGTAAT
1 ATTTAATAAT
*
2024247 ATTTTAAT-GT
1 A-TTTAATAAT
* *
2024257 ATGTAATAAC
1 ATTTAATAAT
*
2024267 ATTTTA-AAT
1 ATTTAATAAT
*
2024276 ATTTATATGAT
1 ATTTA-ATAAT
*
2024287 ATATAATAAT
1 ATTTAATAAT
*
2024297 ATTTAGAAAAT
1 ATTTA-ATAAT
*
2024308 ATTTAAGAAT
1 ATTTAATAAT
2024318 ATTTTAA-AAT
1 A-TTTAATAAT
*
2024328 ATAGTAATAAT
1 AT-TTAATAAT
* *
2024339 ATATT-TTTAT
1 AT-TTAATAAT
* *
2024349 AATAAAT-AT
1 ATTTAATAAT
2024358 ATCTTAA-AAT
1 AT-TTAATAAT
2024368 ATTCTAATAATAT
1 ATT-TAAT-A-AT
*
2024381 ATTTTATAAT
1 ATTTAATAAT
2024391 ATTTGAATAAT
1 ATTT-AATAAT
* *
2024402 AATT-ATATT
1 ATTTAATAAT
* *
2024411 A-ATAACTATT
1 ATTTAA-TAAT
2024421 ATTTTAAT-AT
1 A-TTTAATAAT
* *
2024431 ATTAAAAAAT
1 ATTTAATAAT
*
2024441 ATATTTA-AAT
1 AT-TTAATAAT
2024451 ATTTAATAAT
1 ATTTAATAAT
*
2024461 ATATAA-AAT
1 ATTTAATAAT
2024470 ATTTAATAAT
1 ATTTAATAAT
2024480 AT
1 AT
2024482 GTTTAATAAA
Statistics
Matches: 602, Mismatches: 113, Indels: 182
0.67 0.13 0.20
Matches are distributed among these distances:
6 3 0.00
7 3 0.00
8 6 0.01
9 73 0.12
10 241 0.40
11 190 0.32
12 52 0.09
13 19 0.03
14 15 0.02
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (10 bp):
ATTTAATAAT
Found at i:2023904 original size:34 final size:32
Alignment explanation
Indices: 2023853--2024147 Score: 122
Period size: 31 Copynumber: 9.2 Consensus size: 32
2023843 TAACATTTAA
*
2023853 TAAT-ATATATTAAAATATTTTAATAACAATATTT
1 TAATAATAT-TTATAATATTTTAA-AA-AATATTT
*
2023887 TAATAATATTTATAATATATT-AAAAATATTT
1 TAATAATATTTATAATATTTTAAAAAATATTT
2023918 TAATAATATTTAATAATATATTT-----ATATTT
1 TAATAATATTT-ATAATAT-TTTAAAAAATATTT
* * * *
2023947 T-ATAATTAATAATTAATATTTT-AATAGTATTT
1 TAATAA-TATTTA-TAATATTTTAAAAAATATTT
* * ** *
2023979 TAATGATAGTTAATTAATATGTTATAATTAAT-TAT
1 TAATAATA-TTTA-TAATAT-TT-TAAAAAATATTT
* *
2024014 TAA-AAGATTTTAATAATTATTTT--ATAATATTT
1 TAATAATA-TTT-ATAA-TATTTTAAAAAATATTT
* * * *
2024046 TAAT-GTATTCAATAATATTTTAAAATATATAT
1 TAATAATATT-TATAATATTTTAAAAAATATTT
2024078 TAA-AATATATTATAATATTTT-AAAAATATTT
1 TAATAATAT-TTATAATATTTTAAAAAATATTT
* * * *
2024109 TAA-AATATTTAT-ATAATATATAATAATAATT
1 TAATAATATTTATAATATTTTA-AAAAATATTT
2024140 TAATAATA
1 TAATAATA
2024148 AATATATATT
Statistics
Matches: 204, Mismatches: 31, Indels: 54
0.71 0.11 0.19
Matches are distributed among these distances:
28 8 0.04
29 21 0.10
30 10 0.05
31 55 0.27
32 49 0.24
33 18 0.09
34 25 0.12
35 14 0.07
36 4 0.02
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (32 bp):
TAATAATATTTATAATATTTTAAAAAATATTT
Found at i:2023954 original size:151 final size:151
Alignment explanation
Indices: 2023723--2024102 Score: 387
Period size: 151 Copynumber: 2.5 Consensus size: 151
2023713 ATAACATATG
* * *
2023723 TAAT-AATA-TTTAATAATATATTAGAATATCTTAATAAT-TTTTCATAATATATTAAAATA-AC
1 TAATAAATATTTTAATAATAT-TTATAATATATTAATAATATTTTAATAATATATTAAAATATA-
* *
2023784 TTAATAATATATTAAAATTATGTAAATAATTATATTTAA-A-T-TTTTAATGATATATTACA-TA
64 TT-ATAATATTTTAAAATTA-ATAAATAA-TAT-TTTAATAGTATTTTAATGATA-ATTA-ATTA
*
2023845 ACAT-TTAATAA-T-ATATATTAAAATATTT
123 ACATGTT-ATAATTAAT-TATTAAAAGATTT
*
2023873 TAATAACAATATTTTAATAATATTTATAATATATTAAAAATATTTTAATAATAT-TTAATAATAT
1 TAAT-A-AATATTTTAATAATATTTATAATATATTAATAATATTTTAATAATATATTAA-AATAT
* * * *
2023937 ATT-T-ATATTTTATAATTAATAATTAATATTTTAATAGTATTTTAATGATAGTTAATTAATATG
63 ATTATAATATTTTAAAATTAATAAATAATATTTTAATAGTATTTTAATGATAATTAATTAACATG
2024000 TTATAATTAATTATTAAAAGATTT
128 TTATAATTAATTATTAAAAGATTT
* * *
2024024 TAATAATTATTTT-ATAATATTT-TAATGTATTCAATAATATTTTAAAATATATATTAAAATATA
1 TAATAAATATTTTAATAATATTTATAATATATT-AATAATATTTTAATA-ATATATTAAAATATA
2024087 TTATAATATTTTAAAA
64 TTATAATATTTTAAAA
2024103 ATATTTTAAA
Statistics
Matches: 195, Mismatches: 16, Indels: 37
0.79 0.06 0.15
Matches are distributed among these distances:
147 8 0.04
148 27 0.14
149 24 0.12
150 29 0.15
151 52 0.27
152 3 0.02
153 23 0.12
154 28 0.14
155 1 0.01
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (151 bp):
TAATAAATATTTTAATAATATTTATAATATATTAATAATATTTTAATAATATATTAAAATATATT
ATAATATTTTAAAATTAATAAATAATATTTTAATAGTATTTTAATGATAATTAATTAACATGTTA
TAATTAATTATTAAAAGATTT
Found at i:2024016 original size:61 final size:61
Alignment explanation
Indices: 2023899--2024237 Score: 141
Period size: 61 Copynumber: 5.4 Consensus size: 61
2023889 ATAATATTTA
* * * *
2023899 TAATATATTAAAAATATTTTAATAATATTTAATAATATATTTATATTTTATAATTAATAAT
1 TAATATATTAAAAATATTTTAATAATAGTTAATAATATAGTTATAATTAATAATTAATAAT
* * * * * *
2023960 TAATATTTTAATAGTATTTTAATGATAGTTAATTAATAT-GTTATAATTAATTATTAAAAGATTT
1 TAATATATTAAAAATATTTTAATAATAGTTAA-TAATATAGTTATAATTAATAATTAATA-A--T
* * * * *
2024024 TAATAATTATTTTATAATATTTTAAT-GTA-TTCAATAATAT-TTTA-AAAT-ATATATTAAAAT
1 TAAT-A-TA-TTAAAAATATTTTAATAATAGTT-AATAATATAGTTATAATTAATA-ATT--AAT
2024084 ATATT
59 A-A-T
* * *
2024089 ATAATATTTTAAAAATATTTTAA-AATATTTATATAATATA-TAATAA-TAAT--TTAATAAT
1 -TAATATATTAAAAATATTTTAATAATAGTTA-ATAATATAGTTATAATTAATAATTAATAAT
* ** * * * * *
2024147 AAATATATATTGAAATATTTAATAATAAATATTTATTTTATTGATAG-T-TAATTAATATTTTAT
1 TAATATAT-TAAAAATATTT--TAAT-AATAGTTA--ATAAT-ATAGTTATAATTAATAATTAAT
2024210 AAT
59 AAT
2024213 TAAT-TATT-AAAATATTTTAATAATA
1 TAATATATTAAAAATATTTTAATAATA
2024238 TTTTGTAATA
Statistics
Matches: 215, Mismatches: 34, Indels: 59
0.70 0.11 0.19
Matches are distributed among these distances:
57 6 0.03
58 10 0.05
59 1 0.00
60 11 0.05
61 46 0.21
62 17 0.08
63 33 0.15
64 32 0.15
65 22 0.10
66 23 0.11
67 14 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (61 bp):
TAATATATTAAAAATATTTTAATAATAGTTAATAATATAGTTATAATTAATAATTAATAAT
Found at i:2024044 original size:10 final size:10
Alignment explanation
Indices: 2023880--2024329 Score: 125
Period size: 11 Copynumber: 43.5 Consensus size: 10
2023870 TTTTAATAAC
2023880 AATATTTTAAT
1 AATATTTT-AT
2023891 AATA-TTTAT
1 AATATTTTAT
* *
2023900 AATATATTAAA
1 AATAT-TTTAT
2023911 AATATTTTAAT
1 AATATTTT-AT
*
2023922 AATATTTAAT
1 AATATTTTAT
*
2023932 AATATATT-T
1 AATATTTTAT
2023941 -ATATTTTAT
1 AATATTTTAT
* *
2023950 AAT-TAATAATT
1 AATAT-TTTA-T
2023961 AATATTTTAAT
1 AATATTTT-AT
*
2023972 AGTATTTTAAT
1 AATATTTT-AT
* * *
2023983 GATAGTTAATT
1 AATATTTTA-T
*
2023994 AATATGTTAT
1 AATATTTTAT
*
2024004 AATTAATTATTAA
1 AA-T-ATT-TTAT
*
2024017 AAGATTTTAAT
1 AATATTTT-AT
2024028 AATTATTTTAT
1 AA-TATTTTAT
2024039 AATATTTTA-
1 AATATTTTAT
* **
2024048 ATGTATTCAAT
1 A-ATATTTTAT
*
2024059 AATATTTTAA
1 AATATTTTAT
*
2024069 AATATATATTAA
1 AATAT-T-TTAT
*
2024081 AATATATTAT
1 AATATTTTAT
*
2024091 AATATTTTAAA
1 AATATTTT-AT
*
2024102 AATATTTTAA
1 AATATTTTAT
2024112 AATATTTATAT
1 AATATTT-TAT
* *
2024123 AATATATAAT
1 AATATTTTAT
*
2024133 AATAATTTAAT
1 AAT-ATTTTAT
**
2024144 AATA-AATAT
1 AATATTTTAT
*
2024153 -ATA-TTGA-
1 AATATTTTAT
*
2024160 AATATTTAAT
1 AATATTTTAT
**
2024170 AATA-AATAT
1 AATATTTTAT
*
2024179 -TTATTTTATT
1 AATATTTTA-T
* * *
2024189 GATAGTTAATT
1 AATATTTTA-T
2024200 AATATTTTAT
1 AATATTTTAT
*
2024210 AATTAATTATTAA
1 AA-T-ATT-TTAT
2024223 AATATTTTAAT
1 AATATTTT-AT
*
2024234 AATATTTTGT
1 AATATTTTAT
2024244 AATATTTTA-
1 AATATTTTAT
* * *
2024253 ATGTATGTAAT
1 A-ATATTTTAT
*
2024264 AACATTTTA-
1 AATATTTTAT
2024273 AATATTTATAT
1 AATATTT-TAT
* * *
2024284 GATATATAAT
1 AATATTTTAT
* *
2024294 AATATTTAGAA
1 AATATTT-TAT
* *
2024305 AATATTTAAG
1 AATATTTTAT
*
2024315 AATATTTTAA
1 AATATTTTAT
2024325 AATAT
1 AATAT
2024330 AGTAATAATA
Statistics
Matches: 319, Mismatches: 83, Indels: 75
0.67 0.17 0.16
Matches are distributed among these distances:
8 15 0.05
9 26 0.08
10 121 0.38
11 125 0.39
12 22 0.07
13 10 0.03
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.49
Consensus pattern (10 bp):
AATATTTTAT
Found at i:2024178 original size:14 final size:14
Alignment explanation
Indices: 2024128--2024181 Score: 53
Period size: 14 Copynumber: 4.0 Consensus size: 14
2024118 TATATAATAT
2024128 ATAAT-AATAATTTA
1 ATAATAAAT-ATTTA
2024142 ATAATAAATA--T-
1 ATAATAAATATTTA
*
2024153 ATATTGAAATATTTA
1 ATAAT-AAATATTTA
2024168 ATAATAAATATTTA
1 ATAATAAATATTTA
2024182 TTTTATTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
11 4 0.12
12 6 0.18
14 16 0.48
15 7 0.21
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (14 bp):
ATAATAAATATTTA
Found at i:2024217 original size:206 final size:205
Alignment explanation
Indices: 2023974--2024387 Score: 581
Period size: 206 Copynumber: 2.0 Consensus size: 205
2023964 ATTTTAATAG
2023974 TATTTTAATGATAGTTAATTAATATGTTATAATTAATTATTAAAAGATTTTAATAATTATTTTAT
1 TATTTTAATGATAGTTAATTAATATGTTATAATTAATTATTAAAAGATTTTAATAA-TATTTTAT
* *
2024039 AATATTTTAATGTAT-TCAATAATATTTTAAAATATATATTAAAATATATTATAATATTTTA-AA
65 AATATTTTAATGTATGT-AATAACATTTT-AAATATATA-TAAAATATATAATAATA-TTTAGAA
* *
2024102 AATATTTTAA-AATATTTATATAATATA-TAATAATA-A-TTTAATAATAAATATATATTGAAAT
126 AATA-TTTAAGAATATTT-TAAAATATAGTAATAATATATTTTAATAATAAATATATATTAAAAT
2024163 ATT-TAATAATAAATATT
189 ATTCTAATAATAAAT-TT
* * * *
2024180 TATTTTATTGATAGTTAATTAATATTTTATAATTAATTATTAAAATATTTTAATAATATTTTGTA
1 TATTTTAATGATAGTTAATTAATATGTTATAATTAATTATTAAAAGATTTTAATAATATTTTATA
* **
2024245 ATATTTTAATGTATGTAATAACATTTTAAATATTTATATGATATATAATAATATTTAGAAAATAT
66 ATATTTTAATGTATGTAATAACATTTTAAATATATATAAAATATATAATAATATTTAGAAAATAT
* *
2024310 TTAAGAATATTTTAAAATATAGTAATAATATATTTTTATAATAAATATATCTTAAAATATTCTAA
131 TTAAGAATATTTTAAAATATAGTAATAATATATTTTAATAATAAATATATATTAAAATATTCTAA
*
2024375 TAATATATTT
196 TAATAAATTT
2024385 TAT
1 TAT
2024388 AATATTTGAA
Statistics
Matches: 187, Mismatches: 14, Indels: 15
0.87 0.06 0.07
Matches are distributed among these distances:
202 17 0.09
203 35 0.19
204 9 0.05
205 62 0.33
206 64 0.34
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.49
Consensus pattern (205 bp):
TATTTTAATGATAGTTAATTAATATGTTATAATTAATTATTAAAAGATTTTAATAATATTTTATA
ATATTTTAATGTATGTAATAACATTTTAAATATATATAAAATATATAATAATATTTAGAAAATAT
TTAAGAATATTTTAAAATATAGTAATAATATATTTTAATAATAAATATATATTAAAATATTCTAA
TAATAAATTT
Found at i:2024480 original size:29 final size:30
Alignment explanation
Indices: 2024423--2024508 Score: 76
Period size: 29 Copynumber: 3.0 Consensus size: 30
2024413 TAACTATTAT
* *
2024423 TTTAAT-ATATTAAAAAATATATTTAAATA-
1 TTTAATAATA-TATAAAATATATTAAAATAG
2024452 TTTAATAATATATAAAATAT-TTAATAATATG
1 TTTAATAATATATAAAATATATTAA-AATA-G
*
2024483 TTTAATAA-A-ATAAAATA-AATAAAATA
1 TTTAATAATATATAAAATATATTAAAATA
2024509 TGAAAGGGTA
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
28 7 0.14
29 30 0.61
30 4 0.08
31 8 0.16
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (30 bp):
TTTAATAATATATAAAATATATTAAAATAG
Found at i:2026127 original size:26 final size:27
Alignment explanation
Indices: 2026098--2026154 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
2026088 ATTATATCCT
2026098 TTTTTA-TTTT-TAAATATTTAAAAATA
1 TTTTTACTTTTCTAAAT-TTTAAAAATA
* *
2026124 TTTTTACTTTTCTATATTTTAAAAATG
1 TTTTTACTTTTCTAAATTTTAAAAATA
2026151 TTTT
1 TTTT
2026155 GAGATTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 6 0.22
27 17 0.63
28 4 0.15
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (27 bp):
TTTTTACTTTTCTAAATTTTAAAAATA
Found at i:2028981 original size:3 final size:3
Alignment explanation
Indices: 2028973--2029013 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
2028963 TTAAAAGCTA
2028973 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2029014 GAAGCTTAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2035091 original size:3 final size:3
Alignment explanation
Indices: 2035078--2035114 Score: 65
Period size: 3 Copynumber: 12.0 Consensus size: 3
2035068 GTTCATTAAA
2035078 ATT ATT AATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2035115 TTAAATAGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2042366 original size:12 final size:12
Alignment explanation
Indices: 2042351--2042385 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2042341 TTCAGCTTCA
2042351 GGTTCTGGCTCT
1 GGTTCTGGCTCT
*
2042363 GGTTCTGGTTCT
1 GGTTCTGGCTCT
*
2042375 GGTTTTGGCTC
1 GGTTCTGGCTC
2042386 ATCTTCCGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.34, T:0.46
Consensus pattern (12 bp):
GGTTCTGGCTCT
Found at i:2044327 original size:32 final size:32
Alignment explanation
Indices: 2044291--2044354 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
2044281 TACAATCACA
*
2044291 ATATCTAGCAAAGTTTAACTTCATCTATAATT
1 ATATCTAGCAAAGTTTAACATCATCTATAATT
2044323 ATATCTAGCAAAGTTTAACATCATCTATAATT
1 ATATCTAGCAAAGTTTAACATCATCTATAATT
2044355 GCTTATCTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.39, C:0.16, G:0.06, T:0.39
Consensus pattern (32 bp):
ATATCTAGCAAAGTTTAACATCATCTATAATT
Found at i:2047865 original size:2 final size:2
Alignment explanation
Indices: 2047858--2047883 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2047848 ACGTTGAGAA
2047858 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
2047884 GGAACTTAAG
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:2048165 original size:11 final size:12
Alignment explanation
Indices: 2048146--2048186 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 12
2048136 CCTGATTATA
2048146 TAAATATAATAT
1 TAAATATAATAT
2048158 TAAA-ATAAT-T
1 TAAATATAATAT
*
2048168 AAAATATAATA-
1 TAAATATAATAT
2048179 TAAATATA
1 TAAATATA
2048187 TAATTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
TAAATATAATAT
Found at i:2048208 original size:33 final size:33
Alignment explanation
Indices: 2048171--2048290 Score: 98
Period size: 32 Copynumber: 3.9 Consensus size: 33
2048161 AATAATTAAA
*
2048171 ATATAATATAAATATA-TAATTATTTTAAAATTT
1 ATATAATATAAATATATTAA-TATATTAAAATTT
*
2048204 ATATAATAT-AATTTATTAATATATTAAAATTT
1 ATATAATATAAATATATTAATATATTAAAATTT
* * * *
2048236 ATTTAA-ATAAA-AAATATAAAATA-TATAA--T
1 ATATAATATAAATATAT-TAATATATTAAAATTT
2048265 -TATAATATAAATA-ATTAAT-TATTAAA
1 ATATAATATAAATATATTAATATATTAAA
2048291 TTTTTTTTAC
Statistics
Matches: 71, Mismatches: 10, Indels: 17
0.72 0.10 0.17
Matches are distributed among these distances:
27 2 0.03
28 10 0.14
29 8 0.11
30 1 0.01
31 8 0.11
32 30 0.42
33 12 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (33 bp):
ATATAATATAAATATATTAATATATTAAAATTT
Found at i:2048225 original size:18 final size:18
Alignment explanation
Indices: 2048204--2048250 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
2048194 TTTAAAATTT
*
2048204 ATATAATATAATTTATTA
1 ATATAATAAAATTTATTA
*
2048222 ATATATTAAAATTTATTTA
1 ATATAATAAAATTTA-TTA
2048241 A-ATAA-AAAAT
1 ATATAATAAAAT
2048251 ATAAAATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 5 0.20
18 16 0.64
19 4 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATATAATAAAATTTATTA
Found at i:2048278 original size:15 final size:15
Alignment explanation
Indices: 2048240--2048281 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
2048230 AAATTTATTT
*
2048240 AAATAAA-AAATATA
1 AAATAAATAATTATA
*
2048254 AAATATATAATTATA
1 AAATAAATAATTATA
*
2048269 ATATAAATAATTA
1 AAATAAATAATTA
2048282 ATTATTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
14 6 0.26
15 17 0.74
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATAAATAATTATA
Found at i:2049696 original size:18 final size:18
Alignment explanation
Indices: 2049675--2049709 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2049665 GGTGAAATTT
* *
2049675 AAATTTTAATAGTTATTA
1 AAATATTAATAATTATTA
2049693 AAATATTAATAATTATT
1 AAATATTAATAATTATT
2049710 TAACCAAACT
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:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (18 bp):
AAATATTAATAATTATTA
Found at i:2051855 original size:13 final size:13
Alignment explanation
Indices: 2051837--2051861 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2051827 ATTTTTAAAA
2051837 TATTTATATTTAT
1 TATTTATATTTAT
2051850 TATTTATATTTA
1 TATTTATATTTA
2051862 AGACATATAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TATTTATATTTAT
Found at i:2052540 original size:15 final size:16
Alignment explanation
Indices: 2052520--2052556 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
2052510 TAACAATGAA
2052520 TAAAAT-AATTTAAAT
1 TAAAATAAATTTAAAT
2052535 TAAAATAAATTTAAAT
1 TAAAATAAATTTAAAT
*
2052551 AAAAAT
1 TAAAAT
2052557 TATTATGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TAAAATAAATTTAAAT
Found at i:2052639 original size:28 final size:29
Alignment explanation
Indices: 2052580--2052639 Score: 79
Period size: 27 Copynumber: 2.1 Consensus size: 29
2052570 ATTCACTTTA
***
2052580 TTTTTTAAATAAATTTTATGTTATTTAAT
1 TTTTTTAAATAAATTTTAAAATATTTAAT
2052609 TTTTTTAAA-AAATTTTAAAAT-TTTAAT
1 TTTTTTAAATAAATTTTAAAATATTTAAT
2052636 TTTT
1 TTTT
2052640 AACTCCCTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 10 0.36
28 9 0.32
29 9 0.32
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (29 bp):
TTTTTTAAATAAATTTTAAAATATTTAAT
Found at i:2053388 original size:17 final size:16
Alignment explanation
Indices: 2053362--2053394 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
2053352 CTTGGATATT
2053362 TTTATTATTTATTTTA
1 TTTATTATTTATTTTA
2053378 TTTATTTATTTATTTTA
1 TTTA-TTATTTATTTTA
2053395 CAGACTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTATTATTTATTTTA
Found at i:2053389 original size:12 final size:13
Alignment explanation
Indices: 2053361--2053392 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
2053351 TCTTGGATAT
2053361 TTTTA-TTATTTA
1 TTTTATTTATTTA
2053373 TTTTATTTATTTA
1 TTTTATTTATTTA
2053386 -TTTATTT
1 TTTTATTT
2053393 TACAGACTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTATTTATTTA
Found at i:2053452 original size:13 final size:13
Alignment explanation
Indices: 2053428--2053478 Score: 59
Period size: 14 Copynumber: 3.8 Consensus size: 13
2053418 AAAGATATTG
2053428 TAAATGTTAAAATT
1 TAAAT-TTAAAATT
2053442 TAAATTTAAAATT
1 TAAATTTAAAATT
*
2053455 TAAAATTTAATA-T
1 T-AAATTTAAAATT
*
2053468 TATATTTAAAA
1 TAAATTTAAAA
2053479 ATAATTATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
12 8 0.24
13 11 0.33
14 14 0.42
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (13 bp):
TAAATTTAAAATT
Found at i:2056874 original size:16 final size:16
Alignment explanation
Indices: 2056853--2056945 Score: 52
Period size: 16 Copynumber: 5.8 Consensus size: 16
2056843 GATTTAATTT
2056853 TAAATATTAAATAATA
1 TAAATATTAAATAATA
2056869 TAAATA-T-AA-AATA
1 TAAATATTAAATAATA
*
2056882 AAAATAATTAAAATATATA
1 TAAAT-ATT-AAATA-ATA
* * *
2056901 AAAATATGATATAATA
1 TAAATATTAAATAATA
* *
2056917 TTAAA-AATATATAATA
1 -TAAATATTAAATAATA
2056933 -AAATATATAAATA
1 TAAATAT-TAAATA
2056946 TTTTAAAATT
Statistics
Matches: 60, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
13 8 0.13
14 6 0.10
15 3 0.05
16 23 0.38
17 9 0.15
18 3 0.05
19 8 0.13
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (16 bp):
TAAATATTAAATAATA
Found at i:2056901 original size:19 final size:20
Alignment explanation
Indices: 2056861--2056943 Score: 82
Period size: 19 Copynumber: 4.0 Consensus size: 20
2056851 TTTAAATATT
*
2056861 AAATAATATAAATATAAAATAA
1 AAATAATATAAA-AT-ATATAA
2056883 AAATAAT-TAAAATATATAA
1 AAATAATATAAAATATATAA
*
2056902 AAAT-ATGATATAATAT-TAA
1 AAATAAT-ATAAAATATATAA
2056921 AAATATATAATAAAATATATAA
1 AAATA-AT-ATAAAATATATAA
2056943 A
1 A
2056944 TATTTTAAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
18 2 0.04
19 16 0.31
20 9 0.17
21 14 0.27
22 11 0.21
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.31
Consensus pattern (20 bp):
AAATAATATAAAATATATAA
Found at i:2056904 original size:10 final size:10
Alignment explanation
Indices: 2056879--2056943 Score: 64
Period size: 10 Copynumber: 6.5 Consensus size: 10
2056869 TAAATATAAA
2056879 ATAAAAATA-
1 ATAAAAATAT
*
2056888 ATTAAAATAT
1 ATAAAAATAT
2056898 ATAAAAATAT
1 ATAAAAATAT
*
2056908 GAT-ATAATAT
1 -ATAAAAATAT
2056918 -TAAAAATAT
1 ATAAAAATAT
2056927 ATAATAAAATAT
1 AT-A-AAAATAT
2056939 ATAAA
1 ATAAA
2056944 TATTTTAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
8 1 0.02
9 14 0.30
10 18 0.39
11 4 0.09
12 9 0.20
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (10 bp):
ATAAAAATAT
Found at i:2056926 original size:29 final size:29
Alignment explanation
Indices: 2056853--2056947 Score: 101
Period size: 29 Copynumber: 3.3 Consensus size: 29
2056843 GATTTAATTT
2056853 TAAATATTAAATAATATA-AATATAAA-ATA
1 TAAATATTAAA-AATATATAATA-AAATATA
*
2056882 AAAATAATT-AAAATATAT-A-AAAATATGA
1 TAAAT-ATTAAAAATATATAATAAAATAT-A
2056910 TATAATATTAAAAATATATAATAAAATATA
1 TA-AATATTAAAAATATATAATAAAATATA
2056940 TAAATATT
1 TAAATATT
2056948 TTAAAATTTA
Statistics
Matches: 56, Mismatches: 2, Indels: 16
0.76 0.03 0.22
Matches are distributed among these distances:
26 3 0.05
27 3 0.05
28 12 0.21
29 24 0.43
30 7 0.12
31 7 0.12
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (29 bp):
TAAATATTAAAAATATATAATAAAATATA
Found at i:2056960 original size:32 final size:32
Alignment explanation
Indices: 2056914--2056994 Score: 103
Period size: 32 Copynumber: 2.6 Consensus size: 32
2056904 ATATGATATA
*
2056914 ATATTAAAA-ATATATAATA-AAATATATAAAT
1 ATATTAAAATTTATATAATACAAAT-TATAAAT
* * *
2056945 ATTTTAAAATTTATATAATACGAATTATTAAT
1 ATATTAAAATTTATATAATACAAATTATAAAT
2056977 ATATTAAAATTTATATAA
1 ATATTAAAATTTATATAA
2056995 ATATTTTATA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
31 8 0.19
32 32 0.74
33 3 0.07
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (32 bp):
ATATTAAAATTTATATAATACAAATTATAAAT
Found at i:2058151 original size:15 final size:15
Alignment explanation
Indices: 2058133--2058163 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2058123 TTAATTAAAT
*
2058133 TTTTTATTTTTAATA
1 TTTTAATTTTTAATA
2058148 TTTTAATTTTTAATA
1 TTTTAATTTTTAATA
2058163 T
1 T
2058164 AAATTTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTAATTTTTAATA
Found at i:2058209 original size:12 final size:12
Alignment explanation
Indices: 2058192--2058227 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 12
2058182 AAATATAAAT
2058192 AATTAAATTTAA
1 AATTAAATTTAA
*
2058204 AATTAAATATAAA
1 AATTAAAT-TTAA
2058217 AATTAAATTTA
1 AATTAAATTTA
2058228 TTTTTTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
AATTAAATTTAA
Found at i:2058209 original size:26 final size:26
Alignment explanation
Indices: 2058159--2058227 Score: 90
Period size: 26 Copynumber: 2.8 Consensus size: 26
2058149 TTTAATTTTT
* **
2058159 AATATAAAT--TTTAATTTAATTTTA
1 AATATAAATAATTAAATTTAAAATTA
2058183 AATATAAATAATTAAATTTAAAATTA
1 AATATAAATAATTAAATTTAAAATTA
2058209 AATATAAA-AATTAAATTTA
1 AATATAAATAATTAAATTTA
2058228 TTTTTTATTA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
24 9 0.22
25 11 0.28
26 20 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
AATATAAATAATTAAATTTAAAATTA
Found at i:2058210 original size:20 final size:21
Alignment explanation
Indices: 2058170--2058212 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2058160 ATATAAATTT
* *
2058170 TAATTTAATTTTAAATATAAA
1 TAATTAAATTTAAAATATAAA
2058191 TAATTAAATTTAAAAT-TAAA
1 TAATTAAATTTAAAATATAAA
2058211 TA
1 TA
2058213 TAAAAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TAATTAAATTTAAAATATAAA
Found at i:2067455 original size:2 final size:2
Alignment explanation
Indices: 2067448--2067474 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2067438 CCAAATGTTT
2067448 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2067475 GCTCCGATCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2067710 original size:2 final size:2
Alignment explanation
Indices: 2067697--2067734 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2067687 CATCCGGAGA
*
2067697 AT AT AA 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
2067735 TTCTGCAGAC
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2068046 original size:13 final size:13
Alignment explanation
Indices: 2068028--2068052 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2068018 TTTTTAAAAA
2068028 TAATTATATTAAT
1 TAATTATATTAAT
2068041 TAATTATATTAA
1 TAATTATATTAA
2068053 ATTACAGATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TAATTATATTAAT
Found at i:2068091 original size:23 final size:23
Alignment explanation
Indices: 2068050--2068093 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2068040 TTAATTATAT
*
2068050 TAAATTACAGATTCAATTAATCA
1 TAAATTACAGATTAAATTAATCA
2068073 TAAATTACA-ATTAATATTAAT
1 TAAATTACAGATTAA-ATTAAT
2068094 TTTTTTTGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.39
Consensus pattern (23 bp):
TAAATTACAGATTAAATTAATCA
Found at i:2068908 original size:27 final size:26
Alignment explanation
Indices: 2068874--2068927 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
2068864 GTATTATAAT
*
2068874 TAAATTTAAAAT-TTTATATATTTATA
1 TAAATTTAAAATATTAATA-ATTTATA
*
2068900 TAAATTTTAATATATTAATAATTTATA
1 TAAA-TTTAAAATATTAATAATTTATA
2068927 T
1 T
2068928 TTTATAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 4 0.17
27 15 0.62
28 5 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
TAAATTTAAAATATTAATAATTTATA
Found at i:2068936 original size:32 final size:32
Alignment explanation
Indices: 2068890--2068958 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 32
2068880 TAAAATTTTA
*
2068890 TATATTTATATAAATTTTAATATATTAATAATT
1 TATATTTATATAAATTTAAATATATTAAT-ATT
*
2068923 TATATTT-TATAAATTTAAATATATTAATTTT
1 TATATTTATATAAATTTAAATATATTAATATT
2068954 TATAT
1 TATAT
2068959 CATACTTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 7 0.21
32 20 0.59
33 7 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (32 bp):
TATATTTATATAAATTTAAATATATTAATATT
Found at i:2068975 original size:21 final size:20
Alignment explanation
Indices: 2068949--2068992 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
2068939 AAATATATTA
2068949 ATTTTTATATCATACTTATAT
1 ATTTTTATATCATA-TTATAT
* *
2068970 ATTTTTATATTATATTTTAT
1 ATTTTTATATCATATTATAT
2068990 ATT
1 ATT
2068993 AAATTTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.64
Consensus pattern (20 bp):
ATTTTTATATCATATTATAT
Found at i:2070661 original size:2 final size:2
Alignment explanation
Indices: 2070654--2070679 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2070644 TTTACTTTGC
2070654 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
2070680 TCCAACTAAT
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:2071382 original size:12 final size:12
Alignment explanation
Indices: 2071361--2071407 Score: 76
Period size: 12 Copynumber: 3.9 Consensus size: 12
2071351 AATTTATTTG
2071361 TTTTCATCTTTC
1 TTTTCATCTTTC
*
2071373 TTTTCGTCTTTC
1 TTTTCATCTTTC
2071385 TTTTCATCTTTC
1 TTTTCATCTTTC
*
2071397 TTTTCTTCTTT
1 TTTTCATCTTT
2071408 AGCAGGTCCC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.04, C:0.23, G:0.02, T:0.70
Consensus pattern (12 bp):
TTTTCATCTTTC
Found at i:2071388 original size:24 final size:24
Alignment explanation
Indices: 2071361--2071407 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
2071351 AATTTATTTG
2071361 TTTTCATCTTTCTTTTCGTCTTTC
1 TTTTCATCTTTCTTTTCGTCTTTC
*
2071385 TTTTCATCTTTCTTTTCTTCTTT
1 TTTTCATCTTTCTTTTCGTCTTT
2071408 AGCAGGTCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.04, C:0.23, G:0.02, T:0.70
Consensus pattern (24 bp):
TTTTCATCTTTCTTTTCGTCTTTC
Found at i:2073321 original size:36 final size:36
Alignment explanation
Indices: 2073268--2073350 Score: 130
Period size: 36 Copynumber: 2.3 Consensus size: 36
2073258 TGAGATAAGG
* *
2073268 AAATTTAAAGTAAAATTTAATTTAGTTAATTTATAT
1 AAATTTAAAATAAAATTTAATTTAATTAATTTATAT
* *
2073304 ATATTTAAAATAGAATTTAATTTAATTAATTTATAT
1 AAATTTAAAATAAAATTTAATTTAATTAATTTATAT
2073340 AAATTTAAAAT
1 AAATTTAAAAT
2073351 TAATTATATA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (36 bp):
AAATTTAAAATAAAATTTAATTTAATTAATTTATAT
Found at i:2073359 original size:20 final size:21
Alignment explanation
Indices: 2073327--2073370 Score: 81
Period size: 20 Copynumber: 2.1 Consensus size: 21
2073317 AATTTAATTT
2073327 AATTAATTTATATAAATTTAA
1 AATTAATTTATATAAATTTAA
2073348 AATTAA-TTATATAAATTTAA
1 AATTAATTTATATAAATTTAA
2073368 AAT
1 AAT
2073371 GAAACTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AATTAATTTATATAAATTTAA
Done.