Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold59
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: 3999109
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.32
Warning! 268233 characters in sequence are not A, C, G, or T
File 12 of 25
Found at i:1876846 original size:4 final size:4
Alignment explanation
Indices: 1876816--1876865 Score: 55
Period size: 4 Copynumber: 12.5 Consensus size: 4
1876806 TGTGTGTGTG
* * * * *
1876816 TATA TCTA TCTA TCTA TACA TACA TATA TATA TATA TATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
1876864 TA
1 TA
1876866 AGGTACTGAC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (4 bp):
TATA
Found at i:1876852 original size:10 final size:10
Alignment explanation
Indices: 1876816--1876865 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 10
1876806 TGTGTGTGTG
* *
1876816 TATATCTATC
1 TATATATATA
* *
1876826 TATCTATACA
1 TATATATATA
*
1876836 TACATATATA
1 TATATATATA
1876846 TATATATATA
1 TATATATATA
1876856 TATATATATA
1 TATATATATA
1876866 AGGTACTGAC
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
10 32 1.00
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (10 bp):
TATATATATA
Found at i:1878687 original size:15 final size:15
Alignment explanation
Indices: 1878655--1878698 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1878645 TGGGTTTAAT
* *
1878655 ATTTTATTTATATTA
1 ATTTTATTTAAATAA
*
1878670 ATTTGATTTAAATAA
1 ATTTTATTTAAATAA
1878685 ATTTTTATTTAAAT
1 A-TTTTATTTAAAT
1878699 TTAATTATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (15 bp):
ATTTTATTTAAATAA
Found at i:1878691 original size:27 final size:27
Alignment explanation
Indices: 1878661--1878713 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
1878651 TAATATTTTA
*
1878661 TTTATATT-AATTTGATT-TAAATAAATT
1 TTTAT-TTAAATTTAATTATAAA-AAATT
1878688 TTTATTTAAATTTAATTATAAAAAAT
1 TTTATTTAAATTTAATTATAAAAAAT
1878714 ATAAATTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 2 0.09
27 17 0.74
28 4 0.17
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (27 bp):
TTTATTTAAATTTAATTATAAAAAATT
Found at i:1878701 original size:10 final size:10
Alignment explanation
Indices: 1878688--1878774 Score: 52
Period size: 10 Copynumber: 8.4 Consensus size: 10
1878678 TAAATAAATT
1878688 TTTATTTAAA
1 TTTATTTAAA
1878698 TTTAATTATAAA
1 TTT-ATT-TAAA
** *
1878710 -AAATATAAA
1 TTTATTTAAA
* *
1878719 TTAATATAAA
1 TTTATTTAAA
*
1878729 TTTTTTTAAA
1 TTTATTTAAA
1878739 TTATAATTTAAA
1 TT-T-ATTTAAA
*
1878751 TTTA-TAAAA
1 TTTATTTAAA
1878760 TTATATTTAAA
1 TT-TATTTAAA
1878771 TTTA
1 TTTA
1878775 AATAAAAATT
Statistics
Matches: 60, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
9 10 0.17
10 27 0.45
11 11 0.18
12 12 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (10 bp):
TTTATTTAAA
Found at i:1878750 original size:22 final size:21
Alignment explanation
Indices: 1878720--1878805 Score: 72
Period size: 22 Copynumber: 4.2 Consensus size: 21
1878710 AAATATAAAT
* *
1878720 TAATATAAATTTTTTTAAATTA
1 TAATTTAAA-TTTTTTAAATAA
* * *
1878742 TAATTTAAATTTATAAAATTA
1 TAATTTAAATTTTTTAAATAA
1878763 T-ATTTAAA---TTTAAATAA
1 TAATTTAAATTTTTTAAATAA
*
1878780 AAATTTAAAATTTTTTAAATAA
1 TAATTT-AAATTTTTTAAATAA
1878802 TAAT
1 TAAT
1878806 ACACCTTAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
17 6 0.12
18 4 0.08
19 3 0.06
20 7 0.14
21 11 0.22
22 20 0.39
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TAATTTAAATTTTTTAAATAA
Found at i:1878762 original size:21 final size:20
Alignment explanation
Indices: 1878736--1878774 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1878726 AAATTTTTTT
1878736 AAATTATAATTTAAATTTATA
1 AAATTAT-ATTTAAATTTATA
1878757 AAATTATATTTAAATTTA
1 AAATTATATTTAAATTTA
1878775 AATAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AAATTATATTTAAATTTATA
Found at i:1878769 original size:32 final size:30
Alignment explanation
Indices: 1878723--1878805 Score: 89
Period size: 30 Copynumber: 2.8 Consensus size: 30
1878713 TATAAATTAA
*
1878723 TATAAATTTTTTTAAATTATAATTTAAATT
1 TATAAAATTTTTTAAATTATAATTTAAATT
* * *
1878753 TATAAAATTATATTTAAATT-TAAATAAAAAT
1 TATAAAATT-T-TTTAAATTATAATTTAAATT
*
1878784 T-TAAAATTTTTTAAATAATAAT
1 TATAAAATTTTTTAAATTATAAT
1878806 ACACCTTAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
28 7 0.16
29 4 0.09
30 15 0.34
31 10 0.23
32 8 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
TATAAAATTTTTTAAATTATAATTTAAATT
Found at i:1879170 original size:17 final size:17
Alignment explanation
Indices: 1879133--1879184 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
1879123 ATATTATTCT
1879133 TTAAA-AATATTTTTTAA
1 TTAAATAATA-TTTTTAA
1879150 -TAAATAATATTTTTAA
1 TTAAATAATATTTTTAA
1879166 TTAAATTAA-A-TTTTAA
1 TTAAA-TAATATTTTTAA
1879182 TTA
1 TTA
1879185 TAAAAATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
16 20 0.62
17 9 0.28
18 3 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTAAATAATATTTTTAA
Found at i:1879193 original size:15 final size:15
Alignment explanation
Indices: 1879144--1879198 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 15
1879134 TAAAAATATT
1879144 TTTTAA-TAAATAATA
1 TTTTAATTAAATAA-A
1879159 TTTTTAATTAAATTAAA
1 -TTTTAATTAAA-TAAA
1879176 TTTTAATTATAA-AAA
1 TTTTAATTA-AATAAA
*
1879191 TTTAAATT
1 TTTTAATT
1879199 TATATGCACT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
15 10 0.29
16 15 0.43
17 7 0.20
18 3 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTTTAATTAAATAAA
Found at i:1879793 original size:19 final size:19
Alignment explanation
Indices: 1879761--1879814 Score: 62
Period size: 18 Copynumber: 3.0 Consensus size: 19
1879751 TTTTATTAAA
1879761 TATATAAA-TA-TAAATAT
1 TATATAAATTATTAAATAT
1879778 TATATAAATTATTAAATA-
1 TATATAAATTATTAAATAT
*
1879796 TATTTAAAATT-TTAAATAT
1 TATAT-AAATTATTAAATAT
1879815 AAATATTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
17 8 0.25
18 13 0.41
19 11 0.34
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TATATAAATTATTAAATAT
Found at i:1880055 original size:27 final size:26
Alignment explanation
Indices: 1880010--1880060 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
1880000 AATTAAATAT
1880010 AATAATTTTTATTATAATTATATTTAA
1 AATAATTTTTATTATAATTA-ATTTAA
*
1880037 AATATTTTTTATT-TAAATTAATTT
1 AATAATTTTTATTAT-AATTAATTT
1880061 TTATGTGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (26 bp):
AATAATTTTTATTATAATTAATTTAA
Found at i:1880062 original size:17 final size:16
Alignment explanation
Indices: 1880030--1880064 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1880020 ATTATAATTA
1880030 TATTTAAAATATTTTT
1 TATTTAAAATATTTTT
* *
1880046 TATTTAAATTAATTTT
1 TATTTAAAATATTTTT
1880062 TAT
1 TAT
1880065 GTGTTAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TATTTAAAATATTTTT
Found at i:1880127 original size:24 final size:24
Alignment explanation
Indices: 1880082--1880160 Score: 81
Period size: 24 Copynumber: 3.2 Consensus size: 24
1880072 TAATTTGAAG
*
1880082 TATATAA-ATTTTTATATATTTATA
1 TATATAATATTTTTAT-TTTTTATA
*
1880106 TATATAATATTTTTATTTTTTACA
1 TATATAATATTTTTATTTTTTATA
* *
1880130 TCT-TATTATATTTTATTTTTTATTA
1 TATATAATAT-TTTTATTTTTTA-TA
1880155 TATATA
1 TATATA
1880161 TAATGTAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
23 5 0.11
24 27 0.60
25 11 0.24
26 2 0.04
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (24 bp):
TATATAATATTTTTATTTTTTATA
Found at i:1880451 original size:21 final size:22
Alignment explanation
Indices: 1880427--1880469 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
1880417 AAATAAAATG
1880427 ATATAATATAAT-ATATTTAAT
1 ATATAATATAATCATATTTAAT
*
1880448 ATATATTATAATCATATTTAAT
1 ATATAATATAATCATATTTAAT
1880470 CTTTTGATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
ATATAATATAATCATATTTAAT
Found at i:1881772 original size:13 final size:12
Alignment explanation
Indices: 1881750--1881795 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
1881740 TAATTAACCA
1881750 TAAAAAATTCAT
1 TAAAAAATTCAT
1881762 TAAAAACATTCAT
1 TAAAAA-ATTCAT
* *
1881775 TAACAAATTCCT
1 TAAAAAATTCAT
*
1881787 AAAAAAATT
1 TAAAAAATT
1881796 AGGTTAAACA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
12 18 0.62
13 11 0.38
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (12 bp):
TAAAAAATTCAT
Found at i:1886931 original size:20 final size:20
Alignment explanation
Indices: 1886862--1886932 Score: 56
Period size: 20 Copynumber: 3.5 Consensus size: 20
1886852 TATAAATATC
*
1886862 TTATAAT-TTATATAATATGAA
1 TTATAATATTTTA-AATAT-AA
*
1886883 TTATTAATATATTAAATAT-A
1 TTA-TAATATTTTAAATATAA
* *
1886903 TAAAAAATATTTTAAATATAA
1 T-TATAATATTTTAAATATAA
1886924 TTATAATAT
1 TTATAATAT
1886933 GGTAAAATAT
Statistics
Matches: 39, Mismatches: 7, Indels: 9
0.71 0.13 0.16
Matches are distributed among these distances:
20 21 0.54
21 6 0.15
22 9 0.23
23 3 0.08
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (20 bp):
TTATAATATTTTAAATATAA
Found at i:1890582 original size:19 final size:17
Alignment explanation
Indices: 1890549--1890583 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 17
1890539 TATGTAAAAA
1890549 ATTATTTTTATATTAAT
1 ATTATTTTTATATTAAT
1890566 ATTATATTTTATAATTAA
1 ATTAT-TTTTAT-ATTAA
1890584 ATTTAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 6 0.38
19 5 0.31
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTATTTTTATATTAAT
Found at i:1897520 original size:22 final size:22
Alignment explanation
Indices: 1897494--1897538 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
1897484 TTTTATGATA
1897494 TTAT-TTTATT-A-AAAAATTAT
1 TTATATTTATTGATAAAAATT-T
1897514 TTATATTTATTGATAAAAATTT
1 TTATATTTATTGATAAAAATTT
1897536 TTA
1 TTA
1897539 ATAAAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.18
21 6 0.27
22 5 0.23
23 7 0.32
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TTATATTTATTGATAAAAATTT
Found at i:1898342 original size:20 final size:20
Alignment explanation
Indices: 1898317--1898361 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1898307 ATATTATTTA
*
1898317 TAAATTTAAAAAAAAATATT
1 TAAATTTAAAAAAAAATAAT
* *
1898337 TAAATTTAAATAAAATTAAT
1 TAAATTTAAAAAAAAATAAT
1898357 TAAAT
1 TAAAT
1898362 ATTTATTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAATTTAAAAAAAAATAAT
Found at i:1898417 original size:37 final size:34
Alignment explanation
Indices: 1898332--1898417 Score: 86
Period size: 37 Copynumber: 2.4 Consensus size: 34
1898322 TTAAAAAAAA
**
1898332 ATATTTA-AATTTAAATAAAATTAATTAAATATTT
1 ATATTTATAA-TTAAATAAAATTAAAAAAATATTT
*
1898366 AT-TTTATTATTTAAAGTAAAATATAAAAAATATATTT
1 ATATTTA-TAATTAAA-TAAAAT-TAAAAAA-ATATTT
1898403 ATATTTATAATTAAA
1 ATATTTATAATTAAA
1898418 ATTAAATAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
33 4 0.10
34 7 0.17
35 7 0.17
36 5 0.12
37 15 0.36
38 4 0.10
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (34 bp):
ATATTTATAATTAAATAAAATTAAAAAAATATTT
Found at i:1898425 original size:37 final size:36
Alignment explanation
Indices: 1898360--1898429 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 36
1898350 AATTAATTAA
* *
1898360 ATATTTATTTTATTATTTAAAGTAAAATATAAAAAAT
1 ATATTTATTTTATTAATTAAAATAAAATA-AAAAAAT
*
1898397 ATATTTATATTTA-TAATTAAAATTAAATAAAAA
1 ATATTTAT-TTTATTAATTAAAATAAAATAAAAA
1898430 TAAATTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
36 4 0.14
37 21 0.72
38 4 0.14
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (36 bp):
ATATTTATTTTATTAATTAAAATAAAATAAAAAAAT
Found at i:1899378 original size:15 final size:15
Alignment explanation
Indices: 1899358--1899390 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1899348 TTGCAAATAA
1899358 TTTTT-AATCTTTAAT
1 TTTTTAAAT-TTTAAT
1899373 TTTTTAAATTTTAAT
1 TTTTTAAATTTTAAT
1899388 TTT
1 TTT
1899391 AATTTAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 14 0.82
16 3 0.18
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTTAAATTTTAAT
Found at i:1899406 original size:12 final size:11
Alignment explanation
Indices: 1899360--1899409 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 11
1899350 GCAAATAATT
1899360 TTTAATCTTTAA
1 TTTAAT-TTTAA
*
1899372 TTT--TTTAAA
1 TTTAATTTTAA
1899381 TTTTAATTTTAA
1 -TTTAATTTTAA
1899393 TTTAATTTTCAA
1 TTTAATTTT-AA
1899405 TTTAA
1 TTTAA
1899410 AAATTAAGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
9 4 0.12
10 4 0.12
11 9 0.28
12 15 0.47
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTAATTTTAA
Found at i:1900613 original size:18 final size:18
Alignment explanation
Indices: 1900572--1900621 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
1900562 TTATTTTATT
1900572 TAAATTTAATTATAAAATA
1 TAAATTTAA-TATAAAATA
1900591 TAAATATTAATATAAAA-A
1 TAAAT-TTAATATAAAATA
1900609 TAAATTTTAATAT
1 TAAA-TTTAATAT
1900622 TTTAATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 12 0.41
19 13 0.45
20 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAATTTAATATAAAATA
Found at i:1900704 original size:9 final size:9
Alignment explanation
Indices: 1900692--1900726 Score: 52
Period size: 9 Copynumber: 3.7 Consensus size: 9
1900682 AAAACAAGTA
1900692 AATTATTTT
1 AATTATTTT
1900701 AATTATTTT
1 AATTATTTT
1900710 AATTATATTT
1 AATTAT-TTT
1900720 AAATTAT
1 -AATTAT
1900727 AAACATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 15 0.62
10 3 0.12
11 6 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
AATTATTTT
Found at i:1901119 original size:26 final size:27
Alignment explanation
Indices: 1901090--1901178 Score: 89
Period size: 27 Copynumber: 3.4 Consensus size: 27
1901080 AATAAAAATA
*
1901090 AAAATTATTCAA-TTATATTTATATTT
1 AAAATTATTAAAGTTATATTTATATTT
1901116 AAAATTATTAAAGTTATATTTATA-TT
1 AAAATTATTAAAGTTATATTTATATTT
* * * *
1901142 -AAA-TAATAAA-TTACATTTATGTTG
1 AAAATTATTAAAGTTATATTTATATTT
1901166 AATAATTATTAAA
1 AA-AATTATTAAA
1901179 AATTATTAAC
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
23 9 0.17
24 7 0.13
25 4 0.08
26 15 0.29
27 17 0.33
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (27 bp):
AAAATTATTAAAGTTATATTTATATTT
Found at i:1901160 original size:23 final size:23
Alignment explanation
Indices: 1901100--1901171 Score: 72
Period size: 23 Copynumber: 3.0 Consensus size: 23
1901090 AAAATTATTC
*
1901100 AATTATATTTATATTTAAAATTATTA
1 AATTATATTTATA-TT-AAA-TAATA
1901126 AAGTTATATTTATATTAAATAATA
1 AA-TTATATTTATATTAAATAATA
* * *
1901150 AATTACATTTATGTTGAATAAT
1 AATTATATTTATATTAAATAAT
1901172 TATTAAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
23 17 0.41
24 6 0.15
25 3 0.07
26 4 0.10
27 11 0.27
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (23 bp):
AATTATATTTATATTAAATAATA
Found at i:1901262 original size:27 final size:27
Alignment explanation
Indices: 1901232--1901296 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
1901222 ATAATAAAAA
1901232 ATATATAAAAAATTA-AAAAT-TATATTT
1 ATAT-TAAAAAATTACAAAATAT-TATTT
*
1901259 ATATT-AATAATTATCAAAATATTATTT
1 ATATTAAAAAATTA-CAAAATATTATTT
1901286 ATATTAAAAAA
1 ATATTAAAAAA
1901297 AAAGAGTTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
25 7 0.22
26 1 0.03
27 19 0.59
28 5 0.16
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (27 bp):
ATATTAAAAAATTACAAAATATTATTT
Found at i:1901524 original size:18 final size:18
Alignment explanation
Indices: 1901503--1901613 Score: 57
Period size: 18 Copynumber: 5.7 Consensus size: 18
1901493 AAAATAATAT
1901503 AAATATAAAAATATTTTA
1 AAATATAAAAATATTTTA
1901521 AAAT-TAATATAATGTAAATTATTA
1 AAATATAA-A-AA--T--ATT-TTA
* *
1901545 ATATATAAAAAT-TTATA
1 AAATATAAAAATATTTTA
*
1901562 TAAATAT-AAAATAATTTA
1 -AAATATAAAAATATTTTA
**
1901580 AAATATAATTATAATATAATA
1 AAATATAA--A-AATATTTTA
1901601 AAATATAAAAATA
1 AAATATAAAAATA
1901614 AATAATCAAA
Statistics
Matches: 71, Mismatches: 8, Indels: 28
0.66 0.07 0.26
Matches are distributed among these distances:
17 16 0.23
18 20 0.28
19 3 0.04
20 1 0.01
21 16 0.23
23 5 0.07
24 7 0.10
25 3 0.04
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (18 bp):
AAATATAAAAATATTTTA
Found at i:1901528 original size:28 final size:28
Alignment explanation
Indices: 1901492--1901598 Score: 76
Period size: 28 Copynumber: 3.7 Consensus size: 28
1901482 ATATTCTATA
*
1901492 AAAAATAATATAAATATAAAAATATTTT
1 AAAATTAATATAAATATAAAAATATTTT
* * *
1901520 AAAATTAATAT-AATGTAAATTATTAATATATA
1 AAAATTAATATAAATAT-AA--A--AATATTTT
* *
1901552 AAAATTTATATAAATAT-AAAATAATTT
1 AAAATTAATATAAATATAAAAATATTTT
1901579 AAAATATAAT-TATAATATAA
1 AAAAT-TAATATA-AATATAA
1901599 TAAAATATAA
Statistics
Matches: 60, Mismatches: 10, Indels: 17
0.69 0.11 0.20
Matches are distributed among these distances:
27 16 0.27
28 20 0.33
29 2 0.03
30 1 0.02
31 1 0.02
32 16 0.27
33 4 0.07
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (28 bp):
AAAATTAATATAAATATAAAAATATTTT
Found at i:1901585 original size:23 final size:22
Alignment explanation
Indices: 1901559--1901619 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 22
1901549 ATAAAAATTT
1901559 ATATAAATATAAAATAATTTAAA
1 ATATAAATATAAAATAA-TTAAA
* *
1901582 ATATAATTATAATATAA-TAAA
1 ATATAAATATAAAATAATTAAA
*
1901603 ATATAAAAAT-AAATAAT
1 ATATAAATATAAAATAAT
1901620 CAAATCTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
20 5 0.16
21 12 0.38
23 15 0.47
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
ATATAAATATAAAATAATTAAA
Found at i:1901602 original size:21 final size:20
Alignment explanation
Indices: 1901559--1901624 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 20
1901549 ATAAAAATTT
1901559 ATATAAATATAAAATAATTTAAA
1 ATATAAATAT-AAATAA--TAAA
*
1901582 ATATAATTATAATATAATAAA
1 ATATAAATATAA-ATAATAAA
* *
1901603 ATATAAAAATAAATAATCAA
1 ATATAAATATAAATAATAAA
1901623 AT
1 AT
1901625 CTAATTTGCT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
20 9 0.24
21 14 0.37
22 2 0.05
23 13 0.34
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
ATATAAATATAAATAATAAA
Found at i:1902766 original size:24 final size:23
Alignment explanation
Indices: 1902738--1902788 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
1902728 TAACTATAAA
*
1902738 ATTAATATAATCTA-TTAAAACATG
1 ATTAA-ATAATATATTTAAAA-ATG
*
1902762 ATTAACTAATATATTTAAAAATG
1 ATTAAATAATATATTTAAAAATG
1902785 ATTA
1 ATTA
1902789 TTTTATATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 13 0.54
24 11 0.46
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (23 bp):
ATTAAATAATATATTTAAAAATG
Found at i:1905247 original size:27 final size:28
Alignment explanation
Indices: 1905213--1905281 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
1905203 TCTATTGTGG
1905213 AAATGAAGGGAGCCTA-TTTGATCATGA
1 AAATGAAGGGAGCCTAGTTTGATCATGA
*
1905240 AAATGAAGGGAGCC-AGTTTGATCATGC
1 AAATGAAGGGAGCCTAGTTTGATCATGA
*
1905267 AAATGAAGGTAGCCT
1 AAATGAAGGGAGCCT
1905282 TTGTGCTCAG
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
26 1 0.03
27 37 0.97
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.23
Consensus pattern (28 bp):
AAATGAAGGGAGCCTAGTTTGATCATGA
Found at i:1909105 original size:17 final size:18
Alignment explanation
Indices: 1909065--1909108 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
1909055 TTGTAACCTT
*
1909065 ATAATAAAAATAATGATA
1 ATAATAAAAATAATCATA
1909083 ATAATAAAAA-AATCAT-
1 ATAATAAAAATAATCATA
1909099 ATCAATAAAA
1 AT-AATAAAA
1909109 TCTTTTTGCC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 2 0.08
17 12 0.50
18 10 0.42
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (18 bp):
ATAATAAAAATAATCATA
Found at i:1909350 original size:20 final size:20
Alignment explanation
Indices: 1909288--1909351 Score: 56
Period size: 24 Copynumber: 3.0 Consensus size: 20
1909278 TATTTATATT
* *
1909288 TAAAAATAATTATAAAAATTT
1 TAAAAATAATAATAAAAA-TA
1909309 TAAATTAATTAATAAGTAAAAATA
1 TAAA--AA-TAATAA-TAAAAATA
*
1909333 TAAAAATAATCATAAAAAT
1 TAAAAATAATAATAAAAAT
1909352 TAATTTATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
20 7 0.19
21 9 0.25
22 2 0.06
23 2 0.06
24 10 0.28
25 6 0.17
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (20 bp):
TAAAAATAATAATAAAAATA
Found at i:1909795 original size:29 final size:28
Alignment explanation
Indices: 1909734--1909796 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
1909724 TAGAATGGTT
* *
1909734 TTTAAATTTTTTTTTATAATTTAAAAAA
1 TTTATATTTTTTTTCATAATTTAAAAAA
* * *
1909762 ATTATATTTTTTATTCATATTTTAAAATA
1 TTTATATTTTTT-TTCATAATTTAAAAAA
1909791 TTTATA
1 TTTATA
1909797 ACTATATATA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
28 10 0.36
29 18 0.64
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (28 bp):
TTTATATTTTTTTTCATAATTTAAAAAA
Found at i:1910110 original size:21 final size:21
Alignment explanation
Indices: 1910086--1910146 Score: 56
Period size: 21 Copynumber: 2.9 Consensus size: 21
1910076 ATTTAAAATT
1910086 TTATTTATATAAAAATTATAA
1 TTATTTATATAAAAATTATAA
*
1910107 TTATATTAT-T-AAATTTAATAA
1 TTAT-TTATATAAAAATT-ATAA
1910128 TTAATTTA-ATAAAATATTA
1 TT-ATTTATATAAAA-ATTA
1910147 ACTGTATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 11
0.71 0.04 0.24
Matches are distributed among these distances:
20 5 0.16
21 15 0.47
22 10 0.31
23 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTATTTATATAAAAATTATAA
Found at i:1911981 original size:13 final size:14
Alignment explanation
Indices: 1911965--1911994 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1911955 TCAATTATTA
1911965 AAAATAATT-AAAT
1 AAAATAATTGAAAT
1911978 AAAATAATTGAAAT
1 AAAATAATTGAAAT
1911992 AAA
1 AAA
1911995 TTTATATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (14 bp):
AAAATAATTGAAAT
Found at i:1913820 original size:43 final size:43
Alignment explanation
Indices: 1913773--1913859 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 43
1913763 TTTTTATTTT
* * *
1913773 TGTAAAATTGAGTACTCTGTTATCGGATTAATTATAAACTAAA
1 TGTAAAATTGAGTACTCTATCATCAGATTAATTATAAACTAAA
* *
1913816 TGTAAAATTGAGTACTCTATCATCATATTAATTATAAGCTAAA
1 TGTAAAATTGAGTACTCTATCATCAGATTAATTATAAACTAAA
1913859 T
1 T
1913860 TATTTTTAGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.38
Consensus pattern (43 bp):
TGTAAAATTGAGTACTCTATCATCAGATTAATTATAAACTAAA
Found at i:1914072 original size:165 final size:165
Alignment explanation
Indices: 1913800--1914299 Score: 973
Period size: 165 Copynumber: 3.0 Consensus size: 165
1913790 TGTTATCGGA
*
1913800 TTAATTATAAACTAAATGTAAAATTGAGTACTCTATCATCATATTAATTATAAGCTAAATTATTT
1 TTAATTATAAACTAAATGTAAAATTGAGTACTCTGTCATCATATTAATTATAAGCTAAATTATTT
1913865 TTAGATTAAAAGTTATTAAAATTTGGTATTTGTTTAACTACATTTTGCATTATTTATTTATCTTT
66 TTAGATTAAAAGTTATTAAAATTTGGTATTTGTTTAACTACATTTTGCATTATTTATTTATCTTT
1913930 ATTGCATTATCAATTATTAGATTAGGTACCAACAC
131 ATTGCATTATCAATTATTAGATTAGGTACCAACAC
1913965 TTAATTATAAACTAAATGTAAAATTGAGTACTCTGTCATCATATTAATTATAAGCTAAATTATTT
1 TTAATTATAAACTAAATGTAAAATTGAGTACTCTGTCATCATATTAATTATAAGCTAAATTATTT
*
1914030 TTAGATTAAAAGTTATTAAATTTTGGTATTTGTTTAACTACATTTTGCATTATTTATTTATCTTT
66 TTAGATTAAAAGTTATTAAAATTTGGTATTTGTTTAACTACATTTTGCATTATTTATTTATCTTT
1914095 ATTGCATTATCAATTATTAGATTAGGTACCAACAC
131 ATTGCATTATCAATTATTAGATTAGGTACCAACAC
*
1914130 TTAATTATAAACTAAATGTAAAATTAAGTACTCTGTCATCATATTAATTATAAGCTAAATTATTT
1 TTAATTATAAACTAAATGTAAAATTGAGTACTCTGTCATCATATTAATTATAAGCTAAATTATTT
1914195 TTAGATTAAAAGTTATTAAAATTTGGTATTTGTTTAACTACATTTTGCATTATTTATTTATCTTT
66 TTAGATTAAAAGTTATTAAAATTTGGTATTTGTTTAACTACATTTTGCATTATTTATTTATCTTT
1914260 ATTGCATTATCAATTATTAGATTAGGTACCAACAC
131 ATTGCATTATCAATTATTAGATTAGGTACCAACAC
1914295 TTAAT
1 TTAAT
1914300 CGCTTCATGT
Statistics
Matches: 331, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
165 331 1.00
ACGTcount: A:0.37, C:0.10, G:0.09, T:0.45
Consensus pattern (165 bp):
TTAATTATAAACTAAATGTAAAATTGAGTACTCTGTCATCATATTAATTATAAGCTAAATTATTT
TTAGATTAAAAGTTATTAAAATTTGGTATTTGTTTAACTACATTTTGCATTATTTATTTATCTTT
ATTGCATTATCAATTATTAGATTAGGTACCAACAC
Found at i:1914652 original size:4 final size:4
Alignment explanation
Indices: 1914643--1914677 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
1914633 AACAATTTCA
*
1914643 AAAT AAAT AAAT AACT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1914678 AGAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:1915452 original size:3 final size:3
Alignment explanation
Indices: 1915444--1915478 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
1915434 AAGATTTATG
*
1915444 ATA ATA ATA ATA ATA ATA AT- ATA ATA TTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1915479 TTTTCATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:1915528 original size:33 final size:34
Alignment explanation
Indices: 1915472--1915538 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 34
1915462 ATATAATATT
* *
1915472 AATAATATTTTCATTTAATATATTAAAAATAATA
1 AATAATATTGTCAATTAATATATTAAAAATAATA
* * *
1915506 AATAA-ATTGTCAATTATTATATTTAATATAATA
1 AATAATATTGTCAATTAATATATTAAAAATAATA
1915539 TTATTATAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 23 0.82
34 5 0.18
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (34 bp):
AATAATATTGTCAATTAATATATTAAAAATAATA
Found at i:1915570 original size:22 final size:20
Alignment explanation
Indices: 1915518--1915555 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1915508 TAAATTGTCA
**
1915518 ATTATTATATTTAATATAAT
1 ATTATTATAAATAATATAAT
1915538 ATTATTATAAATAATATA
1 ATTATTATAAATAATATA
1915556 TTAATTAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTATTATAAATAATATAAT
Found at i:1916134 original size:22 final size:22
Alignment explanation
Indices: 1916100--1916161 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
1916090 TATAAATAAT
*
1916100 AATATATAATTTATTTTTAATTA
1 AATAT-TAATTTATTTATAATTA
* *
1916123 AATATTAATTTATTCAATAATTT
1 AATATTAATTTATT-TATAATTA
1916146 AAT-TTAATTTATTTAT
1 AATATTAATTTATTTAT
1916162 TTAATCAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
21 2 0.06
22 19 0.56
23 13 0.38
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
AATATTAATTTATTTATAATTA
Found at i:1917446 original size:18 final size:20
Alignment explanation
Indices: 1917410--1917451 Score: 61
Period size: 18 Copynumber: 2.1 Consensus size: 20
1917400 GAGGCAGTGC
1917410 CGGTGGTGGAGGGCATGGTGG
1 CGGTGGTGGAGGG-ATGGTGG
1917431 CGGTGG-GGAGGG-TGGTGG
1 CGGTGGTGGAGGGATGGTGG
1917449 CGG
1 CGG
1917452 ACTTTGTGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.43
20 6 0.29
21 6 0.29
ACGTcount: A:0.07, C:0.10, G:0.67, T:0.17
Consensus pattern (20 bp):
CGGTGGTGGAGGGATGGTGG
Found at i:1918799 original size:2 final size:2
Alignment explanation
Indices: 1918792--1918823 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1918782 TTAAATACAA
1918792 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
1918824 TTGATTCTTT
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:1919150 original size:22 final size:22
Alignment explanation
Indices: 1919124--1919198 Score: 55
Period size: 22 Copynumber: 3.2 Consensus size: 22
1919114 AAAACATGGT
1919124 ATAATTGAAGAATAACTAAAAA
1 ATAATTGAAGAATAACTAAAAA
*
1919146 ATAATATG-AGAAAAAC-AAAACA
1 ATAAT-TGAAGAATAACTAAAA-A
* *
1919168 TGGTATAATTAAAGAATAATTAAAAA
1 ----ATAATTGAAGAATAACTAAAAA
1919194 ATAAT
1 ATAAT
1919199 ATGGGTTTCC
Statistics
Matches: 41, Mismatches: 4, Indels: 16
0.67 0.07 0.26
Matches are distributed among these distances:
21 4 0.10
22 18 0.44
23 2 0.05
25 1 0.02
26 12 0.29
27 4 0.10
ACGTcount: A:0.63, C:0.04, G:0.09, T:0.24
Consensus pattern (22 bp):
ATAATTGAAGAATAACTAAAAA
Found at i:1919171 original size:48 final size:47
Alignment explanation
Indices: 1919107--1919201 Score: 163
Period size: 48 Copynumber: 2.0 Consensus size: 47
1919097 TTTTATTTTA
*
1919107 AGAAAAAAAAACATGGTATAATTGAAGAATAACTAAAAAATAATATG
1 AGAAAAAAAAACATGGTATAATTAAAGAATAACTAAAAAATAATATG
*
1919154 AGAAAAACAAAACATGGTATAATTAAAGAATAATTAAAAAATAATATG
1 AGAAAAA-AAAACATGGTATAATTAAAGAATAACTAAAAAATAATATG
1919202 GGTTTCCCTA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
47 7 0.16
48 38 0.84
ACGTcount: A:0.62, C:0.04, G:0.12, T:0.22
Consensus pattern (47 bp):
AGAAAAAAAAACATGGTATAATTAAAGAATAACTAAAAAATAATATG
Found at i:1920454 original size:17 final size:16
Alignment explanation
Indices: 1920416--1920454 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1920406 AAATTTAATT
1920416 TTAAATTATTTTAAAA
1 TTAAATTATTTTAAAA
*
1920432 TTAAATTATTTTTAAA
1 TTAAATTATTTTAAAA
1920448 TTCAAAT
1 TT-AAAT
1920455 CGTTTTAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (16 bp):
TTAAATTATTTTAAAA
Found at i:1921855 original size:17 final size:17
Alignment explanation
Indices: 1921835--1921873 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1921825 TTATATTTTA
1921835 ATTTAA-AATTTTAATAT
1 ATTTAATAA-TTTAATAT
*
1921852 ATTTAATAATTTATTAT
1 ATTTAATAATTTAATAT
1921869 ATTTA
1 ATTTA
1921874 TGTTTACATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 18 0.90
18 2 0.10
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTAATAATTTAATAT
Found at i:1921874 original size:9 final size:9
Alignment explanation
Indices: 1921810--1921873 Score: 52
Period size: 9 Copynumber: 7.9 Consensus size: 9
1921800 ATTAATGTGG
1921810 TATATTTAA
1 TATATTTAA
*
1921819 TATA--TAT
1 TATATTTAA
1921826 TATATTT--
1 TATATTTAA
1921833 TA-ATTTAA
1 TATATTTAA
*
1921841 AAT-TTTAA
1 TATATTTAA
1921849 TATATTTAA
1 TATATTTAA
*
1921858 TA-ATTTAT
1 TATATTTAA
1921866 TATATTTA
1 TATATTTA
1921874 TGTTTACATA
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
6 4 0.09
7 8 0.18
8 15 0.34
9 17 0.39
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
TATATTTAA
Found at i:1923525 original size:18 final size:18
Alignment explanation
Indices: 1923504--1923573 Score: 62
Period size: 18 Copynumber: 4.1 Consensus size: 18
1923494 ATCAAAATTT
1923504 ATATATTATAAATTATTA
1 ATATATTATAAATTATTA
1923522 ATATATTA-AAA-T-TT-
1 ATATATTATAAATTATTA
1923536 ATATA-TAT-AATATATTTA
1 ATATATTATAAAT-TA-TTA
*
1923554 ATATGATTATAATTTATTA
1 ATAT-ATTATAAATTATTA
1923573 A
1 A
1923574 AATAATCAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 17
0.70 0.02 0.28
Matches are distributed among these distances:
13 4 0.10
14 5 0.12
15 3 0.07
16 1 0.02
17 5 0.12
18 12 0.29
19 5 0.12
20 5 0.12
21 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (18 bp):
ATATATTATAAATTATTA
Found at i:1923533 original size:32 final size:33
Alignment explanation
Indices: 1923497--1923570 Score: 100
Period size: 32 Copynumber: 2.3 Consensus size: 33
1923487 TAAATTTATC
1923497 AAAATTTATATATTATAA-AT-TATTAATAT-ATT
1 AAAATTTATATA-TATAATATAT-TTAATATGATT
1923529 AAAATTTATATATATAATATATTTAATATGATT
1 AAAATTTATATATATAATATATTTAATATGATT
*
1923562 ATAATTTAT
1 AAAATTTAT
1923571 TAAAATAATC
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
31 5 0.13
32 21 0.55
33 12 0.32
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (33 bp):
AAAATTTATATATATAATATATTTAATATGATT
Found at i:1923541 original size:16 final size:16
Alignment explanation
Indices: 1923497--1923570 Score: 57
Period size: 16 Copynumber: 4.6 Consensus size: 16
1923487 TAAATTTATC
1923497 AAAATTTATATAT-TAT
1 AAAATTTATATATAT-T
*
1923513 AAATTATTA-ATATATT
1 AAAAT-TTATATATATT
1923529 AAAATTTATATATA-T
1 AAAATTTATATATATT
1923544 AATATATTTA-ATATGATT
1 AA-A-ATTTATATAT-ATT
*
1923562 ATAATTTAT
1 AAAATTTAT
1923571 TAAAATAATC
Statistics
Matches: 47, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
15 6 0.13
16 28 0.60
17 11 0.23
18 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (16 bp):
AAAATTTATATATATT
Found at i:1923712 original size:18 final size:18
Alignment explanation
Indices: 1923686--1923734 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
1923676 TTTAATAAGA
* *
1923686 TATACAAAAATTAAAAGT
1 TATAAAAAAATTAAAACT
*
1923704 TATAAAAAAATAAAAACT
1 TATAAAAAAATTAAAACT
*
1923722 TTTAAAAAAATTA
1 TATAAAAAAATTA
1923735 TAAATAAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (18 bp):
TATAAAAAAATTAAAACT
Found at i:1927407 original size:17 final size:17
Alignment explanation
Indices: 1927387--1927419 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1927377 ATTTTAAAAA
*
1927387 TTATTTTTAATTATTTT
1 TTATTCTTAATTATTTT
1927404 TTATTCTTAATTATTT
1 TTATTCTTAATTATTT
1927420 CAAATAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (17 bp):
TTATTCTTAATTATTTT
Found at i:1928830 original size:19 final size:22
Alignment explanation
Indices: 1928783--1928836 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 22
1928773 AATTTTTATT
1928783 TAAA-TTTAATTATAAAAATATA
1 TAAATTTTAA-TATAAAAATATA
1928805 TAAATTTTAATAT-AAAA-ATA
1 TAAATTTTAATATAAAAATATA
1928825 -AAATTTTAATAT
1 TAAATTTTAATAT
1928837 TTTTAAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 12 0.39
20 3 0.10
21 4 0.13
22 7 0.23
23 5 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TAAATTTTAATATAAAAATATA
Found at i:1931012 original size:40 final size:41
Alignment explanation
Indices: 1930936--1931021 Score: 122
Period size: 42 Copynumber: 2.1 Consensus size: 41
1930926 TAATGCTTTT
*
1930936 AAAAAATTTCTCCTTCTTTTTGTTATCTCTTACAAATTTTAC
1 AAAAAATTTCTCCTCCTTTTTGTTATCTC-TACAAATTTTAC
*
1930978 AAAAAATTTCT-CTCCCTTTTTGTTATCTC-CCAAATTTTAC
1 AAAAAATTTCTCCT-CCTTTTTGTTATCTCTACAAATTTTAC
1931018 AAAA
1 AAAA
1931022 TTTTCACAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
40 14 0.34
41 2 0.05
42 25 0.61
ACGTcount: A:0.31, C:0.21, G:0.02, T:0.45
Consensus pattern (41 bp):
AAAAAATTTCTCCTCCTTTTTGTTATCTCTACAAATTTTAC
Found at i:1935247 original size:16 final size:19
Alignment explanation
Indices: 1935221--1935285 Score: 57
Period size: 18 Copynumber: 3.6 Consensus size: 19
1935211 TATTAAATTT
1935221 AATATTTAATT-TAT-TAA
1 AATATTTAATTATATATAA
1935238 AATA-TTAATTATATATAA
1 AATATTTAATTATATATAA
* **
1935256 AAT-TATAAAAATATATAA
1 AATATTTAATTATATATAA
* *
1935274 ATTAATTAATTA
1 AATATTTAATTA
1935286 ATTAATATAA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
16 6 0.17
17 7 0.19
18 19 0.53
19 4 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AATATTTAATTATATATAA
Found at i:1936895 original size:23 final size:22
Alignment explanation
Indices: 1936868--1936913 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
1936858 ACATGTATTT
1936868 TAATTTAATTTACAATTTATAAA
1 TAATTTAATTTAC-ATTTATAAA
** *
1936891 TAATTTTTTTTACTTTTATAAA
1 TAATTTAATTTACATTTATAAA
1936913 T
1 T
1936914 TAAAAATCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (22 bp):
TAATTTAATTTACATTTATAAA
Found at i:1936981 original size:15 final size:16
Alignment explanation
Indices: 1936957--1936999 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
1936947 TTTATTAAAA
1936957 ATAT-TTATTATAATT
1 ATATATTATTATAATT
*
1936972 ATA-ATTATTATTATT
1 ATATATTATTATAATT
*
1936987 ATATTTTATTATA
1 ATATATTATTATA
1937000 CAAAATGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATATATTATTATAATT
Found at i:1939693 original size:5 final size:5
Alignment explanation
Indices: 1939673--1939792 Score: 54
Period size: 5 Copynumber: 24.2 Consensus size: 5
1939663 TATTCAAACT
* * * **
1939673 AATT- AATTA AATTTA AATTA AATCA AATTTA AAATA AAATA TTTTA AATTTA
1 AATTA AATTA AA-TTA AATTA AATTA AA-TTA AATTA AATTA AATTA AA-TTA
* * * * *
1939725 TATT- AATGTA ATTTA ATTTA AATTA TATTT AA-TA AA-TA AA--A AATTA
1 AATTA AAT-TA AATTA AATTA AATTA AATTA AATTA AATTA AATTA AATTA
*
1939771 ACTTA AATTTA AATTA AATTA A
1 AATTA AA-TTA AATTA AATTA A
1939793 TAAAAAATTT
Statistics
Matches: 89, Mismatches: 18, Indels: 17
0.72 0.15 0.14
Matches are distributed among these distances:
3 3 0.03
4 13 0.15
5 53 0.60
6 20 0.22
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (5 bp):
AATTA
Found at i:1939800 original size:32 final size:31
Alignment explanation
Indices: 1939737--1939801 Score: 85
Period size: 32 Copynumber: 2.1 Consensus size: 31
1939727 TTAATGTAAT
* * *
1939737 TTAATTTAAATTATATTTAATAAATAAAAAA
1 TTAACTTAAATTAAATTAAATAAATAAAAAA
*
1939768 TTAACTTAAATTTAAATTAAATTAATAAAAAA
1 TTAACTTAAA-TTAAATTAAATAAATAAAAAA
1939800 TT
1 TT
1939802 TATTAATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 9 0.31
32 20 0.69
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (31 bp):
TTAACTTAAATTAAATTAAATAAATAAAAAA
Found at i:1940314 original size:2 final size:2
Alignment explanation
Indices: 1940307--1940331 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1940297 AGAATCTGTA
1940307 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1940332 ATTGGTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1943873 original size:31 final size:31
Alignment explanation
Indices: 1943799--1943860 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
1943789 TATGCCAAAC
1943799 CCATGAAATAAAAATGAAAAAGAAATATCCA
1 CCATGAAATAAAAATGAAAAAGAAATATCCA
1943830 CCATGAAATAAAAATGAAAAAGAAATATCCA
1 CCATGAAATAAAAATGAAAAAGAAATATCCA
1943861 ATCATACATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.61, C:0.13, G:0.10, T:0.16
Consensus pattern (31 bp):
CCATGAAATAAAAATGAAAAAGAAATATCCA
Found at i:1946677 original size:17 final size:16
Alignment explanation
Indices: 1946655--1946704 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 16
1946645 ACGTCAAATT
1946655 TAAATATATCTTTTATA
1 TAAATATAT-TTTTATA
*
1946672 TAAATATATTTATT-TT
1 TAAATATATTT-TTATA
1946688 TAAA-ATATTTTTATA
1 TAAATATATTTTTATA
1946703 TA
1 TA
1946705 TTTAAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
14 2 0.07
15 9 0.31
16 7 0.24
17 11 0.38
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (16 bp):
TAAATATATTTTTATA
Found at i:1946710 original size:19 final size:17
Alignment explanation
Indices: 1946673--1946716 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1946663 TCTTTTATAT
*
1946673 AAATATATTTATTTTTA
1 AAATATTTTTATTTTTA
1946690 AAATATTTTTATATATTTA
1 AAATATTTTTAT-T-TTTA
*
1946709 AAAAATTT
1 AAATATTT
1946717 ATAAAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 11 0.48
18 1 0.04
19 11 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
AAATATTTTTATTTTTA
Found at i:1947179 original size:12 final size:12
Alignment explanation
Indices: 1947162--1947198 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1947152 TGGTCCTGAT
1947162 ATATATACATAC
1 ATATATACATAC
1947174 ATATATAC--AC
1 ATATATACATAC
*
1947184 ACATATACATAC
1 ATATATACATAC
1947196 ATA
1 ATA
1947199 CACACACGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
10 9 0.43
12 12 0.57
ACGTcount: A:0.51, C:0.19, G:0.00, T:0.30
Consensus pattern (12 bp):
ATATATACATAC
Found at i:1947193 original size:18 final size:18
Alignment explanation
Indices: 1947170--1947204 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1947160 ATATATATAC
*
1947170 ATACATATATACACACAT
1 ATACATACATACACACAT
1947188 ATACATACATACACACA
1 ATACATACATACACACA
1947205 CGAAAAGAAT
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:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (18 bp):
ATACATACATACACACAT
Found at i:1947205 original size:22 final size:22
Alignment explanation
Indices: 1947164--1947205 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1947154 GTCCTGATAT
* *
1947164 ATATACATACATATATACACAC
1 ATATACATACATACACACACAC
1947186 ATATACATACATACACACAC
1 ATATACATACATACACACAC
1947206 GAAAAGAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (22 bp):
ATATACATACATACACACACAC
Found at i:1947269 original size:20 final size:17
Alignment explanation
Indices: 1947246--1947291 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 17
1947236 TTTTAAATTT
1947246 TATAAAAATAATATATTAAA
1 TATAAAAATAAT-TA--AAA
1947266 TATAAAAA-AATTAAAA
1 TATAAAAATAATTAAAA
1947282 TA-AAAAATAA
1 TATAAAAATAA
1947292 AAAATTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 5 0.20
16 7 0.28
18 2 0.08
19 3 0.12
20 8 0.32
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
TATAAAAATAATTAAAA
Found at i:1947284 original size:14 final size:15
Alignment explanation
Indices: 1947260--1947288 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1947250 AAAATAATAT
1947260 ATTAAATATAAAAAA
1 ATTAAATATAAAAAA
1947275 ATTAAA-ATAAAAAA
1 ATTAAATATAAAAAA
1947289 TAAAAAATTT
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
ATTAAATATAAAAAA
Found at i:1949824 original size:2 final size:2
Alignment explanation
Indices: 1949819--1949849 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1949809 AAAGAAAAAA
*
1949819 AG AG AG AG AG AG AA 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 A
1949850 AAAAGATTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1950975 original size:18 final size:17
Alignment explanation
Indices: 1950937--1951001 Score: 61
Period size: 17 Copynumber: 4.0 Consensus size: 17
1950927 AAATTAACGT
1950937 AATTTATAT-AATA-AA
1 AATTTATATAAATATAA
1950952 AA-TTAT-TAAAATATTAA
1 AATTTATAT-AAATA-TAA
1950969 AATTTATATAAATATAA
1 AATTTATATAAATATAA
1950986 AATATT-T-TAAATATAA
1 AAT-TTATATAAATATAA
1951002 TTATAATATA
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 1 0.02
14 4 0.09
15 6 0.14
16 9 0.21
17 11 0.26
18 11 0.26
19 1 0.02
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTTATATAAATATAA
Found at i:1951018 original size:22 final size:21
Alignment explanation
Indices: 1950974--1951027 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
1950964 ATTAAAATTT
* *
1950974 ATATAAATATAAAATATTTTAA
1 ATAT-AATATAAAATAATATAA
*
1950996 ATATAATTATAATATAATATAA
1 ATATAA-TATAAAATAATATAA
1951018 ATA-AATATAA
1 ATATAATATAA
1951028 CGTAAAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 5 0.18
21 4 0.14
22 19 0.68
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
ATATAATATAAAATAATATAA
Found at i:1951146 original size:21 final size:20
Alignment explanation
Indices: 1951117--1951182 Score: 69
Period size: 21 Copynumber: 3.2 Consensus size: 20
1951107 AAATCAAGTT
*
1951117 TTTATAATAAAATTTTATATA
1 TTTAAAATAAAATTTTAT-TA
* *
1951138 TTTAAAATAAGATTTTATTT
1 TTTAAAATAAAATTTTATTA
* *
1951158 TTTAAAATTAAAAATTTATTT
1 TTTAAAA-TAAAATTTTATTA
1951179 TTTA
1 TTTA
1951183 TTTAAAATTA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
20 8 0.21
21 31 0.79
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
TTTAAAATAAAATTTTATTA
Found at i:1952989 original size:23 final size:24
Alignment explanation
Indices: 1952953--1953009 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 24
1952943 GAATACATAA
** *
1952953 ATAATAATAATAAT-TATTATAAT
1 ATAATAATTTTAATATATTAAAAT
*
1952976 TTAATAATTTTAATATATTAAAAT
1 ATAATAATTTTAATATATTAAAAT
1953000 AT-ATAATTTT
1 ATAATAATTTT
1953010 TTAATAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
23 19 0.68
24 9 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
ATAATAATTTTAATATATTAAAAT
Found at i:1953336 original size:7 final size:7
Alignment explanation
Indices: 1953326--1953364 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
1953316 ACACTTACTT
*
1953326 TTTTGTT
1 TTTTGTG
1953333 TTTTGTG
1 TTTTGTG
1953340 TTTTGTG
1 TTTTGTG
1953347 TTTTGTG
1 TTTTGTG
*
1953354 TTTTGCG
1 TTTTGTG
1953361 TTTT
1 TTTT
1953365 TACAGTGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.00, C:0.03, G:0.23, T:0.74
Consensus pattern (7 bp):
TTTTGTG
Found at i:1953512 original size:24 final size:23
Alignment explanation
Indices: 1953460--1953517 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 23
1953450 TTATTGATAT
* ** *
1953460 AAAATTATAATAAAATAACGATT
1 AAAATAATAATAAAATAAAAATA
*
1953483 ATAATAAATAATAAAATAAAAATA
1 AAAAT-AATAATAAAATAAAAATA
1953507 AAAATAATAAT
1 AAAATAATAAT
1953518 TATAATGTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
23 10 0.36
24 18 0.64
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (23 bp):
AAAATAATAATAAAATAAAAATA
Found at i:1953851 original size:21 final size:20
Alignment explanation
Indices: 1953822--1953882 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 20
1953812 ATTTAATTAA
1953822 AAATA-ATTAAAAGATAATAT
1 AAATATATTAAAA-ATAATAT
*
1953842 AAATATATTATAAAT-ATAT
1 AAATATATTAAAAATAATAT
1953861 AAA-ATATTAAAATATATATAT
1 AAATATATTAAAA-ATA-ATAT
1953882 A
1 A
1953883 GTATATAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
18 8 0.23
19 9 0.26
20 7 0.20
21 11 0.31
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (20 bp):
AAATATATTAAAAATAATAT
Found at i:1953887 original size:28 final size:28
Alignment explanation
Indices: 1953842--1953898 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
1953832 AAGATAATAT
1953842 AAATATATTATAAATATATAAAATATTA
1 AAATATATTATAAATATATAAAATATTA
* *
1953870 AAATATA-TATATAGTATATAAATTATTA
1 AAATATATTATA-AATATATAAAATATTA
1953898 A
1 A
1953899 TTTATTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 4 0.15
28 22 0.85
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (28 bp):
AAATATATTATAAATATATAAAATATTA
Found at i:1954236 original size:17 final size:17
Alignment explanation
Indices: 1954210--1954244 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
1954200 AAATTTAAAT
1954210 TTATTAATTT-AATTTC
1 TTATTAATTTAAATTTC
1954226 TTATCTAATTTAAATTTC
1 TTAT-TAATTTAAATTTC
1954244 T
1 T
1954245 CTTGATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 6 0.35
18 7 0.41
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (17 bp):
TTATTAATTTAAATTTC
Found at i:1954397 original size:18 final size:18
Alignment explanation
Indices: 1954376--1954420 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1954366 ACACATATGT
*
1954376 ATTTATATAAAAATATAA
1 ATTTAAATAAAAATATAA
* *
1954394 ATTTAAATAAATATTTAA
1 ATTTAAATAAAAATATAA
1954412 ATTTTAAAT
1 A-TTTAAAT
1954421 TTTTAAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTTAAATAAAAATATAA
Found at i:1954435 original size:15 final size:15
Alignment explanation
Indices: 1954402--1954454 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
1954392 AAATTTAAAT
* *
1954402 AAATATTTAAATTTT
1 AAATATTTAAATATA
* *
1954417 AAATTTTTAAATATC
1 AAATATTTAAATATA
**
1954432 AAATAAATAAATATA
1 AAATATTTAAATATA
1954447 AAATATTT
1 AAATATTT
1954455 TAAAAAATAT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
AAATATTTAAATATA
Found at i:1954462 original size:23 final size:25
Alignment explanation
Indices: 1954436--1954482 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
1954426 AATATCAAAT
1954436 AAATAAAT-ATAAAATATT-TTAAA
1 AAATAAATAATAAAATATTGTTAAA
* *
1954459 AAATATATAATAAATTATTGTTAA
1 AAATAAATAATAAAATATTGTTAA
1954483 TTAGGTCTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 7 0.35
24 9 0.45
25 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (25 bp):
AAATAAATAATAAAATATTGTTAAA
Found at i:1954648 original size:14 final size:14
Alignment explanation
Indices: 1954629--1954656 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1954619 GTTATAAAAA
1954629 ATTAATATTTTATT
1 ATTAATATTTTATT
1954643 ATTAATATTTTATT
1 ATTAATATTTTATT
1954657 TTATTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTAATATTTTATT
Found at i:1955119 original size:19 final size:20
Alignment explanation
Indices: 1955091--1955141 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
1955081 TATTATAAGA
*
1955091 TAAAAAATTAATAAAT-TAT
1 TAAAATATTAATAAATATAT
1955110 TAAAATATTACATAAATATAT
1 TAAAATATTA-ATAAATATAT
*
1955131 TAATATATTAA
1 TAAAATATTAA
1955142 ATTTTATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 9 0.32
20 7 0.25
21 12 0.43
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
TAAAATATTAATAAATATAT
Found at i:1955164 original size:32 final size:33
Alignment explanation
Indices: 1955121--1955193 Score: 96
Period size: 32 Copynumber: 2.2 Consensus size: 33
1955111 AAAATATTAC
*
1955121 ATAAATATATTAATATATT-AAATTTTATATAAT
1 ATAAATATATTAATATATTAAAATTATAT-TAAT
*
1955154 ATAAAT-TATTAATCTATTAAAATTATATTAAT
1 ATAAATATATTAATATATTAAAATTATATTAAT
1955186 ATATAATA
1 ATA-AATA
1955194 CTTTACATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
32 18 0.51
33 17 0.49
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (33 bp):
ATAAATATATTAATATATTAAAATTATATTAAT
Found at i:1955165 original size:24 final size:25
Alignment explanation
Indices: 1955101--1955165 Score: 69
Period size: 28 Copynumber: 2.5 Consensus size: 25
1955091 TAAAAAATTA
1955101 ATAAATTATTAAAATATTACATAAAT
1 ATAAATTATT-AAATATTACATAAAT
* *
1955127 ATATTAATATATTAAATTTTATAT-AAT
1 ATA--AAT-TATTAAATATTACATAAAT
1955154 ATAAATTATTAA
1 ATAAATTATTAA
1955166 TCTATTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
24 6 0.18
25 3 0.09
26 3 0.09
27 6 0.18
28 12 0.35
29 4 0.12
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
ATAAATTATTAAATATTACATAAAT
Found at i:1955484 original size:10 final size:10
Alignment explanation
Indices: 1955449--1955506 Score: 55
Period size: 10 Copynumber: 5.9 Consensus size: 10
1955439 TTTTTATAAT
*
1955449 TTATATTATA
1 TTATATTTTA
*
1955459 -TAAATTTTA
1 TTATATTTTA
* *
1955468 ATATATTATA
1 TTATATTTTA
1955478 TTATATTTTA
1 TTATATTTTA
*
1955488 TTTTATTTTA
1 TTATATTTTA
*
1955498 TAATATTTT
1 TTATATTTT
1955507 TTAATTTAAT
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
9 7 0.18
10 31 0.82
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TTATATTTTA
Found at i:1955487 original size:20 final size:20
Alignment explanation
Indices: 1955450--1955506 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
1955440 TTTTATAATT
*
1955450 TATATTATA-TAAATTTTAA
1 TATATTATATTATATTTTAA
*
1955469 TATATTATATTATATTTTAT
1 TATATTATATTATATTTTAA
* * *
1955489 TTTATTTTATAATATTTT
1 TATATTATATTATATTTT
1955507 TTAATTTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 9 0.28
20 23 0.72
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TATATTATATTATATTTTAA
Found at i:1955961 original size:152 final size:153
Alignment explanation
Indices: 1955772--1956076 Score: 470
Period size: 152 Copynumber: 2.0 Consensus size: 153
1955762 GGTCTTTTAT
* *
1955772 TTTTATTTTATTTTGTTGTCGATTAATTAATGTTATTTTCGGTACTTGCAAAGGCTAGATTTCAT
1 TTTTATTTTATTTTGGTGTCGATTAATTAATGTTATTTTCGGTACTTGCAAAGGCTAGATTTCAA
* *
1955837 GTACAAAGAT-TTTTTTTGTAATTTATTCGGAAAATTATGATGCTCAATTGCTTTATATT-ATTT
66 GTACAAAGATATATTTTT-TAATTTATTCGGAAAATTATGATGCTCAATTGCTTTATATTAAGTT
1955900 TCAAATACTTTAATAAAAATGTTA
130 TCAAATACTTTAATAAAAATGTTA
* *
1955924 TTTTATTTTATTTTGGTGTCGATTAATTAATGTTATTTTTGGTACTTGTAAAGGCTAGATTTCAA
1 TTTTATTTTATTTTGGTGTCGATTAATTAATGTTATTTTCGGTACTTGCAAAGGCTAGATTTCAA
** * * *
1955989 GTGTAAATATATATTTTTTAATTTATTCTGAAAATTATGATGCTCAGTTGCTTTATATTAAAGTT
66 GTACAAAGATATATTTTTTAATTTATTCGGAAAATTATGATGCTCAATTGCTTTATATT-AAGTT
*
1956054 TCAAATACTTTAATACAAATGTT
130 TCAAATACTTTAATAAAAATGTT
1956077 TCTTTCTTTC
Statistics
Matches: 138, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
152 107 0.78
153 6 0.04
154 25 0.18
ACGTcount: A:0.30, C:0.08, G:0.13, T:0.49
Consensus pattern (153 bp):
TTTTATTTTATTTTGGTGTCGATTAATTAATGTTATTTTCGGTACTTGCAAAGGCTAGATTTCAA
GTACAAAGATATATTTTTTAATTTATTCGGAAAATTATGATGCTCAATTGCTTTATATTAAGTTT
CAAATACTTTAATAAAAATGTTA
Found at i:1957984 original size:14 final size:13
Alignment explanation
Indices: 1957960--1957989 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1957950 AATGGTTAAT
1957960 AATTATTTTAAAA
1 AATTATTTTAAAA
*
1957973 AATTATTTTTAAA
1 AATTATTTTAAAA
1957986 AATT
1 AATT
1957990 TTAATTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AATTATTTTAAAA
Found at i:1958520 original size:2 final size:2
Alignment explanation
Indices: 1958515--1958545 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1958505 TATATAACGC
*
1958515 TA TA TA TT 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 T
1958546 GAAATGTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:1960366 original size:2 final size:2
Alignment explanation
Indices: 1960359--1960386 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1960349 AAGAAAAACC
1960359 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
1960387 GCTTGACACA
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:1962553 original size:15 final size:15
Alignment explanation
Indices: 1962530--1962561 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1962520 ACATATTAAA
*
1962530 TTAATAAATTATTAT
1 TTAAAAAATTATTAT
1962545 TTAAAAAATTATTAT
1 TTAAAAAATTATTAT
1962560 TT
1 TT
1962562 TTATAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTAAAAAATTATTAT
Found at i:1962603 original size:21 final size:22
Alignment explanation
Indices: 1962561--1962603 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
1962551 AATTATTATT
* **
1962561 TTTATAATATTTTTTATTTATA
1 TTTATAATATTTATTAAATATA
1962583 TTTA-AATATTTATTAAATATA
1 TTTATAATATTTATTAAATATA
1962604 AATATCAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTATAATATTTATTAAATATA
Found at i:1964796 original size:18 final size:18
Alignment explanation
Indices: 1964763--1964898 Score: 71
Period size: 18 Copynumber: 6.9 Consensus size: 18
1964753 TATTGAAACT
*
1964763 ATTTT-ATATTAATATAA
1 ATTTTAATATTTATATAA
*
1964780 ATTTTAATATTTTTATATTAT
1 ATTTTAATA--TTTATA-TAA
*
1964801 ATTAATAATTTATATTATATAA
1 ATT-TTAA--TAT-TTATATAA
*
1964823 ATTTTAAAATATTTATATACTT
1 ATTTT--AATATTTATATA--A
1964845 ATTTT-ATATTTATATAAA
1 ATTTTAATATTTATAT-AA
*
1964863 ATTTTAATA-TAATATAA
1 ATTTTAATATTTATATAA
*
1964880 TATTTTAATTATTTTTATA
1 -ATTTTAA-TATTTATATA
1964899 TTTATATTTA
Statistics
Matches: 92, Mismatches: 10, Indels: 31
0.69 0.08 0.23
Matches are distributed among these distances:
17 7 0.08
18 20 0.22
19 15 0.16
20 18 0.20
21 9 0.10
22 14 0.15
23 7 0.08
24 2 0.02
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTTAATATTTATATAA
Found at i:1964815 original size:26 final size:26
Alignment explanation
Indices: 1964764--1964816 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
1964754 ATTGAAACTA
*
1964764 TTTTATATTAATATAAATTTTAATAT
1 TTTTATATTAATATAAAATTTAATAT
1964790 TTTTATATT-ATATTAATAATTT-ATAT
1 TTTTATATTAATA-TAA-AATTTAATAT
1964816 T
1 T
1964817 ATATAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 3 0.12
26 17 0.71
27 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (26 bp):
TTTTATATTAATATAAAATTTAATAT
Found at i:1964816 original size:44 final size:38
Alignment explanation
Indices: 1964762--1964891 Score: 126
Period size: 43 Copynumber: 3.3 Consensus size: 38
1964752 ATATTGAAAC
*
1964762 TATTTTATATTAATATAAATTTTAATATTTTTATATTATAT
1 TATTTTATATT-ATATAAATTTTAATATATTTATA-TA-AT
* *
1964803 TAATAATTTATATTATATAAATTTTAAAATATTTATATACT
1 T-AT--TTTATATTATATAAATTTTAATATATTTATATAAT
1964844 TATTTTATATTTATATAAAATTTTAATATA---ATATAA-
1 TATTTTATA-TTATAT-AAATTTTAATATATTTATATAAT
1964880 TATTTTA-ATTAT
1 TATTTTATATTAT
1964892 TTTTATATTT
Statistics
Matches: 79, Mismatches: 5, Indels: 17
0.78 0.05 0.17
Matches are distributed among these distances:
34 4 0.05
35 1 0.01
36 7 0.09
37 5 0.06
38 6 0.08
39 6 0.08
40 14 0.18
41 3 0.04
42 4 0.05
43 21 0.27
44 8 0.10
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (38 bp):
TATTTTATATTATATAAATTTTAATATATTTATATAAT
Found at i:1964838 original size:20 final size:20
Alignment explanation
Indices: 1964768--1964841 Score: 60
Period size: 20 Copynumber: 3.5 Consensus size: 20
1964758 AAACTATTTT
* *
1964768 ATATTAATATAAATTTTAAT
1 ATATTTATATAAATTTTAAA
* * *
1964788 ATTTTTATAT-TATATTAATA
1 ATATTTATATAAATTTTAA-A
1964808 ATTTATATTATATAAATTTTAAA
1 A--TAT-TTATATAAATTTTAAA
1964831 ATATTTATATA
1 ATATTTATATA
1964842 CTTATTTTAT
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
19 6 0.15
20 16 0.39
21 3 0.07
22 2 0.05
23 8 0.20
24 6 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
ATATTTATATAAATTTTAAA
Found at i:1964858 original size:57 final size:57
Alignment explanation
Indices: 1964790--1964912 Score: 146
Period size: 57 Copynumber: 2.2 Consensus size: 57
1964780 ATTTTAATAT
*
1964790 TTTTATA-TTATATTAATAA-TTT-ATATTATATAA-ATTTTAAAATATTTATATACTTA
1 TTTTATATTTATA-TAA-AATTTTAATATAATATAATATTTT-AAATATTTATATACTTA
* * *
1964846 TTTTATATTTATATAAAATTTTAATATAATATAATATTTTAATTATTTTTATATTTA
1 TTTTATATTTATATAAAATTTTAATATAATATAATATTTTAAATATTTATATACTTA
1964903 TATTTATATT
1 T-TTTATATT
1964913 ATTATATTGA
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
55 2 0.03
56 13 0.22
57 30 0.52
58 13 0.22
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.59
Consensus pattern (57 bp):
TTTTATATTTATATAAAATTTTAATATAATATAATATTTTAAATATTTATATACTTA
Found at i:1964917 original size:14 final size:13
Alignment explanation
Indices: 1964831--1964920 Score: 52
Period size: 11 Copynumber: 7.4 Consensus size: 13
1964821 AAATTTTAAA
1964831 ATATTTATATACTT
1 ATATTTATATA-TT
1964845 AT-TTTATAT-TT
1 ATATTTATATATT
* * *
1964856 ATA-TAAAATTTT
1 ATATTTATATATT
* *
1964868 A-ATATA-ATATA
1 ATATTTATATATT
1964879 ATATTT-TA-ATT
1 ATATTTATATATT
*
1964890 ATTTTTATAT-TT
1 ATATTTATATATT
1964902 ATATTTATATTATT
1 ATATTTATA-TATT
1964916 ATATT
1 ATATT
1964921 GAGAATTATA
Statistics
Matches: 57, Mismatches: 10, Indels: 18
0.67 0.12 0.21
Matches are distributed among these distances:
11 20 0.35
12 20 0.35
13 8 0.14
14 9 0.16
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (13 bp):
ATATTTATATATT
Found at i:1965684 original size:2 final size:2
Alignment explanation
Indices: 1965679--1965715 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1965669 CAAGTAAAAA
1965679 AT 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 AT A
1965716 ATTTTAATAT
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:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1970485 original size:14 final size:14
Alignment explanation
Indices: 1970468--1970550 Score: 94
Period size: 14 Copynumber: 5.4 Consensus size: 14
1970458 TTATATATTT
1970468 TATATAAATTTTAA
1 TATATAAATTTTAA
1970482 TATATTAATAATTTATAA
1 TATA-T-A-AATTT-TAA
1970500 TATATAAATTTTAA
1 TATATAAATTTTAA
1970514 TATATTAATAATTTATAA
1 TATA-T-A-AATTT-TAA
1970532 TATATAAATTTTAA
1 TATATAAATTTTAA
1970546 TATAT
1 TATAT
1970551 TTGTATTCAT
Statistics
Matches: 61, Mismatches: 0, Indels: 16
0.79 0.00 0.21
Matches are distributed among these distances:
14 19 0.31
15 12 0.20
16 4 0.07
17 12 0.20
18 14 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TATATAAATTTTAA
Found at i:1970509 original size:32 final size:32
Alignment explanation
Indices: 1970468--1970551 Score: 168
Period size: 32 Copynumber: 2.6 Consensus size: 32
1970458 TTATATATTT
1970468 TATATAAATTTTAATATATTAATAATTTATAA
1 TATATAAATTTTAATATATTAATAATTTATAA
1970500 TATATAAATTTTAATATATTAATAATTTATAA
1 TATATAAATTTTAATATATTAATAATTTATAA
1970532 TATATAAATTTTAATATATT
1 TATATAAATTTTAATATATT
1970552 TGTATTCATA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (32 bp):
TATATAAATTTTAATATATTAATAATTTATAA
Found at i:1971033 original size:2 final size:2
Alignment explanation
Indices: 1971021--1971072 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
1971011 CTTGCATCTA
*
1971021 AT AT GT 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
1971063 AT AT A- AT AT A
1 AT AT AT AT AT A
1971073 CCGTAACCTG
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1974022 original size:123 final size:123
Alignment explanation
Indices: 1973803--1974049 Score: 494
Period size: 123 Copynumber: 2.0 Consensus size: 123
1973793 ACAACAGTTC
1973803 TGGATTGATAGATGTACCAATAAAATTGTTATCAGTTTATTTCTGCATTATTAAAACTGTCCAAA
1 TGGATTGATAGATGTACCAATAAAATTGTTATCAGTTTATTTCTGCATTATTAAAACTGTCCAAA
1973868 ATATAAATGATTTGCGATCCAATGCTTCCATCACTTCATTCAGGAGAAAATCTTACAT
66 ATATAAATGATTTGCGATCCAATGCTTCCATCACTTCATTCAGGAGAAAATCTTACAT
1973926 TGGATTGATAGATGTACCAATAAAATTGTTATCAGTTTATTTCTGCATTATTAAAACTGTCCAAA
1 TGGATTGATAGATGTACCAATAAAATTGTTATCAGTTTATTTCTGCATTATTAAAACTGTCCAAA
1973991 ATATAAATGATTTGCGATCCAATGCTTCCATCACTTCATTCAGGAGAAAATCTTACAT
66 ATATAAATGATTTGCGATCCAATGCTTCCATCACTTCATTCAGGAGAAAATCTTACAT
1974049 T
1 T
1974050 TAAGCAAAAT
Statistics
Matches: 124, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
123 124 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (123 bp):
TGGATTGATAGATGTACCAATAAAATTGTTATCAGTTTATTTCTGCATTATTAAAACTGTCCAAA
ATATAAATGATTTGCGATCCAATGCTTCCATCACTTCATTCAGGAGAAAATCTTACAT
Found at i:1976847 original size:18 final size:19
Alignment explanation
Indices: 1976820--1976861 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
1976810 TTGATCATTG
1976820 AAAAAAAAAT-TAAAAATT
1 AAAAAAAAATATAAAAATT
* *
1976838 AAAAATAAATGATAAATATT
1 AAAAAAAAAT-ATAAAAATT
1976858 AAAA
1 AAAA
1976862 TTCAAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 9 0.45
20 11 0.55
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (19 bp):
AAAAAAAAATATAAAAATT
Found at i:1981749 original size:30 final size:30
Alignment explanation
Indices: 1981688--1981751 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
1981678 GGTAGGTTAG
* * **
1981688 ATTTAAATTAATTTAAAATTTTATATTATT
1 ATTTAAAATAATTTAAAAATTTATAAAATT
1981718 ATTTAAAATAATATTAAAAATTTA-AAAATT
1 ATTTAAAATAAT-TTAAAAATTTATAAAATT
1981748 ATTT
1 ATTT
1981752 TATATTAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 19 0.66
31 10 0.34
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (30 bp):
ATTTAAAATAATTTAAAAATTTATAAAATT
Found at i:1981784 original size:40 final size:41
Alignment explanation
Indices: 1981705--1981797 Score: 109
Period size: 43 Copynumber: 2.3 Consensus size: 41
1981695 TTAATTTAAA
* *
1981705 ATTTTATATTATTATTTAAAATAATATTAAAAATTTAAAAATT
1 ATTTTATATTAATATTTAAAATAAAATTAAAAA-TTAAAAA-T
* *
1981748 ATTTTATATTAATATTTATAATAAAATT-TAAA-TAAAAAT
1 ATTTTATATTAATATTTAAAATAAAATTAAAAATTAAAAAT
*
1981787 AATTTATATTA
1 ATTTTATATTA
1981798 TATAAATAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
39 11 0.24
40 6 0.13
42 3 0.07
43 25 0.56
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (41 bp):
ATTTTATATTAATATTTAAAATAAAATTAAAAATTAAAAAT
Found at i:1981826 original size:36 final size:38
Alignment explanation
Indices: 1981742--1981828 Score: 99
Period size: 36 Copynumber: 2.3 Consensus size: 38
1981732 TAAAAATTTA
* *
1981742 AAAATTATTTTATATTAATATTTATAATAAAATTTAAAT
1 AAAATTAATTTATATTAATA-TTATAATAAAATCTAAAT
*
1981781 AAAAATAATTTATATT-ATA-TA-AATAATAATCTAAAT
1 AAAATTAATTTATATTAATATTATAATAA-AATCTAAAT
*
1981817 CAAATTAATTTA
1 AAAATTAATTTA
1981829 AAACGTAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
35 5 0.12
36 20 0.48
38 3 0.07
39 14 0.33
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (38 bp):
AAAATTAATTTATATTAATATTATAATAAAATCTAAAT
Found at i:1981981 original size:15 final size:16
Alignment explanation
Indices: 1981963--1982028 Score: 61
Period size: 15 Copynumber: 4.4 Consensus size: 16
1981953 TTTTTATTTT
*
1981963 ATATTAATTAT-ATAA
1 ATATTAAATATAATAA
1981978 ATA-TAAATATAATAA
1 ATATTAAATATAATAA
*
1981993 ATATT--ATAAAAT-A
1 ATATTAAATATAATAA
*
1982006 ATTTTAAATATAATTAA
1 ATATTAAATATAA-TAA
1982023 ATATTA
1 ATATTA
1982029 TATTAATCGT
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
13 5 0.12
14 12 0.30
15 15 0.38
16 2 0.05
17 6 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATTAAATATAATAA
Found at i:1982885 original size:22 final size:23
Alignment explanation
Indices: 1982860--1982906 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 23
1982850 ATAAAATAAA
*
1982860 TCAAAATTTGAT-TTTTATTAAT
1 TCAAAATATGATATTTTATTAAT
*
1982882 TC--AATATGATATTTTGTTAAT
1 TCAAAATATGATATTTTATTAAT
1982903 TCAA
1 TCAA
1982907 CCTTTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 5
0.74 0.07 0.19
Matches are distributed among these distances:
20 7 0.35
21 11 0.55
22 2 0.10
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.51
Consensus pattern (23 bp):
TCAAAATATGATATTTTATTAAT
Found at i:1982901 original size:21 final size:20
Alignment explanation
Indices: 1982868--1982906 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1982858 AATCAAAATT
1982868 TGATTTTTATTAATTCAATA
1 TGATTTTTATTAATTCAATA
*
1982888 TGATATTTTGTTAATTCAA
1 TGAT-TTTTATTAATTCAA
1982907 CCTTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.05, G:0.08, T:0.54
Consensus pattern (20 bp):
TGATTTTTATTAATTCAATA
Found at i:1983838 original size:21 final size:20
Alignment explanation
Indices: 1983799--1983860 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 20
1983789 ATAAATCAAA
1983799 TTTAAT-ATATAAATTAATTT
1 TTTAATAAT-TAAATTAATTT
*
1983819 TTT-ATCAATTTAATTTAATTT
1 TTTAAT-AA-TTAAATTAATTT
1983840 TTTAATAATTAAATTAATTT
1 TTTAATAATTAAATTAATTT
1983860 T
1 T
1983861 GACTAAGTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
19 2 0.06
20 15 0.42
21 16 0.44
22 3 0.08
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTAATAATTAAATTAATTT
Found at i:1984933 original size:12 final size:13
Alignment explanation
Indices: 1984911--1984961 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
1984901 TCCGTTTATA
1984911 TTATATTTTT-AAT
1 TTAT-TTTTTAAAT
*
1984924 TTATTTTTTAAAA
1 TTATTTTTTAAAT
*
1984937 ATATTTTTTAAAAT
1 TTATTTTTT-AAAT
*
1984951 TTAATTTTTAA
1 TTATTTTTTAA
1984962 TAATTTAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
12 5 0.16
13 16 0.52
14 10 0.32
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTATTTTTTAAAT
Done.