Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold206
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: 2736418
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 22040 characters in sequence are not A, C, G, or T
File 8 of 20
Found at i:1006588 original size:21 final size:21
Alignment explanation
Indices: 1006530--1006589 Score: 52
Period size: 21 Copynumber: 2.8 Consensus size: 21
1006520 TGATATAAAA
1006530 ATATATTATAAATATAATACTT
1 ATATATTA-AAATATAATACTT
* *
1006552 TTA-ATTAATATAATAATA-TT
1 ATATATTAAAAT-ATAATACTT
*
1006572 GATATATTAAGATATAAT
1 -ATATATTAAAATATAAT
1006590 TAACATGACA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
20 5 0.16
21 17 0.55
22 9 0.29
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (21 bp):
ATATATTAAAATATAATACTT
Found at i:1009069 original size:28 final size:27
Alignment explanation
Indices: 1009038--1009147 Score: 73
Period size: 28 Copynumber: 3.9 Consensus size: 27
1009028 TCTCTTGCAC
1009038 TTATATTTAAATTTGATAATATAAAAAA
1 TTATA-TTAAATTTGATAATATAAAAAA
* *
1009066 TTATA-TAAATTTAATATATAATTAAAAA
1 TTATATTAAATTTGATA-AT-ATAAAAAA
* *
1009094 TTATAATAAAGATATGATGAATATATAAAAA
1 TTAT-ATTAA-ATTTGAT-AATATA-AAAAA
* *
1009125 TT-T-TAAAATTTATATAATATAAA
1 TTATATTAAATTT-GATAATATAAA
1009148 TTATTAAAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 18
0.72 0.09 0.20
Matches are distributed among these distances:
26 12 0.18
27 11 0.17
28 22 0.33
29 1 0.02
30 5 0.08
31 14 0.21
32 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (27 bp):
TTATATTAAATTTGATAATATAAAAAA
Found at i:1009157 original size:24 final size:22
Alignment explanation
Indices: 1009114--1009157 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
1009104 GATATGATGA
1009114 ATATATAAAAATTTTAAAATTT
1 ATATATAAAAATTTTAAAATTT
*
1009136 ATATAATATAAATTATTAAAAT
1 ATAT-ATAAAAATT-TTAAAAT
1009158 ATAAAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 8 0.42
24 7 0.37
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
ATATATAAAAATTTTAAAATTT
Found at i:1009175 original size:18 final size:17
Alignment explanation
Indices: 1009128--1009195 Score: 58
Period size: 18 Copynumber: 4.2 Consensus size: 17
1009118 ATAAAAATTT
1009128 TAAAATTTATAT-AATA
1 TAAAATTTATATAAATA
1009144 T-AAA-TTAT-TAAAATA
1 TAAAATTTATAT-AAATA
1009159 TAAAAATTTATATAAATA
1 T-AAAATTTATATAAATA
*
1009177 TTAAATATT-T-TAAATA
1 TAAAAT-TTATATAAATA
1009193 TAA
1 TAA
1009196 TTATAATATA
Statistics
Matches: 43, Mismatches: 2, Indels: 14
0.73 0.03 0.24
Matches are distributed among these distances:
13 1 0.02
14 4 0.09
15 8 0.19
16 9 0.21
17 8 0.19
18 12 0.28
19 1 0.02
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:1009192 original size:34 final size:32
Alignment explanation
Indices: 1009129--1009195 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 32
1009119 TAAAAATTTT
1009129 AAAATTTATATAATATAAATTATTAAAATATA
1 AAAATTTATATAATATAAATTATTAAAATATA
*
1009161 AAAATTTATATAAATATTAAA-TATTTTAAATATA
1 AAAATTTATAT-AATA-TAAATTA-TTAAAATATA
1009195 A
1 A
1009196 TTATAATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
32 11 0.35
33 6 0.19
34 14 0.45
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (32 bp):
AAAATTTATATAATATAAATTATTAAAATATA
Found at i:1009543 original size:23 final size:21
Alignment explanation
Indices: 1009502--1009543 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
1009492 AAATTTTAAA
1009502 TTTTTATCTAAAAAATAAAAT
1 TTTTTATCTAAAAAATAAAAT
*
1009523 TTTTTGATTTAAAAAACTAAA
1 TTTTT-ATCTAAAAAA-TAAA
1009544 TCATTCGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 9 0.50
23 4 0.22
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (21 bp):
TTTTTATCTAAAAAATAAAAT
Found at i:1009544 original size:22 final size:20
Alignment explanation
Indices: 1009498--1009544 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 20
1009488 AATAAAATTT
1009498 TAAA-TTTTTATCTAAAAAA
1 TAAATTTTTTATCTAAAAAA
*
1009517 TAAAATTTTTTGATTTAAAAAA
1 T-AAATTTTTT-ATCTAAAAAA
1009539 CTAAAT
1 -TAAAT
1009545 CATTCGAGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 1 0.04
20 3 0.13
21 5 0.22
22 13 0.57
23 1 0.04
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (20 bp):
TAAATTTTTTATCTAAAAAA
Found at i:1009716 original size:10 final size:10
Alignment explanation
Indices: 1009701--1009741 Score: 55
Period size: 10 Copynumber: 3.8 Consensus size: 10
1009691 ACACGACCAC
1009701 ATATTTTTTT
1 ATATTTTTTT
1009711 ATATTTTTTT
1 ATATTTTTTT
1009721 CATATTTTATATT
1 -ATATTTT-T-TT
1009734 ATATTTTT
1 ATATTTTT
1009742 ACTTATATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 10 0.36
11 8 0.29
12 8 0.29
13 2 0.07
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (10 bp):
ATATTTTTTT
Found at i:1009726 original size:21 final size:23
Alignment explanation
Indices: 1009700--1009763 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
1009690 GACACGACCA
1009700 CATATTTT-T-TTATATTTTTTT
1 CATATTTTATATTATATTTTTTT
1009721 CATATTTTATATTATATTTTTACTT
1 CATATTTTATATTATATTTTT--TT
*
1009746 -ATATTATATATTAT-TTTT
1 CATATTTTATATTATATTTT
1009764 ATGTTATAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
21 8 0.21
22 1 0.03
23 14 0.37
24 13 0.34
25 2 0.05
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.69
Consensus pattern (23 bp):
CATATTTTATATTATATTTTTTT
Found at i:1009737 original size:12 final size:11
Alignment explanation
Indices: 1009701--1009763 Score: 60
Period size: 12 Copynumber: 5.6 Consensus size: 11
1009691 ACACGACCAC
1009701 ATATTTTT-TT
1 ATATTTTTATT
1009711 ATATTTTT-TT
1 ATATTTTTATT
1009721 CATATTTTATATT
1 -ATATTTT-TATT
1009734 ATATTTTTACTT
1 ATATTTTTA-TT
*
1009746 ATATTATATATT
1 ATATT-TTTATT
1009758 AT-TTTT
1 ATATTTT
1009764 ATGTTATAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
10 11 0.24
11 11 0.24
12 19 0.41
13 5 0.11
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (11 bp):
ATATTTTTATT
Found at i:1009752 original size:22 final size:22
Alignment explanation
Indices: 1009709--1009764 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
1009699 ACATATTTTT
* *
1009709 TTATATTTTTTTCATATTTTATA
1 TTATA-TTTTTACATATATTATA
*
1009732 TTATATTTTTACTTATATTATA
1 TTATATTTTTACATATATTATA
1009754 -TATTATTTTTA
1 TTA-TATTTTTA
1009765 TGTTATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.07
22 22 0.76
23 5 0.17
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.68
Consensus pattern (22 bp):
TTATATTTTTACATATATTATA
Found at i:1011603 original size:206 final size:208
Alignment explanation
Indices: 1011231--1011604 Score: 585
Period size: 206 Copynumber: 1.8 Consensus size: 208
1011221 TTCACGGATA
* * *
1011231 TATTCAATTCTTTTAAAGTGTTTTTCATGTATTTGGAGGAGGCTTTGGACAGTTATATCCCTATA
1 TATTCAATTCTTTTAAAATGTTTTTCATGTATTTAGAGGAGGCATTGGACAGTTATATCCC-ATA
* * *
1011296 TTTATGTCTAAAAATGTATCAAACATGAGTGTTGAATTCGAGTACTTAAAGAAAAATGAAGAGTC
65 TCTATGTCTAAAAATGTATCAAACATGAGTGTCGAATTCGAGTACTTAAAAAAAAATGAAGAGTC
1011361 AGAGCAACATAAGTTATGTGATTACATAGATGCATTTCACTCGAAGTTCACTTTATAAGTTTTTC
130 AGAGCAACATAAGTTATGTGATTACATAGATGCATTTCACTCGAAGTTCACTTTATAAGTTTTTC
1011426 CATGTATTTGGGTG
195 CATGTATTTGGGTG
1011440 TATTCAATT-TTTTAAAAAT-TTTTTCATGTATTTAGAGG-GGACATTGGACAGTTATATCCC-T
1 TATTCAATTCTTTT-AAAATGTTTTTCATGTATTTAGAGGAGG-CATTGGACAGTTATATCCCAT
** * *
1011501 ATCTATGTCTGGAAATGTATCAGACATGAGTGTCGAATTCGGGTACTTAAAAAAAAATGAAGAGT
64 ATCTATGTCTAAAAATGTATCAAACATGAGTGTCGAATTCGAGTACTTAAAAAAAAATGAAGAGT
* *
1011566 CAGAGCAGCATAAGTTATGTGATTACATAGGTGCATTTC
129 CAGAGCAACATAAGTTATGTGATTACATAGATGCATTTC
1011605 GCTTGATCTG
Statistics
Matches: 151, Mismatches: 12, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
206 96 0.64
207 2 0.01
208 40 0.26
209 13 0.09
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.36
Consensus pattern (208 bp):
TATTCAATTCTTTTAAAATGTTTTTCATGTATTTAGAGGAGGCATTGGACAGTTATATCCCATAT
CTATGTCTAAAAATGTATCAAACATGAGTGTCGAATTCGAGTACTTAAAAAAAAATGAAGAGTCA
GAGCAACATAAGTTATGTGATTACATAGATGCATTTCACTCGAAGTTCACTTTATAAGTTTTTCC
ATGTATTTGGGTG
Found at i:1021049 original size:2 final size:2
Alignment explanation
Indices: 1021042--1021077 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1021032 ATTTAAGATC
1021042 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1021078 ACTGACTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1021326 original size:35 final size:35
Alignment explanation
Indices: 1021280--1021349 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
1021270 GAGGCAAAGG
1021280 GAAGGATGCTTCTCCCTCAACCCTCCAACCAAACC
1 GAAGGATGCTTCTCCCTCAACCCTCCAACCAAACC
1021315 GAAGGATGCTTCTCCCTCAACCCTCCAACCAAACC
1 GAAGGATGCTTCTCCCTCAACCCTCCAACCAAACC
1021350 ATCTCTCTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.29, C:0.43, G:0.11, T:0.17
Consensus pattern (35 bp):
GAAGGATGCTTCTCCCTCAACCCTCCAACCAAACC
Found at i:1030324 original size:9 final size:10
Alignment explanation
Indices: 1030308--1030349 Score: 50
Period size: 12 Copynumber: 4.0 Consensus size: 10
1030298 AAATTTTTAA
1030308 TAATTTAAAT
1 TAATTTAAAT
1030318 TAA-TTAAAT
1 TAATTTAAAT
1030327 TAAATTTAAAT
1 T-AATTTAAAT
1030338 TATTATTTAAAT
1 TA--ATTTAAAT
1030350 AATATAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 7 0.25
10 6 0.21
11 7 0.25
12 8 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
TAATTTAAAT
Found at i:1030337 original size:11 final size:11
Alignment explanation
Indices: 1030269--1030349 Score: 53
Period size: 11 Copynumber: 7.5 Consensus size: 11
1030259 AATTATTCGA
*
1030269 TAAATTTAATT
1 TAAATTAAATT
*
1030280 TATATTAAATT
1 TAAATTAAATT
* *
1030291 GATATTAAAATTT
1 TAAATT-AAA-TT
*
1030304 TTAA-T-AATT
1 TAAATTAAATT
1030313 TAAATT-AA-T
1 TAAATTAAATT
1030322 TAAATTAAATT
1 TAAATTAAATT
*
1030333 TAAATTATTATT
1 TAAATTA-AATT
1030345 TAAAT
1 TAAAT
1030350 AATATAAAAT
Statistics
Matches: 56, Mismatches: 8, Indels: 11
0.75 0.11 0.15
Matches are distributed among these distances:
9 12 0.21
10 7 0.12
11 22 0.39
12 12 0.21
13 3 0.05
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (11 bp):
TAAATTAAATT
Found at i:1030358 original size:58 final size:58
Alignment explanation
Indices: 1030269--1030398 Score: 149
Period size: 58 Copynumber: 2.2 Consensus size: 58
1030259 AATTATTCGA
* * *
1030269 TAAATTTAATTTATATTAAATTGATATTAAAAT-TTTTAATAATTTAAATTAATTAAAT
1 TAAATTTAAATTATATTAAATTAATATTAAAATATTTTAATAATTTAAA-TAATAAAAT
* *
1030327 TAAATTTAAATTATTATTTAAA-TAATA-TAAAATATTTTTATATTTTAAATAATAAAAT
1 TAAATTTAAATTA-TA-TTAAATTAATATTAAAATATTTTAATAATTTAAATAATAAAAT
*
1030385 AAAATTTTAAATTA
1 TAAA-TTTAAATTA
1030399 ATAAACTTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
58 29 0.47
59 28 0.45
60 5 0.08
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (58 bp):
TAAATTTAAATTATATTAAATTAATATTAAAATATTTTAATAATTTAAATAATAAAAT
Found at i:1031798 original size:14 final size:15
Alignment explanation
Indices: 1031759--1031801 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1031749 AATCATAATA
* **
1031759 ATAATTATTATATTT
1 ATAATTATAATAAAT
1031774 ATAATTATAATAAAT
1 ATAATTATAATAAAT
1031789 ATAA-TATAATAAA
1 ATAATTATAATAAA
1031802 AATATATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 9 0.36
15 16 0.64
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAATTATAATAAAT
Found at i:1032173 original size:21 final size:20
Alignment explanation
Indices: 1032120--1032175 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 20
1032110 TTAGCTCATT
1032120 ATAAAAATAAAATTTTTTTA
1 ATAAAAATAAAATTTTTTTA
1032140 ATATCAAATATAAAATTTTATTTTA
1 ATA--AAA-ATAAAA-TTT-TTTTA
1032165 A-AAAAATAAAA
1 ATAAAAATAAAA
1032176 ATTAAATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
20 3 0.10
21 6 0.19
22 6 0.19
23 6 0.19
24 4 0.13
25 6 0.19
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
ATAAAAATAAAATTTTTTTA
Found at i:1032281 original size:13 final size:15
Alignment explanation
Indices: 1032250--1032282 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
1032240 CATATCATCC
1032250 ATTTTCTAAAATAAT
1 ATTTTCTAAAATAAT
1032265 ATTTT-TAAAAT-AT
1 ATTTTCTAAAATAAT
1032278 ATTTT
1 ATTTT
1032283 GACACGTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 6 0.33
15 5 0.28
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTTTCTAAAATAAT
Found at i:1033413 original size:16 final size:15
Alignment explanation
Indices: 1033388--1033417 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1033378 AGTTGAGTAT
1033388 ATTTAATTTAAATTA
1 ATTTAATTTAAATTA
1033403 ATTTAAATTTAAATT
1 ATTT-AATTTAAATT
1033418 TTTGTGATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTTAATTTAAATTA
Found at i:1033874 original size:11 final size:11
Alignment explanation
Indices: 1033842--1033876 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
1033832 AATATAATTT
1033842 TATAAAAAAAA
1 TATAAAAAAAA
1033853 T-TAAAATAAAA
1 TATAAAA-AAAA
1033864 TATAAAAAAAA
1 TATAAAAAAAA
1033875 TA
1 TA
1033877 AATACAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 5 0.23
11 12 0.55
12 5 0.23
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
TATAAAAAAAA
Found at i:1042795 original size:6 final size:6
Alignment explanation
Indices: 1042784--1042815 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
1042774 GTCAAACTTC
1042784 TTTATT TTTATT TTTATT TTTATT TTTATT TT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TT
1042816 CAAAAGCTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTATT
Found at i:1043682 original size:22 final size:22
Alignment explanation
Indices: 1043646--1043695 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
1043636 AAAAGAAAAC
1043646 AAAAAATTTATTTT-ATAAAATT
1 AAAAAATTTATTTTAAT-AAATT
*
1043668 AAAAAA-TTATCTTTAATATATT
1 AAAAAATTTAT-TTTAATAAATT
1043690 AAAAAA
1 AAAAAA
1043696 AAAAAGAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 4 0.16
22 19 0.76
23 2 0.08
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAAAATTTATTTTAATAAATT
Found at i:1044501 original size:3 final size:3
Alignment explanation
Indices: 1044454--1044487 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1044444 AGAAAACAAT
1044454 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1044488 TAGGTGGAAG
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:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1046777 original size:9 final size:9
Alignment explanation
Indices: 1046763--1046828 Score: 53
Period size: 9 Copynumber: 7.0 Consensus size: 9
1046753 AAATAAATTA
1046763 AATTTAAAT
1 AATTTAAAT
*
1046772 ATTTTAATATTT
1 AATTTAA-A--T
1046784 AATTTAAAT
1 AATTTAAAT
1046793 AATTTAAA-
1 AATTTAAAT
* *
1046801 ATTTTAATT
1 AATTTAAAT
*
1046810 AATATTAAAA
1 AAT-TTAAAT
1046820 AATTTAAAT
1 AATTTAAAT
1046829 TTAAATTTAA
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
8 6 0.14
9 22 0.50
10 8 0.18
11 1 0.02
12 7 0.16
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
AATTTAAAT
Found at i:1046787 original size:21 final size:21
Alignment explanation
Indices: 1046757--1046834 Score: 79
Period size: 21 Copynumber: 3.7 Consensus size: 21
1046747 ATGATCAAAT
*
1046757 AAATTAAATTTAAATATTTTA
1 AAATTTAATTTAAATATTTTA
* *
1046778 ATATTTAATTTAAATAATTTA
1 AAATTTAATTTAAATATTTTA
**
1046799 AAATTTTAA-TT-AATATTAAA
1 AAA-TTTAATTTAAATATTTTA
1046819 AAATTTAAATTTAAAT
1 AAATTT-AATTTAAAT
1046835 TTAAACATAA
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
19 3 0.07
20 11 0.24
21 24 0.52
22 8 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AAATTTAATTTAAATATTTTA
Found at i:1046811 original size:26 final size:27
Alignment explanation
Indices: 1046762--1046835 Score: 80
Period size: 26 Copynumber: 2.7 Consensus size: 27
1046752 CAAATAAATT
1046762 AAATTTAAATATTTTAATATTTAAT-TTAAA
1 AAATTTAAA-ATTTT-A-A-TTAATATTAAA
*
1046792 TAATTTAAAATTTTAATTAATATTAAA
1 AAATTTAAAATTTTAATTAATATTAAA
*
1046819 AAATTT-AAATTTAAATT
1 AAATTTAAAATTTTAATT
1046836 TAAACATAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
26 15 0.38
27 11 0.28
28 1 0.03
29 5 0.12
30 8 0.20
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
AAATTTAAAATTTTAATTAATATTAAA
Found at i:1046838 original size:27 final size:27
Alignment explanation
Indices: 1046762--1046838 Score: 86
Period size: 27 Copynumber: 2.8 Consensus size: 27
1046752 CAAATAAATT
1046762 AAATTTAAATATTTTAATATTTAATTTAAA
1 AAATTTAAA-A-TTTAA-ATTTAATTTAAA
* *
1046792 TAATTTAAAATTTTAA-TTAATATTAAA
1 AAATTTAAAATTTAAATTTAAT-TTAAA
1046819 AAATTT-AAATTTAAATTTAA
1 AAATTTAAAATTTAAATTTAA
1046839 ACATAAATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
26 13 0.32
27 15 0.37
28 4 0.10
29 1 0.02
30 8 0.20
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
AAATTTAAAATTTAAATTTAATTTAAA
Found at i:1047200 original size:20 final size:21
Alignment explanation
Indices: 1047151--1047202 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 21
1047141 TTTGAGATAA
1047151 ATTTATTT-AAT-TTTTATAT
1 ATTTATTTAAATATTTTATAT
**
1047170 ATTTA-AAAAATATTTTATAT
1 ATTTATTTAAATATTTTATAT
1047190 -TTTATTTAAATAT
1 ATTTATTTAAATAT
1047203 ATCAAATACA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTATTTAAATATTTTATAT
Found at i:1049826 original size:143 final size:147
Alignment explanation
Indices: 1049568--1049905 Score: 425
Period size: 143 Copynumber: 2.3 Consensus size: 147
1049558 CCATTCAGAT
* * *
1049568 GCATATACGACAAGGATTGAATCTATCACATCTATTGAGGCATATAT-TCGAATATCCAAAACAG
1 GCATATACCACAAAGACTGAATCTATCACATCTATTGAGGCATATATCTCGAATATCCAAAACAG
** *** *
1049632 TAACCAACTCCAACCCGAAAATGTTAAAAGAGAATACATGTATCAGCTAGAACTAGAGTGCAA-A
66 TAACCAACTCCAACAAGAAAATGTTAAAAGAGAATACAACCATCAGCTAGAACTAGAGTACAAGA
*
1049696 -ACA-AACTATTTGAAC
131 CAAATAACTATTTGAAC
* * *
1049711 GCATATACCACAAAGACCGAATCTATCACATCTATTGAGGCATATATCT-GAATATCCAAAAGAT
1 GCATATACCACAAAGACTGAATCTATCACATCTATTGAGGCATATATCTCGAATATCCAAAACAG
* * * * *
1049775 TGACCGACTCCGACAAGATAATGTTAAAAGAGAATACAACCATCAGCTAGAACTAGGGTACAAGA
66 TAACCAACTCCAACAAGAAAATGTTAAAAGAGAATACAACCATCAGCTAGAACTAGAGTACAAGA
*
1049840 CAAATTAATTATTTGAAC
131 CAAA-TAACTATTTGAAC
* * * *
1049858 ACATCTACCACAAAGACTGAATCTATCACATCCATTGAGTCATATATC
1 GCATATACCACAAAGACTGAATCTATCACATCTATTGAGGCATATATC
1049906 CAAATGATTG
Statistics
Matches: 166, Mismatches: 24, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
143 108 0.65
144 2 0.01
145 2 0.01
147 54 0.33
ACGTcount: A:0.42, C:0.21, G:0.14, T:0.24
Consensus pattern (147 bp):
GCATATACCACAAAGACTGAATCTATCACATCTATTGAGGCATATATCTCGAATATCCAAAACAG
TAACCAACTCCAACAAGAAAATGTTAAAAGAGAATACAACCATCAGCTAGAACTAGAGTACAAGA
CAAATAACTATTTGAAC
Found at i:1049966 original size:138 final size:140
Alignment explanation
Indices: 1049586--1049977 Score: 391
Period size: 143 Copynumber: 2.8 Consensus size: 140
1049576 GACAAGGATT
* * * * * * * *
1049586 GAATCTATCACATCTATTGAGGCATATATTCGAATATCCAAAACAGTAACCAACTCCAACCCGAA
1 GAATCTATCACATCCATTGAGG-ATACA--CTAATATCCAAAAGATTGACCAACTCCGACACGAA
* * * * *
1049651 AATGTTAAAAGAGAATACATGTATCAGCTAGAACTAGAGTGCAAAACAAACTATTTGAACGCATA
63 AATGTTAAAAGAGAATACAAGTATCAGCTAGAACTAGGGTACAAAAAAAACTATTTGAACACATA
1049716 TACCACAAAGACC
128 TACCACAAAGACC
* * * * *
1049729 GAATCTATCACATCTATTGAGGCATATATCTGAATATCCAAAAGATTGACCGACTCCGACAAGAT
1 GAATCTATCACATCCATTGAGG-ATACA-CT-AATATCCAAAAGATTGACCAACTCCGACACGAA
** *
1049794 AATGTTAAAAGAGAATACAACCATCAGCTAGAACTAGGGTACAAGACAAATTAATTATTTGAACA
63 AATGTTAAAAGAGAATACAAGTATCAGCTAGAACTAGGGTACAA-A-AAA--AACTATTTGAACA
* *
1049859 CATCTACCACAAAGACT
124 CATATACCACAAAGACC
* *
1049876 GAATCTATCACATCCATTGA-G-T-CA-T-ATATCCAAATGATTGGCCAACTCCGACACGAAAAT
1 GAATCTATCACATCCATTGAGGATACACTAATATCCAAAAGATTGACCAACTCCGACACGAAAAT
* * * *
1049936 ATT-AAAGAGAATGCAGGTATCAGCTAGAACTAGGGTGCAAAA
66 GTTAAAAGAGAATACAAGTATCAGCTAGAACTAGGGTACAAAA
1049978 TCTTTTGGGG
Statistics
Matches: 212, Mismatches: 32, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
136 1 0.00
137 1 0.00
138 32 0.15
139 32 0.15
141 1 0.00
142 2 0.01
143 93 0.44
144 2 0.01
145 2 0.01
146 1 0.00
147 45 0.21
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.23
Consensus pattern (140 bp):
GAATCTATCACATCCATTGAGGATACACTAATATCCAAAAGATTGACCAACTCCGACACGAAAAT
GTTAAAAGAGAATACAAGTATCAGCTAGAACTAGGGTACAAAAAAAACTATTTGAACACATATAC
CACAAAGACC
Found at i:1050182 original size:102 final size:101
Alignment explanation
Indices: 1050006--1050201 Score: 313
Period size: 102 Copynumber: 1.9 Consensus size: 101
1049996 AGCACTACGA
* * * *
1050006 AAATTTGTTTAATTAGCTCAGCAAGTGATTAGAAAACATTTTCGACCAGTCAAATCCGAGCTTGA
1 AAATTTGTTTAATTAGCTCAGCAAGTGATTACAAAACAATTTCGACCAGTCAAATACAAGCTTGA
1050071 AGATTGATAACATGGTTACCTTCAAATGTCATTTTGC
66 AGATTGATAACAT-GTTACCTTCAAATGTCATTTTGC
*
1050108 AAATTTGTTTAATTAGCTCAGCAAGTGATTACAAAACAATTTCTACC-GCTCAAATACAAGCTTG
1 AAATTTGTTTAATTAGCTCAGCAAGTGATTACAAAACAATTTCGACCAG-TCAAATACAAGCTTG
*
1050172 AAGATTGATAACATTTTACCTTCAAATGTC
65 AAGATTGATAACATGTTACCTTCAAATGTC
1050202 CCAACAGGCA
Statistics
Matches: 87, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
101 16 0.18
102 71 0.82
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.33
Consensus pattern (101 bp):
AAATTTGTTTAATTAGCTCAGCAAGTGATTACAAAACAATTTCGACCAGTCAAATACAAGCTTGA
AGATTGATAACATGTTACCTTCAAATGTCATTTTGC
Found at i:1051893 original size:21 final size:22
Alignment explanation
Indices: 1051867--1051911 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1051857 TAAATATATA
*
1051867 AAAAATTATAA-AAA-TATTTTT
1 AAAAA-TATAATAAATTATTATT
1051888 AAAAATATAATAAATTATTATT
1 AAAAATATAATAAATTATTATT
1051910 AA
1 AA
1051912 TTAAGTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAAATATAATAAATTATTATT
Found at i:1051906 original size:22 final size:21
Alignment explanation
Indices: 1051858--1051911 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
1051848 TTTAAACATT
*
1051858 AAATA-TATAAAAAATTATAA
1 AAATATTATTAAAAATTATAA
*
1051878 AAATATTTTTAAAAA-TATAA
1 AAATATTATTAAAAATTATAA
1051898 TAAATTATTATTAA
1 -AAA-TATTATTAA
1051912 TTAAGTTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 10 0.36
21 10 0.36
22 8 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
AAATATTATTAAAAATTATAA
Found at i:1056303 original size:30 final size:30
Alignment explanation
Indices: 1056269--1056380 Score: 143
Period size: 30 Copynumber: 3.7 Consensus size: 30
1056259 TTTACCTAAG
* *
1056269 TAAGCCCCTAACCTTTAATTTGCACTCAAA
1 TAAGCCCTTAACCTTTAATTTGCACCCAAA
* * * **
1056299 TAAGCCTTTAAACTTTAATTTGTACCCGGA
1 TAAGCCCTTAACCTTTAATTTGCACCCAAA
* *
1056329 TAAGCCTTTAACCTTTAATATGCACCCAAA
1 TAAGCCCTTAACCTTTAATTTGCACCCAAA
1056359 TAAGCCCTTAACCTTTAATTTG
1 TAAGCCCTTAACCTTTAATTTG
1056381 TACACAAAGG
Statistics
Matches: 68, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 68 1.00
ACGTcount: A:0.32, C:0.25, G:0.09, T:0.34
Consensus pattern (30 bp):
TAAGCCCTTAACCTTTAATTTGCACCCAAA
Found at i:1056399 original size:30 final size:30
Alignment explanation
Indices: 1056277--1056411 Score: 94
Period size: 30 Copynumber: 4.5 Consensus size: 30
1056267 AGTAAGCCCC
* * *
1056277 TAACCTTTAATTTGCACTCAAATAAGC-CTT
1 TAACCTTTAATTTGTACACAAAGAAGCAC-T
* * ** *
1056307 TAAACTTTAATTTGTACCCGGATAAGC-CTT
1 TAACCTTTAATTTGTACACAAAGAAGCAC-T
* * * * *
1056337 TAACCTTTAATATGCACCCAAATAAGCCCT
1 TAACCTTTAATTTGTACACAAAGAAGCACT
*
1056367 TAACCTTTAATTTGTACACAAAGGAGCACT
1 TAACCTTTAATTTGTACACAAAGAAGCACT
* *
1056397 TAAACTCTAATTTGT
1 TAACCTTTAATTTGT
1056412 GCCAAATAAA
Statistics
Matches: 86, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
30 85 0.99
31 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.34
Consensus pattern (30 bp):
TAACCTTTAATTTGTACACAAAGAAGCACT
Found at i:1057633 original size:20 final size:21
Alignment explanation
Indices: 1057608--1057674 Score: 86
Period size: 20 Copynumber: 3.3 Consensus size: 21
1057598 TATTAGATAC
*
1057608 AATATAAATATGACATAAAA-
1 AATATAAATATGATATAAAAT
* *
1057628 AATATAAATATAATAAAAAAT
1 AATATAAATATGATATAAAAT
1057649 AATATAAATATGATAT-AAAT
1 AATATAAATATGATATAAAAT
1057669 -ATATAA
1 AATATAA
1057675 GTGTTTAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
19 6 0.15
20 21 0.51
21 14 0.34
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (21 bp):
AATATAAATATGATATAAAAT
Found at i:1057642 original size:11 final size:11
Alignment explanation
Indices: 1057594--1057671 Score: 72
Period size: 11 Copynumber: 7.3 Consensus size: 11
1057584 AATAAGTATG
*
1057594 ATAATATTAGAT
1 ATAATA-TAAAT
*
1057606 ACAATATAAAT
1 ATAATATAAAT
* *
1057617 ATGACATAAA-
1 ATAATATAAAT
1057627 A-AATATAAAT
1 ATAATATAAAT
*
1057637 ATAATA-AAAA
1 ATAATATAAAT
1057647 ATAATATAAAT
1 ATAATATAAAT
*
1057658 ATGATATAAAT
1 ATAATATAAAT
1057669 ATA
1 ATA
1057672 TAAGTGTTTA
Statistics
Matches: 52, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
9 6 0.12
10 11 0.21
11 30 0.58
12 5 0.10
ACGTcount: A:0.63, C:0.03, G:0.04, T:0.31
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:1057793 original size:48 final size:50
Alignment explanation
Indices: 1057680--1057793 Score: 121
Period size: 48 Copynumber: 2.3 Consensus size: 50
1057670 TATAAGTGTT
* * *
1057680 TAAAAATTTATATAATATGAATTATTAATATATTAAGATTTATAAAAGTAT
1 TAAAAATATATA-AATATGAATTATTAATATATTAAAATTTATAAAAGTAA
*
1057731 TAAAAA-ATCTTAAATAT-AATTA-TAATATGA-TAAAATTTATAAACA-TAA
1 TAAAAATAT-ATAAATATGAATTATTAATAT-ATTAAAATTTATAAA-AGTAA
1057779 TAAAAATATATAAAT
1 TAAAAATATATAAAT
1057794 TACAAATCTA
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
48 31 0.57
49 9 0.17
50 6 0.11
51 8 0.15
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.39
Consensus pattern (50 bp):
TAAAAATATATAAATATGAATTATTAATATATTAAAATTTATAAAAGTAA
Found at i:1058316 original size:5 final size:5
Alignment explanation
Indices: 1058264--1058359 Score: 89
Period size: 5 Copynumber: 20.0 Consensus size: 5
1058254 CTATTAACAA
* * *
1058264 ATATT ATATTT ATATT A-ATT ATATTT AAATAT ATATC ATAAT -TATT
1 ATATT ATA-TT ATATT ATATT ATA-TT ATAT-T ATATT ATATT ATATT
1058310 ATATT AT-TT -T-TT ATATT -TATT ATA-T ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
1058355 ATATT
1 ATATT
1058360 TTTAAAAAAT
Statistics
Matches: 76, Mismatches: 6, Indels: 18
0.76 0.06 0.18
Matches are distributed among these distances:
3 3 0.04
4 18 0.24
5 42 0.55
6 13 0.17
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (5 bp):
ATATT
Found at i:1058563 original size:22 final size:21
Alignment explanation
Indices: 1058537--1058600 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 21
1058527 ATATTATTTT
1058537 TTATTTAAATTAATTTAAATTA
1 TTATTT-AATTAATTTAAATTA
*
1058559 TTATTT-ATTAATTAAAATAATA
1 TTATTTAATTAATTTAAAT--TA
1058581 TT-TTTAATTAATTT-AATTA
1 TTATTTAATTAATTTAAATTA
1058600 T
1 T
1058601 AATATATGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
19 3 0.08
20 11 0.30
21 6 0.16
22 17 0.46
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTATTTAATTAATTTAAATTA
Found at i:1058597 original size:18 final size:19
Alignment explanation
Indices: 1058545--1058597 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
1058535 TTTTATTTAA
*
1058545 ATTAATTTAAATTATTATTT
1 ATTAA-TTAAATTAATATTT
*
1058565 ATTAATTAAAATAATATTT
1 ATTAATTAAATTAATATTT
*
1058584 -TTAATTAATTTAAT
1 ATTAATTAAATTAAT
1058598 TATAATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 12 0.41
19 12 0.41
20 5 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTAATTAAATTAATATTT
Found at i:1060465 original size:25 final size:27
Alignment explanation
Indices: 1060435--1060490 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
1060425 ATTTATATTT
*
1060435 AATAT-ATA-TTTGAATAAAAATAAAA
1 AATATAATATTTTAAATAAAAATAAAA
* *
1060460 AATATAATATTTTAAATATATATAAAA
1 AATATAATATTTTAAATAAAAATAAAA
1060487 AATA
1 AATA
1060491 AAATTAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 5 0.19
26 3 0.12
27 18 0.69
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (27 bp):
AATATAATATTTTAAATAAAAATAAAA
Found at i:1061360 original size:15 final size:15
Alignment explanation
Indices: 1061357--1061910 Score: 357
Period size: 15 Copynumber: 36.7 Consensus size: 15
1061347 AAGAGATTAA
*
1061357 AAAACAAAAAAAGAAA
1 AAAA-AAAAAAAGAAT
1061373 AAAAAAAAAAAG-AT
1 AAAAAAAAAAAGAAT
1061387 -AAAAAAAAAAGAAT
1 AAAAAAAAAAAGAAT
*
1061401 AAAAATAAAAAAAGGAAAAA
1 -AAAA-AAAAAAA-G--AAT
*
1061421 AAGAAAAAAAAAGAGT
1 AA-AAAAAAAAAGAAT
*
1061437 AAAAAAAGAAGAAAAAT
1 AAAAAAA-AA-AAGAAT
1061454 AAAAAAAAAAACGAA-
1 AAAAAAAAAAA-GAAT
*
1061469 AAAGAGAAAAAAA-AAG
1 AAA-A-AAAAAAAGAAT
1061485 AGAAAAAAAAAA-AA-
1 A-AAAAAAAAAAGAAT
1061499 AAAAAAAAAAA-AAT
1 AAAAAAAAAAAGAAT
1061513 AAAAGAAAAAAA-AA-
1 AAAA-AAAAAAAGAAT
* *
1061527 AAAAAAAAAAAAAAA
1 AAAAAAAAAAAGAAT
1061542 AAAAAAAAAAAGAGA-
1 AAAAAAAAAAAGA-AT
*
1061557 AAAAAAAAAAA-AAA
1 AAAAAAAAAAAGAAT
*
1061571 AAAAAGAGAAAAAGAAA
1 AAAAA-A-AAAAAGAAT
*
1061588 AAAAAAAAAAAGAAA
1 AAAAAAAAAAAGAAT
1061603 AAAAAAAAAAAGAA-
1 AAAAAAAAAAAGAAT
* **
1061617 AAAACAAAAACCAA-
1 AAAAAAAAAAAGAAT
* *
1061631 AAAAAAGAAAAAAAAA
1 AAAAAA-AAAAAGAAT
1061647 AAAAAAAAAAAG-AT
1 AAAAAAAAAAAGAAT
* *
1061661 AAAAAAAACAGAGAAA
1 AAAAAAAA-AAAGAAT
1061677 AAAAAAAAAAAGAA-
1 AAAAAAAAAAAGAAT
*
1061691 AAAAAAAAAAA-AAA
1 AAAAAAAAAAAGAAT
* *
1061705 AAAAAAAAAAAAAAC
1 AAAAAAAAAAAGAAT
*
1061720 AAAAAAAAAAA-AAA
1 AAAAAAAAAAAGAAT
* *
1061734 AAAAAAAAAAACAAC
1 AAAAAAAAAAAGAAT
1061749 ACAAAAAAAAAAG-A-
1 A-AAAAAAAAAAGAAT
1061763 AAAAAAAAAAAGAAT
1 AAAAAAAAAAAGAAT
*
1061778 AAAAAAAAAAA-AAA
1 AAAAAAAAAAAGAAT
*
1061792 AGAAAAAAAAAAGGGGGGGA-
1 A-AAAAAAAAAA-----GAAT
**
1061812 AAAAAAAAAAAGAGG
1 AAAAAAAAAAAGAAT
*
1061827 AAGAAAAAAGAA-AAT
1 AA-AAAAAAAAAGAAT
*
1061842 AAAAAAAAGAAAAAAT
1 AAAAAAAA-AAAGAAT
* *
1061858 AAAGAAAAAAA-AAC
1 AAAAAAAAAAAGAAT
* * **
1061872 AAAGAAAGAGTGAA-
1 AAAAAAAAAAAGAAT
1061886 AAAAAAAAAAAGAA-
1 AAAAAAAAAAAGAAT
1061900 AAAAAATAAAA
1 AAAAAA-AAAA
1061911 CCACATTAAA
Statistics
Matches: 451, Mismatches: 40, Indels: 95
0.77 0.07 0.16
Matches are distributed among these distances:
13 44 0.10
14 118 0.26
15 158 0.35
16 69 0.15
17 35 0.08
18 2 0.00
19 19 0.04
20 5 0.01
21 1 0.00
ACGTcount: A:0.87, C:0.02, G:0.09, T:0.02
Consensus pattern (15 bp):
AAAAAAAAAAAGAAT
Found at i:1061376 original size:30 final size:26
Alignment explanation
Indices: 1061355--1061910 Score: 489
Period size: 28 Copynumber: 20.5 Consensus size: 26
1061345 AAAAGAGATT
*
1061355 AAAAAACAAAAAAAGAAAAAAAAAAA
1 AAAAAAAAAAAAAAGAAAAAAAAAAA
* *
1061381 AAAGATAAAAAAAAAAGAATAAAAATAA
1 AAA-A-AAAAAAAAAAGAAAAAAAAAAA
**
1061409 AAAAAGGAAAAAAAG--AAAAAAAAA
1 AAAAAAAAAAAAAAGAAAAAAAAAAA
* ** *
1061433 GAGTAAAAAAAGAAGAAAAATAAAAAA
1 AAAAAAAAAAAAAAGAAAAA-AAAAAA
** *
1061460 AAAAACGAAAAAGAGAAAAAAAAAGAGA
1 AAAAAAAAAAAAAAGAAAAAAAAA-A-A
1061488 AAAAAAAAAAAAAA-AAAAAAAAAATA
1 AAAAAAAAAAAAAAGAAAAAAAAAA-A
1061514 AAAGAAAAAAAAAAA-AAAAAAAAAAA
1 AAA-AAAAAAAAAAAGAAAAAAAAAAA
1061540 AAAAAAAAAAAAAGAGAAAAAAAAAAAA
1 AAAAAAAAAAAAA-AG-AAAAAAAAAAA
1061568 AAAAAAAAGAGAAAAAGAAAAAAAAAAA
1 AAAAAAAA-A-AAAAAGAAAAAAAAAAA
*
1061596 AAAGAAAAAAAAAAA-AAAGAAAAAACA
1 AAA-AAAAAAAAAAAGAAA-AAAAAAAA
**
1061623 AAAACCAAAAAAAAGAAAAAAAAAAA
1 AAAAAAAAAAAAAAGAAAAAAAAAAA
1061649 AAAAAAAAAGATAAAA-AAAACAGAGAAAAA
1 AAAAAAAAA-A-AAAAGAAAA-A-A-AAAAA
1061679 AAAAAAAAAGAAAAA-AAAAAAAAAAA
1 AAAAAAAAA-AAAAAGAAAAAAAAAAA
*
1061705 AAAAAAAAAAAAAACAAAAAAAAAAA
1 AAAAAAAAAAAAAAGAAAAAAAAAAA
*
1061731 AAAAAAAAAAAAAACAACACAAAAAAAA
1 AAAAAAAAAAAAAAGAA-A-AAAAAAAA
1061759 AAGAAAAAAAAAAAAGAATAAAAAAAAA
1 AA-AAAAAAAAAAAAGAA-AAAAAAAAA
*****
1061787 AAAAAAGAAAAAAAA-AAGGGGGGGAAAA
1 AAAAAA-AAAAAAAAGAA--AAAAAAAAA
* **
1061815 AAAAAAAAGAGGAAGAAAAAAGAAAATA
1 AAAAAAAAAAAAAAGAAAAAA-AAAA-A
* * *
1061843 AAAAAAAGAAAAAATAAAGAAAAAAA
1 AAAAAAAAAAAAAAGAAAAAAAAAAA
* * * **
1061869 AACAAAGAAAGAGTGAAAAAAAAAAA
1 AAAAAAAAAAAAAAGAAAAAAAAAAA
1061895 AAGAAAAAAAATAAAA
1 AA-AAAAAAAA-AAAA
1061911 CCACATTAAA
Statistics
Matches: 433, Mismatches: 65, Indels: 62
0.77 0.12 0.11
Matches are distributed among these distances:
24 16 0.04
25 15 0.03
26 118 0.27
27 101 0.23
28 131 0.30
29 32 0.07
30 20 0.05
ACGTcount: A:0.87, C:0.02, G:0.09, T:0.02
Consensus pattern (26 bp):
AAAAAAAAAAAAAAGAAAAAAAAAAA
Found at i:1061593 original size:135 final size:128
Alignment explanation
Indices: 1061339--1061910 Score: 537
Period size: 134 Copynumber: 4.3 Consensus size: 128
1061329 TAAGCTACAG
* * * *
1061339 AAAAAAAAAAGAGATTAAAAAACAAAAAAAGAAAAAAAAAAAAAAGATAAAAAAAAAAGAATAAA
1 AAAAAAAAAAAAGA--AAAAAA-AAAAAAA-AAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAA
* ** * ** * * * *
1061404 AATAAAAAAAGGAAAAAA-AGAAAAAAAAAGAGTAAAAAAAGAAGAAAAATAAAAAAAAAAACGA
62 AAAAAAAAAAAAAAAAAAGAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAGA
1061468 AA
127 AA
1061470 AAGAGAAAAAAAAAGAGAAAAAAAAAAAAAAAAAAAAAAAAATAAAAGAAAAAAAAAAA-AAAAA
1 AA-A-AAAAAAAAAGA-AAAAAAAAAAAAAAAAAAAAAAAAA-AAAA-AAAAAAAAAAAGAAAAA
*
1061534 AAAAAAAAAAAAAAAAAAAGAGAAAAAAAAAAAAAAAAAAAAGAGAAAAAGAA-AAAAAAAAAAA
61 AAAAAAAAAAAAAAAAAAAGAGAAAAAAAAAAAAAAAAAAAA-A-AAAAAAAACAAAAAAAAAAA
1061598 AG-AA
124 AGAAA
* *
1061602 AAAAAAAAAAAAGAAAAAACAAAAACCAAAAAAAAGAAAAAAAAAAAAAAAAAAAAGATAAAAAA
1 AAAAAAAAAAAAGAAAAAA-AAAAA-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGA-AAAAAA
1061667 AACAGAGAAAAAAAAAAAAA-AGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAA
63 AA-A-A-AAAAAAAAAAAAAGAG-AAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAA
1061731 A-AAA
124 AGAAA
* *
1061735 AAAAAAAAAACAACACAAAAAAAAAAGAAAAAAAAAAAAGAATAAAAAAAAAAAAAAAGAAAAAA
1 AAAAAAAAAA-AAGA-AAAAAAAAAA-AAAAAAAAAAAA-AAAAAAAAAAAAAAAAAAGAAAAAA
** *
1061800 AAAAGGGGGGGAAAAAAAAAAAAGAGGAAGAAAAAAGAAAATAAAAAAAAGAAAAAATAAAGAAA
62 AAAA-----AAAAAAAAAAAAAAGA-GAA-AAAAAA-AAAA-AAAAAAAA-AAAAAA-AAACAAA
1061865 AAAAAACAAAGAAA
116 AAAAAA-AAAGAAA
* *** * *
1061879 GAGTGAAAAAAA-AAAAAAGAAAAAAAATAAAA
1 AAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAA
1061911 CCACATTAAA
Statistics
Matches: 376, Mismatches: 32, Indels: 57
0.81 0.07 0.12
Matches are distributed among these distances:
129 16 0.04
130 33 0.09
131 54 0.14
132 48 0.13
133 51 0.14
134 65 0.17
135 24 0.06
136 12 0.03
137 4 0.01
138 7 0.02
139 4 0.01
140 16 0.04
141 15 0.04
142 13 0.03
143 5 0.01
144 9 0.02
ACGTcount: A:0.87, C:0.02, G:0.09, T:0.02
Consensus pattern (128 bp):
AAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAA
AAAAAAAAAAAAAAGAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAGAAA
Found at i:1061802 original size:120 final size:117
Alignment explanation
Indices: 1061355--1061910 Score: 566
Period size: 122 Copynumber: 4.6 Consensus size: 117
1061345 AAAAGAGATT
* * * * *
1061355 AAAAAACAAAAAAAGAAAAAAAAAAAAAAGATAAAAA-AAAAAGAATAAAAATAAAAAAAGGAAA
1 AAAAAAGAAAAAAA-AAAAAAAAAAAAAA-A-AAAAACAAAAAAAAAAAAAAAAAAAAAAAGAAA
* ** * *
1061419 AAAAGAAAAAAAAAGAGTAAAAAAAGAAGAAAAATAAAAAAAAAAACGAAAAAGAGAAA
63 AAAA-AAAAAAAAAGAG-AAAAAAA-AA-AAAAAGAAAAAAAAAAAAAAAAAAAAAAAA
* *
1061478 AAAAAAGAGAAAAAAAAAAAAAAAAAAAAAAAAATAAAAGAAAAAAAAAAAAAAAAAAA-AAAAA
1 AAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAA-AAAAAAAAAAAAAAAAAAAGAAAAA
* * *
1061542 AAAAAAAAAAAGAG-AAAAAAAAAAAAA-AAAAAAAGAGAAAAAGAAAAAAAA
65 AAAAAAAAAAAGAGAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAA
* *
1061593 AAAAAAGAAAAAAAAAAAAAAGAAAAAACAAAAACCAAAAAAAAGAAAAAAAAAAAAAAA-AAAA
1 AAAAAAGAAAAAAAAAAAAAA-AAAAAAAAAAAAACAAAAAAAA-AAAAAAAAAAAAAAAGAAAA
*
1061657 AGATAAAAAAAACAGAGAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAA
64 A-A-AAAAAAAAAAGAGAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAA
*
1061713 AAAAAACAAAAAAAAAAAAAAAAAAAAAAAAACAACACAAAAAAAAAAGAAAAAAAAAAAAGAAT
1 AAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAA-AACA-AAAAAAAAAA-AAAAAAAAAAAAGAA-
**** * ** *
1061778 AAAAAAAAAAAAAA-AGAAAAAAAAAAGGGGGGGAAAAAAAAAAAAGAGGAAGAAAAA
62 AAAAAAAAAAAAAAGAGAAAAAAAAAA--AAAAGAAAAAAAAAAAAAAAAAAAAAAAA
* * * ***
1061835 AGAAAATAAAAAAAAGAAAAAATAAAGAAAAAAAAACAAAGAAAGAGTGAAAAAAAAAAAAAGAA
1 AAAAAAGAAAAAAAA-AAAAAA-AAAAAAAAAAAAACAAA-AAA-AAAAAAAAAAAAAAAAAGAA
*
1061900 AAAAAATAAAA
62 AAAAAAAAAAA
1061911 CCACATTAAA
Statistics
Matches: 374, Mismatches: 40, Indels: 39
0.83 0.09 0.09
Matches are distributed among these distances:
115 41 0.11
116 40 0.11
117 3 0.01
118 18 0.05
119 23 0.06
120 76 0.20
121 40 0.11
122 78 0.21
123 43 0.11
124 12 0.03
ACGTcount: A:0.87, C:0.02, G:0.09, T:0.02
Consensus pattern (117 bp):
AAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAGAAAAAA
AAAAAAAAAAGAGAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAA
Found at i:1061815 original size:32 final size:32
Alignment explanation
Indices: 1061337--1061910 Score: 369
Period size: 31 Copynumber: 18.0 Consensus size: 32
1061327 TCTAAGCTAC
** *
1061337 AGAAAAAAAAAAGAG-ATTAAAAAACAAAAAA
1 AGAAAAAAAAAAGAGAAGAAAAAAAAAAAAAA
*
1061368 AGAAAAAAAAAA-AAAAGATAAAAAAAAAAGAATA
1 AGAAAAAAAAAAGAGAAGA-AAAAAAAAAA-AA-A
*
1061402 A-AAATAAAAAAAG-GAA-AAAAAGAAAAAAAA
1 AGAAA-AAAAAAAGAGAAGAAAAAAAAAAAAAA
**
1061432 AGAGTAAAAAAAGAAGAA-AAATAAAAAAAAAAA
1 AGAAAAAAAAAAG-AGAAGAAA-AAAAAAAAAAA
* * *
1061465 CGAAAAAGAGAAAAAAAAAGAGAAAAAAAAAAAAA
1 AGAAAAA-A-AAAAGAGAAGA-AAAAAAAAAAAAA
* * *
1061500 AAAAAAAAAAAATAAAAGAAAAAAAAAAAAAA
1 AGAAAAAAAAAAGAGAAGAAAAAAAAAAAAAA
* *
1061532 A-AAAAAAAAAA-AAAAAAAAAAGAGAAAAAAAA
1 AGAAAAAAAAAAGAGAAGAAAAA-A-AAAAAAAA
* *
1061564 AAAAAAAAAAAAGAGAAAAAGAAAAAAAAAAAAA
1 AGAAAAAAAAAAGAG-AAGA-AAAAAAAAAAAAA
* **
1061598 AGAAAAAAAAAA-AAAAGAAAAAACAAAAACCA
1 AGAAAAAAAAAAGAGAAGAAAAAA-AAAAAAAA
*
1061630 A-AAAAAAGAAA-A-AA-AAAAAAAAAAAAAA
1 AGAAAAAAAAAAGAGAAGAAAAAAAAAAAAAA
* *
1061658 -GATAAAAAAAACAG-AG-AAAAAAAAAAAAA
1 AGAAAAAAAAAAGAGAAGAAAAAAAAAAAAAA
* *
1061687 AGAAAAAAAAAA-AAAAAAAAAAAAAAAAAAA
1 AGAAAAAAAAAAGAGAAGAAAAAAAAAAAAAA
*
1061718 ACAAAAAAAAAA-A-AA-AAAAAAAAAAAACAA
1 AGAAAAAAAAAAGAGAAGAAAAAAAAAAAA-AA
*
1061748 CACAAAAAAAAAAGA-AA-AAAAAAAAAGAATAAA
1 -AGAAAAAAAAAAGAGAAGAAAAAAAAA-AA-AAA
*****
1061781 A-AAAAAAAAAA-AGAA-AAAAAAAAGGGGGGGA
1 AGAAAAAAAAAAGAGAAGAAAAAAAA--AAAAAA
1061812 A-AAAAAAAAAAGAGGAAGAAAAAAGAAAATAAAA
1 AGAAAAAAAAAAGA-GAAGAAAAAA-AAAA-AAAA
* *
1061846 A-AAAGAAAAAATA-AAGAAAAAAAAACAAAGAA
1 AGAAAAAAAAAAGAGAAGAAAAAAAAA-AAA-AA
* *
1061878 AGAGTGAAAAAAAAA-AAAAGAAAAAAAATAAAA
1 AGA---AAAAAAAAAGAGAAGAAAAAAAAAAAAA
1061911 CCACATTAAA
Statistics
Matches: 448, Mismatches: 47, Indels: 93
0.76 0.08 0.16
Matches are distributed among these distances:
28 14 0.03
29 34 0.08
30 38 0.08
31 116 0.26
32 84 0.19
33 49 0.11
34 56 0.12
35 32 0.07
36 25 0.06
ACGTcount: A:0.86, C:0.02, G:0.09, T:0.02
Consensus pattern (32 bp):
AGAAAAAAAAAAGAGAAGAAAAAAAAAAAAAA
Found at i:1061822 original size:1 final size:1
Alignment explanation
Indices: 1061355--1061803 Score: 457
Period size: 1 Copynumber: 449.0 Consensus size: 1
1061345 AAAAGAGATT
* * * * * * * **
1061355 AAAAAACAAAAAAAGAAAAAAAAAAAAAAGATAAAAAAAAAAGAATAAAAATAAAAAAAGGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * ** * * * ** * * *
1061420 AAAGAAAAAAAAAGAGTAAAAAAAGAAGAAAAATAAAAAAAAAAACGAAAAAGAGAAAAAAAAAG
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
1061485 AGAAAAAAAAAAAAAAAAAAAAAAAAATAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * *
1061550 AAAGAGAAAAAAAAAAAAAAAAAAAAGAGAAAAAGAAAAAAAAAAAAAAGAAAAAAAAAAAAAAG
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* ** * * * * * *
1061615 AAAAAACAAAAACCAAAAAAAAGAAAAAAAAAAAAAAAAAAAAGATAAAAAAAACAGAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
1061680 AAAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * *
1061745 CAACACAAAAAAAAAAGAAAAAAAAAAAAGAATAAAAAAAAAAAAAAAGAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1061804 GGGGGGGAAA
Statistics
Matches: 356, Mismatches: 92, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 356 1.00
ACGTcount: A:0.89, C:0.02, G:0.07, T:0.02
Consensus pattern (1 bp):
A
Found at i:1061889 original size:74 final size:69
Alignment explanation
Indices: 1061355--1061910 Score: 515
Period size: 69 Copynumber: 8.1 Consensus size: 69
1061345 AAAAGAGATT
* * * *
1061355 AAAAAACAAAAAAAGAAAAAAAAA-AAAAAGATAAAAAAAAAAGA-ATAAAAATAAAAAAAG-G-
1 AAAAAAAAAAAAAAGAAAAAAAAAGAAAAA-AAAAAAAAAAAAGAGAGAAAAAAAAAAAAAGAGA
1061416 AAAAA
65 AAAAA
* * *
1061421 AAGAAAAAAAAAGAGTAAAAAAAGAAGAAAAATAAAAAAAAAAACGA-A-AAAGAGAAAAAAAAA
1 AAAAAAAAAAAAAAG-AAAAAAA-AAGAAAAA-AAAAAAAAAAAAGAGAGAAA-A-AAAAAAAAA
1061484 GAGAAAAAA
61 GAGAAAAAA
* * *
1061493 AAAAAAAAAAAAAA-AAAAATAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAGA
1 AAAAAAAAAAAAAAGAAAAA-AAAAGAAAAAAAAAAAAAAAAAGAGAGAAAAAAAAAAAAAGAGA
1061557 AAAAA
65 AAAAA
* *
1061562 AAAAAAAAAAAAAAGAGAAAAAGAAA-AAAAAAAAAAAGAAAAAA-A-A-AAAAAAGAAAAAACA
1 AAAAAAAAAAAAAAGA-AAAAA-AAAGAAAAAAAAAAA-AAAAAAGAGAGAAAAAAAAAAAAAGA
**
1061623 -AAAACC
63 GAAAAAA
* * * *
1061629 AAAAAAAAGAAAAA-AAAAAAAAA-AAAAAAGATAAAAAAAACAGAGAAAAAAAAAAAAA-AGAA
1 AAAAAAAAAAAAAAGAAAAAAAAAGAAAAAAAAAAAAAAAAAGAGAGAAAAAAAAAAAAAGAGAA
1061691 AAAA
66 AAAA
* * * *
1061695 AAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAA-A-A-AAAAAACAACACAA-A-A
1 AAAAAAAAAAAAAAGAAAAAAAAAGAAAAAAAAAAAAAAAAAGAGAGAAAAAA-AAAAAAAGAGA
1061755 AAAAA
65 AAAAA
* * * * *
1061760 AGAAAAAAAAAAAAGAATAAAAAAAAAAAAAAAGAAAAAAAAAAGGGGGGGAAAAAAAAAAAAGA
1 AAAAAAAAAAAAAAGAA-AAAAAAAGAAAAAAA-AAAAAAAAAA-GAGAGAAAAAAAAAAAAAGA
1061825 GGAAGAAAA
63 -GAA-AAAA
* * *
1061834 AAGAAAATAAAAAAAAGAAAAAATAAAGAAAAAAAAACAAAGAAAGAGTGAAAAAAAAAAAAAGA
1 AA-AAAA-AAAAAAAAGAAAAAA-AAAGAAAAAAAAAAAAAAAAAGAGAGAAAAAAAAAAAAAGA
1061899 -AAAAAA
63 GAAAAAA
*
1061905 ATAAAA
1 AAAAAA
1061911 CCACATTAAA
Statistics
Matches: 414, Mismatches: 42, Indels: 64
0.80 0.08 0.12
Matches are distributed among these distances:
63 6 0.01
64 13 0.03
65 34 0.08
66 63 0.15
67 44 0.11
68 33 0.08
69 64 0.15
70 47 0.11
71 30 0.07
72 19 0.05
73 2 0.00
74 22 0.05
75 16 0.04
76 21 0.05
ACGTcount: A:0.87, C:0.02, G:0.09, T:0.02
Consensus pattern (69 bp):
AAAAAAAAAAAAAAGAAAAAAAAAGAAAAAAAAAAAAAAAAAGAGAGAAAAAAAAAAAAAGAGAA
AAAA
Found at i:1061931 original size:152 final size:134
Alignment explanation
Indices: 1061370--1062002 Score: 547
Period size: 135 Copynumber: 4.5 Consensus size: 134
1061360 ACAAAAAAAG
* *
1061370 AAAAAAAAAAAAAAGATAAAAAAAAA-AGA-ATAAAAATAAAAAA-AGGAAAAAAAGAAAAAAAA
1 AAAAAAAAAAAAAAGA-AAAAAAAAACAGAGA-AAAAA-AAAAAAGAGAAAAAAAAAAAAAAAAA
*
1061432 AGAGTAAAAAAAGAAGAAAAATAAAAAAAAAAACGAAAAAGAGAAAAAAAAAGAGAAAAAAAAAA
63 AAAG-AAAAAAA-AAG-AAAA-AAAAAAAAAAA-G--AAA-A-AAAAAAAAA-AGAAAAAAAAAA
** *
1061497 AAAAAAAAAAAAAAATA
118 AACCAAAAAAGAAAATA
1061514 AAAGAAAAAAAAAAA-AAAAAAAAAA-A-A-AAAAAAAAAAAAGAGAAAAAAAAAAAAAAAAAAA
1 AAA-AAAAAAAAAAAGAAAAAAAAAACAGAGAAAAAAAAAAAAGAGAAAAAAAAAAAAAAAAAAA
* *
1061575 AG--AGAAAAAG-AAAAAAAAAAAAAAGAAAAAAAAAAAAAAGAAAAAACAAAAACCAAAAAAAA
65 AGAAAAAAAAAGAAAAAAAAAAAAAAAGAAAAAAAAAAAAAAGAAAAAAAAAAAACC--AAAAAA
*
1061637 GAAAAAA
128 GAAAATA
* *
1061644 AAAAAAAAAAAAAAGATAAAAAAAACAGAGAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAGAAAAAAAAAACAGAGAAAAAAAAAAAAGAGAAAAAAAAAAAAAAAAAAAA
* * * * * *
1061709 AAAAAAAAAACAAAAAAAAAAAAAAA-AAAAAAAAAACAACACAAAAAAAAAAGAA-AAAAAAAA
66 GAAAAAAAAAGAAAAAAAAAAAAAAAGAAAAAAAAAA-AAAAGAAAAAAAAAA-AACCAAAAAAG
1061772 AAGAATA
129 AA-AATA
** *
1061779 AAAAAAAAAAAAAAGAAAAAAAAAAGGGGGGGAAAAAAAAAAAAGAGGAAGAAAAAAGAAAATAA
1 AAAAAAAAAAAAAAGAAAAAAAAAA--CAGAGAAAAAAAAAAAAGA-GAA-AAAAAA-AAAA-AA
1061844 AAAAAAGAAAAAATAAAGAAAAAAAAACAAAGAAAGAGTGAAAAAAAAAAAAAGAAAAAAAATAA
60 AAAAAAGAAAAAA-AAAGAAAAAAAAA-AAA-AAAGA---AAAAAAAAAAAAAGAAAAAAAA-AA
1061909 AACCACATTAAAAGCAACAATA
118 AACCA-A--AAAAG-AA-AATA
* * * * * *
1061931 AAAATTAAAACAAAAAAAACAAAAAATAAATCATA-AAGAAAAAAATA-AGAACAAAAAAAAACA
1 AAAA--AAAA-AAAAAAGA-AAAAAA-AAA-CAGAGAAAAAAAAAAAAGAGAAAAAAAAAAAAAA
1061994 AAAAAAGAA
60 AAAAAAGAA
1062003 GGCTGCAAAC
Statistics
Matches: 409, Mismatches: 42, Indels: 70
0.79 0.08 0.13
Matches are distributed among these distances:
128 13 0.03
129 20 0.05
130 24 0.06
131 4 0.01
132 1 0.00
133 35 0.09
134 19 0.05
135 46 0.11
136 26 0.06
137 20 0.05
138 7 0.02
139 6 0.01
140 10 0.02
141 39 0.10
142 14 0.03
143 13 0.03
144 7 0.02
145 12 0.03
147 13 0.03
148 12 0.03
149 1 0.00
150 10 0.02
151 8 0.02
152 15 0.04
153 3 0.01
154 5 0.01
155 17 0.04
156 6 0.01
157 3 0.01
ACGTcount: A:0.85, C:0.03, G:0.08, T:0.03
Consensus pattern (134 bp):
AAAAAAAAAAAAAAGAAAAAAAAAACAGAGAAAAAAAAAAAAGAGAAAAAAAAAAAAAAAAAAAA
GAAAAAAAAAGAAAAAAAAAAAAAAAGAAAAAAAAAAAAAAGAAAAAAAAAAAACCAAAAAAGAA
AATA
Found at i:1061990 original size:156 final size:142
Alignment explanation
Indices: 1061356--1061999 Score: 469
Period size: 141 Copynumber: 4.5 Consensus size: 142
1061346 AAAGAGATTA
* *
1061356 AAAAACAAAAAAAGAAAAAAAAAAAAAA-GATAAAAAAAAAAGAATAAAAATAAAAAAAGGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAATGATAAAAAAAAAA-AA-AAAAA-AAAAAAA-GAAAA
* * * * *
1061420 AAAGAAAAA-AAAAGAGTAAAAAAAGAAGAA-AAATAAAAA-AAAAAACGAAAAAGAGAAAAAAA
62 AAA-AAAAAGAAAA-A--AAAAAAAAAAAAACAAAGAAAAAGAAAAAA-AAAAAAAAGAAAAAAA
*
1061482 AAGAGAAAAAAAAAA-AAAAA-
122 AA-AAAAAAAAAAAACAAAAAT
* * *
1061502 AAAAAAAAAATAAAAGAAAAAAAAAAAA--A-AAAAAAAAAAAAAAAAAAAAAAGAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAATGATAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAA
* * *
1061564 AAAA-AAAAAAAAGAGAAAAAGAAAAAAAAAAAAAAGAAAAAAAAAAAAAAGAAAAAACAAAAAC
66 AAAAGAAAAAAAA-A-AAAAA-AAAACAAAGAAAAAGAAAAAAAAAAAAAAGAAAAAA-AAAAAA
* *
1061628 CAAAAAAAAGAAAAA-
127 AAAAAAAAACAAAAAT
* * * * *
1061643 AAAAAAAAAAAAAAAGATAAAAAAAACA-GAGAAAAAAAAAAAAAAGAAAAAAAAA-AAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAATGATAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAA
* * * * *
1061706 AAAA-AAAAAAAAACAAAAAAAA-AAA-AAAAA-AAAAAAAAACAACACAAAAAAAAAAGAAAAA
66 AAAAGAAAAAAAAAAAAAAAAAACAAAGAAAAAGAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAA
*
1061767 AAAAA-AAGAAT
131 AAAAACAAAAAT
**** ** ** *
1061778 AAAAAAAAAAAAAAAGAAAAAAAAAAGGGGGGGAAAAAAAAAAAAGAGGAAGAAAAAAGAAAATA
1 AAAAAAAAAAAAAAA-AAAAAAAAAAAAATGATAAAAAAAAAAAA-AAAAAAAAAAAAGAAAA-A
* *
1061843 AAAAAAAGAAAAAATAAAGAAAAAAAAACAAAGAAAGAGTGAAAAAAAAAAAAAGAAAAAAAATA
63 AAAAAAAGAAAAAA-AAA-AAAAAAAAACAAAGAAAAAG-AAAAAAAAAAAAAAGAAAAAAAA-A
** * *
1061908 AAACCACATTAAAAGCAACAAT
124 AAA--A-AAAAAAAACAAAAAT
* * * * *
1061930 AAAAATTAAAACAAAAAAAACAAAAAATAAATCATAAAGAAAAAAATAAGAACAAAAAAAAACAA
1 AAAAA--AAAA-AAAAAAAAAAAAAAAAAAATGATAAA-AAAAAAA-AA-AAAAAAAAAAAAGAA
1061995 AAAAA
60 AAAAA
1062000 GAAGGCTGCA
Statistics
Matches: 408, Mismatches: 58, Indels: 55
0.78 0.11 0.11
Matches are distributed among these distances:
134 4 0.01
135 27 0.07
136 29 0.07
137 20 0.05
138 18 0.04
139 20 0.05
140 50 0.12
141 52 0.13
142 29 0.07
143 32 0.08
144 13 0.03
145 5 0.01
146 24 0.06
147 19 0.05
148 3 0.01
150 1 0.00
151 5 0.01
152 10 0.02
154 15 0.04
155 16 0.04
156 16 0.04
ACGTcount: A:0.85, C:0.03, G:0.08, T:0.03
Consensus pattern (142 bp):
AAAAAAAAAAAAAAAAAAAAAAAAAAAATGATAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAA
AAAAGAAAAAAAAAAAAAAAAAACAAAGAAAAAGAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAA
AAAAACAAAAAT
Found at i:1062606 original size:23 final size:21
Alignment explanation
Indices: 1062573--1062615 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
1062563 TATTTTAAAA
*
1062573 TATATTTAATAATATAAATTTTT
1 TATATTAAATAA-AT-AATTTTT
1062596 TATATTAAATAAATAATTTT
1 TATATTAAATAAATAATTTT
1062616 ATATTTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 2 0.11
23 11 0.58
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TATATTAAATAAATAATTTTT
Found at i:1063339 original size:23 final size:23
Alignment explanation
Indices: 1063313--1063361 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
1063303 AATAAAAATT
* *
1063313 TAAAATT-TTTAACTTAATATAAA
1 TAAAATTAATTAAATTAA-ATAAA
1063336 TAAAATTAATTAAATTAAATAAA
1 TAAAATTAATTAAATTAAATAAA
1063359 TAA
1 TAA
1063362 TTTAACCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
TAAAATTAATTAAATTAAATAAA
Found at i:1063348 original size:19 final size:20
Alignment explanation
Indices: 1063321--1063358 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
1063311 TTTAAAATTT
1063321 TTAACTT-AATATAAATAAAA
1 TTAACTTAAAT-TAAATAAAA
1063341 TTAA-TTAAATTAAATAAA
1 TTAACTTAAATTAAATAAA
1063359 TAATTTAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (20 bp):
TTAACTTAAATTAAATAAAA
Found at i:1063641 original size:11 final size:11
Alignment explanation
Indices: 1063625--1063758 Score: 70
Period size: 11 Copynumber: 12.5 Consensus size: 11
1063615 AAGTATTTAA
1063625 ATATTTATATT
1 ATATTTATATT
1063636 ATATTTATATT
1 ATATTTATATT
1063647 AT-TTT-TA-T
1 ATATTTATATT
*
1063655 ATA-TTATGATG
1 ATATTTAT-ATT
1063666 ATATTTAAGGTATT
1 ATATTT-A--TATT
*
1063680 AT-GTTA-A-T
1 ATATTTATATT
1063688 A-ATTTATATT
1 ATATTTATATT
** *
1063698 ATATAAATTTT
1 ATATTTATATT
*
1063709 GATATTTTTATT
1 -ATATTTATATT
* *
1063721 -TATTTGTATC
1 ATATTTATATT
1063731 ATATTTATATT
1 ATATTTATATT
* *
1063742 ATTTTTGTATT
1 ATATTTATATT
1063753 ATATTT
1 ATATTT
1063759 TTATATCGTT
Statistics
Matches: 91, Mismatches: 18, Indels: 28
0.66 0.13 0.20
Matches are distributed among these distances:
8 10 0.11
9 5 0.05
10 14 0.15
11 44 0.48
12 10 0.11
13 3 0.03
14 4 0.04
15 1 0.01
ACGTcount: A:0.33, C:0.01, G:0.06, T:0.60
Consensus pattern (11 bp):
ATATTTATATT
Found at i:1064206 original size:29 final size:29
Alignment explanation
Indices: 1064174--1064240 Score: 66
Period size: 29 Copynumber: 2.3 Consensus size: 29
1064164 TAAATTTATC
* *
1064174 ATATCATATTTATTAT-ATTATTTTTATAT
1 ATATCATATTTATAATAATT-TTATTATAT
* * *
1064203 ATATTAAATTTGTAATAATTTTATTATAT
1 ATATCATATTTATAATAATTTTATTATAT
1064232 AT-TCATATT
1 ATATCATATT
1064241 ATGTTCAATT
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
28 5 0.17
29 22 0.73
30 3 0.10
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.58
Consensus pattern (29 bp):
ATATCATATTTATAATAATTTTATTATAT
Found at i:1064207 original size:12 final size:13
Alignment explanation
Indices: 1064167--1064207 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
1064157 TTAAATTTAA
*
1064167 ATTTATCATATCAT
1 ATTTATTATAT-AT
1064181 ATTTATTATAT-T
1 ATTTATTATATAT
1064193 ATTT-TTATATAT
1 ATTTATTATATAT
1064205 ATT
1 ATT
1064208 AAATTTGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
11 6 0.24
12 9 0.36
14 10 0.40
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (13 bp):
ATTTATTATATAT
Found at i:1064314 original size:22 final size:21
Alignment explanation
Indices: 1064271--1064327 Score: 53
Period size: 22 Copynumber: 2.7 Consensus size: 21
1064261 TATTTAATAT
**
1064271 ACATTTTAATTTTATGTCTTG
1 ACATTTTAATTTTAAATCTTG
1064292 AGCATTTTAATTTTTAAAT-TTG
1 A-CATTTTAA-TTTTAAATCTTG
* *
1064314 ACATATTAAATTTA
1 ACATTTTAATTTTA
1064328 TATAATTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
20 4 0.13
21 8 0.27
22 12 0.40
23 6 0.20
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (21 bp):
ACATTTTAATTTTAAATCTTG
Found at i:1065642 original size:3 final size:3
Alignment explanation
Indices: 1065634--1065679 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
1065624 ATTAAGGATG
1065634 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1065680 AATCCATCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1066413 original size:3 final size:3
Alignment explanation
Indices: 1066407--1066439 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1066397 TTCAAACTAC
1066407 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1066440 AACTTAACCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1067879 original size:21 final size:21
Alignment explanation
Indices: 1067811--1067889 Score: 85
Period size: 21 Copynumber: 3.9 Consensus size: 21
1067801 GTTTTGTATT
*
1067811 TTATATTTATTTTTAAATATAA
1 TTATATTTA-TTATAAATATAA
* *
1067833 TTATATTTATAATAAAAATAA
1 TTATATTTATTATAAATATAA
*
1067854 TTATTTTTATTATAAATAT-A
1 TTATATTTATTATAAATATAA
1067874 TT-TATTT-TT-TAAATAT
1 TTATATTTATTATAAATAT
1067890 TTTTATATAA
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
17 7 0.14
18 2 0.04
19 4 0.08
20 3 0.06
21 25 0.50
22 9 0.18
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTATATTTATTATAAATATAA
Found at i:1068264 original size:18 final size:19
Alignment explanation
Indices: 1068231--1068287 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 19
1068221 TTATTTAATT
* *
1068231 ATTTAAAATAATATTAAAA
1 ATTTATAATTATATTAAAA
* *
1068250 ATTTAT-GTTATATT-AAT
1 ATTTATAATTATATTAAAA
1068267 ATTTATAATTATACTTAAAA
1 ATTTATAATTATA-TTAAAA
1068287 A
1 A
1068288 AATTATTTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
17 8 0.28
18 11 0.38
19 7 0.24
20 3 0.10
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (19 bp):
ATTTATAATTATATTAAAA
Found at i:1068285 original size:37 final size:36
Alignment explanation
Indices: 1068219--1068305 Score: 99
Period size: 36 Copynumber: 2.4 Consensus size: 36
1068209 TAACTCGAAA
*
1068219 ATTTAT-TTAATTATTTAAAATAATATT-AAAAATTT
1 ATTTATATTAA-TATTTAAAATAATATTAAAAAAATT
* *
1068254 ATGTTATATTAATATTTATAATTATACTTAAAAAAATT
1 AT-TTATATTAATATTTAAAATAATA-TTAAAAAAATT
1068292 ATTTATA-TAATATT
1 ATTTATATTAATATT
1068306 AGTGAATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
35 2 0.04
36 23 0.51
37 11 0.24
38 9 0.20
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (36 bp):
ATTTATATTAATATTTAAAATAATATTAAAAAAATT
Found at i:1069202 original size:174 final size:174
Alignment explanation
Indices: 1068893--1069220 Score: 425
Period size: 174 Copynumber: 1.9 Consensus size: 174
1068883 TGACTGCCAC
* *
1068893 ACAACATAAACATTATTCAAAACGATTACCTCTTGATCTCATTACATTGATGATTGGAAAAAGTT
1 ACAACATAAACATTATTCAAAACGATTACCTCTTGACCTCATTACATTGATGATCGGAAAAAGTT
* * *
1068958 GCAGACATATTCACTGAATCATCGGCAAGCAAAGATTCCTAGTAGCCGGATGTCTAAATACCGTG
66 GCAGACATATTCACTAAATCATCCGCAAGCAAAGATTCCTAGTAGCCGGATGTCTAAATACCGCG
*
1069023 CAACTTTCCTAGTCTCACGGAGTTTGATATAAACAAACGACTAG
131 CAACTTTCCCAGTCTCACGGAGTTTGATATAAACAAACGACTAG
* * * **
1069067 ACAACAT-AACGTTATTC-AAACTGATTACCTCTTGACCTCGTTAC-TTGATGGTCGG-AGTAGT
1 ACAACATAAACATTATTCAAAAC-GATTACCTCTTGACCTCATTACATTGATGATCGGAAAAAGT
* * *
1069128 TGCAGGCATATTCACTAAAATCATCCGCAAG-AGAAGATTTGCCTAGTA-CCTGGGTGTCTGAAT
65 TGCAGACATATTCACT-AAATCATCCGCAAGCA-AAGA-TT-CCTAGTAGCC-GGATGTCTAAAT
*
1069191 ATCGCGCAACTTTCCCAGTCTCACGGAGTT
125 ACCGCGCAACTTTCCCAGTCTCACGGAGTT
1069221 GATGTAATTT
Statistics
Matches: 133, Mismatches: 15, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
171 20 0.15
172 29 0.22
173 33 0.25
174 51 0.38
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (174 bp):
ACAACATAAACATTATTCAAAACGATTACCTCTTGACCTCATTACATTGATGATCGGAAAAAGTT
GCAGACATATTCACTAAATCATCCGCAAGCAAAGATTCCTAGTAGCCGGATGTCTAAATACCGCG
CAACTTTCCCAGTCTCACGGAGTTTGATATAAACAAACGACTAG
Found at i:1071210 original size:15 final size:16
Alignment explanation
Indices: 1071190--1071232 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
1071180 TAACTAACTT
1071190 ATATATATATATAT-A
1 ATATATATATATATCA
1071205 ATATATATATTATATCA
1 ATATATATA-TATATCA
1071222 ATATAT-TATAT
1 ATATATATATAT
1071233 TGTTTATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 12 0.46
16 7 0.27
17 7 0.27
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
ATATATATATATATCA
Found at i:1071243 original size:2 final size:2
Alignment explanation
Indices: 1071189--1071232 Score: 51
Period size: 2 Copynumber: 23.5 Consensus size: 2
1071179 TTAACTAACT
1071189 TA TA TA TA TA TA TA TA -A TA TA TA TA T- TA TA TCA -A TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA
1071228 TA TA T
1 TA TA T
1071233 TGTTTATATA
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
1 4 0.11
2 32 0.86
3 1 0.03
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1072047 original size:23 final size:21
Alignment explanation
Indices: 1072020--1072064 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 21
1072010 AATATACAAT
1072020 TAATATTTATGTATTAATTATAA
1 TAATATTTAT-TA-TAATTATAA
*
1072043 TAATATTTATTATATTTATAA
1 TAATATTTATTATAATTATAA
1072064 T
1 T
1072065 TATAATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.43
22 2 0.10
23 10 0.48
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
TAATATTTATTATAATTATAA
Found at i:1073082 original size:20 final size:21
Alignment explanation
Indices: 1073043--1073082 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1073033 TTTAATTATC
* *
1073043 AATTTAATTTGATTTTTAATA
1 AATTTAATTTAATATTTAATA
1073064 AATTTAA-TTAATATTTAAT
1 AATTTAATTTAATATTTAAT
1073083 CACTTAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (21 bp):
AATTTAATTTAATATTTAATA
Found at i:1073988 original size:4 final size:4
Alignment explanation
Indices: 1073979--1074009 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
1073969 TGAGATTATG
1073979 ATTT ATTT ATTT ATTT A-TT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1074010 TTTTCAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:1073999 original size:15 final size:15
Alignment explanation
Indices: 1073981--1074009 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1073971 AGATTATGAT
1073981 TTATTTATTTATTTA
1 TTATTTATTTATTTA
1073996 TTATTTATTTATTT
1 TTATTTATTTATTT
1074010 TTTTCAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTATTTATTTATTTA
Found at i:1074215 original size:2 final size:2
Alignment explanation
Indices: 1074208--1074250 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
1074198 TAGGAATGCA
* *
1074208 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1074250 A
1 A
1074251 ATTTGAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1079815 original size:12 final size:13
Alignment explanation
Indices: 1079791--1079829 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
1079781 CAAGTTTGAG
1079791 TATAAATAATTAAA
1 TATAAA-AATTAAA
*
1079805 T-TTAAAATTAAA
1 TATAAAAATTAAA
1079817 TATAAAAATTAAA
1 TATAAAAATTAAA
1079830 CATATTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 8 0.36
13 13 0.59
14 1 0.05
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TATAAAAATTAAA
Found at i:1080411 original size:31 final size:33
Alignment explanation
Indices: 1080371--1080435 Score: 82
Period size: 31 Copynumber: 2.0 Consensus size: 33
1080361 AATTTATATT
*
1080371 TATATAAATTTTGAT-ACATT-ATA-ATTAATAC
1 TATACAAATTTT-ATGACATTCATATATTAATAC
*
1080402 TATACAAATTTTATGACATTCATATATTTATAC
1 TATACAAATTTTATGACATTCATATATTAATAC
1080435 T
1 T
1080436 CAAAATATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 2 0.07
31 16 0.55
32 3 0.10
33 8 0.28
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.46
Consensus pattern (33 bp):
TATACAAATTTTATGACATTCATATATTAATAC
Found at i:1082050 original size:21 final size:20
Alignment explanation
Indices: 1082005--1082124 Score: 73
Period size: 21 Copynumber: 5.8 Consensus size: 20
1081995 GGGATGATCC
*
1082005 TTTTTAAGAGGGATCAATTCCT
1 TTTTTAAGAAGGATCAATT--T
1082027 TTTTTAAGAAGGATCAATTAT
1 TTTTTAAGAAGGATCAATT-T
* * * * * *
1082048 TTTCTAACAATGAACTATTC
1 TTTTTAAGAAGGATCAATTT
* *
1082068 TTTTTAAGAGGGATC-TTTAT
1 TTTTTAAGAAGGATCAATT-T
*
1082088 TTTTTAA-ACAGGATCAGTTT
1 TTTTTAAGA-AGGATCAATTT
*
1082108 CTTTTCAAGAAGGATCA
1 -TTTTTAAGAAGGATCA
1082125 CTCTTTTTAT
Statistics
Matches: 75, Mismatches: 18, Indels: 11
0.72 0.17 0.11
Matches are distributed among these distances:
19 3 0.04
20 23 0.31
21 30 0.40
22 19 0.25
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.42
Consensus pattern (20 bp):
TTTTTAAGAAGGATCAATTT
Found at i:1086521 original size:12 final size:11
Alignment explanation
Indices: 1086504--1086544 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
1086494 TAAAAATATT
1086504 TTTATATTAATA
1 TTTATATT-ATA
1086516 TTTATA-TAT-
1 TTTATATTATA
1086525 TTTATATTATA
1 TTTATATTATA
*
1086536 TTTAAATTA
1 TTTATATTA
1086545 AAATAATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
9 6 0.23
10 5 0.19
11 9 0.35
12 6 0.23
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTATATTATA
Found at i:1086536 original size:20 final size:20
Alignment explanation
Indices: 1086499--1086539 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
1086489 AATATTAAAA
1086499 ATATTTTTATATTAATATTT
1 ATATTTTTATATTAATATTT
1086519 ATATATTTTATATT-ATATTT
1 ATAT-TTTTATATTAATATTT
1086539 A
1 A
1086540 AATTAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
ATATTTTTATATTAATATTT
Found at i:1086907 original size:37 final size:35
Alignment explanation
Indices: 1086866--1086981 Score: 100
Period size: 35 Copynumber: 3.3 Consensus size: 35
1086856 TTTTTATCTT
1086866 ATAAAAATATATATGTAATTTTATAATGTAAATATTA
1 ATAAAAATAT-TATGTAATTTTATAAT-TAAATATTA
* * *
1086903 ATAAATATATTAAGTTA-TTTATAATTTAAA-ACTTA
1 ATAAAAATATTATGTAATTTTATAA-TTAAATA-TTA
1086938 ATAAAAA-ATTAT-TAAATTATTATAAATTAAAT-TTA
1 ATAAAAATATTATGT-AATT-TTAT-AATTAAATATTA
1086973 A-AAAAATAT
1 ATAAAAATAT
1086982 ATTTTAAAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
33 1 0.02
34 11 0.17
35 27 0.42
36 15 0.23
37 11 0.17
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (35 bp):
ATAAAAATATTATGTAATTTTATAATTAAATATTA
Found at i:1087000 original size:13 final size:13
Alignment explanation
Indices: 1086965--1087008 Score: 61
Period size: 13 Copynumber: 3.2 Consensus size: 13
1086955 TATTATAAAT
1086965 TAAATTTAAAAAAA
1 TAAATTT-AAAAAA
*
1086979 TATATTTTAAAAAA
1 TA-AATTTAAAAAA
1086993 TAAATTTAAAAAA
1 TAAATTTAAAAAA
1087006 TAA
1 TAA
1087009 TAAACAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
13 13 0.48
14 10 0.37
15 4 0.15
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
TAAATTTAAAAAA
Found at i:1088419 original size:49 final size:49
Alignment explanation
Indices: 1088355--1088458 Score: 190
Period size: 49 Copynumber: 2.1 Consensus size: 49
1088345 TCCTTCCCTA
1088355 CTTTCGAGAGAAAGTTCGAATGTTTATGAGTCATAACTATGATCCTAAG
1 CTTTCGAGAGAAAGTTCGAATGTTTATGAGTCATAACTATGATCCTAAG
*
1088404 CTTTCGAGAGAAAGTTCGAATGTTTATGAGTCATAACTGTGATCCTAAG
1 CTTTCGAGAGAAAGTTCGAATGTTTATGAGTCATAACTATGATCCTAAG
1088453 CGTTTC
1 C-TTTC
1088459 AATTTTAACT
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
49 49 0.92
50 4 0.08
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (49 bp):
CTTTCGAGAGAAAGTTCGAATGTTTATGAGTCATAACTATGATCCTAAG
Found at i:1088650 original size:26 final size:27
Alignment explanation
Indices: 1088603--1088658 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
1088593 ATTTAATTTA
1088603 ATTCACTTTTTAATTATATAATATATT
1 ATTCACTTTTTAATTATATAATATATT
* * *
1088630 ATTCATTTTTTAATT-TTTAATGTATT
1 ATTCACTTTTTAATTATATAATATATT
1088656 ATT
1 ATT
1088659 TATATATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 12 0.46
27 14 0.54
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (27 bp):
ATTCACTTTTTAATTATATAATATATT
Found at i:1090131 original size:9 final size:9
Alignment explanation
Indices: 1090117--1090142 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1090107 ATTTTAAAAA
1090117 TAAATTAAT
1 TAAATTAAT
1090126 TAAATTAAT
1 TAAATTAAT
1090135 TAAATTAA
1 TAAATTAA
1090143 GTGTTAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
TAAATTAAT
Found at i:1091967 original size:18 final size:18
Alignment explanation
Indices: 1091939--1091979 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1091929 ATATAAATTT
*
1091939 TATTT-AAAATTTTTATA
1 TATTTAAAAATTTATATA
1091956 TATTTAAAAATTTATATA
1 TATTTAAAAATTTATATA
*
1091974 TTTTTA
1 TATTTA
1091980 TATATGTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TATTTAAAAATTTATATA
Found at i:1091971 original size:16 final size:17
Alignment explanation
Indices: 1091939--1091976 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
1091929 ATATAAATTT
*
1091939 TATTTAAAATTTTTATA
1 TATTTAAAATATTTATA
1091956 TATTTAAAA-ATTTATA
1 TATTTAAAATATTTATA
1091972 TATTT
1 TATTT
1091977 TTATATATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATTTAAAATATTTATA
Found at i:1098488 original size:2 final size:2
Alignment explanation
Indices: 1098471--1098527 Score: 57
Period size: 2 Copynumber: 30.0 Consensus size: 2
1098461 TATTTTTATC
* * * *
1098471 AT AT GT AT AT -T AT AT AT AT AT TT TT AT AT -T AT AT -T AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1098510 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
1098528 TTTTATGAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
1 3 0.07
2 43 0.93
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (2 bp):
AT
Found at i:1098494 original size:36 final size:36
Alignment explanation
Indices: 1098454--1098530 Score: 95
Period size: 36 Copynumber: 2.1 Consensus size: 36
1098444 ATTTTAATAC
*
1098454 ATTTTAATATT-T-TTATCATATGTATATTATATATAT
1 ATTTTAATATTATATTAT-ATATATATA-TATATATAT
* *
1098490 ATTTTTATATTATATTATTTATATATATATATATAT
1 ATTTTAATATTATATTATATATATATATATATATAT
1098526 ATTTT
1 ATTTT
1098531 TATGAATACG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
36 24 0.67
37 8 0.22
38 4 0.11
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (36 bp):
ATTTTAATATTATATTATATATATATATATATATAT
Found at i:1098511 original size:28 final size:30
Alignment explanation
Indices: 1098463--1098528 Score: 84
Period size: 28 Copynumber: 2.3 Consensus size: 30
1098453 CATTTTAATA
*
1098463 TTTT-TATCATATGTATATTATATATATAT
1 TTTTATATTATATGTATATTATATATATAT
1098492 TTTTATATTATAT-TAT-TTATATATATAT
1 TTTTATATTATATGTATATTATATATATAT
* *
1098520 ATATATATT
1 TTTTATATT
1098529 TTTATGAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 19 0.58
29 7 0.21
30 7 0.21
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (30 bp):
TTTTATATTATATGTATATTATATATATAT
Found at i:1098980 original size:19 final size:18
Alignment explanation
Indices: 1098949--1098991 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
1098939 TATTATGTAT
*
1098949 TTATATAGATTTAATATA
1 TTATATAAATTTAATATA
1098967 TTATATAAATTTTAATATA
1 TTATATAAA-TTTAATATA
*
1098986 ATATAT
1 TTATAT
1098992 TTGTATAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
TTATATAAATTTAATATA
Found at i:1100198 original size:16 final size:18
Alignment explanation
Indices: 1100175--1100216 Score: 61
Period size: 16 Copynumber: 2.4 Consensus size: 18
1100165 ATGAATTTTA
1100175 ATTAATTTAAA-AATTAT
1 ATTAATTTAAATAATTAT
1100192 A-TAATTTAAATTAATTAT
1 ATTAATTTAAA-TAATTAT
1100210 ATTAATT
1 ATTAATT
1100217 ATTATATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 9 0.41
17 1 0.05
18 7 0.32
19 5 0.23
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTAATTTAAATAATTAT
Found at i:1100345 original size:135 final size:135
Alignment explanation
Indices: 1100152--1100395 Score: 372
Period size: 136 Copynumber: 1.8 Consensus size: 135
1100142 TAGAGAGAAG
*
1100152 TTTTTAATAGTTTATGAATTTTAATTAATTTAAAAATTATATAATTTAAATTAATTATATT-AAT
1 TTTTTAATAGTTTATGAATTTTAATTAAATTAAAAATTATATAATTTAAATTAATTATATTAAAT
1100216 TATTATATTTTATTTAAATAATTTTTTATATAGTTTTA-TCTTAAATAATAAATCACTTCATTTC
66 TATT-TA-TTTATTT-AATAATTTTTTATAT--TTTTATTCTTAAATAATAAATCACTTCATTTC
1100280 GTTAGATAGA
126 GTTAGATAGA
* *
1100290 TTTTTAATA-TTTA-GAATTTTACTTAAATTAAAAATTA-CTAATTTAAATTAATTATATTAAAT
1 TTTTTAATAGTTTATGAATTTTAATTAAATTAAAAATTATATAATTTAAATTAATTATATTAAAT
*
1100352 TATTTATTTATTTAATAATTTTTTCTATTTTTATTCTTAAATAA
66 TATTTATTTATTTAATAATTTTTTATATTTTTATTCTTAAATAA
1100396 ATCCTATACA
Statistics
Matches: 100, Mismatches: 4, Indels: 10
0.88 0.04 0.09
Matches are distributed among these distances:
131 5 0.05
132 10 0.10
133 14 0.14
134 7 0.07
135 22 0.22
136 29 0.29
137 4 0.04
138 9 0.09
ACGTcount: A:0.40, C:0.04, G:0.03, T:0.54
Consensus pattern (135 bp):
TTTTTAATAGTTTATGAATTTTAATTAAATTAAAAATTATATAATTTAAATTAATTATATTAAAT
TATTTATTTATTTAATAATTTTTTATATTTTTATTCTTAAATAATAAATCACTTCATTTCGTTAG
ATAGA
Found at i:1100885 original size:11 final size:11
Alignment explanation
Indices: 1100833--1100885 Score: 51
Period size: 10 Copynumber: 5.2 Consensus size: 11
1100823 AATAAAAAAT
1100833 AAATATA-ATA
1 AAATATATATA
*
1100843 AAA-ATATA-G
1 AAATATATATA
1100852 AAATATAT-TA
1 AAATATATATA
*
1100862 AAATATATGTA
1 AAATATATATA
*
1100873 AAATTTATATA
1 AAATATATATA
1100884 AA
1 AA
1100886 TTTATAACAC
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
9 6 0.17
10 16 0.46
11 13 0.37
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (11 bp):
AAATATATATA
Found at i:1102893 original size:24 final size:25
Alignment explanation
Indices: 1102866--1102912 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
1102856 TATTTTAAAA
1102866 TTTTAATAGAT-ATATATTAAATTT
1 TTTTAATAGATAATATATTAAATTT
* *
1102890 TTTTAATATATAATATTTTAAAT
1 TTTTAATAGATAATATATTAAAT
1102913 ATAATTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (25 bp):
TTTTAATAGATAATATATTAAATTT
Found at i:1103105 original size:9 final size:9
Alignment explanation
Indices: 1103091--1103125 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
1103081 AATTTTAAAT
1103091 TTTAAATAA
1 TTTAAATAA
1103100 TTTAAATAA
1 TTTAAATAA
*
1103109 TTTAATTTAA
1 TTTAA-ATAA
1103119 TTTAAAT
1 TTTAAAT
1103126 TATTATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
TTTAAATAA
Found at i:1103166 original size:16 final size:15
Alignment explanation
Indices: 1103107--1103163 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 15
1103097 TAATTTAAAT
1103107 AATTTAATTTAATTTA
1 AATTTAATTT-ATTTA
*
1103123 AATTATTATTTATTTA
1 AATT-TAATTTATTTA
** *
1103139 ATATAAAATATATTTA
1 A-ATTTAATTTATTTA
1103155 AATTTAATT
1 AATTTAATT
1103164 ATAAAATATA
Statistics
Matches: 31, Mismatches: 8, Indels: 5
0.70 0.18 0.11
Matches are distributed among these distances:
15 5 0.16
16 19 0.61
17 7 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
AATTTAATTTATTTA
Found at i:1103166 original size:23 final size:21
Alignment explanation
Indices: 1103103--1103208 Score: 105
Period size: 21 Copynumber: 5.1 Consensus size: 21
1103093 TAAATAATTT
*
1103103 AAATA-ATTTAATTTAATTTA
1 AAATATATTTAATTTAATATA
*
1103123 AATTATTATTT-ATTTAATATA
1 AAATA-TATTTAATTTAATATA
1103144 AAATATATTTAAATTTAATTATA
1 AAATATATTT-AATTTAA-TATA
1103167 AAATATA-TTAATATTAATATA
1 AAATATATTTAAT-TTAATATA
* *
1103188 AAA-ATA-ATATTTTAATATA
1 AAATATATTTAATTTAATATA
1103207 AA
1 AA
1103209 TAAAAAATTT
Statistics
Matches: 75, Mismatches: 5, Indels: 13
0.81 0.05 0.14
Matches are distributed among these distances:
19 10 0.13
20 15 0.20
21 23 0.31
22 16 0.21
23 11 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AAATATATTTAATTTAATATA
Found at i:1103196 original size:25 final size:24
Alignment explanation
Indices: 1103168--1103216 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
1103158 TTAATTATAA
*
1103168 AATATATTAATATTAATATAAAAAT
1 AATATATTAATATAAATA-AAAAAT
*
1103193 AATATTTTAATATAAATAAAAAAT
1 AATATATTAATATAAATAAAAAAT
1103217 TTTAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
AATATATTAATATAAATAAAAAAT
Found at i:1103204 original size:19 final size:19
Alignment explanation
Indices: 1103157--1103221 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
1103147 TATATTTAAA
*
1103157 TTTAATTATAAAATATATTAAT
1 TTTAA-TATAAAA-ATAAT-AT
*
1103179 ATTAATATAAAAATAATAT
1 TTTAATATAAAAATAATAT
*
1103198 TTTAATATAAATAA-AAAAT
1 TTTAATATAAA-AATAATAT
1103217 TTTAA
1 TTTAA
1103222 AAAAATTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
19 21 0.55
20 6 0.16
21 7 0.18
22 4 0.11
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTAATATAAAAATAATAT
Found at i:1130436 original size:14 final size:14
Alignment explanation
Indices: 1130386--1130445 Score: 50
Period size: 14 Copynumber: 4.3 Consensus size: 14
1130376 CTATTTAGAT
1130386 TATTAATATTTAT-
1 TATTAATATTTATA
** *
1130399 TATTTTTAATTAATA
1 TATTAAT-ATTTATA
* * *
1130414 AAATAATATTTTTA
1 TATTAATATTTATA
1130428 TATTAATATTTATA
1 TATTAATATTTATA
1130442 TATT
1 TATT
1130446 TTATAATTAT
Statistics
Matches: 33, Mismatches: 12, Indels: 3
0.69 0.25 0.06
Matches are distributed among these distances:
13 5 0.15
14 25 0.76
15 3 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TATTAATATTTATA
Found at i:1130447 original size:21 final size:22
Alignment explanation
Indices: 1130387--1130460 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 22
1130377 TATTTAGATT
1130387 ATTAATATTTAT-TATTTT-TA
1 ATTAATATTTATATATTTTATA
**
1130407 ATTAATA-AAATAATATTTT-TA
1 ATTAATATTTAT-ATATTTTATA
1130428 TATTAATATTTATATATTTTATA
1 -ATTAATATTTATATATTTTATA
1130451 ATT-ATATTTA
1 ATTAATATTTA
1130461 AATAAAAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
19 2 0.04
20 7 0.16
21 15 0.33
22 17 0.38
23 4 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTAATATTTATATATTTTATA
Found at i:1130509 original size:15 final size:15
Alignment explanation
Indices: 1130489--1130524 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
1130479 ATTATTACTT
1130489 ATTAATTTAAATC-AA
1 ATTAATTT-AATCTAA
1130504 ATTAATTTAATCTAA
1 ATTAATTTAATCTAA
1130519 ATTAAT
1 ATTAAT
1130525 AAAAAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTAATTTAATCTAA
Found at i:1131268 original size:25 final size:25
Alignment explanation
Indices: 1131210--1131276 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 25
1131200 TTGATAAAAA
**
1131210 TAAATTTAATTTTTATACTCAATTT
1 TAAATTTAATTTTTATACTCAAGCT
*
1131235 TAAATTTAATTTTTTATACTCGAGCT
1 TAAATTTAA-TTTTTATACTCAAGCT
*
1131261 TAAATTAAAATTTTTA
1 TAAATT-TAATTTTTA
1131277 ATATTAATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
25 9 0.25
26 25 0.69
27 2 0.06
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.52
Consensus pattern (25 bp):
TAAATTTAATTTTTATACTCAAGCT
Found at i:1131368 original size:17 final size:18
Alignment explanation
Indices: 1131336--1131370 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1131326 TTAAAATATT
1131336 TAAATTAAATTTATTCAA
1 TAAATTAAATTTATTCAA
1131354 TAAATTAAA-TTATTCAA
1 TAAATTAAATTTATTCAA
1131371 ACTTAATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (18 bp):
TAAATTAAATTTATTCAA
Found at i:1133056 original size:2 final size:2
Alignment explanation
Indices: 1133049--1133077 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1133039 CAGAGCTGTT
1133049 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 T
1133078 TTCATTTTTC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1141506 original size:21 final size:21
Alignment explanation
Indices: 1141476--1141515 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1141466 TTATAATCTT
1141476 TTAAAAATTTTTTAATAAAAA
1 TTAAAAATTTTTTAATAAAAA
* *
1141497 TTAAATATTTTTTATTAAA
1 TTAAAAATTTTTTAATAAA
1141516 TATATATTTA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TTAAAAATTTTTTAATAAAAA
Found at i:1142645 original size:17 final size:17
Alignment explanation
Indices: 1142620--1142671 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 17
1142610 ACTTACATTT
* *
1142620 ATATATATTTTTATTAA
1 ATATTTATTTATATTAA
*
1142637 ATATTTA-TTATATTTA
1 ATATTTATTTATATTAA
1142653 ATATTTATTTATAATTAA
1 ATATTTATTTAT-ATTAA
1142671 A
1 A
1142672 ATTACATATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 14 0.48
17 10 0.34
18 5 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATATTTATTTATATTAA
Found at i:1142657 original size:23 final size:23
Alignment explanation
Indices: 1142616--1142705 Score: 59
Period size: 20 Copynumber: 4.1 Consensus size: 23
1142606 AATCACTTAC
*
1142616 ATTTATATATATTT-TTATTAAAT
1 ATTTAT-TATATTTAATATTAAAT
1142639 ATTTATTATATTTAATATT---T
1 ATTTATTATATTTAATATTAAAT
* *
1142659 ATTTA-TA-A-TTAAAATTACAT
1 ATTTATTATATTTAATATTAAAT
* *
1142679 ATTTAATATTTTTAAAATATTAAAT
1 ATTTATTATATTT--AATATTAAAT
1142704 AT
1 AT
1142706 AATATGTTAA
Statistics
Matches: 53, Mismatches: 5, Indels: 16
0.72 0.07 0.22
Matches are distributed among these distances:
17 7 0.13
18 1 0.02
19 2 0.04
20 12 0.23
21 2 0.04
22 7 0.13
23 12 0.23
25 10 0.19
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (23 bp):
ATTTATTATATTTAATATTAAAT
Found at i:1143509 original size:18 final size:20
Alignment explanation
Indices: 1143475--1143512 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1143465 TTTTCAATCG
1143475 ATAAAAAATTAATTTAAATA
1 ATAAAAAATTAATTTAAATA
1143495 ATAAAAAA-TAA-TTAAATA
1 ATAAAAAATTAATTTAAATA
1143513 TATTTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
19 3 0.17
20 8 0.44
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
ATAAAAAATTAATTTAAATA
Found at i:1143617 original size:27 final size:28
Alignment explanation
Indices: 1143587--1143653 Score: 64
Period size: 27 Copynumber: 2.4 Consensus size: 28
1143577 AAATTATACT
*
1143587 ATTAAAAAATATATATAATTTTTA-TTA
1 ATTAAAAAATATATATAATATTTATTTA
*** *
1143614 ATTATTTATTATATATAATATTTATTTA
1 ATTAAAAAATATATATAATATTTATTTA
*
1143642 ATATTAAAAATA
1 AT-TAAAAAATA
1143654 ATTTTTAAAT
Statistics
Matches: 28, Mismatches: 10, Indels: 2
0.70 0.25 0.05
Matches are distributed among these distances:
27 19 0.68
28 5 0.18
29 4 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
ATTAAAAAATATATATAATATTTATTTA
Found at i:1143682 original size:21 final size:20
Alignment explanation
Indices: 1143630--1143684 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
1143620 TATTATATAT
*
1143630 AATATTTATTTAATATTAAA
1 AATATTTATTAAATATTAAA
*
1143650 AATAATTT-TTAAATATTTAA
1 AAT-ATTTATTAAATATTAAA
1143670 AATATTTAATTAAAT
1 AATATTT-ATTAAAT
1143685 CGATCGATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 4 0.13
20 16 0.53
21 10 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATATTTATTAAATATTAAA
Found at i:1143899 original size:18 final size:18
Alignment explanation
Indices: 1143878--1143955 Score: 63
Period size: 18 Copynumber: 4.3 Consensus size: 18
1143868 CTCATATAAA
1143878 TATATTA-ATTTATATATT
1 TATATTATATTT-TATATT
1143896 TATATTATATTTTATATTT
1 TATATTATATTTTATA-TT
* *
1143915 TATAGTATCATAATTAT-TT
1 TATATTAT-AT-TTTATATT
**
1143934 T-TAAAATATTTTATATT
1 TATATTATATTTTATATT
1143951 TATAT
1 TATAT
1143956 AAATTTTAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
16 4 0.08
17 5 0.10
18 17 0.35
19 16 0.33
20 2 0.04
21 4 0.08
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (18 bp):
TATATTATATTTTATATT
Found at i:1143967 original size:18 final size:18
Alignment explanation
Indices: 1143941--1143996 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 18
1143931 TTTTTAAAAT
1143941 ATTTT-ATATTTATATAA
1 ATTTTAATATTTATATAA
1143958 ATTTTAATATATTA-AT-A
1 ATTTTAATAT-TTATATAA
*
1143975 A--TAAATA-TTATATAA
1 ATTTTAATATTTATATAA
1143990 ATTTTAA
1 ATTTTAA
1143997 ATAAACTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
13 3 0.10
14 2 0.06
15 7 0.23
17 10 0.32
18 6 0.19
19 3 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATTTTAATATTTATATAA
Found at i:1143987 original size:20 final size:19
Alignment explanation
Indices: 1143937--1143988 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
1143927 ATTATTTTTA
* *
1143937 AAATATTTTATATTTATAT
1 AAATATTATATATTAATAT
*
1143956 AAATTTTAATATATTAATAAT
1 AAATATT-ATATATTAAT-AT
1143977 AAATATTATATA
1 AAATATTATATA
1143989 AATTTTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 6 0.22
20 13 0.48
21 8 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AAATATTATATATTAATAT
Found at i:1143997 original size:18 final size:18
Alignment explanation
Indices: 1143941--1143999 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 18
1143931 TTTTTAAAAT
*
1143941 ATTTTATAT-TTATATAA
1 ATTTTAAATATTATATAA
1143958 ATTTTAATATATTA-AT-A
1 ATTTTAA-ATATTATATAA
1143975 A---TAAATATTATATAA
1 ATTTTAAATATTATATAA
1143990 ATTTTAAATA
1 ATTTTAAATA
1144000 AACTTATTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 13
0.71 0.02 0.27
Matches are distributed among these distances:
13 6 0.18
14 5 0.15
15 2 0.06
17 8 0.24
18 10 0.29
19 3 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTTAAATATTATATAA
Found at i:1144504 original size:3 final size:3
Alignment explanation
Indices: 1144496--1144529 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1144486 AAATCAAAGA
1144496 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1144530 CAAGCATCAA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1145901 original size:17 final size:16
Alignment explanation
Indices: 1145879--1145921 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
1145869 AATTTAAATA
1145879 TAATTTTTTTATTGATT
1 TAATTTTTTTATT-ATT
**
1145896 TAATTTAAATTATTATT
1 TAATTT-TTTTATTATT
1145913 TAATTTTTT
1 TAATTTTTT
1145922 ATTTAAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
16 1 0.05
17 15 0.71
18 5 0.24
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (16 bp):
TAATTTTTTTATTATT
Found at i:1145913 original size:29 final size:29
Alignment explanation
Indices: 1145866--1145939 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 29
1145856 TAATATTAAA
1145866 TTAAATTTAAA-TATAATTT-TTTTATTGAT
1 TTAAATTTAAATTATAATTTATTTT-TT-AT
*
1145895 TT-AATTTAAATTATTATTTAATTTTTTAT
1 TTAAATTTAAATTATAATTT-ATTTTTTAT
1145924 TTAAATTT-AATTATAA
1 TTAAATTTAAATTATAA
1145940 ATATTAATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
28 8 0.21
29 20 0.51
30 7 0.18
31 4 0.10
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (29 bp):
TTAAATTTAAATTATAATTTATTTTTTAT
Found at i:1145952 original size:24 final size:24
Alignment explanation
Indices: 1145925--1145979 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
1145915 ATTTTTTATT
* *
1145925 TAAATTTAA-TTATAAATATTAATA
1 TAAATTTAATTTA-AAATAATAAAA
**
1145949 TAAAAATAATTTAAAATAATAAAA
1 TAAATTTAATTTAAAATAATAAAA
1145973 TAAATTT
1 TAAATTT
1145980 TTGAATCGAT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
TAAATTTAATTTAAAATAATAAAA
Found at i:1146731 original size:25 final size:24
Alignment explanation
Indices: 1146680--1146733 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
1146670 TATTAAAAAT
*
1146680 TAATATTTATTTCATTTATTATAA
1 TAATATTTATTTCATTTATAATAA
*
1146704 TAATATTTAATTAT-ATTTATAATTA
1 TAATATTT-ATT-TCATTTATAATAA
1146729 TAATA
1 TAATA
1146734 AATATAATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 8 0.31
25 17 0.65
26 1 0.04
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (24 bp):
TAATATTTATTTCATTTATAATAA
Found at i:1147069 original size:11 final size:10
Alignment explanation
Indices: 1147040--1147141 Score: 64
Period size: 10 Copynumber: 9.5 Consensus size: 10
1147030 TATGATAATA
*
1147040 TTATTTATAT
1 TTATTTAAAT
1147050 TTATTTAAAT
1 TTATTTAAAT
1147060 TTAGTTTAAAAT
1 TTA-TTT-AAAT
*
1147072 ATAAATTTTAAATT
1 -T-TA-TTTAAA-T
1147086 TTATTTAAAT
1 TTATTTAAAT
**
1147096 TTATTTTTAT
1 TTATTTAAAT
1147106 TTA--TAAAT
1 TTATTTAAAT
*
1147114 AGATAATTTAAAT
1 ---TTATTTAAAT
1147127 TTATTTAAAT
1 TTATTTAAAT
1147137 TTATT
1 TTATT
1147142 ATATTATAAT
Statistics
Matches: 72, Mismatches: 10, Indels: 20
0.71 0.10 0.20
Matches are distributed among these distances:
8 3 0.04
10 38 0.53
11 11 0.15
12 5 0.07
13 10 0.14
14 5 0.07
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (10 bp):
TTATTTAAAT
Done.