Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold223
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: 4172444
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 17292 characters in sequence are not A, C, G, or T
File 23 of 26
Found at i:3648167 original size:55 final size:55
Alignment explanation
Indices: 3648107--3648213 Score: 135
Period size: 55 Copynumber: 1.9 Consensus size: 55
3648097 ATCTTTATGT
** * *
3648107 TTTAAAAATTCATTTTTATTTTTTTAAATTTTTATTCCGTGA-ATATTTTTTGTGC
1 TTTAAAAATTCATACTTATTTTTTTAAACTTTTATCCCGTGATA-ATTTTTTGTGC
* * *
3648162 TTTAAAAATTGATACTTATTTTTTTATACTTTTATCCCTTGATAATTTTTTG
1 TTTAAAAATTCATACTTATTTTTTTAAACTTTTATCCCGTGATAATTTTTTG
3648214 CACCAAATCT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
55 43 0.98
56 1 0.02
ACGTcount: A:0.26, C:0.08, G:0.07, T:0.59
Consensus pattern (55 bp):
TTTAAAAATTCATACTTATTTTTTTAAACTTTTATCCCGTGATAATTTTTTGTGC
Found at i:3649362 original size:18 final size:19
Alignment explanation
Indices: 3649329--3649364 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3649319 CACTAAAATC
*
3649329 AAATATACAAAGATGAAAA
1 AAATATACAAACATGAAAA
3649348 AAATAT-CAAACATGAAA
1 AAATATACAAACATGAAA
3649365 TACTTTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.67, C:0.08, G:0.08, T:0.17
Consensus pattern (19 bp):
AAATATACAAACATGAAAA
Found at i:3649879 original size:2 final size:2
Alignment explanation
Indices: 3649872--3649901 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3649862 TCTAAATCTA
*
3649872 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3649902 GTGACTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3651061 original size:20 final size:20
Alignment explanation
Indices: 3651035--3651076 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
3651025 TTTAAATAAA
* *
3651035 TTTAAAAATTTTTA-TTATT
1 TTTAAAAAATATTATTTATT
3651054 TTTAAAAAATATTATTTATT
1 TTTAAAAAATATTATTTATT
3651074 TTT
1 TTT
3651077 TTATAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTAAAAAATATTATTTATT
Found at i:3655711 original size:32 final size:32
Alignment explanation
Indices: 3655653--3655724 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 32
3655643 TATAATAATT
*
3655653 TAATTAATATAAAAATAATATTATAAATGTTAAA
1 TAATTAATAT-AAAATAATATGATAAAT-TTAAA
*
3655687 TAATTAATAT-AATTAATATGATAAATTTAAA
1 TAATTAATATAAAATAATATGATAAATTTAAA
3655718 TATATTA
1 TA-ATTA
3655725 TTATGTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 7 0.20
32 18 0.51
34 10 0.29
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (32 bp):
TAATTAATATAAAATAATATGATAAATTTAAA
Found at i:3655716 original size:23 final size:24
Alignment explanation
Indices: 3655690--3655751 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 24
3655680 TGTTAAATAA
3655690 TTAATATAATTAATATG-ATAAATT
1 TTAATATAATTAATATGTA-AAATT
* *
3655714 TAAATAT-ATTATTATGTAAAATT
1 TTAATATAATTAATATGTAAAATT
* *
3655737 TTATTATATTTAATA
1 TTAATATAATTAATA
3655752 ATTTATATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
23 18 0.60
24 12 0.40
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (24 bp):
TTAATATAATTAATATGTAAAATT
Found at i:3655743 original size:18 final size:20
Alignment explanation
Indices: 3655718--3655764 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
3655708 TAAATTTAAA
3655718 TATATTATTATGTAA-AATT
1 TATATTATTATGTAATAATT
*
3655737 T-TATTA-TATTTAATAATT
1 TATATTATTATGTAATAATT
3655755 TATATT-TTAT
1 TATATTATTAT
3655765 TTATATTTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
17 6 0.25
18 10 0.42
19 8 0.33
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TATATTATTATGTAATAATT
Found at i:3656098 original size:15 final size:17
Alignment explanation
Indices: 3656078--3656110 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
3656068 TATTTTTATT
3656078 TATTTTT-ATTA-AAAA
1 TATTTTTAATTATAAAA
3656093 TATTTTTAATTATAAAA
1 TATTTTTAATTATAAAA
3656110 T
1 T
3656111 TACCTTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 4 0.25
17 5 0.31
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TATTTTTAATTATAAAA
Found at i:3656744 original size:22 final size:21
Alignment explanation
Indices: 3656673--3656745 Score: 76
Period size: 22 Copynumber: 3.3 Consensus size: 21
3656663 TATATTATTG
**
3656673 AATTAAAAATAATTTACACTTT
1 AATTAAAAATAATTTA-AAATT
3656695 AATTAAAATATAATTTAATAA-T
1 AATTAAAA-ATAATTTAA-AATT
*
3656717 ATTTAAAAATAATTTTAAAATT
1 AATTAAAAATAA-TTTAAAATT
3656739 AATTAAA
1 AATTAAA
3656746 TCTCATTATT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
21 6 0.14
22 29 0.67
23 8 0.19
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (21 bp):
AATTAAAAATAATTTAAAATT
Found at i:3656869 original size:28 final size:27
Alignment explanation
Indices: 3656838--3656917 Score: 117
Period size: 28 Copynumber: 2.9 Consensus size: 27
3656828 ATTTAAAATT
3656838 AATTTTAAAAAATAAATATATTTTTTA
1 AATTTTAAAAAATAAATATATTTTTTA
*
3656865 AAATTTAAAAAA-AAATAAATATTTTTTA
1 AATTTTAAAAAATAAAT--ATATTTTTTA
*
3656893 AATATTAAAAAATAAATATATTTTT
1 AATTTTAAAAAATAAATATATTTTT
3656918 AATAAAAAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
26 4 0.09
27 19 0.40
28 20 0.43
29 4 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
AATTTTAAAAAATAAATATATTTTTTA
Found at i:3656872 original size:27 final size:26
Alignment explanation
Indices: 3656836--3656917 Score: 112
Period size: 27 Copynumber: 3.0 Consensus size: 26
3656826 TCATTTAAAA
*
3656836 TTAATTTTAAAAAATAAATATATTTT
1 TTAAATTTAAAAAATAAATATATTTT
3656862 TTAAAATTTAAAAAA-AAATAAATATTTT
1 TT-AAATTTAAAAAATAAAT--ATATTTT
3656890 TTAAATATTAAAAAATAAATATATTTT
1 TTAAAT-TTAAAAAATAAATATATTTT
3656917 T
1 T
3656918 AATAAAAAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
26 6 0.12
27 23 0.46
28 17 0.34
29 4 0.08
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
TTAAATTTAAAAAATAAATATATTTT
Found at i:3657342 original size:20 final size:21
Alignment explanation
Indices: 3657308--3657350 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
3657298 GTTAGAATGC
3657308 ATTTAATAAATATAAAA-ATA
1 ATTTAATAAATATAAAATATA
3657328 ATTTATATAAA-ATAAAATATA
1 ATTTA-ATAAATATAAAATATA
3657349 AT
1 AT
3657351 ATATTTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
ATTTAATAAATATAAAATATA
Found at i:3657353 original size:19 final size:20
Alignment explanation
Indices: 3657313--3657354 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
3657303 AATGCATTTA
3657313 ATAAATATAAAAATAATTTAT
1 ATAAATATAAAAATAA-TTAT
3657334 ATAAA-ATAAAATATAA-TAT
1 ATAAATATAAAA-ATAATTAT
3657353 AT
1 AT
3657355 TTCATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 5 0.25
20 6 0.30
21 9 0.45
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
ATAAATATAAAAATAATTAT
Found at i:3659418 original size:16 final size:16
Alignment explanation
Indices: 3659369--3659439 Score: 51
Period size: 16 Copynumber: 4.6 Consensus size: 16
3659359 TGGAATATCA
*
3659369 ATAAATATAAATTGAT
1 ATAAATATAAATTAAT
* *
3659385 AT--ATAT-CATTATT
1 ATAAATATAAATTAAT
3659398 GATAAATATAAATTAAT
1 -ATAAATATAAATTAAT
* *
3659415 ATAAAAATTAAAATAAT
1 ATAAATA-TAAATTAAT
3659432 AT-AATATA
1 ATAAATATA
3659440 GGTACATTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 11
0.69 0.13 0.18
Matches are distributed among these distances:
13 4 0.10
14 6 0.14
15 2 0.05
16 15 0.36
17 15 0.36
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (16 bp):
ATAAATATAAATTAAT
Found at i:3659426 original size:17 final size:18
Alignment explanation
Indices: 3659401--3659435 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
3659391 CATTATTGAT
*
3659401 AAATATAAATTAATATAA
1 AAATATAAAATAATATAA
3659419 AAAT-TAAAATAATATAA
1 AAATATAAAATAATATAA
3659436 TATAGGTACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AAATATAAAATAATATAA
Found at i:3659915 original size:20 final size:21
Alignment explanation
Indices: 3659890--3659929 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
3659880 AGATGTAATT
*
3659890 TAATTTGATAA-TAATTAAAA
1 TAATTTGAAAATTAATTAAAA
*
3659910 TAATTTTAAAATTAATTAAA
1 TAATTTGAAAATTAATTAAA
3659930 TTTTATGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (21 bp):
TAATTTGAAAATTAATTAAAA
Found at i:3662156 original size:22 final size:22
Alignment explanation
Indices: 3662131--3662184 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
3662121 GTTCATGAAC
3662131 AAGTTTATTTA-TAAATTGTTTA
1 AAGTTTATTTATTAAATT-TTTA
*
3662153 AAGTTCATTTATTAAATTTTTA
1 AAGTTTATTTATTAAATTTTTA
*
3662175 AAGCTTATTT
1 AAGTTTATTT
3662185 GAAACTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 22 0.79
23 6 0.21
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (22 bp):
AAGTTTATTTATTAAATTTTTA
Found at i:3662400 original size:24 final size:22
Alignment explanation
Indices: 3662348--3662406 Score: 57
Period size: 24 Copynumber: 2.6 Consensus size: 22
3662338 TTGCTTATTG
*
3662348 TTTATGAATATATTTTTAATTA
1 TTTATGAATATGTTTTTAATTA
*
3662370 TTCATGAATATGTTTGATT-ATATA
1 TTTATGAATATGTTT--TTAAT-TA
*
3662394 TTTATGAACATGT
1 TTTATGAATATGT
3662407 CCTTTTATTG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
22 13 0.43
23 2 0.07
24 15 0.50
ACGTcount: A:0.34, C:0.03, G:0.10, T:0.53
Consensus pattern (22 bp):
TTTATGAATATGTTTTTAATTA
Found at i:3662838 original size:16 final size:16
Alignment explanation
Indices: 3662819--3662867 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
3662809 AATATAATTT
*
3662819 TATAATAAAAATTTAA
1 TATAATAAAAATTAAA
3662835 TATAA-AAATAATTAAA
1 TATAATAAA-AATTAAA
*
3662851 TATAATATAAAAATAAA
1 TATAATA-AAAATTAAA
3662868 ATTAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
15 3 0.11
16 16 0.57
17 7 0.25
18 2 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TATAATAAAAATTAAA
Found at i:3662856 original size:21 final size:22
Alignment explanation
Indices: 3662827--3662893 Score: 75
Period size: 21 Copynumber: 3.0 Consensus size: 22
3662817 TTTATAATAA
*
3662827 AAATTTAATATAAAAAT-AATT
1 AAATATAATATAAAAATAAATT
3662848 AAATATAATATAAAAATAAAATT
1 AAATATAATATAAAAAT-AAATT
*
3662871 -AATATAATTATAATATATAAATT
1 AAATATAA-TATAA-AAATAAATT
3662894 TATAAAAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
21 16 0.40
22 7 0.17
23 14 0.35
24 3 0.08
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
AAATATAATATAAAAATAAATT
Found at i:3662884 original size:11 final size:11
Alignment explanation
Indices: 3662795--3662927 Score: 83
Period size: 11 Copynumber: 11.7 Consensus size: 11
3662785 ATTTGATTTG
3662795 ATAATTATAAAT
1 ATAA-TATAAAT
*
3662807 ATAATATAATTTT
1 ATAATATAA--AT
*
3662820 ATAATAAAAAT
1 ATAATATAAAT
* *
3662831 TTAATATAAAA
1 ATAATATAAAT
3662842 ATAAT-TAAAT
1 ATAATATAAAT
*
3662852 ATAATATAAAA
1 ATAATATAAAT
* *
3662863 ATAAAATTAAT
1 ATAATATAAAT
3662874 ATAATTATAATAT
1 ATAA-TATAA-AT
**
3662887 ATAA-ATTTAT
1 ATAATATAAAT
* *
3662897 A-AAAATATAT
1 ATAATATAAAT
3662907 ATAATATAAATT
1 ATAATATAAA-T
3662919 ATTAATATA
1 A-TAATATA
3662928 CCAATCATTA
Statistics
Matches: 93, Mismatches: 19, Indels: 17
0.72 0.15 0.13
Matches are distributed among these distances:
9 2 0.02
10 18 0.19
11 42 0.45
12 9 0.10
13 22 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:3662898 original size:38 final size:38
Alignment explanation
Indices: 3662795--3662927 Score: 103
Period size: 38 Copynumber: 3.4 Consensus size: 38
3662785 ATTTGATTTG
* *
3662795 ATAATTATAAATATAATATAATTTTATAATAA-AAATTTAAT
1 ATAATTAT-AATAT-ATA-AA-TTTATAAAAATAAAATTAAT
** *
3662836 ATAAAAATAAT-TA-AATATAATATAAAAATAAAATTAAT
1 ATAATTATAATATATAA-AT-TTATAAAAATAAAATTAAT
*
3662874 ATAATTATAATATATAAATTTATAAAAAT-ATATATAAT
1 ATAATTATAATATATAAATTTATAAAAATAAAAT-TAAT
3662912 ATAAATTATTAATATA
1 AT-AATTA-TAATATA
3662928 CCAATCATTA
Statistics
Matches: 75, Mismatches: 9, Indels: 17
0.74 0.09 0.17
Matches are distributed among these distances:
36 2 0.03
37 12 0.16
38 33 0.44
39 10 0.13
40 12 0.16
41 6 0.08
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (38 bp):
ATAATTATAATATATAAATTTATAAAAATAAAATTAAT
Found at i:3663712 original size:19 final size:18
Alignment explanation
Indices: 3663679--3663720 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
3663669 GGTGGTTTTA
*
3663679 TTTT-ATTTTTAATTATT
1 TTTTAATTTTTAATTAAT
3663696 TTTTAATTTTTAGATTAAT
1 TTTTAATTTTTA-ATTAAT
3663715 TTTTAA
1 TTTTAA
3663721 ATAATAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 4 0.18
18 7 0.32
19 11 0.50
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (18 bp):
TTTTAATTTTTAATTAAT
Found at i:3663966 original size:16 final size:16
Alignment explanation
Indices: 3663920--3663973 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
3663910 AAAAATATAA
3663920 ATTTTATTAATTATTT-T
1 ATTTTATT-A-TATTTAT
*
3663937 ATTTT-TGTAGATTTAT
1 ATTTTAT-TATATTTAT
3663953 ATTTTATTATATTTAT
1 ATTTTATTATATTTAT
3663969 -TTTTA
1 ATTTTA
3663974 AATGATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
15 9 0.28
16 16 0.50
17 7 0.22
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.69
Consensus pattern (16 bp):
ATTTTATTATATTTAT
Found at i:3664517 original size:17 final size:17
Alignment explanation
Indices: 3664495--3664527 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3664485 ATTATTATTT
3664495 AATAAAATTTAATTAAA
1 AATAAAATTTAATTAAA
*
3664512 AATAAAATTTTATTAA
1 AATAAAATTTAATTAA
3664528 TAATTAATTA
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:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AATAAAATTTAATTAAA
Found at i:3664858 original size:23 final size:21
Alignment explanation
Indices: 3664805--3664891 Score: 61
Period size: 21 Copynumber: 3.9 Consensus size: 21
3664795 TATTTTACTA
3664805 TTATATA-ATATATATTAATT
1 TTATATATATATATATTAATT
*
3664825 TTATATTTATATATTATATAATTT
1 TTATATATATATA-TAT-TAA-TT
* *
3664849 TTATCATATAAAAATATATGTAATA
1 TTAT-ATAT--ATATATAT-TAATT
*
3664874 TTATA-ATATAAATATTAA
1 TTATATATATATATATTAA
3664892 AAATTAAGTT
Statistics
Matches: 53, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
20 9 0.17
21 11 0.21
22 3 0.06
23 5 0.09
24 7 0.13
25 8 0.15
26 6 0.11
27 4 0.08
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (21 bp):
TTATATATATATATATTAATT
Found at i:3669477 original size:15 final size:16
Alignment explanation
Indices: 3669457--3669490 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3669447 TAATTATTAA
*
3669457 TTATATT-TTTTAAGT
1 TTATATTATTTTAAAT
3669472 TTATATTATTTTAAAT
1 TTATATTATTTTAAAT
3669488 TTA
1 TTA
3669491 AATAGAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (16 bp):
TTATATTATTTTAAAT
Found at i:3669576 original size:19 final size:19
Alignment explanation
Indices: 3669554--3669600 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
3669544 AAATTATAAA
*
3669554 TAATTTATTTAAAAAATTT
1 TAATTTATATAAAAAATTT
*
3669573 TAATTGTA-ATAATAAATTT
1 TAATT-TATATAAAAAATTT
3669592 TATATTTAT
1 TA-ATTTAT
3669601 GTAGTGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
TAATTTATATAAAAAATTT
Found at i:3670905 original size:31 final size:32
Alignment explanation
Indices: 3670859--3670920 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
3670849 ATGAAAAATA
*
3670859 TTTAAGAATTGAAAAACTT-TA-TTTATTTAAT
1 TTTAAGAATT-AAAAAATTATATTTTATTTAAT
*
3670890 TTTAAGAGTTAAAAAATTATATTTTATTTAA
1 TTTAAGAATTAAAAAATTATATTTTATTTAA
3670921 ATATATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 7 0.26
31 11 0.41
32 9 0.33
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (32 bp):
TTTAAGAATTAAAAAATTATATTTTATTTAAT
Found at i:3670961 original size:13 final size:13
Alignment explanation
Indices: 3670943--3670967 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3670933 TGAACGTTAT
3670943 ATTATTTAATTTA
1 ATTATTTAATTTA
3670956 ATTATTTAATTT
1 ATTATTTAATTT
3670968 TTTAATCTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
ATTATTTAATTTA
Found at i:3671630 original size:16 final size:15
Alignment explanation
Indices: 3671601--3671654 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 15
3671591 AGTTTTGGGT
*
3671601 TTTTTTTAAGTTCAAA
1 TTTTTTCAA-TTCAAA
*
3671617 TTTTTTCGAATTCAAG
1 TTTTTTC-AATTCAAA
*
3671633 TTTTGTTCAATTTAAA
1 TTTT-TTCAATTCAAA
3671649 TTTTTT
1 TTTTTT
3671655 TTGAATTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
15 2 0.06
16 25 0.78
17 5 0.16
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.59
Consensus pattern (15 bp):
TTTTTTCAATTCAAA
Found at i:3671907 original size:26 final size:25
Alignment explanation
Indices: 3671877--3671931 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
3671867 TCTTAAAATC
*
3671877 TTCATACATTTATTATTCATA-TTAAA
1 TTCATACA-TT-TTATTCAAATTTAAA
3671903 TTCATACATTTTATTCAAATTTAAA
1 TTCATACATTTTATTCAAATTTAAA
3671928 TTCA
1 TTCA
3671932 AATTTAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 8 0.30
25 11 0.41
26 8 0.30
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (25 bp):
TTCATACATTTTATTCAAATTTAAA
Found at i:3674347 original size:20 final size:20
Alignment explanation
Indices: 3674322--3674360 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3674312 TAATTAATAA
3674322 TAATTT-TAATAATATTTAAT
1 TAATTTATAATAA-ATTTAAT
*
3674342 TAATTTATTATAAATTTAA
1 TAATTTATAATAAATTTAA
3674361 CTAAATTCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TAATTTATAATAAATTTAAT
Found at i:3677836 original size:54 final size:54
Alignment explanation
Indices: 3677770--3677928 Score: 239
Period size: 54 Copynumber: 3.0 Consensus size: 54
3677760 GTTTAATTAA
* * * *
3677770 AAAAATT-GAAGCATTTGAAAAAGTTAAAATTTTTAAATCTGAGATGGAAAAAG
1 AAAAATTAAAAGCATTTGAAAAAGTCAAAATTTTTAAAACTGAAATGGAAAAAG
* * **
3677823 AAAGATTCAAAGCATTTGAAAAAGTCAAAATTTTTAAAACAAAAATGGAAAAAG
1 AAAAATTAAAAGCATTTGAAAAAGTCAAAATTTTTAAAACTGAAATGGAAAAAG
3677877 AAAAATTAAAAGCATTTGAAAAAGTCAAAATTTTTAAAACTGAAATGGAAAA
1 AAAAATTAAAAGCATTTGAAAAAGTCAAAATTTTTAAAACTGAAATGGAAAA
3677929 GCAATTAGGA
Statistics
Matches: 94, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
53 6 0.06
54 88 0.94
ACGTcount: A:0.55, C:0.06, G:0.14, T:0.25
Consensus pattern (54 bp):
AAAAATTAAAAGCATTTGAAAAAGTCAAAATTTTTAAAACTGAAATGGAAAAAG
Found at i:3678403 original size:19 final size:19
Alignment explanation
Indices: 3678381--3678421 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3678371 GGATCCGAAA
3678381 TAATTTGGA-TTATTTCTTT
1 TAATTTGGACTT-TTTCTTT
*
3678400 TAATTTGGACTTTTTTTTT
1 TAATTTGGACTTTTTCTTT
3678419 TAA
1 TAA
3678422 AAAAAGGTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.22, C:0.05, G:0.10, T:0.63
Consensus pattern (19 bp):
TAATTTGGACTTTTTCTTT
Found at i:3686273 original size:28 final size:25
Alignment explanation
Indices: 3686239--3686309 Score: 65
Period size: 25 Copynumber: 2.8 Consensus size: 25
3686229 ATATTCTATA
*
3686239 AATTTATATATAATTAATAAATCAAAT
1 AATTTATATAT-ATTAA-AAATAAAAT
3686266 AATATTAT-T-TATTAAAAATAAAAT
1 AAT-TTATATATATTAAAAATAAAAT
* * *
3686290 TATTTATATATTTTTAAAAT
1 AATTTATATATATTAAAAAT
3686310 TTTTTAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
23 4 0.11
24 11 0.30
25 13 0.35
26 1 0.03
27 4 0.11
28 4 0.11
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (25 bp):
AATTTATATATATTAAAAATAAAAT
Found at i:3688545 original size:17 final size:16
Alignment explanation
Indices: 3688513--3688544 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3688503 AGGATTAAAT
3688513 TTTTAAAAAATATATA
1 TTTTAAAAAATATATA
3688529 TTTTAAAAAATA-ATA
1 TTTTAAAAAATATATA
3688544 T
1 T
3688545 AATAAGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTTAAAAAATATATA
Found at i:3692978 original size:20 final size:19
Alignment explanation
Indices: 3692950--3693055 Score: 73
Period size: 20 Copynumber: 5.7 Consensus size: 19
3692940 AGACAATACG
* *
3692950 ATAAAAATAATATGATTAT
1 ATAATAATAATATAATTAT
3692969 AATAATAATAATATAATTAT
1 -ATAATAATAATATAATTAT
* *
3692989 ATAAT-ATATTA-AATTTT
1 ATAATAATAATATAATTAT
*
3693006 AT-ATAATATATTTAA-TAT
1 ATAATAATA-ATATAATTAT
*
3693024 CATAATTATAATTATAATT-T
1 -ATAATAATAA-TATAATTAT
3693044 ATAA-AA-AATATA
1 ATAATAATAATATA
3693056 TAATACACAA
Statistics
Matches: 69, Mismatches: 10, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
16 6 0.09
17 12 0.17
18 9 0.13
19 14 0.20
20 27 0.39
21 1 0.01
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (19 bp):
ATAATAATAATATAATTAT
Found at i:3693616 original size:2 final size:2
Alignment explanation
Indices: 3693609--3693635 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3693599 TTTATCTATC
3693609 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3693636 GTTCTTAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3696697 original size:2 final size:2
Alignment explanation
Indices: 3696692--3696717 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3696682 CTATATACTC
3696692 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
3696718 CTGAACATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3699567 original size:22 final size:20
Alignment explanation
Indices: 3699525--3699567 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
3699515 CAGAAACAAG
**
3699525 AAATTTTCAATATTATTTAT
1 AAATTTTCAATATTAAATAT
3699545 AAATTATTACAATATTAAATAT
1 AAATT-TT-CAATATTAAATAT
3699567 A
1 A
3699568 TTTTCATGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 5 0.26
21 2 0.11
22 12 0.63
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATTTTCAATATTAAATAT
Found at i:3700103 original size:14 final size:14
Alignment explanation
Indices: 3700086--3700112 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3700076 ATTATTAATA
3700086 TATTTTTAAAATTT
1 TATTTTTAAAATTT
3700100 TATTTTTAAAATT
1 TATTTTTAAAATT
3700113 AAAAAAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TATTTTTAAAATTT
Found at i:3704970 original size:28 final size:31
Alignment explanation
Indices: 3704921--3704977 Score: 84
Period size: 28 Copynumber: 1.9 Consensus size: 31
3704911 ATATGATTGT
3704921 TTAATTTATAAATATTTATTTTATAAAATGA
1 TTAATTTATAAATATTTATTTTATAAAATGA
*
3704952 TTAATTT-T-AATA-TTATTTTTTAAAAT
1 TTAATTTATAAATATTTATTTTATAAAAT
3704978 TTTGAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 13 0.52
29 4 0.16
30 1 0.04
31 7 0.28
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (31 bp):
TTAATTTATAAATATTTATTTTATAAAATGA
Found at i:3705637 original size:12 final size:12
Alignment explanation
Indices: 3705620--3705657 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3705610 AATTAAATAA
3705620 ATTATATTTTAT
1 ATTATATTTTAT
3705632 ATTATATTTTA-
1 ATTATATTTTAT
*
3705643 AATATAATTTTAT
1 ATTAT-ATTTTAT
3705656 AT
1 AT
3705658 ATTATTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 4 0.18
12 17 0.77
13 1 0.05
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
ATTATATTTTAT
Found at i:3705663 original size:24 final size:23
Alignment explanation
Indices: 3705617--3705672 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 23
3705607 AAAAATTAAA
3705617 TAAAT-TATATTTTATATTATATTT
1 TAAATATATATTTTATATTATA--T
3705641 TAAATATA-ATTTTATA-TATTAT
1 TAAATATATATTTTATATTA-TAT
3705663 TAAATATATA
1 TAAATATATA
3705673 ACATTTAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
22 9 0.31
23 3 0.10
24 15 0.52
25 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TAAATATATATTTTATATTATAT
Found at i:3705730 original size:27 final size:26
Alignment explanation
Indices: 3705680--3705731 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
3705670 ATAACATTTA
* **
3705680 ATAATTTAAATTTTATTTTTAATATC
1 ATAAATTAAATTTTATTTAAAATATC
3705706 ATAAATTAAACTTTTATTTAAAATAT
1 ATAAATTAAA-TTTTATTTAAAATAT
3705732 ATATTAAGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (26 bp):
ATAAATTAAATTTTATTTAAAATATC
Found at i:3707597 original size:38 final size:38
Alignment explanation
Indices: 3707555--3707630 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 38
3707545 ATCGGGATAG
* *
3707555 GTAGCTTTTAGCCTTGAACTTTCTATAGCGACAACTAT
1 GTAGCTTTTAGCCTTGAACTTTCCATAACGACAACTAT
*
3707593 GTAGCTTTTGGCCTTGAACTTTCCATAACGACAACTAT
1 GTAGCTTTTAGCCTTGAACTTTCCATAACGACAACTAT
3707631 CGGATTTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (38 bp):
GTAGCTTTTAGCCTTGAACTTTCCATAACGACAACTAT
Found at i:3712407 original size:2 final size:2
Alignment explanation
Indices: 3712400--3712446 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
3712390 TTTAATATTA
3712400 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3712442 AT AT A
1 AT AT A
3712447 CAAGAAATCA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3712695 original size:54 final size:54
Alignment explanation
Indices: 3712623--3713070 Score: 284
Period size: 54 Copynumber: 8.0 Consensus size: 54
3712613 ATCTATATAA
3712623 TATATATAAAATATAATTTTTTTTACATAAATATTAATATTTATTATAAATTTT
1 TATATATAAAATATAATTTTTTTTACATAAATATTAATATTTATTATAAATTTT
* * *
3712677 TATATATAAAATATAATTTTTTTGACAT-AA-ATTAATATTTATTATGAGTTTT
1 TATATATAAAATATAATTTTTTTTACATAAATATTAATATTTATTATAAATTTT
* * * * * *
3712729 TATATATAAAATA-CAGTTTTTTAAC-TTAATATTTATTATGAGTTTTTTATAAA---G
1 TATATATAAAATATAATTTTTTTTACATAAATA-TTA--AT-A-TTTATTATAAATTTT
* * * ** **
3712783 AATATATAAAATACAGTTTTTTGGACATAAATATTAATATTTATTATGAGTTTCTTTT
1 TATATATAAAATATAATTTTTTTTACATAAATATTAATATTTATTAT-A---AATTTT
* * * * *
3712841 TCTATATAATATATATAAAATACAGTTTTTTTAACATAAATGTTAATATTTATTTTGAGTTTT
1 TATATATAA-A-ATAT--AAT----TTTTTTT-ACATAAATATTAATATTTATTATAAATTTT
* * * *
3712904 TATATATAAAATACAGTTTTTTTTACATAAATATTAATATTTATTATGAGTTTT
1 TATATATAAAATATAATTTTTTTTACATAAATATTAATATTTATTATAAATTTT
* * * * **
3712958 TATATATAAAATA-CAGTTTTTTTATATAAATGTTAATATTTATTATGAGCTTTT
1 TATATATAAAATATAATTTTTTTTACATAAATATTAATATTTATTAT-AAATTTT
* * * *
3713012 TATAGGGAATATATAAA-ATACAATTTTTTGACATAAATGTTAATATTTATTATGAATTT
1 TAT-----ATATA-AAATATA-ATTTTTTTTACATAAATATTAATATTTATTATAAATTT
3713071 CTTTTATAGA
Statistics
Matches: 308, Mismatches: 52, Indels: 62
0.73 0.12 0.15
Matches are distributed among these distances:
50 1 0.00
51 18 0.06
52 36 0.12
53 35 0.11
54 87 0.28
55 19 0.06
56 6 0.02
57 8 0.03
58 7 0.02
59 9 0.03
60 9 0.03
61 32 0.10
62 3 0.01
63 12 0.04
66 5 0.02
67 21 0.07
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (54 bp):
TATATATAAAATATAATTTTTTTTACATAAATATTAATATTTATTATAAATTTT
Found at i:3712760 original size:27 final size:28
Alignment explanation
Indices: 3712730--3712804 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 28
3712720 ATGAGTTTTT
***
3712730 ATATATAAAATACAGTTTTTTA-ACTTA
1 ATATATAAAATACAGTTTTTTATAAAGA
* ** *
3712757 ATATTTATTAT-GAGTTTTTTATAAAGA
1 ATATATAAAATACAGTTTTTTATAAAGA
3712784 ATATATAAAATACAGTTTTTT
1 ATATATAAAATACAGTTTTTT
3712805 GGACATAAAT
Statistics
Matches: 35, Mismatches: 11, Indels: 3
0.71 0.22 0.06
Matches are distributed among these distances:
26 9 0.26
27 18 0.51
28 8 0.23
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (28 bp):
ATATATAAAATACAGTTTTTTATAAAGA
Found at i:3712860 original size:121 final size:118
Alignment explanation
Indices: 3712729--3713090 Score: 318
Period size: 121 Copynumber: 3.1 Consensus size: 118
3712719 TATGAGTTTT
3712729 TATATATAAAATACAGTTTTTTAACTTAATATTTATTATGAGTTTTTTATAAAGAATATATAAAA
1 TATATATAAAATACAGTTTTTTAACTTAATATTTATTATGAGTTTTTTATAAAGAATATATAAAA
3712794 TACAGTTTTTTGGACATAAATATTAATATTTATTATGAGTTTCTTTTTCTATATAA
66 TACAGTTTTTT-GACATAAATATTAATATTTATTATGAGTTTCTTTTT-TATAT-A
* * ****
3712850 TATATATAAAATACAGTTTTTTTAACATAA-ATGTTA--AT-ATTTATTTTGAGT-TTTTATATA
1 TATATATAAAATACAG-TTTTTTAACTTAATAT-TTATTATGAGTT-TTTT-A-TAAAGAATATA
*
3712910 TAAAATACAGTTTTTTTTACATAAATATTAATATTTATTATGAG-----TTTTTATATA
61 TAAAATACAG-TTTTTTGACATAAATATTAATATTTATTATGAGTTTCTTTTTTATATA
* * * ** * * **
3712964 TA-AAATACAGT--TTTTTTATATAAATGTTAATATTTATTATGAGCTTTTTATAGGGAATATAT
1 TATATATAAAATACAGTTTT-T-T-AA-CTTAATATTTATTATGAGTTTTTTATAAAGAATATAT
* * * * * *
3713026 AAAATACAATTTTTTGACATAAATGTTAATATTTATTATGAATTTCTTTTATAGAGA
62 AAAATACAGTTTTTTGACATAAATATTAATATTTATTATGAGTTTCTTTTTTATATA
3713083 TATATATA
1 TATATATA
3713091 TTTATTAATT
Statistics
Matches: 192, Mismatches: 28, Indels: 43
0.73 0.11 0.16
Matches are distributed among these distances:
110 4 0.02
111 1 0.01
112 1 0.01
113 8 0.04
114 40 0.21
115 22 0.11
116 10 0.05
117 2 0.01
119 12 0.06
120 10 0.05
121 60 0.31
122 22 0.11
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.49
Consensus pattern (118 bp):
TATATATAAAATACAGTTTTTTAACTTAATATTTATTATGAGTTTTTTATAAAGAATATATAAAA
TACAGTTTTTTGACATAAATATTAATATTTATTATGAGTTTCTTTTTTATATA
Found at i:3712966 original size:175 final size:164
Alignment explanation
Indices: 3712624--3713066 Score: 457
Period size: 175 Copynumber: 2.7 Consensus size: 164
3712614 TCTATATAAT
* * * **
3712624 ATATATAAAATATAATTTTTTTTACATAAATATTAATATTTATTAT-AAATTTTTAT----ATAT
1 ATATATAAAATA-CAGTTTTTTGACATAAATATTAATATTTATTATGAGCTTTTTATAGGAATAT
*
3712684 A-A-AATATA-ATTTTTTTGACATAAA--TTAATATTTATTATGAGTTTTTATATATAAAATACA
65 ATATAAAATACATTTTTTTGACATAAATGTTAATATTTATTATGAGTTTTTATATATAAAATACA
*
3712744 GTTTTTTAACTTAATATTTATTATGAGTTTTTTATAAAGA
130 GTTTTTTAAATTAATATTTATTATGAG-TTTTTAT----A
*
3712784 ATATATAAAATACAGTTTTTTGGACATAAATATTAATATTTATTATGAGTTTCTTTTTCTATA-T
1 ATATATAAAATACAGTTTTTT-GACATAAATATTAATATTTATTATGAG---C-TTTT-TATAGG
* *
3712848 AATATATATAAAATACAGTTTTTTTAACATAAATGTTAATATTTATTTTGAGTTTTTATATATAA
60 AATATATATAAAATACA-TTTTTTTGACATAAATGTTAATATTTATTATGAGTTTTTATATATAA
3712913 AATACAGTTTTTTTTACATAAATATTAATATTTATTATGAG-TTTT-T-
124 AATACAG---TTTTT---T-AA-ATTAATATTTATTATGAGTTTTTATA
* * * *
3712959 ATATATAAAATACAGTTTTTTTATATAAATGTTAATATTTATTATGAGCTTTTTATAGGGA-ATA
1 ATATATAAAATACAGTTTTTTGACATAAATATTAATATTTATTATGAGCTTTTTATAGGAATATA
*
3713023 TATAAAATACAATTTTTTGACATAAATGTTAATATTTATTATGA
66 TATAAAATACATTTTTTTGACATAAATGTTAATATTTATTATGA
3713067 ATTTCTTTTA
Statistics
Matches: 241, Mismatches: 17, Indels: 42
0.80 0.06 0.14
Matches are distributed among these distances:
159 7 0.03
160 35 0.15
161 1 0.00
165 4 0.02
166 3 0.01
168 30 0.12
169 23 0.10
170 6 0.02
171 6 0.02
172 1 0.00
173 14 0.06
174 24 0.10
175 57 0.24
178 5 0.02
180 1 0.00
181 5 0.02
182 2 0.01
183 17 0.07
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.50
Consensus pattern (164 bp):
ATATATAAAATACAGTTTTTTGACATAAATATTAATATTTATTATGAGCTTTTTATAGGAATATA
TATAAAATACATTTTTTTGACATAAATGTTAATATTTATTATGAGTTTTTATATATAAAATACAG
TTTTTTAAATTAATATTTATTATGAGTTTTTATA
Found at i:3713001 original size:53 final size:53
Alignment explanation
Indices: 3712850--3713066 Score: 299
Period size: 54 Copynumber: 3.9 Consensus size: 53
3712840 TTCTATATAA
*
3712850 TATATATAAAATACAGTTTTTTTAACATAAATGTTAATATTTATTTTGAGTTTT
1 TATATATAAAATACAGTTTTTTT-ACATAAATGTTAATATTTATTATGAGTTTT
*
3712904 TATATATAAAATACAGTTTTTTTTACATAAATATTAATATTTATTATGAGTTTT
1 TATATATAAAATACAG-TTTTTTTACATAAATGTTAATATTTATTATGAGTTTT
*
3712958 TATATATAAAATACAGTTTTTTTATATAAATGTTAATATTTATTATGAGCTTTTT
1 TATATATAAAATACAGTTTTTTTACATAAATGTTAATATTTATTATGAG--TTTT
* *
3713013 ATAGGGAATATATAAAATACAATTTTTTGACATAAATGTTAATATTTATTATGA
1 -T-----ATATATAAAATACAGTTTTTTTACATAAATGTTAATATTTATTATGA
3713067 ATTTCTTTTA
Statistics
Matches: 147, Mismatches: 7, Indels: 11
0.89 0.04 0.07
Matches are distributed among these distances:
53 31 0.21
54 60 0.41
55 11 0.07
56 1 0.01
61 44 0.30
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.49
Consensus pattern (53 bp):
TATATATAAAATACAGTTTTTTTACATAAATGTTAATATTTATTATGAGTTTT
Found at i:3713226 original size:43 final size:43
Alignment explanation
Indices: 3713178--3713259 Score: 119
Period size: 43 Copynumber: 1.9 Consensus size: 43
3713168 TTTTATCATA
* * *
3713178 TTAAATTAATCAATAGATGTATAGAGATATATATTCATTGATT
1 TTAAATAAATCAATAGATATATAGAGATATAGATTCATTGATT
* *
3713221 TTAAATAAATTAATAGATATATAGATATATAGATTCATT
1 TTAAATAAATCAATAGATATATAGAGATATAGATTCATT
3713260 AAGTATTAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.41
Consensus pattern (43 bp):
TTAAATAAATCAATAGATATATAGAGATATAGATTCATTGATT
Found at i:3713367 original size:135 final size:136
Alignment explanation
Indices: 3713142--3713397 Score: 415
Period size: 135 Copynumber: 1.8 Consensus size: 136
3713132 AAGTATTAAT
* *
3713142 TAAATATTAATATTTATTATGAGTTTTTTTATCATATTAAATTAATCAATAGATGTATAGAGATA
1 TAAATATTAATATTTATTATGAGTTTTTTTATAATATTAAATTAATC-----A-GTATAGAAATA
*
3713207 TATATTCATTGATTTTAAATAAATTAATAGATATATAGATATATAGATTCATTAAGTATTAATTA
60 TATATTCATTGACTTTAAATAAATTAATAGATATATAGATATATAGATTCATTAAGTATTAATTA
3713272 ATTTTTTTGATA
125 ATTTTTTTGATA
3713284 TAAATATTAATATTTATTATGAGTTTTTTTATAATATTAAATTAATC-GTATAGAAATATATATT
1 TAAATATTAATATTTATTATGAGTTTTTTTATAATATTAAATTAATCAGTATAGAAATATATATT
*
3713348 CATTGACTTTAAATTAATTAATAGATATATAGATATATAGATTCATTAAG
66 CATTGACTTTAAATAAATTAATAGATATATAGATATATAGATTCATTAAG
3713398 AATAATGCAT
Statistics
Matches: 110, Mismatches: 4, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
135 64 0.58
142 46 0.42
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.46
Consensus pattern (136 bp):
TAAATATTAATATTTATTATGAGTTTTTTTATAATATTAAATTAATCAGTATAGAAATATATATT
CATTGACTTTAAATAAATTAATAGATATATAGATATATAGATTCATTAAGTATTAATTAATTTTT
TTGATA
Found at i:3713627 original size:15 final size:15
Alignment explanation
Indices: 3713604--3713644 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
3713594 CTAATTAATT
*
3713604 AATTAAATTACTAAA
1 AATTTAATTACTAAA
3713619 AATTTAATTA-T-AA
1 AATTTAATTACTAAA
3713632 AATTT-ATTACTAA
1 AATTTAATTACTAA
3713645 TTAATTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
12 4 0.17
13 8 0.35
14 2 0.09
15 9 0.39
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (15 bp):
AATTTAATTACTAAA
Found at i:3713648 original size:23 final size:23
Alignment explanation
Indices: 3713591--3713650 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
3713581 ATTTATTGAT
*
3713591 TTACTAATTAATTAATTAAATTA
1 TTACTAATTAATTAATAAAATTA
* **
3713614 CTAAAAATTTAATT-ATAAAATTTA
1 TTACTAA-TTAATTAATAAAA-TTA
3713638 TTACTAATTAATT
1 TTACTAATTAATT
3713651 TTTTTGTAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
23 15 0.54
24 13 0.46
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (23 bp):
TTACTAATTAATTAATAAAATTA
Found at i:3718146 original size:21 final size:20
Alignment explanation
Indices: 3718120--3718159 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3718110 TATTAAAATT
*
3718120 AATTTTATTATTTATTTTTTA
1 AATTTTATT-TTAATTTTTTA
*
3718141 AATTTTGTTTTAATTTTTT
1 AATTTTATTTTAATTTTTT
3718160 TAATAGAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (20 bp):
AATTTTATTTTAATTTTTTA
Found at i:3718180 original size:73 final size:72
Alignment explanation
Indices: 3718046--3718190 Score: 256
Period size: 73 Copynumber: 2.0 Consensus size: 72
3718036 ATATCATATT
3718046 TTAATTTTATTATTTATTTTAAATTTTGTTTTAACTCTTTTTAATAGAATTTGAATGGTTAAATT
1 TTAATTTTATTATTTATTTTAAATTTTGTTTTAACTCTTTTTAATAGAATTTGAATGGTTAAATT
3718111 ATTAAAA
66 ATTAAAA
*
3718118 TTAATTTTATTATTTATTTTTTAAATTTTGTTTTAA-TTTTTTTAATAGAATTTGAATGGTTAAA
1 TTAATTTTATTATTTA--TTTTAAATTTTGTTTTAACTCTTTTTAATAGAATTTGAATGGTTAAA
3718182 TTATTAAAA
64 TTATTAAAA
3718191 ATATTATTAC
Statistics
Matches: 70, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
72 16 0.23
73 36 0.51
74 18 0.26
ACGTcount: A:0.34, C:0.01, G:0.07, T:0.57
Consensus pattern (72 bp):
TTAATTTTATTATTTATTTTAAATTTTGTTTTAACTCTTTTTAATAGAATTTGAATGGTTAAATT
ATTAAAA
Found at i:3727453 original size:2 final size:2
Alignment explanation
Indices: 3727446--3727477 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3727436 AACTTGATTA
3727446 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
3727478 CACAGAAGTA
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:3727708 original size:157 final size:157
Alignment explanation
Indices: 3727490--3727799 Score: 421
Period size: 157 Copynumber: 2.0 Consensus size: 157
3727480 CAGAAGTAAC
* *
3727490 CCATACTTCATCAGTGAGATTGCTTACAATCTTACACTAACAACCAAACTTTTTTCCTTTTTAAG
1 CCATACTTCATCACTGAGATTGCTTACAACCTTACACTAACAACCAAACTTTTTTCCTTTTTAAG
* * * *
3727555 TGAACATAATGAGATC-AATTTCTT-ATTCATTATGGATATTAATCGTGCAATGTATTTATGTAT
66 TGAACATAATAAGA-CAAATTT-TTCATTCATCATGAATATTAATCATGCAATGTATTTATGTAT
* *
3727618 TGTGTATCTACGTACGATAATTTATATGT
129 CGTATATCTACGTACGATAATTTATATGT
*
3727647 CCATACTTCATCACTG-GAATTGCTTATC-ACCTTACACTAACAACCAAACTTTTTTCTTTTTTA
1 CCATACTTCATCACTGAG-ATTGCTTA-CAACCTTACACTAACAACCAAACTTTTTTCCTTTTTA
** * *
3727710 AGTGGGCATAATAAGACAAATTTTTCATTTATCATGAATATTAATCATGTAATGTATTTATGTAT
64 AGTGAACATAATAAGACAAATTTTTCATTCATCATGAATATTAATCATGCAATGTATTTATGTAT
* *
3727775 CGTATATTTATGTACGATAATTTAT
129 CGTATATCTACGTACGATAATTTAT
3727800 GTATTGATAT
Statistics
Matches: 134, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
156 4 0.03
157 129 0.96
158 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (157 bp):
CCATACTTCATCACTGAGATTGCTTACAACCTTACACTAACAACCAAACTTTTTTCCTTTTTAAG
TGAACATAATAAGACAAATTTTTCATTCATCATGAATATTAATCATGCAATGTATTTATGTATCG
TATATCTACGTACGATAATTTATATGT
Found at i:3727784 original size:15 final size:14
Alignment explanation
Indices: 3727764--3727809 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
3727754 TCATGTAATG
3727764 TATTTATGTATCGTA
1 TATTTATGTATCG-A
3727779 TATTTATGTA-CGA
1 TATTTATGTATCGA
*
3727792 TAATTTATGTATTGA
1 T-ATTTATGTATCGA
3727807 TAT
1 TAT
3727810 ACATAATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 2 0.07
14 13 0.46
15 13 0.46
ACGTcount: A:0.30, C:0.04, G:0.13, T:0.52
Consensus pattern (14 bp):
TATTTATGTATCGA
Found at i:3729767 original size:18 final size:20
Alignment explanation
Indices: 3729739--3729791 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 20
3729729 GTTGAAAACT
*
3729739 CTTACTATTTTTTTAAGT-A
1 CTTACTATTTTTTTAAATAA
*
3729758 CTTA-TA-TTTTCTAAATAA
1 CTTACTATTTTTTTAAATAA
*
3729776 CTTATTATTTTTTTAA
1 CTTACTATTTTTTTAA
3729792 TTGAAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 8 0.29
18 7 0.25
19 6 0.21
20 7 0.25
ACGTcount: A:0.30, C:0.09, G:0.02, T:0.58
Consensus pattern (20 bp):
CTTACTATTTTTTTAAATAA
Found at i:3739495 original size:16 final size:16
Alignment explanation
Indices: 3739476--3739507 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3739466 TTGTTCAATT
3739476 TTTATTTTTATTTTTA
1 TTTATTTTTATTTTTA
*
3739492 TTTATTTTTCTTTTTA
1 TTTATTTTTATTTTTA
3739508 CTTTCCCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTATTTTTATTTTTA
Found at i:3739634 original size:13 final size:13
Alignment explanation
Indices: 3739616--3739662 Score: 51
Period size: 14 Copynumber: 3.6 Consensus size: 13
3739606 CACCAAGCTG
*
3739616 TCTTTTTTCTTTT
1 TCTTTTTTCTTTC
3739629 TCTTTTTTTCTTTC
1 TC-TTTTTTCTTTC
**
3739643 TCTTTCAT-TTTC
1 TCTTTTTTCTTTC
3739655 TCTTTTTT
1 TCTTTTTT
3739663 TTCCTCATCT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
12 10 0.36
13 6 0.21
14 12 0.43
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (13 bp):
TCTTTTTTCTTTC
Found at i:3739648 original size:18 final size:18
Alignment explanation
Indices: 3739621--3739659 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
3739611 AGCTGTCTTT
* * *
3739621 TTTCTTTTTCTTTTTTTC
1 TTTCTCTTTCATTTTCTC
3739639 TTTCTCTTTCATTTTCTC
1 TTTCTCTTTCATTTTCTC
3739657 TTT
1 TTT
3739660 TTTTTCCTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTCTCTTTCATTTTCTC
Found at i:3741897 original size:23 final size:25
Alignment explanation
Indices: 3741842--3741899 Score: 66
Period size: 26 Copynumber: 2.4 Consensus size: 25
3741832 TGAAGTATCC
* *
3741842 TTCTTTTTCCCTCTCTTATTTTCTT
1 TTCTTTTTTCCTCTCATATTTTCTT
*
3741867 TTGTTTTTTTCCTCT-AT-TTTTCTT
1 TT-CTTTTTTCCTCTCATATTTTCTT
3741891 TTCTTTTTT
1 TTCTTTTTT
3741900 AGATCTTTAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 6 0.21
24 9 0.32
25 3 0.11
26 10 0.36
ACGTcount: A:0.03, C:0.21, G:0.02, T:0.74
Consensus pattern (25 bp):
TTCTTTTTTCCTCTCATATTTTCTT
Found at i:3743033 original size:21 final size:21
Alignment explanation
Indices: 3743007--3743069 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
3742997 ACTTAACATA
3743007 TGGCAATTGTATCGATATAAT
1 TGGCAATTGTATCGATATAAT
* * *
3743028 TGGCAATTGTGTTGATACAAT
1 TGGCAATTGTATCGATATAAT
*
3743049 AT-GC-CTTGTATCGATATAAT
1 -TGGCAATTGTATCGATATAAT
3743069 T
1 T
3743070 ATTACCTTCA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
19 1 0.03
20 12 0.35
21 20 0.59
22 1 0.03
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.40
Consensus pattern (21 bp):
TGGCAATTGTATCGATATAAT
Found at i:3746518 original size:36 final size:37
Alignment explanation
Indices: 3746463--3746536 Score: 105
Period size: 36 Copynumber: 2.0 Consensus size: 37
3746453 GTAAATTTAG
* * *
3746463 ATTTTATTTAATTTGTAATAACAAACAT-TAAAGAAA
1 ATTTTATTTAACTTATAATAACAAACATAAAAAGAAA
*
3746499 ATTTTATTTAACTTATAATAATAAACATAAAAAGAAA
1 ATTTTATTTAACTTATAATAACAAACATAAAAAGAAA
3746536 A
1 A
3746537 AAAAAGTTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
36 25 0.76
37 8 0.24
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.36
Consensus pattern (37 bp):
ATTTTATTTAACTTATAATAACAAACATAAAAAGAAA
Found at i:3748973 original size:12 final size:11
Alignment explanation
Indices: 3748943--3748972 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
3748933 AAAAAACTAA
3748943 GAAAAAAATCT
1 GAAAAAAATCT
3748954 GAAAAAAATCT
1 GAAAAAAATCT
3748965 GAAAAAAA
1 GAAAAAAA
3748973 AAAAGAGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.70, C:0.07, G:0.10, T:0.13
Consensus pattern (11 bp):
GAAAAAAATCT
Found at i:3754767 original size:34 final size:35
Alignment explanation
Indices: 3754729--3754795 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
3754719 CCTTACAACA
3754729 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
3754763 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
3754796 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:3755272 original size:13 final size:13
Alignment explanation
Indices: 3755254--3755279 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3755244 CAATTTTTTG
3755254 TGTATCGATACAT
1 TGTATCGATACAT
3755267 TGTATCGATACAT
1 TGTATCGATACAT
3755280 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3756006 original size:21 final size:21
Alignment explanation
Indices: 3755963--3756008 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
3755953 TAATTCACGC
* *
3755963 ATTCTCCCCCGTTTATTAATA
1 ATTCTCCCCCGTTAATCAATA
3755984 ATTCTCCCCC-TTAATCAAGTA
1 ATTCTCCCCCGTTAATCAA-TA
3756005 ATTC
1 ATTC
3756009 ATATCAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.26, C:0.30, G:0.04, T:0.39
Consensus pattern (21 bp):
ATTCTCCCCCGTTAATCAATA
Found at i:3756290 original size:30 final size:30
Alignment explanation
Indices: 3756255--3756314 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
3756245 ACTAATACCA
* *
3756255 AAAATTTATGCAAGCTCTCCCCCTTAATAC
1 AAAATTTATACAAACTCTCCCCCTTAATAC
3756285 AAAATTTATACAAACTCTCCCCCTTAATAC
1 AAAATTTATACAAACTCTCCCCCTTAATAC
3756315 GTTGTCACCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.37, C:0.30, G:0.03, T:0.30
Consensus pattern (30 bp):
AAAATTTATACAAACTCTCCCCCTTAATAC
Found at i:3756919 original size:13 final size:13
Alignment explanation
Indices: 3756901--3756930 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
3756891 CATACTGAAG
3756901 CAATGTATCGATA
1 CAATGTATCGATA
3756914 CAATGTATCGATA
1 CAATGTATCGATA
3756927 CAAT
1 CAAT
3756931 CTGGAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:3760165 original size:34 final size:35
Alignment explanation
Indices: 3760127--3760193 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
3760117 CCTTACAACA
3760127 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
3760161 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
3760194 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:3764735 original size:21 final size:22
Alignment explanation
Indices: 3764695--3764735 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
3764685 TCAAACCATC
* *
3764695 ATATTTATAAAGTTGAAATTGG
1 ATATTTATAAACTAGAAATTGG
3764717 ATATTTA-AAACTAGAAATT
1 ATATTTATAAACTAGAAATT
3764736 AATTTAATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.46, C:0.02, G:0.12, T:0.39
Consensus pattern (22 bp):
ATATTTATAAACTAGAAATTGG
Found at i:3765732 original size:22 final size:22
Alignment explanation
Indices: 3765707--3765759 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
3765697 AAAGCTTGTG
*
3765707 ATATAATTTACTTTTTGATAAA
1 ATATAATTTACTTTTTAATAAA
3765729 ATATAATTTACTTTTTAATAAA
1 ATATAATTTACTTTTTAATAAA
* *
3765751 TTATTATTT
1 ATATAATTT
3765760 CATCATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.55
Consensus pattern (22 bp):
ATATAATTTACTTTTTAATAAA
Found at i:3766892 original size:30 final size:30
Alignment explanation
Indices: 3766775--3766893 Score: 107
Period size: 30 Copynumber: 4.0 Consensus size: 30
3766765 ATGTTAAATA
* * * *
3766775 AAATATTAATTTAAG-TAAAAGCTTTATTT
1 AAATATAAATTAAAGATTAAAGATTTATTT
** * * *
3766804 AGTTACAAATTAAATATTAAA-ATTTTATTC
1 AAATATAAATTAAAGATTAAAGA-TTTATTT
* * *
3766834 GAATAAAAATTAAAGATTAAAGACTTATTT
1 AAATATAAATTAAAGATTAAAGATTTATTT
3766864 AAATATAAATTAAAGATTAAAGATTTATTT
1 AAATATAAATTAAAGATTAAAGATTTATTT
3766894 TAGTCTAATA
Statistics
Matches: 68, Mismatches: 19, Indels: 5
0.74 0.21 0.05
Matches are distributed among these distances:
29 9 0.13
30 58 0.85
31 1 0.01
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (30 bp):
AAATATAAATTAAAGATTAAAGATTTATTT
Found at i:3767250 original size:3 final size:3
Alignment explanation
Indices: 3767242--3767280 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
3767232 ATTCAATTAA
3767242 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3767281 GTAATAAGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3767352 original size:16 final size:15
Alignment explanation
Indices: 3767331--3767360 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3767321 ACAAAGTAGA
3767331 TAAAAATAGTATTTTT
1 TAAAAATA-TATTTTT
3767347 TAAAAATATATTTT
1 TAAAAATATATTTT
3767361 AAAAAGAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
TAAAAATATATTTTT
Found at i:3767655 original size:24 final size:25
Alignment explanation
Indices: 3767626--3767693 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 25
3767616 ATACTTAGGA
3767626 TGAAAAGATATATTTTTTAAAAA-AT
1 TGAAAA-ATATATTTTTTAAAAAGAT
* * *
3767651 T-AAAAATAAATATTTAAAAAAGAT
1 TGAAAAATATATTTTTTAAAAAGAT
*
3767675 TGATAAAT-TATTTTTTAAA
1 TGAAAAATATATTTTTTAAA
3767694 TGAATAGTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
23 13 0.38
24 15 0.44
25 6 0.18
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (25 bp):
TGAAAAATATATTTTTTAAAAAGAT
Found at i:3768843 original size:15 final size:16
Alignment explanation
Indices: 3768825--3768858 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
3768815 TTTACTTTAA
3768825 AAAATT-AATTAATAT
1 AAAATTAAATTAATAT
3768840 AAAATTAAAATTAATAT
1 AAAATT-AAATTAATAT
3768857 AA
1 AA
3768859 TTAATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
17 11 0.65
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAATTAAATTAATAT
Found at i:3781455 original size:4 final size:4
Alignment explanation
Indices: 3781446--3781495 Score: 73
Period size: 4 Copynumber: 12.5 Consensus size: 4
3781436 TCTGTGAAAG
** *
3781446 CATA CATA CATA CATA CATA CATA TGTG CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
3781494 CA
1 CA
3781496 CTTGCACAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.46, C:0.24, G:0.04, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:3782221 original size:20 final size:20
Alignment explanation
Indices: 3782177--3782218 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
3782167 AATTTGATTG
3782177 TTTAAAATATTATAATATTA
1 TTTAAAATATTATAATATTA
*
3782197 ATTAAATATATT-TAATA-TA
1 TTTAAA-ATATTATAATATTA
3782216 TTT
1 TTT
3782219 TAATGGTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
19 4 0.21
20 10 0.53
21 5 0.26
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTTAAAATATTATAATATTA
Found at i:3783677 original size:2 final size:2
Alignment explanation
Indices: 3783670--3783724 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
3783660 TGAACTGGTT
3783670 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3783712 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
3783725 TTCATCATGC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3784073 original size:166 final size:171
Alignment explanation
Indices: 3783775--3784111 Score: 443
Period size: 166 Copynumber: 2.0 Consensus size: 171
3783765 TGATGGGACT
* * *
3783775 TTCTGGAGTCGTTGGATAAAACCAGATGCCATTGCCCAAGCCGAAGTATGATCTTTATATATATA
1 TTCTGGAGTCGATGGATAAAACCAGATGCCATTGCCCAAGCCGAACTATGATC--TATAGATATA
* * *
3783840 TATATTTTTTACCAATCTTATTCTATCCAAGGTTTCTTGAATGTTGGTTGTACATGTTTAAGTTC
64 TATATTTTTTACCAATCTTATTCTATCCAAAGTTTCTTGAATGTTAGTTATACATGTTTAAGTTC
* *
3783905 TATGTTCATATAAGACAATTAATT-GATCCATCTGGCTAAGCA
129 TATCTTCATATAAGACAATTAATTGGATCCATCTGCCTAAGCA
* * *
3783947 TTCTGGAGTCGATGGATAAAACCAGATGTCATTGCCTAAGCTGAACTATGATC-AT-GATATAT-
1 TTCTGGAGTCGATGGATAAAACCAGATGCCATTGCCCAAGCCGAACTATGATCTATAGATATATA
* * * *
3784009 T-TTTTTTATCAATCTTATTCTA-CCAAAAGTTTCTTGATTGTTAGTTATAGATTTTTAAGTTCT
66 TATTTTTTACCAATCTTATTCTATCC-AAAGTTTCTTGAATGTTAGTTATACATGTTTAAGTTCT
* * *
3784072 ATCTTCATATTAGACAATTAGTTGGATCCATTTGCCTAAG
130 ATCTTCATATAAGACAATTAATTGGATCCATCTGCCTAAG
3784112 TTATTTTTCT
Statistics
Matches: 145, Mismatches: 18, Indels: 9
0.84 0.10 0.05
Matches are distributed among these distances:
165 2 0.01
166 72 0.50
167 15 0.10
168 6 0.04
169 2 0.01
172 48 0.33
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (171 bp):
TTCTGGAGTCGATGGATAAAACCAGATGCCATTGCCCAAGCCGAACTATGATCTATAGATATATA
TATTTTTTACCAATCTTATTCTATCCAAAGTTTCTTGAATGTTAGTTATACATGTTTAAGTTCTA
TCTTCATATAAGACAATTAATTGGATCCATCTGCCTAAGCA
Found at i:3789330 original size:24 final size:24
Alignment explanation
Indices: 3789302--3789360 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
3789292 TTCTAAATTT
*
3789302 ATATTAAAATTTATATAAATATAA
1 ATATTAAAATATATATAAATATAA
* * *
3789326 ATATTTAAATATATATATATATAT
1 ATATTAAAATATATATAAATATAA
3789350 ATA-T-AAATATA
1 ATATTAAAATATA
3789361 AAGTTTGAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 7 0.23
23 1 0.03
24 23 0.74
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
ATATTAAAATATATATAAATATAA
Found at i:3789334 original size:14 final size:14
Alignment explanation
Indices: 3789313--3789360 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
3789303 TATTAAAATT
3789313 TATATAAATATAAA
1 TATATAAATATAAA
*
3789327 TATTTAAATATATATA
1 TATATAAATATA-A-A
*
3789343 TATATATATATAAA
1 TATATAAATATAAA
3789357 TATA
1 TATA
3789361 AAGTTTGAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 16 0.55
15 2 0.07
16 11 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TATATAAATATAAA
Found at i:3789345 original size:8 final size:8
Alignment explanation
Indices: 3789313--3789360 Score: 51
Period size: 8 Copynumber: 6.0 Consensus size: 8
3789303 TATTAAAATT
*
3789313 TATATAAA
1 TATATATA
*
3789321 TATAAATA
1 TATATATA
* *
3789329 TTTAAATA
1 TATATATA
3789337 TATATATA
1 TATATATA
3789345 TATATATA
1 TATATATA
*
3789353 TAAATATA
1 TATATATA
3789361 AAGTTTGAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 34 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (8 bp):
TATATATA
Found at i:3789725 original size:18 final size:19
Alignment explanation
Indices: 3789692--3789728 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
3789682 TAAAATAAAT
*
3789692 TAGATAAATTAATTGATCA
1 TAGATAAATAAATTGATCA
3789711 TAGATAAA-AAATTGATCA
1 TAGATAAATAAATTGATCA
3789729 AATTTATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.51, C:0.05, G:0.11, T:0.32
Consensus pattern (19 bp):
TAGATAAATAAATTGATCA
Found at i:3790011 original size:4 final size:4
Alignment explanation
Indices: 3790004--3790034 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
3789994 AAAAACCAAC
3790004 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
3790035 AACAATTGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:3790862 original size:21 final size:21
Alignment explanation
Indices: 3790822--3790863 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3790812 TTCCGTTTGT
*
3790822 AACTGCAATTAACATGTCTGC
1 AACTGCAATTAACATCTCTGC
3790843 AACTGCAATTTAA-ATCTCTGC
1 AACTGCAA-TTAACATCTCTGC
3790864 TATAGCCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.31
Consensus pattern (21 bp):
AACTGCAATTAACATCTCTGC
Found at i:3794829 original size:24 final size:24
Alignment explanation
Indices: 3794802--3794851 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
3794792 GTTGCAACTC
*
3794802 AAGGAATG-CCCCTCAATAAGTAAA
1 AAGGAATGTCCAC-CAATAAGTAAA
3794826 AAGGAATGTCCACCAATAAGTAAA
1 AAGGAATGTCCACCAATAAGTAAA
3794850 AA
1 AA
3794852 TTAAGTAGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.50, C:0.18, G:0.16, T:0.16
Consensus pattern (24 bp):
AAGGAATGTCCACCAATAAGTAAA
Found at i:3799397 original size:45 final size:45
Alignment explanation
Indices: 3799333--3799424 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 45
3799323 TACTTACCAG
*
3799333 AAAATGCTATGGACATTTCTTAGCAGACTATTGAATATGAAACAA
1 AAAATGCTATGGACATTTCTTAGCAGACTATGGAATATGAAACAA
3799378 AAAATGCTATGGACATTTCTTAGCAGACTATGGAATATGAAACAA
1 AAAATGCTATGGACATTTCTTAGCAGACTATGGAATATGAAACAA
3799423 AA
1 AA
3799425 CTAATAGGCC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.27
Consensus pattern (45 bp):
AAAATGCTATGGACATTTCTTAGCAGACTATGGAATATGAAACAA
Found at i:3801488 original size:2 final size:2
Alignment explanation
Indices: 3801481--3801517 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3801471 ATTTTATTCT
3801481 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3801518 TAGAATTACT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3802391 original size:16 final size:16
Alignment explanation
Indices: 3802372--3802431 Score: 66
Period size: 16 Copynumber: 3.8 Consensus size: 16
3802362 TTAAGTAACT
3802372 TTTAAATTTAAAATGA
1 TTTAAATTTAAAATGA
* *
3802388 TTTAAATTTTACATGA
1 TTTAAATTTAAAATGA
* * *
3802404 CTCAAATTTAAAATAA
1 TTTAAATTTAAAATGA
*
3802420 TTTAAAATTAAA
1 TTTAAATTTAAA
3802432 TATTCAATCA
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (16 bp):
TTTAAATTTAAAATGA
Found at i:3808283 original size:19 final size:19
Alignment explanation
Indices: 3808261--3808300 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
3808251 TCAATTATTT
3808261 AAGATTAAAGTAATTACAC
1 AAGATTAAAGTAATTACAC
3808280 AAGATTAAAGTAATTACAC
1 AAGATTAAAGTAATTACAC
3808299 AA
1 AA
3808301 TGAATGTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.55, C:0.10, G:0.10, T:0.25
Consensus pattern (19 bp):
AAGATTAAAGTAATTACAC
Found at i:3809447 original size:12 final size:12
Alignment explanation
Indices: 3809432--3809456 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3809422 GTTGTCAGCA
3809432 TAGTTAAAAACT
1 TAGTTAAAAACT
3809444 TAGTTAAAAACT
1 TAGTTAAAAACT
3809456 T
1 T
3809457 TATCAAAATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (12 bp):
TAGTTAAAAACT
Found at i:3811843 original size:37 final size:36
Alignment explanation
Indices: 3811802--3811921 Score: 116
Period size: 37 Copynumber: 3.2 Consensus size: 36
3811792 TTGGGTGTCA
*
3811802 AAATTTAAAAATTCTTAAAATTTTAAAATTTGATCTT
1 AAATTTAAAAATT-TTAAAATTTTAAAATTTAATCTT
** * * *
3811839 AAATTTAAAAATTTTTAATTTTTTTAAATTTTTATCTCA
1 AAATTTAAAAA-TTTTAA-AATTTTAAAATTTAATCT-T
* * *
3811878 AAATTTAAAAATTTTTAAATTTCAAAATTCAATCTT
1 AAATTTAAAAATTTTAAAATTTTAAAATTTAATCTT
3811914 -AATTTAAA
1 AAATTTAAA
3811922 GAATGCTATA
Statistics
Matches: 67, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
35 8 0.12
37 27 0.40
38 21 0.31
39 11 0.16
ACGTcount: A:0.45, C:0.06, G:0.01, T:0.48
Consensus pattern (36 bp):
AAATTTAAAAATTTTAAAATTTTAAAATTTAATCTT
Found at i:3811844 original size:20 final size:21
Alignment explanation
Indices: 3811814--3811852 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
3811804 ATTTAAAAAT
*
3811814 TCTTAAAATTTTAAAATTTGA
1 TCTTAAAATTTAAAAATTTGA
3811835 TCTT-AAATTTAAAAATTT
1 TCTTAAAATTTAAAAATTT
3811853 TTAATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.49
Consensus pattern (21 bp):
TCTTAAAATTTAAAAATTTGA
Found at i:3812954 original size:15 final size:14
Alignment explanation
Indices: 3812934--3812965 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
3812924 TAGAACATGT
3812934 AATTTAAATAAATCA
1 AATTTAAATAAAT-A
3812949 AATTTAAATAAATA
1 AATTTAAATAAATA
3812963 AAT
1 AAT
3812966 AAATATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTTAAATAAATA
Found at i:3812986 original size:10 final size:10
Alignment explanation
Indices: 3812968--3813029 Score: 56
Period size: 10 Copynumber: 6.1 Consensus size: 10
3812958 AAATAAATAA
3812968 ATATTTATTT
1 ATATTTATTT
*
3812978 ATGTTTA-TT
1 ATATTTATTT
*
3812987 -TAGTTATTTT
1 ATATTTA-TTT
*
3812997 AAATTTATTT
1 ATATTTATTT
3813007 ATATTTAATTT
1 ATATTT-ATTT
3813018 ATATTTTATTT
1 ATA-TTTATTT
3813029 A
1 A
3813030 AAAAGAAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
8 4 0.10
9 2 0.05
10 16 0.39
11 16 0.39
12 3 0.07
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (10 bp):
ATATTTATTT
Found at i:3813008 original size:15 final size:15
Alignment explanation
Indices: 3812970--3813030 Score: 63
Period size: 15 Copynumber: 4.1 Consensus size: 15
3812960 ATAAATAAAT
*
3812970 ATTTATTTATGTTT-
1 ATTTATTTATATTTA
*
3812984 ATTTAGTTAT-TTTAA
1 ATTTATTTATATTT-A
3812999 ATTTATTTATATTTA
1 ATTTATTTATATTTA
*
3813014 ATTTATATTTTATTTA
1 ATTTAT-TTATATTTA
3813030 A
1 A
3813031 AAAGAAATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
13 3 0.08
14 9 0.22
15 16 0.40
16 12 0.30
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (15 bp):
ATTTATTTATATTTA
Found at i:3813013 original size:29 final size:28
Alignment explanation
Indices: 3812970--3813025 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
3812960 ATAAATAAAT
*
3812970 ATTTATTTATGTTT-ATTTAGTTATTTTAA
1 ATTTATTTATATTTAATTTA--TATTTTAA
3812999 ATTTATTTATATTTAATTTATATTTTA
1 ATTTATTTATATTTAATTTATATTTTA
3813026 TTTAAAAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 7 0.28
29 13 0.52
30 5 0.20
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (28 bp):
ATTTATTTATATTTAATTTATATTTTAA
Found at i:3813029 original size:11 final size:11
Alignment explanation
Indices: 3813000--3813029 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
3812990 TTATTTTAAA
3813000 TTTATTTATAT
1 TTTATTTATAT
*
3813011 TTAATTTATAT
1 TTTATTTATAT
3813022 TTTATTTA
1 TTTATTTA
3813030 AAAAGAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTATTTATAT
Found at i:3814159 original size:2 final size:2
Alignment explanation
Indices: 3814152--3814181 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3814142 AACATGTGTT
3814152 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3814182 ATTTTGTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3814402 original size:20 final size:21
Alignment explanation
Indices: 3814379--3814421 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
3814369 ATTATAAATA
3814379 TTAAAAT-A-AAAATAATATTT
1 TTAAAATAATAAAATAA-ATTT
3814399 TT-AAATAATAAAATAAATTT
1 TTAAAATAATAAAATAAATTT
3814419 TTA
1 TTA
3814422 TATCATTGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
19 4 0.20
20 9 0.45
21 7 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAAAATAATAAAATAAATTT
Found at i:3815024 original size:21 final size:21
Alignment explanation
Indices: 3814937--3815026 Score: 76
Period size: 21 Copynumber: 4.3 Consensus size: 21
3814927 AATATATTTT
* *
3814937 GATGAATGAATGCATTTGTTG
1 GATGAATGAATGTATTTATTG
* * *
3814958 AATAAAT-AGATGTATTTGTTG
1 GATGAATGA-ATGTATTTATTG
* *
3814979 GATGAATGAATGTATTTCTTA
1 GATGAATGAATGTATTTATTG
*
3815000 GATGAGA-GAATGTACTTATTG
1 GATGA-ATGAATGTATTTATTG
3815021 GATGAA
1 GATGAA
3815027 AAAAATGTAC
Statistics
Matches: 56, Mismatches: 10, Indels: 7
0.77 0.14 0.10
Matches are distributed among these distances:
20 2 0.04
21 52 0.93
22 2 0.04
ACGTcount: A:0.34, C:0.03, G:0.24, T:0.38
Consensus pattern (21 bp):
GATGAATGAATGTATTTATTG
Found at i:3815085 original size:16 final size:16
Alignment explanation
Indices: 3815064--3815094 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3815054 ATCATAGTTC
3815064 GTGAAAAAACTTATTT
1 GTGAAAAAACTTATTT
3815080 GTGAAAAAACTTATT
1 GTGAAAAAACTTATT
3815095 AATTAAGACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.35
Consensus pattern (16 bp):
GTGAAAAAACTTATTT
Found at i:3816146 original size:13 final size:13
Alignment explanation
Indices: 3816128--3816154 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3816118 AAATTATGCT
3816128 TTGTATCGATACA
1 TTGTATCGATACA
3816141 TTGTATCGATACA
1 TTGTATCGATACA
3816154 T
1 T
3816155 GATCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3816184 original size:20 final size:20
Alignment explanation
Indices: 3816140--3816213 Score: 107
Period size: 20 Copynumber: 3.8 Consensus size: 20
3816130 GTATCGATAC
3816140 ATTGTATCGATACATGATC-
1 ATTGTATCGATACATGATCA
3816159 ATTGTATCGATACATGGA-CA
1 ATTGTATCGATACAT-GATCA
* *
3816179 ATTGTATCGATACATTATGA
1 ATTGTATCGATACATGATCA
3816199 ATTGTATCGATACAT
1 ATTGTATCGATACAT
3816214 TGCTTCTAAC
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
19 17 0.34
20 33 0.66
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (20 bp):
ATTGTATCGATACATGATCA
Found at i:3821395 original size:13 final size:13
Alignment explanation
Indices: 3821377--3821416 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
3821367 ACAATATTTC
3821377 TTGTATCGATACA
1 TTGTATCGATACA
3821390 TTGTATCGATACA
1 TTGTATCGATACA
*
3821403 TTATATCGATACA
1 TTGTATCGATACA
3821416 T
1 T
3821417 GGGTTACTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3823980 original size:19 final size:19
Alignment explanation
Indices: 3823952--3824003 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
3823942 CAATATATTA
*
3823952 TATCGTTACATGATC-ATTG
1 TATCGATACATGA-CAATTG
3823971 TATCGATACATGGACAATTG
1 TATCGATACAT-GACAATTG
3823991 TATCGATACATGA
1 TATCGATACATGA
3824004 AACTGGCAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 13 0.43
20 17 0.57
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (19 bp):
TATCGATACATGACAATTG
Found at i:3828016 original size:18 final size:18
Alignment explanation
Indices: 3827993--3828028 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3827983 CTTAAAATGT
3827993 ATCGATACAAAACCACCC
1 ATCGATACAAAACCACCC
3828011 ATCGATACAAAACCACCC
1 ATCGATACAAAACCACCC
3828029 TGCATACTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.39, G:0.06, T:0.11
Consensus pattern (18 bp):
ATCGATACAAAACCACCC
Found at i:3828110 original size:20 final size:20
Alignment explanation
Indices: 3828047--3828122 Score: 82
Period size: 20 Copynumber: 3.7 Consensus size: 20
3828037 ATCAAGGAAA
* *
3828047 TGTATCGATACA-TAAGTAAA
1 TGTATCGATACATTTA-TAAT
3828067 TGTATCGATACATACTTATAAT
1 TGTATCGATACAT--TTATAAT
* *
3828089 TGTATCAATACATTTATCAT
1 TGTATCGATACATTTATAAT
3828109 TGTATCGATACATT
1 TGTATCGATACATT
3828123 CTGGGTTTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
20 31 0.65
22 15 0.31
23 2 0.04
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATTTATAAT
Found at i:3830611 original size:78 final size:79
Alignment explanation
Indices: 3830495--3830665 Score: 190
Period size: 78 Copynumber: 2.2 Consensus size: 79
3830485 CATTAATGTT
* * * * *
3830495 TTTTATTTCTAAAATATCAATTTTCCACCCTCGGGGATACTCCAATCCC-GTTA-TTTC-TGAGG
1 TTTTATTTCTAAAACATCAAGTTTCCACCATCAGGGATACTCCAA-CCCTGTTATTTTCAAGA-G
*
3830557 GCATACTTCAA-CCTCGA
64 G-ATACTTCAACCCT-AA
* * *
3830574 TTTTATTTCTAAAACA-CCAGTTTCCACCATTAGGGATACTCCAACCCTGTTGTTTTCAAGAGGA
1 TTTTATTTCTAAAACATCAAGTTTCCACCATCAGGGATACTCCAACCCTGTTATTTTCAAGAGGA
3830638 TACTTCAACCCTAA
66 TACTTCAACCCTAA
3830652 TTTTATTTCTAAAA
1 TTTTATTTCTAAAA
3830666 TACCGATTTT
Statistics
Matches: 79, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
77 3 0.04
78 50 0.63
79 24 0.30
80 2 0.03
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.36
Consensus pattern (79 bp):
TTTTATTTCTAAAACATCAAGTTTCCACCATCAGGGATACTCCAACCCTGTTATTTTCAAGAGGA
TACTTCAACCCTAA
Found at i:3830693 original size:20 final size:20
Alignment explanation
Indices: 3830651--3830695 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
3830641 TTCAACCCTA
* * *
3830651 ATTTTATTTCTAAAATACCG
1 ATTTTATTTATAAAACAACG
*
3830671 ATTTTATTTATAAAACAATG
1 ATTTTATTTATAAAACAACG
3830691 ATTTT
1 ATTTT
3830696 TCACTATCGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.38, C:0.09, G:0.04, T:0.49
Consensus pattern (20 bp):
ATTTTATTTATAAAACAACG
Found at i:3830802 original size:79 final size:79
Alignment explanation
Indices: 3830691--3830876 Score: 223
Period size: 79 Copynumber: 2.4 Consensus size: 79
3830681 TAAAACAATG
* * * * *
3830691 ATTTTTCACTATCGGGGATACTCCAACCCCGTTATTT-TCGAGGGGATACTCTAACTCTGATTTT
1 ATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTCT-AAGGGGATACTCCAACCCTAATTTT
* *
3830755 A-TTTCTACAGCATCA
65 ATTTTC-AAAACATCA
* *
3830770 ATTTTTCACCATCGGGGATACTCCAACTCCGTTATTTCTAAGGGGATTCTCCAACCCTAATTTTA
1 ATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTCTAAGGGGATACTCCAACCCTAATTTTA
* *
3830835 TTTTCAAAATATCG
66 TTTTCAAAACATCA
* *
3830849 ACTTTTCACCATCGGGGATGCTCCAACC
1 ATTTTTCACCATCGGGGATACTCCAACC
3830877 GTATTTTCAC
Statistics
Matches: 91, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
79 86 0.95
80 5 0.05
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.35
Consensus pattern (79 bp):
ATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTCTAAGGGGATACTCCAACCCTAATTTTA
TTTTCAAAACATCA
Found at i:3830896 original size:29 final size:29
Alignment explanation
Indices: 3830851--3830910 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
3830841 AAATATCGAC
* * * *
3830851 TTTTCACCATCGGGGATGCTCCAACCGTA
1 TTTTCACCATCGAGGATACCCCAACCCTA
3830880 TTTTCACCATCGAGGATACCCCAACCCTA
1 TTTTCACCATCGAGGATACCCCAACCCTA
3830909 TT
1 TT
3830911 GTTTTCGAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.23, C:0.33, G:0.15, T:0.28
Consensus pattern (29 bp):
TTTTCACCATCGAGGATACCCCAACCCTA
Done.