Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold189
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: 2243555
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 25 characters in sequence are not A, C, G, or T
File 8 of 9
Found at i:1830538 original size:34 final size:34
Alignment explanation
Indices: 1830492--1830707 Score: 278
Period size: 34 Copynumber: 6.4 Consensus size: 34
1830482 GTAAAAACCA
*
1830492 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1830526 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
1830560 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
1830594 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
1830627 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
1830661 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
1830694 CCATTTAATCAACA
1 CCATTTAATCAACA
1830708 GTCCGATCGT
Statistics
Matches: 160, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
33 43 0.27
34 115 0.72
35 2 0.01
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:1830606 original size:68 final size:67
Alignment explanation
Indices: 1830490--1830707 Score: 319
Period size: 67 Copynumber: 3.2 Consensus size: 67
1830480 TGGTAAAAAC
* * *
1830490 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
1830555 AT
66 AT
* * *
1830557 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
1830622 AAT
65 AAT
* * * * * *
1830625 CTCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACTAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
1830690 AT
66 AT
1830692 CACCATTTAATCAACA
1 CACCATTTAATCAACA
1830708 GTCCGATCGT
Statistics
Matches: 134, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
67 73 0.54
68 61 0.46
ACGTcount: A:0.40, C:0.28, G:0.08, T:0.24
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:1838444 original size:21 final size:21
Alignment explanation
Indices: 1838402--1838444 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1838392 TTTCTCTATA
*
1838402 TTATAATTAGTTATATTATTT
1 TTATAATTAGTTATAATATTT
*
1838423 TTATAATTAGTTATAATCTTT
1 TTATAATTAGTTATAATATTT
1838444 T
1 T
1838445 AATTTTAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (21 bp):
TTATAATTAGTTATAATATTT
Found at i:1838856 original size:34 final size:34
Alignment explanation
Indices: 1838813--1838883 Score: 115
Period size: 34 Copynumber: 2.1 Consensus size: 34
1838803 CTTACTCACT
*
1838813 TAACATTCTCACTAAATACATCACCTAACACACC
1 TAACATTCTCACCAAATACATCACCTAACACACC
* *
1838847 TAACATTCTCACCAAATATATCATCTAACACACC
1 TAACATTCTCACCAAATACATCACCTAACACACC
1838881 TAA
1 TAA
1838884 TATGCTTCAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.25
Consensus pattern (34 bp):
TAACATTCTCACCAAATACATCACCTAACACACC
Found at i:1843596 original size:34 final size:34
Alignment explanation
Indices: 1843558--1843673 Score: 117
Period size: 34 Copynumber: 3.4 Consensus size: 34
1843548 AAATATCTTA
* * *
1843558 CTCACCTAACATATTACCTAACACACTTAATATT
1 CTCACCAAACACATCACCTAACACACTTAATATT
* * *
1843592 CTCACCAAATACATCACTTAACACA-TCTAACATT
1 CTCACCAAACACATCACCTAACACACT-TAATATT
* * *
1843626 CTCACCAAATACATCACCTAACACACCTAATATG
1 CTCACCAAACACATCACCTAACACACTTAATATT
*
1843660 CTTCACCTAACACA
1 C-TCACCAAACACA
1843674 CTTAACAAAA
Statistics
Matches: 67, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
33 1 0.01
34 56 0.84
35 10 0.15
ACGTcount: A:0.40, C:0.34, G:0.01, T:0.26
Consensus pattern (34 bp):
CTCACCAAACACATCACCTAACACACTTAATATT
Found at i:1843657 original size:21 final size:22
Alignment explanation
Indices: 1843628--1843674 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
1843618 CTAACATTCT
1843628 CACCAAATA-CATCACCTAACA
1 CACCAAATAGCATCACCTAACA
* *
1843649 CACCTAATATGCTTCACCTAACA
1 CACCAAATA-GCATCACCTAACA
1843672 CAC
1 CAC
1843675 TTAACAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 8 0.36
23 14 0.64
ACGTcount: A:0.40, C:0.38, G:0.02, T:0.19
Consensus pattern (22 bp):
CACCAAATAGCATCACCTAACA
Found at i:1852187 original size:2 final size:2
Alignment explanation
Indices: 1852180--1852220 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
1852170 TCAGAAAGAC
* * *
1852180 AT AT AT AT AT AT AT AT AT CT AT AT AT AT TT AT AT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1852221 GAAATAATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:1852362 original size:13 final size:13
Alignment explanation
Indices: 1852337--1852370 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1852327 GTCTCAGATT
1852337 TATA-ATATGATA
1 TATATATATGATA
*
1852349 TATATATATTATA
1 TATATATATGATA
1852362 TATATATAT
1 TATATATAT
1852371 CCTTGTAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 4 0.20
13 16 0.80
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (13 bp):
TATATATATGATA
Found at i:1856211 original size:2 final size:2
Alignment explanation
Indices: 1856204--1856234 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1856194 TGAGAACATA
*
1856204 AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1856235 GAGAGAGAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1865369 original size:34 final size:34
Alignment explanation
Indices: 1865326--1865394 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
1865316 GCCTAGACTT
1865326 AGTTCAATAATCAAGTATTATTATTGTCTATAAC
1 AGTTCAATAATCAAGTATTATTATTGTCTATAAC
1865360 AGTTCAATAATCAAGTATTATTATTGTCTATAAC
1 AGTTCAATAATCAAGTATTATTATTGTCTATAAC
1865394 A
1 A
1865395 CAATGTTACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.41
Consensus pattern (34 bp):
AGTTCAATAATCAAGTATTATTATTGTCTATAAC
Found at i:1866129 original size:24 final size:24
Alignment explanation
Indices: 1866097--1866144 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1866087 GAAAGTTAAG
1866097 GAAATTAAAGATCAACAGCAAAGC
1 GAAATTAAAGATCAACAGCAAAGC
1866121 GAAATTAAAGATCAACAGCAAAGC
1 GAAATTAAAGATCAACAGCAAAGC
1866145 AGTTCTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.17, G:0.17, T:0.12
Consensus pattern (24 bp):
GAAATTAAAGATCAACAGCAAAGC
Found at i:1867355 original size:32 final size:32
Alignment explanation
Indices: 1867306--1867367 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 32
1867296 AAAAATTATA
1867306 TATTTATATAAATTTTTGATATATTAATAATT
1 TATTTATATAAATTTTTGATATATTAATAATT
*
1867338 TATTTCATATAAA-TTTTGATATATTTATAA
1 TATTT-ATATAAATTTTTGATATATTAATAA
1867368 AATAATATCG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 21 0.75
33 7 0.25
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (32 bp):
TATTTATATAAATTTTTGATATATTAATAATT
Found at i:1867404 original size:19 final size:19
Alignment explanation
Indices: 1867380--1867418 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1867370 TAATATCGTA
1867380 TTATTTT-TTATATTATATT
1 TTATTTTATT-TATTATATT
*
1867399 TTATTTTATTTATTTTATT
1 TTATTTTATTTATTATATT
1867418 T
1 T
1867419 ATGTTAGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 16 0.89
20 2 0.11
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (19 bp):
TTATTTTATTTATTATATT
Found at i:1867418 original size:14 final size:14
Alignment explanation
Indices: 1867380--1867418 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
1867370 TAATATCGTA
*
1867380 TTATTTT-TTATAT
1 TTATTTTATTTTAT
1867393 TATATTTTATTTTAT
1 T-TATTTTATTTTAT
1867408 TTATTTTATTT
1 TTATTTTATTT
1867419 ATGTTAGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 1 0.04
14 16 0.70
15 6 0.26
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTATTTTATTTTAT
Found at i:1867813 original size:17 final size:19
Alignment explanation
Indices: 1867776--1867813 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
1867766 ATATTATATA
1867776 ATTATATAAAATTTTACAT
1 ATTATATAAAATTTTACAT
*
1867795 ATTA-ATAAATTTTTA-AT
1 ATTATATAAAATTTTACAT
1867812 AT
1 AT
1867814 AAAATTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 10 0.56
19 4 0.22
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTATATAAAATTTTACAT
Found at i:1870046 original size:3 final size:3
Alignment explanation
Indices: 1870038--1870065 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1870028 TTCATGTTTT
1870038 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1870066 AAATTACCCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1877332 original size:25 final size:26
Alignment explanation
Indices: 1877292--1877355 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
1877282 TTATCTAATA
*
1877292 AAATT-AAATTTGATTA-TTATATTT-
1 AAATTCAAATTTAATTATTTAT-TTTC
*
1877316 AATTTCAAATTTAATTATTTATTTTC
1 AAATTCAAATTTAATTATTTATTTTC
1877342 AAATTCAAATTTAA
1 AAATTCAAATTTAA
1877356 ATATCAAACA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 4 0.12
25 13 0.38
26 17 0.50
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.52
Consensus pattern (26 bp):
AAATTCAAATTTAATTATTTATTTTC
Found at i:1877348 original size:26 final size:25
Alignment explanation
Indices: 1877292--1877355 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
1877282 TTATCTAATA
*
1877292 AAATT-AAATTTGATTATTATATTT
1 AAATTCAAATTTAATTATTATATTT
*
1877316 AATTTCAAATTTAATTATT-TATTTT
1 AAATTCAAATTTAATTATTATA-TTT
1877341 CAAATTCAAATTTAA
1 -AAATTCAAATTTAA
1877356 ATATCAAACA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 6 0.18
25 15 0.44
26 13 0.38
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.52
Consensus pattern (25 bp):
AAATTCAAATTTAATTATTATATTT
Found at i:1877380 original size:19 final size:19
Alignment explanation
Indices: 1877358--1877407 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1877348 AAATTTAAAT
1877358 ATCAAACATATAAAT-ATAC
1 ATCAAACATA-AAATCATAC
*
1877377 ATCAAAGATAAAATCATAC
1 ATCAAACATAAAATCATAC
* *
1877396 ATTAAAAATAAA
1 ATCAAACATAAA
1877408 CTTTTTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 4 0.15
19 23 0.85
ACGTcount: A:0.62, C:0.12, G:0.02, T:0.24
Consensus pattern (19 bp):
ATCAAACATAAAATCATAC
Found at i:1881907 original size:18 final size:18
Alignment explanation
Indices: 1881884--1881922 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1881874 CGCAAATCCT
1881884 TGAAGAAGAAGATGATGA
1 TGAAGAAGAAGATGATGA
* *
1881902 TGAAGACGACGATGATGA
1 TGAAGAAGAAGATGATGA
1881920 TGA
1 TGA
1881923 TCAATTCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.44, C:0.05, G:0.33, T:0.18
Consensus pattern (18 bp):
TGAAGAAGAAGATGATGA
Found at i:1888653 original size:6 final size:6
Alignment explanation
Indices: 1888642--1888667 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1888632 TATATATTTT
1888642 TTTTAA TTTTAA TTTTAA TTTTAA TT
1 TTTTAA TTTTAA TTTTAA TTTTAA TT
1888668 ATATTAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTTAA
Found at i:1888714 original size:13 final size:13
Alignment explanation
Indices: 1888696--1888725 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1888686 TTTTAAATTT
*
1888696 AATAATATTAAAA
1 AATAATATAAAAA
1888709 AATAATATAAAAA
1 AATAATATAAAAA
1888722 AATA
1 AATA
1888726 TAACTTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
AATAATATAAAAA
Found at i:1888762 original size:16 final size:14
Alignment explanation
Indices: 1888738--1888785 Score: 62
Period size: 15 Copynumber: 3.4 Consensus size: 14
1888728 ACTTTTAAAT
*
1888738 TTTTTAAAAATATTA
1 TTTTAAAAAATA-TA
1888753 TTTTAAAAAATA-A
1 TTTTAAAAAATATA
1888766 TTATTAAAAAATATA
1 TT-TTAAAAAATATA
1888781 TTTTA
1 TTTTA
1888786 TTTTATTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 3 0.10
14 13 0.43
15 14 0.47
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TTTTAAAAAATATA
Found at i:1888814 original size:55 final size:53
Alignment explanation
Indices: 1888703--1888827 Score: 162
Period size: 55 Copynumber: 2.3 Consensus size: 53
1888693 TTTAATAATA
*
1888703 TTAAAAAATAA-TATAAAAAAATATAACTTTTAAATTTTTTAAAAATATTATT
1 TTAAAAAATAATTATTAAAAAATATAACTTTTAAATTTTTTAAAAATATTATT
** ** *
1888755 TTAAAAAATAATTATTAAAAAATATATTTTATTTTATTTTTTAAAAATTATTTTT
1 TTAAAAAATAATTATTAAAAAATATAACTT-TTAAATTTTTTAAAAA-TATTATT
*
1888810 TTAAAAAATAATTTTTAA
1 TTAAAAAATAATTATTAA
1888828 TTCTTTAAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
52 11 0.17
53 15 0.24
54 14 0.22
55 23 0.37
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (53 bp):
TTAAAAAATAATTATTAAAAAATATAACTTTTAAATTTTTTAAAAATATTATT
Found at i:1888816 original size:16 final size:15
Alignment explanation
Indices: 1888791--1888825 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
1888781 TTTTATTTTA
*
1888791 TTTTTTAAAAATTAT
1 TTTTTTAAAAATAAT
1888806 TTTTTTAAAAAATAAT
1 TTTTTT-AAAAATAAT
1888822 TTTT
1 TTTT
1888826 AATTCTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTTTTAAAAATAAT
Found at i:1888824 original size:14 final size:14
Alignment explanation
Indices: 1888735--1888827 Score: 57
Period size: 14 Copynumber: 6.6 Consensus size: 14
1888725 ATAACTTTTA
*
1888735 AATTTTTTAAAAAT
1 AATTTTTAAAAAAT
*
1888749 ATTATTTTAAAAAAT
1 AAT-TTTTAAAAAAT
*
1888764 AATTATTAAAAAAT
1 AATTTTTAAAAAAT
***
1888778 -ATATTTT--ATTTT
1 AAT-TTTTAAAAAAT
* *
1888790 ATTTTTTAAAAATT
1 AATTTTTAAAAAAT
*
1888804 ATTTTTTTAAAAAAT
1 A-ATTTTTAAAAAAT
1888819 AATTTTTAA
1 AATTTTTAA
1888828 TTCTTTAAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
12 6 0.10
13 3 0.05
14 26 0.43
15 25 0.42
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
AATTTTTAAAAAAT
Found at i:1888919 original size:3 final size:3
Alignment explanation
Indices: 1888904--1888935 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1888894 CCCTCTTTCT
*
1888904 GAA GAA AAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1888936 GTGTTGGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1892258 original size:29 final size:29
Alignment explanation
Indices: 1892184--1892263 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 29
1892174 GATTCAAAAA
* * *
1892184 TTAATTTAAA-TCAAATTAAAGTATTTAT
1 TTAATTTAAATTTAAATTAAAATATCTAT
* *
1892212 TTAATTCAAATATAAATTAAAATATCTAT
1 TTAATTTAAATTTAAATTAAAATATCTAT
*
1892241 TTAATTTAAATTTGAATTGAAAA
1 TTAATTTAAATTTAAATT-AAAA
1892264 GATTTAAATC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
28 9 0.21
29 29 0.69
30 4 0.10
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.44
Consensus pattern (29 bp):
TTAATTTAAATTTAAATTAAAATATCTAT
Found at i:1896147 original size:2 final size:2
Alignment explanation
Indices: 1896140--1896168 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1896130 ATAGTCGCTT
1896140 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
1896169 GCCCTTTTGT
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:1898904 original size:2 final size:2
Alignment explanation
Indices: 1898897--1898931 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1898887 ATGATAATTG
1898897 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 T
1898932 TTTTAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1899764 original size:2 final size:2
Alignment explanation
Indices: 1899757--1899787 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1899747 TTATCTAATA
*
1899757 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1899788 GTGCAGGATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1903209 original size:19 final size:19
Alignment explanation
Indices: 1903187--1903235 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
1903177 ATTCAGACTT
1903187 AATAATTTAAATTATATAA
1 AATAATTTAAATTATATAA
* * * *
1903206 AATAATATGATTTATTTAA
1 AATAATTTAAATTATATAA
1903225 AATAAATTTAA
1 AAT-AATTTAA
1903236 TACTTGAAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
AATAATTTAAATTATATAA
Found at i:1907538 original size:19 final size:18
Alignment explanation
Indices: 1907498--1907547 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
1907488 AATAGTATTC
* *
1907498 CTCTATATTTTTCTTTAT
1 CTCTAAATTTTTCTTTAA
*
1907516 CTCTAAATTTTCTGTTTAA
1 CTCTAAATTTT-TCTTTAA
1907535 CTCTAAATCTTTT
1 CTCTAAAT-TTTT
1907548 AGTTTTAGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 10 0.37
19 14 0.52
20 3 0.11
ACGTcount: A:0.22, C:0.18, G:0.02, T:0.58
Consensus pattern (18 bp):
CTCTAAATTTTTCTTTAA
Found at i:1910780 original size:16 final size:16
Alignment explanation
Indices: 1910761--1910793 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1910751 GCTTTGGAAT
1910761 TAAACCAGTTAGCAAA
1 TAAACCAGTTAGCAAA
*
1910777 TAAACCAGTTTGCAAA
1 TAAACCAGTTAGCAAA
1910793 T
1 T
1910794 TAGGCAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.18, G:0.12, T:0.24
Consensus pattern (16 bp):
TAAACCAGTTAGCAAA
Found at i:1912383 original size:24 final size:24
Alignment explanation
Indices: 1912331--1912383 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
1912321 TTGCTTTCTT
* * *
1912331 CTCAGTGTCTTCATCCTCACTTTT
1 CTCAGCGTCTTCATCCTCACCTTC
* *
1912355 TTCAGCGTCTTCATCCTCTCCTTC
1 CTCAGCGTCTTCATCCTCACCTTC
1912379 CTCAG
1 CTCAG
1912384 AAGAGCTGCT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.11, C:0.38, G:0.09, T:0.42
Consensus pattern (24 bp):
CTCAGCGTCTTCATCCTCACCTTC
Found at i:1914597 original size:20 final size:21
Alignment explanation
Indices: 1914572--1914611 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1914562 GGTTTTGTAA
*
1914572 ACGTGG-CGCATTACGATTTG
1 ACGTGGACGAATTACGATTTG
*
1914592 ACGTGGATGAATTACGATTT
1 ACGTGGACGAATTACGATTT
1914612 CGAGATAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.33
Consensus pattern (21 bp):
ACGTGGACGAATTACGATTTG
Found at i:1920504 original size:5 final size:5
Alignment explanation
Indices: 1920494--1920518 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1920484 ACAAAACCCT
1920494 AGCTC AGCTC AGCTC AGCTC AGCTC
1 AGCTC AGCTC AGCTC AGCTC AGCTC
1920519 CAATAGAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.40, G:0.20, T:0.20
Consensus pattern (5 bp):
AGCTC
Found at i:1920961 original size:12 final size:13
Alignment explanation
Indices: 1920939--1920973 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
1920929 ATTTTAATAT
*
1920939 GAAATTGAAAAAA
1 GAAAATGAAAAAA
1920952 -AAAATGAAAAAA
1 GAAAATGAAAAAA
1920964 GAAAATGAAA
1 GAAAATGAAA
1920974 GACAATTGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.11
Consensus pattern (13 bp):
GAAAATGAAAAAA
Found at i:1921169 original size:3 final size:3
Alignment explanation
Indices: 1921161--1921188 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1921151 GAAAATTGTA
1921161 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1921189 GATATTAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1923724 original size:32 final size:31
Alignment explanation
Indices: 1923683--1923746 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 31
1923673 ATTGTCAGTT
1923683 GTTACATAAA-AGTCAAAACCCAAGAAGAAGCA
1 GTTACATAAATA-T-AAAACCCAAGAAGAAGCA
* * *
1923715 GTTATATAAATATAAAACCCTAGAAGGAGCA
1 GTTACATAAATATAAAACCCAAGAAGAAGCA
1923746 G
1 G
1923747 ACGACTCGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 17 0.61
32 10 0.36
33 1 0.04
ACGTcount: A:0.50, C:0.16, G:0.17, T:0.17
Consensus pattern (31 bp):
GTTACATAAATATAAAACCCAAGAAGAAGCA
Found at i:1937016 original size:24 final size:24
Alignment explanation
Indices: 1936989--1937037 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
1936979 GCATTACGTC
*
1936989 TCCTCCTCATCATTCTCACAACTT
1 TCCTCCTCATCATTCGCACAACTT
*
1937013 TCCTCCTCATCGTTCGCACAACTT
1 TCCTCCTCATCATTCGCACAACTT
1937037 T
1 T
1937038 GATCGATCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.18, C:0.41, G:0.04, T:0.37
Consensus pattern (24 bp):
TCCTCCTCATCATTCGCACAACTT
Found at i:1937831 original size:2 final size:2
Alignment explanation
Indices: 1937824--1937864 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1937814 ATAGCTTCAA
1937824 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1937865 GTATATTAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1941823 original size:2 final size:2
Alignment explanation
Indices: 1941816--1941856 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1941806 AAACTTGCTC
1941816 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1941857 CTAAAACAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1945721 original size:2 final size:2
Alignment explanation
Indices: 1945714--1945785 Score: 81
Period size: 2 Copynumber: 36.0 Consensus size: 2
1945704 GAAACCCCCG
* * * *
1945714 AT AT AT AT AC AT AT AT AC AT AT AT AT AT AT AT AT AC AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
1945756 AT AC AT AC AT AC 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
1945786 CAAGGGAAGA
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (2 bp):
AT
Found at i:1946864 original size:18 final size:17
Alignment explanation
Indices: 1946816--1946864 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
1946806 TCATACATAG
1946816 TTAATAAATATTTAATAT
1 TTAA-AAATATTTAATAT
* *
1946834 ATAAAATTAATTTAGATAT
1 TTAAAAAT-ATTTA-ATAT
1946853 TTAAAAATATTT
1 TTAAAAATATTT
1946865 TTTATTCAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 3 0.12
18 12 0.48
19 10 0.40
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (17 bp):
TTAAAAATATTTAATAT
Found at i:1947812 original size:3 final size:3
Alignment explanation
Indices: 1947806--1947845 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
1947796 TTTTGTTGTT
1947806 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1947846 GTGTTCCAGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1949385 original size:2 final size:2
Alignment explanation
Indices: 1949378--1949404 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1949368 AATTTGACAA
1949378 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1949405 CACACTACCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1949859 original size:2 final size:2
Alignment explanation
Indices: 1949854--1949889 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
1949844 TCCTACCAAG
*
1949854 TA TA TA TA TA TA TA TA TA TA TA TT TA TA CTA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA T
1949890 GAAAATTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1953519 original size:3 final size:3
Alignment explanation
Indices: 1953511--1953542 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
1953501 TAGTTAGTAG
1953511 ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1953543 TGGTTGAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1954009 original size:3 final size:3
Alignment explanation
Indices: 1954001--1954034 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1953991 ATTACATGGA
1954001 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1954035 TCCCTTTTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1954114 original size:29 final size:29
Alignment explanation
Indices: 1954077--1954146 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
1954067 TCTTTTAAAA
*
1954077 TTAAGATTATGAATG-ACGAATATAATTTT
1 TTAAAATTATGAATGAACGAATATAA-TTT
* *
1954106 TTAAAATTATAAATGAATGAATATAATTT
1 TTAAAATTATGAATGAACGAATATAATTT
1954135 TTAAAAGTTATG
1 TTAAAA-TTATG
1954147 GACAAAAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 22 0.63
30 13 0.37
ACGTcount: A:0.46, C:0.01, G:0.11, T:0.41
Consensus pattern (29 bp):
TTAAAATTATGAATGAACGAATATAATTT
Found at i:1956338 original size:2 final size:2
Alignment explanation
Indices: 1956331--1956356 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1956321 CCATACAACA
1956331 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
1956357 TCATTCTATG
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:1957994 original size:14 final size:14
Alignment explanation
Indices: 1957977--1958027 Score: 57
Period size: 15 Copynumber: 3.5 Consensus size: 14
1957967 TTTGACACAA
*
1957977 ATATTTTGATATAG
1 ATATTTTGAAATAG
1957991 ATATTTTTGAAATAG
1 ATA-TTTTGAAATAG
* *
1958006 ATATTTTCAACACAG
1 ATATTTTGAA-ATAG
1958021 ATATTTT
1 ATATTTT
1958028 AACACAAGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
14 9 0.28
15 23 0.72
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.47
Consensus pattern (14 bp):
ATATTTTGAAATAG
Found at i:1958031 original size:14 final size:14
Alignment explanation
Indices: 1958004--1958043 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 14
1957994 TTTTTGAAAT
1958004 AGATATTTTCAACAC
1 AGATATTTT-AACAC
1958019 AGATATTTTAACAC
1 AGATATTTTAACAC
1958033 A-AGTATTTTAA
1 AGA-TATTTTAA
1958044 TATAAGTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 1 0.04
14 14 0.58
15 9 0.38
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.38
Consensus pattern (14 bp):
AGATATTTTAACAC
Found at i:1977592 original size:78 final size:77
Alignment explanation
Indices: 1977459--1977700 Score: 313
Period size: 78 Copynumber: 3.0 Consensus size: 77
1977449 AGAAAACCCA
** * * * *
1977459 CCACGGCTGCCTTGGGGAGCGGCTTCGTAATTGTAGCCTCCGTCTTGTTGACTATCAACCTGAGG
1 CCACGGCCACCTTGGGGAG-GGGTTCATAATTGTAGCCTCCATCTTGTTGCCTATCAACCTGAGG
1977524 TCCATTGTATCCT
65 TCCATTGTATCCT
* * *
1977537 CCACGGCCACCTTGGGGAGTGGGTTCATAACTGTAGCCTACATCTCGTTGCCTATCAACCTGAGG
1 CCACGGCCACCTTGGGGAG-GGGTTCATAATTGTAGCCTCCATCTTGTTGCCTATCAACCTGAGG
1977602 TCCATTGTATCCT
65 TCCATTGTATCCT
*
1977615 CCACGTCCTCGGCCACCTTGAGGAGGGGCTTCATAATTGTAGCCTCCATCTTGTTGCCTATCAAC
1 CCA------CGGCCACCTTGGGGAGGGG-TTCATAATTGTAGCCTCCATCTTGTTGCCTATCAAC
1977680 CTGAGGTCCATTGTATCCT
59 CTGAGGTCCATTGTATCCT
1977699 CC
1 CC
1977701 GCGTCCACGG
Statistics
Matches: 143, Mismatches: 14, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
78 71 0.50
83 3 0.02
84 69 0.48
ACGTcount: A:0.17, C:0.30, G:0.23, T:0.29
Consensus pattern (77 bp):
CCACGGCCACCTTGGGGAGGGGTTCATAATTGTAGCCTCCATCTTGTTGCCTATCAACCTGAGGT
CCATTGTATCCT
Found at i:1977671 original size:84 final size:83
Alignment explanation
Indices: 1977468--1977714 Score: 344
Period size: 84 Copynumber: 3.0 Consensus size: 83
1977458 ACCACGGCTG
* * * *
1977468 CCTTGGGGAGCGGCTTCGTAATTGTAGCCTCCGTCTTGTTGACTATCAACCTGAGGTCCATTGTA
1 CCTTGGGGAGGGGCTTCATAATTGTAGCCTCCATCTTGTTGCCTATCAACCTGAGGTCCATTGTA
1977533 TCCTCCA-----CGGCCA
66 TCCTCCACGTCCCGGCCA
* * *
1977546 CCTTGGGGAGTGGG-TTCATAACTGTAGCCTACATCTCGTTGCCTATCAACCTGAGGTCCATTGT
1 CCTTGGGGAG-GGGCTTCATAATTGTAGCCTCCATCTTGTTGCCTATCAACCTGAGGTCCATTGT
1977610 ATCCTCCACGTCCTCGGCCA
65 ATCCTCCACGTCC-CGGCCA
*
1977630 CCTTGAGGAGGGGCTTCATAATTGTAGCCTCCATCTTGTTGCCTATCAACCTGAGGTCCATTGTA
1 CCTTGGGGAGGGGCTTCATAATTGTAGCCTCCATCTTGTTGCCTATCAACCTGAGGTCCATTGTA
*
1977695 TCCTCCGCGTCCACGGCCA
66 TCCTCCACGTCC-CGGCCA
1977714 C
1 C
1977715 GGAAACCACG
Statistics
Matches: 148, Mismatches: 13, Indels: 10
0.87 0.08 0.06
Matches are distributed among these distances:
78 62 0.42
79 2 0.01
83 3 0.02
84 81 0.55
ACGTcount: A:0.17, C:0.31, G:0.23, T:0.29
Consensus pattern (83 bp):
CCTTGGGGAGGGGCTTCATAATTGTAGCCTCCATCTTGTTGCCTATCAACCTGAGGTCCATTGTA
TCCTCCACGTCCCGGCCA
Found at i:1983706 original size:32 final size:31
Alignment explanation
Indices: 1983670--1983800 Score: 106
Period size: 32 Copynumber: 4.2 Consensus size: 31
1983660 AATATAAGCT
*
1983670 TTTAAAAAAATTAAATCGATATTATTTATATA
1 TTTAAAAAAATTAAATC-ATATTATTTATAAA
*
1983702 TTT-AAAGAATTAAA-CATAATTATTTATAAA
1 TTTAAAAAAATTAAATCAT-ATTATTTATAAA
* * * * *
1983732 TTTGATAAATATTAAATAAAATTATTCATAAA
1 TTT-AAAAAAATTAAATCATATTATTTATAAA
* * *
1983764 TTTAATAAATATTAAATACA-ATTACTCATAAA
1 TTTAA-AAAAATTAAAT-CATATTATTTATAAA
1983796 TTTAA
1 TTTAA
1983801 CAGATTAATA
Statistics
Matches: 82, Mismatches: 11, Indels: 12
0.78 0.10 0.11
Matches are distributed among these distances:
29 2 0.02
30 15 0.18
31 11 0.13
32 52 0.63
33 2 0.02
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (31 bp):
TTTAAAAAAATTAAATCATATTATTTATAAA
Found at i:1983856 original size:21 final size:20
Alignment explanation
Indices: 1983814--1983858 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1983804 ATTAATATTG
*
1983814 ATTTTTTTATATTTAATGAA
1 ATTTTTTTAAATTTAATGAA
1983834 ATTTTTTTAAATATTATAT-AA
1 ATTTTTTTAAAT-TTA-ATGAA
1983855 ATTT
1 ATTT
1983859 ATAAGTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 11 0.50
21 9 0.41
22 2 0.09
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
ATTTTTTTAAATTTAATGAA
Found at i:1983921 original size:17 final size:18
Alignment explanation
Indices: 1983896--1983934 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1983886 TAATTTTATT
*
1983896 TATTTTATAT-TTAAAAA
1 TATTATATATATTAAAAA
1983913 TATTATATATATTAAAAA
1 TATTATATATATTAAAAA
1983931 TATT
1 TATT
1983935 TAAAATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTATATATATTAAAAA
Found at i:1983961 original size:28 final size:30
Alignment explanation
Indices: 1983900--1983961 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 30
1983890 TTTATTTATT
*
1983900 TTATATTTAAAAATATTATATATATTAAAA
1 TTATATTTAAAAATATTATATAAATTAAAA
1983930 --ATATTT-AAAAT-TTA-ATAAACTTAAAA
1 TTATATTTAAAAATATTATATAAA-TTAAAA
1983956 TTATAT
1 TTATAT
1983962 ATCAAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
25 4 0.14
26 9 0.32
27 5 0.18
28 10 0.36
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (30 bp):
TTATATTTAAAAATATTATATAAATTAAAA
Found at i:1989297 original size:21 final size:20
Alignment explanation
Indices: 1989263--1989306 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
1989253 ATATTATTTT
1989263 ATTAATTTTTTTAAAAATAA
1 ATTAATTTTTTTAAAAATAA
*
1989283 ATTATTTTATTTTAAAAATAA
1 ATTAATTT-TTTTAAAAATAA
1989304 ATT
1 ATT
1989307 TATATGTGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATTAATTTTTTTAAAAATAA
Found at i:1992216 original size:2 final size:2
Alignment explanation
Indices: 1992209--1992234 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1992199 AGTCAATGAG
1992209 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
1992235 GCATCATCAT
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:1993776 original size:13 final size:12
Alignment explanation
Indices: 1993752--1993785 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
1993742 ATTCAACTTA
1993752 TATTTATATTAT
1 TATTTATATTAT
1993764 TATTTATTATTAT
1 TATTTA-TATTAT
*
1993777 TATATATAT
1 TATTTATAT
1993786 AATTTAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TATTTATATTAT
Found at i:1994701 original size:17 final size:16
Alignment explanation
Indices: 1994675--1994736 Score: 56
Period size: 17 Copynumber: 3.8 Consensus size: 16
1994665 TGTGGGAATC
*
1994675 AAATTGTTTTTATATAT
1 AAATTATTTTTATAT-T
1994692 AAATTA-TTTTATACTT
1 AAATTATTTTTATA-TT
*
1994708 AAATT-TAGTTTATATTT
1 AAATTAT-TTTTATA-TT
1994725 AAATTATTTTTA
1 AAATTATTTTTA
1994737 ATTTTTAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
16 13 0.35
17 23 0.62
18 1 0.03
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (16 bp):
AAATTATTTTTATATT
Found at i:1994784 original size:16 final size:16
Alignment explanation
Indices: 1994675--1994875 Score: 81
Period size: 16 Copynumber: 12.0 Consensus size: 16
1994665 TGTGGGAATC
* *
1994675 AAATTGTTTTTATATAT
1 AAATTATTTTTA-ATTT
*
1994692 AAATTA-TTTTATACTT
1 AAATTATTTTTA-ATTT
*
1994708 AAATT-TAGTTTATATTT
1 AAATTAT-TTTTA-ATTT
1994725 AAATTATTTTTAATTTTT
1 AAATTATTTTTAA--TTT
* * *
1994743 AATTTTTTTTTGAAGTT
1 AAATTATTTTT-AATTT
* *
1994760 AGATAATTTTTAATTT
1 AAATTATTTTTAATTT
*
1994776 AAATTA-TTTTAA-AT
1 AAATTATTTTTAATTT
*
1994790 ATATT-TTTTTAAGTTT
1 AAATTATTTTTAA-TTT
* *
1994806 AGATTA-TTTAAGATTT
1 AAATTATTTTTA-ATTT
*
1994822 AAATTAATTTTAATTTT
1 AAATTATTTTTAA-TTT
*
1994839 AATAATTAATTTTAATTTT
1 -A-AATTATTTTTAA-TTT
*
1994858 AATAATTAATTTTAATTT
1 -A-AATTATTTTTAATTT
1994876 TATATAATTA
Statistics
Matches: 146, Mismatches: 23, Indels: 29
0.74 0.12 0.15
Matches are distributed among these distances:
14 11 0.08
15 6 0.04
16 40 0.27
17 39 0.27
18 17 0.12
19 33 0.23
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (16 bp):
AAATTATTTTTAATTT
Found at i:1994836 original size:6 final size:6
Alignment explanation
Indices: 1994825--1994877 Score: 70
Period size: 6 Copynumber: 8.5 Consensus size: 6
1994815 AAGATTTAAA
* *
1994825 TTAATT TTAATT TTAATAA TTAATT TTAATT TTAATAA TTAATT TTAATT
1 TTAATT TTAATT TTAAT-T TTAATT TTAATT TTAAT-T TTAATT TTAATT
1994875 TTA
1 TTA
1994878 TATAATTATA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
6 31 0.76
7 10 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (6 bp):
TTAATT
Found at i:1994847 original size:19 final size:19
Alignment explanation
Indices: 1994823--1994885 Score: 117
Period size: 19 Copynumber: 3.3 Consensus size: 19
1994813 TTAAGATTTA
1994823 AATTAATTTTAATTTTAAT
1 AATTAATTTTAATTTTAAT
1994842 AATTAATTTTAATTTTAAT
1 AATTAATTTTAATTTTAAT
1994861 AATTAATTTTAATTTTATAT
1 AATTAATTTTAATTTTA-AT
1994881 AATTA
1 AATTA
1994886 TAAAAATATT
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
19 36 0.84
20 7 0.16
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
AATTAATTTTAATTTTAAT
Found at i:1994849 original size:13 final size:12
Alignment explanation
Indices: 1994819--1994873 Score: 58
Period size: 13 Copynumber: 4.5 Consensus size: 12
1994809 TTATTTAAGA
1994819 TTTAA-ATTAAT
1 TTTAATATTAAT
*
1994830 TTTAATTTTAAT
1 TTTAATATTAAT
* *
1994842 AATTAATTTTAAT
1 -TTTAATATTAAT
1994855 TTTAATAATTAAT
1 TTTAAT-ATTAAT
1994868 TTTAAT
1 TTTAAT
1994874 TTTATATAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
11 5 0.14
12 10 0.27
13 22 0.59
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TTTAATATTAAT
Found at i:1994858 original size:25 final size:25
Alignment explanation
Indices: 1994825--1994877 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
1994815 AAGATTTAAA
*
1994825 TTAATTTTAAT-TTTAATAATTAATT
1 TTAATTTTAATAATTAAT-ATTAATT
*
1994850 TTAATTTTAATAATTAATTTTAATT
1 TTAATTTTAATAATTAATATTAATT
1994875 TTA
1 TTA
1994878 TATAATTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 20 0.80
26 5 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
TTAATTTTAATAATTAATATTAATT
Found at i:1995031 original size:11 final size:11
Alignment explanation
Indices: 1995015--1995040 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1995005 TTAATATAAT
1995015 AATATTTTTAA
1 AATATTTTTAA
1995026 AATATTTTTAA
1 AATATTTTTAA
1995037 AATA
1 AATA
1995041 AATATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
AATATTTTTAA
Found at i:1997018 original size:16 final size:16
Alignment explanation
Indices: 1996948--1997018 Score: 65
Period size: 15 Copynumber: 4.5 Consensus size: 16
1996938 TTTGATTTTG
*
1996948 AATTTTCTCAAATTTA
1 AATTTTTTCAAATTTA
1996964 AATTTTTT-AAATTTA
1 AATTTTTTCAAATTTA
* * *
1996979 AGTTTTTTTTAATTTTA
1 A-ATTTTTTCAAATTTA
* *
1996996 AA-CTTTTCAAGTTTA
1 AATTTTTTCAAATTTA
1997011 AATTTTTT
1 AATTTTTT
1997019 ATATCAAATT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
15 20 0.45
16 17 0.39
17 7 0.16
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (16 bp):
AATTTTTTCAAATTTA
Found at i:1999529 original size:2 final size:2
Alignment explanation
Indices: 1999522--1999546 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1999512 ATCTTTTATG
1999522 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1999547 ATTATAATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2000988 original size:23 final size:23
Alignment explanation
Indices: 2000958--2001003 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
2000948 CTATAAACCA
2000958 ACGGAACTTGAATGAACAGATTT
1 ACGGAACTTGAATGAACAGATTT
2000981 ACGGAACTTGAATGAACAGATTT
1 ACGGAACTTGAATGAACAGATTT
2001004 TTTTTTGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.26
Consensus pattern (23 bp):
ACGGAACTTGAATGAACAGATTT
Found at i:2001141 original size:22 final size:23
Alignment explanation
Indices: 2001099--2001166 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 23
2001089 GTTTATTTAA
* *
2001099 ATTAAATAAACTTATTTATAAAT
1 ATTAAATAAACATATTCATAAAT
*
2001122 ATTAAATAAA-ATATTCATAAAC
1 ATTAAATAAACATATTCATAAAT
* * *
2001144 ATATAATTGAACATATTTATAAA
1 AT-TAAATAAACATATTCATAAA
2001167 CTAAAAATCT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
22 11 0.30
23 16 0.43
24 10 0.27
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.38
Consensus pattern (23 bp):
ATTAAATAAACATATTCATAAAT
Found at i:2001284 original size:24 final size:24
Alignment explanation
Indices: 2001252--2001299 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
2001242 ATTAAATATA
*
2001252 AAATAATAAAATACAAATATTATT
1 AAATAATAAAACACAAATATTATT
*
2001276 AAATAATAAAACGCAAATATTATT
1 AAATAATAAAACACAAATATTATT
2001300 CAATTATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.31
Consensus pattern (24 bp):
AAATAATAAAACACAAATATTATT
Found at i:2001296 original size:21 final size:22
Alignment explanation
Indices: 2001245--2001297 Score: 54
Period size: 24 Copynumber: 2.4 Consensus size: 22
2001235 AGTTATTATT
* *
2001245 AAATATAAAATAATAAAATACA
1 AAATATTAAATAATAAAACACA
*
2001267 AATATTATTAAATAATAAAACGC-
1 AA-A-TATTAAATAATAAAACACA
2001290 AAATATTA
1 AAATATTA
2001298 TTCAATTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 5 0.19
22 3 0.12
23 3 0.12
24 15 0.58
ACGTcount: A:0.64, C:0.06, G:0.02, T:0.28
Consensus pattern (22 bp):
AAATATTAAATAATAAAACACA
Found at i:2006102 original size:15 final size:15
Alignment explanation
Indices: 2006082--2006125 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
2006072 CGTCATTTAA
2006082 AAAAATTAAATATAT
1 AAAAATTAAATATAT
*
2006097 AAAAATTAAAT-TTT
1 AAAAATTAAATATAT
2006111 AAAATTATTAAATAT
1 AAAA--ATTAAATAT
2006126 TATTTATTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 6 0.24
15 11 0.44
16 7 0.28
17 1 0.04
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAAAATTAAATATAT
Found at i:2011029 original size:6 final size:6
Alignment explanation
Indices: 2011018--2011046 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2011008 AAGACGGGGA
2011018 TGGCAT TGGCAT TGGCAT TGGCAT TGGCA
1 TGGCAT TGGCAT TGGCAT TGGCAT TGGCA
2011047 AAGAGAGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.34, T:0.31
Consensus pattern (6 bp):
TGGCAT
Found at i:2014577 original size:6 final size:6
Alignment explanation
Indices: 2014566--2014591 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2014556 CCTGTGACTT
2014566 GTCATA GTCATA GTCATA GTCATA GT
1 GTCATA GTCATA GTCATA GTCATA GT
2014592 TTACTCATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (6 bp):
GTCATA
Found at i:2015807 original size:14 final size:13
Alignment explanation
Indices: 2015791--2015859 Score: 58
Period size: 12 Copynumber: 5.4 Consensus size: 13
2015781 ACATTTTGAC
2015791 ATATTTTTATATT
1 ATATTTTTATATT
2015804 CATATCATGTTTATATT
1 -ATAT--T-TTTATATT
*
2015821 AT-TTTTTGTATT
1 ATATTTTTATATT
2015833 ATA-TTTTA-ATT
1 ATATTTTTATATT
2015844 AT-TTTTTAT-TT
1 ATATTTTTATATT
2015855 ATATT
1 ATATT
2015860 ATACTCATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
11 14 0.30
12 15 0.33
13 1 0.02
14 4 0.09
15 1 0.02
16 3 0.07
17 8 0.17
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (13 bp):
ATATTTTTATATT
Found at i:2016217 original size:32 final size:33
Alignment explanation
Indices: 2016164--2016226 Score: 85
Period size: 32 Copynumber: 1.9 Consensus size: 33
2016154 GTATTATAAA
2016164 TTTATATAAACTTTTAAATATTAATA-ATTTGT
1 TTTATATAAACTTTTAAATATTAATATATTTGT
* *
2016196 TTTATATAAA-TTTTGATATATTCATATATTT
1 TTTATATAAACTTTT-AAATATTAATATATTT
2016227 ATGTCATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 4 0.15
32 19 0.70
33 4 0.15
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (33 bp):
TTTATATAAACTTTTAAATATTAATATATTTGT
Found at i:2018540 original size:19 final size:19
Alignment explanation
Indices: 2018516--2018555 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
2018506 GGGTGAGTTT
2018516 AAGTTTCATAGCAGGGAAC
1 AAGTTTCATAGCAGGGAAC
2018535 AAGTTTCATAGCAGGGAAC
1 AAGTTTCATAGCAGGGAAC
2018554 AA
1 AA
2018556 ACGCAGGCAG
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:0.40, C:0.15, G:0.25, T:0.20
Consensus pattern (19 bp):
AAGTTTCATAGCAGGGAAC
Found at i:2018814 original size:5 final size:6
Alignment explanation
Indices: 2018800--2018824 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2018790 GATTATTTAT
2018800 AAAAGA AAAAGA AAAAGA AAAAGA A
1 AAAAGA AAAAGA AAAAGA AAAAGA A
2018825 TCGAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:2020434 original size:6 final size:6
Alignment explanation
Indices: 2020423--2020449 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2020413 AACTGAGAGA
2020423 AAAAGC AAAAGC AAAAGC AAAAGC AAA
1 AAAAGC AAAAGC AAAAGC AAAAGC AAA
2020450 GAGGCAAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.70, C:0.15, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAGC
Found at i:2023452 original size:3 final size:3
Alignment explanation
Indices: 2023444--2023483 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
2023434 TGTTGATTAA
*
2023444 AAT AAT AAT ACT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2023484 CAGTGATGCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2023733 original size:3 final size:3
Alignment explanation
Indices: 2023725--2023757 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2023715 TTAATTTGGA
2023725 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2023758 ATATCTCAAA
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2024048 original size:7 final size:7
Alignment explanation
Indices: 2024036--2024069 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
2024026 GTATAACAAT
2024036 AAAAATA
1 AAAAATA
2024043 AAAAAT-
1 AAAAATA
2024049 AAAAATA
1 AAAAATA
2024056 AAAAATA
1 AAAAATA
2024063 ATAAAAT
1 A-AAAAT
2024070 TCACCATTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.24
7 14 0.56
8 5 0.20
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (7 bp):
AAAAATA
Found at i:2024051 original size:13 final size:13
Alignment explanation
Indices: 2024033--2024063 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
2024023 TACGTATAAC
2024033 AATAAAAATAAAA
1 AATAAAAATAAAA
2024046 AATAAAAATAAAA
1 AATAAAAATAAAA
2024059 AATAA
1 AATAA
2024064 TAAAATTCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
AATAAAAATAAAA
Found at i:2024228 original size:19 final size:18
Alignment explanation
Indices: 2024204--2024241 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
2024194 TCTTTTAAAA
2024204 ATTTAT-TTTATATAGTATT
1 ATTTATATTTA-ATA-TATT
2024223 ATTTATATTTAATATATT
1 ATTTATATTTAATATATT
2024241 A
1 A
2024242 AAAACAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 9 0.50
20 4 0.22
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
ATTTATATTTAATATATT
Found at i:2025268 original size:24 final size:25
Alignment explanation
Indices: 2025228--2025291 Score: 78
Period size: 24 Copynumber: 2.6 Consensus size: 25
2025218 GTTCTAAGGA
2025228 GTTAAAAT-ATAAAAAATATAAATAT
1 GTTAAAATAAT-AAAAATATAAATAT
* *
2025253 -TTAAAATAATAAAAATTTAAATGT
1 GTTAAAATAATAAAAATATAAATAT
*
2025277 GTGAAAATAATAAAA
1 GTTAAAATAATAAAA
2025292 TTATTTAATC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 19 0.56
25 15 0.44
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (25 bp):
GTTAAAATAATAAAAATATAAATAT
Found at i:2031320 original size:16 final size:15
Alignment explanation
Indices: 2031299--2031329 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
2031289 GCTTAATTGG
2031299 TCTTTTGTTTTTTTTT
1 TCTTTT-TTTTTTTTT
2031315 TCTTTTTTTTTTTTT
1 TCTTTTTTTTTTTTT
2031330 ATAACAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.00, C:0.06, G:0.03, T:0.90
Consensus pattern (15 bp):
TCTTTTTTTTTTTTT
Found at i:2032968 original size:38 final size:38
Alignment explanation
Indices: 2032917--2032996 Score: 151
Period size: 38 Copynumber: 2.1 Consensus size: 38
2032907 AAGAACAAGA
*
2032917 TGAGAATTTAGAGGCACTAGATTATCGTACTTTGGGAT
1 TGAGAATTTAGAGGCACTAGATTATCCTACTTTGGGAT
2032955 TGAGAATTTAGAGGCACTAGATTATCCTACTTTGGGAT
1 TGAGAATTTAGAGGCACTAGATTATCCTACTTTGGGAT
2032993 TGAG
1 TGAG
2032997 GATGTATGTA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.29, C:0.11, G:0.26, T:0.34
Consensus pattern (38 bp):
TGAGAATTTAGAGGCACTAGATTATCCTACTTTGGGAT
Found at i:2033669 original size:2 final size:2
Alignment explanation
Indices: 2033662--2033696 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2033652 TTTCAACAGC
2033662 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2033697 CACACTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2043395 original size:2 final size:2
Alignment explanation
Indices: 2043388--2043422 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2043378 TCCATACACT
2043388 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2043423 TTTGGTTAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2045856 original size:2 final size:2
Alignment explanation
Indices: 2045851--2045880 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2045841 ATATATAGAT
*
2045851 AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2045881 GTGATGCGTA
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:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2047054 original size:4 final size:4
Alignment explanation
Indices: 2047029--2047068 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
2047019 AATTGATGAA
* * *
2047029 GCAT GCAC GCAT GCAC GCAT GCAT GCAT GCAT GCAG GCAT
1 GCAT GCAT GCAT GCAT GCAT GCAT GCAT GCAT GCAT GCAT
2047069 CACTGGATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.25, C:0.30, G:0.28, T:0.17
Consensus pattern (4 bp):
GCAT
Found at i:2047343 original size:6 final size:6
Alignment explanation
Indices: 2047334--2047369 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
2047324 GTTTTAATTT
*
2047334 TTATAA TTATAT TTATAA TTATAA TTATAA TATATA
1 TTATAA TTATAA TTATAA TTATAA TTATAA T-TATA
2047370 TGCTAAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 23 0.85
7 4 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
TTATAA
Found at i:2048971 original size:18 final size:18
Alignment explanation
Indices: 2048940--2048991 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
2048930 CTATTATTAT
2048940 TTATGTTTTAATTTATATAA
1 TTAT-TTTT-ATTTATATAA
*
2048960 TTATTTTTATTTTAAATAA
1 TTATTTTTA-TTTATATAA
2048979 -TATTTTT-TTTATA
1 TTATTTTTATTTATA
2048992 AAAATGTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 5 0.17
18 8 0.28
19 12 0.41
20 4 0.14
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (18 bp):
TTATTTTTATTTATATAA
Found at i:2048981 original size:24 final size:24
Alignment explanation
Indices: 2048918--2048981 Score: 58
Period size: 24 Copynumber: 2.7 Consensus size: 24
2048908 ATATTGACTA
* * *
2048918 TATATTTT-ACTACTATTATTATT
1 TATATTTTAAATAATATAATTATT
* * *
2048941 TATGTTTTAATTTATATAATTATT
1 TATATTTTAAATAATATAATTATT
*
2048965 TTTATTTTAAATAATAT
1 TATATTTTAAATAATAT
2048982 TTTTTTTATA
Statistics
Matches: 31, Mismatches: 9, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
23 7 0.23
24 24 0.77
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (24 bp):
TATATTTTAAATAATATAATTATT
Found at i:2048993 original size:18 final size:19
Alignment explanation
Indices: 2048940--2048985 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
2048930 CTATTATTAT
* *
2048940 TTATGTTTTAATTTATATAA
1 TTAT-TTTTATTTTAAATAA
2048960 TTATTTTTATTTTAAATAA
1 TTATTTTTATTTTAAATAA
2048979 -TATTTTT
1 TTATTTTT
2048986 TTTATAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 7 0.29
19 13 0.54
20 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
TTATTTTTATTTTAAATAA
Found at i:2049668 original size:2 final size:2
Alignment explanation
Indices: 2049663--2049695 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2049653 GTTATATAAC
2049663 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2049696 GCTGATTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2054181 original size:21 final size:22
Alignment explanation
Indices: 2054143--2054188 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2054133 ATCTGTTGAA
* **
2054143 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
2054164 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
2054186 ACT
1 ACT
2054189 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:2056666 original size:20 final size:20
Alignment explanation
Indices: 2056641--2056686 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
2056631 AAGAATTGAA
*
2056641 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGGGAG
* **
2056661 GAGGGATGCTTGAGAGGGAG
1 GAGGGATACAAGAGAGGGAG
2056681 GAGGGA
1 GAGGGA
2056687 GCCTCTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.04, G:0.52, T:0.11
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGGAG
Found at i:2056771 original size:25 final size:25
Alignment explanation
Indices: 2056743--2056802 Score: 111
Period size: 25 Copynumber: 2.4 Consensus size: 25
2056733 AGTCACAAAT
2056743 TTTGACAAATAAATAAACCTCTATA
1 TTTGACAAATAAATAAACCTCTATA
*
2056768 TTTGACAAATAAATAAATCTCTATA
1 TTTGACAAATAAATAAACCTCTATA
2056793 TTTGACAAAT
1 TTTGACAAAT
2056803 CTAAAGGAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.47, C:0.13, G:0.05, T:0.35
Consensus pattern (25 bp):
TTTGACAAATAAATAAACCTCTATA
Found at i:2062254 original size:4 final size:4
Alignment explanation
Indices: 2062245--2062279 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
2062235 AAGGGAATAA
*
2062245 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTGT GTA
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTA
2062280 CGTAATTAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.23, C:0.00, G:0.29, T:0.49
Consensus pattern (4 bp):
GTAT
Found at i:2063586 original size:7 final size:7
Alignment explanation
Indices: 2063550--2063582 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
2063540 ATAGATCAAT
2063550 GGCTGGA
1 GGCTGGA
2063557 GGCTGGA
1 GGCTGGA
2063564 GGCTGGA
1 GGCTGGA
*
2063571 GGCTGAA
1 GGCTGGA
2063578 GGCTG
1 GGCTG
2063583 AAGGGCGGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.15, C:0.15, G:0.55, T:0.15
Consensus pattern (7 bp):
GGCTGGA
Found at i:2066220 original size:3 final size:3
Alignment explanation
Indices: 2066212--2066246 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2066202 ACTCACAAAT
2066212 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
2066247 TAATAATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:2067569 original size:2 final size:2
Alignment explanation
Indices: 2067562--2067598 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2067552 AGTTATACAT
2067562 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
2067599 TATATATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2069138 original size:25 final size:25
Alignment explanation
Indices: 2069103--2069152 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
2069093 ATTAAAGAAC
*
2069103 AATATTCGAAGCATAGAAATTAAAT
1 AATATTCGAAGCAAAGAAATTAAAT
*
2069128 AATATTGGAAGCAAAGAAATTAAAT
1 AATATTCGAAGCAAAGAAATTAAAT
2069153 TCGAACATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.54, C:0.06, G:0.14, T:0.26
Consensus pattern (25 bp):
AATATTCGAAGCAAAGAAATTAAAT
Found at i:2072901 original size:13 final size:13
Alignment explanation
Indices: 2072883--2072910 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2072873 CTTCAAATGG
2072883 ATAAAGCCCTCTA
1 ATAAAGCCCTCTA
2072896 ATAAAGCCCTCTA
1 ATAAAGCCCTCTA
2072909 AT
1 AT
2072911 TATATAGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.29, G:0.07, T:0.25
Consensus pattern (13 bp):
ATAAAGCCCTCTA
Found at i:2083518 original size:2 final size:2
Alignment explanation
Indices: 2083511--2083540 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2083501 AAGTTATTTG
*
2083511 AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2083541 GTTAATGCTT
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:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2090229 original size:3 final size:3
Alignment explanation
Indices: 2090221--2090247 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2090211 TGTGTAATAG
2090221 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
2090248 ATAAATGTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2091985 original size:20 final size:22
Alignment explanation
Indices: 2091956--2092003 Score: 64
Period size: 20 Copynumber: 2.2 Consensus size: 22
2091946 AGAAAACTAA
*
2091956 AATAATAAAATTT-AAA-AAGC
1 AATAAAAAAATTTGAAAGAAGC
2091976 AATAAAAAAATTTGAAAGAAGC
1 AATAAAAAAATTTGAAAGAAGC
2091998 ATATAA
1 A-ATAA
2092004 TATATGATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 12 0.50
21 3 0.12
22 5 0.21
23 4 0.17
ACGTcount: A:0.65, C:0.04, G:0.08, T:0.23
Consensus pattern (22 bp):
AATAAAAAAATTTGAAAGAAGC
Found at i:2096377 original size:2 final size:2
Alignment explanation
Indices: 2096370--2096399 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2096360 TCACTTTTAC
*
2096370 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2096400 GTATTTATGT
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:2096404 original size:12 final size:12
Alignment explanation
Indices: 2096370--2096407 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
2096360 TCACTTTTAC
*
2096370 ATATATATATAT
1 ATATATATATTT
2096382 ATATATATATTT
1 ATATATATATTT
*
2096394 ATATATGTATTT
1 ATATATATATTT
2096406 AT
1 AT
2096408 GTAAGTATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (12 bp):
ATATATATATTT
Found at i:2103008 original size:112 final size:112
Alignment explanation
Indices: 2102858--2103072 Score: 299
Period size: 112 Copynumber: 1.9 Consensus size: 112
2102848 ACCATGTTGT
* * *
2102858 GTCACAGGCCTAGATTTTAGCTTAGCAAATTAAAAATTG-TGTCTTTATATGCATAAGTCAATCT
1 GTCACAGGCCTAGATTTTAACCTAGCAAATTAAAAATTGCT-TCTTTATATGCATAAGTCAACCT
2102922 TCAAACA-TTCAAAAGTGAAAATCTAAATTCCCTAAAGTAGTAAAGTGA
65 TCAAACACTT-AAAAGTGAAAATCTAAATTCCCTAAAGTAGTAAAGTGA
* * * *
2102970 GTCACGGGCCTAGATTTTAACCTAGCAAATTGAAAATTGCTTCTTTGTATGCTTAAGTCAACCTT
1 GTCACAGGCCTAGATTTTAACCTAGCAAATTAAAAATTGCTTCTTTATATGCATAAGTCAACCTT
* * * *
2103035 TAAATACTTAAAAGTGAAAATCTGAATTCCTTAAAGTA
66 CAAACACTTAAAAGTGAAAATCTAAATTCCCTAAAGTA
2103073 TTGAAGTTAA
Statistics
Matches: 90, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
112 87 0.97
113 3 0.03
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (112 bp):
GTCACAGGCCTAGATTTTAACCTAGCAAATTAAAAATTGCTTCTTTATATGCATAAGTCAACCTT
CAAACACTTAAAAGTGAAAATCTAAATTCCCTAAAGTAGTAAAGTGA
Found at i:2110813 original size:16 final size:16
Alignment explanation
Indices: 2110780--2110821 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
2110770 CCAATGCCCG
* *
2110780 AAAAGAAGAAAGTAGA
1 AAAAGAAAAAAGGAGA
*
2110796 AAAAGAAAAAAGGGGA
1 AAAAGAAAAAAGGAGA
2110812 AAAA-AAAAAA
1 AAAAGAAAAAA
2110822 AAAAAAGGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 6 0.26
16 17 0.74
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.02
Consensus pattern (16 bp):
AAAAGAAAAAAGGAGA
Found at i:2112654 original size:2 final size:2
Alignment explanation
Indices: 2112641--2112675 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2112631 TGGTTAGTAT
*
2112641 TA TA TC 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 T
2112676 TTGGTTAGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2120037 original size:6 final size:6
Alignment explanation
Indices: 2120026--2120061 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
2120016 AAACATACCC
2120026 GAGAGG GAGAGG GAGAGG GAGA-G G-GAGG GAGAGG GA
1 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GA
2120062 AGGCAGACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 2 0.07
5 4 0.14
6 22 0.79
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (6 bp):
GAGAGG
Found at i:2120055 original size:10 final size:10
Alignment explanation
Indices: 2120028--2120061 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
2120018 ACATACCCGA
2120028 GAGGGAGAGGG
1 GAGGGAGA-GG
2120039 AGAGGGAGAGG
1 -GAGGGAGAGG
2120050 GAGGGAGAGG
1 GAGGGAGAGG
2120060 GA
1 GA
2120062 AGGCAGACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 12 0.55
11 2 0.09
12 8 0.36
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (10 bp):
GAGGGAGAGG
Done.