Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 129432109
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: 129432109
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 218 of 425
Found at i:66219874 original size:12 final size:12
Alignment explanation
Indices: 66219857--66219900 Score: 54
Period size: 11 Copynumber: 3.6 Consensus size: 12
66219847 TATACAAGTC
66219857 AAAAAAATTTGA
1 AAAAAAATTTGA
*
66219869 AAAAAAA-TTCA
1 AAAAAAATTTGA
66219880 AAAAAAATTTCGA
1 AAAAAAATTT-GA
66219893 AAAGAAAA
1 AAA-AAAA
66219901 AAAAATCTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 10 0.37
12 9 0.33
13 4 0.15
14 4 0.15
ACGTcount: A:0.70, C:0.05, G:0.07, T:0.18
Consensus pattern (12 bp):
AAAAAAATTTGA
Found at i:66220842 original size:9 final size:10
Alignment explanation
Indices: 66220835--66220890 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
66220825 AAGAGAAAAC
66220835 AAAGAAAAGA
1 AAAGAAAAGA
66220845 AAAGAAAAAGCA
1 AAAG-AAAAG-A
66220857 AAAG--AAGA
1 AAAGAAAAGA
66220865 AAAGAAAACGA
1 AAAGAAAA-GA
66220876 AATA-AAAAGA
1 AA-AGAAAAGA
66220886 AAAGA
1 AAAGA
66220891 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
8 5 0.13
9 4 0.10
10 11 0.28
11 13 0.33
12 6 0.15
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.02
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:66220858 original size:21 final size:20
Alignment explanation
Indices: 66220824--66220890 Score: 73
Period size: 20 Copynumber: 3.2 Consensus size: 20
66220814 ACATTCTTGT
66220824 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAA-AAAAGA
*
66220845 AAAGAAAAAGCAAAAGAAGA
1 AAAGAAAAAGCAAAAAAAGA
* *
66220865 AAAGAAAACGAAATAAAAAGA
1 AAAGAAAAAGCAA-AAAAAGA
66220886 AAAGA
1 AAAGA
66220891 GAGGCAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
20 20 0.50
21 20 0.50
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.01
Consensus pattern (20 bp):
AAAGAAAAAGCAAAAAAAGA
Found at i:66220859 original size:6 final size:5
Alignment explanation
Indices: 66220835--66220890 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
66220825 AAGAGAAAAC
66220835 AAAGA AAAGA AAAGAA AAAGCA AAAG- -AAGA AAAGA AAACGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
66220881 AAAGA AAAGA
1 AAAGA AAAGA
66220891 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
3 3 0.07
4 1 0.02
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:66220973 original size:12 final size:12
Alignment explanation
Indices: 66220958--66220982 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
66220948 TTTGAAAAGC
66220958 AAAAAGAAAATG
1 AAAAAGAAAATG
66220970 AAAAAGAAAATG
1 AAAAAGAAAATG
66220982 A
1 A
66220983 GATTGAAAAA
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:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:66220979 original size:18 final size:18
Alignment explanation
Indices: 66220952--66221007 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
66220942 AAAAGCTTTG
66220952 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
66220971 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
66220989 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
66221006 AA
1 AA
66221008 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:66220994 original size:30 final size:31
Alignment explanation
Indices: 66220958--66221038 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 31
66220948 TTTGAAAAGC
*
66220958 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
66220988 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
66221018 AAAAA-AAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
66221039 TGAAACAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
29 11 0.26
30 31 0.74
ACGTcount: A:0.65, C:0.01, G:0.21, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:66223184 original size:30 final size:31
Alignment explanation
Indices: 66223150--66223246 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
66223140 AGCTCACTCC
*
66223150 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
66223180 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
66223210 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
66223240 TAGCTCA
1 TAGCTCA
66223247 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:66224907 original size:12 final size:12
Alignment explanation
Indices: 66224890--66224931 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
66224880 TTATACAAGT
66224890 AAAAAAATTCGA
1 AAAAAAATTCGA
66224902 AAAAAAATTC--
1 AAAAAAATTCGA
66224912 AAAAAAATTCGA
1 AAAAAAATTCGA
66224924 AAAGAAAA
1 AAA-AAAA
66224932 AAAATCTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 10 0.37
12 13 0.48
13 4 0.15
ACGTcount: A:0.71, C:0.07, G:0.07, T:0.14
Consensus pattern (12 bp):
AAAAAAATTCGA
Found at i:66225867 original size:9 final size:10
Alignment explanation
Indices: 66225860--66225916 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
66225850 AAGAGAAAAT
66225860 AAAGAAAAGA
1 AAAGAAAAGA
66225870 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
66225882 AAAGAAGA-A
1 AAAGAAAAGA
66225891 AAAGAAAATGA
1 AAAGAAAA-GA
66225902 AATA-AAAAGA
1 AA-AGAAAAGA
66225912 AAAGA
1 AAAGA
66225917 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:66225884 original size:6 final size:5
Alignment explanation
Indices: 66225860--66225916 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
66225850 AAGAGAAAAT
*
66225860 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
66225907 AAAGA AAAGA
1 AAAGA AAAGA
66225917 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:66225891 original size:15 final size:14
Alignment explanation
Indices: 66225860--66225916 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
66225850 AAGAGAAAAT
66225860 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
66225876 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
66225891 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
66225907 AAAGAAAAGA
1 AAAGAAAAGA
66225917 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:66225993 original size:12 final size:12
Alignment explanation
Indices: 66225985--66226009 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
66225975 TTTGAAAAGC
66225985 AAAAAGAAAATG
1 AAAAAGAAAATG
66225997 AAAAAGAAAATG
1 AAAAAGAAAATG
66226009 A
1 A
66226010 GATTGAAAAA
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:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:66226006 original size:18 final size:18
Alignment explanation
Indices: 66225979--66226034 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
66225969 AAAGCCTTTG
66225979 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
66225998 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
66226016 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
66226033 AA
1 AA
66226035 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:66226019 original size:30 final size:31
Alignment explanation
Indices: 66225985--66226066 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
66225975 TTTGAAAAGC
*
66225985 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
66226015 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
66226045 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
66226067 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.01, G:0.22, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:66228243 original size:30 final size:30
Alignment explanation
Indices: 66228149--66228244 Score: 79
Period size: 30 Copynumber: 3.2 Consensus size: 30
66228139 AGCTAAACCG
* * *
66228149 AGCTC-ACTTTCAACTCATGAGCTAAACCTT
1 AGCTCAACTTT-AGCTCACGAGCTAAAGCTT
* * * ** *
66228179 AGCTCAACTTCAGCTTAGGAG-TTTAGCCTC
1 AGCTCAACTTTAGCTCACGAGCTAAAG-CTT
66228209 AGCTCAACTTTAGCTCACGAGCTAAAGCTT
1 AGCTCAACTTTAGCTCACGAGCTAAAGCTT
66228239 AGCTCA
1 AGCTCA
66228245 TTTTAGTTTA
Statistics
Matches: 49, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 40 0.82
31 7 0.14
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (30 bp):
AGCTCAACTTTAGCTCACGAGCTAAAGCTT
Found at i:66231682 original size:27 final size:26
Alignment explanation
Indices: 66231652--66231707 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 26
66231642 ACATAGCTTA
*
66231652 AATGTGTCTAGTTTAG-GACATCAATTT
1 AATGTGCCTAGTTTAGAGACA--AATTT
66231679 AATGTGCCTAGTTTAGAGACAAATTT
1 AATGTGCCTAGTTTAGAGACAAATTT
66231705 AAT
1 AAT
66231708 TAGTTATAGC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 8 0.30
27 15 0.56
28 4 0.15
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.38
Consensus pattern (26 bp):
AATGTGCCTAGTTTAGAGACAAATTT
Found at i:66234566 original size:14 final size:14
Alignment explanation
Indices: 66234547--66234591 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
66234537 AACTCATCTT
*
66234547 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
66234561 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
66234574 AATTTAATTTAATG
1 AGTTTAATTTAATG
66234588 AGTT
1 AGTT
66234592 ACTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:66235598 original size:29 final size:29
Alignment explanation
Indices: 66235566--66235625 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
66235556 ATAACCAAAC
66235566 CTACAAAAACGTT-ATATCCATAAACCCAT
1 CTACAAAAAC-TTCATATCCATAAACCCAT
* *
66235595 CTACATAAACTTCATATCTATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
66235624 CT
1 CT
66235626 TTGAATCCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 2 0.07
29 26 0.93
ACGTcount: A:0.42, C:0.28, G:0.02, T:0.28
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:66236967 original size:18 final size:19
Alignment explanation
Indices: 66236924--66236969 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
66236914 CGAGAGAAGC
*
66236924 GAAAAAG-AGAAAGAATGT
1 GAAAAAGAAAAAAGAATGT
* *
66236942 GAACAAGAAAAAAGAGTG-
1 GAAAAAGAAAAAAGAATGT
66236960 GAAAAAGAAA
1 GAAAAAGAAA
66236970 TTGAGATAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.65, C:0.02, G:0.26, T:0.07
Consensus pattern (19 bp):
GAAAAAGAAAAAAGAATGT
Found at i:66239398 original size:14 final size:14
Alignment explanation
Indices: 66239379--66239423 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
66239369 AACTCATCTT
*
66239379 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
66239393 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
66239406 AATTTAATTTAATG
1 AGTTTAATTTAATG
66239420 AGTT
1 AGTT
66239424 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:66240447 original size:15 final size:15
Alignment explanation
Indices: 66240401--66240448 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
66240391 AAACCTATAA
*
66240401 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
66240416 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
66240430 AAACTTCATATCCAT
1 AAACTTCATATCCAT
66240445 AAAC
1 AAAC
66240449 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:66252670 original size:14 final size:15
Alignment explanation
Indices: 66252651--66252681 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
66252641 AATGATCAAA
66252651 TTTTCAG-ATTTTTT
1 TTTTCAGAATTTTTT
66252665 TTTTCAGAATTTTTT
1 TTTTCAGAATTTTTT
66252680 TT
1 TT
66252682 GAAAATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.16, C:0.06, G:0.06, T:0.71
Consensus pattern (15 bp):
TTTTCAGAATTTTTT
Found at i:66252677 original size:13 final size:13
Alignment explanation
Indices: 66252651--66252693 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
66252641 AATGATCAAA
*
66252651 TTTTCAGATTTTTT
1 TTTTCAGA-ATTTT
66252665 TTTTCAGAATTTT
1 TTTTCAGAATTTT
* *
66252678 TTTTGAAAATTTT
1 TTTTCAGAATTTT
66252691 TTT
1 TTT
66252694 CGTTTTTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 18 0.69
14 8 0.31
ACGTcount: A:0.21, C:0.05, G:0.07, T:0.67
Consensus pattern (13 bp):
TTTTCAGAATTTT
Found at i:66252701 original size:21 final size:19
Alignment explanation
Indices: 66252675--66252721 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
66252665 TTTTCAGAAT
*
66252675 TTTTTTTGAAAATTTTTTTCG
1 TTTTTTTG-AAA-TTTTTTCA
66252696 TTTTTTTGAAATTTTTTCA
1 TTTTTTTGAAATTTTTTCA
66252715 TTTTTTT
1 TTTTTTT
66252722 TAAACTTACT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 14 0.56
20 3 0.12
21 8 0.32
ACGTcount: A:0.17, C:0.04, G:0.06, T:0.72
Consensus pattern (19 bp):
TTTTTTTGAAATTTTTTCA
Found at i:66252719 original size:20 final size:22
Alignment explanation
Indices: 66252673--66252722 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 22
66252663 TTTTTTCAGA
66252673 ATTTTTTTTGAAAATTTTTTTC
1 ATTTTTTTTGAAAATTTTTTTC
*
66252695 -GTTTTTTTG-AAA-TTTTTTC
1 ATTTTTTTTGAAAATTTTTTTC
66252714 ATTTTTTTT
1 ATTTTTTTT
66252723 AAACTTACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 7 0.28
20 10 0.40
21 8 0.32
ACGTcount: A:0.18, C:0.04, G:0.06, T:0.72
Consensus pattern (22 bp):
ATTTTTTTTGAAAATTTTTTTC
Found at i:66262337 original size:36 final size:36
Alignment explanation
Indices: 66262297--66262371 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 36
66262287 ATTTTACGGA
*
66262297 ATTGAATTTCGAGTTTTGTAACTCGTGTTATGATTT
1 ATTGAATTTCGAGTTTTGTAACTCGAGTTATGATTT
*
66262333 ATTGAATTTTGAGTTTTGTAACTCGAGTTATGATTT
1 ATTGAATTTCGAGTTTTGTAACTCGAGTTATGATTT
66262369 ATT
1 ATT
66262372 TAGTGAGTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.24, C:0.07, G:0.19, T:0.51
Consensus pattern (36 bp):
ATTGAATTTCGAGTTTTGTAACTCGAGTTATGATTT
Found at i:66263108 original size:30 final size:30
Alignment explanation
Indices: 66263072--66263169 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
66263062 AGCTCACTCC
66263072 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
66263102 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * *
66263132 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
66263162 TAGCTCAT
1 TAGCTCAT
66263170 TTTAGTTTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:66264851 original size:11 final size:11
Alignment explanation
Indices: 66264835--66264869 Score: 61
Period size: 11 Copynumber: 3.1 Consensus size: 11
66264825 GTTATACAAG
66264835 TCAAAAAAAAT
1 TCAAAAAAAAT
66264846 TCAAAAAAAAAT
1 TC-AAAAAAAAT
66264858 TCAAAAAAAAT
1 TCAAAAAAAAT
66264869 T
1 T
66264870 TTGAAAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 12 0.52
12 11 0.48
ACGTcount: A:0.71, C:0.09, G:0.00, T:0.20
Consensus pattern (11 bp):
TCAAAAAAAAT
Found at i:66264854 original size:12 final size:12
Alignment explanation
Indices: 66264837--66264867 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
66264827 TATACAAGTC
66264837 AAAAAAAATTCA
1 AAAAAAAATTCA
66264849 AAAAAAAATTCA
1 AAAAAAAATTCA
66264861 AAAAAAA
1 AAAAAAA
66264868 TTTTGAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.13
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:66264895 original size:19 final size:18
Alignment explanation
Indices: 66264860--66264898 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
66264850 AAAAAAATTC
* *
66264860 AAAAAAAATTTTGAAAAG
1 AAAAAAAAATCTGAAAAG
66264878 AAAAAAAAATCTGAAAA-
1 AAAAAAAAATCTGAAAAG
66264895 AAAA
1 AAAA
66264899 GTGTTTAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.74, C:0.03, G:0.08, T:0.15
Consensus pattern (18 bp):
AAAAAAAAATCTGAAAAG
Found at i:66265819 original size:9 final size:10
Alignment explanation
Indices: 66265812--66265868 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
66265802 AAGAGAAAAT
66265812 AAAGAAAAGA
1 AAAGAAAAGA
66265822 AAAGAAAAAGA
1 AAAG-AAAAGA
*
66265833 AAA-AGAAGAA
1 AAAGAAAAG-A
66265843 AAAGAAAATGA
1 AAAGAAAA-GA
66265854 AATA-AAAAGA
1 AA-AGAAAAGA
66265864 AAAGA
1 AAAGA
66265869 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 5 0.13
10 13 0.33
11 19 0.49
12 2 0.05
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:66265822 original size:5 final size:5
Alignment explanation
Indices: 66265812--66265868 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
66265802 AAGAGAAAAT
*
66265812 AAAGA AAAGA AAAGAA AAAGA AAA-A GAAGAA AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAGA AAAGA AAAG-A AAAGA AAA-GA AA-AGA
66265859 AAAGA AAAGA
1 AAAGA AAAGA
66265869 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 26 0.59
6 13 0.30
7 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:66265948 original size:11 final size:12
Alignment explanation
Indices: 66265916--66265946 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
66265906 TTGAGAGAAC
66265916 TTGAAAAAGCCT
1 TTGAAAAAGCCT
66265928 TTGAAAAAGCCT
1 TTGAAAAAGCCT
66265940 TTGAAAA
1 TTGAAAA
66265947 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:66265957 original size:12 final size:12
Alignment explanation
Indices: 66265949--66265973 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
66265939 TTTGAAAAGC
66265949 AAAAAGAAAATG
1 AAAAAGAAAATG
66265961 AAAAAGAAAATG
1 AAAAAGAAAATG
66265973 A
1 A
66265974 GATTGAAAAA
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:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:66265970 original size:18 final size:18
Alignment explanation
Indices: 66265943--66265995 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
66265933 AAAGCCTTTG
*
66265943 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAATGAAAATGA
* *
66265962 AAAAGAAAATGAGATTGA
1 AAAAGAAAATGAAAATGA
*
66265980 AAAAGAGAATGAAAAT
1 AAAAGAAAATGAAAAT
66265996 AAATTTGAGA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 23 0.82
19 5 0.18
ACGTcount: A:0.68, C:0.02, G:0.19, T:0.11
Consensus pattern (18 bp):
AAAAGAAAATGAAAATGA
Found at i:66265983 original size:30 final size:30
Alignment explanation
Indices: 66265949--66266029 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 30
66265939 TTTGAAAAGC
*
66265949 AAAAAGAAAATGAAAAAGAAAATGAGATTG
1 AAAAAGAAAATGAAAAAGAAAATGAGAGTG
* **
66265979 AAAAAGAGAATGAAAATA-AATTTGAGAGTG
1 AAAAAGAAAATGAAAA-AGAAAATGAGAGTG
*
66266009 AAAAAGAAGATGAAAAAGAAA
1 AAAAAGAAAATGAAAAAGAAA
66266030 TTGAAACAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
29 1 0.02
30 40 0.95
31 1 0.02
ACGTcount: A:0.65, C:0.00, G:0.21, T:0.14
Consensus pattern (30 bp):
AAAAAGAAAATGAAAAAGAAAATGAGAGTG
Found at i:66268216 original size:30 final size:30
Alignment explanation
Indices: 66268180--66268277 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
66268170 AGCTCACTCC
66268180 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
66268210 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * *
66268240 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
66268270 TAGCTCAT
1 TAGCTCAT
66268278 TTTAGTTTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:66271396 original size:14 final size:14
Alignment explanation
Indices: 66271374--66271421 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
66271364 ACCTAAACCG
* *
66271374 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
66271388 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
*
66271402 ACCCTTTTGTTCCT
1 ACCATTTTGTTCCT
66271416 ACCATT
1 ACCATT
66271422 CCATTCGTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.19, C:0.29, G:0.06, T:0.46
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:66272047 original size:20 final size:20
Alignment explanation
Indices: 66272002--66272047 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 20
66271992 AACTAGGTTC
* *
66272002 GTTGTGAAAAAAAAATTCGA
1 GTTGTAAAAAAAAAATTCAA
*
66272022 -CT-TAAAAAAAAAATTCAA
1 GTTGTAAAAAAAAAATTCAA
66272040 GTTGTAAA
1 GTTGTAAA
66272048 TTTTCGTTCT
Statistics
Matches: 20, Mismatches: 4, Indels: 4
0.71 0.14 0.14
Matches are distributed among these distances:
18 14 0.70
19 2 0.10
20 4 0.20
ACGTcount: A:0.54, C:0.07, G:0.13, T:0.26
Consensus pattern (20 bp):
GTTGTAAAAAAAAAATTCAA
Found at i:66273080 original size:9 final size:10
Alignment explanation
Indices: 66273073--66273129 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
66273063 AAGAGAAAAC
66273073 AAAGAAAAGA
1 AAAGAAAAGA
66273083 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
66273095 AAAGAAGA-A
1 AAAGAAAAGA
66273104 AAAGAAAATGA
1 AAAGAAAA-GA
66273115 AATA-AAAAGA
1 AA-AGAAAAGA
66273125 AAAGA
1 AAAGA
66273130 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:66273096 original size:21 final size:20
Alignment explanation
Indices: 66273062--66273129 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
66273052 ACATTCTTGT
66273062 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAA-AAAAGA
*
66273083 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAGCAAAAAAAG-A
* *
66273104 AAAGAAAATGAAATAAAAAGA
1 AAAGAAAAAGCAA-AAAAAGA
66273125 AAAGA
1 AAAGA
66273130 GAGGCAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 8 0.20
21 27 0.68
22 5 0.12
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (20 bp):
AAAGAAAAAGCAAAAAAAGA
Found at i:66273097 original size:6 final size:5
Alignment explanation
Indices: 66273073--66273129 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
66273063 AAGAGAAAAC
*
66273073 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
66273120 AAAGA AAAGA
1 AAAGA AAAGA
66273130 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:66273104 original size:15 final size:14
Alignment explanation
Indices: 66273073--66273129 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
66273063 AAGAGAAAAC
66273073 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
66273089 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
66273104 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
66273120 AAAGAAAAGA
1 AAAGAAAAGA
66273130 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:66275377 original size:22 final size:22
Alignment explanation
Indices: 66275352--66275420 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
66275342 AGCTAAACCG
66275352 AGCTCACTCCTAGCTCATATTC
1 AGCTCACTCCTAGCTCATATTC
* **
66275374 AGCTCA---CGAGCT-A-AACC
1 AGCTCACTCCTAGCTCATATTC
66275391 AAGCTCACTCCTAGCTCATATTC
1 -AGCTCACTCCTAGCTCATATTC
66275414 AGCTCAC
1 AGCTCAC
66275421 GAGCTAAACC
Statistics
Matches: 35, Mismatches: 6, Indels: 12
0.66 0.11 0.23
Matches are distributed among these distances:
17 2 0.06
18 7 0.20
19 5 0.14
21 5 0.14
22 14 0.40
23 2 0.06
ACGTcount: A:0.28, C:0.36, G:0.12, T:0.25
Consensus pattern (22 bp):
AGCTCACTCCTAGCTCATATTC
Found at i:66275385 original size:40 final size:40
Alignment explanation
Indices: 66275341--66275430 Score: 171
Period size: 40 Copynumber: 2.2 Consensus size: 40
66275331 CAACTTGCCT
*
66275341 GAGCTAAACCGAGCTCACTCCTAGCTCATATTCAGCTCAC
1 GAGCTAAACCAAGCTCACTCCTAGCTCATATTCAGCTCAC
66275381 GAGCTAAACCAAGCTCACTCCTAGCTCATATTCAGCTCAC
1 GAGCTAAACCAAGCTCACTCCTAGCTCATATTCAGCTCAC
66275421 GAGCTAAACC
1 GAGCTAAACC
66275431 TTAGCTCAAC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.30, C:0.34, G:0.14, T:0.21
Consensus pattern (40 bp):
GAGCTAAACCAAGCTCACTCCTAGCTCATATTCAGCTCAC
Found at i:66275438 original size:30 final size:30
Alignment explanation
Indices: 66275402--66275498 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
66275392 AGCTCACTCC
66275402 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
66275432 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
66275462 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
66275492 TAGCTCA
1 TAGCTCA
66275499 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:66277224 original size:30 final size:30
Alignment explanation
Indices: 66277190--66277274 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 30
66277180 TTAATTAAAA
*
66277190 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
* * * * * * *
66277220 TGAGCTGAGATTAAACTCCTAAGTTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
* *
66277250 TAAGCTAAGGTTTAGCTCGTGAGCT
1 TGAGCTAAGATTTAGCTCGTGAGCT
66277275 GAATATGAGC
Statistics
Matches: 39, Mismatches: 16, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
Found at i:66280799 original size:30 final size:30
Alignment explanation
Indices: 66280765--66280861 Score: 83
Period size: 30 Copynumber: 3.2 Consensus size: 30
66280755 TAAACTAAAA
66280765 TGAGCTAAGCTTTAGCTCCTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCCTGAGCTAAAGT
* * * * *
66280795 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCCTGAGCTAAAGT
* *
66280825 TGAGCTAA-CGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGC-TTTAGCTCCTGAGCT-AAAGT
66280855 TGAGCTA
1 TGAGCTA
66280862 GGAGTAAGCT
Statistics
Matches: 51, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
28 1 0.02
29 1 0.02
30 43 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCCTGAGCTAAAGT
Found at i:66280901 original size:20 final size:20
Alignment explanation
Indices: 66280873--66280962 Score: 64
Period size: 20 Copynumber: 4.5 Consensus size: 20
66280863 GAGTAAGCTC
66280873 GGTTT-AGCTCAGGTAAGAT
1 GGTTTGAGCTCAGGTAAGAT
* *
66280892 GGTTTGAGCTC-GAATAAGCT
1 GGTTTGAGCTCAG-GTAAGAT
* *
66280912 GGATTTGAGCTGGACGG--AGCT
1 GG-TTTGAGCT-CA-GGTAAGAT
66280933 CGGTTT-AGCTCAGGTAAGAT
1 -GGTTTGAGCTCAGGTAAGAT
66280953 GGTTTGAGCT
1 GGTTTGAGCT
66280963 GGAAATGAGC
Statistics
Matches: 55, Mismatches: 6, Indels: 19
0.69 0.08 0.24
Matches are distributed among these distances:
18 2 0.04
19 12 0.22
20 23 0.42
21 15 0.27
22 2 0.04
24 1 0.02
ACGTcount: A:0.22, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
GGTTTGAGCTCAGGTAAGAT
Found at i:66284929 original size:13 final size:13
Alignment explanation
Indices: 66284911--66284935 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
66284901 TAACCTACAA
66284911 AATTAAATAACAT
1 AATTAAATAACAT
66284924 AATTAAATAACA
1 AATTAAATAACA
66284936 CACAACTATT
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:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (13 bp):
AATTAAATAACAT
Found at i:66285157 original size:10 final size:10
Alignment explanation
Indices: 66285142--66285187 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
66285132 AAAAAGGAAT
66285142 GAGCTAAAAC
1 GAGCTAAAAC
**
66285152 GAGCTAAATTT
1 GAGCTAAA-AC
*
66285163 GAGCTCAAAC
1 GAGCTAAAAC
66285173 GAGCTAAAAC
1 GAGCTAAAAC
66285183 GAGCT
1 GAGCT
66285188 CAAGTGAGCT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
10 22 0.76
11 7 0.24
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.17
Consensus pattern (10 bp):
GAGCTAAAAC
Found at i:66285167 original size:21 final size:21
Alignment explanation
Indices: 66285141--66285180 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
66285131 GAAAAAGGAA
66285141 TGAGCTAAAACGAGCTAAATT
1 TGAGCTAAAACGAGCTAAATT
*
66285162 TGAGCTCAAACGAGCTAAA
1 TGAGCTAAAACGAGCTAAA
66285181 ACGAGCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.20
Consensus pattern (21 bp):
TGAGCTAAAACGAGCTAAATT
Found at i:66286674 original size:14 final size:14
Alignment explanation
Indices: 66286632--66286676 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
66286622 TTAAAGAAGC
66286632 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
66286646 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
66286659 AACTCATTTAATTA
1 AACTCATTAAATTA
66286673 AACT
1 AACT
66286677 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:66290453 original size:15 final size:15
Alignment explanation
Indices: 66290433--66290480 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
66290423 TCAAAGATGG
66290433 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
66290448 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
66290462 GTTTATGGATATAAA
1 GTTTATGGATATGAA
66290477 GTTT
1 GTTT
66290481 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:66290467 original size:14 final size:14
Alignment explanation
Indices: 66290427--66290470 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
66290417 AAGGATTCAA
66290427 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
66290441 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
66290456 AGATGGGTTTATGG
1 AGATGGGTTTATGG
66290470 A
1 A
66290471 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:66290496 original size:29 final size:29
Alignment explanation
Indices: 66290427--66290486 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
66290417 AAGGATTCAA
*
66290427 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
66290456 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
66290485 AG
1 AG
66290487 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:66291499 original size:14 final size:14
Alignment explanation
Indices: 66291457--66291501 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
66291447 TTAAAGAAGC
66291457 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
66291471 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
66291484 AACTCATTTAATTA
1 AACTCATTAAATTA
66291498 AACT
1 AACT
66291502 AAGATGACTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:66291923 original size:10 final size:10
Alignment explanation
Indices: 66291910--66291956 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
66291900 GAGCTCCGTC
*
66291910 CAGCTCAATT
1 CAGCTCATTT
66291920 CAGCTCATTT
1 CAGCTCATTT
*
66291930 GAGCTCATTT
1 CAGCTCATTT
*
66291940 CAGCTCGTTT
1 CAGCTCATTT
*
66291950 GAGCTCA
1 CAGCTCA
66291957 ACCGAGCTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (10 bp):
CAGCTCATTT
Found at i:66291934 original size:20 final size:20
Alignment explanation
Indices: 66291911--66291957 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
66291901 AGCTCCGTCC
66291911 AGCTCAATTCAGCTCATTTG
1 AGCTCAATTCAGCTCATTTG
* *
66291931 AGCTCATTTCAGCTCGTTTG
1 AGCTCAATTCAGCTCATTTG
66291951 AGCTCAA
1 AGCTCAA
66291958 CCGAGCTTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (20 bp):
AGCTCAATTCAGCTCATTTG
Found at i:66297683 original size:30 final size:30
Alignment explanation
Indices: 66297649--66297745 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
66297639 TAAACTAAAA
66297649 TGAGCTAAGCTTTAGCTCGTAAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTAAGCTAAAGT
* * * * *
66297679 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTAAGCTAAAGT
* * *
66297709 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTAAGCT-AAAGT
66297739 TGAGCTA
1 TGAGCTA
66297746 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 2 0.04
30 43 0.84
31 6 0.12
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTAAGCTAAAGT
Found at i:66311628 original size:30 final size:30
Alignment explanation
Indices: 66311532--66311628 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
66311522 TAAACTAAAA
* *
66311532 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
66311562 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
*
66311592 TAAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
66311621 ATGAGCTA
1 -TGAGCTA
66311629 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
29 1 0.02
30 49 0.98
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:66311948 original size:13 final size:13
Alignment explanation
Indices: 66311930--66311967 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
66311920 CATAATTCAC
66311930 TTTTTTTTTCAAA
1 TTTTTTTTTCAAA
**
66311943 TTTTTTTTTCGGA
1 TTTTTTTTTCAAA
66311956 -TTTTTTTTCAAA
1 TTTTTTTTTCAAA
66311968 CTTGTATAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.18, C:0.08, G:0.05, T:0.68
Consensus pattern (13 bp):
TTTTTTTTTCAAA
Found at i:66317690 original size:30 final size:30
Alignment explanation
Indices: 66317656--66317752 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
66317646 TAAACTAAAA
66317656 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
66317686 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
66317716 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
66317746 TGAGCTA
1 TGAGCTA
66317753 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:66319454 original size:30 final size:30
Alignment explanation
Indices: 66319369--66319456 Score: 86
Period size: 30 Copynumber: 2.9 Consensus size: 30
66319359 TAAACTAAAA
* * * *
66319369 TGAGCTAAGCTTTAGCTCGTAAGTTAAAGT
1 TGAGCTAAGATTTAGCTCGTAAGCTGAAGC
* * * *
66319399 TGAGCTGAGATTAAACTCCTAAGCTGAAGC
1 TGAGCTAAGATTTAGCTCGTAAGCTGAAGC
* *
66319429 TGAGCTAAGGTTTAGCTCGTGAGCTGAA
1 TGAGCTAAGATTTAGCTCGTAAGCTGAA
66319457 TATGAGATAA
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTAAGCTGAAGC
Found at i:66323036 original size:30 final size:30
Alignment explanation
Indices: 66323002--66323098 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
66322992 TAAACTAAAA
66323002 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
66323032 TGAGCTGAGAC-TAAACTCCTAAGCTGAAGT
1 TGAGCTAAG-CTTTAGCTCGTGAGCTAAAGT
* *
66323062 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
66323092 TGAGCTA
1 TGAGCTA
66323099 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
30 46 0.92
31 4 0.08
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:66327750 original size:13 final size:12
Alignment explanation
Indices: 66327723--66327754 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
66327713 GTTCTTTTTG
66327723 TTTTTCAAAGGC
1 TTTTTCAAAGGC
66327735 TTTTTCAAAGGC
1 TTTTTCAAAGGC
*
66327747 CTTTTCAA
1 TTTTTCAA
66327755 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.44
Consensus pattern (12 bp):
TTTTTCAAAGGC
Found at i:66327812 original size:5 final size:5
Alignment explanation
Indices: 66327802--66327858 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
66327792 CTTTTGCCTC
*
66327802 TCTTT TCTTT T-TATT TCGTTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
66327849 TCTTT TCTTT
1 TCTTT TCTTT
66327859 GTTTTCTCGT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:66327842 original size:15 final size:14
Alignment explanation
Indices: 66327802--66327858 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
66327792 CTTTTGCCTC
*
66327802 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
66327817 TCGTTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
66327832 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
66327849 TCTTTTCTTT
1 TCTTTTCTTT
66327859 GTTTTCTCGT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:66327859 original size:21 final size:21
Alignment explanation
Indices: 66327802--66327863 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
66327792 CTTTTGCCTC
* *
66327802 TCTTTTCTTTT-TATTTCGTTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
66327823 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCTTTTC-TTTGCTTTT
66327844 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
66327864 CTCGTTACAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
20 7 0.21
21 22 0.65
22 5 0.15
ACGTcount: A:0.02, C:0.16, G:0.05, T:0.77
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTGCTTTT
Found at i:66328830 original size:34 final size:32
Alignment explanation
Indices: 66328782--66328845 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 32
66328772 CAACTATAAA
*
66328782 TTTTTTTTTAATTTT-GAATTTTTTTCTCTTTC
1 TTTTTTTTTAATTTTCG-ACTTTTTTCTCTTTC
66328814 TTTTTTTTTACTATTTTCGACTTTTTTCTCTT
1 TTTTTTTTTA--ATTTTCGACTTTTTTCTCTT
66328846 CAAATAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 10 0.36
34 17 0.61
35 1 0.04
ACGTcount: A:0.11, C:0.12, G:0.03, T:0.73
Consensus pattern (32 bp):
TTTTTTTTTAATTTTCGACTTTTTTCTCTTTC
Found at i:66328893 original size:29 final size:27
Alignment explanation
Indices: 66328861--66328943 Score: 85
Period size: 29 Copynumber: 2.9 Consensus size: 27
66328851 AAATATGTTC
66328861 TTTTTTTTCAACTTTTTTTTAATTTTGAA
1 TTTTTTTTC-ACTTTTTTTTAATTTTG-A
* *
66328890 TTTTTTTTCTCTTTTTTTCACTATTTTGA
1 TTTTTTTTCACTTTTTTTTA--ATTTTGA
* * *
66328919 CTTTTTTTGACTTTTTTTTATTTTT
1 TTTTTTTTCACTTTTTTTTAATTTT
66328944 TTAACGATAC
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
27 4 0.09
28 9 0.20
29 26 0.58
30 6 0.13
ACGTcount: A:0.13, C:0.10, G:0.04, T:0.73
Consensus pattern (27 bp):
TTTTTTTTCACTTTTTTTTAATTTTGA
Found at i:66328916 original size:19 final size:19
Alignment explanation
Indices: 66328894--66328945 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
66328884 TTTGAATTTT
66328894 TTTTCTCTTTTTTTCACTA
1 TTTTCTCTTTTTTTCACTA
** * *
66328913 TTTTGACTTTTTTTGACTT
1 TTTTCTCTTTTTTTCACTA
* *
66328932 TTTTTTATTTTTTT
1 TTTTCTCTTTTTTT
66328946 AACGATACGA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.10, C:0.12, G:0.04, T:0.75
Consensus pattern (19 bp):
TTTTCTCTTTTTTTCACTA
Found at i:66328916 original size:30 final size:29
Alignment explanation
Indices: 66328861--66328926 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 29
66328851 AAATATGTTC
*
66328861 TTTTTTTTCAACTTTTTTTTAATTTTGAA
1 TTTTTTTTCAACTTTTTTTCAATTTTGAA
* *
66328890 TTTTTTTTC-TCTTTTTTTCACTATTTTGAC
1 TTTTTTTTCAACTTTTTTTCA--ATTTTGAA
66328920 TTTTTTT
1 TTTTTTT
66328927 GACTTTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 9 0.28
29 9 0.28
30 14 0.44
ACGTcount: A:0.14, C:0.11, G:0.03, T:0.73
Consensus pattern (29 bp):
TTTTTTTTCAACTTTTTTTCAATTTTGAA
Found at i:66328942 original size:9 final size:10
Alignment explanation
Indices: 66328900--66328945 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
66328890 TTTTTTTTCT
*
66328900 CTTTTTTTCA
1 CTTTTTTTGA
*
66328910 C-TATTTTGA
1 CTTTTTTTGA
66328919 CTTTTTTTGA
1 CTTTTTTTGA
*
66328929 CTTTTTTTTA
1 CTTTTTTTGA
66328939 -TTTTTTT
1 CTTTTTTT
66328946 AACGATACGA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
9 14 0.45
10 17 0.55
ACGTcount: A:0.11, C:0.11, G:0.04, T:0.74
Consensus pattern (10 bp):
CTTTTTTTGA
Found at i:66328945 original size:29 final size:27
Alignment explanation
Indices: 66328862--66328944 Score: 78
Period size: 30 Copynumber: 2.9 Consensus size: 27
66328852 AATATGTTCT
66328862 TTTTTTTCAACTTTTTTTTA-ATTTTGAA
1 TTTTTTT--ACTTTTTTTTATATTTTGAA
* *
66328890 TTTTTTTTCTCTTTTTTTCACTATTTTGAC
1 TTTTTTTACT-TTTTTTT-A-TATTTTGAA
*
66328920 TTTTTTTGACTTTTTTTTATTTTTT
1 TTTTTTT-ACTTTTTTTTATATTTT
66328945 TAACGATACG
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
26 2 0.04
27 7 0.15
28 13 0.28
29 1 0.02
30 21 0.46
31 2 0.04
ACGTcount: A:0.13, C:0.10, G:0.04, T:0.73
Consensus pattern (27 bp):
TTTTTTTACTTTTTTTTATATTTTGAA
Found at i:66330939 original size:19 final size:19
Alignment explanation
Indices: 66330915--66330954 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
66330905 AGCTTCCATG
66330915 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
66330934 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
66330953 TA
1 TA
66330955 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:66333674 original size:13 final size:12
Alignment explanation
Indices: 66333656--66333687 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
66333646 ATACAAGTTT
66333656 AAAAAAAATCCG
1 AAAAAAAATCCG
*
66333668 AAAAAAAATTCG
1 AAAAAAAATCCG
66333680 AAAAAAAA
1 AAAAAAAA
66333688 GTGAATTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.75, C:0.09, G:0.06, T:0.09
Consensus pattern (12 bp):
AAAAAAAATCCG
Found at i:66342449 original size:30 final size:30
Alignment explanation
Indices: 66342415--66342511 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
66342405 TAAACTAAAA
66342415 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
66342445 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
66342475 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
66342505 TGAGCTA
1 TGAGCTA
66342512 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:66344693 original size:30 final size:30
Alignment explanation
Indices: 66344622--66344704 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
66344612 CTTTTGTTTC
* *
66344622 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
66344653 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
66344682 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
66344705 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:66344704 original size:18 final size:18
Alignment explanation
Indices: 66344655--66344710 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
66344645 CACTCTCAAA
* *
66344655 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
66344672 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
66344690 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
66344709 TT
1 TT
66344711 CAAAGGCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:66344711 original size:12 final size:12
Alignment explanation
Indices: 66344680--66344704 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
66344670 TTTTTCAATC
66344680 TCATTTTCTTTT
1 TCATTTTCTTTT
66344692 TCATTTTCTTTT
1 TCATTTTCTTTT
66344704 T
1 T
66344705 GCTTTTCAAA
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:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:66344783 original size:5 final size:5
Alignment explanation
Indices: 66344773--66344829 Score: 53
Period size: 5 Copynumber: 11.0 Consensus size: 5
66344763 CTCTTGCCTC
* * *
66344773 TCTTT TCTTTT TATTT TATTT TCTTT T-TCT TCATTT TCTGTT TCTTT
1 TCTTT TC-TTT TCTTT TCTTT TCTTT TCTTT TC-TTT TCT-TT TCTTT
66344820 TCTTT TCTTT
1 TCTTT TCTTT
66344830 GTTTTCTCTT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
4 3 0.07
5 28 0.64
6 13 0.30
ACGTcount: A:0.05, C:0.16, G:0.02, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:66345774 original size:16 final size:17
Alignment explanation
Indices: 66345747--66345778 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
66345737 AAACACTGTT
66345747 TTTTCAGATTTTTTTTC
1 TTTTCAGATTTTTTTTC
66345764 TTTTC-GATTTTTTTT
1 TTTTCAGATTTTTTTT
66345779 TGATTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.09, C:0.09, G:0.06, T:0.75
Consensus pattern (17 bp):
TTTTCAGATTTTTTTTC
Found at i:66345778 original size:11 final size:11
Alignment explanation
Indices: 66345759--66345801 Score: 59
Period size: 11 Copynumber: 3.7 Consensus size: 11
66345749 TTCAGATTTT
66345759 TTTTCTTTTCGA
1 TTTT-TTTTCGA
*
66345771 TTTTTTTTTGA
1 TTTTTTTTCGA
66345782 TTTTTTTTCGAA
1 TTTTTTTTCG-A
66345794 TTTTTTTT
1 TTTTTTTT
66345802 GACTTGTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 15 0.54
12 13 0.46
ACGTcount: A:0.09, C:0.07, G:0.07, T:0.77
Consensus pattern (11 bp):
TTTTTTTTCGA
Found at i:66345792 original size:22 final size:23
Alignment explanation
Indices: 66345759--66345803 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
66345749 TTCAGATTTT
*
66345759 TTTTCTTTTCGATTTTTTTTTGA
1 TTTTCTTTTCGAATTTTTTTTGA
66345782 TTTT-TTTTCGAATTTTTTTTGA
1 TTTTCTTTTCGAATTTTTTTTGA
66345804 CTTGTGTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.11, C:0.07, G:0.09, T:0.73
Consensus pattern (23 bp):
TTTTCTTTTCGAATTTTTTTTGA
Found at i:66347546 original size:30 final size:30
Alignment explanation
Indices: 66347512--66347608 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
66347502 TAAACTAAAA
66347512 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
66347542 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
66347572 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
66347602 TGAGCTA
1 TGAGCTA
66347609 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:66350916 original size:4 final size:4
Alignment explanation
Indices: 66350909--66350943 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
66350899 GCTAGAAGCA
66350909 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
66350944 AGATGAAGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:66352946 original size:13 final size:13
Alignment explanation
Indices: 66352912--66352945 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
66352902 ATACAAGTTT
66352912 GAAAAAAAATTCC
1 GAAAAAAAATTCC
66352925 GAAAAAAAATT-C
1 GAAAAAAAATTCC
66352937 GAAAAAAAA
1 GAAAAAAAA
66352946 AAGTGATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.71, C:0.09, G:0.09, T:0.12
Consensus pattern (13 bp):
GAAAAAAAATTCC
Found at i:66362577 original size:27 final size:27
Alignment explanation
Indices: 66362547--66362599 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
66362537 CCCAAATTGA
66362547 TAAAATGACTGTTATGCCCCTATGAGG
1 TAAAATGACTGTTATGCCCCTATGAGG
*
66362574 TAAAATGACTGTTATGCCCTTATGAG
1 TAAAATGACTGTTATGCCCCTATGAG
66362600 ATGTATGACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (27 bp):
TAAAATGACTGTTATGCCCCTATGAGG
Found at i:66368892 original size:11 final size:11
Alignment explanation
Indices: 66368876--66368906 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
66368866 ATATATTTCT
66368876 TTTTTTTTGAA
1 TTTTTTTTGAA
66368887 TTTTTTTTGAA
1 TTTTTTTTGAA
66368898 TTTTTTTTG
1 TTTTTTTTG
66368907 GCTAATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.13, C:0.00, G:0.10, T:0.77
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:66370214 original size:30 final size:31
Alignment explanation
Indices: 66370180--66370276 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
66370170 AGCTCACTCC
*
66370180 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
66370210 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
66370240 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
66370270 TAGCTCA
1 TAGCTCA
66370277 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:66371697 original size:9 final size:10
Alignment explanation
Indices: 66371690--66371751 Score: 56
Period size: 11 Copynumber: 6.0 Consensus size: 10
66371680 AAGAGAAAAC
66371690 AAAGAAAAGA
1 AAAGAAAAGA
*
66371700 AAAGAAAAAGC
1 AAAG-AAAAGA
66371711 AAAGCAAAAGA
1 AAAG-AAAAGA
*
66371722 AGA-AAAAGA
1 AAAGAAAAGA
66371731 AAATGAAATA-A
1 AAA-GAAA-AGA
66371742 AAAGAAAAGA
1 AAAGAAAAGA
66371752 GAGGCAAGAG
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
9 9 0.21
10 9 0.21
11 23 0.55
12 1 0.02
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:66371720 original size:6 final size:5
Alignment explanation
Indices: 66371690--66371751 Score: 56
Period size: 5 Copynumber: 12.0 Consensus size: 5
66371680 AAGAGAAAAC
* *
66371690 AAAGA AAAGA AAAGAA AAAGC AAAGCA AAAGA AGA-A AAAGA AAATGA
1 AAAGA AAAGA AAAG-A AAAGA AAAG-A AAAGA AAAGA AAAGA AAA-GA
66371737 AATA-A AAAGA AAAGA
1 AA-AGA AAAGA AAAGA
66371752 GAGGCAAGAG
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
4 4 0.09
5 29 0.62
6 13 0.28
7 1 0.02
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:66371721 original size:17 final size:16
Alignment explanation
Indices: 66371690--66371751 Score: 58
Period size: 16 Copynumber: 3.9 Consensus size: 16
66371680 AAGAGAAAAC
66371690 AAAGAAAAGAAAAGAA
1 AAAGAAAAGAAAAGAA
*
66371706 AAAGCAAAGCAAAAG-A
1 AAAGAAAAG-AAAAGAA
*
66371722 AGA-AAAAGAAAATGAA
1 AAAGAAAAGAAAA-GAA
*
66371738 ATA-AAAAGAAAAGA
1 AAAGAAAAGAAAAGA
66371752 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
14 4 0.10
15 7 0.18
16 23 0.59
17 5 0.13
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (16 bp):
AAAGAAAAGAAAAGAA
Found at i:66371828 original size:12 final size:12
Alignment explanation
Indices: 66371820--66371844 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
66371810 TTTGAAAAGC
66371820 AAAAAGAAAATG
1 AAAAAGAAAATG
66371832 AAAAAGAAAATG
1 AAAAAGAAAATG
66371844 A
1 A
66371845 GATTGAAAAA
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:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:66371841 original size:18 final size:18
Alignment explanation
Indices: 66371814--66371869 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
66371804 AAAGCCTTTG
66371814 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
66371833 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
66371851 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
66371868 AA
1 AA
66371870 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:66371854 original size:30 final size:31
Alignment explanation
Indices: 66371820--66371901 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
66371810 TTTGAAAAGC
*
66371820 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
66371850 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
66371880 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
66371902 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.01, G:0.22, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:66374041 original size:30 final size:31
Alignment explanation
Indices: 66374007--66374103 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
66373997 AGCTCACTCC
*
66374007 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
66374037 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
66374067 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
66374097 TAGCTCA
1 TAGCTCA
66374104 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:66377212 original size:12 final size:14
Alignment explanation
Indices: 66377184--66377219 Score: 58
Period size: 12 Copynumber: 2.7 Consensus size: 14
66377174 ATACAAGTTT
66377184 GAAAAAAAAATTCC
1 GAAAAAAAAATTCC
66377198 GAAAAAAAAA-T-C
1 GAAAAAAAAATTCC
66377210 GAAAAAAAAA
1 GAAAAAAAAA
66377220 AGTGATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 11 0.50
13 1 0.05
14 10 0.45
ACGTcount: A:0.75, C:0.08, G:0.08, T:0.08
Consensus pattern (14 bp):
GAAAAAAAAATTCC
Found at i:66377220 original size:13 final size:14
Alignment explanation
Indices: 66377184--66377220 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
66377174 ATACAAGTTT
*
66377184 GAAAAAAAAATTCC
1 GAAAAAAAAAATCC
66377198 G-AAAAAAAAAT-C
1 GAAAAAAAAAATCC
66377210 GAAAAAAAAAA
1 GAAAAAAAAAA
66377221 GTGATTTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
12 2 0.10
13 18 0.86
14 1 0.05
ACGTcount: A:0.76, C:0.08, G:0.08, T:0.08
Consensus pattern (14 bp):
GAAAAAAAAAATCC
Found at i:66384104 original size:27 final size:26
Alignment explanation
Indices: 66384055--66384114 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 26
66384045 TAGCAGCAAC
*
66384055 AATTAAATTTGTCCCTAAGCTAGACA
1 AATTAAATTTGTCCCTAAACTAGACA
66384081 AATTAAATTGATGT-CCTAAACTAGACA
1 AATTAAATT--TGTCCCTAAACTAGACA
*
66384108 CATTAAA
1 AATTAAA
66384115 GCTGGGTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 9 0.30
27 18 0.60
28 3 0.10
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.30
Consensus pattern (26 bp):
AATTAAATTTGTCCCTAAACTAGACA
Found at i:66390390 original size:17 final size:17
Alignment explanation
Indices: 66390368--66390400 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
66390358 ATAAGAACTA
66390368 TGAATATTCTTCCAATT
1 TGAATATTCTTCCAATT
66390385 TGAATATTCTTCCAAT
1 TGAATATTCTTCCAAT
66390401 CATAAGTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.18, G:0.06, T:0.45
Consensus pattern (17 bp):
TGAATATTCTTCCAATT
Found at i:66390952 original size:42 final size:42
Alignment explanation
Indices: 66390885--66391000 Score: 169
Period size: 42 Copynumber: 2.7 Consensus size: 42
66390875 GGCATCGACT
* * * *
66390885 TCTGTTTTACGTGTAAGACCATGTCTGGGACATCGGCATTGTA
1 TCTGATTT-CGTGTAAAACCCTGTCTGGGACATCGACATTGTA
*
66390928 TCTGATTTCGTGTAAAACCCTGTCTGAGACATCGACATTGTA
1 TCTGATTTCGTGTAAAACCCTGTCTGGGACATCGACATTGTA
*
66390970 TCTGATTTCGTGTAAAACCCTGCCTGGGACA
1 TCTGATTTCGTGTAAAACCCTGTCTGGGACA
66391001 GTGGCATCAA
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
42 59 0.89
43 7 0.11
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.33
Consensus pattern (42 bp):
TCTGATTTCGTGTAAAACCCTGTCTGGGACATCGACATTGTA
Found at i:66395656 original size:43 final size:43
Alignment explanation
Indices: 66395593--66395711 Score: 132
Period size: 43 Copynumber: 2.8 Consensus size: 43
66395583 TCTGAACTCA
* * **
66395593 TTCACCGACATT-TCGCCTGCTAGGCTTGAAGCCCAATATCAT
1 TTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCAATATCAT
* * *
66395635 TTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCGATGTTAT
1 TTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCAATATCAT
* * * *
66395678 CTCACCAGTATTATAGCCTGCTAGACCCGAAGCC
1 TTCACCGGCATTATAGCCTGCTAGGCCCGAAGCC
66395712 TGATAATATT
Statistics
Matches: 65, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
42 11 0.17
43 54 0.83
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (43 bp):
TTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCAATATCAT
Found at i:66399651 original size:10 final size:10
Alignment explanation
Indices: 66399636--66399664 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
66399626 TTCGAGAACT
66399636 TTAGAAAAAC
1 TTAGAAAAAC
66399646 TTAGAAAAAC
1 TTAGAAAAAC
66399656 TTAGAAAAA
1 TTAGAAAAA
66399665 TTTTCATGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.62, C:0.07, G:0.10, T:0.21
Consensus pattern (10 bp):
TTAGAAAAAC
Found at i:66401348 original size:19 final size:19
Alignment explanation
Indices: 66401324--66401363 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
66401314 AGCTCCCATG
66401324 TAGCTC-CACACCAGCTCAT
1 TAGCTCGCA-ACCAGCTCAT
*
66401343 TAGCTCGGAACCAGCTCAT
1 TAGCTCGCAACCAGCTCAT
66401362 TA
1 TA
66401364 TCAACTCACG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.28, C:0.35, G:0.15, T:0.23
Consensus pattern (19 bp):
TAGCTCGCAACCAGCTCAT
Found at i:66411981 original size:31 final size:31
Alignment explanation
Indices: 66411943--66412052 Score: 175
Period size: 31 Copynumber: 3.5 Consensus size: 31
66411933 TTTAACGGTT
*
66411943 ACTGGGCCGAAGCCTTTTTATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
**
66411974 ACTGGGCCGAAGCGATTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
*
66412005 ACTGGGCCAAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
*
66412036 ACTGGGCCGAATCCTTT
1 ACTGGGCCGAAGCCTTT
66412053 ACTGTAAACG
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 71 1.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTTTCATAAATCATATC
Found at i:66412123 original size:42 final size:42
Alignment explanation
Indices: 66412076--66412167 Score: 175
Period size: 42 Copynumber: 2.2 Consensus size: 42
66412066 TAGCCCTTAG
*
66412076 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGCCAATGAATGTATGCAA
66412118 GCCCATTTCAATATCACATGTAATGCCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGCCAATGAATGTATGCAA
66412160 GCCCATTT
1 GCCCATTT
66412168 GGGGAGACTA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGTAATGCCAATGAATGTATGCAA
Found at i:66413201 original size:27 final size:27
Alignment explanation
Indices: 66413171--66413235 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
66413161 GGGCATATTC
66413171 GTCATTTTACCATACAAGGG-TATTACG
1 GTCATTTTACCATACAAGGGCT-TTACG
* * * *
66413198 GTCACTTTACCCTATAGGGGCTTTACG
1 GTCATTTTACCATACAAGGGCTTTACG
*
66413225 GTCTTTTTACC
1 GTCATTTTACC
66413236 TATTAGGGGT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
27 30 0.97
28 1 0.03
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (27 bp):
GTCATTTTACCATACAAGGGCTTTACG
Found at i:66413237 original size:26 final size:28
Alignment explanation
Indices: 66413193--66413244 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
66413183 TACAAGGGTA
66413193 TTACGGTCACTTTACCCTA-TAGGGGCT
1 TTACGGTCACTTTACCCTATTAGGGGCT
**
66413220 TTACGGTCTTTTTA-CCTATTAGGGG
1 TTACGGTCACTTTACCCTATTAGGGG
66413245 TATTTTAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.38
Consensus pattern (28 bp):
TTACGGTCACTTTACCCTATTAGGGGCT
Found at i:66413319 original size:27 final size:27
Alignment explanation
Indices: 66413289--66413374 Score: 86
Period size: 27 Copynumber: 3.1 Consensus size: 27
66413279 GTAAATCTAC
66413289 AAACCAAGGGTATTTCAGTAATTTTGT
1 AAACCAAGGGTATTTCAGTAATTTTGT
*
66413316 AAACCAATGGTATTTCTA-TAATTTT-T
1 AAACCAAGGGTATTTC-AGTAATTTTGT
* **
66413342 AGAAAGTCAAGGGTATTTTTGTAATTTTGT
1 --AAA-CCAAGGGTATTTCAGTAATTTTGT
66413372 AAA
1 AAA
66413375 TTAGGGGTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
26 1 0.02
27 22 0.46
28 7 0.15
29 17 0.35
30 1 0.02
ACGTcount: A:0.35, C:0.08, G:0.16, T:0.41
Consensus pattern (27 bp):
AAACCAAGGGTATTTCAGTAATTTTGT
Found at i:66413392 original size:27 final size:27
Alignment explanation
Indices: 66413352--66413505 Score: 175
Period size: 27 Copynumber: 5.7 Consensus size: 27
66413342 AGAAAGTCAA
* ** *
66413352 GGGTATTTTTGTAATTTTGTAAATTAG
1 GGGTATTTTGGTAATTTTACAAACTAG
*
66413379 GGGTATTTTGGTAATTTTACAAA-TTG
1 GGGTATTTTGGTAATTTTACAAACTAG
* * * *
66413405 AGGGTATTTCGATAATTTCACAAACCAG
1 -GGGTATTTTGGTAATTTTACAAACTAG
* *
66413433 TGGTATTTCGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACTAG
* *
66413460 GGATATTTTGGTAATGTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACTAG
66413487 GGGTATTTTGGTAATTTTA
1 GGGTATTTTGGTAATTTTA
66413506 TCCTACAGGG
Statistics
Matches: 106, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
26 2 0.02
27 103 0.97
28 1 0.01
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.42
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACTAG
Found at i:66413491 original size:81 final size:81
Alignment explanation
Indices: 66413353--66413503 Score: 196
Period size: 81 Copynumber: 1.9 Consensus size: 81
66413343 GAAAGTCAAG
** ** * * * *
66413353 GGTATTTTTGTAATTTTGTAAATTAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGAT
1 GGTATTTCGGTAATTTTACAAACTAGGGATATTTTGGTAATGTTACAAATAGAGGGTATTTCGAT
66413418 AATTTCACAAACCAGT
66 AATTTCACAAACCAGT
* *
66413434 GGTATTTCGGTAATTTTACAAACTAGGGATATTTTGGTAATGTTACAAACTAG-GGGTATTTTGG
1 GGTATTTCGGTAATTTTACAAACTAGGGATATTTTGGTAATGTTACAAA-TAGAGGGTATTTCGA
66413498 TAATTT
65 TAATTT
66413504 TATCCTACAG
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
81 57 0.97
82 2 0.03
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.42
Consensus pattern (81 bp):
GGTATTTCGGTAATTTTACAAACTAGGGATATTTTGGTAATGTTACAAATAGAGGGTATTTCGAT
AATTTCACAAACCAGT
Found at i:66413569 original size:27 final size:27
Alignment explanation
Indices: 66413533--66413784 Score: 360
Period size: 27 Copynumber: 9.3 Consensus size: 27
66413523 GTAATTTCAC
*
66413533 AATCGAGGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTCTGTA
*
66413560 AATCGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAATGGTAATTCTGTA
*
66413587 AATCGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAATGGTAATTCTGTA
* * *
66413614 AATCGAGGGTAAAACGATAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTCTGTA
66413641 AATCGAGGGTAAAATGGTAATTCTGTA
1 AATCGAGGGTAAAATGGTAATTCTGTA
*
66413668 AATCGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAATGGTAATTCTGTA
* *
66413695 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTCTGTA
* * * *
66413722 AATTGAGGGTGAAACGGTAATTCTATA
1 AATCGAGGGTAAAATGGTAATTCTGTA
* **
66413749 AATCGAGGGTAAAGTGGTAATTCTACA
1 AATCGAGGGTAAAATGGTAATTCTGTA
66413776 AATCGAGGG
1 AATCGAGGG
66413785 CATTTCAGTA
Statistics
Matches: 201, Mismatches: 24, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 201 1.00
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.29
Consensus pattern (27 bp):
AATCGAGGGTAAAATGGTAATTCTGTA
Found at i:66413635 original size:81 final size:81
Alignment explanation
Indices: 66413533--66413784 Score: 432
Period size: 81 Copynumber: 3.1 Consensus size: 81
66413523 GTAATTTCAC
*
66413533 AATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTA
1 AATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTA
66413598 AAATGGTAATTCTATA
66 AAATGGTAATTCTATA
* *
66413614 AATCGAGGGTAAAACGATAATTTTGTAAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTA
1 AATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTA
66413679 AAATGGTAATTCTATA
66 AAATGGTAATTCTATA
* * *
66413695 AATCGAGGGTAAAACGGTAATTTTGTAAATTGAGGGTGAAACGGTAATTCTATAAATCGAGGGTA
1 AATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTA
* *
66413760 AAGTGGTAATTCTACA
66 AAATGGTAATTCTATA
66413776 AATCGAGGG
1 AATCGAGGG
66413785 CATTTCAGTA
Statistics
Matches: 161, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 161 1.00
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.29
Consensus pattern (81 bp):
AATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTA
AAATGGTAATTCTATA
Found at i:66416214 original size:21 final size:22
Alignment explanation
Indices: 66416174--66416214 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
66416164 TTCCAAATAA
* *
66416174 AACATTATATCATTTCTAATTC
1 AACATTATATCAATTATAATTC
66416196 AACATT-TATCAATTATAAT
1 AACATTATATCAATTATAAT
66416215 CGGGCATGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (22 bp):
AACATTATATCAATTATAATTC
Found at i:66418540 original size:34 final size:34
Alignment explanation
Indices: 66418493--66418599 Score: 160
Period size: 34 Copynumber: 3.1 Consensus size: 34
66418483 ATTTGCCTTT
*
66418493 CTGATACTATTACTGTAATGGGCTAAGGCCCACA
1 CTGATACTGTTACTGTAATGGGCTAAGGCCCACA
*
66418527 CTGATACTGTTACTGTAATAGGCTAAGGCCCACA
1 CTGATACTGTTACTGTAATGGGCTAAGGCCCACA
* * * *
66418561 CTAATACTGCTATTATAATGGGCTAAGGCCCACA
1 CTGATACTGTTACTGTAATGGGCTAAGGCCCACA
66418595 CTGAT
1 CTGAT
66418600 GCTGGACTGT
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 65 1.00
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (34 bp):
CTGATACTGTTACTGTAATGGGCTAAGGCCCACA
Found at i:66422863 original size:30 final size:30
Alignment explanation
Indices: 66422829--66422889 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
66422819 TCCTTAACTC
66422829 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
66422859 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
66422889 A
1 A
66422890 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:66426857 original size:30 final size:30
Alignment explanation
Indices: 66426823--66426883 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
66426813 TCCTTAACTC
66426823 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
66426853 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
66426883 A
1 A
66426884 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Done.