Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2450_ERROPOS131173+
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: 114056
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:12581 original size:15 final size:15
Alignment explanation
Indices: 12561--12615 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
12551 ACTCTCCTCA
*
12561 TTCTTTTCTTTCTTT
1 TTCTTTTCTCTCTTT
*
12576 TTCTTTTCACTCTTT
1 TTCTTTTCTCTCTTT
*
12591 TTGTTTT-TCTCTTT
1 TTCTTTTCTCTCTTT
12605 TTCTTTT-TCTC
1 TTCTTTTCTCTC
12616 GCTCAATAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
14 16 0.46
15 19 0.54
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75
Consensus pattern (15 bp):
TTCTTTTCTCTCTTT
Found at i:14712 original size:11 final size:11
Alignment explanation
Indices: 14696--14736 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
14686 GAATACAAAC
14696 TTTTTTTTGAA
1 TTTTTTTTGAA
*
14707 TTTTTTTCGAA
1 TTTTTTTTGAA
*
14718 TTTTTTTTCAA
1 TTTTTTTTGAA
14729 TTTTTTTT
1 TTTTTTTT
14737 ACAATCTCGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.15, C:0.05, G:0.05, T:0.76
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:14741 original size:12 final size:11
Alignment explanation
Indices: 14696--14741 Score: 58
Period size: 11 Copynumber: 4.1 Consensus size: 11
14686 GAATACAAAC
*
14696 TTTTTTTTGAA
1 TTTTTTTTCAA
14707 -TTTTTTTCGAA
1 TTTTTTTTC-AA
14718 TTTTTTTTCAA
1 TTTTTTTTCAA
14729 TTTTTTTTACAA
1 TTTTTTTT-CAA
14741 T
1 T
14742 CTCGTAATAC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
10 7 0.23
11 12 0.39
12 12 0.39
ACGTcount: A:0.20, C:0.07, G:0.04, T:0.70
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:17053 original size:13 final size:13
Alignment explanation
Indices: 17035--17083 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
17025 TAGTTTCTTC
17035 AAAAAAATTTCAAA
1 AAAAAAATTT-AAA
*
17049 AAAAAAA-TTGAA
1 AAAAAAATTTAAA
*
17061 AAAAAAATTGAAA
1 AAAAAAATTTAAA
17074 AAAAAAATTT
1 AAAAAAATTT
17084 GGTTTCCATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
12 9 0.30
13 14 0.47
14 7 0.23
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.20
Consensus pattern (13 bp):
AAAAAAATTTAAA
Found at i:17062 original size:11 final size:12
Alignment explanation
Indices: 17047--17079 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
17037 AAAAATTTCA
17047 AAAAAAAAATTG
1 AAAAAAAAATTG
17059 AAAAAAAAATTG
1 AAAAAAAAATTG
17071 AAAAAAAAA
1 AAAAAAAAA
17080 ATTTGGTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (12 bp):
AAAAAAAAATTG
Found at i:17142 original size:14 final size:15
Alignment explanation
Indices: 17120--17158 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
17110 GATATCAAGT
* *
17120 TGAAAAAAAAATTCG
1 TGAAAAAAATATTCA
*
17135 TGAAAAAAATTTTCA
1 TGAAAAAAATATTCA
17150 TGAAAAAAA
1 TGAAAAAAA
17159 GAAGAAGAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.23
Consensus pattern (15 bp):
TGAAAAAAATATTCA
Found at i:18867 original size:20 final size:20
Alignment explanation
Indices: 18844--18897 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
18834 AGTTTTCCCC
*
18844 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
18864 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
18884 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
18898 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:18879 original size:30 final size:30
Alignment explanation
Indices: 18844--18917 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
18834 AGTTTTCCCC
18844 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
18874 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
18904 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
18918 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:18907 original size:20 final size:20
Alignment explanation
Indices: 18844--18908 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
18834 AGTTTTCCCC
* * * *
18844 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
18864 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
18883 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
18904 AGCTC
1 AGCTC
18909 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:20542 original size:10 final size:11
Alignment explanation
Indices: 20520--20555 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
20510 AAAAGAGAAG
20520 AAATTCAAAAA
1 AAATTCAAAAA
20531 AAATTCAAAAA
1 AAATTCAAAAA
20542 AAA-TCGAAAAA
1 AAATTC-AAAAA
20553 AAA
1 AAA
20556 AAGAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 2 0.08
11 22 0.92
ACGTcount: A:0.75, C:0.08, G:0.03, T:0.14
Consensus pattern (11 bp):
AAATTCAAAAA
Found at i:20562 original size:22 final size:21
Alignment explanation
Indices: 20506--20566 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
20496 TATTGGATTT
* *
20506 AAAAAAAAGAGAAGAAATTCAA
1 AAAAAAAAGA-AAAAAAATCAA
***
20528 AAAAAATTCAAAAAAAATCGAA
1 AAAAAAAAGAAAAAAAATC-AA
20550 AAAAAAAAGAAAAAAAA
1 AAAAAAAAGAAAAAAAA
20567 GAAGTGACAA
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
21 7 0.23
22 23 0.77
ACGTcount: A:0.79, C:0.05, G:0.08, T:0.08
Consensus pattern (21 bp):
AAAAAAAAGAAAAAAAATCAA
Found at i:21610 original size:11 final size:11
Alignment explanation
Indices: 21594--21679 Score: 66
Period size: 11 Copynumber: 7.0 Consensus size: 11
21584 AGAAAGAGAT
21594 TGAAAAAGAAA
1 TGAAAAAGAAA
21605 TGAAAAAGAAGA
1 TGAAAAAGAA-A
21617 -GAAAAAGAAAA
1 TGAAAAAG-AAA
21628 TGAAGAAAAGAAAA
1 TG-A-AAAAG-AAA
21642 TTGAAAAAGAAA
1 -TGAAAAAGAAA
*
21654 TGAGAATGAAAAAA
1 TGA-AA--AAGAAA
21668 TTGAAAAAGAAA
1 -TGAAAAAGAAA
21680 AAGCGAAAAA
Statistics
Matches: 63, Mismatches: 2, Indels: 19
0.75 0.02 0.23
Matches are distributed among these distances:
11 21 0.33
12 14 0.22
13 6 0.10
14 17 0.27
15 5 0.08
ACGTcount: A:0.70, C:0.00, G:0.20, T:0.10
Consensus pattern (11 bp):
TGAAAAAGAAA
Found at i:21653 original size:18 final size:17
Alignment explanation
Indices: 21597--21666 Score: 61
Period size: 20 Copynumber: 3.9 Consensus size: 17
21587 AAGAGATTGA
21597 AAAAG-AAATGAAAAAG
1 AAAAGAAAATGAAAAAG
* *
21613 AAGAGAAAAAGAAAATGAAG
1 AAAAGAAAATG-AAA--AAG
21633 AAAAGAAAATTGAAAAAG
1 AAAAGAAAA-TGAAAAAG
* *
21651 AAATGAGAATGAAAAA
1 AAAAGAAAATGAAAAA
21667 ATTGAAAAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
16 4 0.09
17 11 0.26
18 13 0.30
20 14 0.33
21 1 0.02
ACGTcount: A:0.71, C:0.00, G:0.20, T:0.09
Consensus pattern (17 bp):
AAAAGAAAATGAAAAAG
Found at i:21654 original size:26 final size:25
Alignment explanation
Indices: 21592--21679 Score: 103
Period size: 26 Copynumber: 3.5 Consensus size: 25
21582 GGAGAAAGAG
*
21592 ATTGAAAAAGAAATGA-AAAAGAAG
1 ATTGAAAAAGAAATGAGAAAAGAAA
21616 A--GAAAAAGAAAATGAAGAAAAGAAA
1 ATTGAAAAAG-AAATG-AGAAAAGAAA
21641 ATTGAAAAAGAAATGAGAATGAA-AAA
1 ATTGAAAAAGAAATGAGAA--AAGAAA
21667 ATTGAAAAAGAAA
1 ATTGAAAAAGAAA
21680 AAGCGAAAAA
Statistics
Matches: 56, Mismatches: 1, Indels: 12
0.81 0.01 0.17
Matches are distributed among these distances:
22 7 0.12
23 5 0.09
24 2 0.04
25 12 0.21
26 21 0.38
27 9 0.16
ACGTcount: A:0.69, C:0.00, G:0.19, T:0.11
Consensus pattern (25 bp):
ATTGAAAAAGAAATGAGAAAAGAAA
Found at i:21695 original size:27 final size:26
Alignment explanation
Indices: 21592--21700 Score: 102
Period size: 27 Copynumber: 4.3 Consensus size: 26
21582 GGAGAAAGAG
* *
21592 ATTGAAAAAG-AAATGA-AAAAGAAG
1 ATTGAAAAAGAAAATGAGAAAAAAAA
*
21616 A--GAAAAAGAAAATGAAGAAAAGAAA
1 ATTGAAAAAGAAAATG-AGAAAAAAAA
*
21641 ATTGAAAAAG-AAATGAGAATGAAAAA
1 ATTGAAAAAGAAAATGAGAA-AAAAAA
* *
21667 ATTGAAAAAGAAAAAGCGAAAAAAGAA
1 ATTGAAAAAGAAAATGAGAAAAAA-AA
21694 ATTGAAA
1 ATTGAAA
21701 GAGAGCTTGA
Statistics
Matches: 71, Mismatches: 6, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
22 7 0.10
23 5 0.07
24 2 0.03
25 12 0.17
26 22 0.31
27 23 0.32
ACGTcount: A:0.69, C:0.01, G:0.19, T:0.11
Consensus pattern (26 bp):
ATTGAAAAAGAAAATGAGAAAAAAAA
Found at i:21734 original size:33 final size:33
Alignment explanation
Indices: 21697--21759 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
21687 AAAAGAAATT
21697 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
21730 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
21760 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.56, C:0.06, G:0.25, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTATAAAAGAAACAAGTGAAAAA
Found at i:23557 original size:20 final size:20
Alignment explanation
Indices: 23534--23587 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
23524 AGTTTTTCCC
*
23534 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
23554 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
23574 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
23588 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:23569 original size:30 final size:30
Alignment explanation
Indices: 23534--23607 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
23524 AGTTTTTCCC
23534 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
23564 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
23594 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
23608 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:23597 original size:20 final size:20
Alignment explanation
Indices: 23534--23598 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
23524 AGTTTTTCCC
* * * *
23534 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
23554 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
23573 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
23594 AGCTC
1 AGCTC
23599 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:31778 original size:19 final size:20
Alignment explanation
Indices: 31754--31798 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
31744 TTTTTCACTC
* *
31754 TCTTTTTTTGAGTTTTC-TT
1 TCTTTTTCTCAGTTTTCTTT
*
31773 TCTTTTTCTCATTTTTCTTT
1 TCTTTTTCTCAGTTTTCTTT
31793 TCTTTT
1 TCTTTT
31799 GTAGTTTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.04, C:0.16, G:0.04, T:0.76
Consensus pattern (20 bp):
TCTTTTTCTCAGTTTTCTTT
Found at i:35113 original size:13 final size:13
Alignment explanation
Indices: 35095--35119 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35085 TGAAAAATGA
35095 AAAACCTCACAAC
1 AAAACCTCACAAC
35108 AAAACCTCACAA
1 AAAACCTCACAA
35120 ATCTCTCAAA
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:0.56, C:0.36, G:0.00, T:0.08
Consensus pattern (13 bp):
AAAACCTCACAAC
Found at i:37452 original size:23 final size:24
Alignment explanation
Indices: 37403--37463 Score: 79
Period size: 23 Copynumber: 2.6 Consensus size: 24
37393 ATGGAGTTGG
* **
37403 TTTTGGTACAAAATGGTATGG-GG
1 TTTTGGTACGAAATGGTATGGAAT
*
37426 TTTTGGTATGAAATGGTATGGAAT
1 TTTTGGTACGAAATGGTATGGAAT
37450 TTTTGGTACGAAAT
1 TTTTGGTACGAAAT
37464 AAACCAAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 19 0.59
24 13 0.41
ACGTcount: A:0.28, C:0.03, G:0.30, T:0.39
Consensus pattern (24 bp):
TTTTGGTACGAAATGGTATGGAAT
Found at i:42895 original size:18 final size:18
Alignment explanation
Indices: 42874--42912 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
42864 TTTCTTCAAC
* *
42874 TTCTTTTTCAAATTTCTT
1 TTCTGTTTCAAATTCCTT
*
42892 TTCTGTTTCACATTCCTT
1 TTCTGTTTCAAATTCCTT
42910 TTC
1 TTC
42913 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.03, T:0.62
Consensus pattern (18 bp):
TTCTGTTTCAAATTCCTT
Found at i:48854 original size:19 final size:18
Alignment explanation
Indices: 48818--48857 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
48808 TTTCCACTCG
*
48818 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
48836 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
48855 TTT
1 TTT
48858 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:49932 original size:12 final size:12
Alignment explanation
Indices: 49915--49962 Score: 71
Period size: 13 Copynumber: 4.0 Consensus size: 12
49905 TAGCTCTCTT
49915 TTTTTTTCACAA
1 TTTTTTTCACAA
49927 TTTTTTTTCACAA
1 -TTTTTTTCACAA
49940 TTTTTTTCA-AA
1 TTTTTTTCACAA
*
49951 TTTTTTTTACAA
1 TTTTTTTCACAA
49963 CTTGATATCA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
11 10 0.30
12 11 0.33
13 12 0.36
ACGTcount: A:0.25, C:0.12, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTTTTTCACAA
Found at i:49932 original size:13 final size:13
Alignment explanation
Indices: 49914--49962 Score: 77
Period size: 12 Copynumber: 4.0 Consensus size: 13
49904 CTAGCTCTCT
49914 TTTTTTTTCACAA
1 TTTTTTTTCACAA
49927 TTTTTTTTCACAA
1 TTTTTTTTCACAA
49940 -TTTTTTTCA-AA
1 TTTTTTTTCACAA
49951 TTTTTTTT-ACAA
1 TTTTTTTTCACAA
49963 CTTGATATCA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
11 3 0.09
12 18 0.53
13 13 0.38
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTTTTTTCACAA
Found at i:50018 original size:13 final size:13
Alignment explanation
Indices: 50000--50044 Score: 58
Period size: 12 Copynumber: 3.6 Consensus size: 13
49990 TGGAAACTAG
50000 TTTTTTTTTC-AA
1 TTTTTTTTTCGAA
*
50012 ATTTTTTTT-GAA
1 TTTTTTTTTCGAA
*
50024 TTTTTTTTTCGAG
1 TTTTTTTTTCGAA
50037 TTTTTTTT
1 TTTTTTTT
50045 CGAGAAACTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 18 0.64
13 10 0.36
ACGTcount: A:0.13, C:0.04, G:0.07, T:0.76
Consensus pattern (13 bp):
TTTTTTTTTCGAA
Found at i:52832 original size:12 final size:12
Alignment explanation
Indices: 52815--52874 Score: 77
Period size: 12 Copynumber: 5.1 Consensus size: 12
52805 TAGTAGTTTC
52815 TTCAAAAAAAAT
1 TTCAAAAAAAAT
*
52827 TTCAAAAAAAAA
1 TTCAAAAAAAAT
52839 TTCAAAAAAAA-
1 TTCAAAAAAAAT
*
52850 TTGAAAAAAAAT
1 TTCAAAAAAAAT
**
52862 TGAAAAAAAAAT
1 TTCAAAAAAAAT
52874 T
1 T
52875 GGTTTCCATT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
11 10 0.23
12 33 0.77
ACGTcount: A:0.70, C:0.05, G:0.03, T:0.22
Consensus pattern (12 bp):
TTCAAAAAAAAT
Found at i:52835 original size:11 final size:11
Alignment explanation
Indices: 52815--52871 Score: 78
Period size: 11 Copynumber: 5.0 Consensus size: 11
52805 TAGTAGTTTC
52815 TTCAAAAAAAA
1 TTCAAAAAAAA
52826 TTTCAAAAAAAAA
1 -TTC-AAAAAAAA
52839 TTCAAAAAAAA
1 TTCAAAAAAAA
*
52850 TTGAAAAAAAA
1 TTCAAAAAAAA
*
52861 TTGAAAAAAAA
1 TTCAAAAAAAA
52872 ATTGGTTTCC
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
11 29 0.67
12 6 0.14
13 8 0.19
ACGTcount: A:0.72, C:0.05, G:0.04, T:0.19
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:52872 original size:23 final size:22
Alignment explanation
Indices: 52831--52875 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
52821 AAAAATTTCA
*
52831 AAAAAAAATTCAAAAAAAATTG
1 AAAAAAAATTAAAAAAAAATTG
52853 AAAAAAAATTGAAAAAAAAATTG
1 AAAAAAAATT-AAAAAAAAATTG
52876 GTTTCCATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (22 bp):
AAAAAAAATTAAAAAAAAATTG
Found at i:52934 original size:15 final size:15
Alignment explanation
Indices: 52911--52950 Score: 71
Period size: 15 Copynumber: 2.6 Consensus size: 15
52901 GATATCAAGT
52911 TGAAAAAAAAATTTCG
1 TGAAAAAAAAA-TTCG
52927 TGAAAAAAAAATTCG
1 TGAAAAAAAAATTCG
52942 TGAAAAAAA
1 TGAAAAAAA
52951 GAAGAAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.62, C:0.05, G:0.12, T:0.20
Consensus pattern (15 bp):
TGAAAAAAAAATTCG
Found at i:54210 original size:14 final size:14
Alignment explanation
Indices: 54191--54221 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
54181 GTTGTTTAAG
54191 TTAATTTTTAAGTT
1 TTAATTTTTAAGTT
54205 TTAATTTTTAAGTT
1 TTAATTTTTAAGTT
54219 TTA
1 TTA
54222 GGAATATCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (14 bp):
TTAATTTTTAAGTT
Found at i:62965 original size:10 final size:11
Alignment explanation
Indices: 62942--62992 Score: 57
Period size: 11 Copynumber: 4.4 Consensus size: 11
62932 GGAGAAGAGG
62942 AAATTCGAAAAA
1 AAATT-GAAAAA
*
62954 AAATTTAAAAAAA
1 AAA-TT-GAAAAA
62967 AAATTGAAAAA
1 AAATTGAAAAA
*
62978 AAATTTAAAAA
1 AAATTGAAAAA
62989 AAAT
1 AAAT
62993 CGAAGTATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
11 19 0.56
12 5 0.15
13 10 0.29
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.22
Consensus pattern (11 bp):
AAATTGAAAAA
Found at i:62965 original size:11 final size:11
Alignment explanation
Indices: 62949--62992 Score: 61
Period size: 11 Copynumber: 3.8 Consensus size: 11
62939 AGGAAATTCG
62949 AAAAAAAATTT
1 AAAAAAAATTT
*
62960 AAAAAAAAAATTG
1 --AAAAAAAATTT
62973 AAAAAAAATTT
1 AAAAAAAATTT
62984 AAAAAAAAT
1 AAAAAAAAT
62993 CGAAGTATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 19 0.66
13 10 0.34
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.20
Consensus pattern (11 bp):
AAAAAAAATTT
Found at i:62975 original size:24 final size:25
Alignment explanation
Indices: 62942--62991 Score: 93
Period size: 24 Copynumber: 2.0 Consensus size: 25
62932 GGAGAAGAGG
62942 AAATTCGAAAAAAAATTTAAAAAAA
1 AAATTCGAAAAAAAATTTAAAAAAA
62967 AAATT-GAAAAAAAATTTAAAAAAA
1 AAATTCGAAAAAAAATTTAAAAAAA
62991 A
1 A
62992 TCGAAGTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 20 0.80
25 5 0.20
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (25 bp):
AAATTCGAAAAAAAATTTAAAAAAA
Found at i:74250 original size:18 final size:18
Alignment explanation
Indices: 74221--74265 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
74211 TACTTCCTTT
74221 TCTTTCTTCAATCTCACTC
1 TCTTT-TTCAATCTCACTC
* **
74240 TCTTTTTCAATTTCTTTC
1 TCTTTTTCAATCTCACTC
74258 TCTTTTTC
1 TCTTTTTC
74266 TTCTTTTGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.11, C:0.29, G:0.00, T:0.60
Consensus pattern (18 bp):
TCTTTTTCAATCTCACTC
Found at i:77721 original size:21 final size:21
Alignment explanation
Indices: 77676--77761 Score: 149
Period size: 21 Copynumber: 4.2 Consensus size: 21
77666 ATTTTCGAGG
*
77676 ATATACAATCTTAGATATG--
1 ATATGCAATCTTAGATATGAT
77695 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
77716 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
77737 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
77758 ATAT
1 ATAT
77762 ACAAATCCAA
Statistics
Matches: 64, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
19 18 0.28
21 46 0.72
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:82668 original size:21 final size:22
Alignment explanation
Indices: 82642--82700 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 22
82632 TCAATTTCAA
82642 CTCACT-TTTTCTTTTTGTTTT
1 CTCACTCTTTTCTTTTTGTTTT
*
82663 CTCACTCTTTT-TTTCT-TTTT
1 CTCACTCTTTTCTTTTTGTTTT
82683 C-CA-TCTTTTCTTTTTGTT
1 CTCACTCTTTTCTTTTTGTT
82701 CCTTTGCCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
18 6 0.18
19 6 0.18
20 7 0.21
21 10 0.30
22 4 0.12
ACGTcount: A:0.05, C:0.22, G:0.03, T:0.69
Consensus pattern (22 bp):
CTCACTCTTTTCTTTTTGTTTT
Found at i:82696 original size:20 final size:20
Alignment explanation
Indices: 82642--82700 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 20
82632 TCAATTTCAA
82642 CTCACTTTTTCTTTTTGTTTT
1 CTCAC-TTTTCTTTTTGTTTT
82663 CTCACTCTTT-TTTTCT-TTTT
1 CTCACT-TTTCTTTT-TGTTTT
82683 C-CATCTTTTCTTTTTGTT
1 CTCA-CTTTTCTTTTTGTT
82701 CCTTTGCCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
19 6 0.18
20 18 0.55
21 9 0.27
ACGTcount: A:0.05, C:0.22, G:0.03, T:0.69
Consensus pattern (20 bp):
CTCACTTTTCTTTTTGTTTT
Found at i:82702 original size:18 final size:19
Alignment explanation
Indices: 82644--82702 Score: 52
Period size: 18 Copynumber: 3.1 Consensus size: 19
82634 AATTTCAACT
82644 CACT-TTTTCTTTTTGTTTTC
1 CACTCTTTTCTTTTTG--TTC
*
82664 TCACTCTTTT-TTTCTTTTTC
1 -CACTCTTTTCTTT-TTGTTC
82684 CA-TCTTTTCTTTTTGTTC
1 CACTCTTTTCTTTTTGTTC
82702 C
1 C
82703 TTTGCCTTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
18 12 0.36
19 5 0.15
20 3 0.09
21 7 0.21
22 6 0.18
ACGTcount: A:0.05, C:0.24, G:0.03, T:0.68
Consensus pattern (19 bp):
CACTCTTTTCTTTTTGTTC
Found at i:84952 original size:21 final size:19
Alignment explanation
Indices: 84896--84957 Score: 61
Period size: 21 Copynumber: 3.1 Consensus size: 19
84886 CCGTATACAA
*
84896 TTTTCTTTTTCAATTAATTT
1 TTTTCTTTTTCAATT-TTTT
* **
84916 TTTTATTTTTTTATTTTTGAT
1 TTTTCTTTTTCAATTTTT--T
84937 TTTTCTTTTTCAATTTTTT
1 TTTTCTTTTTCAATTTTTT
84956 TT
1 TT
84958 CACGAATCTA
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
19 5 0.15
20 12 0.36
21 16 0.48
ACGTcount: A:0.15, C:0.06, G:0.02, T:0.77
Consensus pattern (19 bp):
TTTTCTTTTTCAATTTTTT
Found at i:85005 original size:17 final size:17
Alignment explanation
Indices: 84979--85020 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
84969 TTACTCCGGC
*
84979 TCTTCCCGAACGTCCGT
1 TCTTCTCGAACGTCCGT
*
84996 TCTTCTCGAATGTCCGT
1 TCTTCTCGAACGTCCGT
85013 TCTTCTCG
1 TCTTCTCG
85021 TTTTAACCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.10, C:0.36, G:0.17, T:0.38
Consensus pattern (17 bp):
TCTTCTCGAACGTCCGT
Found at i:86105 original size:11 final size:11
Alignment explanation
Indices: 86089--86140 Score: 83
Period size: 11 Copynumber: 5.0 Consensus size: 11
86079 TAGTAATTTC
86089 TTCAAAAAAAA
1 TTCAAAAAAAA
86100 TTCAAAAAAAA
1 TTCAAAAAAAA
86111 TT--AAAAAAA
1 TTCAAAAAAAA
86120 TT-AAAAAAAA
1 TTCAAAAAAAA
86130 TTCAAAAAAAA
1 TTCAAAAAAAA
86141 ATTGGTTTCC
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 21 0.54
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:86108 original size:10 final size:10
Alignment explanation
Indices: 86093--86139 Score: 69
Period size: 10 Copynumber: 4.7 Consensus size: 10
86083 AATTTCTTCA
86093 AAAAAAATTC
1 AAAAAAATTC
86103 AAAAAAAATT-
1 -AAAAAAATTC
*
86113 AAAAAAATTA
1 AAAAAAATTC
86123 AAAAAAATTC
1 AAAAAAATTC
86133 AAAAAAA
1 AAAAAAA
86140 AATTGGTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
9 9 0.26
10 16 0.47
11 9 0.26
ACGTcount: A:0.79, C:0.04, G:0.00, T:0.17
Consensus pattern (10 bp):
AAAAAAATTC
Found at i:86118 original size:19 final size:19
Alignment explanation
Indices: 86093--86139 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
86083 AATTTCTTCA
86093 AAAAAAATTCAAAAAAAATT
1 AAAAAAATT-AAAAAAAATT
86113 AAAAAAATTAAAAAAAATT
1 AAAAAAATTAAAAAAAATT
86132 CAAAAAAA
1 -AAAAAAA
86140 AATTGGTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.79, C:0.04, G:0.00, T:0.17
Consensus pattern (19 bp):
AAAAAAATTAAAAAAAATT
Found at i:86200 original size:15 final size:16
Alignment explanation
Indices: 86180--86221 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
86170 GATATCAAGT
86180 TGAAAAAAAAA-TTCG
1 TGAAAAAAAAATTTCG
86195 TGAAAAAAAAATTTCG
1 TGAAAAAAAAATTTCG
86211 TGAAAAAAAAA
1 TGAAAAAAAAA
86222 GAAGCTAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 11 0.42
16 15 0.58
ACGTcount: A:0.64, C:0.05, G:0.12, T:0.19
Consensus pattern (16 bp):
TGAAAAAAAAATTTCG
Found at i:98462 original size:20 final size:19
Alignment explanation
Indices: 98439--98503 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
98429 AAGCTCAAAC
98439 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
98459 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
98479 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
98499 GAGCT
1 GAGCT
98504 GGAAAAACTA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:99315 original size:14 final size:13
Alignment explanation
Indices: 99291--99324 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
99281 TTGTAAAGTT
99291 TTATTTTTATTTA
1 TTATTTTTATTTA
99304 TTATTATTTATTTA
1 TTATT-TTTATTTA
99318 TTTATTT
1 -TTATTT
99325 ACTTAGTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 5 0.26
14 9 0.47
15 5 0.26
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTATTTTTATTTA
Found at i:104339 original size:15 final size:15
Alignment explanation
Indices: 104319--104352 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
104309 TTTTTAAAAA
*
104319 AAAAGAGAAAGAAAG
1 AAAAGAAAAAGAAAG
104334 AAAAGAAAAAGAAAG
1 AAAAGAAAAAGAAAG
104349 AAAA
1 AAAA
104353 AGGAAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAAGAAAG
Found at i:104346 original size:19 final size:20
Alignment explanation
Indices: 104314--104351 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
104304 AAATTTTTTT
104314 AAAAAAAAAGAGAAAGAAAG
1 AAAAAAAAAGAGAAAGAAAG
*
104334 AAAAGAAAA-AGAAAGAAA
1 AAAAAAAAAGAGAAAGAAA
104352 AAGGAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAGAGAAAGAAAG
Found at i:105854 original size:132 final size:132
Alignment explanation
Indices: 105617--107077 Score: 2427
Period size: 132 Copynumber: 11.1 Consensus size: 132
105607 GTGAAACACT
* * * *
105617 AAGCCTTGTCTCCCTGAGCTGCAGTGGAGTAGGTTGAAGATTGTATATCTTATCTCTCTAAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
* * ** *
105682 TAGTAGAGAAGATTGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
66 TAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
105747 CC
131 CC
** * *
105749 AAGCCTTGTCTCCCTGAGCAGCAATGGAGTAGGCTGAAGATTGTAGATCTTATCTCCCTAAGCAA
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
*
105814 AAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
66 TAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
105879 CC
131 CC
* *
105881 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAAGCTGAAGATTGTAGATCTTATCTCCCTAAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
* * *
105946 TAGTGGAGCAGATCAAAGATGACAAATCTTATCTTTCCAAGATAGTGGGAAGTAAATTTAAGCCA
66 TAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
106011 CC
131 CC
106013 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
*
106078 TAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAAATTTAAGCCA
66 TAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
106143 CC
131 CC
* * *
106145 AAGCCTTGTCTTCCTAAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGTAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
* ** *
106210 TAGTGGACCAGATCAAAGATAACAAATCTTATCTTTCGAAGATAGTGGGAAGCAGATTTAAGCCA
66 TAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
106275 CC
131 CC
* * * *
106277 AAGCCTTGTCTCCCTGAGCTGCAGTGGAGTAGGTTGAAGATTGTATATCTTATCTCTCTAAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
* * ** *
106342 TAGTAGAGAAGATTGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
66 TAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
106407 CC
131 CC
** * *
106409 AAGCCTTGTCTCCCTGAGCAGCAATGGAGTAGGCTGAAGATTGTAGATCTTATCTCCCTAAGCAA
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
*
106474 AAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
66 TAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
*
106539 CT
131 CC
*
106541 AAGCCTTGTCTCCCTGAGCAGCAGCGGATTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
*
106606 TAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
66 TAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
106671 CC
131 CC
*
106673 AAGCCTTGTCTCCCTGAGCAGTAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
*
106738 TAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAAATTTAAGCCA
66 TAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
106803 CC
131 CC
* *
106805 AAGCCTTGTCTTCCTGAGCAACAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
* *
106870 TAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCGAAGATAGTGGGAAGCAGATTTAAGCCA
66 TAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
106935 CC
131 CC
*
106937 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATATCCCTAAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
* * *
107002 TAGGGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
66 TAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
*
107067 GC
131 CC
107069 AAGCCTTGT
1 AAGCCTTGT
107078 GATACGACCA
Statistics
Matches: 1243, Mismatches: 86, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 1243 1.00
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.26
Consensus pattern (132 bp):
AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
TAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
CC
Found at i:106635 original size:44 final size:44
Alignment explanation
Indices: 105663--107035 Score: 277
Period size: 44 Copynumber: 31.2 Consensus size: 44
105653 AAGATTGTAT
* * *
105663 ATCTTATCTCTCTAAGCAGTAGTAGAGAAGATTGAAGACGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
* * * **
105707 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACGGCAA
** * * * * * ** ** * *
105751 GCCTTGTCTCCCTGAGCAGCAATGGAGTAGGCTGAAGATTGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
** ** *
105795 ATCTTATCTCCCTAAGCAAAAGTGGAGCAGATCAAAGATGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
* * * **
105839 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACGGCAA
** * * * * * * ** * *
105883 GCCTTGTCTCCCTGAGCAGCAGCGGAGTA-AGCTGAAGATTGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGA-TTGAAGACGGCAA
** * *
105927 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGACAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
* * * * * **
105971 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGTAAATTTAAGCCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACGGCAA
** * * * * * * ** * *
106015 GCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
** *
106059 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
* * * * **
106103 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAAATTTAAGCCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACGGCAA
** * * * * * * ** * *
106147 GCCTTGTCTTCCTAAGCAGCAGCGGAGTAGGTTGAAGATTGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
* * ** ***
106191 ATCTTATCTCCCTAAGTAGTAGTGGACCAGATCAAAGATAACAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
** * * * **
106235 ATCTTATCTTTCGAAG-A-TAGTGGGAAGCAGATTTAAGCCACCAA
1 ATCTTATCTCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACGGCAA
** * * * * * * ** * *
106279 GCCTTGTCTCCCTGAGCTGCAGTGGAGTAGGTTGAAGATTGTAT
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
* * *
106323 ATCTTATCTCTCTAAGCAGTAGTAGAGAAGATTGAAGACGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
* * * **
106367 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACGGCAA
** * * * * * ** ** * *
106411 GCCTTGTCTCCCTGAGCAGCAATGGAGTAGGCTGAAGATTGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
** ** *
106455 ATCTTATCTCCCTAAGCAAAAGTGGAGCAGATCAAAGATGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
* * **
106499 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAG-CCACTAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACGGC-AA
** * * * * ** * ** * *
106543 GCCTTGTCTCCCTGAGCAGCAGCGGATTAGGTTGAAGATTGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
**
106587 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
* * * **
106631 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACGGCAA
** * * * * * ** * *
106675 GCCTTGTCTCCCTGAGCAGTAGCGGAGTAGGTTGAAGATTGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
** *
106719 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
* * * * **
106763 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAAATTTAAGCCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACGGCAA
** * * * ** * * * ** * *
106807 GCCTTGTCTTCCTGAGCAACAGCGGAGTAGGTTGAAGATTGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
**
106851 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
** * * * **
106895 ATCTTATCTTTCGAAG-A-TAGTGGGAAGCAGATTTAAGCCACCAA
1 ATCTTATCTCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACGGCAA
** * * * * * * ** * *
106939 GCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
* * *
106983 ATCTTATATCCCTAAGCAGTAGGGGAGCAGATCGAAGACGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
107027 ATCTTATCT
1 ATCTTATCT
107036 TTCCAAGATA
Statistics
Matches: 881, Mismatches: 388, Indels: 120
0.63 0.28 0.09
Matches are distributed among these distances:
42 38 0.04
43 56 0.06
44 713 0.81
45 52 0.06
46 22 0.02
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (44 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
Found at i:108864 original size:12 final size:11
Alignment explanation
Indices: 108836--108891 Score: 62
Period size: 12 Copynumber: 5.1 Consensus size: 11
108826 GTATTACGGT
*
108836 ATTGTAAAAAA
1 ATTGAAAAAAA
108847 A-T-AAAAAAA
1 ATTGAAAAAAA
108856 ACTTGAAAAAAA
1 A-TTGAAAAAAA
108868 ATTCGAAAAAAA
1 ATT-GAAAAAAA
*
108880 ATTCAAAAAAA
1 ATTGAAAAAAA
108891 A
1 A
108892 AGTTTGTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
9 7 0.18
10 1 0.03
11 12 0.31
12 19 0.49
ACGTcount: A:0.71, C:0.05, G:0.05, T:0.18
Consensus pattern (11 bp):
ATTGAAAAAAA
Found at i:108979 original size:29 final size:28
Alignment explanation
Indices: 108937--109002 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 28
108927 AGTATTGAAG
* * *
108937 AAAAAAAAGAAAAAAAATTTGGAATTAA
1 AAAAAAAAGAAAAAAAAATCGAAATTAA
*
108965 AAAAAAAAGAAAAAAAAATCGAAATTGA
1 AAAAAAAAGAAAAAAAAATCGAAATTAA
108993 AAAAAAAAGA
1 AAAAAAAAGA
109003 GTGATTGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.76, C:0.02, G:0.11, T:0.12
Consensus pattern (28 bp):
AAAAAAAAGAAAAAAAAATCGAAATTAA
Found at i:109980 original size:12 final size:12
Alignment explanation
Indices: 109963--110036 Score: 55
Period size: 12 Copynumber: 6.2 Consensus size: 12
109953 AGTGAAAAGC
109963 AAAAAGAGATTG
1 AAAAAGAGATTG
*
109975 AAAAAGAAATTG
1 AAAAAGAGATTG
109987 AAAAAGA-A--G
1 AAAAAGAGATTG
*
109996 AAAAAGAAAGAGTGG
1 AAAAAG--AGA-TTG
*
110011 AAAAAGAAATTG
1 AAAAAGAGATTG
* *
110023 AAAGAGAGCTTG
1 AAAAAGAGATTG
110035 AA
1 AA
110037 CAGAAATTGA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
9 7 0.14
11 2 0.04
12 32 0.64
13 2 0.04
15 7 0.14
ACGTcount: A:0.62, C:0.01, G:0.24, T:0.12
Consensus pattern (12 bp):
AAAAAGAGATTG
Found at i:111378 original size:20 final size:20
Alignment explanation
Indices: 111346--111400 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
111336 TGTGGTTCAA
*
111346 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
* *
111366 CTTATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
111386 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
111401 TTTAACTCGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.31
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Done.