Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2574
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: 63210
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:6528 original size:23 final size:22
Alignment explanation
Indices: 6476--6528 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
6466 TCCACGTCTT
*
6476 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
6498 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
6521 TTTCTTTT
1 TTTCTTTT
6529 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:8005 original size:20 final size:20
Alignment explanation
Indices: 7959--8005 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
7949 AGCTCGTTTC
*
7959 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
7979 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
7999 CAGCTCA
1 CAGCTCA
8006 AGCTCAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:8007 original size:16 final size:16
Alignment explanation
Indices: 7970--8014 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
7960 AGCTCACTCG
*
7970 AGCTCAAG-TCAACTC
1 AGCTCAAGCTCAATTC
7985 A-CTCAAGCTCAATTC
1 AGCTCAAGCTCAATTC
8000 AGCTCAAGCTCAATT
1 AGCTCAAGCTCAATT
8015 TAACCCAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 6 0.22
15 8 0.30
16 13 0.48
ACGTcount: A:0.33, C:0.31, G:0.11, T:0.24
Consensus pattern (16 bp):
AGCTCAAGCTCAATTC
Found at i:15053 original size:22 final size:21
Alignment explanation
Indices: 15022--15072 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
15012 ACCTCTTTGA
15022 ACCATTACCAATTCGTACCAAAT
1 ACCA-TACCAATTCGTACC-AAT
*
15045 ACCATACCATTTCGTACCAAT
1 ACCATACCAATTCGTACCAAT
*
15066 TCCATAC
1 ACCATAC
15073 TATTTCAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 9 0.35
22 13 0.50
23 4 0.15
ACGTcount: A:0.35, C:0.33, G:0.04, T:0.27
Consensus pattern (21 bp):
ACCATACCAATTCGTACCAAT
Found at i:15072 original size:21 final size:21
Alignment explanation
Indices: 15027--15089 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
15017 TTTGAACCAT
* *
15027 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
15049 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* **
15070 TACTATTTCAAACCAATTCC
1 TACCATTTCGTACCAATTCC
15090 CAAATACCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 23 0.64
22 13 0.36
ACGTcount: A:0.35, C:0.32, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:15441 original size:17 final size:16
Alignment explanation
Indices: 15420--15460 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
15410 AGTCAAAATC
*
15420 GAAAAAAAATTGAAAG
1 GAAAAAAAATTGAAAA
15436 GAAAAAAAATTGAAAA
1 GAAAAAAAATTGAAAA
15452 GAAAAAAAA
1 GAAAAAAAA
15461 ATTGCATACG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.10
Consensus pattern (16 bp):
GAAAAAAAATTGAAAA
Found at i:15461 original size:17 final size:16
Alignment explanation
Indices: 15421--15464 Score: 70
Period size: 17 Copynumber: 2.7 Consensus size: 16
15411 GTCAAAATCG
*
15421 AAAAAAAATTGAAAGG
1 AAAAAAAATTGAAAGA
15437 AAAAAAAATTGAAAAGA
1 AAAAAAAATTG-AAAGA
15454 AAAAAAAATTG
1 AAAAAAAATTG
15465 CATACGGTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 11 0.42
17 15 0.58
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (16 bp):
AAAAAAAATTGAAAGA
Found at i:17695 original size:20 final size:20
Alignment explanation
Indices: 17670--17714 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
17660 GCGAAAATAC
*
17670 AAAAGAAAAGAAAAATGAAA
1 AAAAGAAAAGAAAAATCAAA
*
17690 AAAAG-AAAGAAAATTCAAA
1 AAAAGAAAAGAAAAATCAAA
17709 AAAAGA
1 AAAAGA
17715 GAATGAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.78, C:0.02, G:0.13, T:0.07
Consensus pattern (20 bp):
AAAAGAAAAGAAAAATCAAA
Found at i:29441 original size:4 final size:4
Alignment explanation
Indices: 29432--29468 Score: 56
Period size: 4 Copynumber: 9.0 Consensus size: 4
29422 AAATTACTAG
*
29432 TAAA TAAA TAAA TAAA TAAA TAAA TAATA AAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAA-A TAAA TAAA
29469 ACTTTACAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 27 0.90
5 3 0.10
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:35064 original size:30 final size:30
Alignment explanation
Indices: 35030--35115 Score: 102
Period size: 30 Copynumber: 2.9 Consensus size: 30
35020 GCTCACTCCT
35030 AGCTCATA-TTTAGCTCACGAGCTAAACCTC
1 AGCTCA-ACTTTAGCTCACGAGCTAAACCTC
* * * * * *
35060 AGCTCAACTTCAGCTTAGGAGTTTAGCCTC
1 AGCTCAACTTTAGCTCACGAGCTAAACCTC
35090 AGCTCAACTTTAGCTCACGAGCTAAA
1 AGCTCAACTTTAGCTCACGAGCTAAA
35116 GCGTAGCTCA
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
29 1 0.02
30 42 0.98
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (30 bp):
AGCTCAACTTTAGCTCACGAGCTAAACCTC
Found at i:35124 original size:30 final size:31
Alignment explanation
Indices: 35030--35125 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
35020 GCTCACTCCT
35030 AGCTCATA-TTTAGCTCACGAGCTAAA-CCTC
1 AGCTCA-ACTTTAGCTCACGAGCTAAAGCCTC
* * * **
35060 AGCTCAACTTCAGCTTAGGAG-TTTAGCCTC
1 AGCTCAACTTTAGCTCACGAGCTAAAGCCTC
*
35090 AGCTCAACTTTAGCTCACGAGCTAAAGCGT-
1 AGCTCAACTTTAGCTCACGAGCTAAAGCCTC
35120 AGCTCA
1 AGCTCA
35126 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
29 3 0.06
30 44 0.85
31 5 0.10
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (31 bp):
AGCTCAACTTTAGCTCACGAGCTAAAGCCTC
Found at i:36127 original size:4 final size:4
Alignment explanation
Indices: 36118--36151 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
36108 GTTGTAAAGT
36118 TTTA TTTA -TT- TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
36152 CTTAGTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 4 0.14
4 24 0.86
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:42564 original size:20 final size:20
Alignment explanation
Indices: 42539--42593 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
42529 ACGAGTTAAA
* *
42539 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
42559 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
42579 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
42594 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:44049 original size:20 final size:20
Alignment explanation
Indices: 44026--44071 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
44016 CCAGCTCGAA
*
44026 TTAGCTCACATGAGCTTAAT
1 TTAGCTCACATGAGCTCAAT
***
44046 TTAGCTCGTTTGAGCTCAAT
1 TTAGCTCACATGAGCTCAAT
44066 TTAGCT
1 TTAGCT
44072 TACTTTAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (20 bp):
TTAGCTCACATGAGCTCAAT
Found at i:44053 original size:30 final size:30
Alignment explanation
Indices: 44018--44091 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
44008 AGTTTTTCCC
44018 AGCTCGAATT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-ATTGAGCTCA-ATTGAGCTTAATTT
* * *
44048 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGATTGAGCTCAATTGAGCTTAATTT
*
44078 AGCTCGTTTGAGCT
1 AGCTCGATTGAGCT
44092 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 3 0.08
30 36 0.92
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCGATTGAGCTCAATTGAGCTTAATTT
Found at i:45689 original size:10 final size:12
Alignment explanation
Indices: 45674--45745 Score: 53
Period size: 11 Copynumber: 6.0 Consensus size: 12
45664 TTGGAGTAAC
45674 AAAAAAA-TC-A
1 AAAAAAATTCGA
45684 AAAAAAATTCGAA
1 AAAAAAATTCG-A
*
45697 AAAAAAATTGATTGA
1 AAAAAAA-T--TCGA
45712 AAAAAAATTC-A
1 AAAAAAATTCGA
*
45723 AAAAAAAGT-GA
1 AAAAAAATTCGA
*
45734 AAAAAAAATCGA
1 AAAAAAATTCGA
45746 GCAAAAAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
10 7 0.14
11 20 0.40
12 3 0.06
13 8 0.16
14 2 0.04
15 8 0.16
16 2 0.04
ACGTcount: A:0.71, C:0.06, G:0.08, T:0.15
Consensus pattern (12 bp):
AAAAAAATTCGA
Found at i:45699 original size:13 final size:13
Alignment explanation
Indices: 45683--45755 Score: 57
Period size: 12 Copynumber: 5.6 Consensus size: 13
45673 CAAAAAAATC
45683 AAAAAAAATTCGA
1 AAAAAAAATTCGA
45696 AAAAAAAATT-GA
1 AAAAAAAATTCGA
45708 TTGAAAAAAAATTC--
1 ---AAAAAAAATTCGA
*
45722 AAAAAAAAGT-GA
1 AAAAAAAATTCGA
45734 AAAAAAAA-TCGA
1 AAAAAAAATTCGA
45746 GCAAAAAAAA
1 --AAAAAAAA
45756 AAGAAAAAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 17
0.74 0.01 0.25
Matches are distributed among these distances:
11 10 0.20
12 12 0.24
13 10 0.20
14 8 0.16
15 10 0.20
ACGTcount: A:0.71, C:0.05, G:0.10, T:0.14
Consensus pattern (13 bp):
AAAAAAAATTCGA
Found at i:45750 original size:26 final size:26
Alignment explanation
Indices: 45721--45782 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
45711 AAAAAAAATT
**
45721 CAAAAAAAAGTGAAAAAAAA-ATCGAG
1 CAAAAAAAAAAGAAAAAAAAGAT-GAG
*
45747 CAAAAAAAAAAGAAAAAAAAGGTGAG
1 CAAAAAAAAAAGAAAAAAAAGATGAG
45773 CAAAAAAAAA
1 CAAAAAAAAA
45783 TCAAGTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
26 31 0.97
27 1 0.03
ACGTcount: A:0.74, C:0.06, G:0.15, T:0.05
Consensus pattern (26 bp):
CAAAAAAAAAAGAAAAAAAAGATGAG
Found at i:45753 original size:38 final size:38
Alignment explanation
Indices: 45674--45767 Score: 111
Period size: 37 Copynumber: 2.5 Consensus size: 38
45664 TTGGAGTAAC
* *
45674 AAAAAAATCAAAAAAAATTCGAAAAAAAAATTGATTG-AA
1 AAAAAAATCAAAAAAAAGTCGAAAAAAAAATCGA--GCAA
*
45713 AAAAAATTCAAAAAAAAGT-GAAAAAAAAATCGAGCAA
1 AAAAAAATCAAAAAAAAGTCGAAAAAAAAATCGAGCAA
**
45750 AAAAAAAAGAAAAAAAAG
1 AAAAAAATCAAAAAAAAG
45768 GTGAGCAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
36 1 0.02
37 17 0.35
38 13 0.27
39 17 0.35
ACGTcount: A:0.73, C:0.05, G:0.10, T:0.12
Consensus pattern (38 bp):
AAAAAAATCAAAAAAAAGTCGAAAAAAAAATCGAGCAA
Found at i:45754 original size:39 final size:38
Alignment explanation
Indices: 45674--45767 Score: 102
Period size: 38 Copynumber: 2.5 Consensus size: 38
45664 TTGGAGTAAC
* * **
45674 AAAAAAATCAAAAAAAATTCGAAAAAAAAATTGATTGAA
1 AAAAAAATCAAAAAAAAGTCGAAAAAAAAATCGA-CAAA
*
45713 AAAAAATTCAAAAAAAAGT-GAAAAAAAAATCGAGCAAA
1 AAAAAAATCAAAAAAAAGTCGAAAAAAAAATCGA-CAAA
*
45751 AAAAAAA-GAAAAAAAAG
1 AAAAAAATCAAAAAAAAG
45768 GTGAGCAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
37 9 0.19
38 21 0.45
39 17 0.36
ACGTcount: A:0.73, C:0.05, G:0.10, T:0.12
Consensus pattern (38 bp):
AAAAAAATCAAAAAAAAGTCGAAAAAAAAATCGACAAA
Found at i:46862 original size:6 final size:6
Alignment explanation
Indices: 46815--46920 Score: 56
Period size: 6 Copynumber: 17.7 Consensus size: 6
46805 AAAGAAATTG
* * ** *
46815 AAAG-A AAACAA AAA-AA AACG-A AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
46860 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
46911 AAAGAA AAAG
1 AAAGAA AAAG
46921 CGAAAAAAGA
Statistics
Matches: 72, Mismatches: 23, Indels: 11
0.68 0.22 0.10
Matches are distributed among these distances:
5 11 0.15
6 50 0.69
7 7 0.10
8 4 0.06
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:46874 original size:18 final size:18
Alignment explanation
Indices: 46804--46875 Score: 65
Period size: 18 Copynumber: 3.9 Consensus size: 18
46794 AAAGAGATTG
* *
46804 AAAAGAAATTGAAAGAAAA
1 AAAAGAAATCGAAA-AAGA
* *
46823 CAAAAAAAAACG-AAAAGA
1 -AAAAGAAATCGAAAAAGA
* *
46841 AAAAGAAATTGCAAAAGA
1 AAAAGAAATCGAAAAAGA
46859 AAAAGAAATCGAAAAAG
1 AAAAGAAATCGAAAAAG
46876 TGAGAGAAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
17 8 0.19
18 24 0.57
19 2 0.05
20 8 0.19
ACGTcount: A:0.72, C:0.06, G:0.15, T:0.07
Consensus pattern (18 bp):
AAAAGAAATCGAAAAAGA
Found at i:46902 original size:14 final size:13
Alignment explanation
Indices: 46881--46918 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
46871 AAAAGTGAGA
46881 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
46893 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
46908 GAAAAAGAAAA
1 GAAAAAGAAAA
46919 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:46932 original size:21 final size:21
Alignment explanation
Indices: 46882--46932 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
46872 AAAGTGAGAG
*
46882 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
46903 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
46924 AAAAAGAAA
1 AAAAAGAAA
46933 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:46972 original size:33 final size:33
Alignment explanation
Indices: 46935--46997 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
46925 AAAAGAAATT
46935 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
46968 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
46998 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:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:53557 original size:20 final size:20
Alignment explanation
Indices: 53534--53579 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
53524 CCAGCTCGAA
*
53534 TTAGCTCACATGAGCTTAAT
1 TTAGCTCACATGAGCTCAAT
***
53554 TTAGCTCGTTTGAGCTCAAT
1 TTAGCTCACATGAGCTCAAT
53574 TTAGCT
1 TTAGCT
53580 TACTTTAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (20 bp):
TTAGCTCACATGAGCTCAAT
Found at i:53561 original size:30 final size:30
Alignment explanation
Indices: 53526--53599 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
53516 AGTTTTTCCC
53526 AGCTCGAATT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-ATTGAGCTCA-ATTGAGCTTAATTT
* * *
53556 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGATTGAGCTCAATTGAGCTTAATTT
*
53586 AGCTCGTTTGAGCT
1 AGCTCGATTGAGCT
53600 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 3 0.08
30 36 0.92
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCGATTGAGCTCAATTGAGCTTAATTT
Found at i:61378 original size:11 final size:11
Alignment explanation
Indices: 61364--61393 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
61354 CAGCTCGGGT
61364 CCAGCTCACTA
1 CCAGCTCACTA
61375 CCAGCTCACTA
1 CCAGCTCACTA
61386 CCAGCTCA
1 CCAGCTCA
61394 TGGGTCCAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.27, C:0.47, G:0.10, T:0.17
Consensus pattern (11 bp):
CCAGCTCACTA
Found at i:63030 original size:26 final size:26
Alignment explanation
Indices: 63001--63050 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
62991 TTATAATATG
* *
63001 AAAAATGACTATTTTAC-CCCTAGGT
1 AAAAATGACCATTATACACCCTAGGT
63026 AAAAATGACCATTATACACCCTAGG
1 AAAAATGACCATTATACACCCTAGG
63051 GTTTAATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.40, C:0.22, G:0.12, T:0.26
Consensus pattern (26 bp):
AAAAATGACCATTATACACCCTAGGT
Found at i:63116 original size:11 final size:11
Alignment explanation
Indices: 63087--63139 Score: 56
Period size: 11 Copynumber: 5.0 Consensus size: 11
63077 ATATTGTTAT
63087 ACATGATATG-
1 ACATGATATGC
*
63097 ACATAATATGC
1 ACATGATATGC
63108 ACATGATATG-
1 ACATGATATGC
** *
63118 TTATGAGATGC
1 ACATGATATGC
63129 ACATGATATGC
1 ACATGATATGC
63140 TATGATATTA
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
10 16 0.48
11 17 0.52
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (11 bp):
ACATGATATGC
Found at i:63143 original size:21 final size:21
Alignment explanation
Indices: 63087--63144 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
63077 ATATTGTTAT
* *
63087 ACATGATATGAC-ATAATATGC
1 ACATGATATG-CTATGAGATGC
*
63108 ACATGATATGTTATGAGATGC
1 ACATGATATGCTATGAGATGC
63129 ACATGATATGCTATGA
1 ACATGATATGCTATGA
63145 TATTACTCAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (21 bp):
ACATGATATGCTATGAGATGC
Done.