Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold832
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: 18140
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Found at i:161 original size:31 final size:31
Alignment explanation
Indices: 121--189 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
111 AATATGTTCC
*
121 AACAAATCTTATCTCCCTAAAGTTACAGTGG
1 AACAGATCTTATCTCCCTAAAGTTACAGTGG
* * **
152 AGCAGATCTTATTTCCCTAAAGTTGTAGTGG
1 AACAGATCTTATCTCCCTAAAGTTACAGTGG
183 AACAGAT
1 AACAGAT
190 TAAAGCTACG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Consensus pattern (31 bp):
AACAGATCTTATCTCCCTAAAGTTACAGTGG
Found at i:1968 original size:27 final size:27
Alignment explanation
Indices: 1937--2114 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
1927 TAAATTGTAC
1937 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
1964 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
1990 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
2018 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
2046 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
2073 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
2100 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
2115 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:2051 original size:82 final size:81
Alignment explanation
Indices: 1938--2093 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
1928 AAATTGTACA
* *
1938 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
2002 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
2019 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
2084 TGCGAGTTGA
65 TGCGAATTGA
2094 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:2105 original size:82 final size:81
Alignment explanation
Indices: 1934--2114 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
1924 GATTAAATTG
* *
1934 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
1999 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
2015 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
2079 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
2097 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
2115 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:10010 original size:27 final size:27
Alignment explanation
Indices: 9979--10156 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
9969 TAAATTGTAC
9979 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
10006 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
10032 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
10060 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
10088 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
10115 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
10142 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
10157 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:10093 original size:82 final size:81
Alignment explanation
Indices: 9980--10135 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
9970 AAATTGTACA
* *
9980 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
10044 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
10061 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
10126 TGCGAGTTGA
65 TGCGAATTGA
10136 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:10147 original size:82 final size:81
Alignment explanation
Indices: 9976--10156 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
9966 GATTAAATTG
* *
9976 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
10041 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
10057 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
10121 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
10139 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
10157 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:16261 original size:40 final size:40
Alignment explanation
Indices: 16217--16411 Score: 263
Period size: 40 Copynumber: 4.9 Consensus size: 40
16207 GCATATAGCT
* *
16217 ACTCGCTCAAATGCCTTCGGGACATAGCCCGGTTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
* *
16257 ACTCGCACCAATGCCTTCGGGACTTAGCCCGGATT-TGGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG-TTATAGTA
* *
16297 ACTCGCACAAATGCCTTTGGGACTTAGCCCGG-AATTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTA
* *
16337 ACTCGGACAAATGCCTTC-GGACTTAGCCCGGATT-TGGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG-TTATAGTA
16376 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
16412 CATCCGAATA
Statistics
Matches: 135, Mismatches: 13, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
39 36 0.27
40 97 0.72
41 2 0.01
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.25
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
Found at i:16398 original size:79 final size:80
Alignment explanation
Indices: 16217--16407 Score: 305
Period size: 79 Copynumber: 2.4 Consensus size: 80
16207 GCATATAGCT
* * * *
16217 ACTCGCTCAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACCAATGCCTTCGGGACTT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTT
16282 AGCCCGGATTTGGTA
66 AGCCCGGATTTGGTA
* *
16297 ACTCGCACAAATGCCTTTGGGACTTAGCCCGGA-ATTAGTAACTCGGACAAATGCCTTC-GGACT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGACT
16360 TAGCCCGGATTTGGTA
65 TAGCCCGGATTTGGTA
16376 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
16408 TTATCATCCG
Statistics
Matches: 103, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
79 53 0.51
80 50 0.49
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (80 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTT
AGCCCGGATTTGGTA
Found at i:17595 original size:13 final size:13
Alignment explanation
Indices: 17571--17613 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
17561 ATTAAGAAAG
17571 GGAAAAAAAAGG-
1 GGAAAAAAAAGGA
17583 GGAAAAGAAAAGGAA
1 GGAAAA-AAAAGG-A
*
17598 GGAAGAAAAAGGA
1 GGAAAAAAAAGGA
17611 GGA
1 GGA
17614 GAAAGAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 6 0.22
13 10 0.37
14 6 0.22
15 5 0.19
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (13 bp):
GGAAAAAAAAGGA
Found at i:17607 original size:19 final size:18
Alignment explanation
Indices: 17584--17657 Score: 64
Period size: 19 Copynumber: 4.2 Consensus size: 18
17574 AAAAAAAGGG
*
17584 GAAAAGAAAAGGAAGGAA
1 GAAAAAAAAAGGAAGGAA
** *
17602 G-AAAAAGGAGG-AGAAA
1 GAAAAAAAAAGGAAGGAA
*
17618 G-AAAAAAGAGAGAAGGAA
1 GAAAAAAAAAG-GAAGGAA
17636 GAAAAAAAAAGGAGAGGAA
1 GAAAAAAAAAGGA-AGGAA
17655 GAA
1 GAA
17658 GGAAAGAAAG
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
16 13 0.29
17 8 0.18
18 8 0.18
19 16 0.36
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (18 bp):
GAAAAAAAAAGGAAGGAA
Found at i:17630 original size:15 final size:16
Alignment explanation
Indices: 17600--17642 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
17590 AAAAGGAAGG
*
17600 AAGAAAAAGGAGGAGA
1 AAGAAAAAAGAGGAGA
*
17616 AAGAAAAAAGAGAGAAGG
1 AAGAAAAAAGAG-G-AGA
17634 AAGAAAAAA
1 AAGAAAAAA
17643 AAAGGAGAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 11 0.48
17 1 0.04
18 11 0.48
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (16 bp):
AAGAAAAAAGAGGAGA
Found at i:17634 original size:38 final size:37
Alignment explanation
Indices: 17584--17820 Score: 116
Period size: 38 Copynumber: 6.2 Consensus size: 37
17574 AAAAAAAGGG
17584 GAAAAGAA-AAGGAAGGAAGAAAAAGGAGGAGAAAGAA
1 GAAAAGAAGAAGGAAGGAAGAAAAAGGA-GAGAAAGAA
* * *
17621 -AAAAGAGAGAAGGAAGAAAAAAAAAGGAGAGGAAGAA
1 GAAAAGA-AGAAGGAAGGAAGAAAAAGGAGAGAAAGAA
* * * *
17658 GGAAAGAAAGAAGGGAGGGAGAAGAAGGAAGCAGGGAAAGAA
1 GAAAAG-AAGAAGGAAGGAAGAAAAAGG-AG-A--GAAAGAA
* * *
17700 -AAAGGAAGAAAGGAA-AAAGAGAAAGAGAGAGAAAGAA
1 GAAAAGAAG-AAGGAAGGAAGAAAAAG-GAGAGAAAGAA
* * * * *
17737 GAAGAA-AAAAAGAAAAGGAAGAAAATGAGAAATGGAAG-A
1 GAA-AAGAAGAAG-GAAGGAAGAAAAAG-GAGA-GAAAGAA
*
17776 GAATAAGAAGAA-AAGAGGAA-AAAAA-GAGAGGAAAGAA
1 GAA-AAGAAGAAGGA-AGGAAGAAAAAGGAGA-GAAAGAA
17813 -AAAAGAAG
1 GAAAAGAAG
17821 GGGACAGAAG
Statistics
Matches: 151, Mismatches: 31, Indels: 38
0.69 0.14 0.17
Matches are distributed among these distances:
35 6 0.04
36 15 0.10
37 20 0.13
38 48 0.32
39 27 0.18
40 20 0.13
41 9 0.06
42 6 0.04
ACGTcount: A:0.65, C:0.00, G:0.34, T:0.01
Consensus pattern (37 bp):
GAAAAGAAGAAGGAAGGAAGAAAAAGGAGAGAAAGAA
Found at i:17640 original size:16 final size:18
Alignment explanation
Indices: 17595--17640 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 18
17585 AAAAGAAAAG
17595 GAAGGAAGAAAAAGGAGGA
1 GAAGGAAG-AAAAGGAGGA
*
17614 GAAAGAA-AAAA-GA-GA
1 GAAGGAAGAAAAGGAGGA
17629 GAAGGAAGAAAA
1 GAAGGAAGAAAA
17641 AAAAAGGAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
15 8 0.33
16 6 0.25
17 4 0.17
19 6 0.25
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (18 bp):
GAAGGAAGAAAAGGAGGA
Found at i:17644 original size:22 final size:20
Alignment explanation
Indices: 17609--17657 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
17599 GAAGAAAAAG
*
17609 GAGG-AGAAAGAAAAAAGAGA
1 GAGGAAGAAAAAAAAAAG-GA
17629 GAAGGAAG-AAAAAAAAAGGA
1 G-AGGAAGAAAAAAAAAAGGA
17649 GAGGAAGAA
1 GAGGAAGAA
17658 GGAAAGAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
19 6 0.24
20 5 0.20
21 12 0.48
22 2 0.08
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (20 bp):
GAGGAAGAAAAAAAAAAGGA
Found at i:17661 original size:26 final size:27
Alignment explanation
Indices: 17624--17688 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 27
17614 GAAAGAAAAA
17624 AGAG-AGAAGGAAGAAAAAAAAAGGAG
1 AGAGAAGAAGGAAGAAAAAAAAAGGAG
* * *
17650 AG-GAAGAAGGAA-AGAAAGAAGGGAG
1 AGAGAAGAAGGAAGAAAAAAAAAGGAG
*
17675 GGAGAAGAAGGAAG
1 AGAGAAGAAGGAAG
17689 CAGGGAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
25 12 0.38
26 20 0.62
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (27 bp):
AGAGAAGAAGGAAGAAAAAAAAAGGAG
Found at i:17757 original size:17 final size:17
Alignment explanation
Indices: 17737--17816 Score: 65
Period size: 17 Copynumber: 4.6 Consensus size: 17
17727 AGAGAAAGAA
17737 GAAGAAAAAAAGAAAAG
1 GAAGAAAAAAAGAAAAG
** *
17754 GAAGAAAATGAGAAATG
1 GAAGAAAAAAAGAAAAG
17771 GAAGAGAATAAGAAGAAAA-
1 GAAGA-AA-AA-AAGAAAAG
* *
17790 GAGGAAAAAAAG-AGAG
1 GAAGAAAAAAAGAAAAG
17806 GAAAGAAAAAA
1 G-AAGAAAAAA
17817 GAAGGGGACA
Statistics
Matches: 49, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
15 2 0.04
16 4 0.08
17 29 0.59
18 4 0.08
19 5 0.10
20 5 0.10
ACGTcount: A:0.69, C:0.00, G:0.28, T:0.04
Consensus pattern (17 bp):
GAAGAAAAAAAGAAAAG
Found at i:17854 original size:16 final size:16
Alignment explanation
Indices: 17833--17867 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
17823 GACAGAAGAG
17833 AGGGAGGAG-GAGAGAA
1 AGGGAGGAGAG-GAGAA
17849 AGGGAGGAGAGGAGAA
1 AGGGAGGAGAGGAGAA
17865 AGG
1 AGG
17868 AAAAAGCGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 17 0.94
17 1 0.06
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (16 bp):
AGGGAGGAGAGGAGAA
Done.