Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold6328.1
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: 12338
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:61 original size:28 final size:26
Alignment explanation
Indices: 3--61 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
1 AC
* **
3 GAAAAAAAAGGAAAAAAAAATCGAGT
1 GAAAAAAAAGAAAAAAAAAATAAAGT
*
29 TAAAAAAAAGAAGAAAAAAAATAAAAGT
1 GAAAAAAAAGAA-AAAAAAAAT-AAAGT
57 GAAAA
1 GAAAA
62 GTCTTGTGAG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 10 0.38
27 9 0.35
28 7 0.27
ACGTcount: A:0.75, C:0.02, G:0.15, T:0.08
Consensus pattern (26 bp):
GAAAAAAAAGAAAAAAAAAATAAAGT
Found at i:993 original size:37 final size:37
Alignment explanation
Indices: 942--1012 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
932 CATTCTTGTA
942 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
979 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
1013 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:1012 original size:6 final size:6
Alignment explanation
Indices: 952--1001 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
942 AAGAGAAAAC
*
952 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
1001 A
1 A
1002 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:1094 original size:11 final size:12
Alignment explanation
Indices: 1062--1092 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
1052 TTGAGAGAAC
1062 TTGAAAAAGCCT
1 TTGAAAAAGCCT
1074 TTGAAAAAGCCT
1 TTGAAAAAGCCT
1086 TTGAAAA
1 TTGAAAA
1093 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:3164 original size:17 final size:17
Alignment explanation
Indices: 3142--3174 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
3132 CCCATTTGAT
3142 CGAGGAAAACCATGCAC
1 CGAGGAAAACCATGCAC
3159 CGAGGAAAACCATGCA
1 CGAGGAAAACCATGCA
3175 TGAGTCAAAG
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:0.42, C:0.27, G:0.24, T:0.06
Consensus pattern (17 bp):
CGAGGAAAACCATGCAC
Found at i:3443 original size:30 final size:30
Alignment explanation
Indices: 3409--3505 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
3399 AGCTCACTCC
3409 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
3439 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
3469 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
3499 TAGCTCA
1 TAGCTCA
3506 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:6395 original size:12 final size:12
Alignment explanation
Indices: 6378--6416 Score: 71
Period size: 12 Copynumber: 3.3 Consensus size: 12
6368 CAAAAAAAAA
6378 TTTTGAATTTTT
1 TTTTGAATTTTT
6390 TTTTGAA-TTTT
1 TTTTGAATTTTT
6401 TTTTGAATTTTT
1 TTTTGAATTTTT
6413 TTTT
1 TTTT
6417 CATATTTCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 11 0.42
12 15 0.58
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (12 bp):
TTTTGAATTTTT
Found at i:6400 original size:11 final size:11
Alignment explanation
Indices: 6378--6415 Score: 67
Period size: 11 Copynumber: 3.4 Consensus size: 11
6368 CAAAAAAAAA
6378 TTTTGAATTTTT
1 TTTTGAA-TTTT
6390 TTTTGAATTTT
1 TTTTGAATTTT
6401 TTTTGAATTTT
1 TTTTGAATTTT
6412 TTTT
1 TTTT
6416 TCATATTTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 19 0.73
12 7 0.27
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (11 bp):
TTTTGAATTTT
Found at i:7593 original size:57 final size:57
Alignment explanation
Indices: 7503--7616 Score: 219
Period size: 57 Copynumber: 2.0 Consensus size: 57
7493 AATGTGAACG
*
7503 CATAGGTGCTGTTTTGGGAAGTGCATCGGCCAGCTTTTGGAGAATGAATTTAGTTGC
1 CATAGGTGCTGTTTTGGGAAGTGCATCGACCAGCTTTTGGAGAATGAATTTAGTTGC
7560 CATAGGTGCTGTTTTGGGAAGTGCATCGACCAGCTTTTGGAGAATGAATTTAGTTGC
1 CATAGGTGCTGTTTTGGGAAGTGCATCGACCAGCTTTTGGAGAATGAATTTAGTTGC
7617 TCTTCTGATA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.22, C:0.14, G:0.31, T:0.33
Consensus pattern (57 bp):
CATAGGTGCTGTTTTGGGAAGTGCATCGACCAGCTTTTGGAGAATGAATTTAGTTGC
Found at i:8532 original size:13 final size:13
Alignment explanation
Indices: 8514--8538 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8504 TGGTCATCAT
8514 GGTGTGAACACAA
1 GGTGTGAACACAA
8527 GGTGTGAACACA
1 GGTGTGAACACA
8539 TGATCAATAC
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:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:9057 original size:10 final size:10
Alignment explanation
Indices: 9044--9081 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
9034 TTGTAGCTAA
9044 ATTGAGCTCG
1 ATTGAGCTCG
9054 ATTGAGCT-G
1 ATTGAGCTCG
9063 ACTTGAGCTCG
1 A-TTGAGCTCG
*
9074 AGTGAGCT
1 ATTGAGCT
9082 GGAAACGAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (10 bp):
ATTGAGCTCG
Found at i:9061 original size:20 final size:20
Alignment explanation
Indices: 9021--9081 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
9011 ACCAATAAAA
9021 TAAA-TGAGCT-GAATTGTAGC
1 TAAATTGAGCTCG-ATTG-AGC
9041 TAAATTGAGCTCGATTGAGC
1 TAAATTGAGCTCGATTGAGC
* * *
9061 TGACTTGAGCTCGAGTGAGC
1 TAAATTGAGCTCGATTGAGC
9081 T
1 T
9082 GGAAACGAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 25 0.69
21 10 0.28
22 1 0.03
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (20 bp):
TAAATTGAGCTCGATTGAGC
Found at i:9082 original size:20 final size:20
Alignment explanation
Indices: 9045--9082 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
9035 TGTAGCTAAA
*
9045 TTGAGCTCGATTGAGCTGAC
1 TTGAGCTCGAGTGAGCTGAC
9065 TTGAGCTCGAGTGAGCTG
1 TTGAGCTCGAGTGAGCTG
9083 GAAACGAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.34, T:0.29
Consensus pattern (20 bp):
TTGAGCTCGAGTGAGCTGAC
Found at i:9656 original size:60 final size:60
Alignment explanation
Indices: 9584--9699 Score: 214
Period size: 60 Copynumber: 1.9 Consensus size: 60
9574 AAAGAGCTAA
*
9584 TAATGAGCTGAATTGAATTTAAACCAAGCTCAACCGAGATGAATTAAGCTCATGTGCGCT
1 TAATGAGCTGAATTGAATTTAAACCAAGCTCAAACGAGATGAATTAAGCTCATGTGCGCT
*
9644 TAATGAGCTGAATTGAATTTAAACCAAGCTCAAACGAGCTGAATTAAGCTCATGTG
1 TAATGAGCTGAATTGAATTTAAACCAAGCTCAAACGAGATGAATTAAGCTCATGTG
9700 AGCTAAAATA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (60 bp):
TAATGAGCTGAATTGAATTTAAACCAAGCTCAAACGAGATGAATTAAGCTCATGTGCGCT
Found at i:10678 original size:29 final size:29
Alignment explanation
Indices: 10645--10704 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
10635 TGGCTGAATT
10645 AACCTTAACGAAATGAAATACGAACTTCA
1 AACCTTAACGAAATGAAATACGAACTTCA
*
10674 AACCTTAACGAAATGAAATGCGAACTTCA
1 AACCTTAACGAAATGAAATACGAACTTCA
10703 AA
1 AA
10705 TACAACCACA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.48, C:0.20, G:0.12, T:0.20
Consensus pattern (29 bp):
AACCTTAACGAAATGAAATACGAACTTCA
Found at i:11083 original size:37 final size:37
Alignment explanation
Indices: 11041--11113 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
11031 TAATTGGTGC
*
11041 ACAAAATTGTCACAAATGAAGAATTTAATCGCCTTTT
1 ACAAAATTGTCACAAATGAAAAATTTAATCGCCTTTT
11078 ACAAAATTGTCACAAATGAAAAATTTAATCGCCTTT
1 ACAAAATTGTCACAAATGAAAAATTTAATCGCCTTT
11114 CGTGAAAAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (37 bp):
ACAAAATTGTCACAAATGAAAAATTTAATCGCCTTTT
Done.