Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold6317.1
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: 12384
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:2136 original size:10 final size:10
Alignment explanation
Indices: 2123--2160 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
2113 AAGAAGCTAA
2123 ATTGAGCTCG
1 ATTGAGCTCG
2133 ATTGAGCT-G
1 ATTGAGCTCG
2142 ACTTGAGCTCG
1 A-TTGAGCTCG
*
2153 AGTGAGCT
1 ATTGAGCT
2161 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:2147 original size:20 final size:20
Alignment explanation
Indices: 2124--2161 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2114 AGAAGCTAAA
*
2124 TTGAGCTCGATTGAGCTGAC
1 TTGAGCTCGAGTGAGCTGAC
2144 TTGAGCTCGAGTGAGCTG
1 TTGAGCTCGAGTGAGCTG
2162 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:3825 original size:18 final size:18
Alignment explanation
Indices: 3804--3838 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3794 TTTTTCTTTT
3804 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
3822 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
3839 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:4877 original size:14 final size:14
Alignment explanation
Indices: 4860--4922 Score: 65
Period size: 14 Copynumber: 4.3 Consensus size: 14
4850 TTTTTTTCAA
*
4860 TTTTCAATTTTTCT
1 TTTTCAATTTTTTT
*
4874 TTTTC-CTTCTTTTT
1 TTTTCAATT-TTTTT
4888 TTTTCAGATTTTTTT
1 TTTTCA-ATTTTTTT
4903 TTTTCGAACTTTTTTT
1 TTTTC-AA-TTTTTTT
4919 TTTT
1 TTTT
4923 ACGCACCTAC
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
13 2 0.05
14 14 0.34
15 11 0.27
16 14 0.34
ACGTcount: A:0.10, C:0.13, G:0.03, T:0.75
Consensus pattern (14 bp):
TTTTCAATTTTTTT
Found at i:4901 original size:15 final size:16
Alignment explanation
Indices: 4883--4922 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
4873 TTTTTCCTTC
4883 TTTTTTTTTC-AGA-TT
1 TTTTTTTTTCGA-ACTT
4898 TTTTTTTTTCGAACTT
1 TTTTTTTTTCGAACTT
4914 TTTTTTTTT
1 TTTTTTTTT
4923 ACGCACCTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.10, C:0.07, G:0.05, T:0.78
Consensus pattern (16 bp):
TTTTTTTTTCGAACTT
Found at i:4914 original size:29 final size:28
Alignment explanation
Indices: 4860--4920 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
4850 TTTTTTTCAA
**
4860 TTTTCAATTTTTCTTTTTCCTTCTTTTT
1 TTTTCAATTTTTCTTTTTCCAACTTTTT
* *
4888 TTTTCAGATTTTTTTTTTTCGAACTTTTT
1 TTTTCA-ATTTTTCTTTTTCCAACTTTTT
4917 TTTT
1 TTTT
4921 TTACGCACCT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 6 0.21
29 22 0.79
ACGTcount: A:0.10, C:0.13, G:0.03, T:0.74
Consensus pattern (28 bp):
TTTTCAATTTTTCTTTTTCCAACTTTTT
Found at i:4915 original size:16 final size:15
Alignment explanation
Indices: 4883--4922 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 15
4873 TTTTTCCTTC
4883 TTTTTTTTTCAGATT
1 TTTTTTTTTCAGATT
4898 TTTTTTTTTC-GAACTT
1 TTTTTTTTTCAG-A-TT
4914 TTTTTTTTT
1 TTTTTTTTT
4923 ACGCACCTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 1 0.04
15 11 0.48
16 11 0.48
ACGTcount: A:0.10, C:0.07, G:0.05, T:0.78
Consensus pattern (15 bp):
TTTTTTTTTCAGATT
Found at i:6224 original size:28 final size:28
Alignment explanation
Indices: 6184--6242 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
6174 TAATTCAGCC
6184 AAATCAAGACATA-TTAAACA-CTTGTAAT
1 AAATCAAGACATATTTAAA-AGC-TGTAAT
*
6212 AAATTAAGACATATTTAAAAGCTGTAAT
1 AAATCAAGACATATTTAAAAGCTGTAAT
6240 AAA
1 AAA
6243 ACTTATTTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 22 0.79
29 6 0.21
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.29
Consensus pattern (28 bp):
AAATCAAGACATATTTAAAAGCTGTAAT
Found at i:8457 original size:20 final size:20
Alignment explanation
Indices: 8432--8486 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
8422 TGTGGTTCAA
*
8432 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
8452 CTCATTCGTA-CTCAAGTCAG
1 CTCATTCG-AGCTCAAGTCAG
*
8472 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
8487 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:10523 original size:11 final size:11
Alignment explanation
Indices: 10474--10523 Score: 59
Period size: 11 Copynumber: 4.6 Consensus size: 11
10464 ACGGTATTGT
10474 AAAAAAA-T-A
1 AAAAAAATTCA
*
10483 AAAAAAACTTGA
1 AAAAAAA-TTCA
*
10495 AAAAAAATTCG
1 AAAAAAATTCA
10506 AAAAAAATTCA
1 AAAAAAATTCA
10517 AAAAAAA
1 AAAAAAA
10524 GTTTGTATTC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
9 7 0.20
11 20 0.57
12 8 0.23
ACGTcount: A:0.76, C:0.06, G:0.04, T:0.14
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:11512 original size:15 final size:16
Alignment explanation
Indices: 11492--11522 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
11482 GAAAATGAAC
11492 ATGAAAAAGAA-ATGA
1 ATGAAAAAGAAGATGA
11507 ATGAAAAAGAAGATGA
1 ATGAAAAAGAAGATGA
11523 GTGGGAGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.65, C:0.00, G:0.23, T:0.13
Consensus pattern (16 bp):
ATGAAAAAGAAGATGA
Done.