Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3828
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: 23567
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:781 original size:12 final size:13
Alignment explanation
Indices: 759--787 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
749 AAGTTTTATT
759 TTTATTTTATTTA
1 TTTATTTTATTTA
772 TTTA-TTTATTTA
1 TTTATTTTATTTA
784 TTTA
1 TTTA
788 CTTAGTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:3177 original size:13 final size:12
Alignment explanation
Indices: 3147--3202 Score: 53
Period size: 12 Copynumber: 4.7 Consensus size: 12
3137 AATGTGAAAC
*
3147 AAAAAGAAATTG
1 AAAAAGAAGTTG
3159 AAAAAGAAGTTG
1 AAAAAGAAGTTG
*
3171 AAGAAAGAAG-AG
1 AA-AAAGAAGTTG
*
3183 AAAATG-AGTTAG
1 AAAAAGAAGTT-G
3195 AAAAAGAA
1 AAAAAGAA
3203 ACAAAAGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
10 2 0.06
11 3 0.09
12 22 0.63
13 8 0.23
ACGTcount: A:0.64, C:0.00, G:0.23, T:0.12
Consensus pattern (12 bp):
AAAAAGAAGTTG
Found at i:6181 original size:34 final size:34
Alignment explanation
Indices: 6138--6213 Score: 125
Period size: 34 Copynumber: 2.2 Consensus size: 34
6128 AAATTTAAAC
*
6138 AAATTAATTACTAACACTTATTTAAGCTGAACTA
1 AAATTAATTACCAACACTTATTTAAGCTGAACTA
*
6172 AAATTAATTACCAACACTTATTTGAGCTGAACTA
1 AAATTAATTACCAACACTTATTTAAGCTGAACTA
*
6206 AAGTTAAT
1 AAATTAAT
6214 AAACTAACTC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.08, T:0.34
Consensus pattern (34 bp):
AAATTAATTACCAACACTTATTTAAGCTGAACTA
Found at i:9863 original size:12 final size:12
Alignment explanation
Indices: 9848--9872 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9838 TTTCACAAAT
9848 CTCTTCAAACGG
1 CTCTTCAAACGG
9860 CTCTTCAAACGG
1 CTCTTCAAACGG
9872 C
1 C
9873 ACAAGTATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.16, T:0.24
Consensus pattern (12 bp):
CTCTTCAAACGG
Found at i:10404 original size:19 final size:17
Alignment explanation
Indices: 10368--10406 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
10358 TCAGTTGCTG
10368 ATTAGTTAAATAAATTA
1 ATTAGTTAAATAAATTA
*
10385 ATTAGCTTAAGATTAATTA
1 ATTAG-TTAA-ATAAATTA
10404 ATT
1 ATT
10407 TAATAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 4 0.21
19 10 0.53
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (17 bp):
ATTAGTTAAATAAATTA
Found at i:15336 original size:9 final size:9
Alignment explanation
Indices: 15322--15353 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
15312 TGGTATCAGA
15322 TTTTGGGCG
1 TTTTGGGCG
15331 TTTTGGGCG
1 TTTTGGGCG
15340 TTTTGGGCG
1 TTTTGGGCG
15349 TTTTG
1 TTTTG
15354 TAAAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.00, C:0.09, G:0.41, T:0.50
Consensus pattern (9 bp):
TTTTGGGCG
Found at i:17834 original size:23 final size:22
Alignment explanation
Indices: 17782--17834 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
17772 TCCACGTCTT
*
17782 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
17804 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
17827 TTTCTTTT
1 TTTCTTTT
17835 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
Done.