Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold317
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: 33873
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:2255 original size:23 final size:22
Alignment explanation
Indices: 2203--2255 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
2193 TCCACGTCTT
*
2203 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
2225 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
2248 TTTCTTTT
1 TTTCTTTT
2256 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:10740 original size:11 final size:10
Alignment explanation
Indices: 10715--10775 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
10705 ACCAATAAAA
10715 TAAA-TGAGC
1 TAAATTGAGC
*
10724 TGAATTGTAGC
1 TAAATTG-AGC
10735 TAAATTGAGC
1 TAAATTGAGC
**
10745 TCGATTGAGC
1 TAAATTGAGC
10755 TGAAA-TGAGC
1 T-AAATTGAGC
*
10765 TCAATTGAGC
1 TAAATTGAGC
10775 T
1 T
10776 GGTCGAAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:10776 original size:20 final size:20
Alignment explanation
Indices: 10716--10776 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
10706 CCAATAAAAT
*
10716 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
10736 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
10757 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
10777 GTCGAAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:14753 original size:12 final size:11
Alignment explanation
Indices: 14722--14752 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
14712 CAAAAATTTT
14722 ATTTTTTTTGA
1 ATTTTTTTTGA
14733 ATTTTTTTTGA
1 ATTTTTTTTGA
14744 ATTTTTTTT
1 ATTTTTTTT
14753 TCAAATTTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.77
Consensus pattern (11 bp):
ATTTTTTTTGA
Found at i:15988 original size:22 final size:22
Alignment explanation
Indices: 15958--16001 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
15948 TTTGGTATTT
15958 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
15980 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
16002 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:22070 original size:18 final size:18
Alignment explanation
Indices: 22049--22083 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
22039 TTTTTCTTTT
22049 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
22067 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
22084 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
Done.