Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold847
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: 16123
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.37
Found at i:4396 original size:2 final size:2
Alignment explanation
Indices: 4389--4429 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
4379 GAGCTTTAAA
*
4389 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
4430 TAACTGTGAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5120 original size:2 final size:2
Alignment explanation
Indices: 5113--5139 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5103 ATTAAAACAT
5113 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
5140 TTGCATTGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5583 original size:13 final size:13
Alignment explanation
Indices: 5567--5605 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
5557 TTTTATATAT
*
5567 TTTTATGATTAAA
1 TTTTATTATTAAA
*
5580 TTTTATTA-AAAA
1 TTTTATTATTAAA
5592 TTTTATTATTAAA
1 TTTTATTATTAAA
5605 T
1 T
5606 AGTAATTCGG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (13 bp):
TTTTATTATTAAA
Found at i:7184 original size:15 final size:15
Alignment explanation
Indices: 7160--7190 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
7150 ATTTGAATAA
*
7160 ATTTTTTTAAAAAAT
1 ATTTTATTAAAAAAT
7175 ATTTTATTAAAAAAT
1 ATTTTATTAAAAAAT
7190 A
1 A
7191 ATATAGAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTTTATTAAAAAAT
Found at i:9607 original size:8 final size:8
Alignment explanation
Indices: 9594--9619 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
9584 CAAAATACAT
9594 AAAAAATA
1 AAAAAATA
9602 AAAAAATA
1 AAAAAATA
9610 AAAAAATA
1 AAAAAATA
9618 AA
1 AA
9620 TAATACTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAAATA
Found at i:11706 original size:5 final size:5
Alignment explanation
Indices: 11684--11774 Score: 51
Period size: 5 Copynumber: 17.8 Consensus size: 5
11674 TAATTTTTTA
** *
11684 AAAAG AAAA- AAATC AAAAG AAAAG GAAAG AGAAAG AAAAAG AAAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG A-AAAG -AAAAG -AAAAG
* * * * * *
11731 AAAAG TACAG -TAAG TAAAG AAAAA AAAAG AAAAT AAATAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA-AG AAAA
11775 AAATTATGTA
Statistics
Matches: 66, Mismatches: 15, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
4 5 0.08
5 42 0.64
6 18 0.27
7 1 0.02
ACGTcount: A:0.75, C:0.02, G:0.16, T:0.07
Consensus pattern (5 bp):
AAAAG
Found at i:11720 original size:16 final size:16
Alignment explanation
Indices: 11699--11733 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
11689 AAAAAAATCA
* *
11699 AAAGAAAAGGAAAGAG
1 AAAGAAAAAGAAAAAG
11715 AAAGAAAAAGAAAAAG
1 AAAGAAAAAGAAAAAG
11731 AAA
1 AAA
11734 AGTACAGTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAGAAAAAG
Found at i:11855 original size:28 final size:30
Alignment explanation
Indices: 11799--11855 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 30
11789 TTTCATGTTA
* **
11799 TTTTTATGTTTAAAAAAAATTGTGTATTTT
1 TTTTTATGTTTAAAAAAAATTATAAATTTT
11829 TTTTTATG-TT-AAAAAAATTATAAATTT
1 TTTTTATGTTTAAAAAAAATTATAAATTT
11856 ATGTAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 14 0.58
29 2 0.08
30 8 0.33
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (30 bp):
TTTTTATGTTTAAAAAAAATTATAAATTTT
Found at i:12092 original size:23 final size:24
Alignment explanation
Indices: 12066--12128 Score: 60
Period size: 23 Copynumber: 2.7 Consensus size: 24
12056 TGACTATTCG
12066 TGTTGTATTAATGTTAGTTTTC-A
1 TGTTGTATTAATGTTAGTTTTCTA
* *
12089 TGTTGTGTTTTAA--TTATTTTTCTA
1 TG-T-TGTATTAATGTTAGTTTTCTA
*
12113 TGTTGTATTCATGTTA
1 TGTTGTATTAATGTTA
12129 TATTTTAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
22 6 0.19
23 11 0.35
24 7 0.23
25 7 0.23
ACGTcount: A:0.19, C:0.05, G:0.16, T:0.60
Consensus pattern (24 bp):
TGTTGTATTAATGTTAGTTTTCTA
Found at i:15280 original size:2 final size:2
Alignment explanation
Indices: 15271--15307 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
15261 TAAAAAAGTC
15271 AT AT -T AT AT AT -T A- AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15308 CAGATAATCA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.09
2 29 0.91
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:15967 original size:16 final size:18
Alignment explanation
Indices: 15936--15968 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
15926 AATTTAAAAT
15936 TTTAACAAAATAATATTA
1 TTTAACAAAATAATATTA
15954 TTTAA-AAAAT-ATATT
1 TTTAACAAAATAATATT
15969 GCAGTCAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
TTTAACAAAATAATATTA
Done.