Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold469
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: 21142
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:5400 original size:18 final size:18
Alignment explanation
Indices: 5377--5411 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
5367 TATTTTGGTT
5377 ATTTATTTATTT-ATTTTG
1 ATTTATTT-TTTGATTTTG
5395 ATTTATTTTTTGATTTT
1 ATTTATTTTTTGATTTT
5412 TTGTGTAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.20, C:0.00, G:0.06, T:0.74
Consensus pattern (18 bp):
ATTTATTTTTTGATTTTG
Found at i:6582 original size:15 final size:15
Alignment explanation
Indices: 6544--6599 Score: 51
Period size: 17 Copynumber: 3.5 Consensus size: 15
6534 CTTACCTTTG
6544 TTTATTTATTTATTATA
1 TTTATTTA--TATTATA
6561 TTTATTTATATTA-A
1 TTTATTTATATTATA
*
6575 TTTGATTTGATTTTATA
1 TTT-ATTT-ATATTATA
*
6592 ATTATTTA
1 TTTATTTA
6600 GACATACCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
14 4 0.12
15 10 0.29
16 9 0.26
17 11 0.32
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (15 bp):
TTTATTTATATTATA
Found at i:6805 original size:15 final size:15
Alignment explanation
Indices: 6785--6816 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
6775 ACAAAGGGCT
6785 TTCTATTTGATTAAA
1 TTCTATTTGATTAAA
6800 TTCTATTTGATTAAA
1 TTCTATTTGATTAAA
6815 TT
1 TT
6817 GATACACAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.56
Consensus pattern (15 bp):
TTCTATTTGATTAAA
Found at i:8198 original size:23 final size:22
Alignment explanation
Indices: 8163--8213 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
8153 ATGTCACTTT
8163 TTAGAA-TAATGCAGCCAAGCCG
1 TTAGAATTAATGCAG-CAAGCCG
* *
8185 TTAGAATTAATGCAGTAATCCG
1 TTAGAATTAATGCAGCAAGCCG
8207 TTAGAAT
1 TTAGAAT
8214 CAAGTAGGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (22 bp):
TTAGAATTAATGCAGCAAGCCG
Found at i:10040 original size:41 final size:42
Alignment explanation
Indices: 9987--10101 Score: 135
Period size: 42 Copynumber: 2.8 Consensus size: 42
9977 TTTTCTATAG
* * * *
9987 CCCAAATATGGTCTTACAC-AATTCTCATATCGATGCCATGT
1 CCCAAATATGGTCTTACACAAAATCTCATAACAATGCCATAT
*
10028 CCCAAACATGGTCTTACACAAAATCTCATAACAATGCCATAT
1 CCCAAATATGGTCTTACACAAAATCTCATAACAATGCCATAT
* * *
10070 CTCAGATATGGTCTTACACGTAAA-CTCATAAC
1 CCCAAATATGGTCTTACAC-AAAATCTCATAAC
10102 CCTAATGTCA
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
41 18 0.29
42 42 0.67
43 3 0.05
ACGTcount: A:0.35, C:0.27, G:0.10, T:0.28
Consensus pattern (42 bp):
CCCAAATATGGTCTTACACAAAATCTCATAACAATGCCATAT
Found at i:17995 original size:6 final size:6
Alignment explanation
Indices: 17960--18015 Score: 62
Period size: 6 Copynumber: 9.5 Consensus size: 6
17950 TCCTCCTATC
* *
17960 TTTTTA TTCTTA TTTATT- TATTTA -TTTTA TTTTTA TTTTTA TTTTTA
1 TTTTTA TTTTTA TTT-TTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
*
18007 TTTTCA TTT
1 TTTTTA TTT
18016 CAATTTGATT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
5 6 0.14
6 34 0.81
7 2 0.05
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTTA
Found at i:17995 original size:23 final size:23
Alignment explanation
Indices: 17961--18015 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
17951 CCTCCTATCT
*
17961 TTTTATTCTTATTTATT-TATTTA
1 TTTTATTTTTATTT-TTATATTTA
*
17984 TTTTATTTTTATTTTTATTTTTA
1 TTTTATTTTTATTTTTATATTTA
18007 TTTTCATTT
1 TTTT-ATTT
18016 CAATTTGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 2 0.07
23 22 0.79
24 4 0.14
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (23 bp):
TTTTATTTTTATTTTTATATTTA
Found at i:20931 original size:13 final size:13
Alignment explanation
Indices: 20915--20947 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
20905 TTTAATTAAA
*
20915 TTAGTTAATTAGT
1 TTAGATAATTAGT
20928 TTAGATAATTAGT
1 TTAGATAATTAGT
20941 TTA-ATAA
1 TTAGATAA
20948 AAAACCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Done.