Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold296
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: 15328
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Found at i:2828 original size:12 final size:12
Alignment explanation
Indices: 2811--2836 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2801 TATGACCATG
2811 AGATTGGCGCTA
1 AGATTGGCGCTA
2823 AGATTGGCGCTA
1 AGATTGGCGCTA
2835 AG
1 AG
2837 TGCGCGGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.15, G:0.35, T:0.23
Consensus pattern (12 bp):
AGATTGGCGCTA
Found at i:2920 original size:27 final size:27
Alignment explanation
Indices: 2857--2984 Score: 127
Period size: 27 Copynumber: 4.7 Consensus size: 27
2847 AAATTGTACA
*
2857 GCACTAAGTGTGCG-ATTCGACTA-GTT
1 GCACTAAGTGTGCGAATT-GACTATGAT
* *
2883 GCACTAAGTGTGCGAAATGAATATGAT
1 GCACTAAGTGTGCGAATTGACTATGAT
* **
2910 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTGACTATGAT
* *
2937 GCACTAAGTGTGCGAGTCTAACTATG-T
1 GCACTAAGTGTGCGAAT-TGACTATGAT
*
2964 AGCACTAAGTGTGCGATTTGA
1 -GCACTAAGTGTGCGAATTGA
2985 TTACGTGGCA
Statistics
Matches: 84, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
26 18 0.21
27 44 0.52
28 22 0.26
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.27
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTGACTATGAT
Found at i:2995 original size:55 final size:51
Alignment explanation
Indices: 2856--3008 Score: 155
Period size: 55 Copynumber: 2.9 Consensus size: 51
2846 TAAATTGTAC
* * *
2856 AGCACTAAGTGTGCGATTCGACTAGTTGCACTAAGTGTGCGAAATGAATATG
1 AGCACTAAGTGTGCGATTTGACTAGTGGCACTAAGTGTGCG-AGTGAATATG
* * * *
2908 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTCTAACTATG
1 A-GCACTAAGTGTGCGATTTGACTA-GTGGCACTAAGTGTGCGAGT-GAA-TATG
*
2963 TAGCACTAAGTGTGCGATTTGATTACGTGGCACCTAAGTGT-CGAGT
1 -AGCACTAAGTGTGCGATTTGACTA-GTGGCA-CTAAGTGTGCGAGT
3009 TGATTGTATA
Statistics
Matches: 83, Mismatches: 12, Indels: 9
0.80 0.12 0.09
Matches are distributed among these distances:
52 1 0.01
53 22 0.27
54 17 0.20
55 34 0.41
56 9 0.11
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.27
Consensus pattern (51 bp):
AGCACTAAGTGTGCGATTTGACTAGTGGCACTAAGTGTGCGAGTGAATATG
Found at i:8626 original size:35 final size:37
Alignment explanation
Indices: 8578--8661 Score: 127
Period size: 35 Copynumber: 2.3 Consensus size: 37
8568 TCGGGACCTG
*
8578 TAACCCGGATTTAATAACTGAACGAATG-CTCGGACT
1 TAACCCGGATTTAATAACCGAACGAATGCCTCGGACT
*
8614 TAACCC-GATTTAATAACCGCACGAATGCCTCGGACT
1 TAACCCGGATTTAATAACCGAACGAATGCCTCGGACT
8650 TAACACCGGATT
1 TAAC-CCGGATT
8662 AGTATCTCGT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
35 19 0.44
36 18 0.42
37 2 0.05
38 4 0.09
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (37 bp):
TAACCCGGATTTAATAACCGAACGAATGCCTCGGACT
Found at i:13458 original size:1 final size:1
Alignment explanation
Indices: 13452--13535 Score: 141
Period size: 1 Copynumber: 84.0 Consensus size: 1
13442 CACTTTGTCG
*
13452 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
13517 TTTTTTTTTCTTGTTTTTT
1 TTTTTTTTTTTTTTTTTTT
13536 GAGTTGTGAA
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 77 1.00
ACGTcount: A:0.01, C:0.01, G:0.01, T:0.96
Consensus pattern (1 bp):
T
Done.