Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_3960
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: 16550
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:737 original size:10 final size:10
Alignment explanation
Indices: 709--740 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
699 TTTTTTCTTT
709 TTTTTTTG-A
1 TTTTTTTGAA
718 TTTTTTTGAA
1 TTTTTTTGAA
728 TTTTTTTGAA
1 TTTTTTTGAA
738 TTT
1 TTT
741 CTCTCTCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.16, C:0.00, G:0.09, T:0.75
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:3342 original size:14 final size:14
Alignment explanation
Indices: 3312--3341 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
3302 CAATTTTTCA
3312 TTCACTTTTTCTTT
1 TTCACTTTTTCTTT
3326 TTCATCTTTTTCTTT
1 TTCA-CTTTTTCTTT
3341 T
1 T
3342 CTCGCTCTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.73
Consensus pattern (14 bp):
TTCACTTTTTCTTT
Found at i:3384 original size:19 final size:20
Alignment explanation
Indices: 3360--3404 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
3350 CTTTTCATTC
*
3360 TCTTTTTTTGAATTTTC-TT
1 TCTTTTTTTCAATTTTCTTT
*
3379 TCTTTTTTTCATTTTTCTTT
1 TCTTTTTTTCAATTTTCTTT
3399 TCTTTT
1 TCTTTT
3405 GTATTTTCGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.07, C:0.13, G:0.02, T:0.78
Consensus pattern (20 bp):
TCTTTTTTTCAATTTTCTTT
Found at i:7155 original size:21 final size:21
Alignment explanation
Indices: 7128--7181 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
7118 TAGACTTATA
7128 CAATTTTTTTTCT-TTTTTTT
1 CAATTTTTTTTCTATTTTTTT
7148 CAAATTTTTTATT-TATTTTTTT
1 C-AATTTTTT-TTCTATTTTTTT
7170 CAATTTTTTTTC
1 CAATTTTTTTTC
7182 ACAAGTCTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
20 3 0.10
21 17 0.57
22 10 0.33
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (21 bp):
CAATTTTTTTTCTATTTTTTT
Found at i:7516 original size:22 final size:23
Alignment explanation
Indices: 7488--7530 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
7478 TATTTAGGGA
7488 TTGGTACGAAATGGT-ATGGTAT
1 TTGGTACGAAATGGTAATGGTAT
*
7510 TTGGTACGAATTGGTAATGGT
1 TTGGTACGAAATGGTAATGGT
7531 TCAAAAAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.26, C:0.05, G:0.33, T:0.37
Consensus pattern (23 bp):
TTGGTACGAAATGGTAATGGTAT
Found at i:10081 original size:20 final size:20
Alignment explanation
Indices: 10058--10142 Score: 82
Period size: 20 Copynumber: 4.2 Consensus size: 20
10048 AAGCTCAAAC
*
10058 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGTGAGCTAAATT
*
10078 GAGCTCAAA-CGAGCTAAATT
1 GAGCT-AAAGTGAGCTAAATT
* *
10098 GAGCTCAAGCGAGCTAAATT
1 GAGCTAAAGTGAGCTAAATT
* * * *
10118 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGTGAGCTAAATT
10138 GAGCT
1 GAGCT
10143 GGGAAAAACT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.04
20 50 0.91
21 3 0.05
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (20 bp):
GAGCTAAAGTGAGCTAAATT
Found at i:10082 original size:10 final size:10
Alignment explanation
Indices: 10058--10142 Score: 57
Period size: 10 Copynumber: 8.5 Consensus size: 10
10048 AAGCTCAAAC
*
10058 GAGCTAAAGT
1 GAGCTAAATT
*
10068 AAGCTAAATT
1 GAGCTAAATT
*
10078 GAGCTCAAA-C
1 GAGCT-AAATT
10088 GAGCTAAATT
1 GAGCTAAATT
* **
10098 GAGCTCAAGC
1 GAGCTAAATT
10108 GAGCTAAATT
1 GAGCTAAATT
* *
10118 AAGCT-CATGT
1 GAGCTAAAT-T
*
10128 GAGCTAAATC
1 GAGCTAAATT
10138 GAGCT
1 GAGCT
10143 GGGAAAAACT
Statistics
Matches: 55, Mismatches: 16, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
9 5 0.09
10 45 0.82
11 5 0.09
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (10 bp):
GAGCTAAATT
Found at i:10112 original size:30 final size:30
Alignment explanation
Indices: 10049--10112 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
10039 ACTTAAGCCA
**
10049 AGCTCAAACGAGCTAAAGTAAGCTAAATTG
1 AGCTCAAACGAGCTAAAGTAAGCTAAAGCG
* * *
10079 AGCTCAAACGAGCTAAATTGAGCTCAAGCG
1 AGCTCAAACGAGCTAAAGTAAGCTAAAGCG
10109 AGCT
1 AGCT
10113 AAATTAAGCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.19
Consensus pattern (30 bp):
AGCTCAAACGAGCTAAAGTAAGCTAAAGCG
Done.