Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold358
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: 17970
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31
Found at i:2101 original size:17 final size:17
Alignment explanation
Indices: 2076--2129 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
2066 TCTCTTTTCA
*
2076 TTCTCTTTTTTTGAATT
1 TTCTTTTTTTTTGAATT
* * *
2093 TTCTTTTTTTATCATTT
1 TTCTTTTTTTTTGAATT
* *
2110 TTCTTTTCTTTTGTATT
1 TTCTTTTTTTTTGAATT
2127 TTC
1 TTC
2130 GCTCTTTTCT
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.09, C:0.13, G:0.04, T:0.74
Consensus pattern (17 bp):
TTCTTTTTTTTTGAATT
Found at i:4357 original size:12 final size:12
Alignment explanation
Indices: 4340--4376 Score: 65
Period size: 12 Copynumber: 3.0 Consensus size: 12
4330 AAACCGTATG
4340 CAATTTTTTTTT
1 CAATTTTTTTTT
4352 CAATTTTTTTTTT
1 CAA-TTTTTTTTT
4365 CAATTTTTTTTT
1 CAATTTTTTTTT
4377 TTGAACTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 12 0.50
13 12 0.50
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (12 bp):
CAATTTTTTTTT
Found at i:4378 original size:14 final size:14
Alignment explanation
Indices: 4343--4390 Score: 71
Period size: 13 Copynumber: 3.4 Consensus size: 14
4333 CCGTATGCAA
4343 TTTTTTTTTCAA-T
1 TTTTTTTTTCAATT
4356 TTTTTTTTTCAATT
1 TTTTTTTTTCAATT
*
4370 TTTTTTTTTGAACTT
1 TTTTTTTTTCAA-TT
4385 TTTTTT
1 TTTTTT
4391 ACGCACCTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.38
14 12 0.38
15 8 0.25
ACGTcount: A:0.12, C:0.06, G:0.02, T:0.79
Consensus pattern (14 bp):
TTTTTTTTTCAATT
Found at i:4707 original size:24 final size:23
Alignment explanation
Indices: 4653--4730 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 23
4643 GGATAATTAA
**
4653 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
4676 GTTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
*
4700 GAAATGGTA--TGGAATTGGTAT
1 GAAATGGTATTTGGAATTGGTAC
*
4721 GAAATAGTAT
1 GAAATGGTAT
4731 GGTATTTGGT
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
21 18 0.42
22 1 0.02
23 9 0.21
24 15 0.35
ACGTcount: A:0.27, C:0.03, G:0.31, T:0.40
Consensus pattern (23 bp):
GAAATGGTATTTGGAATTGGTAC
Found at i:4715 original size:21 final size:21
Alignment explanation
Indices: 4689--4755 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
4679 TTGGTATTTG
4689 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
4710 GGAATTGGTATGAAATAGTAT
1 GGAATTGGTACGAAATGGTAT
* *
4731 GGTATTTGGTACGAATTGGTTAT
1 GG-AATTGGTACGAAATGG-TAT
4754 GG
1 GG
4756 TTCAAAGAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 21 0.55
22 12 0.32
23 5 0.13
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.34
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:10602 original size:23 final size:22
Alignment explanation
Indices: 10550--10602 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
10540 TCCACGTCTT
*
10550 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
10572 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
10595 TTTCTTTT
1 TTTCTTTT
10603 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
Done.