Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1370
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: 21449
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:1964 original size:22 final size:22
Alignment explanation
Indices: 1934--1980 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
1924 TTTTGTATTT
1934 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
1956 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
1978 GGG
1 GGG
1981 TTCAAAAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.32, C:0.04, G:0.40, T:0.23
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:3499 original size:12 final size:13
Alignment explanation
Indices: 3482--3510 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
3472 TTAAACTAAG
3482 TAAATAAAT-AAA
1 TAAATAAATAAAA
3494 TAAATAAATAAAA
1 TAAATAAATAAAA
3507 TAAA
1 TAAA
3511 AATAAAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAATAAATAAAA
Found at i:4911 original size:23 final size:22
Alignment explanation
Indices: 4859--4911 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
4849 TCCACGTCTT
*
4859 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
4881 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
4904 TTTCTTTT
1 TTTCTTTT
4912 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
Found at i:7282 original size:15 final size:15
Alignment explanation
Indices: 7264--7297 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
7254 TTAAACTAAG
7264 TAAAT-AAATAATAAA
1 TAAATAAAATAA-AAA
7279 TAAATAAAATAAAAA
1 TAAATAAAATAAAAA
7294 TAAA
1 TAAA
7298 ACTTTACAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
TAAATAAAATAAAAA
Found at i:11057 original size:17 final size:17
Alignment explanation
Indices: 11032--11086 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
11022 TCTCTTTTCA
*
11032 TTCTCTTTTTTTGAATT
1 TTCTTTTTTTTTGAATT
* *
11049 TTCTTTTTTTTTTCATTT
1 TTC-TTTTTTTTTGAATT
* *
11067 TTCTTTTCTTTTGTATT
1 TTCTTTTTTTTTGAATT
11084 TTC
1 TTC
11087 GCTCTTTTCT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 16 0.53
18 14 0.47
ACGTcount: A:0.07, C:0.13, G:0.04, T:0.76
Consensus pattern (17 bp):
TTCTTTTTTTTTGAATT
Found at i:11060 original size:18 final size:18
Alignment explanation
Indices: 11037--11078 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
11027 TTTCATTCTC
*
11037 TTTTTTTGAATTTTCTTT
1 TTTTTTTCAATTTTCTTT
*
11055 TTTTTTTCATTTTTCTTT
1 TTTTTTTCAATTTTCTTT
11073 TCTTTT
1 T-TTTT
11079 GTATTTTCGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.07, C:0.10, G:0.02, T:0.81
Consensus pattern (18 bp):
TTTTTTTCAATTTTCTTT
Found at i:13639 original size:22 final size:22
Alignment explanation
Indices: 13609--13652 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
13599 TTTGGTATTT
13609 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
13631 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
13653 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:17909 original size:18 final size:17
Alignment explanation
Indices: 17878--17913 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
17868 AATTCTGTTA
*
17878 AAAAAGTGAAGAAAAAG
1 AAAAAGAGAAGAAAAAG
17895 AAAAAGAGAATGAAAAAG
1 AAAAAGAGAA-GAAAAAG
17913 A
1 A
17914 GCAAAAAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (17 bp):
AAAAAGAGAAGAAAAAG
Done.