Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1960
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: 35420
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:5285 original size:20 final size:20
Alignment explanation
Indices: 5262--5308 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
5252 GGGTTAAGAT
*
5262 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
5282 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
5302 TGAGCTG
1 TGAGCTG
5309 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:7056 original size:48 final size:47
Alignment explanation
Indices: 6978--7083 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
6968 TTGTCTTTTC
*
6978 TTTCTTTTTCAATTTTCTCTTTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTTCTCTTTTT-CTCACATCCTTT-TTCAATCTCAA
* *
7026 TTTCTTTTTCGATTTCTTTCTCTTTT-TCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTT-TCTCT-TTTTCTCACATCCTTTTTCAATCTCAA
7074 TTTCTTTTTC
1 TTTCTTTTTC
7084 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (47 bp):
TTTCTTTTTCAATTTTCTCTTTTTCTCACATCCTTTTTCAATCTCAA
Found at i:10708 original size:20 final size:20
Alignment explanation
Indices: 10685--10731 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
10675 GGGTTAAGAT
*
10685 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
10705 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
10725 TGAGCTG
1 TGAGCTG
10732 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:11789 original size:30 final size:30
Alignment explanation
Indices: 11755--11851 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
11745 TAAACTAAAA
11755 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
11785 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
11815 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
11845 TGAGCTA
1 TGAGCTA
11852 GAAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:12860 original size:18 final size:18
Alignment explanation
Indices: 12817--12860 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
12807 AAAAGAATGA
12817 GAAAAAGAAAAAGAAATT
1 GAAAAAGAAAAAGAAATT
**
12835 GATCAAG-AAAAGAAAATT
1 GAAAAAGAAAAAG-AAATT
12853 GAAAAAGA
1 GAAAAAGA
12861 GAGTGAGTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.68, C:0.02, G:0.18, T:0.11
Consensus pattern (18 bp):
GAAAAAGAAAAAGAAATT
Found at i:25116 original size:23 final size:22
Alignment explanation
Indices: 25064--25116 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
25054 TCCACGTCTT
*
25064 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
25086 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
25109 TTTCTTTT
1 TTTCTTTT
25117 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:29803 original size:21 final size:22
Alignment explanation
Indices: 29764--29807 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
29754 ATGCATACTC
29764 CTTCAAGCTCAAATCAGCTCAA
1 CTTCAAGCTCAAATCAGCTCAA
* *
29786 CTTCAA-CTCAACTTAGCTCAA
1 CTTCAAGCTCAAATCAGCTCAA
29807 C
1 C
29808 GAGCTCGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.34, C:0.34, G:0.07, T:0.25
Consensus pattern (22 bp):
CTTCAAGCTCAAATCAGCTCAA
Done.