Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2010
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: 29662
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.30
Found at i:7799 original size:4 final size:4
Alignment explanation
Indices: 7790--7820 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
7780 TTAAACTAAG
7790 TAAA TAAA TAAA TAAA TAAA T-AA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
7821 AATAAAACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:7807 original size:12 final size:11
Alignment explanation
Indices: 7790--7826 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
7780 TTAAACTAAG
7790 TAAATAAATAAA
1 TAAATAAAT-AA
7802 TAAATAAATAA
1 TAAATAAATAA
7813 TAAATAAA-AA
1 TAAATAAATAA
7823 TAAA
1 TAAA
7827 ACTTTACAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 6 0.24
11 10 0.40
12 9 0.36
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
TAAATAAATAA
Found at i:9225 original size:23 final size:22
Alignment explanation
Indices: 9173--9225 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
9163 TCCACGTCTT
*
9173 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
9195 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
9218 TTTCTTTT
1 TTTCTTTT
9226 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:17193 original size:23 final size:22
Alignment explanation
Indices: 17141--17193 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
17131 TCCACGTCTT
*
17141 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
17163 -TTCATTTTCTCTTCATTTTTC-AA
1 TTTC-TTTTCT-TTC-TTTTTCTAA
17186 TTTCTTTT
1 TTTCTTTT
17194 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 9 0.35
24 9 0.35
ACGTcount: A:0.11, C:0.17, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:21212 original size:20 final size:20
Alignment explanation
Indices: 21187--21233 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
21177 AGCTCGTTTC
21187 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCGAGCTCAAGT
* * *
21207 CAGCTCATTCGAGTTCAATT
1 CAGCTCACTCGAGCTCAAGT
21227 CAGCTCA
1 CAGCTCA
21234 ACCTCAACCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCACTCGAGCTCAAGT
Found at i:22841 original size:13 final size:13
Alignment explanation
Indices: 22823--22868 Score: 76
Period size: 13 Copynumber: 3.6 Consensus size: 13
22813 TAGTTTCTTC
22823 AAAAAAAAATTC-
1 AAAAAAAAATTCA
22835 AAAAAAAAATTCA
1 AAAAAAAAATTCA
*
22848 AAAAAAAATTTCA
1 AAAAAAAAATTCA
22861 AAAAAAAA
1 AAAAAAAA
22869 TTTGGTTTCC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
12 12 0.38
13 20 0.62
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAAAAAATTCA
Found at i:22860 original size:25 final size:24
Alignment explanation
Indices: 22820--22870 Score: 93
Period size: 25 Copynumber: 2.1 Consensus size: 24
22810 TAGTAGTTTC
22820 TTCAAAAAAAAATTCAAAAAAAAA
1 TTCAAAAAAAAATTCAAAAAAAAA
22844 TTCAAAAAAAAATTTCAAAAAAAAA
1 TTCAAAAAAAAA-TTCAAAAAAAAA
22869 TT
1 TT
22871 TGGTTTCCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 12 0.46
25 14 0.54
ACGTcount: A:0.71, C:0.08, G:0.00, T:0.22
Consensus pattern (24 bp):
TTCAAAAAAAAATTCAAAAAAAAA
Found at i:22871 original size:13 final size:12
Alignment explanation
Indices: 22820--22870 Score: 93
Period size: 12 Copynumber: 4.2 Consensus size: 12
22810 TAGTAGTTTC
22820 TTCAAAAAAAAA
1 TTCAAAAAAAAA
22832 TTCAAAAAAAAA
1 TTCAAAAAAAAA
22844 TTCAAAAAAAAA
1 TTCAAAAAAAAA
22856 TTTCAAAAAAAAA
1 -TTCAAAAAAAAA
22869 TT
1 TT
22871 TGGTTTCCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
12 26 0.68
13 12 0.32
ACGTcount: A:0.71, C:0.08, G:0.00, T:0.22
Consensus pattern (12 bp):
TTCAAAAAAAAA
Found at i:22929 original size:16 final size:16
Alignment explanation
Indices: 22908--22963 Score: 98
Period size: 16 Copynumber: 3.6 Consensus size: 16
22898 GATATCAAGT
22908 TGAAAAAAAAAATTCG
1 TGAAAAAAAAAATTCG
22924 TG--AAAAAAAATTCG
1 TGAAAAAAAAAATTCG
22938 TGAAAAAAAAAATTCG
1 TGAAAAAAAAAATTCG
22954 TGAAAAAAAA
1 TGAAAAAAAA
22964 GAAGAAGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
14 14 0.37
16 24 0.63
ACGTcount: A:0.64, C:0.05, G:0.12, T:0.18
Consensus pattern (16 bp):
TGAAAAAAAAAATTCG
Found at i:22931 original size:14 final size:14
Alignment explanation
Indices: 22912--22963 Score: 86
Period size: 14 Copynumber: 3.6 Consensus size: 14
22902 TCAAGTTGAA
22912 AAAAAAAATTCGTG
1 AAAAAAAATTCGTG
22926 AAAAAAAATTCGTG
1 AAAAAAAATTCGTG
22940 AAAAAAAAAATTCGTG
1 --AAAAAAAATTCGTG
22956 AAAAAAAA
1 AAAAAAAA
22964 GAAGAAGCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
14 22 0.61
16 14 0.39
ACGTcount: A:0.65, C:0.06, G:0.12, T:0.17
Consensus pattern (14 bp):
AAAAAAAATTCGTG
Done.