Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_5211
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: 11856
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:1755 original size:30 final size:30
Alignment explanation
Indices: 1700--1756 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
1690 ACAAACATAT
* * *
1700 AAAATAATAATTAAATGATGCATGATATAA
1 AAAACAATAATCAAATAATGCATGATATAA
*
1730 AAAACAATAATCAAATAATGTATGATA
1 AAAACAATAATCAAATAATGCATGATA
1757 CAAATAGAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.58, C:0.05, G:0.09, T:0.28
Consensus pattern (30 bp):
AAAACAATAATCAAATAATGCATGATATAA
Found at i:1966 original size:13 final size:13
Alignment explanation
Indices: 1944--1973 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1934 ACAATTTAAA
*
1944 AATATTAATATAT
1 AATATAAATATAT
1957 AATATAAATATAT
1 AATATAAATATAT
1970 AATA
1 AATA
1974 ACAAGAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AATATAAATATAT
Found at i:2179 original size:18 final size:18
Alignment explanation
Indices: 2144--2181 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2134 ATTTACAAAT
*
2144 TTAAAATAATATATATAA
1 TTAAAATAATATAAATAA
2162 TTAAACATAA-ATAAATAA
1 TTAAA-ATAATATAAATAA
2180 TT
1 TT
2182 GTAATATGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (18 bp):
TTAAAATAATATAAATAA
Found at i:2283 original size:12 final size:13
Alignment explanation
Indices: 2237--2286 Score: 50
Period size: 12 Copynumber: 3.9 Consensus size: 13
2227 CAAGTAAAAC
2237 ATAATAAATATTAT
1 ATAATAAATA-TAT
2251 ATAATAAA-ATAT
1 ATAATAAATATAT
***
2263 ATGGGAAATA-AT
1 ATAATAAATATAT
2275 ATAATAAATATA
1 ATAATAAATATA
2287 GCATGTAATA
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
12 17 0.61
13 3 0.11
14 8 0.29
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (13 bp):
ATAATAAATATAT
Found at i:2358 original size:20 final size:21
Alignment explanation
Indices: 2332--2373 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
2322 ATGTATATAT
*
2332 AATATATGTAAAAATATAATAA
1 AATATATAT-AAAATATAATAA
2354 AATATATATAAAA-ATAATAA
1 AATATATATAAAATATAATAA
2374 TTATGAGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 4 0.21
22 8 0.42
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (21 bp):
AATATATATAAAATATAATAA
Found at i:6076 original size:14 final size:14
Alignment explanation
Indices: 6057--6093 Score: 56
Period size: 16 Copynumber: 2.5 Consensus size: 14
6047 CAAAAGAGTT
6057 AAGCAAATTGTTGA
1 AAGCAAATTGTTGA
6071 AAGCAAAAATTGTTGA
1 AAGC--AAATTGTTGA
6087 AAGCAAA
1 AAGCAAA
6094 AGTCGTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 7 0.33
16 14 0.67
ACGTcount: A:0.51, C:0.08, G:0.19, T:0.22
Consensus pattern (14 bp):
AAGCAAATTGTTGA
Found at i:6082 original size:16 final size:16
Alignment explanation
Indices: 6061--6094 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
6051 AGAGTTAAGC
6061 AAATTGTTGAAAGCAA
1 AAATTGTTGAAAGCAA
6077 AAATTGTTGAAAGCAA
1 AAATTGTTGAAAGCAA
6093 AA
1 AA
6095 GTCGTCGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.53, C:0.06, G:0.18, T:0.24
Consensus pattern (16 bp):
AAATTGTTGAAAGCAA
Found at i:8205 original size:15 final size:15
Alignment explanation
Indices: 8185--8214 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
8175 CATTTCATTT
*
8185 ATATTAGGATAATTA
1 ATATTAAGATAATTA
8200 ATATTAAGATAATTA
1 ATATTAAGATAATTA
8215 TTAGAATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (15 bp):
ATATTAAGATAATTA
Found at i:11670 original size:18 final size:18
Alignment explanation
Indices: 11642--11686 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
11632 CAACCTAATT
* *
11642 TTTATTTTTATTTTATTT
1 TTTATTATTATTTTATTA
*
11660 TTTCTTATTATTTTATTA
1 TTTATTATTATTTTATTA
11678 TTTATTATT
1 TTTATTATT
11687 TTTAGATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTATTATTATTTTATTA
Done.