Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3757
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: 37151
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1140 original size:36 final size:36
Alignment explanation
Indices: 1100--1173 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
1090 TTTTTAATAC
1100 TTGATCAAAATAGAATCCTTCTTTTGGATGACTGCA
1 TTGATCAAAATAGAATCCTTCTTTTGGATGACTGCA
1136 TTGATCAAAATAGAATCCTTCTTTTGGATGACTGCA
1 TTGATCAAAATAGAATCCTTCTTTTGGATGACTGCA
1172 TT
1 TT
1174 ATTAATTTGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (36 bp):
TTGATCAAAATAGAATCCTTCTTTTGGATGACTGCA
Found at i:3314 original size:21 final size:21
Alignment explanation
Indices: 3285--3334 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
3275 TGAATAGATT
*
3285 TAATATTTATTGTTTAAACAA
1 TAATATTTATTGTGTAAACAA
*
3306 TATTATTTATTGTGTAAACAA
1 TAATATTTATTGTGTAAACAA
3327 TAATATTT
1 TAATATTT
3335 TTAAAGTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (21 bp):
TAATATTTATTGTGTAAACAA
Found at i:11446 original size:22 final size:22
Alignment explanation
Indices: 11421--11469 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 22
11411 ACTTTCGCTC
11421 AATA-ATTAAATTTAGAAT-TAAT
1 AATATATTAAA-TTA-AATATAAT
11443 AATATATTAAATTAAATATAAT
1 AATATATTAAATTAAATATAAT
11465 AATAT
1 AATAT
11470 GATATAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 3 0.12
22 16 0.64
23 6 0.24
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
AATATATTAAATTAAATATAAT
Found at i:16156 original size:36 final size:36
Alignment explanation
Indices: 16116--16189 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
16106 TTTTTAATAC
16116 TTGATCAAAATAGAATCCTTCTTTTGGATGACTGCA
1 TTGATCAAAATAGAATCCTTCTTTTGGATGACTGCA
16152 TTGATCAAAATAGAATCCTTCTTTTGGATGACTGCA
1 TTGATCAAAATAGAATCCTTCTTTTGGATGACTGCA
16188 TT
1 TT
16190 ATTAATTTGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (36 bp):
TTGATCAAAATAGAATCCTTCTTTTGGATGACTGCA
Found at i:18331 original size:21 final size:21
Alignment explanation
Indices: 18302--18351 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
18292 TGAATAGATT
*
18302 TAATATTTATTGTTTAAACAA
1 TAATATTTATTGTGTAAACAA
*
18323 TATTATTTATTGTGTAAACAA
1 TAATATTTATTGTGTAAACAA
18344 TAATATTT
1 TAATATTT
18352 TTAAAGTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (21 bp):
TAATATTTATTGTGTAAACAA
Found at i:26472 original size:22 final size:22
Alignment explanation
Indices: 26447--26495 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 22
26437 ACTTTCGCTC
26447 AATA-ATTAAATTTAGAAT-TAAT
1 AATATATTAAA-TTA-AATATAAT
26469 AATATATTAAATTAAATATAAT
1 AATATATTAAATTAAATATAAT
26491 AATAT
1 AATAT
26496 GATATAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 3 0.12
22 16 0.64
23 6 0.24
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
AATATATTAAATTAAATATAAT
Found at i:31183 original size:36 final size:36
Alignment explanation
Indices: 31143--31216 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
31133 TTTTTAATAC
31143 TTGATCAAAATAGAATCCTTCTTTTGGATGACTGCA
1 TTGATCAAAATAGAATCCTTCTTTTGGATGACTGCA
31179 TTGATCAAAATAGAATCCTTCTTTTGGATGACTGCA
1 TTGATCAAAATAGAATCCTTCTTTTGGATGACTGCA
31215 TT
1 TT
31217 ATTAATTTGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (36 bp):
TTGATCAAAATAGAATCCTTCTTTTGGATGACTGCA
Found at i:33964 original size:33 final size:34
Alignment explanation
Indices: 33922--33987 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 34
33912 GTGGATGATA
33922 ATCGAGATCTTATACTTGATAC-TTGATAGTTTT
1 ATCGAGATCTTATACTTGATACTTTGATAGTTTT
33955 ATCGAGATCTTATACTTGATACTTTGATAGTTT
1 ATCGAGATCTTATACTTGATACTTTGATAGTTT
33988 GTCTTTCTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 22 0.69
34 10 0.31
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.45
Consensus pattern (34 bp):
ATCGAGATCTTATACTTGATACTTTGATAGTTTT
Done.