Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2549
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: 12872
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:88 original size:34 final size:34
Alignment explanation
Indices: 44--189 Score: 202
Period size: 34 Copynumber: 4.3 Consensus size: 34
34 GTTGGTGCCA
*
44 GTTGACTAAATGGGAGATTTGGTAGCTTACCATT
1 GTTGATTAAATGGGAGATTTGGTAGCTTACCATT
* *
78 GTTGATTAAATGAGAAATTTGGTAGCTTACCATT
1 GTTGATTAAATGGGAGATTTGGTAGCTTACCATT
* * *
112 ATTGATTAAATGGGTGATTTGGTGGCTTACCATT
1 GTTGATTAAATGGGAGATTTGGTAGCTTACCATT
* * * *
146 GTTGACTAAATGGTAGATTTGGTAGGTTGCCATT
1 GTTGATTAAATGGGAGATTTGGTAGCTTACCATT
180 GTTGATTAAA
1 GTTGATTAAA
190 AGGTGGTTTT
Statistics
Matches: 96, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 96 1.00
ACGTcount: A:0.27, C:0.09, G:0.25, T:0.38
Consensus pattern (34 bp):
GTTGATTAAATGGGAGATTTGGTAGCTTACCATT
Found at i:3010 original size:25 final size:24
Alignment explanation
Indices: 2972--3020 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
2962 TTACCCTACA
*
2972 AAAATATAAAATATTAAAATAATT
1 AAAATATAAAATATCAAAATAATT
* *
2996 AAAATGTAAATATATCAAGATAATT
1 AAAATATAAA-ATATCAAAATAATT
3021 TTTTTATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (24 bp):
AAAATATAAAATATCAAAATAATT
Found at i:3585 original size:5 final size:5
Alignment explanation
Indices: 3577--3636 Score: 58
Period size: 5 Copynumber: 12.6 Consensus size: 5
3567 TGATCACATG
*
3577 ATATA ATATA ATATA A-A-A A-ATA ATTAAA ATATA ATATA ATA-A A-ATA
1 ATATA ATATA ATATA ATATA ATATA A-TATA ATATA ATATA ATATA ATATA
3623 ATATAA ATATA ATA
1 ATAT-A ATATA ATA
3637 CAAATACATG
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
3 4 0.09
4 7 0.15
5 28 0.60
6 8 0.17
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (5 bp):
ATATA
Found at i:3630 original size:24 final size:23
Alignment explanation
Indices: 3577--3636 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 23
3567 TGATCACATG
3577 ATAT-AATATAATATAAAAAATA
1 ATATAAATATAATATAAAAAATA
3599 AT-TAAAATATAATATAATAAAATA
1 ATAT-AAATATAATATAA-AAAATA
3623 ATATAAATATAATA
1 ATATAAATATAATA
3637 CAAATACATG
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
21 1 0.03
22 2 0.06
23 12 0.35
24 18 0.53
25 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
ATATAAATATAATATAAAAAATA
Found at i:3636 original size:11 final size:12
Alignment explanation
Indices: 3581--3636 Score: 71
Period size: 11 Copynumber: 4.8 Consensus size: 12
3571 CACATGATAT
3581 AATATAATATAA
1 AATATAATATAA
*
3593 AAAATAAT-TAA
1 AATATAATATAA
3604 AATATAATATAA
1 AATATAATATAA
*
3616 TAAAATAATAT-A
1 -AATATAATATAA
3628 AATATAATA
1 AATATAATA
3637 CAAATACATG
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
11 18 0.47
12 11 0.29
13 9 0.24
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AATATAATATAA
Found at i:4332 original size:4 final size:4
Alignment explanation
Indices: 4325--4351 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
4315 TATCTTTATT
4325 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
4352 GTTTGTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:4431 original size:14 final size:15
Alignment explanation
Indices: 4412--4441 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4402 TAGCTGAGTT
4412 TTTATTT-TTTTTTA
1 TTTATTTATTTTTTA
4426 TTTATTTATTTTTTA
1 TTTATTTATTTTTTA
4441 T
1 T
4442 AACAAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTATTTATTTTTTA
Found at i:4871 original size:18 final size:16
Alignment explanation
Indices: 4841--4888 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 16
4831 AATTTTTTTT
4841 TAATTTAATTATAAAATA
1 TAATTTAA-TATAAAA-A
4859 TAATATTAATATAAAAA
1 TAAT-TTAATATAAAAA
4876 TAAATTTTAATAT
1 T-AA-TTTAATAT
4889 TTTAATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
17 2 0.07
18 20 0.74
19 5 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAATTTAATATAAAAA
Found at i:5168 original size:2 final size:2
Alignment explanation
Indices: 5161--5193 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5151 TCTAGGATAA
*
5161 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5194 ACTTAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:10802 original size:20 final size:19
Alignment explanation
Indices: 10769--10820 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
10759 ATTATGTGTT
*
10769 ATATTT-ATTTTTTATTTA
1 ATATTTAATTATTTATTTA
*
10787 GTATTTAAATTATTTATTTA
1 ATATTT-AATTATTTATTTA
10807 ATATTTAATTATTT
1 ATATTTAATTATTT
10821 TTCATTAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 5 0.17
19 8 0.28
20 16 0.55
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
ATATTTAATTATTTATTTA
Done.