Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1702
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: 13748
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Found at i:189 original size:32 final size:31
Alignment explanation
Indices: 143--203 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 31
133 TTTAATTTAA
143 TAAATATAAAATTAAAAATATTTATTTTTATT
1 TAAATATAAAATTAAAAATATTT-TTTTTATT
**
175 TAAA-ATAATAATTAACTATATTTTTTTTA
1 TAAATATAA-AATTAAAAATATTTTTTTTA
204 AATTACCTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 10 0.38
32 16 0.62
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (31 bp):
TAAATATAAAATTAAAAATATTTTTTTTATT
Found at i:4071 original size:20 final size:19
Alignment explanation
Indices: 4048--4085 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
4038 TTTAAAATAA
4048 ATCAATAAG-CCAATGATTAT
1 ATCAA-AAGTCCAA-GATTAT
4068 ATCAAAAGTCCAAGATTA
1 ATCAAAAGTCCAAGATTA
4086 AGTAGATACG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.26
Consensus pattern (19 bp):
ATCAAAAGTCCAAGATTAT
Found at i:4212 original size:22 final size:20
Alignment explanation
Indices: 4186--4260 Score: 71
Period size: 20 Copynumber: 3.5 Consensus size: 20
4176 AGATTAACTT
4186 AATTTAATAATTAAAAATATTA
1 AATTTAATAA-TAAAAATA-TA
4208 AATTTAAATTAATAAAAATATA
1 AATTT-AA-TAATAAAAATATA
*
4230 AATATTAAT-ATAAAATTATA
1 AAT-TTAATAATAAAAATATA
**
4250 TTTTTAATAAT
1 AATTTAATAAT
4261 TATAATAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
19 5 0.11
20 13 0.28
21 1 0.02
22 12 0.26
23 12 0.26
24 3 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AATTTAATAATAAAAATATA
Found at i:4244 original size:20 final size:19
Alignment explanation
Indices: 4186--4249 Score: 56
Period size: 22 Copynumber: 3.0 Consensus size: 19
4176 AGATTAACTT
4186 AATTTAATAATTAAAAATATTA
1 AATTTAAT-A-TAAAAATA-TA
4208 AATTTAAATTAATAAAAATATA
1 AATTT-AA-T-ATAAAAATATA
*
4230 AATATTAATATAAAATTATA
1 AAT-TTAATATAAAAATATA
4250 TTTTTAATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
20 10 0.26
21 1 0.03
22 12 0.32
23 12 0.32
24 3 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AATTTAATATAAAAATATA
Found at i:4293 original size:31 final size:30
Alignment explanation
Indices: 4258--4317 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
4248 TATTTTTAAT
*
4258 AATTATAATAAAAT-ATAAATATATATAAACA
1 AATTA-AATAAAATAAAAAATATAT-TAAACA
*
4289 AATTAAATCAAATAAAAAATATATTAAAC
1 AATTAAATAAAATAAAAAATATATTAAAC
4318 TAAAAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (30 bp):
AATTAAATAAAATAAAAAATATATTAAACA
Found at i:4370 original size:2 final size:2
Alignment explanation
Indices: 4363--4399 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
4353 TCCAATATTA
4363 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4400 GGCCTTCGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9421 original size:21 final size:19
Alignment explanation
Indices: 9397--9459 Score: 58
Period size: 20 Copynumber: 3.3 Consensus size: 19
9387 TAAAACAAAG
*
9397 TTTTAAATATTTAAAAATTAA
1 TTTTAAATATTT--AAATAAA
9418 TTTT-AATA-TTAAATAAA
1 TTTTAAATATTTAAATAAA
* *
9435 TTTTAAATATAGTAAATAAT
1 TTTTAAATAT-TTAAATAAA
9455 TTTTA
1 TTTTA
9460 CTGTATTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 10 0.28
18 4 0.11
19 2 0.06
20 16 0.44
21 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
TTTTAAATATTTAAATAAA
Found at i:11841 original size:16 final size:15
Alignment explanation
Indices: 11816--11857 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
11806 TTATATTAAT
11816 ATTATAAAAATAAAAA
1 ATTATAAAAA-AAAAA
* *
11832 ATTATTAAAAAAGAA
1 ATTATAAAAAAAAAA
11847 ATTA-AAAAAAA
1 ATTATAAAAAAA
11858 TGTTAGTTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 6 0.26
15 8 0.35
16 9 0.39
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (15 bp):
ATTATAAAAAAAAAA
Found at i:13678 original size:25 final size:24
Alignment explanation
Indices: 13643--13694 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
13633 ATACATTGTT
* * *
13643 ATTTTATTTAATTTTATTAATTTTA
1 ATTTTAATTAAGTTTA-AAATTTTA
13668 ATTTTAATTAAGTTTAAAATTTTA
1 ATTTTAATTAAGTTTAAAATTTTA
13692 ATT
1 ATT
13695 CATACGTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
ATTTTAATTAAGTTTAAAATTTTA
Found at i:13683 original size:16 final size:16
Alignment explanation
Indices: 13649--13694 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 16
13639 TGTTATTTTA
*
13649 TTTAATTTT-ATTAAT
1 TTTAATTTTAATTAAG
13664 TTTAATTTTAATTAAG
1 TTTAATTTTAATTAAG
13680 TTTAAAATTTTAATT
1 TTT--AATTTTAATT
13695 CATACGTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 9 0.33
16 8 0.30
18 10 0.37
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (16 bp):
TTTAATTTTAATTAAG
Done.