Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2739
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: 34167
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:4977 original size:2 final size:2
Alignment explanation
Indices: 4970--5002 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
4960 TAACATTGTG
*
4970 AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5003 ATCTGTTTTA
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:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5827 original size:2 final size:2
Alignment explanation
Indices: 5820--5856 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5810 ATGAATCTGA
5820 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5857 ATAGTACAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9618 original size:15 final size:14
Alignment explanation
Indices: 9598--9627 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
9588 AATTGACAAT
9598 TATTTCTATTATTTC
1 TATTTCTATT-TTTC
9613 TATTTCTATTTTTC
1 TATTTCTATTTTTC
9627 T
1 T
9628 CTTTATTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (14 bp):
TATTTCTATTTTTC
Found at i:11516 original size:35 final size:35
Alignment explanation
Indices: 11470--11541 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
11460 AAAGGATTGA
11470 ATAAAACCGGAAATTATTTTAAAAATACCAAAAAT
1 ATAAAACCGGAAATTATTTTAAAAATACCAAAAAT
11505 ATAAAACCGGAAATTATTTTAAAAATACCAAAAAT
1 ATAAAACCGGAAATTATTTTAAAAATACCAAAAAT
11540 AT
1 AT
11542 GTTTTATTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.57, C:0.11, G:0.06, T:0.26
Consensus pattern (35 bp):
ATAAAACCGGAAATTATTTTAAAAATACCAAAAAT
Found at i:15400 original size:15 final size:15
Alignment explanation
Indices: 15380--15410 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
15370 TAAAAATGTC
*
15380 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
15395 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
15410 C
1 C
15411 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:17510 original size:13 final size:13
Alignment explanation
Indices: 17492--17530 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
17482 ACATTTTTCT
17492 TTGTATCGATACA
1 TTGTATCGATACA
17505 TTGTATCGATACA
1 TTGTATCGATACA
*
17518 CTGTATCGATACA
1 TTGTATCGATACA
17531 GGGGGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:19329 original size:13 final size:13
Alignment explanation
Indices: 19311--19336 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19301 ACACCAAAGT
19311 ATGTATCGATACA
1 ATGTATCGATACA
19324 ATGTATCGATACA
1 ATGTATCGATACA
19337 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:19334 original size:33 final size:33
Alignment explanation
Indices: 19292--19356 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
19282 TAGCCAAACT
* *
19292 TGTATCGATACAC-CAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAAT-TGTATCGATACAA
19325 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
19357 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 25 0.86
34 4 0.14
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:25264 original size:33 final size:33
Alignment explanation
Indices: 25222--25287 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
25212 AAATTTCCAG
*
25222 ATGTATCGATACAAAGATCAATGTGTCGATACA
1 ATGTATCGATACAAAGATCAATGTATCGATACA
** *
25255 ATGTATCGATACATTGATTAATGTATCGATACA
1 ATGTATCGATACAAAGATCAATGTATCGATACA
25288 TTTCCTTGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.32
Consensus pattern (33 bp):
ATGTATCGATACAAAGATCAATGTATCGATACA
Found at i:26817 original size:13 final size:13
Alignment explanation
Indices: 26799--26823 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26789 TTCAACAATT
26799 TGTATCGATACAA
1 TGTATCGATACAA
26812 TGTATCGATACA
1 TGTATCGATACA
26824 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:31499 original size:21 final size:21
Alignment explanation
Indices: 31471--31528 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
31461 AAAAAAAATT
*
31471 CAAATGTATCGATACATT-TG
1 CAAATGTATCGATACATTCTA
*
31491 CGGAATGTATCGATACATTCTA
1 C-AAATGTATCGATACATTCTA
31513 CAAATGTATCGATACA
1 CAAATGTATCGATACA
31529 GGGTCCCAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 1 0.03
21 30 0.91
22 2 0.06
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (21 bp):
CAAATGTATCGATACATTCTA
Found at i:31588 original size:19 final size:19
Alignment explanation
Indices: 31564--31630 Score: 83
Period size: 19 Copynumber: 3.8 Consensus size: 19
31554 AATTCAACAA
31564 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
31583 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
31598 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
31615 ATTGTATCGATACATA
1 TTTGTATCGATACATA
31631 TTTAGCTACT
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 27 0.64
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:31603 original size:13 final size:13
Alignment explanation
Indices: 31585--31609 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31575 ACATAAGTTT
31585 TGTATCGATACAA
1 TGTATCGATACAA
31598 TGTATCGATACA
1 TGTATCGATACA
31610 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:31607 original size:32 final size:32
Alignment explanation
Indices: 31566--31628 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
31556 TTCAACAATT
*
31566 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
31598 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
31629 TATTTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Done.