Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold667
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: 11219
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Found at i:497 original size:2 final size:2
Alignment explanation
Indices: 490--561 Score: 85
Period size: 2 Copynumber: 37.0 Consensus size: 2
480 ATCAACATGA
* * *
490 AT AT AT AT AT AT AT AT AT TT AC AT -T AT -T AT AT AT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
530 AC AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
562 TTAAAGTTTT
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
1 2 0.03
2 56 0.97
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:522 original size:20 final size:18
Alignment explanation
Indices: 494--564 Score: 110
Period size: 16 Copynumber: 3.9 Consensus size: 18
484 ACATGAATAT
494 ATATATATATATATTTAC
1 ATATATATATATATTTAC
512 ATTATTATATATATATTTAC
1 A-TA-TATATATATATTTAC
532 ATATATATATATATTT--
1 ATATATATATATATTTAC
548 ATATATATATATATTTA
1 ATATATATATATATTTA
565 AAGTTTTGCT
Statistics
Matches: 50, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
16 16 0.32
18 14 0.28
19 4 0.08
20 16 0.32
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
ATATATATATATATTTAC
Found at i:3516 original size:18 final size:18
Alignment explanation
Indices: 3490--3524 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3480 CAAAGAATAA
*
3490 AAAGCAAAAGGAAAAAAG
1 AAAGAAAAAGGAAAAAAG
3508 AAAGAAAAAGGAAAAAA
1 AAAGAAAAAGGAAAAAA
3525 AAGGAAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.77, C:0.03, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAGAAAAAGGAAAAAAG
Found at i:3526 original size:20 final size:20
Alignment explanation
Indices: 3501--3545 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
3491 AAGCAAAAGG
3501 AAAAAAGAAAGAAAAAG-GAA
1 AAAAAAGAAA-AAAAAGAGAA
* *
3521 AAAAAAGGAAAACAAGAGAA
1 AAAAAAGAAAAAAAAGAGAA
3541 AAAAA
1 AAAAA
3546 TCATCCAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (20 bp):
AAAAAAGAAAAAAAAGAGAA
Found at i:10646 original size:16 final size:16
Alignment explanation
Indices: 10623--10709 Score: 86
Period size: 16 Copynumber: 5.4 Consensus size: 16
10613 TCAATTATTT
10623 TTTTAAATTTAAATTA
1 TTTTAAATTTAAATTA
* *
10639 TATTAAATTTAAAATAA
1 TTTTAAATTT-AAATTA
* *
10656 TTTTTATTTTAAATTA
1 TTTTAAATTTAAATTA
*
10672 TTTTAAATTTAATTTA
1 TTTTAAATTTAAATTA
* *
10688 TTTTCAA-TTCAATTA
1 TTTTAAATTTAAATTA
10703 TTCTTAA
1 TT-TTAA
10710 GTTAATCAAA
Statistics
Matches: 56, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
15 8 0.14
16 36 0.64
17 12 0.21
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTTAAATTTAAATTA
Found at i:10762 original size:15 final size:15
Alignment explanation
Indices: 10742--10797 Score: 58
Period size: 16 Copynumber: 3.6 Consensus size: 15
10732 AAATTAAAAT
10742 TTTTAAATTGATTAA
1 TTTTAAATTGATTAA
* **
10757 TTTTAAATTAAATCGA
1 TTTTAAATT-GATTAA
*
10773 TCTTATAATTGATTAA
1 TTTTA-AATTGATTAA
10789 TTTTAAATT
1 TTTTAAATT
10798 AAATCGATCT
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
15 13 0.42
16 14 0.45
17 4 0.13
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.52
Consensus pattern (15 bp):
TTTTAAATTGATTAA
Found at i:10823 original size:32 final size:32
Alignment explanation
Indices: 10747--10811 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
10737 AAAATTTTTA
10747 AATTGATTAATTTTAAATTAAATCGATCTTAT
1 AATTGATTAATTTTAAATTAAATCGATCTTAT
10779 AATTGATTAATTTTAAATTAAATCGATCTTAT
1 AATTGATTAATTTTAAATTAAATCGATCTTAT
10811 A
1 A
10812 TTATTACAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (32 bp):
AATTGATTAATTTTAAATTAAATCGATCTTAT
Done.