Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold3226
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, 468
Length: 781
ACGTcount: A:0.24, C:0.22, G:0.07, T:0.47
Found at i:475 original size:10 final size:10
Alignment explanation
Indices: 462--630 Score: 65
Period size: 10 Copynumber: 17.1 Consensus size: 10
452 TCCTTCCCTC
462 TTCTTCTTCT
1 TTCTTCTTCT
472 TTCTTTCTTC-
1 TTC-TTCTTCT
482 TTCTTCTTTCT
1 TTCTTC-TTCT
* *
493 TTTTTTTTC-
1 TTCTTCTTCT
* *
502 CTCTTCTCCT
1 TTCTTCTTCT
512 TTCCTT-TTCT
1 TT-CTTCTTCT
*
522 TTC--CTTAT
1 TTCTTCTTCT
530 TT-TTCTTTCT
1 TTCTTC-TTCT
* *
540 TTCCTC-CCAT
1 TTCTTCTTC-T
550 TTCCTT-TTCT
1 TT-CTTCTTCT
560 TTC--CTTCT
1 TTCTTCTTCT
568 TT-TTCTTTCT
1 TTCTTC-TTCT
* *
578 TTCCTCTCCT
1 TTCTTCTTCT
*
588 TTCCTT-TTCC
1 TT-CTTCTTCT
*
598 TTCTTTTTCT
1 TTCTTCTTCT
608 TTCTTCCTTTCT
1 TTCTT-C-TTCT
620 TTCTTCTTCT
1 TTCTTCTTCT
630 T
1 T
631 CCCCTCTCCT
Statistics
Matches: 116, Mismatches: 21, Indels: 44
0.64 0.12 0.24
Matches are distributed among these distances:
8 11 0.09
9 16 0.14
10 57 0.49
11 23 0.20
12 9 0.08
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.67
Consensus pattern (10 bp):
TTCTTCTTCT
Found at i:501 original size:23 final size:23
Alignment explanation
Indices: 460--541 Score: 76
Period size: 23 Copynumber: 3.5 Consensus size: 23
450 CTTCCTTCCC
*
460 TCTTC-TTCTTCTTTCTTTCTTCT
1 TCTTCTTTCTT-TTTTTTTCTTCT
*
483 TCTTCTTTCTTTTTTTTTCCTCT
1 TCTTCTTTCTTTTTTTTTCTTCT
* * * *
506 TCTCCTTTCCTTTTCTTTCCTTAT
1 TCTTCTTT-CTTTTTTTTTCTTCT
*
530 TTTTCTTTCTTT
1 TCTTCTTTCTTT
542 CCTCCCATTT
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
23 26 0.54
24 22 0.46
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.71
Consensus pattern (23 bp):
TCTTCTTTCTTTTTTTTTCTTCT
Found at i:540 original size:18 final size:18
Alignment explanation
Indices: 517--582 Score: 71
Period size: 18 Copynumber: 3.6 Consensus size: 18
507 CTCCTTTCCT
517 TTTCTTTCCTTATTTTTC
1 TTTCTTTCCTTATTTTTC
* *
535 TTTCTTTCCTCCCA-TTTCC
1 TTTCTTTCCT--TATTTTTC
*
554 TTTTCTTTCCTTCTTTTTC
1 -TTTCTTTCCTTATTTTTC
573 TTTCTTTCCT
1 TTTCTTTCCT
583 CTCCTTTCCT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
18 20 0.51
19 8 0.21
20 11 0.28
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTCTTTCCTTATTTTTC
Found at i:558 original size:38 final size:38
Alignment explanation
Indices: 506--618 Score: 158
Period size: 38 Copynumber: 3.0 Consensus size: 38
496 TTTTTCCTCT
506 TCTCCTTTCCTTTTCTTTCCTTATTTTTCTTTCTTTCC
1 TCTCCTTTCCTTTTCTTTCCTTATTTTTCTTTCTTTCC
*
544 TC-CCATTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCC
1 TCTCC-TTTCCTTTTCTTTCCTTATTTTTCTTTCTTTCC
* * *
582 TCTCCTTTCCTTTTCCTT-CTTTTTCTTTCTTCCTTTC
1 TCTCCTTTCCTTTTCTTTCCTTATT-TTTCTTTCTTTC
619 TTTCTTCTTC
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
37 7 0.10
38 59 0.87
39 2 0.03
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.65
Consensus pattern (38 bp):
TCTCCTTTCCTTTTCTTTCCTTATTTTTCTTTCTTTCC
Found at i:628 original size:28 final size:30
Alignment explanation
Indices: 438--631 Score: 103
Period size: 34 Copynumber: 6.2 Consensus size: 30
428 TTACCTTATT
**
438 TTCTT-TTT-TTTCCTTCC-TTCCCTCTTC
1 TTCTTCTTTCTTTCCTTCCTTTCTTTCTTC
* *
465 TTCTTCTTTCTTTCTTCTTCTTCTTTCTTTTTTT
1 TTCTTCTTTCTTTC--CTTC--CTTTCTTTCTTC
* * * * *
499 TTCCTCTTCTCCTTTCCTTTTCTTTCCTTATTT
1 TTCTTCTT-T-CTTTCC-TTCCTTTCTTTCTTC
* *
532 TTCTTTCTTTCCTCCCATTTCCTTTTCTTTCCTTC
1 TTC-TTCTTTCTTTCC--TTCC-TTTCTTT-CTTC
* *
567 TTTTTCTTTCTTTCCTCTCCTTTCCTTT-TCC
1 TTCTTCTTTCTTTCCT-TCCTTT-CTTTCTTC
598 TTCTT-TTTCTTT-CTTCCTTTCTTTCTTC
1 TTCTTCTTTCTTTCCTTCCTTTCTTTCTTC
626 TTCTTC
1 TTCTTC
632 CCCTCTCCTT
Statistics
Matches: 128, Mismatches: 21, Indels: 34
0.70 0.11 0.19
Matches are distributed among these distances:
27 9 0.07
28 16 0.12
29 6 0.05
30 7 0.05
31 10 0.08
32 8 0.06
33 26 0.20
34 34 0.27
35 7 0.05
36 5 0.04
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.66
Consensus pattern (30 bp):
TTCTTCTTTCTTTCCTTCCTTTCTTTCTTC
Found at i:641 original size:42 final size:40
Alignment explanation
Indices: 564--644 Score: 99
Period size: 42 Copynumber: 2.0 Consensus size: 40
554 TTTTCTTTCC
* * *
564 TTCTTTTTCTTTCTTTCCTCTCCTTTCCTTTTCCTTCTTT
1 TTCTTTTTCTTTCTTTCCTCTCCTTCCCCTCTCCTTCTTT
* *
604 TTCTTTCTTCCTTTCTTTCTTCTTCTTCCCCTCTCCTTCTT
1 TTCTTT-TT-CTTTCTTTCCTCTCCTTCCCCTCTCCTTCTT
645 CCCCCCACCA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
40 6 0.18
41 2 0.06
42 26 0.76
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (40 bp):
TTCTTTTTCTTTCTTTCCTCTCCTTCCCCTCTCCTTCTTT
Done.