Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_628 ID=scaffold_628-JGI_221_v2.0
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: 5140
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.33
Found at i:530 original size:1 final size:1
Alignment explanation
Indices: 515--627 Score: 64
Period size: 1 Copynumber: 113.0 Consensus size: 1
505 CCGGTAGAGG
* * * * * * * * * * * *
515 TTTTTTGTTTCTTTTTGTTTTTTTGTTTTTTGTTCTTTTTTGTTCTCTTTTTCTTTTTTCTCTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * *
580 TTTTCTTTTTTTTGTTTTTTTGTTTTTTTGTTTTTTTCTCTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
628 GAACTGAATC
Statistics
Matches: 76, Mismatches: 36, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
1 76 1.00
ACGTcount: A:0.00, C:0.09, G:0.07, T:0.84
Consensus pattern (1 bp):
T
Found at i:536 original size:17 final size:16
Alignment explanation
Indices: 515--625 Score: 107
Period size: 18 Copynumber: 6.4 Consensus size: 16
505 CCGGTAGAGG
*
515 TTTTTTGTTTCTTTTTGT
1 TTTTTTGTTT-TTTTT-C
533 TTTTTTGTTTTTTGTTC
1 TTTTTTGTTTTTT-TTC
550 TTTTTTGTTCTCTTTTTC
1 TTTTTTGTT-T-TTTTTC
*
568 TTTTTTCTCTTTTTTTC
1 TTTTTTGT-TTTTTTTC
585 TTTTTTTTGTTTTTTTGT-
1 --TTTTTTGTTTTTTT-TC
603 TTTTTTGTTTTTTTCTC
1 TTTTTTGTTTTTTT-TC
620 TTTTTT
1 TTTTTT
626 TTGAACTGAA
Statistics
Matches: 81, Mismatches: 4, Indels: 17
0.79 0.04 0.17
Matches are distributed among these distances:
16 15 0.19
17 24 0.30
18 30 0.37
19 12 0.15
ACGTcount: A:0.00, C:0.09, G:0.07, T:0.84
Consensus pattern (16 bp):
TTTTTTGTTTTTTTTC
Found at i:539 original size:8 final size:8
Alignment explanation
Indices: 515--616 Score: 89
Period size: 8 Copynumber: 11.8 Consensus size: 8
505 CCGGTAGAGG
515 TTTTTTGTT
1 TTTTTTG-T
524 TCTTTTTGT
1 T-TTTTTGT
533 TTTTTTG-
1 TTTTTTGT
540 TTTTTTGTT
1 TTTTTTG-T
549 CTTTTTTGTT
1 -TTTTTTG-T
*
559 CTCTTTTTCT
1 -T-TTTTTGT
*
569 TTTTTCTCT
1 TTTTT-TGT
*
578 TTTTTTCTT
1 TTTTTT-GT
587 TTTTTTGT
1 TTTTTTGT
595 TTTTTTGT
1 TTTTTTGT
603 TTTTTTGT
1 TTTTTTGT
611 TTTTTT
1 TTTTTT
617 CTCTTTTTTT
Statistics
Matches: 83, Mismatches: 3, Indels: 15
0.82 0.03 0.15
Matches are distributed among these distances:
7 7 0.08
8 34 0.41
9 19 0.23
10 18 0.22
11 5 0.06
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.84
Consensus pattern (8 bp):
TTTTTTGT
Found at i:548 original size:25 final size:25
Alignment explanation
Indices: 514--624 Score: 103
Period size: 25 Copynumber: 4.7 Consensus size: 25
504 CCCGGTAGAG
514 GTTTTTTGTTTCTTTTTGTTTTTTT
1 GTTTTTTGTTTCTTTTTGTTTTTTT
*
539 GTTTTTTG-TTCTTTTTTGTTCTCTTT
1 GTTTTTTGTTTC-TTTTTGTT-TTTTT
* * *
565 -TTCTTT-TTTCTCTTT-TTTTCTT
1 GTTTTTTGTTTCTTTTTGTTTTTTT
587 -TTTTTTG-TT-TTTTTGTTTTTTT
1 GTTTTTTGTTTCTTTTTGTTTTTTT
*
609 GTTTTTT-TCTCTTTTT
1 GTTTTTTGTTTCTTTTT
625 TTTGAACTGA
Statistics
Matches: 69, Mismatches: 9, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
21 4 0.06
22 16 0.23
23 9 0.13
24 12 0.17
25 24 0.35
26 4 0.06
ACGTcount: A:0.00, C:0.09, G:0.08, T:0.83
Consensus pattern (25 bp):
GTTTTTTGTTTCTTTTTGTTTTTTT
Found at i:626 original size:35 final size:34
Alignment explanation
Indices: 515--628 Score: 131
Period size: 34 Copynumber: 3.2 Consensus size: 34
505 CCGGTAGAGG
515 TTTTTTGTTTCTTTTTGTTTTTTTGTTTTTTGTTCTT
1 TTTTTTG-TT-TTTTTGTTTTTTTGTTTTTT-TTCTT
* * * *
552 TTTTGTTCTCTTTTTCTTTTTTCT-CTTTTTTTCTT
1 TTTT-TTGTTTTTTTGTTTTTT-TGTTTTTTTTCTT
587 TTTTTTGTTTTTTTGTTTTTTTGTTTTTTTCTCTT
1 TTTTTTGTTTTTTTGTTTTTTTGTTTTTTT-TCTT
622 TTTTTTG
1 TTTTTTG
629 AACTGAATCT
Statistics
Matches: 65, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
33 1 0.02
34 20 0.31
35 20 0.31
36 16 0.25
37 6 0.09
38 2 0.03
ACGTcount: A:0.00, C:0.09, G:0.08, T:0.83
Consensus pattern (34 bp):
TTTTTTGTTTTTTTGTTTTTTTGTTTTTTTTCTT
Done.