Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001344.1 Kokia drynarioides strain JFW-HI SEQ_112790, whole genome shotgun sequence
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: 3255
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Found at i:535 original size:27 final size:29
Alignment explanation
Indices: 488--545 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 29
478 TCACGTTCCC
*
488 TCCCTCCTTTTCTTTCCTTC-TT-CTTCT
1 TCCCTCATTTTCTTTCCTTCTTTCCTTCT
*
515 TCCCTCATTTTCTCTT-TTTCTTTCCTTCT
1 TCCCTCATTTTCT-TTCCTTCTTTCCTTCT
544 TC
1 TC
546 TCCTTTCACA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
27 15 0.58
28 4 0.15
29 7 0.27
ACGTcount: A:0.02, C:0.38, G:0.00, T:0.60
Consensus pattern (29 bp):
TCCCTCATTTTCTTTCCTTCTTTCCTTCT
Found at i:565 original size:35 final size:35
Alignment explanation
Indices: 495--566 Score: 83
Period size: 35 Copynumber: 2.1 Consensus size: 35
485 CCCTCCCTCC
* * **
495 TTTTCTTTCCTTCTTCTTCTTCCCTCATTTTCTCT
1 TTTTCTTTCCTTCTTCTCCTTCCCACATTCACTCT
*
530 TTTTCTTTCCTTCTTCTCCTT-TCACATTCCACTCT
1 TTTTCTTTCCTTCTTCTCCTTCCCACATT-CACTCT
565 TT
1 TT
567 GATATGAGGA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
34 5 0.16
35 26 0.84
ACGTcount: A:0.06, C:0.35, G:0.00, T:0.60
Consensus pattern (35 bp):
TTTTCTTTCCTTCTTCTCCTTCCCACATTCACTCT
Found at i:2738 original size:26 final size:26
Alignment explanation
Indices: 2709--2801 Score: 91
Period size: 26 Copynumber: 3.5 Consensus size: 26
2699 AAGATGAAGA
2709 AATGAGAGAAGAGAAAAATAAGTTTG
1 AATGAGAGAAGAGAAAAATAAGTTTG
** *
2735 AATGAGAGAAGA-ATTAAGTTTA-TTTG
1 AATGAGAGAAGAGA--AAAATAAGTTTG
*
2761 ATTGACGAGAGAAGAGAAAAATAAGTTTG
1 A---ATGAGAGAAGAGAAAAATAAGTTTG
2790 AATGAGAGAAGA
1 AATGAGAGAAGA
2802 ATTAAGTTTA
Statistics
Matches: 52, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
25 1 0.02
26 27 0.52
27 4 0.08
28 4 0.08
29 15 0.29
30 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.27, T:0.23
Consensus pattern (26 bp):
AATGAGAGAAGAGAAAAATAAGTTTG
Found at i:2796 original size:55 final size:55
Alignment explanation
Indices: 2712--2818 Score: 214
Period size: 55 Copynumber: 1.9 Consensus size: 55
2702 ATGAAGAAAT
2712 GAGAGAAGAGAAAAATAAGTTTGAATGAGAGAAGAATTAAGTTTATTTGATTGAC
1 GAGAGAAGAGAAAAATAAGTTTGAATGAGAGAAGAATTAAGTTTATTTGATTGAC
2767 GAGAGAAGAGAAAAATAAGTTTGAATGAGAGAAGAATTAAGTTTATTTGATT
1 GAGAGAAGAGAAAAATAAGTTTGAATGAGAGAAGAATTAAGTTTATTTGATT
2819 CAGAGGAGAG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.46, C:0.01, G:0.25, T:0.28
Consensus pattern (55 bp):
GAGAGAAGAGAAAAATAAGTTTGAATGAGAGAAGAATTAAGTTTATTTGATTGAC
Found at i:2815 original size:26 final size:26
Alignment explanation
Indices: 2731--2816 Score: 77
Period size: 26 Copynumber: 3.2 Consensus size: 26
2721 GAAAAATAAG
2731 TTTGAATGAGAGAAGAATTAAGTTTA
1 TTTGAATGAGAGAAGAATTAAGTTTA
* ** *
2757 TTTGATTGACGAGAGAAGAGA--AAAATAA
1 TTTGA---ATGAGAGAAGA-ATTAAGTTTA
2785 GTTTGAATGAGAGAAGAATTAAGTTTA
1 -TTTGAATGAGAGAAGAATTAAGTTTA
2812 TTTGA
1 TTTGA
2817 TTCAGAGGAG
Statistics
Matches: 45, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
25 1 0.02
26 20 0.44
27 4 0.09
28 4 0.09
29 15 0.33
30 1 0.02
ACGTcount: A:0.43, C:0.01, G:0.24, T:0.31
Consensus pattern (26 bp):
TTTGAATGAGAGAAGAATTAAGTTTA
Done.