Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002105.1 Kokia drynarioides strain JFW-HI SEQ_114026, 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: 7014
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:722 original size:16 final size:17
Alignment explanation
Indices: 691--773 Score: 71
Period size: 18 Copynumber: 4.7 Consensus size: 17
681 ATATTCAATT
*
691 TATTTATATATTATATC
1 TATTTATATATTATATA
*
708 TATTT-TATTTTATATA
1 TATTTATATATTATATA
*
724 TATTCTAAATATT-TGATA
1 TATT-TATATATTAT-ATA
*
742 TATTTTTATATTTATATA
1 TATTTATATA-TTATATA
760 TTATTATATATATT
1 -TATT-TATATATT
774 TTTATTTCTA
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
16 13 0.25
17 11 0.21
18 16 0.31
19 7 0.13
20 5 0.10
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.61
Consensus pattern (17 bp):
TATTTATATATTATATA
Found at i:730 original size:21 final size:20
Alignment explanation
Indices: 680--744 Score: 62
Period size: 20 Copynumber: 3.1 Consensus size: 20
670 TGTATAATAT
680 TATATTC-AATTTATTTATA
1 TATATTCTAATTTATTTATA
*
699 TATTATATCTATTTTATTTTATA
1 TA-TAT-TCTAATTTA-TTTATA
*
722 TATATTCTAA-ATATTTGATA
1 TATATTCTAATTTATTT-ATA
742 TAT
1 TAT
745 TTTTATATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
19 5 0.13
20 11 0.29
21 6 0.16
22 8 0.21
23 8 0.21
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (20 bp):
TATATTCTAATTTATTTATA
Found at i:768 original size:26 final size:26
Alignment explanation
Indices: 722--780 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
712 TTATTTTATA
722 TATATTCTAAATATTTGATATAT-TTT
1 TATATT-TAAATATTTGATATATATTT
* *
748 TATATTTATATATTATTATATATATTT
1 TATATTTAAATATT-TGATATATATTT
775 T-TATTT
1 TATATTT
781 CTATTTTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 7 0.24
26 18 0.62
27 4 0.14
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (26 bp):
TATATTTAAATATTTGATATATATTT
Found at i:2398 original size:13 final size:13
Alignment explanation
Indices: 2380--2404 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2370 TATATTTTAC
2380 TTTATTTACTTTT
1 TTTATTTACTTTT
2393 TTTATTTACTTT
1 TTTATTTACTTT
2405 ACCACTCTCA
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:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTATTTACTTTT
Found at i:3390 original size:16 final size:16
Alignment explanation
Indices: 3371--3414 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
3361 AGCAAATATG
*
3371 CTAGTAAATAAATACA
1 CTAGTAAATAAACACA
3387 CTAGTAAATAAACACA
1 CTAGTAAATAAACACA
3403 CTAGTAAATAAA
1 CTAGTAAATAAA
3415 ATACTAGATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.57, C:0.14, G:0.07, T:0.23
Consensus pattern (16 bp):
CTAGTAAATAAACACA
Done.