Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001428.1 Kokia drynarioides strain JFW-HI SEQ_112933, 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: 3928
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.35
Found at i:879 original size:17 final size:17
Alignment explanation
Indices: 857--889 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
847 TAATTTTTAA
857 TTTGAATTTGGTAAAAG
1 TTTGAATTTGGTAAAAG
874 TTTGAATTTGGTAAAA
1 TTTGAATTTGGTAAAA
890 TTATTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.42
Consensus pattern (17 bp):
TTTGAATTTGGTAAAAG
Found at i:987 original size:12 final size:12
Alignment explanation
Indices: 963--1014 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
953 AATTATCATT
963 TTTTAAA-AT-A
1 TTTTAAATATAA
973 TTTTAAATATAA
1 TTTTAAATATAA
* *
985 TTTGAAATATGGTA
1 TTTTAAATAT--AA
999 TTTTAAATATAA
1 TTTTAAATATAA
1011 TTTT
1 TTTT
1015 TTTGTATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
10 7 0.21
11 2 0.06
12 15 0.44
14 10 0.29
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (12 bp):
TTTTAAATATAA
Found at i:1045 original size:23 final size:23
Alignment explanation
Indices: 973--1046 Score: 62
Period size: 23 Copynumber: 3.1 Consensus size: 23
963 TTTTAAAATA
*
973 TTTTAAATATAATTTGAAATATGGTA-
1 TTTTAAATATAATTT----TATTGTAT
*
999 TTTTAAATATAATTTTTTTGTAT
1 TTTTAAATATAATTTTATTGTAT
*
1022 TTTTAAATTTAATTATTATT-TAT
1 TTTTAAATATAATT-TTATTGTAT
1045 TT
1 TT
1047 AAATATTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
22 5 0.12
23 18 0.43
24 4 0.10
26 15 0.36
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.59
Consensus pattern (23 bp):
TTTTAAATATAATTTTATTGTAT
Found at i:1337 original size:11 final size:11
Alignment explanation
Indices: 1295--1371 Score: 73
Period size: 11 Copynumber: 6.8 Consensus size: 11
1285 CAAATTAAAT
*
1295 ATTTAATTTTA
1 ATTTAATTTGA
*
1306 ATTTTAATTTTA
1 A-TTTAATTTGA
* *
1318 GTTTCATTTGA
1 ATTTAATTTGA
1329 ATTTAATTTGA
1 ATTTAATTTGA
* *
1340 AGTTCATTTGA
1 ATTTAATTTGA
*
1351 AATTAATTTGA
1 ATTTAATTTGA
1362 ATTTCAATTT
1 ATTT-AATTT
1372 TAACTTAGTG
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
11 39 0.72
12 15 0.28
ACGTcount: A:0.32, C:0.04, G:0.08, T:0.56
Consensus pattern (11 bp):
ATTTAATTTGA
Found at i:1484 original size:7 final size:6
Alignment explanation
Indices: 1459--1499 Score: 66
Period size: 6 Copynumber: 6.8 Consensus size: 6
1449 TTCAACTTCG
1459 ATTTTA ATTTTA ATTTTA ATTTTTA ATTTTA A-TTTA ATTTT
1 ATTTTA ATTTTA ATTTTA A-TTTTA ATTTTA ATTTTA ATTTT
1500 TTAAGTTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 5 0.15
6 22 0.67
7 6 0.18
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
ATTTTA
Found at i:1484 original size:13 final size:13
Alignment explanation
Indices: 1460--1541 Score: 64
Period size: 13 Copynumber: 6.2 Consensus size: 13
1450 TCAACTTCGA
1460 TTTTAATTTTAA-
1 TTTTAATTTTAAT
1472 TTTTAATTTTTAA-
1 TTTTAA-TTTTAAT
1485 TTTTAA-TTTAATT
1 TTTTAATTTTAA-T
*
1498 TTTTAA-GTTAATT
1 TTTTAATTTTAA-T
1511 TTTTAAAATTTTAAAT
1 TTTT--AATTTT-AAT
*
1527 TTTAAATTTTAAT
1 TTTTAATTTTAAT
1540 TT
1 TT
1542 AAAATTATTT
Statistics
Matches: 60, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
11 5 0.08
12 6 0.10
13 33 0.55
14 6 0.10
15 2 0.03
16 6 0.10
17 2 0.03
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (13 bp):
TTTTAATTTTAAT
Found at i:1528 original size:7 final size:7
Alignment explanation
Indices: 1459--1547 Score: 57
Period size: 6 Copynumber: 13.4 Consensus size: 7
1449 TTCAACTTCG
1459 ATTTT-A
1 ATTTTAA
1465 ATTTT-A
1 ATTTTAA
1471 ATTTT-A
1 ATTTTAA
*
1477 ATTTTTA
1 ATTTTAA
1484 ATTTT-A
1 ATTTTAA
1490 A-TTTAA
1 ATTTTAA
* *
1496 TTTTTTA
1 ATTTTAA
*
1503 A-GTTAA
1 ATTTTAA
*
1509 TTTTTTAAA
1 -ATTTT-AA
1518 ATTTTAA
1 ATTTTAA
1525 ATTTTAA
1 ATTTTAA
1532 ATTTT-A
1 ATTTTAA
*
1538 ATTTAAA
1 ATTTTAA
1545 ATT
1 ATT
1548 ATTTTTAATA
Statistics
Matches: 67, Mismatches: 9, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
5 3 0.04
6 28 0.42
7 28 0.42
8 6 0.09
9 2 0.03
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (7 bp):
ATTTTAA
Found at i:1555 original size:17 final size:17
Alignment explanation
Indices: 1533--1575 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
1523 AAATTTTAAA
1533 TTTTAATTTAAAAT-TAT
1 TTTTAATTTAAAATAT-T
*
1550 TTTTAATAT-AAATATT
1 TTTTAATTTAAAATATT
1566 TTTTAATTTA
1 TTTTAATTTA
1576 TTTATTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTTAATTTAAAATATT
Found at i:1611 original size:21 final size:21
Alignment explanation
Indices: 1561--1611 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1551 TTTAATATAA
* *
1561 ATATTTTTTAATTTATTTATT
1 ATATTTTTTAATTAATTAATT
*
1582 ATATATTTTAATTAATTAATT
1 ATATTTTTTAATTAATTAATT
* *
1603 TTTTTTTTT
1 ATATTTTTT
1612 GCAGTTGGGA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (21 bp):
ATATTTTTTAATTAATTAATT
Done.