Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004398.1 Kokia drynarioides strain JFW-HI SEQ_117775, 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: 2392
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Found at i:521 original size:30 final size:30
Alignment explanation
Indices: 483--610 Score: 143
Period size: 30 Copynumber: 4.3 Consensus size: 30
473 CCCAGAAGGT
*
483 CCCGAAACTTCCAAAAATTCAATTTTTAAC
1 CCCGAAACTTCCAAAAATTCCATTTTTAAC
* *
513 CTCGAAACTTCCAAAAATTCCATTTTTACC
1 CCCGAAACTTCCAAAAATTCCATTTTTAAC
*
543 CCCGAAACTTCCAAAAATTGCCA-TTTTACC
1 CCCGAAACTTCCAAAAATT-CCATTTTTAAC
** * * *
573 CCCGAATGTT-CAAAAACTCTATTTTCAAC
1 CCCGAAACTTCCAAAAATTCCATTTTTAAC
*
602 CTCGAAACT
1 CCCGAAACT
611 CTCAAAATTA
Statistics
Matches: 83, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
28 2 0.02
29 18 0.22
30 60 0.72
31 3 0.04
ACGTcount: A:0.35, C:0.30, G:0.05, T:0.30
Consensus pattern (30 bp):
CCCGAAACTTCCAAAAATTCCATTTTTAAC
Found at i:1486 original size:17 final size:17
Alignment explanation
Indices: 1441--1520 Score: 94
Period size: 17 Copynumber: 4.8 Consensus size: 17
1431 GGACTTAGTG
1441 GAAATTG-AATTTATTT
1 GAAATTGAAATTTATTT
* *
1457 -AAATTTAAGTTTATTT
1 GAAATTGAAATTTATTT
1473 GAAATTGAAATTTATTT
1 GAAATTGAAATTTATTT
*
1490 GAAATTTAAATTTATTAT
1 GAAATTGAAATTTATT-T
*
1508 AAAATT-AAATTTA
1 GAAATTGAAATTTA
1521 GAAAGTCCAA
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
15 5 0.09
16 8 0.15
17 36 0.65
18 6 0.11
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (17 bp):
GAAATTGAAATTTATTT
Found at i:1504 original size:34 final size:34
Alignment explanation
Indices: 1441--1520 Score: 112
Period size: 34 Copynumber: 2.4 Consensus size: 34
1431 GGACTTAGTG
*
1441 GAAATTG-AATTTATTTAAATTTAAGTTTATT-T
1 GAAATTGAAATTTATTTAAATTTAAATTTATTAT
1473 GAAATTGAAATTTATTTGAAATTTAAATTTATTAT
1 GAAATTGAAATTTATTT-AAATTTAAATTTATTAT
*
1508 AAAATT-AAATTTA
1 GAAATTGAAATTTA
1521 GAAAGTCCAA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
32 7 0.16
33 9 0.21
34 21 0.49
35 6 0.14
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (34 bp):
GAAATTGAAATTTATTTAAATTTAAATTTATTAT
Found at i:1577 original size:15 final size:15
Alignment explanation
Indices: 1553--1623 Score: 88
Period size: 15 Copynumber: 4.7 Consensus size: 15
1543 AAAACAAAGT
1553 CCAATTACAAATGAC
1 CCAATTACAAATGAC
* *
1568 CCAATAACAAATGGC
1 CCAATTACAAATGAC
* *
1583 CCAGTTACAGATGAC
1 CCAATTACAAATGAC
* *
1598 CCAAATACAAATGGC
1 CCAATTACAAATGAC
1613 CCAATTACAAA
1 CCAATTACAAA
1624 CTACCCAAAA
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.45, C:0.27, G:0.11, T:0.17
Consensus pattern (15 bp):
CCAATTACAAATGAC
Found at i:1597 original size:30 final size:30
Alignment explanation
Indices: 1553--1632 Score: 110
Period size: 30 Copynumber: 2.7 Consensus size: 30
1543 AAAACAAAGT
1553 CCAATTACAAATGACCC-AATAACAAATGGC
1 CCAATTACAAATGACCCAAAT-ACAAATGGC
* *
1583 CCAGTTACAGATGACCCAAATACAAATGGC
1 CCAATTACAAATGACCCAAATACAAATGGC
1613 CCAATTACAAACT-ACCCAAA
1 CCAATTACAAA-TGACCCAAA
1633 AGCCCAAACT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
30 40 0.91
31 4 0.09
ACGTcount: A:0.45, C:0.29, G:0.10, T:0.16
Consensus pattern (30 bp):
CCAATTACAAATGACCCAAATACAAATGGC
Found at i:2259 original size:15 final size:15
Alignment explanation
Indices: 2239--2284 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
2229 AAATGTTTTG
2239 ATATTAATAATAATA
1 ATATTAATAATAATA
* *
2254 ATATTAATAATTATT
1 ATATTAATAATAATA
2269 A-ATTAATAATTAATA
1 ATATTAATAA-TAATA
2284 A
1 A
2285 AAAAAACGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 8 0.31
15 18 0.69
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATATTAATAATAATA
Found at i:2271 original size:7 final size:7
Alignment explanation
Indices: 2246--2284 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
2236 TTGATATTAA
2246 TAATAA-
1 TAATAAT
2252 TAAT-AT
1 TAATAAT
2258 TAATAAT
1 TAATAAT
*
2265 TATTAAT
1 TAATAAT
2272 TAATAAT
1 TAATAAT
2279 TAATAA
1 TAATAA
2285 AAAAAACGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
5 1 0.03
6 8 0.28
7 20 0.69
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TAATAAT
Done.