Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012548.1 Kokia drynarioides strain JFW-HI SEQ_127557, 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: 17845
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1547 original size:2 final size:2
Alignment explanation
Indices: 1540--1565 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1530 ATTAAATCAA
1540 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1566 GTAGATACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6039 original size:21 final size:21
Alignment explanation
Indices: 6014--6061 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
6004 AATTAATAGA
**
6014 AAGTACCAAAGTACTTAGTAG
1 AAGTACCAAAGTACTTAACAG
6035 AAGTACCAAAGTACTTAACAG
1 AAGTACCAAAGTACTTAACAG
6056 AAGTAC
1 AAGTAC
6062 ATAACTGCTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.46, C:0.17, G:0.17, T:0.21
Consensus pattern (21 bp):
AAGTACCAAAGTACTTAACAG
Found at i:6108 original size:23 final size:23
Alignment explanation
Indices: 6076--6132 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
6066 CTGCTGGGGA
6076 AACAG-AAGCACACACAGTACTG
1 AACAGTAAGCACACACAGTACTG
* *
6098 AACAGTAAGCATACACAGTGCTG
1 AACAGTAAGCACACACAGTACTG
6121 AACAGTAAGCAC
1 AACAGTAAGCAC
6133 GCTAGCATTC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
22 5 0.16
23 26 0.84
ACGTcount: A:0.44, C:0.25, G:0.19, T:0.12
Consensus pattern (23 bp):
AACAGTAAGCACACACAGTACTG
Found at i:12508 original size:13 final size:13
Alignment explanation
Indices: 12487--12520 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
12477 ACAATATAAT
12487 AATAATAATCCTA
1 AATAATAATCCTA
*
12500 AATATTAATCCTA
1 AATAATAATCCTA
*
12513 AAAAATAA
1 AATAATAA
12521 AGTTTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:13480 original size:22 final size:21
Alignment explanation
Indices: 13452--13498 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
13442 CCTTTTCTTC
** *
13452 TTTTTTTCTGATTTTTCTTTTT
1 TTTTTTTCAAATTTTT-TTATT
13474 TTTTTTTCAAATTTTTTTATT
1 TTTTTTTCAAATTTTTTTATT
13495 TTTT
1 TTTT
13499 CGACTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.11, C:0.06, G:0.02, T:0.81
Consensus pattern (21 bp):
TTTTTTTCAAATTTTTTTATT
Found at i:13490 original size:18 final size:18
Alignment explanation
Indices: 13469--13511 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
13459 CTGATTTTTC
13469 TTTTTTTTTTTTCAAATT
1 TTTTTTTTTTTTCAAATT
* * *
13487 TTTTTATTTTTTCGACTT
1 TTTTTTTTTTTTCAAATT
13505 TTTTTTT
1 TTTTTTT
13512 AAATAATAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.12, C:0.07, G:0.02, T:0.79
Consensus pattern (18 bp):
TTTTTTTTTTTTCAAATT
Found at i:14442 original size:5 final size:5
Alignment explanation
Indices: 14427--14486 Score: 57
Period size: 5 Copynumber: 10.6 Consensus size: 5
14417 AAAATATTGC
14427 AAAATT AAAAT AAAATT AAAAAT AAAAT AAAAT AAAACT AAAAAT GAAAAT
1 AAAA-T AAAAT AAAA-T -AAAAT AAAAT AAAAT AAAA-T -AAAAT -AAAAT
14478 AAAAAT AAA
1 -AAAAT AAA
14487 TATACTAATT
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
5 22 0.46
6 18 0.38
7 8 0.17
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:14484 original size:6 final size:6
Alignment explanation
Indices: 14427--14486 Score: 70
Period size: 6 Copynumber: 10.3 Consensus size: 6
14417 AAAATATTGC
* * * *
14427 AAAATT AAAATA AAATTA AAAAT- AAAAT- AAAATA AAACTA AAAATG
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
14473 AAAATA AAAATA AA
1 AAAATA AAAATA AA
14487 TATACTAATT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
5 10 0.22
6 36 0.78
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.20
Consensus pattern (6 bp):
AAAATA
Done.