Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000328.1 Kokia drynarioides strain JFW-HI SEQ_111098, 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: 108544
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:4309 original size:18 final size:19
Alignment explanation
Indices: 4273--4311 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
4263 TATTTGTAAG
4273 AAATTAAAAATCATATAAA
1 AAATTAAAAATCATATAAA
4292 AAATATAAAAA-C-TATAAA
1 AAAT-TAAAAATCATATAAA
4310 AA
1 AA
4312 TATTTCTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.42
19 5 0.26
20 6 0.32
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (19 bp):
AAATTAAAAATCATATAAA
Found at i:4928 original size:51 final size:51
Alignment explanation
Indices: 4818--4929 Score: 129
Period size: 52 Copynumber: 2.2 Consensus size: 51
4808 ACGTAAATAG
* * *
4818 TTATTCAATTATGAAAAATTATAAAATTATCAATTAATTATTAATATATTT
1 TTATTTAATTATAAAAAATTATAAAATTATCAATTAATTATTAATATATCT
** *
4869 TTCATTTAATTATAAAAAATTATAAAA-TATCTTTTAATTATTTAATTTTATCT
1 TT-ATTTAATTATAAAAAATTATAAAATTATCAATTAATTA-TTAA-TATATCT
4922 TT-TTTAAT
1 TTATTTAAT
4930 CATCCAATCA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
51 19 0.37
52 26 0.50
53 7 0.13
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.52
Consensus pattern (51 bp):
TTATTTAATTATAAAAAATTATAAAATTATCAATTAATTATTAATATATCT
Found at i:5502 original size:45 final size:49
Alignment explanation
Indices: 5451--5554 Score: 117
Period size: 51 Copynumber: 2.2 Consensus size: 49
5441 GGATCCTCCT
* *
5451 TCAATGCC-AAC-A-ACAGAACCAA-AACAAGTTCAAACTCAGGAAGTA
1 TCAATGCCAAACAAGACAGAACCAACAACAAGTTCAAACCCAGAAAGTA
** *
5496 TCAATGCCTCAAACAAGACAGCCCCAACAAGAAGTTCAAACCCAGAAAGTA
1 TCAATG-C-CAAACAAGACAGAACCAACAACAAGTTCAAACCCAGAAAGTA
5547 TCAATGCC
1 TCAATGCC
5555 TGAAGCTCAA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
45 6 0.12
46 1 0.02
47 1 0.02
48 3 0.06
49 2 0.04
50 9 0.19
51 26 0.54
ACGTcount: A:0.45, C:0.28, G:0.13, T:0.13
Consensus pattern (49 bp):
TCAATGCCAAACAAGACAGAACCAACAACAAGTTCAAACCCAGAAAGTA
Found at i:23050 original size:22 final size:22
Alignment explanation
Indices: 23016--23060 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
23006 ACACTTTTAT
23016 AAATCTTAAAAAAATGTGTCAAA
1 AAATCTTAAAAAAATGTGT-AAA
* *
23039 AAAT-TTATAAAAGTGTGTAAA
1 AAATCTTAAAAAAATGTGTAAA
23060 A
1 A
23061 TTTTCTTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 4 0.20
22 12 0.60
23 4 0.20
ACGTcount: A:0.56, C:0.04, G:0.11, T:0.29
Consensus pattern (22 bp):
AAATCTTAAAAAAATGTGTAAA
Found at i:34294 original size:2 final size:2
Alignment explanation
Indices: 34289--34313 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
34279 CTTTTGTCTT
34289 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
34314 TGCTGGTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35070 original size:25 final size:24
Alignment explanation
Indices: 35020--35074 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
35010 ATATTAGATC
* *
35020 AAAAATTAAATTAATTTTTTTGTT
1 AAAAATTAAATTAATTTTTCTATT
**
35044 AAAAATTTCATTAATTTTTACTATT
1 AAAAATTAAATTAATTTTT-CTATT
35069 AAAAAT
1 AAAAAT
35075 GAGTTACTAC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 17 0.65
25 9 0.35
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (24 bp):
AAAAATTAAATTAATTTTTCTATT
Found at i:45312 original size:2 final size:2
Alignment explanation
Indices: 45301--45340 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
45291 CTTCATTTTC
45301 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
45341 TTGATGACCT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:59080 original size:16 final size:15
Alignment explanation
Indices: 59059--59088 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
59049 TTATTTTCTA
59059 TTGATTATATATAATG
1 TTGATTAT-TATAATG
59075 TTGATTATTATAAT
1 TTGATTATTATAAT
59089 AACAAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (15 bp):
TTGATTATTATAATG
Found at i:65346 original size:2 final size:2
Alignment explanation
Indices: 65339--65373 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
65329 GCTCTGCCCC
65339 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
65374 GTATGTTTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:78400 original size:35 final size:35
Alignment explanation
Indices: 78360--78429 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
78350 TTTAGGTTAT
78360 CCAATCACACAAAATAAAAAGATTGGTGGCGACTC
1 CCAATCACACAAAATAAAAAGATTGGTGGCGACTC
**
78395 CCAATCACACCGAATAAAAAGATTGGTGGCGACTC
1 CCAATCACACAAAATAAAAAGATTGGTGGCGACTC
78430 TCATTTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.40, C:0.24, G:0.19, T:0.17
Consensus pattern (35 bp):
CCAATCACACAAAATAAAAAGATTGGTGGCGACTC
Found at i:91237 original size:3 final size:3
Alignment explanation
Indices: 91231--91257 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
91221 AATGCAGCAG
91231 CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA
91258 AGGAACCGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Done.