Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007113.1 Kokia drynarioides strain JFW-HI SEQ_121723, 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: 38269
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:13707 original size:24 final size:21
Alignment explanation
Indices: 13680--13728 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
13670 TCTCACAATT
13680 TATTTATATGGTAATATAATTCTA
1 TATTTATAT--TAATATAA-TCTA
* *
13704 TATTTTTATTTATATAATCTA
1 TATTTATATTAATATAATCTA
13725 TATT
1 TATT
13729 CTTTTTATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 8 0.35
22 7 0.30
24 8 0.35
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (21 bp):
TATTTATATTAATATAATCTA
Found at i:13726 original size:21 final size:21
Alignment explanation
Indices: 13693--13736 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
13683 TTATATGGTA
*
13693 ATATAATTCTATATTTTTATTT
1 ATATAATTCTATATTCTT-TTT
13715 ATATAA-TCTATATTCTTTTT
1 ATATAATTCTATATTCTTTTT
13735 AT
1 AT
13737 GTCAGGTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.24
21 10 0.48
22 6 0.29
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (21 bp):
ATATAATTCTATATTCTTTTT
Found at i:14425 original size:17 final size:18
Alignment explanation
Indices: 14394--14428 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
14384 GACAAACAAA
*
14394 ATTTTAATAATTTTTTAT
1 ATTTTAATAAGTTTTTAT
14412 ATTTT-ATAAGTTTTTAT
1 ATTTTAATAAGTTTTTAT
14429 TTATATTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (18 bp):
ATTTTAATAAGTTTTTAT
Found at i:18222 original size:24 final size:24
Alignment explanation
Indices: 18173--18223 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
18163 AAGCCAATGT
**
18173 TATTTATTATATATATTTTTTGAA
1 TATTTATTATATATATTTTTAAAA
18197 TATTTATTATATAT-TATTTTAAAA
1 TATTTATTATATATAT-TTTTAAAA
18221 TAT
1 TAT
18224 ACATCTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
TATTTATTATATATATTTTTAAAA
Found at i:19036 original size:24 final size:25
Alignment explanation
Indices: 19004--19055 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 25
18994 CTTTTTAAAA
*
19004 TAAATTAATTTTAATTATTA-ATCTT
1 TAAATTAATTTAAATTATTATAT-TT
19029 TAAA-TAATTTAAATTATTATATTT
1 TAAATTAATTTAAATTATTATATTT
19053 TAA
1 TAA
19056 TGAAAAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 19 0.76
25 6 0.24
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (25 bp):
TAAATTAATTTAAATTATTATATTT
Found at i:19331 original size:23 final size:22
Alignment explanation
Indices: 19305--19347 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
19295 TTTAATGTTT
19305 TAATTAACATTTTTATTAAAAAA
1 TAATTAA-ATTTTTATTAAAAAA
* *
19328 TAATTTAATTTTTTTTAAAA
1 TAATTAAATTTTTATTAAAA
19348 TGTTGAGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
TAATTAAATTTTTATTAAAAAA
Found at i:25078 original size:52 final size:52
Alignment explanation
Indices: 25000--25290 Score: 404
Period size: 52 Copynumber: 5.6 Consensus size: 52
24990 TAAATGAAAT
25000 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATA
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATA
* ** * *
25052 AGGTCCGATGACTATGTATCATCGTGAGTATATGGTTACTTTACTGATTATA
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATA
* *
25104 AGGTCCGATAACTATGTGTCATCATGAGTATATGAATCCTTTACGGATTATA
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATA
* *
25156 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATA
* * * * * *
25208 AGGTCTGATGATTATGTGTCATCGTAAGTATATGATTCCCATTACAGATTA-A
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAAT-CCTTTACGGATTATA
* * *
25260 AGGTCCGGTTACTCTGTGTCATCGTGAGTAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTAT
25291 CAAATATGCA
Statistics
Matches: 208, Mismatches: 30, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
52 198 0.95
53 10 0.05
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATA
Found at i:26582 original size:314 final size:315
Alignment explanation
Indices: 26007--26641 Score: 1148
Period size: 314 Copynumber: 2.0 Consensus size: 315
25997 ATTTTTGAAC
26007 TATTTACTGACTTGACAACTACCGATACTTGTCCAACAAATACCGGTAGAAGTCTCAAAGAATTT
1 TATTTACTGACTTGACAACTACCGATACTTGTCCAACAAATACCGGTAGAAGTCTCAAAGAATTT
*
26072 TAGAAATGACATTTTTACCCTTTTTGAGTCGTACTGACATCCAATTTATGATTCATGTTGTGAAT
66 TAAAAATGACATTTTTACCCTTTTTGAGTCGTACTGACATCCAATTTATGATTCATGTTGTGAAT
26137 TCTGAAATTACTCTATTAAAATACGATTAAACGAAATAGTAGCGGGAGATTTAATGCAATATAAG
131 TCTGAAATTACTCTATTAAAATACGATTAAACGAAATAGTAGCGGGAGATTTAATGCAATATAAG
* *
26202 TTTGGACGGACATCAGGCCCCTAACCGACGACGGTTTCGAGTTTTGGGTGTTACACCAATGATCG
196 TTTGGACGGACATCAGGCCCCTAACCAACGACGGTTTCGAGTTTTGGGTGTTACACCAACGATCG
*
26267 AATCGGGTAATGGGGTGTTGCAGTGGTTGAAAACATCAACCACATACATAGGGTT
261 AATCGGGTAATAGGGTGTTGCAGTGGTTGAAAACATCAACCACATACATAGGGTT
* * *
26322 TATTTACTGACTTGACAATTATCGATACTTGTCCAACAAATACCGGTAGAAGTCTCCAAG-ATTT
1 TATTTACTGACTTGACAACTACCGATACTTGTCCAACAAATACCGGTAGAAGTCTCAAAGAATTT
26386 TAAAAATGACATTTTTACCCTTTTTGAGTCGTACTGACATCCAATTTATGATTCATGTTGTGAAT
66 TAAAAATGACATTTTTACCCTTTTTGAGTCGTACTGACATCCAATTTATGATTCATGTTGTGAAT
26451 TCTGAAATTACTCTATTAAAATAC-AGTTAAACGAAATAGTAGCGGGAGATTTAATGCAATATAA
131 TCTGAAATTACTCTATTAAAATACGA-TTAAACGAAATAGTAGCGGGAGATTTAATGCAATATAA
* * *
26515 GTTTGGACGGACATCAGGCCTCTAATCAACGACGGTTTCGAGTTTTGGGTGTTACACCAGCGATC
195 GTTTGGACGGACATCAGGCCCCTAACCAACGACGGTTTCGAGTTTTGGGTGTTACACCAACGATC
*
26580 GAATCGGGTAATAGGGTGTTGTAGTGGTTGAAAACATCAACCACATACATAGGGTT
260 GAATCGGGTAATAGGGTGTTGCAGTGGTTGAAAACATCAACCACATACATAGGGTT
26636 TATTTA
1 TATTTA
26642 ATGTCCATAT
Statistics
Matches: 308, Mismatches: 11, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
313 1 0.00
314 250 0.81
315 57 0.19
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (315 bp):
TATTTACTGACTTGACAACTACCGATACTTGTCCAACAAATACCGGTAGAAGTCTCAAAGAATTT
TAAAAATGACATTTTTACCCTTTTTGAGTCGTACTGACATCCAATTTATGATTCATGTTGTGAAT
TCTGAAATTACTCTATTAAAATACGATTAAACGAAATAGTAGCGGGAGATTTAATGCAATATAAG
TTTGGACGGACATCAGGCCCCTAACCAACGACGGTTTCGAGTTTTGGGTGTTACACCAACGATCG
AATCGGGTAATAGGGTGTTGCAGTGGTTGAAAACATCAACCACATACATAGGGTT
Found at i:27493 original size:33 final size:32
Alignment explanation
Indices: 27455--27551 Score: 102
Period size: 33 Copynumber: 3.2 Consensus size: 32
27445 TTATTTTTTT
27455 TCAATTTAATCGTATATTAATGATATAAATATA
1 TCAATTTAATCGTATATTAATGA-ATAAATATA
**
27488 TCAATTTAATTTTAT-TTAA--AAT-AA-ATA
1 TCAATTTAATCGTATATTAATGAATAAATATA
27515 --AA-TTAATCGTATATTAATGACATAAATATA
1 TCAATTTAATCGTATATTAATGA-ATAAATATA
27545 TCAATTT
1 TCAATTT
27552 CTTGTTTGTT
Statistics
Matches: 51, Mismatches: 4, Indels: 18
0.70 0.05 0.25
Matches are distributed among these distances:
24 8 0.16
25 6 0.12
27 4 0.08
28 4 0.08
29 4 0.08
30 4 0.08
32 6 0.12
33 15 0.29
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.43
Consensus pattern (32 bp):
TCAATTTAATCGTATATTAATGAATAAATATA
Done.