Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002805.1 Kokia drynarioides strain JFW-HI SEQ_115152, 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, 685
Length: 1143
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Found at i:231 original size:28 final size:28
Alignment explanation
Indices: 174--232 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
164 AAATGAGACT
* *
174 TTTCGGATTCTCGAGAGCAAAATGATAA
1 TTTCGGATTCTCGAGAGCAAAACGAAAA
* * *
202 TTTCGGATTCTCGGGGGCAGAACGAAAA
1 TTTCGGATTCTCGAGAGCAAAACGAAAA
230 TTT
1 TTT
233 TGGAAAAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (28 bp):
TTTCGGATTCTCGAGAGCAAAACGAAAA
Found at i:292 original size:59 final size:57
Alignment explanation
Indices: 244--585 Score: 339
Period size: 59 Copynumber: 5.8 Consensus size: 57
234 GGAAAAATTT
* * *
244 GGGGTCAAAAATGGGATTTTT-TAAGGTTTAGGGGTAAAAATGGGATTTTTAGAAGTTTC
1 GGGGTCAAAAATGGGATTTTTGGAA-G-TTAGGGGTAAAAATGGAATTTTGA-AAGTTTC
* * *
303 GGGGTTAAAAATGAGATTTTTGGAAGTTAGAGGGTAAAAATAGAATTTTTAGAAA-TTTC
1 GGGGTCAAAAATGGGATTTTTGGAAGTTAG-GGGTAAAAATGGAA-TTTT-GAAAGTTTC
* * * * *
362 GGGGTCAAAAATGGGTTTTTTGGAAGTTCGATGGTAAAAATAGAATTTTTGGAAGTTTC
1 GGGGTCAAAAATGGGATTTTTGGAAGTTAG-GGGTAAAAATGGAA-TTTTGAAAGTTTC
* * * *
421 GGGGTCGAAAATGAGATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAGTTTC
1 GGGGTCAAAAATGGGATTTTTGGAAG-TTAGGGGTAAAAATGGAA-TTTTGAAAGTTTC
** * * * *
480 GGGGTTGAAAATGGGATTTTTGGAAGTTCGGGGTAAAAATGAAATTTTTAGAAGTTTT
1 GGGGTCAAAAATGGGATTTTTGGAAGTTAGGGGTAAAAATGGAATTTTGA-AAGTTTC
* * *
538 GAGGTC-AAAATGGGATTTTTAGAAGTTTAGGGGTAAAAATGAAATTTT
1 GGGGTCAAAAATGGGATTTTTGGAAG-TTAGGGGTAAAAATGGAATTTT
586 TTGACAGTTA
Statistics
Matches: 246, Mismatches: 29, Indels: 17
0.84 0.10 0.06
Matches are distributed among these distances:
57 22 0.09
58 54 0.22
59 158 0.64
60 11 0.04
61 1 0.00
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.35
Consensus pattern (57 bp):
GGGGTCAAAAATGGGATTTTTGGAAGTTAGGGGTAAAAATGGAATTTTGAAAGTTTC
Found at i:374 original size:118 final size:114
Alignment explanation
Indices: 238--586 Score: 398
Period size: 118 Copynumber: 3.0 Consensus size: 114
228 AATTTTGGAA
* *
238 AAATTT-GGGGTCAAAAATGGGATTTTTTAAGGTTTAGGGGTAAAAATGGGATTTTTAGAAGTTT
1 AAATTTCGGGGTCAAAAATGGGATTTTTTAA-G-TTCGGGGTAAAAATGGAATTTTTAGAAGTTT
302 CGGGGTTAAAAATGAGATTTTTGGAAGTTAGAGGGTAAAAATAGAATTTTTAG
64 CGGGGTTAAAAATGAGATTTTTGGAAGTTAG-GGGTAAAAAT-GAATTTTTAG
* * *
355 AAATTTCGGGGTCAAAAATGGG-TTTTTTGGAAGTTCGATGGTAAAAATAGAATTTTTGGAAGTT
1 AAATTTCGGGGTCAAAAATGGGATTTTTT--AAGTTCG-GGGTAAAAATGGAATTTTTAGAAGTT
** * *
419 TCGGGGTCGAAAATGAGATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGG
63 TCGGGGTTAAAAATGAGATTTTTGGAAG-TTAGGGGTAAAAAT-GAATTTTTAG
* ** * * *
473 AAGTTTCGGGGTTGAAAATGGGATTTTTGGAAGTTCGGGGTAAAAATGAAATTTTTAGAAGTTTT
1 AAATTTCGGGGTCAAAAATGGGATTTTT-TAAGTTCGGGGTAAAAATGGAATTTTTAGAAGTTTC
* * * *
538 GAGG-TCAAAATGGGATTTTTAGAAGTTTAGGGGTAAAAATGAAATTTTT
65 GGGGTTAAAAATGAGATTTTTGGAAG-TTAGGGGTAAAAATG-AATTTTT
587 TGACAGTTAG
Statistics
Matches: 199, Mismatches: 25, Indels: 17
0.83 0.10 0.07
Matches are distributed among these distances:
115 1 0.01
116 38 0.19
117 41 0.21
118 109 0.55
119 10 0.05
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (114 bp):
AAATTTCGGGGTCAAAAATGGGATTTTTTAAGTTCGGGGTAAAAATGGAATTTTTAGAAGTTTCG
GGGTTAAAAATGAGATTTTTGGAAGTTAGGGGTAAAAATGAATTTTTAG
Found at i:598 original size:29 final size:29
Alignment explanation
Indices: 244--586 Score: 322
Period size: 29 Copynumber: 11.7 Consensus size: 29
234 GGAAAAATTT
* * *
244 GGGGTCAAAAATGGGATTTTT-TAAGGTTTA
1 GGGGT-AAAAATGAGATTTTTGGAA-GTTTC
* *
274 GGGGTAAAAATGGGATTTTTAGAAGTTTC
1 GGGGTAAAAATGAGATTTTTGGAAGTTTC
*
303 GGGGTTAAAAATGAGATTTTTGGAAG-TTA
1 GGGG-TAAAAATGAGATTTTTGGAAGTTTC
* *
332 GAGGGTAAAAAT-AGAATTTTTAGAAATTTC
1 G-GGGTAAAAATGAG-ATTTTTGGAAGTTTC
* *
362 GGGGTCAAAAATGGGTTTTTTGGAAG-TTC
1 GGGGT-AAAAATGAGATTTTTGGAAGTTTC
*
391 GATGGTAAAAAT-AGAATTTTTGGAAGTTTC
1 G-GGGTAAAAATGAG-ATTTTTGGAAGTTTC
* *
421 GGGGTCGAAAATGAGATTTTTGGAAGTTTG
1 GGGGT-AAAAATGAGATTTTTGGAAGTTTC
451 GGGGTAAAAATG-GAATTTTTGGAAGTTTC
1 GGGGTAAAAATGAG-ATTTTTGGAAGTTTC
* *
480 GGGGTTGAAAATGGGATTTTTGGAAG-TTC
1 GGGG-TAAAAATGAGATTTTTGGAAGTTTC
* * *
509 GGGGTAAAAATGAAATTTTTAGAAGTTTT
1 GGGGTAAAAATGAGATTTTTGGAAGTTTC
* * * * *
538 GAGGTCAAAATGGGATTTTTAGAAGTTTA
1 GGGGTAAAAATGAGATTTTTGGAAGTTTC
*
567 GGGGTAAAAATGAAATTTTT
1 GGGGTAAAAATGAGATTTTT
587 TGACAGTTAG
Statistics
Matches: 262, Mismatches: 35, Indels: 33
0.79 0.11 0.10
Matches are distributed among these distances:
28 21 0.08
29 142 0.54
30 95 0.36
31 4 0.02
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (29 bp):
GGGGTAAAAATGAGATTTTTGGAAGTTTC
Done.