Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009634.1 Kokia drynarioides strain JFW-HI SEQ_124351, 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: 28959
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:3725 original size:13 final size:14
Alignment explanation
Indices: 3707--3736 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
3697 TTTAGCCATT
3707 TTTTTATTTT-TTA
1 TTTTTATTTTATTA
3720 TTTTTATTTTATTA
1 TTTTTATTTTATTA
3734 TTT
1 TTT
3737 GCATATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTATTTTATTA
Found at i:9287 original size:21 final size:20
Alignment explanation
Indices: 9261--9320 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 20
9251 TTTTTTAAAA
*
9261 AAAAAAATTGAAAAGAAAATT
1 AAAAAAATTGAAAA-AAAATC
9282 AAAAAAATTTGAAAAAAAATC
1 AAAAAAA-TTGAAAAAAAATC
* *
9303 GAAAAAATTCAAAAAAAA
1 AAAAAAATTGAAAAAAAA
9321 AATTAGTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 10 0.29
21 18 0.51
22 7 0.20
ACGTcount: A:0.73, C:0.03, G:0.07, T:0.17
Consensus pattern (20 bp):
AAAAAAATTGAAAAAAAATC
Found at i:9288 original size:22 final size:21
Alignment explanation
Indices: 9260--9320 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
9250 TTTTTTTAAA
9260 AAAAAAAATTGAAAAGAAAATT
1 AAAAAAAATTGAAAA-AAAATT
*
9282 AAAAAAATTTGAAAAAAAA-T
1 AAAAAAAATTGAAAAAAAATT
** *
9302 CGAAAAAATTCAAAAAAAA
1 AAAAAAAATTGAAAAAAAA
9321 AATTAGTATA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
20 16 0.47
21 4 0.12
22 14 0.41
ACGTcount: A:0.74, C:0.03, G:0.07, T:0.16
Consensus pattern (21 bp):
AAAAAAAATTGAAAAAAAATT
Found at i:9391 original size:5 final size:6
Alignment explanation
Indices: 9331--9390 Score: 79
Period size: 6 Copynumber: 10.3 Consensus size: 6
9321 AATTAGTATA
* * *
9331 TTTATT TTCATT TTCATT TTTATT TTTAGT TTTA-T TTTA-T TTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
9377 TTTATT TTTATT TT
1 TTTATT TTTATT TT
9391 AATTATGCAA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
5 10 0.20
6 40 0.80
ACGTcount: A:0.17, C:0.03, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTATT
Found at i:10331 original size:16 final size:17
Alignment explanation
Indices: 10310--10341 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
10300 TATTGTTTAG
10310 AAAAAAAAGA-AAAAGA
1 AAAAAAAAGACAAAAGA
10326 AAAAAAAAGACAAAAG
1 AAAAAAAAGACAAAAG
10342 TGTGTTTGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.84, C:0.03, G:0.12, T:0.00
Consensus pattern (17 bp):
AAAAAAAAGACAAAAGA
Found at i:11405 original size:25 final size:23
Alignment explanation
Indices: 11364--11409 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
11354 CTAATTAGGG
11364 AATTATTATTTAGATTTAATTCA
1 AATTATTATTTAGATTTAATTCA
*
11387 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TATTTAG-ATTTAATT
11410 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.54
Consensus pattern (23 bp):
AATTATTATTTAGATTTAATTCA
Found at i:16240 original size:6 final size:6
Alignment explanation
Indices: 16229--16299 Score: 79
Period size: 6 Copynumber: 11.8 Consensus size: 6
16219 TAATAAGATA
* * * * *
16229 AAAATG AAAATG AAAATG AAATTG GAAATG AAAGTG AAAGTG AAAGTG
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG
* *
16277 AAAGTG AAAGTG AAAATG AAAAT
1 AAAATG AAAATG AAAATG AAAAT
16300 ACAAATATAA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 59 1.00
ACGTcount: A:0.58, C:0.00, G:0.24, T:0.18
Consensus pattern (6 bp):
AAAATG
Found at i:16246 original size:12 final size:12
Alignment explanation
Indices: 16229--16297 Score: 93
Period size: 12 Copynumber: 5.8 Consensus size: 12
16219 TAATAAGATA
*
16229 AAAATGAAAATG
1 AAAATGAAAGTG
*
16241 AAAATGAAATTG
1 AAAATGAAAGTG
*
16253 GAAATGAAAGTG
1 AAAATGAAAGTG
*
16265 AAAGTGAAAGTG
1 AAAATGAAAGTG
*
16277 AAAGTGAAAGTG
1 AAAATGAAAGTG
16289 AAAATGAAA
1 AAAATGAAA
16298 ATACAAATAT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 51 1.00
ACGTcount: A:0.58, C:0.00, G:0.25, T:0.17
Consensus pattern (12 bp):
AAAATGAAAGTG
Found at i:16423 original size:13 final size:14
Alignment explanation
Indices: 16398--16428 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
16388 ACATGAAAGC
16398 AAAATAAATAAATA
1 AAAATAAATAAATA
16412 AAAATAAA-AAATA
1 AAAATAAATAAATA
16425 AAAA
1 AAAA
16429 CACAAGGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (14 bp):
AAAATAAATAAATA
Found at i:19230 original size:20 final size:20
Alignment explanation
Indices: 19202--19260 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
19192 AATAAAAAGG
19202 AAATATAAAAATATAAAAATT
1 AAAT-TAAAAATATAAAAATT
19223 AAATTAAAAA-A-AAATATATT
1 AAATTAAAAATATAAA-A-ATT
19243 AAATTAAAAAT-TAAAAAT
1 AAATTAAAAATATAAAAAT
19261 GGCTAAATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
18 3 0.09
19 4 0.12
20 20 0.59
21 7 0.21
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
AAATTAAAAATATAAAAATT
Found at i:19236 original size:25 final size:26
Alignment explanation
Indices: 19208--19259 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
19198 AAGGAAATAT
19208 AAAAATATA-AAAATT-AAATTAAAA
1 AAAAATATATAAAATTAAAATTAAAA
*
19232 AAAAATATATTAAATTAAAAATTAAAA
1 AAAAATATATAAAATT-AAAATTAAAA
19259 A
1 A
19260 TGGCTAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 9 0.38
25 5 0.21
27 10 0.42
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (26 bp):
AAAAATATATAAAATTAAAATTAAAA
Done.