Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001189.1 Kokia drynarioides strain JFW-HI SEQ_112528, 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: 27086
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Found at i:143 original size:23 final size:23
Alignment explanation
Indices: 117--194 Score: 70
Period size: 23 Copynumber: 3.3 Consensus size: 23
107 CTATAACAAC
*
117 ATTAAATAACAAATAAATTAAAA
1 ATTAAATAACAAATAAACTAAAA
*
140 ATTAAATTAA-AAA-AAACAAAAA
1 ATTAAA-TAACAAATAAACTAAAA
*
162 ACTTAAAATAATCAAATTAACTAACAA
1 A-TT-AAATAA-CAAATAAACTAA-AA
189 ATTAAA
1 ATTAAA
195 ATATTTTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
22 8 0.18
23 14 0.32
24 6 0.14
25 6 0.14
26 7 0.16
27 3 0.07
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (23 bp):
ATTAAATAACAAATAAACTAAAA
Found at i:432 original size:4 final size:4
Alignment explanation
Indices: 423--461 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
413 TTATTCCTTC
*
423 TTCT TTCT TTCT TTCT TTCT CTTTT TTCT TTCT TT-T TTC
1 TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTC
462 CTTCAATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 3 0.10
4 25 0.81
5 3 0.10
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:450 original size:21 final size:20
Alignment explanation
Indices: 421--465 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
411 CATTATTCCT
421 TCTTCTTTCTTTCTTTCTTTC
1 TCTTCTTTCTTTCTTT-TTTC
*
442 TCTTTTTTCTTTCTTTTTTC
1 TCTTCTTTCTTTCTTTTTTC
462 -CTTC
1 TCTTC
466 AATTTTTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 4 0.18
21 15 0.68
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (20 bp):
TCTTCTTTCTTTCTTTTTTC
Found at i:2276 original size:8 final size:8
Alignment explanation
Indices: 2263--2287 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
2253 AGAGACGTGG
2263 TTCACCGC
1 TTCACCGC
2271 TTCACCGC
1 TTCACCGC
2279 TTCACCGC
1 TTCACCGC
2287 T
1 T
2288 AAGACATCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.48, G:0.12, T:0.28
Consensus pattern (8 bp):
TTCACCGC
Found at i:6424 original size:30 final size:31
Alignment explanation
Indices: 6362--6425 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
6352 AACAACTCAG
6362 TGACTTAAATAAAAACTTTTGAAAAATTTAA
1 TGACTTAAATAAAAACTTTTGAAAAATTTAA
*
6393 TGACTTAAATAAAAA-TTTT-AAATAGTTTAA
1 TGACTTAAATAAAAACTTTTGAAA-AATTTAA
6423 TGA
1 TGA
6426 TCAAATTGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
29 3 0.10
30 13 0.42
31 15 0.48
ACGTcount: A:0.50, C:0.05, G:0.08, T:0.38
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTTGAAAAATTTAA
Found at i:8245 original size:6 final size:6
Alignment explanation
Indices: 8234--8280 Score: 85
Period size: 6 Copynumber: 7.8 Consensus size: 6
8224 TGATCAAAAT
*
8234 TGAAAG TGAAAG TAAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAA
8281 TTAGAATTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.53, C:0.00, G:0.30, T:0.17
Consensus pattern (6 bp):
TGAAAG
Found at i:8253 original size:12 final size:12
Alignment explanation
Indices: 8236--8294 Score: 73
Period size: 12 Copynumber: 4.9 Consensus size: 12
8226 ATCAAAATTG
8236 AAAGTGAAAGTA
1 AAAGTGAAAGTA
*
8248 AAAGTGAAAGTG
1 AAAGTGAAAGTA
*
8260 AAAGTGAAAGTG
1 AAAGTGAAAGTA
*
8272 AAAGTGAAATTA
1 AAAGTGAAAGTA
* *
8284 GAATTGAAAGT
1 AAAGTGAAAGT
8295 GATATGGATT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 41 1.00
ACGTcount: A:0.53, C:0.00, G:0.27, T:0.20
Consensus pattern (12 bp):
AAAGTGAAAGTA
Found at i:8255 original size:18 final size:18
Alignment explanation
Indices: 8229--8296 Score: 91
Period size: 18 Copynumber: 3.8 Consensus size: 18
8219 ATTTGTGATC
*
8229 AAAATTGAAAGTGAAAGT
1 AAAAGTGAAAGTGAAAGT
8247 AAAAGTGAAAGTGAAAGT
1 AAAAGTGAAAGTGAAAGT
* *
8265 GAAAGTGAAAGTGAAATT
1 AAAAGTGAAAGTGAAAGT
* *
8283 AGAATTGAAAGTGA
1 AAAAGTGAAAGTGA
8297 TATGGATTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.53, C:0.00, G:0.26, T:0.21
Consensus pattern (18 bp):
AAAAGTGAAAGTGAAAGT
Found at i:11792 original size:18 final size:18
Alignment explanation
Indices: 11769--11811 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
11759 TTTTCAGTTG
11769 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
11787 TAATTAATTAAACTTATT
1 TAATTAATTAAAATTATT
11805 TAATTAA
1 TAATTAA
11812 AAATTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:12095 original size:24 final size:24
Alignment explanation
Indices: 12045--12105 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
12035 AAATTTTATA
* *
12045 AATATTT-AT-ATTATATTATTTT
1 AATATTTAATAATTTTATAATTTT
12067 AATATTTAATAATTTTATAATTTT
1 AATATTTAATAATTTTATAATTTT
*
12091 TATATATTAA-AATTT
1 AATAT-TTAATAATTT
12106 ATTATAGATC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 7 0.21
23 2 0.06
24 20 0.61
25 4 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
AATATTTAATAATTTTATAATTTT
Found at i:16739 original size:22 final size:21
Alignment explanation
Indices: 16714--16756 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
16704 TTAATTTATG
*
16714 AATTCAAATATTATAATAAAAA
1 AATTCAAA-ATAATAATAAAAA
* *
16736 AATTTAAAATAATAATTAAAA
1 AATTCAAAATAATAATAAAAA
16757 TATTTTTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
AATTCAAAATAATAATAAAAA
Found at i:18555 original size:2 final size:2
Alignment explanation
Indices: 18548--18584 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
18538 TACATATAAA
18548 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18585 CACACACTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20378 original size:8 final size:8
Alignment explanation
Indices: 20365--20389 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
20355 TACTTTTATT
20365 AATTTTAA
1 AATTTTAA
20373 AATTTTAA
1 AATTTTAA
20381 AATTTTAA
1 AATTTTAA
20389 A
1 A
20390 GGATTAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
AATTTTAA
Found at i:21580 original size:24 final size:24
Alignment explanation
Indices: 21547--21608 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
21537 ATTTCTTACC
*
21547 AAAGTTTAATGGAT-ACTCAACCAA
1 AAAGATTAATGGATAAC-CAACCAA
*
21571 GAAGATTAATGGATAACCAACCAA
1 AAAGATTAATGGATAACCAACCAA
*
21595 AAAGTTTAATGGAT
1 AAAGATTAATGGAT
21609 TCCTCCATGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 31 0.94
25 2 0.06
ACGTcount: A:0.47, C:0.13, G:0.16, T:0.24
Consensus pattern (24 bp):
AAAGATTAATGGATAACCAACCAA
Found at i:24596 original size:21 final size:23
Alignment explanation
Indices: 24551--24597 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
24541 AACTATAATA
* *
24551 TTTTACATTTTTACCCCAAACCT
1 TTTTACATTTTTACCCAAAAACT
24574 TTTTAC-TTTTT-CCCAAAAACT
1 TTTTACATTTTTACCCAAAAACT
24595 TTT
1 TTT
24598 ACCCCTCCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 11 0.50
22 5 0.23
23 6 0.27
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.49
Consensus pattern (23 bp):
TTTTACATTTTTACCCAAAAACT
Found at i:25090 original size:18 final size:18
Alignment explanation
Indices: 25067--25112 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
25057 CGATTTATAT
*
25067 TATTGAATTTTTTAATAA
1 TATTGAATTTTATAATAA
*
25085 TATTGAATATTTATATTAA
1 TATTGAAT-TTTATAATAA
*
25104 AATTGAATT
1 TATTGAATT
25113 ATTAATGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (18 bp):
TATTGAATTTTATAATAA
Done.