Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007668.1 Kokia drynarioides strain JFW-HI SEQ_122299, 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: 2515
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Found at i:275 original size:6 final size:6
Alignment explanation
Indices: 264--335 Score: 64
Period size: 6 Copynumber: 12.3 Consensus size: 6
254 CTGGGCCCAA
* *
264 TAAATT TAAATT T-ATTT TAAAAT TAAATT T--ATT CTAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT -TAAATT TAAATT
310 T--ATT ATAAATT TAAATT TAAAATT TA
1 TAAATT -TAAATT TAAATT T-AAATT TA
336 TTTTAAATGT
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
4 6 0.11
5 6 0.11
6 30 0.56
7 12 0.22
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (6 bp):
TAAATT
Found at i:305 original size:23 final size:23
Alignment explanation
Indices: 270--333 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 23
260 CCAATAAATT
*
270 TAAATTT-ATTTTAAAATTA-AA
1 TAAATTTAAATTTAAAATTATAA
** * *
291 TTTATTCTAAATTTAAATTTATTA
1 TAAATT-TAAATTTAAAATTATAA
315 TAAATTTAAATTTAAAATT
1 TAAATTTAAATTTAAAATT
334 TATTTTAAAT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
21 4 0.12
22 1 0.03
23 22 0.69
24 5 0.16
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
TAAATTTAAATTTAAAATTATAA
Found at i:337 original size:24 final size:23
Alignment explanation
Indices: 298--343 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
288 AAATTTATTC
298 TAAATTTAAATTTATTATAAATT
1 TAAATTTAAATTTATTATAAATT
*
321 TAAATTTAAAATTTATTTTAAAT
1 TAAATTT-AAATTTATTATAAAT
344 GTCCAAAGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TAAATTTAAATTTATTATAAATT
Found at i:338 original size:17 final size:17
Alignment explanation
Indices: 263--328 Score: 105
Period size: 17 Copynumber: 3.9 Consensus size: 17
253 TCTGGGCCCA
263 ATAAATTTAAATTTATT
1 ATAAATTTAAATTTATT
* *
280 TTAAAATTAAATTTATT
1 ATAAATTTAAATTTATT
*
297 CTAAATTTAAATTTATT
1 ATAAATTTAAATTTATT
314 ATAAATTTAAATTTA
1 ATAAATTTAAATTTA
329 AAATTTATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 44 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (17 bp):
ATAAATTTAAATTTATT
Found at i:1017 original size:15 final size:16
Alignment explanation
Indices: 990--1025 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
980 AATTTATTAT
990 TAATAAGTATTAAGAA
1 TAATAAGTATTAAGAA
*
1006 TAATAA-TATTAATAA
1 TAATAAGTATTAAGAA
1021 TAATA
1 TAATA
1026 TTTATAGCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (16 bp):
TAATAAGTATTAAGAA
Found at i:1454 original size:79 final size:78
Alignment explanation
Indices: 1305--1459 Score: 202
Period size: 79 Copynumber: 2.0 Consensus size: 78
1295 CTTTGAACTC
* * * *
1305 ACCGATGACCGGATATGTGGGGCGCGTGGACGATCGGACGTTACCATGGCGGAAACGCGCAACGG
1 ACCGATGACCGGAGATGTGGGGCACGCGGACGATCGGACGTTACCATGGCGGAAACGCGCAACGA
1370 CGCGTGACTACGG
66 CGCGTGACTACGG
* * * * * *
1383 ACCGGTGACTGGAGATGTGGGGGCACGCGGACGATCGGACGTTGCCATGGCGGAGACGCTCAGCG
1 ACCGATGACCGGAGATGT-GGGGCACGCGGACGATCGGACGTTACCATGGCGGAAACGCGCAACG
*
1448 ACGCGTGGCTAC
65 ACGCGTGACTAC
1460 AAACTCGCGA
Statistics
Matches: 65, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
78 15 0.23
79 50 0.77
ACGTcount: A:0.20, C:0.26, G:0.40, T:0.14
Consensus pattern (78 bp):
ACCGATGACCGGAGATGTGGGGCACGCGGACGATCGGACGTTACCATGGCGGAAACGCGCAACGA
CGCGTGACTACGG
Found at i:2132 original size:29 final size:29
Alignment explanation
Indices: 2088--2515 Score: 361
Period size: 29 Copynumber: 14.6 Consensus size: 29
2078 CCTTGGAGGT
*
2088 CCCC-AAACTTCTC-AAAATCCCATTTTTGA
1 CCCCGAAACTTC-CAAAAATTCCATTTTT-A
***
2117 CCCCGAAACTTCCAAAAATTTTGTTTTTA
1 CCCCGAAACTTCCAAAAATTCCATTTTTA
*** *
2146 CCCTCG-AACTTTTGAAAATTTCATTTTTGA
1 CCC-CGAAACTTCCAAAAATTCCATTTTT-A
*
2176 CCTCGAAACTTCCAAAAATTCCATTTTTA
1 CCCCGAAACTTCCAAAAATTCCATTTTTA
* ** *
2205 ACCATAAACTTTCAAAAA-TCCTATTTTTGA
1 CCCCGAAACTTCCAAAAATTCC-ATTTTT-A
* *
2235 CCCCAAAACTTCC-AAAATTCTATTTTTA
1 CCCCGAAACTTCCAAAAATTCCATTTTTA
* *
2263 CCCTC-AAACTTCCAAAAATCCCATTTTGA
1 CCC-CGAAACTTCCAAAAATTCCATTTTTA
***
2292 CCCCGAAACTTCCAAAAATTTTGTTTTTA
1 CCCCGAAACTTCCAAAAATTCCATTTTTA
2321 CCCCCG-AACTTCCAAAAA-TCTCATTTTTAA
1 -CCCCGAAACTTCCAAAAATTC-CATTTTT-A
* * *
2351 CTCCGAAACTTTCAAAAATTCCAATTTTA
1 CCCCGAAACTTCCAAAAATTCCATTTTTA
* * *
2380 CTCCTG-AACTTCAAAAAATCCCATTTTTAA
1 C-CCCGAAACTTCCAAAAATTCCATTTTT-A
* *
2410 CCCCAAAAACTTCCAAAAATTTCATTTTTA
1 CCCC-GAAACTTCCAAAAATTCCATTTTTA
* *
2440 CCCCCAAACTTCCAAAAATCCCATTTTTAA
1 CCCCGAAACTTCCAAAAATTCCATTTTT-A
* *
2470 CTCCAAAACTTCCAAAAATTCCATTTTTA
1 CCCCGAAACTTCCAAAAATTCCATTTTTA
* *
2499 CCCCCAAATTTCCAAAA
1 CCCCGAAACTTCCAAAA
Statistics
Matches: 320, Mismatches: 58, Indels: 42
0.76 0.14 0.10
Matches are distributed among these distances:
28 17 0.05
29 172 0.54
30 110 0.34
31 21 0.07
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.33
Consensus pattern (29 bp):
CCCCGAAACTTCCAAAAATTCCATTTTTA
Found at i:2185 original size:59 final size:59
Alignment explanation
Indices: 2091--2515 Score: 448
Period size: 59 Copynumber: 7.2 Consensus size: 59
2081 TGGAGGTCCC
* *
2091 CAAACTTCTC-AAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTTTGTTTTTACCCT
1 CAAACTTC-CAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTCTATTTTTACCCT
* *** ** * * *
2150 CGAACTTTTGAAAATTTCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTAACCAT
1 CAAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTCTATTTTT-ACCCT
* * *
2210 -AAACTTTCAAAAATCCTATTTTTGACCCCAAAACTTCC-AAAATTCTATTTTTACCCT
1 CAAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTCTATTTTTACCCT
* * *
2267 CAAACTTCCAAAAATCCCA-TTTTGACCCCGAAACTTCCAAAAATTTTGTTTTTACCCC
1 CAAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTCTATTTTTACCCT
* * * * * * *
2325 CGAACTTCCAAAAATCTCATTTTTAACTCCGAAACTTTCAAAAATTCCAATTTTACTCCT
1 CAAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTCTATTTTTAC-CCT
* * * * *
2385 -GAACTTCAAAAAATCCCATTTTTAACCCCAAAAACTTCCAAAAATT-TCATTTTTACCCC
1 CAAACTTCCAAAAATCCCATTTTTGACCCC-GAAACTTCCAAAAATTCT-ATTTTTACCCT
* * * * *
2444 CAAACTTCCAAAAATCCCATTTTTAACTCCAAAACTTCCAAAAATTCCATTTTTACCCC
1 CAAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTCTATTTTTACCCT
*
2503 CAAATTTCCAAAA
1 CAAACTTCCAAAA
Statistics
Matches: 307, Mismatches: 49, Indels: 20
0.82 0.13 0.05
Matches are distributed among these distances:
57 22 0.07
58 62 0.20
59 170 0.55
60 53 0.17
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (59 bp):
CAAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTCTATTTTTACCCT
Done.