Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007667.1 Kokia drynarioides strain JFW-HI SEQ_122298, 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: 2514
ACGTcount: A:0.35, C:0.20, G:0.15, 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: 220
Period size: 79 Copynumber: 2.0 Consensus size: 78
1295 CTTTGAACTC
* * *
1305 ACCGATGACCGGATATGTGGGGCGCGTGGACGATCGGACGTTACCATGGCGGAAACGCGCAACGG
1 ACCGATGACCGGAGATGTGGGGCGCGCGGACGATCGGACGTTACCATGGCGGAAACGCGCAACGA
1370 CGCGTGACTACGG
66 CGCGTGACTACGG
* * * * *
1383 ACCGGTGACTGGAGATGTGGGGGCGCGCGGACGATCGGACGTTGCCATGGCGGAGACGCGCAGCG
1 ACCGATGACCGGAGATGT-GGGGCGCGCGGACGATCGGACGTTACCATGGCGGAAACGCGCAACG
*
1448 ACGCGTGGCTAC
65 ACGCGTGACTAC
1460 AAACTCGCGG
Statistics
Matches: 67, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
78 15 0.22
79 52 0.78
ACGTcount: A:0.19, C:0.26, G:0.41, T:0.14
Consensus pattern (78 bp):
ACCGATGACCGGAGATGTGGGGCGCGCGGACGATCGGACGTTACCATGGCGGAAACGCGCAACGA
CGCGTGACTACGG
Found at i:2131 original size:29 final size:29
Alignment explanation
Indices: 2087--2514 Score: 370
Period size: 29 Copynumber: 14.6 Consensus size: 29
2077 CCTTGGAGGT
*
2087 CCCC-AAACTTCTC-AAAATCCCATTTTTGA
1 CCCCGAAACTTC-CAAAAATTCCATTTTT-A
***
2116 CCCCGAAACTTCCAAAAATTTTGTTTTTA
1 CCCCGAAACTTCCAAAAATTCCATTTTTA
* *
2145 CCCTCG-AACTTCTAAAAATTTCATTTTTGA
1 CCC-CGAAACTTCCAAAAATTCCATTTTT-A
*
2175 CCTCGAAACTTCCAAAAATTCCATTTTTA
1 CCCCGAAACTTCCAAAAATTCCATTTTTA
* ** * *
2204 ACCATAAACTTTCGAAAA-TCCTATTTTTGA
1 CCCCGAAACTTCCAAAAATTCC-ATTTTT-A
* *
2234 CCCCAAAACTTCC-AAAATTCTATTTTTA
1 CCCCGAAACTTCCAAAAATTCCATTTTTA
* *
2262 CCCTC-AAACTTCCAAAAATCCCATTTTGA
1 CCC-CGAAACTTCCAAAAATTCCATTTTTA
* ***
2291 CCCTGAAACTTCCAAAAATTTTGTTTTTA
1 CCCCGAAACTTCCAAAAATTCCATTTTTA
*
2320 CCCCCG-AACTT-CAAAAAATCTCATTTTTAA
1 -CCCCGAAACTTCCAAAAATTC-CATTTTT-A
* *
2350 CTCCGAAACTTCCAAAAATTCCAATTTTA
1 CCCCGAAACTTCCAAAAATTCCATTTTTA
* * *
2379 CTCCTG-AACTTCAAAAAATCCCATTTTTAA
1 C-CCCGAAACTTCCAAAAATTCCATTTTT-A
*
2409 CCCCAAAAACTTCCAAAAATTCCATTTTTA
1 CCCC-GAAACTTCCAAAAATTCCATTTTTA
* *
2439 CCCCCAAACTTCCAAAAATCCCATTTTTAA
1 CCCCGAAACTTCCAAAAATTCCATTTTT-A
* *
2469 CTCCAAAACTTCCAAAAATTCCATTTTTA
1 CCCCGAAACTTCCAAAAATTCCATTTTTA
* *
2498 CCCCCAAATTTCCAAAA
1 CCCCGAAACTTCCAAAA
Statistics
Matches: 323, Mismatches: 55, Indels: 42
0.77 0.13 0.10
Matches are distributed among these distances:
28 22 0.07
29 168 0.52
30 105 0.33
31 28 0.09
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (29 bp):
CCCCGAAACTTCCAAAAATTCCATTTTTA
Found at i:2184 original size:59 final size:59
Alignment explanation
Indices: 2090--2514 Score: 446
Period size: 59 Copynumber: 7.2 Consensus size: 59
2080 TGGAGGTCCC
* ***
2090 CAAACTTCTCAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTTTGTTTTTACCCT
1 CAAACTTCTAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCCT
* ** * *
2149 CGAACTTCTAAAAATTTCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTAACCAT
1 CAAACTTCTAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTT-ACCCT
* * * *
2209 -AAACTT-TCGAAAATCCTATTTTTGACCCCAAAACTTCC-AAAATTCTATTTTTACCCT
1 CAAACTTCT-AAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCCT
* * *** *
2266 CAAACTTCCAAAAATCCCA-TTTTGACCCTGAAACTTCCAAAAATTTTGTTTTTACCCC
1 CAAACTTCTAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCCT
* * * * * *
2324 CGAACTTCAAAAAATCTCATTTTTAACTCCGAAACTTCCAAAAATTCCAATTTTACTCCT
1 CAAACTTCTAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTAC-CCT
* * * * *
2384 -GAACTTCAAAAAATCCCATTTTTAACCCCAAAAACTTCCAAAAATTCCATTTTTACCCC
1 CAAACTTCTAAAAATCCCATTTTTGACCCC-GAAACTTCCAAAAATTCCATTTTTACCCT
* * * * *
2443 CAAACTTCCAAAAATCCCATTTTTAACTCCAAAACTTCCAAAAATTCCATTTTTACCCC
1 CAAACTTCTAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCCT
* *
2502 CAAATTTCCAAAA
1 CAAACTTCTAAAA
Statistics
Matches: 311, Mismatches: 46, Indels: 18
0.83 0.12 0.05
Matches are distributed among these distances:
57 21 0.07
58 60 0.19
59 174 0.56
60 56 0.18
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.33
Consensus pattern (59 bp):
CAAACTTCTAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCCT
Done.