Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005610.1 Kokia drynarioides strain JFW-HI SEQ_119757, 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: 1692
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.36
Found at i:334 original size:29 final size:29
Alignment explanation
Indices: 293--590 Score: 307
Period size: 30 Copynumber: 10.0 Consensus size: 29
283 TTTGGGAAAA
*
293 TTCGGGGTCAAAAATGGGATTTTTAGAAG-
1 TTCGGGGT-AAAAATGGGATTTTTGGAAGT
* * *
322 TTCGGGTGTAAAAAT-TGACCTTTTGAAAGT
1 TTCGGG-GTAAAAATGGGA-TTTTTGGAAGT
* * *
352 TTTGGGGTTAAAAATGGGATTTTTTGTAG-
1 TTCGGGG-TAAAAATGGGATTTTTGGAAGT
*
381 TTCGGGGGTAAAAATGGAATTTTTGGAAGT
1 TTC-GGGGTAAAAATGGGATTTTTGGAAGT
* * *
411 TTTGGGGTTAAAATTGAGATTTTTGGAAGT
1 TTCGGGG-TAAAAATGGGATTTTTGGAAGT
*
441 TTCGAGGTTAAAAATGGGATTTTTGGAAGT
1 TTCG-GGGTAAAAATGGGATTTTTGGAAGT
471 TTCGGGGTAAAAATGGGATTTTTGGAAGT
1 TTCGGGGTAAAAATGGGATTTTTGGAAGT
* * *
500 TTCGGGGTTAAAAATGGGATTTCTAGAA-A
1 TTCGGGG-TAAAAATGGGATTTTTGGAAGT
529 TTCGAGGGTAAAAATGGGATTTTTTGGAAGT
1 TTCG-GGGTAAAAATGGGA-TTTTTGGAAGT
* * *
560 TTTGGGGTTAAAAATGGGATTTCTAGAAGT
1 TTCGGGG-TAAAAATGGGATTTTTGGAAGT
590 T
1 T
591 ACATAAAATA
Statistics
Matches: 223, Mismatches: 32, Indels: 27
0.79 0.11 0.10
Matches are distributed among these distances:
28 2 0.01
29 90 0.40
30 113 0.51
31 18 0.08
ACGTcount: A:0.29, C:0.04, G:0.30, T:0.37
Consensus pattern (29 bp):
TTCGGGGTAAAAATGGGATTTTTGGAAGT
Found at i:365 original size:59 final size:59
Alignment explanation
Indices: 296--590 Score: 282
Period size: 59 Copynumber: 5.0 Consensus size: 59
286 GGGAAAATTC
* * * * *
296 GGGGTCAAAAATGGGATTTTTAGAAG-TTCGGGTGTAAAAATTGACCTTTTGAAAGTTTT
1 GGGGTTAAAAATGGGATTTTTGGAAGTTTCGGGTGTAAAAATGGA-TTTTTGGAAGTTTT
* * *
355 GGGGTTAAAAATGGGATTTTTTGTAG-TTCGGGGGTAAAAATGGAATTTTTGGAAGTTTT
1 GGGGTTAAAAATGGGATTTTTGGAAGTTTCGGGTGTAAAAATGG-ATTTTTGGAAGTTTT
* * *
414 GGGGTTAAAATTGAGATTTTTGGAAGTTTCGAGGT-TAAAAATGGGATTTTTGGAAGTTTC
1 GGGGTTAAAAATGGGATTTTTGGAAGTTTCG-GGTGTAAAAAT-GGATTTTTGGAAGTTTT
* * * *
474 GGGG-TAAAAATGGGATTTTTGGAAGTTTCGGG-GTTAAAAATGGGATTTCTAGAA-ATTC
1 GGGGTTAAAAATGGGATTTTTGGAAGTTTCGGGTG-TAAAAAT-GGATTTTTGGAAGTTTT
* * *
532 GAGGG-TAAAAATGGGATTTTTTGGAAGTTTTGGG-GTTAAAAATGGGATTTCTAGAAGTT
1 G-GGGTTAAAAATGGGA-TTTTTGGAAGTTTCGGGTG-TAAAAAT-GGATTTTTGGAAGTT
591 ACATAAAATA
Statistics
Matches: 207, Mismatches: 20, Indels: 16
0.85 0.08 0.07
Matches are distributed among these distances:
58 6 0.03
59 128 0.62
60 68 0.33
61 5 0.02
ACGTcount: A:0.29, C:0.04, G:0.31, T:0.36
Consensus pattern (59 bp):
GGGGTTAAAAATGGGATTTTTGGAAGTTTCGGGTGTAAAAATGGATTTTTGGAAGTTTT
Found at i:452 original size:89 final size:90
Alignment explanation
Indices: 296--590 Score: 339
Period size: 89 Copynumber: 3.3 Consensus size: 90
286 GGGAAAATTC
* ** * * *
296 GGGGTCAAAAATGGGATTTTTAGAAG-TTCGGGTGTAAAAATTGA-CCTTTTGAAAGTTTTGGGG
1 GGGGT-AAAAATGGGATTTTTAGAAGTTTCGGG-GTTAAAATTGAGATTTTTGGAAGTTTCGAGG
*
359 TTAAAAATGGGATTTTTTGTAG-TTCG
64 TTAAAAATGGGATTTTTTGAAGTTTCG
* * *
385 GGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTTAAAATTGAGATTTTTGGAAGTTTCGAGGTT
1 GGGGTAAAAATGGGATTTTTAGAAGTTTCGGGGTTAAAATTGAGATTTTTGGAAGTTTCGAGGTT
*
450 AAAAATGGGATTTTTGGAAGTTTC-
66 AAAAATGGGATTTTTTGAAGTTTCG
* * * * * * *
474 GGGGTAAAAATGGGATTTTTGGAAGTTTCGGGGTTAAAAATGGGATTTCTAGAA-ATTCGAGGGT
1 GGGGTAAAAATGGGATTTTTAGAAGTTTCGGGGTTAAAATTGAGATTTTTGGAAGTTTCGAGGTT
*
538 AAAAATGGGATTTTTTGGAAGTTTTG
66 AAAAATGGGATTTTTT-GAAGTTTCG
* *
564 GGGTTAAAAATGGGATTTCTAGAAGTT
1 GGGGTAAAAATGGGATTTTTAGAAGTT
591 ACATAAAATA
Statistics
Matches: 177, Mismatches: 24, Indels: 9
0.84 0.11 0.04
Matches are distributed among these distances:
88 51 0.29
89 99 0.56
90 27 0.15
ACGTcount: A:0.29, C:0.04, G:0.31, T:0.36
Consensus pattern (90 bp):
GGGGTAAAAATGGGATTTTTAGAAGTTTCGGGGTTAAAATTGAGATTTTTGGAAGTTTCGAGGTT
AAAAATGGGATTTTTTGAAGTTTCG
Found at i:1283 original size:12 final size:12
Alignment explanation
Indices: 1257--1289 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1247 AAACAATTCA
*
1257 TTCTCTCT-TTT
1 TTCTCTCTAGTT
1268 TTCTCTCTAGTT
1 TTCTCTCTAGTT
1280 TTCTCTCTAG
1 TTCTCTCTAG
1290 CCTTCCATCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.06, C:0.27, G:0.06, T:0.61
Consensus pattern (12 bp):
TTCTCTCTAGTT
Found at i:1524 original size:12 final size:12
Alignment explanation
Indices: 1507--1531 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1497 TGCTATCATG
1507 ATGAATGCTATT
1 ATGAATGCTATT
1519 ATGAATGCTATT
1 ATGAATGCTATT
1531 A
1 A
1532 ATTATTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (12 bp):
ATGAATGCTATT
Done.