Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001139.1 Kokia drynarioides strain JFW-HI SEQ_112437, 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: 1875
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Found at i:203 original size:29 final size:28
Alignment explanation
Indices: 171--231 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
161 AAAATGAGAC
*
171 TTTTCGGA-TACCTAGGGGCAAAATGGTAA
1 TTTT-GGATTACC-AGGGGCAAAAGGGTAA
* *
200 TTTTGGATTATCGGGGGCAAAAGGGTAA
1 TTTTGGATTACCAGGGGCAAAAGGGTAA
228 TTTT
1 TTTT
232 TGGGAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 21 0.75
29 7 0.25
ACGTcount: A:0.28, C:0.10, G:0.30, T:0.33
Consensus pattern (28 bp):
TTTTGGATTACCAGGGGCAAAAGGGTAA
Found at i:382 original size:30 final size:30
Alignment explanation
Indices: 288--588 Score: 249
Period size: 30 Copynumber: 10.1 Consensus size: 30
278 GAAAGGGTAA
* * * *
288 TTTTGGGAGTTTTGAGGTCGAAAATGGAGT
1 TTTTGGAAGTTTCGAGGTCAAAAATGGAAT
* * * *
318 TTTTGGACA--TCCGGGGGC-AAAATGGTATT
1 TTTTGGA-AGTTTCGAGGTCAAAAATGG-AAT
*
347 TTTTGGAAGTTTCGAGGTTAAAAATGGAAT
1 TTTTGGAAGTTTCGAGGTCAAAAATGGAAT
* *
377 TTTTGGAAATTTTGAGGTCAAAAATGGAAT
1 TTTTGGAAGTTTCGAGGTCAAAAATGGAAT
* **
407 TTTTCGAAGTTTTAAGTGT-AAAAATAGG-AT
1 TTTTGGAAGTTTCGAG-GTCAAAAAT-GGAAT
* * * * *
437 TTTTAGATGTTTTGAGGTCAAAAACGAAAT
1 TTTTGGAAGTTTCGAGGTCAAAAATGGAAT
* *
467 TTTTGGAAGTTTCAAGGGT-AAAAATGGGAT
1 TTTTGGAAGTTTCGA-GGTCAAAAATGGAAT
* **
497 TTTTTGAAGTTTTTAGGTCAAAAATGGAAT
1 TTTTGGAAGTTTCGAGGTCAAAAATGGAAT
* *
527 TTTTGGAAGTTTCGGGGTCAAAAATGGGAT
1 TTTTGGAAGTTTCGAGGTCAAAAATGGAAT
*
557 TTTTGGAAG-TTCGAGGAT-AAAAATGAAAT
1 TTTTGGAAGTTTCGAGG-TCAAAAATGGAAT
586 TTT
1 TTT
589 CGAACAGTTT
Statistics
Matches: 218, Mismatches: 41, Indels: 25
0.77 0.14 0.09
Matches are distributed among these distances:
28 8 0.04
29 38 0.17
30 157 0.72
31 15 0.07
ACGTcount: A:0.32, C:0.05, G:0.26, T:0.37
Consensus pattern (30 bp):
TTTTGGAAGTTTCGAGGTCAAAAATGGAAT
Found at i:429 original size:60 final size:60
Alignment explanation
Indices: 336--588 Score: 278
Period size: 60 Copynumber: 4.2 Consensus size: 60
326 ATCCGGGGGC
* ** * * *
336 AAAATGGTATTTTTTGGAAGTTTCGAGGTTAAAAATGGAATTTTTGGAAATTTTGAGGTCA
1 AAAATGG-AATTTTTGGAAGTTTTAAGGGTAAAAATGGGATTTTTGGAAGTTTTGAGGTCA
* * * * *
397 AAAATGGAATTTTTCGAAGTTTTAAGTGTAAAAATAGGATTTTTAGATGTTTTGAGGTCA
1 AAAATGGAATTTTTGGAAGTTTTAAGGGTAAAAATGGGATTTTTGGAAGTTTTGAGGTCA
* * * * *
457 AAAACGAAATTTTTGGAAGTTTCAAGGGTAAAAATGGGATTTTTTGAAGTTTTTAGGTCA
1 AAAATGGAATTTTTGGAAGTTTTAAGGGTAAAAATGGGATTTTTGGAAGTTTTGAGGTCA
** *
517 AAAATGGAATTTTTGGAAG-TTTCGGGGTCAAAAATGGGATTTTTGGAAG-TTCGAGGAT-A
1 AAAATGGAATTTTTGGAAGTTTTAAGGGT-AAAAATGGGATTTTTGGAAGTTTTGAGG-TCA
*
576 AAAATGAAATTTT
1 AAAATGGAATTTT
589 CGAACAGTTT
Statistics
Matches: 161, Mismatches: 29, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
59 24 0.15
60 130 0.81
61 7 0.04
ACGTcount: A:0.35, C:0.04, G:0.24, T:0.37
Consensus pattern (60 bp):
AAAATGGAATTTTTGGAAGTTTTAAGGGTAAAAATGGGATTTTTGGAAGTTTTGAGGTCA
Found at i:598 original size:90 final size:88
Alignment explanation
Indices: 336--592 Score: 277
Period size: 90 Copynumber: 2.9 Consensus size: 88
326 ATCCGGGGGC
* * * *
336 AAAATGGTATTTTTTGGAAGTTTCGAGGTTAAAAATGGAATTTTTGGAAATTTTGAGGTCAAAAA
1 AAAATGG-AATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGG-AAGTTCGAGGT-AAAAA
401 TGGAATTTTTCGAAGTTTTAAGTGTA
63 TGGAATTTTTCGAAGTTTTAAGTGTA
* * * * * *
427 AAAATAGG-ATTTTTAGATGTTTTGAGGTCAAAAACGAAATTTTTGGAAGTTTCAAGGGTAAAAA
1 AAAAT-GGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAG-TTCGA-GGTAAAAA
* * *
491 TGGGATTTTTTGAAGTTTTTAG-GTCA
63 TGGAATTTTTCGAAGTTTTAAGTGT-A
* *
517 AAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGATAAAAAT-
1 AAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTCGAGG-TAAAAATG
*
581 GAAATTTTCGAA
65 GAATTTTTCGAA
593 CAGTTTAGGG
Statistics
Matches: 136, Mismatches: 24, Indels: 15
0.78 0.14 0.09
Matches are distributed among these distances:
88 11 0.08
89 17 0.12
90 98 0.72
91 8 0.06
92 2 0.01
ACGTcount: A:0.35, C:0.04, G:0.24, T:0.37
Consensus pattern (88 bp):
AAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTCGAGGTAAAAATGG
AATTTTTCGAAGTTTTAAGTGTA
Found at i:1486 original size:34 final size:32
Alignment explanation
Indices: 1447--1515 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
1437 TTCGTATTAA
*
1447 ATAATAAATAGAT-AGTTAATGAACATATTAATAT
1 ATAATAAATA-ATAAGTAAAT--ACATATTAATAT
*
1481 ATAATAAATAATAAGTAAATATATATTAATAT
1 ATAATAAATAATAAGTAAATACATATTAATAT
1513 ATA
1 ATA
1516 TTTATATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 14 0.44
33 2 0.06
34 16 0.50
ACGTcount: A:0.57, C:0.01, G:0.06, T:0.36
Consensus pattern (32 bp):
ATAATAAATAATAAGTAAATACATATTAATAT
Done.