Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010519.1 Kokia drynarioides strain JFW-HI SEQ_125431, 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: 16302
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Warning! 60 characters in sequence are not A, C, G, or T
Found at i:499 original size:29 final size:29
Alignment explanation
Indices: 460--629 Score: 147
Period size: 29 Copynumber: 5.8 Consensus size: 29
450 GTCCCTGAAC
*
460 CTTCCAAAAATTACCGTTTTACCCCCGAA
1 CTTCCAAAAATTACCATTTTACCCCCGAA
* *
489 -TTCCCAAAAA-TCCCATTTTTAACCCCGAA
1 CTT-CCAAAAATTACCA-TTTTACCCCCGAA
** **
518 CCTTTTAAAAATTATAATTTTACCCCCGAA
1 -CTTCCAAAAATTACCATTTTACCCCCGAA
548 -TTCCCAAAAA-T-CCAATTTTTGA-CCCCGAA
1 CTT-CCAAAAATTACC-A-TTTT-ACCCCCGAA
*
577 CCTTCCAAAAATTACCATTTTATCCCCGAA
1 -CTTCCAAAAATTACCATTTTACCCCCGAA
607 CTTCC-AAAATTACCATTTTACCC
1 CTTCCAAAAATTACCATTTTACCC
630 TCGAGTTGCT
Statistics
Matches: 113, Mismatches: 14, Indels: 29
0.72 0.09 0.19
Matches are distributed among these distances:
28 26 0.23
29 41 0.36
30 36 0.32
31 8 0.07
32 2 0.02
ACGTcount: A:0.34, C:0.32, G:0.04, T:0.31
Consensus pattern (29 bp):
CTTCCAAAAATTACCATTTTACCCCCGAA
Found at i:548 original size:59 final size:59
Alignment explanation
Indices: 456--625 Score: 225
Period size: 59 Copynumber: 2.9 Consensus size: 59
446 GAATGTCCCT
**
456 GAACCTTCCAAAAATTACCGTTTTACCCCCGAATTCCCAAAAATCCCATTTTTAACCCC
1 GAACCTTCCAAAAATTACAATTTTACCCCCGAATTCCCAAAAATCCCATTTTTAACCCC
** * * *
515 GAACCTTTTAAAAATTATAATTTTACCCCCGAATTCCCAAAAATCCAATTTTTGACCCC
1 GAACCTTCCAAAAATTACAATTTTACCCCCGAATTCCCAAAAATCCCATTTTTAACCCC
* * * *
574 GAACCTTCCAAAAATTACCATTTTATCCCCGAACTT-CCAAAATTACCATTTT
1 GAACCTTCCAAAAATTACAATTTTACCCCCGAA-TTCCCAAAAATCCCATTTT
626 ACCCTCGAGT
Statistics
Matches: 95, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
59 93 0.98
60 2 0.02
ACGTcount: A:0.34, C:0.31, G:0.05, T:0.31
Consensus pattern (59 bp):
GAACCTTCCAAAAATTACAATTTTACCCCCGAATTCCCAAAAATCCCATTTTTAACCCC
Found at i:643 original size:28 final size:28
Alignment explanation
Indices: 451--626 Score: 108
Period size: 28 Copynumber: 6.0 Consensus size: 28
441 ACCCCGAATG
* *
451 TCCCTGAACCTTCCAAAAATTACCGTTTTA
1 TCCCCGAA-CTTCC-AAAATTACCATTTTA
* * *
481 CCCCCGAA-TTCCCAAAAATCCCATTTTTA
1 TCCCCGAACTT-CCAAAATTACCA-TTTTA
* ** **
510 ACCCCGAACCTTTTAAAAATTATAATTTTA
1 TCCCCGAA-C-TTCCAAAATTACCATTTTA
* *
540 CCCCCGAA-TTCCCAAAAAT-CCAATTTT-
1 TCCCCGAACTT-CCAAAATTACC-ATTTTA
567 TGACCCCGAACCTTCCAAAAATTACCATTTTA
1 T--CCCCGAA-CTTCC-AAAATTACCATTTTA
599 TCCCCGAACTTCCAAAATTACCATTTTA
1 TCCCCGAACTTCCAAAATTACCATTTTA
627 CCCTCGAGTT
Statistics
Matches: 112, Mismatches: 20, Indels: 30
0.69 0.12 0.19
Matches are distributed among these distances:
27 2 0.02
28 34 0.30
29 26 0.23
30 27 0.24
31 18 0.16
32 5 0.04
ACGTcount: A:0.34, C:0.31, G:0.05, T:0.31
Consensus pattern (28 bp):
TCCCCGAACTTCCAAAATTACCATTTTA
Found at i:15234 original size:90 final size:90
Alignment explanation
Indices: 15081--15264 Score: 368
Period size: 90 Copynumber: 2.0 Consensus size: 90
15071 TCAGGACCTT
15081 GAAGATAATCAAGATTGCGATTTACCTTCGGATCTGTTAAGAATGATGGAACAGGAAGAAAGACA
1 GAAGATAATCAAGATTGCGATTTACCTTCGGATCTGTTAAGAATGATGGAACAGGAAGAAAGACA
15146 GATCCTCCCTCATGCTGACCCGGTA
66 GATCCTCCCTCATGCTGACCCGGTA
15171 GAAGATAATCAAGATTGCGATTTACCTTCGGATCTGTTAAGAATGATGGAACAGGAAGAAAGACA
1 GAAGATAATCAAGATTGCGATTTACCTTCGGATCTGTTAAGAATGATGGAACAGGAAGAAAGACA
15236 GATCCTCCCTCATGCTGACCCGGTA
66 GATCCTCCCTCATGCTGACCCGGTA
15261 GAAG
1 GAAG
15265 TTATTAATCT
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 94 1.00
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.23
Consensus pattern (90 bp):
GAAGATAATCAAGATTGCGATTTACCTTCGGATCTGTTAAGAATGATGGAACAGGAAGAAAGACA
GATCCTCCCTCATGCTGACCCGGTA
Done.