Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012145.1 Kokia drynarioides strain JFW-HI SEQ_127144, 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: 5733
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.32
Warning! 74 characters in sequence are not A, C, G, or T
Found at i:3772 original size:17 final size:17
Alignment explanation
Indices: 3738--3817 Score: 108
Period size: 17 Copynumber: 4.7 Consensus size: 17
3728 TCTGGGTCTA
*
3738 TTGAAATTTGAATTTAT
1 TTGAAATTTAAATTTAT
* * *
3755 TTTAAAATTAAGTTTAT
1 TTGAAATTTAAATTTAT
3772 TTGAAATTTAAATTTAT
1 TTGAAATTTAAATTTAT
3789 TTGAAATTTAAATTTAT
1 TTGAAATTTAAATTTAT
3806 TAT-AAATTTAAA
1 T-TGAAATTTAAA
3818 ATGTCTAATT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
17 54 0.98
18 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.51
Consensus pattern (17 bp):
TTGAAATTTAAATTTAT
Found at i:5458 original size:30 final size:29
Alignment explanation
Indices: 5426--5733 Score: 325
Period size: 29 Copynumber: 10.4 Consensus size: 29
5416 GAAGGTCCCT
* *
5426 AAACTATCCAAAAATTTCATTTTTACCCCT
1 AAACT-TCCAAAAATTCCATTTTTACCCCA
*
5456 AAACTTCCAAAAA-TCCAATTTCTAACCCCA
1 AAACTTCCAAAAATTCC-ATTT-TTACCCCA
* * *
5486 AAACTTCTAAAAATTCTATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCA
* * *
5515 AAACTTCCAAAAATCCCATTTTTGATCCCG
1 AAACTTCCAAAAATTCCATTTTT-ACCCCA
* *
5545 AAACTTCTAAAAATTCCATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCA
5574 AAACTTCCAAAAA-TCCAATTTTTGACCCCA
1 AAACTTCCAAAAATTCC-ATTTTT-ACCCCA
* * ***
5604 AAACTTCTAAAAATTCCAATTTTACCTTT
1 AAACTTCCAAAAATTCCATTTTTACCCCA
**
5633 AAACTTCCAAAAAACCCATTTTTAACCCCA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCA
** * *
5663 AAACTTTTAAAAATTCCATTTTTAGCCCT
1 AAACTTCCAAAAATTCCATTTTTACCCCA
5692 AAACTTCCAAAAATTCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCA
5722 AAACTT-CAAAAA
1 AAACTTCCAAAAA
Statistics
Matches: 229, Mismatches: 40, Indels: 19
0.80 0.14 0.07
Matches are distributed among these distances:
28 5 0.02
29 113 0.49
30 106 0.46
31 5 0.02
ACGTcount: A:0.39, C:0.28, G:0.02, T:0.32
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCA
Found at i:5527 original size:59 final size:59
Alignment explanation
Indices: 5426--5733 Score: 422
Period size: 59 Copynumber: 5.2 Consensus size: 59
5416 GAAGGTCCCT
* * * *
5426 AAACTATCCAAAAATTTCATTTTTACCCCTAAACTTCCAAAAATCCAATTTCTAACCCCA
1 AAACT-TCTAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCCAATTTTTGACCCCA
* * * * *
5486 AAACTTCTAAAAATTCTATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTGATCCCG
1 AAACTTCTAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCCAATTTTTGACCCCA
*
5545 AAACTTCTAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCAATTTTTGACCCCA
1 AAACTTCTAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCCAATTTTTGACCCCA
* ** * * *
5604 AAACTTCTAAAAATTCCAATTTTACCTTTAAACTTCCAAAAAACCCATTTTTAACCCCA
1 AAACTTCTAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCCAATTTTTGACCCCA
* *
5663 AAACTTTTAAAAATTCCATTTTTAGCCCTAAACTTCCAAAAATTCC-ATTTTTGACCCCA
1 AAACTTCTAAAAATTCCATTTTTACCCCTAAACTTCCAAAAA-TCCAATTTTTGACCCCA
5722 AAACTTC-AAAAA
1 AAACTTCTAAAAA
Statistics
Matches: 219, Mismatches: 28, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
58 5 0.02
59 207 0.95
60 7 0.03
ACGTcount: A:0.39, C:0.28, G:0.02, T:0.32
Consensus pattern (59 bp):
AAACTTCTAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCCAATTTTTGACCCCA
Done.