Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012573.1 Kokia drynarioides strain JFW-HI SEQ_127582, 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: 1716
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.30
Warning! 22 characters in sequence are not A, C, G, or T
Found at i:548 original size:30 final size:28
Alignment explanation
Indices: 486--804 Score: 300
Period size: 30 Copynumber: 10.8 Consensus size: 28
476 ATCTCGAGGT
*
486 AAAATGGTAATTTTTGAAAGTTTCGGGGTAA
1 AAAATGG-AATTTTTGGAAGTTT-GGGGT-A
* *
517 AAAATGGAATTGTTAGAAGTTTGGGGCTA
1 AAAATGGAATTTTTGGAAGTTTGGGG-TA
546 AAAATGGAATTTTTGGAAGTTTGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTG-GGGTA
*
575 AAAATGGGATTTTTTGGAAGTTTGAGGGTA
1 AAAAT-GGAATTTTTGGAAGTTTG-GGGTA
*
605 AAAATGAAATTTTT-GATAGTTTTGGGGTTA
1 AAAATGGAATTTTTGGA-AG-TTTGGGG-TA
635 AAAAT-GAGATTTTTGGAAGTTTAGGGGTA
1 AAAATGGA-ATTTTTGGAAGTTT-GGGGTA
* ** *
664 AAAATAGAATTTTTACAAGTTTTAGGGTA
1 AAAATGGAATTTTTGGAAG-TTTGGGGTA
* * *
693 AAATATGGGATTTTTCGAAGTTCGAGGGTA
1 AAA-ATGGAATTTTTGGAAGTTTG-GGGTA
* *
723 AAAATAGAATTTTTAGAAGTTTTGGGGTCA
1 AAAATGGAATTTTTGGAAG-TTTGGGGT-A
* *
753 AAAATGGGATTTTTGGAAGTTTAAGGGTA
1 AAAATGGAATTTTTGGAAGTTT-GGGGTA
*
782 AAAATGAAATTTTTGGATAGTTT
1 AAAATGGAATTTTTGGA-AGTTT
805 AGGGACCTAC
Statistics
Matches: 243, Mismatches: 28, Indels: 35
0.79 0.09 0.11
Matches are distributed among these distances:
28 2 0.01
29 111 0.46
30 121 0.50
31 9 0.04
ACGTcount: A:0.35, C:0.02, G:0.27, T:0.36
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAAGTTTGGGGTA
Found at i:548 original size:59 final size:59
Alignment explanation
Indices: 494--796 Score: 318
Period size: 59 Copynumber: 5.1 Consensus size: 59
484 GTAAAATGGT
* * * *
494 AATTTTTGAAAGTTTCGGGGTAAAAAATGGAATTGTTAGAAGTTTG-GGGCTAAAAATGG
1 AATTTTTGAAAGTTTTGGGGTAAAAAATGGAATTTTTGGAAGTTTGAGGG-TAAAAATAG
* *
553 AATTTTTGGAAG-TTTGAGGGT-AAAAATGGGATTTTTTGGAAGTTTGAGGGTAAAAAT-G
1 AATTTTTGAAAGTTTTG-GGGTAAAAAAT-GGAATTTTTGGAAGTTTGAGGGTAAAAATAG
* *
611 AAATTTTTGATAGTTTTGGGGTTAAAAAT-GAGATTTTTGGAAGTTT-AGGGGTAAAAATAG
1 -AATTTTTGAAAGTTTTGGGGTAAAAAATGGA-ATTTTTGGAAGTTTGA-GGGTAAAAATAG
* * * * *
671 AATTTTT-ACAAGTTTTAGGGTAAAATATGGGATTTTTCGAAGTTCGAGGGTAAAAATAG
1 AATTTTTGA-AAGTTTTGGGGTAAAAAATGGAATTTTTGGAAGTTTGAGGGTAAAAATAG
* * *
730 AATTTTT-AGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTTAAGGGTAAAAAT-G
1 AATTTTTGA-AAGTTTTGGGGTAAAAAATGGAATTTTTGGAAGTTTGAGGGTAAAAATAG
788 AAATTTTTG
1 -AATTTTTG
797 GATAGTTTAG
Statistics
Matches: 208, Mismatches: 22, Indels: 27
0.81 0.09 0.11
Matches are distributed among these distances:
58 15 0.07
59 177 0.85
60 16 0.08
ACGTcount: A:0.35, C:0.02, G:0.27, T:0.36
Consensus pattern (59 bp):
AATTTTTGAAAGTTTTGGGGTAAAAAATGGAATTTTTGGAAGTTTGAGGGTAAAAATAG
Found at i:626 original size:118 final size:116
Alignment explanation
Indices: 494--808 Score: 395
Period size: 118 Copynumber: 2.7 Consensus size: 116
484 GTAAAATGGT
* * *
494 AATTTTTGAAAGTTTCGGGGTAAAAAATGGAATTGTTAGAAGTTT-GGGGCTAAAAATGGAATTT
1 AATTTTTG-AAGTTTTGGGGTAAAAAATGGAATTTTTGGAAGTTTAGGGG-TAAAAATGGAATTT
* *
558 TTGGAAGTTTGAGGGTAAAA-ATGGGATTTTTTGGAAGTTTGAGGGTAAAAAT-G
64 TTGGAAGTTT-AGGGTAAAATATGGGA-TTTTTCGAAGTTCGAGGGTAAAAATAG
* *
611 AAATTTTTGATAGTTTTGGGGTTAAAAAT-GAGATTTTTGGAAGTTTAGGGGTAAAAATAGAATT
1 -AATTTTTGA-AGTTTTGGGGTAAAAAATGGA-ATTTTTGGAAGTTTAGGGGTAAAAATGGAATT
**
675 TTTACAAGTTTTAGGGTAAAATATGGGATTTTTCGAAGTTCGAGGGTAAAAATAG
63 TTTGGAAG-TTTAGGGTAAAATATGGGATTTTTCGAAGTTCGAGGGTAAAAATAG
* * * *
730 AATTTTTAGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTTAAGGGTAAAAATGAAATTTT
1 AATTTTT-GAAGTTTTGGGGTAAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTT
795 TGGATAGTTTAGGG
65 TGGA-AGTTTAGGG
809 ACCTACAGGG
Statistics
Matches: 172, Mismatches: 16, Indels: 18
0.83 0.08 0.09
Matches are distributed among these distances:
117 3 0.02
118 150 0.87
119 19 0.11
ACGTcount: A:0.34, C:0.02, G:0.28, T:0.36
Consensus pattern (116 bp):
AATTTTTGAAGTTTTGGGGTAAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTTT
GGAAGTTTAGGGTAAAATATGGGATTTTTCGAAGTTCGAGGGTAAAAATAG
Done.