Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003925.1 Kokia drynarioides strain JFW-HI SEQ_117001, 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: 5170
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Found at i:400 original size:29 final size:29
Alignment explanation
Indices: 349--817 Score: 401
Period size: 30 Copynumber: 16.0 Consensus size: 29
339 GAGGTCCCTA
349 AACTGTCCAAAAATTCCATTTTTACCCCCG
1 AACT-TCCAAAAATTCCATTTTTACCCCCG
* *
379 AACTTCCAAAAATTCCAATTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTACCCCCG
* * * **
408 AACTTCAAAAAATCCCATTTTTGACCTCAA
1 AACTTCCAAAAATTCCATTTTT-ACCCCCG
438 AACTTCCAAAAATTCCATTTTTACCCCCG
1 AACTTCCAAAAATTCCATTTTTACCCCCG
* * * *
467 AACTTCCAAAAATCCCATTTTCAACCTCG
1 AACTTCCAAAAATTCCATTTTTACCCCCG
* **
496 AAACGTCCAAAAATTCCATTTTTGA-CCTTG
1 -AACTTCCAAAAATTCCATTTTT-ACCCCCG
*
526 AAACTTCCAAAAATTCCATTTTTACCCTCG
1 -AACTTCCAAAAATTCCATTTTTACCCCCG
* * *
556 AACTTCAAAAAATTCCATTTTTGA-TCTCG
1 AACTTCCAAAAATTCCATTTTT-ACCCCCG
*
585 AAACTTCCAAAAATTCCATTTTTACCCCTG
1 -AACTTCCAAAAATTCCATTTTTACCCCCG
* * ***
615 AACTACCTAAAATTCCATTTTT-CCCGTA
1 AACTTCCAAAAATTCCATTTTTACCCCCG
**
643 AACTTCCAAAAA-TCACATTTTTGA-CCTTG
1 AACTTCCAAAAATTC-CATTTTT-ACCCCCG
*
672 AAACTTCTAAAAATTCCATTTTTACCCCCG
1 -AACTTCCAAAAATTCCATTTTTACCCCCG
** * * * *
702 AACTT-CTGAAATCCCAATTTTAACCCTG
1 AACTTCCAAAAATTCCATTTTTACCCCCG
* * *
730 AAACTTCAAAAAATTCCATTTTTATCCCTG
1 -AACTTCCAAAAATTCCATTTTTACCCCCG
* ** * **
760 AACATCCAAAAACACCATTTTTTATCCCAA
1 AACTTCCAAAAATTCCA-TTTTTACCCCCG
*
790 AATTTCCAAAAATTCCATTTTTACCCCC
1 AACTTCCAAAAATTCCATTTTTACCCCC
818 CGAATGTTTA
Statistics
Matches: 357, Mismatches: 66, Indels: 33
0.78 0.14 0.07
Matches are distributed among these distances:
27 2 0.01
28 37 0.10
29 154 0.43
30 161 0.45
31 3 0.01
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTACCCCCG
Found at i:449 original size:30 final size:29
Alignment explanation
Indices: 348--814 Score: 404
Period size: 29 Copynumber: 15.9 Consensus size: 29
338 GGAGGTCCCT
*
348 AAACTGTCCAAAAATTCCATTTTTACCCCCG
1 AAACT-TCCAAAAATTCCATTTTTA-CCTCG
*
379 -AACTTCCAAAAATTCCAATTTTACCCTCG
1 AAACTTCCAAAAATTCCATTTTTA-CCTCG
* * *
408 -AACTTCAAAAAATCCCATTTTTGACCTCA
1 AAACTTCCAAAAATTCCATTTTT-ACCTCG
*
437 AAACTTCCAAAAATTCCATTTTTACCCCCG
1 AAACTTCCAAAAATTCCATTTTTA-CCTCG
* *
467 -AACTTCCAAAAATCCCATTTTCAACCTCG
1 AAACTTCCAAAAATTCCATTTT-TACCTCG
* *
496 AAACGTCCAAAAATTCCATTTTTGACCTTG
1 AAACTTCCAAAAATTCCATTTTT-ACCTCG
526 AAACTTCCAAAAATTCCATTTTTACCCTCG
1 AAACTTCCAAAAATTCCATTTTTA-CCTCG
* *
556 -AACTTCAAAAAATTCCATTTTTGATCTCG
1 AAACTTCCAAAAATTCCATTTTT-ACCTCG
*
585 AAACTTCCAAAAATTCCATTTTTACCCCTG
1 AAACTTCCAAAAATTCCATTTTTACCTC-G
* *
615 -AACTACCTAAAATTCCATTTTT-CC-CG
1 AAACTTCCAAAAATTCCATTTTTACCTCG
*
641 TAAACTTCCAAAAA-TCACATTTTTGACCTTG
1 -AAACTTCCAAAAATTC-CATTTTT-ACCTCG
* *
672 AAACTTCTAAAAATTCCATTTTTACCCCCG
1 AAACTTCCAAAAATTCCATTTTTA-CCTCG
** * *
702 -AACTT-CTGAAATCCCAATTTTAACC-CTG
1 AAACTTCCAAAAATTCC-ATTTTTACCTC-G
*
730 AAACTTCAAAAAATTCCATTTTTATCC-CTG
1 AAACTTCCAAAAATTCCATTTTTA-CCTC-G
* ** *
760 -AACATCCAAAAACACCATTTTTTATCC-CA
1 AAACTTCCAAAAATTCCA-TTTTTA-CCTCG
*
789 AAATTTCCAAAAATTCCATTTTTACC
1 AAACTTCCAAAAATTCCATTTTTACC
815 CCCCGAATGT
Statistics
Matches: 360, Mismatches: 51, Indels: 53
0.78 0.11 0.11
Matches are distributed among these distances:
26 1 0.00
27 4 0.01
28 30 0.08
29 162 0.45
30 160 0.44
31 3 0.01
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCTCG
Found at i:451 original size:59 final size:58
Alignment explanation
Indices: 349--815 Score: 436
Period size: 59 Copynumber: 7.9 Consensus size: 58
339 GAGGTCCCTA
* * *
349 AACTGTCCAAAAATTCCATTTTTACCCCCG-AACTTCCAAAAATTCCAATTTTACCCTCG
1 AACT-TCCAAAAATCCCATTTTTA-CCTCGAAACTTCCAAAAATTCCATTTTTACCCTCG
* * *
408 AACTTCAAAAAATCCCATTTTTGACCTCAAAACTTCCAAAAATTCCATTTTTACCCCCG
1 AACTTCCAAAAATCCCATTTTT-ACCTCGAAACTTCCAAAAATTCCATTTTTACCCTCG
* * *
467 AACTTCCAAAAATCCCATTTTCAACCTCGAAACGTCCAAAAATTCCATTTTTGA-CCTTG
1 AACTTCCAAAAATCCCATTTT-TACCTCGAAACTTCCAAAAATTCCATTTTT-ACCCTCG
* * *
526 AAACTTCCAAAAATTCCATTTTTACCCTCG-AACTTCAAAAAATTCCATTTTTGA-TCTCG
1 -AACTTCCAAAAATCCCATTTTTA-CCTCGAAACTTCCAAAAATTCCATTTTT-ACCCTCG
* * * * *
585 AAACTTCCAAAAATTCCATTTTTACCCCTG-AACTACCTAAAATTCCATTTTT-CCCGT-A
1 -AACTTCCAAAAATCCCATTTTTACCTC-GAAACTTCCAAAAATTCCATTTTTACCC-TCG
* * * *
643 AACTTCCAAAAATCACATTTTTGACCTTGAAACTTCTAAAAATTCCATTTTTACCCCCG
1 AACTTCCAAAAATCCCATTTTT-ACCTCGAAACTTCCAAAAATTCCATTTTTACCCTCG
** * *
702 AACTT-CTGAAATCCCAATTTTAACC-CTGAAACTTCAAAAAATTCCATTTTTATCCCT-G
1 AACTTCCAAAAATCCC-ATTTTTACCTC-GAAACTTCCAAAAATTCCATTTTTA-CCCTCG
* * *
760 AACATCCAAAAA-CACCATTTTTTATCC-CAAAATTTCCAAAAATTCCATTTTTACCC
1 AACTTCCAAAAATC-CCA-TTTTTA-CCTCGAAACTTCCAAAAATTCCATTTTTACCC
816 CCCGAATGTT
Statistics
Matches: 341, Mismatches: 47, Indels: 41
0.79 0.11 0.10
Matches are distributed among these distances:
57 21 0.06
58 89 0.26
59 202 0.59
60 29 0.09
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.33
Consensus pattern (58 bp):
AACTTCCAAAAATCCCATTTTTACCTCGAAACTTCCAAAAATTCCATTTTTACCCTCG
Done.