Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009910.1 Kokia drynarioides strain JFW-HI SEQ_124650, 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: 1957
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:361 original size:9 final size:9
Alignment explanation
Indices: 346--422 Score: 50
Period size: 9 Copynumber: 8.4 Consensus size: 9
336 ATTAATGACA
346 ATAATAATT
1 ATAATAATT
*
355 ATTATAATGTT
1 ATAATAA--TT
* *
366 ATTATTATT
1 ATAATAATT
*
375 A-ATATAATA
1 ATA-ATAATT
*
384 ATAATAATA
1 ATAATAATT
*
393 ATAATAATA
1 ATAATAATT
402 ATAATAATT
1 ATAATAATT
*
411 A-AATAATA
1 ATAATAATT
419 ATAA
1 ATAA
423 GGGAAGACAA
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
8 7 0.12
9 40 0.71
10 1 0.02
11 8 0.14
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (9 bp):
ATAATAATT
Found at i:384 original size:3 final size:3
Alignment explanation
Indices: 374--422 Score: 75
Period size: 3 Copynumber: 17.0 Consensus size: 3
364 TTATTATTAT
*
374 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TTA -AA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
420 TAA
1 TAA
423 GGGAAGACAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 3 0.07
3 39 0.93
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1540 original size:30 final size:30
Alignment explanation
Indices: 1491--1799 Score: 245
Period size: 30 Copynumber: 10.5 Consensus size: 30
1481 TAAACTTTCT
1491 AAAAATTACCA-TTTTACCCTCGAA-CTTCC
1 AAAAA-TACCATTTTTACCCTCGAACCTTCC
* **
1520 AAAAATCCCATTTTTGACCCT-GAACCTTTT
1 AAAAATACCATTTTT-ACCCTCGAACCTTCC
1550 AAAAATTACCA-TTTTACCCTCGAA-CTTCC
1 AAAAA-TACCATTTTTACCCTCGAACCTTCC
*
1579 AAAAAT-CTCATTTTTGACCCT-GAACCTTCT
1 AAAAATAC-CATTTTT-ACCCTCGAACCTTCC
*
1609 AAAAATTACCA-TTTTACCCCCGAA-CTTCC
1 AAAAA-TACCATTTTTACCCTCGAACCTTCC
* * *
1638 AAAAATATCATTTTTGACCC-CAAACCTTCT
1 AAAAATACCATTTTT-ACCCTCGAACCTTCC
* *
1668 AAAAATTACCA-TTTTACCC-CCAAACTTCC
1 AAAAA-TACCATTTTTACCCTCGAACCTTCC
* * *
1697 AAAAATCCCATTTTTGA-CCTCTAACCTTCT
1 AAAAATACCATTTTT-ACCCTCGAACCTTCC
*
1727 AAAAATTACCA-TTTTACCCCCGAA-CTTCC
1 AAAAA-TACCATTTTTACCCTCGAACCTTCC
* * *
1756 AAAAATCCCATTTTTGACTCT-GAACCCTCC
1 AAAAATACCATTTTT-ACCCTCGAACCTTCC
*
1786 AAAACTACCATTTT
1 AAAAATACCATTTT
1800 GCCCCCGTGC
Statistics
Matches: 226, Mismatches: 30, Indels: 47
0.75 0.10 0.16
Matches are distributed among these distances:
27 1 0.00
28 19 0.08
29 91 0.40
30 99 0.44
31 15 0.07
32 1 0.00
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (30 bp):
AAAAATACCATTTTTACCCTCGAACCTTCC
Found at i:1582 original size:59 final size:59
Alignment explanation
Indices: 1487--1806 Score: 491
Period size: 59 Copynumber: 5.4 Consensus size: 59
1477 TCCATAAACT
*
1487 TTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCTGAACC
1 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCTGAACC
* * *
1546 TTTTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCCTGAACC
1 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCTGAACC
** **
1605 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATATCATTTTTGACCCCAAACC
1 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCTGAACC
*
1664 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTCT-AACC
1 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACC-CTGAACC
*
1723 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACTCTGAACC
1 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCTGAACC
* * * *
1782 CTC-CAAAACTACCATTTTGCCCCCG
1 TTCTAAAAATTACCATTTTACCCCCG
1807 TGCATCCTAA
Statistics
Matches: 242, Mismatches: 17, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
58 21 0.09
59 220 0.91
60 1 0.00
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.32
Consensus pattern (59 bp):
TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCTGAACC
Done.