Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004021.1 Kokia drynarioides strain JFW-HI SEQ_117143, 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, 911
Length: 1519
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.27
Found at i:287 original size:30 final size:29
Alignment explanation
Indices: 244--710 Score: 331
Period size: 30 Copynumber: 15.9 Consensus size: 29
234 TTCGGATGCA
* *
244 CGGGGGCAAAATGGTAGTTTTGGAAGGTT
1 CGGGGTCAAAATGGTATTTTTGGAAGGTT
* *
273 CGGAGTCAAAAATGGGATTTTTGGAA-GTT
1 CGGGGTC-AAAATGGTATTTTTGGAAGGTT
* *
302 CGAGGGT-AAAATGGCAATTTTTGAAAGGTT
1 CG-GGGTCAAAATGG-TATTTTTGGAAGGTT
* *
332 CGGGGTCAAAAATGGAACTTTTGGAA-GTT
1 CGGGGTC-AAAATGGTATTTTTGGAAGGTT
* *
361 CGGGGGT-AAAATGGTAATTTTTGAAAAGTT
1 C-GGGGTCAAAATGGT-ATTTTTGGAAGGTT
*
391 CGGGGTCAAAAATGGGATTTTTGGAA-GTT
1 CGGGGTC-AAAATGGTATTTTTGGAAGGTT
***
420 CGGGGGT-AAAATGGTAATTTTAAAAAGGTT
1 C-GGGGTCAAAATGGT-ATTTTTGGAAGGTT
*
450 CGAGGTCAAAAATGAG-ATTTTTGGAA-GTT
1 CGGGGTC-AAAATG-GTATTTTTGGAAGGTT
* *
479 CGGGGGT-AAAATGGTAATTTTTAGACGGTT
1 C-GGGGTCAAAATGGT-ATTTTTGGAAGGTT
* *
509 CGAGGTCGAAAATAGG-ATTTTTGGGA-GTT
1 CGGGGTC-AAAAT-GGTATTTTTGGAAGGTT
*
538 CGGGGGT-AAAATGGTAATTTTTAGAAGGTT
1 C-GGGGTCAAAATGGT-ATTTTTGGAAGGTT
* *
568 CAGGGTCAAAAATGGTATTTTTTAGAAGGTT
1 CGGGGTC-AAAATGGTA-TTTTTGGAAGGTT
** *
599 CGGCATCAAAATGGTATTTTTGGGA-GTT
1 CGGGGTCAAAATGGTATTTTTGGAAGGTT
*
627 CGAGGGT-AAAATGGTAATTTTT-AAATGGTT
1 CG-GGGTCAAAATGGT-ATTTTTGGAA-GGTT
*
657 TGGGGTCAAAAGTGAG-ATTTTTGGAA-GTT
1 CGGGGTCAAAA-TG-GTATTTTTGGAAGGTT
*
686 CGGGGGT-AAAATGGTAATTTTGGAA
1 C-GGGGTCAAAATGGTATTTTTGGAA
711 AGTTTAAGGA
Statistics
Matches: 351, Mismatches: 46, Indels: 83
0.73 0.10 0.17
Matches are distributed among these distances:
27 4 0.01
28 57 0.16
29 113 0.32
30 119 0.34
31 54 0.15
32 4 0.01
ACGTcount: A:0.30, C:0.06, G:0.32, T:0.32
Consensus pattern (29 bp):
CGGGGTCAAAATGGTATTTTTGGAAGGTT
Found at i:333 original size:59 final size:59
Alignment explanation
Indices: 244--589 Score: 443
Period size: 59 Copynumber: 5.9 Consensus size: 59
234 TTCGGATGCA
* * *
244 CGGGGGCAAAATGGT-AGTTTTGGAAGGTTCGGAGTCAAAAATGGGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTGAAAGGTTCGGAGTCAAAAATGGGATTTTTGGAAGTT
* * * * *
302 CGAGGGTAAAATGGCAATTTTTGAAAGGTTCGGGGTCAAAAATGGAACTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTGAAAGGTTCGGAGTCAAAAATGGGATTTTTGGAAGTT
* *
361 CGGGGGTAAAATGGTAATTTTTGAAAAGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTGAAAGGTTCGGAGTCAAAAATGGGATTTTTGGAAGTT
** *
420 CGGGGGTAAAATGGTAATTTTAAAAAGGTTC-GAGGTCAAAAATGAGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTGAAAGGTTCGGA-GTCAAAAATGGGATTTTTGGAAGTT
* * * *
479 CGGGGGTAAAATGGTAATTTTT-AGACGGTTC-GAGGTCGAAAATAGGATTTTTGGGAGTT
1 CGGGGGTAAAATGGTAATTTTTGA-AAGGTTCGGA-GTCAAAAATGGGATTTTTGGAAGTT
*
538 CGGGGGTAAAATGGTAATTTTT-AGAAGGTTCAGG-GTCAAAAATGGTATTTTT
1 CGGGGGTAAAATGGTAATTTTTGA-AAGGTTC-GGAGTCAAAAATGGGATTTTT
590 TAGAAGGTTC
Statistics
Matches: 255, Mismatches: 28, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
58 14 0.05
59 240 0.94
61 1 0.00
ACGTcount: A:0.31, C:0.06, G:0.32, T:0.31
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTTGAAAGGTTCGGAGTCAAAAATGGGATTTTTGGAAGTT
Found at i:630 original size:177 final size:177
Alignment explanation
Indices: 250--631 Score: 481
Period size: 177 Copynumber: 2.2 Consensus size: 177
240 TGCACGGGGG
* *
250 CAAAATGGTAGTTTTGGAAGGTTCG-GAGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAT
1 CAAAATGGTATTTTTGGAAGGTTCGAG-GTCAAAAATGAGATTTTTGGAAGTTCGAGGGTAAAAT
*
314 GGCAATTTTTGAAAGGTTCGGGGTCAAAAATGGAACTTTTGGAAGTTCGGGGGTAAAATGGTAAT
65 GGCAATTTTTGAAAGGTTCGAGGTCAAAAATGGAACTTTTGGAAGTTCGGGGGTAAAATGGTAAT
* * **
379 TTTTGAAAAGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
130 TTTTGAAAAGTTCAGGGTCAAAAATGGGATTTTTAGAAGTTCGGGCAT
*** *
427 -AAAATGGTAATTTTAAAAAGGTTCGAGGTCAAAAATGAGATTTTTGGAAGTTCGGGGGTAAAAT
1 CAAAATGGT-ATTTTTGGAAGGTTCGAGGTCAAAAATGAGATTTTTGGAAGTTCGAGGGTAAAAT
* * * * *
491 GGTAATTTTT-AGACGGTTCGAGGTCGAAAATAGG-ATTTTTGGGAGTTCGGGGGTAAAATGGTA
65 GGCAATTTTTGA-AAGGTTCGAGGTCAAAAAT-GGAACTTTTGGAAGTTCGGGGGTAAAATGGTA
* *
554 ATTTTT-AGAAGGTTCAGGGTCAAAAATGGTATTTTTTAGAAGGTTC-GGCAT
128 ATTTTTGA-AAAGTTCAGGGTCAAAAATGGGA-TTTTTAGAA-GTTCGGGCAT
*
605 CAAAATGGTATTTTTGGGA-GTTCGAGG
1 CAAAATGGTATTTTTGGAAGGTTCGAGG
632 GTAAAATGGT
Statistics
Matches: 175, Mismatches: 22, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
176 10 0.06
177 133 0.76
178 20 0.11
179 12 0.07
ACGTcount: A:0.31, C:0.07, G:0.31, T:0.32
Consensus pattern (177 bp):
CAAAATGGTATTTTTGGAAGGTTCGAGGTCAAAAATGAGATTTTTGGAAGTTCGAGGGTAAAATG
GCAATTTTTGAAAGGTTCGAGGTCAAAAATGGAACTTTTGGAAGTTCGGGGGTAAAATGGTAATT
TTTGAAAAGTTCAGGGTCAAAAATGGGATTTTTAGAAGTTCGGGCAT
Found at i:676 original size:148 final size:149
Alignment explanation
Indices: 427--706 Score: 390
Period size: 148 Copynumber: 1.9 Consensus size: 149
417 GTTCGGGGGT
* *
427 AAAATGGTAATTTTAAAAAGGTTCGAGGTCAAAAATGAGATTTTTGGAAGTTCGGGGGTAAAATG
1 AAAATGGTAATTTTAAAAAGGTTCGAGATCAAAAATGAGATTTTTGGAAGTTCGAGGGTAAAATG
* *
492 GTAATTTTTAGACGGTTCGAGGTCGAAAATAGGATTTTTGGGAGTTCGGGGGTAAAATGGTAATT
66 GTAATTTTTAAACGGTTCGAGGTCGAAAATAGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATT
557 TTTAGAAGGTTCAGGGTCA
131 TTTAGAAGGTTCAGGGTCA
* * * *
576 AAAATGGTATTTTTTAGAAGGTTCG-GCATC-AAAATG-GTATTTTTGGGAGTTCGAGGGTAAAA
1 AAAATGGTAATTTTAAAAAGGTTCGAG-ATCAAAAATGAG-ATTTTTGGAAGTTCGAGGGTAAAA
* * *
638 TGGTAATTTTTAAATGGTTTGGGGTC-AAAAGT-GAGATTTTTGGAAGTTCGGGGGTAAAATGGT
64 TGGTAATTTTTAAACGGTTCGAGGTCGAAAA-TAG-GATTTTTGGAAGTTCGGGGGTAAAATGGT
701 AATTTT
127 AATTTT
707 GGAAAGTTTA
Statistics
Matches: 116, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
147 6 0.05
148 86 0.74
149 24 0.21
ACGTcount: A:0.31, C:0.05, G:0.30, T:0.34
Consensus pattern (149 bp):
AAAATGGTAATTTTAAAAAGGTTCGAGATCAAAAATGAGATTTTTGGAAGTTCGAGGGTAAAATG
GTAATTTTTAAACGGTTCGAGGTCGAAAATAGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATT
TTTAGAAGGTTCAGGGTCA
Found at i:686 original size:59 final size:58
Alignment explanation
Indices: 545--706 Score: 177
Period size: 59 Copynumber: 2.7 Consensus size: 58
535 GTTCGGGGGT
* *
545 AAAATGGTAATTTTTAGAAGGTTC-AGGGTCAAAAATGGTATTTTTTAGAAGGTTCGGCATC
1 AAAATGGT-ATTTTTGGAA-GTTCGAGGGT--AAAATGGTAATTTTTAGAAGGTTCGGCATC
* * **
606 AAAATGGTATTTTTGGGAGTTCGAGGGTAAAATGGTAATTTTTA-AATGGTTTGGGGTC
1 AAAATGGTATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAA-GGTTCGGCATC
*
664 AAAAGTGAG-ATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTT
1 AAAA-TG-GTATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTT
707 GGAAAGTTTA
Statistics
Matches: 89, Mismatches: 8, Indels: 10
0.83 0.07 0.09
Matches are distributed among these distances:
57 2 0.02
58 27 0.30
59 38 0.43
60 14 0.16
61 8 0.09
ACGTcount: A:0.31, C:0.05, G:0.28, T:0.36
Consensus pattern (58 bp):
AAAATGGTATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGGTTCGGCATC
Done.