Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001525.1 Kokia drynarioides strain JFW-HI SEQ_113089, 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: 1919
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Found at i:513 original size:57 final size:56
Alignment explanation
Indices: 435--743 Score: 240
Period size: 57 Copynumber: 5.4 Consensus size: 56
425 AAAATTAGGA
* *
435 TAAAAGTGAAATTTTTGGATATTCGGGAGT-AATGGTAATTTTTGAGAGTTTTGAGG
1 TAAAAATGGAATTTTTGGATATTCGGG-GTAAATGGTAATTTTTGAGAGTTTTGAGG
* * * * *
491 TCAAAAATGGAGTTTTTAGATATTCGAGGGTAAAATGGTAATTTTTGAAAGTGTTGGGG
1 T-AAAAATGGAATTTTTGGATATTCG-GGGT-AAATGGTAATTTTTGAGAGTTTTGAGG
** * *
550 TTAAAAATGGAATTTTTGGAGGTTCGGGGTAAATATGTAATTTTT-AGAAGTTTCGAGG
1 -TAAAAATGGAATTTTTGGATATTCGGGGTAAAT-GGTAATTTTTGAG-AGTTTTGAGG
** *
608 TAAAAATGGAATTTTTGGA-AGTTCGAGGGTAAAAAT-GTAATTTTCAAAAGTTTTCG-GG
1 TAAAAATGGAATTTTTGGATA-TTCG-GGGT--AAATGGTAATTTTTGAGAGTTTT-GAGG
* * *
666 TCAAAAATGGAA-TTTTGGA-AGTTCGAGGGAAAAAT-ATAATTTTTG-GAAGTTTTGGGG
1 T-AAAAATGGAATTTTTGGATA-TTCG-GGG-TAAATGGTAATTTTTGAG-AGTTTTGAGG
*
723 TCAAAATGGAATTTTTGGATA
1 TAAAAATGGAATTTTTGGATA
744 GTTTAGGGAC
Statistics
Matches: 208, Mismatches: 26, Indels: 36
0.77 0.10 0.13
Matches are distributed among these distances:
56 11 0.05
57 77 0.37
58 60 0.29
59 55 0.26
60 5 0.02
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.36
Consensus pattern (56 bp):
TAAAAATGGAATTTTTGGATATTCGGGGTAAATGGTAATTTTTGAGAGTTTTGAGG
Found at i:613 original size:116 final size:115
Alignment explanation
Indices: 401--746 Score: 350
Period size: 116 Copynumber: 3.0 Consensus size: 115
391 TTAAACATTT
* * * * * *
401 GAGGGTAAAACGGTAATTTTTAGAAA-AATTAGGATAAAAGTGAAATTTTTGGATA-TTCGGGAG
1 GAGGGTAAAATGGTAATTTTT-GAAAGTATTGGGTTAAAAATGGAATTTTTGGA-AGTTCGGG-G
* * *
464 T-AAT-GGTAATTTTTGAGAGTTTTGAGGTCAAAAATGGAGTTTTTAGATA-TTC
63 TAAATATGTAATTTTTGA-AGTTTTGAGGT-AAAAATGGAATTTTTGGATAGTTC
* *
516 GAGGGTAAAATGGTAATTTTTGAAAGTGTTGGGGTTAAAAATGGAATTTTTGGAGGTTCGGGGTA
1 GAGGGTAAAATGGTAATTTTTGAAAGTATT-GGGTTAAAAATGGAATTTTTGGAAGTTCGGGGTA
*
581 AATATGTAATTTTTAGAAGTTTCGAGGTAAAAATGGAATTTTTGGA-AGTTC
65 AATATGTAATTTTT-GAAGTTTTGAGGTAAAAATGGAATTTTTGGATAGTTC
** * *
632 GAGGGTAAAAAT-GTAATTTTCAAAAGTTTTCGGGTCAAAAATGGAA-TTTTGGAAGTTCGAGGG
1 GAGGGT-AAAATGGTAATTTTTGAAAGTATT-GGGTTAAAAATGGAATTTTTGGAAGTTCG-GGG
* * * *
695 -AAAAATATAATTTTTGGAAGTTTTGGGGTCAAAATGGAATTTTTGGATAGTT
63 TAAATATGTAATTTTT-GAAGTTTTGAGGTAAAAATGGAATTTTTGGATAGTT
747 TAGGGACCTC
Statistics
Matches: 197, Mismatches: 24, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
114 4 0.02
115 78 0.40
116 89 0.45
117 24 0.12
118 2 0.01
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.36
Consensus pattern (115 bp):
GAGGGTAAAATGGTAATTTTTGAAAGTATTGGGTTAAAAATGGAATTTTTGGAAGTTCGGGGTAA
ATATGTAATTTTTGAAGTTTTGAGGTAAAAATGGAATTTTTGGATAGTTC
Found at i:739 original size:29 final size:29
Alignment explanation
Indices: 465--747 Score: 210
Period size: 29 Copynumber: 9.7 Consensus size: 29
455 ATTCGGGAGT
* *
465 AATGGTAATTTTT-GAGAGTTTTGAGGTCAAA
1 AATGG-AATTTTTGGA-AGTTTCGGGGT-AAA
* *
496 AATGGAGTTTTTAG-A-TATTCGAGGGT-AA
1 AATGGAATTTTTGGAAGT-TTCG-GGGTAAA
*
524 AATGGTAATTTTTGAAAGTGTT-GGGGTTAAA
1 AATGG-AATTTTTGGAAGT-TTCGGGG-TAAA
*
555 AATGGAATTTTTGG-AGGTTCGGGGTAAA
1 AATGGAATTTTTGGAAGTTTCGGGGTAAA
* * * *
583 TATGTAATTTTTAGAAGTTTCGAGGTAAA
1 AATGGAATTTTTGGAAGTTTCGGGGTAAA
612 AATGGAATTTTTGGAAG-TTCGAGGGTAAA
1 AATGGAATTTTTGGAAGTTTCG-GGGTAAA
* ***
641 AATGTAATTTTCAAAAGTTTTC-GGGTCAAA
1 AATGGAATTTTTGGAAG-TTTCGGGGT-AAA
671 AATGGAA-TTTTGGAAG-TTCGAGGG-AAA
1 AATGGAATTTTTGGAAGTTTCG-GGGTAAA
** * *
698 AATATAATTTTTGGAAGTTTTGGGGTCAA
1 AATGGAATTTTTGGAAGTTTCGGGGTAAA
727 AATGGAATTTTTGGATAGTTT
1 AATGGAATTTTTGGA-AGTTT
748 AGGGACCTCC
Statistics
Matches: 200, Mismatches: 32, Indels: 41
0.73 0.12 0.15
Matches are distributed among these distances:
27 11 0.05
28 41 0.20
29 95 0.47
30 34 0.17
31 19 0.09
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.37
Consensus pattern (29 bp):
AATGGAATTTTTGGAAGTTTCGGGGTAAA
Found at i:752 original size:57 final size:57
Alignment explanation
Indices: 469--746 Score: 287
Period size: 58 Copynumber: 4.8 Consensus size: 57
459 GGGAGTAATG
* * * *
469 GTAATTTTT-GAGAGTTTTGAGGTCAAAAATGGAGTTTTTAGATA-TTCGAGGGTAAAAT
1 GTAATTTTTAGA-AGTTTTGGGGTC-AAAATGGAATTTTTGGA-AGTTCGAGGGAAAAAT
* * * *
527 GGTAATTTTT-GAAAGTGTTGGGGTTAAAAATGGAATTTTTGGAGGTTCG-GGGTAAATAT
1 -GTAATTTTTAG-AAGTTTTGGGG-TCAAAATGGAATTTTTGGAAGTTCGAGGG-AAAAAT
* * *
586 GTAATTTTTAGAAGTTTCGAGGTAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAAT
1 GTAATTTTTAGAAGTTTTGGGGTCAAAATGGAATTTTTGGAAGTTCGAGGG-AAAAAT
* * *
644 GTAATTTTCAAAAGTTTTCGGGTCAAAAATGGAA-TTTTGGAAGTTCGAGGGAAAAAT
1 GTAATTTTTAGAAGTTTTGGGGTC-AAAATGGAATTTTTGGAAGTTCGAGGGAAAAAT
* *
701 ATAATTTTTGGAAGTTTTGGGGTCAAAATGGAATTTTTGGATAGTT
1 GTAATTTTTAGAAGTTTTGGGGTCAAAATGGAATTTTTGGA-AGTT
747 TAGGGACCTC
Statistics
Matches: 186, Mismatches: 24, Indels: 19
0.81 0.10 0.08
Matches are distributed among these distances:
56 9 0.05
57 56 0.30
58 68 0.37
59 51 0.27
60 2 0.01
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.37
Consensus pattern (57 bp):
GTAATTTTTAGAAGTTTTGGGGTCAAAATGGAATTTTTGGAAGTTCGAGGGAAAAAT
Found at i:1776 original size:3 final size:3
Alignment explanation
Indices: 1763--1846 Score: 53
Period size: 3 Copynumber: 28.0 Consensus size: 3
1753 TTTTTTATAT
* * * * *
1763 TTA TTA ATA TTA TTA TAA TTA TTA ATA -TA TTA TTA TTTA ATG TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
* * * ** *
1808 TTA GTA TTA TTA TTA ATG TTA TTA TGG CTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1847 CTAATGATAT
Statistics
Matches: 58, Mismatches: 21, Indels: 4
0.70 0.25 0.05
Matches are distributed among these distances:
2 2 0.03
3 53 0.91
4 3 0.05
ACGTcount: A:0.36, C:0.01, G:0.06, T:0.57
Consensus pattern (3 bp):
TTA
Done.