Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007540.1 Kokia drynarioides strain JFW-HI SEQ_122166, 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, 774
Length: 1290
ACGTcount: A:0.38, C:0.09, G:0.24, T:0.30
Found at i:359 original size:30 final size:29
Alignment explanation
Indices: 324--810 Score: 348
Period size: 30 Copynumber: 16.9 Consensus size: 29
314 ATTTTAGGAT
*
324 TTAAAAATGGAATTTTTAGAAGTTTCGGG
1 TTAAAAATGGAATTTTTGGAAGTTTCGGG
* *
353 CTT-AAAATGGGATTTTTTAGAAGTTT-GGG
1 -TTAAAAAT-GGAATTTTTGGAAGTTTCGGG
*** *
382 GGCAAAATGGAATTTTTGGAAGTTTTGAGG
1 TTAAAAATGGAATTTTTGGAAGTTTCG-GG
* *
412 TTAAAAATGGGATTTTTGGAA-ATTCGAGGG
1 TTAAAAATGGAATTTTTGGAAGTTTC--GGG
* * *
442 TT-AAATTGGAATTTTTAGAAGTTTCGAGA
1 TTAAAAATGGAATTTTTGGAAGTTTCG-GG
*
471 TTAAAAATGGGATTTTTGGAAG-TTCAGAGG
1 TTAAAAATGGAATTTTTGGAAGTTTC-G-GG
* * *
501 TTAAAAATGGGATTTTTGAAAGTTTAGGG
1 TTAAAAATGGAATTTTTGGAAGTTTCGGG
* *
530 -TAAAAATAGAATTTTTGGAAGCTTCGGGG
1 TTAAAAATGGAATTTTTGGAAGTTTC-GGG
* *
559 TT-AAATTGGGATTTTTGGAAG-TTCGGGG
1 TTAAAAATGGAATTTTTGGAAGTTTC-GGG
* * *
587 GTAAAATTGGAATTTTTGGAAGTTTTGGGG
1 TTAAAAATGGAATTTTTGGAAG-TTTCGGG
617 TTAAAAATAGG-ATTTTTGGAAGTTT-GAGG
1 TTAAAAAT-GGAATTTTTGGAAGTTTCG-GG
* * *
646 GTAAAAATGGAGTTTTTGGAAGTTTTGAGG
1 TTAAAAATGGAATTTTTGGAAGTTTCG-GG
*
676 TTAAAAAT-GAGATTTTTAGAAG-TTCGGGG
1 TTAAAAATGGA-ATTTTTGGAAGTTTC-GGG
*
705 GTAAAAATGGAATTTTT-G-A------GG
1 TTAAAAATGGAATTTTTGGAAGTTTCGGG
* *
726 TTAAAAATGGGATTTTTGGAAGTTTAGGG
1 TTAAAAATGGAATTTTTGGAAGTTTCGGG
* *** *
755 GTAAAAACAAAATTTTTAGAAGTTTCGGGG
1 TTAAAAATGGAATTTTTGGAAGTTTC-GGG
*
785 GTAAAAATGGAATTTTTGGAAAGTTT
1 TTAAAAATGGAATTTTTGG-AAGTTT
811 AGGGACCTTC
Statistics
Matches: 369, Mismatches: 55, Indels: 65
0.75 0.11 0.13
Matches are distributed among these distances:
21 17 0.05
22 1 0.00
23 1 0.00
27 1 0.00
28 48 0.13
29 141 0.38
30 147 0.40
31 13 0.04
ACGTcount: A:0.33, C:0.02, G:0.29, T:0.36
Consensus pattern (29 bp):
TTAAAAATGGAATTTTTGGAAGTTTCGGG
Found at i:452 original size:59 final size:57
Alignment explanation
Indices: 331--722 Score: 308
Period size: 59 Copynumber: 6.7 Consensus size: 57
321 GATTTAAAAA
* * * * * ** *
331 TGGAATTTTTAGAAGTTTCG-GGCTTAAAATGGGATTTTTTAGAAGTTTGGGGGCAAAA
1 TGGAATTTTTGGAAG-TTCGAGGGTAAAAATGGGA-TTTTTGGAAGTTCGGGGTTAAAT
* * *
389 TGGAATTTTTGGAAGTTTTGAGGTTAAAAATGGGATTTTTGGAAATTCGAGGGTTAAAT
1 TGGAATTTTTGGAAG-TTCGAGGGTAAAAATGGGATTTTTGGAAGTTCG-GGGTTAAAT
* ** * *
448 TGGAATTTTTAGAAGTTTCGAGATTAAAAATGGGATTTTTGGAAGTTCAGAGGTTAAAAA
1 TGGAATTTTTGGAAG-TTCGAGGGTAAAAATGGGATTTTTGGAAGTTC-GGGGTT-AAAT
* * * * *
508 TGGGATTTTTGAAAGTT-TAGGGTAAAAATAGAATTTTTGGAAGCTTCGGGGTTAAAT
1 TGGAATTTTTGGAAGTTCGAGGGTAAAAATGGGATTTTTGGAAG-TTCGGGGTTAAAT
* * * * *
565 TGGGATTTTTGGAAGTTCGGGGGTAAAATTGGAATTTTTGGAAGTTTTGGGGTTAAAAAT
1 TGGAATTTTTGGAAGTTCGAGGGTAAAAATGGGATTTTTGGAAG-TTCGGGGTT--AAAT
* * * * *
625 AGG-ATTTTTGGAAGTTTGAGGGTAAAAAT-GGAGTTTTTGGAAGTTTTGAGGTTAAAAA
1 TGGAATTTTTGGAAGTTCGAGGGTAAAAATGGGA-TTTTTGGAAG-TTCGGGGTT-AAAT
* * *
683 T-GAGATTTTTAGAAGTTCGGGGGTAAAAATGGAATTTTTG
1 TGGA-ATTTTTGGAAGTTCGAGGGTAAAAATGGGATTTTTG
723 AGGTTAAAAA
Statistics
Matches: 277, Mismatches: 45, Indels: 23
0.80 0.13 0.07
Matches are distributed among these distances:
57 20 0.07
58 91 0.33
59 142 0.51
60 24 0.09
ACGTcount: A:0.31, C:0.03, G:0.29, T:0.37
Consensus pattern (57 bp):
TGGAATTTTTGGAAGTTCGAGGGTAAAAATGGGATTTTTGGAAGTTCGGGGTTAAAT
Found at i:740 original size:50 final size:50
Alignment explanation
Indices: 662--761 Score: 155
Period size: 50 Copynumber: 2.0 Consensus size: 50
652 ATGGAGTTTT
*
662 TGGAAGTTTTGAGGTTAAAAATGAGATTTTTAGAAGTTCGGGGGTAAAAA
1 TGGAAGTTTTGAGGTTAAAAATGAGATTTTTAGAAGTTCAGGGGTAAAAA
* * * *
712 TGGAATTTTTGAGGTTAAAAATGGGATTTTTGGAAGTTTAGGGGTAAAAA
1 TGGAAGTTTTGAGGTTAAAAATGAGATTTTTAGAAGTTCAGGGGTAAAAA
762 CAAAATTTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.35, C:0.01, G:0.30, T:0.34
Consensus pattern (50 bp):
TGGAAGTTTTGAGGTTAAAAATGAGATTTTTAGAAGTTCAGGGGTAAAAA
Found at i:782 original size:80 final size:80
Alignment explanation
Indices: 639--802 Score: 242
Period size: 80 Copynumber: 2.0 Consensus size: 80
629 TTTTTGGAAG
* * ** *
639 TTTGAGGGTAAAAATGGAGTTTTTGGAAGTTTTGAGGTTAAAAATGAGATTTTTAGAAGTTCGGG
1 TTTGAGGGTAAAAATGGAGTTTTTGGAAGTTTAGAGGGTAAAAACAAAATTTTTAGAAGTTCGGG
704 GGTAAAAATGGAATT
66 GGTAAAAATGGAATT
*
719 TTTGAGGTTAAAAATGG-GATTTTTGGAAGTTTAG-GGGTAAAAACAAAATTTTTAGAAGTTTCG
1 TTTGAGGGTAAAAATGGAG-TTTTTGGAAGTTTAGAGGGTAAAAACAAAATTTTTAGAAG-TTCG
782 GGGGTAAAAATGGAATT
64 GGGGTAAAAATGGAATT
799 TTTG
1 TTTG
803 GAAAGTTTAG
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
79 21 0.28
80 55 0.72
ACGTcount: A:0.34, C:0.02, G:0.29, T:0.35
Consensus pattern (80 bp):
TTTGAGGGTAAAAATGGAGTTTTTGGAAGTTTAGAGGGTAAAAACAAAATTTTTAGAAGTTCGGG
GGTAAAAATGGAATT
Found at i:800 original size:109 final size:109
Alignment explanation
Indices: 603--801 Score: 267
Period size: 109 Copynumber: 1.8 Consensus size: 109
593 TTGGAATTTT
* *** * *
603 TGGAAGTTTTGGGGTTAAAAATAGGATTTTTGGAAGTTTGAGGGTAAAAATGGAGTTTTTGGAAG
1 TGGAAGTTTTGAGGTTAAAAATAGGATTTTTGGAAGTTTGAGGGTAAAAACAAAATTTTTAGAAG
* *
668 TTTTGAGGTTAAAAATGAGATTTTTAGAAGTTCGGGGGTAAAAA
66 TTTCGAGGGTAAAAATGAGATTTTTAGAAGTTCGGGGGTAAAAA
* *
712 TGGAATTTTTGAGGTTAAAAATGGGATTTTTGGAAGTTT-AGGGGTAAAAACAAAATTTTTAGAA
1 TGGAAGTTTTGAGGTTAAAAATAGGATTTTTGGAAGTTTGA-GGGTAAAAACAAAATTTTTAGAA
*
776 GTTTCGGGGGTAAAAATG-GAATTTTT
65 GTTTCGAGGGTAAAAATGAG-ATTTTT
802 GGAAAGTTTA
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
108 2 0.03
109 75 0.97
ACGTcount: A:0.34, C:0.02, G:0.29, T:0.36
Consensus pattern (109 bp):
TGGAAGTTTTGAGGTTAAAAATAGGATTTTTGGAAGTTTGAGGGTAAAAACAAAATTTTTAGAAG
TTTCGAGGGTAAAAATGAGATTTTTAGAAGTTCGGGGGTAAAAA
Done.