Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006682.1 Kokia drynarioides strain JFW-HI SEQ_121276, 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: 2809
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Found at i:298 original size:29 final size:28
Alignment explanation
Indices: 266--328 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
256 AAAATGAGAC
266 TTTTCGGATACTCGGGGGTAAAATGGTAA
1 TTTT-GGATACTCGGGGGTAAAATGGTAA
* * *
295 TTTTGGATTCTTGGGGGTGAAATGGTAA
1 TTTTGGATACTCGGGGGTAAAATGGTAA
323 TTTTGG
1 TTTTGG
329 GAAAATTCGG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
28 27 0.87
29 4 0.13
ACGTcount: A:0.22, C:0.06, G:0.33, T:0.38
Consensus pattern (28 bp):
TTTTGGATACTCGGGGGTAAAATGGTAA
Found at i:466 original size:30 final size:28
Alignment explanation
Indices: 430--748 Score: 284
Period size: 30 Copynumber: 10.8 Consensus size: 28
420 ATTCAAGGGC
430 AAAATGGTAATTTTTGGAAGTTTAGGGTCA
1 AAAATGG-AATTTTTGGAAGTTTAGGGT-A
* * *
460 AAAATGGAGTTTTTAGAAGTTCAGGGGTA
1 AAAATGGAATTTTTGGAAGTTTA-GGGTA
* * *
489 AAATTAGAATTTTTTGAAGTTTTAGGGGTA
1 AAAATGGAATTTTTGGAAG-TTTA-GGGTA
* *
519 AAAATGAAATTTTT-GAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTT-TAGGGTA
*
547 AAAATGGAATTTTTGGAAGTTTTGAGGTCA
1 AAAATGGAATTTTTGGAAGTTTAG-GGT-A
* *
577 AAAATGGGATTTTTAGAAGTTTTAGGGTCA
1 AAAATGGAATTTTTGGAAG-TTTAGGGT-A
*
607 AAAATGGAATTTTTGGAAGTTTTGGGGTTA
1 AAAATGGAATTTTTGGAAG-TTTAGGG-TA
* *
637 AAAATGGGATTTTTGGAAGTTCAGAGGGTA
1 AAAATGGAATTTTTGGAAGTT--TAGGGTA
*
667 AAAATGGAATTTTTGGAAG-TTCGAGGTCA
1 AAAATGGAATTTTTGGAAGTTTAG-GGT-A
* *
696 AAAATGGAATTTTTAGAAGTTTCGAGGTAAA
1 AAAATGGAATTTTTGGAAGTTTAG-GGT--A
727 AAAATGTG-ATTTTTGGAAGTTT
1 AAAATG-GAATTTTTGGAAGTTT
749 CGGGACCTCT
Statistics
Matches: 244, Mismatches: 30, Indels: 29
0.81 0.10 0.10
Matches are distributed among these distances:
27 1 0.00
28 24 0.10
29 65 0.27
30 125 0.51
31 28 0.11
32 1 0.00
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.36
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAAGTTTAGGGTA
Found at i:492 original size:58 final size:57
Alignment explanation
Indices: 308--752 Score: 304
Period size: 58 Copynumber: 7.5 Consensus size: 57
298 TGGATTCTTG
* * ** * * *
308 GGGGTGAAATGGTAATTTTGGGAAAATTCGGAGTTAAAAAAGGAATTTTTAGACA-TTC-
1 GGGGTAAAATGG-AATTTTTGGAAGTTTCGG-GTCAAAAATGGAGTTTTTAGA-AGTTCA
* ** * *
366 GGAGGTAAAAGGGTAATTTTAAG-AGTTTCGAGGTCGAAAATGGAGTTTTTGGACA-TTCA
1 GG-GGTAAAATGG-AATTTTTGGAAGTTTCG-GGTCAAAAATGGAGTTTTTAGA-AGTTCA
* * *
425 AGGGCAAAATGGTAATTTTTGGAAGTTTAGGGTCAAAAATGGAGTTTTTAGAAGTTCA
1 GGGGTAAAATGG-AATTTTTGGAAGTTTCGGGTCAAAAATGGAGTTTTTAGAAGTTCA
* * * * *
483 GGGGTAAAATTAGAATTTTTTGAAGTTTTAGGGGT-AAAAATGAAATTTTT-GAAGTTC-
1 GGGGTAAAA-TGGAATTTTTGGAAG-TTT-CGGGTCAAAAATGGAGTTTTTAGAAGTTCA
* *
540 GAGGGTAAAAATGGAATTTTTGGAAGTTTTGAGGTCAAAAATGG-GATTTTTAGAAGTTTTA
1 G-GGGT-AAAATGGAATTTTTGGAAGTTTCG-GGTCAAAAATGGAG-TTTTTAGAAG-TTCA
* * *
601 -GGGTCAAAAATGGAATTTTTGGAAGTTTTGGGGTTAAAAATGG-GATTTTTGGAAGTTCA
1 GGGGT--AAAATGGAATTTTTGGAAG-TTTCGGGTCAAAAATGGAG-TTTTTAGAAGTTCA
*
660 GAGGGTAAAAATGGAATTTTTGGAAG-TTCGAGGTCAAAAATGGAATTTTTAGAAGTTTC-
1 G-GGGT-AAAATGGAATTTTTGGAAGTTTCG-GGTCAAAAATGGAGTTTTTAGAAG-TTCA
*
719 GAGGTAAAAAAATGTG-ATTTTTGGAAGTTTCGGG
1 GGGGT---AAAATG-GAATTTTTGGAAGTTTCGGG
753 ACCTCTTAGA
Statistics
Matches: 319, Mismatches: 41, Indels: 52
0.77 0.10 0.13
Matches are distributed among these distances:
56 1 0.00
57 8 0.03
58 128 0.40
59 78 0.24
60 91 0.29
61 13 0.04
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (57 bp):
GGGGTAAAATGGAATTTTTGGAAGTTTCGGGTCAAAAATGGAGTTTTTAGAAGTTCA
Found at i:626 original size:60 final size:59
Alignment explanation
Indices: 430--748 Score: 348
Period size: 60 Copynumber: 5.4 Consensus size: 59
420 ATTCAAGGGC
* *
430 AAAATGGTAATTTTTGGAAGTTTAG-GGTCAAAAAT-GGAGTTTTTAGAAG-TTCAGGGGTA
1 AAAATGG-AATTTTTGGAAGTTTTGAGGTCAAAAATGGGA-TTTTTAGAAGTTTGA-GGGTA
* * * * ** *
489 AAATTAGAATTTTTTGAAGTTTTAGGGGT-AAAAATGAAATTTTT-GAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTT-GAGGTCAAAAATGGGATTTTTAGAAGTTTGAGGGTA
*
547 AAAATGGAATTTTTGGAAGTTTTGAGGTCAAAAATGGGATTTTTAGAAGTTTTAGGGTCA
1 AAAATGGAATTTTTGGAAGTTTTGAGGTCAAAAATGGGATTTTTAGAAGTTTGAGGGT-A
* * * *
607 AAAATGGAATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCAGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTTGAGGTCAAAAATGGGATTTTTAGAAGTT-TGAGGGTA
* *
667 AAAATGGAATTTTTGGAAG-TTCGAGGTCAAAAATGGAATTTTTAGAAGTTTCGA-GGTAAA
1 AAAATGGAATTTTTGGAAGTTTTGAGGTCAAAAATGGGATTTTTAGAAGTTT-GAGGGT--A
727 AAAATGTG-ATTTTTGGAAGTTT
1 AAAATG-GAATTTTTGGAAGTTT
749 CGGGACCTCT
Statistics
Matches: 220, Mismatches: 27, Indels: 24
0.81 0.10 0.09
Matches are distributed among these distances:
57 4 0.02
58 59 0.27
59 58 0.26
60 91 0.41
61 8 0.04
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.36
Consensus pattern (59 bp):
AAAATGGAATTTTTGGAAGTTTTGAGGTCAAAAATGGGATTTTTAGAAGTTTGAGGGTA
Found at i:2630 original size:23 final size:22
Alignment explanation
Indices: 2600--2645 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
2590 ATGGGACATT
*
2600 ATTTAAATAAATTTAAATTTAA
1 ATTTAAATAAACTTAAATTTAA
*
2622 ATTTCAAATAAACTTAATTTTAA
1 ATTT-AAATAAACTTAAATTTAA
2645 A
1 A
2646 ATAAATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTTAAATAAACTTAAATTTAA
Found at i:2638 original size:17 final size:17
Alignment explanation
Indices: 2613--2659 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
2603 TAAATAAATT
*
2613 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTAAAA
* *
2630 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
2647 TAAATTTAAATTT
1 TAAATTTAAATTT
2660 TGTTGGGCCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Done.