Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012331.1 Kokia drynarioides strain JFW-HI SEQ_127333, 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, 698
Length: 1164
ACGTcount: A:0.36, C:0.11, G:0.26, T:0.27
Found at i:399 original size:30 final size:28
Alignment explanation
Indices: 338--719 Score: 333
Period size: 29 Copynumber: 12.9 Consensus size: 28
328 ACGGAGTGGC
* * **
338 AAAATGGTAGTTTTGGAATGTTCGGAATAA
1 AAAATGGGATTTTTGGAA-GTTCGGGGT-A
* * *
368 AAAATAGGATTCTTGGAAGTTCAAGGGT-
1 AAAATGGGATTTTTGGAAGTTC-GGGGTA
* * **
396 AAAATGGTATTTTTTGGAAAGCTCAAGGTCA
1 AAAATGGGA-TTTTTGG-AAGTTCGGGGT-A
427 AAAATGGGATTTTTGGAAGTTCGAGGGT-
1 AAAATGGGATTTTTGGAAGTTCG-GGGTA
*
455 AAAATGGTGATTTTTGGAAGGTTTGGGGTTA
1 AAAATGG-GATTTTTGGAA-GTTCGGGG-TA
486 AAAATGGGATTTTTGGAAGTTCGGGGGT-
1 AAAATGGGATTTTTGGAAGTTC-GGGGTA
514 AAAATGGTGATTTTTGGAAGGTTCGGGGTCA
1 AAAATGG-GATTTTTGGAA-GTTCGGGGT-A
545 AAAATGGGATTTTTGGAAGTTCGGGGTCA
1 AAAATGGGATTTTTGGAAGTTCGGGGT-A
*
574 AAAATGGTGATTTTTGGAAGGTTTGGGGT-
1 AAAATGG-GATTTTTGGAA-GTTCGGGGTA
* * *
603 AAAATGGTAATTTTTAGAAGGTTCGAGGTAA
1 AAAATGG-GATTTTTGGAA-GTTCGGGGT-A
634 AAAATGGGACTTTTTGGAAGTTCGGGG-A
1 AAAATGGGA-TTTTTGGAAGTTCGGGGTA
* *
662 TAAAATGGTGATTTTAGGATGGTTCGGGGTCA
1 -AAAATGG-GATTTTTGGA-AGTTCGGGGT-A
*
694 AAAATGGGATTTTTGGTAGTTCGGGG
1 AAAATGGGATTTTTGGAAGTTCGGGG
720 ACCTCCGGAG
Statistics
Matches: 296, Mismatches: 31, Indels: 51
0.78 0.08 0.13
Matches are distributed among these distances:
28 22 0.07
29 118 0.40
30 103 0.35
31 52 0.18
32 1 0.00
ACGTcount: A:0.29, C:0.05, G:0.33, T:0.33
Consensus pattern (28 bp):
AAAATGGGATTTTTGGAAGTTCGGGGTA
Found at i:430 original size:59 final size:59
Alignment explanation
Indices: 338--719 Score: 367
Period size: 59 Copynumber: 6.5 Consensus size: 59
328 ACGGAGTGGC
* * ** * * * *
338 AAAATGGT-AGTTTTGGAATGTTCGGAATAAAAAATAGGATTCTTGGAAGTTCAAGGGT
1 AAAATGGTGATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
* * **
396 AAAATGGT-ATTTTTTGGAAAGCTCAAGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
1 AAAATGGTGA-TTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
* * *
455 AAAATGGTGATTTTTGGAAGGTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGT
1 AAAATGGTGATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
514 AAAATGGTGATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCG-GGGT
1 AAAATGGTGATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
* * *
572 CAAAAATGGTGATTTTTGGAAGGTTTGGGGT--AAAATGGTAATTTTTAGAAGGTTCGA-GGT
1 --AAAATGGTGATTTTTGGAAGGTTCGGGGTCAAAAATGG-GATTTTTGGAA-GTTCGAGGGT
* *
632 AAAAAATGG-GACTTTTTGGAA-GTTCGGGG--ATAAAATGGTGATTTTAGGATGGTTCG-GGGT
1 --AAAATGGTGA-TTTTTGGAAGGTTCGGGGTCA-AAAATGG-GATTTTTGGA-AGTTCGAGGGT
*
692 CAAAAATGG-GATTTTTGGTA-GTTCGGGG
1 --AAAATGGTGATTTTTGGAAGGTTCGGGG
720 ACCTCCGGAG
Statistics
Matches: 281, Mismatches: 31, Indels: 23
0.84 0.09 0.07
Matches are distributed among these distances:
58 20 0.07
59 174 0.62
60 87 0.31
ACGTcount: A:0.29, C:0.05, G:0.33, T:0.33
Consensus pattern (59 bp):
AAAATGGTGATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
Found at i:488 original size:89 final size:88
Alignment explanation
Indices: 367--709 Score: 346
Period size: 89 Copynumber: 3.9 Consensus size: 88
357 GTTCGGAATA
* * * * **
367 AAAAATAGGATTCTTGGAAGTTCAAGGG-TAAAATGGT-ATTTTTTGGAAAGCTCAAGGTCAAAA
1 AAAAATGGGATTTTTGGAAGTTC-GGGGTTAAAATGGTGA-TTTTTGGAAAGTTCGGGGT--AAA
430 ATGG-GATTTTTGGAA-GTTCGAGGGT
62 ATGGTGATTTTTGGAAGGTTCGAGGGT
*
455 -AAAATGGTGATTTTTGGAAGGTTTGGGGTTAAAAATGG-GATTTTTGG-AAGTTCGGGGGTAAA
1 AAAAATGG-GATTTTTGGAA-GTTCGGGGTT-AAAATGGTGATTTTTGGAAAGTTC-GGGGTAAA
517 ATGGTGATTTTTGGAAGGTTCG-GGGT
62 ATGGTGATTTTTGGAAGGTTCGAGGGT
* * *
543 CAAAAATGGGATTTTTGGAAGTTCGGGGTCAAAAATGGTGATTTTTGGAAGGTTTGGGGTAAAAT
1 -AAAAATGGGATTTTTGGAAGTTCGGGGT-TAAAATGGTGATTTTTGGAAAGTTCGGGGTAAAAT
* *
608 GGTAATTTTTAGAAGGTTCGA-GGT
64 GGTGATTTTTGGAAGGTTCGAGGGT
* * **
632 AAAAAATGGGACTTTTTGGAAGTTCGGGGATAAAATGGTGATTTTAGGATGGTTCGGGGTCAAAA
1 -AAAAATGGGA-TTTTTGGAAGTTCGGGGTTAAAATGGTGATTTTTGGAAAGTTCGGGGT--AAA
697 ATGG-GATTTTTGG
62 ATGGTGATTTTTGG
710 TAGTTCGGGG
Statistics
Matches: 217, Mismatches: 21, Indels: 32
0.80 0.08 0.12
Matches are distributed among these distances:
87 13 0.06
88 48 0.22
89 106 0.49
90 43 0.20
91 7 0.03
ACGTcount: A:0.29, C:0.05, G:0.33, T:0.33
Consensus pattern (88 bp):
AAAAATGGGATTTTTGGAAGTTCGGGGTTAAAATGGTGATTTTTGGAAAGTTCGGGGTAAAATGG
TGATTTTTGGAAGGTTCGAGGGT
Done.