Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011459.1 Kokia drynarioides strain JFW-HI SEQ_126443, 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, 930
Length: 1550
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Found at i:1017 original size:431 final size:431
Alignment explanation
Indices: 222--1017 Score: 1025
Period size: 431 Copynumber: 1.8 Consensus size: 431
212 AACACAAAAT
** * *
222 AAGTGGTATATAATGTTAAATGATAAAAGAAAAAAACTACTGTTTTTGAAGATATTTAAGCGAAA
1 AAGTGGTATATAATGTTAAAAAATAAAAGAAAAAAACTAC--TTTTTGAAGATATTTAAACAAAA
* * * *
287 TTTTCAAAGAAAGATTAGAGTCTTAATTACAATGGAAACAACAAACAAATATGGTAGGAAATATG
64 TTTCCAAAGAAAGATTAGAGTCATAACTACAATGGAAACAACAAACAAATATGGTAGGAAACATG
* * * *
352 TATCATGGCTCCCATCTAAGAAATTGGATACACTCTATTTTTAGACTTTTTAAATGGGTTCGCCT
129 TATCATGGCTCCCATCTAACAAATTGGATACACTCCATTTTCAGACTTTTTAAATGGGTTCACCT
* **
417 CGATTTTGTCTTCACTTCTCTTTTTTATTTATTTCCAGCCCTCAATATCGCTGCATGTTGCAATG
194 CGATTTTGTCTTCACTTCTCTTTTTTATTTATTTCCACCCCTCAATATCGCAACATGTTGCAATG
* *
482 CAATTACACTCTATTTATTGATATGGATATTCTGGAAACATATAGAAATTTGGCACTTTTACCGT
259 CAATTACACTCTATTTATTGATATGGATATTCTGGAAACATATAGAAACTTGGCACATTTACCGT
** * * *
547 GAGTTGTTACTTTCTTCTTGAGATTGTTTAGACAATTTTTTTGCCATCCTTTTTCCACTCGGTTC
324 GAGCCGTTACTTTATTCTTAAGATTGTTTAAACAATTTTTTTGCCATCCTTTTTCCACTCGGTTC
612 ATATGGGAAACTTGAATTGCTGTGAATGTTGGTAATGCGAAAC
389 ATATGGGAAACTTGAATTGCTGTGAATGTTGGTAATGCGAAAC
655 AAGTGGTATATAATGTTAAAAAAATAAAAGAAAAATAA-TA-TTTTTGAAGATATTTAAACAAAA
1 AAGTGGTATATAATGTT-AAAAAATAAAAGAAAAA-AACTACTTTTTGAAGATATTTAAACAAAA
* * * * *
718 TTTCCAATGAAAGGTTGGAGTCATAACTACGATGGAAACAACAGACAAATATGGTAGGAAACATG
64 TTTCCAAAGAAAGATTAGAGTCATAACTACAATGGAAACAACAAACAAATATGGTAGGAAACATG
** * **
783 TATCATGTTTGGCC-TCTAACAAATTGGATACTTTCCATTTTCAGACTTTTTAAATGGG-TCAAC
129 TATCATGGCT-CCCATCTAACAAATTGGATACACTCCATTTTCAGACTTTTTAAATGGGTTC-AC
* *
846 CTCGATTTTGTCTTCA--TCTCTCTTTTTATTTATTTCC-CCCCTCAATATTGCAATATGTTGCA
192 CTCGATTTTGTCTTCACTTCTCT-TTTTTATTTATTTCCACCCCTCAATATCGCAACATGTTGCA
* * * * * * * *
908 CTGTAGTTACTCTCTATTTATTTTATATGG-TAATTCTTGAAACATATAGGAACTTGTCACATTT
256 ATGCAATTACACTCTATTTA-TTGATATGGAT-ATTCTGGAAACATATAGAAACTTGGCACATTT
* * * *
972 ACTGTGAGCCGTTAGTTTATTGTTAAGATAT-TTTAAACAAATTTTT
319 ACCGTGAGCCGTTACTTTATTCTTAAGAT-TGTTTAAACAATTTTTT
1018 ATGTATAAAA
Statistics
Matches: 309, Mismatches: 46, Indels: 19
0.83 0.12 0.05
Matches are distributed among these distances:
429 42 0.14
430 87 0.28
431 142 0.46
432 2 0.01
433 17 0.06
434 17 0.06
435 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (431 bp):
AAGTGGTATATAATGTTAAAAAATAAAAGAAAAAAACTACTTTTTGAAGATATTTAAACAAAATT
TCCAAAGAAAGATTAGAGTCATAACTACAATGGAAACAACAAACAAATATGGTAGGAAACATGTA
TCATGGCTCCCATCTAACAAATTGGATACACTCCATTTTCAGACTTTTTAAATGGGTTCACCTCG
ATTTTGTCTTCACTTCTCTTTTTTATTTATTTCCACCCCTCAATATCGCAACATGTTGCAATGCA
ATTACACTCTATTTATTGATATGGATATTCTGGAAACATATAGAAACTTGGCACATTTACCGTGA
GCCGTTACTTTATTCTTAAGATTGTTTAAACAATTTTTTTGCCATCCTTTTTCCACTCGGTTCAT
ATGGGAAACTTGAATTGCTGTGAATGTTGGTAATGCGAAAC
Done.