Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006962.1 Kokia drynarioides strain JFW-HI SEQ_121567, 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: 9554
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35


Found at i:1012 original size:36 final size:36

Alignment explanation


    Indices: 952--1035  Score: 123
    Period size: 36  Copynumber: 2.3  Consensus size: 36

        942 TATCAATCGC

                        * *                     
        952 CAAGACAAGAATCTGCTTTCGCAAGCAGTGGATTGG
          1 CAAGACAAGAATATACTTTCGCAAGCAGTGGATTGG

                      *        *     *          
        988 CAAGACAAGATTATACTTTTGCAAGTAGTGGATTGG
          1 CAAGACAAGAATATACTTTCGCAAGCAGTGGATTGG

                        
       1024 CAAGACAAGAAT
          1 CAAGACAAGAAT

       1036 CTATTTTCTC


Statistics
Matches: 42,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  36   42  1.00

ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24


Consensus pattern (36 bp):   
CAAGACAAGAATATACTTTCGCAAGCAGTGGATTGG

Found at i:1319 original size:18 final size:18

Alignment explanation


    Indices: 1298--1340  Score: 52
    Period size: 18  Copynumber: 2.4  Consensus size: 18

       1288 TTTCATCAAT

                      *       
       1298 ATTTATTTTATTTTTTAA
          1 ATTTATTTTAATTTTTAA

                *  *          
       1316 ATTTCTTATAATTTTTAA
          1 ATTTATTTTAATTTTTAA

                    
       1334 A-TTATTT
          1 ATTTATTT

       1341 GTTGTTGTGA


Statistics
Matches: 20,  Mismatches: 5, Indels: 1
        0.77            0.19        0.04

Matches are distributed among these distances:
  17    4  0.20
  18   16  0.80

ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67


Consensus pattern (18 bp):   
ATTTATTTTAATTTTTAA

Found at i:3565 original size:28 final size:28

Alignment explanation


    Indices: 3533--3614  Score: 112
    Period size: 27  Copynumber: 3.0  Consensus size: 28

       3523 ACATAATCCA

                      *                 
       3533 GTGAAAGTTCGTTAGGACTATCGTATAT
          1 GTGAAAGTTCATTAGGACTATCGTATAT

                   **                *  
       3561 GTG-AAGCCCATTAGGACTATCGTACAT
          1 GTGAAAGTTCATTAGGACTATCGTATAT

                                  *    
       3588 GTGAAAGTTCATTAGGACTATCTTATA
          1 GTGAAAGTTCATTAGGACTATCGTATA

       3615 AGTGGAGGTC


Statistics
Matches: 45,  Mismatches: 8, Indels: 2
        0.82            0.15        0.04

Matches are distributed among these distances:
  27   23  0.51
  28   22  0.49

ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33


Consensus pattern (28 bp):   
GTGAAAGTTCATTAGGACTATCGTATAT

Done.