Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012706.1 Kokia drynarioides strain JFW-HI SEQ_127717, 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: 12243
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.27


Found at i:1582 original size:60 final size:59

Alignment explanation


    Indices: 1480--1680  Score: 273
    Period size: 60  Copynumber: 3.4  Consensus size: 59

       1470 GGAGGTCCCT

                                              * **                      
       1480 AAACTGTCCAAAAATTCCATTTTTACCCTCGAACATAAAAAAAATTCCATTTTTGACCCC
          1 AAACT-TCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAAATTCCATTTTTGACCCC

                                                                    *     
       1540 GAAACTTCCAAAAATTCCATTTTTATCCC-CGAACTTCC-AAAAATTCCATTTTTTTACCCC
          1 -AAACTTCCAAAAATTCCATTTTTA-CCCTCGAACTTCCAAAAAATTCCA-TTTTTGACCCC

                             *                                          
       1600 AAAACTTCCAAAAATTCTATTTTTACCCTCGAACTTCCAAAAAA-TCCATTTTTGACCCC
          1 -AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAAATTCCATTTTTGACCCC

                          *       
       1659 AGAACTTCCAAAAACTCCATTT
          1 A-AACTTCCAAAAATTCCATTT

       1681 CTGACCATTA


Statistics
Matches: 126,  Mismatches: 9, Indels: 12
        0.86            0.06        0.08

Matches are distributed among these distances:
  58    1  0.01
  59   41  0.33
  60   71  0.56
  61   13  0.10

ACGTcount: A:0.36, C:0.28, G:0.04, T:0.32


Consensus pattern (59 bp):   
AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAAATTCCATTTTTGACCCC

Found at i:1686 original size:30 final size:29

Alignment explanation


    Indices: 1481--1686  Score: 229
    Period size: 30  Copynumber: 6.9  Consensus size: 29

       1471 GAGGTCCCTA

                                           
       1481 AACTGTCCAAAAATTCCATTTTT-ACCCTCG
          1 AACT-TCCAAAAATTCCATTTTTGACCC-CG

                 ***                      
       1511 AACATAAAAAAAATTCCATTTTTGACCCCG
          1 AAC-TTCCAAAAATTCCATTTTTGACCCCG

                                           
       1541 AAACTTCCAAAAATTCCATTTTT-ATCCCCG
          1 -AACTTCCAAAAATTCCATTTTTGA-CCCCG

                                   *      *
       1571 AACTTCCAAAAATTCCATTTTTTTACCCCAA
          1 AACTTCCAAAAATTCCA-TTTTTGACCCC-G

                           *              
       1602 AACTTCCAAAAATTCTATTTTT-ACCCTCG
          1 AACTTCCAAAAATTCCATTTTTGACCC-CG

                        *                 
       1631 AACTTCCAAAAAATCCATTTTTGACCCCAG
          1 AACTTCCAAAAATTCCATTTTTGACCCC-G

                        *       *     
       1661 AACTTCCAAAAACTCCATTTCTGACC
          1 AACTTCCAAAAATTCCATTTTTGACC

       1687 ATTAAACTCT


Statistics
Matches: 153,  Mismatches: 13, Indels: 20
        0.82            0.07        0.11

Matches are distributed among these distances:
  29   43  0.28
  30   85  0.56
  31   25  0.16

ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32


Consensus pattern (29 bp):   
AACTTCCAAAAATTCCATTTTTGACCCCG

Done.