Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006097.1 Kokia drynarioides strain JFW-HI SEQ_120597, 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: 10578
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:634 original size:24 final size:25

Alignment explanation


    Indices: 607--654  Score: 64
    Period size: 26  Copynumber: 1.9  Consensus size: 25

        597 AGAGAAATGT

                                      
        607 AAATG-TG-ATATATGAAATTATGAA
          1 AAATGATGAATATA-GAAATTATGAA

                                    
        631 AAATGATGAATATGAGAAATTATG
          1 AAATGATGAATAT-AGAAATTATG

        655 CCCATGTAGA


Statistics
Matches: 21,  Mismatches: 0, Indels: 4
        0.84            0.00        0.16

Matches are distributed among these distances:
  24    5  0.24
  25    2  0.10
  26   13  0.62
  27    1  0.05

ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31


Consensus pattern (25 bp):   
AAATGATGAATATAGAAATTATGAA

Found at i:747 original size:23 final size:23

Alignment explanation


    Indices: 717--770  Score: 74
    Period size: 23  Copynumber: 2.3  Consensus size: 23

        707 ACGTTAGCAC

                                    
        717 GCTTACTGTTTCACACTT-TGTGT
          1 GCTTACTGTTTCACACTTCT-TGT

                        *          
        740 GCTTACTGTTTCGCACTTCTTGT
          1 GCTTACTGTTTCACACTTCTTGT

              *     
        763 GCCTACTG
          1 GCTTACTG

        771 ACTTGCGCTA


Statistics
Matches: 28,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  23   27  0.96
  24    1  0.04

ACGTcount: A:0.11, C:0.26, G:0.19, T:0.44


Consensus pattern (23 bp):   
GCTTACTGTTTCACACTTCTTGT

Found at i:806 original size:22 final size:23

Alignment explanation


    Indices: 763--815  Score: 63
    Period size: 22  Copynumber: 2.3  Consensus size: 23

        753 CACTTCTTGT

                          *        
        763 GCCTACTGACTTGCGCTATGTGC
          1 GCCTACTGACTTGCACTATGTGC

                             *    *
        786 GCCTACTGA-TTGCACTGTGTGT
          1 GCCTACTGACTTGCACTATGTGC

              *     
        808 GCTTACTG
          1 GCCTACTG

        816 TTTCCCCAGC


Statistics
Matches: 26,  Mismatches: 4, Indels: 1
        0.84            0.13        0.03

Matches are distributed among these distances:
  22   17  0.65
  23    9  0.35

ACGTcount: A:0.13, C:0.26, G:0.26, T:0.34


Consensus pattern (23 bp):   
GCCTACTGACTTGCACTATGTGC

Found at i:1088 original size:26 final size:24

Alignment explanation


    Indices: 1048--1095  Score: 62
    Period size: 26  Copynumber: 1.9  Consensus size: 24

       1038 TCTACATGGG

                                      
       1048 CATAATTTCTCATATTCATCATTTCT
          1 CATAATTTCTCATA-TCA-CATTTCT

                                   
       1074 CATAATTTCAT-ATATCACATTT
          1 CATAATTTC-TCATATCACATTT

       1096 ACATTTCTCT


Statistics
Matches: 21,  Mismatches: 0, Indels: 4
        0.84            0.00        0.16

Matches are distributed among these distances:
  24    5  0.24
  25    3  0.14
  26   12  0.57
  27    1  0.05

ACGTcount: A:0.31, C:0.21, G:0.00, T:0.48


Consensus pattern (24 bp):   
CATAATTTCTCATATCACATTTCT
Done.