Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002447.1 Kokia drynarioides strain JFW-HI SEQ_114560, 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: 13291
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37


Found at i:859 original size:19 final size:18

Alignment explanation


    Indices: 824--867  Score: 52
    Period size: 19  Copynumber: 2.4  Consensus size: 18

        814 TTAACTTTGT

                        *     
        824 AATTTTTATTTTCATTTC
          1 AATTTTTATTTTAATTTC

                   *          *
        842 AATTTTTGTTCTTAATTTT
          1 AATTTTTATT-TTAATTTC

                   
        861 AATTTTT
          1 AATTTTT

        868 TTATGTTTAA


Statistics
Matches: 22,  Mismatches: 3, Indels: 1
        0.85            0.12        0.04

Matches are distributed among these distances:
  18    9  0.41
  19   13  0.59

ACGTcount: A:0.23, C:0.07, G:0.02, T:0.68


Consensus pattern (18 bp):   
AATTTTTATTTTAATTTC

Found at i:3125 original size:13 final size:14

Alignment explanation


    Indices: 3102--3132  Score: 55
    Period size: 13  Copynumber: 2.3  Consensus size: 14

       3092 GGTTTTGTTT

                          
       3102 TGATAGTTTAGAAA
          1 TGATAGTTTAGAAA

                          
       3116 TGAT-GTTTAGAAA
          1 TGATAGTTTAGAAA

                
       3129 TGAT
          1 TGAT

       3133 TTTTTGTGTA


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13   13  0.76
  14    4  0.24

ACGTcount: A:0.39, C:0.00, G:0.23, T:0.39


Consensus pattern (14 bp):   
TGATAGTTTAGAAA

Found at i:3646 original size:12 final size:12

Alignment explanation


    Indices: 3629--3654  Score: 52
    Period size: 12  Copynumber: 2.2  Consensus size: 12

       3619 ATTAAAGCAC

                        
       3629 TTGATCATGGTT
          1 TTGATCATGGTT

                        
       3641 TTGATCATGGTT
          1 TTGATCATGGTT

              
       3653 TT
          1 TT

       3655 ATTGTGTTTA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   14  1.00

ACGTcount: A:0.15, C:0.08, G:0.23, T:0.54


Consensus pattern (12 bp):   
TTGATCATGGTT

Found at i:12037 original size:19 final size:20

Alignment explanation


    Indices: 12002--12040  Score: 62
    Period size: 19  Copynumber: 2.0  Consensus size: 20

      11992 CTCAAAACCT

                                
      12002 CTTCCCCATTTCCCCTTTCC
          1 CTTCCCCATTTCCCCTTTCC

                        *       
      12022 CTTCCCC-TTTCTCCTTTCC
          1 CTTCCCCATTTCCCCTTTCC

      12041 ACCATTGTAC


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  19   11  0.61
  20    7  0.39

ACGTcount: A:0.03, C:0.54, G:0.00, T:0.44


Consensus pattern (20 bp):   
CTTCCCCATTTCCCCTTTCC
Done.