Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016137.1 Corchorus olitorius cultivar O-4 contig16170, 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: 21692
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35


Found at i:6272 original size:22 final size:22

Alignment explanation


    Indices: 6247--6299  Score: 72
    Period size: 22  Copynumber: 2.4  Consensus size: 22

       6237 GTATAATTAT

                          *        
       6247 CAAAATTTCATACAGAAG-TTAC
          1 CAAAATTTCAT-CAAAAGTTTAC

                                 *
       6269 CAAAATTTCATCAAAAGTTTAT
          1 CAAAATTTCATCAAAAGTTTAC

                     
       6291 CAAAATTTC
          1 CAAAATTTC

       6300 TTAGGGAGAT


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

Matches are distributed among these distances:
  21    5  0.18
  22   23  0.82

ACGTcount: A:0.45, C:0.17, G:0.06, T:0.32


Consensus pattern (22 bp):   
CAAAATTTCATCAAAAGTTTAC

Found at i:14920 original size:31 final size:31

Alignment explanation


    Indices: 14882--14986  Score: 90
    Period size: 31  Copynumber: 3.4  Consensus size: 31

      14872 AATGGCTAAT

                                           
      14882 TGCTCAAATAAGGGTTTAACGTTTGTCAAAA
          1 TGCTCAAATAAGGGTTTAACGTTTGTCAAAA

                             * * **        **
      14913 TGCTCAAATGAGAGGGTCTGATATTT-T-AATT
          1 TGCTCAAAT-A-AGGGTTTAACGTTTGTCAAAA

                          **                
      14944 TGGC-CAAATAAGGACTTAACGTTTGTCAAAA
          1 T-GCTCAAATAAGGGTTTAACGTTTGTCAAAA

                        
      14975 TGCTCAAATAAG
          1 TGCTCAAATAAG

      14987 AGCCCAATCT


Statistics
Matches: 54,  Mismatches: 14, Indels: 12
        0.68            0.17        0.15

Matches are distributed among these distances:
  29    8  0.15
  30    4  0.07
  31   28  0.52
  32    4  0.07
  33   10  0.19

ACGTcount: A:0.35, C:0.13, G:0.20, T:0.31


Consensus pattern (31 bp):   
TGCTCAAATAAGGGTTTAACGTTTGTCAAAA

Found at i:14983 original size:62 final size:60

Alignment explanation


    Indices: 14886--15014  Score: 177
    Period size: 62  Copynumber: 2.1  Consensus size: 60

      14876 GCTAATTGCT

                     **                              * * **               
      14886 CAAATAAGGGTTTAACGTTTGTCAAAATGCTCAAATGAGAGGGTCTGATATTTTAATTTGGC
          1 CAAATAAGGACTTAACGTTTGTCAAAATGCTCAAAT-A-AGAGCCCAATATTTTAATTTGGC

                                                           *            
      14948 CAAATAAGGACTTAACGTTTGTCAAAATGCTCAAATAAGAGCCCAATCTTTTAATTTGGC
          1 CAAATAAGGACTTAACGTTTGTCAAAATGCTCAAATAAGAGCCCAATATTTTAATTTGGC

                   
      15008 CAAATAA
          1 CAAATAA

      15015 AATCCAAACC


Statistics
Matches: 60,  Mismatches: 7, Indels: 2
        0.87            0.10        0.03

Matches are distributed among these distances:
  60   25  0.42
  61    1  0.02
  62   34  0.57

ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31


Consensus pattern (60 bp):   
CAAATAAGGACTTAACGTTTGTCAAAATGCTCAAATAAGAGCCCAATATTTTAATTTGGC

Found at i:20532 original size:43 final size:43

Alignment explanation


    Indices: 20452--20538  Score: 113
    Period size: 43  Copynumber: 2.0  Consensus size: 43

      20442 TCTCTTTGTG

                                                   *   
      20452 TCTGCGTTTTTAATCTGAAAAAAAAAAGGTTTCTTTTCCGTTT
          1 TCTGCGTTTTTAATCTGAAAAAAAAAAGGTTTCTTTTCCATTT

                        *              **    *          
      20495 TCTGCGTTTTT-TTCTGAAAAAAAAAATTTTGTGTTTTCCATTT
          1 TCTGCGTTTTTAATCTGAAAAAAAAAAGGTT-TCTTTTCCATTT

             
      20538 T
          1 T

      20539 TTTTTAATTT


Statistics
Matches: 38,  Mismatches: 5, Indels: 2
        0.84            0.11        0.04

Matches are distributed among these distances:
  42   16  0.42
  43   22  0.58

ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48


Consensus pattern (43 bp):   
TCTGCGTTTTTAATCTGAAAAAAAAAAGGTTTCTTTTCCATTT
Done.