Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006946.1 Corchorus capsularis cultivar CVL-1 contig06967, 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: 29292
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:314 original size:2 final size:2

Alignment explanation


    Indices: 307--332  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

        297 CCTTTACTAA

                                                  
        307 AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT

        333 CATAATAAAG


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:581 original size:22 final size:23

Alignment explanation


    Indices: 556--609  Score: 74
    Period size: 23  Copynumber: 2.4  Consensus size: 23

        546 TTTGTGTCTT

                    *              
        556 AATCGTGTGA-CACGATTAAGAA
          1 AATCGTGTCATCACGATTAAGAA

                *  *               
        578 AATCATGCCATCACGATTAAGAA
          1 AATCGTGTCATCACGATTAAGAA

                     
        601 AATCGTGTC
          1 AATCGTGTC

        610 CCGTTTCTTA


Statistics
Matches: 26,  Mismatches: 5, Indels: 1
        0.81            0.16        0.03

Matches are distributed among these distances:
  22    7  0.27
  23   19  0.73

ACGTcount: A:0.39, C:0.19, G:0.19, T:0.24


Consensus pattern (23 bp):   
AATCGTGTCATCACGATTAAGAA

Found at i:1753 original size:16 final size:17

Alignment explanation


    Indices: 1732--1768  Score: 58
    Period size: 16  Copynumber: 2.2  Consensus size: 17

       1722 CCATCACAAT

                       *     
       1732 TCACCTTGAACCAA-CC
          1 TCACCTTGAACAAACCC

                             
       1748 TCACCTTGAACAAACCC
          1 TCACCTTGAACAAACCC

                
       1765 TCAC
          1 TCAC

       1769 TTTGGGCTTC


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  16   13  0.68
  17    6  0.32

ACGTcount: A:0.32, C:0.43, G:0.05, T:0.19


Consensus pattern (17 bp):   
TCACCTTGAACAAACCC

Found at i:15911 original size:23 final size:24

Alignment explanation


    Indices: 15859--15914  Score: 89
    Period size: 24  Copynumber: 2.4  Consensus size: 24

      15849 AATGTTCTTA

                                    
      15859 ACCTTATAATTAAGGGGAAAAATG
          1 ACCTTATAATTAAGGGGAAAAATG

                                     
      15883 ACCTTATAATT-AGGAGGAAAAATG
          1 ACCTTATAATTAAGG-GGAAAAATG

                     
      15907 A-CTTATAA
          1 ACCTTATAA

      15915 GCTGAATAAT


Statistics
Matches: 31,  Mismatches: 0, Indels: 3
        0.91            0.00        0.09

Matches are distributed among these distances:
  23   10  0.32
  24   21  0.68

ACGTcount: A:0.46, C:0.09, G:0.18, T:0.27


Consensus pattern (24 bp):   
ACCTTATAATTAAGGGGAAAAATG

Found at i:16153 original size:69 final size:69

Alignment explanation


    Indices: 16073--16201  Score: 249
    Period size: 69  Copynumber: 1.9  Consensus size: 69

      16063 TCAAATAGCC

                                                   *                         
      16073 GTAAAAAAAGAAATTAAGAATAATACTAAAATATAAGAGTTATTTAAGTGTTTGAATATAAAATT
          1 GTAAAAAAAGAAATTAAGAATAATACTAAAATATAAGAGGTATTTAAGTGTTTGAATATAAAATT

                
      16138 TTCT
         66 TTCT

                                                                        
      16142 GTAAAAAAAGAAATTAAGAATAATACTAAAATATAAGAGGTATTTAAGTGTTTGAATATA
          1 GTAAAAAAAGAAATTAAGAATAATACTAAAATATAAGAGGTATTTAAGTGTTTGAATATA

      16202 TTTTTTTTTG


Statistics
Matches: 59,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  69   59  1.00

ACGTcount: A:0.52, C:0.02, G:0.13, T:0.33


Consensus pattern (69 bp):   
GTAAAAAAAGAAATTAAGAATAATACTAAAATATAAGAGGTATTTAAGTGTTTGAATATAAAATT
TTCT

Found at i:18182 original size:27 final size:27

Alignment explanation


    Indices: 18144--18205  Score: 115
    Period size: 27  Copynumber: 2.3  Consensus size: 27

      18134 TGTCACTCTT

                                       
      18144 CTCCTGATCTCTTTGCTTCCATGATTG
          1 CTCCTGATCTCTTTGCTTCCATGATTG

                                       
      18171 CTCCTGATCTCTTTGCTTCCATGATTG
          1 CTCCTGATCTCTTTGCTTCCATGATTG

               *    
      18198 CTCTTGAT
          1 CTCCTGAT

      18206 AATGATCTCT


Statistics
Matches: 34,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  27   34  1.00

ACGTcount: A:0.11, C:0.29, G:0.15, T:0.45


Consensus pattern (27 bp):   
CTCCTGATCTCTTTGCTTCCATGATTG

Found at i:26533 original size:2 final size:2

Alignment explanation


    Indices: 26526--26608  Score: 159
    Period size: 2  Copynumber: 42.0  Consensus size: 2

      26516 TGAGCATTCA

                                                                          
      26526 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC

                                                                          
      26568 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T- TC TC
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC

      26609 AATAGGGCAA


Statistics
Matches: 80,  Mismatches: 0, Indels: 2
        0.98            0.00        0.02

Matches are distributed among these distances:
   1    1  0.01
   2   79  0.99

ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51


Consensus pattern (2 bp):   
TC

Done.