Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016245.1 Corchorus capsularis cultivar CVL-1 contig16266, 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: 16609
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31


Found at i:6131 original size:30 final size:30

Alignment explanation


    Indices: 6095--6157  Score: 108
    Period size: 30  Copynumber: 2.1  Consensus size: 30

       6085 TCGCGCGGGA

                                          
       6095 CATCGCACGAGCCATCCGGCCACAACCGGC
          1 CATCGCACGAGCCATCCGGCCACAACCGGC

                   * *                    
       6125 CATCGCATGGGCCATCCGGCCACAACCGGC
          1 CATCGCACGAGCCATCCGGCCACAACCGGC

               
       6155 CAT
          1 CAT

       6158 TCGACCCTTT


Statistics
Matches: 31,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  30   31  1.00

ACGTcount: A:0.22, C:0.44, G:0.24, T:0.10


Consensus pattern (30 bp):   
CATCGCACGAGCCATCCGGCCACAACCGGC

Found at i:7184 original size:8 final size:8

Alignment explanation


    Indices: 7165--7195  Score: 53
    Period size: 8  Copynumber: 3.8  Consensus size: 8

       7155 AGTTATATCG

                     
       7165 AAAAATATA
          1 AAAAATA-A

                    
       7174 AAAAATAA
          1 AAAAATAA

                    
       7182 AAAAATAA
          1 AAAAATAA

                  
       7190 AAAAAT
          1 AAAAAT

       7196 TTCAACCAGA


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   8   15  0.68
   9    7  0.32

ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16


Consensus pattern (8 bp):   
AAAAATAA

Found at i:12631 original size:12 final size:12

Alignment explanation


    Indices: 12614--12644  Score: 53
    Period size: 12  Copynumber: 2.6  Consensus size: 12

      12604 GGCCACAACC

                        
      12614 GGCCATCGCACG
          1 GGCCATCGCACG

                      * 
      12626 GGCCATCGCATG
          1 GGCCATCGCACG

                   
      12638 GGCCATC
          1 GGCCATC

      12645 CGGCCACAAC


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  12   18  1.00

ACGTcount: A:0.16, C:0.39, G:0.32, T:0.13


Consensus pattern (12 bp):   
GGCCATCGCACG

Found at i:12661 original size:42 final size:42

Alignment explanation


    Indices: 12544--12661  Score: 139
    Period size: 42  Copynumber: 2.8  Consensus size: 42

      12534 AGACCGGCCA

                            *       **        *    *   
      12544 CCATCGCATGGAG-CAACCGGCCATGACCGGCCAACGCATGGG
          1 CCATCGCATGG-GCCATCCGGCCACAACCGGCCATCGCACGGG

            *       * **                              
      12586 ACATCGCACGATCCATCCGGCCACAACCGGCCATCGCACGGG
          1 CCATCGCATGGGCCATCCGGCCACAACCGGCCATCGCACGGG

                                              
      12628 CCATCGCATGGGCCATCCGGCCACAACCGGCCAT
          1 CCATCGCATGGGCCATCCGGCCACAACCGGCCAT

      12662 TCGACCCTTT


Statistics
Matches: 62,  Mismatches: 13, Indels: 2
        0.81            0.17        0.03

Matches are distributed among these distances:
  42   62  1.00

ACGTcount: A:0.23, C:0.41, G:0.26, T:0.10


Consensus pattern (42 bp):   
CCATCGCATGGGCCATCCGGCCACAACCGGCCATCGCACGGG

Found at i:16007 original size:19 final size:18

Alignment explanation


    Indices: 15983--16018  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      15973 TGAAGATTTC

                               
      15983 TTGAAGATAATTTGAAGAT
          1 TTGAAGATAA-TTGAAGAT

                    *        
      16002 TTGAAGATCATTGAAGA
          1 TTGAAGATAATTGAAGA

      16019 ATTATTTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33


Consensus pattern (18 bp):   
TTGAAGATAATTGAAGAT
Done.