Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008027.1 Corchorus capsularis cultivar CVL-1 contig08048, 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: 38064
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32


Found at i:54 original size:37 final size:38

Alignment explanation


    Indices: 13--92  Score: 128
    Period size: 38  Copynumber: 2.1  Consensus size: 38

          3 AGTTTTTGTT

                                                   
         13 TTTTTCCGTTTTTACTA-AAAAAAAAAAGT-TTTTTCCG
          1 TTTTTCCGTTTTTACTATAAAAAAAAAA-TATTTTTCCG

                         *                        
         50 TTTTTCCGTTTTTTCTATAAAAAAAAAATATTTTTCCG
          1 TTTTTCCGTTTTTACTATAAAAAAAAAATATTTTTCCG

                 
         88 TTTTT
          1 TTTTT

         93 AATTTTAGGG


Statistics
Matches: 40,  Mismatches: 1, Indels: 3
        0.91            0.02        0.07

Matches are distributed among these distances:
  37   17  0.43
  38   23  0.57

ACGTcount: A:0.30, C:0.12, G:0.06, T:0.51


Consensus pattern (38 bp):   
TTTTTCCGTTTTTACTATAAAAAAAAAATATTTTTCCG

Found at i:10921 original size:20 final size:20

Alignment explanation


    Indices: 10885--10922  Score: 58
    Period size: 20  Copynumber: 1.9  Consensus size: 20

      10875 TGACCGGCCA

                        *       
      10885 CCATCGCATGGATCAACCGG
          1 CCATCGCATGGAGCAACCGG

                       *      
      10905 CCATCGCATGGGGCAACC
          1 CCATCGCATGGAGCAACC

      10923 AGTCACAACC


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   16  1.00

ACGTcount: A:0.24, C:0.37, G:0.26, T:0.13


Consensus pattern (20 bp):   
CCATCGCATGGAGCAACCGG

Found at i:10934 original size:30 final size:30

Alignment explanation


    Indices: 10898--10968  Score: 97
    Period size: 30  Copynumber: 2.4  Consensus size: 30

      10888 TCGCATGGAT

                               *       *  
      10898 CAACCGGCCATCGCATGGGGCAACCAGTCA
          1 CAACCGGCCATCGCATGGGCCAACCAGCCA

                          *       *  *    
      10928 CAACCGGCCATCGCTTGGGCCATCCGGCCA
          1 CAACCGGCCATCGCATGGGCCAACCAGCCA

                       
      10958 CAACCGGCCAT
          1 CAACCGGCCAT

      10969 TTGATCCCTT


Statistics
Matches: 36,  Mismatches: 5, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  30   36  1.00

ACGTcount: A:0.23, C:0.41, G:0.25, T:0.11


Consensus pattern (30 bp):   
CAACCGGCCATCGCATGGGCCAACCAGCCA

Found at i:12849 original size:30 final size:30

Alignment explanation


    Indices: 12800--12862  Score: 99
    Period size: 30  Copynumber: 2.1  Consensus size: 30

      12790 TCGCATGGAA

                       *                  
      12800 CATCGCATGGGGCAACCGGCCACAACCGGC
          1 CATCGCATGGGCCAACCGGCCACAACCGGC

                  *       *               
      12830 CATCGCTTGGGCCATCCGGCCACAACCGGC
          1 CATCGCATGGGCCAACCGGCCACAACCGGC

               
      12860 CAT
          1 CAT

      12863 TTGATCACTT


Statistics
Matches: 30,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  30   30  1.00

ACGTcount: A:0.21, C:0.41, G:0.27, T:0.11


Consensus pattern (30 bp):   
CATCGCATGGGCCAACCGGCCACAACCGGC

Found at i:36064 original size:30 final size:30

Alignment explanation


    Indices: 36028--36087  Score: 111
    Period size: 30  Copynumber: 2.0  Consensus size: 30

      36018 CAAAGGAACA

                                          
      36028 AATGGCATCTTTGGTGCGATTCCTCCATCC
          1 AATGGCATCTTTGGTGCGATTCCTCCATCC

                         *                
      36058 AATGGCATCTTTGTTGCGATTCCTCCATCC
          1 AATGGCATCTTTGGTGCGATTCCTCCATCC

      36088 TTTGATGTAT


Statistics
Matches: 29,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  30   29  1.00

ACGTcount: A:0.17, C:0.30, G:0.18, T:0.35


Consensus pattern (30 bp):   
AATGGCATCTTTGGTGCGATTCCTCCATCC

Found at i:36106 original size:30 final size:30

Alignment explanation


    Indices: 36028--36107  Score: 79
    Period size: 30  Copynumber: 2.7  Consensus size: 30

      36018 CAAAGGAACA

                *   *                     
      36028 AATGGCATCTTTGGTGCGATTCCTCCATCC
          1 AATGACATATTTGGTGCGATTCCTCCATCC

                *   *    *                
      36058 AATGGCATCTTTGTTGCGATTCCTCCATCC
          1 AATGACATATTTGGTGCGATTCCTCCATCC

            **   **             
      36088 TTTGATGTATTTGGTGCGAT
          1 AATGACATATTTGGTGCGAT

      36108 CCCATCTCTT


Statistics
Matches: 42,  Mismatches: 8, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  30   42  1.00

ACGTcount: A:0.16, C:0.24, G:0.21, T:0.39


Consensus pattern (30 bp):   
AATGACATATTTGGTGCGATTCCTCCATCC
Done.