Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005875.1 Corchorus capsularis cultivar CVL-1 contig05893, 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: 3130
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36


Found at i:769 original size:7 final size:7

Alignment explanation


    Indices: 759--836  Score: 52
    Period size: 7  Copynumber: 10.7  Consensus size: 7

        749 TCATCATTCA

                   
        759 TTTTTCT
          1 TTTTTCT

                   
        766 TTTTTCT
          1 TTTTTCT

             *     
        773 TCTTTCT
          1 TTTTTCT

                    
        780 TTTTTCTT
          1 TTTTTC-T

                    
        788 TCTTTTCT
          1 T-TTTTCT

              **  *
        796 TTCATCA
          1 TTTTTCT

                   
        803 TTTTTCT
          1 TTTTTCT

                     
        810 TCCTTTT-T
          1 T--TTTTCT

            *      
        818 GTTTTCT
          1 TTTTTCT

                    
        825 TGTTTT-T
          1 T-TTTTCT

                 
        832 TTTTT
          1 TTTTT

        837 TACATGCACT


Statistics
Matches: 55,  Mismatches: 10, Indels: 13
        0.71            0.13        0.17

Matches are distributed among these distances:
   6    8  0.15
   7   29  0.53
   8    9  0.16
   9    9  0.16

ACGTcount: A:0.03, C:0.17, G:0.03, T:0.78


Consensus pattern (7 bp):   
TTTTTCT

Found at i:780 original size:14 final size:16

Alignment explanation


    Indices: 760--797  Score: 62
    Period size: 14  Copynumber: 2.5  Consensus size: 16

        750 CATCATTCAT

                            
        760 TTTTCTTTTTTC-TTC
          1 TTTTCTTTTTTCTTTC

                            
        775 -TTTCTTTTTTCTTTC
          1 TTTTCTTTTTTCTTTC

                    
        790 TTTTCTTT
          1 TTTTCTTT

        798 CATCATTTTT


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  14   11  0.52
  15    3  0.14
  16    7  0.33

ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82


Consensus pattern (16 bp):   
TTTTCTTTTTTCTTTC

Found at i:788 original size:11 final size:11

Alignment explanation


    Indices: 759--793  Score: 54
    Period size: 11  Copynumber: 3.3  Consensus size: 11

        749 TCATCATTCA

                       
        759 TTTTTCTTT-T
          1 TTTTTCTTTCT

              *        
        769 TTCTTCTTTCT
          1 TTTTTCTTTCT

                       
        780 TTTTTCTTTCT
          1 TTTTTCTTTCT

               
        791 TTT
          1 TTT

        794 CTTTCATCAT


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  10    8  0.36
  11   14  0.64

ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83


Consensus pattern (11 bp):   
TTTTTCTTTCT

Found at i:1623 original size:44 final size:43

Alignment explanation


    Indices: 1513--1656  Score: 180
    Period size: 44  Copynumber: 3.2  Consensus size: 43

       1503 TGCAACTTTG

                   *                           * *    *  
       1513 GAAAACCCTTTTATCAAAACCCTCTTTAAAACCATAATTCTTCTT
          1 GAAAACCATTTTATCAAAA-CCT-TTTAAAACCATGACTCTTTTT

                  *                                      
       1558 GAAAAAACATTTTATCAAAACCTTTTGAAAACCATGACTCTTTTT
          1 G-AAAACCATTTTATCAAAACCTTTT-AAAACCATGACTCTTTTT

                                                   *     
       1603 GAAAACCATTTTATCAAAACCTTTTAAAAACCATGACTATTTTTT
          1 GAAAACCATTTTATCAAAACCTTTT-AAAACCATGACT-CTTTTT

                     
       1648 GAAAACCAT
          1 GAAAACCAT

       1657 CGTTGCTCTT


Statistics
Matches: 88,  Mismatches: 8, Indels: 6
        0.86            0.08        0.06

Matches are distributed among these distances:
  44   38  0.43
  45   34  0.39
  46   16  0.18

ACGTcount: A:0.40, C:0.21, G:0.05, T:0.35


Consensus pattern (43 bp):   
GAAAACCATTTTATCAAAACCTTTTAAAACCATGACTCTTTTT

Found at i:1699 original size:16 final size:17

Alignment explanation


    Indices: 1665--1708  Score: 54
    Period size: 17  Copynumber: 2.5  Consensus size: 17

       1655 ATCGTTGCTC

                       *      
       1665 TTTCTCTTTTCTTTCTTT
          1 TTTCT-TTTTCATTCTTT

                             
       1683 TTTCTTTTTCATT-TTT
          1 TTTCTTTTTCATTCTTT

                      
       1699 TTTCATTTTT
          1 TTTC-TTTTT

       1709 TCCACGTATC


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  16    7  0.29
  17   12  0.50
  18    5  0.21

ACGTcount: A:0.05, C:0.16, G:0.00, T:0.80


Consensus pattern (17 bp):   
TTTCTTTTTCATTCTTT
Done.