Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013234.1 Corchorus capsularis cultivar CVL-1 contig13255, 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: 22132
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:475 original size:11 final size:11

Alignment explanation


    Indices: 432--469  Score: 51
    Period size: 11  Copynumber: 3.5  Consensus size: 11

        422 TTCATATATA

                *      
        432 AAATAAATTAT
          1 AAATTAATTAT

                        
        443 CAAA-TAATTAT
          1 -AAATTAATTAT

                       
        454 AAATTAATTAT
          1 AAATTAATTAT

                 
        465 AAATT
          1 AAATT

        470 TGTTATGAAT


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

Matches are distributed among these distances:
  10    3  0.12
  11   18  0.75
  12    3  0.12

ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39


Consensus pattern (11 bp):   
AAATTAATTAT

Found at i:6500 original size:92 final size:92

Alignment explanation


    Indices: 6343--6515  Score: 249
    Period size: 92  Copynumber: 1.9  Consensus size: 92

       6333 TTACAATTGA

                                            *        *  *                    
       6343 TTCTGTTCGAGTTGAGTCGGTCCATTATAAGGTAAACCACTTTTGATGATGATCTCGTAAATTCA
          1 TTCTGTTCGAGTTGAGTCGGTCCATTATAAGGCAAACCACTCTTAATGATGATCTCGTAAATTCA

                                       
       6408 CAAAACTTAAATTCGATACCTTATTAG
         66 CAAAACTTAAATTCGATACCTTATTAG

                             *                  *                      **    
       6435 TTCTGTTCGAGTTGAGTTGGTCCATTATAAGGCAAATCACTCTTAATGATGATCTTC-TTGATTC
          1 TTCTGTTCGAGTTGAGTCGGTCCATTATAAGGCAAACCACTCTTAATGATGATC-TCGTAAATTC

              **             
       6499 ACTCAACTTAAATTCGA
         65 ACAAAACTTAAATTCGA

       6516 GACCCTAAAT


Statistics
Matches: 71,  Mismatches: 9, Indels: 2
        0.87            0.11        0.02

Matches are distributed among these distances:
  92   69  0.97
  93    2  0.03

ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37


Consensus pattern (92 bp):   
TTCTGTTCGAGTTGAGTCGGTCCATTATAAGGCAAACCACTCTTAATGATGATCTCGTAAATTCA
CAAAACTTAAATTCGATACCTTATTAG

Found at i:19677 original size:29 final size:29

Alignment explanation


    Indices: 19623--19682  Score: 75
    Period size: 29  Copynumber: 2.1  Consensus size: 29

      19613 ATGTTTATCT

                             * * *    *  
      19623 TATAATGAGTAGTTTTTTTTTTAAATTGG
          1 TATAATGAGTAGTTTTTATCTAAAATGGG

                   *                     
      19652 TATAATGGGTAGTTTTTATCTAAAATGGG
          1 TATAATGAGTAGTTTTTATCTAAAATGGG

              
      19681 TA
          1 TA

      19683 GTTTTTATTT


Statistics
Matches: 26,  Mismatches: 5, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  29   26  1.00

ACGTcount: A:0.30, C:0.02, G:0.20, T:0.48


Consensus pattern (29 bp):   
TATAATGAGTAGTTTTTATCTAAAATGGG
Done.