Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001645.1 Corchorus capsularis cultivar CVL-1 contig01645, 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: 4394
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30


Found at i:12 original size:2 final size:2

Alignment explanation


    Indices: 6--48  Score: 86
    Period size: 2  Copynumber: 21.5  Consensus size: 2

          1 CGTAG

                                                                          
          6 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

             
         48 T
          1 T

         49 GCATAGTAAC


Statistics
Matches: 41,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   41  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:2841 original size:11 final size:11

Alignment explanation


    Indices: 2827--2864  Score: 51
    Period size: 11  Copynumber: 3.5  Consensus size: 11

       2817 ATTCATAACA

                       
       2827 AATTTATAATT
          1 AATTTATAATT

                       
       2838 AATTTATAATT
          1 AATTTATAATT

                        
       2849 -ATTTGATAATT
          1 AATTT-ATAATT

            *    
       2860 TATTT
          1 AATTT

       2865 TATATAGGAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 3
        0.89            0.00        0.11

Matches are distributed among these distances:
  10    4  0.16
  11   17  0.68
  12    4  0.16

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


Consensus pattern (11 bp):   
AATTTATAATT

Found at i:3774 original size:107 final size:105

Alignment explanation


    Indices: 3550--3811  Score: 411
    Period size: 107  Copynumber: 2.5  Consensus size: 105

       3540 AATTTTTTTA

                             **                                              
       3550 ACCCTTAAAATAAAAATTTAATTTTAATTT-GGGCTAAACTTAGTG-AATTAGTTATATATTTTA
          1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA

                     *                        *     
       3613 TTTCTAAAATCCTATAACAATATTATTAATTATGGAATTT
         66 TTTCTAAAACCCTATAACAATATTATTAATTATGAAATTT

                                                                   * *       
       3653 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
          1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA

                    *        *               *        
       3718 TTTCTAAACCCCTATAATAATAAATTATTAATTTTGAAATTT
         66 TTTCTAAAACCCTATAACAAT--ATTATTAATTATGAAATTT

                                                                
       3760 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
          1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA

       3812 AGACTAAACT


Statistics
Matches: 146,  Mismatches: 9, Indels: 4
        0.92            0.06        0.03

Matches are distributed among these distances:
 103   28  0.19
 104   15  0.10
 105   34  0.23
 107   69  0.47

ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41


Consensus pattern (105 bp):   
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
TTTCTAAAACCCTATAACAATATTATTAATTATGAAATTT

Found at i:4245 original size:2 final size:2

Alignment explanation


    Indices: 4238--4268  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       4228 AAATAAGATA

                                                          
       4238 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       4269 AAGTAAAGCA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Done.