Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005121.1 Corchorus capsularis cultivar CVL-1 contig05139, 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: 3795
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.40


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--39  Score: 78
    Period size: 2  Copynumber: 19.5  Consensus size: 2

                                                                      
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

         40 CTTTATCTTT


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   37  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:278 original size:28 final size:29

Alignment explanation


    Indices: 237--301  Score: 96
    Period size: 28  Copynumber: 2.3  Consensus size: 29

        227 TTACACGTTG

                                  *      
        237 AACATCTTTCTTTTTTAGATATTACATTA
          1 AACATCTTTCTTTTTTAGATATCACATTA

                     *               *   
        266 AACA-CTTTTTTTTTTAGATATCACGTTA
          1 AACATCTTTCTTTTTTAGATATCACATTA

                    
        294 AACATCTT
          1 AACATCTT

        302 AGTATGATAT


Statistics
Matches: 32,  Mismatches: 3, Indels: 2
        0.86            0.08        0.05

Matches are distributed among these distances:
  28   25  0.78
  29    7  0.22

ACGTcount: A:0.31, C:0.15, G:0.05, T:0.49


Consensus pattern (29 bp):   
AACATCTTTCTTTTTTAGATATCACATTA

Found at i:821 original size:48 final size:48

Alignment explanation


    Indices: 750--847  Score: 160
    Period size: 48  Copynumber: 2.0  Consensus size: 48

        740 AAAAACTAAT

                     *                                  *   
        750 TTGATTCATGAGTGTCATGATTTGCTCTAATCTCATAATATTTTTGTA
          1 TTGATTCATAAGTGTCATGATTTGCTCTAATCTCATAATATTTTGGTA

                           *        *                       
        798 TTGATTCATAAGTGTTATGATTTGTTCTAATCTCATAATATTTTGGTA
          1 TTGATTCATAAGTGTCATGATTTGCTCTAATCTCATAATATTTTGGTA

              
        846 TT
          1 TT

        848 AAATTAACAT


Statistics
Matches: 46,  Mismatches: 4, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  48   46  1.00

ACGTcount: A:0.26, C:0.10, G:0.14, T:0.50


Consensus pattern (48 bp):   
TTGATTCATAAGTGTCATGATTTGCTCTAATCTCATAATATTTTGGTA

Found at i:1957 original size:20 final size:19

Alignment explanation


    Indices: 1932--1969  Score: 58
    Period size: 19  Copynumber: 1.9  Consensus size: 19

       1922 GAATTTATTA

                                
       1932 ATAACCTTATAATTGTTTTG
          1 ATAACC-TATAATTGTTTTG

                   *          
       1952 ATAACCTCTAATTGTTTT
          1 ATAACCTATAATTGTTTT

       1970 TTAGTAATCA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  19   11  0.65
  20    6  0.35

ACGTcount: A:0.29, C:0.13, G:0.08, T:0.50


Consensus pattern (19 bp):   
ATAACCTATAATTGTTTTG
Done.