Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006221.1 Corchorus capsularis cultivar CVL-1 contig06240, 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: 3438
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36


Found at i:155 original size:30 final size:29

Alignment explanation


    Indices: 99--155  Score: 69
    Period size: 30  Copynumber: 1.9  Consensus size: 29

         89 ATTGCAAATA

                   *      *      *       
         99 TTTTAAGTACATGGTAAAAGTGTAAATCT
          1 TTTTAAGGACATGGCAAAAGTATAAATCT

                                *       
        128 TTTTAGAGGACATGGCAAAATTATAAAT
          1 TTTTA-AGGACATGGCAAAAGTATAAAT

        156 TTTCACCTAC


Statistics
Matches: 23,  Mismatches: 4, Indels: 1
        0.82            0.14        0.04

Matches are distributed among these distances:
  29    5  0.22
  30   18  0.78

ACGTcount: A:0.40, C:0.07, G:0.18, T:0.35


Consensus pattern (29 bp):   
TTTTAAGGACATGGCAAAAGTATAAATCT

Found at i:2945 original size:17 final size:17

Alignment explanation


    Indices: 2893--2933  Score: 52
    Period size: 15  Copynumber: 2.5  Consensus size: 17

       2883 CTAGCCGAAC

                              
       2893 CTTCTT-TTTCTCCTT-T
          1 CTTCTTCTTT-TCCTTCT

                             
       2909 -TTCTTCTTTTCCTTCT
          1 CTTCTTCTTTTCCTTCT

                     
       2925 CTTCTTCTT
          1 CTTCTTCTT

       2934 CTTCTTTTCT


Statistics
Matches: 22,  Mismatches: 0, Indels: 5
        0.81            0.00        0.19

Matches are distributed among these distances:
  15   10  0.45
  16    4  0.18
  17    8  0.36

ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68


Consensus pattern (17 bp):   
CTTCTTCTTTTCCTTCT

Found at i:3339 original size:21 final size:21

Alignment explanation


    Indices: 3314--3355  Score: 59
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       3304 GCACCAGGTA

                                  
       3314 TCTTCTGCTTC-TCTTTTCTTT
          1 TCTTCTGCTTCTTC-TTTCTTT

                  *              
       3335 TCTTCTTCTTCTTCTTTCTTT
          1 TCTTCTGCTTCTTCTTTCTTT

       3356 CCTTTTTTTT


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  21   17  0.89
  22    2  0.11

ACGTcount: A:0.00, C:0.29, G:0.02, T:0.69


Consensus pattern (21 bp):   
TCTTCTGCTTCTTCTTTCTTT
Done.