Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005695.1 Corchorus capsularis cultivar CVL-1 contig05713, 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: 4682
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.37


Found at i:234 original size:2 final size:2

Alignment explanation


    Indices: 214--262  Score: 73
    Period size: 2  Copynumber: 25.0  Consensus size: 2

        204 GTGAAGACTA

                            *  *                                          
        214 AT AT A- AT AT AA AG AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                       
        255 AT AT AT AT
          1 AT AT AT AT

        263 GGTGATTGCT


Statistics
Matches: 43,  Mismatches: 3, Indels: 2
        0.90            0.06        0.04

Matches are distributed among these distances:
   1    1  0.02
   2   42  0.98

ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45


Consensus pattern (2 bp):   
AT

Found at i:4050 original size:17 final size:17

Alignment explanation


    Indices: 4028--4061  Score: 68
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       4018 TTCTCTATAA

                             
       4028 GGATTTTATCGACTGTG
          1 GGATTTTATCGACTGTG

                             
       4045 GGATTTTATCGACTGTG
          1 GGATTTTATCGACTGTG

       4062 TTTCTCAATA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.18, C:0.12, G:0.29, T:0.41


Consensus pattern (17 bp):   
GGATTTTATCGACTGTG

Found at i:4458 original size:2 final size:2

Alignment explanation


    Indices: 4451--4480  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

       4441 AATTTGTAGT

                                                        
       4451 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

       4481 ATGAAATCGG


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:4598 original size:24 final size:23

Alignment explanation


    Indices: 4543--4598  Score: 60
    Period size: 23  Copynumber: 2.4  Consensus size: 23

       4533 GGATGAAAGG

                  *          *     
       4543 TTACTTATTTCTTTATAGCATTA
          1 TTACTTTTTTCTTTATACCATTA

                                 *   
       4566 TTA-TGTTTTTCTTTATAACCTTTA
          1 TTACT-TTTTTCTTTAT-ACCATTA

                     
       4590 TTACTTTTT
          1 TTACTTTTT

       4599 AGTAACCTTA


Statistics
Matches: 27,  Mismatches: 3, Indels: 5
        0.77            0.09        0.14

Matches are distributed among these distances:
  22    1  0.04
  23   13  0.48
  24   12  0.44
  25    1  0.04

ACGTcount: A:0.21, C:0.12, G:0.04, T:0.62


Consensus pattern (23 bp):   
TTACTTTTTTCTTTATACCATTA
Done.