Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015584.1 Corchorus capsularis cultivar CVL-1 contig15605, 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: 13182
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35


Found at i:6161 original size:29 final size:29

Alignment explanation


    Indices: 6119--6177  Score: 118
    Period size: 29  Copynumber: 2.0  Consensus size: 29

       6109 AGCAAGTCGG

                                         
       6119 GACTCTTCATCAAGCATCTGTTATATGAT
          1 GACTCTTCATCAAGCATCTGTTATATGAT

                                         
       6148 GACTCTTCATCAAGCATCTGTTATATGAT
          1 GACTCTTCATCAAGCATCTGTTATATGAT

             
       6177 G
          1 G

       6178 TTCTAAAATG


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  29   30  1.00

ACGTcount: A:0.27, C:0.20, G:0.15, T:0.37


Consensus pattern (29 bp):   
GACTCTTCATCAAGCATCTGTTATATGAT

Found at i:10153 original size:3 final size:3

Alignment explanation


    Indices: 10147--10174  Score: 56
    Period size: 3  Copynumber: 9.3  Consensus size: 3

      10137 GAAGAAGAGG

                                                 
      10147 GTT GTT GTT GTT GTT GTT GTT GTT GTT G
          1 GTT GTT GTT GTT GTT GTT GTT GTT GTT G

      10175 GTTGGAAAGG


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   25  1.00

ACGTcount: A:0.00, C:0.00, G:0.36, T:0.64


Consensus pattern (3 bp):   
GTT

Found at i:12762 original size:4 final size:4

Alignment explanation


    Indices: 12753--12780  Score: 56
    Period size: 4  Copynumber: 7.0  Consensus size: 4

      12743 TAGTTGATTA

                                              
      12753 TTAG TTAG TTAG TTAG TTAG TTAG TTAG
          1 TTAG TTAG TTAG TTAG TTAG TTAG TTAG

      12781 ATTGTTAATA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   24  1.00

ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50


Consensus pattern (4 bp):   
TTAG

Found at i:12969 original size:60 final size:60

Alignment explanation


    Indices: 12846--12971  Score: 146
    Period size: 60  Copynumber: 2.1  Consensus size: 60

      12836 ATGATAAGCG

                *              *                  *             * *     
      12846 ACAAAAACTAATAGTACAGGGACCCATATGACCCAAAATTTTGTACAGAGACTTGTTTAC
          1 ACAATAACTAATAGTACAGAGACCCATATGACCCAAAAGTTTGTACAGAGACGTATTTAC

                            * *    *          *                        * 
      12906 ACAATAACTAATAGTATATAGACTCATATGACCCGAAAGTTTGTACA-AGAACGTATTTGC
          1 ACAATAACTAATAGTACAGAGACCCATATGACCCAAAAGTTTGTACAGAG-ACGTATTTAC

                  
      12966 ACAATA
          1 ACAATA

      12972 CTTGATAGTA


Statistics
Matches: 55,  Mismatches: 10, Indels: 2
        0.82            0.15        0.03

Matches are distributed among these distances:
  59    2  0.04
  60   53  0.96

ACGTcount: A:0.41, C:0.18, G:0.14, T:0.26


Consensus pattern (60 bp):   
ACAATAACTAATAGTACAGAGACCCATATGACCCAAAAGTTTGTACAGAGACGTATTTAC
Done.