Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014165.1 Corchorus capsularis cultivar CVL-1 contig14186, 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: 14270
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


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

Alignment explanation


    Indices: 1--32  Score: 57
    Period size: 2  Copynumber: 16.5  Consensus size: 2

                                                             
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

         33 GTGGCTAGGT


Statistics
Matches: 29,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   28  0.97

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


Consensus pattern (2 bp):   
TA

Found at i:7176 original size:17 final size:17

Alignment explanation


    Indices: 7154--7199  Score: 78
    Period size: 15  Copynumber: 2.8  Consensus size: 17

       7144 TGGGTCTAAT

                             
       7154 AGAAATCTTAGGCATTA
          1 AGAAATCTTAGGCATTA

                             
       7171 AGAAATCTT--GCATTA
          1 AGAAATCTTAGGCATTA

                          
       7186 AGAAATCTTAGGCA
          1 AGAAATCTTAGGCA

       7200 ATTGCATTAA


Statistics
Matches: 27,  Mismatches: 0, Indels: 4
        0.87            0.00        0.13

Matches are distributed among these distances:
  15   15  0.56
  17   12  0.44

ACGTcount: A:0.41, C:0.13, G:0.17, T:0.28


Consensus pattern (17 bp):   
AGAAATCTTAGGCATTA

Found at i:10830 original size:41 final size:42

Alignment explanation


    Indices: 10773--10879  Score: 159
    Period size: 41  Copynumber: 2.6  Consensus size: 42

      10763 ATTTTATTAA

                                        *              
      10773 TTTCCAAAAGTCTTCTCTCTTGGAATT-TTAAAA-ACATTTAC
          1 TTTCCAAAAGTCTT-TCTCTTGGAATTACTAAAACACATTTAC

                                                     *
      10814 TTTCCAAAAGTC-TTCTCTTGGAATTACTAAAACACATTTAT
          1 TTTCCAAAAGTCTTTCTCTTGGAATTACTAAAACACATTTAC

                                      
      10855 TTTCCAAAAGTCTTT-TCTTGGAATT
          1 TTTCCAAAAGTCTTTCTCTTGGAATT

      10880 GCTTAAATAA


Statistics
Matches: 61,  Mismatches: 2, Indels: 6
        0.88            0.03        0.09

Matches are distributed among these distances:
  39   12  0.20
  40    6  0.10
  41   41  0.67
  42    2  0.03

ACGTcount: A:0.31, C:0.19, G:0.08, T:0.42


Consensus pattern (42 bp):   
TTTCCAAAAGTCTTTCTCTTGGAATTACTAAAACACATTTAC

Done.