Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01002846.1 Corchorus capsularis cultivar CVL-1 contig02854, 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: 1986
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30


Found at i:641 original size:30 final size:31

Alignment explanation


    Indices: 600--685  Score: 102
    Period size: 33  Copynumber: 2.7  Consensus size: 31

        590 TCTTTCTCGT

                         *  *               
        600 CACCTAAAACAGATTTATTTTCAATGCTA-TC
          1 CACC-AAAACAGAATTGTTTTCAATGCTACTC

                                *            
        631 CACCAAAACAGAATTGTTTTTAATGCTACGTTC
          1 CACCAAAACAGAATTGTTTTCAATGCTAC--TC

            *                     
        664 AACCAAAACAGAATTGTTTTCA
          1 CACCAAAACAGAATTGTTTTCA

        686 TCACAATTAG


Statistics
Matches: 47,  Mismatches: 5, Indels: 4
        0.84            0.09        0.07

Matches are distributed among these distances:
  30   21  0.45
  31    4  0.09
  33   22  0.47

ACGTcount: A:0.37, C:0.21, G:0.09, T:0.33


Consensus pattern (31 bp):   
CACCAAAACAGAATTGTTTTCAATGCTACTC

Found at i:746 original size:33 final size:33

Alignment explanation


    Indices: 721--829  Score: 148
    Period size: 33  Copynumber: 3.3  Consensus size: 33

        711 TAGTTTTATT

                                             
        721 GCAAACAACACTCAAATTAGGTTTAGTATCATC
          1 GCAAACAACACTCAAATTAGGTTTAGTATCATC

                             **  *      *    *
        754 GCAAACAACA-TCTAAAACAGATTTAGTGTCATT
          1 GCAAACAACACTC-AAATTAGGTTTAGTATCATC

                           *                 
        787 GCAAACAACACTCAATTTAGGTTTAGTATCATC
          1 GCAAACAACACTCAAATTAGGTTTAGTATCATC

                      
        820 GCAAACAACA
          1 GCAAACAACA

        830 TCTAAAAGAC


Statistics
Matches: 63,  Mismatches: 11, Indels: 4
        0.81            0.14        0.05

Matches are distributed among these distances:
  32    2  0.03
  33   59  0.94
  34    2  0.03

ACGTcount: A:0.41, C:0.21, G:0.12, T:0.26


Consensus pattern (33 bp):   
GCAAACAACACTCAAATTAGGTTTAGTATCATC

Found at i:753 original size:66 final size:66

Alignment explanation


    Indices: 696--836  Score: 219
    Period size: 66  Copynumber: 2.1  Consensus size: 66

        686 TCACAATTAG

                               * *                                    *      
        696 CATCCAAAACAGATTTAGTTTTATTGCAAACAACACTCAAATTAGGTTTAGTATCATCGCAAACA
          1 CATCCAAAACAGATTTAGTGTCATTGCAAACAACACTCAAATTAGGTTTAGTATCATCACAAACA

             
        761 A
         66 A

                *                                   *                 *      
        762 CATCTAAAACAGATTTAGTGTCATTGCAAACAACACTCAATTTAGGTTTAGTATCATCGCAAACA
          1 CATCCAAAACAGATTTAGTGTCATTGCAAACAACACTCAAATTAGGTTTAGTATCATCACAAACA

             
        827 A
         66 A

                *    
        828 CATCTAAAA
          1 CATCCAAAA

        837 GACTCTTTTC


Statistics
Matches: 71,  Mismatches: 4, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  66   71  1.00

ACGTcount: A:0.41, C:0.20, G:0.11, T:0.28


Consensus pattern (66 bp):   
CATCCAAAACAGATTTAGTGTCATTGCAAACAACACTCAAATTAGGTTTAGTATCATCACAAACA
A
Done.