Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020883.1 Corchorus olitorius cultivar O-4 contig20916, 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, 609

Length: 1016
ACGTcount: A:0.12, C:0.25, G:0.21, T:0.43


Found at i:706 original size:34 final size:34

Alignment explanation


    Indices: 668--807  Score: 163
    Period size: 34  Copynumber: 3.8  Consensus size: 34

        658 AGCACCACTG

                                              
        668 TGTCTTCTCGTGTACCTTCGTGTCTGTCTTCCTC
          1 TGTCTTCTCGTGTACCTTCGTGTCTGTCTTCCTC

                   *                          
        702 TGTCTTCCCGTGTACCTTCGTGTCTGTCTTCCTC
          1 TGTCTTCTCGTGTACCTTCGTGTCTGTCTTCCTC

                                                         
        736 TGTCTTCTCGTGTACTGCTGGTGTACCTTCGTGTCTGTCTTCCTC
          1 TG-----TC-T-T-CT-C--GTGTACCTTCGTGTCTGTCTTCCTC

                                  *    
        781 TGTCTTCTCGTGTACCTTCGTGCCTGT
          1 TGTCTTCTCGTGTACCTTCGTGTCTGT

        808 TGGCCTCACC


Statistics
Matches: 92,  Mismatches: 3, Indels: 22
        0.79            0.03        0.19

Matches are distributed among these distances:
  34   52  0.57
  36    1  0.01
  37    2  0.02
  38    1  0.01
  39    3  0.03
  40    3  0.03
  41    1  0.01
  42    1  0.01
  43    1  0.01
  45   27  0.29

ACGTcount: A:0.04, C:0.31, G:0.20, T:0.45


Consensus pattern (34 bp):   
TGTCTTCTCGTGTACCTTCGTGTCTGTCTTCCTC

Found at i:727 original size:24 final size:24

Alignment explanation


    Indices: 700--778  Score: 71
    Period size: 24  Copynumber: 3.4  Consensus size: 24

        690 TCTGTCTTCC

                                    
        700 TCTGTCTTCCCGTGTACCTTCGTG
          1 TCTGTCTTCCCGTGTACCTTCGTG

                              *       
        724 TCTGTCTTCCTC-TGT-CTTCTCGTG
          1 TCTGTCTTCC-CGTGTACCT-TCGTG

                       *             
        748 TACTG-C-T--GGTGTACCTTCGTG
          1 T-CTGTCTTCCCGTGTACCTTCGTG

                      
        769 TCTGTCTTCC
          1 TCTGTCTTCC

        779 TCTGTCTTCT


Statistics
Matches: 43,  Mismatches: 3, Indels: 18
        0.67            0.05        0.28

Matches are distributed among these distances:
  20    3  0.07
  21   10  0.23
  22    3  0.07
  23    3  0.07
  24   20  0.47
  25    4  0.09

ACGTcount: A:0.04, C:0.32, G:0.20, T:0.44


Consensus pattern (24 bp):   
TCTGTCTTCCCGTGTACCTTCGTG

Found at i:923 original size:62 final size:62

Alignment explanation


    Indices: 774--1016  Score: 443
    Period size: 62  Copynumber: 3.9  Consensus size: 62

        764 TCGTGTCTGT

                                                     *                    
        774 CTTCCTCTGTCTTCTCGTGTACCTTCGTGCCTGTTGGCCTCACCTCCTGCGG-GGCCTCTTC
          1 CTTCCTCTGTCTTCTCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCTTC

                      *                                                   
        835 CTTCCTCTGTGTTCTCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCTTC
          1 CTTCCTCTGTCTTCTCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCTTC

                            *                                             
        897 CTTCCTCTGTCTTCTCATGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCTTC
          1 CTTCCTCTGTCTTCTCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCTTC

                                             *                        
        959 CTTCCTCTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCT
          1 CTTCCTCTGTCTTCTCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCT


Statistics
Matches: 175,  Mismatches: 6, Indels: 1
        0.96            0.03        0.01

Matches are distributed among these distances:
  61   50  0.29
  62  125  0.71

ACGTcount: A:0.04, C:0.39, G:0.23, T:0.35


Consensus pattern (62 bp):   
CTTCCTCTGTCTTCTCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCTTC

Done.