Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008059.1 Corchorus olitorius cultivar O-4 contig08086, 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, 627

Length: 1046
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36


Found at i:703 original size:41 final size:41

Alignment explanation


    Indices: 632--873  Score: 308
    Period size: 41  Copynumber: 5.9  Consensus size: 41

        622 GTTTGATTTG

                *                       *           * 
        632 ATTTGATTCAAGGG--TCGAATGACTTGGTCTTGAATTGACA
          1 ATTTAATTCAAGGGTCTCG-ATGACTTGATCTTGAATTGATA

              *              *  *      *             
        672 ATCTAATTCAAGGGTCTTGACGACTTGGTCTTGAATTGATA
          1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA

                   *                      *             
        713 ATAATTCGATTCAAGGGTCTCGATGACTTGTTCTTGAATTGATA
          1 AT--TT-AATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA

                        *            **              
        757 ATTTAATTCAAGAGTCTCGATGACTCAATCTTGAATTGATA
          1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA

                                     **              
        798 ATTTAATTCAAGGGTCTCGATGACTCAATCTTGAATTGATA
          1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA

                                               
        839 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAA
          1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAA

        874 CAAACGAAAA


Statistics
Matches: 179,  Mismatches: 18, Indels: 9
        0.87            0.09        0.04

Matches are distributed among these distances:
  40   12  0.07
  41  127  0.71
  42    4  0.02
  43    1  0.01
  44   35  0.20

ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37


Consensus pattern (41 bp):   
ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA

Found at i:990 original size:16 final size:16

Alignment explanation


    Indices: 969--1003  Score: 70
    Period size: 16  Copynumber: 2.2  Consensus size: 16

        959 TCTGAAAATA

                            
        969 CTTCAGAGCTTTTCTG
          1 CTTCAGAGCTTTTCTG

                            
        985 CTTCAGAGCTTTTCTG
          1 CTTCAGAGCTTTTCTG

               
       1001 CTT
          1 CTT

       1004 TCTGAATTGT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   19  1.00

ACGTcount: A:0.11, C:0.26, G:0.17, T:0.46


Consensus pattern (16 bp):   
CTTCAGAGCTTTTCTG
Done.