Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018796.1 Corchorus olitorius cultivar O-4 contig18829, 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: 41955
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31


Found at i:1849 original size:21 final size:20

Alignment explanation


    Indices: 1816--1858  Score: 50
    Period size: 21  Copynumber: 2.1  Consensus size: 20

       1806 AAGAATTGTA

                         **     
       1816 GCTTCTTGGAAATGGCTCTT
          1 GCTTCTTGGAAATCCCTCTT

                    *            
       1836 GCTTCCTTTGAAATCCCTCTT
          1 GCTT-CTTGGAAATCCCTCTT

              
       1857 GC
          1 GC

       1859 AATCCTAAAG


Statistics
Matches: 19,  Mismatches: 3, Indels: 1
        0.83            0.13        0.04

Matches are distributed among these distances:
  20    4  0.21
  21   15  0.79

ACGTcount: A:0.14, C:0.28, G:0.19, T:0.40


Consensus pattern (20 bp):   
GCTTCTTGGAAATCCCTCTT

Found at i:3812 original size:76 final size:76

Alignment explanation


    Indices: 3675--3826  Score: 191
    Period size: 76  Copynumber: 2.0  Consensus size: 76

       3665 ACAAGGACCC

                                            *                  *           * 
       3675 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
          1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTAAGCACCCATGTGGTTTGCCTGAGAACCCAGAT

                       
       3740 GGGCAGTGTCA
         66 GGGCAGTGTCA

                    *     *              *                           **      
       3751 CGACTCCAGCTGGGTGCCCACATGGTTTGTCTTAAG-ACCCATGT-GTTTCGCCTGATCACCCAG
          1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTAAGCACCCATGTGGTTT-GCCTGAGAACCCAG

                  *      
       3814 ATGGGCTGTGTCA
         64 ATGGGCAGTGTCA

       3827 TAGCTCATCA


Statistics
Matches: 65,  Mismatches: 9, Indels: 4
        0.83            0.12        0.05

Matches are distributed among these distances:
  75    4  0.06
  76   53  0.82
  77    8  0.12

ACGTcount: A:0.17, C:0.30, G:0.28, T:0.25


Consensus pattern (76 bp):   
CGACTCCACCTGGGCGCCCACATGGTTGCCTTAAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA

Found at i:10807 original size:12 final size:12

Alignment explanation


    Indices: 10790--10819  Score: 51
    Period size: 12  Copynumber: 2.5  Consensus size: 12

      10780 TTTAAATGTT

                        
      10790 TATATTTCTTTA
          1 TATATTTCTTTA

                        
      10802 TATATTTCTTTA
          1 TATATTTCTTTA

            *     
      10814 AATATT
          1 TATATT

      10820 ATCGAATAAT


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  12   17  1.00

ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63


Consensus pattern (12 bp):   
TATATTTCTTTA

Found at i:24740 original size:15 final size:15

Alignment explanation


    Indices: 24720--24752  Score: 66
    Period size: 15  Copynumber: 2.2  Consensus size: 15

      24710 TACATTATAT

                           
      24720 ATTATATTATTTGCA
          1 ATTATATTATTTGCA

                           
      24735 ATTATATTATTTGCA
          1 ATTATATTATTTGCA

               
      24750 ATT
          1 ATT

      24753 TGCAATGATG


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   18  1.00

ACGTcount: A:0.33, C:0.06, G:0.06, T:0.55


Consensus pattern (15 bp):   
ATTATATTATTTGCA
Done.