Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021722.1 Corchorus olitorius cultivar O-4 contig21755, 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: 19263
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34


Found at i:4521 original size:76 final size:76

Alignment explanation


    Indices: 4382--4522  Score: 185
    Period size: 76  Copynumber: 1.9  Consensus size: 76

       4372 TGACAAGGGC

                     *                                     *       *  *      
       4382 CCCGACTCCTCCTAGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTTAAGACCCAG
          1 CCCGACTCCACCTAGGCGCCCACATGGTTGCCTTGAGCACCCATGTGATTTGCCTGAACACCCAG

                       
       4447 CTGGGCAGTGT
         66 CTGGGCAGTGT

                         *  *              *      *                   *      
       4458 CCCGACTCCACCTGGGTGCCCACATGGTTTGTC-TGAGGACCCATGTGATTTGCCTGATCACCCA
          1 CCCGACTCCACCTAGGCGCCCACATGG-TTGCCTTGAGCACCCATGTGATTTGCCTGAACACCCA

             
       4522 G
         65 G

       4523 GTAGGCTGTG


Statistics
Matches: 55,  Mismatches: 9, Indels: 2
        0.83            0.14        0.03

Matches are distributed among these distances:
  76   51  0.93
  77    4  0.07

ACGTcount: A:0.16, C:0.34, G:0.26, T:0.24


Consensus pattern (76 bp):   
CCCGACTCCACCTAGGCGCCCACATGGTTGCCTTGAGCACCCATGTGATTTGCCTGAACACCCAG
CTGGGCAGTGT

Found at i:15568 original size:20 final size:20

Alignment explanation


    Indices: 15543--15581  Score: 69
    Period size: 20  Copynumber: 1.9  Consensus size: 20

      15533 TTCTCTTATA

                       *        
      15543 CGTATTTAAATGAGGGTAAC
          1 CGTATTTAAATAAGGGTAAC

                               
      15563 CGTATTTAAATAAGGGTAA
          1 CGTATTTAAATAAGGGTAA

      15582 TTTGGAAAAC


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  20   18  1.00

ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31


Consensus pattern (20 bp):   
CGTATTTAAATAAGGGTAAC

Found at i:19239 original size:80 final size:80

Alignment explanation


    Indices: 19110--19263  Score: 236
    Period size: 80  Copynumber: 1.9  Consensus size: 80

      19100 TCCCTTTTTT

                 *       *                **                          *      
      19110 TTCTTCGATTCCTCTCTTTAAACCCTCTTCTGCCAAAACCCTAATTTCAAAAACTTTTTATCAAA
          1 TTCTTAGATTCCTATCTTTAAACCCTCTTCCACCAAAACCCTAATTTCAAAAACTTTTCATCAAA

             *             
      19175 CGAAAATCCAATTTC
         66 CAAAAATCCAATTTC

                                    *             *                          
      19190 TTCTTAGATTCCTATCTTTAAACCTTCTTCCACCAAAATCCTAATTTCAAAAACTTTTCATCAAA
          1 TTCTTAGATTCCTATCTTTAAACCCTCTTCCACCAAAACCCTAATTTCAAAAACTTTTCATCAAA

                     
      19255 CAAAAATCC
         66 CAAAAATCC


Statistics
Matches: 66,  Mismatches: 8, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  80   66  1.00

ACGTcount: A:0.34, C:0.28, G:0.03, T:0.36


Consensus pattern (80 bp):   
TTCTTAGATTCCTATCTTTAAACCCTCTTCCACCAAAACCCTAATTTCAAAAACTTTTCATCAAA
CAAAAATCCAATTTC
Done.