Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020163.1 Corchorus olitorius cultivar O-4 contig20196, 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: 15164
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:4781 original size:14 final size:14

Alignment explanation


    Indices: 4762--4789  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

       4752 CAACAATCAC

                          
       4762 GTACTTTTATATAT
          1 GTACTTTTATATAT

                          
       4776 GTACTTTTATATAT
          1 GTACTTTTATATAT

       4790 ATTATATGTA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57


Consensus pattern (14 bp):   
GTACTTTTATATAT

Found at i:9530 original size:25 final size:26

Alignment explanation


    Indices: 9495--9571  Score: 106
    Period size: 25  Copynumber: 3.0  Consensus size: 26

       9485 CTGTGCTTAT

                                      
       9495 TTTCTCTCAGGCCCTGCGCCACTTCC
          1 TTTCTCTCAGGCCCTGCGCCACTTCC

                                      
       9521 TTTC-CTCAGGCCCTGCGCCAC-T-C
          1 TTTCTCTCAGGCCCTGCGCCACTTCC

                      *        *       
       9544 TCTTCTCTCAAGCCCTGCGTCACTTCC
          1 T-TTCTCTCAGGCCCTGCGCCACTTCC

             
       9571 T
          1 T

       9572 GCAGCAACCC


Statistics
Matches: 45,  Mismatches: 2, Indels: 7
        0.83            0.04        0.13

Matches are distributed among these distances:
  23    2  0.04
  24    4  0.09
  25   32  0.71
  26    5  0.11
  27    2  0.04

ACGTcount: A:0.09, C:0.45, G:0.14, T:0.31


Consensus pattern (26 bp):   
TTTCTCTCAGGCCCTGCGCCACTTCC

Found at i:11902 original size:31 final size:31

Alignment explanation


    Indices: 11825--11902  Score: 113
    Period size: 30  Copynumber: 2.5  Consensus size: 31

      11815 CCATGTAATT

                           *               
      11825 ACAAGATTGGGTCAAATTAATCCTTGAACTC
          1 ACAAGATTGGGTCAATTTAATCCTTGAACTC

                                      *   *
      11856 ACAAGATT-GGTCAATTTAATCCTTGTACTT
          1 ACAAGATTGGGTCAATTTAATCCTTGAACTC

            *                
      11886 GCAAGATTGGGTCAATT
          1 ACAAGATTGGGTCAATT

      11903 GAGTCCTCAT


Statistics
Matches: 42,  Mismatches: 4, Indels: 2
        0.88            0.08        0.04

Matches are distributed among these distances:
  30   26  0.62
  31   16  0.38

ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Consensus pattern (31 bp):   
ACAAGATTGGGTCAATTTAATCCTTGAACTC
Done.