Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000539.1 Corchorus olitorius cultivar O-4 contig00539, 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, 751

Length: 1253
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.32


Found at i:97 original size:15 final size:15

Alignment explanation


    Indices: 77--108  Score: 55
    Period size: 15  Copynumber: 2.1  Consensus size: 15

         67 AAACTAAGTG

                           
         77 GAGCTTGTCGATTTT
          1 GAGCTTGTCGATTTT

                    *      
         92 GAGCTTGTTGATTTT
          1 GAGCTTGTCGATTTT

              
        107 GA
          1 GA

        109 AACCCCAAGG


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.16, C:0.09, G:0.28, T:0.47


Consensus pattern (15 bp):   
GAGCTTGTCGATTTT

Found at i:909 original size:10 final size:9

Alignment explanation


    Indices: 893--917  Score: 50
    Period size: 9  Copynumber: 2.8  Consensus size: 9

        883 TCTGGTCAAA

                     
        893 ATTTTTTTT
          1 ATTTTTTTT

                     
        902 ATTTTTTTT
          1 ATTTTTTTT

                   
        911 ATTTTTT
          1 ATTTTTT

        918 GATATTTTTC


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   16  1.00

ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88


Consensus pattern (9 bp):   
ATTTTTTTT

Found at i:1076 original size:25 final size:24

Alignment explanation


    Indices: 1039--1085  Score: 69
    Period size: 26  Copynumber: 1.9  Consensus size: 24

       1029 CTAGAAAATT

                                      
       1039 TGAAAAACTTTGATGGATGAGATGGA
          1 TGAAAAACTTTGAT-GAT-AGATGGA

                                  
       1065 TGAAAAAC-TTGATGATAGATG
          1 TGAAAAACTTTGATGATAGATG

       1086 AATAGAAGGA


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  23    5  0.24
  24    3  0.14
  25    5  0.24
  26    8  0.38

ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28


Consensus pattern (24 bp):   
TGAAAAACTTTGATGATAGATGGA
Done.