Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023176.1 Corchorus olitorius cultivar O-4 contig23209, 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: 5465
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30


Found at i:76 original size:15 final size:15

Alignment explanation


    Indices: 56--87  Score: 64
    Period size: 15  Copynumber: 2.1  Consensus size: 15

         46 AAACTAAGTG

                           
         56 GAGCTTGTTGATTTT
          1 GAGCTTGTTGATTTT

                           
         71 GAGCTTGTTGATTTT
          1 GAGCTTGTTGATTTT

              
         86 GA
          1 GA

         88 ACCCCCAAGG


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.16, C:0.06, G:0.28, T:0.50


Consensus pattern (15 bp):   
GAGCTTGTTGATTTT

Found at i:910 original size:10 final size:10

Alignment explanation


    Indices: 895--919  Score: 50
    Period size: 10  Copynumber: 2.5  Consensus size: 10

        885 GGTCGAAAAC

                      
        895 TTTTTTTATT
          1 TTTTTTTATT

                      
        905 TTTTTTTATT
          1 TTTTTTTATT

                 
        915 TTTTT
          1 TTTTT

        920 AATATTTTTC


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   15  1.00

ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92


Consensus pattern (10 bp):   
TTTTTTTATT

Found at i:1078 original size:25 final size:24

Alignment explanation


    Indices: 1041--1087  Score: 60
    Period size: 26  Copynumber: 1.9  Consensus size: 24

       1031 CTAGAAAATT

                                      
       1041 TGAAAAACTTTGATGGATGAGATGGA
          1 TGAAAAACTTTGAT-GAT-AGATGGA

                  *               
       1067 TGAAAAGC-TTGATGATAGATG
          1 TGAAAAACTTTGATGATAGATG

       1088 AATAGAAGTA


Statistics
Matches: 20,  Mismatches: 1, Indels: 3
        0.83            0.04        0.12

Matches are distributed among these distances:
  23    5  0.25
  24    3  0.15
  25    5  0.25
  26    7  0.35

ACGTcount: A:0.38, C:0.04, G:0.30, T:0.28


Consensus pattern (24 bp):   
TGAAAAACTTTGATGATAGATGGA

Found at i:3154 original size:28 final size:28

Alignment explanation


    Indices: 3115--3173  Score: 118
    Period size: 28  Copynumber: 2.1  Consensus size: 28

       3105 CAAAGGTTGA

                                        
       3115 TGTTGTTCAAAATTTGCCTTATCCAACT
          1 TGTTGTTCAAAATTTGCCTTATCCAACT

                                        
       3143 TGTTGTTCAAAATTTGCCTTATCCAACT
          1 TGTTGTTCAAAATTTGCCTTATCCAACT

               
       3171 TGT
          1 TGT

       3174 GTTAGATCAT


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  28   31  1.00

ACGTcount: A:0.24, C:0.20, G:0.12, T:0.44


Consensus pattern (28 bp):   
TGTTGTTCAAAATTTGCCTTATCCAACT
Done.