Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006177.1 Corchorus olitorius cultivar O-4 contig06202, 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: 1934
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32


Found at i:961 original size:15 final size:15

Alignment explanation


    Indices: 941--981  Score: 66
    Period size: 14  Copynumber: 2.8  Consensus size: 15

        931 AACATAATTA

                          *
        941 AAAACATTTTTTTTT
          1 AAAACATTTTTTTTG

                           
        956 AAAACA-TTTTTTTG
          1 AAAACATTTTTTTTG

                        
        970 AAAACATTTTTT
          1 AAAACATTTTTT

        982 ATTACATCTT


Statistics
Matches: 24,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  14   13  0.54
  15   11  0.46

ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54


Consensus pattern (15 bp):   
AAAACATTTTTTTTG

Found at i:1039 original size:16 final size:17

Alignment explanation


    Indices: 998--1041  Score: 54
    Period size: 16  Copynumber: 2.6  Consensus size: 17

        988 TCTTTTAATT

                             *
        998 TTCTGTTTTTTCCATTTT
          1 TTCT-TTTTTTCCATTTC

               *             
       1016 TTCATTTTTTCC-TTTC
          1 TTCTTTTTTTCCATTTC

                      
       1032 TTCTTTTTTT
          1 TTCTTTTTTT

       1042 TCTTCGACTT


Statistics
Matches: 23,  Mismatches: 3, Indels: 2
        0.82            0.11        0.07

Matches are distributed among these distances:
  16   12  0.52
  17    8  0.35
  18    3  0.13

ACGTcount: A:0.05, C:0.18, G:0.02, T:0.75


Consensus pattern (17 bp):   
TTCTTTTTTTCCATTTC

Found at i:1041 original size:17 final size:18

Alignment explanation


    Indices: 998--1043  Score: 51
    Period size: 17  Copynumber: 2.7  Consensus size: 18

        988 TCTTTTAATT

                *            *
        998 TTCTGTTTTTTCCATTTT
          1 TTCTATTTTTTCCATTTC

                              
       1016 TTC-ATTTTTTCC-TTTC
          1 TTCTATTTTTTCCATTTC

                *       
       1032 TTCTTTTTTTTC
          1 TTCTATTTTTTC

       1044 TTCGACTTTG


Statistics
Matches: 24,  Mismatches: 3, Indels: 3
        0.80            0.10        0.10

Matches are distributed among these distances:
  16    6  0.25
  17   15  0.62
  18    3  0.12

ACGTcount: A:0.04, C:0.20, G:0.02, T:0.74


Consensus pattern (18 bp):   
TTCTATTTTTTCCATTTC
Done.