Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013148.1 Corchorus olitorius cultivar O-4 contig13181, 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: 2148
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30


Found at i:942 original size:14 final size:15

Alignment explanation


    Indices: 923--952  Score: 53
    Period size: 14  Copynumber: 2.1  Consensus size: 15

        913 GATTCCTAAT

                           
        923 AAAACTCAAAA-AAA
          1 AAAACTCAAAAGAAA

                           
        937 AAAACTCAAAAGAAA
          1 AAAACTCAAAAGAAA

             
        952 A
          1 A

        953 TTGTTAGTTG


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14   11  0.73
  15    4  0.27

ACGTcount: A:0.77, C:0.13, G:0.03, T:0.07


Consensus pattern (15 bp):   
AAAACTCAAAAGAAA

Found at i:1158 original size:29 final size:30

Alignment explanation


    Indices: 1075--1161  Score: 79
    Period size: 29  Copynumber: 2.9  Consensus size: 30

       1065 GAAATTTCGT

                      *      *              
       1075 TTTTTTTTTTTAATATATGACGCAAAA-AACG
          1 TTTTTTTTTTCAA-A-ACGACGCAAAACAACG

                       * ** *  *          
       1106 TTTTTTTTTTCGATGCAACACAAAACAA-G
          1 TTTTTTTTTTCAAAACGACGCAAAACAACG

                                       
       1135 TTTTTTTTTTCAAAACGACGCAAAACA
          1 TTTTTTTTTTCAAAACGACGCAAAACA

       1162 CACAAAATTA


Statistics
Matches: 43,  Mismatches: 12, Indels: 4
        0.73            0.20        0.07

Matches are distributed among these distances:
  29   30  0.70
  30    2  0.05
  31   11  0.26

ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40


Consensus pattern (30 bp):   
TTTTTTTTTTCAAAACGACGCAAAACAACG

Found at i:1511 original size:16 final size:15

Alignment explanation


    Indices: 1473--1514  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       1463 ACAGAGGTTG

                       *   
       1473 ACAGAAAACAATTAA
          1 ACAGAAAACAACTAA

                           
       1488 ACAGAAAACAACTAA
          1 ACAGAAAACAACTAA

                        
       1503 ACTAGAAAACAA
          1 AC-AGAAAACAA

       1515 AGCAAAGTAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.67, C:0.17, G:0.07, T:0.10


Consensus pattern (15 bp):   
ACAGAAAACAACTAA
Done.