Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012016.1 Corchorus olitorius cultivar O-4 contig12049, 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: 5769
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31


Found at i:1241 original size:15 final size:14

Alignment explanation


    Indices: 1223--1252  Score: 51
    Period size: 15  Copynumber: 2.1  Consensus size: 14

       1213 TAATTTTCAA

                           
       1223 TAAAATAAAATATAT
          1 TAAAATAAAA-ATAT

                          
       1238 TAAAATAAAAATAT
          1 TAAAATAAAAATAT

             
       1252 T
          1 T

       1253 TATTTTTATT


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

Matches are distributed among these distances:
  14    5  0.33
  15   10  0.67

ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33


Consensus pattern (14 bp):   
TAAAATAAAAATAT

Found at i:3864 original size:45 final size:45

Alignment explanation


    Indices: 3815--3944  Score: 190
    Period size: 45  Copynumber: 2.9  Consensus size: 45

       3805 AGATCTTTTC

                     *                                 * 
       3815 TTTGTTTGTAAAGGAGAAGATTCTGATTTTGTTCTTGATGAAGGA
          1 TTTGTTTGTGAAGGAGAAGATTCTGATTTTGTTCTTGATGAAGAA

                                                         
       3860 TTTGTTTGTGAAGGAGAAGATTCTGATTTTGTTCTTGATGAAGAA
          1 TTTGTTTGTGAAGGAGAAGATTCTGATTTTGTTCTTGATGAAGAA

                       *     *  *     *              
       3905 TTTGTTTGTGAGGGAGAGGAGTCTGAGTTTG-TCATTGATG
          1 TTTGTTTGTGAAGGAGAAGATTCTGATTTTGTTC-TTGATG

       3945 GAAAAAGATT


Statistics
Matches: 78,  Mismatches: 6, Indels: 2
        0.91            0.07        0.02

Matches are distributed among these distances:
  44    2  0.03
  45   76  0.97

ACGTcount: A:0.24, C:0.05, G:0.30, T:0.42


Consensus pattern (45 bp):   
TTTGTTTGTGAAGGAGAAGATTCTGATTTTGTTCTTGATGAAGAA
Done.