Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018430.1 Corchorus olitorius cultivar O-4 contig18463, 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: 7478
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.35


Found at i:1825 original size:5 final size:5

Alignment explanation


    Indices: 1817--1850  Score: 68
    Period size: 5  Copynumber: 6.8  Consensus size: 5

       1807 CTACTTTTCT

                                                    
       1817 TTTAG TTTAG TTTAG TTTAG TTTAG TTTAG TTTA
          1 TTTAG TTTAG TTTAG TTTAG TTTAG TTTAG TTTA

       1851 TTATTTTTAT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   29  1.00

ACGTcount: A:0.21, C:0.00, G:0.18, T:0.62


Consensus pattern (5 bp):   
TTTAG

Found at i:4721 original size:14 final size:15

Alignment explanation


    Indices: 4702--4730  Score: 51
    Period size: 14  Copynumber: 2.0  Consensus size: 15

       4692 ATAGTTAGTT

                           
       4702 TTTCTTTTTC-TTTA
          1 TTTCTTTTTCGTTTA

                           
       4716 TTTCTTTTTCGTTTA
          1 TTTCTTTTTCGTTTA

       4731 GCATTTAGTT


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  14   10  0.71
  15    4  0.29

ACGTcount: A:0.07, C:0.14, G:0.03, T:0.76


Consensus pattern (15 bp):   
TTTCTTTTTCGTTTA

Found at i:6524 original size:22 final size:22

Alignment explanation


    Indices: 6496--6539  Score: 63
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       6486 TTTTCCTGTT

                                   
       6496 TCAACCTTCATCGGGGTC-AAAC
          1 TCAACCTTC-TCGGGGTCTAAAC

                       *          
       6518 TCAACCTTCTCTGGGTCTAAAC
          1 TCAACCTTCTCGGGGTCTAAAC

       6540 AGGATTGGAA


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  21    7  0.35
  22   13  0.65

ACGTcount: A:0.25, C:0.32, G:0.16, T:0.27


Consensus pattern (22 bp):   
TCAACCTTCTCGGGGTCTAAAC
Done.