Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002424.1 Corchorus olitorius cultivar O-4 contig02424, 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: 3819
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38


Found at i:1715 original size:40 final size:40

Alignment explanation


    Indices: 1670--1746  Score: 136
    Period size: 40  Copynumber: 1.9  Consensus size: 40

       1660 TTCTGATTTG

                                        *           
       1670 ATTCTAAATTCTAATTTCTAACTTATAACTTGGTTTCCGA
          1 ATTCTAAATTCTAATTTCTAACTTATAAATTGGTTTCCGA

                   *                             
       1710 ATTCTAATTTCTAATTTCTAACTTATAAATTGGTTTC
          1 ATTCTAAATTCTAATTTCTAACTTATAAATTGGTTTC

       1747 TGATTTCTGA


Statistics
Matches: 35,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  40   35  1.00

ACGTcount: A:0.30, C:0.16, G:0.06, T:0.48


Consensus pattern (40 bp):   
ATTCTAAATTCTAATTTCTAACTTATAAATTGGTTTCCGA

Found at i:1871 original size:34 final size:35

Alignment explanation


    Indices: 1831--1896  Score: 98
    Period size: 34  Copynumber: 1.9  Consensus size: 35

       1821 TATAACTTGG

                        *         *            
       1831 TTTCTGATTTCTGATATG-CTGCATTCTGATGTGA
          1 TTTCTGATTTCTAATATGTCTGAATTCTGATGTGA

                           *                
       1865 TTTCTGATTTCTAATCTGTCTGAATTCTGATG
          1 TTTCTGATTTCTAATATGTCTGAATTCTGATG

       1897 CATTTGCCTA


Statistics
Matches: 28,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  34   16  0.57
  35   12  0.43

ACGTcount: A:0.18, C:0.15, G:0.18, T:0.48


Consensus pattern (35 bp):   
TTTCTGATTTCTAATATGTCTGAATTCTGATGTGA

Found at i:3785 original size:2 final size:2

Alignment explanation


    Indices: 3778--3819  Score: 84
    Period size: 2  Copynumber: 21.0  Consensus size: 2

       3768 AAGGCAGATC

                                                                          
       3778 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT


Statistics
Matches: 40,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   40  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.