Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014144.1 Corchorus olitorius cultivar O-4 contig14177, 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: 19606
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--34  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

                                                              
          1 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

         35 TAAAACAAAA


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:3898 original size:15 final size:16

Alignment explanation


    Indices: 3865--3904  Score: 55
    Period size: 15  Copynumber: 2.6  Consensus size: 16

       3855 TTTGTTTGTT

                            
       3865 TTGTTTTCTAGTATAA
          1 TTGTTTTCTAGTATAA

                        *   
       3881 TTGTTTTCT-GTTTAA
          1 TTGTTTTCTAGTATAA

               *     
       3896 TTGCTTTCT
          1 TTGTTTTCT

       3905 TTCAACCTCT


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  15   13  0.59
  16    9  0.41

ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62


Consensus pattern (16 bp):   
TTGTTTTCTAGTATAA

Found at i:8047 original size:28 final size:28

Alignment explanation


    Indices: 7959--8037  Score: 140
    Period size: 28  Copynumber: 2.8  Consensus size: 28

       7949 GGGTCACTTA

                     *                  
       7959 AGGGGCATTCTGGTCATTTTACATGTCC
          1 AGGGGCATTTTGGTCATTTTACATGTCC

                                *       
       7987 AGGGGCATTTTGGTCATTTTGCATGTCC
          1 AGGGGCATTTTGGTCATTTTACATGTCC

                                   
       8015 AGGGGCATTTTGGTCATTTTACA
          1 AGGGGCATTTTGGTCATTTTACA

       8038 CATCTAGGGG


Statistics
Matches: 48,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  28   48  1.00

ACGTcount: A:0.18, C:0.18, G:0.27, T:0.38


Consensus pattern (28 bp):   
AGGGGCATTTTGGTCATTTTACATGTCC

Found at i:12872 original size:20 final size:20

Alignment explanation


    Indices: 12843--12901  Score: 100
    Period size: 20  Copynumber: 3.0  Consensus size: 20

      12833 GTTGAAGTGG

                 *              
      12843 CATAGCTGCGGCAGAGACAA
          1 CATAGTTGCGGCAGAGACAA

                                
      12863 CATAGTTGCGGCAGAGACAA
          1 CATAGTTGCGGCAGAGACAA

                       *       
      12883 CATAGTTGCGGTAGAGACA
          1 CATAGTTGCGGCAGAGACA

      12902 GAAGCATGGC


Statistics
Matches: 37,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  20   37  1.00

ACGTcount: A:0.34, C:0.20, G:0.31, T:0.15


Consensus pattern (20 bp):   
CATAGTTGCGGCAGAGACAA
Done.