Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023425.1 Corchorus olitorius cultivar O-4 contig23458, 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: 9184
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.30


Found at i:1919 original size:2 final size:2

Alignment explanation


    Indices: 1912--1945  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       1902 ATCAATCATA

                                                              
       1912 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

       1946 TGTTTAAGAT


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:3865 original size:34 final size:34

Alignment explanation


    Indices: 3821--3885  Score: 94
    Period size: 34  Copynumber: 1.9  Consensus size: 34

       3811 TGCCATAAAC

                 *       *         *          
       3821 TATATTAGGCCAATAGACCAGAATAGTGCATAGT
          1 TATATCAGGCCAAGAGACCAGAAAAGTGCATAGT

                            *              
       3855 TATATCAGGCCAAGAGGCCAGAAAAGTGCAT
          1 TATATCAGGCCAAGAGACCAGAAAAGTGCAT

       3886 TACATGCTGC


Statistics
Matches: 27,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  34   27  1.00

ACGTcount: A:0.38, C:0.17, G:0.23, T:0.22


Consensus pattern (34 bp):   
TATATCAGGCCAAGAGACCAGAAAAGTGCATAGT

Found at i:6795 original size:21 final size:22

Alignment explanation


    Indices: 6762--6802  Score: 57
    Period size: 21  Copynumber: 1.9  Consensus size: 22

       6752 AGAAACAGTG

                                  
       6762 AAGGATTGAGAAAAAGGGTTAA
          1 AAGGATTGAGAAAAAGGGTTAA

                *        *      
       6784 AAGGTTTG-GAAACAGGGTT
          1 AAGGATTGAGAAAAAGGGTT

       6803 TGTGTTTTTT


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  21   10  0.59
  22    7  0.41

ACGTcount: A:0.41, C:0.02, G:0.34, T:0.22


Consensus pattern (22 bp):   
AAGGATTGAGAAAAAGGGTTAA
Done.