Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010142.1 Corchorus olitorius cultivar O-4 contig10174, 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: 29523
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30


Found at i:4474 original size:12 final size:12

Alignment explanation


    Indices: 4457--4501  Score: 54
    Period size: 12  Copynumber: 3.8  Consensus size: 12

       4447 GCACAGCCAC

                        
       4457 AAACATGCCTGA
          1 AAACATGCCTGA

                     * *
       4469 AAACATGCCGGG
          1 AAACATGCCTGA

               *        
       4481 AAATATGCCTGA
          1 AAACATGCCTGA

                *    
       4493 AAACCTGCC
          1 AAACATGCC

       4502 GGAAGAAGTA


Statistics
Matches: 26,  Mismatches: 7, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
  12   26  1.00

ACGTcount: A:0.38, C:0.27, G:0.20, T:0.16


Consensus pattern (12 bp):   
AAACATGCCTGA

Found at i:4990 original size:24 final size:24

Alignment explanation


    Indices: 4958--5015  Score: 71
    Period size: 24  Copynumber: 2.4  Consensus size: 24

       4948 ATGAGGATGC

                *           * *     
       4958 AAAGTCTAAAGCAGCAGCTAAAGG
          1 AAAGGCTAAAGCAGCACCCAAAGG

                          *         
       4982 AAAGGCTAAAGCAGTACCCAAAGG
          1 AAAGGCTAAAGCAGCACCCAAAGG

                 *    
       5006 AAAGGGTAAA
          1 AAAGGCTAAA

       5016 CCTCCAAAGA


Statistics
Matches: 29,  Mismatches: 5, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  24   29  1.00

ACGTcount: A:0.48, C:0.16, G:0.26, T:0.10


Consensus pattern (24 bp):   
AAAGGCTAAAGCAGCACCCAAAGG

Found at i:5623 original size:40 final size:40

Alignment explanation


    Indices: 5565--5643  Score: 122
    Period size: 40  Copynumber: 2.0  Consensus size: 40

       5555 AGAATATCTT

                 *      **                   *      
       5565 TTATGTTGTCTTTTATATTTGGTGGTTTGTAAATCAATGA
          1 TTATGATGTCTTGAATATTTGGTGGTTTGTAAAACAATGA

                                                   
       5605 TTATGATGTCTTGAATATTTGGTGGTTTGTAAAACAATG
          1 TTATGATGTCTTGAATATTTGGTGGTTTGTAAAACAATG

       5644 TCTTTTATTG


Statistics
Matches: 35,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  40   35  1.00

ACGTcount: A:0.25, C:0.05, G:0.22, T:0.48


Consensus pattern (40 bp):   
TTATGATGTCTTGAATATTTGGTGGTTTGTAAAACAATGA

Found at i:24892 original size:23 final size:21

Alignment explanation


    Indices: 24854--24899  Score: 56
    Period size: 23  Copynumber: 2.1  Consensus size: 21

      24844 TTTGGAGGGA

                             *   
      24854 GGGAAAGAGGAGGGAATTGGG
          1 GGGAAAGAGGAGGGAATCGGG

                       *           
      24875 GGGAAAGAGAGGGTGGAATCGGG
          1 GGGAAAGAG-GAG-GGAATCGGG

              
      24898 GG
          1 GG

      24900 ATTTGATGGC


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  21    9  0.43
  22    2  0.10
  23   10  0.48

ACGTcount: A:0.30, C:0.02, G:0.59, T:0.09


Consensus pattern (21 bp):   
GGGAAAGAGGAGGGAATCGGG
Done.