Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013860.1 Corchorus olitorius cultivar O-4 contig13893, 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: 4776
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31


Found at i:2524 original size:26 final size:26

Alignment explanation


    Indices: 2477--2544  Score: 84
    Period size: 27  Copynumber: 2.6  Consensus size: 26

       2467 CACGCGCGAT

                 *           *         
       2477 GTCACATGTGGAGGTGTCCG-TTGGAG
          1 GTCACGTGT-GAGGTGTACGTTTGGAG

                                       
       2503 GTCACGTGTGAGGTCGTACGTTTGGAG
          1 GTCACGTGTGAGGT-GTACGTTTGGAG

                      *    
       2530 GTCACGTGTGGGGTG
          1 GTCACGTGTGAGGTG

       2545 CCAGCTGGTT


Statistics
Matches: 37,  Mismatches: 3, Indels: 4
        0.84            0.07        0.09

Matches are distributed among these distances:
  25    5  0.14
  26   13  0.35
  27   19  0.51

ACGTcount: A:0.13, C:0.15, G:0.44, T:0.28


Consensus pattern (26 bp):   
GTCACGTGTGAGGTGTACGTTTGGAG

Found at i:2658 original size:24 final size:22

Alignment explanation


    Indices: 2626--2730  Score: 81
    Period size: 23  Copynumber: 4.7  Consensus size: 22

       2616 TTGTGGTCAC

                            *       
       2626 AAGTGGTCGAGCGCCGCGATATGG
          1 AAGTGGTCG-GCGCC-AGATATGG

                               *   
       2650 AAGTGGTCGGTCGCCAGATTTGG
          1 AAGTGGTCGG-CGCCAGATATGG

                            *     
       2673 AAGTGGTCGG-G-C-GCTATGG
          1 AAGTGGTCGGCGCCAGATATGG

              * *            * *   
       2692 AAATAGTCGGTCGCCAGGTTTGG
          1 AAGTGGTCGG-CGCCAGATATGG

                            
       2715 AAGTGGTCGGGCGCCA
          1 AAGTGGTC-GGCGCCA

       2731 AGCAATTATG


Statistics
Matches: 65,  Mismatches: 10, Indels: 13
        0.74            0.11        0.15

Matches are distributed among these distances:
  19   13  0.20
  20    1  0.02
  21    2  0.03
  22    1  0.02
  23   33  0.51
  24   15  0.23

ACGTcount: A:0.19, C:0.19, G:0.41, T:0.21


Consensus pattern (22 bp):   
AAGTGGTCGGCGCCAGATATGG

Found at i:2677 original size:23 final size:23

Alignment explanation


    Indices: 2647--2730  Score: 86
    Period size: 23  Copynumber: 3.8  Consensus size: 23

       2637 CGCCGCGATA

                                   
       2647 TGGAAGTGGTCGGTCGCCAGATT
          1 TGGAAGTGGTCGGTCGCCAGATT

                                * *
       2670 TGGAAGTGGTCGG--G-C-GCTA
          1 TGGAAGTGGTCGGTCGCCAGATT

                 * *            *  
       2689 TGGAAATAGTCGGTCGCCAGGTT
          1 TGGAAGTGGTCGGTCGCCAGATT

                         *     
       2712 TGGAAGTGGTCGGGCGCCA
          1 TGGAAGTGGTCGGTCGCCA

       2731 AGCAATTATG


Statistics
Matches: 48,  Mismatches: 9, Indels: 8
        0.74            0.14        0.12

Matches are distributed among these distances:
  19   13  0.27
  20    1  0.02
  21    2  0.04
  22    1  0.02
  23   31  0.65

ACGTcount: A:0.18, C:0.18, G:0.42, T:0.23


Consensus pattern (23 bp):   
TGGAAGTGGTCGGTCGCCAGATT

Found at i:2704 original size:42 final size:42

Alignment explanation


    Indices: 2645--2728  Score: 141
    Period size: 42  Copynumber: 2.0  Consensus size: 42

       2635 AGCGCCGCGA

                   * *                                
       2645 TATGGAAGTGGTCGGTCGCCAGATTTGGAAGTGGTCGGGCGC
          1 TATGGAAATAGTCGGTCGCCAGATTTGGAAGTGGTCGGGCGC

                                  *                   
       2687 TATGGAAATAGTCGGTCGCCAGGTTTGGAAGTGGTCGGGCGC
          1 TATGGAAATAGTCGGTCGCCAGATTTGGAAGTGGTCGGGCGC

       2729 CAAGCAATTA


Statistics
Matches: 39,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  42   39  1.00

ACGTcount: A:0.18, C:0.17, G:0.42, T:0.24


Consensus pattern (42 bp):   
TATGGAAATAGTCGGTCGCCAGATTTGGAAGTGGTCGGGCGC
Done.