Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023183.1 Corchorus olitorius cultivar O-4 contig23216, 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: 24922
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31


Found at i:609 original size:38 final size:39

Alignment explanation


    Indices: 522--630  Score: 152
    Period size: 39  Copynumber: 2.9  Consensus size: 39

        512 GGCTGTGCAT

                   *   *      **          *        
        522 AGTGGACTCGTACCTCAGTTGGTTAAACTGATGGTAAAG
          1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGGTAAAG

                                                   
        561 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGGT-AAG
          1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGGTAAAG

                                              
        599 AGTGGACCCGTGCCTCA-GGGGTT-AACTGTTGG
          1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGG

        631 CTAGACTCGA


Statistics
Matches: 65,  Mismatches: 5, Indels: 3
        0.89            0.07        0.04

Matches are distributed among these distances:
  36    9  0.14
  37    6  0.09
  38   20  0.31
  39   30  0.46

ACGTcount: A:0.22, C:0.18, G:0.34, T:0.26


Consensus pattern (39 bp):   
AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGGTAAAG

Found at i:14759 original size:38 final size:38

Alignment explanation


    Indices: 14672--14764  Score: 125
    Period size: 38  Copynumber: 2.4  Consensus size: 38

      14662 AATGGCCGAT

                                                  
      14672 AGAGACATAAGCAGGTTTGATTAAACGACACCCTAAAC
          1 AGAGACATAAGCAGGTTTGATTAAACGACACCCTAAAC

               *                            *    * 
      14710 AGATACATAAGCAGGTTTGATTAAACGA-AGCTCTAAGC
          1 AGAGACATAAGCAGGTTTGATTAAACGACA-CCCTAAAC

                * *          
      14748 AGAGGCCTAAGCAGGTT
          1 AGAGACATAAGCAGGTT

      14765 CACTGAAATG


Statistics
Matches: 48,  Mismatches: 6, Indels: 2
        0.86            0.11        0.04

Matches are distributed among these distances:
  37    1  0.02
  38   47  0.98

ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20


Consensus pattern (38 bp):   
AGAGACATAAGCAGGTTTGATTAAACGACACCCTAAAC

Found at i:21342 original size:76 final size:76

Alignment explanation


    Indices: 21192--21335  Score: 177
    Period size: 76  Copynumber: 1.9  Consensus size: 76

      21182 ACAAGGACCC

                    *                                          *           * 
      21192 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
          1 CGACTCCAACTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT

                       
      21257 GGGTAGTGTCA
         66 GGGTAGTGTCA

                          *              *                            **     
      21268 CGACTCCAACTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
          1 CGACTCCAACTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA

                  
      21330 GATGGG
         63 GATGGG

      21336 CTGTGTCGTA


Statistics
Matches: 58,  Mismatches: 7, Indels: 6
        0.82            0.10        0.08

Matches are distributed among these distances:
  75    4  0.07
  76   48  0.83
  77    6  0.10

ACGTcount: A:0.18, C:0.29, G:0.28, T:0.24


Consensus pattern (76 bp):   
CGACTCCAACTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGTAGTGTCA

Found at i:23488 original size:18 final size:18

Alignment explanation


    Indices: 23465--23499  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

      23455 TCTTCATCAA

                              
      23465 CTTCCAAAGGTGGTTGTC
          1 CTTCCAAAGGTGGTTGTC

                  * *        
      23483 CTTCCACATGTGGTTGT
          1 CTTCCAAAGGTGGTTGT

      23500 TCAAGTCCTT


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   15  1.00

ACGTcount: A:0.14, C:0.23, G:0.26, T:0.37


Consensus pattern (18 bp):   
CTTCCAAAGGTGGTTGTC
Done.