Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017158.1 Corchorus olitorius cultivar O-4 contig17191, 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: 5729
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33


Found at i:804 original size:21 final size:21

Alignment explanation


    Indices: 771--810  Score: 55
    Period size: 21  Copynumber: 1.9  Consensus size: 21

        761 GCGTTTTATT

                                 
        771 CTTGTCAACTCTTT-AACTTC
          1 CTTGTCAACTCTTTCAACTTC

                    *           
        791 CTTGTTCATCTCTTTCAACT
          1 CTTG-TCAACTCTTTCAACT

        811 CAAACGATTA


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

Matches are distributed among these distances:
  20    4  0.24
  21    9  0.53
  22    4  0.24

ACGTcount: A:0.17, C:0.30, G:0.05, T:0.47


Consensus pattern (21 bp):   
CTTGTCAACTCTTTCAACTTC

Found at i:3257 original size:15 final size:15

Alignment explanation


    Indices: 3199--3258  Score: 57
    Period size: 15  Copynumber: 4.0  Consensus size: 15

       3189 GGGTTGGTAT

                       *   
       3199 GGCATAGGTGGCAAC
          1 GGCATAGGTGGAAAC

                  * *   *  
       3214 GGCATACGCGGATAC
          1 GGCATAGGTGGAAAC

                *    *     
       3229 GGCAAAGGTTGAAAC
          1 GGCATAGGTGGAAAC

             *             
       3244 GCCATAGGTGGAAAC
          1 GGCATAGGTGGAAAC

       3259 ATCATTGGCG


Statistics
Matches: 33,  Mismatches: 12, Indels: 0
        0.73            0.27        0.00

Matches are distributed among these distances:
  15   33  1.00

ACGTcount: A:0.32, C:0.20, G:0.35, T:0.13


Consensus pattern (15 bp):   
GGCATAGGTGGAAAC

Found at i:5667 original size:15 final size:15

Alignment explanation


    Indices: 5649--5679  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       5639 ACTAATTAAG

                      *    
       5649 TTAAAATTTATTTAT
          1 TTAAAATTTAATTAT

                           
       5664 TTAAAATTTAATTAT
          1 TTAAAATTTAATTAT

             
       5679 T
          1 T

       5680 GTGATTAACC


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58


Consensus pattern (15 bp):   
TTAAAATTTAATTAT
Done.