Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018863.1 Corchorus olitorius cultivar O-4 contig18896, 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: 13316
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36


Found at i:2945 original size:17 final size:17

Alignment explanation


    Indices: 2923--2971  Score: 55
    Period size: 17  Copynumber: 2.9  Consensus size: 17

       2913 AGGCAACAAA

                             
       2923 ATATAAATAAAAAATAC
          1 ATATAAATAAAAAATAC

                     *      *
       2940 ATATAAAT-TAAAATAT
          1 ATATAAATAAAAAATAC

              * *           
       2956 ATCTGAATAAAAAATA
          1 ATATAAATAAAAAATA

       2972 AAGAAAAGTA


Statistics
Matches: 26,  Mismatches: 5, Indels: 2
        0.79            0.15        0.06

Matches are distributed among these distances:
  16   12  0.46
  17   14  0.54

ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29


Consensus pattern (17 bp):   
ATATAAATAAAAAATAC

Found at i:10197 original size:23 final size:23

Alignment explanation


    Indices: 10169--10222  Score: 99
    Period size: 23  Copynumber: 2.3  Consensus size: 23

      10159 TAGTTGATAC

                                   
      10169 ATTAACCGGCTAATTAATTTGAT
          1 ATTAACCGGCTAATTAATTTGAT

                                   
      10192 ATTAACCGGCTAATTAATTTGAT
          1 ATTAACCGGCTAATTAATTTGAT

                    
      10215 ATTGAACC
          1 ATT-AACC

      10223 ATTTTTCTTT


Statistics
Matches: 30,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  23   26  0.87
  24    4  0.13

ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37


Consensus pattern (23 bp):   
ATTAACCGGCTAATTAATTTGAT

Found at i:12877 original size:129 final size:130

Alignment explanation


    Indices: 12744--13005  Score: 429
    Period size: 129  Copynumber: 2.0  Consensus size: 130

      12734 TTGTTTAAAC

                   *                         *        *                      
      12744 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAACTA
          1 TTTTATAATTTTACTCAACTAAAAACTCTATTTCTATTTAATAAAATCTAATATCTTTATAACTA

                       *          *                                   *      
      12809 TTTTATTTTTATCATTTTACTATTTTAATTAAAAAATCTT-ATATATTAGAATTTTT-TAATATA
         66 TTTTATTTTTACCATTTTACTAATTTAATTAAAAAA-CTTAATATATTAGAATTTTTAAAATATA

             
      12872 T
        130 T

                                                                         *   
      12873 TTTTATAATTTTACTCAACTAAAAACTCTATTTCTATTTAATAAAATCTAATATCTTTATACCTA
          1 TTTTATAATTTTACTCAACTAAAAACTCTATTTCTATTTAATAAAATCTAATATCTTTATAACTA

                                                                             
      12938 TTTTATTTTTACCATTTTACTAATTTAATTAAAAAACTTAGATATATTAGAATTTTTAAAATATA
         66 TTTTATTTTTACCATTTTACTAATTTAATTAAAAAACTTA-ATATATTAGAATTTTTAAAATATA

             
      13003 T
        130 T

              
      13004 TT
          1 TT

      13006 CTTAAATGAC


Statistics
Matches: 123,  Mismatches: 7, Indels: 4
        0.92            0.05        0.03

Matches are distributed among these distances:
 128    3  0.02
 129   95  0.77
 130   16  0.13
 131    9  0.07

ACGTcount: A:0.38, C:0.10, G:0.02, T:0.51


Consensus pattern (130 bp):   
TTTTATAATTTTACTCAACTAAAAACTCTATTTCTATTTAATAAAATCTAATATCTTTATAACTA
TTTTATTTTTACCATTTTACTAATTTAATTAAAAAACTTAATATATTAGAATTTTTAAAATATAT
Done.