Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01003459.1 Corchorus olitorius cultivar O-4 contig03467, 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, 758

Length: 1264
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.36


Found at i:631 original size:18 final size:19

Alignment explanation


    Indices: 602--662  Score: 81
    Period size: 19  Copynumber: 3.3  Consensus size: 19

        592 ACTAAGTCTG

                               
        602 AATAGTTTTTTTAATCTCT
          1 AATAGTTTTTTTAATCTCT

                            *  *
        621 AATAGTTTTTTTCAA-GT-G
          1 AATAGTTTTTTT-AATCTCT

                               
        639 AATAGTTTTTTTAATCTCT
          1 AATAGTTTTTTTAATCTCT

                 
        658 AATAG
          1 AATAG

        663 AGAGAAGATG


Statistics
Matches: 35,  Mismatches: 4, Indels: 6
        0.78            0.09        0.13

Matches are distributed among these distances:
  17    2  0.06
  18   13  0.37
  19   18  0.51
  20    2  0.06

ACGTcount: A:0.30, C:0.08, G:0.10, T:0.52


Consensus pattern (19 bp):   
AATAGTTTTTTTAATCTCT

Found at i:1012 original size:21 final size:21

Alignment explanation


    Indices: 986--1264  Score: 297
    Period size: 21  Copynumber: 13.0  Consensus size: 21

        976 TGTTTCTAAA

                        *        
        986 TTTGGGGTTTGATTATCAAAT
          1 TTTGGGGTTTGACTATCAAAT

                           *     
       1007 TTTGGGGTTTGACTACCAAAT
          1 TTTGGGGTTTGACTATCAAAT

                                  *    *
       1028 TTTGGGGTTTGACTCTCAAAAGACAAAA
          1 TTTGGGGTTTGA--CT----A-TCAAAT

            *   *               *
       1056 ATTGCGGTTTGACTATCAAAC
          1 TTTGGGGTTTGACTATCAAAT

               *         *    *  
       1077 TTTAGGGTTTGACGATCACAT
          1 TTTGGGGTTTGACTATCAAAT

                      *    *    *
       1098 TTTGGGGTTTTACTACCAAAC
          1 TTTGGGGTTTGACTATCAAAT

                            *    
       1119 TTTGGGGTTTGACTATAAAAT
          1 TTTGGGGTTTGACTATCAAAT

                        * *     *
       1140 TTTGGGGTTTGATTTTCAAAA
          1 TTTGGGGTTTGACTATCAAAT

                                 
       1161 TTTGGGGTTTGACTATCAAAT
          1 TTTGGGGTTTGACTATCAAAT

                          *      
       1182 TTTGGGGTTTGACTTTCAAAT
          1 TTTGGGGTTTGACTATCAAAT

                *               *
       1203 TTTGCGGTTTGACTATCAAAC
          1 TTTGGGGTTTGACTATCAAAT

                                 
       1224 TTTGGGGTTTGACTATCAAAT
          1 TTTGGGGTTTGACTATCAAAT

                      *    *    
       1245 TTTGGGGTTTTACTACCAAA
          1 TTTGGGGTTTGACTATCAAA


Statistics
Matches: 212,  Mismatches: 39, Indels: 14
        0.80            0.15        0.05

Matches are distributed among these distances:
  21  192  0.91
  22    1  0.00
  23    2  0.01
  26    2  0.01
  27    1  0.00
  28   14  0.07

ACGTcount: A:0.25, C:0.12, G:0.22, T:0.40


Consensus pattern (21 bp):   
TTTGGGGTTTGACTATCAAAT

Done.