Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010228.1 Corchorus capsularis cultivar CVL-1 contig10249, 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: 45387
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33


Found at i:332 original size:31 final size:31

Alignment explanation


    Indices: 290--349  Score: 84
    Period size: 31  Copynumber: 1.9  Consensus size: 31

        280 ATGCAAATAG

                  *                        
        290 GTCCCTGAAGTGAACTTAAGTGAGCAATTGA
          1 GTCCCTAAAGTGAACTTAAGTGAGCAATTGA

                        * *    *         
        321 GTCCCTAAAGTGGAGTTAATTGAGCAATT
          1 GTCCCTAAAGTGAACTTAAGTGAGCAATT

        350 AGGCCCCTGA


Statistics
Matches: 25,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  31   25  1.00

ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28


Consensus pattern (31 bp):   
GTCCCTAAAGTGAACTTAAGTGAGCAATTGA

Found at i:29668 original size:67 final size:67

Alignment explanation


    Indices: 29591--29728  Score: 249
    Period size: 67  Copynumber: 2.1  Consensus size: 67

      29581 ACCGGACAAA

                                                          *         *        
      29591 ATTTTAGCAAAACGGTCTCGAAGGAGACGTTCGTCTTACTTAAGTTTACGATTCAATGATCGTTT
          1 ATTTTAGCAAAACGGTCTCGAAGGAGACGTTCGTCTTACTTAAGTTCACGATTCAAGGATCGTTT

            * 
      29656 TT
         66 AT

                                                                             
      29658 ATTTTAGCAAAACGGTCTCGAAGGAGACGTTCGTCTTACTTAAGTTCACGATTCAAGGATCGTTT
          1 ATTTTAGCAAAACGGTCTCGAAGGAGACGTTCGTCTTACTTAAGTTCACGATTCAAGGATCGTTT

              
      29723 AT
         66 AT

                
      29725 ATTT
          1 ATTT

      29729 GGTCCTCAAG


Statistics
Matches: 68,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  67   68  1.00

ACGTcount: A:0.28, C:0.17, G:0.20, T:0.36


Consensus pattern (67 bp):   
ATTTTAGCAAAACGGTCTCGAAGGAGACGTTCGTCTTACTTAAGTTCACGATTCAAGGATCGTTT
AT

Found at i:41111 original size:26 final size:25

Alignment explanation


    Indices: 41064--41112  Score: 64
    Period size: 26  Copynumber: 1.9  Consensus size: 25

      41054 TTAATGTTTA

                            *        
      41064 AATTTTATTTTTTTATTAAAAATTT
          1 AATTTTATTTTTTTATAAAAAATTT

                                     
      41089 AATTATTATTTTATTT-TAAAAAAT
          1 AATT-TTATTTT-TTTATAAAAAAT

      41113 AAATATAAGC


Statistics
Matches: 21,  Mismatches: 1, Indels: 3
        0.84            0.04        0.12

Matches are distributed among these distances:
  25    4  0.19
  26   14  0.67
  27    3  0.14

ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59


Consensus pattern (25 bp):   
AATTTTATTTTTTTATAAAAAATTT
Done.