Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015225.1 Corchorus capsularis cultivar CVL-1 contig15246, 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: 2857
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:75 original size:15 final size:15

Alignment explanation


    Indices: 51--122  Score: 54
    Period size: 11  Copynumber: 5.4  Consensus size: 15

         41 AAATTACTTA

                           
         51 GTTT-ATTAGTTTAT
          1 GTTTAATTAGTTTAT

                           
         65 GTTTAATTAG--TA-
          1 GTTTAATTAGTTTAT

              *            
         77 -TCTAATTAGTTTAT
          1 GTTTAATTAGTTTAT

             *             
         91 GATTAATTAG--TA-
          1 GTTTAATTAGTTTAT

                           
        103 -TTTAATTAGTTTAT
          1 GTTTAATTAGTTTAT

             *    
        117 GATTAA
          1 GTTTAA

        123 AATGAAGGAA


Statistics
Matches: 44,  Mismatches: 5, Indels: 17
        0.67            0.08        0.26

Matches are distributed among these distances:
  11   16  0.36
  13    8  0.18
  14    4  0.09
  15   16  0.36

ACGTcount: A:0.32, C:0.01, G:0.12, T:0.54


Consensus pattern (15 bp):   
GTTTAATTAGTTTAT

Found at i:84 original size:26 final size:26

Alignment explanation


    Indices: 55--122  Score: 118
    Period size: 26  Copynumber: 2.6  Consensus size: 26

         45 TACTTAGTTT

                       *              
         55 ATTAGTTTATGTTTAATTAGTATCTA
          1 ATTAGTTTATGATTAATTAGTATCTA

                                   *  
         81 ATTAGTTTATGATTAATTAGTATTTA
          1 ATTAGTTTATGATTAATTAGTATCTA

                            
        107 ATTAGTTTATGATTAA
          1 ATTAGTTTATGATTAA

        123 AATGAAGGAA


Statistics
Matches: 40,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  26   40  1.00

ACGTcount: A:0.34, C:0.01, G:0.12, T:0.53


Consensus pattern (26 bp):   
ATTAGTTTATGATTAATTAGTATCTA

Found at i:300 original size:22 final size:21

Alignment explanation


    Indices: 271--314  Score: 70
    Period size: 21  Copynumber: 2.1  Consensus size: 21

        261 CAAAAGTGTA

                      *          
        271 AAAAGGGGGGTGGTATTTAGC
          1 AAAAGGGGGGCGGTATTTAGC

                          *      
        292 AAAAGGGGGGCGGTGTTTAGC
          1 AAAAGGGGGGCGGTATTTAGC

              
        313 AA
          1 AA

        315 TCCAGTTGAT


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.30, C:0.07, G:0.43, T:0.20


Consensus pattern (21 bp):   
AAAAGGGGGGCGGTATTTAGC
Done.