Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005519.1 Corchorus capsularis cultivar CVL-1 contig05537, 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, 684

Length: 1141
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.40


Found at i:85 original size:2 final size:2

Alignment explanation


    Indices: 78--119  Score: 66
    Period size: 2  Copynumber: 20.5  Consensus size: 2

         68 TAATATGTAG

                                        *                                 
         78 TA TA TA TA TA TA TA TA CTA CA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA T

        120 GTATTTTTGG


Statistics
Matches: 37,  Mismatches: 2, Indels: 2
        0.90            0.05        0.05

Matches are distributed among these distances:
   2   35  0.95
   3    2  0.05

ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48


Consensus pattern (2 bp):   
TA

Found at i:362 original size:22 final size:22

Alignment explanation


    Indices: 334--378  Score: 63
    Period size: 22  Copynumber: 2.0  Consensus size: 22

        324 TATTTATTTT

                     *            
        334 TAACGTTACGTAAATTAAATTC
          1 TAACGTTACATAAATTAAATTC

                    *   *         
        356 TAACGTTATATATATTAAATTC
          1 TAACGTTACATAAATTAAATTC

             
        378 T
          1 T

        379 TAATGTTATG


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  22   20  1.00

ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42


Consensus pattern (22 bp):   
TAACGTTACATAAATTAAATTC

Found at i:422 original size:23 final size:23

Alignment explanation


    Indices: 395--439  Score: 72
    Period size: 23  Copynumber: 2.0  Consensus size: 23

        385 TATGTAACTT

                  *         *      
        395 TATATTTAATTCTTAAGGTTATA
          1 TATATTAAATTCTTAACGTTATA

                                  
        418 TATATTAAATTCTTAACGTTAT
          1 TATATTAAATTCTTAACGTTAT

        440 GTTTAGGGTT


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  23   20  1.00

ACGTcount: A:0.36, C:0.07, G:0.07, T:0.51


Consensus pattern (23 bp):   
TATATTAAATTCTTAACGTTATA
Done.