Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014623.1 Corchorus capsularis cultivar CVL-1 contig14644, 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: 3066
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34


Found at i:2130 original size:31 final size:31

Alignment explanation


    Indices: 2088--2195  Score: 96
    Period size: 31  Copynumber: 3.5  Consensus size: 31

       2078 GCTAAATAAC

                 *                   **     
       2088 CAATTCAGGATATAACGTTTGCT-GCCACGAT
          1 CAATTTAGGATATAACGTTT-CTGGAAACGAT

                  *        *               
       2119 CAATTTGGGATATAAAGTTTCTGGAAACGAT
          1 CAATTTAGGATATAACGTTTCTGGAAACGAT

              *                   **        
       2150 CATTTTAGGATATAACGTTTC-AAAAAGCGAT
          1 CAATTTAGGATATAACGTTTCTGGAAA-CGAT

                            
       2181 C-ATTTCAGGATATAA
          1 CAATTT-AGGATATAA

       2196 AGAATGATTA


Statistics
Matches: 63,  Mismatches: 11, Indels: 6
        0.79            0.14        0.08

Matches are distributed among these distances:
  30    8  0.13
  31   55  0.87

ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31


Consensus pattern (31 bp):   
CAATTTAGGATATAACGTTTCTGGAAACGAT

Found at i:2376 original size:29 final size:31

Alignment explanation


    Indices: 2310--2377  Score: 86
    Period size: 31  Copynumber: 2.3  Consensus size: 31

       2300 TTCCGTCATA

                       *    *         *    
       2310 TTATATCCTGATTTGATCGTTTCAAGTAACG
          1 TTATATCCTGAATTGAGCGTTTCAAGAAACG

                                    *      
       2341 TTATATCCTGAATTG-GCGTTTC-TGAAACG
          1 TTATATCCTGAATTGAGCGTTTCAAGAAACG

                    
       2370 TTATATCC
          1 TTATATCC

       2378 CAAATTGATC


Statistics
Matches: 33,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
  29   13  0.39
  30    6  0.18
  31   14  0.42

ACGTcount: A:0.25, C:0.18, G:0.16, T:0.41


Consensus pattern (31 bp):   
TTATATCCTGAATTGAGCGTTTCAAGAAACG
Done.