Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005601.1 Corchorus capsularis cultivar CVL-1 contig05619, 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: 9782
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34


Found at i:67 original size:31 final size:29

Alignment explanation


    Indices: 29--196  Score: 119
    Period size: 31  Copynumber: 5.6  Consensus size: 29

         19 ATCTGACACC

                                           
         29 AGGCCCTTATTTGAGCATTTTCGATAACGTT
          1 AGGCCCTTATTTGAGCATTTT-GA-AACGTT

                              **      * * 
         60 AGGCCCTTATTTG-GCCAAATT-AAAAGAT
          1 AGGCCCTTATTTGAG-CATTTTGAAACGTT

            *                               
         88 CGGACCCTTATTTGAGCATTTTCGATAACGTT
          1 AGG-CCCTTATTTGAGCATTTT-GA-AACGTT

                              **      *   *
        120 AGGCCCTTATTTG-GCCAAATT-AAAAGATC
          1 AGGCCCTTATTTGAG-CATTTTGAAACG-TT

            *  *                           
        149 GGGTCCTTATTTGAGCATTTTGGCAAACGTT
          1 AGGCCCTTATTTGAGCATTTT-G-AAACGTT

                             
        180 AGGCCCTTATTTGAGCA
          1 AGGCCCTTATTTGAGCA

        197 ATTAACCTAC


Statistics
Matches: 103,  Mismatches: 22, Indels: 24
        0.69            0.15        0.16

Matches are distributed among these distances:
  28    9  0.09
  29   32  0.31
  30    4  0.04
  31   48  0.47
  32   10  0.10

ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34


Consensus pattern (29 bp):   
AGGCCCTTATTTGAGCATTTTGAAACGTT

Found at i:125 original size:60 final size:60

Alignment explanation


    Indices: 32--192  Score: 279
    Period size: 60  Copynumber: 2.7  Consensus size: 60

         22 TGACACCAGG

                                                                        
         32 CCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGA
          1 CCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGA

                                                                       *
         92 CCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGG
          1 CCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGA

            *                 *                       
        152 TCCTTATTTGAGCATTTTGGCA-AACGTTAGGCCCTTATTTG
          1 CCCTTATTTGAGCATTTTCG-ATAACGTTAGGCCCTTATTTG

        193 AGCAATTAAC


Statistics
Matches: 97,  Mismatches: 3, Indels: 2
        0.95            0.03        0.02

Matches are distributed among these distances:
  60   96  0.99
  61    1  0.01

ACGTcount: A:0.25, C:0.20, G:0.19, T:0.35


Consensus pattern (60 bp):   
CCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGA
Done.