Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008777.1 Corchorus capsularis cultivar CVL-1 contig08798, 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: 1850
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35


Found at i:720 original size:33 final size:32

Alignment explanation


    Indices: 683--789  Score: 119
    Period size: 33  Copynumber: 3.2  Consensus size: 32

        673 GTTTGCGAAA

                                             
        683 ATACTAAACCTAATTTGAGTGTTGGTTTTGATG
          1 ATACTAAACCTAATTTGAGTGTT-GTTTTGATG

                                              
        716 ATACTAAACCTAATTTGAGTGTTG-TTTGCAATG
          1 ATACTAAACCTAATTTGAGTGTTGTTTTG--ATG

             *      *  *                      
        749 ACACTAAATCTGATTT-AGGTGTTGTTTGTGATG
          1 ATACTAAACCTAATTTGA-GTGTTGTTT-TGATG

             *      
        782 AAACTAAA
          1 ATACTAAA

        790 TCTGTTTTGG


Statistics
Matches: 65,  Mismatches: 4, Indels: 10
        0.82            0.05        0.13

Matches are distributed among these distances:
  31    4  0.06
  32    2  0.03
  33   55  0.85
  34    2  0.03
  35    2  0.03

ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39


Consensus pattern (32 bp):   
ATACTAAACCTAATTTGAGTGTTGTTTTGATG

Found at i:883 original size:30 final size:31

Alignment explanation


    Indices: 813--895  Score: 105
    Period size: 30  Copynumber: 2.6  Consensus size: 31

        803 CTAATTGTGA

                  *  *                       
        813 TGAAAACAAATCTGTTTTGGTTGATCATAGCAT
          1 TGAAAATAATTCTGTTTTGGTTGA--ATAGCAT

              *                       *    
        846 TGCAAATAATTCTGTTTTGGTTG-ATGGCAT
          1 TGAAAATAATTCTGTTTTGGTTGAATAGCAT

                                
        876 TGAAAATAATTCTGTTTTGG
          1 TGAAAATAATTCTGTTTTGG

        896 GTGAGAAGAA


Statistics
Matches: 45,  Mismatches: 5, Indels: 3
        0.85            0.09        0.06

Matches are distributed among these distances:
  30   25  0.56
  33   20  0.44

ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41


Consensus pattern (31 bp):   
TGAAAATAATTCTGTTTTGGTTGAATAGCAT
Done.