Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009886.1 Corchorus capsularis cultivar CVL-1 contig09907, 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: 9026
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34


Found at i:3204 original size:78 final size:78

Alignment explanation


    Indices: 2994--3227  Score: 409
    Period size: 77  Copynumber: 3.0  Consensus size: 78

       2984 TTTTTTAATT

                                         *                                   
       2994 AATAGTAAAATGGTAAAATATAATAGTTACAAGGATATTAGATTTAATTATATAAAAATAGAGTT
          1 AATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTT

                         
       3059 TTTAGTTGAGT-A
         66 TTTAGTTGAGTAA

                                                                             
       3071 AATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTT
          1 AATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTT

                         
       3136 TTTAGTTGAGTAA
         66 TTTAGTTGAGTAA

                                *           *       *         *              
       3149 AATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTATATTTAATTAAAT-AAAATAGAGTT
          1 AATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTT

                         
       3213 TTTAGTTGAGTAA
         66 TTTAGTTGAGTAA

              
       3226 AA
          1 AA

       3228 CTATAAATAC


Statistics
Matches: 151,  Mismatches: 5, Indels: 2
        0.96            0.03        0.01

Matches are distributed among these distances:
  77  101  0.67
  78   50  0.33

ACGTcount: A:0.49, C:0.00, G:0.15, T:0.36


Consensus pattern (78 bp):   
AATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTT
TTTAGTTGAGTAA

Found at i:8262 original size:23 final size:23

Alignment explanation


    Indices: 8217--8263  Score: 67
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       8207 TTTTCCCCCG

                             *     
       8217 AAAAAATTAAATTTTCAGGTAAA
          1 AAAAAATTAAATTTTCAAGTAAA

                           *  *    
       8240 AAAAAATTAAATTTTGAATTAAA
          1 AAAAAATTAAATTTTCAAGTAAA

             
       8263 A
          1 A

       8264 CCCAAAATGA


Statistics
Matches: 21,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  23   21  1.00

ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32


Consensus pattern (23 bp):   
AAAAAATTAAATTTTCAAGTAAA
Done.