Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011819.1 Corchorus capsularis cultivar CVL-1 contig11840, 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: 15202
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:2239 original size:19 final size:19

Alignment explanation


    Indices: 2215--2281  Score: 71
    Period size: 19  Copynumber: 3.3  Consensus size: 19

       2205 CTTAGGTTTT

                               
       2215 TGGAATTCATTTATAGGGA
          1 TGGAATTCATTTATAGGGA

                    *            **
       2234 TGGAATATAATTTATCAAGGTTT
          1 TGGAAT-TCATTTAT--AGG-GA

                               
       2257 TGGAATTCATTTATAGGGA
          1 TGGAATTCATTTATAGGGA

                  
       2276 TGGAAT
          1 TGGAAT

       2282 ATAATACAGT


Statistics
Matches: 38,  Mismatches: 6, Indels: 8
        0.73            0.12        0.15

Matches are distributed among these distances:
  19   12  0.32
  20   10  0.26
  22   10  0.26
  23    6  0.16

ACGTcount: A:0.33, C:0.04, G:0.24, T:0.39


Consensus pattern (19 bp):   
TGGAATTCATTTATAGGGA

Found at i:2248 original size:20 final size:20

Alignment explanation


    Indices: 2223--2286  Score: 67
    Period size: 20  Copynumber: 3.1  Consensus size: 20

       2213 TTTGGAATTC

                                
       2223 ATTTATAGGGATGGAATATA
          1 ATTTATAGGGATGGAATATA

                        **        *
       2243 ATTTATCAAGGTTTTGGAAT-TC
          1 ATTTAT--AGG-GATGGAATATA

                                
       2265 ATTTATAGGGATGGAATATA
          1 ATTTATAGGGATGGAATATA

              
       2285 AT
          1 AT

       2287 ACAGTGATTC


Statistics
Matches: 34,  Mismatches: 6, Indels: 8
        0.71            0.12        0.17

Matches are distributed among these distances:
  19    6  0.18
  20   12  0.35
  22   10  0.29
  23    6  0.18

ACGTcount: A:0.36, C:0.03, G:0.22, T:0.39


Consensus pattern (20 bp):   
ATTTATAGGGATGGAATATA
Done.