Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012228.1 Corchorus capsularis cultivar CVL-1 contig12249, 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: 4966
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25


Found at i:274 original size:40 final size:39

Alignment explanation


    Indices: 230--324  Score: 118
    Period size: 40  Copynumber: 2.4  Consensus size: 39

        220 CCCAATAATT

                              *            *       
        230 AAAGTCCTCAAACACATATAACACAGAGGCATCTATATC
          1 AAAGTCCTCAAACACATACAACACAGAGGCAACTATATC

                    *                  *       * *  
        269 AAAAGTCCCCAAACACATACAACACAGGGGCAACTCTCTC
          1 -AAAGTCCTCAAACACATACAACACAGAGGCAACTATATC

                       *    
        309 AAAGTCCTCAAGCACA
          1 AAAGTCCTCAAACACA

        325 AGGGCATCTA


Statistics
Matches: 47,  Mismatches: 8, Indels: 1
        0.84            0.14        0.02

Matches are distributed among these distances:
  39   14  0.30
  40   33  0.70

ACGTcount: A:0.42, C:0.31, G:0.12, T:0.16


Consensus pattern (39 bp):   
AAAGTCCTCAAACACATACAACACAGAGGCAACTATATC

Found at i:343 original size:30 final size:30

Alignment explanation


    Indices: 327--384  Score: 107
    Period size: 30  Copynumber: 1.9  Consensus size: 30

        317 CAAGCACAAG

                                          
        327 GGCATCTATACTAAAGTCCCTATACACAGA
          1 GGCATCTATACTAAAGTCCCTATACACAGA

                                  *     
        357 GGCATCTATACTAAAGTCCCTAAACACA
          1 GGCATCTATACTAAAGTCCCTATACACA

        385 TATAACACAA


Statistics
Matches: 27,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  30   27  1.00

ACGTcount: A:0.38, C:0.28, G:0.12, T:0.22


Consensus pattern (30 bp):   
GGCATCTATACTAAAGTCCCTATACACAGA
Done.