Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005637.1 Corchorus capsularis cultivar CVL-1 contig05655, 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, 970

Length: 1618
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30


Found at i:865 original size:35 final size:33

Alignment explanation


    Indices: 825--977  Score: 151
    Period size: 29  Copynumber: 4.7  Consensus size: 33

        815 GGTGAAACCA

                                     *         
        825 CTTCAAAGTTCGATTCAGATGACTCGGTGTAGCAT
          1 CTTCAAAG-T-GATTCAGATGACTCAGTGTAGCAT

            *                                
        860 TTTCAAA---ATT-AGATGACTCAGTGTAGCAT
          1 CTTCAAAGTGATTCAGATGACTCAGTGTAGCAT

                                             
        889 CTTCAAA--G--TCAGATGACTCAGTGTAGCAT
          1 CTTCAAAGTGATTCAGATGACTCAGTGTAGCAT

                         *    *            *   
        918 CTTCAAAGTGTAAATCAGGTGACTCAGTGTATCAT
          1 CTTCAAAGTG--ATTCAGATGACTCAGTGTAGCAT

                                     
        953 CTTCAAAGTGGGATTCAGATGACTC
          1 CTTCAAAGT--GATTCAGATGACTC

        978 GATAAAGCAT


Statistics
Matches: 101,  Mismatches: 7, Indels: 20
        0.79            0.05        0.16

Matches are distributed among these distances:
  28    1  0.01
  29   50  0.50
  30    3  0.03
  31    1  0.01
  35   45  0.45
  37    1  0.01

ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31


Consensus pattern (33 bp):   
CTTCAAAGTGATTCAGATGACTCAGTGTAGCAT

Found at i:1408 original size:26 final size:26

Alignment explanation


    Indices: 1379--1430  Score: 104
    Period size: 26  Copynumber: 2.0  Consensus size: 26

       1369 TAGTTACATT

                                      
       1379 TCCCCATTTGGTTGCATCTAAAAGGC
          1 TCCCCATTTGGTTGCATCTAAAAGGC

                                      
       1405 TCCCCATTTGGTTGCATCTAAAAGGC
          1 TCCCCATTTGGTTGCATCTAAAAGGC

       1431 CAAAGTAAAG


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  26   26  1.00

ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31


Consensus pattern (26 bp):   
TCCCCATTTGGTTGCATCTAAAAGGC
Done.