Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005639.1 Corchorus capsularis cultivar CVL-1 contig05657, 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: 2199
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.32


Found at i:719 original size:50 final size:50

Alignment explanation


    Indices: 595--765  Score: 200
    Period size: 50  Copynumber: 3.4  Consensus size: 50

        585 ACTAATGGCC

                 *     *    * *                      *         
        595 TAAAAGTTCAAACTTTAATTCAAAGGTGACATTTTATTTACAAATTACTTT
          1 TAAAAATTCAATCTTTTACTCAAAGGTGACATTTTATTTACTAATTAC-TT

                        *     *        *      *                
        646 TAAAAATTCAATATTTTATTCAAAGGTTACATCTGTATTTACTAATTAC-T
          1 TAAAAATTCAATCTTTTACTCAAAGGTGACAT-TTTATTTACTAATTACTT

                             *       *                          
        696 TAAAAATTCAATCTTTTGCTCAAAGATGACATTTTTATTTACTAATTACTTT
          1 TAAAAATTCAATCTTTTACTCAAAGGTGACA-TTTTATTTACTAATTAC-TT

                              
        748 TAAAAATTCAATCTTTTA
          1 TAAAAATTCAATCTTTTA

        766 AAAAAATTCA


Statistics
Matches: 102,  Mismatches: 14, Indels: 7
        0.83            0.11        0.06

Matches are distributed among these distances:
  50   42  0.41
  51   28  0.27
  52   32  0.31

ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44


Consensus pattern (50 bp):   
TAAAAATTCAATCTTTTACTCAAAGGTGACATTTTATTTACTAATTACTT

Found at i:765 original size:16 final size:16

Alignment explanation


    Indices: 744--783  Score: 62
    Period size: 18  Copynumber: 2.4  Consensus size: 16

        734 TTACTAATTA

                            
        744 CTTTTAAAAATTCAAT
          1 CTTTTAAAAATTCAAT

                              
        760 CTTTTAAAAAAATTCAAT
          1 CTTTT--AAAAATTCAAT

                  
        778 CTTTTA
          1 CTTTTA

        784 CTTAAAAATT


Statistics
Matches: 22,  Mismatches: 0, Indels: 4
        0.85            0.00        0.15

Matches are distributed among these distances:
  16    6  0.27
  18   16  0.73

ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45


Consensus pattern (16 bp):   
CTTTTAAAAATTCAAT

Found at i:790 original size:19 final size:18

Alignment explanation


    Indices: 749--783  Score: 70
    Period size: 18  Copynumber: 1.9  Consensus size: 18

        739 AATTACTTTT

                              
        749 AAAAATTCAATCTTTTAA
          1 AAAAATTCAATCTTTTAA

                             
        767 AAAAATTCAATCTTTTA
          1 AAAAATTCAATCTTTTA

        784 CTTAAAAATT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40


Consensus pattern (18 bp):   
AAAAATTCAATCTTTTAA
Done.