Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005185.1 Corchorus capsularis cultivar CVL-1 contig05203, 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: 1875
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36


Found at i:245 original size:51 final size:50

Alignment explanation


    Indices: 183--398  Score: 215
    Period size: 50  Copynumber: 4.4  Consensus size: 50

        173 AATTACTTTT

                 *            *        *      *                
        183 TAAAACTTCAATCTTTTATTCAAAGGTTACATCTCTATTTACTAATTAATC
          1 TAAAAATTCAATCTTTTACTCAAAGGTGACATCTTTATTTACTAATT-ATC

                  *          *                   *            
        234 TAAAAAATCAATCTTTTGCTCAAAGGTGACATCTTTACTTACTAATTAT-
          1 TAAAAATTCAATCTTTTACTCAAAGGTGACATCTTTATTTACTAATTATC

                  *             *     *      *                 
        283 TAAAAGTTTCAATCTTTTACCCAAAGATGACATTTTTATTTACTAATTA-C
          1 TAAAA-ATTCAATCTTTTACTCAAAGGTGACATCTTTATTTACTAATTATC

               *               *     *      *           *    *
        333 TAAGAATTCAATCTTTTACCCAAAGATGACATTTTTATTTA--AGTTATT
          1 TAAAAATTCAATCTTTTACTCAAAGGTGACATCTTTATTTACTAATTATC

                **            
        381 TAAAGCTTCAATCTTTTA
          1 TAAAAATTCAATCTTTTA

        399 TTTACAAGTT


Statistics
Matches: 141,  Mismatches: 21, Indels: 9
        0.82            0.12        0.05

Matches are distributed among these distances:
  47    4  0.03
  48   15  0.11
  49   40  0.28
  50   42  0.30
  51   40  0.28

ACGTcount: A:0.36, C:0.16, G:0.06, T:0.42


Consensus pattern (50 bp):   
TAAAAATTCAATCTTTTACTCAAAGGTGACATCTTTATTTACTAATTATC

Found at i:403 original size:101 final size:103

Alignment explanation


    Indices: 181--403  Score: 232
    Period size: 101  Copynumber: 2.2  Consensus size: 103

        171 CAAATTACTT

                  *                       * *                                
        181 TTTAAAACTTCAATCTTTTA-TT--CAAAGGTTACATCTCTATTTACTAATTAATCTAAAAAATC
          1 TTTAAAGCTTCAATCTTTTATTTACCAAAGATGACATCTCTATTTACTAATTAATCTAAAAAATC

                    * *     *                      
        243 AATCTTTTGCTCAAAGGTGACATCTTTACTTACTAATTA
         66 AATCTTTTACCCAAAGATGACATCTTTACTTA-TAATTA

              *    *               *             * *                   *  *  
        282 TTAAAAGTTTCAATCTTTTA---CCCAAAGATGACATTTTTATTTACTAATT-A-CTAAGAATTC
          1 TTTAAAGCTTCAATCTTTTATTTACCAAAGATGACATCTCTATTTACTAATTAATCTAAAAAATC

                                   *               
        342 AATCTTTTACCCAAAGATGACATTTTTA-TT-TAAGTTA
         66 AATCTTTTACCCAAAGATGACATCTTTACTTATAA-TTA

                                     
        379 TTTAAAGCTTCAATCTTTTATTTAC
          1 TTTAAAGCTTCAATCTTTTATTTAC

        404 AAGTTACTTG


Statistics
Matches: 100,  Mismatches: 16, Indels: 13
        0.78            0.12        0.10

Matches are distributed among these distances:
  96    3  0.03
  97   21  0.21
  98    2  0.02
  99   32  0.32
 100    2  0.02
 101   40  0.40

ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43


Consensus pattern (103 bp):   
TTTAAAGCTTCAATCTTTTATTTACCAAAGATGACATCTCTATTTACTAATTAATCTAAAAAATC
AATCTTTTACCCAAAGATGACATCTTTACTTATAATTA
Done.