Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003241.1 Corchorus capsularis cultivar CVL-1 contig03249, 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: 2375
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36


Found at i:604 original size:51 final size:50

Alignment explanation


    Indices: 511--957  Score: 439
    Period size: 50  Copynumber: 8.9  Consensus size: 50

        501 AAAGGTGACA

                               *              * *      *     *
        511 TTTTATTTACTAATTACTTGAAAATTCAATCTTTCATTCAAAGGTTAAAG
          1 TTTTATTTACTAATTACTTAAAAATTCAATCTTTTACTCAAAGATTAAAT

            *             *        *              *      ** *  
        561 CTTTATTTACTAATCACTCTAAAGATTCAATCTTTTACCCAAAGACGACAT
          1 TTTTATTTACTAATTACT-TAAAAATTCAATCTTTTACTCAAAGATTAAAT

                      *              *           *      *      
        612 TTTTATTTACCAATTACTTAAAAATCCAAATCTTTTATTCAAAGGTTAAAT
          1 TTTTATTTACTAATTACTTAAAAATTC-AATCTTTTACTCAAAGATTAAAT

            *                      *          *   *       * *  
        663 CTTTATTTACTAATTACTCTAAAGATTCAATCTTCTACCCAAAGATGACAT
          1 TTTTATTTACTAATTACT-TAAAAATTCAATCTTTTACTCAAAGATTAAAT

                      *                                *      
        714 TTTTATTTACCAATTACTTAAAAATTCAATCTTTTACTCAAAGGTTAAAT
          1 TTTTATTTACTAATTACTTAAAAATTCAATCTTTTACTCAAAGATTAAAT

            **                          *         *    *  * *  
        764 CCTTATTTACTAATTACTCTAAAAATTCGATCTTTTACCCAAACATGACAT
          1 TTTTATTTACTAATTACT-TAAAAATTCAATCTTTTACTCAAAGATTAAAT

                 *    *                   *     *      *     *
        815 TTTTACTTACCAATTACTTAAAAATTCAATATTTTATTCAAAGCTTAAAA
          1 TTTTATTTACTAATTACTTAAAAATTCAATCTTTTACTCAAAGATTAAAT

                          *         *             *       * *  
        865 TTTTATTTACTAATCACTCT-AAAGTTCAATCTTTTACCCAAAGATGACAT
          1 TTTTATTTACTAATTACT-TAAAAATTCAATCTTTTACTCAAAGATTAAAT

                                                 *      
        915 TTTTATTTA-TCAATTACTTAAAAATTCAATCTTTTATTCAAAG
          1 TTTTATTTACT-AATTACTTAAAAATTCAATCTTTTACTCAAAG

        958 GTTACATCTT


Statistics
Matches: 312,  Mismatches: 78, Indels: 14
        0.77            0.19        0.03

Matches are distributed among these distances:
  49    2  0.01
  50  159  0.51
  51  144  0.46
  52    7  0.02

ACGTcount: A:0.37, C:0.17, G:0.05, T:0.41


Consensus pattern (50 bp):   
TTTTATTTACTAATTACTTAAAAATTCAATCTTTTACTCAAAGATTAAAT

Found at i:616 original size:101 final size:101

Alignment explanation


    Indices: 500--968  Score: 719
    Period size: 101  Copynumber: 4.7  Consensus size: 101

        490 ACTCCTAATT

                 *                *        *              *              *   
        500 CAAAGGTGACA-TTTTATTTACTAATTACTTGAAAATTCAATCTTTCATTCAAAGGTTAAAGCTT
          1 CAAAGATGACATTTTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTT

                                                
        564 TATTTACTAATCACTCTAAAGATTCAATCTTTTACC
         66 TATTTACTAATCACTCTAAAGATTCAATCTTTTACC

                  *                              *                           
        600 CAAAGACGACATTTTTATTTACCAATTACTTAAAAATCCAAATCTTTTATTCAAAGGTTAAATCT
          1 CAAAGATGACATTTTTATTTACCAATTACTTAAAAATTC-AATCTTTTATTCAAAGGTTAAATCT

                        *                   *    
        665 TTATTTACTAATTACTCTAAAGATTCAATCTTCTACC
         65 TTATTTACTAATCACTCTAAAGATTCAATCTTTTACC

                                                            *              * 
        702 CAAAGATGACATTTTTATTTACCAATTACTTAAAAATTCAATCTTTTACTCAAAGGTTAAATCCT
          1 CAAAGATGACATTTTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTT

                       *        *    *          
        767 TATTTACTAATTACTCTAAAAATTCGATCTTTTACC
         66 TATTTACTAATCACTCTAAAGATTCAATCTTTTACC

                *            *                        *            *         
        803 CAAACATGACATTTTTACTTACCAATTACTTAAAAATTCAATATTTTATTCAAAGCTTAAAAT-T
          1 CAAAGATGACATTTTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTT-AAATCT

                                                 
        867 TTATTTACTAATCACTCTAAAG-TTCAATCTTTTACC
         65 TTATTTACTAATCACTCTAAAGATTCAATCTTTTACC

                                 *                                     *     
        903 CAAAGATGACATTTTTATTTATCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTACATCTT
          1 CAAAGATGACATTTTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTT

             
        968 T
         66 T

        969 TAGCCAAGTA


Statistics
Matches: 334,  Mismatches: 31, Indels: 8
        0.90            0.08        0.02

Matches are distributed among these distances:
  99    3  0.01
 100   78  0.23
 101  154  0.46
 102   99  0.30

ACGTcount: A:0.37, C:0.17, G:0.05, T:0.41


Consensus pattern (101 bp):   
CAAAGATGACATTTTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTT
TATTTACTAATCACTCTAAAGATTCAATCTTTTACC
Done.