Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008112.1 Corchorus capsularis cultivar CVL-1 contig08133, 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: 1922
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.32


Found at i:568 original size:51 final size:50

Alignment explanation


    Indices: 507--838  Score: 264
    Period size: 50  Copynumber: 6.8  Consensus size: 50

        497 GACATTTTAT

                                   *        * *               
        507 TTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTTATTTACTAA
          1 TTACTTAAAAATTCAATCTTTTACTCAAAGGTCACATCTTTATTTACTAA

                                     *     * *    *        *   
        557 TTACTCTAAAAATTCAATCTTTTACCCAAAGATGACATTTTTATTTATTAA
          1 TTACT-TAAAAATTCAATCTTTTACTCAAAGGTCACATCTTTATTTACTAA

                        **       *                             
        608 TTACTTAAAAAAAACAATCTTCTACTCAAAGGTCACATCTTTATTTACTAA
          1 TTACTT-AAAAATTCAATCTTTTACTCAAAGGTCACATCTTTATTTACTAA

                 *                          *   *   *           
        659 TTACCCT-AAAATTCAATCTTTTAC-CTAAAGAT--GAT-ATT-TTTA-T--
          1 TTA-CTTAAAAATTCAATCTTTTACTC-AAAGGTCACATCTTTATTTACTAA

                        *   *   *             *               
        702 TTA---AAAAA-ACAAACTTCTACTCAAAGGTCATATCTTTATTTACTAA
          1 TTACTTAAAAATTCAATCTTTTACTCAAAGGTCACATCTTTATTTACTAA

                 *                          * *    *            
        748 TTACCCT-AAAATTCAATCTTTTAC-CTAAAGATAACATTTTTATTTACTAA
          1 TTA-CTTAAAAATTCAATCTTTTACTC-AAAGGTCACATCTTTATTTACTAA

              *                              *        
        798 TTGCTTAAAAATTCAATCTTTTA-TCCAAAGGTTACATCTTT
          1 TTACTTAAAAATTCAATCTTTTACT-CAAAGGTCACATCTTT

        839 TAGCCAAATA


Statistics
Matches: 220,  Mismatches: 40, Indels: 44
        0.72            0.13        0.14

Matches are distributed among these distances:
  39   14  0.06
  40    5  0.02
  41    2  0.01
  42    2  0.01
  43    7  0.03
  44    1  0.00
  45    1  0.00
  46    7  0.03
  47    2  0.01
  48    2  0.01
  49    8  0.04
  50   84  0.38
  51   83  0.38
  52    2  0.01

ACGTcount: A:0.38, C:0.17, G:0.04, T:0.41


Consensus pattern (50 bp):   
TTACTTAAAAATTCAATCTTTTACTCAAAGGTCACATCTTTATTTACTAA

Found at i:719 original size:89 final size:89

Alignment explanation


    Indices: 615--793  Score: 322
    Period size: 89  Copynumber: 2.0  Consensus size: 89

        605 TAATTACTTA

                      *                                                      
        615 AAAAAAACAATCTTCTACTCAAAGGTCACATCTTTATTTACTAATTACCCTAAAATTCAATCTTT
          1 AAAAAAACAAACTTCTACTCAAAGGTCACATCTTTATTTACTAATTACCCTAAAATTCAATCTTT

                       * *          
        680 TACCTAAAGATGATATTTTTATTT
         66 TACCTAAAGATAACATTTTTATTT

                                        *                                    
        704 AAAAAAACAAACTTCTACTCAAAGGTCATATCTTTATTTACTAATTACCCTAAAATTCAATCTTT
          1 AAAAAAACAAACTTCTACTCAAAGGTCACATCTTTATTTACTAATTACCCTAAAATTCAATCTTT

                                    
        769 TACCTAAAGATAACATTTTTATTT
         66 TACCTAAAGATAACATTTTTATTT

             
        793 A
          1 A

        794 CTAATTGCTT


Statistics
Matches: 86,  Mismatches: 4, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  89   86  1.00

ACGTcount: A:0.40, C:0.18, G:0.04, T:0.39


Consensus pattern (89 bp):   
AAAAAAACAAACTTCTACTCAAAGGTCACATCTTTATTTACTAATTACCCTAAAATTCAATCTTT
TACCTAAAGATAACATTTTTATTT
Done.