Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1386

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: 1867
ACGTcount: A:0.22, C:0.14, G:0.17, T:0.21

Warning! 472 characters in sequence are not A, C, G, or T


Found at i:656 original size:175 final size:175

Alignment explanation


    Indices: 1--1037  Score: 1206
    Period size: 175  Copynumber: 6.0  Consensus size: 175

                                                          * *                
          1 CGTATGGATGTTGAGGCAACTCGGCAACATTGCTCGAGAT-TTCCTGCATGGATTTTCTCGAAAT
          1 CGTATGGATGTTGAGGCAACTCGGCAACATTGCTCGAGATATTCC-CCTTGGATTTTCTCGAAAT

            *    * **       * *     *    * * * *       *   *                 
         65 ATTCCCAACATGGTC-CTGGGAGGTCATAGTCAGTGTAAAATGAGT-GAAATCGGATGAACAAAT
         65 TTTCCGAGGATGGTCTTTAGG-GGCCATACTTACTATAAAATGTGTCAAAAT-GGATGAACAAAT

               *   *                             *  *     *  
        128 GAATTGGTTGAAACGACAGAGCCTGCTCCGAATTTACACGACT-TGACT
        128 GAAATGGATGAAACGACAGAGCCTGCTCCGAATTTACGCGGCTCT-CCT

                          *                            *  *        *  *      
        176 CGTATGGA---TGACG-AACGT-GGCAACATTGCAT-GA-ATTTTTTCCCTTGGAATTACTCGAA
          1 CGTATGGATGTTGAGGCAAC-TCGGCAACATTGC-TCGAGA-TATTCCCCTTGGATTTTCTCGAA

                                * *   *                                      
        234 ATTTTCCGAGGATGGTCTTTTGAGGCTATACTTACTATAAAATGTGTCAAAATGGATGAACAAAT
         63 ATTTTCCGAGGATGGTCTTTAGGGGCCATACTTACTATAAAATGTGTCAAAATGGATGAACAAAT

                              *                  *  *     *  
        299 GAAATGGATGAAACGACACAGCCTGCTCCGAATTTACACGACT-TGACT
        128 GAAATGGATGAAACGACAGAGCCTGCTCCGAATTTACGCGGCTCT-CCT

                          *                                *        *  *     
        347 CGTATGGA---TGACG-AACGT-GGCAACATTG-T-GCATGA-ATTTTCCCTTGGAATTACTCGA
          1 CGTATGGATGTTGAGGCAAC-TCGGCAACATTGCTCG-A-GATA-TTCCCCTTGGATTTTCTCGA

                                 * *   *                                     
        404 AATTTTCCGAGGATGGTCTTTTGAGGCTATACTTACTATAAAATGTGTCAAAATGGATGAACAAA
         62 AATTTTCCGAGGATGGTCTTTAGGGGCCATACTTACTATAAAATGTGTCAAAATGGATGAACAAA

                                                             
        469 TGAAATGGATGAAACGACAGAGCCTGCTCCGAATTTACGCGGCTCTCCT
        127 TGAAATGGATGAAACGACAGAGCCTGCTCCGAATTTACGCGGCTCTCCT

             *         *                                                     
        518 CCTATGGATGTAGAGGCAACTCGGCAACATTGCTCGAGATATTCCCCTTGGATTTTCTCGAAATT
          1 CGTATGGATGTTGAGGCAACTCGGCAACATTGCTCGAGATATTCCCCTTGGATTTTCTCGAAATT

                                      *                                      
        583 TTCCGAGGATGGTCTTTAGGGGCCATTCTTACTATAAAATGTGTCAAAATGGATGAACAAATGAA
         66 TTCCGAGGATGGTCTTTAGGGGCCATACTTACTATAAAATGTGTCAAAATGGATGAACAAATGAA

                          *                              
        648 ATGGATGAAACGACGGAGCCTGCTCCGAATTTACGCGGCTCTCCT
        131 ATGGATGAAACGACAGAGCCTGCTCCGAATTTACGCGGCTCTCCT

                                        *              *                     
        693 CGTATGGATGTTGAGGCAACTCGGCAACTTTGCTCGAGATCA-CCCCCTTGGATTTTCTCGAAAT
          1 CGTATGGATGTTGAGGCAACTCGGCAACATTGCTCGAGAT-ATTCCCCTTGGATTTTCTCGAAAT

                                       *                                     
        757 TTTCCGAGGATGGTCTTTAGGGGCCATTCTTACTATAAAATGTGTCAAAATGGATGAACAAATGA
         65 TTTCCGAGGATGGTCTTTAGGGGCCATACTTACTATAAAATGTGTCAAAATGGATGAACAAATGA

                           *                              
        822 AATGGATGAAACGACGGAGCCTGCTCCGAATTTACGCGGCTCTCCT
        130 AATGGATGAAACGACAGAGCCTGCTCCGAATTTACGCGGCTCTCCT

                                        *              *                     
        868 CGTATGGATGTTGAGGCAACTCGGCAACTTTGCTCGAGATCA-CCCCCTTGGATTTTCTCGAAAT
          1 CGTATGGATGTTGAGGCAACTCGGCAACATTGCTCGAGAT-ATTCCCCTTGGATTTTCTCGAAAT

                            * *           * *           *   *  *    *        
        932 TTTCCGAGGATGGTC-CTGGGAGGCCATTAATGA-TATAAAATGAGTCGAATTGGACGAACAAAT
         65 TTTCCGAGGATGGTCTTTAGG-GGCCA-TACTTACTATAAAATGTGTCAAAATGGATGAACAAAT

                 *       *         *                    
        995 GAAATTGATGAAATGACA-AGGCTTGCTCCGAATTTACGCGGCT
        128 GAAATGGATGAAACGACAGA-GCCTGCTCCGAATTTACGCGGCT

       1038 TGACAGGAAT


Statistics
Matches: 782,  Mismatches: 57, Indels: 46
        0.88            0.06        0.05

Matches are distributed among these distances:
 169    2  0.00
 170    2  0.00
 171  280  0.36
 172   17  0.02
 174    8  0.01
 175  465  0.59
 176    7  0.01
 177    1  0.00

ACGTcount: A:0.29, C:0.20, G:0.24, T:0.28


Consensus pattern (175 bp):   
CGTATGGATGTTGAGGCAACTCGGCAACATTGCTCGAGATATTCCCCTTGGATTTTCTCGAAATT
TTCCGAGGATGGTCTTTAGGGGCCATACTTACTATAAAATGTGTCAAAATGGATGAACAAATGAA
ATGGATGAAACGACAGAGCCTGCTCCGAATTTACGCGGCTCTCCT

Done.