Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold2535

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, 549

Length: 915
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28


Found at i:249 original size:132 final size:131

Alignment explanation


    Indices: 1--814  Score: 1073
    Period size: 132  Copynumber: 6.2  Consensus size: 131

                 *           *                    *  *                   *   
          1 GGAGTAGGTTGAAAATTTTAGATCTTATCTCCCTAAGCTGTTGTGGAGCAGATCGAAGACGGCAA
          1 GGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGT-GAGCAGATCGAAGACGACAA

                   *    *      *              **          *          *      *
         66 ATCTTATTTTTCTAAGATAATGGGAAGCAGATTTCGGTCACCAAGCATTGTCTCCCTAAGCAGCT
         65 ATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCA

              
        131 GC
        130 GC

            *                  *   *          *            *            *    
        133 AGAGTGGGTTGAAAATTGTTGATGTTATCTCCCTTAGCAGTAGTAGAACAGATCGAAGACAACAA
          1 GGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGT-GAGCAGATCGAAGACGACAA

                                                                           * 
        198 ATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGTCACCAAGCCTTGTCTCCCTGAGCAGTA
         65 ATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCA

              
        263 GC
        130 GC

            *                                        *      *            *   
        265 AGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTGGTGTAGTAGATCGAAGACGTCAA
          1 GGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTG-AGCAGATCGAAGACGACAA

                          *              *                                   
        330 ATCTTATCTTTCCATGATAGTGGGAAGCATATTTAAGTCACCAA--C---TCTCCCTGAG-AGCA
         65 ATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCA

             *
        389 GG
        130 GC

                                                                         *   
        391 GGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTAGAGCAGATCGAAGACGGCAA
          1 GGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGT-GAGCAGATCGAAGACGACAA

            *                                    *                         * 
        456 GTCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGGA
         65 ATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCA

              
        521 GC
        130 GC

                                      *          * *       *           *     
        523 GGAGTGGGTTGAAAATTGTAGATCTTCTCTCCCTAAGAACTAGTGGAACAGATCGAAGAAGACAA
          1 GGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGT-GAGCAGATCGAAGACGACAA

              *            **                             *                  
        588 ATTTTATCTTTCCAACTTAGTGGGAAGCAGATTTAAGTCACCAAGCATTGTCTCCCTGAGCAGCA
         65 ATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCA

              
        653 GC
        130 GC

               *                                     *      *            *   
        655 GGAATGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTGGTGTAGTAGATCGAAGACGTCAA
          1 GGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTG-AGCAGATCGAAGACGACAA

                          *              *              *            *   *   
        720 ATCTTATCTTTCCATGATAGTGGGAAGCATATTTAAGTCACCAACCCTTGTCTCCCTAAGCTGCA
         65 ATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCA

              
        785 GC
        130 GC

                     *          *       
        787 GGAGTGGGTCGAAAATTGTAAATCTTAT
          1 GGAGTGGGTTGAAAATTGTAGATCTTAT

        815 TTTTCCAAGA


Statistics
Matches: 595,  Mismatches: 78, Indels: 18
        0.86            0.11        0.03

Matches are distributed among these distances:
 126  103  0.17
 127   11  0.02
 128    1  0.00
 130    1  0.00
 131   12  0.02
 132  467  0.78

ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28


Consensus pattern (131 bp):   
GGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGAGCAGATCGAAGACGACAAA
TCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAG
C

Found at i:726 original size:390 final size:393

Alignment explanation


    Indices: 1--814  Score: 1240
    Period size: 390  Copynumber: 2.1  Consensus size: 393

                 *           *                    *  *  *                    
          1 GGAGTAGGTTGAAAATTTTAGATCTTATCTCCCTAAGCTGTTGTGGAGCAGATCGAAGACGGCAA
          1 GGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTAGAGCAGATCGAAGACGGCAA

                   *    *                     ** *                          *
         66 ATCTTATTTTTCTAAGATAATGGGAAGCAGATTTCGGTCACCAAGCATTGTCTCCCTAAGCAGCT
         66 ATCTTATCTTTCCAAGATAATGGGAAGCAGATTTAAGCCACCAAGCATTGTCTCCCTAAGCAGCA

                                 *   *          *  * *                       
        131 GCAGAGTGGGTTGAAAATTGTTGATGTTATCTCCCTTAGCAGTAGTAGAACAGATCGAAGACAAC
        131 GCAGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGAACTAGTAGAACAGATCGAAGACAAC

                             *                              *                
        196 AAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGTCACCAAGCCTTGTCTCCCTGAGCAG
        196 AAATCTTATCTTTCCAACATAGTGGGAAGCAGATTTAAGTCACCAAGCATTGTCTCCCTGAGCAG

            *      *                                                         
        261 TAGCAGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTGGTGTAGTAGATCGAAGACG
        261 CAGCAGAATGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTGGTGTAGTAGATCGAAGACG

                                                                      *      
        326 TCAAATCTTATCTTTCCATGATAGTGGGAAGCATATTTAAGTCACCAA-C-TCTCCCTGAG-AGC
        326 TCAAATCTTATCTTTCCATGATAGTGGGAAGCATATTTAAGTCACCAACCTTCTCCCTAAGCAGC

              *
        388 AGG
        391 AGC

                                                                             
        391 GGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTAGAGCAGATCGAAGACGGCAA
          1 GGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTAGAGCAGATCGAAGACGGCAA

            *                  *                          *          *     * 
        456 GTCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGGA
         66 ATCTTATCTTTCCAAGATAATGGGAAGCAGATTTAAGCCACCAAGCATTGTCTCCCTAAGCAGCA

              *                         *                 *                  
        521 GCGGAGTGGGTTGAAAATTGTAGATCTTCTCTCCCTAAGAACTAGTGGAACAGATCGAAGA-AGA
        131 GCAGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGAACTAGTAGAACAGATCGAAGACA-A

                 *             *                                             
        585 CAAATTTTATCTTTCCAACTTAGTGGGAAGCAGATTTAAGTCACCAAGCATTGTCTCCCTGAGCA
        195 CAAATCTTATCTTTCCAACATAGTGGGAAGCAGATTTAAGTCACCAAGCATTGTCTCCCTGAGCA

                 *                                                           
        650 GCAGCGGAATGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTGGTGTAGTAGATCGAAGAC
        260 GCAGCAGAATGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTGGTGTAGTAGATCGAAGAC

                                                                             
        715 GTCAAATCTTATCTTTCCATGATAGTGGGAAGCATATTTAAGTCACCAACCCTTGTCTCCCTAAG
        325 GTCAAATCTTATCTTTCCATGATAGTGGGAAGCATATTTAAGTCACCAA-CC-T-TCTCCCTAAG

             *     
        780 CTGCAGC
        387 CAGCAGC

                     *          *       
        787 GGAGTGGGTCGAAAATTGTAAATCTTAT
          1 GGAGTGGGTTGAAAATTGTAGATCTTAT

        815 TTTTCCAAGA


Statistics
Matches: 381,  Mismatches: 36, Indels: 8
        0.90            0.08        0.02

Matches are distributed among these distances:
 389    1  0.00
 390  340  0.89
 392    1  0.00
 395    9  0.02
 396   30  0.08

ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28


Consensus pattern (393 bp):   
GGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTAGAGCAGATCGAAGACGGCAA
ATCTTATCTTTCCAAGATAATGGGAAGCAGATTTAAGCCACCAAGCATTGTCTCCCTAAGCAGCA
GCAGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGAACTAGTAGAACAGATCGAAGACAAC
AAATCTTATCTTTCCAACATAGTGGGAAGCAGATTTAAGTCACCAAGCATTGTCTCCCTGAGCAG
CAGCAGAATGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTGGTGTAGTAGATCGAAGACG
TCAAATCTTATCTTTCCATGATAGTGGGAAGCATATTTAAGTCACCAACCTTCTCCCTAAGCAGC
AGC

Found at i:880 original size:88 final size:88

Alignment explanation


    Indices: 718--893  Score: 208
    Period size: 88  Copynumber: 2.0  Consensus size: 88

        708 CGAAGACGTC

                            *    *         *                *              * 
        718 AAATCTTATCTTTCCATGATAGTGGGAAGCATATTTAAGTCACCAACCCTTGTCTCCCTAAGCTG
          1 AAATCTTATCTTTCCAAGATAATGGGAAGCAGATTTAAGTCACCAACCATTGTCTCCCTAAGCAG

                *         *        
        783 CAGCGGAGTGGGTCGAAAATTGT
         66 CAGCAGAGTGGGTCAAAAATTGT

                     *                          **      * *            *     
        806 AAATCTTATTTTTCCAAGATAATGGGAAGCAGATTTCGGTCACCGAGCATTGTCTCCCTGAGCAG
          1 AAATCTTATCTTTCCAAGATAATGGGAAGCAGATTTAAGTCACCAACCATTGTCTCCCTAAGCAG

             * *         *         
        871 CGGTAGAGTGGGTTAAAAATTGT
         66 CAGCAGAGTGGGTCAAAAATTGT

        894 TGATGTTATC


Statistics
Matches: 72,  Mismatches: 16, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  88   72  1.00

ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30


Consensus pattern (88 bp):   
AAATCTTATCTTTCCAAGATAATGGGAAGCAGATTTAAGTCACCAACCATTGTCTCCCTAAGCAG
CAGCAGAGTGGGTCAAAAATTGT
Done.