genome.fa.s1870.2.7.7.80.10.50.1000.txt.html

Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1736

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, 809

Length: 1349
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37


Found at i:980 original size:516 final size:516

Alignment explanation


    Indices: 1--1349  Score: 2297
    Period size: 516  Copynumber: 2.6  Consensus size: 516

                        *                                  * **              
          1 TCCCATTTTTCCCTTTTATAACCATAATCACTTTCCATTTTTATCTATAGGATTTGTTAAATTCA
          1 TCCCATTTTTCCTTTTTATAACCATAATCACTTTCCATTTTTATCTAAACCATTTGTTAAATTCA

               *   *     *                     **                            
         66 TACTGGTCCTTTTTCCAATTTCGTATCATTTCAAAAACTTTAATTGTATACACACATTAGTTATT
         66 TACAGGTTCTTTTACCAATTTCGTATCATTTCAAACTCTTTAATTGTATACACACATTAGTTATT

                                                                             
        131 TTGAATAACAATTCTCTATACATTTTAAATTTGCAACATCATCATATACATGCTATCCAACAACA
        131 TTGAATAACAATTCTCTATACATTTTAAATTTGCAACATCATCATATACATGCTATCCAACAACA

                     *               *                *                      
        196 TACCATTCTAACATCCATTCAATGTTATGAATCTCTTCATATGTATCAAGTATTTCTTATTTTAC
        196 TACCATTCTCACATCCATTCAATGTCATGAATCTCTTCATATTTATCAAGTATTTCTTATTTTAC

            *                 * **                   *                       
        261 TATTTGATCCATTTTATAGAGGAAGCCATTAAATCTGCAATCATATATATTTAATATATATACAA
        261 AATTTGATCCATTTTATATAAAAAGCCATTAAATCTGCAATTATATATATTTAATATATATACAA

                                                     *                       
        326 AAACACAATTAAAATATAAAACGAAAATGCAGTAAGTTCCATATGAACTTACATAGAAAATGGCA
        326 AAACACAATTAAAATATAAAACGAAAATGCAGTAAGTTCCACATGAACTTACATAGAAAATGGCA

                                                                             
        391 ACTAGAACGTTTCAGGGACTAATCATCACAGATTGCTATATAAGGATCCGATACGGCTCAGTCGA
        391 ACTAGAACGTTTCAGGGACTAATCATCACAGATTGCTATATAAGGATCCGATACGGCTCAGTCGA

                                                                          
        456 GCTGTCGGGAATCCACAATTTATGCTGGATC-CAAACCATCGAATAAATCTCTAATCACAAT
        456 GCTGTCGGGAATCCACAATTTATGCTGGATCTC-AACCATCGAATAAATCTCTAATCACAAT

                                              * *  *                         
        517 TCCCATTTTTCCTTTTTATAACCATAATCACTTTACGTTCTTATCTAAACCATTTGTTAAATTCA
          1 TCCCATTTTTCCTTTTTATAACCATAATCACTTTCCATTTTTATCTAAACCATTTGTTAAATTCA

             *                                                               
        582 TGCAGGTTCTTTTACCAATTTCGTATCATTTCAAACTCTTTAATTGTATACACACATTAGTTATT
         66 TACAGGTTCTTTTACCAATTTCGTATCATTTCAAACTCTTTAATTGTATACACACATTAGTTATT

                                                       *         *           
        647 TTGAATAACAATTCTCTATACATTTTAAATTTGCAACATCATCGTATACATGCAATCCAACAACA
        131 TTGAATAACAATTCTCTATACATTTTAAATTTGCAACATCATCATATACATGCTATCCAACAACA

                                        *                                    
        712 TACCATTCTCACATCCATTCAATGTCATCAATCTCTTCATATTTATCAAGTATTTCTTATTTTAC
        196 TACCATTCTCACATCCATTCAATGTCATGAATCTCTTCATATTTATCAAGTATTTCTTATTTTAC

            *                                            *                   
        777 GATTTGATCCATTTTATATAAAAAGCCATTAAATCTGCAATTATAAATATTTAATATATATACAA
        261 AATTTGATCCATTTTATATAAAAAGCCATTAAATCTGCAATTATATATATTTAATATATATACAA

                              **                                             
        842 AAACACAATTAAAATATAGTACGAAAATGCAGTAAGTTCCACATGAACTTACATAGAAAATGGCA
        326 AAACACAATTAAAATATAAAACGAAAATGCAGTAAGTTCCACATGAACTTACATAGAAAATGGCA

               *                    *                  *              *      
        907 ACTGGAACGTTTCAGGGACTAATCTTCACAGATTGCTATATAATGATCCGATACGGCTTAGTCGA
        391 ACTAGAACGTTTCAGGGACTAATCATCACAGATTGCTATATAAGGATCCGATACGGCTCAGTCGA

             *                                                           
        972 GTTGTCGGGAATCCACAATTTATGCTGGATCTCAACCATCGAATAAATCTCTAATCACAAT
        456 GCTGTCGGGAATCCACAATTTATGCTGGATCTCAACCATCGAATAAATCTCTAATCACAAT

                                                                             
       1033 TCCCATTTTTCCTTTTTATAACCATAATCACTTTCCATTTTTATCTAAACCATTTGTTAAATTCA
          1 TCCCATTTTTCCTTTTTATAACCATAATCACTTTCCATTTTTATCTAAACCATTTGTTAAATTCA

                                                                             
       1098 TACAGGTTCTTTTACCAATTTCGTATCATTTCAAACTCTTTAATTGTATACACACATTAGTTATT
         66 TACAGGTTCTTTTACCAATTTCGTATCATTTCAAACTCTTTAATTGTATACACACATTAGTTATT

                                                                             
       1163 TTGAATAACAATTCTCTATACATTTTAAATTTGCAACATCATCATATACATGCTATCCAACAACA
        131 TTGAATAACAATTCTCTATACATTTTAAATTTGCAACATCATCATATACATGCTATCCAACAACA

                     *                            *                          
       1228 TACCCATTCCCACA-CCATTCAATGTCATGAATCTCTTTATATTTATCAAGTATTTCTTATTTTA
        196 TA-CCATTCTCACATCCATTCAATGTCATGAATCTCTTCATATTTATCAAGTATTTCTTATTTTA

            *               *                * * *                    
       1292 TAATTTGATCCATTTTGTATAAAAAGCCATTAAGTTTACAATTATATATATTTAATAT
        260 CAATTTGATCCATTTTATATAAAAAGCCATTAAATCTGCAATTATATATATTTAATAT


Statistics
Matches: 782,  Mismatches: 49, Indels: 4
        0.94            0.06        0.00

Matches are distributed among these distances:
 516  771  0.99
 517   11  0.01

ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37


Consensus pattern (516 bp):   
TCCCATTTTTCCTTTTTATAACCATAATCACTTTCCATTTTTATCTAAACCATTTGTTAAATTCA
TACAGGTTCTTTTACCAATTTCGTATCATTTCAAACTCTTTAATTGTATACACACATTAGTTATT
TTGAATAACAATTCTCTATACATTTTAAATTTGCAACATCATCATATACATGCTATCCAACAACA
TACCATTCTCACATCCATTCAATGTCATGAATCTCTTCATATTTATCAAGTATTTCTTATTTTAC
AATTTGATCCATTTTATATAAAAAGCCATTAAATCTGCAATTATATATATTTAATATATATACAA
AAACACAATTAAAATATAAAACGAAAATGCAGTAAGTTCCACATGAACTTACATAGAAAATGGCA
ACTAGAACGTTTCAGGGACTAATCATCACAGATTGCTATATAAGGATCCGATACGGCTCAGTCGA
GCTGTCGGGAATCCACAATTTATGCTGGATCTCAACCATCGAATAAATCTCTAATCACAAT
Done.