Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1551

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, 939

Length: 1565
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33


Found at i:250 original size:132 final size:132

Alignment explanation


    Indices: 5--1560  Score: 1302
    Period size: 132  Copynumber: 11.8  Consensus size: 132

          1 AATT

                    *   *                           *     **                 
          5 TGCTTCTCCACTATATTGGGAAGATAAGATTCACCAT-TTGGATCTTATCCACTACTGCTTAGGG
          1 TGCTTCTCTACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGG

             *          *                           *   *                    
         69 TTACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAA
         66 TGACAGAATCTGTAATCTTCAACCTACTCCACTACTGCTTTGGGAGATAGGACTAATGGCTTAAA

             *
        134 TA
        131 TC

                    *                        *   *      *             *      
        136 TGCTTCTCCACTGTATTGGGAAGATAAGATTCATCATATTCGATTTGCTCCACTACTGTTTAGGG
          1 TGCTTCTCTACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGG

                *  *   *                                       *    *        
        201 TGACTGAGTCTATAATCTTCAACCTACTCCACTACTGCTTTGGGAGATAGGTCTAACGGCTTAAA
         66 TGACAGAATCTGTAATCTTCAACCTACTCCACTACTGCTTTGGGAGATAGGACTAATGGCTTAAA

              
        266 TC
        131 TC

                                                    *                        
        268 TGCTTCTCTACTGTATTGGGAAGATAAGATTCACCATCTTGGATCTGCTCCACTACTGCTTAGGG
          1 TGCTTCTCTACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGG

               ** *              *  *  *  * *                    *  *        
        333 TGATTGGA-C--TAATGGCTTAAATCTGCTTCTCTACTG-TATTGGGAAGATAAGATTCACCAT-
         66 TGACAGAATCTGTAAT--CTTCAACCTACTCCACTACTGCT-TTGGG-AGATAGGACT-A--ATG

                **   
        393 -CTTGGATC
        124 GCTTAAATC

                * *          *    *   **  *            **       * *          
        401 TGCTCCACTACTGCT-TAGGG-TGATTGGACT-A--ATGGCTTAAATCTGCTTCTCTACTG-TAT
          1 TGCTTCTCTACTG-TATTGGGAAGATAAGATTCACCAT--CTTCGATCTGCTCCACTACTGCT-T

            *    *   *   *   ***     ** *  *              *   *   *          
        460 TGGGAAGATAAGATTC-ACCATCTTGGATCTGCTCCACTACTGCTTAGGGTGATTGGACTAATGG
         62 AGGG-TGA-CAGAATCTGTAATCTTCAACCTACTCCACTACTGCTTTGGGAGATAGGACTAATGG

                    
        524 CTTAAATC
        125 CTTAAATC

                                                    *                        
        532 TGCTTCTCTACTGTATTGGGAAGATAAGATTCACCATCTTGGATCTGCTCCACTACTGCTTAGGG
          1 TGCTTCTCTACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGG

               ** *              *  *  *  * *                    *  *        
        597 TGATTGGA-C--TAATGGCTTAAATCTGCTTCTCTACTG-TATTGGGAAGATAAGATTCACCAT-
         66 TGACAGAATCTGTAAT--CTTCAACCTACTCCACTACTGCT-TTGGG-AGATAGGACT-A--ATG

                **   
        657 -CTTGGATC
        124 GCTTAAATC

                * *          *    *   **  *            **       * *          
        665 TGCTCCACTACTGCT-TAGGG-TGATTGGACT-A--ATGGCTTAAATCTGCTTCTCTACTG-TAT
          1 TGCTTCTCTACTG-TATTGGGAAGATAAGATTCACCAT--CTTCGATCTGCTCCACTACTGCT-T

            *    *   *   *   ***     ** *  *              *   *   *          
        724 TGGGAAGATAAGATTC-ACCATCTTGGATCTGCTCCACTACTGCTTAGGGTGATTGGACTAATGG
         62 AGGG-TGA-CAGAATCTGTAATCTTCAACCTACTCCACTACTGCTTTGGGAGATAGGACTAATGG

                    
        788 CTTAAATC
        125 CTTAAATC

                                                             *               
        796 TGCTTCTCTACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTTCACTACTGCTTAGGG
          1 TGCTTCTCTACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGG

                         *   *  **                  *   *   *                
        861 TGACAGAATCTGTGATCCTCGTCCTACTCCACTACTGCTTAGGGTGATTGGACTAATGGCTTAAA
         66 TGACAGAATCTGTAATCTTCAACCTACTCCACTACTGCTTTGGGAGATAGGACTAATGGCTTAAA

              
        926 TC
        131 TC

                    *                        *                         *    *
        928 TGCTTCTCCACTGTATTGGGAAGATAAGATTCATCATAC-TCGATCTGCTCCACTACTGTTTAGT
          1 TGCTTCTCTACTGTATTGGGAAGATAAGATTCACCAT-CTTCGATCTGCTCCACTACTGCTTAGG

                                               *                *    *       
        992 GTGACAGAATCTGTAATCTTCAACCTACTCCACTATTGCTTTGGGAGATAGGTCTAACGGCTTAA
         65 GTGACAGAATCTGTAATCTTCAACCTACTCCACTACTGCTTTGGGAGATAGGACTAATGGCTTAA

               
       1057 ATC
        130 ATC

                                                          *     *            
       1060 TGCTTCTCTACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTACTCCATTACTGCTTAGGG
          1 TGCTTCTCTACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGG

                 *                                            * *            
       1125 TGACAAAATCT-TCAATCTTCAACCTACTCCACTACTGC-TTGGAGAGATTGAACTAATGGCTTA
         66 TGACAGAATCTGT-AATCTTCAACCTACTCCACTACTGCTTTGG-GAGATAGGACTAATGGCTTA

            *   
       1188 CATC
        129 AATC

                  * *   * *   *       *                 *    *   *   *       
       1192 TGCTTCACCACTATCTTGAGAAGATATGATTCACCATCTTCGATATGCTGCACAACTACTTAGGG
          1 TGCTTCTCTACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGG

                 *      *                           *   *                    
       1257 TGACAAAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAA
         66 TGACAGAATCTGTAATCTTCAACCTACTCCACTACTGCTTTGGGAGATAGGACTAATGGCTTAAA

              
       1322 TC
        131 TC

                    *                        *   *                    *      
       1324 TGCTTCTCCACTGTATTGGGAAGATAAGATTCATCATATTCGATCTGCTCCACTACTGTTTAGGG
          1 TGCTTCTCTACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGG

                                                *              **   *        
       1389 TGACAGAATCTGTAATCTTCAACCTACTCCACTACTACTTTGGGAGATAGGTTTAACGGCTTAAA
         66 TGACAGAATCTGTAATCTTCAACCTACTCCACTACTGCTTTGGGAGATAGGACTAATGGCTTAAA

              
       1454 TC
        131 TC

             *     *                               *      *     *        *   
       1456 TACTTCTTTACTGTATTGGGAAGATAAGATTCACCATCTCCGATCTACTCCATTACTGCTTTGGG
          1 TGCTTCTCTACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGG

               * *                                   
       1521 TGATAAAATCT-TCAATCTTCAACCTACTCCACTACTGCTT
         66 TGACAGAATCTGT-AATCTTCAACCTACTCCACTACTGCTT

       1561 AGAGA


Statistics
Matches: 1140,  Mismatches: 228, Indels: 113
        0.77            0.15        0.08

Matches are distributed among these distances:
 129   14  0.01
 130    7  0.01
 131  179  0.16
 132  784  0.69
 133  137  0.12
 134    8  0.01
 135   11  0.01

ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33


Consensus pattern (132 bp):   
TGCTTCTCTACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGG
TGACAGAATCTGTAATCTTCAACCTACTCCACTACTGCTTTGGGAGATAGGACTAATGGCTTAAA
TC

Found at i:324 original size:88 final size:88

Alignment explanation


    Indices: 227--863  Score: 1211
    Period size: 88  Copynumber: 7.2  Consensus size: 88

        217 CTTCAACCTA

                          *   *   *  *    *                                  
        227 CTCCACTACTGCTTTGGGAGATAGGTCTAACGGCTTAAATCTGCTTCTCTACTGTATTGGGAAGA
          1 CTCCACTACTGCTTAGGGTGATTGGACTAATGGCTTAAATCTGCTTCTCTACTGTATTGGGAAGA

                                   
        292 TAAGATTCACCATCTTGGATCTG
         66 TAAGATTCACCATCTTGGATCTG

                                                                             
        315 CTCCACTACTGCTTAGGGTGATTGGACTAATGGCTTAAATCTGCTTCTCTACTGTATTGGGAAGA
          1 CTCCACTACTGCTTAGGGTGATTGGACTAATGGCTTAAATCTGCTTCTCTACTGTATTGGGAAGA

                                   
        380 TAAGATTCACCATCTTGGATCTG
         66 TAAGATTCACCATCTTGGATCTG

                                                                             
        403 CTCCACTACTGCTTAGGGTGATTGGACTAATGGCTTAAATCTGCTTCTCTACTGTATTGGGAAGA
          1 CTCCACTACTGCTTAGGGTGATTGGACTAATGGCTTAAATCTGCTTCTCTACTGTATTGGGAAGA

                                   
        468 TAAGATTCACCATCTTGGATCTG
         66 TAAGATTCACCATCTTGGATCTG

                                                                             
        491 CTCCACTACTGCTTAGGGTGATTGGACTAATGGCTTAAATCTGCTTCTCTACTGTATTGGGAAGA
          1 CTCCACTACTGCTTAGGGTGATTGGACTAATGGCTTAAATCTGCTTCTCTACTGTATTGGGAAGA

                                   
        556 TAAGATTCACCATCTTGGATCTG
         66 TAAGATTCACCATCTTGGATCTG

                                                                             
        579 CTCCACTACTGCTTAGGGTGATTGGACTAATGGCTTAAATCTGCTTCTCTACTGTATTGGGAAGA
          1 CTCCACTACTGCTTAGGGTGATTGGACTAATGGCTTAAATCTGCTTCTCTACTGTATTGGGAAGA

                                   
        644 TAAGATTCACCATCTTGGATCTG
         66 TAAGATTCACCATCTTGGATCTG

                                                                             
        667 CTCCACTACTGCTTAGGGTGATTGGACTAATGGCTTAAATCTGCTTCTCTACTGTATTGGGAAGA
          1 CTCCACTACTGCTTAGGGTGATTGGACTAATGGCTTAAATCTGCTTCTCTACTGTATTGGGAAGA

                                   
        732 TAAGATTCACCATCTTGGATCTG
         66 TAAGATTCACCATCTTGGATCTG

                                                                             
        755 CTCCACTACTGCTTAGGGTGATTGGACTAATGGCTTAAATCTGCTTCTCTACTGTATTGGGAAGA
          1 CTCCACTACTGCTTAGGGTGATTGGACTAATGGCTTAAATCTGCTTCTCTACTGTATTGGGAAGA

                            *      
        820 TAAGATTCACCATCTTCGATCTG
         66 TAAGATTCACCATCTTGGATCTG

              *                  
        843 CTTCACTACTGCTTAGGGTGA
          1 CTCCACTACTGCTTAGGGTGA

        864 CAGAATCTGT


Statistics
Matches: 542,  Mismatches: 7, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  88  542  1.00

ACGTcount: A:0.24, C:0.21, G:0.22, T:0.34


Consensus pattern (88 bp):   
CTCCACTACTGCTTAGGGTGATTGGACTAATGGCTTAAATCTGCTTCTCTACTGTATTGGGAAGA
TAAGATTCACCATCTTGGATCTG

Done.