Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold9040.1

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: 4667
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.34


Found at i:487 original size:114 final size:114

Alignment explanation


    Indices: 242--1597  Score: 1817
    Period size: 114  Copynumber: 11.9  Consensus size: 114

        232 CCCAAAACGT

                      *    **   *            *            * *         *      
        242 GCCGCTAATAATATGTTTTACCGGCGTTTTCCCGTAAGCGCCACTACTACTAATATACATCAAGA
          1 GCCGCTAATACTATGCGTTAGCGGCGTTTTCCCATAAGCGCCACTAATTCTAATATACCTCAAGA

                   *         *             *   *      *  * ** 
        307 CCAAAGCGCTGCGTTTTTGTTAAGATATTTTACGGTGCTTTTCACCAAGC
         66 CCAAA-CTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTGACTATTC

            *                                                                
        357 ACCGCTAATACTATGCGTTAGCGGCGTTTTCCCATAAGCGCCACTAATTCTAATATACCTCAAGA
          1 GCCGCTAATACTATGCGTTAGCGGCGTTTTCCCATAAGCGCCACTAATTCTAATATACCTCAAGA

                                           *                 
        422 CCAAACTCTGCGTTTTGGTTAAGATATTTTGTGGCGCTTTTGACTATTC
         66 CCAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTGACTATTC

                                                                             
        471 GCCGCTAATACTATGCGTTAGCGGCGTTTTCCCATAAGCGCCACTAATTCTAATATACCTCAAGA
          1 GCCGCTAATACTATGCGTTAGCGGCGTTTTCCCATAAGCGCCACTAATTCTAATATACCTCAAGA

                                           *                 
        536 CCAAACTCTGCGTTTTGGTTAAGATATTTTGTGGCGCTTTTGACTATTC
         66 CCAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTGACTATTC

                                                                             
        585 GCCGCTAATACTATGCGTTAGCGGCGTTTTCCCATAAGCGCCACTAATTCTAATATACCTCAAGA
          1 GCCGCTAATACTATGCGTTAGCGGCGTTTTCCCATAAGCGCCACTAATTCTAATATACCTCAAGA

                                           *                 
        650 CCAAACTCTGCGTTTTGGTTAAGATATTTTGTGGCGCTTTTGACTATTC
         66 CCAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTGACTATTC

                                                                             
        699 GCCGCTAATACTATGCGTTAGCGGCGTTTTCCCATAAGCGCCACTAATTCTAATATACCTCAAGA
          1 GCCGCTAATACTATGCGTTAGCGGCGTTTTCCCATAAGCGCCACTAATTCTAATATACCTCAAGA

                                           *                 
        764 CCAAACTCTGCGTTTTGGTTAAGATATTTTGTGGCGCTTTTGACTATTC
         66 CCAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTGACTATTC

                                                                           * 
        813 GCCGCTAATACTATGCGTTAGCGGCGTTTTCCCATAAGCGCCACTAATTCTAATATACCTCAAAA
          1 GCCGCTAATACTATGCGTTAGCGGCGTTTTCCCATAAGCGCCACTAATTCTAATATACCTCAAGA

                       **                          *    * ** 
        878 CCAAACTCTGCACTTTGGTTAAGATATTTTGCGGCGCTTCTGACGACGC
         66 CCAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTGACTATTC

                                   *        *         *              *       
        927 GCCGCTAATACTATGCGTTAGCGACGTTTTCCAATAAGCGCCGCTAATTCTAATATATCTCAAGA
          1 GCCGCTAATACTATGCGTTAGCGGCGTTTTCCCATAAGCGCCACTAATTCTAATATACCTCAAGA

                       *               *                *  *  
        992 CCAAACTCTGCATTTTGGTTAAGATATGTTGCGGCGCTTTTGACGACGT-
         66 CCAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTGACTA-TTC

                            *               *       *                        
       1041 GCCGCTAATACTATGCTTTAGCGGCGTTTTCCAATAAGCGTCACTAATTCTAATATACCTCAAGA
          1 GCCGCTAATACTATGCGTTAGCGGCGTTTTCCCATAAGCGCCACTAATTCTAATATACCTCAAGA

                       *               *                *  *  
       1106 CCAAACTCTGCATTTTGGTTAAGATATGTTGCGGCGCTTTTGACGACGT-
         66 CCAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTGACTA-TTC

                            *               *       *                        
       1155 GCCGCTAATACTATGCTTTAGCGGCGTTTTCCAATAAGCGTCACTAATTCTAATATACCTCAAGA
          1 GCCGCTAATACTATGCGTTAGCGGCGTTTTCCCATAAGCGCCACTAATTCTAATATACCTCAAGA

                       *               *                * ** 
       1220 CCAAACTCTGCATTTTGGTTAAGATATGTTGCGGCGCTTTTGACAACGC
         66 CCAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTGACTATTC

                        * * *               *                                
       1269 GCCGCTAATACTTTCCTTTAGCGGCGTTTTCCAATAAGCGCCACTAATTCTAATATACCTCAAGA
          1 GCCGCTAATACTATGCGTTAGCGGCGTTTTCCCATAAGCGCCACTAATTCTAATATACCTCAAGA

                                * *                  *  * *  
       1334 CCAAACTCTGCGTTTTGGTTTATATATTTTGCGGCGCTTTTCACAAATC
         66 CCAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTGACTATTC

                            *         *    ** *  *                     * *   
       1383 GCCGCTAATACT-TGCTTTAGCGGCATTTTTTTCGTATGCGCCACTAATTCTAATATACATAAAG
          1 GCCGCTAATACTATGCGTTAGCGGC-GTTTTCCCATAAGCGCCACTAATTCTAATATACCTCAAG

                   ***  *     *                      *  *        
       1447 ACCAAAAAGATGTGTTTTCGTTAAGACT-TTTTGCGGCGCTGTTCA-TGA-TC
         65 ACC-AAACTCTGCGTTTTGGTTAAGA-TATTTTGCGGCGCTTTTGACT-ATTC

                   *      * *   *                *              *     *  *   
       1497 GCCGCTAGTACT-TTCTTTAACGGCGTTTTCCCATAATCGCCACTAATTCTAGTATACATCTAGA
          1 GCCGCTAATACTATGCGTTAGCGGCGTTTTCCCATAAGCGCCACTAATTCTAATATACCTCAAGA

                   *          *      *           
       1561 CCAAAACGCTGCGTTTTGATTAAGAGATTTTGCGGCG
         66 CC-AAACTCTGCGTTTTGGTTAAGATATTTTGCGGCG

       1598 GTTGATTGTA


Statistics
Matches: 1143,  Mismatches: 91, Indels: 16
        0.91            0.07        0.01

Matches are distributed among these distances:
 113   72  0.06
 114  977  0.85
 115   93  0.08
 116    1  0.00

ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33


Consensus pattern (114 bp):   
GCCGCTAATACTATGCGTTAGCGGCGTTTTCCCATAAGCGCCACTAATTCTAATATACCTCAAGA
CCAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTGACTATTC

Found at i:3864 original size:58 final size:58

Alignment explanation


    Indices: 3774--3889  Score: 223
    Period size: 58  Copynumber: 2.0  Consensus size: 58

       3764 TGGGAAGAGT

                 *                                                    
       3774 GGAGCGGAGTCCAATGTGCATGGAAAAAGAGAAGAAAAAAAGCAAAGAAAGATGAAAA
          1 GGAGCCGAGTCCAATGTGCATGGAAAAAGAGAAGAAAAAAAGCAAAGAAAGATGAAAA

                                                                      
       3832 GGAGCCGAGTCCAATGTGCATGGAAAAAGAGAAGAAAAAAAGCAAAGAAAGATGAAAA
          1 GGAGCCGAGTCCAATGTGCATGGAAAAAGAGAAGAAAAAAAGCAAAGAAAGATGAAAA

       3890 TGAAGAGAGT


Statistics
Matches: 57,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  58   57  1.00

ACGTcount: A:0.53, C:0.09, G:0.28, T:0.09


Consensus pattern (58 bp):   
GGAGCCGAGTCCAATGTGCATGGAAAAAGAGAAGAAAAAAAGCAAAGAAAGATGAAAA
Done.