Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga10g01168.F1

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, 819

Length: 1365
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23


Found at i:334 original size:24 final size:24

Alignment explanation


    Indices: 302--360  Score: 82
    Period size: 24  Copynumber: 2.5  Consensus size: 24

        292 AGGGCACACA

                         *       *  
        302 TAAACCTCCACGATACTCAGGTGG
          1 TAAACCTCCACGACACTCAGGAGG

                      *       *     
        326 TAAACCTCCAAGACACTCGGGAGG
          1 TAAACCTCCACGACACTCAGGAGG

                       
        350 TAAACCTCCAC
          1 TAAACCTCCAC

        361 ATGTTGAGGG


Statistics
Matches: 30,  Mismatches: 5, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  24   30  1.00

ACGTcount: A:0.32, C:0.32, G:0.19, T:0.17


Consensus pattern (24 bp):   
TAAACCTCCACGACACTCAGGAGG

Found at i:535 original size:24 final size:24

Alignment explanation


    Indices: 503--562  Score: 93
    Period size: 24  Copynumber: 2.5  Consensus size: 24

        493 AGGGCACACA

                                 *  
        503 TAAACCTCCACAACACTCAGGTGG
          1 TAAACCTCCACAACACTCAGGGGG

                       *   *        
        527 TAAACCTCCACGACATTCAGGGGG
          1 TAAACCTCCACAACACTCAGGGGG

                        
        551 TAAACCTCCACA
          1 TAAACCTCCACA

        563 TGTTGAAGGA


Statistics
Matches: 32,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  24   32  1.00

ACGTcount: A:0.33, C:0.33, G:0.17, T:0.17


Consensus pattern (24 bp):   
TAAACCTCCACAACACTCAGGGGG

Found at i:618 original size:171 final size:171

Alignment explanation


    Indices: 401--992  Score: 812
    Period size: 171  Copynumber: 3.4  Consensus size: 171

        391 CCATGAAGCC

                                 *        * *                     *          
        401 ATTCCCTGGTGACAAACCATCTAAGGGTAATGAAAAGGGAGCACCTCATGAACCTAAACCTCCTC
          1 ATTCCCTGGTGACAAACCATCCAAGGGTAAGGGAAAGGGAGCACCTCATGAACCAAAACCTCCTC

                    *                                                        
        466 ATAGACACTTATTGAGTGTGGAAGTTGAGGGCACACATAAACCTCCACAACACTCAGGTGGTAAA
         66 ATAGACACATATTGAGTGTGGAAGTTGAGGGCACACATAAACCTCCACAACACTCAGGTGGTAAA

                                                     
        531 CCTCCACGACATTCAGGGGGTAAACCTCCACATGTTGAAGG
        131 CCTCCACGACATTCAGGGGGTAAACCTCCACATGTTGAAGG

               *                                   *              *          
        572 ATTTCCTGGTGACAAACCATCCAAGGGTAAGGGAAAGGGGGCACCTCATGAACCCAAACCTCCTC
          1 ATTCCCTGGTGACAAACCATCCAAGGGTAAGGGAAAGGGAGCACCTCATGAACCAAAACCTCCTC

             *                               *                  *            
        637 ACAGACACATATTGAGTGTGGAAGTTGAGGGCATACATAAACCTCCACAACAATCAGGTGGTAAA
         66 ATAGACACATATTGAGTGTGGAAGTTGAGGGCACACATAAACCTCCACAACACTCAGGTGGTAAA

                                                     
        702 CCTCCACGACATTCAGGGGGTAAACCTCCACATGTTGAAGG
        131 CCTCCACGACATTCAGGGGGTAAACCTCCACATGTTGAAGG

                                                                             
        743 ATTCCCTGGTGACAAACCATCCAAGGGTAAGGGAAAGGGAGCACCTCATGAACCAAAACCTCCTC
          1 ATTCCCTGGTGACAAACCATCCAAGGGTAAGGGAAAGGGAGCACCTCATGAACCAAAACCTCCTC

                    *      *   *          *         *                 *      
        808 ATAGACACCTATTGAATGTCGAAGTTGAGGACACACATAAGCCTCCACAACACTCAGGGGGTAAA
         66 ATAGACACATATTGAGTGTGGAAGTTGAGGGCACACATAAACCTCCACAACACTCAGGTGGTAAA

                            *      * **     *  *        **  **
        873 CCTCCACATGTTGAAGGATTCCCCGACGGTAAGCCACC-CA--TAAAACC
        131 CCTCCAC-----G-A-CATT--CAGGGGGTAAACCTCCACATGTTGAAGG

                  *                                  *            *          
        920 ATTCCCCGGTGACAAACCATCCAAGGGTAAGGGAAAGGGAGTACCTCATGAACCTAAACCTCCTC
          1 ATTCCCTGGTGACAAACCATCCAAGGGTAAGGGAAAGGGAGCACCTCATGAACCAAAACCTCCTC

                    
        985 ATAGACAC
         66 ATAGACAC

        993 CTCTTAAGTG


Statistics
Matches: 377,  Mismatches: 35, Indels: 12
        0.89            0.08        0.03

Matches are distributed among these distances:
 171  286  0.76
 176    1  0.00
 177   74  0.20
 178    3  0.01
 179    2  0.01
 180   11  0.03

ACGTcount: A:0.33, C:0.27, G:0.22, T:0.18


Consensus pattern (171 bp):   
ATTCCCTGGTGACAAACCATCCAAGGGTAAGGGAAAGGGAGCACCTCATGAACCAAAACCTCCTC
ATAGACACATATTGAGTGTGGAAGTTGAGGGCACACATAAACCTCCACAACACTCAGGTGGTAAA
CCTCCACGACATTCAGGGGGTAAACCTCCACATGTTGAAGG

Found at i:706 original size:24 final size:24

Alignment explanation


    Indices: 674--733  Score: 93
    Period size: 24  Copynumber: 2.5  Consensus size: 24

        664 AGGGCATACA

                                 *  
        674 TAAACCTCCACAACAATCAGGTGG
          1 TAAACCTCCACAACAATCAGGGGG

                       *   *        
        698 TAAACCTCCACGACATTCAGGGGG
          1 TAAACCTCCACAACAATCAGGGGG

                        
        722 TAAACCTCCACA
          1 TAAACCTCCACA

        734 TGTTGAAGGA


Statistics
Matches: 32,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  24   32  1.00

ACGTcount: A:0.35, C:0.32, G:0.17, T:0.17


Consensus pattern (24 bp):   
TAAACCTCCACAACAATCAGGGGG

Done.