Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga08g00102.F2

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: 4111
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33


Found at i:564 original size:100 final size:99

Alignment explanation


    Indices: 428--878  Score: 526
    Period size: 100  Copynumber: 4.5  Consensus size: 99

        418 ACTGTATCGG

                   * *               *           *              *        *   
        428 TCCTTGCTTTGAGAGAAATCGTGTGGTGGCGATGATACGGGATATTTACTTGCATATGAATAATG
          1 TCCTTGCCTCGAGAGAAATCGTGTGATGGCG-TGATATGGGATATTTACTTGTATATGAATCATG

                                      *        
        493 GTTATGTAATATGTAGTCTTAATTTGCTCATTTGA
         65 GTTATGTAATATGTAGTCTTAATTTGATCATTTGA

             *      *                                                        
        528 TACTTGCCACGAGAGAAATCGTGTGATGGCAGTGATATGGGAT-TATTACTTGTATATGAATCAT
          1 TCCTTGCCTCGAGAGAAATCGTGTGATGGC-GTGATATGGGATAT-TTACTTGTATATGAATCAT

                     *           *              
        592 GGTTATGTACTATGTAGTCTTGATTTGATCATTTGA
         64 GGTTATGTAATATGTAGTCTTAATTTGATCATTTGA

                *    **    *   *                                  *        * 
        628 TCCTCGCCTTAAGAGCAATTGTGTGATGGCGATGATATGGGATATTTACTTGTAAATGAATCACG
          1 TCCTTGCCTCGAGAGAAATCGTGTGATGGCG-TGATATGGGATATTTACTTGTATATGAATCATG

                                      *   * ** 
        693 GTTATGTAATATGTAGTCTTAATTTGCTCACTCAA
         65 GTTATGTAATATGTAGTCTTAATTTGATCATTTGA

                               *       * * *     *   * *         *           
        728 TCCTTGCCTCGAGAGAAATTGTGTGACAGCCTTGATAAGGGCTTTTTACTTGTGTATGAATCATG
          1 TCCTTGCCTCGAGAGAAATCGTGTGA-TGGCGTGATATGGGATATTTACTTGTATATGAATCATG

                       *                       
        793 GTTATGTAATACGTAGTCTTAATTTGATCATTTGA
         65 GTTATGTAATATGTAGTCTTAATTTGATCATTTGA

                      *     *         *                 *      
        828 TCCTTGCCTCAAGAGATATCGTGTGACGGCGGTGATATGGGATAATTACTT
          1 TCCTTGCCTCGAGAGAAATCGTGTGATGGC-GTGATATGGGATATTTACTT

        879 CCATATATTT


Statistics
Matches: 291,  Mismatches: 54, Indels: 12
        0.82            0.15        0.03

Matches are distributed among these distances:
  99    4  0.01
 100  283  0.97
 101    4  0.01

ACGTcount: A:0.26, C:0.13, G:0.23, T:0.37


Consensus pattern (99 bp):   
TCCTTGCCTCGAGAGAAATCGTGTGATGGCGTGATATGGGATATTTACTTGTATATGAATCATGG
TTATGTAATATGTAGTCTTAATTTGATCATTTGA

Found at i:797 original size:200 final size:199

Alignment explanation


    Indices: 439--878  Score: 592
    Period size: 200  Copynumber: 2.2  Consensus size: 199

        429 CCTTGCTTTG

                          *           *                *        *            
        439 AGAGAAATCGTGTGGTGGCGATGATACGGGATATTTACTTGCATATGAATAATGGTTATGTAATA
          1 AGAG-AATCGTGTGATGGCGATGATATGGGATATTTACTTGCAAATGAATAACGGTTATGTAATA

                               * **                           **         *   
        504 TGTAGTCTTAATTTGCTCATTTGATACTTGCCACGAGAGAAATCGTGTGATGGCAGTGATATGGG
         65 TGTAGTCTTAATTTGCTCACTCAATACTTGCCACGAGAGAAATCGTGTGACAGCAGTGATAAGGG

                                            *  *        *                    
        569 ATTATTACTTGTATATGAATCATGGTTATGTACTATGTAGTCTTGATTTGATCATTTGATCCTCG
        130 ATTATTACTTGTATATGAATCATGGTTATGTAATACGTAGTCTTAATTTGATCATTTGATCCTCG

               * 
        634 CCTTA
        195 CCTCA

                    *                                *        *              
        639 AGAGCAATTGTGTGATGGCGATGATATGGGATATTTACTTGTAAATGAATCACGGTTATGTAATA
          1 AGAG-AATCGTGTGATGGCGATGATATGGGATATTTACTTGCAAATGAATAACGGTTATGTAATA

                                     *      *          *          **         
        704 TGTAGTCTTAATTTGCTCACTCAATCCTTGCCTCGAGAGAAATTGTGTGACAGCCTTGATAAGGG
         65 TGTAGTCTTAATTTGCTCACTCAATACTTGCCACGAGAGAAATCGTGTGACAGCAGTGATAAGGG

            *  *        *                                                  * 
        769 CTTTTTACTTGTGTATGAATCATGGTTATGTAATACGTAGTCTTAATTTGATCATTTGATCCTTG
        130 ATTATTACTTGTATATGAATCATGGTTATGTAATACGTAGTCTTAATTTGATCATTTGATCCTCG

                 
        834 CCTCA
        195 CCTCA

                           *    *            *      
        839 AGAGATATCGTGTGACGGCGGTGATATGGGATAATTACTT
          1 AGAGA-ATCGTGTGATGGCGATGATATGGGATATTTACTT

        879 CCATATATTT


Statistics
Matches: 208,  Mismatches: 31, Indels: 2
        0.86            0.13        0.01

Matches are distributed among these distances:
 199    1  0.00
 200  207  1.00

ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37


Consensus pattern (199 bp):   
AGAGAATCGTGTGATGGCGATGATATGGGATATTTACTTGCAAATGAATAACGGTTATGTAATAT
GTAGTCTTAATTTGCTCACTCAATACTTGCCACGAGAGAAATCGTGTGACAGCAGTGATAAGGGA
TTATTACTTGTATATGAATCATGGTTATGTAATACGTAGTCTTAATTTGATCATTTGATCCTCGC
CTCA
Done.