Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga06g01809.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: 3134
ACGTcount: A:0.34, C:0.15, G:0.29, T:0.22


Found at i:1358 original size:189 final size:186

Alignment explanation


    Indices: 1038--1679  Score: 758
    Period size: 189  Copynumber: 3.4  Consensus size: 186

       1028 AAAAGTTTGA

                                             *                  *  *     *  *
       1038 GGGTAGTGAATCTGATTCTGATGCTGACAGAGCGAGAGGTCATACAAAGGAATTGATTAAGGAAG
          1 GGGTAGTGAATCTGATTCTGATGCTGACAGAGCAAGAGGTCATA-AAAGGAAATGGTTAAGAAAC

                   *                   *                                     
       1103 GTCGTCAAAGGCATGACTCCAGTGAGGGTGACTCTGATTCTGATGGTGGGAGGCAAAAGAAGAGA
         65 GTCGTCATAGGCATGACTCCAGTGAGGATGACTCTGATTCTGATGGTGGGAGGCAAAAGAAGAGA

                                        **   *                         
       1168 GGTGAAGTTCAAAAACGGAAGATTGAGTCAACTAGGAGCCAGAGGAGAGAGAGGGACAT
        130 GGTGAAGTTCAAAAA-GGAAGATTGAGTTGACTGGGAGCCAGAGGAGAGAGAGGG-CAT

                                                                             
       1227 GGGTAGTGAATCTGATTCTGATGCTGACAGAGCAAGAGGTCATAGAAAGGAAATGGTTAAGAAAC
          1 GGGTAGTGAATCTGATTCTGATGCTGACAGAGCAAGAGGTCATA-AAAGGAAATGGTTAAGAAAC

                         **             **   *                               
       1292 GTCGTCATAGGCACAACTCCAGTGAGGACAACTTTGATTCTGATGGTGGGAGGCAAAAGAAGAGA
         65 GTCGTCATAGGCATGACTCCAGTGAGGATGACTCTGATTCTGATGGTGGGAGGCAAAAGAAGAGA

                                            *                          
       1357 GGTGAAGTTCAAAAAGGAAAGATTGAGTTGACGGGGAGCCAGAGGAGAGAGAGGGCCAT
        130 GGTGAAGTTCAAAAAGG-AAGATTGAGTTGACTGGGAGCCAGAGGAGAGAGAGGG-CAT

                                * **   *    **       *                      *
       1416 GGGTAGTGAATCTGATTCTGGTAATGATAGAGTGAGAGGTCGTAAGAAGGAAATGGTTAAGAAAG
          1 GGGTAGTGAATCTGATTCTGATGCTGACAGAGCAAGAGGTCATAA-AAGGAAATGGTTAAGAAAC

                  *  * *         *                       *  *  * *           
       1481 GTCGTCGTATGAATGACTCCAATGAGGATGACTCTGATTCTGATGTTGAGAAGAAAAAGAAGAGA
         65 GTCGTCATAGGCATGACTCCAGTGAGGATGACTCTGATTCTGATGGTGGGAGGCAAAAGAAGAGA

                           *       *                                  
       1546 GGTGAAGTTCAGAAAGGGAAGATCGAGTTGACTGGGAGCC--A-GAG-GAGA-GGCA-
        130 GGTGAAGTTCA-AAAAGGAAGATTGAGTTGACTGGGAGCCAGAGGAGAGAGAGGGCAT

                      *  *     *                    *               *  *     
       1598 GGGATAGTGACTCAGATTCCGATG-TAGACAGAGCAAGAGATCATAAAAGGGAAATAGTAAAGAA
          1 GGG-TAGTGAATCTGATTCTGATGCT-GACAGAGCAAGAGGTCATAAAA-GGAAATGGTTAAGAA

                *        *    
       1662 ACGTGGTCATAGGTATGA
         63 ACGTCGTCATAGGCATGA

       1680 TACAGGAGAT


Statistics
Matches: 388,  Mismatches: 59, Indels: 18
        0.83            0.13        0.04

Matches are distributed among these distances:
 182    6  0.02
 183   58  0.15
 184    2  0.01
 185    4  0.01
 186    3  0.01
 187    1  0.00
 188    3  0.01
 189  306  0.79
 190    5  0.01

ACGTcount: A:0.35, C:0.12, G:0.34, T:0.20


Consensus pattern (186 bp):   
GGGTAGTGAATCTGATTCTGATGCTGACAGAGCAAGAGGTCATAAAAGGAAATGGTTAAGAAACG
TCGTCATAGGCATGACTCCAGTGAGGATGACTCTGATTCTGATGGTGGGAGGCAAAAGAAGAGAG
GTGAAGTTCAAAAAGGAAGATTGAGTTGACTGGGAGCCAGAGGAGAGAGAGGGCAT

Found at i:2326 original size:39 final size:39

Alignment explanation


    Indices: 2265--2461  Score: 216
    Period size: 39  Copynumber: 5.0  Consensus size: 39

       2255 CCAAAGCTTA

                     *                              
       2265 TGGGGAGAATGATGATCAGAATAGGGATGAATATTCTAGG
          1 TGGGG-GAAAGATGATCAGAATAGGGATGAATATTCTAGG

                          * *     * *              
       2305 TGGGGGAAAGATGACCGGAATAAGCATGAATATTCTAGG
          1 TGGGGGAAAGATGATCAGAATAGGGATGAATATTCTAGG

                    *      * *     *         *     *
       2344 TGGGGG-ATGAGTGACCGGAATAAGGATGAATACTCTAGA
          1 TGGGGGAAAGA-TGATCAGAATAGGGATGAATATTCTAGG

                 *                                 
       2383 TGGGGAAAAGATGATCAGAATAGGGATGAATATTCTAGG
          1 TGGGGGAAAGATGATCAGAATAGGGATGAATATTCTAGG

                *           *   *    *   *         
       2422 TGGGAGAAAGATGATCTGAAAAGGGGTGATTATTCTAGG
          1 TGGGGGAAAGATGATCAGAATAGGGATGAATATTCTAGG

             
       2461 T
          1 T

       2462 CAGTTAGGTC


Statistics
Matches: 133,  Mismatches: 22, Indels: 5
        0.83            0.14        0.03

Matches are distributed among these distances:
  38    3  0.02
  39  122  0.92
  40    8  0.06

ACGTcount: A:0.35, C:0.07, G:0.35, T:0.23


Consensus pattern (39 bp):   
TGGGGGAAAGATGATCAGAATAGGGATGAATATTCTAGG

Done.