Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga09g02364.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, 822

Length: 1370
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24


Found at i:476 original size:120 final size:119

Alignment explanation


    Indices: 284--848  Score: 719
    Period size: 117  Copynumber: 4.7  Consensus size: 119

        274 AGATTATTGG

                               *     *  *     *                             *
        284 AAGAGAATGTCGAGGAAGAAAGTCCGTTTGCCGGTGAGAAACCACCTAGTGACGAAGGAGATAAG
          1 AAGAG-ATGTCGAGGAAGAGAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGATAAT

              *                    *        *                      
        349 CCCCCAGAAAGATTACTAAAAGAAATTGAGGTTATCGGTGAGAAACGAAAACTAC
         65 CCTCCAGAAAGATTACTAAAAGACATTGAGGTCATCGGTGAGAAACGAAAACTAC

                                                       *                 *   
        404 AAGCAGATGTCGAGGAAGAGAGTCCATTCGCCGGCGAGAAACCGCCTAGTGACGAAGGAGACAAT
          1 AAG-AGATGTCGAGGAAGAGAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGATAAT

                                      *                            
        469 CCTCCAGAAAGATTACTAAAAGACATCGAGGTCATCGGTGAGAAACGAAAACTAC
         65 CCTCCAGAAAGATTACTAAAAGACATTGAGGTCATCGGTGAGAAACGAAAACTAC

                     *        *                                              
        524 -A-AGATGTTGAGGAAGAAAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGATAATT
          1 AAGAGATGTCGAGGAAGAGAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGATAA-T

                           *              *     *     *     **     
        587 CC-CCAGAAAGATTATTAAAAGACATTGAGCTCATCCGTGAGGAACGATTACTAC
         65 CCTCCAGAAAGATTACTAAAAGACATTGAGGTCATCGGTGAGAAACGAAAACTAC

                                                                           * 
        641 AAGACG-T-T-GAGGAAGAGAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGATAGT
          1 AAGA-GATGTCGAGGAAGAGAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGATAAT

                              **  *     *                   **     
        703 CCTCCAGAAAGATTACTAGCAGGCATTGGGGTCATCGGTGAGAAACGATTACTAC
         65 CCTCCAGAAAGATTACTAAAAGACATTGAGGTCATCGGTGAGAAACGAAAACTAC

                   *                          *                           * *
        758 AAGCAGACGTCGAGGAAGAGAGTCCATTCGCCGGTGAGAAACCACCTAGTGACGACGAAGGAAAC
          1 AAG-AGATGTCGAGGAAGAGAGTCCATTCGCCGGCGAGAAACCACCTAGT---GACGAAGGAGAT

                 *    *          *    
        823 AATCCACCAGCAAGATTACTAGAAGA
         62 AATCCTCCAGAAAGATTACTAAAAGA

        849 AGAAGACGAC


Statistics
Matches: 391,  Mismatches: 41, Indels: 23
        0.86            0.09        0.05

Matches are distributed among these distances:
 116    3  0.01
 117  200  0.51
 118    6  0.02
 119    4  0.01
 120  145  0.37
 121    2  0.01
 123   31  0.08

ACGTcount: A:0.37, C:0.20, G:0.27, T:0.16


Consensus pattern (119 bp):   
AAGAGATGTCGAGGAAGAGAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGATAATC
CTCCAGAAAGATTACTAAAAGACATTGAGGTCATCGGTGAGAAACGAAAACTAC

Found at i:775 original size:237 final size:237

Alignment explanation


    Indices: 292--812  Score: 744
    Period size: 237  Copynumber: 2.2  Consensus size: 237

        282 GGAAGAGAAT

                             *  *                                            
        292 GTCGAGGAAGAAAGTCCGTTTGCCGGTGAGAAACCACCTAGTGACGAAGGAGATAAGCCCCCAGA
          1 GTCGAGGAAGAAAGTCCATTCGCCGGTGAGAAACCACCTAGTGACGAAGGAGATAAGCCCCCAGA

                                  * *   *                                    
        357 AAGATTACTAAAAGAAATTGAGGTTATCGGTGAGAAACGAAAACTACAAGCAGATGTCGAGGAAG
         66 AAGATTACTAAAAGAAATTGAGCTCATCCGTGAGAAACGAAAACTACAAGCAGATGTCGAGGAAG

                                     *                                       
        422 AGAGTCCATTCGCCGGCGAGAAACCGCCTAGTGACGAAGGAGACAATCCTCCAGAAAGATTACTA
        131 AGAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGAAAGATTACTA

                                                     *
        487 AAAGACATCGAGGTCATCGGTGAGAAACGAAAACTACAAGAT
        196 AAAGACATCGAGGTCATCGGTGAGAAACGAAAACTACAAGAC

              *                       *                             **       
        529 GTTGAGGAAGAAAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGATAATTCCCCAGA
          1 GTCGAGGAAGAAAGTCCATTCGCCGGTGAGAAACCACCTAGTGACGAAGGAGATAAGCCCCCAGA

                   *       *                  *     **                       
        594 AAGATTATTAAAAGACATTGAGCTCATCCGTGAGGAACGATTACTACAAG-ACG-T-T-GAGGAA
         66 AAGATTACTAAAAGAAATTGAGCTCATCCGTGAGAAACGAAAACTACAAGCA-GATGTCGAGGAA

                                                        * *                  
        655 GAGAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGATAGTCCTCCAGAAAGATTACT
        130 GAGAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGAAAGATTACT

             **  *   * *                   **             
        720 AGCAGGCATTGGGGTCATCGGTGAGAAACGATTACTACAAGCAGAC
        195 AAAAGACATCGAGGTCATCGGTGAGAAACGAAAACTAC-A--AGAC

                       *                                   
        766 GTCGAGGAAGAGAGTCCATTCGCCGGTGAGAAACCACCTAGTGACGA
          1 GTCGAGGAAGAAAGTCCATTCGCCGGTGAGAAACCACCTAGTGACGA

        813 CGAAGGAAAC


Statistics
Matches: 252,  Mismatches: 28, Indels: 8
        0.88            0.10        0.03

Matches are distributed among these distances:
 234   99  0.39
 235    2  0.01
 236    2  0.01
 237  149  0.59

ACGTcount: A:0.36, C:0.20, G:0.27, T:0.17


Consensus pattern (237 bp):   
GTCGAGGAAGAAAGTCCATTCGCCGGTGAGAAACCACCTAGTGACGAAGGAGATAAGCCCCCAGA
AAGATTACTAAAAGAAATTGAGCTCATCCGTGAGAAACGAAAACTACAAGCAGATGTCGAGGAAG
AGAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGAAAGATTACTA
AAAGACATCGAGGTCATCGGTGAGAAACGAAAACTACAAGAC
Done.