Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga12g01575.N1

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: 1794
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32


Found at i:1336 original size:132 final size:132

Alignment explanation


    Indices: 1138--1660  Score: 850
    Period size: 132  Copynumber: 4.0  Consensus size: 132

       1128 ACTTTGATTT

                                     *       *        *      *         *     
       1138 TGCTCCACTGCAACTTCAGGGAAA-CAGGATCTGAAATTTCAGCCTACTTCACTACAACTTTAGG
          1 TGCTCCACTGCAACTTCAGGGAAATGA-GATCTAAAATTTCAACCTACTCCACTACAACCTTAGG

                      *                    *                                 
       1202 GAGCTAGGTTGGTGACTTAAATCTGCTTCACTGCAACTTCAGGAAGTCAAGATTCGTCGTCTTCG
         65 GAGCTAGGTTAGTGACTTAAATCTGCTTCACCGCAACTTCAGGAAGTCAAGATTCGTCGTCTTCG

               
       1267 ATC
        130 ATC

                *                                    *                       
       1270 TGCTGCACTGCAACTTCAGGGAAATGAGATCTAAAATTTCAGCCTACTCCACTACAACCTTAGGG
          1 TGCTCCACTGCAACTTCAGGGAAATGAGATCTAAAATTTCAACCTACTCCACTACAACCTTAGGG

                                    *                                        
       1335 AGCTAGGTTAGTGACTTAAATCTGTTTCACCGCAACTTCAGGAAGTCAAGATTCGTCGTCTTCGA
         66 AGCTAGGTTAGTGACTTAAATCTGCTTCACCGCAACTTCAGGAAGTCAAGATTCGTCGTCTTCGA

              
       1400 TC
        131 TC

                     **                                                      
       1402 TGCTCCACTATAACTTCAGGGAAATGAGATCTAAAATTTCAACCTACTCCACTACAACCTTAGGG
          1 TGCTCCACTGCAACTTCAGGGAAATGAGATCTAAAATTTCAACCTACTCCACTACAACCTTAGGG

                                                                             
       1467 AGCTAGGTTAGTGACTTAAATCTGCTTCACCGCAACTTCAGGAAGTCAAGATTCGTCGTCTTCGA
         66 AGCTAGGTTAGTGACTTAAATCTGCTTCACCGCAACTTCAGGAAGTCAAGATTCGTCGTCTTCGA

              
       1532 TC
        131 TC

                                    **    *                          *       
       1534 TGCTCCACTGCAACTTCAGGGAAACAAGATTTAAAATTTCAACCTACTCCACTACAATCTTAGGG
          1 TGCTCCACTGCAACTTCAGGGAAATGAGATCTAAAATTTCAACCTACTCCACTACAACCTTAGGG

                                   *      **             *                
       1599 AGCTAGGTTAGTGACTTAAATCTACTTCACTACAACTTCAGGAAGCCAAGATTCGTCGTCTT
         66 AGCTAGGTTAGTGACTTAAATCTGCTTCACCGCAACTTCAGGAAGTCAAGATTCGTCGTCTT

       1661 GCCACACCAT


Statistics
Matches: 367,  Mismatches: 23, Indels: 2
        0.94            0.06        0.01

Matches are distributed among these distances:
 132  366  1.00
 133    1  0.00

ACGTcount: A:0.29, C:0.24, G:0.18, T:0.28


Consensus pattern (132 bp):   
TGCTCCACTGCAACTTCAGGGAAATGAGATCTAAAATTTCAACCTACTCCACTACAACCTTAGGG
AGCTAGGTTAGTGACTTAAATCTGCTTCACCGCAACTTCAGGAAGTCAAGATTCGTCGTCTTCGA
TC

Found at i:1550 original size:45 final size:45

Alignment explanation


    Indices: 1221--1553  Score: 145
    Period size: 45  Copynumber: 7.5  Consensus size: 45

       1211 TGGTGACTTA

                    *                                    
       1221 AATCTGCTTCACTGCAACTTCAGGAAGTCAAGATTCGTCGTCTTC
          1 AATCTGCTCCACTGCAACTTCAGGAAGTCAAGATTCGTCGTCTTC

            *       *                  *  *          **     
       1266 GATCTGCTGCACTGCAACTTCAGGGAAAT-GAGA-TC-TAAAAT-TTC
          1 AATCTGCTCCACTGCAACTTCA-GGAAGTCAAGATTCGT--CGTCTTC

             **  *       *           *    *  *  *    *   *
       1310 AGCCTACTCCACTACAACCTT-AGGGAG-CTAGGTTAGT-GACTTA
          1 AATCTGCTCCACTGCAA-CTTCAGGAAGTCAAGATTCGTCGTCTTC

                  * *   *                                
       1353 AATCTGTTTCACCGCAACTTCAGGAAGTCAAGATTCGTCGTCTTC
          1 AATCTGCTCCACTGCAACTTCAGGAAGTCAAGATTCGTCGTCTTC

            *            **            *  *          **     
       1398 GATCTGCTCCACTATAACTTCAGGGAAAT-GAGA-TC-TAAAAT-TTC
          1 AATCTGCTCCACTGCAACTTCA-GGAAGTCAAGATTCGT--CGTCTTC

              *  *       *           *    *  *  *    *   *
       1442 AACCTACTCCACTACAACCTT-AGGGAG-CTAGGTTAGT-GACTTA
          1 AATCTGCTCCACTGCAA-CTTCAGGAAGTCAAGATTCGTCGTCTTC

                    *   *                                
       1485 AATCTGCTTCACCGCAACTTCAGGAAGTCAAGATTCGTCGTCTTC
          1 AATCTGCTCCACTGCAACTTCAGGAAGTCAAGATTCGTCGTCTTC

            *                       
       1530 GATCTGCTCCACTGCAACTTCAGG
          1 AATCTGCTCCACTGCAACTTCAGG

       1554 GAAACAAGAT


Statistics
Matches: 197,  Mismatches: 69, Indels: 44
        0.64            0.22        0.14

Matches are distributed among these distances:
  42    6  0.03
  43   48  0.24
  44   52  0.26
  45   81  0.41
  46   10  0.05

ACGTcount: A:0.28, C:0.26, G:0.19, T:0.28


Consensus pattern (45 bp):   
AATCTGCTCCACTGCAACTTCAGGAAGTCAAGATTCGTCGTCTTC

Done.