Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga06g01127.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: 3370
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30


Found at i:1386 original size:27 final size:27

Alignment explanation


    Indices: 1344--1420  Score: 109
    Period size: 27  Copynumber: 2.9  Consensus size: 27

       1334 AATTTAAGAT

                                   * * 
       1344 CAAGCCATGGTGATCAACAACCTTTGC
          1 CAAGCCATGGTGATCAACAACCTGTAC

             * *                *      
       1371 CGATCCATGGTGATCAACAATCTGTAC
          1 CAAGCCATGGTGATCAACAACCTGTAC

                                   
       1398 CAAGCCATGGTGATCAACAACCT
          1 CAAGCCATGGTGATCAACAACCT

       1421 ATGTCAAACC


Statistics
Matches: 42,  Mismatches: 8, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  27   42  1.00

ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22


Consensus pattern (27 bp):   
CAAGCCATGGTGATCAACAACCTGTAC

Found at i:1432 original size:27 final size:27

Alignment explanation


    Indices: 1344--1432  Score: 106
    Period size: 27  Copynumber: 3.3  Consensus size: 27

       1334 AATTTAAGAT

                                   *   
       1344 CAAGCCATGGTGATCAACAACCTTTGC
          1 CAAGCCATGGTGATCAACAACCTATGC

             * *                *  * * 
       1371 CGATCCATGGTGATCAACAATCTGTAC
          1 CAAGCCATGGTGATCAACAACCTATGC

                                      *
       1398 CAAGCCATGGTGATCAACAACCTATGT
          1 CAAGCCATGGTGATCAACAACCTATGC

               *    
       1425 CAAACCAT
          1 CAAGCCAT

       1433 ATTACCAACT


Statistics
Matches: 50,  Mismatches: 12, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  27   50  1.00

ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22


Consensus pattern (27 bp):   
CAAGCCATGGTGATCAACAACCTATGC

Found at i:1553 original size:171 final size:171

Alignment explanation


    Indices: 1261--1602  Score: 612
    Period size: 171  Copynumber: 2.0  Consensus size: 171

       1251 TGTGGCTTAT

                            *                                                
       1261 TATTACCAACTATGATTCCCATCCAGTACAAATCAATGAGCGAGTGGCAAAACAACCTAGGAGGA
          1 TATTACCAACTATGATCCCCATCCAGTACAAATCAATGAGCGAGTGGCAAAACAACCTAGGAGGA

                                         *                                   
       1326 AGAGACCTAATTTAAGATCAAGCCATGGTGATCAACAACCTTTGCCGATCCATGGTGATCAACAA
         66 AGAGACCTAATTTAAGATCAAGCCATGGTCATCAACAACCTTTGCCGATCCATGGTGATCAACAA

                                                     
       1391 TCTGTACCAAGCCATGGTGATCAACAACCTATGTCAAACCA
        131 TCTGTACCAAGCCATGGTGATCAACAACCTATGTCAAACCA

                                                                 *           
       1432 TATTACCAACTATGATCCCCATCCAGTACAAATCAATGAGCGAGTGGCAAAACTACCTAGGAGGA
          1 TATTACCAACTATGATCCCCATCCAGTACAAATCAATGAGCGAGTGGCAAAACAACCTAGGAGGA

                    **                             *         *               
       1497 AGAGACCTCGTTTAAGATCAAGCCATGGTCATCAACAACTTTTGCCGATTCATGGTGATCAACAA
         66 AGAGACCTAATTTAAGATCAAGCCATGGTCATCAACAACCTTTGCCGATCCATGGTGATCAACAA

                   *                                 
       1562 TCTGTACTAAGCCATGGTGATCAACAACCTATGTCAAACCA
        131 TCTGTACCAAGCCATGGTGATCAACAACCTATGTCAAACCA

       1603 CAGTGATCAA


Statistics
Matches: 163,  Mismatches: 8, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
 171  163  1.00

ACGTcount: A:0.35, C:0.25, G:0.18, T:0.23


Consensus pattern (171 bp):   
TATTACCAACTATGATCCCCATCCAGTACAAATCAATGAGCGAGTGGCAAAACAACCTAGGAGGA
AGAGACCTAATTTAAGATCAAGCCATGGTCATCAACAACCTTTGCCGATCCATGGTGATCAACAA
TCTGTACCAAGCCATGGTGATCAACAACCTATGTCAAACCA

Found at i:1577 original size:27 final size:26

Alignment explanation


    Indices: 1547--1642  Score: 113
    Period size: 27  Copynumber: 3.6  Consensus size: 26

       1537 TTTGCCGATT

                                       
       1547 CATGGTGATCAACAATCTGTACTAAGC
          1 CATGGTGATCAACAATCTGTAC-AAGC

                              *       * 
       1574 CATGGTGATCAACAACCTATGT-CAAAC
          1 CATGGTGATCAACAA--TCTGTACAAGC

              **                       
       1601 CACAGTGATCAACAATCTGTACCAAGC
          1 CATGGTGATCAACAATCTGTA-CAAGC

                           
       1628 CATGGTGATCAACAA
          1 CATGGTGATCAACAA

       1643 CCTGGACCAC


Statistics
Matches: 57,  Mismatches: 8, Indels: 8
        0.78            0.11        0.11

Matches are distributed among these distances:
  25    4  0.07
  27   48  0.84
  28    1  0.02
  29    4  0.07

ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22


Consensus pattern (26 bp):   
CATGGTGATCAACAATCTGTACAAGC

Done.