Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga11g00115.F3

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: 2829
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.30


Found at i:1370 original size:6 final size:6

Alignment explanation


    Indices: 1359--1609  Score: 306
    Period size: 6  Copynumber: 41.8  Consensus size: 6

       1349 GGCTTCTTCC

                               *         *   *      *              
       1359 TCAAGT TCAAGT TCAAGA TCAAGT TGAAGA TCAAGA TCAAGT TCAAGT
          1 TCAAGT TCAAGT TCAAGT TCAAGT TCAAGT TCAAGT TCAAGT TCAAGT

                                      *         *   *      *       
       1407 TCAAGT TCAAGT TCAAGT TCAAGA TCAAGT TGAAGA TCAAGA TCAAGT
          1 TCAAGT TCAAGT TCAAGT TCAAGT TCAAGT TCAAGT TCAAGT TCAAGT

                 *      *             *        **                  *
       1455 TCAAGA TCAAGA TCAAGT TCAAGA TCAAGT AGAA-T ATCAAGT TCAAGA
          1 TCAAGT TCAAGT TCAAGT TCAAGT TCAAGT TCAAGT -TCAAGT TCAAGT

                 *      *                           *              
       1503 TCAAGA TCAAGA TCAAGT TCAAGT TCAAGT TCAAGA TCAAGT TCAAGT
          1 TCAAGT TCAAGT TCAAGT TCAAGT TCAAGT TCAAGT TCAAGT TCAAGT

                 *                    *                           *
       1551 TCAAGA TCAAGT TCAAGT TCAAGA TCAAGT TCAAGT TCAAGT TCAAGA
          1 TCAAGT TCAAGT TCAAGT TCAAGT TCAAGT TCAAGT TCAAGT TCAAGT

                        
       1599 TCAAGT TCAAG
          1 TCAAGT TCAAG

       1610 AAAATTTGTT


Statistics
Matches: 213,  Mismatches: 30, Indels: 4
        0.86            0.12        0.02

Matches are distributed among these distances:
   5    1  0.00
   6  211  0.99
   7    1  0.00

ACGTcount: A:0.41, C:0.16, G:0.18, T:0.26


Consensus pattern (6 bp):   
TCAAGT

Found at i:1382 original size:18 final size:18

Alignment explanation


    Indices: 1359--1610  Score: 355
    Period size: 18  Copynumber: 14.0  Consensus size: 18

       1349 GGCTTCTTCC

                              
       1359 TCAAGTTCAAGTTCAAGA
          1 TCAAGTTCAAGTTCAAGA

                   *   *      
       1377 TCAAGTTGAAGATCAAGA
          1 TCAAGTTCAAGTTCAAGA

                             *
       1395 TCAAGTTCAAGTTCAAGT
          1 TCAAGTTCAAGTTCAAGA

                              
       1413 TCAAGTTCAAGTTCAAGA
          1 TCAAGTTCAAGTTCAAGA

                   *   *      
       1431 TCAAGTTGAAGATCAAGA
          1 TCAAGTTCAAGTTCAAGA

                       *      
       1449 TCAAGTTCAAGATCAAGA
          1 TCAAGTTCAAGTTCAAGA

                       *      
       1467 TCAAGTTCAAGATCAAG-
          1 TCAAGTTCAAGTTCAAGA

                 *              
       1484 T-AGAATATCAAGTTCAAGA
          1 TCA-AGT-TCAAGTTCAAGA

                 *     *     *
       1503 TCAAGATCAAGATCAAGT
          1 TCAAGTTCAAGTTCAAGA

                              
       1521 TCAAGTTCAAGTTCAAGA
          1 TCAAGTTCAAGTTCAAGA

                              
       1539 TCAAGTTCAAGTTCAAGA
          1 TCAAGTTCAAGTTCAAGA

                              
       1557 TCAAGTTCAAGTTCAAGA
          1 TCAAGTTCAAGTTCAAGA

                             *
       1575 TCAAGTTCAAGTTCAAGT
          1 TCAAGTTCAAGTTCAAGA

                 *            
       1593 TCAAGATCAAGTTCAAGA
          1 TCAAGTTCAAGTTCAAGA

       1611 AAATTTGTTC


Statistics
Matches: 209,  Mismatches: 21, Indels: 8
        0.88            0.09        0.03

Matches are distributed among these distances:
  16    1  0.00
  17    3  0.01
  18  202  0.97
  19    2  0.01
  20    1  0.00

ACGTcount: A:0.41, C:0.15, G:0.17, T:0.26


Consensus pattern (18 bp):   
TCAAGTTCAAGTTCAAGA
Done.