Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga11g00757.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, 1000

Length: 3110
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.32


Found at i:2413 original size:139 final size:140

Alignment explanation


    Indices: 2041--2413  Score: 414
    Period size: 139  Copynumber: 2.6  Consensus size: 140

       2031 AGATGGGATT

                *                *                     *         *       *   
       2041 TGAAAAAACTGAAGTGAATTATTGAACATGATCAAATGGGGTTATAGAGTTGCATATTCTAAATA
          1 TGAAGAAACTGAAGTGAATTACTGAACATGATCAAATGGGGTTGTAGAGTTGCTTATTCTACATA

                             *                **                             
       2106 TGGAAGAAGCTAGGATACATGCCTGGTTTTGATTGTTTGATACATGATCTTGAAGATAGGACTTC
         66 TGGAAGAAGC-AGGATAAATGCCTGG-TTTGA-TCATTGATACATGATCTTGAAGATAGGACTTC

                *        
       2171 AAAGGAGAAAAGC
        128 AAAGAAGAAAAGC

                               *                                     *       
       2184 TGAAGAAACTGAAGT-AAGGTACTGAACATGATCAAATGGGGTTGTTA-AGTTGCTTGTTCTACA
          1 TGAAGAAACTGAAGTGAA-TTACTGAACATGATCAAATGGGGTTG-TAGAGTTGCTTATTCTACA

                      *    *      *                                  *      *
       2247 TATGGAAGAAACAGGGTAAATGGCTGGTTT-A-CATTGATACATGATCTTGAA-AGTGGGACTTG
         64 TATGGAAGAAGCAGGATAAATGCCTGGTTTGATCATTGATACATGATCTTGAAGA-TAGGACTTC

                     *    
       2309 AAGAGAAGAGAAGC
        128 AA-AGAAGAAAAGC

             *               *        *                  *             *     
       2323 TTAAGAAACTGAAGTGATTTACTGAAAATGATCAAATGGGGTTGTCGAGTTGCTTATTCCACATA
          1 TGAAGAAACTGAAGTGAATTACTGAACATGATCAAATGGGGTTGTAGAGTTGCTTATTCTACATA

                *  *    *   *         
       2388 TGGAGGAGGCAGAATATATGCCTGGT
         66 TGGAAGAAGCAGGATAAATGCCTGGT

       2414 AAAGATGGGA


Statistics
Matches: 193,  Mismatches: 31, Indels: 16
        0.80            0.13        0.07

Matches are distributed among these distances:
 137    1  0.01
 138   28  0.15
 139   82  0.42
 140    2  0.01
 141    3  0.02
 142   14  0.07
 143   61  0.32
 144    2  0.01

ACGTcount: A:0.35, C:0.10, G:0.26, T:0.28


Consensus pattern (140 bp):   
TGAAGAAACTGAAGTGAATTACTGAACATGATCAAATGGGGTTGTAGAGTTGCTTATTCTACATA
TGGAAGAAGCAGGATAAATGCCTGGTTTGATCATTGATACATGATCTTGAAGATAGGACTTCAAA
GAAGAAAAGC

Found at i:2509 original size:18 final size:18

Alignment explanation


    Indices: 2482--2519  Score: 51
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       2472 TGCTTCTAAG

                 *             
       2482 AAGCATTTTTG-GAACAAA
          1 AAGCACTTTTGAG-ACAAA

                              
       2500 AAGCACTTTTGAGACAAA
          1 AAGCACTTTTGAGACAAA

              
       2518 AA
          1 AA

       2520 CATTCCTAAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  18   17  0.94
  19    1  0.06

ACGTcount: A:0.47, C:0.13, G:0.16, T:0.24


Consensus pattern (18 bp):   
AAGCACTTTTGAGACAAA
Done.