Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1501

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, 984

Length: 1640
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.39


Found at i:138 original size:43 final size:43

Alignment explanation


    Indices: 77--370  Score: 373
    Period size: 43  Copynumber: 6.8  Consensus size: 43

         67 GTTTTTCTAA

                         *           *                  
         77 AAGCGCCGCTAAAAACCATGAG-CTTTAGCGGCGTTTG-T-GGT
          1 AAGCGCCGCTAAAGACCATG-GTCTATAGCGGCGTTTGATGGGT

                                    *              *   *   
        118 GAAGGCGCCGCTAAAGACCATGGTTTATAGCGGCGTTT-TTCACGGT
          1 -AA-GCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGAT--GGGT

                          **   *    * *                 
        164 AAGCGCCGCTAAAGGTCATTGTCTTTCGCGGCGTTT-ATTGGGT
          1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGA-TGGGT

                                                 *     
        207 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGTTGGGT
          1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGATGGGT

                                          *            
        250 AAGCGCCGCTAAAGACCATGGTCTATAGCGACGTTTGATGGGT
          1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGATGGGT

                   *                                   
        293 AAGCGCCACTAAAGACCATGGTCTATAGCGGCGTTTGATGGGT
          1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGATGGGT

                                         *     
        336 AAGCGCCGCTAAAGACCATGGTCTATAGCAGCGTT
          1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTT

        371 GTAAAGAAAA


Statistics
Matches: 221,  Mismatches: 23, Indels: 15
        0.85            0.09        0.06

Matches are distributed among these distances:
  42    3  0.01
  43  184  0.83
  44   28  0.13
  45    3  0.01
  46    3  0.01

ACGTcount: A:0.23, C:0.22, G:0.30, T:0.25


Consensus pattern (43 bp):   
AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGATGGGT

Found at i:426 original size:129 final size:129

Alignment explanation


    Indices: 164--435  Score: 298
    Period size: 129  Copynumber: 2.1  Consensus size: 129

        154 TTTTCACGGT

                   *      **   *    * *                                      
        164 AAGCGCCGCTAAAGGTCATTGTCTTTCGCGGCGTTTATTGGGTAAGCGCCGCTAAAGACCATGGT
          1 AAGCGCCACTAAAGACCATGGTCTATAGCGGCGTTTATTGGGTAAGCGCCGCTAAAGACCATGGT

                   *        *** *  *                 *           *       ***
        229 CTATAGCGGCGTTTGTTGGGTAAGCGCCGCTAAAGACCATGGTCTATAGCGACGTTTGATGGGT
         66 CTATAGCAGCGTTTGTAAAGAAAACGCCGCTAAAGACCATGATCTATAGCGACATTTGATGAAA

                                                                             
        293 AAGCGCCACTAAAGACCATGGTCTATAGCGGCGTTTGA-TGGGTAAGCGCCGCTAAAGACCATGG
          1 AAGCGCCACTAAAGACCATGGTCTATAGCGGCGTTT-ATTGGGTAAGCGCCGCTAAAGACCATGG

                                                ** *      *     *            
        357 TCTATAGCAGCG-TTGTAAAGAAAACGCCGCTAAAGGTCTTGATCTTTAGCGGCATTTAGTAT-A
         65 TCTATAGCAGCGTTTGTAAAGAAAACGCCGCTAAAGACCATGATCTATAGCGACATTT-G-ATGA

              
        420 AA
        128 AA

                          
        422 AAGCGCCACTAAAG
          1 AAGCGCCACTAAAG

        436 TTACCGACGC


Statistics
Matches: 118,  Mismatches: 22, Indels: 6
        0.81            0.15        0.04

Matches are distributed among these distances:
 128   33  0.28
 129   82  0.69
 130    3  0.03

ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25


Consensus pattern (129 bp):   
AAGCGCCACTAAAGACCATGGTCTATAGCGGCGTTTATTGGGTAAGCGCCGCTAAAGACCATGGT
CTATAGCAGCGTTTGTAAAGAAAACGCCGCTAAAGACCATGATCTATAGCGACATTTGATGAAA
Done.