Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3608

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: 8496
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30


Found at i:1397 original size:40 final size:40

Alignment explanation


    Indices: 1314--1529  Score: 350
    Period size: 40  Copynumber: 5.5  Consensus size: 40

       1304 AAACCAAGTA

                     *                       *   *  
       1314 CCTTCGGGATTTAG-CCGGATATAGT-ACTCGCTCAACTG
          1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG

                                                    
       1352 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
          1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG

            *                                     *  
       1392 TCTTCGGGACTTAGCCCGGATATAGT-ACTCGCACAATTTG
          1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAA-ATG

                                                    
       1432 CCTTCGGGACTTAGCCCGGA-ATAGTAACTCGCACAAATG
          1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG

                                                    
       1471 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
          1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG

                               
       1511 CCTTCGGGACTTAGCCCGG
          1 CCTTCGGGACTTAGCCCGG

       1530 TTATTATCCG


Statistics
Matches: 166,  Mismatches: 7, Indels: 8
        0.92            0.04        0.04

Matches are distributed among these distances:
  38   13  0.08
  39   48  0.29
  40  105  0.63

ACGTcount: A:0.24, C:0.28, G:0.24, T:0.25


Consensus pattern (40 bp):   
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG

Found at i:1456 original size:79 final size:79

Alignment explanation


    Indices: 1314--1529  Score: 355
    Period size: 79  Copynumber: 2.7  Consensus size: 79

       1304 AAACCAAGTA

                     *                      *   *                            
       1314 CCTTCGGGATTTAG-CCGGATATAGTACTCGCTCAACTGCCTTCGGGACTTAGCCCGGATATAGT
          1 CCTTCGGGACTTAGCCCGGATATAGTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT

                          
       1378 AACTCGCACAAATG
         66 AACTCGCACAAATG

            *                                    *                           
       1392 TCTTCGGGACTTAGCCCGGATATAGTACTCGCACAATTTGCCTTCGGGACTTAGCCCGGA-ATAG
          1 CCTTCGGGACTTAGCCCGGATATAGTACTCGCACAA-ATGCCTTCGGGACTTAGCCCGGATATAG

                           
       1456 TAACTCGCACAAATG
         65 TAACTCGCACAAATG

                                                                       
       1471 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
          1 CCTTCGGGACTTAGCCCGGATATAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGG

       1530 TTATTATCCG


Statistics
Matches: 129,  Mismatches: 6, Indels: 5
        0.92            0.04        0.04

Matches are distributed among these distances:
  78   12  0.09
  79   85  0.66
  80   32  0.25

ACGTcount: A:0.24, C:0.28, G:0.24, T:0.25


Consensus pattern (79 bp):   
CCTTCGGGACTTAGCCCGGATATAGTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
AACTCGCACAAATG

Found at i:1524 original size:119 final size:118

Alignment explanation


    Indices: 1314--1529  Score: 371
    Period size: 119  Copynumber: 1.8  Consensus size: 118

       1304 AAACCAAGTA

                     *                     *   *                             
       1314 CCTTCGGGATTTAGCCGGATATAGTACTCGCTCAACTGCCTTCGGGACTTAGCCCGGATATAGTA
          1 CCTTCGGGACTTAGCCGGATATAGTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTA

                         *                                       
       1379 ACTCGCACAAATGTCTTCGGGACTTAGCCCGGATATAGTACTCGCACAATTTG
         66 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTACTCGCACAATTTG

                                                                             
       1432 CCTTCGGGACTTAGCCCGGA-ATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
          1 CCTTCGGGACTTAG-CCGGATATAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG

                                              
       1496 TAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
         64 TAACTCGCACAAATGCCTTCGGGACTTAGCCCGG

       1530 TTATTATCCG


Statistics
Matches: 92,  Mismatches: 4, Indels: 3
        0.93            0.04        0.03

Matches are distributed among these distances:
 118   18  0.20
 119   74  0.80

ACGTcount: A:0.24, C:0.28, G:0.24, T:0.25


Consensus pattern (118 bp):   
CCTTCGGGACTTAGCCGGATATAGTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTA
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTACTCGCACAATTTG
Done.