Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3573

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: 29904
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31


Found at i:20928 original size:45 final size:46

Alignment explanation


    Indices: 20873--20998  Score: 161
    Period size: 46  Copynumber: 2.8  Consensus size: 46

      20863 ATGGTTGAGC

                                                         * 
      20873 ATCC-AACTCGTTGAGTTGAGTCCGAGTTCACTTATGATGCA-AATG
          1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA-GATGCACAAGG

                                           * *     *  *   
      20918 -TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAGATGTACTAGG
          1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAGATGCACAAGG

                                                 
      20962 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAG
          1 -ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAG

      20999 GGGCGGGTTA


Statistics
Matches: 69,  Mismatches: 7, Indels: 8
        0.82            0.08        0.10

Matches are distributed among these distances:
  43    5  0.07
  44    7  0.10
  45   25  0.36
  46   29  0.42
  47    3  0.04

ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30


Consensus pattern (46 bp):   
ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAGATGCACAAGG

Found at i:28498 original size:47 final size:47

Alignment explanation


    Indices: 28380--28552  Score: 189
    Period size: 47  Copynumber: 3.7  Consensus size: 47

      28370 GGATGGTTGA

                                               *           *
      28380 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAT
          1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGCAAAG

                                             *        *      
      28428 G--TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA-GATGTAACTAG
          1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGCAA--AG

                                               *        *  *
      28473 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCA-TTATGGATGCGAAC
          1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGCAAAG

                    *                          
      28520 GC--CCGAGCTCGTTGAGTTGAGTCCGAGTTCACT
          1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACT

      28553 TAGGGGCGGT


Statistics
Matches: 108,  Mismatches: 9, Indels: 18
        0.80            0.07        0.13

Matches are distributed among these distances:
  43    6  0.06
  45   32  0.30
  46   30  0.28
  47   34  0.31
  48    1  0.01
  49    5  0.05

ACGTcount: A:0.22, C:0.21, G:0.28, T:0.28


Consensus pattern (47 bp):   
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGCAAAG

Found at i:28549 original size:92 final size:93

Alignment explanation


    Indices: 28380--28549  Score: 297
    Period size: 92  Copynumber: 1.8  Consensus size: 93

      28370 GGATGGTTGA

                                                           * *               
      28380 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
          1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT

                                        
      28445 TGAGTCCGAGTTCGTGAGATGTAACTAG
         66 TGAGTCCGAGTTCGTGAGATGTAACTAG

                                                        *         *          
      28473 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCA-TTATGGATGCGAACGCCCGAGCTCGTTGAGT
          1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT

                         
      28537 TGAGTCCGAGTTC
         66 TGAGTCCGAGTTC

      28550 ACTTAGGGGC


Statistics
Matches: 73,  Mismatches: 4, Indels: 1
        0.94            0.05        0.01

Matches are distributed among these distances:
  92   40  0.55
  93   33  0.45

ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28


Consensus pattern (93 bp):   
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Done.