Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1096

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: 16313
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:1354 original size:46 final size:44

Alignment explanation


    Indices: 1250--1357  Score: 144
    Period size: 44  Copynumber: 2.4  Consensus size: 44

       1240 TGTCTTTGAC

                         ** * *            *            
       1250 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
          1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT

                                                     *    
       1294 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
          1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT

                              
       1340 ATGGACTTACATGGCTCA
          1 ATGGACTTACATGGCTCA

       1358 TTTCTGTTCT


Statistics
Matches: 56,  Mismatches: 6, Indels: 2
        0.88            0.09        0.03

Matches are distributed among these distances:
  44   33  0.59
  46   23  0.41

ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33


Consensus pattern (44 bp):   
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT

Found at i:8575 original size:45 final size:46

Alignment explanation


    Indices: 8412--8586  Score: 216
    Period size: 45  Copynumber: 3.8  Consensus size: 46

       8402 TGGTTGAGCA

                                                        * 
       8412 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
          1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG

                                          * *        *       
       8458 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
          1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---G

                                                            
       8503 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
          1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG

                 *                       *       
       8551 -CCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
          1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG

       8587 GCGGGTTACA


Statistics
Matches: 111,  Mismatches: 9, Indels: 19
        0.80            0.06        0.14

Matches are distributed among these distances:
  42    2  0.02
  43    4  0.04
  45   37  0.33
  46   29  0.26
  47   29  0.26
  48    3  0.03
  50    4  0.04
  51    3  0.03

ACGTcount: A:0.21, C:0.21, G:0.30, T:0.29


Consensus pattern (46 bp):   
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG

Found at i:14744 original size:45 final size:46

Alignment explanation


    Indices: 14635--14753  Score: 181
    Period size: 46  Copynumber: 2.6  Consensus size: 46

      14625 AAGCGAACTC

                                  *       *                
      14635 AACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAGTG
          1 AACTCGGACTCAACTCAACGAGTTC-GGACATTCGCATCCATAAGTG

                                                           
      14681 AACTCGGACTC-ACATCAACGAGTTCGGACATTCGCATCCAT-AGTG
          1 AACTCGGACTCAAC-TCAACGAGTTCGGACATTCGCATCCATAAGTG

                                        
      14726 AACTCGGACTCAACTCAACGAGTTCGGA
          1 AACTCGGACTCAACTCAACGAGTTCGGA

      14754 TGCTCAATCA


Statistics
Matches: 68,  Mismatches: 2, Indels: 7
        0.88            0.03        0.09

Matches are distributed among these distances:
  45   33  0.49
  46   35  0.51

ACGTcount: A:0.29, C:0.29, G:0.21, T:0.20


Consensus pattern (46 bp):   
AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTG
Done.