Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold826

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: 47668
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32


Found at i:7404 original size:46 final size:46

Alignment explanation


    Indices: 7354--7526  Score: 219
    Period size: 46  Copynumber: 3.7  Consensus size: 46

       7344 TGGTTGAGCA

                                                          
       7354 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
          1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG

                                          * *        *       
       7400 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
          1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G

                                                          * 
       7445 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
          1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG

            *    *                            
       7493 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
          1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA

       7527 GGGGCGGGTT


Statistics
Matches: 109,  Mismatches: 9, Indels: 18
        0.80            0.07        0.13

Matches are distributed among these distances:
  42    2  0.02
  43    5  0.05
  45    3  0.03
  46   61  0.56
  47   29  0.27
  48    3  0.03
  50    4  0.04
  51    2  0.02

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


Consensus pattern (46 bp):   
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG

Found at i:7510 original size:93 final size:93

Alignment explanation


    Indices: 7351--7521  Score: 315
    Period size: 93  Copynumber: 1.8  Consensus size: 93

       7341 GGATGGTTGA

                                                           * *               
       7351 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
          1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT

                                        
       7416 TGAGTCCGAGTTCGTGAGATGTAACTAG
         66 TGAGTCCGAGTTCGTGAGATGTAACTAG

                                                                  *          
       7444 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
          1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT

                         
       7509 TGAGTCCGAGTTC
         66 TGAGTCCGAGTTC

       7522 ACTTAGGGGC


Statistics
Matches: 75,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  93   75  1.00

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


Consensus pattern (93 bp):   
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG

Found at i:16086 original size:27 final size:27

Alignment explanation


    Indices: 15958--16075  Score: 200
    Period size: 27  Copynumber: 4.4  Consensus size: 27

      15948 GGGGCATTTT

                                       
      15958 AGTCATTTTACCACATAAGGGCAAAAC
          1 AGTCATTTTACCACATAAGGGCAAAAC

                               * *     
      15985 AGTCATTTTACCACATAAGAGAAAAAC
          1 AGTCATTTTACCACATAAGGGCAAAAC

                              *        
      16012 AGTCATTTTACCACATAATGGCAAAAC
          1 AGTCATTTTACCACATAAGGGCAAAAC

                       *               
      16039 AGTCATTTTACAACATAAGGGCAAAAC
          1 AGTCATTTTACCACATAAGGGCAAAAC

                      
      16066 AGTCATTTTA
          1 AGTCATTTTA

      16076 ATCAATTAGG


Statistics
Matches: 84,  Mismatches: 7, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  27   84  1.00

ACGTcount: A:0.42, C:0.19, G:0.13, T:0.25


Consensus pattern (27 bp):   
AGTCATTTTACCACATAAGGGCAAAAC

Found at i:18941 original size:20 final size:19

Alignment explanation


    Indices: 18897--18941  Score: 56
    Period size: 20  Copynumber: 2.3  Consensus size: 19

      18887 TATTTCTTCC

                               
      18897 TTTTTCTTCATCTCATTTT
          1 TTTTTCTTCATCTCATTTT

                                  
      18916 TCTTTTCTTCAT-TCAAGTTTT
          1 T-TTTTCTTCATCTC-A-TTTT

                 
      18937 TTTTT
          1 TTTTT

      18942 GCTTGACTTT


Statistics
Matches: 23,  Mismatches: 0, Indels: 5
        0.82            0.00        0.18

Matches are distributed among these distances:
  19    3  0.13
  20   15  0.65
  21    5  0.22

ACGTcount: A:0.11, C:0.18, G:0.02, T:0.69


Consensus pattern (19 bp):   
TTTTTCTTCATCTCATTTT

Found at i:32924 original size:27 final size:27

Alignment explanation


    Indices: 32885--32941  Score: 69
    Period size: 27  Copynumber: 2.1  Consensus size: 27

      32875 TCATGTGAAA

                           * *         
      32885 TTGAATGGCAAATTATTGTTACATGAG
          1 TTGAATGGCAAATTACTATTACATGAG

                   **                * 
      32912 TTGAATGTTAAATTACTATTACATGGG
          1 TTGAATGGCAAATTACTATTACATGAG

               
      32939 TTG
          1 TTG

      32942 TATGAATTGC


Statistics
Matches: 25,  Mismatches: 5, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  27   25  1.00

ACGTcount: A:0.32, C:0.07, G:0.21, T:0.40


Consensus pattern (27 bp):   
TTGAATGGCAAATTACTATTACATGAG
Done.