Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_3909

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: 16715
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.34


Found at i:3511 original size:93 final size:93

Alignment explanation


    Indices: 3398--3568  Score: 315
    Period size: 93  Copynumber: 1.8  Consensus size: 93

       3388 GCCCATAAGT

                                        * *                                  
       3398 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
          1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA

                                        
       3463 CGAGTTCGGATGCCTAGTTACATCTCAC
         66 CGAGTTCGGATGCCTAGTTACATCTCAC

                                   *                                         
       3491 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
          1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA

                         
       3556 CGAGTTCGGATGC
         66 CGAGTTCGGATGC

       3569 TCAACCATCC


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


Consensus pattern (93 bp):   
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC

Found at i:3565 original size:46 final size:46

Alignment explanation


    Indices: 3390--3565  Score: 225
    Period size: 46  Copynumber: 3.8  Consensus size: 46

       3380 TGTAATCCGC

                                           *    * *       
       3390 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
          1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT

                                                           *   
       3436 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
          1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT

                *  *                                      
       3486 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
          1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT

                                                 
       3529 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
          1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA

       3566 TGCTCAACCA


Statistics
Matches: 112,  Mismatches: 9, Indels: 18
        0.81            0.06        0.13

Matches are distributed among these distances:
  42    2  0.02
  43    4  0.04
  44    2  0.02
  45    2  0.02
  46   64  0.57
  47   29  0.26
  48    2  0.02
  49    2  0.02
  50    3  0.03
  51    2  0.02

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


Consensus pattern (46 bp):   
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT

Found at i:8233 original size:15 final size:15

Alignment explanation


    Indices: 8213--8254  Score: 59
    Period size: 15  Copynumber: 2.8  Consensus size: 15

       8203 ATCCATAACG

                          *
       8213 AGAAATCCAGAATAT
          1 AGAAATCCAGAATAA

                            
       8228 AGAAATCCA-ACATAA
          1 AGAAATCCAGA-ATAA

                        
       8243 AGAAATCCAGAA
          1 AGAAATCCAGAA

       8255 GAAAATATCA


Statistics
Matches: 24,  Mismatches: 1, Indels: 4
        0.83            0.03        0.14

Matches are distributed among these distances:
  14    1  0.04
  15   22  0.92
  16    1  0.04

ACGTcount: A:0.57, C:0.17, G:0.12, T:0.14


Consensus pattern (15 bp):   
AGAAATCCAGAATAA

Found at i:8795 original size:17 final size:17

Alignment explanation


    Indices: 8775--8810  Score: 56
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       8765 AAAAAAAACC

                              
       8775 AAAATAAAATAAA-CAAA
          1 AAAATAAAA-AAACCAAA

                             
       8792 AAAATAAAAAAACCAAA
          1 AAAATAAAAAAACCAAA

              
       8809 AA
          1 AA

       8811 CAGTAGAAGT


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  16    3  0.17
  17   15  0.83

ACGTcount: A:0.83, C:0.08, G:0.00, T:0.08


Consensus pattern (17 bp):   
AAAATAAAAAAACCAAA
Done.