Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1392

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: 17684
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33


Found at i:4724 original size:17 final size:17

Alignment explanation


    Indices: 4702--4736  Score: 70
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       4692 ACTCAATGAG

                             
       4702 GAATCTATACATATAAA
          1 GAATCTATACATATAAA

                             
       4719 GAATCTATACATATAAA
          1 GAATCTATACATATAAA

             
       4736 G
          1 G

       4737 TATAACTCCT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   18  1.00

ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29


Consensus pattern (17 bp):   
GAATCTATACATATAAA

Found at i:8132 original size:40 final size:40

Alignment explanation


    Indices: 8084--8249  Score: 253
    Period size: 40  Copynumber: 4.2  Consensus size: 40

       8074 GGACTAAGAT

                            *   *        **         
       8084 CCGAAGGCATTTGTGCTAGTGACTATATCAAGGCTAAGTC
          1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC

            *                                       
       8124 TCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
          1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC

                                                    
       8164 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
          1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC

                          *      *               *  
       8204 CCGAAGGCATTTGTACGAGTTGCTATATCC-GGCTAAATC
          1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC

                   
       8243 CCGAAGG
          1 CCGAAGG

       8250 TACTTGGGTT


Statistics
Matches: 117,  Mismatches: 9, Indels: 1
        0.92            0.07        0.01

Matches are distributed among these distances:
  39   15  0.13
  40  102  0.87

ACGTcount: A:0.25, C:0.22, G:0.27, T:0.27


Consensus pattern (40 bp):   
CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC

Found at i:16225 original size:39 final size:39

Alignment explanation


    Indices: 16129--16315  Score: 322
    Period size: 40  Copynumber: 4.8  Consensus size: 39

      16119 CCGGACAAGA

                             *   *                 
      16129 TCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAG
          1 TCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAG

                                                    
      16168 TCTCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAG
          1 TC-CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAG

                                                   
      16208 TCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAG
          1 TCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAG

                                                    
      16247 TCCCGAAGGCATTTGTGCGAGTTACTATATCC-GGCTAAG
          1 T-CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAG

                                  *       
      16286 TCCGAAGGCATTTGTGCGAGTTGCTATATC
          1 TCCGAAGGCATTTGTGCGAGTTACTATATC

      16316 GCTAAATCCG


Statistics
Matches: 143,  Mismatches: 3, Indels: 5
        0.95            0.02        0.03

Matches are distributed among these distances:
  38   28  0.20
  39   48  0.34
  40   67  0.47

ACGTcount: A:0.22, C:0.21, G:0.27, T:0.29


Consensus pattern (39 bp):   
TCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAG

Found at i:16260 original size:79 final size:78

Alignment explanation


    Indices: 16129--16315  Score: 329
    Period size: 79  Copynumber: 2.4  Consensus size: 78

      16119 CCGGACAAGA

                             *   *                   *                       
      16129 TCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCTCGAAGGCATTTGTGCGAGTTACT
          1 TCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT

                          
      16194 ATATCCGGGCTAAG
         66 ATATCC-GGCTAAG

                                                                             
      16208 TCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
          1 TCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT

                         
      16273 ATATCCGGCTAAG
         66 ATATCCGGCTAAG

                                  *       
      16286 TCCGAAGGCATTTGTGCGAGTTGCTATATC
          1 TCCGAAGGCATTTGTGCGAGTTACTATATC

      16316 GCTAAATCCG


Statistics
Matches: 104,  Mismatches: 4, Indels: 1
        0.95            0.04        0.01

Matches are distributed among these distances:
  78   36  0.35
  79   68  0.65

ACGTcount: A:0.22, C:0.21, G:0.27, T:0.29


Consensus pattern (78 bp):   
TCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
ATATCCGGCTAAG
Done.