Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold899

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: 10488
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32


Found at i:2364 original size:40 final size:39

Alignment explanation


    Indices: 2273--2485  Score: 305
    Period size: 39  Copynumber: 5.6  Consensus size: 39

       2263 TATTCGGATG

                                            *   *  
       2273 ATATCCGGGCTAAGT-CCGAAGGCATTTGTGCAAGTTCT
          1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGCT

                                                    
       2311 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
          1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTG-CT

                                                   
       2351 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTA--GC-
          1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGCT

                                                    
       2387 -TATCCGGGCTAAGTCCCGAAGGCA-TTGTGCTAGTGACT
          1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTG-CT

                          *                 *       
       2425 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
          1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGCT

                         *        
       2465 ATATCC-GGCTAAATCCCGAAG
          1 ATATCCGGGCTAAGTCCCGAAG

       2486 TACTTGGGTT


Statistics
Matches: 160,  Mismatches: 6, Indels: 17
        0.87            0.03        0.09

Matches are distributed among these distances:
  34    8  0.05
  35   24  0.15
  36    1  0.01
  37    2  0.01
  38   16  0.10
  39   55  0.34
  40   52  0.32
  41    2  0.01

ACGTcount: A:0.23, C:0.23, G:0.27, T:0.26


Consensus pattern (39 bp):   
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGCT

Found at i:2436 original size:74 final size:77

Alignment explanation


    Indices: 2273--2485  Score: 310
    Period size: 74  Copynumber: 2.8  Consensus size: 77

       2263 TATTCGGATG

                                                                             
       2273 ATATCCGGGCTAAGT-CCGAAGGCATTTGTGCAAGTTCTATATCCGGGCTAAGTCCCGAAGGCAT
          1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TC-ATATCCGGGCTAAGTCCCGAAGGCAT

                          
       2337 TTGTGCTAGTGACT
         64 TTGTGCTAGTGACT

                                            *                                
       2351 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-C-TATCCGGGCTAAGTCCCGAAGGCA-TT
          1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTCATATCCGGGCTAAGTCCCGAAGGCATTT

                        
       2413 GTGCTAGTGACT
         66 GTGCTAGTGACT

                          *                 *                    *        
       2425 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCC-GGCTAAATCCCGAAG
          1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-T-C-ATATCCGGGCTAAGTCCCGAAG

       2486 TACTTGGGTT


Statistics
Matches: 125,  Mismatches: 4, Indels: 12
        0.89            0.03        0.09

Matches are distributed among these distances:
  74   47  0.38
  75   24  0.19
  77    2  0.02
  78   29  0.23
  79   23  0.18

ACGTcount: A:0.23, C:0.23, G:0.27, T:0.26


Consensus pattern (77 bp):   
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTCATATCCGGGCTAAGTCCCGAAGGCATTT
GTGCTAGTGACT

Found at i:10469 original size:42 final size:41

Alignment explanation


    Indices: 10334--10485  Score: 208
    Period size: 42  Copynumber: 3.8  Consensus size: 41

      10324 TATTCGGATG

                                                  *  
      10334 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCG-AGTTCCT
          1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGTAGTTGCT

                                                      
      10374 ATATCCGGGCTAAGT-CCGAAGGCATTTGT-C-TAG-TGACT
          1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGTAGTTG-CT

                      *                                
      10412 ATATCCGGGCGAAGTCCCGAAGG-ATTTGTGCGAGTAGTTGCT
          1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC--GTAGTTGCT

               *                            
      10454 ATACCCGGGCTAAGTCCCGAAGGCATTTGTGC
          1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC

      10486 TAG


Statistics
Matches: 99,  Mismatches: 4, Indels: 15
        0.84            0.03        0.13

Matches are distributed among these distances:
  37    1  0.01
  38   25  0.25
  39   22  0.22
  40   15  0.15
  42   26  0.26
  43   10  0.10

ACGTcount: A:0.22, C:0.23, G:0.29, T:0.26


Consensus pattern (41 bp):   
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGTAGTTGCT
Done.