Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_98 ID=scaffold_98-JGI_221_v2.0

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: 14490
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.28


Found at i:53 original size:17 final size:17

Alignment explanation


    Indices: 31--65  Score: 52
    Period size: 17  Copynumber: 2.1  Consensus size: 17

         21 TTCTCTTTTA

                  *          
         31 ATTAATTTAATATTATT
          1 ATTAATCTAATATTATT

                     *       
         48 ATTAATCTATTATTATT
          1 ATTAATCTAATATTATT

             
         65 A
          1 A

         66 CTCATATCAT


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57


Consensus pattern (17 bp):   
ATTAATCTAATATTATT

Found at i:58 original size:14 final size:15

Alignment explanation


    Indices: 40--79  Score: 55
    Period size: 14  Copynumber: 2.7  Consensus size: 15

         30 AATTAATTTA

                           
         40 ATATTATTATTAATC
          1 ATATTATTATTAATC

                        *  
         55 -TATTATTATTACTC
          1 ATATTATTATTAATC

                *      
         69 ATATCATTATT
          1 ATATTATTATT

         80 GATATTGTTA


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  14   13  0.59
  15    9  0.41

ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55


Consensus pattern (15 bp):   
ATATTATTATTAATC

Found at i:12819 original size:44 final size:44

Alignment explanation


    Indices: 12752--13095  Score: 544
    Period size: 44  Copynumber: 7.8  Consensus size: 44

      12742 GATTTAAGCC

                                                        
      12752 GCAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATT
          1 GCAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATT

             * *          *                            *
      12796 GTAGGTCCTATCTCTCTGACCAGCAGTGGAATAGGTTGAAGATC
          1 GCAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATT

                           *                            
      12840 GCAAGTCCTATCTCCTTGACCAGCAGTGGAATAGGTTGAAGATT
          1 GCAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATT

                  *        * *     *                    
      12884 GCAAGTTCTATCTCCTTCACCAGTAGTGGAATAGGTTGAAGATT
          1 GCAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATT

                 *                                      
      12928 GCAAGCCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATT
          1 GCAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATT

                                                        
      12972 GCAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATT
          1 GCAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATT

                 *         *                            
      13016 GCAAGCCCTATCTCCTTGACCAGCAGTGGAATAGGTTGAAGATT
          1 GCAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATT

            *                *   *       *      
      13060 ACAAGTCCTATCTCCCTAACCCGCAGTGGGATAGGT
          1 GCAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGT

      13096 GGAAAATTAG


Statistics
Matches: 274,  Mismatches: 26, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  44  274  1.00

ACGTcount: A:0.27, C:0.23, G:0.25, T:0.26


Consensus pattern (44 bp):   
GCAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATT

Found at i:14409 original size:17 final size:17

Alignment explanation


    Indices: 14387--14421  Score: 52
    Period size: 17  Copynumber: 2.1  Consensus size: 17

      14377 TTCTCTTTTA

                  *          
      14387 ATTAATTTAATATTATT
          1 ATTAATCTAATATTATT

                     *       
      14404 ATTAATCTATTATTATT
          1 ATTAATCTAATATTATT

             
      14421 A
          1 A

      14422 CTCATATCAT


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57


Consensus pattern (17 bp):   
ATTAATCTAATATTATT

Found at i:14414 original size:14 final size:15

Alignment explanation


    Indices: 14396--14435  Score: 55
    Period size: 14  Copynumber: 2.7  Consensus size: 15

      14386 AATTAATTTA

                           
      14396 ATATTATTATTAATC
          1 ATATTATTATTAATC

                        *  
      14411 -TATTATTATTACTC
          1 ATATTATTATTAATC

                *      
      14425 ATATCATTATT
          1 ATATTATTATT

      14436 GATATTGTTA


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  14   13  0.59
  15    9  0.41

ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55


Consensus pattern (15 bp):   
ATATTATTATTAATC
Done.