Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2108

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: 42690
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30


Found at i:4623 original size:39 final size:39

Alignment explanation


    Indices: 4568--4715  Score: 189
    Period size: 39  Copynumber: 3.8  Consensus size: 39

       4558 GATATAGGTA

                *                                  
       4568 TCGCTCAAATGCCTTCGGGACTT-GCCCGTTATAGTAAC
          1 TCGCACAAATGCCTTCGGGACTTAGCCCGTTATAGTAAC

                                    *   *           
       4606 TCGCCACAAATGCCTTCGGGACTTGGCCGGTTATAGTAAC
          1 TCG-CACAAATGCCTTCGGGACTTAGCCCGTTATAGTAAC

                  *                                 
       4646 TCGCACGAATGCCTTCGGG-CTTAGCCCGGTTATAGTAAC
          1 TCGCACAAATGCCTTCGGGACTTAGCCC-GTTATAGTAAC

                  *                           
       4685 TCGCACGAATG-CTTC-GG-CTTAGCCCGGTTAT
          1 TCGCACAAATGCCTTCGGGACTTAGCCC-GTTAT

       4716 CATCCGAATA


Statistics
Matches: 102,  Mismatches: 5, Indels: 7
        0.89            0.04        0.06

Matches are distributed among these distances:
  37   16  0.16
  38   13  0.13
  39   56  0.55
  40   17  0.17

ACGTcount: A:0.20, C:0.28, G:0.24, T:0.27


Consensus pattern (39 bp):   
TCGCACAAATGCCTTCGGGACTTAGCCCGTTATAGTAAC

Found at i:18331 original size:39 final size:40

Alignment explanation


    Indices: 18277--18430  Score: 249
    Period size: 40  Copynumber: 3.9  Consensus size: 40

      18267 ATTCGGATTG

                      *                             
      18277 ATAACCGGGCTAAG-CCCGAAGGCATTCGTGCGAGTTACT
          1 ATAACCGGGCCAAGTCCCGAAGGCATTCGTGCGAGTTACT

                      *                             
      18316 ATAACCGGGCTAAG-CCCGAAGGCATTCGTGCGAGTTACT
          1 ATAACCGGGCCAAGTCCCGAAGGCATTCGTGCGAGTTACT

                                       *            
      18355 ATAACCGGGCCAAGTCCCGAAGGCATTTGTGCGAGTTACT
          1 ATAACCGGGCCAAGTCCCGAAGGCATTCGTGCGAGTTACT

                                       * *      
      18395 ATAACCGGGCCAAGTCCCGAAGGCATTTGAGCGAGT
          1 ATAACCGGGCCAAGTCCCGAAGGCATTCGTGCGAGT

      18431 ACCTATATCC


Statistics
Matches: 111,  Mismatches: 3, Indels: 1
        0.97            0.03        0.01

Matches are distributed among these distances:
  39   52  0.47
  40   59  0.53

ACGTcount: A:0.26, C:0.25, G:0.29, T:0.20


Consensus pattern (40 bp):   
ATAACCGGGCCAAGTCCCGAAGGCATTCGTGCGAGTTACT

Found at i:18453 original size:79 final size:79

Alignment explanation


    Indices: 18291--18456  Score: 219
    Period size: 79  Copynumber: 2.1  Consensus size: 79

      18281 CCGGGCTAAG

                                               *                 *           
      18291 CCCGAAGGCATTCGTGCGAGTTACTATAACCGGGCTAAGCCCGAAGGCATTCGTGCGAGTTACTA
          1 CCCGAAGGCATTCGTGCGAGTTACTATAACCGGGCCAAGCCCGAAGGCATTCGAGCGAGTTACTA

                  *     **
      18356 TAACCGGGCCAAGT
         66 TAACCGAGCCAAAC

                        *                                       *            
      18370 CCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCCAAGTCCCGAAGGCATTTGAGCGAG-TACC
          1 CCCGAAGGCATTCGTGCGAGTTACTATAACCGGGCCAAG-CCCGAAGGCATTCGAGCGAGTTA-C

                *      *    
      18434 TATATCC-AGCTAAAC
         64 TATAACCGAGCCAAAC

                    
      18449 CCCGAAGG
          1 CCCGAAGG

      18457 TACTTGGTTT


Statistics
Matches: 76,  Mismatches: 9, Indels: 4
        0.85            0.10        0.04

Matches are distributed among these distances:
  79   51  0.67
  80   25  0.33

ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20


Consensus pattern (79 bp):   
CCCGAAGGCATTCGTGCGAGTTACTATAACCGGGCCAAGCCCGAAGGCATTCGAGCGAGTTACTA
TAACCGAGCCAAAC

Found at i:34300 original size:26 final size:26

Alignment explanation


    Indices: 34269--34324  Score: 103
    Period size: 26  Copynumber: 2.2  Consensus size: 26

      34259 TGAAATGCCC

                                      
      34269 ATCATGGAACATTTACCTAAACCATT
          1 ATCATGGAACATTTACCTAAACCATT

                                *     
      34295 ATCATGGAACATTTACCTAACCCATT
          1 ATCATGGAACATTTACCTAAACCATT

                
      34321 ATCA
          1 ATCA

      34325 ATTTGTACCA


Statistics
Matches: 29,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  26   29  1.00

ACGTcount: A:0.38, C:0.25, G:0.07, T:0.30


Consensus pattern (26 bp):   
ATCATGGAACATTTACCTAAACCATT

Found at i:41311 original size:26 final size:26

Alignment explanation


    Indices: 41255--41361  Score: 189
    Period size: 26  Copynumber: 4.2  Consensus size: 26

      41245 TGAAATTCCC

                                      
      41255 ATCATGGAACATTTACCTAA-CCATT
          1 ATCATGGAACATTTACCTAACCCATT

                                      
      41280 ATCATGGAACATTTACCTAACCCATT
          1 ATCATGGAACATTTACCTAACCCATT

                     *          *     
      41306 ATCATGGAATATTTACCTAATCCATT
          1 ATCATGGAACATTTACCTAACCCATT

                                      
      41332 ATCATGGAACATTTACCTAACCCATT
          1 ATCATGGAACATTTACCTAACCCATT

                
      41358 ATCA
          1 ATCA

      41362 ATTTGTACCA


Statistics
Matches: 77,  Mismatches: 4, Indels: 1
        0.94            0.05        0.01

Matches are distributed among these distances:
  25   20  0.26
  26   57  0.74

ACGTcount: A:0.36, C:0.24, G:0.07, T:0.33


Consensus pattern (26 bp):   
ATCATGGAACATTTACCTAACCCATT

Done.