Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold989

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: 37890
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28


Found at i:5999 original size:14 final size:14

Alignment explanation


    Indices: 5952--6008  Score: 55
    Period size: 14  Copynumber: 4.1  Consensus size: 14

       5942 AGAAACCAGC

                 *        
       5952 AAAAAGATAA-CAA
          1 AAAAAAATAACCAA

                      **  
       5965 AAAAAAA-AAAAAA
          1 AAAAAAATAACCAA

                           
       5978 ATAAAAAATAACCAA
          1 A-AAAAAATAACCAA

                   *      
       5993 AAAAAAAAAACCAA
          1 AAAAAAATAACCAA

              
       6007 AA
          1 AA

       6009 GTAATATGTC


Statistics
Matches: 36,  Mismatches: 5, Indels: 5
        0.78            0.11        0.11

Matches are distributed among these distances:
  12    2  0.06
  13    9  0.25
  14   20  0.56
  15    5  0.14

ACGTcount: A:0.84, C:0.09, G:0.02, T:0.05


Consensus pattern (14 bp):   
AAAAAAATAACCAA

Found at i:22531 original size:40 final size:40

Alignment explanation


    Indices: 22429--22597  Score: 179
    Period size: 40  Copynumber: 4.3  Consensus size: 40

      22419 AGCTAGAGGA

                  *                *      *          
      22429 CTAAGATCC-AAGGCATTTGTGCGAGTTG-CTATATCCGGG
          1 CTAAGACCCGAAGGCATTTGTGCTAG-TGATTATATCCGGG

                                      *             
      22468 -TAAGACCCGAAGGCATTTGTGCTAGCGATTATATCCGGG
          1 CTAAGACCCGAAGGCATTTGTGCTAGTGATTATATCCGGG

                 *             *         **         
      22507 CTAAGTCCCGAAGGCATTTATGCTAGTGACCATATCCGGG
          1 CTAAGACCCGAAGGCATTTGTGCTAGTGATTATATCCGGG

                            *      *    *           
      22547 CTAAGACCCGAAGGC-CTTGTGCGAGTGGTTATATCC-GG
          1 CTAAGACCCGAAGGCATTTGTGCTAGTGATTATATCCGGG

                          
      22585 CTAA-ATCCCGAAG
          1 CTAAGA-CCCGAAG

      22598 ATACTTGGGT


Statistics
Matches: 110,  Mismatches: 16, Indels: 9
        0.81            0.12        0.07

Matches are distributed among these distances:
  37    1  0.01
  38   21  0.19
  39   40  0.36
  40   48  0.44

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


Consensus pattern (40 bp):   
CTAAGACCCGAAGGCATTTGTGCTAGTGATTATATCCGGG

Found at i:30526 original size:40 final size:40

Alignment explanation


    Indices: 30466--30649  Score: 230
    Period size: 40  Copynumber: 4.6  Consensus size: 40

      30456 TATTCGAATG

                                     *               
      30466 ATATCCGGGCTAAG-TCCCGAAGGCTTTTATGCTAGTGACT
          1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT

                    *                   *   *        
      30506 ATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTG-CT
          1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAG-TGACT

                           *            *      *  * 
      30546 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT
          1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT

                                                    *
      30586 ATATCCGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACC
          1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT

                           *        
      30626 ATATCCGGGCTAAGACCCGAAGGC
          1 ATATCCGGGCTAAGATCCGAAGGC

      30650 CTTGTGCGAG


Statistics
Matches: 124,  Mismatches: 15, Indels: 10
        0.83            0.10        0.07

Matches are distributed among these distances:
  39    1  0.01
  40  120  0.97
  41    3  0.02

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


Consensus pattern (40 bp):   
ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT

Found at i:30599 original size:80 final size:80

Alignment explanation


    Indices: 30466--30685  Score: 279
    Period size: 80  Copynumber: 2.8  Consensus size: 80

      30456 TATTCGAATG

                          *             *         *         *                
      30466 ATATCCGGGCTAAGTCCCGAAGGCTTTTATGCTAGTGACTATATCCGGACTAAGAT-CCGAAGGC
          1 ATATCCGGGCTAAGACCCGAAGGC-TTTGTGCTAGTGATTATATCCGGGCTAAGATCCCGAAGGC

                *           *
      30530 ATTTGTGCGAGTTG-CT
         65 ATTTATGCGAG-TGACC

                                               *                             
      30546 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATTATATCCGGGCTAAG-TCCCGAAGGC
          1 ATATCCGGGCTAAGACCCGAAGGC-TTTGTGCTAGTGATTATATCCGGGCTAAGATCCCGAAGGC

                    *       
      30610 ATTTATGCTAGTGACC
         65 ATTTATGCGAGTGACC

                                    *      *    *                         
      30626 ATATCCGGGCTAAGACCCGAAGGCCTTGTGCGAGTGGTTATATCC-GGCTAA-ATCCCGAAG
          1 ATATCCGGGCTAAGACCCGAAGGCTTTGTGCTAGTGATTATATCCGGGCTAAGATCCCGAAG

      30686 ATACTTGGGT


Statistics
Matches: 124,  Mismatches: 13, Indels: 8
        0.86            0.09        0.06

Matches are distributed among these distances:
  78   14  0.11
  79   20  0.16
  80   90  0.73

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


Consensus pattern (80 bp):   
ATATCCGGGCTAAGACCCGAAGGCTTTGTGCTAGTGATTATATCCGGGCTAAGATCCCGAAGGCA
TTTATGCGAGTGACC
Done.