Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_2353

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: 23834
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30


Found at i:7132 original size:40 final size:40

Alignment explanation


    Indices: 7072--7292  Score: 265
    Period size: 40  Copynumber: 5.5  Consensus size: 40

       7062 TATTCGAATG

                                     *               
       7072 ATATCCGGGCTAAG-TCCCGAAGGCTTTTGTGCTAGTGACT
          1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCTAGTGACT

                    *                       *        
       7112 ATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTG-CT
          1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAG-TGACT

                           *                   *    
       7152 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
          1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT

                                         * *         
       7192 ATATCCGGGCTAAG-TCTCGAAGGCATTTATTCTAGTGACT
          1 ATATCCGGGCTAAGATC-CGAAGGCATTTGTGCTAGTGACT

                           *                *      * 
       7232 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-TT
          1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAG-TGACT

                                   
       7272 ATATCC-GGCTAA-ATCCCGAAG
          1 ATATCCGGGCTAAGAT-CCGAAG

       7293 ATACTTGGGT


Statistics
Matches: 157,  Mismatches: 17, Indels: 15
        0.83            0.09        0.08

Matches are distributed among these distances:
  38    1  0.01
  39   14  0.09
  40  136  0.87
  41    6  0.04

ACGTcount: A:0.24, C:0.22, G:0.26, T:0.27


Consensus pattern (40 bp):   
ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT

Found at i:7559 original size:22 final size:22

Alignment explanation


    Indices: 7519--7560  Score: 59
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       7509 GAATGTGCAT

                        *         
       7519 ATATGAAGTTATTCATTTAGCC
          1 ATATGAAGTTATACATTTAGCC

                                 
       7541 ATATGAATGTTATAC-TTTAG
          1 ATATGAA-GTTATACATTTAG

       7561 TCGAACTAAT


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  22   12  0.67
  23    6  0.33

ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43


Consensus pattern (22 bp):   
ATATGAAGTTATACATTTAGCC

Found at i:12705 original size:38 final size:39

Alignment explanation


    Indices: 12651--12746  Score: 131
    Period size: 38  Copynumber: 2.5  Consensus size: 39

      12641 AATTAGTTTA

                              *  *               * 
      12651 AGTCTTTAATTATGTCATCATTTGAACATCATTAATATG
          1 AGTCTTTAATTATGTCATAATCTGAACATCATTAATAAG

                                          *        
      12690 AG-CTTTAATTATGTCATAATCTGAACATCTTTAATAAG
          1 AGTCTTTAATTATGTCATAATCTGAACATCATTAATAAG

            *  *               
      12728 GGTTTTTAATTATGTCATA
          1 AGTCTTTAATTATGTCATA

      12747 GTTTAGGACA


Statistics
Matches: 50,  Mismatches: 6, Indels: 2
        0.86            0.10        0.03

Matches are distributed among these distances:
  38   33  0.66
  39   17  0.34

ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44


Consensus pattern (39 bp):   
AGTCTTTAATTATGTCATAATCTGAACATCATTAATAAG

Found at i:17387 original size:40 final size:39

Alignment explanation


    Indices: 17307--17446  Score: 117
    Period size: 40  Copynumber: 3.5  Consensus size: 39

      17297 ATGCTGTCCG

                                     *           *    
      17307 GGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACT-ATATCC
          1 GGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-A-TAAAATCC

                                          *   *  *   
      17346 GGACTAAGAT-CCGAAGGCATTTGTGCGAGTTATTAATTCC
          1 GG-CTAAG-TCCCGAAGGCATTTGTGCGAGATATAAAATCC

              *               *                     
      17386 GGGTCAAGTCCCGAAGGCCTTTGTGCGAGATATAAAATCC
          1 GGCT-AAGTCCCGAAGGCATTTGTGCGAGATATAAAATCC

               *                 
      17426 GGGTTAAGTCCCGAAGGCATT
          1 -GGCTAAGTCCCGAAGGCATT

      17447 GTATGAGTTA


Statistics
Matches: 82,  Mismatches: 11, Indels: 15
        0.76            0.10        0.14

Matches are distributed among these distances:
  39    5  0.06
  40   64  0.78
  41   13  0.16

ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26


Consensus pattern (39 bp):   
GGCTAAGTCCCGAAGGCATTTGTGCGAGATATAAAATCC
Done.