Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1356

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: 29819
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31


Found at i:6969 original size:40 final size:40

Alignment explanation


    Indices: 6820--7005  Score: 200
    Period size: 40  Copynumber: 4.7  Consensus size: 40

       6810 TTGAATGATG

                                          *   *  * * 
       6820 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
          1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA

                 *                           *       
       6860 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAA
          1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA

               * *                                   
       6900 TCCAGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
          1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA

            *     *                        *         
       6940 CCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
          1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA

                     *                
       6981 -CCGGGCTATGTCCCGAAGGCATTTG
          1 TCCGGGCTAAGTCCCGAAGGCATTTG

       7006 AACGAGGAGC


Statistics
Matches: 127,  Mismatches: 15, Indels: 8
        0.85            0.10        0.05

Matches are distributed among these distances:
  39    1  0.01
  40  116  0.91
  41   10  0.08

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


Consensus pattern (40 bp):   
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA

Found at i:17060 original size:21 final size:23

Alignment explanation


    Indices: 17015--17061  Score: 62
    Period size: 23  Copynumber: 2.1  Consensus size: 23

      17005 TCACCTGCAA

                           *  *    
      17015 TAAACACATTAAAATGAGTTTAT
          1 TAAACACATTAAAATCAGCTTAT

                                   
      17038 TAAACACATTAAAA-CA-CTTAT
          1 TAAACACATTAAAATCAGCTTAT

               
      17059 TAA
          1 TAA

      17062 TCATAACACA


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

Matches are distributed among these distances:
  21    7  0.32
  22    1  0.05
  23   14  0.64

ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32


Consensus pattern (23 bp):   
TAAACACATTAAAATCAGCTTAT

Found at i:23587 original size:40 final size:40

Alignment explanation


    Indices: 23543--23765  Score: 271
    Period size: 40  Copynumber: 5.7  Consensus size: 40

      23533 GCTCCTCGTT

                            *        *              
      23543 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA

                               *       *            
      23583 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA

                                             *      
      23623 CAAATGCCTTCGGG-CTTAGCCCGGAT-TAGTATCTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA

                                               *      
      23661 CAAATGCCTTC-GGATCTTAG-CCGGA-ATTAGTATCTCGCA
          1 CAAATGCCTTCGGGA-CTTAGCCCGGATA-TAGTAACTCGCA

                                 *        *  *    *   
      23700 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
          1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA

                                      
      23741 CAAA-GCCTTCGGGACTTAGCCCGGA
          1 CAAATGCCTTCGGGACTTAGCCCGGA

      23766 CATCATTCAA


Statistics
Matches: 164,  Mismatches: 11, Indels: 16
        0.86            0.06        0.08

Matches are distributed among these distances:
  37    2  0.01
  38   27  0.16
  39   48  0.29
  40   75  0.46
  41   12  0.07

ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25


Consensus pattern (40 bp):   
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA

Done.