Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2994

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: 26651
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31


Found at i:6853 original size:39 final size:40

Alignment explanation


    Indices: 6771--6954  Score: 234
    Period size: 40  Copynumber: 4.7  Consensus size: 40

       6761 GCTCCTCGTT

                            *        *              
       6771 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA

                               *                    
       6811 CAAATGCCTTCGGGACTTAACCCGGAT-TAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA

                                              *      
       6850 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA

                                 *        *  *    *   
       6889 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
          1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA

                                      
       6930 CAAA-GCCTTCGGGACTTAGCCCGGA
          1 CAAATGCCTTCGGGACTTAGCCCGGA

       6955 CATCATTCAA


Statistics
Matches: 126,  Mismatches: 11, Indels: 14
        0.83            0.07        0.09

Matches are distributed among these distances:
  38   12  0.10
  39   48  0.38
  40   54  0.43
  41   12  0.10

ACGTcount: A:0.26, C:0.28, G:0.23, T:0.24


Consensus pattern (40 bp):   
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA

Found at i:18745 original size:45 final size:44

Alignment explanation


    Indices: 18665--18841  Score: 189
    Period size: 45  Copynumber: 4.0  Consensus size: 44

      18655 ACAGATTCAT

                           * *        *     *            
      18665 GGTGG-ATCAGCACATAGC-ACCACCCTTATAGTCAATGATACTC
          1 GGTGGAATCAGCACACAACAACCACCTTTATAATCAATGATAC-C

            *         *    * *          *                 
      18708 AGTGGAATCAACACATAGCAACCACCTTCATAATCAAT-AGTACCC
          1 GGTGGAATCAGCACACAACAACCACCTTTATAATCAATGA-TA-CC

                    *                         *         
      18753 GGTGGAATTAGCACACAACAACCACCTTTATAATTAATGATACC
          1 GGTGGAATCAGCACACAACAACCACCTTTATAATCAATGATACC

                                                    *    
      18797 TGGTGGAATCAGCACACAACAACCACCTTTATAATCAATGGTACC
          1 -GGTGGAATCAGCACACAACAACCACCTTTATAATCAATGATACC

      18842 CTGTACACGT


Statistics
Matches: 113,  Mismatches: 15, Indels: 10
        0.82            0.11        0.07

Matches are distributed among these distances:
  43    4  0.04
  44   15  0.13
  45   92  0.81
  46    2  0.02

ACGTcount: A:0.36, C:0.27, G:0.15, T:0.23


Consensus pattern (44 bp):   
GGTGGAATCAGCACACAACAACCACCTTTATAATCAATGATACC

Found at i:21920 original size:119 final size:120

Alignment explanation


    Indices: 21738--21960  Score: 292
    Period size: 119  Copynumber: 1.9  Consensus size: 120

      21728 TCCTCGTTCA

                                   *                             *           
      21738 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAGTTAACCCGGAT
          1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT

            *         *                                             
      21803 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTGTGTAACTCGCACC
         66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTGTGTAACTCGCACC

                          *                 *                          **    
      21858 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
          1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG

                *  *                          *      
      21920 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
         64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA

      21961 CATCATTCAA


Statistics
Matches: 89,  Mismatches: 11, Indels: 7
        0.83            0.10        0.07

Matches are distributed among these distances:
 118    4  0.04
 119   65  0.73
 120   20  0.22

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


Consensus pattern (120 bp):   
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTGTGTAACTCGCACC

Found at i:21960 original size:40 final size:40

Alignment explanation


    Indices: 21736--21960  Score: 262
    Period size: 40  Copynumber: 5.7  Consensus size: 40

      21726 GCTCCTCGTT

                            *        *              
      21736 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA

                           *   *       *            
      21776 CAAATGCCTTCGGGAGTTAACCCGGATTTAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA

                               *          *          
      21816 CAAATGCCTTCGGGACTTAACCCGGAT-TGTGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGATAT-AGTAACTCGCA

             *                                *      
      21856 CCAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA

                                 *        *  *    *   
      21895 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
          1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA

                                      
      21936 CAAA-GCCTTCGGGACTTAGCCCGGA
          1 CAAATGCCTTCGGGACTTAGCCCGGA

      21961 CATCATTCAA


Statistics
Matches: 159,  Mismatches: 18, Indels: 16
        0.82            0.09        0.08

Matches are distributed among these distances:
  38    2  0.01
  39   30  0.19
  40  115  0.72
  41   12  0.08

ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24


Consensus pattern (40 bp):   
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Done.