Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1737

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: 32020
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29


Found at i:301 original size:27 final size:27

Alignment explanation


    Indices: 239--360  Score: 133
    Period size: 27  Copynumber: 4.4  Consensus size: 27

        229 TAGATTGGCG

                       *    *            
        239 CTAAGTGTGCGGGTTTAAT-TGTACAGCA
          1 CTAAGTGTGCGAGTTTGATATGT--AGCA

                                       
        267 CTAAGTGTGCGAGTTTGATATGTAGCA
          1 CTAAGTGTGCGAGTTTGATATGTAGCA

                          *             
        294 CTAAGTGTG-GCAGCTTGATATGTAGCA
          1 CTAAGTGTGCG-AGTTTGATATGTAGCA

                                    *     
        321 CTAAGTGTGCGAG-TTGATTTATATTAGCA
          1 CTAAGTGTGCGAGTTTGA--TAT-GTAGCA

                       
        350 CTAAGTGTGCG
          1 CTAAGTGTGCG

        361 GGAGTGAATT


Statistics
Matches: 84,  Mismatches: 4, Indels: 11
        0.85            0.04        0.11

Matches are distributed among these distances:
  26    5  0.06
  27   39  0.46
  28   21  0.25
  29   19  0.23

ACGTcount: A:0.25, C:0.13, G:0.29, T:0.33


Consensus pattern (27 bp):   
CTAAGTGTGCGAGTTTGATATGTAGCA

Found at i:8125 original size:28 final size:28

Alignment explanation


    Indices: 8062--8212  Score: 214
    Period size: 28  Copynumber: 5.4  Consensus size: 28

       8052 ATATTAAGTC

                    *                   
       8062 CGCACACTCAGTGCTATATAATC-AACT
          1 CGCACACTTAGTGCTATATAATCAAACT

                                        
       8089 CGCACACTTAGTGCTATATAATCAAACT
          1 CGCACACTTAGTGCTATATAATCAAACT

                            *        *  
       8117 CGCACACTTAGTGCTACATAATCAAGCT
          1 CGCACACTTAGTGCTATATAATCAAACT

                            *           
       8145 CGCACACTTAGTGCTACATAATCAAACT
          1 CGCACACTTAGTGCTATATAATCAAACT

                           *  *    *    *
       8173 CGCACACTTAGTGCTGTACAATTTAAACC
          1 CGCACACTTAGTGCTATATAA-TCAAACT

                       
       8202 CGCACACTTAG
          1 CGCACACTTAG

       8213 CGCCAATCTC


Statistics
Matches: 113,  Mismatches: 9, Indels: 2
        0.91            0.07        0.02

Matches are distributed among these distances:
  27   22  0.19
  28   75  0.66
  29   16  0.14

ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26


Consensus pattern (28 bp):   
CGCACACTTAGTGCTATATAATCAAACT

Found at i:16826 original size:43 final size:43

Alignment explanation


    Indices: 16760--16916  Score: 205
    Period size: 43  Copynumber: 3.7  Consensus size: 43

      16750 AGCTTGTACA

                                          *            
      16760 ATGCCAACGTCCCAGACGTGGTCTTACATGCAATCAAATATCG
          1 ATGCCAACGTCCCAGACGTGGTCTTACATGAAATCAAATATCG

                                          *              
      16803 ATGCC-ACTGTCCCAGACAG-GGTCTTACACGAAATCAAATA-CG
          1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACATGAAATCAAATATCG

                    *                                *   
      16845 ATGCCAACATCCCAGACGTGGTCTTACATGTAAATCATAA-GTCG
          1 ATGCCAACGTCCCAGACGTGGTCTTACATG-AAATCA-AATATCG

                            *           
      16889 ATGCCAACGTCCCAGATGTGGTCTTACA
          1 ATGCCAACGTCCCAGACGTGGTCTTACA

      16917 CGATAACACA


Statistics
Matches: 100,  Mismatches: 7, Indels: 13
        0.83            0.06        0.11

Matches are distributed among these distances:
  41    1  0.01
  42   27  0.27
  43   41  0.41
  44   31  0.31

ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23


Consensus pattern (43 bp):   
ATGCCAACGTCCCAGACGTGGTCTTACATGAAATCAAATATCG

Found at i:16914 original size:86 final size:85

Alignment explanation


    Indices: 16760--16919  Score: 227
    Period size: 86  Copynumber: 1.9  Consensus size: 85

      16750 AGCTTGTACA

                    *                     *                                  
      16760 ATGCCAACGTCCCAGACGTGGTCTTACATGCAATCAAATATCGATGCCACTGTCCCAGACAGGGT
          1 ATGCCAACATCCCAGACGTGGTCTTACATGAAATCAAATATCGATGCCACTGTCCCAGACAGGGT

                                
      16825 CTTACACGAAATCAAATACG
         66 CTTACACGAAATCAAATACG

                                                     *                     * 
      16845 ATGCCAACATCCCAGACGTGGTCTTACATGTAAATCATAA-GTCGATGCCAAC-GTCCCAGA-TG
          1 ATGCCAACATCCCAGACGTGGTCTTACATG-AAATCA-AATATCGATGCC-ACTGTCCCAGACAG

                         
      16907 TGGTCTTACACGA
         63 -GGTCTTACACGA

      16920 TAACACATAT


Statistics
Matches: 67,  Mismatches: 4, Indels: 7
        0.86            0.05        0.09

Matches are distributed among these distances:
  85   30  0.45
  86   33  0.49
  87    4  0.06

ACGTcount: A:0.31, C:0.28, G:0.19, T:0.23


Consensus pattern (85 bp):   
ATGCCAACATCCCAGACGTGGTCTTACATGAAATCAAATATCGATGCCACTGTCCCAGACAGGGT
CTTACACGAAATCAAATACG
Done.