Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3691

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: 15521
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.30


Found at i:7801 original size:28 final size:27

Alignment explanation


    Indices: 7737--7888  Score: 232
    Period size: 27  Copynumber: 5.6  Consensus size: 27

       7727 TTATTAAGTC

                    *       *          
       7737 CGCACACTCAGTGCTATATAATCAACT
          1 CGCACACTTAGTGCTACATAATCAACT

                                        
       7764 CGCACACTTAGTGCTACATAATCATACT
          1 CGCACACTTAGTGCTACATAATCA-ACT

                                *      
       7792 CGCACACTTAGTGCTACATAGTCAACT
          1 CGCACACTTAGTGCTACATAATCAACT

                                *       
       7819 CGCACACTTAGTGCTACATAGTCAAACT
          1 CGCACACTTAGTGCTACATAATC-AACT

                                *    * 
       7847 CGCACACTTAGTGCTACATATTCAATT
          1 CGCACACTTAGTGCTACATAATCAACT

                           
       7874 CGCACACTTAGTGCT
          1 CGCACACTTAGTGCT

       7889 GCACAATTTA


Statistics
Matches: 118,  Mismatches: 5, Indels: 4
        0.93            0.04        0.03

Matches are distributed among these distances:
  27   66  0.56
  28   52  0.44

ACGTcount: A:0.30, C:0.29, G:0.13, T:0.28


Consensus pattern (27 bp):   
CGCACACTTAGTGCTACATAATCAACT

Found at i:7821 original size:55 final size:55

Alignment explanation


    Indices: 7737--7913  Score: 246
    Period size: 55  Copynumber: 3.2  Consensus size: 55

       7727 TTATTAAGTC

                    *       *                                  *   
       7737 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCATACT
          1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT

                                *                          *       
       7792 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
          1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT

                                *    *                *  *    *    *
       7847 CGCACACTTAGTGCTACATATTCAATTCGCACACTTAGTGCTGCACAATTTAAACC
          1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAA-TCAAACT

                       
       7903 CGCACACTTAG
          1 CGCACACTTAG

       7914 CGCCAATCTC


Statistics
Matches: 109,  Mismatches: 12, Indels: 1
        0.89            0.10        0.01

Matches are distributed among these distances:
  55   93  0.85
  56   16  0.15

ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27


Consensus pattern (55 bp):   
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT

Found at i:14099 original size:40 final size:40

Alignment explanation


    Indices: 14044--14194  Score: 225
    Period size: 40  Copynumber: 3.8  Consensus size: 40

      14034 CGGATGATAA

                                                    
      14044 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT

                                               *  * 
      14084 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAT
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT

                                   *                *
      14124 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACT-ATAA
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-T

                    *                *      
      14164 CCGGGCTATGT-CCGAAGGCATTTGAGCGAGT
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT

      14195 AGCTATATCC


Statistics
Matches: 101,  Mismatches: 9, Indels: 3
        0.89            0.08        0.03

Matches are distributed among these distances:
  39   19  0.19
  40   82  0.81

ACGTcount: A:0.23, C:0.23, G:0.30, T:0.24


Consensus pattern (40 bp):   
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
Done.