Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2504

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: 30119
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32


Found at i:4726 original size:27 final size:27

Alignment explanation


    Indices: 4696--4873  Score: 106
    Period size: 27  Copynumber: 6.6  Consensus size: 27

       4686 ATATTGAGCC

                    *       *        * 
       4696 CGCACACTCAGTGCTATACAATCAACT
          1 CGCACACTTAGTGCTACACAATCAAAT

                          *  **        
       4723 CGCACACTTAGTGCCACGTAATCAAAT
          1 CGCACACTTAGTGCTACACAATCAAAT

                              * * *   * 
       4750 CGCACACTTAGTGCTACATAGTTAGACT
          1 CGCACACTTAGTGCTACACAATCA-AAT

                          **  ***    * 
       4778 CGCACACTTAGTGCCGCATGGTCAATT
          1 CGCACACTTAGTGCTACACAATCAAAT

                               ***   ** 
       4805 CGCACACTTAGTGC-ATCATGTTCATTT
          1 CGCACACTTAGTGCTA-CACAATCAAAT

                          *   * *  *   
       4832 CGCACACTTAGTGCAACATAGTCGAAT
          1 CGCACACTTAGTGCTACACAATCAAAT

                           
       4859 CGCACACTTAGTGCT
          1 CGCACACTTAGTGCT

       4874 GTACAATTTA


Statistics
Matches: 123,  Mismatches: 25, Indels: 6
        0.80            0.16        0.04

Matches are distributed among these distances:
  27  100  0.81
  28   23  0.19

ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26


Consensus pattern (27 bp):   
CGCACACTTAGTGCTACACAATCAAAT

Found at i:4789 original size:55 final size:55

Alignment explanation


    Indices: 4696--4873  Score: 195
    Period size: 54  Copynumber: 3.3  Consensus size: 55

       4686 ATATTGAGCC

                    *             *                       *  *      
       4696 CGCACACTCAGTGCTATACA--ATCAACTCGCACACTTAGTGCCACGTAATCAAAT
          1 CGCACACTTAGTGCTAT-CATGTTCAACTCGCACACTTAGTGCCACATAGTCAAAT

                                                         *   *     * 
       4750 CGCACACTTAGTGCTA-CATAGTT-AGACTCGCACACTTAGTGCCGCATGGTCAATT
          1 CGCACACTTAGTGCTATCAT-GTTCA-ACTCGCACACTTAGTGCCACATAGTCAAAT

                                     **               *        *   
       4805 CGCACACTTAGTGC-ATCATGTTCATTTCGCACACTTAGTGCAACATAGTCGAAT
          1 CGCACACTTAGTGCTATCATGTTCAACTCGCACACTTAGTGCCACATAGTCAAAT

                           
       4859 CGCACACTTAGTGCT
          1 CGCACACTTAGTGCT

       4874 GTACAATTTA


Statistics
Matches: 103,  Mismatches: 14, Indels: 13
        0.79            0.11        0.10

Matches are distributed among these distances:
  52    2  0.02
  54   57  0.55
  55   44  0.43

ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26


Consensus pattern (55 bp):   
CGCACACTTAGTGCTATCATGTTCAACTCGCACACTTAGTGCCACATAGTCAAAT

Found at i:9634 original size:88 final size:88

Alignment explanation


    Indices: 9482--9926  Score: 635
    Period size: 88  Copynumber: 5.1  Consensus size: 88

       9472 GATACTTTGC

                        *    **     *                               *        
       9482 CATAAAATTCAAAAGTTTTTAGCAAGTTATGCCTCATCATAAAATATGTCCT-ATTGAACTGCTA
          1 CATAAAATTCAAGAGTTGCTAGCATGTTATGCCTCATCATAAAATATGT-CTGATTAAACTGCTA

                                  * 
       9546 ACTTTCATTGATGTTCATACATTA
         65 ACTTTCATTGATGTTCATACATCA

            * *          *                                     *             
       9570 TAAAAAATTCAAGTGTTGCTAGCATGTTATGCCTCATCATAAAATATGTCTAATTAAACTGCTAA
          1 CATAAAATTCAAGAGTTGCTAGCATGTTATGCCTCATCATAAAATATGTCTGATTAAACTGCTAA

                             *     
       9635 CTTTCATTGATGTTCATGCATCA
         66 CTTTCATTGATGTTCATACATCA

                                * *           *                              
       9658 CATAAAATTCAAGAGTTGCTGGTATGTTATGCCTTATCATAAAATATGTCTGATTAAACTGCTAA
          1 CATAAAATTCAAGAGTTGCTAGCATGTTATGCCTCATCATAAAATATGTCTGATTAAACTGCTAA

                *  *         *     
       9723 CTTTGATCGATGTTCATGCATCA
         66 CTTTCATTGATGTTCATACATCA

                                                             *               
       9746 CATAAAATTCAAGAGTTGCTAGCATGTTATGCCTCATCATAAAATATGTTTGATTAAACTGCTAA
          1 CATAAAATTCAAGAGTTGCTAGCATGTTATGCCTCATCATAAAATATGTCTGATTAAACTGCTAA

                   *               
       9811 CTTTCATCGATGTTCATACATCA
         66 CTTTCATTGATGTTCATACATCA

                                            *       *                        
       9834 CATAAAATTCAAGAGTTGCTAGCATGTTATGCTTCA-CTACAAAATATGTCTGATTAAACTGCTA
          1 CATAAAATTCAAGAGTTGCTAGCATGTTATGCCTCATC-ATAAAATATGTCTGATTAAACTGCTA

              *               *      
       9898 ACCTTCATT-AGTGTTCAAACATCA
         65 ACTTTCATTGA-TGTTCATACATCA

                 
       9922 CATAA
          1 CATAA

       9927 TCTTTTCAAT


Statistics
Matches: 323,  Mismatches: 31, Indels: 6
        0.90            0.09        0.02

Matches are distributed among these distances:
  87    4  0.01
  88  319  0.99

ACGTcount: A:0.34, C:0.18, G:0.13, T:0.36


Consensus pattern (88 bp):   
CATAAAATTCAAGAGTTGCTAGCATGTTATGCCTCATCATAAAATATGTCTGATTAAACTGCTAA
CTTTCATTGATGTTCATACATCA

Found at i:17405 original size:16 final size:16

Alignment explanation


    Indices: 17384--17418  Score: 61
    Period size: 16  Copynumber: 2.2  Consensus size: 16

      17374 AAAACATGTG

                         *  
      17384 CTAGTAATTCTCTTAA
          1 CTAGTAATTCTCTCAA

                            
      17400 CTAGTAATTCTCTCAA
          1 CTAGTAATTCTCTCAA

               
      17416 CTA
          1 CTA

      17419 TGTGGTTTTT


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  16   18  1.00

ACGTcount: A:0.31, C:0.23, G:0.06, T:0.40


Consensus pattern (16 bp):   
CTAGTAATTCTCTCAA
Done.