Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1032

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: 13622
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.30


Found at i:1527 original size:27 final size:27

Alignment explanation


    Indices: 1350--1527  Score: 171
    Period size: 27  Copynumber: 6.6  Consensus size: 27

       1340 ATATTAAGTC

                    *       *   *    * 
       1350 CGCACACTCAGTGCTATATAATCAACT
          1 CGCACACTTAGTGCTACATAGTCAAAT

                          *      *       
       1377 CGCACACTTAGTGCCACATAACTCAAACT
          1 CGCACACTTAGTGCTACAT-AGTCAAA-T

                           *   *     * 
       1406 CGCACACTTAGTGC-GCATGGTCAATT
          1 CGCACACTTAGTGCTACATAGTCAAAT

                                **   ** 
       1432 CGCACACTTAGTGC-ATCATTTTCATTT
          1 CGCACACTTAGTGCTA-CATAGTCAAAT

                          *    *       
       1459 CGCACACTTAGTGCAACATGGTCAAAT
          1 CGCACACTTAGTGCTACATAGTCAAAT

                                 *     
       1486 CGCACACTTAGTGCTACATAGCCAAAT
          1 CGCACACTTAGTGCTACATAGTCAAAT

                           
       1513 CGCACACTTAGTGCT
          1 CGCACACTTAGTGCT

       1528 GTACAATTTA


Statistics
Matches: 127,  Mismatches: 20, Indels: 8
        0.82            0.13        0.05

Matches are distributed among these distances:
  26   15  0.12
  27   88  0.69
  28    9  0.07
  29   15  0.12

ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26


Consensus pattern (27 bp):   
CGCACACTTAGTGCTACATAGTCAAAT

Found at i:9500 original size:27 final size:28

Alignment explanation


    Indices: 9470--9646  Score: 132
    Period size: 27  Copynumber: 6.5  Consensus size: 28

       9460 ATATTAAGTC

                    *     * *           
       9470 CGCACACTCAGTGCTATATAATC-AACT
          1 CGCACACTTAGTGCCACATAATCAAACT

                                        
       9497 CGCACACTTAGTGCCACATAATCAAACT
          1 CGCACACTTAGTGCCACATAATCAAACT

                         * *   **     * 
       9525 CGCACACTTAGTGTCGCATGGTC-AATT
          1 CGCACACTTAGTGCCACATAATCAAACT

                                **    ** 
       9552 CGCACACTTAGTG-CATCATTTTC-ATTT
          1 CGCACACTTAGTGCCA-CATAATCAAACT

                          *    **       
       9579 CGCACACTTAGTGCAACATGGTCAAA-T
          1 CGCACACTTAGTGCCACATAATCAAACT

                          *     **      
       9606 CGCACACTTAGTGCTACATAGCCAAA-T
          1 CGCACACTTAGTGCCACATAATCAAACT

            *             
       9633 TGCACACTTAGTGC
          1 CGCACACTTAGTGC

       9647 TGTACAATTT


Statistics
Matches: 126,  Mismatches: 20, Indels: 8
        0.82            0.13        0.05

Matches are distributed among these distances:
  26    1  0.01
  27  100  0.79
  28   25  0.20

ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27


Consensus pattern (28 bp):   
CGCACACTTAGTGCCACATAATCAAACT

Found at i:9638 original size:54 final size:52

Alignment explanation


    Indices: 9491--9646  Score: 161
    Period size: 54  Copynumber: 2.9  Consensus size: 52

       9481 TGCTATATAA

                *                             *              *     
       9491 TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGTCGCATGG
          1 TCAAATCGCACACTTAGTG-CACATAATCAAA-TTGCACACTTAGTG-CACATGG

                *                    **    *                       
       9546 TCAATTCGCACACTTAGTGCATCATTTTC-ATTTCGCACACTTAGTGCAACATGG
          1 TCAAATCGCACACTTAGTGCA-CATAATCAAATT-GCACACTTAGTGC-ACATGG

                                      **                   
       9600 TCAAATCGCACACTTAGTGCTACATAGCCAAATTGCACACTTAGTGC
          1 TCAAATCGCACACTTAGTGC-ACATAATCAAATTGCACACTTAGTGC

       9647 TGTACAATTT


Statistics
Matches: 85,  Mismatches: 11, Indels: 11
        0.79            0.10        0.10

Matches are distributed among these distances:
  53    2  0.02
  54   56  0.66
  55   27  0.32

ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28


Consensus pattern (52 bp):   
TCAAATCGCACACTTAGTGCACATAATCAAATTGCACACTTAGTGCACATGG

Found at i:9644 original size:81 final size:82

Alignment explanation


    Indices: 9496--9646  Score: 209
    Period size: 81  Copynumber: 1.9  Consensus size: 82

       9486 TATAATCAAC

                           *                            *   * *              
       9496 TCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGTCGCATGGTCAATTCGCACACTT
          1 TCGCACACTTAGTGCAACATAATCAAACTCGCACACTTAGTGTCACATAGCCAATTCGCACACTT

                             
       9561 AGTGCATCATTTTCATT
         66 AGTGCATCATTTTCATT

                                **                                           
       9578 TCGCACACTTAGTGCAACATGGTCAAA-TCGCACACTTAGTG-CTACATAGCCAAATT-GCACAC
          1 TCGCACACTTAGTGCAACATAATCAAACTCGCACACTTAGTGTC-ACATAGCC-AATTCGCACAC

                   
       9640 TTAGTGC
         64 TTAGTGC

       9647 TGTACAATTT


Statistics
Matches: 61,  Mismatches: 6, Indels: 5
        0.85            0.08        0.07

Matches are distributed among these distances:
  80    1  0.02
  81   32  0.52
  82   28  0.46

ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28


Consensus pattern (82 bp):   
TCGCACACTTAGTGCAACATAATCAAACTCGCACACTTAGTGTCACATAGCCAATTCGCACACTT
AGTGCATCATTTTCATT

Done.