Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3705

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: 25664
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31


Found at i:7563 original size:21 final size:20

Alignment explanation


    Indices: 7517--7569  Score: 52
    Period size: 21  Copynumber: 2.5  Consensus size: 20

       7507 ATAAAATAGT

                     *        *  
       7517 ATTAAAAGAAATAAAAAGTAA
          1 ATTAAAA-ATATAAAAAGAAA

            *                    
       7538 TTTAAAAATATAAAAGAGAAA
          1 ATTAAAAATATAAAA-AGAAA

                       
       7559 ATTAAATAATA
          1 ATTAAA-AATA

       7570 CATAGTTATA


Statistics
Matches: 26,  Mismatches: 4, Indels: 3
        0.79            0.12        0.09

Matches are distributed among these distances:
  20    7  0.27
  21   15  0.58
  22    4  0.15

ACGTcount: A:0.68, C:0.00, G:0.08, T:0.25


Consensus pattern (20 bp):   
ATTAAAAATATAAAAAGAAA

Found at i:22110 original size:25 final size:26

Alignment explanation


    Indices: 22079--22195  Score: 130
    Period size: 27  Copynumber: 4.5  Consensus size: 26

      22069 AAATTGTACA

                        *             
      22079 GCACTAAGTGTGTG-ATGACTATGTT
          1 GCACTAAGTGTGCGAATGACTATGTT

                                *    * 
      22104 GCACTAAGTGTGCGAAATGAATATGAT
          1 GCACTAAGTGTGCG-AATGACTATGTT

                                 *   **
      22131 GCACTAAGTGTGCGAATTGACCATGCG
          1 GCACTAAGTGTGCGAA-TGACTATGTT

                           *         *
      22158 GCACTAAGTGTGCGAGT-ACTATGTA
          1 GCACTAAGTGTGCGAATGACTATGTT

                         
      22183 GCACTAAGTGTGC
          1 GCACTAAGTGTGC

      22196 ATTTGAACGT


Statistics
Matches: 78,  Mismatches: 11, Indels: 6
        0.82            0.12        0.06

Matches are distributed among these distances:
  25   31  0.40
  26    3  0.04
  27   44  0.56

ACGTcount: A:0.28, C:0.16, G:0.28, T:0.27


Consensus pattern (26 bp):   
GCACTAAGTGTGCGAATGACTATGTT

Found at i:22569 original size:28 final size:28

Alignment explanation


    Indices: 22503--22681  Score: 163
    Period size: 28  Copynumber: 6.5  Consensus size: 28

      22493 ATATTGAGTC

                    *       *           
      22503 CGCACACTCAGTGCTATATAATC-AACT
          1 CGCACACTTAGTGCTACATAATCAAACT

                             *        * 
      22530 CGCACACTTAGTGCTACGTAATCAAAAT
          1 CGCACACTTAGTGCTACATAATCAAACT

                                *       
      22558 CGCACACTTAGTGCTACATAGTCAAACT
          1 CGCACACTTAGTGCTACATAATCAAACT

                          **   **     * 
      22586 CGCACACTTAGTGCCGCATGGTC-AATT
          1 CGCACACTTAGTGCTACATAATCAAACT

                                 *     * 
      22613 CGCACACTTAGTGC-ATCATATTC--ATT
          1 CGCACACTTAGTGCTA-CATAATCAAACT

                           *     *       
      22639 CGCACACTTAGTGGCAACATAGTCAAA-T
          1 CGCACACTTAGT-GCTACATAATCAAACT

             *             
      22667 CACACACTTAGTGCT
          1 CGCACACTTAGTGCT

      22682 GTACAATTTA


Statistics
Matches: 129,  Mismatches: 17, Indels: 12
        0.82            0.11        0.08

Matches are distributed among these distances:
  26   15  0.12
  27   52  0.40
  28   61  0.47
  29    1  0.01

ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26


Consensus pattern (28 bp):   
CGCACACTTAGTGCTACATAATCAAACT

Found at i:22616 original size:55 final size:54

Alignment explanation


    Indices: 22503--22681  Score: 191
    Period size: 55  Copynumber: 3.3  Consensus size: 54

      22493 ATATTGAGTC

                    *       *                        *  *  *       
      22503 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACGTAATCAAAAT
          1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCAACATAGTC-AAAT

                                *                     **   *     * 
      22558 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATT
          1 CGCACACTTAGTGCTACATAATC-AACTCGCACACTTAGTGCAACATAGTCAAAT

                                 *    *                             
      22613 CGCACACTTAGTGC-ATCATATTC-ATTCGCACACTTAGTGGCAACATAGTCAAAT
          1 CGCACACTTAGTGCTA-CATAATCAACTCGCACACTTAGT-GCAACATAGTCAAAT

             *             
      22667 CACACACTTAGTGCT
          1 CGCACACTTAGTGCT

      22682 GTACAATTTA


Statistics
Matches: 104,  Mismatches: 16, Indels: 8
        0.81            0.12        0.06

Matches are distributed among these distances:
  53   14  0.13
  54   25  0.24
  55   43  0.41
  56   22  0.21

ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26


Consensus pattern (54 bp):   
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
Done.