Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_242 ID=scaffold_242-JGI_221_v2.0

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: 9033
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.32


Found at i:6819 original size:42 final size:42

Alignment explanation


    Indices: 6753--6864  Score: 143
    Period size: 42  Copynumber: 2.7  Consensus size: 42

       6743 GATGTAGAGG

                              **                      
       6753 ACACACGGCCAAAACACACTCCCATGTGCTAGGTCGTGTGTC
          1 ACACACGGCCAAAACACAAGCCCATGTGCTAGGTCGTGTGTC

                         *                     *      
       6795 ACACACGGCCAAACCACAAGCCCATGTGCTAGGTCTTGTGTC
          1 ACACACGGCCAAAACACAAGCCCATGTGCTAGGTCGTGTGTC

            *        *  *     *    *    
       6837 TCACACGGCTAAGACACACGCCCGTGTG
          1 ACACACGGCCAAAACACAAGCCCATGTG

       6865 GACGAAAATA


Statistics
Matches: 60,  Mismatches: 10, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  42   60  1.00

ACGTcount: A:0.26, C:0.34, G:0.22, T:0.18


Consensus pattern (42 bp):   
ACACACGGCCAAAACACAAGCCCATGTGCTAGGTCGTGTGTC

Found at i:7623 original size:21 final size:20

Alignment explanation


    Indices: 7597--7775  Score: 90
    Period size: 21  Copynumber: 8.6  Consensus size: 20

       7587 AAGCCCGAAG

                                 
       7597 GCTAAACAGAAGCTCATGAGA
          1 GCTAAACAGAAGCTCAT-AGA

                  *    * *    * 
       7618 GCTAAATAGAAACCCATAAA
          1 GCTAAACAGAAGCTCATAGA

              * *   *       *     
       7638 GGTTGAACGGAAGCTCGTAAGA
          1 -GCTAAACAGAAGCTCAT-AGA

               *                  
       7660 GCTGAAC-GAAAGCTCATAAGA
          1 GCTAAACAG-AAGCTCAT-AGA

               *       * *    * 
       7681 GCTTAACAGAAACCCATAAA
          1 GCTAAACAGAAGCTCATAGA

              *                   
       7701 GGTTAAACAGAAGCTCAATAGA
          1 -GCTAAACAGAAGCTC-ATAGA

               *   *   *       * 
       7723 GCTGAACGGAAACTCATATAA
          1 GCTAAACAGAAGCTCATA-GA

             *      *            
       7744 GTTAAACATAAGCTCATGAGA
          1 GCTAAACAGAAGCTCAT-AGA

                       
       7765 GCTAAACAGAA
          1 GCTAAACAGAA

       7776 TGTAAACACG


Statistics
Matches: 114,  Mismatches: 36, Indels: 16
        0.69            0.22        0.10

Matches are distributed among these distances:
  20    8  0.07
  21   98  0.86
  22    8  0.07

ACGTcount: A:0.45, C:0.18, G:0.21, T:0.17


Consensus pattern (20 bp):   
GCTAAACAGAAGCTCATAGA

Found at i:7714 original size:63 final size:64

Alignment explanation


    Indices: 7606--7740  Score: 186
    Period size: 63  Copynumber: 2.1  Consensus size: 64

       7596 GGCTAAACAG

                    *         *                 *   *        *               
       7606 AAGCTCATGAGAGCTAAATAGAAACCCATAAAGGTTGAACGGAAGCTC-GTAAGAGCTGAAC-GA
          1 AAGCTCATAAGAGCTAAACAGAAACCCATAAAGGTTAAACAGAAGCTCAAT-AGAGCTGAACGGA

                           *                                                
       7669 AAGCTCATAAGAGCTTAACAGAAACCCATAAAGGTTAAACAGAAGCTCAATAGAGCTGAACGGA
          1 AAGCTCATAAGAGCTAAACAGAAACCCATAAAGGTTAAACAGAAGCTCAATAGAGCTGAACGGA

                     
       7733 AA-CTCATA
          1 AAGCTCATA

       7741 TAAGTTAAAC


Statistics
Matches: 64,  Mismatches: 6, Indels: 4
        0.86            0.08        0.05

Matches are distributed among these distances:
  63   59  0.92
  64    5  0.08

ACGTcount: A:0.44, C:0.19, G:0.21, T:0.16


Consensus pattern (64 bp):   
AAGCTCATAAGAGCTAAACAGAAACCCATAAAGGTTAAACAGAAGCTCAATAGAGCTGAACGGA

Found at i:7716 original size:42 final size:42

Alignment explanation


    Indices: 7669--7775  Score: 128
    Period size: 42  Copynumber: 2.5  Consensus size: 42

       7659 AGCTGAACGA

                           *                           
       7669 AAGCTCATAAGAGCTTAACAGAAACCCATA-AAGGTTAAACAG
          1 AAGCTCATAAGAGCTAAACAGAAACCCATATAA-GTTAAACAG

                            *   *     *               *
       7711 AAGCTCA-ATAGAGCTGAACGGAAACTCATATAAGTTAAACAT
          1 AAGCTCATA-AGAGCTAAACAGAAACCCATATAAGTTAAACAG

                    *              
       7753 AAGCTCATGAGAGCTAAACAGAA
          1 AAGCTCATAAGAGCTAAACAGAA

       7776 TGTAAACACG


Statistics
Matches: 55,  Mismatches: 7, Indels: 6
        0.81            0.10        0.09

Matches are distributed among these distances:
  41    1  0.02
  42   52  0.95
  43    2  0.04

ACGTcount: A:0.47, C:0.18, G:0.18, T:0.18


Consensus pattern (42 bp):   
AAGCTCATAAGAGCTAAACAGAAACCCATATAAGTTAAACAG

Found at i:8677 original size:26 final size:26

Alignment explanation


    Indices: 8646--8700  Score: 110
    Period size: 26  Copynumber: 2.1  Consensus size: 26

       8636 TGGATAGAAA

                                      
       8646 ATTGGAGAAGAAATTGTCTAGAAACT
          1 ATTGGAGAAGAAATTGTCTAGAAACT

                                      
       8672 ATTGGAGAAGAAATTGTCTAGAAACT
          1 ATTGGAGAAGAAATTGTCTAGAAACT

               
       8698 ATT
          1 ATT

       8701 AAAATCCAAT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  26   29  1.00

ACGTcount: A:0.42, C:0.07, G:0.22, T:0.29


Consensus pattern (26 bp):   
ATTGGAGAAGAAATTGTCTAGAAACT
Done.