Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_633 ID=scaffold_633-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: 5094
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34


Found at i:341 original size:20 final size:20

Alignment explanation


    Indices: 316--372  Score: 71
    Period size: 20  Copynumber: 2.9  Consensus size: 20

        306 TCCATGCGGT

                                
        316 TCAGCTCACTCGAGCTCAAG
          1 TCAGCTCACTCGAGCTCAAG

                     *         *
        336 TCAGCTCACACGAGCTCAAT
          1 TCAGCTCACTCGAGCTCAAG

               *      *       
        356 TCAACTC-CTTGAGCTCA
          1 TCAGCTCACTCGAGCTCA

        373 TTATTAGATT


Statistics
Matches: 32,  Mismatches: 5, Indels: 1
        0.84            0.13        0.03

Matches are distributed among these distances:
  19    8  0.25
  20   24  0.75

ACGTcount: A:0.26, C:0.35, G:0.16, T:0.23


Consensus pattern (20 bp):   
TCAGCTCACTCGAGCTCAAG

Found at i:3009 original size:5 final size:6

Alignment explanation


    Indices: 2988--3083  Score: 50
    Period size: 6  Copynumber: 15.5  Consensus size: 6

       2978 AATAAAAACA

                      **                   **  *                 *  
       2988 AAAAAG AAAGTG AAAAAG AAAAAG AAATTG CAAAAG AAAAAG AAATCA-
          1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAA-AAG

                   ** *              *                *            
       3036 AAAAAG TGAGAG AAAAAG AAAACG AAGAAAAG AAAATTG AAAAAG AAA
          1 AAAAAG AAAAAG AAAAAG AAAAAG -A-AAAAG AAAA-AG AAAAAG AAA

       3084 TTGAGATTGA


Statistics
Matches: 63,  Mismatches: 22, Indels: 10
        0.66            0.23        0.11

Matches are distributed among these distances:
   5    1  0.02
   6   50  0.79
   7    8  0.13
   8    4  0.06

ACGTcount: A:0.71, C:0.03, G:0.19, T:0.07


Consensus pattern (6 bp):   
AAAAAG

Found at i:3033 original size:18 final size:18

Alignment explanation


    Indices: 2988--3083  Score: 75
    Period size: 18  Copynumber: 5.2  Consensus size: 18

       2978 AATAAAAACA

                     *        
       2988 AAAAAGAAAGTGAAAAAG
          1 AAAAAGAAATTGAAAAAG

                        *     
       3006 AAAAAGAAATTGCAAAAG
          1 AAAAAGAAATTGAAAAAG

                      **      
       3024 AAAAAGAAATCAAAAAAG
          1 AAAAAGAAATTGAAAAAG

            ** *     **     * 
       3042 TGAGAGAAAAAGAAAACG
          1 AAAAAGAAATTGAAAAAG

                                 
       3060 AAGAAAAGAAAATTGAAAAAG
          1 -A-AAAAG-AAATTGAAAAAG

               
       3081 AAA
          1 AAA

       3084 TTGAGATTGA


Statistics
Matches: 57,  Mismatches: 18, Indels: 5
        0.71            0.22        0.06

Matches are distributed among these distances:
  18   42  0.74
  19    2  0.04
  20    4  0.07
  21    9  0.16

ACGTcount: A:0.71, C:0.03, G:0.19, T:0.07


Consensus pattern (18 bp):   
AAAAAGAAATTGAAAAAG

Found at i:4822 original size:20 final size:20

Alignment explanation


    Indices: 4797--4835  Score: 69
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       4787 TCCATGCGGT

                     *          
       4797 TCAGCTCACTCGAGCTCAAG
          1 TCAGCTCACACGAGCTCAAG

                               
       4817 TCAGCTCACACGAGCTCAA
          1 TCAGCTCACACGAGCTCAA

       4836 TTCAACTCCT


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

Matches are distributed among these distances:
  20   18  1.00

ACGTcount: A:0.28, C:0.36, G:0.18, T:0.18


Consensus pattern (20 bp):   
TCAGCTCACACGAGCTCAAG
Done.