Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_980 ID=scaffold_980-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: 4273
ACGTcount: A:0.17, C:0.08, G:0.06, T:0.10

Warning! 2525 characters in sequence are not A, C, G, or T


Found at i:17 original size:7 final size:7

Alignment explanation


    Indices: 1--156  Score: 228
    Period size: 7  Copynumber: 22.0  Consensus size: 7

                    
          1 CCCTAAAA
          1 CCCT-AAA

                   
          9 CCCTAAA
          1 CCCTAAA

                   
         16 CCCTAAA
          1 CCCTAAA

                    
         23 CCCTAAAA
          1 CCCT-AAA

                   
         31 CCCTAAA
          1 CCCTAAA

            *      
         38 ACCTAAA
          1 CCCTAAA

                   
         45 CCCTAAA
          1 CCCTAAA

                   
         52 CCCTAAA
          1 CCCTAAA

               *   
         59 -CCAAAA
          1 CCCTAAA

                   
         65 CCCTAAA
          1 CCCTAAA

                   
         72 -CCTAAA
          1 CCCTAAA

                    
         78 CCCTAAAA
          1 CCCT-AAA

                    
         86 CCCTAAAA
          1 CCCT-AAA

                   
         94 CCC-AAA
          1 CCCTAAA

                   
        100 CCCTAAA
          1 CCCTAAA

                   
        107 CCCTAAA
          1 CCCTAAA

                    
        114 CCCTAAAA
          1 CCCT-AAA

                   
        122 CCCTAAA
          1 CCCTAAA

                   
        129 CCCTAAA
          1 CCCTAAA

                   
        136 CCCTAAA
          1 CCCTAAA

                   
        143 CCCTAAA
          1 CCCTAAA

                   
        150 CCCTAAA
          1 CCCTAAA

        157 TCCCACTCTT


Statistics
Matches: 138,  Mismatches: 4, Indels: 13
        0.89            0.03        0.08

Matches are distributed among these distances:
   6   17  0.12
   7   89  0.64
   8   32  0.23

ACGTcount: A:0.47, C:0.40, G:0.00, T:0.13


Consensus pattern (7 bp):   
CCCTAAA

Found at i:50 original size:36 final size:34

Alignment explanation


    Indices: 6--156  Score: 214
    Period size: 36  Copynumber: 4.3  Consensus size: 34

          1 CCCTA

                                                
          6 AAACCCTAAACCCTAAACCCTAAAACCCTAAAACCT
          1 AAACCCTAAACCCTAAACCC--AAACCCTAAAACCT

                               *              
         42 AAACCCTAAACCCTAAACCAAAACCCT-AAACCT
          1 AAACCCTAAACCCTAAACCCAAACCCTAAAACCT

                                            *   
         75 AAACCCTAAAACCCTAAAACCCAAACCCTAAACCCT
          1 AAACCCT-AAACCCT-AAACCCAAACCCTAAAACCT

                                            *   
        111 AAACCCTAAAACCCTAAACCCTAAACCCTAAACCCT
          1 AAACCCT-AAACCCTAAACCC-AAACCCTAAAACCT

                      
        147 AAACCCTAAA
          1 AAACCCTAAA

        157 TCCCACTCTT


Statistics
Matches: 108,  Mismatches: 3, Indels: 9
        0.90            0.03        0.08

Matches are distributed among these distances:
  33   13  0.12
  34   14  0.13
  35   21  0.19
  36   60  0.56

ACGTcount: A:0.48, C:0.40, G:0.00, T:0.13


Consensus pattern (34 bp):   
AAACCCTAAACCCTAAACCCAAACCCTAAAACCT

Found at i:336 original size:31 final size:31

Alignment explanation


    Indices: 301--365  Score: 85
    Period size: 31  Copynumber: 2.1  Consensus size: 31

        291 GATATTCCTA

                    *      *               
        301 GAATAGCTTAATTCATGTTAGGATATCCCGG
          1 GAATAGCTCAATTCACGTTAGGATATCCCGG

                         *     *         * 
        332 GAATAGCTCAATTGACGTTGGGATATCCCTG
          1 GAATAGCTCAATTCACGTTAGGATATCCCGG

               
        363 GAA
          1 GAA

        366 AATCTCTCGA


Statistics
Matches: 29,  Mismatches: 5, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  31   29  1.00

ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29


Consensus pattern (31 bp):   
GAATAGCTCAATTCACGTTAGGATATCCCGG
Done.