Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_672 ID=scaffold_672-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: 4743
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33


Found at i:199 original size:52 final size:51

Alignment explanation


    Indices: 135--266  Score: 167
    Period size: 50  Copynumber: 2.6  Consensus size: 51

        125 ATGAACAAAT

                   *                                      *    *
        135 GAGTTACTTAATGCATGACTTAATTTAATGATGCAAACTTTAACTACCATGG
          1 GAGTTACATAATGCATGACTTAATTTAATGATGCAAAC-TTAACTAACATGA

                             * *                               
        187 GAGTTACATAATGCATGTCATAATTT-ATGATGCAAACTTAACTAACATGA
          1 GAGTTACATAATGCATGACTTAATTTAATGATGCAAACTTAACTAACATGA

            *             *      *   *    
        237 AAGTTACATAATGCTTGACTTTATTAAATG
          1 GAGTTACATAATGCATGACTTAATTTAATG

        267 CATAACACAT


Statistics
Matches: 68,  Mismatches: 11, Indels: 3
        0.83            0.13        0.04

Matches are distributed among these distances:
  50   31  0.46
  51   14  0.21
  52   23  0.34

ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35


Consensus pattern (51 bp):   
GAGTTACATAATGCATGACTTAATTTAATGATGCAAACTTAACTAACATGA

Found at i:4117 original size:25 final size:27

Alignment explanation


    Indices: 4089--4138  Score: 68
    Period size: 27  Copynumber: 1.9  Consensus size: 27

       4079 ATTAAGCATT

                  *                    
       4089 AAACAATA-ACTTAA-AACACTCATAA
          1 AAACAACATACTTAATAACACTCATAA

                      *              
       4114 AAACAACATATTTAATAACACTCAT
          1 AAACAACATACTTAATAACACTCAT

       4139 GCACAAGAAT


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  25    7  0.33
  26    5  0.24
  27    9  0.43

ACGTcount: A:0.56, C:0.20, G:0.00, T:0.24


Consensus pattern (27 bp):   
AAACAACATACTTAATAACACTCATAA

Found at i:4429 original size:50 final size:52

Alignment explanation


    Indices: 4319--4439  Score: 174
    Period size: 50  Copynumber: 2.4  Consensus size: 52

       4309 ATGAACAAAT

                   *          **                      *        *
       4319 GAGTTACTTAATGCATGAGTTAATTTAATGATGCAAACTTTAGCTAACATGG
          1 GAGTTACATAATGCATGACATAATTTAATGATGCAAACTTTAACTAACATGA

                             *                                  
       4371 GAGTTACATAATGCATGTCATAATTT-ATGATGCAAAC-TTAACTAACATGA
          1 GAGTTACATAATGCATGACATAATTTAATGATGCAAACTTTAACTAACATGA

                               
       4421 GAGTTACATAATGCATGAC
          1 GAGTTACATAATGCATGAC

       4440 TTTATTAAAT


Statistics
Matches: 62,  Mismatches: 7, Indels: 2
        0.87            0.10        0.03

Matches are distributed among these distances:
  50   29  0.47
  51   11  0.18
  52   22  0.35

ACGTcount: A:0.37, C:0.13, G:0.17, T:0.32


Consensus pattern (52 bp):   
GAGTTACATAATGCATGACATAATTTAATGATGCAAACTTTAACTAACATGA
Done.