Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_37 ID=scaffold_37-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: 35176
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.28

Warning! 4950 characters in sequence are not A, C, G, or T


Found at i:3117 original size:15 final size:15

Alignment explanation


    Indices: 3089--3124  Score: 56
    Period size: 15  Copynumber: 2.5  Consensus size: 15

       3079 CTCTCCAAAG

                           
       3089 TTTTTT-TTTATTTA
          1 TTTTTTATTTATTTA

                      *    
       3103 TTTTTTATTTTTTTA
          1 TTTTTTATTTATTTA

                   
       3118 TTTTTTA
          1 TTTTTTA

       3125 GGAAGNNNNN


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  14    6  0.30
  15   14  0.70

ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86


Consensus pattern (15 bp):   
TTTTTTATTTATTTA

Found at i:11698 original size:45 final size:47

Alignment explanation


    Indices: 11646--11740  Score: 122
    Period size: 51  Copynumber: 2.0  Consensus size: 47

      11636 AACGGTAGTA

                                        *     *            
      11646 GTAACAGTATTC-A-ACACACAAAGTGCTGAATCTGTAACAGTAACG
          1 GTAACAGTATTCGATACACACAAAGTGCCGAATCAGTAACAGTAACG

                                                              
      11691 GTAACAGTATTCGTATTCGACACACAAAGTGCCGAATCAGTAACAGTAAC
          1 GTAACAGTATTCG-A-T--ACACACAAAGTGCCGAATCAGTAACAGTAAC

      11741 AGTAGTCGGC


Statistics
Matches: 42,  Mismatches: 2, Indels: 6
        0.84            0.04        0.12

Matches are distributed among these distances:
  45   12  0.29
  47    1  0.02
  51   29  0.69

ACGTcount: A:0.39, C:0.21, G:0.18, T:0.22


Consensus pattern (47 bp):   
GTAACAGTATTCGATACACACAAAGTGCCGAATCAGTAACAGTAACG

Found at i:24950 original size:54 final size:54

Alignment explanation


    Indices: 24853--24955  Score: 136
    Period size: 54  Copynumber: 1.9  Consensus size: 54

      24843 CTTGTTGAGC

                      *           *   *      *    *               
      24853 AAGAGTGATCTTGTTTAGAGGGGGGTTGAACTATAATGGATTAACTTTTTGGAA
          1 AAGAGTGATCATGTTTAGAGGGAGGTGGAACTACAATGAATTAACTTTTTGGAA

                                *                             
      24907 AAGAGTGATCATGTTTAGAGTGAGGTGGAAGC-ACAATGAATTAACTTTT
          1 AAGAGTGATCATGTTTAGAGGGAGGTGGAA-CTACAATGAATTAACTTTT

      24956 GGGCAATAGA


Statistics
Matches: 42,  Mismatches: 6, Indels: 2
        0.84            0.12        0.04

Matches are distributed among these distances:
  54   41  0.98
  55    1  0.02

ACGTcount: A:0.32, C:0.07, G:0.28, T:0.33


Consensus pattern (54 bp):   
AAGAGTGATCATGTTTAGAGGGAGGTGGAACTACAATGAATTAACTTTTTGGAA
Done.