Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_290 ID=scaffold_290-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: 11201
ACGTcount: A:0.25, C:0.13, G:0.14, T:0.25

Warning! 2598 characters in sequence are not A, C, G, or T


Found at i:936 original size:22 final size:24

Alignment explanation


    Indices: 902--945  Score: 56
    Period size: 22  Copynumber: 1.9  Consensus size: 24

        892 CTTAGACCAA

                                    
        902 GATTTCCAAGA-T-TTGAAATCTT
          1 GATTTCCAAGATTCTTGAAATCTT

                   **             
        924 GATTTCCTTGATTCTTGAAATC
          1 GATTTCCAAGATTCTTGAAATC

        946 GCTCAAAACA


Statistics
Matches: 18,  Mismatches: 2, Indels: 2
        0.82            0.09        0.09

Matches are distributed among these distances:
  22    9  0.50
  23    1  0.06
  24    8  0.44

ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43


Consensus pattern (24 bp):   
GATTTCCAAGATTCTTGAAATCTT

Found at i:7918 original size:17 final size:17

Alignment explanation


    Indices: 7898--7934  Score: 74
    Period size: 17  Copynumber: 2.2  Consensus size: 17

       7888 GCTTAAAAAC

                             
       7898 AAGAATGAACCAACACT
          1 AAGAATGAACCAACACT

                             
       7915 AAGAATGAACCAACACT
          1 AAGAATGAACCAACACT

               
       7932 AAG
          1 AAG

       7935 GAAAATGTTG


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   20  1.00

ACGTcount: A:0.54, C:0.22, G:0.14, T:0.11


Consensus pattern (17 bp):   
AAGAATGAACCAACACT

Found at i:9117 original size:21 final size:19

Alignment explanation


    Indices: 9074--9118  Score: 54
    Period size: 20  Copynumber: 2.3  Consensus size: 19

       9064 GAGCTCAAAT

                         * *   
       9074 GAGCTGAAATGAGTTCATG
          1 GAGCTGAAATGAGCTAATG

                                 
       9093 GAGCTGGAAATGAGCTAATTG
          1 GAGCT-GAAATGAGCTAA-TG

                 
       9114 GAGCT
          1 GAGCT

       9119 CAATGAAATG


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  19    5  0.23
  20   10  0.45
  21    7  0.32

ACGTcount: A:0.31, C:0.11, G:0.33, T:0.24


Consensus pattern (19 bp):   
GAGCTGAAATGAGCTAATG
Done.