Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006026.1 Corchorus olitorius cultivar O-4 contig06051, whole genome shotgun sequence

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: 9356
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36


Found at i:155 original size:36 final size:36

Alignment explanation


    Indices: 108--177  Score: 113
    Period size: 36  Copynumber: 1.9  Consensus size: 36

         98 GAGATTTTGG

                         *      *               
        108 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
          1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA

                                       *      
        144 AGAAATATGATAACCAAAATCACAAAAGATGTAA
          1 AGAAATATGATAACCAAAATCACAAAAAATGTAA

        178 GGTTATTGAA


Statistics
Matches: 31,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  36   31  1.00

ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21


Consensus pattern (36 bp):   
AGAAATATGATAACCAAAATCACAAAAAATGTAATA

Found at i:988 original size:30 final size:30

Alignment explanation


    Indices: 952--1037  Score: 99
    Period size: 30  Copynumber: 3.0  Consensus size: 30

        942 TACATACCAC

                                          
        952 TAATAATAATTATTATTATAATAATAAGTT
          1 TAATAATAATTATTATTATAATAATAAGTT

                   *    *  **              
        982 TAATAATTA-TAATACCACTAATAATAAG-T
          1 TAATAATAATTATTATTA-TAATAATAAGTT

                                         
       1011 T--TAATAATTATTATTATAATAATAAGT
          1 TAATAATAATTATTATTATAATAATAAGT

       1038 CTAAATTAAC


Statistics
Matches: 45,  Mismatches: 8, Indels: 8
        0.74            0.13        0.13

Matches are distributed among these distances:
  27   15  0.33
  28    5  0.11
  29    7  0.16
  30   18  0.40

ACGTcount: A:0.50, C:0.03, G:0.03, T:0.43


Consensus pattern (30 bp):   
TAATAATAATTATTATTATAATAATAAGTT

Found at i:9256 original size:38 final size:38

Alignment explanation


    Indices: 9205--9281  Score: 154
    Period size: 38  Copynumber: 2.0  Consensus size: 38

       9195 TGAGTTTGTT

                                                  
       9205 TGTAATTTGTTTGTTTATTTGGTAGGTATGTAGTTGAA
          1 TGTAATTTGTTTGTTTATTTGGTAGGTATGTAGTTGAA

                                                  
       9243 TGTAATTTGTTTGTTTATTTGGTAGGTATGTAGTTGAA
          1 TGTAATTTGTTTGTTTATTTGGTAGGTATGTAGTTGAA

             
       9281 T
          1 T

       9282 TCTCATTTAG


Statistics
Matches: 39,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  38   39  1.00

ACGTcount: A:0.21, C:0.00, G:0.26, T:0.53


Consensus pattern (38 bp):   
TGTAATTTGTTTGTTTATTTGGTAGGTATGTAGTTGAA
Done.