Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016530.1 Corchorus olitorius cultivar O-4 contig16563, 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: 9652
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.35


Found at i:882 original size:36 final size:36

Alignment explanation


    Indices: 835--904  Score: 113
    Period size: 36  Copynumber: 1.9  Consensus size: 36

        825 GAGATTTTGG

                         *      *               
        835 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
          1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA

                                       *      
        871 AGAAATATGATAACCAAAATCACAAAAGATGTAA
          1 AGAAATATGATAACCAAAATCACAAAAAATGTAA

        905 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:9442 original size:3 final size:3

Alignment explanation


    Indices: 9436--9465  Score: 60
    Period size: 3  Copynumber: 10.0  Consensus size: 3

       9426 GATCATCAAC

                                                   
       9436 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
          1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG

       9466 TGAGTGAGTT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   27  1.00

ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33


Consensus pattern (3 bp):   
ATG

Found at i:9599 original size:2 final size:2

Alignment explanation


    Indices: 9592--9623  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

       9582 CACCCATGTT

                                                           
       9592 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       9624 ATAATAATAA


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:9629 original size:3 final size:3

Alignment explanation


    Indices: 9621--9652  Score: 64
    Period size: 3  Copynumber: 10.7  Consensus size: 3

       9611 ATATATATAT

                                                      
       9621 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
          1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   29  1.00

ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34


Consensus pattern (3 bp):   
ATA

Done.