Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020301.1 Corchorus olitorius cultivar O-4 contig20334, 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: 4332
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.29


Found at i:471 original size:7 final size:7

Alignment explanation


    Indices: 453--496  Score: 56
    Period size: 7  Copynumber: 6.4  Consensus size: 7

        443 AATTCCCATC

                    
        453 GAAAAAGA
          1 GAAAAA-A

                  *
        461 GAAAAAT
          1 GAAAAAA

                   
        468 G-AAAAA
          1 GAAAAAA

                   
        474 -AAAAAA
          1 GAAAAAA

                   
        480 GAAAAAA
          1 GAAAAAA

                   
        487 GAAAAAA
          1 GAAAAAA

               
        494 GAA
          1 GAA

        497 GAGAAAGGCA


Statistics
Matches: 32,  Mismatches: 2, Indels: 5
        0.82            0.05        0.13

Matches are distributed among these distances:
   6    9  0.28
   7   17  0.53
   8    6  0.19

ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02


Consensus pattern (7 bp):   
GAAAAAA

Found at i:501 original size:19 final size:19

Alignment explanation


    Indices: 454--502  Score: 71
    Period size: 19  Copynumber: 2.6  Consensus size: 19

        444 ATTCCCATCG

                         *     
        454 AAAAAGAGAAAAATGAAAA
          1 AAAAAGAGAAAAAAGAAAA

                 *             
        473 AAAAAAAGAAAAAAGAAAA
          1 AAAAAGAGAAAAAAGAAAA

              *        
        492 AAGAAGAGAAA
          1 AAAAAGAGAAA

        503 GGCACTTGGT


Statistics
Matches: 26,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  19   26  1.00

ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02


Consensus pattern (19 bp):   
AAAAAGAGAAAAAAGAAAA

Found at i:2424 original size:1 final size:1

Alignment explanation


    Indices: 2418--2443  Score: 52
    Period size: 1  Copynumber: 26.0  Consensus size: 1

       2408 TTAAATTTCT

                                      
       2418 AAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAA

       2444 CCTTAAGCTC


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   25  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Done.