Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017495.1 Corchorus olitorius cultivar O-4 contig17528, 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: 18571
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34


Found at i:380 original size:31 final size:31

Alignment explanation


    Indices: 345--445  Score: 98
    Period size: 31  Copynumber: 3.3  Consensus size: 31

        335 CCATTTCACG

                                           
        345 GAGGGACTAAATTGATCTCTTTTCAATAGTA
          1 GAGGGACTAAATTGATCTCTTTTCAATAGTA

                             ***    *   * *
        376 GAGGGACTAAATTGA-CAGATTT-GATAATG
          1 GAGGGACTAAATTGATCTCTTTTCAATAGTA

                            * *     *      
        405 GAGGGACTAAATTGATTTTTTTTCTATAGTA
          1 GAGGGACTAAATTGATCTCTTTTCAATAGTA

            *         
        436 CAGGGACTAA
          1 GAGGGACTAA

        446 TCAGGTACTT


Statistics
Matches: 54,  Mismatches: 14, Indels: 4
        0.75            0.19        0.06

Matches are distributed among these distances:
  29   19  0.35
  30    7  0.13
  31   28  0.52

ACGTcount: A:0.34, C:0.10, G:0.23, T:0.34


Consensus pattern (31 bp):   
GAGGGACTAAATTGATCTCTTTTCAATAGTA

Found at i:701 original size:2 final size:2

Alignment explanation


    Indices: 694--722  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

        684 TTCAAGCAAA

                                                       
        694 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

        723 GAATTCCTCC


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

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Done.