Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001436.1 Corchorus capsularis cultivar CVL-1 contig01436, 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: 6574
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36


Found at i:920 original size:3 final size:3

Alignment explanation


    Indices: 907--974  Score: 84
    Period size: 3  Copynumber: 23.0  Consensus size: 3

        897 AAAACAAATA

                                                                         * 
        907 TAT TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT

             *   *   *   *             
        954 TGT TGT TGT TGT TAT TAT TAT
          1 TAT TAT TAT TAT TAT TAT TAT

        975 ATAGAATTCC


Statistics
Matches: 62,  Mismatches: 2, Indels: 2
        0.94            0.03        0.03

Matches are distributed among these distances:
   2    2  0.03
   3   60  0.97

ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68


Consensus pattern (3 bp):   
TAT

Found at i:2391 original size:37 final size:37

Alignment explanation


    Indices: 2334--2410  Score: 127
    Period size: 37  Copynumber: 2.1  Consensus size: 37

       2324 TTGAACCCAG

                                                 
       2334 AATCTCACGATCCAGACACACGGATTAATCAATACTA
          1 AATCTCACGATCCAGACACACGGATTAATCAATACTA

                   *    *  *                     
       2371 AATCTCATGATCTAGGCACACGGATTAATCAATACTA
          1 AATCTCACGATCCAGACACACGGATTAATCAATACTA

               
       2408 AAT
          1 AAT

       2411 ATGATGATGA


Statistics
Matches: 37,  Mismatches: 3, Indels: 0
        0.93            0.08        0.00

Matches are distributed among these distances:
  37   37  1.00

ACGTcount: A:0.40, C:0.23, G:0.12, T:0.25


Consensus pattern (37 bp):   
AATCTCACGATCCAGACACACGGATTAATCAATACTA
Done.