Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000629.1 Corchorus olitorius cultivar O-4 contig00629, 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, 786

Length: 1310
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35


Found at i:509 original size:31 final size:31

Alignment explanation


    Indices: 474--553  Score: 115
    Period size: 31  Copynumber: 2.6  Consensus size: 31

        464 ACGGCGTCCG

                      *   *            *   
        474 ACATGGCATGCCACGTGTCACTTTTTGGTAC
          1 ACATGGCATGACACATGTCACTTTTTGATAC

                   *                       
        505 ACATGGCTTGACACATGTCACTTTTTGATAC
          1 ACATGGCATGACACATGTCACTTTTTGATAC

                   *          
        536 ACATGGCTTGACACATGT
          1 ACATGGCATGACACATGT

        554 GGCGTGCCAC


Statistics
Matches: 45,  Mismatches: 4, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  31   45  1.00

ACGTcount: A:0.24, C:0.24, G:0.20, T:0.33


Consensus pattern (31 bp):   
ACATGGCATGACACATGTCACTTTTTGATAC

Found at i:816 original size:41 final size:41

Alignment explanation


    Indices: 763--844  Score: 137
    Period size: 41  Copynumber: 2.0  Consensus size: 41

        753 TTTATAACTA

                                   *       *         
        763 GGGGCTAAACCTGGATTTAATTTCTTACCTTGATTATTAGG
          1 GGGGCTAAACCTGGATTTAATTTATTACCTTAATTATTAGG

                                      *              
        804 GGGGCTAAACCTGGATTTAATTTATTTCCTTAATTATTAGG
          1 GGGGCTAAACCTGGATTTAATTTATTACCTTAATTATTAGG

        845 AGGGTTAAGT


Statistics
Matches: 38,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  41   38  1.00

ACGTcount: A:0.26, C:0.13, G:0.21, T:0.40


Consensus pattern (41 bp):   
GGGGCTAAACCTGGATTTAATTTATTACCTTAATTATTAGG

Found at i:1128 original size:27 final size:27

Alignment explanation


    Indices: 1076--1129  Score: 65
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       1066 TAGAAAATAA

                             * * *     
       1076 AAAGGTAGAAGTTTTTTTTTTTGAAAG
          1 AAAGGTAGAAGTTTTTTCTATAGAAAG

                                        
       1103 AAAGGTAGAAAG-TTTTTCTATAGAAAG
          1 AAAGGTAG-AAGTTTTTTCTATAGAAAG

       1130 TTTAGGACTA


Statistics
Matches: 23,  Mismatches: 3, Indels: 2
        0.82            0.11        0.07

Matches are distributed among these distances:
  27   20  0.87
  28    3  0.13

ACGTcount: A:0.39, C:0.02, G:0.22, T:0.37


Consensus pattern (27 bp):   
AAAGGTAGAAGTTTTTTCTATAGAAAG
Done.