Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007639.1 Corchorus olitorius cultivar O-4 contig07665, 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, 800

Length: 1334
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28


Found at i:807 original size:19 final size:20

Alignment explanation


    Indices: 775--812  Score: 53
    Period size: 19  Copynumber: 1.9  Consensus size: 20

        765 ATTAGTAGTC

                                
        775 AAAGTAAATCAAA-TGAAAA
          1 AAAGTAAATCAAATTGAAAA

                                
        794 AAAG-AAATCAAAATTGAAA
          1 AAAGTAAATC-AAATTGAAA

        813 TGGAATAAAA


Statistics
Matches: 17,  Mismatches: 0, Indels: 3
        0.85            0.00        0.15

Matches are distributed among these distances:
  18    5  0.29
  19    7  0.41
  20    5  0.29

ACGTcount: A:0.68, C:0.05, G:0.11, T:0.16


Consensus pattern (20 bp):   
AAAGTAAATCAAATTGAAAA

Found at i:1028 original size:27 final size:27

Alignment explanation


    Indices: 997--1085  Score: 74
    Period size: 27  Copynumber: 3.4  Consensus size: 27

        987 ATCAGCTTTA

                                       
        997 AGTTTTCAAATTGGGAAAGTTCCCGCC
          1 AGTTTTCAAATTGGGAAAGTTCCCGCC

                      * ****      **   
       1024 AGTTTTCAAAGTATTCAA--TCTAGCC
          1 AGTTTTCAAATTGGGAAAGTTCCCGCC

            **                      *  
       1049 CTTTTTCAAATTGGGAAAGTTCCCACC
          1 AGTTTTCAAATTGGGAAAGTTCCCGCC

                      
       1076 AGTTTTCAAA
          1 AGTTTTCAAA

       1086 GTATTCAATC


Statistics
Matches: 41,  Mismatches: 19, Indels: 4
        0.64            0.30        0.06

Matches are distributed among these distances:
  25   16  0.39
  27   25  0.61

ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34


Consensus pattern (27 bp):   
AGTTTTCAAATTGGGAAAGTTCCCGCC

Found at i:1061 original size:52 final size:52

Alignment explanation


    Indices: 999--1134  Score: 227
    Period size: 52  Copynumber: 2.6  Consensus size: 52

        989 CAGCTTTAAG

                                                                
        999 TTTTCAAATTGGGAAAGTTCCCGCCAGTTTTCAAAGTATTCAATCTAGCCCT
          1 TTTTCAAATTGGGAAAGTTCCCGCCAGTTTTCAAAGTATTCAATCTAGCCCT

                                  *                          *  
       1051 TTTTCAAATTGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATCTAGCTCT
          1 TTTTCAAATTGGGAAAGTTCCCGCCAGTTTTCAAAGTATTCAATCTAGCCCT

            *                      *        
       1103 CTTTCAAATTGGGAAAGTTCCCGTCAGGTTTT
          1 TTTTCAAATTGGGAAAGTTCCCGCCA-GTTTT

       1135 AGTTTTCAAT


Statistics
Matches: 78,  Mismatches: 5, Indels: 1
        0.93            0.06        0.01

Matches are distributed among these distances:
  52   73  0.94
  53    5  0.06

ACGTcount: A:0.26, C:0.21, G:0.16, T:0.36


Consensus pattern (52 bp):   
TTTTCAAATTGGGAAAGTTCCCGCCAGTTTTCAAAGTATTCAATCTAGCCCT
Done.