Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019474.1 Corchorus olitorius cultivar O-4 contig19507, 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: 15965
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32


Found at i:1412 original size:19 final size:19

Alignment explanation


    Indices: 1388--1433  Score: 65
    Period size: 19  Copynumber: 2.4  Consensus size: 19

       1378 TTGATGTGGC

                    *          
       1388 AATGCCACCTAGGACAAAA
          1 AATGCCACATAGGACAAAA

                           **  
       1407 AATGCCACATAGGACCTAA
          1 AATGCCACATAGGACAAAA

                    
       1426 AATGCCAC
          1 AATGCCAC

       1434 GTGGCATCGC


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  19   24  1.00

ACGTcount: A:0.43, C:0.28, G:0.15, T:0.13


Consensus pattern (19 bp):   
AATGCCACATAGGACAAAA

Found at i:1565 original size:29 final size:30

Alignment explanation


    Indices: 1524--1597  Score: 89
    Period size: 31  Copynumber: 2.5  Consensus size: 30

       1514 AAATTGCAAA

                *   *                      
       1524 TTCAAGGGTCAAAATGTCCAAAAT-TA-AAG
          1 TTCAGGGGGCAAAATGT-CAAAATATACAAG

              *                            
       1553 TTTAGGGGGCAAAATGTCAAAATCATACAAG
          1 TTCAGGGGGCAAAATGTCAAAAT-ATACAAG

                          
       1584 TTCAGGGGGCAAAA
          1 TTCAGGGGGCAAAA

       1598 AGGACATTAA


Statistics
Matches: 38,  Mismatches: 4, Indels: 4
        0.83            0.09        0.09

Matches are distributed among these distances:
  28    6  0.16
  29   14  0.37
  30    2  0.05
  31   16  0.42

ACGTcount: A:0.42, C:0.14, G:0.23, T:0.22


Consensus pattern (30 bp):   
TTCAGGGGGCAAAATGTCAAAATATACAAG

Found at i:14938 original size:12 final size:12

Alignment explanation


    Indices: 14921--14945  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

      14911 GCTTTAACTA

                        
      14921 GCCATTTCCTTT
          1 GCCATTTCCTTT

                        
      14933 GCCATTTCCTTT
          1 GCCATTTCCTTT

             
      14945 G
          1 G

      14946 AGAGAGAATT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.08, C:0.32, G:0.12, T:0.48


Consensus pattern (12 bp):   
GCCATTTCCTTT

Found at i:15922 original size:15 final size:15

Alignment explanation


    Indices: 15902--15931  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

      15892 ATCAGGCTGC

                      *    
      15902 CACGATACACGATAT
          1 CACGATACACAATAT

                           
      15917 CACGATACACAATAT
          1 CACGATACACAATAT

      15932 TTCAACCGTA


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.43, C:0.27, G:0.10, T:0.20


Consensus pattern (15 bp):   
CACGATACACAATAT
Done.