Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016609.1 Corchorus olitorius cultivar O-4 contig16642, 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: 2246
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29


Found at i:493 original size:10 final size:10

Alignment explanation


    Indices: 478--528  Score: 59
    Period size: 10  Copynumber: 5.2  Consensus size: 10

        468 TTAATTGGCA

                      
        478 TTAGGGTCAT
          1 TTAGGGTCAT

                  *   
        488 TTAGGGGCAT
          1 TTAGGGTCAT

              *       
        498 TTTGGGTCAT
          1 TTAGGGTCAT

                  *   
        508 TTAGGGGCAT
          1 TTAGGGTCAT

               *      
        518 TT-TGGTCAT
          1 TTAGGGTCAT

              
        527 TT
          1 TT

        529 TTACACCTAG


Statistics
Matches: 34,  Mismatches: 7, Indels: 1
        0.81            0.17        0.02

Matches are distributed among these distances:
   9    7  0.21
  10   27  0.79

ACGTcount: A:0.16, C:0.10, G:0.31, T:0.43


Consensus pattern (10 bp):   
TTAGGGTCAT

Found at i:498 original size:19 final size:19

Alignment explanation


    Indices: 474--528  Score: 83
    Period size: 20  Copynumber: 2.8  Consensus size: 19

        464 TTGTTTAATT

                  *            
        474 GGCATTAGGGTCATTTAGG
          1 GGCATTTGGGTCATTTAGG

                                
        493 GGCATTTTGGGTCATTTAGG
          1 GGCA-TTTGGGTCATTTAGG

                   *        
        513 GGCATTTTGGTCATTT
          1 GGCATTTGGGTCATTT

        529 TTACACCTAG


Statistics
Matches: 33,  Mismatches: 2, Indels: 2
        0.89            0.05        0.05

Matches are distributed among these distances:
  19   15  0.45
  20   18  0.55

ACGTcount: A:0.16, C:0.11, G:0.33, T:0.40


Consensus pattern (19 bp):   
GGCATTTGGGTCATTTAGG

Found at i:504 original size:20 final size:20

Alignment explanation


    Indices: 481--528  Score: 89
    Period size: 20  Copynumber: 2.5  Consensus size: 20

        471 ATTGGCATTA

                                
        481 GGGTCATTTAGGGGCATTTT
          1 GGGTCATTTAGGGGCATTTT

                                
        501 GGGTCATTTAGGGGCATTTT
          1 GGGTCATTTAGGGGCATTTT

                     
        521 -GGTCATTT
          1 GGGTCATTT

        529 TTACACCTAG


Statistics
Matches: 28,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  19    8  0.29
  20   20  0.71

ACGTcount: A:0.15, C:0.10, G:0.33, T:0.42


Consensus pattern (20 bp):   
GGGTCATTTAGGGGCATTTT

Found at i:860 original size:17 final size:17

Alignment explanation


    Indices: 838--870  Score: 66
    Period size: 17  Copynumber: 1.9  Consensus size: 17

        828 ATATGCATGC

                             
        838 TTTCACATTAGTTTAAA
          1 TTTCACATTAGTTTAAA

                            
        855 TTTCACATTAGTTTAA
          1 TTTCACATTAGTTTAA

        871 TTAATTATAG


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.33, C:0.12, G:0.06, T:0.48


Consensus pattern (17 bp):   
TTTCACATTAGTTTAAA
Done.