Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01002113.1 Corchorus capsularis cultivar CVL-1 contig02117, 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, 696

Length: 1160
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34


Found at i:214 original size:18 final size:18

Alignment explanation


    Indices: 179--228  Score: 57
    Period size: 18  Copynumber: 2.7  Consensus size: 18

        169 GTTAGAAATC

                          *    
        179 ATTGTATTACT-TATTCTT
          1 ATTGT-TTACTATAATCTT

                              
        197 ATTGTTTACTATAATCTT
          1 ATTGTTTACTATAATCTT

                  *       
        215 ATTGATCTACTATA
          1 ATTG-TTTACTATA

        229 TGATTGCAAT


Statistics
Matches: 28,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  17    5  0.18
  18   15  0.54
  19    8  0.29

ACGTcount: A:0.28, C:0.12, G:0.06, T:0.54


Consensus pattern (18 bp):   
ATTGTTTACTATAATCTT

Found at i:692 original size:16 final size:16

Alignment explanation


    Indices: 671--704  Score: 68
    Period size: 16  Copynumber: 2.1  Consensus size: 16

        661 GTTTTATATA

                            
        671 TAATGCATATTTTATT
          1 TAATGCATATTTTATT

                            
        687 TAATGCATATTTTATT
          1 TAATGCATATTTTATT

              
        703 TA
          1 TA

        705 TTATATTAAT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   18  1.00

ACGTcount: A:0.32, C:0.06, G:0.06, T:0.56


Consensus pattern (16 bp):   
TAATGCATATTTTATT

Found at i:720 original size:10 final size:10

Alignment explanation


    Indices: 705--742  Score: 53
    Period size: 10  Copynumber: 4.0  Consensus size: 10

        695 ATTTTATTTA

                      
        705 TTATATTAAT
          1 TTATATTAAT

                      
        715 TTATA-TAA-
          1 TTATATTAAT

            *         
        723 ATATATTAAT
          1 TTATATTAAT

                      
        733 TTATATTAAT
          1 TTATATTAAT

        743 AATACTCTAT


Statistics
Matches: 24,  Mismatches: 2, Indels: 4
        0.80            0.07        0.13

Matches are distributed among these distances:
   8    4  0.17
   9    6  0.25
  10   14  0.58

ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55


Consensus pattern (10 bp):   
TTATATTAAT

Found at i:727 original size:18 final size:18

Alignment explanation


    Indices: 706--743  Score: 67
    Period size: 18  Copynumber: 2.1  Consensus size: 18

        696 TTTTATTTAT

                              
        706 TATATTAATTTATATAAA
          1 TATATTAATTTATATAAA

                           *  
        724 TATATTAATTTATATTAA
          1 TATATTAATTTATATAAA

              
        742 TA
          1 TA

        744 ATACTCTATT


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  18   19  1.00

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (18 bp):   
TATATTAATTTATATAAA
Done.