Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009453.1 Corchorus capsularis cultivar CVL-1 contig09474, 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: 7451
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36


Found at i:836 original size:26 final size:26

Alignment explanation


    Indices: 760--836  Score: 68
    Period size: 26  Copynumber: 3.0  Consensus size: 26

        750 TATCTTACAT

                *        *  * *       
        760 ATTATTAATGATGAAAAGCTACTAAA
          1 ATTACTAATGATGTAAGGTTACTAAA

                 *              * *    
        786 ATTACAACAT-AT-TAAGGTAAATAAA
          1 ATTACTA-ATGATGTAAGGTTACTAAA

                                      
        811 ATTACTAATGATGTAAGGTTACTAAA
          1 ATTACTAATGATGTAAGGTTACTAAA

        837 TTTATGGAAA


Statistics
Matches: 38,  Mismatches: 10, Indels: 6
        0.70            0.19        0.11

Matches are distributed among these distances:
  24    2  0.05
  25   16  0.42
  26   18  0.47
  27    2  0.05

ACGTcount: A:0.49, C:0.08, G:0.12, T:0.31


Consensus pattern (26 bp):   
ATTACTAATGATGTAAGGTTACTAAA

Found at i:4434 original size:3 final size:3

Alignment explanation


    Indices: 4426--4470  Score: 54
    Period size: 3  Copynumber: 14.7  Consensus size: 3

       4416 ATATATATGA

                         *             *              *                
       4426 ATT ATT ATT ACT ATT ATT ATAA ATT ATT ATT ACT ATT ATT ATT AT
          1 ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT AT

       4471 ATATACTACA


Statistics
Matches: 35,  Mismatches: 6, Indels: 2
        0.81            0.14        0.05

Matches are distributed among these distances:
   3   33  0.94
   4    2  0.06

ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58


Consensus pattern (3 bp):   
ATT

Found at i:4451 original size:22 final size:22

Alignment explanation


    Indices: 4411--4467  Score: 87
    Period size: 22  Copynumber: 2.5  Consensus size: 22

       4401 AAGTGTCGAA

                 *       *         
       4411 TACTAATATATATGAATTATTAT
          1 TACTATTAT-TATAAATTATTAT

                                  
       4434 TACTATTATTATAAATTATTAT
          1 TACTATTATTATAAATTATTAT

                        
       4456 TACTATTATTAT
          1 TACTATTATTAT

       4468 TATATATACT


Statistics
Matches: 32,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  22   24  0.75
  23    8  0.25

ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53


Consensus pattern (22 bp):   
TACTATTATTATAAATTATTAT
Done.