Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006733.1 Corchorus capsularis cultivar CVL-1 contig06754, 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: 16198
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:984 original size:19 final size:18

Alignment explanation


    Indices: 951--986  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

        941 TTGAAATAAT

                              
        951 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
        969 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

        987 GAAATCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA

Found at i:2529 original size:13 final size:12

Alignment explanation


    Indices: 2511--2551  Score: 50
    Period size: 10  Copynumber: 3.5  Consensus size: 12

       2501 AAACTTGAAG

                         
       2511 AATAAAGACATAA
          1 AATAAAG-CATAA

                        
       2524 AATAAAG-A-AA
          1 AATAAAGCATAA

                        
       2534 AATAAAGCATAA
          1 AATAAAGCATAA

             *    
       2546 ACTAAA
          1 AATAAA

       2552 TAGCTAAACC


Statistics
Matches: 25,  Mismatches: 1, Indels: 5
        0.81            0.03        0.16

Matches are distributed among these distances:
  10    9  0.36
  11    2  0.08
  12    7  0.28
  13    7  0.28

ACGTcount: A:0.71, C:0.07, G:0.07, T:0.15


Consensus pattern (12 bp):   
AATAAAGCATAA

Found at i:6340 original size:22 final size:22

Alignment explanation


    Indices: 6305--6385  Score: 58
    Period size: 22  Copynumber: 3.5  Consensus size: 22

       6295 TTTTCTAAAA

                                    
       6305 AAAAAATAATAATTGCGTTTTTCT
          1 AAAAAA-AA-AATTGCGTTTTTCT

                            *   * *
       6329 AAAAAAAAAATTAG-GGTTTGCG
          1 AAAAAAAAAATT-GCGTTTTTCT

              *                    
       6351 ATTAAAAAAAATT-CGTTTTTCT
          1 A-AAAAAAAAATTGCGTTTTTCT

             *           
       6373 CTAAAAAAAAATT
          1 -AAAAAAAAAATT

       6386 ATTTTCTGTT


Statistics
Matches: 44,  Mismatches: 9, Indels: 10
        0.70            0.14        0.16

Matches are distributed among these distances:
  22   25  0.57
  23   13  0.30
  24    6  0.14

ACGTcount: A:0.48, C:0.07, G:0.10, T:0.35


Consensus pattern (22 bp):   
AAAAAAAAAATTGCGTTTTTCT

Found at i:12757 original size:15 final size:16

Alignment explanation


    Indices: 12725--12758  Score: 52
    Period size: 16  Copynumber: 2.2  Consensus size: 16

      12715 AAAGAAGAAT

                 *          
      12725 TAAAATTAAATCTAAC
          1 TAAAAGTAAATCTAAC

                            
      12741 TAAAAGTAAAT-TAAC
          1 TAAAAGTAAATCTAAC

               
      12756 TAA
          1 TAA

      12759 GAAAGCAATT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  15    7  0.41
  16   10  0.59

ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29


Consensus pattern (16 bp):   
TAAAAGTAAATCTAAC
Done.