Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000686.1 Corchorus capsularis cultivar CVL-1 contig00686, 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, 669

Length: 1116
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.33


Found at i:263 original size:28 final size:28

Alignment explanation


    Indices: 203--263  Score: 79
    Period size: 28  Copynumber: 2.2  Consensus size: 28

        193 TTCGTGTGTT

                    *             *    *
        203 AAAATTACCGTTTTGCCCCTACTAGGCT
          1 AAAATTACAGTTTTGCCCCTACGAGGCC

                                        
        231 AAAATTACAGTTTTGCCCCTA-GAGGCC
          1 AAAATTACAGTTTTGCCCCTACGAGGCC

                  
        258 AGAAAT
          1 A-AAAT

        264 GATTAAATGA


Statistics
Matches: 29,  Mismatches: 3, Indels: 2
        0.85            0.09        0.06

Matches are distributed among these distances:
  27    5  0.17
  28   24  0.83

ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28


Consensus pattern (28 bp):   
AAAATTACAGTTTTGCCCCTACGAGGCC

Found at i:443 original size:13 final size:13

Alignment explanation


    Indices: 412--454  Score: 52
    Period size: 13  Copynumber: 3.3  Consensus size: 13

        402 GTCTGACTGT

                   *     
        412 TTTGGTTGATTA-
          1 TTTGGTTTATTAC

                          
        424 TTCTGGTTTATTAC
          1 TT-TGGTTTATTAC

                      *  
        438 TTTGGTTTATAAC
          1 TTTGGTTTATTAC

                
        451 TTTG
          1 TTTG

        455 ATTATGATAC


Statistics
Matches: 27,  Mismatches: 2, Indels: 3
        0.84            0.06        0.09

Matches are distributed among these distances:
  12    2  0.07
  13   23  0.85
  14    2  0.07

ACGTcount: A:0.16, C:0.07, G:0.19, T:0.58


Consensus pattern (13 bp):   
TTTGGTTTATTAC

Found at i:673 original size:13 final size:13

Alignment explanation


    Indices: 624--678  Score: 62
    Period size: 13  Copynumber: 4.4  Consensus size: 13

        614 TTGAGGAACT

                      *  
        624 ATTTTATT-ACTG
          1 ATTTTATTAAATG

                          
        636 -TTTTATTAAATTG
          1 ATTTTATTAAA-TG

            *            
        649 TTTTTA-TAAATG
          1 ATTTTATTAAATG

                         
        661 ATTTTATTAAATG
          1 ATTTTATTAAATG

                 
        674 ATTTT
          1 ATTTT

        679 GGGTGCATGA


Statistics
Matches: 37,  Mismatches: 2, Indels: 7
        0.80            0.04        0.15

Matches are distributed among these distances:
  11    7  0.19
  12    8  0.22
  13   17  0.46
  14    5  0.14

ACGTcount: A:0.31, C:0.02, G:0.07, T:0.60


Consensus pattern (13 bp):   
ATTTTATTAAATG
Done.