Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013816.1 Corchorus capsularis cultivar CVL-1 contig13837, 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: 15086
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.32


Found at i:4227 original size:52 final size:53

Alignment explanation


    Indices: 4141--4321  Score: 283
    Period size: 52  Copynumber: 3.4  Consensus size: 53

       4131 CGAAGATTAC

                    *   *                                         
       4141 TTGAAAGGCCGCACAGGACCATCAGAAGATCAACATAGATTTTCTGAAAATTGA
          1 TTGAAAGGTCGCCCAGGACC-TCAGAAGATCAACATAGATTTTCTGAAAATTGA

                                                                 
       4195 TTGAAAGGTCGCCCAGGA-CTCAGAAGATCAACATAGATTTTCTGAAAATTGA
          1 TTGAAAGGTCGCCCAGGACCTCAGAAGATCAACATAGATTTTCTGAAAATTGA

                                                             *    
       4247 TTGAAAGGTCGCCCAGGACCCTCAGAAGATCAACATAGATTTTCTGAAAGTTGA
          1 TTGAAAGGTCGCCCAGGA-CCTCAGAAGATCAACATAGATTTTCTGAAAATTGA

                       *  *      
       4301 TTTGAAAGGTCACCTAGGACC
          1 -TTGAAAGGTCGCCCAGGACC

       4322 CTCTGAAATG


Statistics
Matches: 119,  Mismatches: 5, Indels: 6
        0.92            0.04        0.05

Matches are distributed among these distances:
  52   51  0.43
  53    1  0.01
  54   51  0.43
  55   16  0.13

ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24


Consensus pattern (53 bp):   
TTGAAAGGTCGCCCAGGACCTCAGAAGATCAACATAGATTTTCTGAAAATTGA

Found at i:5465 original size:19 final size:20

Alignment explanation


    Indices: 5428--5465  Score: 51
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       5418 ATTATTATTA

                      **        
       5428 TTTTTTTTTCTCTTCTCTTT
          1 TTTTTTTTTCAATTCTCTTT

                               
       5448 TTTTTTTTTCAATT-TCTT
          1 TTTTTTTTTCAATTCTCTT

       5466 CTTCCAATCA


Statistics
Matches: 16,  Mismatches: 2, Indels: 1
        0.84            0.11        0.05

Matches are distributed among these distances:
  19    4  0.25
  20   12  0.75

ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79


Consensus pattern (20 bp):   
TTTTTTTTTCAATTCTCTTT
Done.