Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012666.1 Corchorus capsularis cultivar CVL-1 contig12687, 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: 17111
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32


Found at i:4586 original size:15 final size:16

Alignment explanation


    Indices: 4554--4587  Score: 52
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       4544 AAAGAAGAAT

                 *          
       4554 TAAAATTAAATCTAAC
          1 TAAAAGTAAATCTAAC

                            
       4570 TAAAAGTAAAT-TAAC
          1 TAAAAGTAAATCTAAC

               
       4585 TAA
          1 TAA

       4588 GAAAGCAATC


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

Found at i:12454 original size:19 final size:18

Alignment explanation


    Indices: 12421--12456  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      12411 TTAAAATAAT

                              
      12421 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
      12439 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

      12457 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:15554 original size:10 final size:10

Alignment explanation


    Indices: 15539--15564  Score: 52
    Period size: 10  Copynumber: 2.6  Consensus size: 10

      15529 GAGGACTCTA

                      
      15539 GAATTTTCTG
          1 GAATTTTCTG

                      
      15549 GAATTTTCTG
          1 GAATTTTCTG

                  
      15559 GAATTT
          1 GAATTT

      15565 GGCAGCAACT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   16  1.00

ACGTcount: A:0.23, C:0.08, G:0.19, T:0.50


Consensus pattern (10 bp):   
GAATTTTCTG
Done.