Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021919.1 Corchorus olitorius cultivar O-4 contig21952, 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: 17884
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33


Found at i:13771 original size:6 final size:6

Alignment explanation


    Indices: 13760--13784  Score: 50
    Period size: 6  Copynumber: 4.2  Consensus size: 6

      13750 TTATTAGTAC

                                         
      13760 ATACAT ATACAT ATACAT ATACAT A
          1 ATACAT ATACAT ATACAT ATACAT A

      13785 ATATAAAATT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   19  1.00

ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32


Consensus pattern (6 bp):   
ATACAT

Found at i:14554 original size:19 final size:19

Alignment explanation


    Indices: 14508--14578  Score: 65
    Period size: 19  Copynumber: 3.7  Consensus size: 19

      14498 TATATATATC

                           *    
      14508 ATGTTTATTAATATAATATT
          1 ATGTTTATTAATAT-GTATT

                                
      14528 -TGTATTATTAATATGTATT
          1 ATGT-TTATTAATATGTATT

                             *  
      14547 ATGTTTATTTAATA-GTGTT
          1 ATGTTTA-TTAATATGTATT

            * *          
      14566 GTATTTATTAATA
          1 ATGTTTATTAATA

      14579 ATATACACTT


Statistics
Matches: 44,  Mismatches: 4, Indels: 8
        0.79            0.07        0.14

Matches are distributed among these distances:
  18    6  0.14
  19   19  0.43
  20   19  0.43

ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56


Consensus pattern (19 bp):   
ATGTTTATTAATATGTATT

Found at i:14558 original size:20 final size:20

Alignment explanation


    Indices: 14497--14560  Score: 69
    Period size: 20  Copynumber: 3.1  Consensus size: 20

      14487 ATATATATAT

                      *          
      14497 ATATATATATCATGTTTATTA
          1 ATATA-ATATTATGTTTATTA

                                 
      14518 ATATAATATT-TGTATTATTA
          1 ATATAATATTATGT-TTATTA

                 *               
      14538 ATAT-GTATTATGTTTATTTA
          1 ATATAATATTATGTTTA-TTA

               
      14558 ATA
          1 ATA

      14561 GTGTTGTATT


Statistics
Matches: 38,  Mismatches: 2, Indels: 7
        0.81            0.04        0.15

Matches are distributed among these distances:
  19   10  0.26
  20   23  0.61
  21    5  0.13

ACGTcount: A:0.38, C:0.02, G:0.06, T:0.55


Consensus pattern (20 bp):   
ATATAATATTATGTTTATTA
Done.