Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018200.1 Corchorus olitorius cultivar O-4 contig18233, 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: 7785
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.29


Found at i:446 original size:22 final size:22

Alignment explanation


    Indices: 401--453  Score: 63
    Period size: 22  Copynumber: 2.4  Consensus size: 22

        391 TGCTTTCTGA

                              **  
        401 TTAATTGTTTTCTTTAATTTTC
          1 TTAATTGTTTTCTTTAATAGTC

              *                    
        423 TTGATTGTTTTC-TTAGATAGTC
          1 TTAATTGTTTTCTTTA-ATAGTC

                     
        445 TTAATTGTT
          1 TTAATTGTT

        454 AGTTTGATTT


Statistics
Matches: 26,  Mismatches: 4, Indels: 2
        0.81            0.12        0.06

Matches are distributed among these distances:
  21    3  0.12
  22   23  0.88

ACGTcount: A:0.19, C:0.08, G:0.11, T:0.62


Consensus pattern (22 bp):   
TTAATTGTTTTCTTTAATAGTC

Found at i:2573 original size:18 final size:18

Alignment explanation


    Indices: 2550--2585  Score: 72
    Period size: 18  Copynumber: 2.0  Consensus size: 18

       2540 CAAAGAAAAC

                              
       2550 ATAATAAGTAAAAGAAAT
          1 ATAATAAGTAAAAGAAAT

                              
       2568 ATAATAAGTAAAAGAAAT
          1 ATAATAAGTAAAAGAAAT

       2586 CCATAAAAAA


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.67, C:0.00, G:0.11, T:0.22


Consensus pattern (18 bp):   
ATAATAAGTAAAAGAAAT

Found at i:4770 original size:19 final size:18

Alignment explanation


    Indices: 4746--4781  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       4736 TGAAGATTTA

                               
       4746 TTGAAGACAATTTGAAGAT
          1 TTGAAGACAA-TTGAAGAT

                    *        
       4765 TTGAAGACCATTGAAGA
          1 TTGAAGACAATTGAAGA

       4782 ATAATTTCAA


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

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28


Consensus pattern (18 bp):   
TTGAAGACAATTGAAGAT
Done.