Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014086.1 Corchorus olitorius cultivar O-4 contig14119, 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, 874

Length: 1458
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31


Found at i:353 original size:13 final size:12

Alignment explanation


    Indices: 317--363  Score: 51
    Period size: 13  Copynumber: 3.8  Consensus size: 12

        307 TCAATCTTTA

                        *
        317 TATATATTGATAA
          1 TATATATT-ATAT

                 *      
        330 TA-ATGTTATAT
          1 TATATATTATAT

                         
        341 TATATTATTATAT
          1 TATA-TATTATAT

                      
        354 TATATATTAT
          1 TATATATTAT

        364 CAATAAACTT


Statistics
Matches: 29,  Mismatches: 3, Indels: 5
        0.78            0.08        0.14

Matches are distributed among these distances:
  11    5  0.17
  12   11  0.38
  13   13  0.45

ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55


Consensus pattern (12 bp):   
TATATATTATAT

Found at i:510 original size:8 final size:8

Alignment explanation


    Indices: 497--538  Score: 77
    Period size: 8  Copynumber: 5.4  Consensus size: 8

        487 AATAATGTTA

                    
        497 TATTATAT
          1 TATTATAT

                    
        505 TATTATAT
          1 TATTATAT

                    
        513 TATTATAT
          1 TATTATAT

                    
        521 TATTATAT
          1 TATTATAT

                    
        529 TA-TATAT
          1 TATTATAT

               
        536 TAT
          1 TAT

        539 CAATAAACTT


Statistics
Matches: 33,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   7    7  0.21
   8   26  0.79

ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62


Consensus pattern (8 bp):   
TATTATAT

Found at i:687 original size:17 final size:17

Alignment explanation


    Indices: 667--715  Score: 80
    Period size: 17  Copynumber: 2.9  Consensus size: 17

        657 AAATCAAACT

                             
        667 CGAGCCCGAACCCGACC
          1 CGAGCCCGAACCCGACC

                         *   
        684 CGAGCCCGAACCCTACC
          1 CGAGCCCGAACCCGACC

                *          
        701 CGAGACCGAACCCGA
          1 CGAGCCCGAACCCGA

        716 AAATACCCGA


Statistics
Matches: 29,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  17   29  1.00

ACGTcount: A:0.27, C:0.49, G:0.22, T:0.02


Consensus pattern (17 bp):   
CGAGCCCGAACCCGACC

Found at i:727 original size:16 final size:16

Alignment explanation


    Indices: 706--827  Score: 185
    Period size: 16  Copynumber: 7.7  Consensus size: 16

        696 CTACCCGAGA

                            
        706 CCGAACCCGAAAATAC
          1 CCGAACCCGAAAATAC

                       *     
        722 CCGAACCCG-ACATAAC
          1 CCGAACCCGAAAAT-AC

                *           
        738 CCGAGCCCGAAAATAC
          1 CCGAACCCGAAAATAC

                            
        754 CCGAACCCGAAAATAC
          1 CCGAACCCGAAAATAC

                *           
        770 CCGAGCCCGAAAATAC
          1 CCGAACCCGAAAATAC

                            
        786 CCGAACCCGAAAATAC
          1 CCGAACCCGAAAATAC

                        *   
        802 CCGAACCCG-AAGTAC
          1 CCGAACCCGAAAATAC

                       
        817 CCGAACCCGAA
          1 CCGAACCCGAA

        828 CCCGCCCGAG


Statistics
Matches: 96,  Mismatches: 7, Indels: 6
        0.88            0.06        0.06

Matches are distributed among these distances:
  15   17  0.18
  16   76  0.79
  17    3  0.03

ACGTcount: A:0.39, C:0.39, G:0.16, T:0.06


Consensus pattern (16 bp):   
CCGAACCCGAAAATAC

Done.