Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01005670.1 Corchorus olitorius cultivar O-4 contig05694, 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, 660

Length: 1101
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37


Found at i:665 original size:13 final size:12

Alignment explanation


    Indices: 638--676  Score: 53
    Period size: 12  Copynumber: 3.3  Consensus size: 12

        628 CTTTATTTTG

                        
        638 ATTTTTTATATA
          1 ATTTTTTATATA

                        
        650 ATTTTTTATATA
          1 ATTTTTTATATA

             *  *       
        662 AATTATTAT-TA
          1 ATTTTTTATATA

                
        673 ATTT
          1 ATTT

        677 ATATAATTAT


Statistics
Matches: 24,  Mismatches: 3, Indels: 1
        0.86            0.11        0.04

Matches are distributed among these distances:
  11    5  0.21
  12   19  0.79

ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64


Consensus pattern (12 bp):   
ATTTTTTATATA

Found at i:713 original size:20 final size:19

Alignment explanation


    Indices: 654--700  Score: 85
    Period size: 19  Copynumber: 2.4  Consensus size: 19

        644 TATATAATTT

                                
        654 TTTATATAAATTATTATTAA
          1 TTTATAT-AATTATTATTAA

                               
        674 TTTATATAATTATTATTAA
          1 TTTATATAATTATTATTAA

                    
        693 TTTATATA
          1 TTTATATA

        701 GAGTATTAGT


Statistics
Matches: 27,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  19   20  0.74
  20    7  0.26

ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57


Consensus pattern (19 bp):   
TTTATATAATTATTATTAA

Found at i:718 original size:20 final size:19

Alignment explanation


    Indices: 654--718  Score: 76
    Period size: 20  Copynumber: 3.3  Consensus size: 19

        644 TATATAATTT

                      *         
        654 TTTATATAAATTATTATTAA
          1 TTTATAT-AAGTATTATTAA

                     *         
        674 TTTATATAATTATTATTAA
          1 TTTATATAAGTATTATTAA

                            *   
        693 TTTATATAGAGTATTAGTAA
          1 TTTATATA-AGTATTATTAA

             *    
        713 TCTATA
          1 TTTATA

        719 GATATATAGA


Statistics
Matches: 41,  Mismatches: 3, Indels: 2
        0.89            0.07        0.04

Matches are distributed among these distances:
  19   20  0.49
  20   21  0.51

ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52


Consensus pattern (19 bp):   
TTTATATAAGTATTATTAA

Found at i:763 original size:21 final size:21

Alignment explanation


    Indices: 739--828  Score: 180
    Period size: 21  Copynumber: 4.3  Consensus size: 21

        729 TTTTAAAATT

                                 
        739 TTTTATATAGATATATACAAC
          1 TTTTATATAGATATATACAAC

                                 
        760 TTTTATATAGATATATACAAC
          1 TTTTATATAGATATATACAAC

                                 
        781 TTTTATATAGATATATACAAC
          1 TTTTATATAGATATATACAAC

                                 
        802 TTTTATATAGATATATACAAC
          1 TTTTATATAGATATATACAAC

                  
        823 TTTTAT
          1 TTTTAT

        829 CAGTAATTCC


Statistics
Matches: 69,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   69  1.00

ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46


Consensus pattern (21 bp):   
TTTTATATAGATATATACAAC

Found at i:768 original size:42 final size:42

Alignment explanation


    Indices: 721--828  Score: 164
    Period size: 42  Copynumber: 2.6  Consensus size: 42

        711 AATCTATAGA

                       *      *                        
        721 TATATAGAT-TTTAAAATTTTTTATATAGATATATACAACTTT
          1 TATATAGATATATAAAA-CTTTTATATAGATATATACAACTTT

                          *                           
        763 TATATAGATATATACAACTTTTATATAGATATATACAACTTT
          1 TATATAGATATATAAAACTTTTATATAGATATATACAACTTT

                          *         
        805 TATATAGATATATACAACTTTTAT
          1 TATATAGATATATAAAACTTTTAT

        829 CAGTAATTCC


Statistics
Matches: 62,  Mismatches: 3, Indels: 2
        0.93            0.04        0.03

Matches are distributed among these distances:
  42   57  0.92
  43    5  0.08

ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46


Consensus pattern (42 bp):   
TATATAGATATATAAAACTTTTATATAGATATATACAACTTT
Done.