Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012184.1 Corchorus olitorius cultivar O-4 contig12217, 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: 9949
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.30


Found at i:1017 original size:33 final size:31

Alignment explanation


    Indices: 944--1089  Score: 123
    Period size: 33  Copynumber: 4.5  Consensus size: 31

        934 GCTATGATCA

                                       ** * 
        944 ACCAAAACAGATTTGTTTTCATCACAATTAGC
          1 ACCAAAACAGATTTG-TTTCATCACAAACAAC

                                             
        976 ATCCAAAACAGAATTTGTTTCATCACAAACAAC
          1 A-CCAAAACAG-ATTTGTTTCATCACAAACAAC

                              *              
       1009 ACCTAAAACAGATTTAGTGTCATCACAAACAAC
          1 ACC-AAAACAGATTT-GTTTCATCACAAACAAC

                   **  *             *        
       1042 ACTCAAATTAGGTTTAGTATT-ATCGCAAACAAC
          1 AC-CAAAACAGATTT-GT-TTCATCACAAACAAC

               *           
       1075 ATCTAAAACAGATTT
          1 A-CCAAAACAGATTT

       1090 AGAATTACTC


Statistics
Matches: 94,  Mismatches: 13, Indels: 13
        0.78            0.11        0.11

Matches are distributed among these distances:
  32    7  0.07
  33   79  0.84
  34    8  0.09

ACGTcount: A:0.42, C:0.21, G:0.09, T:0.27


Consensus pattern (31 bp):   
ACCAAAACAGATTTGTTTCATCACAAACAAC

Found at i:3575 original size:21 final size:21

Alignment explanation


    Indices: 3551--3667  Score: 166
    Period size: 21  Copynumber: 5.6  Consensus size: 21

       3541 CTTAGGCATT

                    *    *       
       3551 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAACTTGGAACCTTC

                    *            
       3572 TCCAATGATCTTGGAACCTTC
          1 TCCAATGAACTTGGAACCTTC

                                 
       3593 TCCAATGAACTTGGAACCTTC
          1 TCCAATGAACTTGGAACCTTC

                                  
       3614 TCCAATGAACTTGGAA-CTTGC
          1 TCCAATGAACTTGGAACCTT-C

                    *             
       3635 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAACTTGGAACCTT-C

                        
       3656 TCCAATGAACTT
          1 TCCAATGAACTT

       3668 CTAGCATCTT


Statistics
Matches: 90,  Mismatches: 5, Indels: 2
        0.93            0.05        0.02

Matches are distributed among these distances:
  20    3  0.03
  21   87  0.97

ACGTcount: A:0.27, C:0.26, G:0.16, T:0.30


Consensus pattern (21 bp):   
TCCAATGAACTTGGAACCTTC

Found at i:9822 original size:21 final size:21

Alignment explanation


    Indices: 9796--9837  Score: 75
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       9786 TAAGGAAAAA

                                 
       9796 GTTTCAAGCTCATCAGAGTTG
          1 GTTTCAAGCTCATCAGAGTTG

                          *      
       9817 GTTTCAAGCTCATCGGAGTTG
          1 GTTTCAAGCTCATCAGAGTTG

       9838 CCTAAGATGC


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.21, C:0.19, G:0.26, T:0.33


Consensus pattern (21 bp):   
GTTTCAAGCTCATCAGAGTTG
Done.