Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012530.1 Corchorus olitorius cultivar O-4 contig12563, 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: 9337
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29


Found at i:27 original size:21 final size:21

Alignment explanation


    Indices: 1--103  Score: 170
    Period size: 21  Copynumber: 4.9  Consensus size: 21

                                 
          1 AGGTTCCAAGTTCATTGGAGA
          1 AGGTTCCAAGTTCATTGGAGA

                    *            
         22 AGGTTCCATGTTCATTGGAGA
          1 AGGTTCCAAGTTCATTGGAGA

                                 
         43 AGGTTCCAAGTTCATTGGAGA
          1 AGGTTCCAAGTTCATTGGAGA

                      *          
         64 AGGTTCCAAGATCATTGGAGA
          1 AGGTTCCAAGTTCATTGGAGA

                 *    *        
         85 AGGTTTCAAGCTCATTGGA
          1 AGGTTCCAAGTTCATTGGA

        104 ATTGCCTAAG


Statistics
Matches: 77,  Mismatches: 5, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  21   77  1.00

ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29


Consensus pattern (21 bp):   
AGGTTCCAAGTTCATTGGAGA

Found at i:3557 original size:21 final size:21

Alignment explanation


    Indices: 3533--3624  Score: 134
    Period size: 21  Copynumber: 4.4  Consensus size: 21

       3523 CTTAGGCAAT

                         *        
       3533 TCCAATGAGCTTGAAACCTT-C
          1 TCCAATGAGCTTGGAA-CTTGC

                    *             
       3554 TCCAATGAACTTGGAACCTT-C
          1 TCCAATGAGCTTGGAA-CTTGC

                                 
       3575 TCCAATGAGCTTGGAACTTGC
          1 TCCAATGAGCTTGGAACTTGC

                                 
       3596 TCCAATGAGCTTGGAACTTGC
          1 TCCAATGAGCTTGGAACTTGC

                    
       3617 TCCAATGA
          1 TCCAATGA

       3625 ACTTCTAGCA


Statistics
Matches: 67,  Mismatches: 3, Indels: 2
        0.93            0.04        0.03

Matches are distributed among these distances:
  20    3  0.04
  21   64  0.96

ACGTcount: A:0.27, C:0.26, G:0.18, T:0.28


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACTTGC

Found at i:5504 original size:33 final size:31

Alignment explanation


    Indices: 5431--5535  Score: 111
    Period size: 33  Copynumber: 3.2  Consensus size: 31

       5421 GCTATGATCA

                                       ** * 
       5431 ACCAAAACAGATTTGTTTTCATCACAATTAGC
          1 ACCAAAACAGATTTG-TTTCATCACAAACAAC

                                             
       5463 ATCCAAAACAGAATTTGTTTCATCACAAACAAC
          1 A-CCAAAACAG-ATTTGTTTCATCACAAACAAC

                              *   *          
       5496 ACCTAAAACAGATTTAGTGTCACCACAAACAAC
          1 ACC-AAAACAGATTT-GTTTCATCACAAACAAC

                   
       5529 ACTCAAA
          1 AC-CAAA

       5536 TTAGGTTTAG


Statistics
Matches: 63,  Mismatches: 5, Indels: 9
        0.82            0.06        0.12

Matches are distributed among these distances:
  32    7  0.11
  33   50  0.79
  34    6  0.10

ACGTcount: A:0.44, C:0.25, G:0.08, T:0.24


Consensus pattern (31 bp):   
ACCAAAACAGATTTGTTTCATCACAAACAAC

Found at i:5578 original size:33 final size:32

Alignment explanation


    Indices: 5486--5584  Score: 90
    Period size: 33  Copynumber: 3.0  Consensus size: 32

       5476 TTTGTTTCAT

                                        * *  
       5486 CACAAACAACACCTAAAACAGATTTAGTGTCAC
          1 CACAAACAACA-CTAAAACAGATTTAGTATTAC

                             **  *          *
       5519 CACAAACAACACTCAAATTAGGTTTAGTATTAT
          1 CACAAACAACACT-AAAACAGATTTAGTATTAC

            **                         *     
       5552 TGCAAACAACATCTAAAACAGATTTAGAATTAC
          1 CACAAACAACA-CTAAAACAGATTTAGTATTAC

       5585 TCTTTGAAGA


Statistics
Matches: 51,  Mismatches: 13, Indels: 4
        0.75            0.19        0.06

Matches are distributed among these distances:
  32    2  0.04
  33   47  0.92
  34    2  0.04

ACGTcount: A:0.45, C:0.21, G:0.09, T:0.24


Consensus pattern (32 bp):   
CACAAACAACACTAAAACAGATTTAGTATTAC
Done.