Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022810.1 Corchorus olitorius cultivar O-4 contig22843, 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: 18258
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:6473 original size:21 final size:21

Alignment explanation


    Indices: 6449--6519  Score: 117
    Period size: 21  Copynumber: 3.4  Consensus size: 21

       6439 CCTAGGCGAT

                         *       
       6449 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                 
       6470 TCCAATGAGCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                  
       6491 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                    
       6512 TCCAATGA
          1 TCCAATGA

       6520 ACTCCTAGCA


Statistics
Matches: 48,  Mismatches: 1, Indels: 2
        0.94            0.02        0.04

Matches are distributed among these distances:
  20    3  0.06
  21   45  0.94

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


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACCTTC

Found at i:11838 original size:25 final size:24

Alignment explanation


    Indices: 11801--11847  Score: 69
    Period size: 26  Copynumber: 1.9  Consensus size: 24

      11791 CTAGAAAATT

                                      
      11801 TGAAAAACTTTGATGGATGAGATGGA
          1 TGAAAAACTTTGAT-GAT-AGATGGA

                                  
      11827 TGAAAAAC-TTGATGATAGATG
          1 TGAAAAACTTTGATGATAGATG

      11848 AGTAGAAGGA


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  23    5  0.24
  24    3  0.14
  25    5  0.24
  26    8  0.38

ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28


Consensus pattern (24 bp):   
TGAAAAACTTTGATGATAGATGGA

Found at i:12726 original size:21 final size:21

Alignment explanation


    Indices: 12702--12772  Score: 126
    Period size: 21  Copynumber: 3.4  Consensus size: 21

      12692 CTTAGACAAT

                                  
      12702 TCCAATGAGCTTGGAACCTT-C
          1 TCCAATGAGCTTGGAA-CTTGC

                                 
      12723 TCCAATGAGCTTGGAACTTGC
          1 TCCAATGAGCTTGGAACTTGC

                                 
      12744 TCCAATGAGCTTGGAACTTGC
          1 TCCAATGAGCTTGGAACTTGC

                    
      12765 TCCAATGA
          1 TCCAATGA

      12773 ACTCCTAGCA


Statistics
Matches: 49,  Mismatches: 0, Indels: 2
        0.96            0.00        0.04

Matches are distributed among these distances:
  20    3  0.06
  21   46  0.94

ACGTcount: A:0.25, C:0.25, G:0.21, T:0.28


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACTTGC

Found at i:15898 original size:2 final size:2

Alignment explanation


    Indices: 15891--15916  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

      15881 TCTCTTATTA

                                                  
      15891 AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT

      15917 TGTAAAGAAG


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.