Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019495.1 Corchorus olitorius cultivar O-4 contig19528, 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: 16089
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30

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


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

Alignment explanation


    Indices: 1--71  Score: 117
    Period size: 21  Copynumber: 3.4  Consensus size: 21

                         *       
          1 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                 
         22 TCCAATGAGCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                  
         43 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                    
         64 TCCAATGA
          1 TCCAATGA

         72 TCTCCTAGCA


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:3503 original size:25 final size:24

Alignment explanation


    Indices: 3466--3512  Score: 69
    Period size: 26  Copynumber: 1.9  Consensus size: 24

       3456 CTAGAAAATT

                                      
       3466 TGAAAAACTTTGATGGATGAGATGGA
          1 TGAAAAACTTTGAT-GAT-AGATGGA

                                  
       3492 TGAAAAAC-TTGATGATAGATG
          1 TGAAAAACTTTGATGATAGATG

       3513 AATAGAAAGA


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:5718 original size:21 final size:21

Alignment explanation


    Indices: 5692--5732  Score: 66
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       5682 AGAAAAACCC

                                  
       5692 TAGTACCACTTAG-ATCCAATT
          1 TAGTACCACTT-GTATCCAATT

                                
       5713 TAGTACCACTTGTATCCAAT
          1 TAGTACCACTTGTATCCAAT

       5733 AGGGCTCCAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  20    1  0.05
  21   18  0.95

ACGTcount: A:0.32, C:0.24, G:0.10, T:0.34


Consensus pattern (21 bp):   
TAGTACCACTTGTATCCAATT

Found at i:6817 original size:15 final size:15

Alignment explanation


    Indices: 6797--6826  Score: 60
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       6787 TTGGACTTAG

                           
       6797 TCAAACAAGGCCCAA
          1 TCAAACAAGGCCCAA

                           
       6812 TCAAACAAGGCCCAA
          1 TCAAACAAGGCCCAA

       6827 CCCAATGTCA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.47, C:0.33, G:0.13, T:0.07


Consensus pattern (15 bp):   
TCAAACAAGGCCCAA
Done.