Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011040.1 Corchorus olitorius cultivar O-4 contig11073, 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: 2649
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30


Found at i:446 original size:21 final size:20

Alignment explanation


    Indices: 422--597  Score: 235
    Period size: 21  Copynumber: 8.4  Consensus size: 20

        412 CTTAGGCAAT

                         *       
        422 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGGAA-CTTC

                    *            
        443 TCCAATGATCTTGGAACCTTC
          1 TCCAATGAGCTTGGAA-CTTC

                    *            
        464 TCCAATGAACTTGGAACCTTC
          1 TCCAATGAGCTTGGAA-CTTC

                    *            
        485 TCCAATGAACTTGGAACCTTC
          1 TCCAATGAGCTTGGAA-CTTC

                                 
        506 TCCAATGAGCTTGGAACTTGC
          1 TCCAATGAGCTTGGAACTT-C

                    *            
        527 TCCAATGAACTTGGAAACTTC
          1 TCCAATGAGCTTGG-AACTTC

                                 
        548 TCCAATGAGCTTGGAACTTGC
          1 TCCAATGAGCTTGGAACTT-C

                                 
        569 TCCAATGAGCTTGGAACTTGC
          1 TCCAATGAGCTTGGAACTT-C

                    
        590 TCCAATGA
          1 TCCAATGA

        598 ACTTCTAGCA


Statistics
Matches: 146,  Mismatches: 6, Indels: 6
        0.92            0.04        0.04

Matches are distributed among these distances:
  20    8  0.05
  21  133  0.91
  22    5  0.03

ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29


Consensus pattern (20 bp):   
TCCAATGAGCTTGGAACTTC

Found at i:469 original size:42 final size:42

Alignment explanation


    Indices: 422--597  Score: 259
    Period size: 42  Copynumber: 4.2  Consensus size: 42

        412 CTTAGGCAAT

                         *                *            
        422 TCCAATGAGCTTGAAACCTT-CTCCAATGATCTTGGAACCTTC
          1 TCCAATGAGCTTGGAA-CTTGCTCCAATGAACTTGGAACCTTC

                    *                                  
        464 TCCAATGAACTTGGAACCTT-CTCCAATGAACTTGGAACCTTC
          1 TCCAATGAGCTTGGAA-CTTGCTCCAATGAACTTGGAACCTTC

                                                 *    
        506 TCCAATGAGCTTGGAACTTGCTCCAATGAACTTGGAAACTTC
          1 TCCAATGAGCTTGGAACTTGCTCCAATGAACTTGGAACCTTC

                                         *             
        548 TCCAATGAGCTTGGAACTTGCTCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACTTGCTCCAATGAACTTGGAACCTT-C

                    
        590 TCCAATGA
          1 TCCAATGA

        598 ACTTCTAGCA


Statistics
Matches: 126,  Mismatches: 6, Indels: 4
        0.93            0.04        0.03

Matches are distributed among these distances:
  41    6  0.05
  42  120  0.95

ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29


Consensus pattern (42 bp):   
TCCAATGAGCTTGGAACTTGCTCCAATGAACTTGGAACCTTC

Found at i:506 original size:63 final size:63

Alignment explanation


    Indices: 422--601  Score: 292
    Period size: 63  Copynumber: 2.9  Consensus size: 63

        412 CTTAGGCAAT

                         *               *                             *    
        422 TCCAATGAGCTTGAAACCTTCTCCAATGATCTTGGAACCTT-CTCCAATGAACTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTCTCCAATGAGCTTGGAA-CTTGCTCCAATGAACTTGGAAACTTC

                    *                                                      
        485 TCCAATGAACTTGGAACCTTCTCCAATGAGCTTGGAACTTGCTCCAATGAACTTGGAAACTTC
          1 TCCAATGAGCTTGGAACCTTCTCCAATGAGCTTGGAACTTGCTCCAATGAACTTGGAAACTTC

                                                                   
        548 TCCAATGAGCTTGGAA-CTTGCTCCAATGAGCTTGGAACTTGCTCCAATGAACTT
          1 TCCAATGAGCTTGGAACCTT-CTCCAATGAGCTTGGAACTTGCTCCAATGAACTT

        602 CTAGCATCTT


Statistics
Matches: 110,  Mismatches: 5, Indels: 4
        0.92            0.04        0.03

Matches are distributed among these distances:
  62    6  0.05
  63  104  0.95

ACGTcount: A:0.27, C:0.26, G:0.17, T:0.29


Consensus pattern (63 bp):   
TCCAATGAGCTTGGAACCTTCTCCAATGAGCTTGGAACTTGCTCCAATGAACTTGGAAACTTC

Found at i:2172 original size:21 final size:21

Alignment explanation


    Indices: 2148--2260  Score: 158
    Period size: 21  Copynumber: 5.4  Consensus size: 21

       2138 CTTAGGCATT

                         *       
       2148 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *            
       2169 TCCAATGATCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *          * 
       2190 TCCAATGAACTTGGAACCTGC
          1 TCCAATGAGCTTGGAACCTTC

                                  
       2211 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                                  
       2232 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                    
       2253 TCCAATGA
          1 TCCAATGA

       2261 ACTTCTAGCA


Statistics
Matches: 85,  Mismatches: 6, Indels: 2
        0.91            0.06        0.02

Matches are distributed among these distances:
  20    2  0.02
  21   83  0.98

ACGTcount: A:0.27, C:0.27, G:0.19, T:0.28


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACCTTC

Done.