Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011234.1 Corchorus olitorius cultivar O-4 contig11267, 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: 9022
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.31


Found at i:66 original size:2 final size:2

Alignment explanation


    Indices: 59--83  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

         49 CTTTAACTAG

                                                 
         59 TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA T

         84 GTTTTACCAA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:2216 original size:114 final size:114

Alignment explanation


    Indices: 2011--2344  Score: 431
    Period size: 114  Copynumber: 2.9  Consensus size: 114

       2001 CTTGGCAAAT

                *                  *     *                 *              *  
       2011 CCCATTACTGTGTTAAGATCCATTCTTGGTAAGCCCCATCACTACCCACAAGTGTGTCTCTCATC
          1 CCCACTACTGTGTTAAGATCCATCCTTGGCAAGCCCCATCACTACCCGCAAGTGTGTCTCTCGTC

                           *            **             *      
       2076 AT-AGAGCCCTTGGGGTTTAAGAGGGAGTAGGGGATTGAGAGCCCCAAGC
         66 ATGA-AGCCCTTGGGATTTAAGAGGGAGCGGGGGATTGAGAGCACCAAGC

                                       *                 *          * *      
       2125 CCCACTACTGTGTTAAGATCCATCCTTCGCAAGCCCCATCACTACTCGCAAGTGTGCCCCTCGTC
          1 CCCACTACTGTGTTAAGATCCATCCTTGGCAAGCCCCATCACTACCCGCAAGTGTGTCTCTCGTC

                     *                                       
       2190 ATGAAGCCCCTGGGATTTAAGAGGGAGCGGGGGATTGAGAGCACCAAGC
         66 ATGAAGCCCTTGGGATTTAAGAGGGAGCGGGGGATTGAGAGCACCAAGC

                                     *             *    *     *              
       2239 CCCACTACTGTGTTAAGATCCA-CAATTGGCAAGCCCCACCACTGCCCG-TAGATGTGTCTCTCG
          1 CCCACTACTGTGTTAAGATCCATC-CTTGGCAAGCCCCATCACTACCCGCAAG-TGTGTCTCTCG

            *       *          *                       
       2302 CCATGAAGTCCTTGGGATTCAAGAGGGAGCGGGGGATTGAGAG
         64 TCATGAAGCCCTTGGGATTTAAGAGGGAGCGGGGGATTGAGAG

       2345 TCCCTGAGGT


Statistics
Matches: 191,  Mismatches: 26, Indels: 6
        0.86            0.12        0.03

Matches are distributed among these distances:
 113    3  0.02
 114  187  0.98
 115    1  0.01

ACGTcount: A:0.24, C:0.28, G:0.26, T:0.22


Consensus pattern (114 bp):   
CCCACTACTGTGTTAAGATCCATCCTTGGCAAGCCCCATCACTACCCGCAAGTGTGTCTCTCGTC
ATGAAGCCCTTGGGATTTAAGAGGGAGCGGGGGATTGAGAGCACCAAGC

Found at i:6083 original size:22 final size:22

Alignment explanation


    Indices: 6055--6103  Score: 80
    Period size: 22  Copynumber: 2.2  Consensus size: 22

       6045 TTCCAGAATC

                                  
       6055 CGAAGCGACGTGCCTCGAAACT
          1 CGAAGCGACGTGCCTCGAAACT

                           *    * 
       6077 CGAAGCGACGTGCCTTGAAATT
          1 CGAAGCGACGTGCCTCGAAACT

                 
       6099 CGAAG
          1 CGAAG

       6104 TGTCGTTTCC


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  22   25  1.00

ACGTcount: A:0.29, C:0.27, G:0.29, T:0.16


Consensus pattern (22 bp):   
CGAAGCGACGTGCCTCGAAACT

Found at i:8836 original size:27 final size:27

Alignment explanation


    Indices: 8798--8850  Score: 97
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       8788 AAAAACGAGG

                          *            
       8798 GCGACTAGCAGTACTCCTGGGGGGGTC
          1 GCGACTAGCAGTACCCCTGGGGGGGTC

                                      
       8825 GCGACTAGCAGTACCCCTGGGGGGGT
          1 GCGACTAGCAGTACCCCTGGGGGGGT

       8851 TGCCCCTGTT


Statistics
Matches: 25,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  27   25  1.00

ACGTcount: A:0.15, C:0.26, G:0.42, T:0.17


Consensus pattern (27 bp):   
GCGACTAGCAGTACCCCTGGGGGGGTC
Done.