Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020566.1 Corchorus olitorius cultivar O-4 contig20599, 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: 26321
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34


Found at i:2298 original size:31 final size:31

Alignment explanation


    Indices: 2257--2315  Score: 82
    Period size: 31  Copynumber: 1.9  Consensus size: 31

       2247 TTCGTTGAAC

                 *                         
       2257 TTTTTCTTTTTAACTCCTTAAAATAATTCTT
          1 TTTTTATTTTTAACTCCTTAAAATAATTCTT

                        *  *    *       
       2288 TTTTTATTTTTAGCTTCTTACAATAATT
          1 TTTTTATTTTTAACTCCTTAAAATAATT

       2316 TGTCTTTCAT


Statistics
Matches: 24,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  31   24  1.00

ACGTcount: A:0.25, C:0.14, G:0.02, T:0.59


Consensus pattern (31 bp):   
TTTTTATTTTTAACTCCTTAAAATAATTCTT

Found at i:7802 original size:15 final size:15

Alignment explanation


    Indices: 7782--7814  Score: 57
    Period size: 15  Copynumber: 2.2  Consensus size: 15

       7772 GTATTACAAG

                           
       7782 TTTTATTTGTTATTA
          1 TTTTATTTGTTATTA

                    *      
       7797 TTTTATTTTTTATTA
          1 TTTTATTTGTTATTA

               
       7812 TTT
          1 TTT

       7815 GGTATGTGAT


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79


Consensus pattern (15 bp):   
TTTTATTTGTTATTA

Found at i:8895 original size:15 final size:15

Alignment explanation


    Indices: 8875--8912  Score: 76
    Period size: 15  Copynumber: 2.5  Consensus size: 15

       8865 GAAGAAGGGA

                           
       8875 GAGAGAGATTTGGTC
          1 GAGAGAGATTTGGTC

                           
       8890 GAGAGAGATTTGGTC
          1 GAGAGAGATTTGGTC

                    
       8905 GAGAGAGA
          1 GAGAGAGA

       8913 AAGTAAGAAA


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

Matches are distributed among these distances:
  15   23  1.00

ACGTcount: A:0.32, C:0.05, G:0.42, T:0.21


Consensus pattern (15 bp):   
GAGAGAGATTTGGTC

Found at i:9334 original size:2 final size:2

Alignment explanation


    Indices: 9327--9357  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       9317 TAATATCTAG

                                                          
       9327 TA TA TA 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 TA TA TA T

       9358 TATTCAAATT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:14841 original size:83 final size:83

Alignment explanation


    Indices: 14723--14897  Score: 289
    Period size: 85  Copynumber: 2.1  Consensus size: 83

      14713 ACAATTAATG

                                                                             
      14723 TTCTTTGAAAAAATTTTCTTTTATATCTATTACC-TTTAAAATTGTTGCCTTGACTACTTTTTAG
          1 TTCTTTGAAAAAATTTTCTTTTATATCTATTACCTTTTAAAATTGTTGCCTTGACTACTTTTTAG

                             * 
      14787 GTAAAGAAATCATTTCCTC
         66 GTAAAG-AATCATTTCCCC

                      * *                                        *           
      14806 TTCTTTGAAACATTTTTCTTTTATATCTATTACCTTTTTAAAATTGTTGCCTTTACTACTTTTTA
          1 TTCTTTGAAAAAATTTTCTTTTATATCTATTACC-TTTTAAAATTGTTGCCTTGACTACTTTTTA

                               
      14871 GGTAAAGAATCATTTCCCC
         65 GGTAAAGAATCATTTCCCC

                    
      14890 TTCTTTGA
          1 TTCTTTGA

      14898 CATGGCATAT


Statistics
Matches: 86,  Mismatches: 4, Indels: 3
        0.92            0.04        0.03

Matches are distributed among these distances:
  83   32  0.37
  84   19  0.22
  85   35  0.41

ACGTcount: A:0.26, C:0.17, G:0.08, T:0.49


Consensus pattern (83 bp):   
TTCTTTGAAAAAATTTTCTTTTATATCTATTACCTTTTAAAATTGTTGCCTTGACTACTTTTTAG
GTAAAGAATCATTTCCCC

Found at i:25052 original size:58 final size:58

Alignment explanation


    Indices: 24957--25066  Score: 150
    Period size: 58  Copynumber: 1.9  Consensus size: 58

      24947 ATTAATCAAA

                                                          *           
      24957 TATCAAGTGACATGTTCTTCATTAGATGCATAAAAAAAGACGTTTTCGGACCAAGACT
          1 TATCAAGTGACATGTTCTTCATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGACT

                *            *  *         *         *            
      25015 TATCGAGTGACATGTTTTTTTATTAGATGCCT-AAAAAAGGCGTTTTAGGACC
          1 TATCAAGTGACATG-TTCTTCATTAGATGCATAAAAAAAGACGTTTTAGGACC

      25067 GAGGCATGAT


Statistics
Matches: 45,  Mismatches: 6, Indels: 2
        0.85            0.11        0.04

Matches are distributed among these distances:
  58   31  0.69
  59   14  0.31

ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33


Consensus pattern (58 bp):   
TATCAAGTGACATGTTCTTCATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGACT
Done.