Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001438.1 Corchorus olitorius cultivar O-4 contig01438, 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, 927

Length: 1545
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.36


Found at i:352 original size:96 final size:96

Alignment explanation


    Indices: 188--371  Score: 269
    Period size: 96  Copynumber: 1.9  Consensus size: 96

        178 ATCAACCACG

                                      *  *       *                       *   
        188 CTATCTTCAAAAACTGTTTTTGAAAATAACCCATCAATATCAATTTCTGACAATCTAAAAATTTC
          1 CTATCTTCAAAAACTGTTTTTGAAAACAAACCATCAAAATCAATTTCTGACAATCTAAAAACTTC

                *             *            
        253 AGCAGAAAATTTTGCATCCAAACCAGATTTC
         66 AGCAAAAAATTTTGCATCAAAACCAGATTTC

                                  *         *             *         *  *     
        284 CTATCTTCAAAAACTGTTTTTGCAAACAAACCTTCAAAATCAATTTTTGACAATCTCAAGACTTC
          1 CTATCTTCAAAAACTGTTTTTGAAAACAAACCATCAAAATCAATTTCTGACAATCTAAAAACTTC

                                   
        349 AGCAAAAAATTTTGCATCAAAAC
         66 AGCAAAAAATTTTGCATCAAAAC

        372 TAGAATTCAA


Statistics
Matches: 77,  Mismatches: 11, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  96   77  1.00

ACGTcount: A:0.40, C:0.21, G:0.07, T:0.32


Consensus pattern (96 bp):   
CTATCTTCAAAAACTGTTTTTGAAAACAAACCATCAAAATCAATTTCTGACAATCTAAAAACTTC
AGCAAAAAATTTTGCATCAAAACCAGATTTC

Found at i:898 original size:21 final size:22

Alignment explanation


    Indices: 867--908  Score: 68
    Period size: 21  Copynumber: 2.0  Consensus size: 22

        857 TTTTTGGCGC

                                  
        867 GAAATTTCAAAATTCGAATTTT
          1 GAAATTTCAAAATTCGAATTTT

                          *      
        889 GAAA-TTCAAAATTTGAATTT
          1 GAAATTTCAAAATTCGAATTT

        909 CGGAAGTTGG


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  21   15  0.79
  22    4  0.21

ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40


Consensus pattern (22 bp):   
GAAATTTCAAAATTCGAATTTT
Done.