Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020232.1 Corchorus olitorius cultivar O-4 contig20265, 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: 2202
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31


Found at i:424 original size:151 final size:150

Alignment explanation


    Indices: 150--503  Score: 500
    Period size: 151  Copynumber: 2.4  Consensus size: 150

        140 GCTAATATAT

                                   **       *                       *        
        150 ATTGACACCAGAAGTTGTCAATGGCCTTGCAAATGACACCAGAAGTTGTCATGGCCTTGCAATTG
          1 ATTGACACCAGAAGTTGTCAATGATCTTGCAATTGACACCAGAAGTTGTCAT-GCCCTGCAATTG

               *                 *                                           
        215 ACATCAGAACCTGTCATGGCCTTGCAAATGACACCAGAAGTTGTCATGGCCTTGCAATTGACACC
         65 ACACCAGAACCTGTCATGGCCCTGCAAATGACACCAGAAGTTGTCATGGCCTTGCAATTGACACC

                                  
        280 AGAAGTTGTCATAAC-CTTGCA
        130 AGAAGTTGTCAT-ACTCTTGCA

                                                        *              * *   
        301 ATTGACACCAGAAGTTGTCAATGATCTTGCAATTGACACCAGAAATTGTCATGCTCCTGTAGTTG
          1 ATTGACACCAGAAGTTGTCAATGATCTTGCAATTGACACCAGAAGTTGTCATGC-CCTGCAATTG

                      *                 *                       *            
        366 ACACCAGAACTTGTCAT-GCTCCTGCAATTGACACCAGAAGTTGTCAT-GCTGTTGCAATTGACA
         65 ACACCAGAACCTGTCATGGC-CCTGCAAATGACACCAGAAGTTGTCATGGC-CTTGCAATTGACA

                          *  *     
        429 CCAGAAGTTGTCATGCTGTTGCA
        128 CCAGAAGTTGTCATACTCTTGCA

                                   *                             
        452 ATTGACACCAGAAGTTGTC-ATGCTCTTGCAATTGACACCAGAAGTTGTCATG
          1 ATTGACACCAGAAGTTGTCAATGATCTTGCAATTGACACCAGAAGTTGTCATG

        504 ATAATTCAAT


Statistics
Matches: 183,  Mismatches: 16, Indels: 9
        0.88            0.08        0.04

Matches are distributed among these distances:
 150   38  0.21
 151  145  0.79

ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27


Consensus pattern (150 bp):   
ATTGACACCAGAAGTTGTCAATGATCTTGCAATTGACACCAGAAGTTGTCATGCCCTGCAATTGA
CACCAGAACCTGTCATGGCCCTGCAAATGACACCAGAAGTTGTCATGGCCTTGCAATTGACACCA
GAAGTTGTCATACTCTTGCA

Found at i:535 original size:30 final size:31

Alignment explanation


    Indices: 150--533  Score: 477
    Period size: 30  Copynumber: 12.7  Consensus size: 31

        140 GCTAATATAT

                                    *       
        150 ATTGACACCAGAAGTTGTCAATG-GCCTTGCA
          1 ATTGACACCAGAAGTTGTC-ATGCTCCTTGCA

             *                     *       
        181 AATGACACCAGAAGTTGTCATG-GCCTTGCA
          1 ATTGACACCAGAAGTTGTCATGCTCCTTGCA

                   *     **        *       
        211 ATTGACATCAGAACCTGTCATG-GCCTTGCA
          1 ATTGACACCAGAAGTTGTCATGCTCCTTGCA

             *                     *       
        241 AATGACACCAGAAGTTGTCATG-GCCTTGCA
          1 ATTGACACCAGAAGTTGTCATGCTCCTTGCA

                                  **       
        271 ATTGACACCAGAAGTTGTCAT-AACCTTGCA
          1 ATTGACACCAGAAGTTGTCATGCTCCTTGCA

                                   *        
        301 ATTGACACCAGAAGTTGTCAATGAT-CTTGCA
          1 ATTGACACCAGAAGTTGTC-ATGCTCCTTGCA

                         *               * 
        332 ATTGACACCAGAAATTGTCATGCTCC-TGTA
          1 ATTGACACCAGAAGTTGTCATGCTCCTTGCA

            *            *                 
        362 GTTGACACCAGAACTTGTCATGCTCC-TGCA
          1 ATTGACACCAGAAGTTGTCATGCTCCTTGCA

                                     *     
        392 ATTGACACCAGAAGTTGTCATGCT-GTTGCA
          1 ATTGACACCAGAAGTTGTCATGCTCCTTGCA

                                     *     
        422 ATTGACACCAGAAGTTGTCATGCT-GTTGCA
          1 ATTGACACCAGAAGTTGTCATGCTCCTTGCA

                                           
        452 ATTGACACCAGAAGTTGTCATGCT-CTTGCA
          1 ATTGACACCAGAAGTTGTCATGCTCCTTGCA

                                  * **     
        482 ATTGACACCAGAAGTTGTCATGATAATT-CA
          1 ATTGACACCAGAAGTTGTCATGCTCCTTGCA

                                  
        512 ATTGACACCAGAAGTTGTCATG
          1 ATTGACACCAGAAGTTGTCATG

        534 ATTTTACCTT


Statistics
Matches: 323,  Mismatches: 24, Indels: 13
        0.90            0.07        0.04

Matches are distributed among these distances:
  30  275  0.85
  31   47  0.15
  32    1  0.00

ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28


Consensus pattern (31 bp):   
ATTGACACCAGAAGTTGTCATGCTCCTTGCA

Done.