Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008723.1 Corchorus capsularis cultivar CVL-1 contig08744, 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: 12534
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30


Found at i:404 original size:181 final size:183

Alignment explanation


    Indices: 179--524  Score: 405
    Period size: 181  Copynumber: 1.9  Consensus size: 183

        169 TGGTTAAATT

                                           *               *       *  *     *
        179 AGCCAAAAATCAGTACGTAAACCCTCCAAAATTAGGTCATATCACATGAACATAATCCTAATTTG
          1 AGCCAAAAATCAGTACGTAAACCCTCCAAAACTAGGTCATATCACATAAACATAAGCCCAATTTA

                                    *                             * *        
        244 ATGAAAT-CAAGC-AAACCTAATAGGCCGAACCC-CTTTTGC-AAAATTGCAACTTGGGCGGCAA
         66 ATG--ATCCAAGCTAAACCTAATAAGCCGAACCCTCTTTTGCAAAAATTGCAACATAGGCGGCAA

                                                                   
        305 ATTAACTAGCTTGATAAATTAGGGTTCTTGTGATTTCAGCCTAATTGATTAATCA
        129 ATTAACTAGCTTGATAAATTAGGGTTCTTGTGATTTCAGCCTAATTGATTAATCA

                *          *           **         *            *             
        360 AGCCCAAAATCAGTAGGTTAAACCCT-TTAAACTAGGTTATATCACATAAATATAAGCCCAATTT
          1 AGCCAAAAATCAGTACG-TAAACCCTCCAAAACTAGGTCATATCACATAAACATAAGCCCAATTT

                          **         *   *     *                             
        424 AATGATCCAAGCTACCCCTAATAAGTCGAGCCCTTTTTTTGCAAAAATTGCAACATAGGCGGCAA
         65 AATGATCCAAGCTAAACCTAATAAGCCGAACCC-TCTTTTGCAAAAATTGCAACATAGGCGGCAA

                *  *     * *          *         
        489 ATTAGCTTGCTTGGTGAATTAGGGTTTTTGTGATTT
        129 ATTAACTAGCTTGATAAATTAGGGTTCTTGTGATTT

        525 AGGGAAAATT


Statistics
Matches: 135,  Mismatches: 24, Indels: 9
        0.80            0.14        0.05

Matches are distributed among these distances:
 179    2  0.01
 180    5  0.04
 181   63  0.47
 182    8  0.06
 183    6  0.04
 184   51  0.38

ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29


Consensus pattern (183 bp):   
AGCCAAAAATCAGTACGTAAACCCTCCAAAACTAGGTCATATCACATAAACATAAGCCCAATTTA
ATGATCCAAGCTAAACCTAATAAGCCGAACCCTCTTTTGCAAAAATTGCAACATAGGCGGCAAAT
TAACTAGCTTGATAAATTAGGGTTCTTGTGATTTCAGCCTAATTGATTAATCA

Found at i:9518 original size:27 final size:27

Alignment explanation


    Indices: 9480--9535  Score: 112
    Period size: 27  Copynumber: 2.1  Consensus size: 27

       9470 TTCATCACAA

                                       
       9480 CTCCACAAATTCTTCTAAATTTCCTAT
          1 CTCCACAAATTCTTCTAAATTTCCTAT

                                       
       9507 CTCCACAAATTCTTCTAAATTTCCTAT
          1 CTCCACAAATTCTTCTAAATTTCCTAT

              
       9534 CT
          1 CT

       9536 TTCTTGAAGA


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

Matches are distributed among these distances:
  27   29  1.00

ACGTcount: A:0.29, C:0.30, G:0.00, T:0.41


Consensus pattern (27 bp):   
CTCCACAAATTCTTCTAAATTTCCTAT
Done.