Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015780.1 Corchorus capsularis cultivar CVL-1 contig15801, 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: 5841
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32


Found at i:1018 original size:439 final size:438

Alignment explanation


    Indices: 186--1078  Score: 1177
    Period size: 439  Copynumber: 2.0  Consensus size: 438

        176 TCCAAATAAG

                 *      **       *                   *    *     *            
        186 AAAATGTTTGTTGGTGGAGACGAAACATAAAAATTCCCTCTTGAACTCTCCATGAAACTCATTAA
          1 AAAATATTTGTTTATGGAGACCAAACATAAAAATTCCCTCTCGAACCCTCCACGAAACTCATTAA

                              *                                              
        251 TCAAATTAAACTTTCAGGTCCGTAATGAAAGTCGTAAATCACACAATAACCTTTTAACCGACACT
         66 TCAAATTAAACTTTCAGGCCCGTAATGAAAGTCGTAAATCACACAATAACCTTTTAACCGACACT

                                               *  **                         
        316 TAAACAACCTCAATCAGACAAGTGGACCGAAAATTTTATTATATTAAATAGACCGGCAATCGAGA
        131 TAAACAACCTCAATCAGACAAGTGGACCGAAAATTATACAATATTAAATAGACCGGCAATCGAGA

             *         *                  **    *                   *        
        381 TCACAAAATTTTAGAAGCATCTTTTAGAATTGAAACCTCAAAATTGGCTTATGAGTTATTAATGA
        196 TAACAAAATTTCAGAAGCATCTTTTAGAATCAAAACATCAAAATTGGCTTATGAGTCATTAATGA

                                                                *        *   
        446 AAGTTGTAGATCATGAAATTAACTTTTAATAGACACTTGAATCACCTTGATCGGACAAATAGAAC
        261 AAGTTGTAGATCATGAAATTAACTTTTAATAGACACTTGAATCACCTTGATCAGACAAATAAAAC

                                    *                    *            *      
        511 AAAAAATATAAAAATTAAAACCAGCACGTTAAATCGTCCAACCCATAATTGTAAAGGATTAAATA
        326 AAAAAATATAAAAATTAAAACCAGAACGTTAAATCGTCCAACCCAAAATTGTAAAGGACTAAATA

                   **                     * *        *  *     
        576 GCATAAAGTATAAAAAGTAT-GAGGATCATTTGATAAATAATCCGGCAAA
        391 GCATAAACCAT-AAAAGTATAG-GGATCATCTAATAAATAAACCAGCAAA

                                                *                            
        625 AAAATATTTGTTTATGGAGACCAAACATAAAAATTCTCTCTCGAACCCTCCACGAAACTCATTAA
          1 AAAATATTTGTTTATGGAGACCAAACATAAAAATTCCCTCTCGAACCCTCCACGAAACTCATTAA

                   * *           * *            *      *             *       
        690 TCAAATTCAGCTTTCAGGCCCTTGATGAAAGTCGTAGATCACATAATAACCTTTTAATCGACACT
         66 TCAAATTAAACTTTCAGGCCCGTAATGAAAGTCGTAAATCACACAATAACCTTTTAACCGACACT

             *             *  *          *                *     *            
        755 TGAACAACCTCAATCGGAGAAGTGGACCGGAAATTATACAATATTAGATAGATCGGCAATCGAGA
        131 TAAACAACCTCAATCAGACAAGTGGACCGAAAATTATACAATATTAAATAGACCGGCAATCGAGA

                                *                 *           *      *  *   *
        820 TAACAAAATTTCAGAAGCATTTTTTAGAATCAAAACATTAAAATTGGCTTTTGAGTCCTTCATGG
        196 TAACAAAATTTCAGAAGCATCTTTTAGAATCAAAACATCAAAATTGGCTTATGAGTCATTAATGA

                                                         *                   
        885 AAGTTGTAGATCATG-AATT-ACTTTTAAATAGACACTTGAATCATCTTGATCAGACAAGA-AAA
        261 AAGTTGTAGATCATGAAATTAACTTTT-AATAGACACTTGAATCACCTTGATCAGACAA-ATAAA

                                   * *        *                      * *     
        947 ACAAAAAATA-AAAGAATT-AAAGCTGAAACGTTCAATCGTCCAACCCAAAAATTGTGAGGGACT
        324 ACAAAAAATATAAA-AATTAAAACCAG-AACGTTAAATCGTCCAACCC-AAAATTGTAAAGGACT

                                          *                      
       1010 AAATAGCATAAACCATAAAAGTATAGGGATTATCTAATAAATAAACCAGCAAA
        386 AAATAGCATAAACCATAAAAGTATAGGGATCATCTAATAAATAAACCAGCAAA

                            
       1063 AAAATGATTTGTTTAT
          1 AAAAT-ATTTGTTTAT

       1079 TATAAGGGGG


Statistics
Matches: 392,  Mismatches: 55, Indels: 14
        0.85            0.12        0.03

Matches are distributed among these distances:
 437   14  0.04
 438  102  0.26
 439  276  0.70

ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27


Consensus pattern (438 bp):   
AAAATATTTGTTTATGGAGACCAAACATAAAAATTCCCTCTCGAACCCTCCACGAAACTCATTAA
TCAAATTAAACTTTCAGGCCCGTAATGAAAGTCGTAAATCACACAATAACCTTTTAACCGACACT
TAAACAACCTCAATCAGACAAGTGGACCGAAAATTATACAATATTAAATAGACCGGCAATCGAGA
TAACAAAATTTCAGAAGCATCTTTTAGAATCAAAACATCAAAATTGGCTTATGAGTCATTAATGA
AAGTTGTAGATCATGAAATTAACTTTTAATAGACACTTGAATCACCTTGATCAGACAAATAAAAC
AAAAAATATAAAAATTAAAACCAGAACGTTAAATCGTCCAACCCAAAATTGTAAAGGACTAAATA
GCATAAACCATAAAAGTATAGGGATCATCTAATAAATAAACCAGCAAA

Found at i:2253 original size:42 final size:42

Alignment explanation


    Indices: 2194--2279  Score: 172
    Period size: 42  Copynumber: 2.0  Consensus size: 42

       2184 ACATTAAAAA

                                                      
       2194 AAAGCATTTTTCTTGCTAATTAAAGTATATATCTGCAATGGC
          1 AAAGCATTTTTCTTGCTAATTAAAGTATATATCTGCAATGGC

                                                      
       2236 AAAGCATTTTTCTTGCTAATTAAAGTATATATCTGCAATGGC
          1 AAAGCATTTTTCTTGCTAATTAAAGTATATATCTGCAATGGC

              
       2278 AA
          1 AA

       2280 GTCCCAATAC


Statistics
Matches: 44,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  42   44  1.00

ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37


Consensus pattern (42 bp):   
AAAGCATTTTTCTTGCTAATTAAAGTATATATCTGCAATGGC
Done.