Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015174.1 Corchorus capsularis cultivar CVL-1 contig15195, 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, 619

Length: 1032
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28


Found at i:834 original size:153 final size:157

Alignment explanation


    Indices: 527--864  Score: 345
    Period size: 153  Copynumber: 2.2  Consensus size: 157

        517 GATGAACTTT

                             *                                       * *     
        527 TTGGACAGCCCTGTGCAGAAACAAAGCTTACCAAGATGCCCAAAACCTCAACTTTGAGCGGTTGT
          1 TTGGACAGCCCTGTGCACAAACAAAGCTTACCAAGAT-CCCAAAACCTCAACTTTGACCCGTTGT

                           *                         *     *   *             
        592 ATGCAAAACATCATTTTTAGCGAAAGGCTCATTCCAGATGCTTTTTTTGCGCAACGAGTACTCAA
         65 ATGCAAAACATCATTCTTAGCGAAA-GCTCATTCCAGATGCGTTTTTCGCGAAACGAGTACTCAA

             *                **         
        657 ATGTCGTGCGTCGAATTGCGATGAGATTG
        129 AAGTCGTGCGTCGAATTGAAATGAGATTG

                                         *              *                  * 
        686 TTGGACAGCCCTGTGCACAAACAAAGCTTTCACAAG-T-CCAAAGCCTCAACTTTG-CCCGTTTT
          1 TTGGACAGCCCTGTGCACAAACAAAGCTTAC-CAAGATCCCAAAACCTCAACTTTGACCCGTTGT

            *   *                              **                       *    
        748 GTGCTAAACAT-AGTTCTTAGC-AAA-CT-ATTTCTGGATGCGTTTTTCGCGAAACGAGTGCTCA
         65 ATGCAAAACATCA-TTCTTAGCGAAAGCTCA-TTCCAGATGCGTTTTTCGCGAAACGAGTACTCA

                     *                 *   
        809 AAAGTCGTGTGTCGGAA-TGAAATGAGCTTG
        128 AAAGTCGTGCGTC-GAATTGAAATGAGATTG

              *      *  *               
        839 -TAGACAGCGCTATGCAC-AACAAAGCT
          1 TTGGACAGCCCTGTGCACAAACAAAGCT

        865 CTCCTCGAAG


Statistics
Matches: 152,  Mismatches: 23, Indels: 16
        0.80            0.12        0.08

Matches are distributed among these distances:
 151    9  0.06
 152   15  0.10
 153   50  0.33
 154    3  0.02
 155    4  0.03
 156   21  0.14
 157   16  0.11
 159   30  0.20
 160    4  0.03

ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27


Consensus pattern (157 bp):   
TTGGACAGCCCTGTGCACAAACAAAGCTTACCAAGATCCCAAAACCTCAACTTTGACCCGTTGTA
TGCAAAACATCATTCTTAGCGAAAGCTCATTCCAGATGCGTTTTTCGCGAAACGAGTACTCAAAA
GTCGTGCGTCGAATTGAAATGAGATTG

Found at i:912 original size:427 final size:427

Alignment explanation


    Indices: 2--1032  Score: 1750
    Period size: 427  Copynumber: 2.4  Consensus size: 427

          1 C

                                                                             
          2 CACACAAACAAAGCTCTCCTCGAAGTCTAAAGCATCAACTTTGCGAGTTTGTATGCAACACTTCG
          1 CACACAAACAAAGCTCTCCTCGAAGTCTAAAGCATCAACTTTGCGAGTTTGTATGCAACACTTCG

                                                                             
         67 TTCTTAGTGGTTTGTCGGAGTGAGATGAACTTTTTGGACAGCCCTGTGCAGAAACAAAGCTTACC
         66 TTCTTAGTGGTTTGTCGGAGTGAGATGAACTTTTTGGACAGCCCTGTGCAGAAACAAAGCTTACC

                                                                             
        132 AAGATGCCCAAAACCTCAACTTTGAGCGGTTGTATGCAAAACATCATTTTTAGCGAAAGGCTCAT
        131 AAGATGCCCAAAACCTCAACTTTGAGCGGTTGTATGCAAAACATCATTTTTAGCGAAAGGCTCAT

              *                                                              
        197 TCTAGATGCTTTTTTTGCGCAACGAGTACTCAAATGTCGTGCGTCGAATTGCGATGAGATTGTTG
        196 TCCAGATGCTTTTTTTGCGCAACGAGTACTCAAATGTCGTGCGTCGAATTGCGATGAGATTGTTG

                                                           *        *        
        262 GACAGCCCTGTGCACAAACAAAGCTTTCACGAAGTCCAAAGCCTCAAGTTTGCACATTTTTGTGC
        261 GACAGCCCTGTGCACAAACAAAGCTTTCACGAAGTCCAAAGCCTCAACTTTGCACAGTTTTGTGC

                                   *   *                      *              
        327 TAAACATAGTTCTTAGCAGAACTCTTTTTGGATGCGTTTTTTCGCGAAACTAGTGCTCAAAAGTC
        326 TAAACATAGTTCTTAGCAGAACTATTTCTGGATGCGTTTTTTCGCGAAACGAGTGCTCAAAAGTC

                          *                      
        392 GTGTGTCGGAATGAGATGAGCTTGTTAGACAGCGCTA
        391 GTGTGTCGGAATGAAATGAGCTTGTTAGACAGCGCTA

                                                                             
        429 CACACAAACAAAGCTCTCCTCGAAGTCTAAAGCATCAACTTTGCGAGTTTGTATGCAACACTTCG
          1 CACACAAACAAAGCTCTCCTCGAAGTCTAAAGCATCAACTTTGCGAGTTTGTATGCAACACTTCG

                                                                             
        494 TTCTTAGTGGTTTGTCGGAGTGAGATGAACTTTTTGGACAGCCCTGTGCAGAAACAAAGCTTACC
         66 TTCTTAGTGGTTTGTCGGAGTGAGATGAACTTTTTGGACAGCCCTGTGCAGAAACAAAGCTTACC

                                                                             
        559 AAGATGCCCAAAACCTCAACTTTGAGCGGTTGTATGCAAAACATCATTTTTAGCGAAAGGCTCAT
        131 AAGATGCCCAAAACCTCAACTTTGAGCGGTTGTATGCAAAACATCATTTTTAGCGAAAGGCTCAT

                                                                             
        624 TCCAGATGCTTTTTTTGCGCAACGAGTACTCAAATGTCGTGCGTCGAATTGCGATGAGATTGTTG
        196 TCCAGATGCTTTTTTTGCGCAACGAGTACTCAAATGTCGTGCGTCGAATTGCGATGAGATTGTTG

                                                                   *         
        689 GACAGCCCTGTGCACAAACAAAGCTTTCAC-AAGTCCAAAGCCTCAACTTTGC-CCGTTTTGTGC
        261 GACAGCCCTGTGCACAAACAAAGCTTTCACGAAGTCCAAAGCCTCAACTTTGCACAGTTTTGTGC

                                                                             
        752 TAAACATAGTTCTTAGCA-AACTATTTCTGGATGCG-TTTTTCGCGAAACGAGTGCTCAAAAGTC
        326 TAAACATAGTTCTTAGCAGAACTATTTCTGGATGCGTTTTTTCGCGAAACGAGTGCTCAAAAGTC

                                                 
        815 GTGTGTCGGAATGAAATGAGCTTG-TAGACAGCGCTA
        391 GTGTGTCGGAATGAAATGAGCTTGTTAGACAGCGCTA

            **                         *          *                         *
        851 TGCAC-AACAAAGCTCTCCTCGAAGTCCAAACGCTACTAAACTTTGTCGACGTTTGGTATGCAAG
          1 CACACAAACAAAGCTCTCCTCGAAGTCTAAA-GC-A-TCAACTTTG-CGA-GTTT-GTATGCAAC

              *          *                                                 * 
        915 ACATCGTTCTTAGAGGTTTGTCGGAGTGAGATGAACTTTTTGGACAGCCCCTAGTGCAGAAAGAA
         60 ACTTCGTTCTTAGTGGTTTGTCGGAGTGAGATGAACTTTTTGGACAG-CCCT-GTGCAGAAA-CA

                  *  *   *             *       *                 
        980 AAGCTTTCCTAGACGCCCAAAACCTCATCTTTGAGTGGTTGTATGCAAAACAT
        122 AAGCTTACCAAGATGCCCAAAACCTCAACTTTGAGCGGTTGTATGCAAAACAT


Statistics
Matches: 574,  Mismatches: 21, Indels: 15
        0.94            0.03        0.02

Matches are distributed among these distances:
 421   24  0.04
 422   17  0.03
 423   51  0.09
 424   23  0.04
 425   30  0.05
 426   25  0.04
 427  342  0.60
 428    4  0.01
 429    9  0.02
 430   49  0.09

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


Consensus pattern (427 bp):   
CACACAAACAAAGCTCTCCTCGAAGTCTAAAGCATCAACTTTGCGAGTTTGTATGCAACACTTCG
TTCTTAGTGGTTTGTCGGAGTGAGATGAACTTTTTGGACAGCCCTGTGCAGAAACAAAGCTTACC
AAGATGCCCAAAACCTCAACTTTGAGCGGTTGTATGCAAAACATCATTTTTAGCGAAAGGCTCAT
TCCAGATGCTTTTTTTGCGCAACGAGTACTCAAATGTCGTGCGTCGAATTGCGATGAGATTGTTG
GACAGCCCTGTGCACAAACAAAGCTTTCACGAAGTCCAAAGCCTCAACTTTGCACAGTTTTGTGC
TAAACATAGTTCTTAGCAGAACTATTTCTGGATGCGTTTTTTCGCGAAACGAGTGCTCAAAAGTC
GTGTGTCGGAATGAAATGAGCTTGTTAGACAGCGCTA
Done.