Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005303.1 Corchorus capsularis cultivar CVL-1 contig05321, 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: 2851
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30


Found at i:1827 original size:100 final size:100

Alignment explanation


    Indices: 1654--1855  Score: 350
    Period size: 100  Copynumber: 2.0  Consensus size: 100

       1644 ATATGGGAGA

                                                                             
       1654 AATTATTAAGTGGGACGGACCCACCACGTCATCTATAGGACCAACCAATAATATGAAGACAACTC
          1 AATTATTAAGTGGGACGGACCCACCACGTCATCTATAGGACCAACCAATAATATGAAGACAACTC

                                   * *         
       1719 ATCAATTTTCTAAAACTCTATCCTAGTAAAACCTC
         66 ATCAATTTTCTAAAACTCTATCCCAATAAAACCTC

                    *                           *                            
       1754 AATTATTAGGTGGGACGGACCCACCACGTCATCTATGGGACCAACCAATAATATGAAGACAACTC
          1 AATTATTAAGTGGGACGGACCCACCACGTCATCTATAGGACCAACCAATAATATGAAGACAACTC

                             *             *   
       1819 ATCAATTTTCTAAAACTTTATCCCAATAAAATCTC
         66 ATCAATTTTCTAAAACTCTATCCCAATAAAACCTC

              
       1854 AA
          1 AA

       1856 ATTTGGGGAC


Statistics
Matches: 96,  Mismatches: 6, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
 100   96  1.00

ACGTcount: A:0.38, C:0.24, G:0.12, T:0.25


Consensus pattern (100 bp):   
AATTATTAAGTGGGACGGACCCACCACGTCATCTATAGGACCAACCAATAATATGAAGACAACTC
ATCAATTTTCTAAAACTCTATCCCAATAAAACCTC

Found at i:2049 original size:160 final size:161

Alignment explanation


    Indices: 1853--2173  Score: 446
    Period size: 161  Copynumber: 2.0  Consensus size: 161

       1843 AATAAAATCT

                      *                                                *     
       1853 CAAATTTGGGGACTTACCCTTTACAGAGGGTTTGTTTTAAAAGGGGACTAAACCTTGGATTAAAA
          1 CAAATTTGGGAACTTACCCTTTACAGAGGGTTTGTTTTAAAAGGGGACTAAACCTTGGACTAAAA

                            *  ** **                          *              
       1918 TCGTGC-CAAATTTAAGGAGTTCTTTTGACATGACAAAATTCTATTGGTTGGTCCCATAGATGAC
         66 TCGTGCTCAAATTTAAAGAAATAATTTGACATGACAAAATTCTATTGGTTAGTCCCATAGATGAC

               *   *                       
       1982 GTGGTGGGTCCGTCCCACCTAATAATTTCTC
        131 GTGATGGATCCGTCCCACCTAATAATTTCTC

                                   * *   *                *           *      
       2013 CAAATTTGGGAACTTACCCTTTATATAGGTTTTGTTTTAAAAGGGGGCTAAACCTTGGGCTAAAA
          1 CAAATTTGGGAACTTACCCTTTACAGAGGGTTTGTTTTAAAAGGGGACTAAACCTTGGACTAAAA

                   *                         *    *              *          *
       2078 TCGTGCTTAAATTTAAAGAAATAATTTGACATGGCAAACTTCTATTGGTTAGTTCCATAGATGAT
         66 TCGTGCTCAAATTTAAAGAAATAATTTGACATGACAAAATTCTATTGGTTAGTCCCATAGATGAC

            *                              
       2143 TTGATGGATCCGTCCCACCTAATAATTTCTC
        131 GTGATGGATCCGTCCCACCTAATAATTTCTC

       2174 GGCACATGAA


Statistics
Matches: 139,  Mismatches: 21, Indels: 1
        0.86            0.13        0.01

Matches are distributed among these distances:
 160   64  0.46
 161   75  0.54

ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34


Consensus pattern (161 bp):   
CAAATTTGGGAACTTACCCTTTACAGAGGGTTTGTTTTAAAAGGGGACTAAACCTTGGACTAAAA
TCGTGCTCAAATTTAAAGAAATAATTTGACATGACAAAATTCTATTGGTTAGTCCCATAGATGAC
GTGATGGATCCGTCCCACCTAATAATTTCTC

Done.