Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012082.1 Corchorus capsularis cultivar CVL-1 contig12103, 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: 24001
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


Found at i:8167 original size:195 final size:196

Alignment explanation


    Indices: 7830--8187  Score: 612
    Period size: 195  Copynumber: 1.8  Consensus size: 196

       7820 TGTCACAACT

                                              *                              
       7830 TTTGAAATTTTAACTCTTCCACCACTTTTTATGATATAAAATATTGAAATTTAGACTATCTCACT
          1 TTTGAAATTTTAACTCTTCCACCACTTTTTATGACATAAAATATTGAAATTTAGACTATCTCACT

                                  *                             *            
       7895 TAGGGTTTAATATAGTTTTGGGGCATTTCTTTATCTCACTTAGGGTTTATATTTCATGTATTATA
         66 TAGGGTTTAATATAGTTTTGGGACATTTCTTTATCTCACTTAGGGTTTATATATCATGTATTATA

               * *                                                           
       7960 TCTTATTTAGGGTTTAGATTTCATG-CATGTCATGCCATTTTTTGTCTCTCATAGCCATTTTTTT
        131 TCTCACTTAGGGTTTAGATTTCATGTCATGTCATGCCATTTTTTGTCTCTCATAGCCATTTTTTT

             
       8024 A
        196 A

                       *                          *   *                      
       8025 TTTGAAATTTTGACTCTTCCACCACTTTTTATGACATAGAATGTTGAAATTTAGACTATCTCACT
          1 TTTGAAATTTTAACTCTTCCACCACTTTTTATGACATAAAATATTGAAATTTAGACTATCTCACT

                                                                           * 
       8090 TAGGGTTTAATATAGTTTTGGGACATTT-TTGTATCTCACTTAGGGTTTATATATCATGTATTTT
         66 TAGGGTTTAATATAGTTTTGGGACATTTCTT-TATCTCACTTAGGGTTTATATATCATGTATTAT

                                              
       8154 ATCTCACTTAGGGTTTAGATTTCATGTCATGTCA
        130 ATCTCACTTAGGGTTTAGATTTCATGTCATGTCA

       8188 ATTTTTTTTT


Statistics
Matches: 152,  Mismatches: 9, Indels: 3
        0.93            0.05        0.02

Matches are distributed among these distances:
 194    2  0.01
 195  143  0.94
 196    7  0.05

ACGTcount: A:0.25, C:0.14, G:0.14, T:0.46


Consensus pattern (196 bp):   
TTTGAAATTTTAACTCTTCCACCACTTTTTATGACATAAAATATTGAAATTTAGACTATCTCACT
TAGGGTTTAATATAGTTTTGGGACATTTCTTTATCTCACTTAGGGTTTATATATCATGTATTATA
TCTCACTTAGGGTTTAGATTTCATGTCATGTCATGCCATTTTTTGTCTCTCATAGCCATTTTTTT
A

Found at i:9347 original size:15 final size:15

Alignment explanation


    Indices: 9286--9347  Score: 56
    Period size: 15  Copynumber: 4.1  Consensus size: 15

       9276 GAGTTAAAGG

                            
       9286 AAGAAAGAAAATGAGA
          1 AAGAAAGAAAA-GAGA

                    *     * 
       9302 AAGAAA-ATAAGTAAA
          1 AAGAAAGAAAAG-AGA

                        *  
       9317 AAG-AAGAAAAGGGA
          1 AAGAAAGAAAAGAGA

                   *       
       9331 AAGAAAGGAAAGAGA
          1 AAGAAAGAAAAGAGA

              
       9346 AA
          1 AA

       9348 ATGGAGTCCC


Statistics
Matches: 36,  Mismatches: 7, Indels: 7
        0.72            0.14        0.14

Matches are distributed among these distances:
  14    7  0.19
  15   23  0.64
  16    6  0.17

ACGTcount: A:0.69, C:0.00, G:0.26, T:0.05


Consensus pattern (15 bp):   
AAGAAAGAAAAGAGA

Found at i:10305 original size:55 final size:55

Alignment explanation


    Indices: 10190--10358  Score: 196
    Period size: 55  Copynumber: 3.0  Consensus size: 55

      10180 AGTCTGGGAA

                                            **   * *           *      
      10190 TATGATACCCATATGAATTGTATTATTTTTTCAATCTCTGTATAGAAGAATATTGTGT
          1 TATGATACCCATATGAATTGTA-T-TTTTTTCTTTCTATATATAGAAG-ATGTTGTGT

                                              *     *              
      10248 TATGATACCCATATGAATTGTATTTTTTTCTTTCAATATACAGAAGATGTTGTGT
          1 TATGATACCCATATGAATTGTATTTTTTTCTTTCTATATATAGAAGATGTTGTGT

                        *    *                                       
      10303 TATGATACCCATGTGAACTGTATTTTTTT-TTCAATCTATATATAGAAGATGTTGTG
          1 TATGATACCCATATGAATTGTATTTTTTTCTT---TCTATATATAGAAGATGTTGTG

      10359 CCCACGCTAA


Statistics
Matches: 97,  Mismatches: 11, Indels: 7
        0.84            0.10        0.06

Matches are distributed among these distances:
  54    2  0.02
  55   35  0.36
  56   17  0.18
  57   21  0.22
  58   22  0.23

ACGTcount: A:0.30, C:0.11, G:0.15, T:0.45


Consensus pattern (55 bp):   
TATGATACCCATATGAATTGTATTTTTTTCTTTCTATATATAGAAGATGTTGTGT
Done.