Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013943.1 Corchorus capsularis cultivar CVL-1 contig13964, 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: 17919
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29


Found at i:8405 original size:110 final size:112

Alignment explanation


    Indices: 8206--8423  Score: 307
    Period size: 110  Copynumber: 2.0  Consensus size: 112

       8196 TTTTAATGAA

                                       *    *        *  *                    
       8206 ATCAGGAAACCTCCGGGAAGCAATTCTTGACAGCCTCCGGGCAGGTTATAAGACCTCCCGGCACA
          1 ATCAGGAAACCTCCGGGAAGCAATTCTAGACACCCTCCGGGAAGATTATAAGACCTCCCGGCACA

               *                         *                 
       8271 ACGTCAGAAACCTCCCGGTAGTAATTCTGGCAGCCTCCGGGCATTAT
         66 ACGCCAGAAACCTCCCGGTAGTAATTCTGACAGCCTCCGGGCATTAT

                             *            *            *                     
       8318 ATCA-GAAACCTCCGGGTAGCAATTC-AGATACCCTCCGGGAATATTATAAGACCT-CCGGACAC
          1 ATCAGGAAACCTCCGGGAAGCAATTCTAGACACCCTCCGGGAAGATTATAAGACCTCCCGG-CAC

                          * *                           
       8380 AACGCCAGAAACCTTCGGGTAGTAATTCTGACAGCCTCCGGGCA
         65 AACGCCAGAAACCTCCCGGTAGTAATTCTGACAGCCTCCGGGCA

       8424 CAAAATCCGA


Statistics
Matches: 94,  Mismatches: 11, Indels: 4
        0.86            0.10        0.04

Matches are distributed among these distances:
 109    4  0.04
 110   66  0.70
 111   20  0.21
 112    4  0.04

ACGTcount: A:0.28, C:0.30, G:0.23, T:0.19


Consensus pattern (112 bp):   
ATCAGGAAACCTCCGGGAAGCAATTCTAGACACCCTCCGGGAAGATTATAAGACCTCCCGGCACA
ACGCCAGAAACCTCCCGGTAGTAATTCTGACAGCCTCCGGGCATTAT

Found at i:8450 original size:110 final size:110

Alignment explanation


    Indices: 8204--8452  Score: 275
    Period size: 110  Copynumber: 2.2  Consensus size: 110

       8194 CTTTTTAATG

                            *  *         *  * *        * **                  
       8204 AAATCAGGAAACCTCCGGGAAGCAATTCTTGACAGCCTCCGGGCAGGTTATAAGACCTCCCGGCA
          1 AAATCA-GAAACCTCCAGGCAGCAATTC-AGATACCCTCCGGGAATATTATAAGACCTCCCGGCA

                 *                         *             **
       8269 CAACGTCAGAAACCTCCCGGTAGTAATTCTGGCAGCCTCCGGGCATT
         64 CAACGCCAGAAACCTCCCGGTAGTAATTCTGACAGCCTCCGGGCACA

             *             *  *                                              
       8316 ATATCAGAAACCTCCGGGTAGCAATTCAGATACCCTCCGGGAATATTATAAGACCT-CCGGACAC
          1 AAATCAGAAACCTCCAGGCAGCAATTCAGATACCCTCCGGGAATATTATAAGACCTCCCGG-CAC

                          * *                             
       8380 AACGCCAGAAACCTTCGGGTAGTAATTCTGACAGCCTCCGGGCACA
         65 AACGCCAGAAACCTCCCGGTAGTAATTCTGACAGCCTCCGGGCACA

                 *   *    *    *       
       8426 AAATCCGAAGCCTCTAGGCCGCAATTC
          1 AAATCAGAAACCTCCAGGCAGCAATTC

       8453 TGATTGCCTT


Statistics
Matches: 115,  Mismatches: 21, Indels: 4
        0.82            0.15        0.03

Matches are distributed among these distances:
 109    4  0.03
 110   86  0.75
 111   20  0.17
 112    5  0.04

ACGTcount: A:0.29, C:0.30, G:0.22, T:0.19


Consensus pattern (110 bp):   
AAATCAGAAACCTCCAGGCAGCAATTCAGATACCCTCCGGGAATATTATAAGACCTCCCGGCACA
ACGCCAGAAACCTCCCGGTAGTAATTCTGACAGCCTCCGGGCACA
Done.