Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000576.1 Corchorus olitorius cultivar O-4 contig00576, 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: 1755
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.34


Found at i:1432 original size:22 final size:22

Alignment explanation


    Indices: 1394--1609  Score: 152
    Period size: 22  Copynumber: 9.8  Consensus size: 22

       1384 AGATTTGAGA

                         *        
       1394 AGGTTATC-AAATCTCATAGAG
          1 AGGTTATCAAAATTTCATAGAG

            *       *             
       1415 TGGTTATCGAAATTTCATAGAG
          1 AGGTTATCAAAATTTCATAGAG

                 *                   
       1437 ATCAGATTATCAAAATTT-ATA-AG
          1 ---AGGTTATCAAAATTTCATAGAG

               *            *    * 
       1460 AAGATTATCAAAATTTTATAGTG
          1 -AGGTTATCAAAATTTCATAGAG

            ***              *  * 
       1483 TTATTATCAAAATTTCAAAGCG
          1 AGGTTATCAAAATTTCATAGAG

                          *        
       1505 AGGTTATCAAAATTACATA-ATG
          1 AGGTTATCAAAATTTCATAGA-G

            * *  *         *      
       1527 TGATTTTCAAAATTTTATAGAG
          1 AGGTTATCAAAATTTCATAGAG

            *   * *        *      
       1549 GGGTCAACAAAATTTTATAGAG
          1 AGGTTATCAAAATTTCATAGAG

                               *  
       1571 AGGTTATCAAAATTTCATAAAG
          1 AGGTTATCAAAATTTCATAGAG

                       *     
       1593 AGGTTATCAAATTTTCA
          1 AGGTTATCAAAATTTCA

       1610 AAATGTGATT


Statistics
Matches: 153,  Mismatches: 34, Indels: 15
        0.76            0.17        0.07

Matches are distributed among these distances:
  21   22  0.14
  22  112  0.73
  23    4  0.03
  24    3  0.02
  25   12  0.08

ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35


Consensus pattern (22 bp):   
AGGTTATCAAAATTTCATAGAG

Found at i:1561 original size:88 final size:88

Alignment explanation


    Indices: 1468--1634  Score: 219
    Period size: 88  Copynumber: 1.9  Consensus size: 88

       1458 AGAAGATTAT

                         * **                   *                  *         
       1468 CAAAATTTTATAGTGTTATTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAATGTGATT
          1 CAAAATTTTATAGAGAGATTATCAAAATTTCATAA-AGAGGTTATCAAAATTACAAAATGTGATT

            **        *             
       1532 TTCAAAATTTTATAGAGGGGTCAA
         65 ACCAAAATTTCATAGAGGGGTCAA

                             *                              *  *             
       1556 CAAAATTTTATAGAGAGGTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTGATTA
          1 CAAAATTTTATAGAGAGATTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATGTGATTA

                          
       1621 CCAAAATTTCATAG
         66 CCAAAATTTCATAG

       1635 TGGTATTTCT


Statistics
Matches: 67,  Mismatches: 11, Indels: 2
        0.84            0.14        0.03

Matches are distributed among these distances:
  88   65  0.97
  89    2  0.03

ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35


Consensus pattern (88 bp):   
CAAAATTTTATAGAGAGATTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATGTGATTA
CCAAAATTTCATAGAGGGGTCAA

Found at i:1603 original size:66 final size:66

Alignment explanation


    Indices: 1443--1607  Score: 174
    Period size: 66  Copynumber: 2.5  Consensus size: 66

       1433 AGAGATCAGA

                                                    * **  * *             *  
       1443 TTATCAAAATTT-AT-AAGAAGATTATCAAAATTTTATAGTGTTATTATCAAAATTTCAAAGCGA
          1 TTATCAAAATTTCATAAAG-AGATTATCAAAATTTTATAGAGGGATCAACAAAATTTCAAAGAGA

              
       1506 GG
         65 GG

                       *     * *    *                  *            * *      
       1508 TTATCAAAATTACATAATGTGATTTTCAAAATTTTATAGAGGGGTCAACAAAATTTTATAGAGAG
          1 TTATCAAAATTTCATAAAGAGATTATCAAAATTTTATAGAGGGATCAACAAAATTTCAAAGAGAG

             
       1573 G
         66 G

                                 *             
       1574 TTATCAAAATTTCATAAAGAGGTTATC-AAATTTT
          1 TTATCAAAATTTCATAAAGAGATTATCAAAATTTT

       1608 CAAAATGTGA


Statistics
Matches: 80,  Mismatches: 18, Indels: 4
        0.78            0.18        0.04

Matches are distributed among these distances:
  65   18  0.22
  66   60  0.75
  67    2  0.03

ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37


Consensus pattern (66 bp):   
TTATCAAAATTTCATAAAGAGATTATCAAAATTTTATAGAGGGATCAACAAAATTTCAAAGAGAG
G

Done.