Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019780.1 Corchorus olitorius cultivar O-4 contig19813, 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: 1776
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29


Found at i:1413 original size:91 final size:93

Alignment explanation


    Indices: 1299--1482  Score: 275
    Period size: 91  Copynumber: 2.0  Consensus size: 93

       1289 CCTTCAAGCA

                                              *                        *     
       1299 CCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGATTTAAGTTGATCTTAAGA-GA-CCATTTGCGG
          1 CCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGATCTTAAGATGACCCA-GTGCGG

                               *         
       1362 TCTTTAATAGAAGCTTTCAGAGATCTAAG
         65 TCTTTAATAGAAGCTTTCAAAGATCTAAG

                                                        *  *                 
       1391 CCCTG-GCGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGATTTTCAGATGACCCAGTGCGGT
          1 CCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGATCTTAAGATGACCCAGTGCGGT

                *       *               
       1455 CTTTCATAGAAGTTTTCAAAGATCTAAG
         66 CTTTAATAGAAGCTTTCAAAGATCTAAG

       1483 TTGATTTTAA


Statistics
Matches: 83,  Mismatches: 7, Indels: 4
        0.88            0.07        0.04

Matches are distributed among these distances:
  91   42  0.51
  92   38  0.46
  93    3  0.04

ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34


Consensus pattern (93 bp):   
CCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGATCTTAAGATGACCCAGTGCGGT
CTTTAATAGAAGCTTTCAAAGATCTAAG

Found at i:1462 original size:54 final size:54

Alignment explanation


    Indices: 1396--1776  Score: 298
    Period size: 54  Copynumber: 7.1  Consensus size: 54

       1386 CTAAGCCCTG

                                                  * *             
       1396 GCGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGATTTTCAGATGACCCAGT
          1 GCGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGATCTCCAGATGACCCAGT

                                   *              * **        **  
       1450 GCGGTCTTTCATAGAAGTTTTCAAAGATCTAAGTTGATTTTAAGATGACCTTGT
          1 GCGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGATCTCCAGATGACCCAGT

                             *                      *        * *  
       1504 GCGGTCTTTCATAGAAGCTTTCAGAGA--TAAGTTGATCTTCAGATGACTCGGT
          1 GCGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGATCTCCAGATGACCCAGT

             **                  *                  *       **     
       1556 GTTGTCTTTCATAGAAGTTTTTAGAGATC-AGAGTTGATCCCCAGATGGTCCAGT
          1 GCGGTCTTTCATAGAAGTTTTCAGAGATCTA-AGTTGATCTCCAGATGACCCAGT

             * *     *                                 *   *    * *   
       1610 GAGATCATTCCA-AGAAG-TTTC-GAATGAT-TAGAGTTGATCCCCAAATGATCTAGT
          1 GCGGTC-TTTCATAGAAGTTTTCAG-A-GATCTA-AGTTGATCTCCAGATGACCCAGT

              **                     *    *         *        *     
       1664 GCAATCATTTCA-AGAAGTTTTCAGTGATCAAAGTTGATCCCCAGATGATCCAGT
          1 GCGGTC-TTTCATAGAAGTTTTCAGAGATCTAAGTTGATCTCCAGATGACCCAGT

                     *                *    *                 *      
       1718 GCGGTCATTCCA-AGAAGTTTTC-GTTGATCAAAGTTGAT-TCCAGATGGCCCAGT
          1 GCGGTC-TTTCATAGAAGTTTTCAG-AGATCTAAGTTGATCTCCAGATGACCCAGT

                  
       1771 GCGGTC
          1 GCGGTC


Statistics
Matches: 274,  Mismatches: 42, Indels: 23
        0.81            0.12        0.07

Matches are distributed among these distances:
  52   44  0.16
  53   24  0.09
  54  196  0.72
  55    9  0.03
  56    1  0.00

ACGTcount: A:0.27, C:0.18, G:0.23, T:0.33


Consensus pattern (54 bp):   
GCGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGATCTCCAGATGACCCAGT

Found at i:1584 original size:106 final size:107

Alignment explanation


    Indices: 1396--1593  Score: 292
    Period size: 106  Copynumber: 1.9  Consensus size: 107

       1386 CTAAGCCCTG

                             *                    *                          
       1396 GCGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGATTTTCAGATGACCCAGTGCGGTCTTTCA
          1 GCGGTCTTTCATAGAAGCTTTCAGAGA-CTAAGTTGATCTTCAGATGACCCAGTGCGGTCTTTCA

                                                        
       1461 TAGAAGTTTTCAAAGATCTA-AGTTGATTTTAAGATGACCTTGT
         65 TAGAAGTTTTCAAAGATC-AGAGTTGATTTTAAGATGACCTTGT

                                                            * *   **         
       1504 GCGGTCTTTCATAGAAGCTTTCAGAGA-TAAGTTGATCTTCAGATGACTCGGTGTTGTCTTTCAT
          1 GCGGTCTTTCATAGAAGCTTTCAGAGACTAAGTTGATCTTCAGATGACCCAGTGCGGTCTTTCAT

                     * *              
       1568 AGAAGTTTTTAGAGATCAGAGTTGAT
         66 AGAAGTTTTCAAAGATCAGAGTTGAT

       1594 CCCCAGATGG


Statistics
Matches: 81,  Mismatches: 8, Indels: 4
        0.87            0.09        0.04

Matches are distributed among these distances:
 105    1  0.01
 106   54  0.67
 108   26  0.32

ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37


Consensus pattern (107 bp):   
GCGGTCTTTCATAGAAGCTTTCAGAGACTAAGTTGATCTTCAGATGACCCAGTGCGGTCTTTCAT
AGAAGTTTTCAAAGATCAGAGTTGATTTTAAGATGACCTTGT

Done.