Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010910.1 Corchorus olitorius cultivar O-4 contig10942, 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: 6236
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29


Found at i:1463 original size:21 final size:21

Alignment explanation


    Indices: 1437--1478  Score: 75
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       1427 GCATCTTAGG

                                 
       1437 CAACTCCGATGAGCTTGAAAC
          1 CAACTCCGATGAGCTTGAAAC

                  *              
       1458 CAACTCTGATGAGCTTGAAAC
          1 CAACTCCGATGAGCTTGAAAC

       1479 TTCTTCCTTA


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.33, C:0.26, G:0.19, T:0.21


Consensus pattern (21 bp):   
CAACTCCGATGAGCTTGAAAC

Found at i:1844 original size:274 final size:281

Alignment explanation


    Indices: 1303--1861  Score: 681
    Period size: 274  Copynumber: 2.0  Consensus size: 281

       1293 CAATGGGCTT

                                                        **              *    
       1303 CAAATGATCTCCGATGGCTTTAAACTCTTCAAGATGAACTCTAATGAGGCCAAACAAAGCTTCCT
          1 CAAATGATCTCCGATGGCTTTAAACTCTTCAAGATGAACTCTAACAAGGCCAAACAAAGCATCCT

                                          *              *                   
       1368 TGAACTTTTAGCTCTTACCCTTGTCATTGGGCCTAATGGCATCTTTAATGGATCAAATGGCATCT
         66 TGAACTTTTAGCTCTTACCCTTGTCATTGGACCTAATGGCATCTTCAATGGATCAAATGGCATCT

                               *                                             
       1433 TAGGCAACTCCGATGAGCTTGAAACCAACTCTGATGAGCTTGAAACTTCTTCCTTAGCATCTTCA
        131 TAGGCAACTCCGATGAGCTAGAAACCAA--CTGATGAGC-TGAAAC-TCTTCCTTAGCATCTTCA

                                 **                                          
       1498 AGCTTCTCCAAGCCTCCTTGCCGCATATGCACATCCTCTCCATGATCTCCATTGGGCTCTTCAAG
        192 AGCTTCTCCAAGCCTCCTTGCAACATATGCACATCCTCTCCATGATCTCCATTGGGCTCTTCAAG

                    *                
       1563 ACCATGATGAGTCCTTGGCGCATCA
        257 ACCATGATAAGTCCTTGGCGCATCA

                                                 **               *  *       
       1588 CAAATGATCTCCGATGGCTTTAAACTCTTCAAGATGAGTTCTAACAAGGCCAAATAATGCATCCT
          1 CAAATGATCTCCGATGGCTTTAAACTCTTCAAGATGAACTCTAACAAGGCCAAACAAAGCATCCT

                      *      * *                                             
       1653 TGAATCTTTTGGCTCTTGCTCTTGTCATTGGACCTAATGGCATCTTCAATGGATCAAATGGCATC
         66 TGAA-CTTTTAGCTCTTACCCTTGTCATTGGACCTAATGGCATCTTCAATGGATCAAATGGCATC

              *    *     *   *               *  *     *                    * 
       1718 TTTGGCATCTCC-TTGGTGCTAGAAA-C-A-TGTTGTG-TGATA-TC-TCCTT-G-ATCTTCATG
        130 TTAGGCAACTCCGAT-GAGCTAGAAACCAACTGATGAGCTGAAACTCTTCCTTAGCATCTTCAAG

                    *  *                        *   *  *          *          
       1774 CTTCTCCATGCTTCCTTGCAAC-TCATGCACATCCTTTCCTTGCTCTCCATT-GTCATCTTCAAG
        194 CTTCTCCAAGCCTCCTTGCAACAT-ATGCACATCCTCTCCATGATCTCCATTGGGC-TCTTCAAG

            *                 *      
       1837 TCCATGATAAGTCCTTGGTGCATCA
        257 ACCATGATAAGTCCTTGGCGCATCA

       1862 TAGCCTCAAA


Statistics
Matches: 238,  Mismatches: 32, Indels: 19
        0.82            0.11        0.07

Matches are distributed among these distances:
 273    3  0.01
 274   80  0.34
 275    1  0.00
 276    5  0.02
 277    2  0.01
 279    4  0.02
 281    5  0.02
 284    1  0.00
 285   64  0.27
 286   73  0.31

ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33


Consensus pattern (281 bp):   
CAAATGATCTCCGATGGCTTTAAACTCTTCAAGATGAACTCTAACAAGGCCAAACAAAGCATCCT
TGAACTTTTAGCTCTTACCCTTGTCATTGGACCTAATGGCATCTTCAATGGATCAAATGGCATCT
TAGGCAACTCCGATGAGCTAGAAACCAACTGATGAGCTGAAACTCTTCCTTAGCATCTTCAAGCT
TCTCCAAGCCTCCTTGCAACATATGCACATCCTCTCCATGATCTCCATTGGGCTCTTCAAGACCA
TGATAAGTCCTTGGCGCATCA
Done.