Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011646.1 Corchorus olitorius cultivar O-4 contig11679, 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, 601

Length: 1003
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21


Found at i:380 original size:154 final size:154

Alignment explanation


    Indices: 3--1003  Score: 1556
    Period size: 154  Copynumber: 6.5  Consensus size: 154

          1 CA

                                                         *                   
          3 AAATCGAAGACGATTCAAAACGTCACAAATGGACCCCGATAGGCCAAAAATAACAAGTGTTCCAA
          1 AAATCGAAGACGATTCAAAACGTCACAAATGGACCCCGATAGGCCCAAAATAACAAGTGTTCCAA

                                                                             
         68 ATGAGCTAAAAACTTCAAAGTGGACTAATCTCACCAAAATAGATTATAGTTAGGCCATAAACAAT
         66 ATGAGCTAAAAACTTCAAAGTGGACTAATCTCACCAAAAT-GATTATAGTTAGGCCATAAACAAT

                                       
        133 GGAAAGAAAAGACATTGAGGTTTTGCC
        130 GGAAAGAAAAG-CATTGAGG-TTTGCC

                      *                                             *    *   
        160 AAATCGAAGAAGAGTTACAAAACGTCACAAATGGACCCCGATAGGCCCAAAATAACCAGTGCTCC
          1 AAATCGAAGACGA-TT-CAAAACGTCACAAATGGACCCCGATAGGCCCAAAATAACAAGTGTTCC

                     *             *                                         
        225 AAATGAGCTGAAAACTTCAAAGTTGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
         64 AAATGAGCTAAAAACTTCAAAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA

                                      
        290 TGGAAAGAAAAGCATTGAGGTTTGCC
        129 TGGAAAGAAAAGCATTGAGGTTTGCC

                                                                             
        316 AAATCGAAGACGATTCAAAACGTCACAAATGGACCCCGATAGGCCCAAAATAACAAGTGTTCCAA
          1 AAATCGAAGACGATTCAAAACGTCACAAATGGACCCCGATAGGCCCAAAATAACAAGTGTTCCAA

                    *             *                     *                    
        381 ATGAGCTAGAAACTTCAAAAGTTGACTAATCTCACCAAAATGATCATAGTTAGGCCATAAACAAT
         66 ATGAGCTAAAAACTTC-AAAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT

                                     
        446 GGAAAGAAAAGCATTGAGGTTTGCC
        130 GGAAAGAAAAGCATTGAGGTTTGCC

                                                         *     *             
        471 AAATCGAAGACGATTCAAAACGTCACAAATGGACCCCGATAGGCCAAAAATCACAAGTGTTCCAA
          1 AAATCGAAGACGATTCAAAACGTCACAAATGGACCCCGATAGGCCCAAAATAACAAGTGTTCCAA

                           *                                                 
        536 ATGAGCT-AAAACTTTAAAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATG
         66 ATGAGCTAAAAACTTCAAAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATG

                                    
        600 GAAAGAAAAGCATTGAGGTTTGCC
        131 GAAAGAAAAGCATTGAGGTTTGCC

                                      *                                      
        624 AAATCGAAGACGATTCAAAACGTCACTAATGGACCCCGATAGGCCCAAAATAACAAGTGTTCCAA
          1 AAATCGAAGACGATTCAAAACGTCACAAATGGACCCCGATAGGCCCAAAATAACAAGTGTTCCAA

                             *                                               
        689 ATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATG
         66 ATGAGCTAAAAACTTCAAAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATG

                 *                * 
        754 GAAAGGAAAGCATTGAGGTTTGTC
        131 GAAAGAAAAGCATTGAGGTTTGCC

              *  *    *     * *   **  *     *         *                      
        778 AACTCCAAGATGATTCGAGACGGAACTAATGGGCCCCGATAGTCCCAAAATAACAAGTGTTCCAA
          1 AAATCGAAGACGATTCAAAACGTCACAAATGGACCCCGATAGGCCCAAAATAACAAGTGTTCCAA

                           * *               *       *           *  *    *   
        843 ATGAGCTAAAAACTTTACAGTGGAAC-AATCTCGCCAAAATAATTATAGTTAGTCCGTAAAAAAT
         66 ATGAGCTAAAAACTTCAAAGTGG-ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT

                *       *            
        907 GGAATGAAAAGCTTTGAGGTTTGCC
        130 GGAAAGAAAAGCATTGAGGTTTGCC

                 *  *  *      *       *     *                                
        932 AAATCAAATACAATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAA
          1 AAATCGAAGACGATTCAAAACGTCACAAATGGACCCCGATAGGCCCAAAATAACAAGTGTTCCAA

                   
        997 ATGAGCT
         66 ATGAGCT


Statistics
Matches: 785,  Mismatches: 54, Indels: 13
        0.92            0.06        0.02

Matches are distributed among these distances:
 153  140  0.18
 154  339  0.43
 155  146  0.19
 156   18  0.02
 157   20  0.03
 158   37  0.05
 159   85  0.11

ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21


Consensus pattern (154 bp):   
AAATCGAAGACGATTCAAAACGTCACAAATGGACCCCGATAGGCCCAAAATAACAAGTGTTCCAA
ATGAGCTAAAAACTTCAAAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATG
GAAAGAAAAGCATTGAGGTTTGCC

Done.