Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004974.1 Corchorus capsularis cultivar CVL-1 contig04992, 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: 1716
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37


Found at i:1174 original size:335 final size:332

Alignment explanation


    Indices: 559--1716  Score: 1594
    Period size: 335  Copynumber: 3.5  Consensus size: 332

        549 ATAGATATAG

                   * *          *                                          **
        559 AAAATTTTAGCCAAAATCGTTTACTAACCATCACGAGTTTTTT-GCGAAAAACGCGTTTTGGGGT
          1 AAAATTTCAACCAAAATCGTGTACTAACCATCACG-GTTTTTTGGCGAAAAACGCGTTTTGGGAC

                                     *   *           *                    *  
        623 CCTGACTCAGTTTTGAATGATTTTTTGCGCCGAAACTCCTTAAAATATCTATATTCATTTTCAAA
         65 CCTGACTCAGTTTTGAATGATTTTTGGCGACGAAACTCCTTGAAATATCTATATTCA---TCTAA

                 *   *                 *     *                               
        688 AAAAATCTTTGCCACATTGCATTTAAGGATTTGATTTTACGAGCATCTGAATCTTGTTTCGATTT
        127 AAAAAGCTTAGCCACATTGCATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTT

                                                *               *  *   *     
        753 AATTA-AAATTAATTCAAAAAAAATATAAGAAATGAAATTAAAAGCGTGAAAGGTCCTCTAATCT
        192 AATTAGAAATTAATTCAAAAAAAATATAA-AAATGATATTAAAAGCGTGAAAAGTTCTCCAATCT

                                                            *                
        817 TTTTGGCGTTAAATTATATATAATTTATGAGTATTTTATCCAAAAATTAAGGAAAAAATTTTCGG
        256 TTTTGGCGTTAAATTATATATAATTTATGAGTATTTTATCCAAAAATTGAGGAAAAAATTTTCGG

                        
        882 GTAATTTTTTAC
        321 GTAATTTTTTAC

                                     *                     **           *    
        894 AAAATTTCAACCAAAATCGTGTATGTTAACCATCACGGTTTTTTGGCTCAAAACGCGTTTCGGGA
          1 AAAATTTCAACCAAAATCGTGTA--CTAACCATCACGGTTTTTTGGCGAAAAACGCGTTTTGGGA

                            *                 *            *      *          
        959 CCCTGACTCAGTTTTGTATGATTTTTGGCGACGAGACTCCTTGAAATGTCTATACTCATCTAAAA
         64 CCCTGACTCAGTTTTGAATGATTTTTGGCGACGAAACTCCTTGAAATATCTATATTCATCTAAAA

                                                    **                       
       1024 AAAGCTTAGCCACATTGCATTTAAGAATTTGTTTTTACGAATATCTGAATCTTGTTTCGATTTAA
        129 AAAGCTTAGCCACATTGCATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAA

                           *               *           *                 *   
       1089 TTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGGGTGAAAAGTTCTCCAATATTT
        194 TTAGAAATTAATTCAAAAAAAATAT-AAAAATGATATTAAAAGCGTGAAAAGTTCTCCAATCTTT

                         *                                         *         
       1154 TTGGCGTTAAATTGTATATAATTTATGAGTATTTTATCCAAAAATTGAGGAAAAATTTTTCGGGT
        258 TTGGCGTTAAATTATATATAATTTATGAGTATTTTATCCAAAAATTGAGGAAAAAATTTTCGGGT

            *  *      
       1219 TATATTTTAC
        323 AATTTTTTAC

                   * *                                                       
       1229 AAAATTTTAGCCAAAATCGTGTACTAACCATCACGGTTTTTTTGGCGAAAAACGCGTTTTGAGG-
          1 AAAATTTCAACCAAAATCGTGTACTAACCATCACGG-TTTTTTGGCGAAAAACGCGTTTTG-GGA

                                       *   *   *                             
       1293 CCCTGACTCAGTTTTGAATGATTTTTTTGCGTCGAGACTCCTTGAAATATCTATATTCATCTAAA
         64 CCCTGACTCAGTTTTGAATGA-TTTTTGGCGACGAAACTCCTTGAAATATCTATATTCATCTAAA

                **    *               *    *               *                 
       1358 AAAAATTTAGTCACATTGCATTTAAGGATTTTTTTTTACGAGCATCTAAATCTTGTTTCGATTTA
        128 AAAAGCTTAGCCACATTGCATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTA

                            *                                                
       1423 ATTAGAAATTAATTCATAAAAAATATAAAAAATGATATTAAAAGCGTGAAAAGTTCTCCAATCTT
        193 ATTAGAAATTAATTCAAAAAAAATAT-AAAAATGATATTAAAAGCGTGAAAAGTTCTCCAATCTT

              *  *    *                                         *            
       1488 TTCGGTGTTAGATTATATATAATTTATGAGTATTTTATCC-AAAATTGA-G-TAAAATTTTCGGG
        257 TTTGGCGTTAAATTATATATAATTTATGAGTATTTTATCCAAAAATTGAGGAAAAAATTTTCGGG

             *         
       1550 TCA-TTTTTAC
        322 TAATTTTTTAC

                 *                                    *  *                   
       1560 AAAATGTCAACCAAAATCGTGTACTAACCATCACGGTTTTTTAGCTAAAAACGCGTTTTGGGACC
          1 AAAATTTCAACCAAAATCGTGTACTAACCATCACGGTTTTTTGGCGAAAAACGCGTTTTGGGACC

                          *   **                          *         *        
       1625 CTGACTCAGTTTTGTATGCCTTTTGGC-ACCGAAACTCCTTGAAATGTCTATATTCCTCTAAAAA
         66 CTGACTCAGTTTTGAATGATTTTTGGCGA-CGAAACTCCTTGAAATATCTATATTCATCTAAAAA

                                        
       1689 AAGCTTAGCCACATTGCATTTAAGAATT
        130 AAGCTTAGCCACATTGCATTTAAGAATT


Statistics
Matches: 728,  Mismatches: 85, Indels: 26
        0.87            0.10        0.03

Matches are distributed among these distances:
 329   64  0.09
 330   41  0.06
 331   39  0.05
 332   13  0.02
 333   13  0.02
 334  117  0.16
 335  355  0.49
 336    9  0.01
 337   77  0.11

ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37


Consensus pattern (332 bp):   
AAAATTTCAACCAAAATCGTGTACTAACCATCACGGTTTTTTGGCGAAAAACGCGTTTTGGGACC
CTGACTCAGTTTTGAATGATTTTTGGCGACGAAACTCCTTGAAATATCTATATTCATCTAAAAAA
AGCTTAGCCACATTGCATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATT
AGAAATTAATTCAAAAAAAATATAAAAATGATATTAAAAGCGTGAAAAGTTCTCCAATCTTTTTG
GCGTTAAATTATATATAATTTATGAGTATTTTATCCAAAAATTGAGGAAAAAATTTTCGGGTAAT
TTTTTAC

Done.