Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016458.1 Corchorus olitorius cultivar O-4 contig16491, 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: 2330
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:629 original size:332 final size:329

Alignment explanation


    Indices: 1--779  Score: 1087
    Period size: 332  Copynumber: 2.3  Consensus size: 329

                  *        *                                     * *        *
          1 GATTTATTTGGAAATCAATTCGGAAAAGCATAGGAAAAAT-GATATTCGAAGCTTTAAAAACC-C
          1 GATTTAATTGGAAATTAATTCGGAAAAGCATAGG-AAAATCGATATTCGAAGCGTAAAAAACCTT

                                        *       *        *                   
         64 TACAATCTTTTTGGCGATGATTTATATACTTTTTATTAGTATTTTAGCCAAAATTTGAGGAAAAA
         65 TA-AAT-TTTTTGGCGATGATTTATATATTTTTTATAAGTATTTTGGCCAAAA-TTGAGGAAAAA

                                         *                               *   
        129 TCATTCGGGTCAATTTTTGCAAAATAATGGCCGAAATCGTGTGCTCCATCACAATTTTCAGTTAA
        127 TCATTCGGGTCAATTTTTGCAAAATAATGACCGAAATCGTGTGCTCCATCACAATTTTCAGCTAA

               * *               *            *                              
        194 AAATGTGTTCCGGAGCCCCGGTTCAGTTTTGTATTATTTTTGGCGCCAAGACTCCTTGGAATATC
        192 AAACGCGTTCCGGAGCCCCGGCTCAGTTTTGTATGATTTTTGGCGCCAAGACTCCTTGGAATATC

                                    *              *  *                  *   
        259 TATATTCATCTACCCAAATCTCAGGCACATAAGATTTAATGATTTCTTTTCACGAGCATCAGAAT
        257 TATATTCATCTACCCAAATCTCAGACACATAAGATTTAAAGAATTCTTTTCACGAGCATCAAAAT

                   *
        324 CCAATTTG
        322 CCAATTTC

                    *                    * *        *                        
        332 GATTTAATAGGAAATTAATTCGGAAAAGCGTTGGAAAATCAATATTCGAAGCGTAAAAAACCTTT
          1 GATTTAATTGGAAATTAATTCGGAAAAGCATAGGAAAATCGATATTCGAAGCGTAAAAAACCTTT

                                                                            *
        397 AAATTTTTTGGCGATGATTTATATATTTTTTATAAGTATTTTGGCCGAAAATTGAGGAAAAATCT
         66 AAATTTTTTGGCGATGATTTATATATTTTTTATAAGTATTTTGGCC-AAAATTGAGGAAAAATCA

                                  **                     *            *     *
        462 TTCGGGTCAATTTTTGCAAAATCTTGACCGAAATCGTGTGCTAACTATCACAATTTTCGGCTAAG
        130 TTCGGGTCAATTTTTGCAAAATAATGACCGAAATCGTGTGCT--CCATCACAATTTTCAGCTAAA

                                                       *             *       
        527 AACGCGTTCCAGG-GCCCCGGCTCAGTTTTGTATGATTTTTGGTGCCAAGACTCCTTTGAATATC
        193 AACGCGTTCC-GGAGCCCCGGCTCAGTTTTGTATGATTTTTGGCGCCAAGACTCCTTGGAATATC

                         *                 *             *    *              
        591 TATATTCATCTACGCAAATCTCAGACACATATGATTTAAAGAATTGTTTTTACGAGCATCAAAAT
        257 TATATTCATCTACCCAAATCTCAGACACATAAGATTTAAAGAATTCTTTTCACGAGCATCAAAAT

                    
        656 CCAATTTC
        322 CCAATTTC

                                                  *        *      *          
        664 GATTTAATTGGAAATTAATTCGGAAAAGCATAGGAAAAACGATATTCAAAGCGTGAAAAACCATT
          1 GATTTAATTGGAAATTAATTCGGAAAAGCATAGGAAAATCGATATTCGAAGCGTAAAAAACC-TT

            *  *                              *                
        729 CAATTTTTTTGGCGATGATTTATATATTTTTTATGAGTATTTTGGCCAAAA
         65 TAAATTTTTTGGCGATGATTTATATATTTTTTATAAGTATTTTGGCCAAAA

        780 ATTAAGTGGG


Statistics
Matches: 396,  Mismatches: 45, Indels: 13
        0.87            0.10        0.03

Matches are distributed among these distances:
 330   96  0.24
 331   55  0.14
 332  197  0.50
 333   48  0.12

ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35


Consensus pattern (329 bp):   
GATTTAATTGGAAATTAATTCGGAAAAGCATAGGAAAATCGATATTCGAAGCGTAAAAAACCTTT
AAATTTTTTGGCGATGATTTATATATTTTTTATAAGTATTTTGGCCAAAATTGAGGAAAAATCAT
TCGGGTCAATTTTTGCAAAATAATGACCGAAATCGTGTGCTCCATCACAATTTTCAGCTAAAAAC
GCGTTCCGGAGCCCCGGCTCAGTTTTGTATGATTTTTGGCGCCAAGACTCCTTGGAATATCTATA
TTCATCTACCCAAATCTCAGACACATAAGATTTAAAGAATTCTTTTCACGAGCATCAAAATCCAA
TTTC

Found at i:2261 original size:2 final size:2

Alignment explanation


    Indices: 2254--2330  Score: 154
    Period size: 2  Copynumber: 38.5  Consensus size: 2

       2244 GAATCTTGGT

                                                                          
       2254 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
          1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA

                                                                
       2296 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
          1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G


Statistics
Matches: 75,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   75  1.00

ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00


Consensus pattern (2 bp):   
GA

Done.