Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01003470.1 Corchorus olitorius cultivar O-4 contig03478, 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, 614

Length: 1024
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.32


Found at i:624 original size:334 final size:331

Alignment explanation


    Indices: 1--911  Score: 1206
    Period size: 334  Copynumber: 2.7  Consensus size: 331

                                  **         *                       *       
          1 GGAACGCGTTTTTAGCCAAAAATTGTGATGGTTTGTACACGATTTCATCTAAAACTTCGCAAAAA
          1 GGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCATCTAAAA-TTTGCAAAAA

               *  *             *    *                        *              
         66 AATTACACGAAAAA-TTTTCGTCAATTTTTGACCACAATTCTCATAAAGATATATATAATTCAAC
         65 AATGACCCGAAAAATTTTTCCTCAAATTTTGACCACAATTCTCAT-AAGAAATATATAATTCAAC

                                                       *                     
        130 GCCAAAAAGATTGAAGGGATTTTCAAGTATCTAATATCGTTTTTCATTTTTTTTCTAAATTAATT
        129 GCCAAAAAGATTGAAGGGATTTTCAAGTATCTAATATCGTTTTCCATTTTTTTTCTAAATTAATT

                   *                                **               *    *  
        195 TCTAATTGAATCGAAACAAGATTCAAATGCTCGTAAAAACTGATCCTTAAGTCCAATTTGGCTGA
        194 TCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAGTCCAATGTGGCCGA

                                *  *        *  *    *                        
        260 GATTTGGTTAGATGAATATATATGTTTCAAGGGGTTTGGGTGCCAAAAATCAAGCAAAACTAAGT
        259 GATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGCCAAAAATCAAGCAAAACTAAG-

             *       
        325 TGGGGCCCC
        323 TCGGGCCCC

                 *       *                            *   *                  
        334 GGAACACGTTTTTGGCCAAAAACCGTGATGGTTAGTACACGGTTTTGA-CTAAACA-TTGCAAAA
          1 GGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACAC-GATTTCATCTAAA-ATTTGCAAAA

                                            *       *      *       *   *     
        397 AAA-GACCCGAAAAATTTTTCCTCAAATTTTGTCCACAATACTCATATGAAATATGTAACTCAAC
         64 AAATGACCCGAAAAATTTTTCCTCAAATTTTGACCACAATTCTCATAAGAAATATATAATTCAAC

                        *  *  *        *                               *     
        461 GCCAAAAAGATTCAAAGGCTTTTCAAGCATCTAATATCGCTTTTCCTATTTTCTTTTCTGAATTA
        129 GCCAAAAAGATTGAAGGGATTTTCAAGTATCTAATATCG-TTTTCC-ATTTT-TTTTCTAAATTA

                  *        *             *            *           *          
        526 ATTTCTGATTAAATCCAAACATA-ATTCAGATGCTCGTAAAATCAAATCCTTAATTCCAATGTGG
        191 ATTTCTAATTAAATCGAAACA-AGATTCAAATGCTCGTAAAAACAAATCCTTAAGTCCAATGTGG

                                                           *                 
        590 CCGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGCTAAAAATCAAGCAAAACT
        255 CCGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGCCAAAAATCAAGCAAAACT

            *      *    
        655 GAGTCGGTCCCC
        320 AAGTCGGGCCCC

                     *                   *                                   
        667 GGAACGCGTATTTAGCCAAAAACCGTGATTGTTAGTACACGATTTCATCTAAAATTTTGCAAAAA
          1 GGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCATCTAAAA-TTTGCAAAAA

                         *                                 *                 
        732 AATGACCCGAAAATTTTTTCCTCAAATTTTGACCACAATTCTCATAAAAATATATATAATTCAAC
         65 AATGACCCGAAAAATTTTTCCTCAAATTTTGACCACAATTCTCATAAGAA-ATATATAATTCAAC

                    *                     *             *                    
        797 GCCAAAAAAATTGAAGGGATTTTCAAGTATATAATATCGTTTTTGCATTTTTTTTCTAAATTAAT
        129 GCCAAAAAGATTGAAGGGATTTTCAAGTATCTAATATCG-TTTTCCATTTTTTTTCTAAATTAAT

                                                                
        862 TTCTAATTAAATCGAAACAAGATTCAAATGCTCG-AAAAGA-AAATCCTTAA
        193 TTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAA-ACAAATCCTTAA

        912 ATACAACATG


Statistics
Matches: 495,  Mismatches: 69, Indels: 28
        0.84            0.12        0.05

Matches are distributed among these distances:
 331   59  0.12
 332   47  0.09
 333  108  0.22
 334  183  0.37
 335   48  0.10
 336   50  0.10

ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32


Consensus pattern (331 bp):   
GGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCATCTAAAATTTGCAAAAAA
ATGACCCGAAAAATTTTTCCTCAAATTTTGACCACAATTCTCATAAGAAATATATAATTCAACGC
CAAAAAGATTGAAGGGATTTTCAAGTATCTAATATCGTTTTCCATTTTTTTTCTAAATTAATTTC
TAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAGTCCAATGTGGCCGAGA
TTTGGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGCCAAAAATCAAGCAAAACTAAGTCG
GGCCCC
Done.