Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017682.1 Corchorus olitorius cultivar O-4 contig17715, 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, 858

Length: 1431
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33


Found at i:1227 original size:317 final size:315

Alignment explanation


    Indices: 698--1271  Score: 789
    Period size: 317  Copynumber: 1.8  Consensus size: 315

        688 TGCAATGTGC

                                                         * *                 
        698 CTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCAACGCCAAAAATCATGCAAAACT
          1 CTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCAACACAAAAAATCATGCAAAACT

               *        *     *                                **            
        763 GAGTCAGGGCCCGAAACATGTTTTTAGCAAAAAACCGTGATTAGTACACGATTTCGGCTAAAATT
         66 GAGACAGGGCCCCAAACACGTTTTTAGCAAAAAACCGTGATTAGTACACGAAATCGGCTAAAATT

                    *              *                                         
        828 TTGCAAAAGATTATCAGAAAAATTTTTCCTCAATTTTTAACCACAATACTCATAAAAAATATATA
        131 TTGCAAAAAATTATCAGAAAAATATTTCCTCAATTTTTAACCACAATACTCATAAAAAATATATA

                 *  * *                                                      
        893 ATTCATCGTCGAAAAGATTGAAGGGCTTTTCACG-CTTCTAATA-TCGTTTTTCCTATTTTTTCT
        196 ATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGTCTTCTAATATTCGTTTTT-CTATTTTTTCT

                                                                    
        956 GAATTAATTTCTAATTAAAACGAAACATGATTCAGATTTTTGTAAAAAAAAAATGG
        260 GAATTAATTTCTAATTAAAACGAAACATGATTCAGATTTTTGTAAAAAAAAAATGG

                      *                       *    *  **             *     * 
       1012 CTGAGATTTGGTTAGATGAAT-TAGATATTTCAATGAGTTTCGGCACAAAAAATCATTCAAAATT
          1 CTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCAACACAAAAAATCATGCAAAACT

                 *            *                            *     *           
       1076 GA-ACCGGGCCCCAGAACGCGTTTTTAGCAAAAAACCGTGAAGATTATTACACTAAATCGGCTAA
         66 GAGACAGGGCCCCA-AACACGTTTTTAGCAAAAAACCGT---GATTAGTACACGAAATCGGCTAA

                                *                *       *   *          *    
       1140 AATTTTGCAAAAAATTGA-CTGAAAAGATATTTCCTCGATTTTTAGCCATAATACTCATAGAAAA
        127 AATTTTGCAAAAAATT-ATCAGAAAA-ATATTTCCTCAATTTTTAACCACAATACTCATAAAAAA

                                                        *                    
       1204 TATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGTCTTTTAATATTCGTTTTTCTATTT
        190 TATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGTCTTCTAATATTCGTTTTTCTATTT

               
       1269 TTT
        255 TTT

       1272 TTCTAAATTA


Statistics
Matches: 223,  Mismatches: 29, Indels: 12
        0.84            0.11        0.05

Matches are distributed among these distances:
 312    8  0.04
 313   59  0.26
 314   20  0.09
 316   40  0.18
 317   71  0.32
 318   17  0.08
 319    8  0.04

ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33


Consensus pattern (315 bp):   
CTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCAACACAAAAAATCATGCAAAACT
GAGACAGGGCCCCAAACACGTTTTTAGCAAAAAACCGTGATTAGTACACGAAATCGGCTAAAATT
TTGCAAAAAATTATCAGAAAAATATTTCCTCAATTTTTAACCACAATACTCATAAAAAATATATA
ATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGTCTTCTAATATTCGTTTTTCTATTTTTTCTG
AATTAATTTCTAATTAAAACGAAACATGATTCAGATTTTTGTAAAAAAAAAATGG
Done.