Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008498.1 Corchorus olitorius cultivar O-4 contig08525, 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, 927

Length: 1546
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37


Found at i:953 original size:332 final size:331

Alignment explanation


    Indices: 1--1421  Score: 1478
    Period size: 332  Copynumber: 4.3  Consensus size: 331

                                                    *         *              
          1 AAAACAATATTAGAAGCGTT-AAAACCCTTCAATCTTTTTGATGTCGAATCATATATTTTTTATG
          1 AAAACAATATTAGAAGCGTTAAAAACCCTTCAATCTTTTTTATGTCGAATTATATATTTTTTATG

                  *              *           *             *                 
         65 AGTATTGTAGCCAAAATTGAGGAAATATATTTCAGGTCAATTTTTGCCAAATTTTAACCGAAATC
         66 AGTATTTTAGCCAAAATTGAGAAAATATATTTCGGGTCAATTTTTGCAAAATTTTAACCGAAATC

            *                     *                     *        *           
        130 GTG---T-ACCATCACGGTTTTTGGCTAAAAACGCATTCCAGGGTCACAGCTCTGTTTTGCATGA
        131 ATGAACTAACCATCACGGTTTTCGGCTAAAAACGCATTCCAGGGCCACAGCTCAGTTTTGCATGA

                            *             *                *     *      **   
        191 TTTTTGGCACCGAGACACCTTGAAATATCTTTATTCATCTAATCAAACCTCAGGCACATTGGATT
        196 TTTTTGGCACCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTAAATT

             *              *                                 *              
        256 TTA--ATTT-TTTTTATGTGAATCTGAATCTTGTTTCGATTCAATTAGAAGTTAATTCAT-AAAA
        261 TAAGGATTTGTTTTTACGTGAATCTGAATCTTGTTTCGATTCAATTAGAAATTAATTC-TGAAAA

                *  
        317 AATATGA
        325 AATAGGA

                **      *            ***  *            **                    
        324 AAAATGATATTAAAAGC-TTGAAAAGTTCTCCAAATACTTTTGGCA-GT-GAATTATAGT-TTTT
          1 AAAACAATATTAGAAGCGTT-AAAAACCCTTC-AAT-CTTTT-TTATGTCGAATTATA-TATTTT

                  *        *  *      **      *                              *
        385 TTAATAAAGTATTTTTGCTAGAAATCAAGAAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAG
         61 TT-AT-GAGTATTTTAGCCA-AAATTGAGAAAATATATTTCGGGTCAATTTTTGCAAAATTTTAA

                       *                            *   *            *       
        450 CCGAAATCATGTACTTAA-CATCACGGTTTTCGGCTAAAACCGCGTTCCAGGGCC-CGGCTCAGT
        123 CCGAAATCATGAAC-TAACCATCACGGTTTTCGGCTAAAAACGCATTCCAGGGCCACAGCTCAGT

                 *               *                        *      *           
        513 TTTGCTTGATTTTTTGTGC-CAG-GACTCCTTGAAATATCTATATTTATCTAACCAAATCTCAGC
        187 TTTGCATGA-TTTTTG-GCACCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGC

                                          *                      *           
        576 CACATTAAATTTAAGGATTTGTTTTTACG-AACATCTGAATCTTGTTTCGATTTAATTAGAAATT
        250 CACATTAAATTTAAGGATTTGTTTTTACGTGA-ATCTGAATCTTGTTTCGATTCAATTAGAAATT

                              
        640 AATT-TGAAAAAATAGGA
        314 AATTCTGAAAAAATAGGA

                                    *                     *                  
        657 AAAACAATATTAGAAGCGTTAAAAGCCCTTCAATCTTTTTTATGTCAAATTATATAATTTTTTAT
          1 AAAACAATATTAGAAGCGTTAAAAACCCTTCAATCTTTTTTATGTCGAATTATAT-ATTTTTTAT

                                          *                   *              
        722 GAGTATTTTAGCCAATAATTGAGAAAATATGTTTCGGGTCAATTTTTGCATAATTTTAACCGAAA
         65 GAGTATTTTAGCCAA-AATTGAGAAAATATATTTCGGGTCAATTTTTGCAAAATTTTAACCGAAA

              *         *           *                                        
        787 TCTTGAACTAACTATCACGGTTTTTGGCTAAAAACGCGA-TCCAGGGCCACAGCT-ATGTTTTGC
        129 TCATGAACTAACCATCACGGTTTTCGGCTAAAAACGC-ATTCCAGGGCCACAGCTCA-GTTTTGC

                          *    *           *  *                      *      *
        850 ATGATTTTTGGCACTGAGATTCCTTGAAATAGCTTTATTCATCTAATCAAATCTCAGGCACATTG
        192 ATGATTTTTGGCACCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTA

            *             *     *                                *        *  
        915 GATTTAAGGATTTGCTTTTATGTGAATCTGAATCTTGTTTCGATTCAATTAGATATTAATTCAGA
        257 AATTTAAGGATTTGTTTTTACGTGAATCTGAATCTTGTTTCGATTCAATTAGAAATTAATTCTGA

                   *  
        980 AAAAATATGA
        322 AAAAATAGGA

                 *      *  *   *     **  *          ** *              *      
        990 AAAACGATATTAAAAACGTGAAAAATTCTCCAATCCTTTTGAAAGT-GAATTATAGT-GTTTTTA
          1 AAAACAATATTAGAAGCGTTAAAAACCCTTCAAT-CTTTTTTATGTCGAATTATA-TATTTTTTA

                      *  *      *                             *         *    
       1053 TGAGTATTTTCGCTAGAAATCGAAGAAAA-ATATTTCGGGTCAATTTTTGGAAAATTTTAGCCGA
         64 TGAGTATTTTAGCCA-AAATTG-AGAAAATATATTTCGGGTCAATTTTTGCAAAATTTTAACCGA

                                         **     *             *              
       1117 AATCAT-ATACTAACCATCACGGTTTTCGAATAAAACCGCATTCCAGGG-AACA-CTCAGTTTTG
        127 AATCATGA-ACTAACCATCACGGTTTTCGGCTAAAAACGCATTCCAGGGCCACAGCTCAGTTTTG

             *          **  *                             *    *             
       1179 CTTG-TTTTTGGTGCCAAGACTCCTTGAAATATCTATATTCATCTATTCAATTCTCAGCCACATT
        191 CATGATTTTTGGCACCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATT

                                   * *    *               *                  
       1243 AAATTTAAGGATTTGTTTTTACGGGCATCTAAATCTTGTTTCGATTTAATTAGAAAATTAATT-T
        256 AAATTTAAGGATTTGTTTTTACGTGAATCTGAATCTTGTTTCGATTCAATTAG-AAATTAATTCT

             *          
       1307 GGAAAAATAGGA
        320 GAAAAAATAGGA

                                                                   *  *   *  
       1319 AAAACAATATTTAGAAGCGTTAAAAACCCTTCAATCTTTTTTATGTCGAATTATACATCTTTAAT
          1 AAAACAATA-TTAGAAGCGTTAAAAACCCTTCAATCTTTTTTATGTCGAATTATATATTTTTTA-

                        *            *      *     
       1384 TGAGTATTTTATCCCAAAAATTGAGGAAATATGTTTCG
         64 TGAGTATTTTA-GCC-AAAATTGAGAAAATATATTTCG

       1422 CATGATTTTG


Statistics
Matches: 892,  Mismatches: 156, Indels: 91
        0.78            0.14        0.08

Matches are distributed among these distances:
 322    2  0.00
 323   14  0.02
 324    6  0.01
 325   16  0.02
 326   10  0.01
 327   11  0.01
 328   47  0.05
 329  121  0.14
 330   57  0.06
 331  190  0.21
 332  267  0.30
 333   99  0.11
 334   52  0.06

ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37


Consensus pattern (331 bp):   
AAAACAATATTAGAAGCGTTAAAAACCCTTCAATCTTTTTTATGTCGAATTATATATTTTTTATG
AGTATTTTAGCCAAAATTGAGAAAATATATTTCGGGTCAATTTTTGCAAAATTTTAACCGAAATC
ATGAACTAACCATCACGGTTTTCGGCTAAAAACGCATTCCAGGGCCACAGCTCAGTTTTGCATGA
TTTTTGGCACCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTAAATT
TAAGGATTTGTTTTTACGTGAATCTGAATCTTGTTTCGATTCAATTAGAAATTAATTCTGAAAAA
ATAGGA
Done.