Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013903.1 Corchorus olitorius cultivar O-4 contig13936, 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, 711

Length: 1186
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.25


Found at i:340 original size:154 final size:155

Alignment explanation


    Indices: 12--763  Score: 1117
    Period size: 154  Copynumber: 4.9  Consensus size: 155

          2 TTTAAAACGG

                            *                       *  *                     
         12 ACTAATGGGCCCCCGAAAGGCCCAAAATTAACAAGTGTTCGAATTGAAGCTAAAAACTTCACAGT
          1 ACTAATGGG-CCCCGATAGGCCCAAAA-TAACAAGTGTTCCAAATG-AGCTAAAAACTTCACAGT

                       *                      *                              
         77 GGACTAATCTCCCCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG-AATTGAGGTT
         63 GGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAACAATGGAAAGAAAAGCAATTGAGGTT

                                        
        141 TGCCAAATCGAAGACGATTCAAAACGTC
        128 TGCCAAATCGAAGACGATTCAAAACGTC

             * *        *                                                    
        169 ATTGATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
          1 ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA

                        *                *    *                              
        234 CTAATCTCACCATAATGATTATAGTTAGGTCGTACACAATGGAAAGAAAAGCAA-TGAGGTTTGC
         66 CTAATCTCACCAAAATGATTATAGTTAGGCCGTAAACAATGGAAAGAAAAGCAATTGAGGTTTGC

                        *            
        298 CAAATCGAAGACAATTCAAAACGTC
        131 CAAATCGAAGACGATTCAAAACGTC

                 *  *                  *         **                          
        323 ACTAAAGGTCCCCGATAGGCCCAAAATGACAAGTGTTTTAAATGAGCTAAAAACTTCACAGTGGA
          1 ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA

                   * *              *      *         *                       
        388 CTAATCTTATCAAAATGATTATAGATAGGCCATAAACAATGAAAAGAAAAG-AATTGAGGTTTGC
         66 CTAATCTCACCAAAATGATTATAGTTAGGCCGTAAACAATGGAAAGAAAAGCAATTGAGGTTTGC

                                     
        452 CAAATCGAAGACGATTCAAAACGTC
        131 CAAATCGAAGACGATTCAAAACGTC

             * *                                                             
        477 ATTGATGGGCCCTC-ATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
          1 ACTAATGGGCCC-CGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG

                                          *    *                             
        541 ACTAATCTCACCAAAATGATTATAGTTAGGTCGTACACAATGGAAAGAAAAGC-ATTGAGGTTTG
         65 ACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAACAATGGAAAGAAAAGCAATTGAGGTTTG

                                      
        605 CCAAATCGAAGACGATTCAAAACGTC
        130 CCAAATCGAAGACGATTCAAAACGTC

                    *                        *           *                   
        631 ACTAATGGTCCCCGATAGGCCCAAAATAACAAGCGTTCCAAATGAACTAAAAAC-TCACAGTGGA
          1 ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA

                                                                          *  
        695 CTAATCTCACCAAAATGATTATAGTTAGG-CGATAAACAATGGAAAGAAAAGC-ATTG-GGAATT
         66 CTAATCTCACCAAAATGATTATAGTTAGGCCG-TAAACAATGGAAAGAAAAGCAATTGAGG-TTT

                   
        757 GCCAAAT
        129 GCCAAAT

        764 TGATGCGCCA


Statistics
Matches: 538,  Mismatches: 50, Indels: 18
        0.89            0.08        0.03

Matches are distributed among these distances:
 152    4  0.01
 153   74  0.14
 154  419  0.78
 155   19  0.04
 156   15  0.03
 157    7  0.01

ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22


Consensus pattern (155 bp):   
ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
CTAATCTCACCAAAATGATTATAGTTAGGCCGTAAACAATGGAAAGAAAAGCAATTGAGGTTTGC
CAAATCGAAGACGATTCAAAACGTC

Found at i:617 original size:308 final size:308

Alignment explanation


    Indices: 22--763  Score: 1254
    Period size: 308  Copynumber: 2.4  Consensus size: 308

         12 ACTAATGGGC

                  *                       *  *                               
         22 CCCCGAAAGGCCCAAAATTAACAAGTGTTCGAATTGAAGCTAAAAACTTCACAGTGGACTAATCT
          1 CCCCGATAGGCCCAAAA-TAACAAGTGTTCCAAATG-AGCTAAAAACTTCACAGTGGACTAATCT

             *                                                               
         87 CCCCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGAATTGAGGTTTGCCAAATCGA
         64 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGAATTGAGGTTTGCCAAATCGA

                                          *                                  
        152 AGACGATTCAAAACGTCATTGATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT
        129 AGACGATTCAAAACGTCATTGATGGGCCCTCATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT

                                         *                                   
        217 AAAAACTTCACAGTGGACTAATCTCACCATAATGATTATAGTTAGGTCGTACACAATGGAAAGAA
        194 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGTCGTACACAATGGAAAGAA

                                                              
        282 AAGCAATGAGGTTTGCCAAATCGAAGACAATTCAAAACGTCACTAAAGGT
        259 AAGCAATGAGGTTTGCCAAATCGAAGACAATTCAAAACGTCACTAAAGGT

                              *         **                                 * 
        332 CCCCGATAGGCCCAAAATGACAAGTGTTTTAAATGAGCTAAAAACTTCACAGTGGACTAATCTTA
          1 CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA

            *              *                *                                
        397 TCAAAATGATTATAGATAGGCCATAAACAATGAAAAGAAAAGAATTGAGGTTTGCCAAATCGAAG
         66 CCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGAATTGAGGTTTGCCAAATCGAAG

                                                                             
        462 ACGATTCAAAACGTCATTGATGGGCCCTCATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
        131 ACGATTCAAAACGTCATTGATGGGCCCTCATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA

                                                                             
        527 AAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGTCGTACACAATGGAAAGAAAA
        196 AAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGTCGTACACAATGGAAAGAAAA

               *                      *                 *   
        592 GCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGT
        261 GCAATGAGGTTTGCCAAATCGAAGACAATTCAAAACGTCACTAAAGGT

                                    *           *                            
        640 CCCCGATAGGCCCAAAATAACAAGCGTTCCAAATGAACTAAAAAC-TCACAGTGGACTAATCTCA
          1 CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA

                                 *                    *        *         
        704 CCAAAATGATTATAGTTAGGCGATAAACAATGGAAAGAAAAGCATTG-GGAATTGCCAAAT
         66 CCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGAATTGAGG-TTTGCCAAAT

        764 TGATGCGCCA


Statistics
Matches: 404,  Mismatches: 27, Indels: 5
        0.93            0.06        0.01

Matches are distributed among these distances:
 306    2  0.00
 307   69  0.17
 308  303  0.75
 309   14  0.03
 310   16  0.04

ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22


Consensus pattern (308 bp):   
CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA
CCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGAATTGAGGTTTGCCAAATCGAAG
ACGATTCAAAACGTCATTGATGGGCCCTCATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
AAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGTCGTACACAATGGAAAGAAAA
GCAATGAGGTTTGCCAAATCGAAGACAATTCAAAACGTCACTAAAGGT
Done.