Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011496.1 Corchorus olitorius cultivar O-4 contig11529, 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: 2016
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25


Found at i:314 original size:154 final size:154

Alignment explanation


    Indices: 1--1286  Score: 1930
    Period size: 154  Copynumber: 8.4  Consensus size: 154

                                  *                             *  *         
          1 CAAAAT-ACAAGTGTTCCAAATTAGCTAAAAACTTCACAGTGGACTAATCTCGCTAAAAATGATT
          1 CAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCAC-CAAAATGATT

                                                   *               *         
         65 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCAT-----TTTGCCAAATCGAAGATGATTCAAAA
         65 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGATTGCCAAATCGAAGACGATTCAAAA

              **            *  *    *
        125 CGTCACTAATGGGCCCTGATAGGCC
        130 CGGAACTAATGGGCCCCGAAAGGCA

                                                                             
        150 CAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA
          1 CAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA

                                            *                          *     
        215 TAGTTAGGCCATAAACAATGGAAAGAAAAGCAACGAGGATTGCCAAATCGAAGACGATTGAAAAC
         66 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGATTGCCAAATCGAAGACGATTCAAAAC

                                    
        280 GGAACTAATGGGCCCCGAAAGGCA
        131 GGAACTAATGGGCCCCGAAAGGCA

                                                                  *          
        304 CAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTA
          1 CAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA

                        *  *                 *    *                          
        369 TAGTTAGGCCATGAAGAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC
         66 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGATTGCCAAATCGAAGACGATTCAAAAC

            ***            *  *      
        434 TTCACTAATGGGCCCTGATAGGTC-
        131 GGAACTAATGGGCCCCGAAAGG-CA

                                    *          *                             
        458 CAAAATAACAAGTGTTCCAAATGAACTAAAAACTTTACAGTGGACTAATCTCACCAAAATGATTA
          1 CAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA

                    *                        *    *                          
        523 TAGTTAGGGCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC
         66 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGATTGCCAAATCGAAGACGATTCAAAAC

             **            *  *    *
        588 GTCACTAATGGGCCCTGATAGGCC
        131 GGAACTAATGGGCCCCGAAAGGCA

                                    *          *                  *          
        612 CAAAATAACAAGTGTTCCAAATGAACTAAAAACTTTACAGTGGACTAATCTCACAAAAATGATTA
          1 CAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA

                                                  *                          
        677 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAAAC
         66 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGATTGCCAAATCGAAGACGATTCAAAAC

                                    
        742 GGAACTAATGGGCCCCGAAAGGCA
        131 GGAACTAATGGGCCCCGAAAGGCA

                                                                             
        766 CAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA
          1 CAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA

                                        *                                    
        831 TAGTTAGGCCATAAACAATGGAAAGAAAGGCATCGAGGATTGCCAAATCGAAGACGATTCAAAAC
         66 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGATTGCCAAATCGAAGACGATTCAAAAC

                                *   
        896 GGAACTAATGGGCCCCGAAATGCA
        131 GGAACTAATGGGCCCCGAAAGGCA

                                                               *  *          
        920 CAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTGACTAAAATGATTA
          1 CAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA

                                                  *                          
        985 TAGTTAGGCCATAAACAATGGAAAGAAAAGCAT-GCA-AATTTGCCAAATCGAAGACGATTCAAA
         66 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATCG-AGGA-TTGCCAAATCGAAGACGATTCAAA

                *      *      *  *      
       1048 A-GAAAACTAAAGGGCCCTGATAGGTC-
        129 ACG-GAACTAATGGGCCCCGAAAGG-CA

                                    *          *                             
       1074 CAAAATAACAAGTGTTCCAAATGAACTAAAAACTTTACAGTGGACTAATCTCACCAAAATGATTA
          1 CAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA

                    *                             *                    *    *
       1139 TAGTTAGGGCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTTAAAAT
         66 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGATTGCCAAATCGAAGACGATTCAAAAC

                               *    
       1204 GGAACTAATGGGCCCCGAATGGCA
        131 GGAACTAATGGGCCCCGAAAGGCA

                              *      *                             *    
       1228 CAAAATAACAAAGTGTTCGAAATGAAC-AAAAACTTCACAGTGGACTAATCTCACTAAAA
          1 CAAAATAAC-AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAA

       1287 GGTGATGCGC


Statistics
Matches: 1049,  Mismatches: 71, Indels: 29
        0.91            0.06        0.03

Matches are distributed among these distances:
 149   48  0.05
 150   45  0.04
 153    5  0.00
 154  931  0.89
 155   20  0.02

ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21


Consensus pattern (154 bp):   
CAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA
TAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGATTGCCAAATCGAAGACGATTCAAAAC
GGAACTAATGGGCCCCGAAAGGCA

Found at i:1423 original size:21 final size:21

Alignment explanation


    Indices: 1395--1486  Score: 123
    Period size: 21  Copynumber: 4.4  Consensus size: 21

       1385 TGCTAGAAGT

                                  
       1395 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

             *       *          *
       1416 TAATTGGAGCAGGTTCCAAGT
          1 TCATTGGAGAAGGTTCCAAGC

                                *
       1437 TCATTGGAGAAGGTTCCAAGT
          1 TCATTGGAGAAGGTTCCAAGC

                           *     
       1458 TCATTGGAGAAGGTTTCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                    
       1479 TCATTGGA
          1 TCATTGGA

       1487 AATGCCTAAG


Statistics
Matches: 63,  Mismatches: 7, Indels: 2
        0.88            0.10        0.03

Matches are distributed among these distances:
  20    1  0.02
  21   62  0.98

ACGTcount: A:0.28, C:0.16, G:0.27, T:0.28


Consensus pattern (21 bp):   
TCATTGGAGAAGGTTCCAAGC

Done.