Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012045.1 Corchorus olitorius cultivar O-4 contig12078, 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: 9825
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29


Found at i:7977 original size:33 final size:36

Alignment explanation


    Indices: 7900--7981  Score: 100
    Period size: 33  Copynumber: 2.4  Consensus size: 36

       7890 GTGGTCTTTT

                                     *       *  
       7900 TAATGATGTTGGGTTAGGGTTATGTGATGGTATTTA
          1 TAATGATGTTGGGTTAGGGTTATGTCATGGTATATA

               *                                 
       7936 TAAGGATGTTGGGTTAGGG-T-T-TCACT-GTATATA
          1 TAATGATGTTGGGTTAGGGTTATGTCA-TGGTATATA

                         
       7969 TAATGATGTTGGG
          1 TAATGATGTTGGG

       7982 GACTTATCTT


Statistics
Matches: 41,  Mismatches: 4, Indels: 5
        0.82            0.08        0.10

Matches are distributed among these distances:
  33   20  0.49
  34    2  0.05
  35    1  0.02
  36   18  0.44

ACGTcount: A:0.23, C:0.02, G:0.33, T:0.41


Consensus pattern (36 bp):   
TAATGATGTTGGGTTAGGGTTATGTCATGGTATATA

Found at i:8686 original size:154 final size:154

Alignment explanation


    Indices: 8394--9822  Score: 2323
    Period size: 154  Copynumber: 9.3  Consensus size: 154

       8384 AAATTCTGGT

                *                       *                                    
       8394 TTAGGCCATAAA-AATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTC
          1 TTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTC

                  *                                                          
       8458 ACTAATAGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
         66 ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA

                                    
       8523 CTAATCTCACCAAAATGATTATAG
        131 CTAATCTCACCAAAATGATTATAG

                                                                             
       8547 TTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTC
          1 TTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTC

                                                          *                  
       8612 ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGA
         66 ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA

                                    
       8677 CTAATCTCACCAAAATGATTATAG
        131 CTAATCTCACCAAAATGATTATAG

                *                *     *            **       *  *            
       8701 TTAGGCCATAAACAATGGAAAAAAAAGAATTGAGGTTTGCTGAATCGAACACAATTCAAAACGTC
          1 TTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTC

                *      *                                   *                 
       8766 ACTAGTGGGCCTCGATAGGCCCAAAATAACAAGTGTT-CAGAATGAGGTAAAAACTTCACAGTGG
         66 ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCA-AATGAGCTAAAAACTTCACAGTGG

                                    *
       8830 ACTAATCTCACCAAAATGATTATAT
        130 ACTAATCTCACCAAAATGATTATAG

                                                                             
       8855 TTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTC
          1 TTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTC

                                           *                                 
       8920 ACTAATGGGCCCCGATAGGCCCAAAATAACATGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
         66 ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA

                               *    
       8985 CTAATCTCACCAAAATGATGATAG
        131 CTAATCTCACCAAAATGATTATAG

              *                                                              
       9009 TTCGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTC
          1 TTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTC

                       *                                    *                
       9074 ACTAATGGGCCACGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTGAAAACTTCACAGTGGA
         66 ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA

            *      *       *        
       9139 ATAATCTTACCAAAAGGATTATAG
        131 CTAATCTCACCAAAATGATTATAG

                           *   *                                    *        
       9163 TTAGTCGC-TAAACAGTGGTAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATCCAAAACGG
          1 TTAGTC-CATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC-G

                * *       *  *                                               
       9227 T-ACGAGTGGGCCCTGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG
         64 TCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG

                     *                
       9291 GACTAATCTGACCAAAATGATTATAG
        129 GACTAATCTCACCAAAATGATTATAG

                * *                                                          
       9317 TTAGGCAATAAACAATGGAAA-AAAAGCATTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGT
          1 TTAGTCCATAAACAATGGAAAGAAAAGCA-TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGT

                                              *                              
       9381 CACTAATGGGCCCCGATAGGCCCAAAATAACAAGGGTTCCAAATGAGCTAAAAACTTCACAGTGG
         65 CACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG

                                     
       9446 ACTAATCTCACCAAAATGATTATAG
        130 ACTAATCTCACCAAAATGATTATAG

                *                     *                        *       * *   
       9471 TTAGGCCATAAACAATGGAAAGAAAAACATTGAGGTTTGCCAAATCGAAGAGGATTCAATATGTC
          1 TTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTC

                                        *                                    
       9536 ACTAATGGGCCCCGATAGGCCCAAAATATCAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
         66 ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA

                                    
       9601 CTAATCTCACCAAAATGATTATAG
        131 CTAATCTCACCAAAATGATTATAG

                   *                  *            *                         
       9625 TTAGTCCCTAAACAATGGAAAGAAAACCATTGAGGTTTGTCAAATCGAAGACGATTCAAAACGTC
          1 TTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTC

                       *                                    *            *   
       9690 ACTAAT-GGCCACGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTGAAAACTTCACAGAGGA
         66 ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA

            *      *       *        
       9754 ATAATCTTACCAAAAGGATTATAG
        131 CTAATCTCACCAAAATGATTATAG

                                                          
       9778 TTAGTCTC-TAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAAT
          1 TTAGTC-CATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAAT

       9823 GCA


Statistics
Matches: 1183,  Mismatches: 83, Indels: 20
        0.92            0.06        0.02

Matches are distributed among these distances:
 153  138  0.12
 154  1034  0.87
 155   11  0.01

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


Consensus pattern (154 bp):   
TTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTC
ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
CTAATCTCACCAAAATGATTATAG

Done.