Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024388.1 Corchorus olitorius cultivar O-4 contig24421, 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: 29666
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.28


Found at i:1136 original size:22 final size:23

Alignment explanation


    Indices: 1110--1162  Score: 56
    Period size: 22  Copynumber: 2.4  Consensus size: 23

       1100 ATTGATTGAG

                               *   
       1110 AAAATTGGAAA-AATGTAGGAAT
          1 AAAATTGGAAATAATGTAGAAAT

            *     *      *         
       1132 TAAA-TAGAAATAGTGTAGAAAT
          1 AAAATTGGAAATAATGTAGAAAT

                     
       1154 AAAATTGGA
          1 AAAATTGGA

       1163 CTTATTCATG


Statistics
Matches: 23,  Mismatches: 6, Indels: 3
        0.72            0.19        0.09

Matches are distributed among these distances:
  21    5  0.22
  22   15  0.65
  23    3  0.13

ACGTcount: A:0.55, C:0.00, G:0.21, T:0.25


Consensus pattern (23 bp):   
AAAATTGGAAATAATGTAGAAAT

Found at i:14824 original size:132 final size:130

Alignment explanation


    Indices: 14589--14840  Score: 450
    Period size: 132  Copynumber: 1.9  Consensus size: 130

      14579 ATAGCAGAAG

                                               *                             
      14589 AACACTTATTTATTATATTTATTCAATGCACCAACTAGAAAACTTAACAGCTTCTGCTATACAAG
          1 AACACTTATTTATTATATTTATTCAATGCACCAACCAGAAAACTTAACAGCTTCTGCTATACAAG

                                                                             
      14654 CGAGAGCAAAAACATGAAAGGGAAGTCATACCTATCAGCAAAAGCTGCTCGCAAGCGAGAGCAAA
         66 CGAGAGCAAAAACATGAAAGGGAAGTCATACCTATCAGCAAAAGCTGCTCGCAAGCGAGAGCAAA

                                                   *                    *    
      14719 AACACTTATTTATTATATTTATTCAATGCACCAACAACATAAAACTTAACAGCTTCTGCTTTACA
          1 AACACTTATTTATTATATTTATTCAATGCACCAAC--CAGAAAACTTAACAGCTTCTGCTATACA

              *                                                      
      14784 AGTGAGAGCAAAAACATGAAAGGGAAGTCATACCTATCAGCAAAAGCTGCTCGCAAG
         64 AGCGAGAGCAAAAACATGAAAGGGAAGTCATACCTATCAGCAAAAGCTGCTCGCAAG

      14841 GCAGCCACAA


Statistics
Matches: 116,  Mismatches: 4, Indels: 2
        0.95            0.03        0.02

Matches are distributed among these distances:
 130   35  0.30
 132   81  0.70

ACGTcount: A:0.40, C:0.21, G:0.15, T:0.24


Consensus pattern (130 bp):   
AACACTTATTTATTATATTTATTCAATGCACCAACCAGAAAACTTAACAGCTTCTGCTATACAAG
CGAGAGCAAAAACATGAAAGGGAAGTCATACCTATCAGCAAAAGCTGCTCGCAAGCGAGAGCAAA

Found at i:26656 original size:30 final size:30

Alignment explanation


    Indices: 26595--26674  Score: 92
    Period size: 30  Copynumber: 2.7  Consensus size: 30

      26585 GCTAAATACC

                            *              
      26595 CAAAA-AATCCCTTATATTTTGCTTTTAGGA
          1 CAAAATAATCCCTTATGTTTT-CTTTTAGGA

                                       *   
      26625 CAAAATAATCCCTTATGTTTT-TTTTCGGGA
          1 CAAAATAATCCCTTATGTTTTCTTTT-AGGA

                *          *    
      26655 CAAATTAATCCCTTACGTTT
          1 CAAAATAATCCCTTATGTTT

      26675 CAAAAATGAG


Statistics
Matches: 44,  Mismatches: 4, Indels: 4
        0.85            0.08        0.08

Matches are distributed among these distances:
  29    4  0.09
  30   26  0.59
  31   14  0.32

ACGTcount: A:0.30, C:0.19, G:0.10, T:0.41


Consensus pattern (30 bp):   
CAAAATAATCCCTTATGTTTTCTTTTAGGA

Found at i:26827 original size:31 final size:31

Alignment explanation


    Indices: 26792--26888  Score: 158
    Period size: 31  Copynumber: 3.1  Consensus size: 31

      26782 AAGGGACTGA

                                           
      26792 TTTGTCCCAAAAGAAAAATATAAGGGATTTT
          1 TTTGTCCCAAAAGAAAAATATAAGGGATTTT

                              *        *   
      26823 TTTGTCCCAAAAGAAAAACATAAGGGAGTTT
          1 TTTGTCCCAAAAGAAAAATATAAGGGATTTT

                                      *     
      26854 TTTGTCCCAAAAGAAAAATATAAGAGAATTTT
          1 TTTGTCCCAAAAGAAAAATATAAG-GGATTTT

               
      26886 TTT
          1 TTT

      26889 AATATTTAGT


Statistics
Matches: 60,  Mismatches: 5, Indels: 1
        0.91            0.08        0.02

Matches are distributed among these distances:
  31   52  0.87
  32    8  0.13

ACGTcount: A:0.42, C:0.10, G:0.15, T:0.32


Consensus pattern (31 bp):   
TTTGTCCCAAAAGAAAAATATAAGGGATTTT

Found at i:27658 original size:50 final size:50

Alignment explanation


    Indices: 27600--27694  Score: 172
    Period size: 50  Copynumber: 1.9  Consensus size: 50

      27590 TTTATAACTA

                                         *          *         
      27600 TTTTATTTTTACCATTTTACTATTTTAATTAAATATATTTTTTAATATAC
          1 TTTTATTTTTACCATTTTACTATTTTAATAAAATATATTTCTTAATATAC

                                                         
      27650 TTTTATTTTTACCATTTTACTATTTTAATAAAATATATTTCTTAA
          1 TTTTATTTTTACCATTTTACTATTTTAATAAAATATATTTCTTAA

      27695 ATGACATTAT


Statistics
Matches: 43,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  50   43  1.00

ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59


Consensus pattern (50 bp):   
TTTTATTTTTACCATTTTACTATTTTAATAAAATATATTTCTTAATATAC

Found at i:27977 original size:22 final size:24

Alignment explanation


    Indices: 27942--28000  Score: 61
    Period size: 22  Copynumber: 2.5  Consensus size: 24

      27932 ATAAATGTTG

                            *      *
      27942 CTGATAA-TCTTCT-CTTTTATCT
          1 CTGATAATTCTTCTCCATTTATCA

                                    
      27964 CTGATAATTC-TCTCCATTTATCA
          1 CTGATAATTCTTCTCCATTTATCA

                          
      27987 CTTGATAATATCTT
          1 C-TGATAAT-TCTT

      28001 GCCAGATAAA


Statistics
Matches: 30,  Mismatches: 2, Indels: 6
        0.79            0.05        0.16

Matches are distributed among these distances:
  22   10  0.33
  23   10  0.33
  24    7  0.23
  25    2  0.07
  26    1  0.03

ACGTcount: A:0.24, C:0.22, G:0.05, T:0.49


Consensus pattern (24 bp):   
CTGATAATTCTTCTCCATTTATCA
Done.