Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019095.1 Corchorus olitorius cultivar O-4 contig19128, 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: 16477
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.32


Found at i:10546 original size:23 final size:21

Alignment explanation


    Indices: 10511--10553  Score: 59
    Period size: 23  Copynumber: 2.0  Consensus size: 21

      10501 TTTGATTACT

                                 
      10511 ATTTAGCTTGGTTTGTTCGTC
          1 ATTTAGCTTGGTTTGTTCGTC

                            *     
      10532 ATTTGAGCATTGGTTTTTTCGT
          1 ATTT-AGC-TTGGTTTGTTCGT

      10554 TATTCTCACA


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  21    4  0.21
  22    3  0.16
  23   12  0.63

ACGTcount: A:0.12, C:0.12, G:0.23, T:0.53


Consensus pattern (21 bp):   
ATTTAGCTTGGTTTGTTCGTC

Found at i:12763 original size:28 final size:29

Alignment explanation


    Indices: 12690--12764  Score: 75
    Period size: 30  Copynumber: 2.5  Consensus size: 29

      12680 AATTCAGGAC

                              *            
      12690 AAGTTCAAGGGGCAAAATGTCCTGAATTTGG
          1 AAGTTC-A-GGGCAAAATATCCTGAATTTGG

                                           
      12721 AAGTT-ATGAGGCAAAATATCCTG-ATTT-G
          1 AAGTTCA-G-GGCAAAATATCCTGAATTTGG

                            
      12749 AAGTTCAGGGACAAAA
          1 AAGTTCAGGG-CAAAA

      12765 CGTCATTGAC


Statistics
Matches: 39,  Mismatches: 2, Indels: 9
        0.78            0.04        0.18

Matches are distributed among these distances:
  27    2  0.05
  28   12  0.31
  29    7  0.18
  30   13  0.33
  31    5  0.13

ACGTcount: A:0.37, C:0.12, G:0.25, T:0.25


Consensus pattern (29 bp):   
AAGTTCAGGGCAAAATATCCTGAATTTGG

Found at i:14688 original size:19 final size:20

Alignment explanation


    Indices: 14664--14705  Score: 68
    Period size: 20  Copynumber: 2.1  Consensus size: 20

      14654 TGGAATCCCA

                     *          
      14664 ACATGCAA-TTCTTGTGCTC
          1 ACATGCAAGATCTTGTGCTC

                                
      14683 ACATGCAAGATCTTGTGCTC
          1 ACATGCAAGATCTTGTGCTC

               
      14703 ACA
          1 ACA

      14706 AATACTATTC


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  19    8  0.38
  20   13  0.62

ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31


Consensus pattern (20 bp):   
ACATGCAAGATCTTGTGCTC

Found at i:15303 original size:39 final size:40

Alignment explanation


    Indices: 15247--15327  Score: 137
    Period size: 39  Copynumber: 2.0  Consensus size: 40

      15237 TTTAATTCCT

                                                    
      15247 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
          1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA

                     *          *                   
      15287 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
          1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA

              
      15326 AT
          1 AT

      15328 TCTTAGGTAT


Statistics
Matches: 39,  Mismatches: 2, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  39   31  0.79
  40    8  0.21

ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37


Consensus pattern (40 bp):   
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA

Found at i:15802 original size:202 final size:202

Alignment explanation


    Indices: 15437--15845  Score: 741
    Period size: 202  Copynumber: 2.0  Consensus size: 202

      15427 TTCCTTAATA

                                                                             
      15437 ATAAATAAATCAGATCTTAATATCTTTTATAATTTTAAAATTTTTTTGACATTGATCTAATTTAA
          1 ATAAATAAATCAGATCTTAATATCTTTTATAATTTTAAAATTTTTTTGACATTGATCTAATTTAA

                                                                          *  
      15502 TTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATATAATAGTA
         66 TTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATATAATAATA

                                                            *                
      15567 ATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTATAAAATTAATAACATTC
        131 ATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTC

                   
      15632 ACCATTG
        196 ACCATTG

                       *                         *                           
      15639 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
          1 ATAAATAAATCAGATC-TTAATATCTTTTATAATTTTAAAATTTT-TTTGACATTGATCTAATTT

                                            *                                
      15704 AATTTAATAAATCAACCACTAATGTTCAACTACTTTTTTTTGGTATAGTT-T-TATATATAATAA
         64 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATATAATAA

                                                                             
      15767 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACAT
        129 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACAT

                     
      15832 TCACCATTG
        194 TCACCATTG

                 
      15841 ATAAA
          1 ATAAA

      15846 GTTATTAAGC


Statistics
Matches: 200,  Mismatches: 5, Indels: 4
        0.96            0.02        0.02

Matches are distributed among these distances:
 202  104  0.52
 203   28  0.14
 204   68  0.34

ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44


Consensus pattern (202 bp):   
ATAAATAAATCAGATCTTAATATCTTTTATAATTTTAAAATTTTTTTGACATTGATCTAATTTAA
TTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATATAATAATA
ATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTC
ACCATTG
Done.