Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012814.1 Corchorus olitorius cultivar O-4 contig12847, 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: 10947
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.39


Found at i:2188 original size:32 final size:33

Alignment explanation


    Indices: 2152--2215  Score: 87
    Period size: 33  Copynumber: 2.0  Consensus size: 33

       2142 ATGTTAATTT

                     *                        
       2152 GCACCTT-CTTTGCCATT-TATTAGTTGATGTTG
          1 GCACCTTGCATTGCCATTGT-TTAGTTGATGTTG

                          *                 
       2184 GCACCTTGCATTGCTATTGTTTAGTTGATGTT
          1 GCACCTTGCATTGCCATTGTTTAGTTGATGTT

       2216 AATACAATGA


Statistics
Matches: 28,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  32    7  0.25
  33   20  0.71
  34    1  0.04

ACGTcount: A:0.16, C:0.17, G:0.20, T:0.47


Consensus pattern (33 bp):   
GCACCTTGCATTGCCATTGTTTAGTTGATGTTG

Found at i:2727 original size:22 final size:22

Alignment explanation


    Indices: 2699--2743  Score: 90
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       2689 TCCCTCCCAT

                                  
       2699 TGGCTACCAGTTTGTTTTTCAC
          1 TGGCTACCAGTTTGTTTTTCAC

                                  
       2721 TGGCTACCAGTTTGTTTTTCAC
          1 TGGCTACCAGTTTGTTTTTCAC

             
       2743 T
          1 T

       2744 CTCTCTCCCT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   23  1.00

ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47


Consensus pattern (22 bp):   
TGGCTACCAGTTTGTTTTTCAC

Found at i:6587 original size:36 final size:36

Alignment explanation


    Indices: 6540--6611  Score: 119
    Period size: 36  Copynumber: 2.0  Consensus size: 36

       6530 ATGAATTCAG

                                                 
       6540 AGATTCAAAGCTGCTCATAT-AAGGAGTAGTGCCTTT
          1 AGATTCAAAGCTGCTCAT-TGAAGGAGTAGTGCCTTT

                                       *        
       6576 AGATTCAAAGCTGCTCATTGAAGGAGTGGTGCCTTT
          1 AGATTCAAAGCTGCTCATTGAAGGAGTAGTGCCTTT

       6612 TCATCCCCAA


Statistics
Matches: 34,  Mismatches: 1, Indels: 2
        0.92            0.03        0.05

Matches are distributed among these distances:
  35    1  0.03
  36   33  0.97

ACGTcount: A:0.28, C:0.17, G:0.25, T:0.31


Consensus pattern (36 bp):   
AGATTCAAAGCTGCTCATTGAAGGAGTAGTGCCTTT

Found at i:7106 original size:20 final size:20

Alignment explanation


    Indices: 7083--7122  Score: 80
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       7073 ATATTCGATC

                                
       7083 TATAGAGTAGATTAAATTTT
          1 TATAGAGTAGATTAAATTTT

                                
       7103 TATAGAGTAGATTAAATTTT
          1 TATAGAGTAGATTAAATTTT

       7123 GCTTCATTCT


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45


Consensus pattern (20 bp):   
TATAGAGTAGATTAAATTTT

Found at i:8615 original size:55 final size:55

Alignment explanation


    Indices: 8526--8632  Score: 198
    Period size: 55  Copynumber: 1.9  Consensus size: 55

       8516 CTGTTTCCTA

                                                                   
       8526 TCACACAATAAATGTTATAAAAATCCTATCCCCCTATCTCTACTTAATTATTCTT
          1 TCACACAATAAATGTTATAAAAATCCTATCCCCCTATCTCTACTTAATTATTCTT

                                                                 
       8581 TCACACAATAAATGTTATAATAAATCCTAT-CCCCTATCTCTACTTAATTATT
          1 TCACACAATAAATGTTATAA-AAATCCTATCCCCCTATCTCTACTTAATTATT

       8633 TTACAAAATA


Statistics
Matches: 51,  Mismatches: 0, Indels: 2
        0.96            0.00        0.04

Matches are distributed among these distances:
  55   42  0.82
  56    9  0.18

ACGTcount: A:0.36, C:0.24, G:0.02, T:0.38


Consensus pattern (55 bp):   
TCACACAATAAATGTTATAAAAATCCTATCCCCCTATCTCTACTTAATTATTCTT

Done.