Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018091.1 Corchorus olitorius cultivar O-4 contig18124, 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: 7499
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.36


Found at i:751 original size:204 final size:202

Alignment explanation


    Indices: 515--923  Score: 705
    Period size: 204  Copynumber: 2.0  Consensus size: 202

        505 CATTTTATAG

                                                                       *     
        515 GAAATAATTAATAAGTAAAAAAAAGAAATAATTAATGTATATCAAAACTGCCTCGTATATTTTAC
          1 GAAATAATTAATAAGTAAAAAAAAGAAATAATTAATGTATATCAAAACTGCCTCGTATAATTTAC

                              *                                              
        580 GATCAATATAAAATTGTGTTAATTGATTACGCGTGCTATATAAAACACATGGTAAGTTTGCAA-A
         66 GATCAATATAAAATTGTGATAATTGATTACGCGTGCTATATAAAACACATGGTAAGTTTGCAATA

                     *                               *             *         
        644 -TTTTTTTTGAGTGGTAAGTGAAATTTCATTACAATCAGAATAAATTTCCATATGTTCAAACATC
        131 TTTTTTTTTAAGTGGTAAGTGAAATTTCATTACAATCAGAAAAAATTTCCATATGCTCAAACATC

                   
        708 TAAATGA
        196 TAAATGA

                                                                   *         
        715 GAAATAATTAATAAGTAGTAAAAAAAAAGAAATAATTAATGTATATCAAAACTGCTTCGTATAAT
          1 GAAATAATTAAT-A--AGT-AAAAAAAAGAAATAATTAATGTATATCAAAACTGCCTCGTATAAT

                                                                             
        780 TTACGATCAATATAAAATTGTGATAATTGATTACGCGTGCTATATAAAACACATGGTAAGTTTGC
         62 TTACGATCAATATAAAATTGTGATAATTGATTACGCGTGCTATATAAAACACATGGTAAGTTTGC

                                                                 *           
        845 AATATTTTTTTTTAAGTGGTAAGTGAAATTTCATTACAATCAGAAAAAATTTCTATATGCTCAAA
        127 AATATTTTTTTTTAAGTGGTAAGTGAAATTTCATTACAATCAGAAAAAATTTCCATATGCTCAAA

                       
        910 CATCTAAATGA
        192 CATCTAAATGA

               
        921 GAA
          1 GAA

        924 TCCAACCCAA


Statistics
Matches: 196,  Mismatches: 7, Indels: 6
        0.94            0.03        0.03

Matches are distributed among these distances:
 200   12  0.06
 201    1  0.01
 203    3  0.02
 204  109  0.56
 205    1  0.01
 206   70  0.36

ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34


Consensus pattern (202 bp):   
GAAATAATTAATAAGTAAAAAAAAGAAATAATTAATGTATATCAAAACTGCCTCGTATAATTTAC
GATCAATATAAAATTGTGATAATTGATTACGCGTGCTATATAAAACACATGGTAAGTTTGCAATA
TTTTTTTTTAAGTGGTAAGTGAAATTTCATTACAATCAGAAAAAATTTCCATATGCTCAAACATC
TAAATGA

Found at i:2596 original size:29 final size:30

Alignment explanation


    Indices: 2541--2597  Score: 89
    Period size: 29  Copynumber: 1.9  Consensus size: 30

       2531 TATATATATA

                                          
       2541 TATATATATACATACATGAAATAATTAAAT
          1 TATATATATACATACATGAAATAATTAAAT

                      *   *             
       2571 TATATATATATAT-GATGAAATAATTAA
          1 TATATATATACATACATGAAATAATTAA

       2598 TCGGTCAGAT


Statistics
Matches: 25,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  29   13  0.52
  30   12  0.48

ACGTcount: A:0.53, C:0.04, G:0.05, T:0.39


Consensus pattern (30 bp):   
TATATATATACATACATGAAATAATTAAAT

Found at i:4796 original size:37 final size:37

Alignment explanation


    Indices: 4746--4820  Score: 141
    Period size: 37  Copynumber: 2.0  Consensus size: 37

       4736 CCAGGAAGCT

                                           *     
       4746 AATATTTGTGCTCATAGTTTAGCTAAATTTGGTTGTA
          1 AATATTTGTGCTCATAGTTTAGCTAAATTTGATTGTA

                                                 
       4783 AATATTTGTGCTCATAGTTTAGCTAAATTTGATTGTA
          1 AATATTTGTGCTCATAGTTTAGCTAAATTTGATTGTA

             
       4820 A
          1 A

       4821 TATGTTTGCT


Statistics
Matches: 37,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  37   37  1.00

ACGTcount: A:0.29, C:0.08, G:0.17, T:0.45


Consensus pattern (37 bp):   
AATATTTGTGCTCATAGTTTAGCTAAATTTGATTGTA

Found at i:6521 original size:28 final size:29

Alignment explanation


    Indices: 6490--6545  Score: 71
    Period size: 29  Copynumber: 2.0  Consensus size: 29

       6480 TCAGTATACG

                                          
       6490 TTTTT-AACAATAA-TCACGAGTTCATGTC
          1 TTTTTGAACAA-AATTCACGAGTTCATGTC

                  **                    
       6518 TTTTTGGCCAAAATTCACGAGTTCATGT
          1 TTTTTGAACAAAATTCACGAGTTCATGT

       6546 AAAGTGTATT


Statistics
Matches: 24,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  28    7  0.29
  29   17  0.71

ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39


Consensus pattern (29 bp):   
TTTTTGAACAAAATTCACGAGTTCATGTC

Found at i:6988 original size:63 final size:63

Alignment explanation


    Indices: 6916--7047  Score: 246
    Period size: 63  Copynumber: 2.1  Consensus size: 63

       6906 TAAAGAATTT

                                                                    *      
       6916 ATTGAATTATAATTATTATTGATTTTTAGTGGAAGTTGATTGAAATAGAAAGGAAATGATTAA
          1 ATTGAATTATAATTATTATTGATTTTTAGTGGAAGTTGATTGAAATAGAAAGGAAAGGATTAA

                                                 *                         
       6979 ATTGAATTATAATTATTATTGATTTTTAGTGGAAGTTTATTGAAATAGAAAGGAAAGGATTAA
          1 ATTGAATTATAATTATTATTGATTTTTAGTGGAAGTTGATTGAAATAGAAAGGAAAGGATTAA

                  
       7042 ATTGAA
          1 ATTGAA

       7048 GTAGAAAATA


Statistics
Matches: 67,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  63   67  1.00

ACGTcount: A:0.42, C:0.00, G:0.19, T:0.39


Consensus pattern (63 bp):   
ATTGAATTATAATTATTATTGATTTTTAGTGGAAGTTGATTGAAATAGAAAGGAAAGGATTAA
Done.