Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021507.1 Corchorus olitorius cultivar O-4 contig21540, 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: 10287
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33


Found at i:428 original size:26 final size:22

Alignment explanation


    Indices: 371--428  Score: 53
    Period size: 26  Copynumber: 2.4  Consensus size: 22

        361 AATTGTGATC

                *                 
        371 ATTATTATATAAATTTTATTAT
          1 ATTAATATATAAATTTTATTAT

                                        
        393 ATTCATATATATAATAGTTTTATTTAAT
          1 ATT-A-ATATATAA-A-TTTTA-TT-AT

                    
        421 ATTAATAT
          1 ATTAATAT

        429 GTTTTTTTTC


Statistics
Matches: 29,  Mismatches: 1, Indels: 8
        0.76            0.03        0.21

Matches are distributed among these distances:
  22    3  0.10
  23    1  0.03
  24    7  0.24
  25    1  0.03
  26    9  0.31
  27    3  0.10
  28    5  0.17

ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55


Consensus pattern (22 bp):   
ATTAATATATAAATTTTATTAT

Found at i:515 original size:17 final size:17

Alignment explanation


    Indices: 489--523  Score: 52
    Period size: 17  Copynumber: 2.1  Consensus size: 17

        479 TCAAATTATT

                 *           
        489 TCGGGTTCGGGCTCGGG
          1 TCGGGCTCGGGCTCGGG

                      *      
        506 TCGGGCTCGGTCTCGGG
          1 TCGGGCTCGGGCTCGGG

             
        523 T
          1 T

        524 TGGGTTTGGG


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.00, C:0.26, G:0.49, T:0.26


Consensus pattern (17 bp):   
TCGGGCTCGGGCTCGGG

Found at i:556 original size:16 final size:16

Alignment explanation


    Indices: 531--566  Score: 54
    Period size: 16  Copynumber: 2.2  Consensus size: 16

        521 GGTTGGGTTT

                 *          
        531 GGGTATTTTCGGGCTC
          1 GGGTAATTTCGGGCTC

                         *  
        547 GGGTAATTTCGGGTTC
          1 GGGTAATTTCGGGCTC

                
        563 GGGT
          1 GGGT

        567 TCGGGACGTT


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  16   18  1.00

ACGTcount: A:0.08, C:0.14, G:0.42, T:0.36


Consensus pattern (16 bp):   
GGGTAATTTCGGGCTC

Found at i:8929 original size:52 final size:52

Alignment explanation


    Indices: 8695--8928  Score: 353
    Period size: 52  Copynumber: 4.5  Consensus size: 52

       8685 CAATTTAAGT

                   * *             *                            
       8695 TTTTCAAATTGGGAAAGTTCCCACCAGTCTTCAAAGTATTTAATTTAGCTCC
          1 TTTTCAAGTCGGGAAAGTTCCCATCAGTCTTCAAAGTATTTAATTTAGCTCC

                                    *                           
       8747 TTTTCAAGTCGGGAAAGTTCCCATTAGTCTTCAAAGTATTTAATTTAGCTCC
          1 TTTTCAAGTCGGGAAAGTTCCCATCAGTCTTCAAAGTATTTAATTTAGCTCC

                                                                
       8799 TTTTCAAGTCGGGAAAGTTCCCATCAGTCTTCAAAGTATTTAATTTAGCTCC
          1 TTTTCAAGTCGGGAAAGTTCCCATCAGTCTTCAAAGTATTTAATTTAGCTCC

                                      * *           *           *
       8851 TTTTCAAGTCGGGAAAGTTCCCATCAATTTTCAAAGTATTCAATTTAGC-CAG
          1 TTTTCAAGTCGGGAAAGTTCCCATCAGTCTTCAAAGTATTTAATTTAGCTC-C

                   * *     *          
       8903 TTTTCAAATTGGGAAGGTTCCCATCA
          1 TTTTCAAGTCGGGAAAGTTCCCATCA

       8929 AGTTTTCGTT


Statistics
Matches: 169,  Mismatches: 12, Indels: 2
        0.92            0.07        0.01

Matches are distributed among these distances:
  51    1  0.01
  52  168  0.99

ACGTcount: A:0.28, C:0.20, G:0.15, T:0.36


Consensus pattern (52 bp):   
TTTTCAAGTCGGGAAAGTTCCCATCAGTCTTCAAAGTATTTAATTTAGCTCC

Found at i:8974 original size:34 final size:35

Alignment explanation


    Indices: 8900--9003  Score: 88
    Period size: 40  Copynumber: 2.9  Consensus size: 35

       8890 TCAATTTAGC

                              *                
       8900 CAGTTTTCAAATTGGGAAGGTTCCCATCAAGTTTT
          1 CAGTTTTCAAATTGGGAAAGTTCCCATCAAGTTTT

                      *                               
       8935 C-GTTTTCAATTTAGGGAAAGTTGCCGTCATTTTC-AGTTTT
          1 CAGTTTTCAAATT-GGGAAAGTT-CC--CA---TCAAGTTTT

                    *  *                  
       8975 -AGTTTTCGAAGTGGGAAAGTTCCCATCAA
          1 CAGTTTTCAAATTGGGAAAGTTCCCATCAA

       9004 AAGAATTTTT


Statistics
Matches: 55,  Mismatches: 5, Indels: 19
        0.70            0.06        0.24

Matches are distributed among these distances:
  33    2  0.04
  34   11  0.20
  35    9  0.16
  36    4  0.07
  38    4  0.07
  39    9  0.16
  40   14  0.25
  41    2  0.04

ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38


Consensus pattern (35 bp):   
CAGTTTTCAAATTGGGAAAGTTCCCATCAAGTTTT
Done.