Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023894.1 Corchorus olitorius cultivar O-4 contig23927, 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: 4262
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32


Found at i:2371 original size:24 final size:24

Alignment explanation


    Indices: 2339--2387  Score: 98
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       2329 ACACACATGA

                                    
       2339 GTATTCATACATTGAGGACAATGT
          1 GTATTCATACATTGAGGACAATGT

                                    
       2363 GTATTCATACATTGAGGACAATGT
          1 GTATTCATACATTGAGGACAATGT

             
       2387 G
          1 G

       2388 AATTTTAAAT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   25  1.00

ACGTcount: A:0.33, C:0.12, G:0.22, T:0.33


Consensus pattern (24 bp):   
GTATTCATACATTGAGGACAATGT

Found at i:2624 original size:41 final size:41

Alignment explanation


    Indices: 2527--2616  Score: 180
    Period size: 41  Copynumber: 2.2  Consensus size: 41

       2517 GTGGGATTTC

                                                     
       2527 ATTCAATTGGGTCCCTAATTTAGGCTGATATTTATTCATTA
          1 ATTCAATTGGGTCCCTAATTTAGGCTGATATTTATTCATTA

                                                     
       2568 ATTCAATTGGGTCCCTAATTTAGGCTGATATTTATTCATTA
          1 ATTCAATTGGGTCCCTAATTTAGGCTGATATTTATTCATTA

                    
       2609 ATTCAATT
          1 ATTCAATT

       2617 TTGTCCCTGA


Statistics
Matches: 49,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  41   49  1.00

ACGTcount: A:0.28, C:0.14, G:0.13, T:0.44


Consensus pattern (41 bp):   
ATTCAATTGGGTCCCTAATTTAGGCTGATATTTATTCATTA

Found at i:2640 original size:41 final size:41

Alignment explanation


    Indices: 2527--2664  Score: 152
    Period size: 41  Copynumber: 3.4  Consensus size: 41

       2517 GTGGGATTTC

                    **         *      *              
       2527 ATTCAATTGGGTCCCTAATTTAGGCTGATATTTATTCATTA
          1 ATTCAATTTTGTCCCTAATCTAGGCTAATATTTATTCATTA

                    **         *      *              
       2568 ATTCAATTGGGTCCCTAATTTAGGCTGATATTTATTCATTA
          1 ATTCAATTTTGTCCCTAATCTAGGCTAATATTTATTCATTA

                            *                    *   *
       2609 ATTCAATTTTGTCCCTGATCTAGAG-TAATATTTATTTATTG
          1 ATTCAATTTTGTCCCTAATCTAG-GCTAATATTTATTCATTA

                  *        
       2650 ATTCAAATTTGTCCC
          1 ATTCAATTTTGTCCC

       2665 AGATTTAAGA


Statistics
Matches: 88,  Mismatches: 8, Indels: 2
        0.90            0.08        0.02

Matches are distributed among these distances:
  41   87  0.99
  42    1  0.01

ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45


Consensus pattern (41 bp):   
ATTCAATTTTGTCCCTAATCTAGGCTAATATTTATTCATTA

Found at i:2725 original size:19 final size:19

Alignment explanation


    Indices: 2698--2757  Score: 66
    Period size: 19  Copynumber: 3.0  Consensus size: 19

       2688 TTATGCGGCC

                               
       2698 TAGTCCCTGATTTAAGATT
          1 TAGTCCCTGATTTAAGATT

              *         *         
       2717 TATTCCCTGATTAAATGCAATT
          1 TAGTCCCTGATTTAA-G--ATT

                          *    
       2739 TAGTCCCTGATTTAGGATT
          1 TAGTCCCTGATTTAAGATT

       2758 GTAATTACTG


Statistics
Matches: 33,  Mismatches: 5, Indels: 6
        0.75            0.11        0.14

Matches are distributed among these distances:
  19   16  0.48
  20    1  0.03
  21    1  0.03
  22   15  0.45

ACGTcount: A:0.27, C:0.17, G:0.15, T:0.42


Consensus pattern (19 bp):   
TAGTCCCTGATTTAAGATT

Found at i:2745 original size:22 final size:19

Alignment explanation


    Indices: 2698--2750  Score: 61
    Period size: 22  Copynumber: 2.6  Consensus size: 19

       2688 TTATGCGGCC

                        *      
       2698 TAGTCCCTGATTTAAGATT
          1 TAGTCCCTGATTAAAGATT

              *                   
       2717 TATTCCCTGATTAAATGCAATT
          1 TAGTCCCTGATTAAA-G--ATT

                        
       2739 TAGTCCCTGATT
          1 TAGTCCCTGATT

       2751 TAGGATTGTA


Statistics
Matches: 28,  Mismatches: 3, Indels: 3
        0.82            0.09        0.09

Matches are distributed among these distances:
  19   13  0.46
  20    1  0.04
  22   14  0.50

ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42


Consensus pattern (19 bp):   
TAGTCCCTGATTAAAGATT
Done.