Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021966.1 Corchorus olitorius cultivar O-4 contig21999, 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: 3393
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31


Found at i:2519 original size:13 final size:13

Alignment explanation


    Indices: 2501--2566  Score: 80
    Period size: 13  Copynumber: 4.9  Consensus size: 13

       2491 CCAGTCCACC

                         
       2501 GCCACGTCATCCT
          1 GCCACGTCATCCT

                           
       2514 GCCACGTCATCCGTT
          1 GCCACGTCATCC--T

               *      *   
       2529 GACTA-GTCAACCT
          1 G-CCACGTCATCCT

                         
       2542 GCCACGTCATCCT
          1 GCCACGTCATCCT

                        
       2555 GCCACGTCATCC
          1 GCCACGTCATCC

       2567 GTTGACAGTT


Statistics
Matches: 45,  Mismatches: 4, Indels: 8
        0.79            0.07        0.14

Matches are distributed among these distances:
  12    2  0.04
  13   33  0.73
  15    8  0.18
  16    2  0.04

ACGTcount: A:0.18, C:0.42, G:0.17, T:0.23


Consensus pattern (13 bp):   
GCCACGTCATCCT

Found at i:2558 original size:41 final size:41

Alignment explanation


    Indices: 2445--2572  Score: 190
    Period size: 41  Copynumber: 3.1  Consensus size: 41

       2435 CCTGTTGACT

                                                      *
       2445 GTTGACCAAGTCAACCTGCCACGTCAT-CTGCCACGTCA-CTA
          1 GTTGACC-AGTCAACCTGCCACGTCATCCTGCCACGTCATC-C

                       *                             
       2486 GTTGACCAGTCCACC-GCCACGTCATCCTGCCACGTCATCC
          1 GTTGACCAGTCAACCTGCCACGTCATCCTGCCACGTCATCC

                  *                                  
       2526 GTTGACTAGTCAACCTGCCACGTCATCCTGCCACGTCATCC
          1 GTTGACCAGTCAACCTGCCACGTCATCCTGCCACGTCATCC

                  
       2567 GTTGAC
          1 GTTGAC

       2573 AGTTGACCAG


Statistics
Matches: 80,  Mismatches: 4, Indels: 6
        0.89            0.04        0.07

Matches are distributed among these distances:
  39   10  0.12
  40   31  0.39
  41   39  0.49

ACGTcount: A:0.20, C:0.39, G:0.18, T:0.23


Consensus pattern (41 bp):   
GTTGACCAGTCAACCTGCCACGTCATCCTGCCACGTCATCC

Found at i:2621 original size:13 final size:13

Alignment explanation


    Indices: 2603--2651  Score: 55
    Period size: 13  Copynumber: 3.7  Consensus size: 13

       2593 ATGTCATCAA

                         
       2603 GTTGACTTTGACT
          1 GTTGACTTTGACT

                         * 
       2616 GTTGACTTTTTG-GT
          1 GTTGAC--TTTGACT

                        *
       2630 GTTGACTTTGACC
          1 GTTGACTTTGACT

                     
       2643 GTTGACTTT
          1 GTTGACTTT

       2652 TTGGTTGACC


Statistics
Matches: 30,  Mismatches: 3, Indels: 6
        0.77            0.08        0.15

Matches are distributed among these distances:
  12    4  0.13
  13   15  0.50
  14    7  0.23
  15    4  0.13

ACGTcount: A:0.12, C:0.14, G:0.24, T:0.49


Consensus pattern (13 bp):   
GTTGACTTTGACT

Found at i:2636 original size:27 final size:27

Alignment explanation


    Indices: 2603--2656  Score: 99
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       2593 ATGTCATCAA

                        *              
       2603 GTTGACTTTGACTGTTGACTTTTTGGT
          1 GTTGACTTTGACCGTTGACTTTTTGGT

                                       
       2630 GTTGACTTTGACCGTTGACTTTTTGGT
          1 GTTGACTTTGACCGTTGACTTTTTGGT

       2657 TGACCAGTTT


Statistics
Matches: 26,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  27   26  1.00

ACGTcount: A:0.11, C:0.13, G:0.26, T:0.50


Consensus pattern (27 bp):   
GTTGACTTTGACCGTTGACTTTTTGGT
Done.