Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020250.1 Corchorus olitorius cultivar O-4 contig20283, 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: 19356
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32


Found at i:6617 original size:17 final size:17

Alignment explanation


    Indices: 6575--6620  Score: 51
    Period size: 17  Copynumber: 2.8  Consensus size: 17

       6565 CGTCTTCCCG

                             
       6575 CTGC-TTCTTCTCGTCT
          1 CTGCTTTCTTCTCGTCT

              *  *            
       6591 CTCCTCTCTTCTC-TCAT
          1 CTGCTTTCTTCTCGTC-T

                         
       6608 CTGCTTTCTTCTC
          1 CTGCTTTCTTCTC

       6621 CCTCCGCCAA


Statistics
Matches: 24,  Mismatches: 4, Indels: 3
        0.77            0.13        0.10

Matches are distributed among these distances:
  16    5  0.21
  17   19  0.79

ACGTcount: A:0.02, C:0.41, G:0.07, T:0.50


Consensus pattern (17 bp):   
CTGCTTTCTTCTCGTCT

Found at i:16679 original size:22 final size:22

Alignment explanation


    Indices: 16650--16709  Score: 102
    Period size: 22  Copynumber: 2.7  Consensus size: 22

      16640 TGAATATTTT

                                 *
      16650 TATGAAATTTTGATAACTACCC
          1 TATGAAATTTTGATAACTACCA

               *                  
      16672 TATTAAATTTTGATAACTACCA
          1 TATGAAATTTTGATAACTACCA

                            
      16694 TATGAAATTTTGATAA
          1 TATGAAATTTTGATAA

      16710 ATTGTGATAA


Statistics
Matches: 35,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  22   35  1.00

ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40


Consensus pattern (22 bp):   
TATGAAATTTTGATAACTACCA

Found at i:16711 original size:32 final size:32

Alignment explanation


    Indices: 16675--16741  Score: 89
    Period size: 32  Copynumber: 2.1  Consensus size: 32

      16665 ACTACCCTAT

                  *      *       *    *     
      16675 TAAATTTTGATAACTACCATATGAAATTTTGA
          1 TAAATTGTGATAAATACCATAAGAAACTTTGA

                           *                
      16707 TAAATTGTGATAAATTCCATAAGAAACTTTGA
          1 TAAATTGTGATAAATACCATAAGAAACTTTGA

               
      16739 TAA
          1 TAA

      16742 CCTAACAATG


Statistics
Matches: 30,  Mismatches: 5, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  32   30  1.00

ACGTcount: A:0.43, C:0.09, G:0.10, T:0.37


Consensus pattern (32 bp):   
TAAATTGTGATAAATACCATAAGAAACTTTGA

Found at i:18650 original size:19 final size:19

Alignment explanation


    Indices: 18609--18650  Score: 50
    Period size: 19  Copynumber: 2.2  Consensus size: 19

      18599 GGGTTGCTCA

                           *  *
      18609 ATAATAATAATAATATAAT
          1 ATAATAATAATAATAAAAC

                                
      18628 ATAAT-ATAATATATAAAAC
          1 ATAATAATAATA-ATAAAAC

                
      18647 ATAA
          1 ATAA

      18651 AAGTCTATTT


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  18    6  0.30
  19   14  0.70

ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33


Consensus pattern (19 bp):   
ATAATAATAATAATAAAAC
Done.