Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009772.1 Corchorus capsularis cultivar CVL-1 contig09793, 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: 20968
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32


Found at i:4215 original size:22 final size:22

Alignment explanation


    Indices: 4190--4231  Score: 75
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       4180 TTGATTACCA

                 *                
       4190 CATAATAATCAATTAATTTTAC
          1 CATAAAAATCAATTAATTTTAC

                                
       4212 CATAAAAATCAATTAATTTT
          1 CATAAAAATCAATTAATTTT

       4232 CAATAATTAC


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  22   19  1.00

ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40


Consensus pattern (22 bp):   
CATAAAAATCAATTAATTTTAC

Found at i:4820 original size:17 final size:18

Alignment explanation


    Indices: 4786--4820  Score: 54
    Period size: 17  Copynumber: 2.0  Consensus size: 18

       4776 AACTCAATTA

                         *    
       4786 GAAATTAATTTAGGAAAT
          1 GAAATTAATTTAGAAAAT

                              
       4804 GAAATTAA-TTAGAAAAT
          1 GAAATTAATTTAGAAAAT

       4821 AATTTAGGAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  17    8  0.50
  18    8  0.50

ACGTcount: A:0.54, C:0.00, G:0.14, T:0.31


Consensus pattern (18 bp):   
GAAATTAATTTAGAAAAT

Found at i:8840 original size:2 final size:2

Alignment explanation


    Indices: 8833--8859  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       8823 GTCTACAGTT

                                                    
       8833 TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA T

       8860 GATTAGAAAT


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

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:17462 original size:17 final size:18

Alignment explanation


    Indices: 17431--17468  Score: 60
    Period size: 17  Copynumber: 2.2  Consensus size: 18

      17421 TCCCTCTCAT

                      *       
      17431 GGTACCTAGGTAACATGA
          1 GGTACCTAGGCAACATGA

                              
      17449 GGTA-CTAGGCAACATGA
          1 GGTACCTAGGCAACATGA

               
      17466 GGT
          1 GGT

      17469 GACAGGCTAC


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  17   15  0.79
  18    4  0.21

ACGTcount: A:0.32, C:0.16, G:0.32, T:0.21


Consensus pattern (18 bp):   
GGTACCTAGGCAACATGA

Found at i:20029 original size:2 final size:2

Alignment explanation


    Indices: 19983--20015  Score: 50
    Period size: 2  Copynumber: 17.0  Consensus size: 2

      19973 CATAAATAAC

                                                *             
      19983 TA TA TA TA TA TA TA TA TA TA TA TA GA -A TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      20016 GTAATTACAT


Statistics
Matches: 29,  Mismatches: 1, Indels: 2
        0.91            0.03        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   28  0.97

ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45


Consensus pattern (2 bp):   
TA
Done.