Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005391.1 Corchorus capsularis cultivar CVL-1 contig05409, 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: 18613
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:3025 original size:55 final size:55

Alignment explanation


    Indices: 2941--3050  Score: 220
    Period size: 55  Copynumber: 2.0  Consensus size: 55

       2931 TTCACACACT

                                                                   
       2941 GCATCATTTAATAAACAAGATTAGAGATTATTAAGATACAAACTAAAACATCATC
          1 GCATCATTTAATAAACAAGATTAGAGATTATTAAGATACAAACTAAAACATCATC

                                                                   
       2996 GCATCATTTAATAAACAAGATTAGAGATTATTAAGATACAAACTAAAACATCATC
          1 GCATCATTTAATAAACAAGATTAGAGATTATTAAGATACAAACTAAAACATCATC

       3051 AAGAGCTTAC


Statistics
Matches: 55,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  55   55  1.00

ACGTcount: A:0.49, C:0.15, G:0.09, T:0.27


Consensus pattern (55 bp):   
GCATCATTTAATAAACAAGATTAGAGATTATTAAGATACAAACTAAAACATCATC

Found at i:5066 original size:52 final size:51

Alignment explanation


    Indices: 5004--5160  Score: 233
    Period size: 52  Copynumber: 3.0  Consensus size: 51

       4994 AACATGACAA

                           *             *                      
       5004 TAAACACCATAAAAATTAAAACTTTTGGACTTGTAACTATATAAATCCCAAC
          1 TAAACACCATAAAAACTAAAACTTTTGGATTTGTAACTATA-AAATCCCAAC

                                       *    *    *              
       5056 TAAACACCATAAAAACTAAAACTTTTGAATTTTTAACCATAAAAATCCCAAC
          1 TAAACACCATAAAAACTAAAACTTTTGGATTTGTAACTAT-AAAATCCCAAC

                                                   *            
       5108 TAAACACCATAAAAACTAAAACTTTTGGATTTGTAACTACAAAAGTCCCAAC
          1 TAAACACCATAAAAACTAAAACTTTTGGATTTGTAACTATAAAA-TCCCAAC

             
       5160 T
          1 T

       5161 TTTAACATCT


Statistics
Matches: 94,  Mismatches: 9, Indels: 4
        0.88            0.08        0.04

Matches are distributed among these distances:
  51    4  0.04
  52   89  0.95
  53    1  0.01

ACGTcount: A:0.47, C:0.20, G:0.05, T:0.27


Consensus pattern (51 bp):   
TAAACACCATAAAAACTAAAACTTTTGGATTTGTAACTATAAAATCCCAAC

Found at i:11637 original size:23 final size:22

Alignment explanation


    Indices: 11607--11650  Score: 54
    Period size: 23  Copynumber: 2.0  Consensus size: 22

      11597 CCTTATCGAA

                                   
      11607 CAGTTCGA-TAGAGGCTCGAGCT
          1 CAGTTCGAGTAGA-GCTCGAGCT

                       *          
      11629 CAGTCTCGAGTCGAGCTCGAGC
          1 CAGT-TCGAGTAGAGCTCGAGC

      11651 CTCCAAAATG


Statistics
Matches: 19,  Mismatches: 1, Indels: 3
        0.83            0.04        0.13

Matches are distributed among these distances:
  22    4  0.21
  23   12  0.63
  24    3  0.16

ACGTcount: A:0.20, C:0.27, G:0.32, T:0.20


Consensus pattern (22 bp):   
CAGTTCGAGTAGAGCTCGAGCT
Done.