Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006787.1 Corchorus capsularis cultivar CVL-1 contig06808, 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: 9609
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32


Found at i:3022 original size:6 final size:6

Alignment explanation


    Indices: 3011--3041  Score: 53
    Period size: 6  Copynumber: 5.2  Consensus size: 6

       3001 CAGGTTGCAC

                                  *             
       3011 CACAAT CACAAT CACAAT CTCAAT CACAAT C
          1 CACAAT CACAAT CACAAT CACAAT CACAAT C

       3042 TTGCCAACAG


Statistics
Matches: 23,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
   6   23  1.00

ACGTcount: A:0.45, C:0.35, G:0.00, T:0.19


Consensus pattern (6 bp):   
CACAAT

Found at i:3098 original size:38 final size:38

Alignment explanation


    Indices: 3040--3153  Score: 194
    Period size: 38  Copynumber: 3.0  Consensus size: 38

       3030 TCAATCACAA

                *                                 
       3040 TCTTGCCAACAG-TTAACCCCCTGAGGCACGGGTCCAC
          1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC

                                                  
       3077 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
          1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC

                    *                   *         
       3115 TCTTACCATCAGTTTAACCCCCTGAGGCGCGGGTCCAC
          1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC

             
       3153 T
          1 T

       3154 ATGTACAGCC


Statistics
Matches: 73,  Mismatches: 3, Indels: 1
        0.95            0.04        0.01

Matches are distributed among these distances:
  37   11  0.15
  38   62  0.85

ACGTcount: A:0.21, C:0.37, G:0.20, T:0.22


Consensus pattern (38 bp):   
TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC

Found at i:7076 original size:10 final size:10

Alignment explanation


    Indices: 7063--7094  Score: 55
    Period size: 10  Copynumber: 3.2  Consensus size: 10

       7053 ACAAAATACA

                      
       7063 CAAGATAAAG
          1 CAAGATAAAG

                      
       7073 CAAGATAAAG
          1 CAAGATAAAG

             *        
       7083 CGAGATAAAG
          1 CAAGATAAAG

              
       7093 CA
          1 CA

       7095 TAAGATAGAT


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  10   20  1.00

ACGTcount: A:0.56, C:0.12, G:0.22, T:0.09


Consensus pattern (10 bp):   
CAAGATAAAG

Found at i:7894 original size:24 final size:25

Alignment explanation


    Indices: 7867--7936  Score: 74
    Period size: 24  Copynumber: 2.9  Consensus size: 25

       7857 GCTCCATCAG

                                *   *
       7867 TCTTTTCT-TTTTTCTGTTGTTCAT
          1 TCTTTTCTCTTTTTCTGTTGCTCAC

                       * *           
       7891 TCTTTT-TCTTCTGCTGTTGCTCAC
          1 TCTTTTCTCTTTTTCTGTTGCTCAC

                             *     
       7915 T-TTTTCTCTTTTTCTGCTGCTC
          1 TCTTTTCTCTTTTTCTGTTGCTC

       7937 TTTGACTTTC


Statistics
Matches: 37,  Mismatches: 7, Indels: 4
        0.77            0.15        0.08

Matches are distributed among these distances:
  23    5  0.14
  24   32  0.86

ACGTcount: A:0.03, C:0.24, G:0.10, T:0.63


Consensus pattern (25 bp):   
TCTTTTCTCTTTTTCTGTTGCTCAC

Found at i:9579 original size:2 final size:2

Alignment explanation


    Indices: 9574--9602  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

       9564 GAGATTAAAT

                                                       
       9574 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A

       9603 AGATTAA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

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


Consensus pattern (2 bp):   
AG

Done.