Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000791.1 Corchorus capsularis cultivar CVL-1 contig00791, 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: 10368
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:2759 original size:14 final size:14

Alignment explanation


    Indices: 2740--2768  Score: 58
    Period size: 14  Copynumber: 2.1  Consensus size: 14

       2730 TTCTTCGATG

                          
       2740 TCGGTTTTTTCGGT
          1 TCGGTTTTTTCGGT

                          
       2754 TCGGTTTTTTCGGT
          1 TCGGTTTTTTCGGT

             
       2768 T
          1 T

       2769 TTTATTTTGG


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   15  1.00

ACGTcount: A:0.00, C:0.14, G:0.28, T:0.59


Consensus pattern (14 bp):   
TCGGTTTTTTCGGT

Found at i:3055 original size:3 final size:3

Alignment explanation


    Indices: 3047--3081  Score: 70
    Period size: 3  Copynumber: 11.7  Consensus size: 3

       3037 ATATATATAT

                                                          
       3047 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
          1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT

       3082 TTACTATGTA


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   32  1.00

ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34


Consensus pattern (3 bp):   
ATA

Found at i:3941 original size:10 final size:10

Alignment explanation


    Indices: 3923--3956  Score: 50
    Period size: 10  Copynumber: 3.4  Consensus size: 10

       3913 GATGTAGGTA

                      
       3923 TTTGAGATTG
          1 TTTGAGATTG

                *    *
       3933 TTTGGGATTA
          1 TTTGAGATTG

                      
       3943 TTTGAGATTG
          1 TTTGAGATTG

                
       3953 TTTG
          1 TTTG

       3957 GGATCGAATC


Statistics
Matches: 20,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  10   20  1.00

ACGTcount: A:0.18, C:0.00, G:0.29, T:0.53


Consensus pattern (10 bp):   
TTTGAGATTG

Found at i:3946 original size:20 final size:20

Alignment explanation


    Indices: 3921--3960  Score: 80
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       3911 TGGATGTAGG

                                
       3921 TATTTGAGATTGTTTGGGAT
          1 TATTTGAGATTGTTTGGGAT

                                
       3941 TATTTGAGATTGTTTGGGAT
          1 TATTTGAGATTGTTTGGGAT

       3961 CGAATCTCAT


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.20, C:0.00, G:0.30, T:0.50


Consensus pattern (20 bp):   
TATTTGAGATTGTTTGGGAT

Found at i:7049 original size:11 final size:11

Alignment explanation


    Indices: 7033--7057  Score: 50
    Period size: 11  Copynumber: 2.3  Consensus size: 11

       7023 TCTTCTTTTT

                       
       7033 TTTTTTTCTTC
          1 TTTTTTTCTTC

                       
       7044 TTTTTTTCTTC
          1 TTTTTTTCTTC

               
       7055 TTT
          1 TTT

       7058 AAAGGCTTTT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   14  1.00

ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84


Consensus pattern (11 bp):   
TTTTTTTCTTC

Found at i:7485 original size:13 final size:13

Alignment explanation


    Indices: 7467--7495  Score: 58
    Period size: 13  Copynumber: 2.2  Consensus size: 13

       7457 TTTACTCTCA

                         
       7467 TTTTTCTTTTTCT
          1 TTTTTCTTTTTCT

                         
       7480 TTTTTCTTTTTCT
          1 TTTTTCTTTTTCT

               
       7493 TTT
          1 TTT

       7496 CCAAAAAATC


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   16  1.00

ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86


Consensus pattern (13 bp):   
TTTTTCTTTTTCT
Done.