Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014180.1 Corchorus capsularis cultivar CVL-1 contig14201, 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: 11850
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31


Found at i:2621 original size:10 final size:10

Alignment explanation


    Indices: 2606--2631  Score: 52
    Period size: 10  Copynumber: 2.6  Consensus size: 10

       2596 AGTTGCTGCC

                      
       2606 AAATTCCAGA
          1 AAATTCCAGA

                      
       2616 AAATTCCAGA
          1 AAATTCCAGA

                  
       2626 AAATTC
          1 AAATTC

       2632 TAGAGTCCTC


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

Matches are distributed among these distances:
  10   16  1.00

ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23


Consensus pattern (10 bp):   
AAATTCCAGA

Found at i:3577 original size:6 final size:6

Alignment explanation


    Indices: 3566--3595  Score: 60
    Period size: 6  Copynumber: 5.0  Consensus size: 6

       3556 ATTCTGCTTC

                                              
       3566 AGATTT AGATTT AGATTT AGATTT AGATTT
          1 AGATTT AGATTT AGATTT AGATTT AGATTT

       3596 GCTTTGCTTT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   24  1.00

ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50


Consensus pattern (6 bp):   
AGATTT

Found at i:9387 original size:79 final size:79

Alignment explanation


    Indices: 9256--9416  Score: 313
    Period size: 79  Copynumber: 2.0  Consensus size: 79

       9246 ATAGATTGCA

                                                                     *       
       9256 TGAGTTGGAGCATGTGATGAAAGACTATATCAACACTAAACTCTATACTAGGTGGGAGTTATATA
          1 TGAGTTGGAGCATGTGATGAAAGACTATATCAACACTAAACTCTATACTAGGTGGGACTTATATA

                          
       9321 TCCCTAGACTTTTG
         66 TCCCTAGACTTTTG

                                                                             
       9335 TGAGTTGGAGCATGTGATGAAAGACTATATCAACACTAAACTCTATACTAGGTGGGACTTATATA
          1 TGAGTTGGAGCATGTGATGAAAGACTATATCAACACTAAACTCTATACTAGGTGGGACTTATATA

                          
       9400 TCCCTAGACTTTTG
         66 TCCCTAGACTTTTG

               
       9414 TGA
          1 TGA

       9417 TGTTTTCCCT


Statistics
Matches: 81,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  79   81  1.00

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


Consensus pattern (79 bp):   
TGAGTTGGAGCATGTGATGAAAGACTATATCAACACTAAACTCTATACTAGGTGGGACTTATATA
TCCCTAGACTTTTG

Found at i:9450 original size:16 final size:16

Alignment explanation


    Indices: 9429--9460  Score: 64
    Period size: 16  Copynumber: 2.0  Consensus size: 16

       9419 TTTTCCCTTC

                            
       9429 GATTGAGTTGTTACTT
          1 GATTGAGTTGTTACTT

                            
       9445 GATTGAGTTGTTACTT
          1 GATTGAGTTGTTACTT

       9461 TTTGTTTGTA


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

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.19, C:0.06, G:0.25, T:0.50


Consensus pattern (16 bp):   
GATTGAGTTGTTACTT
Done.