Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004838.1 Corchorus capsularis cultivar CVL-1 contig04856, 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: 9796
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34


Found at i:29 original size:9 final size:9

Alignment explanation


    Indices: 15--44  Score: 60
    Period size: 9  Copynumber: 3.3  Consensus size: 9

          5 CAGAATTCTT

                     
         15 AATTCCCAG
          1 AATTCCCAG

                     
         24 AATTCCCAG
          1 AATTCCCAG

                     
         33 AATTCCCAG
          1 AATTCCCAG

               
         42 AAT
          1 AAT

         45 ACCTCTCTGT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   21  1.00

ACGTcount: A:0.37, C:0.30, G:0.10, T:0.23


Consensus pattern (9 bp):   
AATTCCCAG

Found at i:1211 original size:30 final size:30

Alignment explanation


    Indices: 1176--1236  Score: 122
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       1166 GATATCATTA

                                          
       1176 AATAATAAGGTTTTAGAAATTATAATAATT
          1 AATAATAAGGTTTTAGAAATTATAATAATT

                                          
       1206 AATAATAAGGTTTTAGAAATTATAATAATT
          1 AATAATAAGGTTTTAGAAATTATAATAATT

             
       1236 A
          1 A

       1237 TTTCCAATGA


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  30   31  1.00

ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39


Consensus pattern (30 bp):   
AATAATAAGGTTTTAGAAATTATAATAATT

Found at i:7002 original size:7 final size:7

Alignment explanation


    Indices: 6990--7014  Score: 50
    Period size: 7  Copynumber: 3.6  Consensus size: 7

       6980 AACGTACTAA

                   
       6990 AGAATTT
          1 AGAATTT

                   
       6997 AGAATTT
          1 AGAATTT

                   
       7004 AGAATTT
          1 AGAATTT

                
       7011 AGAA
          1 AGAA

       7015 AAATACGGTT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   18  1.00

ACGTcount: A:0.48, C:0.00, G:0.16, T:0.36


Consensus pattern (7 bp):   
AGAATTT
Done.