Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005384.1 Corchorus capsularis cultivar CVL-1 contig05402, 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: 6178
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36


Found at i:166 original size:19 final size:19

Alignment explanation


    Indices: 142--180  Score: 78
    Period size: 19  Copynumber: 2.1  Consensus size: 19

        132 AAAAAATTAC

                               
        142 ATTTGAAGCAAATTCCTTT
          1 ATTTGAAGCAAATTCCTTT

                               
        161 ATTTGAAGCAAATTCCTTT
          1 ATTTGAAGCAAATTCCTTT

             
        180 A
          1 A

        181 AAATGTGTTA


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

Matches are distributed among these distances:
  19   20  1.00

ACGTcount: A:0.33, C:0.15, G:0.10, T:0.41


Consensus pattern (19 bp):   
ATTTGAAGCAAATTCCTTT

Found at i:3234 original size:3 final size:3

Alignment explanation


    Indices: 3228--3279  Score: 104
    Period size: 3  Copynumber: 17.3  Consensus size: 3

       3218 AGTAGTATAG

                                                                           
       3228 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
          1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA

                 
       3276 ATA A
          1 ATA A

       3280 GAGTTTTGTT


Statistics
Matches: 49,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   49  1.00

ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33


Consensus pattern (3 bp):   
ATA

Found at i:3541 original size:13 final size:13

Alignment explanation


    Indices: 3523--3547  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       3513 ATATATATAT

                         
       3523 TAACTTCAAATAG
          1 TAACTTCAAATAG

                        
       3536 TAACTTCAAATA
          1 TAACTTCAAATA

       3548 TACATTCTAA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.48, C:0.16, G:0.04, T:0.32


Consensus pattern (13 bp):   
TAACTTCAAATAG

Found at i:5553 original size:70 final size:70

Alignment explanation


    Indices: 5466--5605  Score: 253
    Period size: 70  Copynumber: 2.0  Consensus size: 70

       5456 GAAAGTGATA

                                                                      *      
       5466 CAATATTCAAATCTCATCACAATAAGATAATTCAATATAAATTCAGCATAAATCTGCATAAAATA
          1 CAATATTCAAATCTCATCACAATAAGATAATTCAATATAAATTCAGCATAAATCTGCACAAAATA

                 
       5531 AGCTT
         66 AGCTT

                                                               * *           
       5536 CAATATTCAAATCTCATCACAATAAGATAATTCAATATAAATTCAGCATAATTTTGCACAAAATA
          1 CAATATTCAAATCTCATCACAATAAGATAATTCAATATAAATTCAGCATAAATCTGCACAAAATA

                 
       5601 AGCTT
         66 AGCTT

       5606 AAACAAATTC


Statistics
Matches: 67,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  70   67  1.00

ACGTcount: A:0.46, C:0.17, G:0.06, T:0.31


Consensus pattern (70 bp):   
CAATATTCAAATCTCATCACAATAAGATAATTCAATATAAATTCAGCATAAATCTGCACAAAATA
AGCTT
Done.