Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001520.1 Corchorus capsularis cultivar CVL-1 contig01520, 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, 622

Length: 1037
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40


Found at i:94 original size:13 final size:13

Alignment explanation


    Indices: 76--100  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

         66 ATTCTTAATT

                         
         76 TTATTTATTATTC
          1 TTATTTATTATTC

                        
         89 TTATTTATTATT
          1 TTATTTATTATT

        101 GCTGCTATAG


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:0.24, C:0.04, G:0.00, T:0.72


Consensus pattern (13 bp):   
TTATTTATTATTC

Found at i:290 original size:15 final size:15

Alignment explanation


    Indices: 270--307  Score: 62
    Period size: 15  Copynumber: 2.7  Consensus size: 15

        260 GAACAGATAA

                           
        270 GATAAAATAACATAT
          1 GATAAAATAACATAT

                           
        285 GATAAAATAACATAT
          1 GATAAAATAACATAT

                      
        300 -A-AAAATAA
          1 GATAAAATAA

        308 AATAACATAT


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

Matches are distributed among these distances:
  13    7  0.30
  14    1  0.04
  15   15  0.65

ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24


Consensus pattern (15 bp):   
GATAAAATAACATAT

Found at i:331 original size:20 final size:18

Alignment explanation


    Indices: 286--324  Score: 78
    Period size: 18  Copynumber: 2.2  Consensus size: 18

        276 ATAACATATG

                              
        286 ATAAAATAACATATAAAA
          1 ATAAAATAACATATAAAA

                              
        304 ATAAAATAACATATAAAA
          1 ATAAAATAACATATAAAA

               
        322 ATA
          1 ATA

        325 GAAAATAGTA


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

Matches are distributed among these distances:
  18   21  1.00

ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23


Consensus pattern (18 bp):   
ATAAAATAACATATAAAA

Found at i:385 original size:10 final size:10

Alignment explanation


    Indices: 372--421  Score: 55
    Period size: 11  Copynumber: 4.6  Consensus size: 10

        362 CTTTTTTTCA

                 *    
        372 TTTTTGTATT
          1 TTTTTATATT

                        
        382 TTTTTATAGTCT
          1 TTTTTATA-T-T

                       
        394 TTTTTATTATT
          1 TTTTTA-TATT

                      
        405 TTTTTATATT
          1 TTTTTATATT

                   
        415 CTTTTTA
          1 -TTTTTA

        422 CTAAACATTT


Statistics
Matches: 35,  Mismatches: 1, Indels: 7
        0.81            0.02        0.16

Matches are distributed among these distances:
  10   11  0.31
  11   14  0.40
  12    8  0.23
  13    2  0.06

ACGTcount: A:0.16, C:0.04, G:0.04, T:0.76


Consensus pattern (10 bp):   
TTTTTATATT
Done.