Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004846.1 Corchorus capsularis cultivar CVL-1 contig04864, 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: 4334
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35


Found at i:2093 original size:2 final size:2

Alignment explanation


    Indices: 2086--2115  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

       2076 ACAAGAGGGT

                                                        
       2086 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       2116 CTAGTAATGA


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:2197 original size:18 final size:19

Alignment explanation


    Indices: 2155--2203  Score: 66
    Period size: 18  Copynumber: 2.7  Consensus size: 19

       2145 TTAATAATTT

                               
       2155 ATAAAAT-ATATAAAAATA
          1 ATAAAATAATATAAAAATA

            *              *   
       2173 TTAAAATAATATAAATATA
          1 ATAAAATAATATAAAAATA

                         
       2192 AT-AAATAATATA
          1 ATAAAATAATATA

       2204 TTATAATTTG


Statistics
Matches: 27,  Mismatches: 3, Indels: 2
        0.84            0.09        0.06

Matches are distributed among these distances:
  18   16  0.59
  19   11  0.41

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


Consensus pattern (19 bp):   
ATAAAATAATATAAAAATA

Found at i:2268 original size:27 final size:27

Alignment explanation


    Indices: 2187--2273  Score: 93
    Period size: 27  Copynumber: 3.0  Consensus size: 27

       2177 AATAATATAA

                  *                     *  
       2187 ATATAATAAATAATATATTATAATTTGTAAT
          1 ATATAAAAAATAATA-A-T-TAATTT-TTAT

                 *  *                   
       2218 ATATATAAGATGAATAATTAATTTTTAT
          1 ATATAAAAAAT-AATAATTAATTTTTAT

                                       
       2246 ATATAAAAAATAATAATTAATTTTTAT
          1 ATATAAAAAATAATAATTAATTTTTAT

             
       2273 A
          1 A

       2274 AATTATATAT


Statistics
Matches: 49,  Mismatches: 6, Indels: 6
        0.80            0.10        0.10

Matches are distributed among these distances:
  27   17  0.35
  28   12  0.24
  29    6  0.12
  30    1  0.02
  31    9  0.18
  32    4  0.08

ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45


Consensus pattern (27 bp):   
ATATAAAAAATAATAATTAATTTTTAT
Done.