Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023691.1 Corchorus olitorius cultivar O-4 contig23724, 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: 8839
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33


Found at i:3287 original size:16 final size:16

Alignment explanation


    Indices: 3266--3300  Score: 70
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       3256 TAAGCGTAAG

                            
       3266 CAAAATCTTGTCTAAA
          1 CAAAATCTTGTCTAAA

                            
       3282 CAAAATCTTGTCTAAA
          1 CAAAATCTTGTCTAAA

               
       3298 CAA
          1 CAA

       3301 CCAAGCTGCT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   19  1.00

ACGTcount: A:0.46, C:0.20, G:0.06, T:0.29


Consensus pattern (16 bp):   
CAAAATCTTGTCTAAA

Found at i:4250 original size:49 final size:48

Alignment explanation


    Indices: 4143--4279  Score: 145
    Period size: 49  Copynumber: 2.8  Consensus size: 48

       4133 AGCGTGTCAA

                       *                  *               *  
       4143 TCAATTTTGTTATAAAAATTGATAAGAAGTTC-AGG-AAATGTAAATGT
          1 TCAATTTTGTTGTAAAAATTGATAA-AAGTGCAAGGAAAATGTAAAGGT

             *    *                                           
       4190 TTAATTATGTTGTAAAAATTGATTAAAACGTGCAAGGAAAAT-TAAAGGT
          1 TCAATTTTGTTGTAAAAATTGA-TAAAA-GTGCAAGGAAAATGTAAAGGT

                         *         *                 
       4239 TCAATTTTGTTGTCAAAATTGAGAAAAAGGTGCAAGGAAAA
          1 TCAATTTTGTTGTAAAAATTGA-TAAAA-GTGCAAGGAAAA

       4280 GGAAAGATTG


Statistics
Matches: 75,  Mismatches: 11, Indels: 6
        0.82            0.12        0.07

Matches are distributed among these distances:
  47   21  0.28
  48    6  0.08
  49   44  0.59
  50    4  0.05

ACGTcount: A:0.44, C:0.05, G:0.19, T:0.32


Consensus pattern (48 bp):   
TCAATTTTGTTGTAAAAATTGATAAAAGTGCAAGGAAAATGTAAAGGT
Done.