Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021660.1 Corchorus olitorius cultivar O-4 contig21693, 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: 7691
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36


Found at i:334 original size:13 final size:13

Alignment explanation


    Indices: 316--342  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

        306 GGGGAGGAAA

                         
        316 TAGGTGAATACTT
          1 TAGGTGAATACTT

                         
        329 TAGGTGAATACTT
          1 TAGGTGAATACTT

             
        342 T
          1 T

        343 TAGAAAAAAA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.30, C:0.07, G:0.22, T:0.41


Consensus pattern (13 bp):   
TAGGTGAATACTT

Found at i:4133 original size:192 final size:192

Alignment explanation


    Indices: 3804--4189  Score: 700
    Period size: 192  Copynumber: 2.0  Consensus size: 192

       3794 TTCCAAAATG

                                               *                             
       3804 ATCCAATCAGTCTTTCTACTCTTAAAGAACTCCTATCAAAGTTTTGTTCTTCATCAGGGCAAACT
          1 ATCCAATCAGTCTTTCTACTCTTAAAGAACTCCTACCAAAGTTTTGTTCTTCATCAGGGCAAACT

                                                                             
       3869 ATAAACTTCTCCAAGTGCTCAATTATCTTCTCTCAAAATACCTGCCCTGACATTAAAATTGATGT
         66 ATAAACTTCTCCAAGTGCTCAATTATCTTCTCTCAAAATACCTGCCCTGACATTAAAATTGATGT

            *                             *                      *        
       3934 GTCTCAATTCATCAACATTCCCCTTTCTTCTAGACTTGATAAATATCTTGGGCTACCCATGC
        131 ATCTCAATTCATCAACATTCCCCTTTCTTCCAGACTTGATAAATATCTTGGGCCACCCATGC

                                           *  *                              
       3996 ATCCAATCAGTCTTTCTACTCTTAAAGAACTTCTGCCAAAGTTTTGTTCTTCATCAGGGCAAACT
          1 ATCCAATCAGTCTTTCTACTCTTAAAGAACTCCTACCAAAGTTTTGTTCTTCATCAGGGCAAACT

                                      *                                      
       4061 ATAAACTTCTCCAAGTGCTCAATTATTTTCTCTCAAAATACCTGCCCTGACATTAAAATTGATGT
         66 ATAAACTTCTCCAAGTGCTCAATTATCTTCTCTCAAAATACCTGCCCTGACATTAAAATTGATGT

                      *                                                   
       4126 ATCTCAATTCTTCAACATTCCCCTTTCTTCCAGACTTGATAAATATCTTGGGCCACCCATGC
        131 ATCTCAATTCATCAACATTCCCCTTTCTTCCAGACTTGATAAATATCTTGGGCCACCCATGC

              
       4188 AT
          1 AT

       4190 TTTGGTCGAT


Statistics
Matches: 186,  Mismatches: 8, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
 192  186  1.00

ACGTcount: A:0.28, C:0.26, G:0.10, T:0.35


Consensus pattern (192 bp):   
ATCCAATCAGTCTTTCTACTCTTAAAGAACTCCTACCAAAGTTTTGTTCTTCATCAGGGCAAACT
ATAAACTTCTCCAAGTGCTCAATTATCTTCTCTCAAAATACCTGCCCTGACATTAAAATTGATGT
ATCTCAATTCATCAACATTCCCCTTTCTTCCAGACTTGATAAATATCTTGGGCCACCCATGC

Found at i:6256 original size:2 final size:2

Alignment explanation


    Indices: 6249--6304  Score: 78
    Period size: 2  Copynumber: 28.5  Consensus size: 2

       6239 ATTTTGAACA

                                                               *          
       6249 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

            *  *                  
       6291 CT TT AT AT -T AT AT A
          1 AT AT AT AT AT AT AT A

       6305 AGTCTAAACT


Statistics
Matches: 48,  Mismatches: 5, Indels: 2
        0.87            0.09        0.04

Matches are distributed among these distances:
   1    1  0.02
   2   47  0.98

ACGTcount: A:0.45, C:0.04, G:0.00, T:0.52


Consensus pattern (2 bp):   
AT

Done.