Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012705.1 Corchorus olitorius cultivar O-4 contig12738, 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: 11922
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36


Found at i:84 original size:19 final size:18

Alignment explanation


    Indices: 55--96  Score: 57
    Period size: 19  Copynumber: 2.3  Consensus size: 18

         45 TGAGTAGTTT

                *       *     
         55 TTAAGTAAAAATGTAATA
          1 TTAAATAAAAATATAATA

                               
         73 TATAAATAAAAATATAATA
          1 T-TAAATAAAAATATAATA

                 
         92 TTAAA
          1 TTAAA

         97 ATAACTAATA


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  18    5  0.24
  19   16  0.76

ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33


Consensus pattern (18 bp):   
TTAAATAAAAATATAATA

Found at i:100 original size:19 final size:19

Alignment explanation


    Indices: 60--96  Score: 58
    Period size: 19  Copynumber: 2.0  Consensus size: 19

         50 AGTTTTTAAG

                   *           
         60 TAAAAATGTAATATATAAA
          1 TAAAAATATAATATATAAA

                               
         79 TAAAAATATAATAT-TAAA
          1 TAAAAATATAATATATAAA

         97 ATAACTAATA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  18    4  0.24
  19   13  0.76

ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32


Consensus pattern (19 bp):   
TAAAAATATAATATATAAA

Found at i:2151 original size:19 final size:18

Alignment explanation


    Indices: 2127--2165  Score: 51
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       2117 TTAACCTCTG

                         *     
       2127 TGTGTTTAAATTTTTTTTC
          1 TGTGTTT-AATTTGTTTTC

                   *          
       2146 TGTGTTTCATTTGTTTTC
          1 TGTGTTTAATTTGTTTTC

              
       2164 TG
          1 TG

       2166 ATTTCTTTGG


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  18   11  0.61
  19    7  0.39

ACGTcount: A:0.10, C:0.08, G:0.15, T:0.67


Consensus pattern (18 bp):   
TGTGTTTAATTTGTTTTC

Found at i:2195 original size:14 final size:15

Alignment explanation


    Indices: 2176--2205  Score: 53
    Period size: 14  Copynumber: 2.1  Consensus size: 15

       2166 ATTTCTTTGG

                           
       2176 TGATTCTA-TTTCTT
          1 TGATTCTATTTTCTT

                           
       2190 TGATTCTATTTTCTT
          1 TGATTCTATTTTCTT

             
       2205 T
          1 T

       2206 TGCTCTTCTT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    8  0.53
  15    7  0.47

ACGTcount: A:0.13, C:0.13, G:0.07, T:0.67


Consensus pattern (15 bp):   
TGATTCTATTTTCTT

Found at i:6262 original size:6 final size:6

Alignment explanation


    Indices: 6251--6293  Score: 79
    Period size: 6  Copynumber: 7.3  Consensus size: 6

       6241 TATAGCTTTC

                                                               
       6251 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTT-TT TT
          1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TT

       6294 CAATGTATTT


Statistics
Matches: 37,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
   5    4  0.11
   6   33  0.89

ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86


Consensus pattern (6 bp):   
TTTCTT

Found at i:6507 original size:2 final size:2

Alignment explanation


    Indices: 6500--6526  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       6490 TTGTTGTTGG

                                                    
       6500 AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT A

       6527 AGTTCATTTT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Done.