Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020361.1 Corchorus olitorius cultivar O-4 contig20394, 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: 28371
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:3685 original size:22 final size:22

Alignment explanation


    Indices: 3655--3703  Score: 73
    Period size: 22  Copynumber: 2.2  Consensus size: 22

       3645 TCCATTCGTT

                                  
       3655 TTTTGTTTGACTTTTTT-AGTG
          1 TTTTGTTTGACTTTTTTCAGTG

                       *           
       3676 TTTTGCTTTGATTTTTTTCAGTG
          1 TTTTG-TTTGACTTTTTTCAGTG

                 
       3699 TTTTG
          1 TTTTG

       3704 GTTTTGAATT


Statistics
Matches: 25,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  21    5  0.20
  22   11  0.44
  23    9  0.36

ACGTcount: A:0.08, C:0.06, G:0.18, T:0.67


Consensus pattern (22 bp):   
TTTTGTTTGACTTTTTTCAGTG

Found at i:3715 original size:23 final size:22

Alignment explanation


    Indices: 3655--3715  Score: 61
    Period size: 23  Copynumber: 2.7  Consensus size: 22

       3645 TCCATTCGTT

                       *     *    
       3655 TTTTG-TTTGACTTTTTTAGTG
          1 TTTTGCTTTGAATTTTTCAGTG

                        *          
       3676 TTTTGCTTTGATTTTTTTCAGTG
          1 TTTTGCTTTGA-ATTTTTCAGTG

                  *          
       3699 TTTTGGTTTTGAATTTT
          1 TTTT-GCTTTGAATTTT

       3716 GATGGATCCG


Statistics
Matches: 33,  Mismatches: 4, Indels: 4
        0.80            0.10        0.10

Matches are distributed among these distances:
  21    5  0.15
  22    5  0.15
  23   17  0.52
  24    6  0.18

ACGTcount: A:0.10, C:0.05, G:0.18, T:0.67


Consensus pattern (22 bp):   
TTTTGCTTTGAATTTTTCAGTG

Found at i:3976 original size:13 final size:13

Alignment explanation


    Indices: 3958--3983  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       3948 TTTTATTTCT

                         
       3958 TTCAAAATAAACC
          1 TTCAAAATAAACC

                         
       3971 TTCAAAATAAACC
          1 TTCAAAATAAACC

       3984 AATGAAGTCA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.54, C:0.23, G:0.00, T:0.23


Consensus pattern (13 bp):   
TTCAAAATAAACC

Found at i:4052 original size:71 final size:72

Alignment explanation


    Indices: 3935--4078  Score: 263
    Period size: 71  Copynumber: 2.0  Consensus size: 72

       3925 TATTTTTAAT

                                                                             
       3935 TTATTTTTTTATTTTTTATTTCTTTCAAAATAAACCTTCAAAATAAACCAATGAAGTCATGTAAT
          1 TTATTTTTTTATTTTTTATTTCTTTCAAAATAAACCTTCAAAATAAACCAATGAAGTCATGTAAT

                   
       4000 GTACAAA
         66 GTACAAA

                      *                           *                          
       4007 TTATTTTTTTCTTTTTT-TTTCTTTCAAAATAAACCTTTAAAATAAACCAATGAAGTCATGTAAT
          1 TTATTTTTTTATTTTTTATTTCTTTCAAAATAAACCTTCAAAATAAACCAATGAAGTCATGTAAT

                   
       4071 GTACAAA
         66 GTACAAA

             
       4078 T
          1 T

       4079 GTAAACAAGC


Statistics
Matches: 70,  Mismatches: 2, Indels: 1
        0.96            0.03        0.01

Matches are distributed among these distances:
  71   54  0.77
  72   16  0.23

ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44


Consensus pattern (72 bp):   
TTATTTTTTTATTTTTTATTTCTTTCAAAATAAACCTTCAAAATAAACCAATGAAGTCATGTAAT
GTACAAA

Found at i:9937 original size:13 final size:13

Alignment explanation


    Indices: 9919--9944  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       9909 TTAGGTTTTT

                         
       9919 TTAATTATTAGTA
          1 TTAATTATTAGTA

                         
       9932 TTAATTATTAGTA
          1 TTAATTATTAGTA

       9945 ATAACATGTG


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54


Consensus pattern (13 bp):   
TTAATTATTAGTA
Done.