Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017244.1 Corchorus olitorius cultivar O-4 contig17277, 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: 28963
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33


Found at i:3937 original size:67 final size:67

Alignment explanation


    Indices: 3865--4007  Score: 250
    Period size: 67  Copynumber: 2.1  Consensus size: 67

       3855 GGCCATGGCC

                                         *                                   
       3865 GCTAATGAATTTTTTAACCTGTTGACACTGACGGAATTAAAGGGGACAGGGGCCATGGCCCCCGT
          1 GCTAATGAATTTTTTAACCTGTTGACACTAACGGAATTAAAGGGGACAGGGGCCATGGCCCCCGT

              
       3930 CG
         66 CG

                                                         *      *      *     
       3932 GCTAATGAATTTTTTAACCTGTTGACACTAACGGAATTAAAGGGGGCAGGGGTCATGGCTCCCGT
          1 GCTAATGAATTTTTTAACCTGTTGACACTAACGGAATTAAAGGGGACAGGGGCCATGGCCCCCGT

              
       3997 CG
         66 CG

                     
       3999 GCTAATGAA
          1 GCTAATGAA

       4008 AACTTGGTGT


Statistics
Matches: 72,  Mismatches: 4, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  67   72  1.00

ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25


Consensus pattern (67 bp):   
GCTAATGAATTTTTTAACCTGTTGACACTAACGGAATTAAAGGGGACAGGGGCCATGGCCCCCGT
CG

Found at i:4884 original size:13 final size:14

Alignment explanation


    Indices: 4866--4897  Score: 57
    Period size: 13  Copynumber: 2.4  Consensus size: 14

       4856 GTTCTAGAAG

                          
       4866 GGGACTTAT-AAAA
          1 GGGACTTATAAAAA

                          
       4879 GGGACTTATAAAAA
          1 GGGACTTATAAAAA

                 
       4893 GGGAC
          1 GGGAC

       4898 ATAGGGAGTA


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  13    9  0.50
  14    9  0.50

ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19


Consensus pattern (14 bp):   
GGGACTTATAAAAA

Found at i:9127 original size:1 final size:1

Alignment explanation


    Indices: 9075--9109  Score: 70
    Period size: 1  Copynumber: 35.0  Consensus size: 1

       9065 TTGGAAATAG

                                               
       9075 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

       9110 CGAGCTTGTT


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   34  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T

Found at i:10451 original size:14 final size:13

Alignment explanation


    Indices: 10420--10465  Score: 56
    Period size: 13  Copynumber: 3.3  Consensus size: 13

      10410 GTCGGGTTTT

                         
      10420 AGTCAGTTTGTTG
          1 AGTCAGTTTGTTG

                     *    
      10433 AGTCAGTTTTTTCG
          1 AGTCAGTTTGTT-G

                           
      10447 AGTCAGTTAGTGTTG
          1 AGTCAGTT--TGTTG

                
      10462 AGTC
          1 AGTC

      10466 TGAGTCTGGC


Statistics
Matches: 28,  Mismatches: 2, Indels: 4
        0.82            0.06        0.12

Matches are distributed among these distances:
  13   11  0.39
  14    9  0.32
  15    5  0.18
  16    3  0.11

ACGTcount: A:0.17, C:0.11, G:0.28, T:0.43


Consensus pattern (13 bp):   
AGTCAGTTTGTTG

Found at i:13669 original size:17 final size:17

Alignment explanation


    Indices: 13647--13680  Score: 52
    Period size: 17  Copynumber: 2.0  Consensus size: 17

      13637 TTTATAAGAA

                              
      13647 TATAAA-TACTAATTTTC
          1 TATAAATTA-TAATTTTC

                             
      13664 TATAAATTATAATTTTC
          1 TATAAATTATAATTTTC

      13681 AAATCAAGAT


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  17   14  0.88
  18    2  0.12

ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50


Consensus pattern (17 bp):   
TATAAATTATAATTTTC

Found at i:28389 original size:31 final size:31

Alignment explanation


    Indices: 28351--28413  Score: 117
    Period size: 31  Copynumber: 2.0  Consensus size: 31

      28341 TGTTAGAAAA

                          *                
      28351 ATAAGGGTATAATGTGCAATTCAAAAGTTTT
          1 ATAAGGGTATAATGGGCAATTCAAAAGTTTT

                                           
      28382 ATAAGGGTATAATGGGCAATTCAAAAGTTTT
          1 ATAAGGGTATAATGGGCAATTCAAAAGTTTT

             
      28413 A
          1 A

      28414 CAAAACTCGT


Statistics
Matches: 31,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  31   31  1.00

ACGTcount: A:0.40, C:0.06, G:0.21, T:0.33


Consensus pattern (31 bp):   
ATAAGGGTATAATGGGCAATTCAAAAGTTTT
Done.