Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019871.1 Corchorus olitorius cultivar O-4 contig19904, 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: 30333
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30


Found at i:389 original size:16 final size:15

Alignment explanation


    Indices: 351--392  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

        341 ACAGAGATTG

                   *       
        351 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
        366 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
        381 ACTAGAAAACAA
          1 AC-AGAAAACAA

        393 AGCAGAGTAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA

Found at i:2014 original size:22 final size:21

Alignment explanation


    Indices: 1980--2020  Score: 55
    Period size: 22  Copynumber: 1.9  Consensus size: 21

       1970 AATTAAGCAT

                   **             
       1980 AAATGGGTGTAAAAACATAGTA
          1 AAATGGGCATAAAAA-ATAGTA

                               
       2002 AAATGGGCATAAAAAATAG
          1 AAATGGGCATAAAAAATAG

       2021 GGTTGTTTTT


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  21    4  0.24
  22   13  0.76

ACGTcount: A:0.54, C:0.05, G:0.22, T:0.20


Consensus pattern (21 bp):   
AAATGGGCATAAAAAATAGTA

Found at i:12230 original size:27 final size:26

Alignment explanation


    Indices: 12180--12230  Score: 68
    Period size: 26  Copynumber: 1.9  Consensus size: 26

      12170 ACATATGCAA

                               *      
      12180 AAATGCAATTTTAATAAAATAGAACT
          1 AAATGCAATTTTAATAAAACAGAACT

                                      
      12206 AAATGCAATTTTTAA-AAAAGCAGAA
          1 AAATGCAA-TTTTAATAAAA-CAGAA

      12231 ATAAGATGGA


Statistics
Matches: 22,  Mismatches: 1, Indels: 3
        0.85            0.04        0.12

Matches are distributed among these distances:
  26   12  0.55
  27   10  0.45

ACGTcount: A:0.55, C:0.08, G:0.10, T:0.27


Consensus pattern (26 bp):   
AAATGCAATTTTAATAAAACAGAACT

Found at i:22151 original size:22 final size:21

Alignment explanation


    Indices: 22123--22176  Score: 60
    Period size: 19  Copynumber: 2.6  Consensus size: 21

      22113 GAAGTTCGTG

                                  
      22123 TTTGAAGACTTATTGAAGATAA
          1 TTTGAAGA-TTATTGAAGATAA

                               * 
      22145 TTTGAAGA-T-TTGAAGATCA
          1 TTTGAAGATTATTGAAGATAA

                          
      22164 -TTGAAGAATTATT
          1 TTTGAAG-ATTATT

      22177 TCCAAGAAGC


Statistics
Matches: 28,  Mismatches: 1, Indels: 7
        0.78            0.03        0.19

Matches are distributed among these distances:
  18    6  0.21
  19   10  0.36
  20    2  0.07
  21    2  0.07
  22    8  0.29

ACGTcount: A:0.39, C:0.04, G:0.19, T:0.39


Consensus pattern (21 bp):   
TTTGAAGATTATTGAAGATAA

Found at i:23772 original size:58 final size:58

Alignment explanation


    Indices: 23682--23797  Score: 232
    Period size: 58  Copynumber: 2.0  Consensus size: 58

      23672 CCCTAGCTAT

                                                                      
      23682 CTTTAGTTAGTAATTGTTGGGATTTTTATTTTTATGATTTGCTGACGACCGATCATAA
          1 CTTTAGTTAGTAATTGTTGGGATTTTTATTTTTATGATTTGCTGACGACCGATCATAA

                                                                      
      23740 CTTTAGTTAGTAATTGTTGGGATTTTTATTTTTATGATTTGCTGACGACCGATCATAA
          1 CTTTAGTTAGTAATTGTTGGGATTTTTATTTTTATGATTTGCTGACGACCGATCATAA

      23798 ATTTTGGCGC


Statistics
Matches: 58,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  58   58  1.00

ACGTcount: A:0.24, C:0.10, G:0.19, T:0.47


Consensus pattern (58 bp):   
CTTTAGTTAGTAATTGTTGGGATTTTTATTTTTATGATTTGCTGACGACCGATCATAA
Done.