Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022008.1 Corchorus olitorius cultivar O-4 contig22041, 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: 7420
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36


Found at i:89 original size:32 final size:32

Alignment explanation


    Indices: 53--116  Score: 94
    Period size: 33  Copynumber: 2.0  Consensus size: 32

         43 AAAAAAGCTA

                                             
         53 AAATAGCGGCGTT-TTCATACGGAAACGCCACT
          1 AAATAGCGGCGTTATT-ATACGGAAACGCCACT

                             *              
         85 AAATAGCGGCGTTCATTGTACGGAAACGCCAC
          1 AAATAGCGGCGTT-ATTATACGGAAACGCCAC

        117 CATTTAGCGG


Statistics
Matches: 29,  Mismatches: 1, Indels: 3
        0.88            0.03        0.09

Matches are distributed among these distances:
  32   13  0.45
  33   14  0.48
  34    2  0.07

ACGTcount: A:0.31, C:0.25, G:0.23, T:0.20


Consensus pattern (32 bp):   
AAATAGCGGCGTTATTATACGGAAACGCCACT

Found at i:3471 original size:50 final size:50

Alignment explanation


    Indices: 3374--3474  Score: 141
    Period size: 50  Copynumber: 2.0  Consensus size: 50

       3364 TTCTTCATTA

                                                   * **       
       3374 TTTCTCTCTTTCAATCTTCTCTCCGGACAAAAGAACACTTTTTACGTGTT
          1 TTTCTCTCTTTCAATCTTCTCTCCGGACAAAAGAACACTGTACACGTGTT

                              *           *                    
       3424 TTTCTCTCTTTCAATCTTGTCTCCGGACATTAA-AACACTGTACACGTGTT
          1 TTTCTCTCTTTCAATCTTCTCTCCGGACA-AAAGAACACTGTACACGTGTT

             
       3474 T
          1 T

       3475 CCATTTCAGA


Statistics
Matches: 45,  Mismatches: 5, Indels: 2
        0.87            0.10        0.04

Matches are distributed among these distances:
  50   43  0.96
  51    2  0.04

ACGTcount: A:0.22, C:0.26, G:0.11, T:0.42


Consensus pattern (50 bp):   
TTTCTCTCTTTCAATCTTCTCTCCGGACAAAAGAACACTGTACACGTGTT

Found at i:5181 original size:69 final size:70

Alignment explanation


    Indices: 5094--5229  Score: 204
    Period size: 69  Copynumber: 2.0  Consensus size: 70

       5084 TTAAGATGCG

                                              *          * * *               
       5094 TTGTCTTTATATGTAATTTTAGCATTTG-GATGTGATTAATAGTGTTTCTACCA-TTTTTTCCTT
          1 TTGTCTTTATATGTAATTTTAGCA-TTGAGATGTAATTAATAGTGCTCCCACCATTTTTTTCCTT

                  
       5157 AGTGCA
         65 AGTGCA

                                                    *                        
       5163 TTGTCTTTATATGTAATTTTAGCATTGAGATGTAATTAATGGTGCTCCCACCATTTTTTTCCTTA
          1 TTGTCTTTATATGTAATTTTAGCATTGAGATGTAATTAATAGTGCTCCCACCATTTTTTTCCTTA

              
       5228 GT
         66 GT

       5230 TGTTAATTTT


Statistics
Matches: 60,  Mismatches: 5, Indels: 3
        0.88            0.07        0.04

Matches are distributed among these distances:
  68    3  0.05
  69   44  0.73
  70   13  0.22

ACGTcount: A:0.22, C:0.13, G:0.15, T:0.49


Consensus pattern (70 bp):   
TTGTCTTTATATGTAATTTTAGCATTGAGATGTAATTAATAGTGCTCCCACCATTTTTTTCCTTA
GTGCA

Found at i:6621 original size:2 final size:2

Alignment explanation


    Indices: 6614--6638  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       6604 AGGGTGTATC

                                                 
       6614 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 A

       6639 CTACATATTA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:6916 original size:57 final size:55

Alignment explanation


    Indices: 6826--6939  Score: 183
    Period size: 57  Copynumber: 2.0  Consensus size: 55

       6816 TATCCGTTTC

                                                                     
       6826 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCCTATCTCTACTTAATTATT
          1 CTTTCACACAATAAATGTTATAATAAATCCTAT--CCCCTATCTCTACTTAATTATT

                    *                   *                    *     
       6883 CTTTCACATAATAAATGTTATAATAAATTCTATCCCCTATCTCTACTTAGTTATT
          1 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCTATCTCTACTTAATTATT

              
       6938 CT
          1 CT

       6940 ACAGAATAAA


Statistics
Matches: 54,  Mismatches: 3, Indels: 2
        0.92            0.05        0.03

Matches are distributed among these distances:
  55   23  0.43
  57   31  0.57

ACGTcount: A:0.32, C:0.24, G:0.03, T:0.41


Consensus pattern (55 bp):   
CTTTCACACAATAAATGTTATAATAAATCCTATCCCCTATCTCTACTTAATTATT

Found at i:7065 original size:42 final size:42

Alignment explanation


    Indices: 7006--7085  Score: 142
    Period size: 42  Copynumber: 1.9  Consensus size: 42

       6996 AAGGATTAGG

                                                      
       7006 ATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTATT
          1 ATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTATT

                                        **        
       7048 ATTTGAGTTGAGTATTTCTTAATTTACAGGGAATTTTC
          1 ATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC

       7086 AAGACTTAGC


Statistics
Matches: 36,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  42   36  1.00

ACGTcount: A:0.29, C:0.07, G:0.15, T:0.49


Consensus pattern (42 bp):   
ATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTATT
Done.