Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019664.1 Corchorus olitorius cultivar O-4 contig19697, 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: 25426
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32


Found at i:333 original size:2 final size:2

Alignment explanation


    Indices: 326--351  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

        316 ACTTTCAAAG

                                                  
        326 AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT

        352 TAAATAGTAT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:8297 original size:43 final size:43

Alignment explanation


    Indices: 8236--8321  Score: 172
    Period size: 43  Copynumber: 2.0  Consensus size: 43

       8226 GTCTAGACTT

                                                       
       8236 TTGGGGTTGTTAGAGTAGCTTATATACATCATCCCACGTACGG
          1 TTGGGGTTGTTAGAGTAGCTTATATACATCATCCCACGTACGG

                                                       
       8279 TTGGGGTTGTTAGAGTAGCTTATATACATCATCCCACGTACGG
          1 TTGGGGTTGTTAGAGTAGCTTATATACATCATCCCACGTACGG

       8322 GGGAGATTGT


Statistics
Matches: 43,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  43   43  1.00

ACGTcount: A:0.23, C:0.19, G:0.26, T:0.33


Consensus pattern (43 bp):   
TTGGGGTTGTTAGAGTAGCTTATATACATCATCCCACGTACGG

Found at i:17378 original size:20 final size:21

Alignment explanation


    Indices: 17338--17380  Score: 61
    Period size: 20  Copynumber: 2.1  Consensus size: 21

      17328 TGAGATGTTT

                          *      
      17338 TTATAAAGTCTTTTCCTTTTC
          1 TTATAAAGTCTTTTACTTTTC

                *                
      17359 TTATCAAGTC-TTTACTTTTC
          1 TTATAAAGTCTTTTACTTTTC

              
      17379 TT
          1 TT

      17381 TCTTTCTAAT


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  20   11  0.55
  21    9  0.45

ACGTcount: A:0.19, C:0.19, G:0.05, T:0.58


Consensus pattern (21 bp):   
TTATAAAGTCTTTTACTTTTC

Found at i:25418 original size:205 final size:206

Alignment explanation


    Indices: 25035--25423  Score: 663
    Period size: 205  Copynumber: 1.9  Consensus size: 206

      25025 GGACATATAT

                                   *                             *           
      25035 ATATATATATATAGGGTAATTATTTGATACACCGGCGGTGTAAATTTTGGACTTCACAAGCGGGT
          1 ATATATATATATAGGGTAATTATATGATACACCGGCGGTGTAAATTTTGGACTCCACAAGCGGGT

                                       *                                     
      25100 TGTGGAGTTGACACATGTCCATTTTTTGAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTA
         66 TGTGGAGTTGACACATGTCCATTTTTTAAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTA

                                 *    *                                      
      25165 GAGGACACATGTCACCCTTCAGGACCCGCTTGTGTAGTCTGCTAAACTCCACTGCCGGTGTATTG
        131 GAGGACACATGTCACCCTTCAAGACCAGCTTGTGTAGTCTGCTAAACTCCACTGCCGGTGTATTG

                       
      25230 TATAATTTGCC
        196 TATAATTTGCC

                             *                                               
      25241 ATATATATATATA-GGTGATTATATGATACACCGGCGGTGTAAATTTTGGACTCCACAAGCGGGT
          1 ATATATATATATAGGGTAATTATATGATACACCGGCGGTGTAAATTTTGGACTCCACAAGCGGGT

               *                                        *                    
      25305 TGTTGAGTTGACACATGTCCATTTTTTAAATTAATTAAGTTTTATATATTTCAATCTAGTCCCTA
         66 TGTGGAGTTGACACATGTCCATTTTTTAAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTA

             *                 *    *                *            
      25370 GGGGACACATGTCACCCTTTAAGATCAGCTTGTGTAGTCTGTTAAACTCCACTG
        131 GAGGACACATGTCACCCTTCAAGACCAGCTTGTGTAGTCTGCTAAACTCCACTG

      25424 GCG


Statistics
Matches: 171,  Mismatches: 12, Indels: 1
        0.93            0.07        0.01

Matches are distributed among these distances:
 205  158  0.92
 206   13  0.08

ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35


Consensus pattern (206 bp):   
ATATATATATATAGGGTAATTATATGATACACCGGCGGTGTAAATTTTGGACTCCACAAGCGGGT
TGTGGAGTTGACACATGTCCATTTTTTAAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTA
GAGGACACATGTCACCCTTCAAGACCAGCTTGTGTAGTCTGCTAAACTCCACTGCCGGTGTATTG
TATAATTTGCC
Done.