Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009576.1 Corchorus olitorius cultivar O-4 contig09608, 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: 9016
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31


Found at i:39 original size:20 final size:20

Alignment explanation


    Indices: 3--40  Score: 51
    Period size: 20  Copynumber: 1.9  Consensus size: 20

          1 TT

                     *          
          3 ATTTTTTTTTATCTTCTTAG
          1 ATTTTTTTTAATCTTCTTAG

                               
         23 ATTTTCTTTTAAT-TTCTT
          1 ATTTT-TTTTAATCTTCTT

         41 TTTATCTTTT


Statistics
Matches: 16,  Mismatches: 1, Indels: 2
        0.84            0.05        0.11

Matches are distributed among these distances:
  20   10  0.62
  21    6  0.38

ACGTcount: A:0.16, C:0.11, G:0.03, T:0.71


Consensus pattern (20 bp):   
ATTTTTTTTAATCTTCTTAG

Found at i:6461 original size:262 final size:262

Alignment explanation


    Indices: 5996--6520  Score: 1005
    Period size: 262  Copynumber: 2.0  Consensus size: 262

       5986 GATGATATGA

                                 *                        *                  
       5996 CATACTGCAATTCTTTTTCTTTTGATCTTTTAATAATTAGAGGCTTTTTGCAGGCTGTGACTTGT
          1 CATACTGCAATTCTTTTTCTTCTGATCTTTTAATAATTAGAGGCTTCTTGCAGGCTGTGACTTGT

                                  *                                          
       6061 TAACATACTCATCATCTCTTTCTAGGTAAATTTCTTGAATCTTTCCCTAAGATTCTCAAAAACTT
         66 TAACATACTCATCATCTCTTTCCAGGTAAATTTCTTGAATCTTTCCCTAAGATTCTCAAAAACTT

                                                                             
       6126 AAAAAGGCAGTTAAGACTTCATTTAAGCATAACAACAAACACATAAGATGCAAAGAAAACAAACT
        131 AAAAAGGCAGTTAAGACTTCATTTAAGCATAACAACAAACACATAAGATGCAAAGAAAACAAACT

                                                                             
       6191 TAACATAAGTCAGAAACAATTACCTGGAACGAAACCAACCAAACTTTTAGATTCATTCTCCAGGA
        196 TAACATAAGTCAGAAACAATTACCTGGAACGAAACCAACCAAACTTTTAGATTCATTCTCCAGGA

              
       6256 AC
        261 AC

                                                                  *          
       6258 CATACTGCAATTCTTTTTCTTCTGATCTTTTAATAATTAGAGGCTTCTTGCAGGTTGTGACTTGT
          1 CATACTGCAATTCTTTTTCTTCTGATCTTTTAATAATTAGAGGCTTCTTGCAGGCTGTGACTTGT

                                                                             
       6323 TAACATACTCATCATCTCTTTCCAGGTAAATTTCTTGAATCTTTCCCTAAGATTCTCAAAAACTT
         66 TAACATACTCATCATCTCTTTCCAGGTAAATTTCTTGAATCTTTCCCTAAGATTCTCAAAAACTT

                                                                             
       6388 AAAAAGGCAGTTAAGACTTCATTTAAGCATAACAACAAACACATAAGATGCAAAGAAAACAAACT
        131 AAAAAGGCAGTTAAGACTTCATTTAAGCATAACAACAAACACATAAGATGCAAAGAAAACAAACT

                                              *                              
       6453 TAACATAAGTCAGAAACAATTACCTGGAACGAAATCAACCAAACTTTTAGATTCATTCTCCAGGA
        196 TAACATAAGTCAGAAACAATTACCTGGAACGAAACCAACCAAACTTTTAGATTCATTCTCCAGGA

              
       6518 AC
        261 AC

             
       6520 C
          1 C

       6521 CACAATATGA


Statistics
Matches: 258,  Mismatches: 5, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
 262  258  1.00

ACGTcount: A:0.37, C:0.20, G:0.12, T:0.31


Consensus pattern (262 bp):   
CATACTGCAATTCTTTTTCTTCTGATCTTTTAATAATTAGAGGCTTCTTGCAGGCTGTGACTTGT
TAACATACTCATCATCTCTTTCCAGGTAAATTTCTTGAATCTTTCCCTAAGATTCTCAAAAACTT
AAAAAGGCAGTTAAGACTTCATTTAAGCATAACAACAAACACATAAGATGCAAAGAAAACAAACT
TAACATAAGTCAGAAACAATTACCTGGAACGAAACCAACCAAACTTTTAGATTCATTCTCCAGGA
AC

Found at i:6560 original size:17 final size:19

Alignment explanation


    Indices: 6538--6574  Score: 60
    Period size: 17  Copynumber: 2.1  Consensus size: 19

       6528 TGATGAATAA

                               
       6538 AAAAAACAAA-CAGA-AAG
          1 AAAAAACAAAGCAGAGAAG

                               
       6555 AAAAAACAAAGCAGAGAAG
          1 AAAAAACAAAGCAGAGAAG

             
       6574 A
          1 A

       6575 TCAATTTTTC


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  17   10  0.56
  18    4  0.22
  19    4  0.22

ACGTcount: A:0.73, C:0.11, G:0.16, T:0.00


Consensus pattern (19 bp):   
AAAAAACAAAGCAGAGAAG

Done.