Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013517.1 Corchorus olitorius cultivar O-4 contig13550, 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: 23551
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33


Found at i:206 original size:18 final size:18

Alignment explanation


    Indices: 183--219  Score: 56
    Period size: 18  Copynumber: 2.1  Consensus size: 18

        173 CTCCTCTATC

                     *        
        183 ATGAAAACACTTCTTTTT
          1 ATGAAAACAATTCTTTTT

                        *     
        201 ATGAAAACAATTTTTTTT
          1 ATGAAAACAATTCTTTTT

             
        219 A
          1 A

        220 ATTACCCTTT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46


Consensus pattern (18 bp):   
ATGAAAACAATTCTTTTT

Found at i:9353 original size:30 final size:30

Alignment explanation


    Indices: 9314--9373  Score: 77
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       9304 CAATTCTTGC

                *                *         
       9314 TCTTGAAATTATCCTTCAAT-GGTCTTCAAA
          1 TCTTCAAATTAT-CTTCAATAAGTCTTCAAA

                      *                   
       9344 TCTTCAAATTGTCTTCAATAAGTCTTCAAA
          1 TCTTCAAATTATCTTCAATAAGTCTTCAAA

       9374 CACGAACTTC


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  29    7  0.27
  30   19  0.73

ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40


Consensus pattern (30 bp):   
TCTTCAAATTATCTTCAATAAGTCTTCAAA

Found at i:9949 original size:19 final size:19

Alignment explanation


    Indices: 9927--9977  Score: 61
    Period size: 19  Copynumber: 2.7  Consensus size: 19

       9917 GGGCTGAAAT

                               
       9927 TAATTAATTATTAATTAAA
          1 TAATTAATTATTAATTAAA

                         *   *  
       9946 TAA-TAATTATTTTATTGAA
          1 TAATTAATTA-TTAATTAAA

                          
       9965 TAATT-ATTATTAA
          1 TAATTAATTATTAA

       9978 AAATCCTACA


Statistics
Matches: 27,  Mismatches: 3, Indels: 5
        0.77            0.09        0.14

Matches are distributed among these distances:
  18    9  0.33
  19   17  0.63
  20    1  0.04

ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51


Consensus pattern (19 bp):   
TAATTAATTATTAATTAAA

Found at i:18359 original size:2 final size:2

Alignment explanation


    Indices: 18352--18376  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

      18342 ATAGTTTAAA

                                                 
      18352 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

      18377 AACAAACAAT


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:19731 original size:18 final size:18

Alignment explanation


    Indices: 19708--19747  Score: 62
    Period size: 18  Copynumber: 2.2  Consensus size: 18

      19698 TTGAACTTGG

                   *         *
      19708 ATTTGTTTTTTTATTTTT
          1 ATTTGTTGTTTTATTTTC

                              
      19726 ATTTGTTGTTTTATTTTC
          1 ATTTGTTGTTTTATTTTC

                
      19744 ATTT
          1 ATTT

      19748 TTCTGAATTT


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  18   20  1.00

ACGTcount: A:0.12, C:0.03, G:0.07, T:0.78


Consensus pattern (18 bp):   
ATTTGTTGTTTTATTTTC
Done.