Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016514.1 Corchorus olitorius cultivar O-4 contig16547, 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: 28047
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32


Found at i:9217 original size:17 final size:17

Alignment explanation


    Indices: 9197--9230  Score: 68
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       9187 AATTAGTCTC

                             
       9197 TCTTAATAATTTCTCAA
          1 TCTTAATAATTTCTCAA

                             
       9214 TCTTAATAATTTCTCAA
          1 TCTTAATAATTTCTCAA

       9231 ATAGAGACAT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.35, C:0.18, G:0.00, T:0.47


Consensus pattern (17 bp):   
TCTTAATAATTTCTCAA

Found at i:9889 original size:66 final size:66

Alignment explanation


    Indices: 9783--9912  Score: 251
    Period size: 66  Copynumber: 2.0  Consensus size: 66

       9773 ACATGTTAAT

                                                                             
       9783 TTATTAAATCTAACATCAAGTTACAAATATGGAAATTTAATCTTAGAAAGATTTTAGAACAGTCC
          1 TTATTAAATCTAACATCAAGTTACAAATATGGAAATTTAATCTTAGAAAGATTTTAGAACAGTCC

             
       9848 A
         66 A

                                                         *                  
       9849 TTATTAAATCTAACATCAAGTTACAAATATGGAAATTTAATCTTATAAAGATTTTAGAACAGTC
          1 TTATTAAATCTAACATCAAGTTACAAATATGGAAATTTAATCTTAGAAAGATTTTAGAACAGTC

       9913 AATGTCTTCA


Statistics
Matches: 63,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  66   63  1.00

ACGTcount: A:0.44, C:0.12, G:0.10, T:0.35


Consensus pattern (66 bp):   
TTATTAAATCTAACATCAAGTTACAAATATGGAAATTTAATCTTAGAAAGATTTTAGAACAGTCC
A

Found at i:10395 original size:2 final size:2

Alignment explanation


    Indices: 10388--10415  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

      10378 AAACATTTCA

                                                     
      10388 AT 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 AT

      10416 TCATTGATTT


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:26123 original size:15 final size:15

Alignment explanation


    Indices: 26103--26131  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

      26093 TTCATCTTTC

                           
      26103 CTAATGGTTCTATTA
          1 CTAATGGTTCTATTA

                          
      26118 CTAATGGTTCTATT
          1 CTAATGGTTCTATT

      26132 GTATTAAAGG


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.24, C:0.14, G:0.14, T:0.48


Consensus pattern (15 bp):   
CTAATGGTTCTATTA
Done.