Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016028.1 Corchorus capsularis cultivar CVL-1 contig16049, 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: 11960
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.29


Found at i:55 original size:2 final size:2

Alignment explanation


    Indices: 48--77  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

         38 TTATGGATGA

                                                        
         48 AT 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 AT

         78 GATCATCTTG


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:536 original size:2 final size:2

Alignment explanation


    Indices: 498--522  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

        488 TAGTTTAATG

                                                 
        498 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

        523 CACACACATA


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:2011 original size:29 final size:29

Alignment explanation


    Indices: 1956--2014  Score: 73
    Period size: 29  Copynumber: 2.0  Consensus size: 29

       1946 TTAAAATCTT

                   *     *    *          
       1956 AAGTATATTACTATTTTTTTACAAAAAAA
          1 AAGTATACTACTAATTTTGTACAAAAAAA

                                * *      
       1985 AAGTATACTACTAATTTTGTCCTAAAAAA
          1 AAGTATACTACTAATTTTGTACAAAAAAA

             
       2014 A
          1 A

       2015 CCTATTATTA


Statistics
Matches: 25,  Mismatches: 5, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  29   25  1.00

ACGTcount: A:0.47, C:0.10, G:0.05, T:0.37


Consensus pattern (29 bp):   
AAGTATACTACTAATTTTGTACAAAAAAA

Found at i:10187 original size:30 final size:29

Alignment explanation


    Indices: 10150--10224  Score: 114
    Period size: 29  Copynumber: 2.6  Consensus size: 29

      10140 GTTTTAGAGG

                                          
      10150 GGGCAAAATGTCCAAAATTGAGAGTTCAGA
          1 GGGCAAAATGTCCAAAATTGA-AGTTCAGA

            *                           *
      10180 TGGCAAAATGTCCAAAATTGAAGTTCAGG
          1 GGGCAAAATGTCCAAAATTGAAGTTCAGA

                    *       
      10209 GGGCAAAACGTCCAAA
          1 GGGCAAAATGTCCAAA

      10225 CGCTACAAGT


Statistics
Matches: 41,  Mismatches: 4, Indels: 1
        0.89            0.09        0.02

Matches are distributed among these distances:
  29   21  0.51
  30   20  0.49

ACGTcount: A:0.40, C:0.16, G:0.25, T:0.19


Consensus pattern (29 bp):   
GGGCAAAATGTCCAAAATTGAAGTTCAGA

Found at i:10214 original size:29 final size:30

Alignment explanation


    Indices: 10147--10224  Score: 122
    Period size: 30  Copynumber: 2.6  Consensus size: 30

      10137 ATCGTTTTAG

                                          
      10147 AGGGGGCAAAATGTCCAAAATTGAGAGTTC
          1 AGGGGGCAAAATGTCCAAAATTGAGAGTTC

              **                          
      10177 AGATGGCAAAATGTCCAAAATTGA-AGTTC
          1 AGGGGGCAAAATGTCCAAAATTGAGAGTTC

                       *       
      10206 AGGGGGCAAAACGTCCAAA
          1 AGGGGGCAAAATGTCCAAA

      10225 CGCTACAAGT


Statistics
Matches: 43,  Mismatches: 5, Indels: 1
        0.88            0.10        0.02

Matches are distributed among these distances:
  29   21  0.49
  30   22  0.51

ACGTcount: A:0.40, C:0.15, G:0.27, T:0.18


Consensus pattern (30 bp):   
AGGGGGCAAAATGTCCAAAATTGAGAGTTC
Done.