Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014428.1 Corchorus capsularis cultivar CVL-1 contig14449, 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: 6118
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34


Found at i:855 original size:41 final size:42

Alignment explanation


    Indices: 810--888  Score: 99
    Period size: 42  Copynumber: 1.9  Consensus size: 42

        800 TACACCGGTG

                           *                           
        810 AGATTGGTT-CGGT-GAGAGTAAAATTGGTTACTGTACATGTT
          1 AGATTGGTTACGGTACAGA-TAAAATTGGTTACTGTACATGTT

                 *     *              *           
        851 AGATTTGTTACTGTACAGATAAAATTTGTTACTGTACA
          1 AGATTGGTTACGGTACAGATAAAATTGGTTACTGTACA

        889 AATGAGAATA


Statistics
Matches: 32,  Mismatches: 4, Indels: 3
        0.82            0.10        0.08

Matches are distributed among these distances:
  41    8  0.25
  42   21  0.66
  43    3  0.09

ACGTcount: A:0.30, C:0.09, G:0.23, T:0.38


Consensus pattern (42 bp):   
AGATTGGTTACGGTACAGATAAAATTGGTTACTGTACATGTT

Found at i:862 original size:21 final size:21

Alignment explanation


    Indices: 828--888  Score: 79
    Period size: 21  Copynumber: 2.9  Consensus size: 21

        818 TCGGTGAGAG

                   *              
        828 TAAAATTGGTTACTGTACATG-
          1 TAAAATTTGTTACTGTACA-GA

             * *                 
        849 TTAGATTTGTTACTGTACAGA
          1 TAAAATTTGTTACTGTACAGA

                               
        870 TAAAATTTGTTACTGTACA
          1 TAAAATTTGTTACTGTACA

        889 AATGAGAATA


Statistics
Matches: 34,  Mismatches: 5, Indels: 2
        0.83            0.12        0.05

Matches are distributed among these distances:
  20    1  0.03
  21   33  0.97

ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41


Consensus pattern (21 bp):   
TAAAATTTGTTACTGTACAGA

Found at i:6034 original size:78 final size:78

Alignment explanation


    Indices: 5951--6118  Score: 309
    Period size: 78  Copynumber: 2.2  Consensus size: 78

       5941 TTTTTTTAAC

                          *              *                                *  
       5951 TAAAATAGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGA
          1 TAAAATAGTAAAATGGTAAAATATAATAGCTATAAGGATATTAGATTTAATTATATAAAAATAGA

                         
       6016 GTTTTTAGTTGAG
         66 GTTTTTAGTTGAG

                                                                             
       6029 TAAAATAGTAAAATGGTAAAATATAATAGCTATAAGGATATTAGATTTAATTATATAAAAATAGA
          1 TAAAATAGTAAAATGGTAAAATATAATAGCTATAAGGATATTAGATTTAATTATATAAAAATAGA

                         
       6094 GTTTTTAGTTGAG
         66 GTTTTTAGTTGAG

                        
       6107 TAAAATAGTAAA
          1 TAAAATAGTAAA


Statistics
Matches: 87,  Mismatches: 3, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  78   87  1.00

ACGTcount: A:0.48, C:0.01, G:0.14, T:0.37


Consensus pattern (78 bp):   
TAAAATAGTAAAATGGTAAAATATAATAGCTATAAGGATATTAGATTTAATTATATAAAAATAGA
GTTTTTAGTTGAG
Done.