Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014295.1 Corchorus capsularis cultivar CVL-1 contig14316, 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: 3694
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.30


Found at i:1133 original size:19 final size:18

Alignment explanation


    Indices: 1100--1135  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       1090 TTGAAATAAT

                              
       1100 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
       1118 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

       1136 GAAATCTTGA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA

Found at i:2024 original size:33 final size:32

Alignment explanation


    Indices: 1963--2054  Score: 105
    Period size: 33  Copynumber: 2.8  Consensus size: 32

       1953 TTGGTATGGA

                  *   *      *              
       1963 TTAAATTCCATTATTTATGGGCGTTTTCTT-C
          1 TTAAATGCCACTATTTAGGGGCGTTTTCTTCC

                                    *         
       1994 TTAAATCGCCACTATATTAGGGGCATTTTCTTCC
          1 TTAAAT-GCCACTAT-TTAGGGGCGTTTTCTTCC

               **                      
       2028 TTAGGTGCCACTATTTAGGGGCGTTTT
          1 TTAAATGCCACTATTTAGGGGCGTTTT

       2055 TTTTCATAAA


Statistics
Matches: 51,  Mismatches: 7, Indels: 5
        0.81            0.11        0.08

Matches are distributed among these distances:
  31    6  0.12
  32   18  0.35
  33   22  0.43
  34    5  0.10

ACGTcount: A:0.20, C:0.18, G:0.18, T:0.43


Consensus pattern (32 bp):   
TTAAATGCCACTATTTAGGGGCGTTTTCTTCC

Found at i:2069 original size:33 final size:32

Alignment explanation


    Indices: 1974--2069  Score: 95
    Period size: 33  Copynumber: 2.9  Consensus size: 32

       1964 TAAATTCCAT

                  *             *            
       1974 TATTTATGGGCGTTTTCTTCTTAAA-TCGCCAC
          1 TATTTAGGGGCGTTTTCTTCATAAAGT-GCCAC

                        *        * * *       
       2006 TATATTAGGGGCATTTTCTTCCTTAGGTGCCAC
          1 TAT-TTAGGGGCGTTTTCTTCATAAAGTGCCAC

                             *             
       2039 TATTTAGGGGCGTTTTTTTTCATAAAGTGCC
          1 TATTTAGGGGCG-TTTTCTTCATAAAGTGCC

       2070 CTTATTTTGC


Statistics
Matches: 51,  Mismatches: 10, Indels: 5
        0.77            0.15        0.08

Matches are distributed among these distances:
  32   11  0.22
  33   39  0.76
  34    1  0.02

ACGTcount: A:0.19, C:0.19, G:0.20, T:0.43


Consensus pattern (32 bp):   
TATTTAGGGGCGTTTTCTTCATAAAGTGCCAC

Found at i:3224 original size:27 final size:27

Alignment explanation


    Indices: 3194--3318  Score: 198
    Period size: 27  Copynumber: 4.7  Consensus size: 27

       3184 GTGAACTCAA

                                       
       3194 AATGACCAAAATGCCCCTGAATGTAAG
          1 AATGACCAAAATGCCCCTGAATGTAAG

                  *                    
       3221 AATGACAAAAATGCCCCTGAATGTAA-
          1 AATGACCAAAATGCCCCTGAATGTAAG

                       *          *    
       3247 AATGACCAAAAAGCCCCTGAATATAAG
          1 AATGACCAAAATGCCCCTGAATGTAAG

                  *                   *
       3274 AATGACAAAAATGCCCCTGAATGTAAA
          1 AATGACCAAAATGCCCCTGAATGTAAG

                              
       3301 AATGACCAAAATGCCCCT
          1 AATGACCAAAATGCCCCT

       3319 AGGTGACCCT


Statistics
Matches: 88,  Mismatches: 9, Indels: 2
        0.89            0.09        0.02

Matches are distributed among these distances:
  26   23  0.26
  27   65  0.74

ACGTcount: A:0.45, C:0.22, G:0.15, T:0.18


Consensus pattern (27 bp):   
AATGACCAAAATGCCCCTGAATGTAAG

Found at i:3274 original size:53 final size:54

Alignment explanation


    Indices: 3192--3318  Score: 229
    Period size: 53  Copynumber: 2.4  Consensus size: 54

       3182 AAGTGAACTC

                                    *                             
       3192 AAAATGACCAAAATGCCCCTGAATGTAAGAATGACAAAAATGCCCCTGAATGT-
          1 AAAATGACCAAAATGCCCCTGAATATAAGAATGACAAAAATGCCCCTGAATGTA

                         *                                        
       3245 AAAATGACCAAAAAGCCCCTGAATATAAGAATGACAAAAATGCCCCTGAATGTA
          1 AAAATGACCAAAATGCCCCTGAATATAAGAATGACAAAAATGCCCCTGAATGTA

                                
       3299 AAAATGACCAAAATGCCCCT
          1 AAAATGACCAAAATGCCCCT

       3319 AGGTGACCCT


Statistics
Matches: 70,  Mismatches: 3, Indels: 1
        0.95            0.04        0.01

Matches are distributed among these distances:
  53   51  0.73
  54   19  0.27

ACGTcount: A:0.46, C:0.22, G:0.15, T:0.17


Consensus pattern (54 bp):   
AAAATGACCAAAATGCCCCTGAATATAAGAATGACAAAAATGCCCCTGAATGTA

Found at i:3606 original size:25 final size:26

Alignment explanation


    Indices: 3578--3637  Score: 70
    Period size: 26  Copynumber: 2.3  Consensus size: 26

       3568 GACTAGAGAC

                 *                     
       3578 CTCAAGCAGGA-TTTGAAAT-AAAACT
          1 CTCAAACAGGATTTTG-AATCAAAACT

                    *                 
       3603 CTCAAACATGATTTTGAATCAAAACT
          1 CTCAAACAGGATTTTGAATCAAAACT

               *     
       3629 CTCGAACAG
          1 CTCAAACAG

       3638 AGACCTAAAA


Statistics
Matches: 29,  Mismatches: 4, Indels: 3
        0.81            0.11        0.08

Matches are distributed among these distances:
  25   12  0.41
  26   17  0.59

ACGTcount: A:0.42, C:0.20, G:0.13, T:0.25


Consensus pattern (26 bp):   
CTCAAACAGGATTTTGAATCAAAACT
Done.