Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014516.1 Corchorus capsularis cultivar CVL-1 contig14537, 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: 16946
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32


Found at i:685 original size:40 final size:40

Alignment explanation


    Indices: 640--721  Score: 146
    Period size: 40  Copynumber: 2.0  Consensus size: 40

        630 CTAAAATTGC

                                                *   
        640 GATAATTCCCTTCAAGTAATTCTTTGCTATGAAAATTAAG
          1 GATAATTCCCTTCAAGTAATTCTTTGCTATGAAAATCAAG

                          *                         
        680 GATAATTCCCTTCACGTAATTCTTTGCTATGAAAATCAAG
          1 GATAATTCCCTTCAAGTAATTCTTTGCTATGAAAATCAAG

              
        720 GA
          1 GA

        722 GTGGCTTCGT


Statistics
Matches: 40,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  40   40  1.00

ACGTcount: A:0.34, C:0.17, G:0.13, T:0.35


Consensus pattern (40 bp):   
GATAATTCCCTTCAAGTAATTCTTTGCTATGAAAATCAAG

Found at i:2875 original size:16 final size:16

Alignment explanation


    Indices: 2854--2884  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       2844 AGACCCCCTA

                    *       
       2854 GGGTACTATCAATATG
          1 GGGTACTACCAATATG

                           
       2870 GGGTACTACCAATAT
          1 GGGTACTACCAATAT

       2885 TCAACAATTA


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29


Consensus pattern (16 bp):   
GGGTACTACCAATATG

Found at i:3368 original size:40 final size:40

Alignment explanation


    Indices: 3318--3398  Score: 119
    Period size: 40  Copynumber: 2.0  Consensus size: 40

       3308 CAGGTCTCAG

                                              *      
       3318 ATTCAAGATTTTGCGTCTATTCC-CGTTGGTAGATTCACCC
          1 ATTCAAGATTTTGCGTCTA-TCCTCGTTGGTAGACTCACCC

                *        *                          
       3358 ATTCGAGATTTTGTGTCTATCCTCGTTGGTAGACTCACCC
          1 ATTCAAGATTTTGCGTCTATCCTCGTTGGTAGACTCACCC

             
       3398 A
          1 A

       3399 CTAAGTACGC


Statistics
Matches: 37,  Mismatches: 3, Indels: 2
        0.88            0.07        0.05

Matches are distributed among these distances:
  39    3  0.08
  40   34  0.92

ACGTcount: A:0.20, C:0.25, G:0.19, T:0.37


Consensus pattern (40 bp):   
ATTCAAGATTTTGCGTCTATCCTCGTTGGTAGACTCACCC

Found at i:15986 original size:6 final size:6

Alignment explanation


    Indices: 15973--16015  Score: 68
    Period size: 6  Copynumber: 7.2  Consensus size: 6

      15963 CAGGCTGCAC

                    *      *                                  
      15973 CACAAT CGCAAT CGCAAT CACAAT CACAAT CACAAT CACAAT C
          1 CACAAT CACAAT CACAAT CACAAT CACAAT CACAAT CACAAT C

      16016 TTGCCAACAG


Statistics
Matches: 35,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   6   35  1.00

ACGTcount: A:0.44, C:0.35, G:0.05, T:0.16


Consensus pattern (6 bp):   
CACAAT

Found at i:16070 original size:38 final size:38

Alignment explanation


    Indices: 16014--16280  Score: 435
    Period size: 38  Copynumber: 7.0  Consensus size: 38

      16004 ACAATCACAA

                *               *                 
      16014 TCTTGCCAACAGTTTAACCCTCTGAGGCACGGGTCCAC
          1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC

                                           *      
      16052 TCTTACCAACAGTTTAACCCCCTGAGGCACGAGTCCAC
          1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC

                        *                        *
      16090 TCTTACCAACAGCTTAACCCCCTGAGGCACGGGTCCAT
          1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC

             *      *                   *         
      16128 TTTTACCATCAGTTTAACCCCCTGAGGCGCGGGTCCAC
          1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC

                                                  
      16166 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
          1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC

                    *                             
      16204 TCTTACCATCAGTTTAACCCCCTGAGGCACGGGTCCAC
          1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC

                    *                   *         
      16242 TCTTACCATCAGTTTAACCCCCTGAGGCGCGGGTCCAC
          1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC

             
      16280 T
          1 T

      16281 ATGCACAGCC


Statistics
Matches: 213,  Mismatches: 16, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  38  213  1.00

ACGTcount: A:0.22, C:0.36, G:0.19, T:0.23


Consensus pattern (38 bp):   
TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC

Done.