Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008440.1 Corchorus capsularis cultivar CVL-1 contig08461, 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: 2777
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32


Found at i:1112 original size:16 final size:16

Alignment explanation


    Indices: 1092--1136  Score: 65
    Period size: 16  Copynumber: 2.8  Consensus size: 16

       1082 AACCCGCCCG

                            
       1092 AACCCGAACCCGA-AA
          1 AACCCGAACCCGAGAA

                            *
       1107 ATACCCGAACCCGAGAC
          1 A-ACCCGAACCCGAGAA

                         
       1124 AACCCGAACCCGA
          1 AACCCGAACCCGA

       1137 CCCGAGCCCG


Statistics
Matches: 27,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  15    1  0.04
  16   24  0.89
  17    2  0.07

ACGTcount: A:0.40, C:0.42, G:0.16, T:0.02


Consensus pattern (16 bp):   
AACCCGAACCCGAGAA

Found at i:1909 original size:17 final size:17

Alignment explanation


    Indices: 1887--1927  Score: 55
    Period size: 17  Copynumber: 2.4  Consensus size: 17

       1877 CGAAAGTGAA

                           * 
       1887 CCCGAACCCGACCCGGG
          1 CCCGAACCCGACCCGAG

                    *  *     
       1904 CCCGAACCTGATCCGAG
          1 CCCGAACCCGACCCGAG

                   
       1921 CCCGAAC
          1 CCCGAAC

       1928 GCGAAGTACC


Statistics
Matches: 21,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  17   21  1.00

ACGTcount: A:0.22, C:0.49, G:0.24, T:0.05


Consensus pattern (17 bp):   
CCCGAACCCGACCCGAG

Found at i:2081 original size:9 final size:9

Alignment explanation


    Indices: 2067--2105  Score: 51
    Period size: 9  Copynumber: 4.3  Consensus size: 9

       2057 TTAATTTCTT

                  *  
       2067 TTAATTTAA
          1 TTAATTAAA

                     
       2076 TTAATTAAA
          1 TTAATTAAA

                **   
       2085 TTAAAGAAA
          1 TTAATTAAA

                     
       2094 TTAATTAAA
          1 TTAATTAAA

               
       2103 TTA
          1 TTA

       2106 TGTTGAAAAT


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

Matches are distributed among these distances:
   9   25  1.00

ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44


Consensus pattern (9 bp):   
TTAATTAAA
Done.