Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001936.1 Corchorus capsularis cultivar CVL-1 contig01938, 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: 1862
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31


Found at i:820 original size:21 final size:20

Alignment explanation


    Indices: 782--820  Score: 51
    Period size: 21  Copynumber: 1.9  Consensus size: 20

        772 TTTAGAAGCA

                        **      
        782 ATTAATTAAAACCCTTAAAC
          1 ATTAATTAAAACAATTAAAC

                               
        802 ATTAATTAAAAACAATTAA
          1 ATTAATT-AAAACAATTAA

        821 GGAAGAAAAA


Statistics
Matches: 16,  Mismatches: 2, Indels: 1
        0.84            0.11        0.05

Matches are distributed among these distances:
  20    7  0.44
  21    9  0.56

ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31


Consensus pattern (20 bp):   
ATTAATTAAAACAATTAAAC

Found at i:1009 original size:11 final size:11

Alignment explanation


    Indices: 993--1021  Score: 58
    Period size: 11  Copynumber: 2.6  Consensus size: 11

        983 GTTAAAAATA

                       
        993 ATATATAGTAT
          1 ATATATAGTAT

                       
       1004 ATATATAGTAT
          1 ATATATAGTAT

                   
       1015 ATATATA
          1 ATATATA

       1022 TTAGTATAAA


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   18  1.00

ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45


Consensus pattern (11 bp):   
ATATATAGTAT

Found at i:1181 original size:29 final size:31

Alignment explanation


    Indices: 1149--1206  Score: 75
    Period size: 31  Copynumber: 1.9  Consensus size: 31

       1139 TCAAATCAGA

                 *                         
       1149 ATCCGTACTT-TAGAA-AAGGTCAAATAAAG
          1 ATCCGAACTTATAGAATAAGGTCAAATAAAG

                        *     *          
       1178 ATCCGAACTTATCGAATAGGGTCAAATAA
          1 ATCCGAACTTATAGAATAAGGTCAAATAA

       1207 GTTCAGTCCT


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  29    9  0.38
  30    4  0.17
  31   11  0.46

ACGTcount: A:0.43, C:0.16, G:0.17, T:0.24


Consensus pattern (31 bp):   
ATCCGAACTTATAGAATAAGGTCAAATAAAG
Done.