Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016482.1 Corchorus capsularis cultivar CVL-1 contig16503, 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: 7536
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31


Found at i:185 original size:15 final size:15

Alignment explanation


    Indices: 165--197  Score: 50
    Period size: 15  Copynumber: 2.2  Consensus size: 15

        155 TTAATTTCAA

                            
        165 TAAAATAA-AATATAT
          1 TAAAATAATAATAT-T

                           
        180 TAAAATAATAATATT
          1 TAAAATAATAATATT

               
        195 TAA
          1 TAA

        198 TTTTTATCCA


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  15   12  0.71
  16    5  0.29

ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36


Consensus pattern (15 bp):   
TAAAATAATAATATT

Found at i:1983 original size:17 final size:17

Alignment explanation


    Indices: 1963--1998  Score: 54
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       1953 GTAGATGCAG

                         *   
       1963 CCTAATACCTCATGCTA
          1 CCTAATACCTCATACTA

                *            
       1980 CCTAGTACCTCATACTA
          1 CCTAATACCTCATACTA

              
       1997 CC
          1 CC

       1999 AGGGTACCAT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.28, C:0.39, G:0.06, T:0.28


Consensus pattern (17 bp):   
CCTAATACCTCATACTA

Found at i:2176 original size:21 final size:21

Alignment explanation


    Indices: 2150--2190  Score: 73
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       2140 CAGAAGAGTT

                     *           
       2150 CGCCTTCCTTAGCAAGTAAAA
          1 CGCCTTCCTCAGCAAGTAAAA

                                
       2171 CGCCTTCCTCAGCAAGTAAA
          1 CGCCTTCCTCAGCAAGTAAA

       2191 GCCCACCAGT


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.32, C:0.32, G:0.15, T:0.22


Consensus pattern (21 bp):   
CGCCTTCCTCAGCAAGTAAAA

Found at i:4203 original size:14 final size:14

Alignment explanation


    Indices: 4184--4212  Score: 58
    Period size: 14  Copynumber: 2.1  Consensus size: 14

       4174 AATAAATAAC

                          
       4184 ACCATTTCGTAAAG
          1 ACCATTTCGTAAAG

                          
       4198 ACCATTTCGTAAAG
          1 ACCATTTCGTAAAG

             
       4212 A
          1 A

       4213 ACGCAAAAGC


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   15  1.00

ACGTcount: A:0.38, C:0.21, G:0.14, T:0.28


Consensus pattern (14 bp):   
ACCATTTCGTAAAG

Found at i:4361 original size:69 final size:71

Alignment explanation


    Indices: 4250--4389  Score: 257
    Period size: 69  Copynumber: 2.0  Consensus size: 71

       4240 AGAAATTGTC

                                                                             
       4250 ATTTATTAGTAATTTAAATAAAATAACTGTTGAATACTGATCTTAATTAGCT-A-ATAGCCTTGT
          1 ATTTATTAGTAATTTAAATAAAATAACTGTTGAATACTGATCTTAATTAGCTAATATAGCCTTGT

                  
       4313 TCAAAT
         66 TCAAAT

                                               *                             
       4319 ATTTATTAGTAATTTAAATAAAATAACTGTTGAATGCTGATCTTAATTAGCTAATATAGCCTTGT
          1 ATTTATTAGTAATTTAAATAAAATAACTGTTGAATACTGATCTTAATTAGCTAATATAGCCTTGT

                  
       4384 TCAAAT
         66 TCAAAT

       4390 GGATTAAAAT


Statistics
Matches: 68,  Mismatches: 1, Indels: 2
        0.96            0.01        0.03

Matches are distributed among these distances:
  69   51  0.75
  70    1  0.01
  71   16  0.24

ACGTcount: A:0.39, C:0.10, G:0.11, T:0.41


Consensus pattern (71 bp):   
ATTTATTAGTAATTTAAATAAAATAACTGTTGAATACTGATCTTAATTAGCTAATATAGCCTTGT
TCAAAT

Done.