Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017470.1 Corchorus olitorius cultivar O-4 contig17503, 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: 10723
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32


Found at i:1251 original size:124 final size:126

Alignment explanation


    Indices: 1033--1286  Score: 379
    Period size: 124  Copynumber: 2.0  Consensus size: 126

       1023 ATTTAAGAAA

                                     *                   *                   
       1033 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATATTAAAATGGTAAAAACAAAA
          1 TATATTTAAAAAATTCTAATATATAAAAGTTTTTTAATTAAAATAGTAAAATGGT---AACAAAA

                    **                                                 *     
       1098 TAGGTATATGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAATTGAGTAAAACTGTAAAA
         63 T--GTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAATTGAGTAAAACTATAAAA

             
       1163 G
        126 G

                                                                             
       1164 TATATTTAAAAAATTCTAATATATAAAAGTTTTTTTAATTAAAATAGTAAAATGGT-AC-AAAT-
          1 TATATTTAAAAAATTCTAATATATAAAAG-TTTTTTAATTAAAATAGTAAAATGGTAACAAAATG

                                                      *                  
       1226 TATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
         65 TATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAATTGAGTAAAACTATAAAA

       1287 CTTTAAACAA


Statistics
Matches: 116,  Mismatches: 6, Indels: 9
        0.89            0.05        0.07

Matches are distributed among these distances:
 124   57  0.49
 127    4  0.03
 128    2  0.02
 131   28  0.24
 132   25  0.22

ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38


Consensus pattern (126 bp):   
TATATTTAAAAAATTCTAATATATAAAAGTTTTTTAATTAAAATAGTAAAATGGTAACAAAATGT
ATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAATTGAGTAAAACTATAAAAG

Found at i:1921 original size:14 final size:13

Alignment explanation


    Indices: 1877--1926  Score: 57
    Period size: 14  Copynumber: 3.8  Consensus size: 13

       1867 ATGTAGTTAT

                         
       1877 CAAAAATACTTTA
          1 CAAAAATACTTTA

                 *  *    
       1890 C-AAAGTATTTTA
          1 CAAAAATACTTTA

                          
       1902 CTAAAAATACTTTA
          1 C-AAAAATACTTTA

                       
       1916 CGAAAAATACT
          1 C-AAAAATACT

       1927 CCATTTTTTT


Statistics
Matches: 30,  Mismatches: 5, Indels: 3
        0.79            0.13        0.08

Matches are distributed among these distances:
  12   10  0.33
  13    1  0.03
  14   19  0.63

ACGTcount: A:0.50, C:0.14, G:0.04, T:0.32


Consensus pattern (13 bp):   
CAAAAATACTTTA

Found at i:4206 original size:21 final size:21

Alignment explanation


    Indices: 4182--4226  Score: 63
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       4172 ATGACACTGC

                *     *          
       4182 CCACCTGGGTTCTCAAGCAAA
          1 CCACATGGGTGCTCAAGCAAA

                             *   
       4203 CCACATGGGTGCTCAAGGAAA
          1 CCACATGGGTGCTCAAGCAAA

               
       4224 CCA
          1 CCA

       4227 TGTGGACGCC


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

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.31, C:0.31, G:0.22, T:0.16


Consensus pattern (21 bp):   
CCACATGGGTGCTCAAGCAAA

Found at i:6997 original size:21 final size:21

Alignment explanation


    Indices: 6958--7006  Score: 55
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       6948 TCTAAGCCTT

                         **       
       6958 AGGAATGCAAGAGGGATTTCAA
          1 AGGAA-GCAAGAGCCATTTCAA

                               * 
       6980 AGGAAGCAAGAGCCATTTCCA
          1 AGGAAGCAAGAGCCATTTCAA

                   
       7001 A-GAAGC
          1 AGGAAGC

       7007 TACAATTCTT


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

Matches are distributed among these distances:
  20    5  0.21
  21   14  0.58
  22    5  0.21

ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14


Consensus pattern (21 bp):   
AGGAAGCAAGAGCCATTTCAA
Done.