Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023617.1 Corchorus olitorius cultivar O-4 contig23650, 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: 7183
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.33


Found at i:1788 original size:29 final size:29

Alignment explanation


    Indices: 1747--1956  Score: 226
    Period size: 29  Copynumber: 7.2  Consensus size: 29

       1737 AGAGTATGCG

                                *        
       1747 AAAATGACCAAAATGCCCCTAGATGAGCA
          1 AAAATGACCAAAATGCCCCTGGATGAGCA

               *               *          
       1776 AAAGTGACCAAAATGCCCCGGGATGCA-CA
          1 AAAATGACCAAAATGCCCCTGGATG-AGCA

                   *    *           *  *  
       1805 AAAATGATCAAACTGCCCCTGGA-CATTCA
          1 AAAATGACCAAAATGCCCCTGGATGA-GCA

                      *       *      *   
       1834 AAAATGACCATAATGCCCTTGGATGGGCA
          1 AAAATGACCAAAATGCCCCTGGATGAGCA

                                *    *   
       1863 AAAATGACCAAAATGCCCCTAGATGTGCA
          1 AAAATGACCAAAATGCCCCTGGATGAGCA

                              *    * *   
       1892 AAAATGACCAAAATGCCCATGGACGTGCA
          1 AAAATGACCAAAATGCCCCTGGATGAGCA

              *                   * *    
       1921 AATATGACCAAAATGCCCCTGGGTAAGCA
          1 AAAATGACCAAAATGCCCCTGGATGAGCA

                   
       1950 AAAATGA
          1 AAAATGA

       1957 TCAATTAAAA


Statistics
Matches: 148,  Mismatches: 29, Indels: 8
        0.80            0.16        0.04

Matches are distributed among these distances:
  27    1  0.01
  29  146  0.99
  30    1  0.01

ACGTcount: A:0.40, C:0.24, G:0.20, T:0.16


Consensus pattern (29 bp):   
AAAATGACCAAAATGCCCCTGGATGAGCA

Found at i:1894 original size:87 final size:87

Alignment explanation


    Indices: 1742--1956  Score: 268
    Period size: 87  Copynumber: 2.5  Consensus size: 87

       1732 AACCCAGAGT

                *                    *           *                *          
       1742 ATGCGAAAATGACCAAAATGCCCCTAGATGAGCAAAAGTGACCAAAATGCCCCGGGATGCACAAA
          1 ATGCAAAAATGACCAAAATGCCCCTGGATGAGCAAAAATGACCAAAATGCCCCGAGATGCACAAA

                 *    *     *     
       1807 AATGATCAAACTGCCCCTGGAC
         66 AATGACCAAAATGCCCATGGAC

              *            *       *      *                      *     **    
       1829 ATTCAAAAATGACCATAATGCCCTTGGATGGGCAAAAATGACCAAAATGCCCCTAGATGTGCAAA
          1 ATGCAAAAATGACCAAAATGCCCCTGGATGAGCAAAAATGACCAAAATGCCCCGAGATGCACAAA

                                  
       1894 AATGACCAAAATGCCCATGGAC
         66 AATGACCAAAATGCCCATGGAC

            *      *                   * *           
       1916 GTGCAAATATGACCAAAATGCCCCTGGGTAAGCAAAAATGA
          1 ATGCAAAAATGACCAAAATGCCCCTGGATGAGCAAAAATGA

       1957 TCAATTAAAA


Statistics
Matches: 106,  Mismatches: 22, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  87  106  1.00

ACGTcount: A:0.40, C:0.24, G:0.20, T:0.16


Consensus pattern (87 bp):   
ATGCAAAAATGACCAAAATGCCCCTGGATGAGCAAAAATGACCAAAATGCCCCGAGATGCACAAA
AATGACCAAAATGCCCATGGAC

Found at i:2333 original size:58 final size:58

Alignment explanation


    Indices: 2186--2472  Score: 412
    Period size: 58  Copynumber: 4.9  Consensus size: 58

       2176 TGAAATATAG

                  *              *                   *       *             
       2186 ACTCTCAAACAGAGACCTCGACCAGGATTTTAAAACAAGATGAGATTTTGAATTGAAAAAAAA
          1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTAAATTG-----AAA

                                               * *                    
       2249 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAATAGGATAAGATTTTAAATTGAAA
          1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTAAATTGAAA

                    *                      *         *                
       2307 ACTCTCTAGCAGAGACCTCGAACAGGATTTTGAAACAAGATTAGATTTTAAATTGAAA
          1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTAAATTGAAA

                    *                      *           *              
       2365 ACTCTCTAGCAGAGACCTCGAACAGGATTTTGAAACAAGATAATATTTTAAATTGAAA
          1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTAAATTGAAA

                                 *                            
       2423 ACTCTCTAACAGAGACCTCGATCAGGATTTTAAAACAAGATAAGATTTTA
          1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTA

       2473 TTTTAAACTG


Statistics
Matches: 207,  Mismatches: 17, Indels: 5
        0.90            0.07        0.02

Matches are distributed among these distances:
  58  158  0.76
  63   49  0.24

ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26


Consensus pattern (58 bp):   
ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTAAATTGAAA

Found at i:3391 original size:38 final size:38

Alignment explanation


    Indices: 3319--3391  Score: 96
    Period size: 37  Copynumber: 1.9  Consensus size: 38

       3309 TTATTTTCTT

                       *     *                    
       3319 TTTTCTGACCTCTCTCTGTTTTAGGCCAAGTTTTTTTC
          1 TTTTCTGACCTATCTCTATTTTAGGCCAAGTTTTTTTC

                         *                       
       3357 TTTTC-GACCTATTTCTATTTTAGGTCC-AGTTTTTT
          1 TTTTCTGACCTATCTCTATTTTAGG-CCAAGTTTTTT

       3392 ATTTTTATTT


Statistics
Matches: 31,  Mismatches: 3, Indels: 3
        0.84            0.08        0.08

Matches are distributed among these distances:
  37   24  0.77
  38    7  0.23

ACGTcount: A:0.12, C:0.21, G:0.12, T:0.55


Consensus pattern (38 bp):   
TTTTCTGACCTATCTCTATTTTAGGCCAAGTTTTTTTC
Done.