Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011777.1 Corchorus olitorius cultivar O-4 contig11810, 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, 867

Length: 1446
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33


Found at i:33 original size:13 final size:14

Alignment explanation


    Indices: 15--44  Score: 53
    Period size: 13  Copynumber: 2.2  Consensus size: 14

          5 AACATAACAA

                          
         15 GATAAATAA-TAGT
          1 GATAAATAAGTAGT

                          
         28 GATAAATAAGTAGT
          1 GATAAATAAGTAGT

               
         42 GAT
          1 GAT

         45 TTAGTCCTTA


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13    9  0.56
  14    7  0.44

ACGTcount: A:0.50, C:0.00, G:0.20, T:0.30


Consensus pattern (14 bp):   
GATAAATAAGTAGT

Found at i:1337 original size:333 final size:334

Alignment explanation


    Indices: 730--1386  Score: 919
    Period size: 333  Copynumber: 2.0  Consensus size: 334

        720 AAGAGAAAGA

                                                               **            
        730 AACACGATTGTGGCTAAAATTTTGCAAAAAAATGACCCGAAAAGATTTTCCCCAATCTTTTACCA
          1 AACACGATTGTGGCTAAAATTTTGCAAAAAAATGACCCGAAAAGATTTTCCAAAATCTTTTACCA

                                        **      *       *              *     
        795 CAATACTCAGAAAAATCATATAATTCAATTCCAAAATTATTTTAGTGTTTTTCACGCTTCTAATA
         66 CAATACTCAGAAAAATCATATAATTCAACGCCAAAAATATTTTAATGTTTTTCACGCTTATAATA

                                                               *             
        860 TCGTTTTTCCATTTTCTGCCACAATACATTTCTAATTAAATCGAAACAAGATTCAAATACTAGTA
        131 TCGTTTTTCCATTTTCTGCCACAATACATTTCTAATTAAATCGAAACAAGACTCAAATACTAGTA

                *                     * *                                   *
        925 AAAATAAATCCGTAAATCCAACGTGGTTGAGATTTGGTTAGATGAATACAGATATTTCGAAGAGT
        196 AAAACAAATCCGTAAATCCAACGTGGCTAAGATTTGGTTAGATGAATACAGATATTTCGAAGAGA

            *                            *                     *             
        990 TTTTCTGCCAAAAATCATGCAAAACTGAGTCAGGGACCCAAAACGCATTTTTAACCAAAAACCGT
        261 CTTTCTGCCAAAAATCATGCAAAACTGAGACAGGGACCCAAAACGCATTTTCAACCAAAAACCGT

                     
       1055 TATGGTTAG
        326 TATGGTTAG

                                             *            *           *    * 
       1064 AACACGATT-TCGGCTAAAATTTTGCAAAAATACTGACCCGAAAAGTTTTTCCAAAATTTTTTGC
          1 AACACGATTGT-GGCTAAAATTTTGCAAAAA-AATGACCCGAAAAGATTTTCCAAAATCTTTTAC

                                                                             
       1128 CACAATACTCAGAAAAATCATATAATTCAACGCCAAAAA-ATTTTTAAT-TTTTTCACGCTTATA
         64 CACAATACTCAGAAAAATCATATAATTCAACGCCAAAAATA-TTTTAATGTTTTTCACGCTTATA

              *               * *   *   **                      *      *  *  
       1191 ATTTCGTTTTTCCATTTTTTTCC-GAATTTA-TTCTTAATTAAATCGAAACAGGACTCAGATGCT
        128 ATATCGTTTTTCCATTTTCTGCCACAATACATTTC-TAATTAAATCGAAACAAGACTCAAATACT

            *             *                                                 *
       1254 CGTAAAAACAAATCTGTAAATCCAACGTGGCTAAGATTTGGTTAGATGAATACAGATATTTCGAG
        192 AGTAAAAACAAATCCGTAAATCCAACGTGGCTAAGATTTGGTTAGATGAATACAGATATTTCGAA

                                          *        *   *      *      *       
       1319 GAGACTTTCTGCCAAAAATCATGCAAAACTTAGACAGGGCCCCGAAACGCGTTTTCAGCCAAAAA
        257 GAGACTTTCTGCCAAAAATCATGCAAAACTGAGACAGGGACCCAAAACGCATTTTCAACCAAAAA

               
       1384 CCG
        322 CCG

       1387 CACGATTTCG


Statistics
Matches: 283,  Mismatches: 36, Indels: 9
        0.86            0.11        0.03

Matches are distributed among these distances:
 332    3  0.01
 333  148  0.52
 334   63  0.22
 335   69  0.24

ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31


Consensus pattern (334 bp):   
AACACGATTGTGGCTAAAATTTTGCAAAAAAATGACCCGAAAAGATTTTCCAAAATCTTTTACCA
CAATACTCAGAAAAATCATATAATTCAACGCCAAAAATATTTTAATGTTTTTCACGCTTATAATA
TCGTTTTTCCATTTTCTGCCACAATACATTTCTAATTAAATCGAAACAAGACTCAAATACTAGTA
AAAACAAATCCGTAAATCCAACGTGGCTAAGATTTGGTTAGATGAATACAGATATTTCGAAGAGA
CTTTCTGCCAAAAATCATGCAAAACTGAGACAGGGACCCAAAACGCATTTTCAACCAAAAACCGT
TATGGTTAG
Done.