Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014082.1 Corchorus olitorius cultivar O-4 contig14115, 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: 3524
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33


Found at i:88 original size:29 final size:28

Alignment explanation


    Indices: 49--104  Score: 94
    Period size: 29  Copynumber: 2.0  Consensus size: 28

         39 GTTATTCCAC

                  *                      
         49 GTTCTTTAGCGTTCTTGAAGATTAGAAAT
          1 GTTCTTGAGCGTTCTTGAA-ATTAGAAAT

                                       
         78 GTTCTTGAGCGTTCTTGAAATTAGAAA
          1 GTTCTTGAGCGTTCTTGAAATTAGAAA

        105 GTTTGAAGAA


Statistics
Matches: 26,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  28    8  0.31
  29   18  0.69

ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39


Consensus pattern (28 bp):   
GTTCTTGAGCGTTCTTGAAATTAGAAAT

Found at i:390 original size:13 final size:13

Alignment explanation


    Indices: 363--404  Score: 52
    Period size: 13  Copynumber: 3.4  Consensus size: 13

        353 CAAAAAAATG

                         
        363 TTTTTAAT-A-TA
          1 TTTTTAATAATTA

                         
        374 TTTTTAATAATTA
          1 TTTTTAATAATTA

                   * *   
        387 TTTTTAAGACTTA
          1 TTTTTAATAATTA

                 
        400 TTTTT
          1 TTTTT

        405 GGGGTTAAAA


Statistics
Matches: 27,  Mismatches: 2, Indels: 2
        0.87            0.06        0.06

Matches are distributed among these distances:
  11    8  0.30
  12    1  0.04
  13   18  0.67

ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64


Consensus pattern (13 bp):   
TTTTTAATAATTA

Found at i:1536 original size:30 final size:28

Alignment explanation


    Indices: 1453--1536  Score: 96
    Period size: 30  Copynumber: 2.8  Consensus size: 28

       1443 CTTATAGCGC

                  *                      
       1453 TTGGACGTTTTGCCCTCTAAACTTCAATT
          1 TTGGACATTTTGCCCT-TAAACTTCAATT

                             *            
       1482 TTGGACATTTTTGTCCCATAAACTTCAATT
          1 TTGGACA-TTTTG-CCCTTAAACTTCAATT

                               *     
       1512 TTGGGACATTTTGCCCCTTTAACTT
          1 TT-GGACATTTTG-CCCTTAAACTT

       1537 AACGGCACCC


Statistics
Matches: 47,  Mismatches: 5, Indels: 5
        0.82            0.09        0.09

Matches are distributed among these distances:
  29    6  0.13
  30   33  0.70
  31    8  0.17

ACGTcount: A:0.21, C:0.23, G:0.13, T:0.43


Consensus pattern (28 bp):   
TTGGACATTTTGCCCTTAAACTTCAATT

Found at i:3033 original size:30 final size:30

Alignment explanation


    Indices: 2999--3502  Score: 801
    Period size: 30  Copynumber: 16.7  Consensus size: 30

       2989 ACTCTCTAAA

                                *         
       2999 TGACACCAGAAGTTGTCATGCTCTTGCAAT
          1 TGACACCAGAAGTTGTCATGATCTTGCAAT

                                *         
       3029 TGACACCAGAAGTTGTCATGCTCTTGCAAT
          1 TGACACCAGAAGTTGTCATGATCTTGCAAT

                                *         
       3059 TGACACCAGAAGTTGTCATGCTCTTGCAAT
          1 TGACACCAGAAGTTGTCATGATCTTGCAAT

                                *         
       3089 TGACACCAGAAGTTGTCATGGTCTTGCAAT
          1 TGACACCAGAAGTTGTCATGATCTTGCAAT

                                *         
       3119 TGACACCAGAAGTTGTCATGGTCTTGCAAT
          1 TGACACCAGAAGTTGTCATGATCTTGCAAT

                                          
       3149 TGACACCAGAAGTTGTCATGATCTTGCAAT
          1 TGACACCAGAAGTTGTCATGATCTTGCAAT

                                          
       3179 TGACACCAGAAGTTGTCATGATCTTGCAAT
          1 TGACACCAGAAGTTGTCATGATCTTGCAAT

                                          
       3209 TGACACCAGAAGTTGTCATGATCTTGCAAT
          1 TGACACCAGAAGTTGTCATGATCTTGCAAT

                                *         
       3239 TGACACCAGAAGTTGTCATGGTCTTGCAAT
          1 TGACACCAGAAGTTGTCATGATCTTGCAAT

                                          
       3269 TGACACCAGAAGTTGTCATGATCTTGCAAT
          1 TGACACCAGAAGTTGTCATGATCTTGCAAT

             *          *         *       
       3299 TAACACCAGAAGCTGTCATGATGTTGCAAT
          1 TGACACCAGAAGTTGTCATGATCTTGCAAT

                    *                     
       3329 TGACACCATAAGTTGTCATGATCTTGCAAT
          1 TGACACCAGAAGTTGTCATGATCTTGCAAT

                    *                     
       3359 TGACACCATAAGTTGTCATGATCTTGCAAT
          1 TGACACCAGAAGTTGTCATGATCTTGCAAT

                    *             *       
       3389 TGACACCATAAGTTGTCATGATTTTGCAAT
          1 TGACACCAGAAGTTGTCATGATCTTGCAAT

                    *                     
       3419 TGACACCATAAGTTGTCATGATCTTGCAAT
          1 TGACACCAGAAGTTGTCATGATCTTGCAAT

                  **    *     **   *   *    
       3449 TGACACTTGAAGATGTCACAATTTTATTCAAT
          1 TGACACCAGAAGTTGTCATGA-TCT-TGCAAT

                                  
       3481 TGACACCAGAAGTTGTCATGAT
          1 TGACACCAGAAGTTGTCATGAT

       3503 AAATTTCCAA


Statistics
Matches: 446,  Mismatches: 26, Indels: 3
        0.94            0.05        0.01

Matches are distributed among these distances:
  30  422  0.95
  31    3  0.01
  32   21  0.05

ACGTcount: A:0.29, C:0.20, G:0.19, T:0.31


Consensus pattern (30 bp):   
TGACACCAGAAGTTGTCATGATCTTGCAAT

Done.