Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021052.1 Corchorus olitorius cultivar O-4 contig21085, 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: 8197
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37


Found at i:620 original size:42 final size:43

Alignment explanation


    Indices: 569--662  Score: 129
    Period size: 45  Copynumber: 2.2  Consensus size: 43

        559 AGTGCATTAC

                                    *                  
        569 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATAAAAATAAAG
          1 CTAATATTCTACCTCCATCTCTAGATAATTCATAAAAATAAAG

                                               *         
        610 CTAATATTCTACCCCTCCATCTCTAGATAATTCATCAAAATAAAG
          1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATAAAAATAAAG

            *       
        655 TTAATATT
          1 CTAATATT

        663 AATTGTTGTT


Statistics
Matches: 46,  Mismatches: 3, Indels: 4
        0.87            0.06        0.08

Matches are distributed among these distances:
  41    4  0.09
  42    6  0.13
  45   36  0.78

ACGTcount: A:0.39, C:0.21, G:0.05, T:0.34


Consensus pattern (43 bp):   
CTAATATTCTACCTCCATCTCTAGATAATTCATAAAAATAAAG

Found at i:1790 original size:21 final size:21

Alignment explanation


    Indices: 1734--1792  Score: 57
    Period size: 21  Copynumber: 2.8  Consensus size: 21

       1724 CATATAAGCT

                 *       *       
       1734 TTTATTAATTATTATAATAAC
          1 TTTATAAATTATTTTAATAAC

                     * *     *    
       1755 TTT-TAAAGATGTTTTACTAAC
          1 TTTATAAA-TTATTTTAATAAC

                             
       1776 TTTATAAATTATTTTAA
          1 TTTATAAATTATTTTAA

       1793 AAAAATTTTA


Statistics
Matches: 28,  Mismatches: 8, Indels: 4
        0.70            0.20        0.10

Matches are distributed among these distances:
  20    3  0.11
  21   21  0.75
  22    4  0.14

ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53


Consensus pattern (21 bp):   
TTTATAAATTATTTTAATAAC

Found at i:2976 original size:57 final size:57

Alignment explanation


    Indices: 2905--3023  Score: 213
    Period size: 57  Copynumber: 2.1  Consensus size: 57

       2895 TAAAAACACG

                                                                     
       2905 TTTG-GTTGATTGTTTGTGTTTTTAAATTTTAGGAAACAAAAACTATATTTCTGAAA
          1 TTTGTGTTGATTGTTTGTGTTTTTAAATTTTAGGAAACAAAAACTATATTTCTGAAA

                            *                                  *     
       2961 TTTGTGTTGATTGTTTTTGTTTTTAAATTTTAGGAAACAAAAACTATATTTTTGAAA
          1 TTTGTGTTGATTGTTTGTGTTTTTAAATTTTAGGAAACAAAAACTATATTTCTGAAA

                  
       3018 TTTGTG
          1 TTTGTG

       3024 GAAGCAGGAT


Statistics
Matches: 60,  Mismatches: 2, Indels: 1
        0.95            0.03        0.02

Matches are distributed among these distances:
  56    4  0.07
  57   56  0.93

ACGTcount: A:0.30, C:0.04, G:0.16, T:0.50


Consensus pattern (57 bp):   
TTTGTGTTGATTGTTTGTGTTTTTAAATTTTAGGAAACAAAAACTATATTTCTGAAA

Found at i:3628 original size:52 final size:54

Alignment explanation


    Indices: 3520--3628  Score: 177
    Period size: 54  Copynumber: 2.0  Consensus size: 54

       3510 CTGTTTGGTA

                                                            *      
       3520 ATGTTTTTGTTTTTGTTTTTTTGTTGCCAATTTGGTGTTTTGGAAGCACACCATG
          1 ATGTTTTTGTTTTTGTTTTTTTGTTGCCAATTTGGTGTTTT-GAAGCAAACCATG

                                                             *    
       3575 ATGTTTTTG-TTTTGTTTTTTTGTTGCCAATTTGGTGTTTT-AAGCAAATCATG
          1 ATGTTTTTGTTTTTGTTTTTTTGTTGCCAATTTGGTGTTTTGAAGCAAACCATG

              
       3627 AT
          1 AT

       3629 AAAACACGGT


Statistics
Matches: 52,  Mismatches: 2, Indels: 3
        0.91            0.04        0.05

Matches are distributed among these distances:
  52   12  0.23
  54   31  0.60
  55    9  0.17

ACGTcount: A:0.17, C:0.09, G:0.20, T:0.54


Consensus pattern (54 bp):   
ATGTTTTTGTTTTTGTTTTTTTGTTGCCAATTTGGTGTTTTGAAGCAAACCATG
Done.