Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016001.1 Corchorus olitorius cultivar O-4 contig16034, 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: 3661
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31


Found at i:243 original size:50 final size:50

Alignment explanation


    Indices: 1--236  Score: 427
    Period size: 50  Copynumber: 4.7  Consensus size: 50

                                                              
          1 CGGAAGACGGTCCTTTTAAGATTGAATTGGAAGACAGTTCGAAGGATAAG
          1 CGGAAGACGGTCCTTTTAAGATTGAATTGGAAGACAGTTCGAAGGATAAG

                     *                                        
         51 CGGAAGACGATCCTTTTAAGATTGAATTGGAAGACAGTTCGAAGGATAAG
          1 CGGAAGACGGTCCTTTTAAGATTGAATTGGAAGACAGTTCGAAGGATAAG

                                                              
        101 CGGAAGACGGTCCTTTTAAGATTGAATTGGAAGACAGTTCGAAGGATAAG
          1 CGGAAGACGGTCCTTTTAAGATTGAATTGGAAGACAGTTCGAAGGATAAG

                                                    *  *      
        151 CGGAAGACGGTCCTTTTAAGATTGAATTGGAAGACAGTTCAAACGATAAG
          1 CGGAAGACGGTCCTTTTAAGATTGAATTGGAAGACAGTTCGAAGGATAAG

                               *    *           
        201 CGGAAGACGGTCCTTTTAATATTGGATTGGAAGACA
          1 CGGAAGACGGTCCTTTTAAGATTGAATTGGAAGACA

        237 ATTCAAATAA


Statistics
Matches: 180,  Mismatches: 6, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  50  180  1.00

ACGTcount: A:0.34, C:0.13, G:0.28, T:0.25


Consensus pattern (50 bp):   
CGGAAGACGGTCCTTTTAAGATTGAATTGGAAGACAGTTCGAAGGATAAG

Found at i:300 original size:27 final size:27

Alignment explanation


    Indices: 221--305  Score: 75
    Period size: 27  Copynumber: 3.2  Consensus size: 27

        211 TCCTTTTAAT

                *                  *   
        221 ATTGGATTGGAAGACAATTCAAATAAG
          1 ATTGAATTGGAAGACAATTCAAAGAAG

                     *   *  *    ***    
        248 -TTG-ATTCAGAAAACGATTCCCCGAAG
          1 ATTGAATT-GGAAGACAATTCAAAGAAG

                                       
        274 ATTGAATTGGAAGACAATTCAAAGAAG
          1 ATTGAATTGGAAGACAATTCAAAGAAG

                 
        301 ATTGA
          1 ATTGA

        306 TCGGGAGATA


Statistics
Matches: 42,  Mismatches: 13, Indels: 6
        0.69            0.21        0.10

Matches are distributed among these distances:
  25    3  0.07
  26   15  0.36
  27   21  0.50
  28    3  0.07

ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25


Consensus pattern (27 bp):   
ATTGAATTGGAAGACAATTCAAAGAAG

Found at i:685 original size:21 final size:21

Alignment explanation


    Indices: 656--699  Score: 79
    Period size: 21  Copynumber: 2.1  Consensus size: 21

        646 TTTTGTCTCT

                                 
        656 ATTTCGTTCACCGTAAGTTGC
          1 ATTTCGTTCACCGTAAGTTGC

                *                
        677 ATTTTGTTCACCGTAAGTTGC
          1 ATTTCGTTCACCGTAAGTTGC

              
        698 AT
          1 AT

        700 GGTATTTTTG


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  21   22  1.00

ACGTcount: A:0.20, C:0.20, G:0.18, T:0.41


Consensus pattern (21 bp):   
ATTTCGTTCACCGTAAGTTGC

Found at i:3483 original size:18 final size:18

Alignment explanation


    Indices: 3460--3499  Score: 55
    Period size: 18  Copynumber: 2.2  Consensus size: 18

       3450 GGTAAAGAAG

                               
       3460 AATTTC-TAGAATTAGTTT
          1 AATTTCATAG-ATTAGTTT

                      *       
       3478 AATTTCATAGTTTAGTTT
          1 AATTTCATAGATTAGTTT

                
       3496 AATT
          1 AATT

       3500 GTCAATAGAA


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  18   17  0.85
  19    3  0.15

ACGTcount: A:0.33, C:0.05, G:0.10, T:0.53


Consensus pattern (18 bp):   
AATTTCATAGATTAGTTT
Done.