Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017754.1 Corchorus olitorius cultivar O-4 contig17787, 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: 3498
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.27


Found at i:222 original size:13 final size:13

Alignment explanation


    Indices: 204--228  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

        194 GTAAATTTGA

                         
        204 TAATTACTGTAAC
          1 TAATTACTGTAAC

                        
        217 TAATTACTGTAA
          1 TAATTACTGTAA

        229 ATTTGATAAC


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40


Consensus pattern (13 bp):   
TAATTACTGTAAC

Found at i:1098 original size:68 final size:68

Alignment explanation


    Indices: 1010--1166  Score: 278
    Period size: 68  Copynumber: 2.3  Consensus size: 68

       1000 AGGGATAACA

                           *       *  *                              *       
       1010 GTGGGTCAAGAAAAGTACGGAAGGTGGGTGAGGCTTGGGTTAGGCCATTAATGATGATCTTACTC
          1 GTGGGTCAAGAAAAGCACGGAAGATGAGTGAGGCTTGGGTTAGGCCATTAATGATGACCTTACTC

               
       1075 AAG
         66 AAG

                                                                             
       1078 GTGGGTCAAGAAAAGCACGGAAGATGAGTGAGGCTTGGGTTAGGCCATTAATGATGACCTTACTC
          1 GTGGGTCAAGAAAAGCACGGAAGATGAGTGAGGCTTGGGTTAGGCCATTAATGATGACCTTACTC

               
       1143 AAG
         66 AAG

                                 
       1146 GTGGGTCAAGAAAAGCACGGA
          1 GTGGGTCAAGAAAAGCACGGA

       1167 GCTCCCCACA


Statistics
Matches: 85,  Mismatches: 4, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  68   85  1.00

ACGTcount: A:0.31, C:0.13, G:0.34, T:0.22


Consensus pattern (68 bp):   
GTGGGTCAAGAAAAGCACGGAAGATGAGTGAGGCTTGGGTTAGGCCATTAATGATGACCTTACTC
AAG

Found at i:1514 original size:19 final size:19

Alignment explanation


    Indices: 1490--1528  Score: 69
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       1480 TAGAATACAT

                     *         
       1490 AATTTGGGAGAGGAAAAGA
          1 AATTTGGGAAAGGAAAAGA

                               
       1509 AATTTGGGAAAGGAAAAGA
          1 AATTTGGGAAAGGAAAAGA

             
       1528 A
          1 A

       1529 GAGTCAGTAG


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  19   19  1.00

ACGTcount: A:0.51, C:0.00, G:0.33, T:0.15


Consensus pattern (19 bp):   
AATTTGGGAAAGGAAAAGA
Done.