Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020560.1 Corchorus olitorius cultivar O-4 contig20593, 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: 27931
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34


Found at i:12 original size:2 final size:2

Alignment explanation


    Indices: 6--35  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

          1 TCATA

                                                        
          6 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

         36 GCACCGTCAG


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:488 original size:31 final size:31

Alignment explanation


    Indices: 450--511  Score: 81
    Period size: 31  Copynumber: 2.0  Consensus size: 31

        440 GAGTTTTGTA

                    *                       
        450 AAACTTTTGAATCACCTATT-ATACCCTTATT
          1 AAACTTTTAAATCACCT-TTCATACCCTTATT

                         **                
        481 AAACTTTTAAATCGTCTTTCATACCCTTATT
          1 AAACTTTTAAATCACCTTTCATACCCTTATT

        512 TTTCGAATAT


Statistics
Matches: 27,  Mismatches: 3, Indels: 2
        0.84            0.09        0.06

Matches are distributed among these distances:
  30    2  0.07
  31   25  0.93

ACGTcount: A:0.31, C:0.23, G:0.03, T:0.44


Consensus pattern (31 bp):   
AAACTTTTAAATCACCTTTCATACCCTTATT

Found at i:644 original size:93 final size:93

Alignment explanation


    Indices: 547--731  Score: 307
    Period size: 93  Copynumber: 2.0  Consensus size: 93

        537 TTGTTTAAAT

                         *                                                   
        547 TTTTATAGTTTTAGTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
          1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA

                    *      *      *     
        612 TTTTATTTTTACCATTTTACTATTTTAC
         66 TTTTATTTGTACCATATTACTAATTTAC

                                                           *             *   
        640 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATTTAATATCCTTATACCTA
          1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA

                        *              
        705 TTTTATTTGTACGATATTACTAATTTA
         66 TTTTATTTGTACCATATTACTAATTTA

        732 ATTAAAAAGT


Statistics
Matches: 85,  Mismatches: 7, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  93   85  1.00

ACGTcount: A:0.33, C:0.12, G:0.03, T:0.52


Consensus pattern (93 bp):   
TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
TTTTATTTGTACCATATTACTAATTTAC

Found at i:16314 original size:17 final size:17

Alignment explanation


    Indices: 16292--16325  Score: 68
    Period size: 17  Copynumber: 2.0  Consensus size: 17

      16282 ACAATCCAAA

                             
      16292 TCCCCCACCTTTTTTGT
          1 TCCCCCACCTTTTTTGT

                             
      16309 TCCCCCACCTTTTTTGT
          1 TCCCCCACCTTTTTTGT

      16326 ACAAAAAGTC


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.06, C:0.41, G:0.06, T:0.47


Consensus pattern (17 bp):   
TCCCCCACCTTTTTTGT

Found at i:24103 original size:24 final size:25

Alignment explanation


    Indices: 24074--24124  Score: 68
    Period size: 24  Copynumber: 2.1  Consensus size: 25

      24064 TTATGTGAAC

                       *             
      24074 AATAAAATAAATAAACAAGA-AAAT
          1 AATAAAATAAAGAAACAAGATAAAT

                    *   *            
      24098 AATAAAATTAAGCAACAAGATAAAT
          1 AATAAAATAAAGAAACAAGATAAAT

              
      24123 AA
          1 AA

      24125 ATACTCCAAT


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  24   17  0.74
  25    6  0.26

ACGTcount: A:0.71, C:0.06, G:0.06, T:0.18


Consensus pattern (25 bp):   
AATAAAATAAAGAAACAAGATAAAT
Done.