Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001930.1 Corchorus olitorius cultivar O-4 contig01930, 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, 834

Length: 1390
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.34


Found at i:1071 original size:23 final size:23

Alignment explanation


    Indices: 1028--1071  Score: 54
    Period size: 23  Copynumber: 1.9  Consensus size: 23

       1018 TAAATTTTTT

                            *      
       1028 AATAAAATTAGTAAAATGATAAA
          1 AATAAAATTAGTAAAAGGATAAA

                          *       
       1051 AATAAAA-TAGGTATAAGGATA
          1 AATAAAATTA-GTAAAAGGATA

       1072 TTATATTTAA


Statistics
Matches: 18,  Mismatches: 2, Indels: 2
        0.82            0.09        0.09

Matches are distributed among these distances:
  22    2  0.11
  23   16  0.89

ACGTcount: A:0.61, C:0.00, G:0.14, T:0.25


Consensus pattern (23 bp):   
AATAAAATTAGTAAAAGGATAAA

Found at i:1103 original size:23 final size:27

Alignment explanation


    Indices: 1077--1136  Score: 74
    Period size: 23  Copynumber: 2.4  Consensus size: 27

       1067 GGATATTATA

                                       
       1077 TTTAATTAAAT-AAAA-ATAG-AGT-T
          1 TTTAATTAAATAAAAATATAGAAGTAT

                   * *                 
       1100 TTTAATTGAGTAAAAATATAGAAGTAT
          1 TTTAATTAAATAAAAATATAGAAGTAT

                      
       1127 TTTAATTAAA
          1 TTTAATTAAA

       1137 ATAGTAAAAT


Statistics
Matches: 29,  Mismatches: 4, Indels: 4
        0.78            0.11        0.11

Matches are distributed among these distances:
  23    9  0.31
  24    4  0.14
  25    4  0.14
  26    3  0.10
  27    9  0.31

ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40


Consensus pattern (27 bp):   
TTTAATTAAATAAAAATATAGAAGTAT

Found at i:1142 original size:102 final size:104

Alignment explanation


    Indices: 1024--1223  Score: 307
    Period size: 104  Copynumber: 1.9  Consensus size: 104

       1014 TATCTAAATT

                                                  *              *       *   
       1024 TTTTAATAAAATTAGTAAAATGATAAAAATAAA-A-TAGGTATAAGGATATTATATTTAATTAAA
          1 TTTTAATAAAATTAGTAAAATGATAAAAATAAATAGTACGTATAAGGATATTAGATTTAATCAAA

                       *                           
       1087 TAAAAATAGAGTTTTTAATTGAGTAAAAATATAGAAGTA
         66 TAAAAATAGAGGTTTTAATTGAGTAAAAATATAGAAGTA

                                   *                *                        
       1126 TTTTAATTAAAA-TAGTAAAATGGTAAAAATAAATAGTACTTATAAGGATATTAGATTTAATCAA
          1 TTTTAA-TAAAATTAGTAAAATGATAAAAATAAATAGTACGTATAAGGATATTAGATTTAATCAA

                                         *    
       1190 ATAAAAATAGAGGTTTTAATTGAGTAAAACTATA
         65 ATAAAAATAGAGGTTTTAATTGAGTAAAAATATA

       1224 AAAATTTAAT


Statistics
Matches: 88,  Mismatches: 7, Indels: 4
        0.89            0.07        0.04

Matches are distributed among these distances:
 102   26  0.30
 103    6  0.07
 104   56  0.64

ACGTcount: A:0.52, C:0.01, G:0.12, T:0.35


Consensus pattern (104 bp):   
TTTTAATAAAATTAGTAAAATGATAAAAATAAATAGTACGTATAAGGATATTAGATTTAATCAAA
TAAAAATAGAGGTTTTAATTGAGTAAAAATATAGAAGTA

Done.