Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018888.1 Corchorus olitorius cultivar O-4 contig18921, 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: 6829
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.34


Found at i:3910 original size:107 final size:105

Alignment explanation


    Indices: 3769--4030  Score: 393
    Period size: 107  Copynumber: 2.5  Consensus size: 105

       3759 AGTTTAGTTT

                                                                     *       
       3769 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATT
          1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT

                                                      
       3834 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
         66 AATAA--TATTGTTATAGGGTTTTAGAAATAAAATACAAAAC

                  *     *                                               **   
       3876 TAATTTTACTAAATTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATGATT
          1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT

                                              * *   
       3941 AATAATATTGTTATAGGGTTTTAGAAATAAAATATATAAC
         66 AATAATATTGTTATAGGGTTTTAGAAATAAAATACAAAAC

                               *             ** *               
       3981 TAA-TTCACTAAGTTTAG-TCCAAATTAAAATTAAAATTTTATTTTAAGGGT
          1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGT

       4031 TAGAAAATTT


Statistics
Matches: 142,  Mismatches: 13, Indels: 4
        0.89            0.08        0.03

Matches are distributed among these distances:
 103   29  0.20
 104   12  0.08
 105   36  0.25
 107   65  0.46

ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42


Consensus pattern (105 bp):   
TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
AATAATATTGTTATAGGGTTTTAGAAATAAAATACAAAAC

Found at i:5161 original size:160 final size:159

Alignment explanation


    Indices: 4848--5173  Score: 562
    Period size: 159  Copynumber: 2.0  Consensus size: 159

       4838 GGAAAATTGA

                                  *                                          
       4848 TAAATTTGTTGGAAAGTAATTAGTTTGAATGGAAAAAACATGGATATTACCAGGTCAAATATTTG
          1 TAAATTTGTTGGAAAGTAATTAATTTGAATGGAAAAAACATGGATATTACCAGGTCAAATATTTG

                                                  *                          
       4913 CCAAGTTCAAAGTAGTTGAGAGAATATCTCTCAACTATGCAAATCATGGAATATTTGTTTGTTAA
         66 CCAAGTTCAAAGTAGTTGAGAGAATATCTCTCAACTATACAAATCATGGAATATTTGTTTGTTAA

                *   *                    
       4978 TATCTAATTACCAAATATCTCATTTAAAT
        131 TATCCAATCACCAAATATCTCATTTAAAT

                                            *                                
       5007 TAAATTTGTTGGAAAGTAATTAATTTGAATGGGAAAAACATGGATATTACCAGGTCAAATATTTG
          1 TAAATTTGTTGGAAAGTAATTAATTTGAATGGAAAAAACATGGATATTACCAGGTCAAATATTTG

                     *                                *     *                
       5072 CCAAGTTCATAGTAGTTGAGAGAATATCTCTCAACTACTACATATCATTGAATATTTGTTTGTTA
         66 CCAAGTTCAAAGTAGTTGAGAGAATATCTCTCAACTA-TACAAATCATGGAATATTTGTTTGTTA

                                          
       5137 ATATCCAATCACCAAATATCTCATTTAAAT
        130 ATATCCAATCACCAAATATCTCATTTAAAT

              *    
       5167 TAGATTT
          1 TAAATTT

       5174 TGGCTGATTT


Statistics
Matches: 157,  Mismatches: 9, Indels: 1
        0.94            0.05        0.01

Matches are distributed among these distances:
 159   99  0.63
 160   58  0.37

ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36


Consensus pattern (159 bp):   
TAAATTTGTTGGAAAGTAATTAATTTGAATGGAAAAAACATGGATATTACCAGGTCAAATATTTG
CCAAGTTCAAAGTAGTTGAGAGAATATCTCTCAACTATACAAATCATGGAATATTTGTTTGTTAA
TATCCAATCACCAAATATCTCATTTAAAT

Found at i:6563 original size:2 final size:2

Alignment explanation


    Indices: 6556--6588  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

       6546 GTCTTGATCA

                                                             
       6556 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       6589 GACATTGGAT


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   31  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Done.