Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019733.1 Corchorus olitorius cultivar O-4 contig19766, 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: 7005
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36


Found at i:116 original size:20 final size:20

Alignment explanation


    Indices: 81--118  Score: 58
    Period size: 20  Copynumber: 1.9  Consensus size: 20

         71 ATTACTCATT

                       *        
         81 AAGTTGGTGACGATTCAAAA
          1 AAGTTGGTGACAATTCAAAA

                      *       
        101 AAGTTGGTGATAATTCAA
          1 AAGTTGGTGACAATTCAA

        119 CTCATGATAT


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   16  1.00

ACGTcount: A:0.39, C:0.08, G:0.24, T:0.29


Consensus pattern (20 bp):   
AAGTTGGTGACAATTCAAAA

Found at i:1561 original size:53 final size:53

Alignment explanation


    Indices: 1500--1600  Score: 168
    Period size: 53  Copynumber: 1.9  Consensus size: 53

       1490 TAGCAAATCC

                                           *                      
       1500 TAAATATTTGAATCTTAATAAAAAGATTG-AGCTTTCACCAACAAAATATATCT
          1 TAAATATTTGAATCTTAATAAAAAGATTGAAACTTT-ACCAACAAAATATATCT

                                                  *         
       1553 TAAATATTTGAATCTTAATAAAAAGATTGAAACTTTACTAACAAAATA
          1 TAAATATTTGAATCTTAATAAAAAGATTGAAACTTTACCAACAAAATA

       1601 CTCCCTCCGT


Statistics
Matches: 45,  Mismatches: 2, Indels: 2
        0.92            0.04        0.04

Matches are distributed among these distances:
  53   40  0.89
  54    5  0.11

ACGTcount: A:0.49, C:0.11, G:0.07, T:0.34


Consensus pattern (53 bp):   
TAAATATTTGAATCTTAATAAAAAGATTGAAACTTTACCAACAAAATATATCT

Found at i:2718 original size:24 final size:24

Alignment explanation


    Indices: 2671--2718  Score: 78
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       2661 AAAGTTATCC

                              **    
       2671 CCAAACTGTTGTATGCTCGGTATT
          1 CCAAACTGTTGTATGCTCAATATT

                                    
       2695 CCAAACTGTTGTATGCTCAATATT
          1 CCAAACTGTTGTATGCTCAATATT

       2719 TGACTCTGTT


Statistics
Matches: 22,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  24   22  1.00

ACGTcount: A:0.25, C:0.21, G:0.17, T:0.38


Consensus pattern (24 bp):   
CCAAACTGTTGTATGCTCAATATT
Done.