Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021028.1 Corchorus olitorius cultivar O-4 contig21061, 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: 12350
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:1043 original size:30 final size:30

Alignment explanation


    Indices: 989--1048  Score: 77
    Period size: 30  Copynumber: 2.0  Consensus size: 30

        979 GAAGTTCGTG

                      *              *    
        989 TTTGAAGATTTATTGAAGACAATTTGAAGA
          1 TTTGAAGATTCATTGAAGACAATTTCAAGA

                                *          
       1019 TTTGAAGA-TCATTGAAGAATAATTTCAAGA
          1 TTTGAAGATTCATTGAAG-ACAATTTCAAGA

       1049 GCAAGAATTG


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  29    8  0.31
  30   18  0.69

ACGTcount: A:0.42, C:0.05, G:0.18, T:0.35


Consensus pattern (30 bp):   
TTTGAAGATTCATTGAAGACAATTTCAAGA

Found at i:6535 original size:15 final size:15

Alignment explanation


    Indices: 6515--6552  Score: 58
    Period size: 15  Copynumber: 2.5  Consensus size: 15

       6505 ACAGAGGTTG

                  *        
       6515 ACAGAATGCAATTAA
          1 ACAGAAAGCAATTAA

                           
       6530 ACAGAAAGCAATTAA
          1 ACAGAAAGCAATTAA

                    
       6545 ACTAGAAA
          1 AC-AGAAA

       6553 ACAAAGCAAA


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  15   16  0.76
  16    5  0.24

ACGTcount: A:0.58, C:0.13, G:0.13, T:0.16


Consensus pattern (15 bp):   
ACAGAAAGCAATTAA

Found at i:9523 original size:24 final size:24

Alignment explanation


    Indices: 9496--9552  Score: 114
    Period size: 24  Copynumber: 2.4  Consensus size: 24

       9486 CCAAAGCAAT

                                    
       9496 CGAATGGAGAGCAATTGGAGCTTA
          1 CGAATGGAGAGCAATTGGAGCTTA

                                    
       9520 CGAATGGAGAGCAATTGGAGCTTA
          1 CGAATGGAGAGCAATTGGAGCTTA

                     
       9544 CGAATGGAG
          1 CGAATGGAG

       9553 CTTATGCTGG


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   33  1.00

ACGTcount: A:0.33, C:0.12, G:0.35, T:0.19


Consensus pattern (24 bp):   
CGAATGGAGAGCAATTGGAGCTTA

Found at i:10211 original size:18 final size:18

Alignment explanation


    Indices: 10190--10226  Score: 56
    Period size: 18  Copynumber: 2.1  Consensus size: 18

      10180 AAAGGGTAAT

                     *        
      10190 TAAAAAAAATTGTTTTCA
          1 TAAAAAAAAGTGTTTTCA

                  *           
      10208 TAAAAAGAAGTGTTTTCA
          1 TAAAAAAAAGTGTTTTCA

             
      10226 T
          1 T

      10227 GATAGAGGAG


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.46, C:0.05, G:0.11, T:0.38


Consensus pattern (18 bp):   
TAAAAAAAAGTGTTTTCA

Found at i:11113 original size:19 final size:18

Alignment explanation


    Indices: 11089--11124  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      11079 TTAAGATTTA

                               
      11089 TTGAAGACAATTTGAAGAT
          1 TTGAAGACAA-TTGAAGAT

                    *        
      11108 TTGAAGACCATTGAAGA
          1 TTGAAGACAATTGAAGA

      11125 ATAATTTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28


Consensus pattern (18 bp):   
TTGAAGACAATTGAAGAT
Done.