Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015517.1 Corchorus olitorius cultivar O-4 contig15550, 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: 5473
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36


Found at i:664 original size:27 final size:27

Alignment explanation


    Indices: 582--666  Score: 125
    Period size: 27  Copynumber: 3.1  Consensus size: 27

        572 AAAATGTACT

                                      * 
        582 TGAAGTGACCAAAATGCCCCTGGATGCG
          1 TGAA-TGACCAAAATGCCCCTGGATGAG

            **                         
        610 CAAATGACCAAAATGCCCCTGGATGAG
          1 TGAATGACCAAAATGCCCCTGGATGAG

                    *                  
        637 TGAATGACTAAAATGCCCCTGGATGAG
          1 TGAATGACCAAAATGCCCCTGGATGAG

               
        664 TGA
          1 TGA

        667 CCCTAGTGTC


Statistics
Matches: 51,  Mismatches: 6, Indels: 1
        0.88            0.10        0.02

Matches are distributed among these distances:
  27   49  0.96
  28    2  0.04

ACGTcount: A:0.33, C:0.22, G:0.26, T:0.19


Consensus pattern (27 bp):   
TGAATGACCAAAATGCCCCTGGATGAG

Found at i:823 original size:24 final size:24

Alignment explanation


    Indices: 790--849  Score: 102
    Period size: 24  Copynumber: 2.5  Consensus size: 24

        780 TGAGAACAAG

                 *                  
        790 GAAGACGAAGAGGAGGTTAATCAA
          1 GAAGAGGAAGAGGAGGTTAATCAA

                                    
        814 GAAGAGGAAGAGGAGGTTAATCAA
          1 GAAGAGGAAGAGGAGGTTAATCAA

               *        
        838 GAAAAGGAAGAG
          1 GAAGAGGAAGAG

        850 CTTCACCCTT


Statistics
Matches: 34,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  24   34  1.00

ACGTcount: A:0.48, C:0.05, G:0.37, T:0.10


Consensus pattern (24 bp):   
GAAGAGGAAGAGGAGGTTAATCAA

Found at i:2049 original size:19 final size:18

Alignment explanation


    Indices: 2025--2060  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       2015 TGAAGACTTA

                               
       2025 TTGAAGACAATTTGAAGAT
          1 TTGAAGACAA-TTGAAGAT

                    *        
       2044 TTGAAGACCATTGAAGA
          1 TTGAAGACAATTGAAGA

       2061 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

Found at i:2067 original size:30 final size:30

Alignment explanation


    Indices: 2013--2072  Score: 77
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       2003 GAAGTTCGTG

                      *              *    
       2013 TTTGAAGACTTATTGAAGACAATTTGAAGA
          1 TTTGAAGACTCATTGAAGACAATTTCAAGA

                                *          
       2043 TTTGAAGAC-CATTGAAGAATAATTTCAAGA
          1 TTTGAAGACTCATTGAAG-ACAATTTCAAGA

       2073 GCAAGAATTG


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

Matches are distributed among these distances:
  29    7  0.27
  30   19  0.73

ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32


Consensus pattern (30 bp):   
TTTGAAGACTCATTGAAGACAATTTCAAGA

Found at i:3352 original size:19 final size:20

Alignment explanation


    Indices: 3311--3352  Score: 52
    Period size: 19  Copynumber: 2.1  Consensus size: 20

       3301 TCTTAATTAT

                      *         
       3311 TTTCTCAATTTATTTTTTGC
          1 TTTCTCAATTAATTTTTTGC

                                 
       3331 TTTCT-AATTAATTGTTTT-C
          1 TTTCTCAATTAATT-TTTTGC

               
       3350 TTT
          1 TTT

       3353 AATTTTCTTG


Statistics
Matches: 20,  Mismatches: 1, Indels: 3
        0.83            0.04        0.12

Matches are distributed among these distances:
  19   11  0.55
  20    9  0.45

ACGTcount: A:0.17, C:0.12, G:0.05, T:0.67


Consensus pattern (20 bp):   
TTTCTCAATTAATTTTTTGC
Done.