Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014676.1 Corchorus olitorius cultivar O-4 contig14709, 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: 4809
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36


Found at i:1345 original size:21 final size:21

Alignment explanation


    Indices: 1310--1351  Score: 59
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       1300 TATGGGTGTG

                    *             
       1310 TGTGATTGTTTGGTTTAGTAGA
          1 TGTGATTGATTGGTTTA-TAGA

                                 
       1332 TGTGA-TGATTGGTTTATAGA
          1 TGTGATTGATTGGTTTATAGA

       1352 GACCGAGCGA


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  20    4  0.21
  21   10  0.53
  22    5  0.26

ACGTcount: A:0.21, C:0.00, G:0.31, T:0.48


Consensus pattern (21 bp):   
TGTGATTGATTGGTTTATAGA

Found at i:1381 original size:25 final size:25

Alignment explanation


    Indices: 1347--1396  Score: 100
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       1337 TGATTGGTTT

                                     
       1347 ATAGAGACCGAGCGAGAGTGCTCAA
          1 ATAGAGACCGAGCGAGAGTGCTCAA

                                     
       1372 ATAGAGACCGAGCGAGAGTGCTCAA
          1 ATAGAGACCGAGCGAGAGTGCTCAA

       1397 GATTGTTTGG


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  25   25  1.00

ACGTcount: A:0.36, C:0.20, G:0.32, T:0.12


Consensus pattern (25 bp):   
ATAGAGACCGAGCGAGAGTGCTCAA

Found at i:3078 original size:19 final size:20

Alignment explanation


    Indices: 3054--3094  Score: 59
    Period size: 19  Copynumber: 2.1  Consensus size: 20

       3044 ATATTCATTA

                                 
       3054 AAAAGTTATTT-AA-GTTATC
          1 AAAAGTT-TTTGAATGTTATC

                                
       3073 AAAAGTTTTTGAATGTTATC
          1 AAAAGTTTTTGAATGTTATC

              
       3093 AA
          1 AA

       3095 TAAATTCAGT


Statistics
Matches: 20,  Mismatches: 0, Indels: 3
        0.87            0.00        0.13

Matches are distributed among these distances:
  18    3  0.15
  19    9  0.45
  20    8  0.40

ACGTcount: A:0.41, C:0.05, G:0.12, T:0.41


Consensus pattern (20 bp):   
AAAAGTTTTTGAATGTTATC

Done.