Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014796.1 Corchorus olitorius cultivar O-4 contig14829, 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: 2259
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32


Found at i:1363 original size:20 final size:20

Alignment explanation


    Indices: 1338--1380  Score: 77
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       1328 TATGACGTGT

                                
       1338 CCTCTGATAATTCCACATGG
          1 CCTCTGATAATTCCACATGG

                            *   
       1358 CCTCTGATAATTCCACGTGG
          1 CCTCTGATAATTCCACATGG

               
       1378 CCT
          1 CCT

       1381 ATATTCACGC


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  20   22  1.00

ACGTcount: A:0.21, C:0.33, G:0.16, T:0.30


Consensus pattern (20 bp):   
CCTCTGATAATTCCACATGG

Found at i:1476 original size:31 final size:29

Alignment explanation


    Indices: 1441--1507  Score: 82
    Period size: 29  Copynumber: 2.2  Consensus size: 29

       1431 AAAATAGGCG

                                            
       1441 CAATTTGGTGCCCA-TCGAATAGGTTTAGACC
          1 CAATTTGGTGCCCAGT--AA-AGGTTTAGACC

                       **                
       1472 CAATTTGGTGCTGAGTAAAGGTTTAGACC
          1 CAATTTGGTGCCCAGTAAAGGTTTAGACC

                   
       1501 CAATTTG
          1 CAATTTG

       1508 AGCAGACCGT


Statistics
Matches: 33,  Mismatches: 2, Indels: 4
        0.85            0.05        0.10

Matches are distributed among these distances:
  29   18  0.55
  30    2  0.06
  31   12  0.36
  32    1  0.03

ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31


Consensus pattern (29 bp):   
CAATTTGGTGCCCAGTAAAGGTTTAGACC

Found at i:1526 original size:31 final size:29

Alignment explanation


    Indices: 1461--1540  Score: 90
    Period size: 29  Copynumber: 2.7  Consensus size: 29

       1451 CCCATCGAAT

                               *  *      
       1461 AGGTTTAGACCCAATTTGGTGCTGAGTAA
          1 AGGTTTAGACCCAATTTGGAGCAGAGTAA

                                            
       1490 AGGTTTAGACCCAATTT-GAGCAGACCGTGAA
          1 AGGTTTAGACCCAATTTGGAGCAGA--GT-AA

                    *     *     
       1521 AGGTTTAGGCCCAAATTGGA
          1 AGGTTTAGACCCAATTTGGA

       1541 TATTTAGCCC


Statistics
Matches: 43,  Mismatches: 4, Indels: 5
        0.83            0.08        0.10

Matches are distributed among these distances:
  28    5  0.12
  29   17  0.40
  30    2  0.05
  31   17  0.40
  32    2  0.05

ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26


Consensus pattern (29 bp):   
AGGTTTAGACCCAATTTGGAGCAGAGTAA
Done.