Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013581.1 Corchorus olitorius cultivar O-4 contig13614, 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: 5787
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33


Found at i:1637 original size:4 final size:4

Alignment explanation


    Indices: 1628--1653  Score: 52
    Period size: 4  Copynumber: 6.5  Consensus size: 4

       1618 TCTTTGAAAA

                                            
       1628 AATT AATT AATT AATT AATT AATT AA
          1 AATT AATT AATT AATT AATT AATT AA

       1654 AAGAAAATGT


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   22  1.00

ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46


Consensus pattern (4 bp):   
AATT

Found at i:1761 original size:26 final size:26

Alignment explanation


    Indices: 1718--1767  Score: 64
    Period size: 26  Copynumber: 1.9  Consensus size: 26

       1708 TATCCCTCTG

                         *            
       1718 AAAAAAAAAAGAGTGTTAGTAACCTC
          1 AAAAAAAAAAGAGAGTTAGTAACCTC

                *      *      *     
       1744 AAAAGAAAAAGGGAGTTATTAACC
          1 AAAAAAAAAAGAGAGTTAGTAACC

       1768 CCTAAATCAT


Statistics
Matches: 20,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  26   20  1.00

ACGTcount: A:0.54, C:0.10, G:0.18, T:0.18


Consensus pattern (26 bp):   
AAAAAAAAAAGAGAGTTAGTAACCTC

Found at i:2230 original size:16 final size:15

Alignment explanation


    Indices: 2192--2233  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       2182 ACAGAGATTG

                   *       
       2192 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
       2207 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
       2222 ACTAGAAAACAA
          1 AC-AGAAAACAA

       2234 AGCAAAGTAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA

Found at i:3010 original size:11 final size:11

Alignment explanation


    Indices: 2994--3019  Score: 52
    Period size: 11  Copynumber: 2.4  Consensus size: 11

       2984 CCTTTGCCTA

                       
       2994 AAAACTAGAAG
          1 AAAACTAGAAG

                       
       3005 AAAACTAGAAG
          1 AAAACTAGAAG

                
       3016 AAAA
          1 AAAA

       3020 GAAATTATCT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   15  1.00

ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08


Consensus pattern (11 bp):   
AAAACTAGAAG

Found at i:4660 original size:21 final size:21

Alignment explanation


    Indices: 4610--4654  Score: 63
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       4600 GTGACACTGC

                *     *          
       4610 CCACCTGGGTTCTCAAGCAAA
          1 CCACATGGGTGCTCAAGCAAA

                             *   
       4631 CCACATGGGTGCTCAAGGAAA
          1 CCACATGGGTGCTCAAGCAAA

               
       4652 CCA
          1 CCA

       4655 TGTGGGCGCC


Statistics
Matches: 21,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.31, C:0.31, G:0.22, T:0.16


Consensus pattern (21 bp):   
CCACATGGGTGCTCAAGCAAA
Done.