Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020195.1 Corchorus olitorius cultivar O-4 contig20228, 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: 12473
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31


Found at i:303 original size:28 final size:27

Alignment explanation


    Indices: 233--308  Score: 82
    Period size: 28  Copynumber: 2.7  Consensus size: 27

        223 TCCGACGCTT

                                  *     
        233 AAGGGCAAAACTGTAA-TTTAGTCAACC
          1 AAGGGCAAAAC-GTAATTTTAGCCAACC

                 *     *            *   
        260 AAGGGTAAAATGGTAATTTTAGCCGACC
          1 AAGGGCAAAA-CGTAATTTTAGCCAACC

                                 
        288 AAGGGCAAATACGTAATTTTA
          1 AAGGGCAAA-ACGTAATTTTA

        309 ACATCCTAAG


Statistics
Matches: 40,  Mismatches: 6, Indels: 5
        0.78            0.12        0.10

Matches are distributed among these distances:
  27   13  0.32
  28   26  0.65
  29    1  0.03

ACGTcount: A:0.39, C:0.14, G:0.21, T:0.25


Consensus pattern (27 bp):   
AAGGGCAAAACGTAATTTTAGCCAACC

Found at i:797 original size:6 final size:6

Alignment explanation


    Indices: 781--857  Score: 75
    Period size: 6  Copynumber: 12.8  Consensus size: 6

        771 TCCTATTTAT

                 *             *                          *      *  
        781 TTTTTA TTTTTCC TTTTCC TTTTTC TTTTTC TTTTTC TTTCTC TTTCTC
          1 TTTTTC TTTTT-C TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC

               *    *       *                
        830 TTTCTC TCTTTC TTCTTC TTTTT- TTTTT
          1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTT

        858 TTTCGACTTG


Statistics
Matches: 61,  Mismatches: 9, Indels: 3
        0.84            0.12        0.04

Matches are distributed among these distances:
   5    5  0.08
   6   52  0.85
   7    4  0.07

ACGTcount: A:0.01, C:0.22, G:0.00, T:0.77


Consensus pattern (6 bp):   
TTTTTC

Found at i:803 original size:19 final size:19

Alignment explanation


    Indices: 781--817  Score: 56
    Period size: 19  Copynumber: 1.9  Consensus size: 19

        771 TCCTATTTAT

                               
        781 TTTTTATTTTTCCTTTTCC
          1 TTTTTATTTTTCCTTTTCC

                 *      *     
        800 TTTTTCTTTTTCTTTTTC
          1 TTTTTATTTTTCCTTTTC

        818 TTTCTCTTTC


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  19   16  1.00

ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78


Consensus pattern (19 bp):   
TTTTTATTTTTCCTTTTCC

Found at i:970 original size:29 final size:29

Alignment explanation


    Indices: 885--962  Score: 129
    Period size: 29  Copynumber: 2.7  Consensus size: 29

        875 TGGCATGCCA

                *                        
        885 GGCCCGCGCGGCCTGTCAGGCCCGCGTGT
          1 GGCCAGCGCGGCCTGTCAGGCCCGCGTGT

                                         
        914 GGCCAGCGCGGCCTGTCAGGCCCGCGTGT
          1 GGCCAGCGCGGCCTGTCAGGCCCGCGTGT

                *          *    
        943 GGCCTGCGCGGCCTGCCAGG
          1 GGCCAGCGCGGCCTGTCAGG

        963 TTCGCGTGGC


Statistics
Matches: 46,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  29   46  1.00

ACGTcount: A:0.05, C:0.40, G:0.42, T:0.13


Consensus pattern (29 bp):   
GGCCAGCGCGGCCTGTCAGGCCCGCGTGT

Found at i:2345 original size:13 final size:13

Alignment explanation


    Indices: 2323--2354  Score: 57
    Period size: 13  Copynumber: 2.5  Consensus size: 13

       2313 AAGACATTGA

                         
       2323 AATAGT-ATTAAT
          1 AATAGTAATTAAT

                         
       2335 AATAGTAATTAAT
          1 AATAGTAATTAAT

                   
       2348 AATAGTA
          1 AATAGTA

       2355 TTATTACTTT


Statistics
Matches: 19,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  12    6  0.32
  13   13  0.68

ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38


Consensus pattern (13 bp):   
AATAGTAATTAAT

Found at i:4406 original size:12 final size:13

Alignment explanation


    Indices: 4382--4410  Score: 51
    Period size: 12  Copynumber: 2.3  Consensus size: 13

       4372 GTTTACACTT

                         
       4382 ATATAGTATATAG
          1 ATATAGTATATAG

                         
       4395 ATATAG-ATATAG
          1 ATATAGTATATAG

                
       4407 ATAT
          1 ATAT

       4411 GGCAAAATTT


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  12   10  0.62
  13    6  0.38

ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38


Consensus pattern (13 bp):   
ATATAGTATATAG
Done.