Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018232.1 Corchorus olitorius cultivar O-4 contig18265, 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: 20960
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31


Found at i:370 original size:30 final size:28

Alignment explanation


    Indices: 336--402  Score: 80
    Period size: 28  Copynumber: 2.3  Consensus size: 28

        326 CAAAACGACT

                                *         
        336 AAAATTGAGAGCTCAGAGGATAAAATGTCC
          1 AAAATTGA-AGCTCAG-GGACAAAATGTCC

                      * *               
        366 AAAATTGAAGTTTAGGGACAAAATGTCC
          1 AAAATTGAAGCTCAGGGACAAAATGTCC

              *      
        394 AACATTGAA
          1 AAAATTGAA

        403 ATTTAGGGAA


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

Matches are distributed among these distances:
  28   20  0.61
  29    5  0.15
  30    8  0.24

ACGTcount: A:0.45, C:0.12, G:0.21, T:0.22


Consensus pattern (28 bp):   
AAAATTGAAGCTCAGGGACAAAATGTCC

Found at i:392 original size:28 final size:28

Alignment explanation


    Indices: 357--411  Score: 92
    Period size: 28  Copynumber: 2.0  Consensus size: 28

        347 CTCAGAGGAT

                              *         
        357 AAAATGTCCAAAATTGAAGTTTAGGGAC
          1 AAAATGTCCAAAATTGAAATTTAGGGAC

                       *               
        385 AAAATGTCCAACATTGAAATTTAGGGA
          1 AAAATGTCCAAAATTGAAATTTAGGGA

        412 ATAAAACGTC


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  28   25  1.00

ACGTcount: A:0.44, C:0.11, G:0.20, T:0.25


Consensus pattern (28 bp):   
AAAATGTCCAAAATTGAAATTTAGGGAC

Found at i:777 original size:2 final size:2

Alignment explanation


    Indices: 770--794  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

        760 TACTAATTAT

                                                 
        770 TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA T

        795 CCGTAGGCAT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:9387 original size:40 final size:42

Alignment explanation


    Indices: 9306--9400  Score: 122
    Period size: 40  Copynumber: 2.3  Consensus size: 42

       9296 TGAGAGCATG

                                            *           
       9306 AAATTGATAATAATTTGATTCAAATGTCTTGATGACTTGATCTT
          1 AAATTGATAATAATTTGATTC-AA-GTCTTGACGACTTGATCTT

            *       *                    *            
       9350 GAATTGATGATAATTTGATTC-A-TCTTGGCGACTTGATCTT
          1 AAATTGATAATAATTTGATTCAAGTCTTGACGACTTGATCTT

                       
       9390 AAATTGATAAT
          1 AAATTGATAAT

       9401 TTGATTACTT


Statistics
Matches: 45,  Mismatches: 6, Indels: 4
        0.82            0.11        0.07

Matches are distributed among these distances:
  40   25  0.56
  42    1  0.02
  44   19  0.42

ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42


Consensus pattern (42 bp):   
AAATTGATAATAATTTGATTCAAGTCTTGACGACTTGATCTT

Found at i:9466 original size:29 final size:29

Alignment explanation


    Indices: 9433--9506  Score: 112
    Period size: 29  Copynumber: 2.6  Consensus size: 29

       9423 AATCAACGAC

                                         
       9433 AATTCTTCAATAATAAGCACCAACAAATA
          1 AATTCTTCAATAATAAGCACCAACAAATA

                      *        *  *      
       9462 AATTCTTCAAGAATAAGCAGCAGCAAATA
          1 AATTCTTCAATAATAAGCACCAACAAATA

                 *          
       9491 AATTCATCAATAATAA
          1 AATTCTTCAATAATAA

       9507 TAATAATCTT


Statistics
Matches: 40,  Mismatches: 5, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  29   40  1.00

ACGTcount: A:0.51, C:0.18, G:0.07, T:0.24


Consensus pattern (29 bp):   
AATTCTTCAATAATAAGCACCAACAAATA

Found at i:12128 original size:34 final size:32

Alignment explanation


    Indices: 12084--12151  Score: 91
    Period size: 34  Copynumber: 2.1  Consensus size: 32

      12074 AGAAGTATGT

                                              
      12084 TTTTAATTAATTGTTTTCCAAATCTTTAGTTTAG
          1 TTTTAATTAATTGTTTTCCAAAT-TTTA-TTTAG

                 *            *  *          
      12118 TTTTATTTAATTGTTTTCTAAGTTTTATTTAG
          1 TTTTAATTAATTGTTTTCCAAATTTTATTTAG

              
      12150 TT
          1 TT

      12152 ATTTTGAAAA


Statistics
Matches: 31,  Mismatches: 3, Indels: 2
        0.86            0.08        0.06

Matches are distributed among these distances:
  32    7  0.23
  33    4  0.13
  34   20  0.65

ACGTcount: A:0.24, C:0.06, G:0.09, T:0.62


Consensus pattern (32 bp):   
TTTTAATTAATTGTTTTCCAAATTTTATTTAG
Done.