Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023674.1 Corchorus olitorius cultivar O-4 contig23707, 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: 15702
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32


Found at i:3328 original size:19 final size:18

Alignment explanation


    Indices: 3295--3330  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       3285 TTGAGATAAT

                              
       3295 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
       3313 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

       3331 TAAGTCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA

Found at i:4193 original size:18 final size:18

Alignment explanation


    Indices: 4170--4206  Score: 56
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       4160 CTCCTCTATC

                     *        
       4170 ATGAAAACACTTCTTTTT
          1 ATGAAAACAATTCTTTTT

                        *     
       4188 ATGAAAACAATTTTTTTT
          1 ATGAAAACAATTCTTTTT

             
       4206 A
          1 A

       4207 ATTACCCTTT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46


Consensus pattern (18 bp):   
ATGAAAACAATTCTTTTT

Found at i:4524 original size:22 final size:22

Alignment explanation


    Indices: 4497--4545  Score: 98
    Period size: 22  Copynumber: 2.2  Consensus size: 22

       4487 AAAAGGTTTG

                                  
       4497 AAAAATTCAAAATTTTATCTTC
          1 AAAAATTCAAAATTTTATCTTC

                                  
       4519 AAAAATTCAAAATTTTATCTTC
          1 AAAAATTCAAAATTTTATCTTC

                 
       4541 AAAAA
          1 AAAAA

       4546 GCAATTTTTC


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   27  1.00

ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37


Consensus pattern (22 bp):   
AAAAATTCAAAATTTTATCTTC

Found at i:6878 original size:5 final size:6

Alignment explanation


    Indices: 6845--6877  Score: 57
    Period size: 6  Copynumber: 5.5  Consensus size: 6

       6835 AATTAGTGTA

                       *                          
       6845 AAAATT AAAAAT AAAATT AAAATT AAAATT AAA
          1 AAAATT AAAATT AAAATT AAAATT AAAATT AAA

       6878 TATGCAAAGA


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

Matches are distributed among these distances:
   6   25  1.00

ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27


Consensus pattern (6 bp):   
AAAATT

Found at i:13423 original size:19 final size:18

Alignment explanation


    Indices: 13390--13425  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      13380 TTGAGATAAT

                              
      13390 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
      13408 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

      13426 TAAGTCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA

Found at i:14637 original size:15 final size:15

Alignment explanation


    Indices: 14617--14658  Score: 57
    Period size: 15  Copynumber: 2.7  Consensus size: 15

      14607 ACAGAGATTG

                   *       
      14617 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
      14632 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                 *      
      14647 ACTAGGAAACAA
          1 AC-AGAAAACAA

      14659 AGCAGAGTAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  15   16  0.67
  16    8  0.33

ACGTcount: A:0.62, C:0.14, G:0.12, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA

Found at i:14658 original size:16 final size:15

Alignment explanation


    Indices: 14620--14658  Score: 51
    Period size: 16  Copynumber: 2.5  Consensus size: 15

      14610 GAGATTGACA

                            
      14620 GAAAGCAATTAAACAG
          1 GAAA-CAATTAAACAG

            *               
      14636 AAAACAATTAAACTAG
          1 GAAACAATTAAAC-AG

                   
      14652 GAAACAA
          1 GAAACAA

      14659 AGCAGAGTAA


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  15    9  0.45
  16   11  0.55

ACGTcount: A:0.62, C:0.13, G:0.13, T:0.13


Consensus pattern (15 bp):   
GAAACAATTAAACAG
Done.