Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019955.1 Corchorus olitorius cultivar O-4 contig19988, 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: 36261
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32


Found at i:6254 original size:11 final size:11

Alignment explanation


    Indices: 6228--6268  Score: 57
    Period size: 11  Copynumber: 3.8  Consensus size: 11

       6218 CATGGGATTT

                       
       6228 TTAA-TAATAA
          1 TTAATTAATAA

                   *  *
       6238 TTAATTATTAT
          1 TTAATTAATAA

                       
       6249 TTAATTAATAA
          1 TTAATTAATAA

                     
       6260 TTAATTAAT
          1 TTAATTAAT

       6269 TTCAGCCATT


Statistics
Matches: 26,  Mismatches: 4, Indels: 1
        0.84            0.13        0.03

Matches are distributed among these distances:
  10    4  0.15
  11   22  0.85

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (11 bp):   
TTAATTAATAA

Found at i:6255 original size:15 final size:15

Alignment explanation


    Indices: 6235--6269  Score: 52
    Period size: 15  Copynumber: 2.3  Consensus size: 15

       6225 TTTTTAATAA

                    *    * 
       6235 TAATTAATTATTATT
          1 TAATTAATAATTAAT

                           
       6250 TAATTAATAATTAAT
          1 TAATTAATAATTAAT

                 
       6265 TAATT
          1 TAATT

       6270 TCAGCCATTG


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  15   18  1.00

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


Consensus pattern (15 bp):   
TAATTAATAATTAAT

Found at i:22149 original size:13 final size:13

Alignment explanation


    Indices: 22131--22166  Score: 65
    Period size: 12  Copynumber: 2.8  Consensus size: 13

      22121 AGGTATTGAT

                         
      22131 GGATATATCGAAC
          1 GGATATATCGAAC

                         
      22144 GGATATATCG-AC
          1 GGATATATCGAAC

                       
      22156 GGATATATCGA
          1 GGATATATCGA

      22167 GGTATCGATG


Statistics
Matches: 22,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  12   12  0.55
  13   10  0.45

ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25


Consensus pattern (13 bp):   
GGATATATCGAAC

Found at i:24426 original size:29 final size:29

Alignment explanation


    Indices: 24393--24455  Score: 126
    Period size: 29  Copynumber: 2.2  Consensus size: 29

      24383 ACTGAGATTA

                                         
      24393 GACTCGAAACTGACTAGAAAAAACAAACT
          1 GACTCGAAACTGACTAGAAAAAACAAACT

                                         
      24422 GACTCGAAACTGACTAGAAAAAACAAACT
          1 GACTCGAAACTGACTAGAAAAAACAAACT

                 
      24451 GACTC
          1 GACTC

      24456 AAATAAAAGC


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  29   34  1.00

ACGTcount: A:0.49, C:0.22, G:0.14, T:0.14


Consensus pattern (29 bp):   
GACTCGAAACTGACTAGAAAAAACAAACT

Found at i:24830 original size:2 final size:2

Alignment explanation


    Indices: 24823--24859  Score: 74
    Period size: 2  Copynumber: 18.5  Consensus size: 2

      24813 TGAAAGACAA

                                                                   
      24823 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

      24860 CATACTGGTG


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   35  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:35824 original size:2 final size:2

Alignment explanation


    Indices: 35817--35844  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

      35807 TAAGGGACAG

                                                     
      35817 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      35845 TGACTATAAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.