Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01004854.1 Corchorus olitorius cultivar O-4 contig04871, 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, 638

Length: 1064
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27


Found at i:357 original size:4 final size:4

Alignment explanation


    Indices: 348--388  Score: 54
    Period size: 4  Copynumber: 11.2  Consensus size: 4

        338 GGAGTGGCCT

                                                                    
        348 TTTA TTTA TTTA TTTA -TTA TTTA --TA TTTA TTTA -TTA TTTA T
          1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T

        389 ATTTCTCGTA


Statistics
Matches: 33,  Mismatches: 0, Indels: 8
        0.80            0.00        0.20

Matches are distributed among these distances:
   2    2  0.06
   3    6  0.18
   4   25  0.76

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


Consensus pattern (4 bp):   
TTTA

Found at i:376 original size:17 final size:17

Alignment explanation


    Indices: 354--392  Score: 78
    Period size: 17  Copynumber: 2.3  Consensus size: 17

        344 GCCTTTTATT

                             
        354 TATTTATTTATTATTTA
          1 TATTTATTTATTATTTA

                             
        371 TATTTATTTATTATTTA
          1 TATTTATTTATTATTTA

                 
        388 TATTT
          1 TATTT

        393 CTCGTATATT


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

Matches are distributed among these distances:
  17   22  1.00

ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72


Consensus pattern (17 bp):   
TATTTATTTATTATTTA

Found at i:411 original size:21 final size:21

Alignment explanation


    Indices: 385--428  Score: 79
    Period size: 21  Copynumber: 2.1  Consensus size: 21

        375 TATTTATTAT

                    *            
        385 TTATATTTCTCGTATATTTAC
          1 TTATATTTATCGTATATTTAC

                                 
        406 TTATATTTATCGTATATTTAC
          1 TTATATTTATCGTATATTTAC

              
        427 TT
          1 TT

        429 TTAAATATAG


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  21   22  1.00

ACGTcount: A:0.25, C:0.11, G:0.05, T:0.59


Consensus pattern (21 bp):   
TTATATTTATCGTATATTTAC

Found at i:425 original size:11 final size:11

Alignment explanation


    Indices: 386--425  Score: 55
    Period size: 11  Copynumber: 3.7  Consensus size: 11

        376 ATTTATTATT

                   *   
        386 TATATTTCTCG
          1 TATATTTATCG

                      *
        397 TATATTTA-CT
          1 TATATTTATCG

                       
        407 TATATTTATCG
          1 TATATTTATCG

                    
        418 TATATTTA
          1 TATATTTA

        426 CTTTTAAATA


Statistics
Matches: 25,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  10    9  0.36
  11   16  0.64

ACGTcount: A:0.28, C:0.10, G:0.05, T:0.57


Consensus pattern (11 bp):   
TATATTTATCG

Found at i:441 original size:21 final size:21

Alignment explanation


    Indices: 396--441  Score: 56
    Period size: 21  Copynumber: 2.2  Consensus size: 21

        386 TATATTTCTC

                           **   *
        396 GTATATTTACTTATATTTATC
          1 GTATATTTACTTATAAATATA

                        *        
        417 GTATATTTACTTTTAAATATA
          1 GTATATTTACTTATAAATATA

                
        438 GTAT
          1 GTAT

        442 TCCCGGCCAA


Statistics
Matches: 21,  Mismatches: 4, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.33, C:0.07, G:0.07, T:0.54


Consensus pattern (21 bp):   
GTATATTTACTTATAAATATA
Done.