Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020220.1 Corchorus olitorius cultivar O-4 contig20253, 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: 22475
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33


Found at i:3205 original size:27 final size:27

Alignment explanation


    Indices: 3169--3243  Score: 132
    Period size: 27  Copynumber: 2.8  Consensus size: 27

       3159 GACTGATGCC

                                       
       3169 GCAGTGGATCCTCCCACTTCGACCCCA
          1 GCAGTGGATCCTCCCACTTCGACCCCA

             *           *             
       3196 GTAGTGGATCCTCACACTTCGACCCCA
          1 GCAGTGGATCCTCCCACTTCGACCCCA

                                 
       3223 GCAGTGGATCCTCCCACTTCG
          1 GCAGTGGATCCTCCCACTTCG

       3244 CCTCGGGTCG


Statistics
Matches: 44,  Mismatches: 4, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  27   44  1.00

ACGTcount: A:0.19, C:0.40, G:0.20, T:0.21


Consensus pattern (27 bp):   
GCAGTGGATCCTCCCACTTCGACCCCA

Found at i:4438 original size:14 final size:14

Alignment explanation


    Indices: 4419--4455  Score: 74
    Period size: 14  Copynumber: 2.6  Consensus size: 14

       4409 TCTTAACGTG

                          
       4419 TACAAGAAGACGCA
          1 TACAAGAAGACGCA

                          
       4433 TACAAGAAGACGCA
          1 TACAAGAAGACGCA

                     
       4447 TACAAGAAG
          1 TACAAGAAG

       4456 CAATGGAGCA


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

Matches are distributed among these distances:
  14   23  1.00

ACGTcount: A:0.51, C:0.19, G:0.22, T:0.08


Consensus pattern (14 bp):   
TACAAGAAGACGCA

Found at i:6290 original size:32 final size:32

Alignment explanation


    Indices: 6254--6421  Score: 273
    Period size: 32  Copynumber: 5.2  Consensus size: 32

       6244 GTGTGAAAAG

                                            
       6254 AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC
          1 AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC

                                            
       6286 AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC
          1 AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC

                                   *  *     
       6318 AAAACGCCCTTATTTAGCGGCGTTTACAGAAC
          1 AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC

                     *       *          *   
       6350 AAAACGCCCCTATTTAGTGGCGTCTAAAAAAC
          1 AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC

                                     **     
       6382 AAAACGCCCTTATTTAGCGGCGTCTTTAGAAC
          1 AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC

                    
       6414 AAAACGCC
          1 AAAACGCC

       6422 GCTATATATT


Statistics
Matches: 124,  Mismatches: 12, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  32  124  1.00

ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23


Consensus pattern (32 bp):   
AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC

Found at i:6590 original size:24 final size:24

Alignment explanation


    Indices: 6558--6624  Score: 116
    Period size: 24  Copynumber: 2.8  Consensus size: 24

       6548 ACGTGTCCAG

                *     *             
       6558 ATAGCGGCGTTTAGACGCCATTAA
          1 ATAGTGGCGTCTAGACGCCATTAA

                                    
       6582 ATAGTGGCGTCTAGACGCCATTAA
          1 ATAGTGGCGTCTAGACGCCATTAA

                               
       6606 ATAGTGGCGTCTAGACGCC
          1 ATAGTGGCGTCTAGACGCC

       6625 GCTATATATT


Statistics
Matches: 41,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  24   41  1.00

ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24


Consensus pattern (24 bp):   
ATAGTGGCGTCTAGACGCCATTAA

Found at i:18387 original size:20 final size:20

Alignment explanation


    Indices: 18361--18405  Score: 63
    Period size: 20  Copynumber: 2.2  Consensus size: 20

      18351 CATATAGATT

                 *               
      18361 TTTTTTAATTAATTAATTAAA
          1 TTTTTAAATT-ATTAATTAAA

                      *         
      18382 TTTTTAAATTTTTAATTAAA
          1 TTTTTAAATTATTAATTAAA

                
      18402 TTTT
          1 TTTT

      18406 AATATATGGA


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  20   13  0.59
  21    9  0.41

ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62


Consensus pattern (20 bp):   
TTTTTAAATTATTAATTAAA
Done.