Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006041.1 Corchorus olitorius cultivar O-4 contig06066, 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, 840

Length: 1401
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27


Found at i:279 original size:3 final size:3

Alignment explanation


    Indices: 271--323  Score: 106
    Period size: 3  Copynumber: 17.7  Consensus size: 3

        261 AATTTTACAT

                                                                           
        271 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA

                  
        319 TTA TT
          1 TTA TT

        324 TTACACTAAT


Statistics
Matches: 50,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   50  1.00

ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68


Consensus pattern (3 bp):   
TTA

Found at i:629 original size:27 final size:27

Alignment explanation


    Indices: 567--632  Score: 96
    Period size: 27  Copynumber: 2.4  Consensus size: 27

        557 CAAGGCTGCT

                                  *   *
        567 CCGCAAGGCCGCCCCAGCACCAGCAGT
          1 CCGCAAGGCCGCCCCAGCACCAACAGC

            *                          
        594 TCGCAAGGCCGCCCCAGCACCAACAGC
          1 CCGCAAGGCCGCCCCAGCACCAACAGC

                *       
        621 CCGCCAGGCCGC
          1 CCGCAAGGCCGC

        633 TAACAGCAGC


Statistics
Matches: 34,  Mismatches: 5, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  27   34  1.00

ACGTcount: A:0.21, C:0.50, G:0.26, T:0.03


Consensus pattern (27 bp):   
CCGCAAGGCCGCCCCAGCACCAACAGC

Found at i:1135 original size:16 final size:16

Alignment explanation


    Indices: 1097--1142  Score: 58
    Period size: 16  Copynumber: 2.9  Consensus size: 16

       1087 AGGCCAAATC

                         *  
       1097 GACGATAAGG-AGCAA
          1 GACGATAAGGAAGAAA

                            
       1112 GACGATAAGGAAGAAA
          1 GACGATAAGGAAGAAA

             *      *      
       1128 GTCGATAAAGAAGAA
          1 GACGATAAGGAAGAA

       1143 GCCAAAATTC


Statistics
Matches: 27,  Mismatches: 3, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  15   10  0.37
  16   17  0.63

ACGTcount: A:0.52, C:0.09, G:0.30, T:0.09


Consensus pattern (16 bp):   
GACGATAAGGAAGAAA
Done.