Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012889.1 Corchorus olitorius cultivar O-4 contig12922, 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: 15820
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:4901 original size:46 final size:47

Alignment explanation


    Indices: 4851--4941  Score: 130
    Period size: 46  Copynumber: 2.0  Consensus size: 47

       4841 TACCCATATA

                             *                             
       4851 ACTTTTGGGCTTTCCTTGTCATTAAACGATATTAA-TGGATGGAATG
          1 ACTTTTGGGCTTTCCTTATCATTAAACGATATTAATTGGATGGAATG

                     *                *   *      *       
       4897 ACTTTTGGGTTTTCCTTATCATTAAAGGATTTTAATTTGATGGAA
          1 ACTTTTGGGCTTTCCTTATCATTAAACGATATTAATTGGATGGAA

       4942 CTTCAAATCC


Statistics
Matches: 39,  Mismatches: 5, Indels: 1
        0.87            0.11        0.02

Matches are distributed among these distances:
  46   31  0.79
  47    8  0.21

ACGTcount: A:0.26, C:0.11, G:0.20, T:0.43


Consensus pattern (47 bp):   
ACTTTTGGGCTTTCCTTATCATTAAACGATATTAATTGGATGGAATG

Found at i:14360 original size:106 final size:106

Alignment explanation


    Indices: 14142--14384  Score: 350
    Period size: 106  Copynumber: 2.3  Consensus size: 106

      14132 GCTCGAATGT

                      *   *    *        *                                    
      14142 TGAGAGCTTGACTTCATAACGCA-TCACCCTC-AT-CCTTTGGCTTAATAATGCCTTTGCCTCAT
          1 TGAGAGCTTGGCTTAATAATGCACT-ACTCTCAATCCCTTTGGCTTAATAATGCCTTTGCCTCAT

                            *                *        
      14204 CTTAATGATGATGGGCTAAATCATATAACAAGGGAGATTAAG
         65 CTTAATGATGATGGGCAAAATCATATAACAAGGAAGATTAAG

                             *                                               
      14246 TGAGAGCTTGGCTTAATGATGCACTACTCTCAATCCCTTTGGCTTAATAATGCCTTTGCCTCATC
          1 TGAGAGCTTGGCTTAATAATGCACTACTCTCAATCCCTTTGGCTTAATAATGCCTTTGCCTCATC

                                   *                * 
      14311 TTAATGATGATGGGCAAAATCATGTAACAAGGAAGGA-TAGG
         66 TTAATGATGATGGGCAAAATCATATAACAAGGAA-GATTAAG

                                     *       
      14352 TGAGAGCTTGGCTTAATAATGCACTCCTCTCAA
          1 TGAGAGCTTGGCTTAATAATGCACTACTCTCAA

      14385 CCTTTGCCAT


Statistics
Matches: 124,  Mismatches: 11, Indels: 6
        0.88            0.08        0.04

Matches are distributed among these distances:
 104   24  0.19
 105    3  0.02
 106   95  0.77
 107    2  0.02

ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30


Consensus pattern (106 bp):   
TGAGAGCTTGGCTTAATAATGCACTACTCTCAATCCCTTTGGCTTAATAATGCCTTTGCCTCATC
TTAATGATGATGGGCAAAATCATATAACAAGGAAGATTAAG

Found at i:14985 original size:2 final size:2

Alignment explanation


    Indices: 14978--15006  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

      14968 AGTGGTCATC

                                                       
      14978 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      15007 TAACCGGCCA


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

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Done.