Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013797.1 Corchorus olitorius cultivar O-4 contig13830, 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: 13359
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32


Found at i:12823 original size:20 final size:20

Alignment explanation


    Indices: 12798--12867  Score: 56
    Period size: 20  Copynumber: 3.4  Consensus size: 20

      12788 CATTCTCCTT

                                
      12798 TCATTTTCCATTTCCTTTAA
          1 TCATTTTCCATTTCCTTTAA

                               *     
      12818 TCATTTTGGCCCATTTACTTTTTAA
          1 TCATTTT---CCATTT-C-CTTTAA

                                 
      12843 GTC--TTT-CATTTCCTTTAA
          1 -TCATTTTCCATTTCCTTTAA

                   
      12861 TCATTTT
          1 TCATTTT

      12868 GGCCCATTTA


Statistics
Matches: 40,  Mismatches: 2, Indels: 17
        0.68            0.03        0.29

Matches are distributed among these distances:
  17    2  0.05
  18    5  0.12
  19    4  0.10
  20   12  0.30
  23    6  0.15
  24    4  0.10
  25    5  0.12
  26    2  0.05

ACGTcount: A:0.19, C:0.21, G:0.04, T:0.56


Consensus pattern (20 bp):   
TCATTTTCCATTTCCTTTAA

Found at i:12838 original size:23 final size:23

Alignment explanation


    Indices: 12805--12881  Score: 67
    Period size: 23  Copynumber: 3.5  Consensus size: 23

      12795 CTTTCATTTT

                  *                
      12805 CCATTTCCTTTAATCATTTTGGC
          1 CCATTTACTTTAATCATTTTGGC

                                      
      12828 CCATTTACTTTTTAAGTC--TTT---
          1 CCATTTAC--TTTAA-TCATTTTGGC

                  *                
      12849 -CATTTCCTTTAATCATTTTGGC
          1 CCATTTACTTTAATCATTTTGGC

                       
      12871 CCATTTACTTT
          1 CCATTTACTTT

      12882 TTAAGTCTTT


Statistics
Matches: 42,  Mismatches: 3, Indels: 18
        0.67            0.05        0.29

Matches are distributed among these distances:
  17    2  0.05
  18    5  0.12
  19    3  0.07
  20    6  0.14
  23   16  0.38
  24    3  0.07
  25    5  0.12
  26    2  0.05

ACGTcount: A:0.18, C:0.23, G:0.06, T:0.52


Consensus pattern (23 bp):   
CCATTTACTTTAATCATTTTGGC

Found at i:12867 original size:43 final size:43

Alignment explanation


    Indices: 12806--12891  Score: 172
    Period size: 43  Copynumber: 2.0  Consensus size: 43

      12796 TTTCATTTTC

                                                       
      12806 CATTTCCTTTAATCATTTTGGCCCATTTACTTTTTAAGTCTTT
          1 CATTTCCTTTAATCATTTTGGCCCATTTACTTTTTAAGTCTTT

                                                       
      12849 CATTTCCTTTAATCATTTTGGCCCATTTACTTTTTAAGTCTTT
          1 CATTTCCTTTAATCATTTTGGCCCATTTACTTTTTAAGTCTTT

      12892 GTTTGATCAT


Statistics
Matches: 43,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  43   43  1.00

ACGTcount: A:0.19, C:0.21, G:0.07, T:0.53


Consensus pattern (43 bp):   
CATTTCCTTTAATCATTTTGGCCCATTTACTTTTTAAGTCTTT
Done.