Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01005284.1 Corchorus olitorius cultivar O-4 contig05307, 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, 870

Length: 1450
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29


Found at i:119 original size:18 final size:18

Alignment explanation


    Indices: 96--131  Score: 72
    Period size: 18  Copynumber: 2.0  Consensus size: 18

         86 ATAATAATTG

                              
         96 ATAGTAAGAATTGATAAT
          1 ATAGTAAGAATTGATAAT

                              
        114 ATAGTAAGAATTGATAAT
          1 ATAGTAAGAATTGATAAT

        132 CATTTGAATT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33


Consensus pattern (18 bp):   
ATAGTAAGAATTGATAAT

Found at i:159 original size:17 final size:17

Alignment explanation


    Indices: 139--189  Score: 58
    Period size: 17  Copynumber: 3.2  Consensus size: 17

        129 AATCATTTGA

                             
        139 ATTGATATATAATTTAG
          1 ATTGATATATAATTTAG

                             
        156 ATTG---T-TAATTT-G
          1 ATTGATATATAATTTAG

                              
        168 AATTGATATATAATTTAG
          1 -ATTGATATATAATTTAG

                
        186 ATTG
          1 ATTG

        190 TTAATTGGTT


Statistics
Matches: 28,  Mismatches: 0, Indels: 12
        0.70            0.00        0.30

Matches are distributed among these distances:
  12    1  0.04
  13   10  0.36
  14    1  0.04
  16    1  0.04
  17   14  0.50
  18    1  0.04

ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49


Consensus pattern (17 bp):   
ATTGATATATAATTTAG

Found at i:167 original size:30 final size:30

Alignment explanation


    Indices: 133--195  Score: 126
    Period size: 30  Copynumber: 2.1  Consensus size: 30

        123 ATTGATAATC

                                          
        133 ATTTGAATTGATATATAATTTAGATTGTTA
          1 ATTTGAATTGATATATAATTTAGATTGTTA

                                          
        163 ATTTGAATTGATATATAATTTAGATTGTTA
          1 ATTTGAATTGATATATAATTTAGATTGTTA

               
        193 ATT
          1 ATT

        196 GGTTTAGTAG


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  30   33  1.00

ACGTcount: A:0.37, C:0.00, G:0.13, T:0.51


Consensus pattern (30 bp):   
ATTTGAATTGATATATAATTTAGATTGTTA
Done.