Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012917.1 Corchorus olitorius cultivar O-4 contig12950, 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: 20045
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:2211 original size:27 final size:27

Alignment explanation


    Indices: 2173--2227  Score: 110
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       2163 GGAGCCAAGA

                                       
       2173 TTCCAATTTTGGGGGCCAAACTAAAAT
          1 TTCCAATTTTGGGGGCCAAACTAAAAT

                                       
       2200 TTCCAATTTTGGGGGCCAAACTAAAAT
          1 TTCCAATTTTGGGGGCCAAACTAAAAT

             
       2227 T
          1 T

       2228 AAAAATGTCA


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  27   28  1.00

ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Consensus pattern (27 bp):   
TTCCAATTTTGGGGGCCAAACTAAAAT

Found at i:14786 original size:49 final size:48

Alignment explanation


    Indices: 14709--14802  Score: 143
    Period size: 49  Copynumber: 1.9  Consensus size: 48

      14699 AAGTGCGATG

                *                 **                         
      14709 AAAATTAAAAGATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAAGT
          1 AAAAATAAAAGATCAATTTTGTAGTAAAAATTGAGAAAAA-ATGCAAGT

                       *                                 
      14758 AAAAATAAAAGTTCAATTTTGTAGTAAAAATTGAGAAAAAATGCA
          1 AAAAATAAAAGATCAATTTTGTAGTAAAAATTGAGAAAAAATGCA

      14803 GTGAAAAGTA


Statistics
Matches: 41,  Mismatches: 4, Indels: 1
        0.89            0.09        0.02

Matches are distributed among these distances:
  48    5  0.12
  49   36  0.88

ACGTcount: A:0.53, C:0.05, G:0.14, T:0.28


Consensus pattern (48 bp):   
AAAAATAAAAGATCAATTTTGTAGTAAAAATTGAGAAAAAATGCAAGT

Found at i:16082 original size:9 final size:9

Alignment explanation


    Indices: 16064--16101  Score: 60
    Period size: 9  Copynumber: 4.3  Consensus size: 9

      16054 TTAATTCATT

                     
      16064 TAATTT-CA
          1 TAATTTCCA

                     
      16072 TAATTTCCA
          1 TAATTTCCA

                    *
      16081 TAATTTCCT
          1 TAATTTCCA

                     
      16090 TAATTTCCA
          1 TAATTTCCA

               
      16099 TAA
          1 TAA

      16102 GTAATTTGGG


Statistics
Matches: 27,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
   8    6  0.22
   9   21  0.78

ACGTcount: A:0.34, C:0.18, G:0.00, T:0.47


Consensus pattern (9 bp):   
TAATTTCCA
Done.