Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015135.1 Corchorus olitorius cultivar O-4 contig15168, 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: 16499
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34


Found at i:2266 original size:43 final size:43

Alignment explanation


    Indices: 2217--2317  Score: 168
    Period size: 44  Copynumber: 2.3  Consensus size: 43

       2207 TAAGTTTGAG

                          *                             
       2217 TAAATAATAATTAATAAA-ACTTTTATTCAATTTCTTTTCATCA
          1 TAAATAA-AATTAAGAAATACTTTTATTCAATTTCTTTTCATCA

                                                        
       2260 TAAATAAAATTAAAGAAATACTTTTATTCAATTTCTTTTCATCA
          1 TAAATAAAATT-AAGAAATACTTTTATTCAATTTCTTTTCATCA

                          
       2304 TAAATAAAATTAAG
          1 TAAATAAAATTAAG

       2318 CATGTGTATA


Statistics
Matches: 55,  Mismatches: 1, Indels: 4
        0.92            0.02        0.07

Matches are distributed among these distances:
  42    4  0.07
  43   15  0.27
  44   36  0.65

ACGTcount: A:0.46, C:0.10, G:0.02, T:0.43


Consensus pattern (43 bp):   
TAAATAAAATTAAGAAATACTTTTATTCAATTTCTTTTCATCA

Found at i:4257 original size:21 final size:19

Alignment explanation


    Indices: 4232--4289  Score: 71
    Period size: 21  Copynumber: 2.9  Consensus size: 19

       4222 GCTGCTCTAA

                                 
       4232 TAATCTCATCTGTACAGTACC
          1 TAATCTCATCTGTACAGT--C

                  *           *
       4253 TAATCTAATCTGTACAGTG
          1 TAATCTCATCTGTACAGTC

                     *        
       4272 TAATCTCATATGTACAGT
          1 TAATCTCATCTGTACAGT

       4290 TGCTAAACAG


Statistics
Matches: 33,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
  19   16  0.48
  21   17  0.52

ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36


Consensus pattern (19 bp):   
TAATCTCATCTGTACAGTC

Found at i:11819 original size:14 final size:15

Alignment explanation


    Indices: 11794--11826  Score: 59
    Period size: 14  Copynumber: 2.3  Consensus size: 15

      11784 ATTATATCAT

                           
      11794 TATTATATATATTAA
          1 TATTATATATATTAA

                           
      11809 TATTA-ATATATTAA
          1 TATTATATATATTAA

                
      11823 TATT
          1 TATT

      11827 GTTATTATTA


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  14   13  0.72
  15    5  0.28

ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55


Consensus pattern (15 bp):   
TATTATATATATTAA

Found at i:13208 original size:25 final size:25

Alignment explanation


    Indices: 13174--13223  Score: 100
    Period size: 25  Copynumber: 2.0  Consensus size: 25

      13164 TGCATTCTAA

                                     
      13174 ACTTTTATTTTGGATACTTTTGCAC
          1 ACTTTTATTTTGGATACTTTTGCAC

                                     
      13199 ACTTTTATTTTGGATACTTTTGCAC
          1 ACTTTTATTTTGGATACTTTTGCAC

      13224 CCTAACTCTT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  25   25  1.00

ACGTcount: A:0.20, C:0.16, G:0.12, T:0.52


Consensus pattern (25 bp):   
ACTTTTATTTTGGATACTTTTGCAC
Done.