Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015912.1 Corchorus olitorius cultivar O-4 contig15945, 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: 4677
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.36


Found at i:83 original size:17 final size:16

Alignment explanation


    Indices: 42--91  Score: 50
    Period size: 15  Copynumber: 3.1  Consensus size: 16

         32 CATAACGAAG

                            *
         42 AAGAAAGAGAAAAAGAT
          1 AAGAAA-AGAAAAAGAA

                *            
         59 AAG-GAAGAAGAAAGAA
          1 AAGAAAAGAA-AAAGAA

                            
         75 AAGAAAAG-AAAAGAA
          1 AAGAAAAGAAAAAGAA

              
         90 AA
          1 AA

         92 TAAGGGAAAA


Statistics
Matches: 28,  Mismatches: 3, Indels: 6
        0.76            0.08        0.16

Matches are distributed among these distances:
  15   12  0.43
  16   10  0.36
  17    6  0.21

ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02


Consensus pattern (16 bp):   
AAGAAAAGAAAAAGAA

Found at i:2508 original size:22 final size:22

Alignment explanation


    Indices: 2474--2525  Score: 70
    Period size: 22  Copynumber: 2.3  Consensus size: 22

       2464 CTCTCTGATA

                               *    
       2474 AATTGTTTTTCTTTAATTTTC-TT
          1 AATTG-TTTTC-TTAATTTCCTTT

                                  
       2497 AATTGTTTTCTTAATTTCCTTT
          1 AATTGTTTTCTTAATTTCCTTT

                   
       2519 AATTGTT
          1 AATTGTT

       2526 CTGTTTGCTT


Statistics
Matches: 27,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  21    8  0.30
  22   14  0.52
  23    5  0.19

ACGTcount: A:0.19, C:0.10, G:0.06, T:0.65


Consensus pattern (22 bp):   
AATTGTTTTCTTAATTTCCTTT

Found at i:4122 original size:27 final size:27

Alignment explanation


    Indices: 4092--4217  Score: 171
    Period size: 27  Copynumber: 4.7  Consensus size: 27

       4082 GGTCACCTAG

                      *                
       4092 GGGGCATTTTAGTCATTTGCACATCCA
          1 GGGGCATTTTGGTCATTTGCACATCCA

                      *  *             
       4119 GGGGCATTTTAGTAATTTGCACATCCA
          1 GGGGCATTTTGGTCATTTGCACATCCA

                                  *    
       4146 GGGGCATTTTGGTCATTTGCACTTCCA
          1 GGGGCATTTTGGTCATTTGCACATCCA

                           *     ** ** 
       4173 GGGGCATTTTGGTCACTTGCATGTTTA
          1 GGGGCATTTTGGTCATTTGCACATCCA

                              
       4200 GGGGCATTTTGGTCATTT
          1 GGGGCATTTTGGTCATTT

       4218 TAGGTTCATT


Statistics
Matches: 89,  Mismatches: 10, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  27   89  1.00

ACGTcount: A:0.18, C:0.18, G:0.26, T:0.37


Consensus pattern (27 bp):   
GGGGCATTTTGGTCATTTGCACATCCA

Done.