Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013840.1 Corchorus olitorius cultivar O-4 contig13873, 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: 22434
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:15227 original size:24 final size:24

Alignment explanation


    Indices: 15195--15244  Score: 100
    Period size: 24  Copynumber: 2.1  Consensus size: 24

      15185 GCAAAATTTT

                                    
      15195 GGTGGGGAAGTACTGATGAGAAAA
          1 GGTGGGGAAGTACTGATGAGAAAA

                                    
      15219 GGTGGGGAAGTACTGATGAGAAAA
          1 GGTGGGGAAGTACTGATGAGAAAA

              
      15243 GG
          1 GG

      15245 AAAATACATT


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   26  1.00

ACGTcount: A:0.36, C:0.04, G:0.44, T:0.16


Consensus pattern (24 bp):   
GGTGGGGAAGTACTGATGAGAAAA

Found at i:15314 original size:8 final size:8

Alignment explanation


    Indices: 15301--15325  Score: 50
    Period size: 8  Copynumber: 3.1  Consensus size: 8

      15291 AGGGAGGTTT

                    
      15301 GGGATTTC
          1 GGGATTTC

                    
      15309 GGGATTTC
          1 GGGATTTC

                    
      15317 GGGATTTC
          1 GGGATTTC

             
      15325 G
          1 G

      15326 AGGCATTTAA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   8   17  1.00

ACGTcount: A:0.12, C:0.12, G:0.40, T:0.36


Consensus pattern (8 bp):   
GGGATTTC

Found at i:20434 original size:105 final size:104

Alignment explanation


    Indices: 20253--20461  Score: 355
    Period size: 105  Copynumber: 2.0  Consensus size: 104

      20243 GTAAACCCTA

                                                                 *           
      20253 AATTTGAGGTTAATCAATCATTCAATAATTTTTATTAAATTTATCTTCTCTGAGTTTTCTCTGAG
          1 AATTTGAGGTTAATCAATCATTCAATAATTTTTATTAAATTTATCTTCTCTGAATTTTCTCTGAG

                *                            *     
      20318 TTATTTGTGTGTTTCTGGACTGAACACGTTCCGTTGCGT
         66 TTATCTGTGTGTTTCTGGACTGAACACGTTCCGCTGCGT

                                        *        *                           
      20357 AATTTGAGGTTAATCAATCATTCAATTATTTTTTATTCAATTTATCTTCTCTGAATTTTCTCTGA
          1 AATTTGAGGTTAATCAATCATTCAA-TAATTTTTATTAAATTTATCTTCTCTGAATTTTCTCTGA

                                *                   
      20422 GTTATCTGTGTGTTTCTGGATTGAACACGTTCCGCTGCGT
         65 GTTATCTGTGTGTTTCTGGACTGAACACGTTCCGCTGCGT

      20462 CAGATGATCC


Statistics
Matches: 98,  Mismatches: 6, Indels: 1
        0.93            0.06        0.01

Matches are distributed among these distances:
 104   25  0.26
 105   73  0.74

ACGTcount: A:0.22, C:0.15, G:0.16, T:0.46


Consensus pattern (104 bp):   
AATTTGAGGTTAATCAATCATTCAATAATTTTTATTAAATTTATCTTCTCTGAATTTTCTCTGAG
TTATCTGTGTGTTTCTGGACTGAACACGTTCCGCTGCGT

Found at i:21912 original size:2 final size:2

Alignment explanation


    Indices: 21899--21938  Score: 71
    Period size: 2  Copynumber: 20.0  Consensus size: 2

      21889 CATGTAACAA

                      *                                                
      21899 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      21939 CAAAACAATA


Statistics
Matches: 36,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   2   36  1.00

ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47


Consensus pattern (2 bp):   
AT

Done.