Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014410.1 Corchorus olitorius cultivar O-4 contig14443, 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: 24295
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:11078 original size:19 final size:19

Alignment explanation


    Indices: 11038--11074  Score: 58
    Period size: 19  Copynumber: 2.0  Consensus size: 19

      11028 AATTTTTAAG

                               
      11038 TAAAAATATAATATATAAA
          1 TAAAAATATAATATATAAA

                   *           
      11057 TAAAAATTTAATAT-TAAA
          1 TAAAAATATAATATATAAA

      11075 ATAATTAATT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  18    4  0.24
  19   13  0.76

ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35


Consensus pattern (19 bp):   
TAAAAATATAATATATAAA

Found at i:13379 original size:148 final size:149

Alignment explanation


    Indices: 13083--13379  Score: 542
    Period size: 148  Copynumber: 2.0  Consensus size: 149

      13073 TCAAAATGGC

                                                                       *     
      13083 CTCCACTTCGGATCTGAGATCCGGTCATCATTGCACGTATGCAACCATGTTTCAGCCACGCCATT
          1 CTCCACTTCGGATCTGAGATCCGGTCATCATTGCACGTATGCAACCATGTTTCAGCCACACCATT

                                      *                                      
      13148 ATAGATATTTTCATGTCAAACCCATGGGTGCCAAACTTATAATCAAATAATAAAGCAAAGGCATA
         66 ATAGATATTTTCATGTCAAACCCATGCGTGCCAAACTTATAATCAAATAATAAAGCAAAGGCATA

                               
      13213 AATTCTTGATCCAGTATAT
        131 AATTCTTGATCCAGTATAT

                                 *                                           
      13232 CTCCACTTCGGATCTGAGATCTGGTCATCATTGCACGTATGCAACCATGTTTCAGCCACACCATT
          1 CTCCACTTCGGATCTGAGATCCGGTCATCATTGCACGTATGCAACCATGTTTCAGCCACACCATT

                              *                                     *        
      13297 ATAGATA-TTTCATGTCACACCCATGCGTGCCAAACTTATAATCAAATAATAAAGCGAAGGCATA
         66 ATAGATATTTTCATGTCAAACCCATGCGTGCCAAACTTATAATCAAATAATAAAGCAAAGGCATA

                               
      13361 AATTCTTGATCCAGTATAT
        131 AATTCTTGATCCAGTATAT

      13380 TCTTCAAATC


Statistics
Matches: 143,  Mismatches: 5, Indels: 1
        0.96            0.03        0.01

Matches are distributed among these distances:
 148   73  0.51
 149   70  0.49

ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29


Consensus pattern (149 bp):   
CTCCACTTCGGATCTGAGATCCGGTCATCATTGCACGTATGCAACCATGTTTCAGCCACACCATT
ATAGATATTTTCATGTCAAACCCATGCGTGCCAAACTTATAATCAAATAATAAAGCAAAGGCATA
AATTCTTGATCCAGTATAT

Found at i:19366 original size:7 final size:7

Alignment explanation


    Indices: 19362--19391  Score: 60
    Period size: 7  Copynumber: 4.3  Consensus size: 7

      19352 ATTAAAAAAT

                   
      19362 AAAAAGA
          1 AAAAAGA

                   
      19369 AAAAAGA
          1 AAAAAGA

                   
      19376 AAAAAGA
          1 AAAAAGA

                   
      19383 AAAAAGA
          1 AAAAAGA

              
      19390 AA
          1 AA

      19392 CACAAACAAA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   23  1.00

ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00


Consensus pattern (7 bp):   
AAAAAGA

Done.