Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018799.1 Corchorus olitorius cultivar O-4 contig18832, 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, 702

Length: 1170
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36


Found at i:425 original size:10 final size:10

Alignment explanation


    Indices: 412--453  Score: 70
    Period size: 10  Copynumber: 4.4  Consensus size: 10

        402 AATTTTTTAA

                      
        412 TTTTTTCATT
          1 TTTTTTCATT

                      
        422 TTTTTTCATT
          1 TTTTTTCATT

                      
        432 TTTTTTCA--
          1 TTTTTTCATT

                      
        440 TTTTTTCATT
          1 TTTTTTCATT

                
        450 TTTT
          1 TTTT

        454 CATTTCATCA


Statistics
Matches: 30,  Mismatches: 0, Indels: 4
        0.88            0.00        0.12

Matches are distributed among these distances:
   8    8  0.27
  10   22  0.73

ACGTcount: A:0.10, C:0.10, G:0.00, T:0.81


Consensus pattern (10 bp):   
TTTTTTCATT

Found at i:427 original size:18 final size:17

Alignment explanation


    Indices: 398--453  Score: 60
    Period size: 18  Copynumber: 3.2  Consensus size: 17

        388 AGTGCCTTTA

                *       *    
        398 TTTTAATTTTTTAATTT
          1 TTTTTATTTTTTCATTT

                               
        415 TTTCATT-TTTTTTCATTT
          1 TTT--TTATTTTTTCATTT

                              
        433 TTTTTCATTTTTTCATTT
          1 TTTTT-ATTTTTTCATTT

               
        451 TTT
          1 TTT

        454 CATTTCATCA


Statistics
Matches: 33,  Mismatches: 2, Indels: 7
        0.79            0.05        0.17

Matches are distributed among these distances:
  16    2  0.06
  17    3  0.09
  18   27  0.82
  19    1  0.03

ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79


Consensus pattern (17 bp):   
TTTTTATTTTTTCATTT

Found at i:433 original size:8 final size:8

Alignment explanation


    Indices: 398--477  Score: 70
    Period size: 8  Copynumber: 9.5  Consensus size: 8

        388 AGTGCCTTTA

                *   
        398 TTTTAATT
          1 TTTTCATT

                *   
        406 TTTTAATT
          1 TTTTCATT

                      
        414 TTTTCATTTT
          1 TTTTCA--TT

                      
        424 TTTTCATTTT
          1 TTTTCA--TT

                    
        434 TTTTCATT
          1 TTTTCATT

                    
        442 TTTTCATT
          1 TTTTCATT

                    
        450 TTTTCATT
          1 TTTTCATT

             **     
        458 TCATCATT
          1 TTTTCATT

            **      
        466 CATTCATT
          1 TTTTCATT

                
        474 TTTT
          1 TTTT

        478 TATGGGAATT


Statistics
Matches: 62,  Mismatches: 8, Indels: 4
        0.84            0.11        0.05

Matches are distributed among these distances:
   8   44  0.71
  10   18  0.29

ACGTcount: A:0.16, C:0.11, G:0.00, T:0.72


Consensus pattern (8 bp):   
TTTTCATT

Done.