Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010107.1 Corchorus olitorius cultivar O-4 contig10139, 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: 4515
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--59  Score: 84
    Period size: 2  Copynumber: 29.0  Consensus size: 2

                                                                           
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT A-
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT

                       *            
         43 AT AT ACT AA AT AT AT AT
          1 AT AT A-T AT AT AT AT AT

         60 GCTAAATAGT


Statistics
Matches: 52,  Mismatches: 2, Indels: 6
        0.87            0.03        0.10

Matches are distributed among these distances:
   1    1  0.02
   2   47  0.90
   3    4  0.08

ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46


Consensus pattern (2 bp):   
AT

Found at i:64 original size:13 final size:13

Alignment explanation


    Indices: 1--67  Score: 59
    Period size: 12  Copynumber: 5.2  Consensus size: 13

                        *
          1 ATATATATA-TAT
          1 ATATATATACTAA

                        *
         13 ATATATATA-TAT
          1 ATATATATACTAA

                        *
         25 ATATATATA-TAT
          1 ATATATATACTAA

                           
         37 ATACTAATATACTAA
          1 ATA-T-ATATACTAA

                    *    
         52 ATATATATGCTAA
          1 ATATATATACTAA

               
         65 ATA
          1 ATA

         68 GTATTTGAAA


Statistics
Matches: 50,  Mismatches: 2, Indels: 5
        0.88            0.04        0.09

Matches are distributed among these distances:
  12   27  0.54
  13   12  0.24
  14    6  0.12
  15    5  0.10

ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43


Consensus pattern (13 bp):   
ATATATATACTAA

Found at i:382 original size:19 final size:19

Alignment explanation


    Indices: 358--399  Score: 84
    Period size: 19  Copynumber: 2.2  Consensus size: 19

        348 CTCAATTAGT

                               
        358 CTCTGACCATTCATTTTTC
          1 CTCTGACCATTCATTTTTC

                               
        377 CTCTGACCATTCATTTTTC
          1 CTCTGACCATTCATTTTTC

                
        396 CTCT
          1 CTCT

        400 TATTTTATGA


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

Matches are distributed among these distances:
  19   23  1.00

ACGTcount: A:0.14, C:0.33, G:0.05, T:0.48


Consensus pattern (19 bp):   
CTCTGACCATTCATTTTTC
Done.