Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010746.1 Corchorus capsularis cultivar CVL-1 contig10767, 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: 11659
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:165 original size:15 final size:15

Alignment explanation


    Indices: 145--199  Score: 65
    Period size: 15  Copynumber: 3.5  Consensus size: 15

        135 ATAATATGAT

                           
        145 AATTTTAACTATTGG
          1 AATTTTAACTATTGG

                       *   **
        160 AATTTTAACTTGTTAAT
          1 AATTTTAAC-TATT-GG

                           
        177 AATTTTAACTATTGG
          1 AATTTTAACTATTGG

                    
        192 AATTTTAA
          1 AATTTTAA

        200 TGTTCCTTGA


Statistics
Matches: 32,  Mismatches: 6, Indels: 4
        0.76            0.14        0.10

Matches are distributed among these distances:
  15   17  0.53
  16    6  0.19
  17    9  0.28

ACGTcount: A:0.36, C:0.05, G:0.09, T:0.49


Consensus pattern (15 bp):   
AATTTTAACTATTGG

Found at i:249 original size:17 final size:18

Alignment explanation


    Indices: 229--266  Score: 51
    Period size: 18  Copynumber: 2.2  Consensus size: 18

        219 TAACCTTAAC

                              
        229 ATTT-TTTTTATAAAAAG
          1 ATTTATTTTTATAAAAAG

                      *     * 
        246 ATTTATTTTTGTAAAAGG
          1 ATTTATTTTTATAAAAAG

               
        264 ATT
          1 ATT

        267 AGGATATATT


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  17    4  0.22
  18   14  0.78

ACGTcount: A:0.37, C:0.00, G:0.11, T:0.53


Consensus pattern (18 bp):   
ATTTATTTTTATAAAAAG

Found at i:284 original size:18 final size:21

Alignment explanation


    Indices: 257--299  Score: 56
    Period size: 20  Copynumber: 2.2  Consensus size: 21

        247 TTTATTTTTG

                                *
        257 TAAAAGGATT-AGG-ATATAT
          1 TAAAAGGATTGAGGAATATAA

                                 
        276 TAAAA-GATTGAGGAATATAA
          1 TAAAAGGATTGAGGAATATAA

                
        296 TAAA
          1 TAAA

        300 TATATAGATA


Statistics
Matches: 21,  Mismatches: 1, Indels: 3
        0.84            0.04        0.12

Matches are distributed among these distances:
  18    4  0.19
  19    8  0.38
  20    9  0.43

ACGTcount: A:0.53, C:0.00, G:0.19, T:0.28


Consensus pattern (21 bp):   
TAAAAGGATTGAGGAATATAA

Done.