Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01005660.1 Corchorus olitorius cultivar O-4 contig05684, 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, 611

Length: 1019
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33


Found at i:244 original size:18 final size:18

Alignment explanation


    Indices: 209--254  Score: 67
    Period size: 18  Copynumber: 2.6  Consensus size: 18

        199 AATAAATGAA

                        *     
        209 ATAGAAAT-ATTCGAAAT
          1 ATAGAAATAATTAGAAAT

                              
        226 ATAGAAATAATTAGAAAT
          1 ATAGAAATAATTAGAAAT

                  *    
        244 ATAGAATTAAT
          1 ATAGAAATAAT

        255 AATTAATATA


Statistics
Matches: 26,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
  17    8  0.31
  18   18  0.69

ACGTcount: A:0.57, C:0.02, G:0.11, T:0.30


Consensus pattern (18 bp):   
ATAGAAATAATTAGAAAT

Found at i:271 original size:20 final size:21

Alignment explanation


    Indices: 231--280  Score: 59
    Period size: 20  Copynumber: 2.5  Consensus size: 21

        221 GAAATATAGA

                                 
        231 AATAATTAGAAATATAGAATT
          1 AATAATTAGAAATATAGAATT

                      *     *    
        252 AATAATTA-ATATATATAATT
          1 AATAATTAGAAATATAGAATT

                 *    
        272 -ATAAATAGA
          1 AATAATTAGA

        281 TTAAATCTAT


Statistics
Matches: 25,  Mismatches: 3, Indels: 3
        0.81            0.10        0.10

Matches are distributed among these distances:
  19    6  0.24
  20   11  0.44
  21    8  0.32

ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36


Consensus pattern (21 bp):   
AATAATTAGAAATATAGAATT

Found at i:291 original size:23 final size:23

Alignment explanation


    Indices: 252--295  Score: 63
    Period size: 23  Copynumber: 1.9  Consensus size: 23

        242 ATATAGAATT

                                   
        252 AATAATTAATATATATAATTATA
          1 AATAATTAATATATATAATTATA

                         *        
        275 AATAGATTAA-ATCTATAATTA
          1 AATA-ATTAATATATATAATTA

        296 GAATATTAAA


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  23   14  0.74
  24    5  0.26

ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41


Consensus pattern (23 bp):   
AATAATTAATATATATAATTATA
Done.