Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022689.1 Corchorus olitorius cultivar O-4 contig22722, 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: 1904
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33


Found at i:340 original size:129 final size:134

Alignment explanation


    Indices: 177--432  Score: 344
    Period size: 129  Copynumber: 1.9  Consensus size: 134

        167 CTTCAAAAAC

                                                       * *                  *
        177 CTTAATCTGAAATATATAAAACACCAATTTTAATATTAAACATTAGTTTTAACCTTT-G-GTT-G
          1 CTTAATCTGAAATATATAAAACACCAATTTTAATATTAAACATGAATTTTAACCTTTAGAGTTAA

                 *  *                                          *             
        239 T-TA-GTAGTTTAATATACCAATCTAAAATATATTAAATATAGCAAATA-TCTTTAAAATACCAT
         66 TATATATAATTTAATATACCAATCTAAAATATATTAAATATAGCAAA-AGTATTTAAAATACCAT

                 
        301 ATAAA
        130 ATAAA

                           *     *   **                         *            
        306 CTTAATCTGAAATATCTAAAATACCTCTTTTAATATTAAACATGAATTTTAAGCTTTAGTAGTTA
          1 CTTAATCTGAAATATATAAAACACCAATTTTAATATTAAACATGAATTTTAACCTTTAG-AGTTA

                               *                                          
        371 ATATATATAATTTAATATATCAATCTAAAATATATTAAATATAGCAAAAGTATTTAAAATAC
         65 ATATATATAATTTAATATACCAATCTAAAATATATTAAATATAGCAAAAGTATTTAAAATAC

        433 GTGCAACGCA


Statistics
Matches: 108,  Mismatches: 12, Indels: 8
        0.84            0.09        0.06

Matches are distributed among these distances:
 129   50  0.46
 130    1  0.01
 132    3  0.03
 133    1  0.01
 134    3  0.03
 135   50  0.46

ACGTcount: A:0.45, C:0.11, G:0.06, T:0.39


Consensus pattern (134 bp):   
CTTAATCTGAAATATATAAAACACCAATTTTAATATTAAACATGAATTTTAACCTTTAGAGTTAA
TATATATAATTTAATATACCAATCTAAAATATATTAAATATAGCAAAAGTATTTAAAATACCATA
TAAA

Found at i:542 original size:1 final size:1

Alignment explanation


    Indices: 536--569  Score: 68
    Period size: 1  Copynumber: 34.0  Consensus size: 1

        526 TCTTTGTGGG

                                              
        536 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

        570 CCGCAAAATG


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   33  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T

Found at i:702 original size:15 final size:15

Alignment explanation


    Indices: 682--711  Score: 60
    Period size: 15  Copynumber: 2.0  Consensus size: 15

        672 TTTCTTTTGT

                           
        682 TGATTATTTATGTAC
          1 TGATTATTTATGTAC

                           
        697 TGATTATTTATGTAC
          1 TGATTATTTATGTAC

        712 ATCGGTGTCA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.27, C:0.07, G:0.13, T:0.53


Consensus pattern (15 bp):   
TGATTATTTATGTAC
Done.