Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018382.1 Corchorus olitorius cultivar O-4 contig18415, 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: 6376
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34


Found at i:908 original size:24 final size:24

Alignment explanation


    Indices: 876--927  Score: 86
    Period size: 24  Copynumber: 2.2  Consensus size: 24

        866 TTCGTTTACT

                                    
        876 CACATAAAGATTGATACATCAGCG
          1 CACATAAAGATTGATACATCAGCG

                               *  * 
        900 CACATAAAGATTGATACATTAGTG
          1 CACATAAAGATTGATACATCAGCG

                
        924 CACA
          1 CACA

        928 AAATGCTCAT


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  24   26  1.00

ACGTcount: A:0.42, C:0.19, G:0.15, T:0.23


Consensus pattern (24 bp):   
CACATAAAGATTGATACATCAGCG

Found at i:1080 original size:2 final size:2

Alignment explanation


    Indices: 1073--1101  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

       1063 TTATTTAATT

                                                       
       1073 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       1102 TTGGTATGTC


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:1282 original size:15 final size:15

Alignment explanation


    Indices: 1244--1282  Score: 53
    Period size: 15  Copynumber: 2.6  Consensus size: 15

       1234 GGCCATCCCA

                           
       1244 TTTAGTTTATTGTAC
          1 TTTAGTTTATTGTAC

                 *          
       1259 TTGT-TTTTATTGTAC
          1 TT-TAGTTTATTGTAC

                     
       1274 TTTAGTTTA
          1 TTTAGTTTA

       1283 ATTAAATCGT


Statistics
Matches: 20,  Mismatches: 2, Indels: 4
        0.77            0.08        0.15

Matches are distributed among these distances:
  14    1  0.05
  15   18  0.90
  16    1  0.05

ACGTcount: A:0.18, C:0.05, G:0.13, T:0.64


Consensus pattern (15 bp):   
TTTAGTTTATTGTAC

Found at i:5289 original size:6 final size:6

Alignment explanation


    Indices: 5265--5305  Score: 66
    Period size: 6  Copynumber: 7.0  Consensus size: 6

       5255 GTATAAACAA

                             *                              
       5265 GAACC- GAACCG GAATCG GAACCG GAACCG GAACCG GAACCG
          1 GAACCG GAACCG GAACCG GAACCG GAACCG GAACCG GAACCG

       5306 TGCATATTTT


Statistics
Matches: 33,  Mismatches: 2, Indels: 1
        0.92            0.06        0.03

Matches are distributed among these distances:
   5    5  0.15
   6   28  0.85

ACGTcount: A:0.34, C:0.32, G:0.32, T:0.02


Consensus pattern (6 bp):   
GAACCG

Found at i:6350 original size:2 final size:2

Alignment explanation


    Indices: 6343--6376  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       6333 CGTCGTTTTG

                                                              
       6343 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.