Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011232.1 Corchorus capsularis cultivar CVL-1 contig11253, 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: 9316
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32


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

Alignment explanation


    Indices: 1262--1292  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       1252 CTGTTCTATG

                           
       1262 TTCTATATATTGGGT
          1 TTCTATATATTGGGT

                  *        
       1277 TTCTATGTATTGGGT
          1 TTCTATATATTGGGT

             
       1292 T
          1 T

       1293 CCAGTGATGA


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.16, C:0.06, G:0.23, T:0.55


Consensus pattern (15 bp):   
TTCTATATATTGGGT

Found at i:2536 original size:36 final size:36

Alignment explanation


    Indices: 2496--2566  Score: 142
    Period size: 36  Copynumber: 2.0  Consensus size: 36

       2486 AGAGAGGGAT

                                                
       2496 GTCGGGGTATAAGAAAAGGGAAGAGGAAAGAAAGAC
          1 GTCGGGGTATAAGAAAAGGGAAGAGGAAAGAAAGAC

                                               
       2532 GTCGGGGTATAAGAAAAGGGAAGAGGAAAGAAAGA
          1 GTCGGGGTATAAGAAAAGGGAAGAGGAAAGAAAGA

       2567 TGGAAGTAGA


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  36   35  1.00

ACGTcount: A:0.48, C:0.04, G:0.39, T:0.08


Consensus pattern (36 bp):   
GTCGGGGTATAAGAAAAGGGAAGAGGAAAGAAAGAC

Found at i:5438 original size:21 final size:21

Alignment explanation


    Indices: 5412--5453  Score: 75
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       5402 GCGCAAGTGA

                   *             
       5412 CCGGCCATGCGACTTGGAGAT
          1 CCGGCCACGCGACTTGGAGAT

                                 
       5433 CCGGCCACGCGACTTGGAGAT
          1 CCGGCCACGCGACTTGGAGAT

       5454 GCCCGCGCAA


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.19, C:0.31, G:0.33, T:0.17


Consensus pattern (21 bp):   
CCGGCCACGCGACTTGGAGAT

Found at i:5536 original size:33 final size:32

Alignment explanation


    Indices: 5433--5571  Score: 136
    Period size: 33  Copynumber: 4.2  Consensus size: 32

       5423 ACTTGGAGAT

                         *    *          *   
       5433 CCGGCCACGCGACTTGGAGATGCCCGCGCAACA
          1 CCGGCCACGCGACATGGACATGCCCG-GCCACA

                   *          *              
       5466 CCGGCCATGCGACATGGAGATGCCCGGCCATCA
          1 CCGGCCACGCGACATGGACATGCCCGGCCA-CA

                             *              
       5499 CCGGCCACGCGACATGGCCATGCCCGGCCACA
          1 CCGGCCACGCGACATGGACATGCCCGGCCACA

                  *  **        *               
       5531 CCCGGCAACATGAC-TCGGCCATGCCCGGCCACAA
          1 -CCGGCCACGCGACAT-GGACATGCCCGGCCAC-A

                   
       5565 CCGGCCA
          1 CCGGCCA

       5572 TATGATCCTT


Statistics
Matches: 92,  Mismatches: 10, Indels: 8
        0.84            0.09        0.07

Matches are distributed among these distances:
  32    6  0.07
  33   85  0.92
  34    1  0.01

ACGTcount: A:0.21, C:0.42, G:0.28, T:0.09


Consensus pattern (32 bp):   
CCGGCCACGCGACATGGACATGCCCGGCCACA

Found at i:6836 original size:19 final size:19

Alignment explanation


    Indices: 6812--6851  Score: 55
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       6802 GTTTTTCTTG

                            *   
       6812 TGCAATTGA-TCTAATTAGT
          1 TGCAATT-ACTCTAATCAGT

                               
       6831 TGCAATTACTCTAATCAGT
          1 TGCAATTACTCTAATCAGT

              
       6850 TG
          1 TG

       6852 TGAATTGGGA


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

Matches are distributed among these distances:
  18    1  0.05
  19   18  0.95

ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40


Consensus pattern (19 bp):   
TGCAATTACTCTAATCAGT
Done.