Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007749.1 Corchorus capsularis cultivar CVL-1 contig07770, 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: 5545
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34


Found at i:888 original size:18 final size:17

Alignment explanation


    Indices: 847--889  Score: 50
    Period size: 18  Copynumber: 2.4  Consensus size: 17

        837 ATTTGTTTGC

                *            
        847 TTGTCTTTAGTTTTGTT
          1 TTGTTTTTAGTTTTGTT

              *                
        864 TAAGTTTTTAGTTTTTGTT
          1 T-TGTTTTTAG-TTTTGTT

                   
        883 TTGTTTT
          1 TTGTTTT

        890 CTAGCTTGCT


Statistics
Matches: 21,  Mismatches: 3, Indels: 3
        0.78            0.11        0.11

Matches are distributed among these distances:
  17    1  0.05
  18   12  0.57
  19    8  0.38

ACGTcount: A:0.09, C:0.02, G:0.16, T:0.72


Consensus pattern (17 bp):   
TTGTTTTTAGTTTTGTT

Found at i:2584 original size:20 final size:20

Alignment explanation


    Indices: 2559--2598  Score: 71
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       2549 GAGGAATGGA

                     *          
       2559 TGTAAAAAATTAGATCTAGG
          1 TGTAAAAAAATAGATCTAGG

                                
       2579 TGTAAAAAAATAGATCTAGG
          1 TGTAAAAAAATAGATCTAGG

       2599 GGCTGAGCCG


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.47, C:0.05, G:0.20, T:0.28


Consensus pattern (20 bp):   
TGTAAAAAAATAGATCTAGG

Found at i:2849 original size:32 final size:32

Alignment explanation


    Indices: 2820--2917  Score: 126
    Period size: 32  Copynumber: 3.1  Consensus size: 32

       2810 GGGCGGCCGC

                   *             *          
       2820 GCCACGGTAGGCCGCACCCTGTGGTCGGCCTT
          1 GCCACGGCAGGCCGCACCCTGGGGTCGGCCTT

                *             *             
       2852 GCCAAGGCAGGCCGCACCATGGGGTCGGCCTT
          1 GCCACGGCAGGCCGCACCCTGGGGTCGGCCTT

                                * *          
       2884 GCCACGGCAGGCCGC-CCCTAGAGTGCGGCCTT
          1 GCCACGGCAGGCCGCACCCTGGGGT-CGGCCTT

              
       2916 GC
          1 GC

       2918 AATGGCTGAG


Statistics
Matches: 57,  Mismatches: 8, Indels: 2
        0.85            0.12        0.03

Matches are distributed among these distances:
  31    6  0.11
  32   51  0.89

ACGTcount: A:0.12, C:0.38, G:0.36, T:0.14


Consensus pattern (32 bp):   
GCCACGGCAGGCCGCACCCTGGGGTCGGCCTT

Found at i:2984 original size:13 final size:13

Alignment explanation


    Indices: 2962--3004  Score: 50
    Period size: 14  Copynumber: 3.2  Consensus size: 13

       2952 TTTTTTTTGT

                          
       2962 TTTTTCTTAAATTA
          1 TTTTT-TTAAATTA

                      *   
       2976 TTTTTTTAAGGTTA
          1 TTTTTTTAA-ATTA

                  *      
       2990 TTTTTTAAAATTA
          1 TTTTTTTAAATTA

              
       3003 TT
          1 TT

       3005 AGTTTTAATA


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

Matches are distributed among these distances:
  13    9  0.36
  14   16  0.64

ACGTcount: A:0.28, C:0.02, G:0.05, T:0.65


Consensus pattern (13 bp):   
TTTTTTTAAATTA
Done.