Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001305.1 Corchorus capsularis cultivar CVL-1 contig01305, 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: 4073
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30


Found at i:370 original size:44 final size:44

Alignment explanation


    Indices: 292--377  Score: 104
    Period size: 44  Copynumber: 2.0  Consensus size: 44

        282 TGATTTGCCT

                   *             *    *                 
        292 TCACACCGCCTTGGTCAAATTGAATAGCCAACATGG-CTTTTTA
          1 TCACACCACCTTGGTCAAATTAAATACCCAACATGGTCTTTTTA

                                           *            
        335 TCACAGCCACCTTGGTCAAATTTAAAT-CCCGACATGGTCTTTT
          1 TCACA-CCACCTTGGTCAAA-TTAAATACCCAACATGGTCTTTT

        378 AAAATTCTCC


Statistics
Matches: 36,  Mismatches: 4, Indels: 4
        0.82            0.09        0.09

Matches are distributed among these distances:
  43    5  0.14
  44   21  0.58
  45   10  0.28

ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31


Consensus pattern (44 bp):   
TCACACCACCTTGGTCAAATTAAATACCCAACATGGTCTTTTTA

Found at i:601 original size:22 final size:22

Alignment explanation


    Indices: 575--616  Score: 84
    Period size: 22  Copynumber: 1.9  Consensus size: 22

        565 GACCACTATG

                                  
        575 TGGCCGAATCTCACGGCCACCA
          1 TGGCCGAATCTCACGGCCACCA

                                
        597 TGGCCGAATCTCACGGCCAC
          1 TGGCCGAATCTCACGGCCAC

        617 ATACTAACCC


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   20  1.00

ACGTcount: A:0.21, C:0.40, G:0.24, T:0.14


Consensus pattern (22 bp):   
TGGCCGAATCTCACGGCCACCA

Found at i:1151 original size:16 final size:16

Alignment explanation


    Indices: 1130--1160  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       1120 TTACAGCGTA

                   *        
       1130 ATGGCTCTAATTATAG
          1 ATGGCTCAAATTATAG

                           
       1146 ATGGCTCAAATTATA
          1 ATGGCTCAAATTATA

       1161 ATAAAGCCAA


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35


Consensus pattern (16 bp):   
ATGGCTCAAATTATAG

Found at i:4041 original size:22 final size:22

Alignment explanation


    Indices: 4015--4056  Score: 84
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       4005 GACCACTATG

                                  
       4015 TGGCCGAATCTCACGGCCACCA
          1 TGGCCGAATCTCACGGCCACCA

                                
       4037 TGGCCGAATCTCACGGCCAC
          1 TGGCCGAATCTCACGGCCAC

       4057 ATACTAACCC


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   20  1.00

ACGTcount: A:0.21, C:0.40, G:0.24, T:0.14


Consensus pattern (22 bp):   
TGGCCGAATCTCACGGCCACCA
Done.