Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001500.1 Corchorus capsularis cultivar CVL-1 contig01500, 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: 5434
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:1166 original size:22 final size:22

Alignment explanation


    Indices: 1140--1181  Score: 84
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       1130 ACTAAAGACT

                                  
       1140 GTGGCCGTGAGATTCGGCCATG
          1 GTGGCCGTGAGATTCGGCCATG

                                
       1162 GTGGCCGTGAGATTCGGCCA
          1 GTGGCCGTGAGATTCGGCCA

       1182 CATAATGGTA


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


Consensus pattern (22 bp):   
GTGGCCGTGAGATTCGGCCATG

Found at i:1358 original size:22 final size:22

Alignment explanation


    Indices: 1332--1392  Score: 95
    Period size: 22  Copynumber: 2.8  Consensus size: 22

       1322 GGGTTAGTAT

                                  
       1332 GTGGCCGTGAGATTCGGCCATA
          1 GTGGCCGTGAGATTCGGCCATA

                     *           *
       1354 GTGGCCGTGGGATTCGGCCATG
          1 GTGGCCGTGAGATTCGGCCATA

                *            
       1376 GTGGTCGTGAGATTCGG
          1 GTGGCCGTGAGATTCGG

       1393 TGAGATTCGG


Statistics
Matches: 35,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  22   35  1.00

ACGTcount: A:0.13, C:0.20, G:0.43, T:0.25


Consensus pattern (22 bp):   
GTGGCCGTGAGATTCGGCCATA

Found at i:1680 original size:43 final size:44

Alignment explanation


    Indices: 1594--1680  Score: 106
    Period size: 44  Copynumber: 2.0  Consensus size: 44

       1584 TGGAGAATTT

                 *                             ** *     
       1594 TAAAAGGCCATGTCGGGCTTTCAATTTGACCAAGGTGGCTGTGA
          1 TAAAAAGCCATGTCGGGCTTTCAATTTGACCAAGGACGATGTGA

                          *                              
       1638 TAAAAAGCCATGT-TGGCTTTTCAATTTGACCAA-GACGATGTGA
          1 TAAAAAGCCATGTCGGGC-TTTCAATTTGACCAAGGACGATGTGA

       1681 AGGCAAATCA


Statistics
Matches: 37,  Mismatches: 5, Indels: 3
        0.82            0.11        0.07

Matches are distributed among these distances:
  43   10  0.27
  44   27  0.73

ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29


Consensus pattern (44 bp):   
TAAAAAGCCATGTCGGGCTTTCAATTTGACCAAGGACGATGTGA
Done.