Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005805.1 Corchorus capsularis cultivar CVL-1 contig05823, 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: 6092
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35


Found at i:1296 original size:38 final size:38

Alignment explanation


    Indices: 1246--1323  Score: 104
    Period size: 38  Copynumber: 2.1  Consensus size: 38

       1236 TAAAATTACC

                                             *    
       1246 AAAAATTCAAAGTAATAAATAAGAATGCAAGATTGTTG
          1 AAAAATTCAAAGTAATAAATAAGAATGCAAGATAGTTG

                           *   *        *          
       1284 AAAAATGT-AAAGTATTAAGTAAGAATGTAAGATAGTTG
          1 AAAAAT-TCAAAGTAATAAATAAGAATGCAAGATAGTTG

              
       1322 AA
          1 AA

       1324 TTTGTTGAAA


Statistics
Matches: 35,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
  38   34  0.97
  39    1  0.03

ACGTcount: A:0.53, C:0.03, G:0.18, T:0.27


Consensus pattern (38 bp):   
AAAAATTCAAAGTAATAAATAAGAATGCAAGATAGTTG

Found at i:4788 original size:2 final size:2

Alignment explanation


    Indices: 4781--4807  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       4771 AATTGTACAT

                                                    
       4781 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 T

       4808 CTACATTTTA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:4823 original size:12 final size:13

Alignment explanation


    Indices: 4803--4835  Score: 59
    Period size: 12  Copynumber: 2.6  Consensus size: 13

       4793 TATATATATA

                         
       4803 TATATCTACATTT
          1 TATATCTACATTT

                         
       4816 TATA-CTACATTT
          1 TATATCTACATTT

                    
       4828 TATATCTA
          1 TATATCTA

       4836 GTATTTACTT


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  12   12  0.63
  13    7  0.37

ACGTcount: A:0.33, C:0.15, G:0.00, T:0.52


Consensus pattern (13 bp):   
TATATCTACATTT
Done.