Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005893.1 Corchorus capsularis cultivar CVL-1 contig05911, 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: 14849
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31


Found at i:356 original size:27 final size:27

Alignment explanation


    Indices: 282--356  Score: 123
    Period size: 27  Copynumber: 2.7  Consensus size: 27

        272 AAGTGGACTC

                                        
        282 AAAATGACCAAAATGCCCCCTGAATGTA
          1 AAAATGACCAAAATG-CCCCTGAATGTA

             *      *                  
        310 AGAATGACAAAAATGCCCCTGAATGTA
          1 AAAATGACCAAAATGCCCCTGAATGTA

                                
        337 AAAATGACCAAAATGCCCCT
          1 AAAATGACCAAAATGCCCCT

        357 AGGTGACCCT


Statistics
Matches: 43,  Mismatches: 4, Indels: 1
        0.90            0.08        0.02

Matches are distributed among these distances:
  27   30  0.70
  28   13  0.30

ACGTcount: A:0.44, C:0.24, G:0.15, T:0.17


Consensus pattern (27 bp):   
AAAATGACCAAAATGCCCCTGAATGTA

Found at i:1227 original size:2 final size:2

Alignment explanation


    Indices: 1220--1246  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       1210 TTTCAAAACT

                                                    
       1220 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

       1247 TTTTCTGAGA


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:1662 original size:13 final size:14

Alignment explanation


    Indices: 1646--1674  Score: 51
    Period size: 13  Copynumber: 2.1  Consensus size: 14

       1636 ATCCTTATGG

                          
       1646 TTAGTTTTT-ATTT
          1 TTAGTTTTTAATTT

                          
       1659 TTAGTTTTTAATTT
          1 TTAGTTTTTAATTT

              
       1673 TT
          1 TT

       1675 TAAAAATTGA


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

Matches are distributed among these distances:
  13    9  0.60
  14    6  0.40

ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76


Consensus pattern (14 bp):   
TTAGTTTTTAATTT

Found at i:12159 original size:42 final size:39

Alignment explanation


    Indices: 12068--12175  Score: 162
    Period size: 39  Copynumber: 2.8  Consensus size: 39

      12058 AACAAGCTTC

                                          *        
      12068 ATCAGTTTCTTCTTCTGCAGTCTTAGGAATGTCATCTCG
          1 ATCAGTTTCTTCTTCTGCAGTCTTAGGAATCTCATCTCG

                                               * * 
      12107 ATCAGTTTCTTCTTCTGCAGTCTTAGGAATCTCATTTTG
          1 ATCAGTTTCTTCTTCTGCAGTCTTAGGAATCTCATCTCG

                *  *               *      
      12146 ATCACTTCCTTCTTCTGCAGTCTCAGGAAT
          1 ATCAGTTTCTTCTTCTGCAGTCTTAGGAAT

      12176 TTTGTCATCT


Statistics
Matches: 63,  Mismatches: 6, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  39   63  1.00

ACGTcount: A:0.19, C:0.24, G:0.16, T:0.42


Consensus pattern (39 bp):   
ATCAGTTTCTTCTTCTGCAGTCTTAGGAATCTCATCTCG

Found at i:13829 original size:2 final size:2

Alignment explanation


    Indices: 13822--13868  Score: 85
    Period size: 2  Copynumber: 23.0  Consensus size: 2

      13812 ATAGCCAATC

                                                                           
      13822 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT

                 
      13865 AT AT
          1 AT AT

      13869 TATTTTTTAA


Statistics
Matches: 44,  Mismatches: 0, Indels: 2
        0.96            0.00        0.04

Matches are distributed among these distances:
   2   42  0.95
   3    2  0.05

ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:14772 original size:10 final size:11

Alignment explanation


    Indices: 14757--14785  Score: 51
    Period size: 11  Copynumber: 2.7  Consensus size: 11

      14747 AATTACTTTG

                       
      14757 ATCAATTA-AA
          1 ATCAATTACAA

                       
      14767 ATCAATTACAA
          1 ATCAATTACAA

                    
      14778 ATCAATTA
          1 ATCAATTA

      14786 TTACAAATTA


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  10    8  0.44
  11   10  0.56

ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31


Consensus pattern (11 bp):   
ATCAATTACAA
Done.