Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014657.1 Corchorus capsularis cultivar CVL-1 contig14678, 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: 5057
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32


Found at i:1020 original size:27 final size:27

Alignment explanation


    Indices: 990--1069  Score: 90
    Period size: 27  Copynumber: 2.9  Consensus size: 27

        980 ATTAGAGTCG

                                       
        990 CCCAAGGGTATTTTGGTCATTTTTGCA
          1 CCCAAGGGTATTTTGGTCATTTTTGCA

                                    *   
       1017 CCC-AGGGATATTTTGGTCATTTTCGCA
          1 CCCAAGGG-TATTTTGGTCATTTTTGCA

             *        *     *         
       1044 CTCAGGAGGGCATTTTAGTCATTTTT
          1 CCCA--AGGGTATTTTGGTCATTTTT

       1070 TTTAAGATCA


Statistics
Matches: 44,  Mismatches: 5, Indels: 6
        0.80            0.09        0.11

Matches are distributed among these distances:
  26    4  0.09
  27   23  0.52
  29   13  0.30
  30    4  0.09

ACGTcount: A:0.19, C:0.19, G:0.23, T:0.40


Consensus pattern (27 bp):   
CCCAAGGGTATTTTGGTCATTTTTGCA

Found at i:2933 original size:16 final size:16

Alignment explanation


    Indices: 2910--2958  Score: 73
    Period size: 16  Copynumber: 3.1  Consensus size: 16

       2900 AACAGAGGAC

                            
       2910 AACTAGGGTTTTTGAA
          1 AACTAGGGTTTTTGAA

             *        *     
       2926 ATCTAGGGTTCTTGAA
          1 AACTAGGGTTTTTGAA

                            
       2942 AACTAGGG-TTTTGAA
          1 AACTAGGGTTTTTGAA

              
       2957 AA
          1 AA

       2959 AAGCAGGGGA


Statistics
Matches: 29,  Mismatches: 4, Indels: 1
        0.85            0.12        0.03

Matches are distributed among these distances:
  15    8  0.28
  16   21  0.72

ACGTcount: A:0.33, C:0.08, G:0.24, T:0.35


Consensus pattern (16 bp):   
AACTAGGGTTTTTGAA

Found at i:3785 original size:49 final size:49

Alignment explanation


    Indices: 3729--3831  Score: 129
    Period size: 49  Copynumber: 2.1  Consensus size: 49

       3719 GAAGCTTTTT

                                              **               
       3729 GTAAAAATGCCATCTTTGGA-T-AGAAGATTGAATTTTTAGTAATTAGTAA
          1 GTAAAAATGCCAT-TTTGGAGTGA-AAGATTGAAACTTTAGTAATTAGTAA

                     *      *                       *        
       3778 GTAAAAATGTCATTTTTGAGTGAAAGATTGAAACTTTAGTGATTAGTAA
          1 GTAAAAATGCCATTTTGGAGTGAAAGATTGAAACTTTAGTAATTAGTAA

                 
       3827 GTAAA
          1 GTAAA

       3832 GATGTCACCT


Statistics
Matches: 47,  Mismatches: 5, Indels: 4
        0.84            0.09        0.07

Matches are distributed among these distances:
  48    5  0.11
  49   41  0.87
  50    1  0.02

ACGTcount: A:0.40, C:0.05, G:0.19, T:0.36


Consensus pattern (49 bp):   
GTAAAAATGCCATTTTGGAGTGAAAGATTGAAACTTTAGTAATTAGTAA

Found at i:3853 original size:49 final size:49

Alignment explanation


    Indices: 3752--3857  Score: 131
    Period size: 49  Copynumber: 2.2  Consensus size: 49

       3742 CTTTGGATAG

                     **                           **  *   ** 
       3752 AAGATTGAATTTTTAGTAATTAGTAAGTAAAAATGTCATTTTTGAGTGA
          1 AAGATTGAAACTTTAGTAATTAGTAAGTAAAAATGTCACCTTAGAGCAA

                             *             *                 
       3801 AAGATTGAAACTTTAGTGATTAGTAAGTAAAGATGTCACCTTAGAGCAA
          1 AAGATTGAAACTTTAGTAATTAGTAAGTAAAAATGTCACCTTAGAGCAA

                    
       3850 AAGATTGA
          1 AAGATTGA

       3858 TTTTTAGAGT


Statistics
Matches: 48,  Mismatches: 9, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  49   48  1.00

ACGTcount: A:0.41, C:0.06, G:0.20, T:0.34


Consensus pattern (49 bp):   
AAGATTGAAACTTTAGTAATTAGTAAGTAAAAATGTCACCTTAGAGCAA

Found at i:4736 original size:56 final size:53

Alignment explanation


    Indices: 4669--4783  Score: 167
    Period size: 54  Copynumber: 2.1  Consensus size: 53

       4659 GAAAGGGGGC

                                                                   
       4669 AATCAGTAATTAAGTAAAAAGAGATTAATCAAGAGTCAAAGTAACAGTAATCAGT
          1 AATCAGTAATTAAGT-AAAAGAGATTAATC-AGAGTCAAAGTAACAGTAATCAGT

                                               *  *   **          
       4724 AAATCAGTAATTAAGTAAAAGAGATTAATCAGAGTTAAGGTAGTAGTAATCAGT
          1 -AATCAGTAATTAAGTAAAAGAGATTAATCAGAGTCAAAGTAACAGTAATCAGT

                  
       4778 AATCAG
          1 AATCAG

       4784 GTAAAAGATA


Statistics
Matches: 55,  Mismatches: 4, Indels: 3
        0.89            0.06        0.05

Matches are distributed among these distances:
  53    6  0.11
  54   20  0.36
  55   14  0.25
  56   15  0.27

ACGTcount: A:0.49, C:0.08, G:0.18, T:0.25


Consensus pattern (53 bp):   
AATCAGTAATTAAGTAAAAGAGATTAATCAGAGTCAAAGTAACAGTAATCAGT
Done.