Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004966.1 Corchorus capsularis cultivar CVL-1 contig04984, 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: 10671
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31


Found at i:2432 original size:12 final size:12

Alignment explanation


    Indices: 2415--2444  Score: 51
    Period size: 12  Copynumber: 2.4  Consensus size: 12

       2405 AACAAAGAAG

                        
       2415 AAAGATAATCCA
          1 AAAGATAATCCA

                        
       2427 AAAGATAATCCA
          1 AAAGATAATCCA

                  
       2439 AGAAGA
          1 A-AAGA

       2445 AAGTAACACT


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  12   13  0.76
  13    4  0.24

ACGTcount: A:0.60, C:0.13, G:0.13, T:0.13


Consensus pattern (12 bp):   
AAAGATAATCCA

Found at i:3681 original size:15 final size:14

Alignment explanation


    Indices: 3655--3705  Score: 57
    Period size: 15  Copynumber: 3.4  Consensus size: 14

       3645 GATAATAAAT

                          
       3655 AATGGAAATAGATA
          1 AATGGAAATAGATA

                           *
       3669 AATGGATAATAGAATT
          1 AATGGA-AATAG-ATA

              *            
       3685 AAGGGAAATAGATTA
          1 AATGGAAATAGA-TA

                  
       3700 AATGGA
          1 AATGGA

       3706 GGAATACTTC


Statistics
Matches: 30,  Mismatches: 4, Indels: 5
        0.77            0.10        0.13

Matches are distributed among these distances:
  14    7  0.23
  15   16  0.53
  16    7  0.23

ACGTcount: A:0.53, C:0.00, G:0.24, T:0.24


Consensus pattern (14 bp):   
AATGGAAATAGATA

Found at i:3694 original size:30 final size:29

Alignment explanation


    Indices: 3640--3705  Score: 89
    Period size: 30  Copynumber: 2.2  Consensus size: 29

       3630 TTGTCTTAAG

                *            *           
       3640 AAATAGATAATAAATAATGGAAATAGA-T
          1 AAATGGATAATAAATAAGGGAAATAGATT

                                           
       3668 AAATGGATAATAGAATTAAGGGAAATAGATT
          1 AAATGGATAATA-AA-TAAGGGAAATAGATT

                   
       3699 AAATGGA
          1 AAATGGA

       3706 GGAATACTTC


Statistics
Matches: 33,  Mismatches: 2, Indels: 3
        0.87            0.05        0.08

Matches are distributed among these distances:
  28   11  0.33
  29    2  0.06
  30   12  0.36
  31    8  0.24

ACGTcount: A:0.56, C:0.00, G:0.20, T:0.24


Consensus pattern (29 bp):   
AAATGGATAATAAATAAGGGAAATAGATT

Found at i:4191 original size:19 final size:19

Alignment explanation


    Indices: 4169--4210  Score: 59
    Period size: 19  Copynumber: 2.2  Consensus size: 19

       4159 TTGCTTTGGG

                                
       4169 CTTT-CTTGTTTGGACTTTC
          1 CTTTACTTG-TTGGACTTTC

                              *
       4188 CTTTACTTGTTGGACTTTG
          1 CTTTACTTGTTGGACTTTC

                
       4207 CTTT
          1 CTTT

       4211 GGGTCATAAT


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  19   17  0.81
  20    4  0.19

ACGTcount: A:0.07, C:0.19, G:0.17, T:0.57


Consensus pattern (19 bp):   
CTTTACTTGTTGGACTTTC

Found at i:6457 original size:11 final size:10

Alignment explanation


    Indices: 6423--6460  Score: 53
    Period size: 9  Copynumber: 3.9  Consensus size: 10

       6413 AAGAGAAGTG

                      
       6423 AAAGAAA-AA
          1 AAAGAAAGAA

                      
       6432 AAA-AAAGAA
          1 AAAGAAAGAA

                      
       6441 AAAGAAAGAA
          1 AAAGAAAGAA

                      
       6451 AATAGAAAGA
          1 AA-AGAAAGA

       6461 GGAAAGGTGA


Statistics
Matches: 26,  Mismatches: 0, Indels: 4
        0.87            0.00        0.13

Matches are distributed among these distances:
   8    3  0.12
   9    8  0.31
  10    8  0.31
  11    7  0.27

ACGTcount: A:0.82, C:0.00, G:0.16, T:0.03


Consensus pattern (10 bp):   
AAAGAAAGAA

Found at i:9208 original size:25 final size:25

Alignment explanation


    Indices: 9171--9219  Score: 80
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       9161 GATTGGTTTG

                    *       *        
       9171 TAGAGACCGAGCGAGAGTGCTCAAA
          1 TAGAGACCAAGCGAGAATGCTCAAA

                                    
       9196 TAGAGACCAAGCGAGAATGCTCAA
          1 TAGAGACCAAGCGAGAATGCTCAA

       9220 GATTGTTTGG


Statistics
Matches: 22,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  25   22  1.00

ACGTcount: A:0.39, C:0.20, G:0.29, T:0.12


Consensus pattern (25 bp):   
TAGAGACCAAGCGAGAATGCTCAAA
Done.