Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012592.1 Corchorus capsularis cultivar CVL-1 contig12613, 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: 15181
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33


Found at i:2344 original size:31 final size:31

Alignment explanation


    Indices: 2306--2387  Score: 110
    Period size: 37  Copynumber: 2.5  Consensus size: 31

       2296 ATTTGCTGCA

                                           
       2306 TGATTGTGATTCTGGAAAAATGGTAATATGG
          1 TGATTGTGATTCTGGAAAAATGGTAATATGG

                                                 
       2337 TGATTGTGATTCTGGAAATGGAAAAATGGTAATATGG
          1 TGATTGTGATTC------TGGAAAAATGGTAATATGG

                          
       2374 TGATTGTGATTCTG
          1 TGATTGTGATTCTG

       2388 TGTATGGAAG


Statistics
Matches: 45,  Mismatches: 0, Indels: 12
        0.79            0.00        0.21

Matches are distributed among these distances:
  31   14  0.31
  37   31  0.69

ACGTcount: A:0.30, C:0.04, G:0.29, T:0.37


Consensus pattern (31 bp):   
TGATTGTGATTCTGGAAAAATGGTAATATGG

Found at i:7334 original size:13 final size:13

Alignment explanation


    Indices: 7313--7346  Score: 59
    Period size: 13  Copynumber: 2.6  Consensus size: 13

       7303 GATAATGTTT

                         
       7313 TTTGACCCTCCAA
          1 TTTGACCCTCCAA

                *        
       7326 TTTGTCCCTCCAA
          1 TTTGACCCTCCAA

                    
       7339 TTTGACCC
          1 TTTGACCC

       7347 AATTAAGGAA


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

Matches are distributed among these distances:
  13   19  1.00

ACGTcount: A:0.18, C:0.38, G:0.09, T:0.35


Consensus pattern (13 bp):   
TTTGACCCTCCAA

Found at i:7397 original size:22 final size:22

Alignment explanation


    Indices: 7362--7403  Score: 57
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       7352 AGGAAATAAA

                  *        *      
       7362 TTAAATTCAAGTTTAGCCCCCC
          1 TTAAATCCAAGTTTAACCCCCC

                     *          
       7384 TTAAATCCAGGTTTAACCCC
          1 TTAAATCCAAGTTTAACCCC

       7404 TAGTTATAAA


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  22   17  1.00

ACGTcount: A:0.29, C:0.31, G:0.10, T:0.31


Consensus pattern (22 bp):   
TTAAATCCAAGTTTAACCCCCC

Found at i:8627 original size:138 final size:139

Alignment explanation


    Indices: 8356--8640  Score: 509
    Period size: 138  Copynumber: 2.1  Consensus size: 139

       8346 CTTGTCTAGA

                                                             *          *    
       8356 CCAAGAAAAGAAAATAAACAAAACACAATTGGTATGAAATCAGAGATAACTCAGAGAAAAGCAAA
          1 CCAAGAAAAGAAAATAAACAAAACACAATTGGTATGAAATCAGAGATAAATCAGAGAAAAACAAA

                                                                             
       8421 AGCACTGACCCCTCTTACACCAACGTAGCGGTCATAAAGCACAATTGCATGTGCCAATACTTCCT
         66 AGCACTGACCCCTCTTACACCAACGTAGCGGTCATAAAGCACAATTGCATGTGCCAATACTTCCT

                     
       8486 CATCTTCTC
        131 CATCTTCTC

                                  *                                          
       8495 CCAAGAAAAGAAAATAAA-AAAGCACAATTGGTATGAAATCAGAGATAAATCAGAGAAAAACAAA
          1 CCAAGAAAAGAAAATAAACAAAACACAATTGGTATGAAATCAGAGATAAATCAGAGAAAAACAAA

            *                      *                              *          
       8559 GGCACTGACCCCTCTTACACCAATGTAGCGGTCATAAAGCACAATTGCATGTGCTAATACTTCCT
         66 AGCACTGACCCCTCTTACACCAACGTAGCGGTCATAAAGCACAATTGCATGTGCCAATACTTCCT

                     
       8624 CATCTTCTC
        131 CATCTTCTC

                    
       8633 CCAAGAAA
          1 CCAAGAAA

       8641 TTCAATCTCT


Statistics
Matches: 140,  Mismatches: 6, Indels: 1
        0.95            0.04        0.01

Matches are distributed among these distances:
 138  122  0.87
 139   18  0.13

ACGTcount: A:0.42, C:0.23, G:0.15, T:0.20


Consensus pattern (139 bp):   
CCAAGAAAAGAAAATAAACAAAACACAATTGGTATGAAATCAGAGATAAATCAGAGAAAAACAAA
AGCACTGACCCCTCTTACACCAACGTAGCGGTCATAAAGCACAATTGCATGTGCCAATACTTCCT
CATCTTCTC

Found at i:15137 original size:2 final size:2

Alignment explanation


    Indices: 15130--15155  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

      15120 ATAGTTGTAA

                                                  
      15130 CT CT CT CT CT CT CT CT CT CT CT CT CT
          1 CT CT CT CT CT CT CT CT CT CT CT CT CT

      15156 ATATATATAT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50


Consensus pattern (2 bp):   
CT

Found at i:15160 original size:2 final size:2

Alignment explanation


    Indices: 15155--15181  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

      15145 TCTCTCTCTC

                                                    
      15155 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


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

Done.