Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011153.1 Corchorus capsularis cultivar CVL-1 contig11174, 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: 8467
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.36


Found at i:4628 original size:33 final size:34

Alignment explanation


    Indices: 4558--4645  Score: 101
    Period size: 33  Copynumber: 2.6  Consensus size: 34

       4548 AATTTGGTCT

                            *     *           
       4558 AGCCGCCCCAGTGGGGTGGC-CTGCCCATGGTGA
          1 AGCCGCCCCAGTGGGGAGGCTCCGCCCATGGTGA

                                       *       
       4591 AGCCGCCCCAGTGGGGAGGCTCCG-CCGTGGCTG-
          1 AGCCGCCCCAGTGGGGAGGCTCCGCCCATGG-TGA

                 *  *             
       4624 AGCCGTCCTAGTGGGGAGGCTC
          1 AGCCGCCCCAGTGGGGAGGCTC

       4646 AGTGTAAAAA


Statistics
Matches: 48,  Mismatches: 5, Indels: 4
        0.84            0.09        0.07

Matches are distributed among these distances:
  33   44  0.92
  34    4  0.08

ACGTcount: A:0.11, C:0.33, G:0.41, T:0.15


Consensus pattern (34 bp):   
AGCCGCCCCAGTGGGGAGGCTCCGCCCATGGTGA

Found at i:5544 original size:2 final size:2

Alignment explanation


    Indices: 5537--5561  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       5527 TTTTTCTTAT

                                                 
       5537 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 T

       5562 GTATGTATGT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:7496 original size:113 final size:110

Alignment explanation


    Indices: 7288--7511  Score: 394
    Period size: 113  Copynumber: 2.0  Consensus size: 110

       7278 TAAATTAGGT

                                                                             
       7288 TAAAGTCAGATGTGTTTACCTAAAATGAAAAAGTCGTTCATCCCTCCATTATTATGCTATTCAAT
          1 TAAAGTCAGATGTGTTTACCTAAAATGAAAAAGTCGTTCATCCCTCCATTATTATGCTATTCAAT

                                                  *      
       7353 TTTCAATGCTAAGATAAAAGTATCATAAATTTATAAGCTGAATAA
         66 TTTCAATGCTAAGATAAAAGTATCATAAATTTATAAGCCGAATAA

                                            *               *                
       7398 TAAAGTCAGATGTGTTTACCTAAAATGAAAAATTCGTTCATTCCTCCTTCATTATTATGCTATTC
          1 TAAAGTCAGATGTGTTTACCTAAAATGAAAAAGTCGTTCA-T-C-CCTCCATTATTATGCTATTC

                                                            
       7463 AATTTTCAATGCTAAGATAAAAGTATCATAAATTTATAAGCCGAATAA
         63 AATTTTCAATGCTAAGATAAAAGTATCATAAATTTATAAGCCGAATAA

             
       7511 T
          1 T

       7512 TAATTAGAGG


Statistics
Matches: 108,  Mismatches: 3, Indels: 3
        0.95            0.03        0.03

Matches are distributed among these distances:
 110   39  0.36
 111    1  0.01
 112    1  0.01
 113   67  0.62

ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36


Consensus pattern (110 bp):   
TAAAGTCAGATGTGTTTACCTAAAATGAAAAAGTCGTTCATCCCTCCATTATTATGCTATTCAAT
TTTCAATGCTAAGATAAAAGTATCATAAATTTATAAGCCGAATAA

Done.