Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005197.1 Corchorus capsularis cultivar CVL-1 contig05215, 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: 8457
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:5437 original size:16 final size:16

Alignment explanation


    Indices: 5406--5439  Score: 50
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       5396 TCTCTTCTTC

                     *      
       5406 TACTTTTCTTTAGTTT
          1 TACTTTTCTCTAGTTT

                       *    
       5422 TACTTTTCTCTGGTTT
          1 TACTTTTCTCTAGTTT

              
       5438 TA
          1 TA

       5440 GGTTAAGGGT


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.12, C:0.15, G:0.09, T:0.65


Consensus pattern (16 bp):   
TACTTTTCTCTAGTTT

Found at i:6214 original size:19 final size:20

Alignment explanation


    Indices: 6179--6221  Score: 61
    Period size: 19  Copynumber: 2.2  Consensus size: 20

       6169 ATTTGCTATA

                             *  
       6179 GCTTTATATTTAATTTACTT
          1 GCTTTATATTTAATTTAATT

                        *       
       6199 GCTTTAT-TTTAGTTTAATT
          1 GCTTTATATTTAATTTAATT

                
       6218 GCTT
          1 GCTT

       6222 CCTTTCTAAT


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

Matches are distributed among these distances:
  19   14  0.67
  20    7  0.33

ACGTcount: A:0.21, C:0.09, G:0.09, T:0.60


Consensus pattern (20 bp):   
GCTTTATATTTAATTTAATT

Found at i:6513 original size:30 final size:30

Alignment explanation


    Indices: 6469--6549  Score: 83
    Period size: 36  Copynumber: 2.5  Consensus size: 30

       6459 AGCTTGCATT

                                          
       6469 TTGCATAC-TGCATTACTTCAATTTTAACA
          1 TTGCATACATGCATTACTTCAATTTTAACA

                                                
       6498 TTGCATACATGCATTAGCATTACTTCAATTTTAACA
          1 TTGCAT--A--CA-T-GCATTACTTCAATTTTAACA

               *       *    
       6534 TTGTATACATGTATTA
          1 TTGCATACATGCATTA

       6550 GGATATCATA


Statistics
Matches: 43,  Mismatches: 2, Indels: 13
        0.74            0.03        0.22

Matches are distributed among these distances:
  29    6  0.14
  30    5  0.12
  31    2  0.05
  32    2  0.05
  33    1  0.02
  34    1  0.02
  35    1  0.02
  36   25  0.58

ACGTcount: A:0.32, C:0.17, G:0.09, T:0.42


Consensus pattern (30 bp):   
TTGCATACATGCATTACTTCAATTTTAACA

Found at i:6518 original size:36 final size:36

Alignment explanation


    Indices: 6478--6550  Score: 128
    Period size: 36  Copynumber: 2.0  Consensus size: 36

       6468 TTTGCATACT

                                                
       6478 GCATTACTTCAATTTTAACATTGCATACATGCATTA
          1 GCATTACTTCAATTTTAACATTGCATACATGCATTA

                                   *       *    
       6514 GCATTACTTCAATTTTAACATTGTATACATGTATTA
          1 GCATTACTTCAATTTTAACATTGCATACATGCATTA

             
       6550 G
          1 G

       6551 GATATCATAC


Statistics
Matches: 35,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  36   35  1.00

ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41


Consensus pattern (36 bp):   
GCATTACTTCAATTTTAACATTGCATACATGCATTA

Found at i:8029 original size:67 final size:67

Alignment explanation


    Indices: 7916--8062  Score: 285
    Period size: 67  Copynumber: 2.2  Consensus size: 67

       7906 TTTTTTGTGT

                *                                                            
       7916 GTTTTGTTGCTTTTCTGTTTAAAATTTTGGTGTTTATACTTGTGTTATCTTTTGTGCTATATTAT
          1 GTTTAGTTGCTTTTCTGTTTAAAATTTTGGTGTTTATACTTGTGTTATCTTTTGTGCTATATTAT

              
       7981 TA
         66 TA

                                                                             
       7983 GTTTAGTTGCTTTTCTGTTTAAAATTTTGGTGTTTATACTTGTGTTATCTTTTGTGCTATATTAT
          1 GTTTAGTTGCTTTTCTGTTTAAAATTTTGGTGTTTATACTTGTGTTATCTTTTGTGCTATATTAT

              
       8048 TA
         66 TA

                         
       8050 GTTTAGTTGCTTT
          1 GTTTAGTTGCTTT

       8063 GTTTGGTAGT


Statistics
Matches: 79,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  67   79  1.00

ACGTcount: A:0.16, C:0.07, G:0.17, T:0.59


Consensus pattern (67 bp):   
GTTTAGTTGCTTTTCTGTTTAAAATTTTGGTGTTTATACTTGTGTTATCTTTTGTGCTATATTAT
TA
Done.