Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023201.1 Corchorus olitorius cultivar O-4 contig23234, 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: 8880
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35


Found at i:139 original size:22 final size:21

Alignment explanation


    Indices: 106--158  Score: 79
    Period size: 22  Copynumber: 2.5  Consensus size: 21

         96 AAGGCAAGGT

                              *  
        106 CACTGCACACCAACCCTTGCA
          1 CACTGCACACCAACCCTTACA

              *                   
        127 CATTGTCACACCAACCCTTACA
          1 CACTG-CACACCAACCCTTACA

                      
        149 CACTGCACAC
          1 CACTGCACAC

        159 AACAAACAAA


Statistics
Matches: 28,  Mismatches: 3, Indels: 2
        0.85            0.09        0.06

Matches are distributed among these distances:
  21    9  0.32
  22   19  0.68

ACGTcount: A:0.30, C:0.45, G:0.08, T:0.17


Consensus pattern (21 bp):   
CACTGCACACCAACCCTTACA

Found at i:1668 original size:19 final size:20

Alignment explanation


    Indices: 1633--1672  Score: 73
    Period size: 19  Copynumber: 2.0  Consensus size: 20

       1623 GAGGCTTGGT

                                
       1633 TCTTTGTTTCGGTTTGGGCC
          1 TCTTTGTTTCGGTTTGGGCC

                                
       1653 TCTTTGTTTC-GTTTGGGCC
          1 TCTTTGTTTCGGTTTGGGCC

             
       1672 T
          1 T

       1673 AGTCTTTAAC


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  19   10  0.50
  20   10  0.50

ACGTcount: A:0.00, C:0.20, G:0.28, T:0.53


Consensus pattern (20 bp):   
TCTTTGTTTCGGTTTGGGCC

Found at i:2281 original size:12 final size:12

Alignment explanation


    Indices: 2264--2300  Score: 65
    Period size: 12  Copynumber: 3.0  Consensus size: 12

       2254 GTCATTCTCT

                        
       2264 AAAAAAAAAAGA
          1 AAAAAAAAAAGA

                        
       2276 AAAAAAAAAAGA
          1 AAAAAAAAAAGA

                         
       2288 AAAAAAGAAAAGA
          1 AAAAAA-AAAAGA

       2301 GGATATCAAC


Statistics
Matches: 24,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  12   18  0.75
  13    6  0.25

ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00


Consensus pattern (12 bp):   
AAAAAAAAAAGA

Found at i:2282 original size:13 final size:13

Alignment explanation


    Indices: 2264--2300  Score: 58
    Period size: 13  Copynumber: 2.9  Consensus size: 13

       2254 GTCATTCTCT

                         
       2264 AAAAAAAAAAG-A
          1 AAAAAAAAAAGAA

                         
       2276 AAAAAAAAAAGAA
          1 AAAAAAAAAAGAA

                 *      
       2289 AAAAAGAAAAGA
          1 AAAAAAAAAAGA

       2301 GGATATCAAC


Statistics
Matches: 23,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  12   11  0.48
  13   12  0.52

ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00


Consensus pattern (13 bp):   
AAAAAAAAAAGAA

Found at i:5775 original size:24 final size:25

Alignment explanation


    Indices: 5736--5783  Score: 71
    Period size: 24  Copynumber: 2.0  Consensus size: 25

       5726 CTGTATGAAC

                  *         *        
       5736 AATTTTCTTCTTTTCTTTCTTTATT
          1 AATTTTATTCTTTTCTCTCTTTATT

                                    
       5761 AATTTTATT-TTTTCTCTCTTTAT
          1 AATTTTATTCTTTTCTCTCTTTAT

       5784 GTTGCTATTA


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

Matches are distributed among these distances:
  24   13  0.62
  25    8  0.38

ACGTcount: A:0.15, C:0.15, G:0.00, T:0.71


Consensus pattern (25 bp):   
AATTTTATTCTTTTCTCTCTTTATT

Found at i:7033 original size:28 final size:28

Alignment explanation


    Indices: 6999--7053  Score: 83
    Period size: 28  Copynumber: 2.0  Consensus size: 28

       6989 TATAGAATGT

                                        
       6999 ATGCTTTTGCATATTAATCTTGCCACTC
          1 ATGCTTTTGCATATTAATCTTGCCACTC

                     *      *     *    
       7027 ATGCTTTTGGATATTAGTCTTGGCACT
          1 ATGCTTTTGCATATTAATCTTGCCACT

       7054 TTGATTATTT


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  28   24  1.00

ACGTcount: A:0.20, C:0.20, G:0.16, T:0.44


Consensus pattern (28 bp):   
ATGCTTTTGCATATTAATCTTGCCACTC
Done.