Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013448.1 Corchorus olitorius cultivar O-4 contig13481, 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: 39541
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31


Found at i:13055 original size:14 final size:14

Alignment explanation


    Indices: 13036--13064  Score: 58
    Period size: 14  Copynumber: 2.1  Consensus size: 14

      13026 AGGATTTTAC

                          
      13036 ATTATCACTTATCA
          1 ATTATCACTTATCA

                          
      13050 ATTATCACTTATCA
          1 ATTATCACTTATCA

             
      13064 A
          1 A

      13065 AGTTTTTTGG


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   15  1.00

ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41


Consensus pattern (14 bp):   
ATTATCACTTATCA

Found at i:29614 original size:11 final size:10

Alignment explanation


    Indices: 29598--29644  Score: 53
    Period size: 11  Copynumber: 4.7  Consensus size: 10

      29588 AAGTTTGAGT

                       
      29598 TTGAAGACTTA
          1 TTGAAGAC-TA

                    * 
      29609 TTGAAGACAA
          1 TTGAAGACTA

                       
      29619 TTTGAAGA-T-
          1 -TTGAAGACTA

                      
      29628 TTGAAGACTA
          1 TTGAAGACTA

                   
      29638 TTGAAGA
          1 TTGAAGA

      29645 ATTATCTCAA


Statistics
Matches: 31,  Mismatches: 2, Indels: 7
        0.77            0.05        0.17

Matches are distributed among these distances:
   8    7  0.23
   9    1  0.03
  10    8  0.26
  11   15  0.48

ACGTcount: A:0.40, C:0.06, G:0.21, T:0.32


Consensus pattern (10 bp):   
TTGAAGACTA

Found at i:29633 original size:19 final size:18

Alignment explanation


    Indices: 29609--29644  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      29599 TGAAGACTTA

                               
      29609 TTGAAGACAATTTGAAGAT
          1 TTGAAGACAA-TTGAAGAT

                    *        
      29628 TTGAAGACTATTGAAGA
          1 TTGAAGACAATTGAAGA

      29645 ATTATCTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.06, G:0.22, T:0.31


Consensus pattern (18 bp):   
TTGAAGACAATTGAAGAT

Found at i:35544 original size:21 final size:21

Alignment explanation


    Indices: 35520--35632  Score: 158
    Period size: 21  Copynumber: 5.4  Consensus size: 21

      35510 CTTAGGCATT

                         *       
      35520 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *            
      35541 TCCAATGATCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *          * 
      35562 TCCAATGAACTTGGAACCTGC
          1 TCCAATGAGCTTGGAACCTTC

                                  
      35583 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                                  
      35604 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                    
      35625 TCCAATGA
          1 TCCAATGA

      35633 ACTTCTAGCA


Statistics
Matches: 85,  Mismatches: 6, Indels: 2
        0.91            0.06        0.02

Matches are distributed among these distances:
  20    2  0.02
  21   83  0.98

ACGTcount: A:0.27, C:0.27, G:0.19, T:0.28


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACCTTC

Done.