Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017962.1 Corchorus olitorius cultivar O-4 contig17995, 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: 19528
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33


Found at i:2354 original size:13 final size:14

Alignment explanation


    Indices: 2330--2361  Score: 57
    Period size: 13  Copynumber: 2.4  Consensus size: 14

       2320 AGCCATCAAC

                          
       2330 TATTTGAAATTATA
          1 TATTTGAAATTATA

                          
       2344 TATTT-AAATTATA
          1 TATTTGAAATTATA

                 
       2357 TATTT
          1 TATTT

       2362 TATGAGTATT


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  13   13  0.72
  14    5  0.28

ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56


Consensus pattern (14 bp):   
TATTTGAAATTATA

Found at i:7151 original size:29 final size:30

Alignment explanation


    Indices: 7115--7171  Score: 82
    Period size: 29  Copynumber: 1.9  Consensus size: 30

       7105 TTCAATTTTT

                                           
       7115 GATATTTTG-CTCCTTAAATTT-TTATTTCG
          1 GATATTTTGTCT-CTTAAATTTGTTATTTCG

                           *            
       7144 GATATTTTGTCTCTTGAATTTGTTATTT
          1 GATATTTTGTCTCTTAAATTTGTTATTT

       7172 AAAGCCATTT


Statistics
Matches: 25,  Mismatches: 1, Indels: 3
        0.86            0.03        0.10

Matches are distributed among these distances:
  29   17  0.68
  30    8  0.32

ACGTcount: A:0.19, C:0.11, G:0.12, T:0.58


Consensus pattern (30 bp):   
GATATTTTGTCTCTTAAATTTGTTATTTCG

Found at i:7276 original size:31 final size:32

Alignment explanation


    Indices: 7241--7310  Score: 97
    Period size: 32  Copynumber: 2.2  Consensus size: 32

       7231 ACGTGGTCTC

                                            
       7241 GCCACATGGCA-TTTTGGTCCAACGTGACATT
          1 GCCACATGGCATTTTTGGTCCAACGTGACATT

                 **              *     *    
       7272 GCCACGCGGCATTTTTGGTCCGACGTGGCATT
          1 GCCACATGGCATTTTTGGTCCAACGTGACATT

                   
       7304 GCCACAT
          1 GCCACAT

       7311 CAGCCATACC


Statistics
Matches: 32,  Mismatches: 6, Indels: 1
        0.82            0.15        0.03

Matches are distributed among these distances:
  31    9  0.28
  32   23  0.72

ACGTcount: A:0.19, C:0.29, G:0.26, T:0.27


Consensus pattern (32 bp):   
GCCACATGGCATTTTTGGTCCAACGTGACATT

Found at i:7475 original size:2 final size:2

Alignment explanation


    Indices: 7463--7495  Score: 57
    Period size: 2  Copynumber: 16.5  Consensus size: 2

       7453 AGGAAAGTAT

                  *                                          
       7463 TA TA AA 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 TA TA TA T

       7496 CCTTTAATTG


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   29  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:11180 original size:40 final size:40

Alignment explanation


    Indices: 11125--11206  Score: 164
    Period size: 40  Copynumber: 2.0  Consensus size: 40

      11115 TATGGTCTCA

                                                    
      11125 ATCAATAAAATTGTGATAATTCGGATTTTTTCCTATAATT
          1 ATCAATAAAATTGTGATAATTCGGATTTTTTCCTATAATT

                                                    
      11165 ATCAATAAAATTGTGATAATTCGGATTTTTTCCTATAATT
          1 ATCAATAAAATTGTGATAATTCGGATTTTTTCCTATAATT

              
      11205 AT
          1 AT

      11207 TAAAACCCAA


Statistics
Matches: 42,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  40   42  1.00

ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45


Consensus pattern (40 bp):   
ATCAATAAAATTGTGATAATTCGGATTTTTTCCTATAATT
Done.