Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020085.1 Corchorus olitorius cultivar O-4 contig20118, 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: 8139
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33


Found at i:2182 original size:21 final size:21

Alignment explanation


    Indices: 2158--2249  Score: 150
    Period size: 21  Copynumber: 4.4  Consensus size: 21

       2148 CTTAGGCAAT

                         *       
       2158 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                 
       2179 TCCAATGAGCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                       *         
       2200 TCCAATGAGCTAGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                  
       2221 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                    
       2242 TCCAATGA
          1 TCCAATGA

       2250 TCTCCTAGCA


Statistics
Matches: 67,  Mismatches: 3, Indels: 2
        0.93            0.04        0.03

Matches are distributed among these distances:
  20    3  0.04
  21   64  0.96

ACGTcount: A:0.27, C:0.27, G:0.18, T:0.27


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACCTTC

Found at i:4720 original size:17 final size:17

Alignment explanation


    Indices: 4698--4731  Score: 50
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       4688 TATATCATTC

                   *         
       4698 AAAAATAGATCCTTAAA
          1 AAAAATACATCCTTAAA

                      *      
       4715 AAAAATACATTCTTAAA
          1 AAAAATACATCCTTAAA

       4732 TATCCTTCAA


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.59, C:0.12, G:0.03, T:0.26


Consensus pattern (17 bp):   
AAAAATACATCCTTAAA

Found at i:6570 original size:50 final size:48

Alignment explanation


    Indices: 6468--6614  Score: 176
    Period size: 50  Copynumber: 3.0  Consensus size: 48

       6458 GAGCGTGCCA

                        *          *                  *      
       6468 ATCAATTTTGTCAAAAAATTGA-TAAAAAGTGCAA-TGAAAATTAAAAG
          1 ATCAATTTTGTCTAAAAATTGAGAAAAAAGTGCAAGT-AAAAATAAAAG

                                                              
       6515 ATCAATTTTGTCTTAAAAATTGAGAAAAAAGGTGCAAGTAAAAATAAAAG
          1 ATCAATTTTGTC-TAAAAATTGAGAAAAAA-GTGCAAGTAAAAATAAAAG

            *           *                                     
       6565 TTCAATTTTGTAGTAAAAATTGAGAAAAAA-TGC-AGTAAAAAGTAAAAG
          1 ATCAATTTTGT-CTAAAAATTGAGAAAAAAGTGCAAGTAAAAA-TAAAAG

              
       6613 AT
          1 AT

       6615 TGCTTGGAGT


Statistics
Matches: 88,  Mismatches: 6, Indels: 11
        0.84            0.06        0.10

Matches are distributed among these distances:
  47   20  0.23
  48   19  0.22
  49    5  0.06
  50   43  0.49
  51    1  0.01

ACGTcount: A:0.52, C:0.05, G:0.15, T:0.27


Consensus pattern (48 bp):   
ATCAATTTTGTCTAAAAATTGAGAAAAAAGTGCAAGTAAAAATAAAAG
Done.