Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024172.1 Corchorus olitorius cultivar O-4 contig24205, 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: 23382
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30


Found at i:1338 original size:78 final size:78

Alignment explanation


    Indices: 1191--1338  Score: 228
    Period size: 78  Copynumber: 1.9  Consensus size: 78

       1181 AATGGTAAAC

                                                                          * *
       1191 TAAAATAGTTATAAGGATATTAGATTTAATAAAATGAAAATAGAGTATTTAGTTGAGTAAAATAG
          1 TAAAATAGTTATAAGGATATTAGATTTAATAAAATGAAAATAGAGTATTTAGTTGAGTAAAACAA

                         
       1256 TAAAATTGTGAAA
         66 TAAAATTGTGAAA

                                           *                *                
       1269 TAAAATAGTTAT-AGAGATATTAGATTTAATTAAAT-AAATATAGAGTTTTTAGTTGAGTAAAAC
          1 TAAAATAGTTATAAG-GATATTAGATTTAATAAAATGAAA-ATAGAGTATTTAGTTGAGTAAAAC

                   
       1332 AATAAAA
         64 AATAAAA

       1339 GTTTAAACAA


Statistics
Matches: 64,  Mismatches: 4, Indels: 4
        0.89            0.06        0.06

Matches are distributed among these distances:
  77    5  0.08
  78   59  0.92

ACGTcount: A:0.50, C:0.01, G:0.15, T:0.34


Consensus pattern (78 bp):   
TAAAATAGTTATAAGGATATTAGATTTAATAAAATGAAAATAGAGTATTTAGTTGAGTAAAACAA
TAAAATTGTGAAA

Found at i:8632 original size:49 final size:47

Alignment explanation


    Indices: 8555--8695  Score: 169
    Period size: 49  Copynumber: 2.9  Consensus size: 47

       8545 CAAGCAATCC

                *         *                                 
       8555 TTTACTTTTCACTGTACTTTTTCTCAATTTTTACTACAAAATTGAACT
          1 TTTAATTTTCACTGCACTTTTTCTCAATTTTTA-TACAAAATTGAACT

                     *                          *          *  
       8603 TTT-ATTTTTACTTGCATCTTTTTCTCAATTTTTAAGACAAAATTGATCT
          1 TTTAATTTTCAC-TGCA-CTTTTTCTCAATTTTT-ATACAAAATTGAACT

                                  *                      
       8652 TTTAATTTTCACTGCACTTTTTATCAATTTTT-TGACAAAATTGA
          1 TTTAATTTTCACTGCACTTTTTCTCAATTTTTAT-ACAAAATTGA

       8696 TTGGCACGCT


Statistics
Matches: 80,  Mismatches: 8, Indels: 11
        0.81            0.08        0.11

Matches are distributed among these distances:
  47   16  0.20
  48   21  0.26
  49   35  0.44
  50    8  0.10

ACGTcount: A:0.28, C:0.16, G:0.06, T:0.51


Consensus pattern (47 bp):   
TTTAATTTTCACTGCACTTTTTCTCAATTTTTATACAAAATTGAACT

Found at i:18702 original size:39 final size:39

Alignment explanation


    Indices: 18648--18734  Score: 165
    Period size: 39  Copynumber: 2.2  Consensus size: 39

      18638 CTTTGGTGCA

                                  *                
      18648 GGTGCAGCAGCCTTTTGATTGATCTCAATATTGGGATGT
          1 GGTGCAGCAGCCTTTTGATTGACCTCAATATTGGGATGT

                                                   
      18687 GGTGCAGCAGCCTTTTGATTGACCTCAATATTGGGATGT
          1 GGTGCAGCAGCCTTTTGATTGACCTCAATATTGGGATGT

                     
      18726 GGTGCAGCA
          1 GGTGCAGCA

      18735 CTAGTGGTGT


Statistics
Matches: 47,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  39   47  1.00

ACGTcount: A:0.21, C:0.17, G:0.30, T:0.32


Consensus pattern (39 bp):   
GGTGCAGCAGCCTTTTGATTGACCTCAATATTGGGATGT
Done.