Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021324.1 Corchorus olitorius cultivar O-4 contig21357, 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: 11935
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36


Found at i:719 original size:21 final size:20

Alignment explanation


    Indices: 677--720  Score: 52
    Period size: 21  Copynumber: 2.1  Consensus size: 20

        667 TCTTGTAATC

                             *  
        677 TAAAATTACTAAAAAAGTTA
          1 TAAAATTACTAAAAAAGCTA

                     *     *     
        697 TAAAAGTTATTAAAATAGCTA
          1 TAAAA-TTACTAAAAAAGCTA

               
        718 TAA
          1 TAA

        721 TACTTTCCAC


Statistics
Matches: 20,  Mismatches: 3, Indels: 1
        0.83            0.12        0.04

Matches are distributed among these distances:
  20    5  0.25
  21   15  0.75

ACGTcount: A:0.57, C:0.05, G:0.07, T:0.32


Consensus pattern (20 bp):   
TAAAATTACTAAAAAAGCTA

Found at i:1520 original size:56 final size:56

Alignment explanation


    Indices: 1434--1541  Score: 180
    Period size: 56  Copynumber: 1.9  Consensus size: 56

       1424 TCAAATATCA

                                                       *            
       1434 AGTGACATGTTGTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGGCTTCG
          1 AGTGACATGTTGTTTATTAGATGCATAAAAAAAGACGTTTTAGAACCAAGGCTTCG

                       *            *                      *    
       1490 AGTGACATGTTTTTTATTAGATGCCTAAAAAAAGACGTTTTAGAACCGAGGC
          1 AGTGACATGTTGTTTATTAGATGCATAAAAAAAGACGTTTTAGAACCAAGGC

       1542 ATGATGCTAT


Statistics
Matches: 48,  Mismatches: 4, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  56   48  1.00

ACGTcount: A:0.34, C:0.13, G:0.22, T:0.31


Consensus pattern (56 bp):   
AGTGACATGTTGTTTATTAGATGCATAAAAAAAGACGTTTTAGAACCAAGGCTTCG

Found at i:4981 original size:90 final size:89

Alignment explanation


    Indices: 4873--5048  Score: 307
    Period size: 90  Copynumber: 2.0  Consensus size: 89

       4863 ACATGAATAT

                                                              **             
       4873 GATAAATAATCCTTAATTTAATTGATAAATAAAATTACATATTAAACCTTTCAAGTTATTGATAA
          1 GATAAATAATCCTTAATTTAATTGATAAATAAAATTACATATTAAACCTTAAAAGTTATTGATAA

                                     
       4938 TATTTAAAAATTAAAAAGGACACAA
         66 TATTT-AAAATTAAAAAGGACACAA

                *     *                                                      
       4963 GATATATAATTCTTAATTTAATTGATAAATAAAATTACATATTAAACCTTAAAAGTTATTGATAA
          1 GATAAATAATCCTTAATTTAATTGATAAATAAAATTACATATTAAACCTTAAAAGTTATTGATAA

                                 
       5028 TATTTAAAATTAAAAAGGACA
         66 TATTTAAAATTAAAAAGGACA

       5049 TTTTAGATAT


Statistics
Matches: 82,  Mismatches: 4, Indels: 1
        0.94            0.05        0.01

Matches are distributed among these distances:
  89   16  0.20
  90   66  0.80

ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36


Consensus pattern (89 bp):   
GATAAATAATCCTTAATTTAATTGATAAATAAAATTACATATTAAACCTTAAAAGTTATTGATAA
TATTTAAAATTAAAAAGGACACAA

Found at i:5107 original size:6 final size:6

Alignment explanation


    Indices: 5089--5232  Score: 243
    Period size: 6  Copynumber: 23.8  Consensus size: 6

       5079 GTTTAGACTT

                                            * *                     
       5089 ATATAG TATATAG ATATAG ATATAG ATAGAT ATATAG ATATAG ATATAG
          1 ATATAG -ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG

                                                         * *       
       5138 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATAGAT ATATAG
          1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG

                                                                  
       5186 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATA
          1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATA

       5233 TTTGCAGAGG


Statistics
Matches: 129,  Mismatches: 8, Indels: 1
        0.93            0.06        0.01

Matches are distributed among these distances:
   6  123  0.95
   7    6  0.05

ACGTcount: A:0.50, C:0.00, G:0.16, T:0.34


Consensus pattern (6 bp):   
ATATAG

Found at i:10622 original size:3 final size:3

Alignment explanation


    Indices: 10614--10645  Score: 55
    Period size: 3  Copynumber: 10.7  Consensus size: 3

      10604 TCTCTGATGC

                              *                       
      10614 AAG AAG AAG AAG AAA AAG AAG AAG AAG AAG AA
          1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA

      10646 AGAATTTACT


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   3   27  1.00

ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00


Consensus pattern (3 bp):   
AAG

Done.