Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011965.1 Corchorus olitorius cultivar O-4 contig11998, 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: 30703
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32


Found at i:1393 original size:21 final size:21

Alignment explanation


    Indices: 1368--1407  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       1358 ACGCCTCTTG

                 *    *          
       1368 GGAGGTAGGAGGCATCTCCTA
          1 GGAGGAAGGAAGCATCTCCTA

                               
       1389 GGAGGAAGGAAGCATCTCC
          1 GGAGGAAGGAAGCATCTCC

       1408 CTCTTTGTTG


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.28, C:0.20, G:0.38, T:0.15


Consensus pattern (21 bp):   
GGAGGAAGGAAGCATCTCCTA

Found at i:8168 original size:18 final size:18

Alignment explanation


    Indices: 8131--8168  Score: 67
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       8121 TTTTTTTTTT

                           *  
       8131 AATTTTTCAAAATAATAA
          1 AATTTTTCAAAATAAAAA

                              
       8149 AATTTTTCAAAATAAAAA
          1 AATTTTTCAAAATAAAAA

              
       8167 AA
          1 AA

       8169 GTTGACCAAG


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  18   19  1.00

ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34


Consensus pattern (18 bp):   
AATTTTTCAAAATAAAAA

Found at i:10307 original size:41 final size:44

Alignment explanation


    Indices: 10262--10357  Score: 126
    Period size: 45  Copynumber: 2.2  Consensus size: 44

      10252 AAAGTGCATT

                            *          *                
      10262 ACCTAA-ATTCTACT-GT-ATCTCTAGGTAATCCATCAAAATAA
          1 ACCTAATATTCTACTCCTCATCTCTAGATAATCCATCAAAATAA

                                             *           
      10303 ACCTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAA
          1 ACCTAATATTCTACTCCT-CATCTCTAGATAATCCATCAAAATAA

             *        
      10348 AGCTAATATT
          1 ACCTAATATT

      10358 AATTGTTACT


Statistics
Matches: 47,  Mismatches: 4, Indels: 4
        0.85            0.07        0.07

Matches are distributed among these distances:
  41    6  0.13
  42    8  0.17
  43    1  0.02
  45   32  0.68

ACGTcount: A:0.39, C:0.23, G:0.05, T:0.33


Consensus pattern (44 bp):   
ACCTAATATTCTACTCCTCATCTCTAGATAATCCATCAAAATAA

Found at i:13766 original size:6 final size:6

Alignment explanation


    Indices: 13757--13784  Score: 56
    Period size: 6  Copynumber: 4.7  Consensus size: 6

      13747 GACTGCGATA

                                            
      13757 ATGAAG ATGAAG ATGAAG ATGAAG ATGA
          1 ATGAAG ATGAAG ATGAAG ATGAAG ATGA

      13785 TGTTGAGGAG


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   22  1.00

ACGTcount: A:0.50, C:0.00, G:0.32, T:0.18


Consensus pattern (6 bp):   
ATGAAG

Found at i:20472 original size:16 final size:16

Alignment explanation


    Indices: 20440--20481  Score: 50
    Period size: 16  Copynumber: 2.6  Consensus size: 16

      20430 CCAACTTGTT

                            
      20440 AAGAAAAAAATTAAGA
          1 AAGAAAAAAATTAAGA

                     *       
      20456 AAGAGAAAATATT-AGA
          1 AAGA-AAAAAATTAAGA

             *        
      20472 ATGAAAAAAA
          1 AAGAAAAAAA

      20482 ATAAAAAATA


Statistics
Matches: 22,  Mismatches: 3, Indels: 3
        0.79            0.11        0.11

Matches are distributed among these distances:
  15    5  0.23
  16   10  0.45
  17    7  0.32

ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14


Consensus pattern (16 bp):   
AAGAAAAAAATTAAGA
Done.