Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021847.1 Corchorus olitorius cultivar O-4 contig21880, 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: 6274
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.30


Found at i:3520 original size:10 final size:10

Alignment explanation


    Indices: 3505--3536  Score: 55
    Period size: 10  Copynumber: 3.2  Consensus size: 10

       3495 ACCGCTACCA

                      
       3505 CCACCGTCGG
          1 CCACCGTCGG

                   *  
       3515 CCACCGTTGG
          1 CCACCGTCGG

                      
       3525 CCACCGTCGG
          1 CCACCGTCGG

              
       3535 CC
          1 CC

       3537 GCCGGAATAG


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  10   20  1.00

ACGTcount: A:0.09, C:0.50, G:0.28, T:0.12


Consensus pattern (10 bp):   
CCACCGTCGG

Found at i:4384 original size:3 final size:3

Alignment explanation


    Indices: 4378--4463  Score: 154
    Period size: 3  Copynumber: 28.3  Consensus size: 3

       4368 TTTCTCTAAC

                           *                                            
       4378 ATA ATA ATA TATT ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
          1 ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA

                                                                 
       4424 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
          1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A

       4464 GAGGGAAAAG


Statistics
Matches: 80,  Mismatches: 2, Indels: 2
        0.95            0.02        0.02

Matches are distributed among these distances:
   3   78  0.98
   4    2  0.03

ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35


Consensus pattern (3 bp):   
ATA

Found at i:6186 original size:30 final size:30

Alignment explanation


    Indices: 6150--6268  Score: 141
    Period size: 30  Copynumber: 3.8  Consensus size: 30

       6140 TTAGTTGATC

                                          
       6150 CAGGGCGATCTTTCTTCAGTTTACTTGACT
          1 CAGGGCGATCTTTCTTCAGTTTACTTGACT

                                            *   
       6180 CAGGGCGATCTTTCTTCAGTTTATATCAGTTTTA-T
          1 CAGGGCGATCTTTCTTCAG-TT-TA-C---TTGACT

                           *               
       6215 CCAGGGCGATCTTTCCTCAGTTTACTTGACT
          1 -CAGGGCGATCTTTCTTCAGTTTACTTGACT

                   *               
       6246 CAGGGCGGTCTTTCTTCAGTTTA
          1 CAGGGCGATCTTTCTTCAGTTTA

       6269 TATCAA


Statistics
Matches: 76,  Mismatches: 5, Indels: 16
        0.78            0.05        0.16

Matches are distributed among these distances:
  30   43  0.57
  31    3  0.04
  32    2  0.03
  33    2  0.03
  34    2  0.03
  35    3  0.04
  36   21  0.28

ACGTcount: A:0.17, C:0.23, G:0.20, T:0.40


Consensus pattern (30 bp):   
CAGGGCGATCTTTCTTCAGTTTACTTGACT

Found at i:6224 original size:66 final size:66

Alignment explanation


    Indices: 6147--6273  Score: 236
    Period size: 66  Copynumber: 1.9  Consensus size: 66

       6137 ATTTTAGTTG

                             *                                               
       6147 ATCCAGGGCGATCTTTCTTCAGTTTACTTGACTCAGGGCGATCTTTCTTCAGTTTATATCAGTTT
          1 ATCCAGGGCGATCTTTCCTCAGTTTACTTGACTCAGGGCGATCTTTCTTCAGTTTATATCAGTTT

             
       6212 T
         66 T

                                                    *                    
       6213 ATCCAGGGCGATCTTTCCTCAGTTTACTTGACTCAGGGCGGTCTTTCTTCAGTTTATATCA
          1 ATCCAGGGCGATCTTTCCTCAGTTTACTTGACTCAGGGCGATCTTTCTTCAGTTTATATCA

       6274 A


Statistics
Matches: 59,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  66   59  1.00

ACGTcount: A:0.18, C:0.23, G:0.19, T:0.40


Consensus pattern (66 bp):   
ATCCAGGGCGATCTTTCCTCAGTTTACTTGACTCAGGGCGATCTTTCTTCAGTTTATATCAGTTT
T
Done.