Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010691.1 Corchorus olitorius cultivar O-4 contig10723, 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: 20785
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.32


Found at i:5346 original size:27 final size:27

Alignment explanation


    Indices: 5316--5368  Score: 88
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       5306 GAGTCACTCT

                *                      
       5316 CAGCGTCACTCTCTTCCTCACCACTAC
          1 CAGCCTCACTCTCTTCCTCACCACTAC

                            *         
       5343 CAGCCTCACTCTCTTCTTCACCACTA
          1 CAGCCTCACTCTCTTCCTCACCACTA

       5369 ACTCTACCGC


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  27   24  1.00

ACGTcount: A:0.19, C:0.47, G:0.06, T:0.28


Consensus pattern (27 bp):   
CAGCCTCACTCTCTTCCTCACCACTAC

Found at i:5765 original size:2 final size:2

Alignment explanation


    Indices: 5760--5790  Score: 53
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       5750 ATATATGCGC

                                        *                 
       5760 AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       5791 CACATATAAG


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

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45


Consensus pattern (2 bp):   
AT

Found at i:5791 original size:12 final size:12

Alignment explanation


    Indices: 5760--5798  Score: 60
    Period size: 12  Copynumber: 3.2  Consensus size: 12

       5750 ATATATGCGC

                   *    
       5760 ATATATATATAT
          1 ATATATACATAT

                        
       5772 ATATATACATAT
          1 ATATATACATAT

                     *  
       5784 ATATATACACAT
          1 ATATATACATAT

               
       5796 ATA
          1 ATA

       5799 AGGCACTAAC


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  12   25  1.00

ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41


Consensus pattern (12 bp):   
ATATATACATAT

Found at i:5795 original size:14 final size:14

Alignment explanation


    Indices: 5766--5798  Score: 57
    Period size: 14  Copynumber: 2.4  Consensus size: 14

       5756 GCGCATATAT

                       *  
       5766 ATATATATATATAC
          1 ATATATATATACAC

                          
       5780 ATATATATATACAC
          1 ATATATATATACAC

                 
       5794 ATATA
          1 ATATA

       5799 AGGCACTAAC


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  14   18  1.00

ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39


Consensus pattern (14 bp):   
ATATATATATACAC

Found at i:7727 original size:31 final size:31

Alignment explanation


    Indices: 7661--7729  Score: 102
    Period size: 31  Copynumber: 2.2  Consensus size: 31

       7651 CTATAATATA

                                     *   **
       7661 TAGCGGCGTTTTCTCACCAGACACCGCTAGT
          1 TAGCGGCGTTTTCTCACCAGACACCACTAAC

                                  *        
       7692 TAGCGGCGTTTTCTCACCAGACGCCACTAAC
          1 TAGCGGCGTTTTCTCACCAGACACCACTAAC

                   
       7723 TAGCGGC
          1 TAGCGGC

       7730 ATCTAGGAAA


Statistics
Matches: 34,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  31   34  1.00

ACGTcount: A:0.20, C:0.33, G:0.23, T:0.23


Consensus pattern (31 bp):   
TAGCGGCGTTTTCTCACCAGACACCACTAAC

Found at i:10267 original size:15 final size:16

Alignment explanation


    Indices: 10234--10273  Score: 55
    Period size: 15  Copynumber: 2.6  Consensus size: 16

      10224 TTACTTTGCT

                            
      10234 TTGTTTTCTAGTATAA
          1 TTGTTTTCTAGTATAA

                        *   
      10250 TTGTTTTCT-GTTTAA
          1 TTGTTTTCTAGTATAA

               *     
      10265 TTGCTTTCT
          1 TTGTTTTCT

      10274 TTCAACCTCT


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  15   13  0.59
  16    9  0.41

ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62


Consensus pattern (16 bp):   
TTGTTTTCTAGTATAA

Found at i:13591 original size:21 final size:21

Alignment explanation


    Indices: 13567--13615  Score: 71
    Period size: 21  Copynumber: 2.3  Consensus size: 21

      13557 CCCGGACTCC

                *          *     
      13567 TCCGTGCACCACAACCGGCCA
          1 TCCGCGCACCACAACAGGCCA

                                 
      13588 TCCGCGCACCACAACAGGCCA
          1 TCCGCGCACCACAACAGGCCA

              *    
      13609 TCTGCGC
          1 TCCGCGC

      13616 CGCCTGCCCG


Statistics
Matches: 25,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  21   25  1.00

ACGTcount: A:0.22, C:0.47, G:0.20, T:0.10


Consensus pattern (21 bp):   
TCCGCGCACCACAACAGGCCA

Found at i:17115 original size:15 final size:16

Alignment explanation


    Indices: 17082--17121  Score: 55
    Period size: 15  Copynumber: 2.6  Consensus size: 16

      17072 TTACTTTGCT

                            
      17082 TTGTTTTCTAGTATAA
          1 TTGTTTTCTAGTATAA

                        *   
      17098 TTGTTTTC-AGTTTAA
          1 TTGTTTTCTAGTATAA

               *     
      17113 TTGCTTTCT
          1 TTGTTTTCT

      17122 TTCAACCTCT


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  15   13  0.62
  16    8  0.38

ACGTcount: A:0.17, C:0.10, G:0.12, T:0.60


Consensus pattern (16 bp):   
TTGTTTTCTAGTATAA
Done.