Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015563.1 Corchorus olitorius cultivar O-4 contig15596, 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: 12900
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.31


Found at i:374 original size:2 final size:2

Alignment explanation


    Indices: 362--412  Score: 77
    Period size: 2  Copynumber: 26.0  Consensus size: 2

        352 AAATTACTAG

                     *                                 *                  
        362 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TC TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                          
        404 TA TA T- TA TA
          1 TA TA TA TA TA

        413 CATTTACAAT


Statistics
Matches: 44,  Mismatches: 4, Indels: 2
        0.88            0.08        0.04

Matches are distributed among these distances:
   1    1  0.02
   2   43  0.98

ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49


Consensus pattern (2 bp):   
TA

Found at i:467 original size:13 final size:13

Alignment explanation


    Indices: 449--473  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

        439 AAAAAGTTTC

                         
        449 AAATAATATTTAT
          1 AAATAATATTTAT

                        
        462 AAATAATATTTA
          1 AAATAATATTTA

        474 GAATATTGAA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44


Consensus pattern (13 bp):   
AAATAATATTTAT

Found at i:5583 original size:27 final size:27

Alignment explanation


    Indices: 5546--5597  Score: 86
    Period size: 27  Copynumber: 1.9  Consensus size: 27

       5536 AGATACAGAT

                  *          *         
       5546 TTTTTCTCCCTTGATACTCAAACCATA
          1 TTTTTCCCCCTTGATACGCAAACCATA

                                     
       5573 TTTTTCCCCCTTGATACGCAAACCA
          1 TTTTTCCCCCTTGATACGCAAACCA

       5598 AAGATGACAC


Statistics
Matches: 23,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  27   23  1.00

ACGTcount: A:0.25, C:0.33, G:0.06, T:0.37


Consensus pattern (27 bp):   
TTTTTCCCCCTTGATACGCAAACCATA

Found at i:10310 original size:63 final size:63

Alignment explanation


    Indices: 10187--10312  Score: 171
    Period size: 63  Copynumber: 2.0  Consensus size: 63

      10177 AACGAAGAGT

                                           *               *               
      10187 ACAAAAAGAAATCCCCTAAACCACGTGGCTTTGTAACCGGTTCAGAATGAAGCCACCTTCGAC
          1 ACAAAAAGAAATCCCCTAAACCACGTGGCTTAGTAACCGGTTCAGAAAGAAGCCACCTTCGAC

                        *          *          *       *      *    **       
      10250 ACAAAAAGAAATTCCCTAAACCATGTGGCTTAGTTACCGGTTTAGAAAGCAGCCTTCTTCGAC
          1 ACAAAAAGAAATCCCCTAAACCACGTGGCTTAGTAACCGGTTCAGAAAGAAGCCACCTTCGAC

      10313 CGAATAAAAG


Statistics
Matches: 54,  Mismatches: 9, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  63   54  1.00

ACGTcount: A:0.34, C:0.26, G:0.17, T:0.22


Consensus pattern (63 bp):   
ACAAAAAGAAATCCCCTAAACCACGTGGCTTAGTAACCGGTTCAGAAAGAAGCCACCTTCGAC

Found at i:10559 original size:47 final size:47

Alignment explanation


    Indices: 10505--10598  Score: 188
    Period size: 47  Copynumber: 2.0  Consensus size: 47

      10495 AATGCCCACG

                                                           
      10505 GAAAGTTATTATGAGGGACTGAAACTGACCAAGCCTTCCAAACGGCT
          1 GAAAGTTATTATGAGGGACTGAAACTGACCAAGCCTTCCAAACGGCT

                                                           
      10552 GAAAGTTATTATGAGGGACTGAAACTGACCAAGCCTTCCAAACGGCT
          1 GAAAGTTATTATGAGGGACTGAAACTGACCAAGCCTTCCAAACGGCT

      10599 CTCATACGGA


Statistics
Matches: 47,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  47   47  1.00

ACGTcount: A:0.34, C:0.21, G:0.23, T:0.21


Consensus pattern (47 bp):   
GAAAGTTATTATGAGGGACTGAAACTGACCAAGCCTTCCAAACGGCT

Found at i:10924 original size:28 final size:28

Alignment explanation


    Indices: 10871--10924  Score: 72
    Period size: 28  Copynumber: 1.9  Consensus size: 28

      10861 TGCTATGGCG

                            ***         
      10871 AAATCAATCGATCAATTTTAACAAAAAA
          1 AAATCAATCGATCAATAAGAACAAAAAA

                                 *    
      10899 AAATCAATCGATCAATAAGAATAAAA
          1 AAATCAATCGATCAATAAGAACAAAA

      10925 CGGGACAATG


Statistics
Matches: 22,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  28   22  1.00

ACGTcount: A:0.59, C:0.13, G:0.06, T:0.22


Consensus pattern (28 bp):   
AAATCAATCGATCAATAAGAACAAAAAA

Found at i:11313 original size:24 final size:24

Alignment explanation


    Indices: 11281--11374  Score: 161
    Period size: 24  Copynumber: 3.9  Consensus size: 24

      11271 TTGGAGGAAA

                                    
      11281 GTGAGATTCGGCCACATAGTGGTC
          1 GTGAGATTCGGCCACATAGTGGTC

                             *      
      11305 GTGAGATTCGGCCACATGGTGGTC
          1 GTGAGATTCGGCCACATAGTGGTC

                             *      
      11329 GTGAGATTCGGCCACATGGTGGTC
          1 GTGAGATTCGGCCACATAGTGGTC

             *                    
      11353 GAGAGATTCGGCCACATAGTGG
          1 GTGAGATTCGGCCACATAGTGG

      11375 CCGTTAGAAA


Statistics
Matches: 67,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  24   67  1.00

ACGTcount: A:0.20, C:0.20, G:0.36, T:0.23


Consensus pattern (24 bp):   
GTGAGATTCGGCCACATAGTGGTC

Done.