Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020929.1 Corchorus olitorius cultivar O-4 contig20962, 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: 15134
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32


Found at i:3685 original size:17 final size:16

Alignment explanation


    Indices: 3632--3681  Score: 64
    Period size: 17  Copynumber: 3.0  Consensus size: 16

       3622 TCACCCCCCG

                  *          
       3632 GATCACTAGTGATCTAA
          1 GATCACCAGTGATC-AA

                             
       3649 GATCACCAGTGATGCAA
          1 GATCACCAGTGAT-CAA

                   *        
       3666 GATCACCGGTGATCAA
          1 GATCACCAGTGATCAA

       3682 AGATTACATG


Statistics
Matches: 30,  Mismatches: 2, Indels: 3
        0.86            0.06        0.09

Matches are distributed among these distances:
  16    3  0.10
  17   26  0.87
  18    1  0.03

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


Consensus pattern (16 bp):   
GATCACCAGTGATCAA

Found at i:3932 original size:20 final size:20

Alignment explanation


    Indices: 3907--3947  Score: 82
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       3897 ACCAAATACA

                                
       3907 ATATCAGTAAATAAAAGTAT
          1 ATATCAGTAAATAAAAGTAT

                                
       3927 ATATCAGTAAATAAAAGTAT
          1 ATATCAGTAAATAAAAGTAT

             
       3947 A
          1 A

       3948 CGTACAAATA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   21  1.00

ACGTcount: A:0.56, C:0.05, G:0.10, T:0.29


Consensus pattern (20 bp):   
ATATCAGTAAATAAAAGTAT

Found at i:4949 original size:30 final size:28

Alignment explanation


    Indices: 4843--4949  Score: 106
    Period size: 29  Copynumber: 3.6  Consensus size: 28

       4833 ACTTGTAGCG

                   *                     
       4843 TTTGGACGTTTTGCCCCATGAACTTCAAT
          1 TTTGGACATTTTGCCCC-TGAACTTCAAT

                  *     *                
       4872 TTTGGATATTTTACCCACTGAACTTCAAT
          1 TTTGGACATTTTGCCC-CTGAACTTCAAT

                         *        *       
       4901 TTTGGACATTTTCCCCCCTGAATTATCAAT
          1 TTTGGACATTTT-GCCCCTGAACT-TCAAT

               *    *          
       4931 TTAAGGACGTTTTGCCCCT
          1 TT-TGGACATTTTGCCCCT

       4950 TTCAAACGAT


Statistics
Matches: 65,  Mismatches: 9, Indels: 7
        0.80            0.11        0.09

Matches are distributed among these distances:
  29   41  0.63
  30   16  0.25
  31    8  0.12

ACGTcount: A:0.22, C:0.24, G:0.14, T:0.39


Consensus pattern (28 bp):   
TTTGGACATTTTGCCCCTGAACTTCAAT

Found at i:5173 original size:29 final size:30

Alignment explanation


    Indices: 5111--5173  Score: 92
    Period size: 30  Copynumber: 2.1  Consensus size: 30

       5101 AGAGGGGGCA

                           *              
       5111 AAAATGTCCAAAATTGAGAATTCAAGGGAC
          1 AAAATGTCCAAAATTCAGAATTCAAGGGAC

                               *    *     
       5141 AAAATGTCCAAAATTCA-AGTTCAGGGGAC
          1 AAAATGTCCAAAATTCAGAATTCAAGGGAC

                
       5170 AAAA
          1 AAAA

       5174 CATCTAAACG


Statistics
Matches: 30,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  29   14  0.47
  30   16  0.53

ACGTcount: A:0.48, C:0.14, G:0.19, T:0.19


Consensus pattern (30 bp):   
AAAATGTCCAAAATTCAGAATTCAAGGGAC

Found at i:10646 original size:47 final size:47

Alignment explanation


    Indices: 10592--10685  Score: 188
    Period size: 47  Copynumber: 2.0  Consensus size: 47

      10582 TATATATAAA

                                                           
      10592 AAATCACATATTGATTTGTAGTATAACATAAAAAATATATAATCTTC
          1 AAATCACATATTGATTTGTAGTATAACATAAAAAATATATAATCTTC

                                                           
      10639 AAATCACATATTGATTTGTAGTATAACATAAAAAATATATAATCTTC
          1 AAATCACATATTGATTTGTAGTATAACATAAAAAATATATAATCTTC

      10686 TCTTAACATT


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:0.47, C:0.11, G:0.06, T:0.36


Consensus pattern (47 bp):   
AAATCACATATTGATTTGTAGTATAACATAAAAAATATATAATCTTC
Done.