Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024692.1 Corchorus olitorius cultivar O-4 contig24725, 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: 2872
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28


Found at i:128 original size:31 final size:30

Alignment explanation


    Indices: 70--152  Score: 87
    Period size: 31  Copynumber: 2.7  Consensus size: 30

         60 CTTGAGGTCA

                          * *              
         70 AAACCCGA-ACCCGTACGACCCTAAACCCAG
          1 AAACCCGAGACCCGAATGA-CCTAAACCCAG

                                   *       
        100 CAAACCCGAGACCCGAATGACCTGAACCCAG
          1 -AAACCCGAGACCCGAATGACCTAAACCCAG

              * *                 
        131 ATGAGCCGAGACCCGAATGACC
          1 A-AACCCGAGACCCGAATGACC

        153 CAAGAAAATT


Statistics
Matches: 45,  Mismatches: 5, Indels: 4
        0.83            0.09        0.07

Matches are distributed among these distances:
  30    1  0.02
  31   36  0.80
  32    8  0.18

ACGTcount: A:0.35, C:0.39, G:0.19, T:0.07


Consensus pattern (30 bp):   
AAACCCGAGACCCGAATGACCTAAACCCAG

Found at i:150 original size:16 final size:15

Alignment explanation


    Indices: 105--152  Score: 55
    Period size: 15  Copynumber: 3.1  Consensus size: 15

         95 CCCAGCAAAC

                           
        105 CCGAGACCCGAATGA
          1 CCGAGACCCGAATGA

                             
        120 CCTGA-ACCC-AGATGA
          1 CC-GAGACCCGA-ATGA

                            
        135 GCCGAGACCCGAATGA
          1 -CCGAGACCCGAATGA

              
        151 CC
          1 CC

        153 CAAGAAAATT


Statistics
Matches: 28,  Mismatches: 0, Indels: 10
        0.74            0.00        0.26

Matches are distributed among these distances:
  14    1  0.04
  15   14  0.50
  16   12  0.43
  17    1  0.04

ACGTcount: A:0.31, C:0.35, G:0.25, T:0.08


Consensus pattern (15 bp):   
CCGAGACCCGAATGA

Found at i:1723 original size:13 final size:13

Alignment explanation


    Indices: 1705--1734  Score: 51
    Period size: 13  Copynumber: 2.3  Consensus size: 13

       1695 AACCGTTAAT

                         
       1705 ATCAAAATCATAA
          1 ATCAAAATCATAA

                  *      
       1718 ATCAAAGTCATAA
          1 ATCAAAATCATAA

                
       1731 ATCA
          1 ATCA

       1735 GAGTAAAACC


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  13   16  1.00

ACGTcount: A:0.57, C:0.17, G:0.03, T:0.23


Consensus pattern (13 bp):   
ATCAAAATCATAA

Found at i:2825 original size:2 final size:2

Alignment explanation


    Indices: 2818--2865  Score: 64
    Period size: 2  Copynumber: 24.5  Consensus size: 2

       2808 CTTCATTTAT

                                                             *             
       2818 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TCA -A AA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA

                      
       2859 TA TA TA T
          1 TA TA TA T

       2866 TTTACGG


Statistics
Matches: 42,  Mismatches: 1, Indels: 6
        0.86            0.02        0.12

Matches are distributed among these distances:
   1    2  0.05
   2   39  0.93
   3    1  0.02

ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48


Consensus pattern (2 bp):   
TA

Done.