Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016626.1 Corchorus olitorius cultivar O-4 contig16659, 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: 7816
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38


Found at i:1907 original size:36 final size:36

Alignment explanation


    Indices: 1860--1929  Score: 106
    Period size: 36  Copynumber: 1.9  Consensus size: 36

       1850 TTCAATAACC

                                 *               
       1860 TTACATCTTTTG-AGATTTTGGTTATCATATTTCTTA
          1 TTACATCTTTTGTA-ATTTTGATTATCATATTTCTTA

                  *                           
       1896 TTACATTTTTTGTAATTTTGATTATCATATTTCT
          1 TTACATCTTTTGTAATTTTGATTATCATATTTCT

       1930 CCAAAATCTC


Statistics
Matches: 31,  Mismatches: 2, Indels: 2
        0.89            0.06        0.06

Matches are distributed among these distances:
  36   30  0.97
  37    1  0.03

ACGTcount: A:0.23, C:0.10, G:0.09, T:0.59


Consensus pattern (36 bp):   
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA

Found at i:2961 original size:24 final size:24

Alignment explanation


    Indices: 2929--2974  Score: 76
    Period size: 24  Copynumber: 1.9  Consensus size: 24

       2919 ACGTTTGCAC

                                     
       2929 AAATACCTAAG-ATTTGAATTAAAA
          1 AAATACCTAAGAATTT-AATTAAAA

                                  
       2953 AAATACCTAAGAATTTAATTAA
          1 AAATACCTAAGAATTTAATTAA

       2975 TGTAAGTATT


Statistics
Matches: 21,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  24   17  0.81
  25    4  0.19

ACGTcount: A:0.54, C:0.09, G:0.07, T:0.30


Consensus pattern (24 bp):   
AAATACCTAAGAATTTAATTAAAA

Found at i:4845 original size:14 final size:14

Alignment explanation


    Indices: 4826--4852  Score: 54
    Period size: 14  Copynumber: 1.9  Consensus size: 14

       4816 TTACCCATTG

                          
       4826 CCGTATTTTAATCC
          1 CCGTATTTTAATCC

                         
       4840 CCGTATTTTAATC
          1 CCGTATTTTAATC

       4853 TCGGGTTTTT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   13  1.00

ACGTcount: A:0.22, C:0.26, G:0.07, T:0.44


Consensus pattern (14 bp):   
CCGTATTTTAATCC

Found at i:6686 original size:15 final size:16

Alignment explanation


    Indices: 6666--6703  Score: 53
    Period size: 16  Copynumber: 2.4  Consensus size: 16

       6656 CGTTCAAATG

                            
       6666 TCGGGTC-ATTTGGGT
          1 TCGGGTCAATTTGGGT

                             
       6681 TCGGGTCAATTCTGGGT
          1 TCGGGTCAATT-TGGGT

                   
       6698 T-GGGTC
          1 TCGGGTC

       6704 GTTTTCGGTT


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  15    7  0.33
  16    8  0.38
  17    6  0.29

ACGTcount: A:0.08, C:0.16, G:0.39, T:0.37


Consensus pattern (16 bp):   
TCGGGTCAATTTGGGT
Done.