Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023521.1 Corchorus olitorius cultivar O-4 contig23554, 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: 14143
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:1773 original size:3 final size:3

Alignment explanation


    Indices: 1765--1826  Score: 124
    Period size: 3  Copynumber: 20.7  Consensus size: 3

       1755 TGTTCAAATA

                                                                           
       1765 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
          1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT

                              
       1813 ATT ATT ATT ATT AT
          1 ATT ATT ATT ATT AT

       1827 ATATACTAGT


Statistics
Matches: 59,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   59  1.00

ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66


Consensus pattern (3 bp):   
ATT

Found at i:2626 original size:22 final size:21

Alignment explanation


    Indices: 2591--2656  Score: 64
    Period size: 22  Copynumber: 3.0  Consensus size: 21

       2581 ATATATACTA

                                   
       2591 TTAAATAA-ATAATAAATATATT
          1 TTAAATAATA-AAT-AATATATT

                                  
       2613 TTAAATAATAAATAAT-TAGTT
          1 TTAAATAATAAATAATATA-TT

            **                    
       2634 CAAAATAAATAAATAATATATT
          1 TTAAAT-AATAAATAATATATT

             
       2656 T
          1 T

       2657 AATTACTAAA


Statistics
Matches: 37,  Mismatches: 3, Indels: 8
        0.77            0.06        0.17

Matches are distributed among these distances:
  20    2  0.05
  21    9  0.24
  22   23  0.62
  23    3  0.08

ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39


Consensus pattern (21 bp):   
TTAAATAATAAATAATATATT

Found at i:4602 original size:19 final size:19

Alignment explanation


    Indices: 4567--4607  Score: 66
    Period size: 19  Copynumber: 2.2  Consensus size: 19

       4557 ATATTCCACA

                               
       4567 TACTACTTAATTATATTAT
          1 TACTACTTAATTATATTAT

                                
       4586 TACTA-TTAATTATTATTAT
          1 TACTACTTAATTA-TATTAT

               
       4605 TAC
          1 TAC

       4608 ATGTCATAAT


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

Matches are distributed among these distances:
  18    7  0.33
  19   14  0.67

ACGTcount: A:0.37, C:0.10, G:0.00, T:0.54


Consensus pattern (19 bp):   
TACTACTTAATTATATTAT
Done.