Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009700.1 Corchorus olitorius cultivar O-4 contig09732, 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: 5064
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33


Found at i:971 original size:15 final size:15

Alignment explanation


    Indices: 951--982  Score: 55
    Period size: 15  Copynumber: 2.1  Consensus size: 15

        941 TATGATTTTT

                        *  
        951 TATACATAAAAATAA
          1 TATACATAAAAACAA

                           
        966 TATACATAAAAACAA
          1 TATACATAAAAACAA

              
        981 TA
          1 TA

        983 ATGAAACTAT


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

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.66, C:0.09, G:0.00, T:0.25


Consensus pattern (15 bp):   
TATACATAAAAACAA

Found at i:1227 original size:99 final size:97

Alignment explanation


    Indices: 1100--1277  Score: 295
    Period size: 99  Copynumber: 1.8  Consensus size: 97

       1090 ATAGCCAAAA

                                                                         *  *
       1100 AAAAAAACATCATGAAATAAAGAATCATTTCCATGACTTCAAGAGAAAGATAAGAAATATAGATG
          1 AAAAAAACATCATGAAATAAAGAATCATTTCCATGACTTCAAGAGAAAGATAAGAAATATACATA

                                            
       1165 TGGAGATTAATCCTGTATTTATCATTTATAAC
         66 TGGAGATTAATCCTGTATTTATCATTTATAAC

                                                               *             
       1197 AAAAAAA-ATCATGAAAATAAAAAGAATCATTTCCATGACTTCAAGAGAAATATAAGAAATATAC
          1 AAAAAAACATCATG-AAAT--AAAGAATCATTTCCATGACTTCAAGAGAAAGATAAGAAATATAC

                             
       1261 ATATGGAGATTAATCCT
         63 ATATGGAGATTAATCCT

       1278 AAAAATATAG


Statistics
Matches: 75,  Mismatches: 3, Indels: 4
        0.91            0.04        0.05

Matches are distributed among these distances:
  96    6  0.08
  97   11  0.15
  99   58  0.77

ACGTcount: A:0.49, C:0.11, G:0.12, T:0.27


Consensus pattern (97 bp):   
AAAAAAACATCATGAAATAAAGAATCATTTCCATGACTTCAAGAGAAAGATAAGAAATATACATA
TGGAGATTAATCCTGTATTTATCATTTATAAC

Found at i:4886 original size:13 final size:13

Alignment explanation


    Indices: 4870--4895  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       4860 TTGAAATAAT

                         
       4870 ATTAATAATAGTA
          1 ATTAATAATAGTA

                         
       4883 ATTAATAATAGTA
          1 ATTAATAATAGTA

       4896 TTATTACTTT


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

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38


Consensus pattern (13 bp):   
ATTAATAATAGTA

Found at i:5037 original size:2 final size:2

Alignment explanation


    Indices: 5030--5064  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       5020 CCAAGAATAC

                                                                
       5030 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Done.