Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01003257.1 Corchorus olitorius cultivar O-4 contig03263, 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: 2008
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30


Found at i:1035 original size:14 final size:14

Alignment explanation


    Indices: 995--1035  Score: 57
    Period size: 14  Copynumber: 2.9  Consensus size: 14

        985 TTTGTCGTTT

                          
        995 AGATAAAAGGC-AC
          1 AGATAAAAGGCAAC

               *           
       1008 ATGGTAAAAGGCAAC
          1 A-GATAAAAGGCAAC

                         
       1023 AGATAAAAGGCAA
          1 AGATAAAAGGCAA

       1036 GAGGCAACAG


Statistics
Matches: 24,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  13    1  0.04
  14   20  0.83
  15    3  0.12

ACGTcount: A:0.54, C:0.12, G:0.24, T:0.10


Consensus pattern (14 bp):   
AGATAAAAGGCAAC

Found at i:1053 original size:21 final size:20

Alignment explanation


    Indices: 1014--1063  Score: 55
    Period size: 21  Copynumber: 2.4  Consensus size: 20

       1004 GCACATGGTA

                       ** *     
       1014 AAAGGCAACAGATAAAAGGC
          1 AAAGGCAACAGGCACAAGGC

                                 
       1034 AAGAGGCAACAGGCACAAGGC
          1 AA-AGGCAACAGGCACAAGGC

                     
       1055 ACAAGGCAA
          1 A-AAGGCAA

       1064 AGAGTGGTAA


Statistics
Matches: 25,  Mismatches: 3, Indels: 3
        0.81            0.10        0.10

Matches are distributed among these distances:
  20    2  0.08
  21   22  0.88
  22    1  0.04

ACGTcount: A:0.50, C:0.20, G:0.28, T:0.02


Consensus pattern (20 bp):   
AAAGGCAACAGGCACAAGGC

Found at i:1141 original size:21 final size:21

Alignment explanation


    Indices: 1114--1194  Score: 117
    Period size: 21  Copynumber: 3.9  Consensus size: 21

       1104 AAAAATATTA

                 *               
       1114 TAACACCTAATGCCTAAAAAC
          1 TAACAACTAATGCCTAAAAAC

              *  *           *   
       1135 TATCACCTAATGCCTAACAAC
          1 TAACAACTAATGCCTAAAAAC

                             *   
       1156 TAACAACTAATGCCTAACAAC
          1 TAACAACTAATGCCTAAAAAC

                              
       1177 TAACAACTAATGCCTAAA
          1 TAACAACTAATGCCTAAA

       1195 GCCTATTGCC


Statistics
Matches: 55,  Mismatches: 5, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  21   55  1.00

ACGTcount: A:0.46, C:0.28, G:0.05, T:0.21


Consensus pattern (21 bp):   
TAACAACTAATGCCTAAAAAC

Found at i:1158 original size:7 final size:7

Alignment explanation


    Indices: 1148--1186  Score: 51
    Period size: 7  Copynumber: 5.6  Consensus size: 7

       1138 CACCTAATGC

                   
       1148 CTAACAA
          1 CTAACAA

                   
       1155 CTAACAA
          1 CTAACAA

                ***
       1162 CTAATGC
          1 CTAACAA

                   
       1169 CTAACAA
          1 CTAACAA

                   
       1176 CTAACAA
          1 CTAACAA

                
       1183 CTAA
          1 CTAA

       1187 TGCCTAAAGC


Statistics
Matches: 26,  Mismatches: 6, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
   7   26  1.00

ACGTcount: A:0.51, C:0.28, G:0.03, T:0.18


Consensus pattern (7 bp):   
CTAACAA

Done.