Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021330.1 Corchorus olitorius cultivar O-4 contig21363, 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: 3448
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33


Found at i:1152 original size:27 final size:27

Alignment explanation


    Indices: 1114--1291  Score: 216
    Period size: 27  Copynumber: 6.3  Consensus size: 27

       1104 GAACCGACCC

                                       
       1114 GGGTCGAAGTGGGAGGATCCACTGCTG
          1 GGGTCGAAGTGGGAGGATCCACTGCTG

                                       
       1141 GGGTCGAAGTGGGAGGATCCACTGCTG
          1 GGGTCGAAGTGGGAGGATCCACTGCTG

                                           
       1168 GGGTCGAAGTGGGAGGATCCACTACTGCTGG
          1 GGGTCGAAGTGGGAGGAT-C-C-ACTGCT-G

                            **          
       1199 GGGTCGAAG-GGAGAGCCTCCACTGCTG
          1 GGGTCGAAGTGG-GAGGATCCACTGCTG

                                          
       1226 GGGTCGAAGTGGGAGGATCCACTACTGCTG
          1 GGGTCGAAGTGGGAGGAT-C-C-ACTGCTG

              *             **          
       1256 GGATCGAAG-GGAGAGCCTCCACTGCTG
          1 GGGTCGAAGTGG-GAGGATCCACTGCTG

                     
       1283 GGGTCGAAG
          1 GGGTCGAAG

       1292 GGAGAGCCGG


Statistics
Matches: 133,  Mismatches: 8, Indels: 20
        0.83            0.05        0.12

Matches are distributed among these distances:
  27   74  0.56
  28   11  0.08
  29    6  0.05
  30   28  0.21
  31   14  0.11

ACGTcount: A:0.20, C:0.21, G:0.42, T:0.17


Consensus pattern (27 bp):   
GGGTCGAAGTGGGAGGATCCACTGCTG

Found at i:1228 original size:58 final size:57

Alignment explanation


    Indices: 1114--1291  Score: 283
    Period size: 58  Copynumber: 3.2  Consensus size: 57

       1104 GAACCGACCC

                                                          **          
       1114 GGGTCGAAGTGGGAGGAT-C-C-ACTGCTGGGGTCGAAGTGG-GAGGATCCACTGCTG
          1 GGGTCGAAGTGGGAGGATCCACTACTGCTGGGGTCGAAG-GGAGAGCCTCCACTGCTG

                                                                      
       1168 GGGTCGAAGTGGGAGGATCCACTACTGCTGGGGGTCGAAGGGAGAGCCTCCACTGCTG
          1 GGGTCGAAGTGGGAGGATCCACTACTGCT-GGGGTCGAAGGGAGAGCCTCCACTGCTG

                                            *                        
       1226 GGGTCGAAGTGGGAGGATCCACTACTGCTGGGATCGAAGGGAGAGCCTCCACTGCTG
          1 GGGTCGAAGTGGGAGGATCCACTACTGCTGGGGTCGAAGGGAGAGCCTCCACTGCTG

                     
       1283 GGGTCGAAG
          1 GGGTCGAAG

       1292 GGAGAGCCGG


Statistics
Matches: 116,  Mismatches: 3, Indels: 7
        0.92            0.02        0.06

Matches are distributed among these distances:
  54   18  0.16
  55    1  0.01
  56    1  0.01
  57   44  0.38
  58   52  0.45

ACGTcount: A:0.20, C:0.21, G:0.42, T:0.17


Consensus pattern (57 bp):   
GGGTCGAAGTGGGAGGATCCACTACTGCTGGGGTCGAAGGGAGAGCCTCCACTGCTG

Found at i:1280 original size:85 final size:83

Alignment explanation


    Indices: 1114--1299  Score: 243
    Period size: 85  Copynumber: 2.2  Consensus size: 83

       1104 GAACCGACCC

                            **                                       *       
       1114 GGGTCGAAGTGG-GAGGATCCACTGCTGGGGTCGAAGTGGGAGGATCCACTGCTGGGGTCGAAGT
          1 GGGTCGAAG-GGAGAGCCTCCACTGCTGGGGTCGAAGTGGGAGGATCCACTGCTGGGATCGAAG-

                   *    *        
       1178 GGGAGGATCCACTACTGCTGG
         64 GGGAGGAGCCACCACTGCT-G

                                                                             
       1199 GGGTCGAAGGGAGAGCCTCCACTGCTGGGGTCGAAGTGGGAGGATCCACTACTGCTGGGATCGAA
          1 GGGTCGAAGGGAGAGCCTCCACTGCTGGGGTCGAAGTGGGAGGAT-C-C-ACTGCTGGGATCGAA

                       *         
       1264 -GGGA-GAGCCTCCACTGCTG
         63 GGGGAGGAGCCACCACTGCTG

                             
       1283 GGGTCGAAGGGAGAGCC
          1 GGGTCGAAGGGAGAGCC

       1300 GGACCAGCAA


Statistics
Matches: 91,  Mismatches: 6, Indels: 9
        0.86            0.06        0.08

Matches are distributed among these distances:
  84   20  0.22
  85   51  0.56
  86    5  0.05
  87    1  0.01
  88   14  0.15

ACGTcount: A:0.20, C:0.21, G:0.42, T:0.17


Consensus pattern (83 bp):   
GGGTCGAAGGGAGAGCCTCCACTGCTGGGGTCGAAGTGGGAGGATCCACTGCTGGGATCGAAGGG
GAGGAGCCACCACTGCTG

Found at i:2116 original size:21 final size:22

Alignment explanation


    Indices: 2086--2126  Score: 66
    Period size: 21  Copynumber: 1.9  Consensus size: 22

       2076 TCCACTATCC

                                  
       2086 CTTTCCAAGTAATGTTTTTCCA
          1 CTTTCCAAGTAATGTTTTTCCA

                      *         
       2108 CTTT-CAAGTCATGTTTTTC
          1 CTTTCCAAGTAATGTTTTTC

       2127 AAAGTCTATC


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  21   14  0.78
  22    4  0.22

ACGTcount: A:0.20, C:0.22, G:0.10, T:0.49


Consensus pattern (22 bp):   
CTTTCCAAGTAATGTTTTTCCA
Done.