Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022250.1 Corchorus olitorius cultivar O-4 contig22283, 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: 7166
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30


Found at i:1000 original size:16 final size:16

Alignment explanation


    Indices: 954--1007  Score: 58
    Period size: 15  Copynumber: 3.4  Consensus size: 16

        944 GAACCGTATA

                      *    * 
        954 ACCCGAAACCGAAAACG
          1 ACCCG-AACCCAAAATG

                             
        971 ACCC-AACCCAAAATTG
          1 ACCCGAACCCAAAA-TG

                            
        987 ACCCGAACCC-AAATG
          1 ACCCGAACCCAAAATG

                  
       1002 ACCCGA
          1 ACCCGA

       1008 CATTTGAACG


Statistics
Matches: 33,  Mismatches: 2, Indels: 6
        0.80            0.05        0.15

Matches are distributed among these distances:
  15   16  0.48
  16    8  0.24
  17    9  0.27

ACGTcount: A:0.43, C:0.39, G:0.13, T:0.06


Consensus pattern (16 bp):   
ACCCGAACCCAAAATG

Found at i:4052 original size:19 final size:18

Alignment explanation


    Indices: 4027--4089  Score: 65
    Period size: 19  Copynumber: 3.4  Consensus size: 18

       4017 CCGCGCACCA

                              
       4027 GGCCTGGGCGCTTGGGCC
          1 GGCCTGGGCGCTTGGGCC

                      * *  *   
       4045 GTGCCT-GGCCCGTGCGCC
          1 G-GCCTGGGCGCTTGGGCC

                               
       4063 AGGCCTGGGCGCTTGGGCC
          1 -GGCCTGGGCGCTTGGGCC

                    
       4082 GCGCCTGG
          1 G-GCCTGG

       4090 CCCGCACGCC


Statistics
Matches: 35,  Mismatches: 6, Indels: 7
        0.73            0.12        0.15

Matches are distributed among these distances:
  18   15  0.43
  19   20  0.57

ACGTcount: A:0.02, C:0.37, G:0.46, T:0.16


Consensus pattern (18 bp):   
GGCCTGGGCGCTTGGGCC

Found at i:4066 original size:37 final size:37

Alignment explanation


    Indices: 4024--4128  Score: 165
    Period size: 37  Copynumber: 2.8  Consensus size: 37

       4014 GACCCGCGCA

                                  *          **  
       4024 CCAGGCCTGGGCGCTTGGGCCGTGCCTGGCCCGTGCG
          1 CCAGGCCTGGGCGCTTGGGCCGCGCCTGGCCCGCACG

                                                 
       4061 CCAGGCCTGGGCGCTTGGGCCGCGCCTGGCCCGCACG
          1 CCAGGCCTGGGCGCTTGGGCCGCGCCTGGCCCGCACG

                         *            *    
       4098 CCAGGCCTGGGCGTTTGGGCCGCGCCAGGCC
          1 CCAGGCCTGGGCGCTTGGGCCGCGCCTGGCC

       4129 TGGGCGCTTG


Statistics
Matches: 63,  Mismatches: 5, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  37   63  1.00

ACGTcount: A:0.05, C:0.40, G:0.42, T:0.13


Consensus pattern (37 bp):   
CCAGGCCTGGGCGCTTGGGCCGCGCCTGGCCCGCACG

Found at i:4070 original size:18 final size:18

Alignment explanation


    Indices: 4047--4107  Score: 52
    Period size: 18  Copynumber: 3.3  Consensus size: 18

       4037 CTTGGGCCGT

                              
       4047 GCCTGGCCCGTGCGCCAG
          1 GCCTGGCCCGTGCGCCAG

                    * *  *     
       4065 GCCTGGGCGCTTGGGCC-G
          1 GCCT-GGCCCGTGCGCCAG

                       **      
       4083 CGCCTGGCCCGCACGCCAG
          1 -GCCTGGCCCGTGCGCCAG

                  
       4102 GCCTGG
          1 GCCTGG

       4108 GCGTTTGGGC


Statistics
Matches: 32,  Mismatches: 8, Indels: 6
        0.70            0.17        0.13

Matches are distributed among these distances:
  18   18  0.56
  19   14  0.44

ACGTcount: A:0.05, C:0.43, G:0.41, T:0.11


Consensus pattern (18 bp):   
GCCTGGCCCGTGCGCCAG

Found at i:4123 original size:24 final size:24

Alignment explanation


    Indices: 4096--4147  Score: 95
    Period size: 24  Copynumber: 2.2  Consensus size: 24

       4086 CTGGCCCGCA

                           *        
       4096 CGCCAGGCCTGGGCGTTTGGGCCG
          1 CGCCAGGCCTGGGCGCTTGGGCCG

                                    
       4120 CGCCAGGCCTGGGCGCTTGGGCCG
          1 CGCCAGGCCTGGGCGCTTGGGCCG

                
       4144 CGCC
          1 CGCC

       4148 TGGCTGGCCC


Statistics
Matches: 27,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  24   27  1.00

ACGTcount: A:0.04, C:0.38, G:0.44, T:0.13


Consensus pattern (24 bp):   
CGCCAGGCCTGGGCGCTTGGGCCG

Found at i:5078 original size:21 final size:21

Alignment explanation


    Indices: 5045--5084  Score: 55
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       5035 GTGTTTTATT

                                 
       5045 CTTGTCAACTCTTT-AACTTC
          1 CTTGTCAACTCTTTCAACTTC

                    *           
       5065 CTTGTTCATCTCTTTCAACT
          1 CTTG-TCAACTCTTTCAACT

       5085 CAAACGATTA


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  20    4  0.24
  21    9  0.53
  22    4  0.24

ACGTcount: A:0.17, C:0.30, G:0.05, T:0.47


Consensus pattern (21 bp):   
CTTGTCAACTCTTTCAACTTC
Done.