Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014996.1 Corchorus olitorius cultivar O-4 contig15029, 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: 5005
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:1200 original size:14 final size:16

Alignment explanation


    Indices: 1181--1214  Score: 54
    Period size: 14  Copynumber: 2.2  Consensus size: 16

       1171 AGAAGAAGTA

                            
       1181 TGTTTTC-TTATT-AT
          1 TGTTTTCTTTATTAAT

                            
       1195 TGTTTTCTTTATTAAT
          1 TGTTTTCTTTATTAAT

                
       1211 TGTT
          1 TGTT

       1215 GATCAGTCGT


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  14    7  0.39
  15    5  0.28
  16    6  0.33

ACGTcount: A:0.15, C:0.06, G:0.09, T:0.71


Consensus pattern (16 bp):   
TGTTTTCTTTATTAAT

Found at i:2842 original size:76 final size:76

Alignment explanation


    Indices: 2690--2842  Score: 182
    Period size: 76  Copynumber: 2.0  Consensus size: 76

       2680 GGACAAGGGC

                     *                                     *       *  *   *  
       2690 CCCGACTCCTCCTGGGCGCCCACATGTTTGCCTTGAGCACCCATGTGGTTTGCCTTAAGACCTAG
          1 CCCGACTCCACCTGGGCGCCCACATGTTTGCCTTGAGCACCCATGTGATTTGCCTGAACACCCAG

              *        
       2755 CTGGGCAGTGT
         66 CTAGGCAGTGT

                            *              *      *                   *      
       2766 CCCGACTCCACCTGGGTGCCCACATGGTTTGTC-TGAGGACCCATGTGATTTGCCTGATCACCCA
          1 CCCGACTCCACCTGGGCGCCCACAT-GTTTGCCTTGAGCACCCATGTGATTTGCCTGAACACCCA

             *     *    
       2830 GGTAGGCTGTGT
         65 GCTAGGCAGTGT

             
       2842 C
          1 C

       2843 ATAGCTCATC


Statistics
Matches: 64,  Mismatches: 12, Indels: 2
        0.82            0.15        0.03

Matches are distributed among these distances:
  76   58  0.91
  77    6  0.09

ACGTcount: A:0.15, C:0.32, G:0.27, T:0.26


Consensus pattern (76 bp):   
CCCGACTCCACCTGGGCGCCCACATGTTTGCCTTGAGCACCCATGTGATTTGCCTGAACACCCAG
CTAGGCAGTGT
Done.