Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017060.1 Corchorus olitorius cultivar O-4 contig17093, 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: 16070
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.28


Found at i:169 original size:31 final size:29

Alignment explanation


    Indices: 131--298  Score: 94
    Period size: 31  Copynumber: 5.6  Consensus size: 29

        121 AACTGACGCC

                                           
        131 AGGCCCTTATTTGAGCATTTTCGATAACGTT
          1 AGGCCCTTATTTGAGCATTTT-GA-AACGTT

                              **      * * 
        162 AGGCCCTTATTTG-GTCAAATT-AAAAGAT
          1 AGGCCCTTATTTGAG-CATTTTGAAACGTT

            *   **                          
        190 CGGATTCTTATTTGAGCATTTTCGATAACGTT
          1 AGG-CCCTTATTTGAGCATTTT-GA-AACGTT

                *             **      *    
        222 AGGCTCTTATTTG-GCCAAATT-AAAAGATT
          1 AGGCCCTTATTTGAG-CATTTTGAAACG-TT

                                            
        251 -GGACCCTTATTTGAGCATTTTGGCAAACGTT
          1 AGG-CCCTTATTTGAGCATTTT-G-AAACGTT

               *             
        282 AGGTCCTTATTTGAGCA
          1 AGGCCCTTATTTGAGCA

        299 ATTAACCAAA


Statistics
Matches: 102,  Mismatches: 21, Indels: 28
        0.68            0.14        0.19

Matches are distributed among these distances:
  28   11  0.11
  29   29  0.28
  30    4  0.04
  31   46  0.45
  32   12  0.12

ACGTcount: A:0.27, C:0.17, G:0.20, T:0.37


Consensus pattern (29 bp):   
AGGCCCTTATTTGAGCATTTTGAAACGTT

Found at i:231 original size:60 final size:60

Alignment explanation


    Indices: 134--294  Score: 236
    Period size: 60  Copynumber: 2.7  Consensus size: 60

        124 TGACGCCAGG

                                            *         *                 
        134 CCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGTCAAATTAAAAGATCGGA
          1 CCCTTATTTGAGCATTTTCGATAACGTTAGGCTCTTATTTGGCCAAATTAAAAGATCGGA

            **                                                      *   
        194 TTCTTATTTGAGCATTTTCGATAACGTTAGGCTCTTATTTGGCCAAATTAAAAGATTGGA
          1 CCCTTATTTGAGCATTTTCGATAACGTTAGGCTCTTATTTGGCCAAATTAAAAGATCGGA

                              *                        
        254 CCCTTATTTGAGCATTTTGGCA-AACGTTAGG-TCCTTATTTG
          1 CCCTTATTTGAGCATTTTCG-ATAACGTTAGGCT-CTTATTTG

        295 AGCAATTAAC


Statistics
Matches: 91,  Mismatches: 8, Indels: 4
        0.88            0.08        0.04

Matches are distributed among these distances:
  59    1  0.01
  60   89  0.98
  61    1  0.01

ACGTcount: A:0.26, C:0.17, G:0.19, T:0.39


Consensus pattern (60 bp):   
CCCTTATTTGAGCATTTTCGATAACGTTAGGCTCTTATTTGGCCAAATTAAAAGATCGGA

Found at i:449 original size:15 final size:16

Alignment explanation


    Indices: 430--466  Score: 58
    Period size: 15  Copynumber: 2.4  Consensus size: 16

        420 TATAAATGAT

                            
        430 AATATTATAAT-TAAA
          1 AATATTATAATCTAAA

            *               
        445 TATATTATAATCTAAA
          1 AATATTATAATCTAAA

                  
        461 AATATT
          1 AATATT

        467 TATTAGAAGT


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  15   10  0.53
  16    9  0.47

ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43


Consensus pattern (16 bp):   
AATATTATAATCTAAA

Done.