Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011985.1 Corchorus olitorius cultivar O-4 contig12018, 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: 11773
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34


Found at i:4321 original size:18 final size:19

Alignment explanation


    Indices: 4290--4331  Score: 50
    Period size: 18  Copynumber: 2.2  Consensus size: 19

       4280 CATAATTTGC

                               
       4290 GTGTATATCATCT-CAAAA
          1 GTGTATATCATCTCCAAAA

                    **          
       4308 GTGTATATTGTCTCGCAAAA
          1 GTGTATATCATCTC-CAAAA

                
       4328 GTGT
          1 GTGT

       4332 GTAGTTGCTA


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  18   11  0.55
  20    9  0.45

ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36


Consensus pattern (19 bp):   
GTGTATATCATCTCCAAAA

Found at i:4745 original size:30 final size:30

Alignment explanation


    Indices: 4706--4764  Score: 75
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       4696 TTCTTTTTAA

                                           
       4706 TTTACAGTTTGCCA-CGGGCCTTGCCACGGT
          1 TTTACAGTTT-CCAGCGGGCCTTGCCACGGT

                *     *        *         
       4736 TTTAGAGTTTTCAGCGGGCTTTGCCACGG
          1 TTTACAGTTTCCAGCGGGCCTTGCCACGG

       4765 ATTATTTGTT


Statistics
Matches: 25,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  29    2  0.08
  30   23  0.92

ACGTcount: A:0.14, C:0.25, G:0.29, T:0.32


Consensus pattern (30 bp):   
TTTACAGTTTCCAGCGGGCCTTGCCACGGT

Found at i:5011 original size:21 final size:21

Alignment explanation


    Indices: 4985--5025  Score: 64
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       4975 CAGAAACCCG

                                 
       4985 ACTCACCGATCACCACTCACC
          1 ACTCACCGATCACCACTCACC

                    *     *     
       5006 ACTCACCGGTCACCGCTCAC
          1 ACTCACCGATCACCACTCAC

       5026 TGGTTTACGG


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

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.24, C:0.51, G:0.10, T:0.15


Consensus pattern (21 bp):   
ACTCACCGATCACCACTCACC

Found at i:8911 original size:22 final size:22

Alignment explanation


    Indices: 8886--8927  Score: 75
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       8876 ACTATTTTTT

                      *           
       8886 TTGTTTAGATTATCTTATATTC
          1 TTGTTTAGATGATCTTATATTC

                                
       8908 TTGTTTAGATGATCTTATAT
          1 TTGTTTAGATGATCTTATAT

       8928 GCAGACTGTT


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  22   19  1.00

ACGTcount: A:0.24, C:0.07, G:0.12, T:0.57


Consensus pattern (22 bp):   
TTGTTTAGATGATCTTATATTC
Done.