Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000601.1 Corchorus olitorius cultivar O-4 contig00601, 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: 9624
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30


Found at i:149 original size:16 final size:16

Alignment explanation


    Indices: 113--153  Score: 55
    Period size: 16  Copynumber: 2.5  Consensus size: 16

        103 AGGGAATTAA

                         *  
        113 AAAAATAAAAAATGGT
          1 AAAAATAAAAAATAGT

                           * 
        129 AAAAATAAAAAATATTT
          1 AAAAATAAAAAATA-GT

                    
        146 AAAAATAA
          1 AAAAATAA

        154 TTATTAATAA


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  16   13  0.59
  17    9  0.41

ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22


Consensus pattern (16 bp):   
AAAAATAAAAAATAGT

Found at i:178 original size:29 final size:29

Alignment explanation


    Indices: 132--200  Score: 77
    Period size: 29  Copynumber: 2.3  Consensus size: 29

        122 AAATGGTAAA

                        **           **   
        132 AATAAAAAATATTTAAAAATAATTATTAAT
          1 AATAAAAAATATAAAAAAATAA-TAAAAAT

                                         
        162 AATAAAAAAT-TAAAAAAATAATAAAAAT
          1 AATAAAAAATATAAAAAAATAATAAAAAT

                       
        190 AACTAAAAAAT
          1 AA-TAAAAAAT

        201 CCACACAGAT


Statistics
Matches: 34,  Mismatches: 4, Indels: 3
        0.83            0.10        0.07

Matches are distributed among these distances:
  28    7  0.21
  29   17  0.50
  30   10  0.29

ACGTcount: A:0.71, C:0.01, G:0.00, T:0.28


Consensus pattern (29 bp):   
AATAAAAAATATAAAAAAATAATAAAAAT

Found at i:197 original size:19 final size:18

Alignment explanation


    Indices: 110--198  Score: 51
    Period size: 18  Copynumber: 4.8  Consensus size: 18

        100 AATAGGGAAT

                             **
        110 TAAAAA-AATAAAAAATGG
          1 TAAAAATAAT-AAAAATAA

                              *
        128 TAAAAAT-A-AAAAATATT
          1 TAAAAATAATAAAAATA-A

                        **     
        145 TAAAAATAATTATTAATAA
          1 TAAAAATAA-TAAAAATAA

                                
        164 TAAAAAATTAA-AAAAATAA
          1 T-AAAAA-TAATAAAAATAA

                            
        183 TAAAAATAACTAAAAA
          1 TAAAAATAA-TAAAAA

        199 ATCCACACAG


Statistics
Matches: 55,  Mismatches: 7, Indels: 17
        0.70            0.09        0.22

Matches are distributed among these distances:
  16    6  0.11
  17   10  0.18
  18   13  0.24
  19   13  0.24
  20   10  0.18
  21    3  0.05

ACGTcount: A:0.72, C:0.01, G:0.02, T:0.25


Consensus pattern (18 bp):   
TAAAAATAATAAAAATAA

Found at i:3181 original size:15 final size:15

Alignment explanation


    Indices: 3161--3198  Score: 76
    Period size: 15  Copynumber: 2.5  Consensus size: 15

       3151 GCACGGTTTT

                           
       3161 GGGTGGGAAGCGAAG
          1 GGGTGGGAAGCGAAG

                           
       3176 GGGTGGGAAGCGAAG
          1 GGGTGGGAAGCGAAG

                    
       3191 GGGTGGGA
          1 GGGTGGGA

       3199 TCGAGGATCT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   23  1.00

ACGTcount: A:0.24, C:0.05, G:0.63, T:0.08


Consensus pattern (15 bp):   
GGGTGGGAAGCGAAG

Found at i:5259 original size:34 final size:34

Alignment explanation


    Indices: 5211--5277  Score: 107
    Period size: 34  Copynumber: 2.0  Consensus size: 34

       5201 ATTTCCTAGG

                     *            *           
       5211 GTTTGTTCGTATAATTGGCCTGTAATGACAATGC
          1 GTTTGTTCGAATAATTGGCCTGCAATGACAATGC

                               *             
       5245 GTTTGTTCGAATAATTGGCTTGCAATGACAATG
          1 GTTTGTTCGAATAATTGGCCTGCAATGACAATG

       5278 TTCTTAAGCT


Statistics
Matches: 30,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  34   30  1.00

ACGTcount: A:0.25, C:0.13, G:0.24, T:0.37


Consensus pattern (34 bp):   
GTTTGTTCGAATAATTGGCCTGCAATGACAATGC
Done.