Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012878.1 Corchorus olitorius cultivar O-4 contig12911, 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: 17392
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:308 original size:2 final size:2

Alignment explanation


    Indices: 296--335  Score: 71
    Period size: 2  Copynumber: 20.0  Consensus size: 2

        286 AAATGTTGTA

                     *                                                 
        296 AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

        336 TAGAACTACC


Statistics
Matches: 36,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   2   36  1.00

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (2 bp):   
AT

Found at i:2179 original size:22 final size:21

Alignment explanation


    Indices: 2151--2191  Score: 64
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       2141 TTAATAACAA

                    *             
       2151 AAAAAAATCCTCAACAAAATGT
          1 AAAAAAATAC-CAACAAAATGT

                               
       2173 AAAAAAATACCAACAAAAT
          1 AAAAAAATACCAACAAAAT

       2192 CAACTCAAAC


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  21    9  0.50
  22    9  0.50

ACGTcount: A:0.66, C:0.17, G:0.02, T:0.15


Consensus pattern (21 bp):   
AAAAAAATACCAACAAAATGT

Found at i:6546 original size:6 final size:6

Alignment explanation


    Indices: 6535--6559  Score: 50
    Period size: 6  Copynumber: 4.2  Consensus size: 6

       6525 TTATTTCTTC

                                         
       6535 TTTCCA TTTCCA TTTCCA TTTCCA T
          1 TTTCCA TTTCCA TTTCCA TTTCCA T

       6560 GTGCTATATG


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   19  1.00

ACGTcount: A:0.16, C:0.32, G:0.00, T:0.52


Consensus pattern (6 bp):   
TTTCCA

Found at i:9667 original size:2 final size:2

Alignment explanation


    Indices: 9662--9690  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

       9652 TTCTCTCATT

                                                       
       9662 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       9691 TTTGAATAAC


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:15119 original size:5 final size:5

Alignment explanation


    Indices: 15109--15152  Score: 54
    Period size: 5  Copynumber: 8.8  Consensus size: 5

      15099 TCTTTCTTTC

                      *            *                             
      15109 TTTT- TTTTT TTTTA GTTTTG TTTTA TTTTA TTTTA TTTTA TTTT
          1 TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA TTTT

      15153 TTTGAGGGAT


Statistics
Matches: 35,  Mismatches: 3, Indels: 3
        0.85            0.07        0.07

Matches are distributed among these distances:
   4    4  0.11
   5   27  0.77
   6    4  0.11

ACGTcount: A:0.11, C:0.00, G:0.05, T:0.84


Consensus pattern (5 bp):   
TTTTA

Done.