Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012386.1 Corchorus olitorius cultivar O-4 contig12419, 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: 25360
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32


Found at i:5428 original size:18 final size:19

Alignment explanation


    Indices: 5402--5438  Score: 67
    Period size: 18  Copynumber: 2.0  Consensus size: 19

       5392 TTCTCTTCTT

                               
       5402 TTTTCTCTTCTAGTTCTAG
          1 TTTTCTCTTCTAGTTCTAG

                               
       5421 TTTT-TCTTCTAGTTCTAG
          1 TTTTCTCTTCTAGTTCTAG

       5439 GCTAGGGTGT


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  18   14  0.78
  19    4  0.22

ACGTcount: A:0.11, C:0.19, G:0.11, T:0.59


Consensus pattern (19 bp):   
TTTTCTCTTCTAGTTCTAG

Found at i:6490 original size:31 final size:32

Alignment explanation


    Indices: 6428--6504  Score: 129
    Period size: 31  Copynumber: 2.4  Consensus size: 32

       6418 AGATTGTTTC

                                   *        
       6428 TTGTTTTTGCGTTTTTAATTTTCTAAAAAAAA
          1 TTGTTTTTGCGTTTTTAATTTTCAAAAAAAAA

                  *                         
       6460 TTGTTTCTGCGTTTTTAATTTT-AAAAAAAAA
          1 TTGTTTTTGCGTTTTTAATTTTCAAAAAAAAA

                          
       6491 TTGTTTTTGCGTTT
          1 TTGTTTTTGCGTTT

       6505 GAAAAGAAAA


Statistics
Matches: 42,  Mismatches: 3, Indels: 1
        0.91            0.07        0.02

Matches are distributed among these distances:
  31   21  0.50
  32   21  0.50

ACGTcount: A:0.27, C:0.06, G:0.12, T:0.55


Consensus pattern (32 bp):   
TTGTTTTTGCGTTTTTAATTTTCAAAAAAAAA

Found at i:8113 original size:42 final size:42

Alignment explanation


    Indices: 8054--8137  Score: 168
    Period size: 42  Copynumber: 2.0  Consensus size: 42

       8044 AGTGCCTGCC

                                                      
       8054 AAAGAAATCAAGGTTGAAGATCAACCCATTCCCTTTGAAGCT
          1 AAAGAAATCAAGGTTGAAGATCAACCCATTCCCTTTGAAGCT

                                                      
       8096 AAAGAAATCAAGGTTGAAGATCAACCCATTCCCTTTGAAGCT
          1 AAAGAAATCAAGGTTGAAGATCAACCCATTCCCTTTGAAGCT

       8138 GTTAAGGACG


Statistics
Matches: 42,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  42   42  1.00

ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24


Consensus pattern (42 bp):   
AAAGAAATCAAGGTTGAAGATCAACCCATTCCCTTTGAAGCT

Found at i:11423 original size:18 final size:18

Alignment explanation


    Indices: 11402--11437  Score: 63
    Period size: 18  Copynumber: 2.0  Consensus size: 18

      11392 TCTCTTCTTT

                              
      11402 TTTTTCTTCTAGTTCTAG
          1 TTTTTCTTCTAGTTCTAG

                      *       
      11420 TTTTTCTTCTGGTTCTAG
          1 TTTTTCTTCTAGTTCTAG

      11438 GCTAGGGTGT


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.08, C:0.17, G:0.14, T:0.61


Consensus pattern (18 bp):   
TTTTTCTTCTAGTTCTAG

Found at i:12011 original size:20 final size:20

Alignment explanation


    Indices: 11986--12027  Score: 84
    Period size: 20  Copynumber: 2.1  Consensus size: 20

      11976 TTGCACTATT

                                
      11986 TACACGGATCACTAGTCTGC
          1 TACACGGATCACTAGTCTGC

                                
      12006 TACACGGATCACTAGTCTGC
          1 TACACGGATCACTAGTCTGC

              
      12026 TA
          1 TA

      12028 GTAAATTGCA


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   22  1.00

ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26


Consensus pattern (20 bp):   
TACACGGATCACTAGTCTGC

Found at i:15491 original size:15 final size:15

Alignment explanation


    Indices: 15465--15513  Score: 73
    Period size: 15  Copynumber: 3.3  Consensus size: 15

      15455 TTAACAAAAA

                           
      15465 TCAAGGCTTAATTTT
          1 TCAAGGCTTAATTTT

             *              
      15480 TGAAGG-TATAATTTT
          1 TCAAGGCT-TAATTTT

                           
      15495 TCAAGGCTTAATTTT
          1 TCAAGGCTTAATTTT

                
      15510 TCAA
          1 TCAA

      15514 AGCTAAATAA


Statistics
Matches: 30,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
  14    1  0.03
  15   28  0.93
  16    1  0.03

ACGTcount: A:0.31, C:0.10, G:0.14, T:0.45


Consensus pattern (15 bp):   
TCAAGGCTTAATTTT

Found at i:21061 original size:18 final size:17

Alignment explanation


    Indices: 21036--21071  Score: 54
    Period size: 18  Copynumber: 2.1  Consensus size: 17

      21026 TTTCTTTTCA

                     *       
      21036 TCTATTTTTTTTCTAGT
          1 TCTATTTTTCTTCTAGT

                              
      21053 TCTAGTTTTTCTTCTAGT
          1 TCTA-TTTTTCTTCTAGT

             
      21071 T
          1 T

      21072 TTTCCTAAGG


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  17    4  0.24
  18   13  0.76

ACGTcount: A:0.11, C:0.14, G:0.08, T:0.67


Consensus pattern (17 bp):   
TCTATTTTTCTTCTAGT
Done.