Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014528.1 Corchorus olitorius cultivar O-4 contig14561, 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: 45807
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33


Found at i:17621 original size:21 final size:20

Alignment explanation


    Indices: 17595--17658  Score: 76
    Period size: 21  Copynumber: 3.1  Consensus size: 20

      17585 GTTGCTCTAA

                                 
      17595 TAATCTCATCTGTACAGTATC
          1 TAATCTCATCTGTACAGT-TC

                  *            *
      17616 TAATCTAATCTGTACAG-TG
          1 TAATCTCATCTGTACAGTTC

                       *         
      17635 TAATCTCATCTATACAGTTGC
          1 TAATCTCATCTGTACAGTT-C

               
      17656 TAA
          1 TAA

      17659 ACAGTGTCAA


Statistics
Matches: 36,  Mismatches: 5, Indels: 4
        0.80            0.11        0.09

Matches are distributed among these distances:
  19   16  0.44
  20    1  0.03
  21   19  0.53

ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38


Consensus pattern (20 bp):   
TAATCTCATCTGTACAGTTC

Found at i:21701 original size:18 final size:19

Alignment explanation


    Indices: 21673--21708  Score: 65
    Period size: 18  Copynumber: 1.9  Consensus size: 19

      21663 ATGTCATGTC

                               
      21673 GGACAAAAAATGCCACGTT
          1 GGACAAAAAATGCCACGTT

                              
      21692 GGAC-AAAAATGCCACGT
          1 GGACAAAAAATGCCACGT

      21709 GGCAAGACCA


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

Matches are distributed among these distances:
  18   13  0.76
  19    4  0.24

ACGTcount: A:0.42, C:0.22, G:0.22, T:0.14


Consensus pattern (19 bp):   
GGACAAAAAATGCCACGTT

Found at i:25444 original size:209 final size:209

Alignment explanation


    Indices: 25082--25500  Score: 820
    Period size: 209  Copynumber: 2.0  Consensus size: 209

      25072 AAAATTAATA

                                                                             
      25082 CTTTGTAGAGAACATAATATGCTGAAACTGATACCATTTCCATGTGAATGTAGTGTGTGAACTTA
          1 CTTTGTAGAGAACATAATATGCTGAAACTGATACCATTTCCATGTGAATGTAGTGTGTGAACTTA

                                     *                                       
      25147 GTTACTTTGTGGGTATATTAATGCTCTGTTGAATGATATGATTGTTTCTTTGATCATTTGAAAGA
         66 GTTACTTTGTGGGTATATTAATGCTATGTTGAATGATATGATTGTTTCTTTGATCATTTGAAAGA

                            *                                                
      25212 TATTCAAACTTTGATCGGTCTTATGTGTATCTCTTTATACAACCATAAAAAAATTGAACTGAAAT
        131 TATTCAAACTTTGATCAGTCTTATGTGTATCTCTTTATACAACCATAAAAAAATTGAACTGAAAT

                          
      25277 ATATTCTGCTAGGT
        196 ATATTCTGCTAGGT

                                                                             
      25291 CTTTGTAGAGAACATAATATGCTGAAACTGATACCATTTCCATGTGAATGTAGTGTGTGAACTTA
          1 CTTTGTAGAGAACATAATATGCTGAAACTGATACCATTTCCATGTGAATGTAGTGTGTGAACTTA

                                                                             
      25356 GTTACTTTGTGGGTATATTAATGCTATGTTGAATGATATGATTGTTTCTTTGATCATTTGAAAGA
         66 GTTACTTTGTGGGTATATTAATGCTATGTTGAATGATATGATTGTTTCTTTGATCATTTGAAAGA

                                                                             
      25421 TATTCAAACTTTGATCAGTCTTATGTGTATCTCTTTATACAACCATAAAAAAATTGAACTGAAAT
        131 TATTCAAACTTTGATCAGTCTTATGTGTATCTCTTTATACAACCATAAAAAAATTGAACTGAAAT

                          
      25486 ATATTCTGCTAGGT
        196 ATATTCTGCTAGGT

             
      25500 C
          1 C

      25501 ATTTCTAGCT


Statistics
Matches: 208,  Mismatches: 2, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
 209  208  1.00

ACGTcount: A:0.31, C:0.12, G:0.17, T:0.39


Consensus pattern (209 bp):   
CTTTGTAGAGAACATAATATGCTGAAACTGATACCATTTCCATGTGAATGTAGTGTGTGAACTTA
GTTACTTTGTGGGTATATTAATGCTATGTTGAATGATATGATTGTTTCTTTGATCATTTGAAAGA
TATTCAAACTTTGATCAGTCTTATGTGTATCTCTTTATACAACCATAAAAAAATTGAACTGAAAT
ATATTCTGCTAGGT

Found at i:40266 original size:15 final size:15

Alignment explanation


    Indices: 40246--40280  Score: 61
    Period size: 15  Copynumber: 2.3  Consensus size: 15

      40236 CAATAATAAT

                       *   
      40246 GAAATGCAATTGCTA
          1 GAAATGCAATTACTA

                           
      40261 GAAATGCAATTACTA
          1 GAAATGCAATTACTA

                 
      40276 GAAAT
          1 GAAAT

      40281 ATTATATGGC


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

Matches are distributed among these distances:
  15   19  1.00

ACGTcount: A:0.46, C:0.11, G:0.17, T:0.26


Consensus pattern (15 bp):   
GAAATGCAATTACTA
Done.