Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005402.1 Corchorus capsularis cultivar CVL-1 contig05420, 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: 15164
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32


Found at i:4366 original size:3 final size:3

Alignment explanation


    Indices: 4358--4473  Score: 115
    Period size: 3  Copynumber: 38.7  Consensus size: 3

       4348 CAACATGCCA

                          *       *          *                      *   *  
       4358 ATC ATC ATC ATA ATC ATA ATC ATC ACC ATC ATC ATC ATC ATC CTC CTC
          1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC

            *   *   *   *   *   *                                          
       4406 CTC CTC CTC CTC CTC CTC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
          1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC

                      *   *           
       4454 ATC ATC ATA ATA ATC ATC AT
          1 ATC ATC ATC ATC ATC ATC AT

       4474 TATCGTCATA


Statistics
Matches: 103,  Mismatches: 10, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
   3  103  1.00

ACGTcount: A:0.30, C:0.37, G:0.00, T:0.33


Consensus pattern (3 bp):   
ATC

Found at i:4535 original size:53 final size:53

Alignment explanation


    Indices: 4471--4577  Score: 214
    Period size: 53  Copynumber: 2.0  Consensus size: 53

       4461 TAATAATCAT

                                                                 
       4471 CATTATCGTCATAATCGTAGTCATCAGTAGAATTAGCATTATAATCCTTCCAG
          1 CATTATCGTCATAATCGTAGTCATCAGTAGAATTAGCATTATAATCCTTCCAG

                                                                 
       4524 CATTATCGTCATAATCGTAGTCATCAGTAGAATTAGCATTATAATCCTTCCAG
          1 CATTATCGTCATAATCGTAGTCATCAGTAGAATTAGCATTATAATCCTTCCAG

             
       4577 C
          1 C

       4578 GAAAAAACCA


Statistics
Matches: 54,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  53   54  1.00

ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34


Consensus pattern (53 bp):   
CATTATCGTCATAATCGTAGTCATCAGTAGAATTAGCATTATAATCCTTCCAG

Found at i:9734 original size:211 final size:211

Alignment explanation


    Indices: 9370--9791  Score: 711
    Period size: 211  Copynumber: 2.0  Consensus size: 211

       9360 ATTATATATG

                                                           *                 
       9370 AGATTTTATAAGACATCGAGTTTTCTTCTTTTTAGTATAAATTCTTGTAATAAATAGTCATATAT
          1 AGATTTTATAAGACATCGAGTTTTCTTCTTTTTAGTATAAATTCTTGCAATAAATAGTCATATAT

                         *                 **                                
       9435 ATAAAATCCCGTTGAATTTAGAATCAAGTCATGTTAAATTCAAGATGAGGAAAGCTCTTCCCATA
         66 ATAAAATCCCGTTAAATTTAGAATCAAGTCACATTAAATTCAAGATGAGGAAAGCTCTTCCCATA

                                                                     *       
       9500 AATATTTACCCTTGTAAACTTTCTTCATTCAAAAAAATCAAACCCAAAACCTTACTTGACTAACA
        131 AATATTTACCCTTGTAAACTTTCTTCATTCAAAAAAATCAAACCCAAAACCTTACTTAACTAACA

                            
       9565 TTAAACCCATTATTTA
        196 TTAAACCCATTATTTA

                             *                                               
       9581 AGATTTTATAAGACATCTAGTTTTCTTCTTTTTAGTATAAATTCTTGCAATAAATAGTCATATAT
          1 AGATTTTATAAGACATCGAGTTTTCTTCTTTTTAGTATAAATTCTTGCAATAAATAGTCATATAT

                    *                          *                             
       9646 ATAAAATCTCGTTAAATTTAGAATCAAGTCACATTGAATTCAAGATGAGGAAAGCTCTT-CCAGT
         66 ATAAAATCCCGTTAAATTTAGAATCAAGTCACATTAAATTCAAGATGAGGAAAGCTCTTCCCA-T

                     *                              *  *                  *  
       9710 AAATATTTATCCTTGTAAACTTTCTTCATTCAAAAAAATCGAAGCCAAAACCTTACTTAACTGAC
        130 AAATATTTACCCTTGTAAACTTTCTTCATTCAAAAAAATCAAACCCAAAACCTTACTTAACTAAC

                     *       
       9775 ATTAAACCCCTTATTTA
        195 ATTAAACCCATTATTTA

       9792 TTTAATTTTT


Statistics
Matches: 197,  Mismatches: 13, Indels: 2
        0.93            0.06        0.01

Matches are distributed among these distances:
 210    3  0.02
 211  194  0.98

ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36


Consensus pattern (211 bp):   
AGATTTTATAAGACATCGAGTTTTCTTCTTTTTAGTATAAATTCTTGCAATAAATAGTCATATAT
ATAAAATCCCGTTAAATTTAGAATCAAGTCACATTAAATTCAAGATGAGGAAAGCTCTTCCCATA
AATATTTACCCTTGTAAACTTTCTTCATTCAAAAAAATCAAACCCAAAACCTTACTTAACTAACA
TTAAACCCATTATTTA

Found at i:11382 original size:6 final size:6

Alignment explanation


    Indices: 11371--11396  Score: 52
    Period size: 6  Copynumber: 4.3  Consensus size: 6

      11361 GGGTTCTTCA

                                          
      11371 TCTCGT TCTCGT TCTCGT TCTCGT TC
          1 TCTCGT TCTCGT TCTCGT TCTCGT TC

      11397 AGATTCTGGG


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   20  1.00

ACGTcount: A:0.00, C:0.35, G:0.15, T:0.50


Consensus pattern (6 bp):   
TCTCGT

Done.