Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019670.1 Corchorus olitorius cultivar O-4 contig19703, 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: 14081
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31


Found at i:59 original size:2 final size:2

Alignment explanation


    Indices: 54--87  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

         44 TTTTTACTAA

                                                              
         54 AT 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

         88 CCATGGCCAG


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:6281 original size:148 final size:148

Alignment explanation


    Indices: 6019--6310  Score: 435
    Period size: 148  Copynumber: 1.9  Consensus size: 148

       6009 CATTTACGCG

                                      *                                      
       6019 TAATCACTTATTAATACATATGAATCGTGCATATATAATTGATGTTTTTCGTAATTAGTGATAAA
          1 TAATCACTTATTAATACATATGAATCATGC--A-ATAATTGATGTTTTTCGTAATTAGTGATAAA

                    *                      *                                 
       6084 AATCTCTCCCGTAAATATGTACATATCATCATTGAGAAATACCTTAATTAGGGTTGGAAGAAAGA
         63 AATCTCTCACGTAAATATGTACA-ATCATCACTGAGAAATACCTTAATTAGGGTTGGAAGAAAGA

               *                  
       6149 ATGGGAAATTTCTACGCGTAAT
        127 ATGAGAAATTTCTACGCGTAAT

                                                            *                
       6171 TAATCACTTATTAATACATATGAATCATGC-ATAATTGATGTTTTTTTTGTAATTAGTGATAAAA
          1 TAATCACTTATTAATACATATGAATCATGCAATAATTGATG--TTTTTCGTAATTAGTGATAAAA

                    *                              *          *              
       6235 ATCTCTCATGTAAATATGTAC-ATCATCACTGAGAAATATCTTAATTAGGTTTGGAAGAAAGAAT
         64 ATCTCTCACGTAAATATGTACAATCATCACTGAGAAATACCTTAATTAGGGTTGGAAGAAAGAAT

                 *      
       6299 GAGAAGTTTCTA
        129 GAGAAATTTCTA

       6311 GTTCACCATG


Statistics
Matches: 129,  Mismatches: 9, Indels: 8
        0.88            0.06        0.05

Matches are distributed among these distances:
 148   60  0.47
 150   40  0.31
 152   29  0.22

ACGTcount: A:0.37, C:0.11, G:0.15, T:0.36


Consensus pattern (148 bp):   
TAATCACTTATTAATACATATGAATCATGCAATAATTGATGTTTTTCGTAATTAGTGATAAAAAT
CTCTCACGTAAATATGTACAATCATCACTGAGAAATACCTTAATTAGGGTTGGAAGAAAGAATGA
GAAATTTCTACGCGTAAT

Found at i:8876 original size:33 final size:33

Alignment explanation


    Indices: 8839--8909  Score: 124
    Period size: 33  Copynumber: 2.2  Consensus size: 33

       8829 AGAAAGGAAA

                                        *  * 
       8839 AGTGGGTTTAGTGAAGCAGAGCCAAGGAGAATT
          1 AGTGGGTTTAGTGAAGCAGAGCCAAGGAAAAGT

                                             
       8872 AGTGGGTTTAGTGAAGCAGAGCCAAGGAAAAGT
          1 AGTGGGTTTAGTGAAGCAGAGCCAAGGAAAAGT

                 
       8905 AGTGG
          1 AGTGG

       8910 TGGTTTGGAT


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

Matches are distributed among these distances:
  33   36  1.00

ACGTcount: A:0.34, C:0.08, G:0.38, T:0.20


Consensus pattern (33 bp):   
AGTGGGTTTAGTGAAGCAGAGCCAAGGAAAAGT

Found at i:12474 original size:27 final size:27

Alignment explanation


    Indices: 12444--12504  Score: 113
    Period size: 27  Copynumber: 2.3  Consensus size: 27

      12434 AATTAAATAT

                                       
      12444 AAATATATCCGAGATGACCAATTCATG
          1 AAATATATCCGAGATGACCAATTCATG

                                       
      12471 AAATATATCCGAGATGACCAATTCATG
          1 AAATATATCCGAGATGACCAATTCATG

              *    
      12498 AATTATA
          1 AAATATA

      12505 CACTAATTTC


Statistics
Matches: 33,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  27   33  1.00

ACGTcount: A:0.43, C:0.16, G:0.13, T:0.28


Consensus pattern (27 bp):   
AAATATATCCGAGATGACCAATTCATG
Done.