Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016468.1 Corchorus olitorius cultivar O-4 contig16501, 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: 23276
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


Found at i:360 original size:4 final size:4

Alignment explanation


    Indices: 342--380  Score: 55
    Period size: 4  Copynumber: 10.2  Consensus size: 4

        332 CTTTCCCTTC

                                                       *       
        342 TCTT T-TT TC-T TCTT TCTT TCTT TCTT TCTT TCTA TCTT T
          1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT T

        381 TTCGGCTCTT


Statistics
Matches: 31,  Mismatches: 2, Indels: 4
        0.84            0.05        0.11

Matches are distributed among these distances:
   3    6  0.19
   4   25  0.81

ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74


Consensus pattern (4 bp):   
TCTT

Found at i:9781 original size:21 final size:22

Alignment explanation


    Indices: 9752--9795  Score: 54
    Period size: 21  Copynumber: 2.0  Consensus size: 22

       9742 TCAGTCGCAT

                         *   *    
       9752 TTTAGTATGGTAATTAAGTTAA
          1 TTTAGTATGGTAAGTAAATTAA

                     *            
       9774 TTTA-TATGTTAAGTAAATTAA
          1 TTTAGTATGGTAAGTAAATTAA

             
       9795 T
          1 T

       9796 ATGGTTTAAA


Statistics
Matches: 19,  Mismatches: 3, Indels: 1
        0.83            0.13        0.04

Matches are distributed among these distances:
  21   15  0.79
  22    4  0.21

ACGTcount: A:0.39, C:0.00, G:0.14, T:0.48


Consensus pattern (22 bp):   
TTTAGTATGGTAAGTAAATTAA

Found at i:9787 original size:17 final size:17

Alignment explanation


    Indices: 9765--9798  Score: 50
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       9755 AGTATGGTAA

                  *    *     
       9765 TTAAGTTAATTTATATG
          1 TTAAGTAAATTAATATG

                             
       9782 TTAAGTAAATTAATATG
          1 TTAAGTAAATTAATATG

       9799 GTTTAAATTG


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47


Consensus pattern (17 bp):   
TTAAGTAAATTAATATG

Found at i:10770 original size:14 final size:14

Alignment explanation


    Indices: 10753--10781  Score: 58
    Period size: 14  Copynumber: 2.1  Consensus size: 14

      10743 TTTACTATAA

                          
      10753 TCGTTTCACCATCG
          1 TCGTTTCACCATCG

                          
      10767 TCGTTTCACCATCG
          1 TCGTTTCACCATCG

             
      10781 T
          1 T

      10782 TTTGAATTCA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   15  1.00

ACGTcount: A:0.14, C:0.34, G:0.14, T:0.38


Consensus pattern (14 bp):   
TCGTTTCACCATCG

Found at i:22089 original size:21 final size:19

Alignment explanation


    Indices: 22063--22121  Score: 64
    Period size: 21  Copynumber: 3.0  Consensus size: 19

      22053 GCTGCTATAA

                                 
      22063 TAATCTCATTTGTACAGTACC
          1 TAATCTCATTTGTACAGT--C

                  *  *        *
      22084 TAATCTAATCTGTACAGTG
          1 TAATCTCATTTGTACAGTC

               *               
      22103 TAACCTCATTTGTACAGTC
          1 TAATCTCATTTGTACAGTC

      22122 ACTAAACAGT


Statistics
Matches: 31,  Mismatches: 7, Indels: 2
        0.77            0.17        0.05

Matches are distributed among these distances:
  19   15  0.48
  21   16  0.52

ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37


Consensus pattern (19 bp):   
TAATCTCATTTGTACAGTC
Done.