Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023792.1 Corchorus olitorius cultivar O-4 contig23825, 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: 12031
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28


Found at i:7909 original size:19 final size:19

Alignment explanation


    Indices: 7874--7911  Score: 51
    Period size: 19  Copynumber: 2.0  Consensus size: 19

       7864 AGGTTGAAGC

                    *          
       7874 AAGAAGTGCAAGCCTTAGT
          1 AAGAAGTGAAAGCCTTAGT

                                
       7893 AAGAAGTGGAAAG-CTTAGT
          1 AAGAAGT-GAAAGCCTTAGT

       7912 GATGCGGCAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  19   13  0.76
  20    4  0.24

ACGTcount: A:0.39, C:0.11, G:0.29, T:0.21


Consensus pattern (19 bp):   
AAGAAGTGAAAGCCTTAGT

Found at i:8913 original size:25 final size:23

Alignment explanation


    Indices: 8867--8914  Score: 69
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       8857 CTATCCTTCT

                                   
       8867 ATTCATCTATCATCAAGTTTTTC
          1 ATTCATCTATCATCAAGTTTTTC

                                     
       8890 ATTCATCTCATCCATCAAAGTTTTT
          1 ATTCATCT-AT-CATC-AAGTTTTT

       8915 TAAATTTTCT


Statistics
Matches: 22,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  23    8  0.36
  24    2  0.09
  25    4  0.18
  26    8  0.36

ACGTcount: A:0.27, C:0.23, G:0.04, T:0.46


Consensus pattern (23 bp):   
ATTCATCTATCATCAAGTTTTTC

Found at i:10584 original size:21 final size:21

Alignment explanation


    Indices: 10558--10599  Score: 75
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      10548 TAAGGAAGAA

                                 
      10558 GTTTCAAGCTCATCAGAGTTG
          1 GTTTCAAGCTCATCAGAGTTG

                          *      
      10579 GTTTCAAGCTCATCGGAGTTG
          1 GTTTCAAGCTCATCAGAGTTG

      10600 TCTAAGATGC


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.21, C:0.19, G:0.26, T:0.33


Consensus pattern (21 bp):   
GTTTCAAGCTCATCAGAGTTG
Done.