Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007212.1 Corchorus olitorius cultivar O-4 contig07237, 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: 9105
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.30


Found at i:211 original size:2 final size:2

Alignment explanation


    Indices: 204--235  Score: 57
    Period size: 2  Copynumber: 16.5  Consensus size: 2

        194 AAAGATAAAG

                                                             
        204 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

        236 AGTAAAAAAG


Statistics
Matches: 29,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   28  0.97

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


Consensus pattern (2 bp):   
AT

Found at i:443 original size:2 final size:2

Alignment explanation


    Indices: 436--467  Score: 50
    Period size: 2  Copynumber: 17.0  Consensus size: 2

        426 CTTTAAAAAG

                                                              
        436 TA TA TA TA T- TA TA TA -A TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

        468 ATTTGGCTCA


Statistics
Matches: 28,  Mismatches: 0, Indels: 4
        0.88            0.00        0.12

Matches are distributed among these distances:
   1    2  0.07
   2   26  0.93

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


Consensus pattern (2 bp):   
TA

Found at i:7971 original size:17 final size:17

Alignment explanation


    Indices: 7944--7992  Score: 64
    Period size: 17  Copynumber: 2.9  Consensus size: 17

       7934 TGTAATTTTT

                  *          
       7944 GATCACCGGTGATCTT-
          1 GATCACTGGTGATCTTA

                              
       7960 GCATCACTGGTGATCTTA
          1 G-ATCACTGGTGATCTTA

                   *       
       7978 GATCACTAGTGATCT
          1 GATCACTGGTGATCT

       7993 GGGGGGTGAT


Statistics
Matches: 29,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  16    1  0.03
  17   27  0.93
  18    1  0.03

ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33


Consensus pattern (17 bp):   
GATCACTGGTGATCTTA
Done.