Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018786.1 Corchorus olitorius cultivar O-4 contig18819, 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: 4107
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29


Found at i:219 original size:17 final size:16

Alignment explanation


    Indices: 179--221  Score: 59
    Period size: 17  Copynumber: 2.6  Consensus size: 16

        169 CATGTAATCT

                    *       
        179 TTGATCACCGGTGATC
          1 TTGATCACTGGTGATC

                             
        195 TTGCATCACTGGTGATC
          1 TTG-ATCACTGGTGATC

                      
        212 TTAGATCACT
          1 TT-GATCACT

        222 AGTAATCTGG


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  16    3  0.12
  17   20  0.83
  18    1  0.04

ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35


Consensus pattern (16 bp):   
TTGATCACTGGTGATC

Found at i:229 original size:17 final size:16

Alignment explanation


    Indices: 172--229  Score: 53
    Period size: 17  Copynumber: 3.4  Consensus size: 16

        162 ATAAACCCAT

                           * 
        172 GTAATCTTTGATCACCG
          1 GTAATC-TTGATCACTG

              *              
        189 GTGATCTTGCATCACTG
          1 GTAATCTTG-ATCACTG

              *             *
        206 GTGATCTTAGATCACTA
          1 GTAATCTT-GATCACTG

                   
        223 GTAATCT
          1 GTAATCT

        230 GGGGGGTGAT


Statistics
Matches: 35,  Mismatches: 4, Indels: 4
        0.81            0.09        0.09

Matches are distributed among these distances:
  16    3  0.09
  17   31  0.89
  18    1  0.03

ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36


Consensus pattern (16 bp):   
GTAATCTTGATCACTG

Found at i:3741 original size:21 final size:21

Alignment explanation


    Indices: 3717--3756  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       3707 TAATTAAATG

                    *     *      
       3717 CAATTTGATCCCTGCTTTTTT
          1 CAATTTGACCCCTGATTTTTT

                               
       3738 CAATTTGACCCCTGATTTT
          1 CAATTTGACCCCTGATTTT

       3757 AGAAATTATG


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.17, C:0.25, G:0.10, T:0.47


Consensus pattern (21 bp):   
CAATTTGACCCCTGATTTTTT
Done.