Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021595.1 Corchorus olitorius cultivar O-4 contig21628, 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: 18983
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34


Found at i:1645 original size:2 final size:2

Alignment explanation


    Indices: 1638--1662  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       1628 TTAGGAGTAC

                                                 
       1638 AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT A

       1663 AATAAACGCT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:15854 original size:42 final size:43

Alignment explanation


    Indices: 15802--15884  Score: 141
    Period size: 42  Copynumber: 2.0  Consensus size: 43

      15792 TGCCATACAG

                            *                          
      15802 AATATAATTTAATTATTTCACTATTAAAATATATAAAATTGTC
          1 AATATAATTTAATTATGTCACTATTAAAATATATAAAATTGTC

                                *                    
      15845 AATAT-ATTTAATTATGTCATTATTAAAATATATAAAATTG
          1 AATATAATTTAATTATGTCACTATTAAAATATATAAAATTG

      15885 CCATTATTAA


Statistics
Matches: 38,  Mismatches: 2, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  42   33  0.87
  43    5  0.13

ACGTcount: A:0.47, C:0.05, G:0.04, T:0.45


Consensus pattern (43 bp):   
AATATAATTTAATTATGTCACTATTAAAATATATAAAATTGTC

Found at i:15874 original size:26 final size:25

Alignment explanation


    Indices: 15845--15909  Score: 69
    Period size: 24  Copynumber: 2.5  Consensus size: 25

      15835 TAAAATTGTC

                            *         
      15845 AATATATTTAATTATGTCATTATTAA
          1 AATATATTTAATT-TGCCATTATTAA

                    *  *             
      15871 AATATA-TAAAATTGCCATTATTAA
          1 AATATATTTAATTTGCCATTATTAA

                           
      15895 AATATAATTTCAATT
          1 AATAT-ATTT-AATT

      15910 CCTATCTATA


Statistics
Matches: 31,  Mismatches: 5, Indels: 5
        0.76            0.12        0.12

Matches are distributed among these distances:
  24   16  0.52
  25    5  0.16
  26    7  0.23
  27    3  0.10

ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45


Consensus pattern (25 bp):   
AATATATTTAATTTGCCATTATTAA

Found at i:18208 original size:13 final size:13

Alignment explanation


    Indices: 18190--18225  Score: 56
    Period size: 13  Copynumber: 2.8  Consensus size: 13

      18180 AATCATGCAC

                         
      18190 TCAAAACATTTTA
          1 TCAAAACATTTTA

                         
      18203 TCAAAACATTTTA
          1 TCAAAACATTTTA

                 *     
      18216 T-AAAGCATTT
          1 TCAAAACATTT

      18226 AAATAAAAGT


Statistics
Matches: 22,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  12    8  0.36
  13   14  0.64

ACGTcount: A:0.44, C:0.14, G:0.03, T:0.39


Consensus pattern (13 bp):   
TCAAAACATTTTA
Done.