Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001564.1 Corchorus olitorius cultivar O-4 contig01564, 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: 3902
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37


Found at i:261 original size:50 final size:48

Alignment explanation


    Indices: 161--302  Score: 144
    Period size: 49  Copynumber: 2.9  Consensus size: 48

        151 CAAGCAATCC

                *      *                   * **             
        161 TTTACTTTTCACTGCACTTTTTCTCAATTTTTACTACAAAATTGAACT
          1 TTTAATTTTCATTGCACTTTTTCTCAATTTTAAAGACAAAATTGAACT

                     *                                      *  
        209 TTT-ATTTTTACTTGCATCTTTTTCTCAATTTTAAAAGACAAAATTGATCT
          1 TTTAATTTTCA-TTGCA-CTTTTTCTCAATTTT-AAAGACAAAATTGAACT

                        *         *         **           
        259 TTTAATTTTCATCGCACTTTTTATCAATTTT-TTGACAAAATTGA
          1 TTTAATTTTCATTGCACTTTTTCTCAATTTTAAAGACAAAATTGA

        303 TTGGCACGCT


Statistics
Matches: 78,  Mismatches: 12, Indels: 9
        0.79            0.12        0.09

Matches are distributed among these distances:
  47   16  0.21
  48    7  0.09
  49   29  0.37
  50   20  0.26
  51    6  0.08

ACGTcount: A:0.29, C:0.16, G:0.06, T:0.49


Consensus pattern (48 bp):   
TTTAATTTTCATTGCACTTTTTCTCAATTTTAAAGACAAAATTGAACT

Found at i:1726 original size:15 final size:15

Alignment explanation


    Indices: 1706--1736  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       1696 AGTTTTTAAC

                           
       1706 CAAAAATAAGGATAT
          1 CAAAAATAAGGATAT

                           
       1721 CAAAAATAAGGATAT
          1 CAAAAATAAGGATAT

             
       1736 C
          1 C

       1737 CTTATTTTAG


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.58, C:0.10, G:0.13, T:0.19


Consensus pattern (15 bp):   
CAAAAATAAGGATAT

Found at i:2349 original size:30 final size:30

Alignment explanation


    Indices: 2315--2371  Score: 96
    Period size: 30  Copynumber: 1.9  Consensus size: 30

       2305 TTTATTTAGG

                                          
       2315 AAACGTTTTGCCCTAAATTGACCATTTCGA
          1 AAACGTTTTGCCCTAAATTGACCATTTCGA

                        *        *     
       2345 AAACGTTTTGCCTTAAATTGAGCATTT
          1 AAACGTTTTGCCCTAAATTGACCATTT

       2372 TTTTTAAATT


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  30   25  1.00

ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37


Consensus pattern (30 bp):   
AAACGTTTTGCCCTAAATTGACCATTTCGA

Found at i:3891 original size:17 final size:18

Alignment explanation


    Indices: 3858--3891  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       3848 CATAAGCACT

                      *       
       3858 TTTAGTAATCTTTATAAG
          1 TTTAGTAATCCTTATAAG

                             
       3876 TTTAGTAA-CCTTATAA
          1 TTTAGTAATCCTTATAA

       3892 AATTTTTTAA


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  17    7  0.47
  18    8  0.53

ACGTcount: A:0.35, C:0.09, G:0.09, T:0.47


Consensus pattern (18 bp):   
TTTAGTAATCCTTATAAG
Done.