Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020502.1 Corchorus olitorius cultivar O-4 contig20535, 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: 7202
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31


Found at i:631 original size:14 final size:15

Alignment explanation


    Indices: 612--641  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

        602 CAATCAAAGC

                           
        612 AATAAT-CAAGGAAA
          1 AATAATGCAAGGAAA

                           
        626 AATAATGCAAGGAAA
          1 AATAATGCAAGGAAA

             
        641 A
          1 A

        642 TTAAAAAGAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    6  0.40
  15    9  0.60

ACGTcount: A:0.63, C:0.07, G:0.17, T:0.13


Consensus pattern (15 bp):   
AATAATGCAAGGAAA

Found at i:1017 original size:21 final size:21

Alignment explanation


    Indices: 993--1065  Score: 65
    Period size: 21  Copynumber: 3.4  Consensus size: 21

        983 GGCTTGGAAT

                                 
        993 GGTGATGGCACGGGCATGGCC
          1 GGTGATGGCACGGGCATGGCC

                *          * **  
       1014 GGTGGTGGCACGGGCTTAACC
          1 GGTGATGGCACGGGCATGGCC

                *          *    * 
       1035 GGTGGTGGCACGGTGAATGGTC
          1 GGTGATGGCACGG-GCATGGCC

               *     
       1057 GGTAATGGC
          1 GGTGATGGC

       1066 TTGGTAGTGG


Statistics
Matches: 40,  Mismatches: 11, Indels: 1
        0.77            0.21        0.02

Matches are distributed among these distances:
  21   30  0.75
  22   10  0.25

ACGTcount: A:0.15, C:0.19, G:0.47, T:0.19


Consensus pattern (21 bp):   
GGTGATGGCACGGGCATGGCC

Found at i:4227 original size:24 final size:24

Alignment explanation


    Indices: 4200--4254  Score: 78
    Period size: 22  Copynumber: 2.4  Consensus size: 24

       4190 TTCTTTTTAT

                                    
       4200 GACGCAAAAACTATTTTTTTTTTC
          1 GACGCAAAAACTATTTTTTTTTTC

                      * *           
       4224 GACGC--AAATTTTTTTTTTTTTC
          1 GACGCAAAAACTATTTTTTTTTTC

                     
       4246 GACGCAAAA
          1 GACGCAAAA

       4255 CACAAGCAGA


Statistics
Matches: 27,  Mismatches: 2, Indels: 4
        0.82            0.06        0.12

Matches are distributed among these distances:
  22   20  0.74
  24    7  0.26

ACGTcount: A:0.29, C:0.16, G:0.11, T:0.44


Consensus pattern (24 bp):   
GACGCAAAAACTATTTTTTTTTTC

Found at i:4641 original size:16 final size:15

Alignment explanation


    Indices: 4603--4644  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       4593 ACAAAGATTG

                   *       
       4603 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
       4618 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
       4633 ACTAGAAAACAA
          1 AC-AGAAAACAA

       4645 AGCAGAGTAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA
Done.