Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012243.1 Corchorus olitorius cultivar O-4 contig12276, 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: 13867
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31


Found at i:294 original size:17 final size:17

Alignment explanation


    Indices: 272--312  Score: 82
    Period size: 17  Copynumber: 2.4  Consensus size: 17

        262 CTCAAACGAA

                             
        272 AATTTTTGAAATTTCGG
          1 AATTTTTGAAATTTCGG

                             
        289 AATTTTTGAAATTTCGG
          1 AATTTTTGAAATTTCGG

                   
        306 AATTTTT
          1 AATTTTT

        313 AGATCTAGAA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   24  1.00

ACGTcount: A:0.29, C:0.05, G:0.15, T:0.51


Consensus pattern (17 bp):   
AATTTTTGAAATTTCGG

Found at i:1773 original size:54 final size:54

Alignment explanation


    Indices: 1681--1786  Score: 126
    Period size: 54  Copynumber: 1.9  Consensus size: 54

       1671 CCAAGGCACC

                            *                                      
       1681 GCTCGGACAGCACCGAGCCATGCCGAGACAACCAACCAG-CAGCACCAGGCCGTG
          1 GCTCGGACAGCACCGAACCATGCCGAGAC-ACCAACCAGACAGCACCAGGCCGTG

                  *  *             *                     *       
       1735 GCTCGGCCATCACCGAACCATGCGGAGAC-CCAGCACCAGACAGCGCCAGGCC
          1 GCTCGGACAGCACCGAACCATGCCGAGACACCA--ACCAGACAGCACCAGGCC

       1787 AGCCCGTGCG


Statistics
Matches: 44,  Mismatches: 5, Indels: 5
        0.81            0.09        0.09

Matches are distributed among these distances:
  52    3  0.07
  54   30  0.68
  55   11  0.25

ACGTcount: A:0.26, C:0.41, G:0.27, T:0.06


Consensus pattern (54 bp):   
GCTCGGACAGCACCGAACCATGCCGAGACACCAACCAGACAGCACCAGGCCGTG

Found at i:3575 original size:34 final size:34

Alignment explanation


    Indices: 3532--3596  Score: 121
    Period size: 34  Copynumber: 1.9  Consensus size: 34

       3522 ATATGCTAGT

                                              
       3532 TATTGATTGCATGAGAACCTAGCTTAGAATTTGA
          1 TATTGATTGCATGAGAACCTAGCTTAGAATTTGA

                                  *        
       3566 TATTGATTGCATGAGAACCTAGGTTAGAATT
          1 TATTGATTGCATGAGAACCTAGCTTAGAATT

       3597 CGATTGTTTT


Statistics
Matches: 30,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  34   30  1.00

ACGTcount: A:0.32, C:0.11, G:0.22, T:0.35


Consensus pattern (34 bp):   
TATTGATTGCATGAGAACCTAGCTTAGAATTTGA

Found at i:3713 original size:34 final size:34

Alignment explanation


    Indices: 3670--3734  Score: 121
    Period size: 34  Copynumber: 1.9  Consensus size: 34

       3660 ATATGCTAGT

                                 *            
       3670 TATTGATTGCATGAGAACCTATGTTAGAATTTGA
          1 TATTGATTGCATGAGAACCTAGGTTAGAATTTGA

                                           
       3704 TATTGATTGCATGAGAACCTAGGTTAGAATT
          1 TATTGATTGCATGAGAACCTAGGTTAGAATT

       3735 CGATTGTTTT


Statistics
Matches: 30,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  34   30  1.00

ACGTcount: A:0.32, C:0.09, G:0.22, T:0.37


Consensus pattern (34 bp):   
TATTGATTGCATGAGAACCTAGGTTAGAATTTGA

Found at i:3751 original size:138 final size:138

Alignment explanation


    Indices: 3502--3778  Score: 529
    Period size: 138  Copynumber: 2.0  Consensus size: 138

       3492 TTGATAGGTT

                                                                             
       3502 TATTGTTTGATAATTGAGTCATATGCTAGTTATTGATTGCATGAGAACCTAGCTTAGAATTTGAT
          1 TATTGTTTGATAATTGAGTCATATGCTAGTTATTGATTGCATGAGAACCTAGCTTAGAATTTGAT

                                                                             
       3567 ATTGATTGCATGAGAACCTAGGTTAGAATTCGATTGTTTTTGACTTGATATTATTTTCCCAATTT
         66 ATTGATTGCATGAGAACCTAGGTTAGAATTCGATTGTTTTTGACTTGATATTATTTTCCCAATTT

                    
       3632 TTGACAAA
        131 TTGACAAA

                                                                             
       3640 TATTGTTTGATAATTGAGTCATATGCTAGTTATTGATTGCATGAGAACCTATG-TTAGAATTTGA
          1 TATTGTTTGATAATTGAGTCATATGCTAGTTATTGATTGCATGAGAACCTA-GCTTAGAATTTGA

                                                      *                      
       3704 TATTGATTGCATGAGAACCTAGGTTAGAATTCGATTGTTTTTTACTTGATATTATTTTCCCAATT
         65 TATTGATTGCATGAGAACCTAGGTTAGAATTCGATTGTTTTTGACTTGATATTATTTTCCCAATT

                     
       3769 TTTGACAAA
        130 TTTGACAAA

             
       3778 T
          1 T

       3779 TTTTCGAAAA


Statistics
Matches: 137,  Mismatches: 1, Indels: 2
        0.98            0.01        0.01

Matches are distributed among these distances:
 138  136  0.99
 139    1  0.01

ACGTcount: A:0.29, C:0.10, G:0.18, T:0.43


Consensus pattern (138 bp):   
TATTGTTTGATAATTGAGTCATATGCTAGTTATTGATTGCATGAGAACCTAGCTTAGAATTTGAT
ATTGATTGCATGAGAACCTAGGTTAGAATTCGATTGTTTTTGACTTGATATTATTTTCCCAATTT
TTGACAAA

Found at i:4820 original size:16 final size:15

Alignment explanation


    Indices: 4782--4823  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       4772 ACAGAGATTG

                   *       
       4782 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
       4797 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
       4812 ACTAGAAAACAA
          1 AC-AGAAAACAA

       4824 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.