Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021198.1 Corchorus olitorius cultivar O-4 contig21231, 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: 7979
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33


Found at i:2510 original size:15 final size:15

Alignment explanation


    Indices: 2490--2520  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       2480 CAGAGTTTTA

                           
       2490 CACTCTTTTTGGACC
          1 CACTCTTTTTGGACC

                           
       2505 CACTCTTTTTGGACC
          1 CACTCTTTTTGGACC

             
       2520 C
          1 C

       2521 TAAGATCTAT


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:0.13, C:0.35, G:0.13, T:0.39


Consensus pattern (15 bp):   
CACTCTTTTTGGACC

Found at i:3004 original size:45 final size:45

Alignment explanation


    Indices: 2945--3119  Score: 323
    Period size: 45  Copynumber: 3.9  Consensus size: 45

       2935 CTAAATTCTA

                                                         
       2945 CTCCATCTCTAGGTAATTCAGCAAAATAAAGCTAATATTATACTC
          1 CTCCATCTCTAGGTAATTCAGCAAAATAAAGCTAATATTATACTC

                                                         
       2990 CTCCATCTCTAGGTAATTCAGCAAAATAAAGCTAATATTATACTC
          1 CTCCATCTCTAGGTAATTCAGCAAAATAAAGCTAATATTATACTC

                                *                  *     
       3035 CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTCTACTC
          1 CTCCATCTCTAGGTAATTCAGCAAAATAAAGCTAATATTATACTC

                                *                   
       3080 CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTA
          1 CTCCATCTCTAGGTAATTCAGCAAAATAAAGCTAATATTA

       3120 ATTGTTGCTT


Statistics
Matches: 127,  Mismatches: 3, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  45  127  1.00

ACGTcount: A:0.38, C:0.22, G:0.08, T:0.32


Consensus pattern (45 bp):   
CTCCATCTCTAGGTAATTCAGCAAAATAAAGCTAATATTATACTC

Found at i:4816 original size:45 final size:45

Alignment explanation


    Indices: 4752--4880  Score: 233
    Period size: 45  Copynumber: 2.9  Consensus size: 45

       4742 ATCAACAATT

                                                         
       4752 AATATTAGCTTTATTTTGATGAATTATCCAAAGATGGAGGAGTAG
          1 AATATTAGCTTTATTTTGATGAATTATCCAAAGATGGAGGAGTAG

                                                         
       4797 AATATTAGCTTTATTTTGATGAATTATCCAAAGATGGAGGAGTAG
          1 AATATTAGCTTTATTTTGATGAATTATCCAAAGATGGAGGAGTAG

                                           *        
       4842 AATATTAGCTTTATTTTGATGAATTA-CCTAGAGATGGAG
          1 AATATTAGCTTTATTTTGATGAATTATCC-AAAGATGGAG

       4881 TAGAATTTAG


Statistics
Matches: 82,  Mismatches: 1, Indels: 2
        0.96            0.01        0.02

Matches are distributed among these distances:
  44    2  0.02
  45   80  0.98

ACGTcount: A:0.35, C:0.07, G:0.22, T:0.36


Consensus pattern (45 bp):   
AATATTAGCTTTATTTTGATGAATTATCCAAAGATGGAGGAGTAG

Found at i:6116 original size:22 final size:22

Alignment explanation


    Indices: 6088--6131  Score: 70
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       6078 TTCTTTCCGC

                       *          
       6088 AACAACTTCTGTCCCGAAGTTG
          1 AACAACTTCTGGCCCGAAGTTG

                        *         
       6110 AACAACTTCTGGGCCGAAGTTG
          1 AACAACTTCTGGCCCGAAGTTG

       6132 TCCTGCGCAA


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  22   20  1.00

ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25


Consensus pattern (22 bp):   
AACAACTTCTGGCCCGAAGTTG

Found at i:6141 original size:52 final size:52

Alignment explanation


    Indices: 6085--6185  Score: 177
    Period size: 52  Copynumber: 1.9  Consensus size: 52

       6075 TTTTTCTTTC

                                          *                      
       6085 CGCAACAACTTCTGTCCCGAAGTTGAACAACT-TCTGGGCCGAAGTTGTCCTG
          1 CGCAACAACTTCTGTCCCGAAGTTGAACAAGTCT-TGGGCCGAAGTTGTCCTG

                                                             
       6137 CGCAACAACTTCTGTCCCGAAGTTGAACAAGTCTTGGGCCGAAGTTGTC
          1 CGCAACAACTTCTGTCCCGAAGTTGAACAAGTCTTGGGCCGAAGTTGTC

       6186 ATGTAATTCT


Statistics
Matches: 47,  Mismatches: 1, Indels: 2
        0.94            0.02        0.04

Matches are distributed among these distances:
  52   46  0.98
  53    1  0.02

ACGTcount: A:0.24, C:0.28, G:0.24, T:0.25


Consensus pattern (52 bp):   
CGCAACAACTTCTGTCCCGAAGTTGAACAAGTCTTGGGCCGAAGTTGTCCTG

Found at i:6392 original size:16 final size:16

Alignment explanation


    Indices: 6371--6402  Score: 64
    Period size: 16  Copynumber: 2.0  Consensus size: 16

       6361 ATGAGTTCGA

                            
       6371 ACAAGGCCCATTAATG
          1 ACAAGGCCCATTAATG

                            
       6387 ACAAGGCCCATTAATG
          1 ACAAGGCCCATTAATG

       6403 CATCCTTGAA


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

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.38, C:0.25, G:0.19, T:0.19


Consensus pattern (16 bp):   
ACAAGGCCCATTAATG

Found at i:6456 original size:21 final size:21

Alignment explanation


    Indices: 6432--6475  Score: 61
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       6422 TCTTGCTCTT

                *      *         
       6432 TTCATTGGACCTAATGGCATC
          1 TTCAATGGACCAAATGGCATC

                     *           
       6453 TTCAATGGATCAAATGGCATC
          1 TTCAATGGACCAAATGGCATC

              
       6474 TT
          1 TT

       6476 TGGCATCTCC


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.27, C:0.20, G:0.18, T:0.34


Consensus pattern (21 bp):   
TTCAATGGACCAAATGGCATC
Done.