Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022670.1 Corchorus olitorius cultivar O-4 contig22703, 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: 12667
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33


Found at i:3805 original size:29 final size:29

Alignment explanation


    Indices: 3771--3938  Score: 230
    Period size: 29  Copynumber: 5.8  Consensus size: 29

       3761 AGTGCATTTG

                   *           *         
       3771 AAATGACTAAAATACCCCTAGATGTGCAA
          1 AAATGACCAAAATACCCCTGGATGTGCAA

                         *               
       3800 AAATGACCAAAATGCCCCTGGATGTGC-A
          1 AAATGACCAAAATACCCCTGGATGTGCAA

                                         
       3828 AAATGACCAAAATACCCCTGGATGTGCAA
          1 AAATGACCAAAATACCCCTGGATGTGCAA

                         *  *  **     *  
       3857 AAATGACCAAAATGCCACTATATGTGAAA
          1 AAATGACCAAAATACCCCTGGATGTGCAA

                            *            
       3886 AAATGACCAAAATACCACTGGATGTGCAA
          1 AAATGACCAAAATACCCCTGGATGTGCAA

                         *  *       
       3915 AAATGACCAAAATGCCACTGGATG
          1 AAATGACCAAAATACCCCTGGATG

       3939 AGTGACCTAG


Statistics
Matches: 124,  Mismatches: 14, Indels: 2
        0.89            0.10        0.01

Matches are distributed among these distances:
  28   27  0.22
  29   97  0.78

ACGTcount: A:0.43, C:0.21, G:0.17, T:0.18


Consensus pattern (29 bp):   
AAATGACCAAAATACCCCTGGATGTGCAA

Found at i:3859 original size:57 final size:58

Alignment explanation


    Indices: 3771--3938  Score: 266
    Period size: 58  Copynumber: 2.9  Consensus size: 58

       3761 AGTGCATTTG

                   *           *                         *          * 
       3771 AAATGACTAAAATACCCCTAGATGTGCAAAAATGACCAAAATGCCCCTGGATGTG-CA
          1 AAATGACCAAAATACCCCTGGATGTGCAAAAATGACCAAAATGCCACTGGATGTGAAA

                                                            **        
       3828 AAATGACCAAAATACCCCTGGATGTGCAAAAATGACCAAAATGCCACTATATGTGAAA
          1 AAATGACCAAAATACCCCTGGATGTGCAAAAATGACCAAAATGCCACTGGATGTGAAA

                            *                                    
       3886 AAATGACCAAAATACCACTGGATGTGCAAAAATGACCAAAATGCCACTGGATG
          1 AAATGACCAAAATACCCCTGGATGTGCAAAAATGACCAAAATGCCACTGGATG

       3939 AGTGACCTAG


Statistics
Matches: 101,  Mismatches: 9, Indels: 1
        0.91            0.08        0.01

Matches are distributed among these distances:
  57   50  0.50
  58   51  0.50

ACGTcount: A:0.43, C:0.21, G:0.17, T:0.18


Consensus pattern (58 bp):   
AAATGACCAAAATACCCCTGGATGTGCAAAAATGACCAAAATGCCACTGGATGTGAAA

Found at i:4230 original size:35 final size:35

Alignment explanation


    Indices: 4189--4420  Score: 284
    Period size: 35  Copynumber: 6.3  Consensus size: 35

       4179 TGAGTTCATA

                          *            *       
       4189 TTGAAGATGCTACATCGAGTCATCTGACTTTGTCT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT

                                 *        ** * 
       4224 TTGAAGATGCTACACCGAGTCGTCTGAATTCATTT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT

                                    *  *       
       4259 TTGAAGATGCTACACCGAGTCATCCGAGTTTGTCT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT

                       *                       
       4294 TTGAAGATGCTGCACCGAGTCATCTGAATTTGTCT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT

                                                         
       4329 TTGAAGATGCTACACCGAGTCATCTGAATTTACTTTGAAGATTCT
          1 TTGAAGATGCTACACCGAGTCATCTG-A---A-TTT---G--TCT

                       *                       
       4374 TTGAAGATGCTGCACCGAGTCATCTGAATTTGTCT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT

                        
       4409 TTGAAGATGCTA
          1 TTGAAGATGCTA

       4421 ACCAGTATGA


Statistics
Matches: 169,  Mismatches: 18, Indels: 20
        0.82            0.09        0.10

Matches are distributed among these distances:
  35  129  0.76
  36    1  0.01
  37    1  0.01
  39    1  0.01
  40    6  0.04
  41    1  0.01
  43    1  0.01
  44    1  0.01
  45   28  0.17

ACGTcount: A:0.25, C:0.19, G:0.21, T:0.34


Consensus pattern (35 bp):   
TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT

Found at i:4326 original size:105 final size:109

Alignment explanation


    Indices: 4189--4420  Score: 319
    Period size: 105  Copynumber: 2.1  Consensus size: 109

       4179 TGAGTTCATA

                          *            *                            *        
       4189 TTGAAGATGCTACATCGAGTCATCTGACTTTGTCTTTGAAGATGCTACACCGAGTCGTCTGAA-T
          1 TTGAAGATGCTACACCGAGTCATCTGAATTTGTCTTTGAAGATGCTACACCGAGTCATCTGAATT

                                                *       
       4253 T-C-ATT-TTTGAAGATGCTACACCGAGTCATCCGAGTTTGTCT
         66 TACTATTCTTTGAAGATGCTACACCGAGTCATCCGAATTTGTCT

                       *                                                     
       4294 TTGAAGATGCTGCACCGAGTCATCTGAATTTGTCTTTGAAGATGCTACACCGAGTCATCTGAATT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTTGTCTTTGAAGATGCTACACCGAGTCATCTGAATT

                                      *            *          
       4359 TACTTTGAAGATTCTTTGAAGATGCTGCACCGAGTCATCTGAATTTGTCT
         66 TAC--T----ATTCTTTGAAGATGCTACACCGAGTCATCCGAATTTGTCT

                        
       4409 TTGAAGATGCTA
          1 TTGAAGATGCTA

       4421 ACCAGTATGA


Statistics
Matches: 109,  Mismatches: 8, Indels: 10
        0.86            0.06        0.08

Matches are distributed among these distances:
 105   59  0.54
 106    2  0.02
 107    1  0.01
 114    3  0.03
 115   44  0.40

ACGTcount: A:0.25, C:0.19, G:0.21, T:0.34


Consensus pattern (109 bp):   
TTGAAGATGCTACACCGAGTCATCTGAATTTGTCTTTGAAGATGCTACACCGAGTCATCTGAATT
TACTATTCTTTGAAGATGCTACACCGAGTCATCCGAATTTGTCT

Found at i:4390 original size:45 final size:46

Alignment explanation


    Indices: 4326--4416  Score: 157
    Period size: 45  Copynumber: 2.0  Consensus size: 46

       4316 TCTGAATTTG

                                                          
       4326 TCTTTGAAGATGCTACACCGAGTCATCTGAATTT-ACTTTGAAGAT
          1 TCTTTGAAGATGCTACACCGAGTCATCTGAATTTGACTTTGAAGAT

                          *                    *          
       4371 TCTTTGAAGATGCTGCACCGAGTCATCTGAATTTGTCTTTGAAGAT
          1 TCTTTGAAGATGCTACACCGAGTCATCTGAATTTGACTTTGAAGAT

       4417 GCTAACCAGT


Statistics
Matches: 43,  Mismatches: 2, Indels: 1
        0.93            0.04        0.02

Matches are distributed among these distances:
  45   33  0.77
  46   10  0.23

ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36


Consensus pattern (46 bp):   
TCTTTGAAGATGCTACACCGAGTCATCTGAATTTGACTTTGAAGAT
Done.