Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023680.1 Corchorus olitorius cultivar O-4 contig23713, 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: 33693
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31


Found at i:11845 original size:27 final size:28

Alignment explanation


    Indices: 11814--11889  Score: 91
    Period size: 27  Copynumber: 2.7  Consensus size: 28

      11804 AGGTAAACCT

                                 *      
      11814 AAAATGACCAAAATGCCCCTGGA-CGTG
          1 AAAATGACCAAAATGCCCCTGAATCGTG

            *       *                 *  
      11841 CAAATGACTAAAATGCCCCTGAATTCTTG
          1 AAAATGACCAAAATGCCCCTGAA-TCGTG

                       *        
      11870 AAAATGACCAAGATGCCCCT
          1 AAAATGACCAAAATGCCCCT

      11890 AGGTGATCCT


Statistics
Matches: 40,  Mismatches: 7, Indels: 2
        0.82            0.14        0.04

Matches are distributed among these distances:
  27   20  0.50
  29   20  0.50

ACGTcount: A:0.37, C:0.26, G:0.17, T:0.20


Consensus pattern (28 bp):   
AAAATGACCAAAATGCCCCTGAATCGTG

Found at i:18391 original size:35 final size:35

Alignment explanation


    Indices: 18352--18449  Score: 126
    Period size: 35  Copynumber: 2.8  Consensus size: 35

      18342 TTCAAGGGAC

                    * *                         
      18352 CAGATGACCCGGTGTAGCATCTTCAAAGTT-GAATT
          1 CAGATGACTCAGTGTAGCATCTTCAAAGTTGGAA-T

                               *    *          
      18387 CAGATGACTCAGTGTAGCACCTTCGAAGTTGGAAT
          1 CAGATGACTCAGTGTAGCATCTTCAAAGTTGGAAT

                          *        *    
      18422 CAGATGACTCAGTGAAGCATCTTTAAAG
          1 CAGATGACTCAGTGTAGCATCTTCAAAG

      18450 GATGATTCAG


Statistics
Matches: 54,  Mismatches: 8, Indels: 2
        0.84            0.12        0.03

Matches are distributed among these distances:
  35   51  0.94
  36    3  0.06

ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27


Consensus pattern (35 bp):   
CAGATGACTCAGTGTAGCATCTTCAAAGTTGGAAT

Found at i:18609 original size:90 final size:90

Alignment explanation


    Indices: 18452--18744  Score: 460
    Period size: 90  Copynumber: 3.3  Consensus size: 90

      18442 CTTTAAAGGA

                  *                                                          
      18452 TGATTCAGTGAATCAAGTTAATGCGGTGCATTACTTTTTCAAGATTAGACTCGGTGAGCTCGGTG
          1 TGATTCGGTGAATCAAGTTAATGCGGTGCATTACTTTTTCAAGATTAGACTCGGTGAGCTCGGTG

                                     
      18517 CAGCAAATCTTCAAATAGATCAGGG
         66 CAGCAAATCTTCAAATAGATCAGGG

                                     *                                    *  
      18542 TGATTCGGTGAATCAAGTTAATGCGATGCATTACTTTTTCAAGATTAGACTCGGTGAGCTCGATG
          1 TGATTCGGTGAATCAAGTTAATGCGGTGCATTACTTTTTCAAGATTAGACTCGGTGAGCTCGGTG

                                     
      18607 CAGCAAATCTTCAAATAGATCAGGG
         66 CAGCAAATCTTCAAATAGATCAGGG

                      *   *                                                  
      18632 TGA-TCTGGTTAATTAAGTTAATGCGGTGCATTACTTTTTCAAGA-T----T--G-GAGCTCGGT
          1 TGATTC-GGTGAATCAAGTTAATGCGGTGCATTACTTTTTCAAGATTAGACTCGGTGAGCTCGGT

                                      
      18688 GCAGCAAATCTTCAAATAGATCAGGG
         65 GCAGCAAATCTTCAAATAGATCAGGG

                               *           
      18714 TGATTCGGTGAATCAAGTTGATGCGGTGCAT
          1 TGATTCGGTGAATCAAGTTAATGCGGTGCAT

      18745 CTCTTCAAAG


Statistics
Matches: 191,  Mismatches: 10, Indels: 12
        0.90            0.05        0.06

Matches are distributed among these distances:
  82   59  0.31
  83    3  0.02
  85    1  0.01
  89    3  0.02
  90  125  0.65

ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31


Consensus pattern (90 bp):   
TGATTCGGTGAATCAAGTTAATGCGGTGCATTACTTTTTCAAGATTAGACTCGGTGAGCTCGGTG
CAGCAAATCTTCAAATAGATCAGGG

Found at i:19093 original size:27 final size:27

Alignment explanation


    Indices: 19062--19135  Score: 87
    Period size: 27  Copynumber: 2.7  Consensus size: 27

      19052 TAGGGTCATC

                                       
      19062 CAGGGGCATTTTAGTCATTTACAC-GT
          1 CAGGGGCATTTTAGTCATTTACACAGT

                         *       *    * 
      19088 CAAGGGGCATTTTCGTCATTTGCACATT
          1 C-AGGGGCATTTTAGTCATTTACACAGT

                    *   *       
      19116 CAGGGGCAGTTTGGTCATTT
          1 CAGGGGCATTTTAGTCATTT

      19136 TAAGTTCACT


Statistics
Matches: 41,  Mismatches: 5, Indels: 3
        0.84            0.10        0.06

Matches are distributed among these distances:
  26    1  0.02
  27   38  0.93
  28    2  0.05

ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35


Consensus pattern (27 bp):   
CAGGGGCATTTTAGTCATTTACACAGT

Found at i:22014 original size:14 final size:16

Alignment explanation


    Indices: 21984--22017  Score: 54
    Period size: 14  Copynumber: 2.2  Consensus size: 16

      21974 AATTTTCAGA

                            
      21984 AGTTGGAAATGGGTGC
          1 AGTTGGAAATGGGTGC

                            
      22000 AGTTGG-AAT-GGTGC
          1 AGTTGGAAATGGGTGC

                
      22014 AGTT
          1 AGTT

      22018 CAACAGTTAC


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  14    9  0.50
  15    3  0.17
  16    6  0.33

ACGTcount: A:0.24, C:0.06, G:0.41, T:0.29


Consensus pattern (16 bp):   
AGTTGGAAATGGGTGC
Done.