Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014167.1 Corchorus olitorius cultivar O-4 contig14200, 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: 8551
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34


Found at i:3211 original size:19 final size:19

Alignment explanation


    Indices: 3187--3243  Score: 84
    Period size: 19  Copynumber: 3.2  Consensus size: 19

       3177 TTCCATTCAA

                               
       3187 TTTGATCTTGACATCTTTG
          1 TTTGATCTTGACATCTTTG

                            *  
       3206 TTTGATCTTGACATCTATG
          1 TTTGATCTTGACATCTTTG

                               
       3225 -TT--TCTTGACATCTTTG
          1 TTTGATCTTGACATCTTTG

               
       3241 TTT
          1 TTT

       3244 CTTCCTTTCA


Statistics
Matches: 35,  Mismatches: 2, Indels: 4
        0.85            0.05        0.10

Matches are distributed among these distances:
  16   13  0.37
  17    2  0.06
  18    2  0.06
  19   18  0.51

ACGTcount: A:0.16, C:0.16, G:0.14, T:0.54


Consensus pattern (19 bp):   
TTTGATCTTGACATCTTTG

Found at i:3232 original size:16 final size:16

Alignment explanation


    Indices: 3159--3246  Score: 81
    Period size: 16  Copynumber: 5.2  Consensus size: 16

       3149 ATTAATTTGA

                            
       3159 TCTTGACATCTTTGTT
          1 TCTTGACATCTTTGTT

                 *            *
       3175 TCTT-CCATTCAATTTG-A
          1 TCTTGACA-TC--TTTGTT

                             
       3192 TCTTGACATCTTTGTTT
          1 TCTTGACATCTTTG-TT

                         *    
       3209 GATCTTGACATCTATGTT
          1 --TCTTGACATCTTTGTT

                            
       3227 TCTTGACATCTTTGTT
          1 TCTTGACATCTTTGTT

                
       3243 TCTT
          1 TCTT

       3247 CCTTTCAATC


Statistics
Matches: 58,  Mismatches: 6, Indels: 16
        0.73            0.08        0.20

Matches are distributed among these distances:
  15    6  0.10
  16   25  0.43
  17    6  0.10
  18    8  0.14
  19   13  0.22

ACGTcount: A:0.16, C:0.19, G:0.11, T:0.53


Consensus pattern (16 bp):   
TCTTGACATCTTTGTT

Found at i:3840 original size:27 final size:27

Alignment explanation


    Indices: 3802--3903  Score: 186
    Period size: 27  Copynumber: 3.8  Consensus size: 27

       3792 GACTGTTGCC

                                       
       3802 GCAGTGGATCCTCCCACTTCGACCCCA
          1 GCAGTGGATCCTCCCACTTCGACCCCA

                                       
       3829 GCAGTGGATCCTCCCACTTCGACCCCA
          1 GCAGTGGATCCTCCCACTTCGACCCCA

                         *           * 
       3856 GCAGTGGATCCTCACACTTCGACCCTA
          1 GCAGTGGATCCTCCCACTTCGACCCCA

                                 
       3883 GCAGTGGATCCTCCCACTTCG
          1 GCAGTGGATCCTCCCACTTCG

       3904 CCTCGGGTCG


Statistics
Matches: 72,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  27   72  1.00

ACGTcount: A:0.19, C:0.41, G:0.20, T:0.21


Consensus pattern (27 bp):   
GCAGTGGATCCTCCCACTTCGACCCCA

Found at i:6324 original size:32 final size:32

Alignment explanation


    Indices: 6288--6465  Score: 266
    Period size: 32  Copynumber: 5.5  Consensus size: 32

       6278 GTGTGGAAAG

                                   *        
       6288 AAAACGCCCTTATTTAGCGGCGTTTAAAGAAC
          1 AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC

                                            
       6320 AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC
          1 AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC

                            *         *     
       6352 AAAACGCCCTTATTTAACGGCGTCTAGAGAAC
          1 AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC

                                      * *   
       6384 AAAACGCCCTTATTTAGCGGCGTCTAGACAAC
          1 AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC

                              *      **     
       6416 AAAACGCCCTTATTTAGCAGCGTCTTTAGAAC
          1 AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC

                              
       6448 AAAACGCCGCTATATTTA
          1 AAAACGCC-CT-TATTTA

       6466 ACTGCTTTTA


Statistics
Matches: 135,  Mismatches: 9, Indels: 2
        0.92            0.06        0.01

Matches are distributed among these distances:
  32  127  0.94
  33    2  0.01
  34    6  0.04

ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24


Consensus pattern (32 bp):   
AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC

Found at i:7323 original size:21 final size:21

Alignment explanation


    Indices: 7297--7430  Score: 225
    Period size: 21  Copynumber: 6.4  Consensus size: 21

       7287 TGCTAGTAGT

                                  
       7297 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                                 
       7318 TCATTGGAGAAGGTTCCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                   *             
       7339 TCATTGGGGAAGGTTCCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                       *         
       7360 TCATTGGAGAAAGTTCCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                                 
       7381 TCATTGGAGAAGGTTCCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                           *     
       7402 TCATTGGAGAAGGTTTCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                    
       7423 TCATTGGA
          1 TCATTGGA

       7431 ATTGCCTAAG


Statistics
Matches: 107,  Mismatches: 5, Indels: 2
        0.94            0.04        0.02

Matches are distributed among these distances:
  20    2  0.02
  21  105  0.98

ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25


Consensus pattern (21 bp):   
TCATTGGAGAAGGTTCCAAGC

Done.