Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018616.1 Corchorus olitorius cultivar O-4 contig18649, 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: 11941
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31


Found at i:354 original size:23 final size:21

Alignment explanation


    Indices: 329--401  Score: 52
    Period size: 18  Copynumber: 3.8  Consensus size: 21

        319 TCAATTCTCT

                   * *           
        329 TTTGATTGTGATTTGATTTGA
          1 TTTGATTTTTATTTGATTTGA

                    *            
        350 TTT--TTTAT-TTTGATTTGA
          1 TTTGATTTTTATTTGATTTGA

            *                     
        368 GTT--TTTTTA-TTGACTTTGA
          1 TTTGATTTTTATTTGA-TTTGA

                            
        387 TTTGATTTTT-TTTGA
          1 TTTGATTTTTATTTGA

        402 ATTTTTTTTG


Statistics
Matches: 41,  Mismatches: 6, Indels: 10
        0.72            0.11        0.18

Matches are distributed among these distances:
  18   20  0.49
  19    9  0.22
  21   12  0.29

ACGTcount: A:0.16, C:0.01, G:0.16, T:0.66


Consensus pattern (21 bp):   
TTTGATTTTTATTTGATTTGA

Found at i:363 original size:18 final size:17

Alignment explanation


    Indices: 340--410  Score: 65
    Period size: 18  Copynumber: 4.1  Consensus size: 17

        330 TTGATTGTGA

                              
        340 TTTGATTTGATTTTTTAT
          1 TTTGATTTGATTTTTT-T

                              
        358 TTTGATTTGAGTTTTTTT
          1 TTTGATTTGA-TTTTTTT

            *             **  
        376 ATTGACTTTGATTTGATT
          1 TTTGA-TTTGATTTTTTT

                              
        394 TTT--TTTGAATTTTTTT
          1 TTTGATTTG-ATTTTTTT

             
        410 T
          1 T

        411 GAATTTCTTG


Statistics
Matches: 44,  Mismatches: 6, Indels: 8
        0.76            0.10        0.14

Matches are distributed among these distances:
  15    4  0.09
  16    7  0.16
  18   22  0.50
  19   11  0.25

ACGTcount: A:0.15, C:0.01, G:0.13, T:0.70


Consensus pattern (17 bp):   
TTTGATTTGATTTTTTT

Found at i:405 original size:11 final size:11

Alignment explanation


    Indices: 387--416  Score: 53
    Period size: 11  Copynumber: 2.8  Consensus size: 11

        377 TTGACTTTGA

                       
        387 TTTG-ATTTTT
          1 TTTGAATTTTT

                       
        397 TTTGAATTTTT
          1 TTTGAATTTTT

                     
        408 TTTGAATTT
          1 TTTGAATTT

        417 CTTGATGGAG


Statistics
Matches: 19,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  10    4  0.21
  11   15  0.79

ACGTcount: A:0.17, C:0.00, G:0.10, T:0.73


Consensus pattern (11 bp):   
TTTGAATTTTT

Found at i:3880 original size:21 final size:21

Alignment explanation


    Indices: 3856--3896  Score: 55
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       3846 ACCGTCGTTA

                         *       
       3856 ATTAGTGTTTCTCTATCGCAG
          1 ATTAGTGTTTCTCCATCGCAG

                  *   *         
       3877 ATTAGTTTTTGTCCATCGCA
          1 ATTAGTGTTTCTCCATCGCA

       3897 AATGCGTATA


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.20, C:0.20, G:0.17, T:0.44


Consensus pattern (21 bp):   
ATTAGTGTTTCTCCATCGCAG

Found at i:4326 original size:69 final size:69

Alignment explanation


    Indices: 4215--4354  Score: 228
    Period size: 69  Copynumber: 2.0  Consensus size: 69

       4205 TTTCAAAGTA

                           *                              *                  
       4215 AATTTCAAATAAAATGTAAACAATATGCTGCAATAATGTAATAATAGGTAAGCACAATGCTCAGG
          1 AATTTCAAATAAAATCTAAACAATATGCTGCAATAATGTAATAATAAGTAAGCACAATGCTCAGG

                
       4280 ACAG
         66 ACAG

                                                        *                 *  
       4284 AATTTCAAATAAAATCTAATA-AATATGCTGCAATAATGTAATAGTAAGTAAGCACAATGCTTAG
          1 AATTTCAAATAAAATCTAA-ACAATATGCTGCAATAATGTAATAATAAGTAAGCACAATGCTCAG

                 
       4348 GACAG
         65 GACAG

              
       4353 AA
          1 AA

       4355 AACTTTAGAT


Statistics
Matches: 66,  Mismatches: 4, Indels: 2
        0.92            0.06        0.03

Matches are distributed among these distances:
  69   65  0.98
  70    1  0.02

ACGTcount: A:0.47, C:0.12, G:0.15, T:0.26


Consensus pattern (69 bp):   
AATTTCAAATAAAATCTAAACAATATGCTGCAATAATGTAATAATAAGTAAGCACAATGCTCAGG
ACAG
Done.