Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024657.1 Corchorus olitorius cultivar O-4 contig24690, 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: 7262
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30


Found at i:537 original size:15 final size:15

Alignment explanation


    Indices: 517--545  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

        507 AAACTAAGTG

                           
        517 GAGCTTGTTGATTTT
          1 GAGCTTGTTGATTTT

                          
        532 GAGCTTGTTGATTT
          1 GAGCTTGTTGATTT

        546 CGAACCTCCA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.14, C:0.07, G:0.28, T:0.52


Consensus pattern (15 bp):   
GAGCTTGTTGATTTT

Found at i:2284 original size:21 final size:21

Alignment explanation


    Indices: 2258--2334  Score: 154
    Period size: 21  Copynumber: 3.7  Consensus size: 21

       2248 TCCTTTGGTG

                                 
       2258 ATGATCTCCAATGGGCTTCAA
          1 ATGATCTCCAATGGGCTTCAA

                                 
       2279 ATGATCTCCAATGGGCTTCAA
          1 ATGATCTCCAATGGGCTTCAA

                                 
       2300 ATGATCTCCAATGGGCTTCAA
          1 ATGATCTCCAATGGGCTTCAA

                          
       2321 ATGATCTCCAATGG
          1 ATGATCTCCAATGG

       2335 CCTTGAACTC


Statistics
Matches: 56,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   56  1.00

ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29


Consensus pattern (21 bp):   
ATGATCTCCAATGGGCTTCAA

Found at i:2490 original size:21 final size:21

Alignment explanation


    Indices: 2457--2527  Score: 90
    Period size: 21  Copynumber: 3.4  Consensus size: 21

       2447 CTTAGGCAAT

                    *            
       2457 TCCAATGAACTTGAAACCTTC
          1 TCCAATGAGCTTGAAACCTTC

              *          *       
       2478 TCTAATGAGCTTGGAACCTTC
          1 TCCAATGAGCTTGAAACCTTC

                         *        
       2499 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGAAACCTT-C

                    
       2520 TCCAATGA
          1 TCCAATGA

       2528 TCTCCTAGCA


Statistics
Matches: 45,  Mismatches: 4, Indels: 2
        0.88            0.08        0.04

Matches are distributed among these distances:
  20    3  0.07
  21   42  0.93

ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30


Consensus pattern (21 bp):   
TCCAATGAGCTTGAAACCTTC

Found at i:3529 original size:19 final size:19

Alignment explanation


    Indices: 3505--3542  Score: 76
    Period size: 19  Copynumber: 2.0  Consensus size: 19

       3495 TCACTCACAT

                               
       3505 GAGCAATCGCCTTTGGCGC
          1 GAGCAATCGCCTTTGGCGC

                               
       3524 GAGCAATCGCCTTTGGCGC
          1 GAGCAATCGCCTTTGGCGC

       3543 CTATGAGGGG


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   19  1.00

ACGTcount: A:0.16, C:0.32, G:0.32, T:0.21


Consensus pattern (19 bp):   
GAGCAATCGCCTTTGGCGC

Found at i:7176 original size:2 final size:2

Alignment explanation


    Indices: 7169--7203  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       7159 ACCATTTGCA

                                                                
       7169 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       7204 GAGAGAGAGA


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:7208 original size:2 final size:2

Alignment explanation


    Indices: 7203--7257  Score: 110
    Period size: 2  Copynumber: 27.5  Consensus size: 2

       7193 ATATATATAT

                                                                          
       7203 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG

                               
       7245 AG AG AG AG AG AG A
          1 AG AG AG AG AG AG A

       7258 TGATA


Statistics
Matches: 53,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   53  1.00

ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00


Consensus pattern (2 bp):   
AG

Done.