Multiple sequence alignment - TraesCS1B01G036000

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1B01G036000 chr1B 100.000 2601 0 0 1 2601 17249927 17252527 0.000000e+00 4804.0
1 TraesCS1B01G036000 chr1B 96.733 2357 69 5 246 2601 22279360 22277011 0.000000e+00 3919.0
2 TraesCS1B01G036000 chr1B 97.485 1988 38 7 622 2601 7556987 7555004 0.000000e+00 3384.0
3 TraesCS1B01G036000 chr1B 92.498 1333 77 3 1 1332 22163414 22162104 0.000000e+00 1886.0
4 TraesCS1B01G036000 chr1B 92.188 704 43 7 1353 2046 22162123 22161422 0.000000e+00 985.0
5 TraesCS1B01G036000 chr1B 84.146 574 70 11 2044 2599 6000928 6001498 1.060000e-148 536.0
6 TraesCS1B01G036000 chr1B 93.072 332 20 2 68 399 7557796 7557468 1.400000e-132 483.0
7 TraesCS1B01G036000 chr1B 96.016 251 10 0 1 251 22288581 22288331 2.410000e-110 409.0
8 TraesCS1B01G036000 chr1B 93.878 49 3 0 3 51 154143826 154143778 9.980000e-10 75.0
9 TraesCS1B01G036000 chr1D 86.189 572 50 11 2046 2599 4000694 4000134 2.230000e-165 592.0
10 TraesCS1B01G036000 chr1D 78.378 592 60 35 2044 2599 4989522 4988963 3.230000e-84 322.0
11 TraesCS1B01G036000 chr1D 77.852 596 60 41 2044 2599 3444242 3444805 1.170000e-78 303.0
12 TraesCS1B01G036000 chr7B 94.000 50 3 0 2 51 696913192 696913143 2.780000e-10 76.8
13 TraesCS1B01G036000 chr3A 94.118 51 2 1 1 51 365958285 365958334 2.780000e-10 76.8
14 TraesCS1B01G036000 chr1A 94.000 50 3 0 2 51 9207788 9207837 2.780000e-10 76.8
15 TraesCS1B01G036000 chr5D 93.878 49 3 0 3 51 254537228 254537276 9.980000e-10 75.0
16 TraesCS1B01G036000 chr5D 93.878 49 3 0 3 51 551023560 551023608 9.980000e-10 75.0
17 TraesCS1B01G036000 chr2A 93.878 49 3 0 3 51 195108695 195108647 9.980000e-10 75.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G036000 chr1B 17249927 17252527 2600 False 4804.0 4804 100.0000 1 2601 1 chr1B.!!$F2 2600
1 TraesCS1B01G036000 chr1B 22277011 22279360 2349 True 3919.0 3919 96.7330 246 2601 1 chr1B.!!$R1 2355
2 TraesCS1B01G036000 chr1B 7555004 7557796 2792 True 1933.5 3384 95.2785 68 2601 2 chr1B.!!$R4 2533
3 TraesCS1B01G036000 chr1B 22161422 22163414 1992 True 1435.5 1886 92.3430 1 2046 2 chr1B.!!$R5 2045
4 TraesCS1B01G036000 chr1B 6000928 6001498 570 False 536.0 536 84.1460 2044 2599 1 chr1B.!!$F1 555
5 TraesCS1B01G036000 chr1D 4000134 4000694 560 True 592.0 592 86.1890 2046 2599 1 chr1D.!!$R1 553
6 TraesCS1B01G036000 chr1D 4988963 4989522 559 True 322.0 322 78.3780 2044 2599 1 chr1D.!!$R2 555
7 TraesCS1B01G036000 chr1D 3444242 3444805 563 False 303.0 303 77.8520 2044 2599 1 chr1D.!!$F1 555

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
505 506 0.882474 GTCTCAGGCTGTGTACGACT 59.118 55.0 15.27 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2054 2368 2.5205 AATGCGGGTTGTGTGCCA 60.521 55.556 0.0 0.0 0.0 4.92 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
200 201 3.685550 GCTGATGGCAAGGTATTGGTAGT 60.686 47.826 0.00 0.00 41.35 2.73
227 228 4.201705 CCATGCAACGAATAAAACCAATGC 60.202 41.667 0.00 0.00 0.00 3.56
243 244 0.897621 ATGCCATGACTCACGAGACA 59.102 50.000 0.00 0.99 37.49 3.41
505 506 0.882474 GTCTCAGGCTGTGTACGACT 59.118 55.000 15.27 0.00 0.00 4.18
590 615 1.286880 GCTGCGCATGTGGTTCTTT 59.713 52.632 12.24 0.00 0.00 2.52
660 958 4.333913 TGCAAAAGAAGCCTAATTGCAA 57.666 36.364 0.00 0.00 44.82 4.08
705 1003 1.135373 CAGTTAGTCACCGACAGCGAT 60.135 52.381 0.00 0.00 40.82 4.58
727 1025 7.045804 GCGATAGTAATTAAACGCTGTTGTTTC 60.046 37.037 14.76 0.00 42.19 2.78
738 1036 6.289745 ACGCTGTTGTTTCGAGTAATTAAA 57.710 33.333 0.00 0.00 0.00 1.52
845 1143 2.675603 GCCACATGATGCATTTGCTGAA 60.676 45.455 0.00 0.00 42.66 3.02
890 1189 1.197721 GCACACACATAGCCAAGACAC 59.802 52.381 0.00 0.00 0.00 3.67
936 1235 2.543777 TCCTTTTGTTCCTCTCCACG 57.456 50.000 0.00 0.00 0.00 4.94
983 1282 3.209410 CACCTAGCTATTTCTTGCCCTG 58.791 50.000 0.00 0.00 0.00 4.45
1028 1327 3.750371 CTGTTATCTTGTCCAACACCCA 58.250 45.455 0.00 0.00 0.00 4.51
1252 1551 3.589988 GGCAACTCCATATCTACCATCG 58.410 50.000 0.00 0.00 34.01 3.84
1260 1559 6.719829 ACTCCATATCTACCATCGTGATAACA 59.280 38.462 0.00 0.00 0.00 2.41
1323 1622 9.616156 TGGCTTCGTTAATTAGGATATTTAACA 57.384 29.630 11.70 0.00 42.80 2.41
2054 2368 4.989875 ACATATGATTTCAGGCCTAGCT 57.010 40.909 3.98 0.00 0.00 3.32
2381 2743 3.831323 TCTTTGTTTCCATGAAGCCTCA 58.169 40.909 0.00 0.00 35.56 3.86
2434 2797 2.422939 TGGAGGCTAGGAATATGGCT 57.577 50.000 0.00 0.00 39.33 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 3.245518 GCCACGGGCTTTTGAAATAAT 57.754 42.857 7.58 0.00 46.69 1.28
39 40 7.255139 GCTAAAATAAATGATTAGAGTGCCCGT 60.255 37.037 0.00 0.00 0.00 5.28
40 41 7.041098 AGCTAAAATAAATGATTAGAGTGCCCG 60.041 37.037 0.00 0.00 0.00 6.13
200 201 4.519350 TGGTTTTATTCGTTGCATGGTGTA 59.481 37.500 0.00 0.00 0.00 2.90
206 207 3.932089 GGCATTGGTTTTATTCGTTGCAT 59.068 39.130 0.00 0.00 0.00 3.96
212 213 4.997565 AGTCATGGCATTGGTTTTATTCG 58.002 39.130 0.00 0.00 0.00 3.34
214 215 5.622007 CGTGAGTCATGGCATTGGTTTTATT 60.622 40.000 0.00 0.00 0.00 1.40
227 228 3.303881 TTTCTGTCTCGTGAGTCATGG 57.696 47.619 12.42 3.80 0.00 3.66
505 506 6.594937 GTGTTTGGGTTCTCCGTTATACAATA 59.405 38.462 0.00 0.00 38.76 1.90
590 615 1.947597 GCCGCCATTGGAATGCTCAA 61.948 55.000 6.95 0.00 35.08 3.02
660 958 1.401018 GCTGCGTAAAAACCTGCGATT 60.401 47.619 0.00 0.00 0.00 3.34
705 1003 7.169645 ACTCGAAACAACAGCGTTTAATTACTA 59.830 33.333 0.00 0.00 39.17 1.82
890 1189 8.877808 TCACATGTCTATTTATAGAGTGCTTG 57.122 34.615 0.00 6.53 39.87 4.01
936 1235 2.353109 GGATGTCTCTTGCTTTTTGGCC 60.353 50.000 0.00 0.00 0.00 5.36
983 1282 1.436600 CATGAGTGTGTGCAGAGGAC 58.563 55.000 0.00 0.00 0.00 3.85
1028 1327 4.228666 TGTTATAACTGGTGGGCATAACCT 59.771 41.667 16.33 0.00 38.60 3.50
1252 1551 4.752101 CCTTGGATCCTCGAATGTTATCAC 59.248 45.833 14.23 0.00 0.00 3.06
1260 1559 4.164221 ACATTGTACCTTGGATCCTCGAAT 59.836 41.667 14.23 0.00 0.00 3.34
2054 2368 2.520500 AATGCGGGTTGTGTGCCA 60.521 55.556 0.00 0.00 0.00 4.92
2407 2770 3.492102 TTCCTAGCCTCCATAATGTGC 57.508 47.619 0.00 0.00 0.00 4.57


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.