Multiple sequence alignment - TraesCS1B01G257600

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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 TraesCS1B01G257600 chr1B 100.000 2417 0 0 1 2417 453489564 453491980 0.000000e+00 4464
1 TraesCS1B01G257600 chr1B 94.598 2425 120 6 3 2417 480459252 480461675 0.000000e+00 3742
2 TraesCS1B01G257600 chr1B 77.824 2417 466 49 4 2386 379625347 379622967 0.000000e+00 1430
3 TraesCS1B01G257600 chr5B 92.772 2269 143 10 167 2417 239256319 239254054 0.000000e+00 3262
4 TraesCS1B01G257600 chr5B 80.906 1016 188 6 562 1574 356217474 356218486 0.000000e+00 797
5 TraesCS1B01G257600 chr5B 81.412 850 153 5 1570 2417 356227011 356227857 0.000000e+00 689
6 TraesCS1B01G257600 chr3B 88.559 2360 238 6 2 2345 495715410 495713067 0.000000e+00 2833
7 TraesCS1B01G257600 chr1A 87.722 2313 272 9 2 2303 527675938 527678249 0.000000e+00 2687
8 TraesCS1B01G257600 chr1A 76.432 611 123 13 4 598 11955077 11954472 6.490000e-81 311
9 TraesCS1B01G257600 chr6A 84.650 2417 344 11 4 2408 2158279 2160680 0.000000e+00 2383
10 TraesCS1B01G257600 chr6A 82.424 2162 344 25 275 2417 39434992 39432848 0.000000e+00 1855
11 TraesCS1B01G257600 chr6A 72.850 593 130 27 26 598 431919236 431918655 8.880000e-40 174
12 TraesCS1B01G257600 chr4B 80.837 2390 433 22 5 2383 339474512 339476887 0.000000e+00 1853
13 TraesCS1B01G257600 chr2D 91.892 333 23 3 2 330 296706900 296707232 1.690000e-126 462
14 TraesCS1B01G257600 chr7A 76.211 454 95 8 23 465 435829016 435829467 6.720000e-56 228
15 TraesCS1B01G257600 chr7A 74.172 453 98 13 23 465 78124978 78125421 1.150000e-38 171
16 TraesCS1B01G257600 chr4A 77.143 245 56 0 26 270 572222460 572222704 2.500000e-30 143


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 TraesCS1B01G257600 chr1B 453489564 453491980 2416 False 4464 4464 100.000 1 2417 1 chr1B.!!$F1 2416
1 TraesCS1B01G257600 chr1B 480459252 480461675 2423 False 3742 3742 94.598 3 2417 1 chr1B.!!$F2 2414
2 TraesCS1B01G257600 chr1B 379622967 379625347 2380 True 1430 1430 77.824 4 2386 1 chr1B.!!$R1 2382
3 TraesCS1B01G257600 chr5B 239254054 239256319 2265 True 3262 3262 92.772 167 2417 1 chr5B.!!$R1 2250
4 TraesCS1B01G257600 chr5B 356217474 356218486 1012 False 797 797 80.906 562 1574 1 chr5B.!!$F1 1012
5 TraesCS1B01G257600 chr5B 356227011 356227857 846 False 689 689 81.412 1570 2417 1 chr5B.!!$F2 847
6 TraesCS1B01G257600 chr3B 495713067 495715410 2343 True 2833 2833 88.559 2 2345 1 chr3B.!!$R1 2343
7 TraesCS1B01G257600 chr1A 527675938 527678249 2311 False 2687 2687 87.722 2 2303 1 chr1A.!!$F1 2301
8 TraesCS1B01G257600 chr1A 11954472 11955077 605 True 311 311 76.432 4 598 1 chr1A.!!$R1 594
9 TraesCS1B01G257600 chr6A 2158279 2160680 2401 False 2383 2383 84.650 4 2408 1 chr6A.!!$F1 2404
10 TraesCS1B01G257600 chr6A 39432848 39434992 2144 True 1855 1855 82.424 275 2417 1 chr6A.!!$R1 2142
11 TraesCS1B01G257600 chr4B 339474512 339476887 2375 False 1853 1853 80.837 5 2383 1 chr4B.!!$F1 2378

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
740 759 0.03601 CCTGTCGTTCTCAAGGCCAT 60.036 55.0 5.01 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1690 1725 0.537188 ATTCATCCCTCGCACGTTCT 59.463 50.0 0.0 0.0 0.0 3.01 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
66 67 3.574396 AGAAGATGTCGTTTCACCTCTGA 59.426 43.478 0.00 0.00 0.00 3.27
120 121 1.815421 GTGCATCATCGACCGCCTT 60.815 57.895 0.00 0.00 0.00 4.35
179 180 1.805428 GCATGTTGGGTGTGGGTGTC 61.805 60.000 0.00 0.00 0.00 3.67
740 759 0.036010 CCTGTCGTTCTCAAGGCCAT 60.036 55.000 5.01 0.00 0.00 4.40
880 899 1.568612 CGTGGAAGATGCGCAGTTGT 61.569 55.000 18.32 0.00 0.00 3.32
916 935 2.434884 CCATTGCGCTCGACCAGT 60.435 61.111 9.73 0.00 0.00 4.00
917 936 2.034879 CCATTGCGCTCGACCAGTT 61.035 57.895 9.73 0.00 0.00 3.16
1090 1115 3.170672 CCTCCCCCATCATCGCCA 61.171 66.667 0.00 0.00 0.00 5.69
1288 1316 0.461693 GGCAGAAGCTCTCATTCGCT 60.462 55.000 0.00 0.00 41.70 4.93
1374 1402 2.768492 GGCTCTTCGCATTGCAGGG 61.768 63.158 9.69 0.21 41.67 4.45
1375 1403 1.746615 GCTCTTCGCATTGCAGGGA 60.747 57.895 9.69 2.26 38.92 4.20
1471 1506 1.378762 GCAGGGTTTGGCACTAGGA 59.621 57.895 0.00 0.00 0.00 2.94
1575 1610 0.253044 GCTATTGGTGGTCTCTGGCA 59.747 55.000 0.00 0.00 0.00 4.92
1608 1643 6.349280 GCTATGTTGATGGTGTATGTGTGTTT 60.349 38.462 0.00 0.00 0.00 2.83
1672 1707 5.654603 TCGTTCCATATGAGTAACACACT 57.345 39.130 3.65 0.00 41.47 3.55
1690 1725 4.275689 CACACTTGGTGCAATTCTGAGTTA 59.724 41.667 0.00 0.00 41.36 2.24
1858 1894 4.643387 AGGTTGTGCGTCCTGCCC 62.643 66.667 0.00 0.00 45.60 5.36
2004 2040 0.386476 TGGCTCACGACAGTTTACGT 59.614 50.000 0.00 0.00 43.50 3.57
2032 2068 3.422303 GATGCACGCAAGGACGCA 61.422 61.111 0.00 0.00 43.49 5.24
2048 2084 3.515630 GACGCATTTCTGACTGAGATGA 58.484 45.455 14.63 0.00 38.98 2.92
2059 2095 0.389556 CTGAGATGACACGCACTGCT 60.390 55.000 0.00 0.00 0.00 4.24
2060 2096 0.887933 TGAGATGACACGCACTGCTA 59.112 50.000 0.00 0.00 0.00 3.49
2183 2219 0.745845 CAGGGCAGCTATTGACGCTT 60.746 55.000 0.00 0.00 34.72 4.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
877 896 1.400846 GATGGTCTCGTCGAGCTACAA 59.599 52.381 17.61 5.52 40.75 2.41
902 921 3.345808 GCAACTGGTCGAGCGCAA 61.346 61.111 11.47 0.00 0.00 4.85
916 935 1.737838 CTACCAGCGAATTGGAGCAA 58.262 50.000 7.88 0.00 40.87 3.91
917 936 0.744414 GCTACCAGCGAATTGGAGCA 60.744 55.000 7.88 0.00 40.87 4.26
967 986 1.219124 GATTGGTCTGAGCAGCGGA 59.781 57.895 9.70 0.00 0.00 5.54
1113 1138 3.052082 CTGCTCTTGGGTGGTGCG 61.052 66.667 0.00 0.00 0.00 5.34
1374 1402 3.432445 ATCAGGGCCTGCCATGCTC 62.432 63.158 29.02 0.00 46.33 4.26
1375 1403 3.426836 ATCAGGGCCTGCCATGCT 61.427 61.111 29.02 5.61 46.33 3.79
1471 1506 6.147821 CGATCATGAAACCTAACTCAAGTTGT 59.852 38.462 0.00 0.00 38.90 3.32
1575 1610 1.063717 CCATCAACATAGCAAGGGGGT 60.064 52.381 0.00 0.00 0.00 4.95
1672 1707 4.213270 CGTTCTAACTCAGAATTGCACCAA 59.787 41.667 0.00 0.00 45.00 3.67
1690 1725 0.537188 ATTCATCCCTCGCACGTTCT 59.463 50.000 0.00 0.00 0.00 3.01
1858 1894 1.672356 CCCTCTGGTTCCTGTTGCG 60.672 63.158 0.00 0.00 0.00 4.85
1867 1903 2.936032 GCCACTCCCCCTCTGGTT 60.936 66.667 0.00 0.00 0.00 3.67
1960 1996 2.352127 GGATGAGTTGCTTTGCAGAACC 60.352 50.000 0.00 0.00 40.61 3.62
2004 2040 0.811219 GCGTGCATCATCAGCAGGTA 60.811 55.000 9.20 0.00 46.36 3.08
2032 2068 3.257393 GCGTGTCATCTCAGTCAGAAAT 58.743 45.455 0.00 0.00 33.62 2.17
2059 2095 3.755628 GGCTCACCCGACAGCGTA 61.756 66.667 0.00 0.00 36.41 4.42
2183 2219 3.745975 CACTTAATCTCACGCAAACCTGA 59.254 43.478 0.00 0.00 0.00 3.86
2342 2378 2.434884 CACGAGCGGGCAGTGATT 60.435 61.111 11.99 0.00 38.06 2.57


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

AutoCloner maintained by Alex Coulton.