Multiple sequence alignment - TraesCS2A01G592200

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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 TraesCS2A01G592200 chr2A 100.000 2453 0 0 1 2453 779431891 779434343 0.000000e+00 4530
1 TraesCS2A01G592200 chr2A 96.909 1650 49 2 804 2453 779529454 779531101 0.000000e+00 2763
2 TraesCS2A01G592200 chr2A 89.968 1575 104 19 670 2242 779509807 779511329 0.000000e+00 1984
3 TraesCS2A01G592200 chr2A 91.193 1442 85 22 804 2242 779341454 779342856 0.000000e+00 1921
4 TraesCS2A01G592200 chr2A 90.840 1441 92 7 804 2242 779621614 779623016 0.000000e+00 1893
5 TraesCS2A01G592200 chr2A 95.406 849 16 6 1 849 779528609 779529434 0.000000e+00 1330
6 TraesCS2A01G592200 chr2A 90.756 476 38 2 1 476 779619816 779620285 4.450000e-177 630
7 TraesCS2A01G592200 chr2A 89.916 476 42 2 1 476 779507783 779508252 2.090000e-170 608
8 TraesCS2A01G592200 chr2A 89.706 476 43 3 1 476 779339768 779340237 9.700000e-169 603
9 TraesCS2A01G592200 chr2A 93.103 348 23 1 539 885 779509570 779509917 2.180000e-140 508
10 TraesCS2A01G592200 chr2A 93.567 342 21 1 545 885 779621271 779621612 2.180000e-140 508
11 TraesCS2A01G592200 chr2A 92.258 155 10 2 2298 2451 779626704 779626857 4.110000e-53 219
12 TraesCS2A01G592200 chr2A 83.871 155 23 1 2299 2453 779305497 779305649 1.970000e-31 147
13 TraesCS2A01G592200 chr2D 91.617 1670 122 8 539 2194 634155430 634153765 0.000000e+00 2292
14 TraesCS2A01G592200 chr2D 90.216 1063 76 15 670 1731 634149590 634148555 0.000000e+00 1362
15 TraesCS2A01G592200 chr2D 91.195 477 29 1 422 885 634149956 634149480 9.570000e-179 636
16 TraesCS2A01G592200 chr2D 89.474 475 44 2 1 475 634155908 634155440 1.620000e-166 595
17 TraesCS2A01G592200 chr2D 90.750 400 34 3 1 400 634152141 634151745 4.640000e-147 531
18 TraesCS2A01G592200 chr2D 89.701 301 29 2 1 299 492202538 492202238 1.380000e-102 383
19 TraesCS2A01G592200 chr2D 87.500 288 29 2 2013 2299 634148555 634148274 2.350000e-85 326
20 TraesCS2A01G592200 chr2D 95.425 153 7 0 2299 2451 634145461 634145309 6.780000e-61 244
21 TraesCS2A01G592200 chr2D 84.314 153 24 0 2299 2451 634158385 634158233 1.520000e-32 150
22 TraesCS2A01G592200 chr2B 89.682 1541 115 22 670 2194 777143991 777142479 0.000000e+00 1925
23 TraesCS2A01G592200 chr2B 88.000 325 28 6 539 852 777144238 777143914 8.280000e-100 374
24 TraesCS2A01G592200 chr2B 87.692 130 15 1 2299 2428 777145683 777145555 1.520000e-32 150
25 TraesCS2A01G592200 chr2B 92.771 83 5 1 670 752 777143887 777143806 4.280000e-23 119
26 TraesCS2A01G592200 chr2B 86.916 107 6 3 427 526 777144300 777144195 1.990000e-21 113
27 TraesCS2A01G592200 chr5B 89.667 300 29 2 1 298 340534978 340535277 4.950000e-102 381
28 TraesCS2A01G592200 chrUn 89.298 299 31 1 1 298 336517781 336518079 8.280000e-100 374


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 TraesCS2A01G592200 chr2A 779431891 779434343 2452 False 4530.000000 4530 100.000000 1 2453 1 chr2A.!!$F2 2452
1 TraesCS2A01G592200 chr2A 779528609 779531101 2492 False 2046.500000 2763 96.157500 1 2453 2 chr2A.!!$F5 2452
2 TraesCS2A01G592200 chr2A 779339768 779342856 3088 False 1262.000000 1921 90.449500 1 2242 2 chr2A.!!$F3 2241
3 TraesCS2A01G592200 chr2A 779507783 779511329 3546 False 1033.333333 1984 90.995667 1 2242 3 chr2A.!!$F4 2241
4 TraesCS2A01G592200 chr2A 779619816 779626857 7041 False 812.500000 1893 91.855250 1 2451 4 chr2A.!!$F6 2450
5 TraesCS2A01G592200 chr2D 634145309 634158385 13076 True 767.000000 2292 90.061375 1 2451 8 chr2D.!!$R2 2450
6 TraesCS2A01G592200 chr2B 777142479 777145683 3204 True 536.200000 1925 89.012200 427 2428 5 chr2B.!!$R1 2001

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
994 4938 0.39113 GCCATCCTAACACGCACAGA 60.391 55.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2231 11592 0.668535 AAAGAGCAACCCGTTCTTGC 59.331 50.0 0.0 0.0 43.66 4.01 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
180 2658 4.746535 TCAAGTTTGTAGGTGTGAGTGA 57.253 40.909 0.00 0.00 0.00 3.41
270 2748 0.659427 ATCAATTGATGCAGACGCCG 59.341 50.000 20.11 0.00 37.32 6.46
288 2766 2.555006 GCCGGGGGTTAACCTCTTTTTA 60.555 50.000 23.81 0.00 37.70 1.52
409 2887 3.500680 TGTCGAATTGTTTAACCTCCTGC 59.499 43.478 0.00 0.00 0.00 4.85
410 2888 3.500680 GTCGAATTGTTTAACCTCCTGCA 59.499 43.478 0.00 0.00 0.00 4.41
411 2889 4.156008 GTCGAATTGTTTAACCTCCTGCAT 59.844 41.667 0.00 0.00 0.00 3.96
412 2890 4.155826 TCGAATTGTTTAACCTCCTGCATG 59.844 41.667 0.00 0.00 0.00 4.06
477 2955 2.035632 CTAGGAATCGGGAGTCTTGCT 58.964 52.381 0.00 0.00 0.00 3.91
757 4506 4.211125 TCCTCATCTCGCTCTGAGTTATT 58.789 43.478 6.53 0.00 45.46 1.40
801 4550 1.203052 CCACGCAAATGCTGGAAGATT 59.797 47.619 14.75 0.00 39.83 2.40
834 4770 4.492494 TGACATGTAATCTGCTGACCAT 57.508 40.909 0.00 0.00 0.00 3.55
852 4788 1.980784 ATGCCATCCTCAGCTCGCTT 61.981 55.000 0.00 0.00 0.00 4.68
860 4796 2.093288 TCCTCAGCTCGCTTTGATCATT 60.093 45.455 0.00 0.00 0.00 2.57
872 4808 4.201990 GCTTTGATCATTCCGCTCTTTCAT 60.202 41.667 0.00 0.00 0.00 2.57
888 4824 6.677920 GCTCTTTCATTTGGCACGTACAATAT 60.678 38.462 5.79 1.56 0.00 1.28
907 4843 7.966812 ACAATATCTGCATAGACCTCATTACA 58.033 34.615 0.00 0.00 35.34 2.41
913 4849 6.551227 TCTGCATAGACCTCATTACATACAGT 59.449 38.462 0.00 0.00 0.00 3.55
983 4927 2.076207 TTACCACTAGCGCCATCCTA 57.924 50.000 2.29 0.00 0.00 2.94
994 4938 0.391130 GCCATCCTAACACGCACAGA 60.391 55.000 0.00 0.00 0.00 3.41
1016 4960 5.997746 AGACCAGAATGAAGATTTTGTTCGA 59.002 36.000 0.00 0.00 39.69 3.71
1466 5410 2.489985 CCAAGTAACCACCCATGTCCAA 60.490 50.000 0.00 0.00 0.00 3.53
1472 5416 1.285280 CCACCCATGTCCAAGGTAGA 58.715 55.000 0.00 0.00 30.98 2.59
1919 5871 4.782019 TTCACATAAGTCCCAAATGCAC 57.218 40.909 0.00 0.00 0.00 4.57
2124 11485 4.098196 GGATCTAGCTTACCCCGCTTATAG 59.902 50.000 0.00 0.00 38.86 1.31
2231 11592 3.930336 ACACCACACATCTCACATACTG 58.070 45.455 0.00 0.00 0.00 2.74
2337 15431 2.182858 AATCCTCTCCCAGGGGACGT 62.183 60.000 5.33 0.00 43.67 4.34
2410 15504 1.067821 GGGAACACCGCAAAAATGACA 59.932 47.619 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
180 2658 3.175594 ACATCAAACCATCCAAAGCCAT 58.824 40.909 0.00 0.00 0.00 4.40
409 2887 0.881118 AACTAACCAACAGCGGCATG 59.119 50.000 1.45 0.01 0.00 4.06
410 2888 1.616159 AAACTAACCAACAGCGGCAT 58.384 45.000 1.45 0.00 0.00 4.40
411 2889 1.874872 GTAAACTAACCAACAGCGGCA 59.125 47.619 1.45 0.00 0.00 5.69
412 2890 2.148768 AGTAAACTAACCAACAGCGGC 58.851 47.619 0.00 0.00 0.00 6.53
477 2955 7.040617 CGTAGTATAAGATCACTTAAGCCTCCA 60.041 40.741 1.29 0.00 41.15 3.86
801 4550 7.201522 GCAGATTACATGTCAAACAAGATACGA 60.202 37.037 0.00 0.00 0.00 3.43
818 4671 1.281577 TGGCATGGTCAGCAGATTACA 59.718 47.619 0.00 0.00 0.00 2.41
834 4770 2.189191 AAAGCGAGCTGAGGATGGCA 62.189 55.000 0.00 0.00 35.10 4.92
852 4788 5.393352 CCAAATGAAAGAGCGGAATGATCAA 60.393 40.000 0.00 0.00 34.70 2.57
860 4796 0.881118 GTGCCAAATGAAAGAGCGGA 59.119 50.000 0.00 0.00 0.00 5.54
872 4808 3.339141 TGCAGATATTGTACGTGCCAAA 58.661 40.909 0.00 0.00 32.99 3.28
888 4824 6.551227 ACTGTATGTAATGAGGTCTATGCAGA 59.449 38.462 0.00 0.00 34.05 4.26
907 4843 9.998106 AAATGCGAGGTCTATTTATAACTGTAT 57.002 29.630 0.00 0.00 0.00 2.29
913 4849 6.954944 GCACAAATGCGAGGTCTATTTATAA 58.045 36.000 0.00 0.00 43.33 0.98
964 4900 2.076207 TAGGATGGCGCTAGTGGTAA 57.924 50.000 7.64 0.00 0.00 2.85
983 4927 1.202639 TCATTCTGGTCTGTGCGTGTT 60.203 47.619 0.00 0.00 0.00 3.32
994 4938 5.048713 GGTCGAACAAAATCTTCATTCTGGT 60.049 40.000 0.00 0.00 0.00 4.00
1016 4960 2.691011 GTGAGAGCGAGGAGAAATAGGT 59.309 50.000 0.00 0.00 0.00 3.08
1111 5055 2.293677 CTGACAGAGATATACGGGCGTT 59.706 50.000 0.00 0.00 0.00 4.84
1307 5251 3.056465 GGTGACTTTGTCCACAAACCAAA 60.056 43.478 0.55 0.00 40.55 3.28
1429 5373 2.165167 CTTGGCACAGTCATCCACAAT 58.835 47.619 0.00 0.00 42.39 2.71
1472 5416 8.506437 CAGGCATGTAAAATGATGTATTCGTAT 58.494 33.333 0.00 0.00 0.00 3.06
1725 5671 6.823689 ACTATTTGCTCATTATCGTTGTTCCT 59.176 34.615 0.00 0.00 0.00 3.36
1765 5711 5.773176 TCCTCGTCTATTATGCCAAGACATA 59.227 40.000 0.00 0.00 39.69 2.29
1772 5718 5.353394 AACTTTCCTCGTCTATTATGCCA 57.647 39.130 0.00 0.00 0.00 4.92
1919 5871 5.565592 TCAAAATTCCATGTCCGAATGAG 57.434 39.130 0.00 0.00 30.39 2.90
2124 11485 1.603739 GGGGAGGTTTGTGCAGGAC 60.604 63.158 0.00 0.00 0.00 3.85
2231 11592 0.668535 AAAGAGCAACCCGTTCTTGC 59.331 50.000 0.00 0.00 43.66 4.01
2322 15416 2.037367 TCACGTCCCCTGGGAGAG 59.963 66.667 16.20 7.03 46.16 3.20
2337 15431 2.110188 AGACCCTGTCCTAGACTTGTCA 59.890 50.000 3.49 0.00 32.20 3.58
2410 15504 4.094887 GTCATTCTTCGTGTATGGTGCAAT 59.905 41.667 0.00 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.