Multiple sequence alignment - TraesCS3A01G420700

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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 TraesCS3A01G420700 chr3A 100.000 2626 0 0 1 2626 662138995 662141620 0.000000e+00 4850
1 TraesCS3A01G420700 chr3A 97.111 623 18 0 1 623 598385320 598384698 0.000000e+00 1051
2 TraesCS3A01G420700 chr3A 96.965 626 17 1 1 624 208701681 208702306 0.000000e+00 1050
3 TraesCS3A01G420700 chr3A 96.955 624 19 0 1 624 325521248 325520625 0.000000e+00 1048
4 TraesCS3A01G420700 chr1D 97.514 2011 33 4 624 2626 156777356 156779357 0.000000e+00 3421
5 TraesCS3A01G420700 chr6A 97.445 1996 33 5 646 2626 99978139 99976147 0.000000e+00 3387
6 TraesCS3A01G420700 chr6A 97.432 623 16 0 1 623 376522796 376523418 0.000000e+00 1062
7 TraesCS3A01G420700 chr6A 97.569 617 14 1 7 623 571192529 571191914 0.000000e+00 1055
8 TraesCS3A01G420700 chr5A 97.973 1875 33 3 754 2626 299774058 299772187 0.000000e+00 3247
9 TraesCS3A01G420700 chr5A 97.111 623 18 0 1 623 540882402 540883024 0.000000e+00 1051
10 TraesCS3A01G420700 chr5A 96.955 624 19 0 1 624 256600695 256601318 0.000000e+00 1048
11 TraesCS3A01G420700 chr5A 98.582 141 2 0 624 764 299774388 299774248 1.560000e-62 250
12 TraesCS3A01G420700 chr4A 97.794 1360 27 1 624 1983 41895886 41897242 0.000000e+00 2342
13 TraesCS3A01G420700 chr4A 91.130 1071 49 14 1559 2626 725869206 725868179 0.000000e+00 1410
14 TraesCS3A01G420700 chr4A 92.948 553 39 0 624 1176 725870008 725869456 0.000000e+00 806
15 TraesCS3A01G420700 chr4A 94.615 260 14 0 1252 1511 725869454 725869195 1.130000e-108 403
16 TraesCS3A01G420700 chr1A 97.770 1345 26 2 624 1968 452025995 452024655 0.000000e+00 2314
17 TraesCS3A01G420700 chr1A 94.067 1382 53 9 1252 2624 548228465 548227104 0.000000e+00 2071
18 TraesCS3A01G420700 chr1A 94.756 553 29 0 624 1176 548229019 548228467 0.000000e+00 861
19 TraesCS3A01G420700 chr2B 92.241 1379 60 15 1252 2626 493242792 493244127 0.000000e+00 1910
20 TraesCS3A01G420700 chr2B 94.033 553 33 0 624 1176 493242238 493242790 0.000000e+00 839
21 TraesCS3A01G420700 chr2A 97.432 623 16 0 1 623 688935749 688935127 0.000000e+00 1062
22 TraesCS3A01G420700 chr2A 97.276 624 16 1 1 624 113647109 113646487 0.000000e+00 1057
23 TraesCS3A01G420700 chr4B 90.256 780 61 5 624 1403 570344489 570345253 0.000000e+00 1005
24 TraesCS3A01G420700 chr5B 86.102 295 34 6 1429 1722 468630265 468629977 7.060000e-81 311
25 TraesCS3A01G420700 chr3D 86.111 288 37 2 1429 1715 350130046 350130331 9.130000e-80 307
26 TraesCS3A01G420700 chr7D 84.512 297 38 5 1429 1719 606446030 606446324 1.190000e-73 287
27 TraesCS3A01G420700 chrUn 87.037 108 12 2 2335 2442 31522499 31522394 1.280000e-23 121
28 TraesCS3A01G420700 chr5D 88.298 94 9 2 2533 2625 419805005 419804913 7.680000e-21 111
29 TraesCS3A01G420700 chr7B 86.813 91 11 1 2536 2625 521177405 521177315 1.660000e-17 100


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 TraesCS3A01G420700 chr3A 662138995 662141620 2625 False 4850.0 4850 100.000000 1 2626 1 chr3A.!!$F2 2625
1 TraesCS3A01G420700 chr3A 598384698 598385320 622 True 1051.0 1051 97.111000 1 623 1 chr3A.!!$R2 622
2 TraesCS3A01G420700 chr3A 208701681 208702306 625 False 1050.0 1050 96.965000 1 624 1 chr3A.!!$F1 623
3 TraesCS3A01G420700 chr3A 325520625 325521248 623 True 1048.0 1048 96.955000 1 624 1 chr3A.!!$R1 623
4 TraesCS3A01G420700 chr1D 156777356 156779357 2001 False 3421.0 3421 97.514000 624 2626 1 chr1D.!!$F1 2002
5 TraesCS3A01G420700 chr6A 99976147 99978139 1992 True 3387.0 3387 97.445000 646 2626 1 chr6A.!!$R1 1980
6 TraesCS3A01G420700 chr6A 376522796 376523418 622 False 1062.0 1062 97.432000 1 623 1 chr6A.!!$F1 622
7 TraesCS3A01G420700 chr6A 571191914 571192529 615 True 1055.0 1055 97.569000 7 623 1 chr6A.!!$R2 616
8 TraesCS3A01G420700 chr5A 299772187 299774388 2201 True 1748.5 3247 98.277500 624 2626 2 chr5A.!!$R1 2002
9 TraesCS3A01G420700 chr5A 540882402 540883024 622 False 1051.0 1051 97.111000 1 623 1 chr5A.!!$F2 622
10 TraesCS3A01G420700 chr5A 256600695 256601318 623 False 1048.0 1048 96.955000 1 624 1 chr5A.!!$F1 623
11 TraesCS3A01G420700 chr4A 41895886 41897242 1356 False 2342.0 2342 97.794000 624 1983 1 chr4A.!!$F1 1359
12 TraesCS3A01G420700 chr4A 725868179 725870008 1829 True 873.0 1410 92.897667 624 2626 3 chr4A.!!$R1 2002
13 TraesCS3A01G420700 chr1A 452024655 452025995 1340 True 2314.0 2314 97.770000 624 1968 1 chr1A.!!$R1 1344
14 TraesCS3A01G420700 chr1A 548227104 548229019 1915 True 1466.0 2071 94.411500 624 2624 2 chr1A.!!$R2 2000
15 TraesCS3A01G420700 chr2B 493242238 493244127 1889 False 1374.5 1910 93.137000 624 2626 2 chr2B.!!$F1 2002
16 TraesCS3A01G420700 chr2A 688935127 688935749 622 True 1062.0 1062 97.432000 1 623 1 chr2A.!!$R2 622
17 TraesCS3A01G420700 chr2A 113646487 113647109 622 True 1057.0 1057 97.276000 1 624 1 chr2A.!!$R1 623
18 TraesCS3A01G420700 chr4B 570344489 570345253 764 False 1005.0 1005 90.256000 624 1403 1 chr4B.!!$F1 779

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
65 66 0.165944 GATCGCCGGTGAACAAAGTG 59.834 55.000 23.72 0.0 0.0 3.16 F
777 980 1.065709 GCGGTACAAGGGATTCAAGGA 60.066 52.381 0.00 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1137 1340 3.627395 TCCAATGTACCGAGCTTGATT 57.373 42.857 1.22 0.0 0.0 2.57 R
2563 2850 1.278127 CTCCACCAGTACCCGACAATT 59.722 52.381 0.00 0.0 0.0 2.32 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
65 66 0.165944 GATCGCCGGTGAACAAAGTG 59.834 55.000 23.72 0.00 0.00 3.16
335 336 7.899973 TCCCTTCTCTTTACGTAATGTTACTT 58.100 34.615 17.71 0.00 0.00 2.24
396 397 3.636764 TCACTGAGTGACTGCTTGTTCTA 59.363 43.478 11.93 0.00 37.67 2.10
422 423 6.374417 TGGCTTCATAATATCTTCCTACCC 57.626 41.667 0.00 0.00 0.00 3.69
486 487 9.421399 TCACTCTATTGAATACTTGACTATGGA 57.579 33.333 0.00 0.00 0.00 3.41
572 573 4.877323 ACTTCCACGTTTTGAAGACTTC 57.123 40.909 20.26 8.34 40.30 3.01
673 676 2.330216 AGGCCACTACTCAACTTCAGT 58.670 47.619 5.01 0.00 0.00 3.41
686 689 2.490991 ACTTCAGTTCGGTACTTTGCC 58.509 47.619 0.00 0.00 33.85 4.52
773 976 3.244422 GGATATGCGGTACAAGGGATTCA 60.244 47.826 0.00 0.00 0.00 2.57
777 980 1.065709 GCGGTACAAGGGATTCAAGGA 60.066 52.381 0.00 0.00 0.00 3.36
938 1141 2.871022 GTGCATGTTGTTTGGATTGCAA 59.129 40.909 0.00 0.00 41.26 4.08
990 1193 8.918202 TTTGGATTGTACATGAACTAAGTTCT 57.082 30.769 0.00 0.00 42.39 3.01
1137 1340 3.587061 TGATCTAGAAGCCCTCAAACCAA 59.413 43.478 0.00 0.00 0.00 3.67
1466 1669 7.077095 TGGTAGTGGTTAAGTATGGGATATGA 58.923 38.462 0.00 0.00 0.00 2.15
1494 1710 7.496591 CCTGCCATTTTTCTATGCATATTGTTT 59.503 33.333 6.92 0.00 0.00 2.83
1913 2185 7.048512 AGACCTGCATAAGTATTTAGGTTGAC 58.951 38.462 0.00 0.00 38.57 3.18
2126 2405 3.066291 ACTTGTTGTGACCTGTGACAA 57.934 42.857 0.00 0.00 34.44 3.18
2304 2591 7.615582 TGTAGATGTCAAGCTGGAATAAAAG 57.384 36.000 0.00 0.00 0.00 2.27
2415 2702 5.965486 TCCAGCTACATCTCCCTTAGAATA 58.035 41.667 0.00 0.00 37.89 1.75
2563 2850 4.949856 GGCCTGATGTTTCCTTTGAATCTA 59.050 41.667 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.951655 GAACGCGACGCCTAACCGA 62.952 63.158 15.93 0.0 0.00 4.69
65 66 2.640316 AGACTCCCAAACCTTCACAC 57.360 50.000 0.00 0.0 0.00 3.82
146 147 4.217112 GACACCCAGTCCTCACCT 57.783 61.111 0.00 0.0 41.56 4.00
297 298 3.657727 AGAGAAGGGAAGGATGAAACCAA 59.342 43.478 0.00 0.0 0.00 3.67
335 336 6.430616 TGCAATCATACAATGACTTCACAAGA 59.569 34.615 0.00 0.0 43.01 3.02
396 397 7.890655 GGGTAGGAAGATATTATGAAGCCAAAT 59.109 37.037 0.00 0.0 0.00 2.32
422 423 3.722147 AGCTGCAATGTAGTAAGGATCG 58.278 45.455 1.02 0.0 0.00 3.69
486 487 4.650131 GGAAGGTAGACTACACTAGGCAAT 59.350 45.833 14.48 0.0 35.81 3.56
572 573 4.022329 GGGGTGAATAGGCGATTTTTATGG 60.022 45.833 0.00 0.0 0.00 2.74
686 689 7.610692 TGGAGAATTATGGAGGTATACTCTACG 59.389 40.741 2.25 0.0 45.83 3.51
773 976 5.015603 TCCATCTCCTTCCTCAATTTTCCTT 59.984 40.000 0.00 0.0 0.00 3.36
777 980 4.264083 TGCTCCATCTCCTTCCTCAATTTT 60.264 41.667 0.00 0.0 0.00 1.82
938 1141 3.330701 TGCACTTAAGTTCCCTTCCATCT 59.669 43.478 5.07 0.0 31.89 2.90
990 1193 2.429971 TGCAGTCACCATTTTTCAGCAA 59.570 40.909 0.00 0.0 0.00 3.91
1137 1340 3.627395 TCCAATGTACCGAGCTTGATT 57.373 42.857 1.22 0.0 0.00 2.57
1466 1669 6.736110 ATATGCATAGAAAAATGGCAGGTT 57.264 33.333 12.79 0.0 0.00 3.50
1494 1710 3.966979 AGGATGCAACATACATGGACAA 58.033 40.909 0.00 0.0 0.00 3.18
1913 2185 4.688879 TCCTACTGTAAATTGACTTGTGCG 59.311 41.667 0.00 0.0 0.00 5.34
2126 2405 7.420800 CAAACAGAAGTTCTACAGATTGCTTT 58.579 34.615 4.74 0.0 36.84 3.51
2304 2591 5.994054 TCCATACTGAGAAGCTATTGAATGC 59.006 40.000 0.00 0.0 0.00 3.56
2563 2850 1.278127 CTCCACCAGTACCCGACAATT 59.722 52.381 0.00 0.0 0.00 2.32


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

AutoCloner maintained by Alex Coulton.