Multiple sequence alignment - TraesCS7A01G113500

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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 TraesCS7A01G113500 chr7A 100.000 3005 0 0 1 3005 69617665 69620669 0.000000e+00 5550
1 TraesCS7A01G113500 chr7A 98.666 2474 31 2 532 3005 69567801 69570272 0.000000e+00 4385
2 TraesCS7A01G113500 chr7A 95.409 501 9 4 1 499 69567313 69567801 0.000000e+00 785
3 TraesCS7A01G113500 chr7A 94.643 112 5 1 734 844 137821935 137822046 3.980000e-39 172
4 TraesCS7A01G113500 chr7A 86.486 111 15 0 734 844 82206167 82206277 4.070000e-24 122
5 TraesCS7A01G113500 chr7A 97.015 67 1 1 2390 2455 69569747 69569813 8.810000e-21 111
6 TraesCS7A01G113500 chr7A 97.015 67 1 1 2478 2544 69620054 69620119 8.810000e-21 111
7 TraesCS7A01G113500 chr7A 97.015 67 1 1 2390 2455 69620142 69620208 8.810000e-21 111
8 TraesCS7A01G113500 chr7A 95.522 67 2 1 2478 2544 69569659 69569724 4.100000e-19 106
9 TraesCS7A01G113500 chr7D 95.436 1205 51 1 870 2070 65437190 65438394 0.000000e+00 1917
10 TraesCS7A01G113500 chr7D 92.351 706 36 15 2308 3005 65438556 65439251 0.000000e+00 989
11 TraesCS7A01G113500 chr7D 81.266 758 103 24 11 737 65436385 65437134 7.220000e-161 577
12 TraesCS7A01G113500 chr7D 90.995 422 34 4 1597 2017 65627000 65626582 1.560000e-157 566
13 TraesCS7A01G113500 chr7D 95.035 141 5 2 2189 2327 65438391 65438531 1.400000e-53 220
14 TraesCS7A01G113500 chr7D 97.015 67 1 1 2390 2455 65438727 65438793 8.810000e-21 111
15 TraesCS7A01G113500 chr7D 89.744 78 8 0 1094 1171 65666803 65666726 1.910000e-17 100
16 TraesCS7A01G113500 chr7B 94.637 1212 54 2 870 2070 7038506 7037295 0.000000e+00 1868
17 TraesCS7A01G113500 chr7B 93.947 413 23 2 2587 2998 7036774 7036363 9.150000e-175 623
18 TraesCS7A01G113500 chr7B 79.297 768 111 31 1 737 7039310 7038560 7.480000e-136 494
19 TraesCS7A01G113500 chr7B 84.483 290 29 12 2308 2588 7037139 7036857 3.820000e-69 272
20 TraesCS7A01G113500 chr7B 92.806 139 7 3 2190 2327 7037297 7037161 6.570000e-47 198
21 TraesCS7A01G113500 chr2B 89.581 979 88 4 1072 2037 110417466 110416489 0.000000e+00 1230
22 TraesCS7A01G113500 chr2B 78.378 814 134 33 1181 1985 111035647 111034867 9.680000e-135 490
23 TraesCS7A01G113500 chr2D 89.206 982 92 6 1072 2040 73009969 73008989 0.000000e+00 1214
24 TraesCS7A01G113500 chr2D 79.752 805 121 33 1181 1976 73316904 73317675 2.040000e-151 545
25 TraesCS7A01G113500 chr2D 87.879 99 12 0 734 832 197871612 197871710 1.890000e-22 117
26 TraesCS7A01G113500 chr2A 88.481 981 98 8 1072 2037 71614034 71613054 0.000000e+00 1171
27 TraesCS7A01G113500 chr2A 78.501 814 133 33 1181 1985 72697318 72696538 2.080000e-136 496
28 TraesCS7A01G113500 chr2A 92.857 70 2 2 2097 2163 736754399 736754468 6.860000e-17 99
29 TraesCS7A01G113500 chr4A 89.908 109 10 1 734 841 614024413 614024521 4.040000e-29 139
30 TraesCS7A01G113500 chr4A 84.211 114 17 1 731 844 603530159 603530047 3.170000e-20 110
31 TraesCS7A01G113500 chr3A 87.097 124 15 1 730 853 644239205 644239083 4.040000e-29 139
32 TraesCS7A01G113500 chr5D 86.239 109 14 1 733 841 88914288 88914395 1.890000e-22 117
33 TraesCS7A01G113500 chr1B 87.255 102 11 2 730 830 45710977 45711077 6.810000e-22 115


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 TraesCS7A01G113500 chr7A 69617665 69620669 3004 False 1924.00 5550 98.0100 1 3005 3 chr7A.!!$F4 3004
1 TraesCS7A01G113500 chr7A 69567313 69570272 2959 False 1346.75 4385 96.6530 1 3005 4 chr7A.!!$F3 3004
2 TraesCS7A01G113500 chr7D 65436385 65439251 2866 False 762.80 1917 92.2206 11 3005 5 chr7D.!!$F1 2994
3 TraesCS7A01G113500 chr7B 7036363 7039310 2947 True 691.00 1868 89.0340 1 2998 5 chr7B.!!$R1 2997
4 TraesCS7A01G113500 chr2B 110416489 110417466 977 True 1230.00 1230 89.5810 1072 2037 1 chr2B.!!$R1 965
5 TraesCS7A01G113500 chr2B 111034867 111035647 780 True 490.00 490 78.3780 1181 1985 1 chr2B.!!$R2 804
6 TraesCS7A01G113500 chr2D 73008989 73009969 980 True 1214.00 1214 89.2060 1072 2040 1 chr2D.!!$R1 968
7 TraesCS7A01G113500 chr2D 73316904 73317675 771 False 545.00 545 79.7520 1181 1976 1 chr2D.!!$F1 795
8 TraesCS7A01G113500 chr2A 71613054 71614034 980 True 1171.00 1171 88.4810 1072 2037 1 chr2A.!!$R1 965
9 TraesCS7A01G113500 chr2A 72696538 72697318 780 True 496.00 496 78.5010 1181 1985 1 chr2A.!!$R2 804

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
371 411 0.61326 AGACGCAAGCAGGGATACAA 59.387 50.0 0.32 0.0 45.62 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2099 2204 0.971386 GGGTCTCCAGTTTACGTCCA 59.029 55.0 0.0 0.0 0.0 4.02 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
326 340 7.433680 AGGACATAACTTAACAAGCCAAAAAG 58.566 34.615 0.00 0.00 0.00 2.27
327 341 7.286775 AGGACATAACTTAACAAGCCAAAAAGA 59.713 33.333 0.00 0.00 0.00 2.52
329 343 9.308318 GACATAACTTAACAAGCCAAAAAGAAA 57.692 29.630 0.00 0.00 0.00 2.52
330 344 9.660180 ACATAACTTAACAAGCCAAAAAGAAAA 57.340 25.926 0.00 0.00 0.00 2.29
371 411 0.613260 AGACGCAAGCAGGGATACAA 59.387 50.000 0.32 0.00 45.62 2.41
508 550 3.365265 CCACGGCTGCAGAAACCC 61.365 66.667 20.43 8.07 0.00 4.11
511 553 2.361610 CGGCTGCAGAAACCCCAT 60.362 61.111 20.43 0.00 0.00 4.00
518 560 3.195396 GCTGCAGAAACCCCATCATTTAA 59.805 43.478 20.43 0.00 0.00 1.52
520 562 5.404466 TGCAGAAACCCCATCATTTAAAG 57.596 39.130 0.00 0.00 0.00 1.85
525 567 4.918810 AACCCCATCATTTAAAGATCGC 57.081 40.909 0.00 0.00 0.00 4.58
543 585 1.084370 GCATCAGTAGGTCGGCACAC 61.084 60.000 0.00 0.00 0.00 3.82
741 784 4.714308 CCCTCTGATCCATATTACTCCCTC 59.286 50.000 0.00 0.00 0.00 4.30
748 791 5.871396 TCCATATTACTCCCTCTGTTCAC 57.129 43.478 0.00 0.00 0.00 3.18
760 803 7.016268 ACTCCCTCTGTTCACTTTTATAAGACA 59.984 37.037 0.00 0.00 35.30 3.41
773 816 8.947115 ACTTTTATAAGACACTGTAGCCATTTC 58.053 33.333 0.00 0.00 35.30 2.17
784 827 1.818642 AGCCATTTCAGACAGCAGTC 58.181 50.000 0.05 0.05 45.31 3.51
832 875 9.496873 TCTGAAACGTCTTATAAAAATGAAGGA 57.503 29.630 0.00 0.00 0.00 3.36
938 1010 7.065923 GGTCTTATAAAGATGTTTCGAGCCTTT 59.934 37.037 0.00 0.00 40.18 3.11
1497 1579 2.362369 CGAGTCCCTGGACATGGCT 61.362 63.158 18.12 0.00 46.76 4.75
1500 1582 0.622738 AGTCCCTGGACATGGCTGAT 60.623 55.000 18.12 0.00 46.76 2.90
2014 2119 2.579201 CCTGTTGAGGACGGCGAT 59.421 61.111 16.62 0.00 42.93 4.58
2099 2204 8.707796 AATAATCCTATATGACCGGATCGTAT 57.292 34.615 9.46 15.10 41.56 3.06
2466 2634 9.753674 TGTTCTACTGAATTTGGAATATTCCTT 57.246 29.630 30.07 18.87 40.07 3.36
2948 3202 5.423931 ACCCGGCCAAGTTAAATAAAATCAT 59.576 36.000 2.24 0.00 0.00 2.45
2980 3234 7.261325 AGACACATAGACATGTAATCACACTC 58.739 38.462 0.00 0.00 43.73 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
120 123 1.740380 CGGTCATGAATCGGAGCTTGT 60.740 52.381 0.00 0.00 0.00 3.16
298 312 5.626142 TGGCTTGTTAAGTTATGTCCTCAA 58.374 37.500 0.00 0.00 0.00 3.02
371 411 2.042843 CGAGCCAGACTAGGGGGT 60.043 66.667 0.00 0.00 37.66 4.95
433 474 0.689080 GACCTCATCTCCAGCCTCCA 60.689 60.000 0.00 0.00 0.00 3.86
508 550 6.309712 ACTGATGCGATCTTTAAATGATGG 57.690 37.500 5.29 5.54 0.00 3.51
511 553 6.582636 ACCTACTGATGCGATCTTTAAATGA 58.417 36.000 0.00 0.00 0.00 2.57
518 560 1.338337 CCGACCTACTGATGCGATCTT 59.662 52.381 0.00 0.00 0.00 2.40
520 562 0.664767 GCCGACCTACTGATGCGATC 60.665 60.000 0.00 0.00 0.00 3.69
525 567 0.532573 AGTGTGCCGACCTACTGATG 59.467 55.000 0.00 0.00 0.00 3.07
543 585 0.953471 TGTGATCGGGCGGTTTTCAG 60.953 55.000 0.00 0.00 0.00 3.02
719 762 5.421693 CAGAGGGAGTAATATGGATCAGAGG 59.578 48.000 0.00 0.00 0.00 3.69
741 784 8.436200 GCTACAGTGTCTTATAAAAGTGAACAG 58.564 37.037 0.00 0.00 34.13 3.16
748 791 8.946085 TGAAATGGCTACAGTGTCTTATAAAAG 58.054 33.333 0.00 0.00 0.00 2.27
760 803 2.038952 TGCTGTCTGAAATGGCTACAGT 59.961 45.455 0.00 0.00 39.74 3.55
773 816 5.929697 TGAACTATTTTGACTGCTGTCTG 57.070 39.130 22.31 9.51 43.29 3.51
784 827 7.914871 TCAGACAACACACATTGAACTATTTTG 59.085 33.333 0.00 0.00 33.57 2.44
1497 1579 1.081556 CCATGACGCGGTCGAAATCA 61.082 55.000 12.47 2.91 39.41 2.57
1500 1582 3.115892 GCCATGACGCGGTCGAAA 61.116 61.111 12.47 0.00 39.41 3.46
2055 2160 9.692749 GGATTATTTTCCGTTTCTTTTTCTTCT 57.307 29.630 0.00 0.00 0.00 2.85
2099 2204 0.971386 GGGTCTCCAGTTTACGTCCA 59.029 55.000 0.00 0.00 0.00 4.02
2466 2634 6.208599 GGTTGGGATGATGAAACAAAGTTAGA 59.791 38.462 0.00 0.00 0.00 2.10
2962 3216 7.781056 TGCAATAGAGTGTGATTACATGTCTA 58.219 34.615 0.00 12.32 39.39 2.59


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

AutoCloner maintained by Alex Coulton.