Multiple sequence alignment - TraesCS7B01G434900

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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 TraesCS7B01G434900 chr7B 100.000 4420 0 0 1 4420 701925849 701921430 0.000000e+00 8163
1 TraesCS7B01G434900 chr7B 97.991 4281 80 4 1 4276 702143276 702138997 0.000000e+00 7424
2 TraesCS7B01G434900 chr7B 98.007 3362 60 5 939 4295 702049351 702045992 0.000000e+00 5830
3 TraesCS7B01G434900 chr7B 83.651 2306 279 42 2169 4413 701903799 701901531 0.000000e+00 2080
4 TraesCS7B01G434900 chr7B 83.671 2174 238 50 2162 4279 701992477 701990365 0.000000e+00 1940
5 TraesCS7B01G434900 chr7B 85.723 1737 181 24 312 2001 702063048 702061332 0.000000e+00 1772
6 TraesCS7B01G434900 chr7B 85.657 1736 183 24 312 2001 701994512 701992797 0.000000e+00 1766
7 TraesCS7B01G434900 chr7B 85.066 1741 187 24 312 1990 701905547 701903818 0.000000e+00 1707
8 TraesCS7B01G434900 chr7B 83.692 1533 177 38 2814 4300 702153090 702151585 0.000000e+00 1378
9 TraesCS7B01G434900 chr7B 83.366 1533 181 37 2814 4300 702059910 702058406 0.000000e+00 1351
10 TraesCS7B01G434900 chr7B 97.866 703 15 0 1 703 702050100 702049398 0.000000e+00 1216
11 TraesCS7B01G434900 chr7B 84.205 975 104 16 312 1246 702156317 702155353 0.000000e+00 902
12 TraesCS7B01G434900 chr7B 94.340 106 6 0 4315 4420 702045755 702045650 3.540000e-36 163
13 TraesCS7B01G434900 chr7B 92.784 97 7 0 4324 4420 702138684 702138588 1.660000e-29 141
14 TraesCS7B01G434900 chr7D 91.942 3115 154 32 685 3754 612495907 612492845 0.000000e+00 4272
15 TraesCS7B01G434900 chr7D 92.736 2533 133 31 1246 3754 612507541 612505036 0.000000e+00 3611
16 TraesCS7B01G434900 chr7D 84.505 2291 271 36 2169 4413 612516289 612514037 0.000000e+00 2187
17 TraesCS7B01G434900 chr7D 85.935 1621 159 29 423 2001 612518055 612516462 0.000000e+00 1666
18 TraesCS7B01G434900 chr7D 95.282 657 31 0 1 657 612496552 612495896 0.000000e+00 1042
19 TraesCS7B01G434900 chr7D 89.163 526 50 2 3735 4253 612490827 612490302 0.000000e+00 649
20 TraesCS7B01G434900 chr7D 82.827 757 77 17 423 1150 612518782 612518050 2.900000e-176 628
21 TraesCS7B01G434900 chr7D 96.226 371 14 0 1 371 612508803 612508433 3.780000e-170 608
22 TraesCS7B01G434900 chr7D 94.035 285 17 0 373 657 612508227 612507943 2.440000e-117 433
23 TraesCS7B01G434900 chr7D 95.652 230 10 0 685 914 612507954 612507725 1.940000e-98 370
24 TraesCS7B01G434900 chr7D 75.767 326 65 8 1067 1388 612427864 612428179 7.660000e-33 152
25 TraesCS7B01G434900 chrUn 92.333 2165 100 16 685 2818 341689510 341691639 0.000000e+00 3018
26 TraesCS7B01G434900 chrUn 86.450 1727 182 22 312 2001 335211268 335209557 0.000000e+00 1845
27 TraesCS7B01G434900 chrUn 87.303 1205 112 14 829 2001 355096430 355095235 0.000000e+00 1339
28 TraesCS7B01G434900 chrUn 89.130 552 52 3 3735 4279 343553925 343554475 0.000000e+00 680
29 TraesCS7B01G434900 chrUn 94.035 285 17 0 373 657 341689237 341689521 2.440000e-117 433
30 TraesCS7B01G434900 chr7A 84.127 2268 279 36 2169 4395 702998768 702996541 0.000000e+00 2119
31 TraesCS7B01G434900 chr7A 84.107 2026 250 37 5 1984 703000845 702998846 0.000000e+00 1892


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 TraesCS7B01G434900 chr7B 701921430 701925849 4419 True 8163.000000 8163 100.000000 1 4420 1 chr7B.!!$R1 4419
1 TraesCS7B01G434900 chr7B 702138588 702143276 4688 True 3782.500000 7424 95.387500 1 4420 2 chr7B.!!$R6 4419
2 TraesCS7B01G434900 chr7B 702045650 702050100 4450 True 2403.000000 5830 96.737667 1 4420 3 chr7B.!!$R4 4419
3 TraesCS7B01G434900 chr7B 701901531 701905547 4016 True 1893.500000 2080 84.358500 312 4413 2 chr7B.!!$R2 4101
4 TraesCS7B01G434900 chr7B 701990365 701994512 4147 True 1853.000000 1940 84.664000 312 4279 2 chr7B.!!$R3 3967
5 TraesCS7B01G434900 chr7B 702058406 702063048 4642 True 1561.500000 1772 84.544500 312 4300 2 chr7B.!!$R5 3988
6 TraesCS7B01G434900 chr7B 702151585 702156317 4732 True 1140.000000 1378 83.948500 312 4300 2 chr7B.!!$R7 3988
7 TraesCS7B01G434900 chr7D 612490302 612496552 6250 True 1987.666667 4272 92.129000 1 4253 3 chr7D.!!$R1 4252
8 TraesCS7B01G434900 chr7D 612514037 612518782 4745 True 1493.666667 2187 84.422333 423 4413 3 chr7D.!!$R3 3990
9 TraesCS7B01G434900 chr7D 612505036 612508803 3767 True 1255.500000 3611 94.662250 1 3754 4 chr7D.!!$R2 3753
10 TraesCS7B01G434900 chrUn 335209557 335211268 1711 True 1845.000000 1845 86.450000 312 2001 1 chrUn.!!$R1 1689
11 TraesCS7B01G434900 chrUn 341689237 341691639 2402 False 1725.500000 3018 93.184000 373 2818 2 chrUn.!!$F2 2445
12 TraesCS7B01G434900 chrUn 355095235 355096430 1195 True 1339.000000 1339 87.303000 829 2001 1 chrUn.!!$R2 1172
13 TraesCS7B01G434900 chrUn 343553925 343554475 550 False 680.000000 680 89.130000 3735 4279 1 chrUn.!!$F1 544
14 TraesCS7B01G434900 chr7A 702996541 703000845 4304 True 2005.500000 2119 84.117000 5 4395 2 chr7A.!!$R1 4390

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
152 153 1.514678 GCTTGTCAATGTGGTCGCCA 61.515 55.000 0.0 0.0 0.00 5.69 F
497 1438 2.036475 AGATACATGTCGCCTGATCACC 59.964 50.000 0.0 0.0 0.00 4.02 F
2078 3508 1.994779 CGGCCTGATGTTTTGCATTTC 59.005 47.619 0.0 0.0 38.06 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2078 3508 9.545105 AGAGAGATTTGCTAGAAATTATCACAG 57.455 33.333 0.0 0.00 0.00 3.66 R
2412 3857 0.260230 TGAAACAGGCAGGGGAACAA 59.740 50.000 0.0 0.00 0.00 2.83 R
3800 7825 1.135046 CGGCGATGAGATCACACATC 58.865 55.000 0.0 13.71 39.51 3.06 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
144 145 1.999648 ATGGGTGTGCTTGTCAATGT 58.000 45.000 0.00 0.00 0.00 2.71
152 153 1.514678 GCTTGTCAATGTGGTCGCCA 61.515 55.000 0.00 0.00 0.00 5.69
227 228 2.801483 TGGGGACAATAATGTGTGTGG 58.199 47.619 0.00 0.00 40.74 4.17
229 230 2.099405 GGGACAATAATGTGTGTGGGG 58.901 52.381 0.00 0.00 40.74 4.96
497 1438 2.036475 AGATACATGTCGCCTGATCACC 59.964 50.000 0.00 0.00 0.00 4.02
705 1743 3.039588 GTTTGCGCGGGAGTCGAA 61.040 61.111 8.83 0.00 42.43 3.71
837 1891 5.277490 GGAAATGCTTGGCTGAAAAGAAAAC 60.277 40.000 0.00 0.00 0.00 2.43
2078 3508 1.994779 CGGCCTGATGTTTTGCATTTC 59.005 47.619 0.00 0.00 38.06 2.17
2412 3857 6.909550 AGAGAGATCGCTGGTAATTATTCT 57.090 37.500 2.76 0.00 0.00 2.40
2414 3859 7.151308 AGAGAGATCGCTGGTAATTATTCTTG 58.849 38.462 2.76 0.00 0.00 3.02
2787 4250 6.398234 TGAGAGCTCTGGTGAGTATTTATC 57.602 41.667 23.91 1.62 42.13 1.75
3310 5266 5.781210 TTGCCAGTGACAACAATCATTAA 57.219 34.783 0.00 0.00 0.00 1.40
3387 5343 2.303022 TCTGTCTCCTTTGCAGGGTTAG 59.697 50.000 7.51 0.42 41.25 2.34
3414 5370 3.890756 TGGCAGCCATATTTATCTGTTGG 59.109 43.478 11.22 0.00 0.00 3.77
3475 5431 5.939883 TCATCGACAAACATCATCCTTTTCT 59.060 36.000 0.00 0.00 0.00 2.52
3800 7825 4.498241 CATCCACATATCCATCTACCACG 58.502 47.826 0.00 0.00 0.00 4.94
3953 7979 0.250234 CCCGATGACACACCAGACAT 59.750 55.000 0.00 0.00 0.00 3.06
4045 8085 9.203421 CTTATGTGTACACAACTCATGTCTTAA 57.797 33.333 31.01 18.59 45.41 1.85
4116 8175 5.245531 TGCTAAAGAGTAATGTTGGTCCAG 58.754 41.667 0.00 0.00 0.00 3.86
4163 8244 2.102588 TGGAAGAATAGCTAGAACCCGC 59.897 50.000 0.00 0.00 0.00 6.13
4168 8249 1.793134 ATAGCTAGAACCCGCGTCCG 61.793 60.000 4.92 0.00 0.00 4.79
4297 8383 2.263545 AGTGGACAACCTTAGTACCCC 58.736 52.381 0.00 0.00 37.04 4.95
4363 8714 1.682849 GGATGTGCCACTACCACCA 59.317 57.895 0.00 0.00 36.34 4.17
4370 8721 1.586154 GCCACTACCACCATGCACAC 61.586 60.000 0.00 0.00 0.00 3.82
4417 8768 2.617532 GCCAGCCTCTGATTCAGTTTCT 60.618 50.000 13.23 6.14 32.44 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
152 153 3.066198 GGTGTTAGACGGCCACCT 58.934 61.111 7.84 0.48 44.21 4.00
165 166 2.808315 CGCGAGGCTAGATGGTGT 59.192 61.111 0.00 0.00 0.00 4.16
250 251 2.203983 TCCTCCCCAAGCAGCTCA 60.204 61.111 0.00 0.00 0.00 4.26
497 1438 2.673043 GCAACAATGGCATGACAGAAGG 60.673 50.000 7.63 0.00 0.00 3.46
705 1743 5.598005 TCATTCAAACCAACAGAGAAACCAT 59.402 36.000 0.00 0.00 0.00 3.55
837 1891 5.288712 GCCGACCATCTTTATCATATACACG 59.711 44.000 0.00 0.00 0.00 4.49
2078 3508 9.545105 AGAGAGATTTGCTAGAAATTATCACAG 57.455 33.333 0.00 0.00 0.00 3.66
2412 3857 0.260230 TGAAACAGGCAGGGGAACAA 59.740 50.000 0.00 0.00 0.00 2.83
2414 3859 2.507407 TATGAAACAGGCAGGGGAAC 57.493 50.000 0.00 0.00 0.00 3.62
2663 4126 5.763698 CCTTCTGTGACAGATGCAATATCAT 59.236 40.000 16.98 0.00 40.39 2.45
2787 4250 3.850122 CATGCTAATCATGGATGCTGG 57.150 47.619 0.00 0.00 46.81 4.85
3387 5343 3.508793 AGATAAATATGGCTGCCATGCAC 59.491 43.478 37.64 22.97 44.84 4.57
3414 5370 2.325583 TGTAAGGACGGGAATCATGC 57.674 50.000 0.00 0.00 0.00 4.06
3475 5431 7.335627 ACTAGGTAATTCATTGTTCCGAATGA 58.664 34.615 0.00 0.00 39.96 2.57
3683 5666 1.495951 CCAAACGAGGCGTAGTTGC 59.504 57.895 5.66 0.00 39.99 4.17
3741 5724 1.135721 CACCAGGGGTTACGCTAGTAC 59.864 57.143 0.00 0.00 37.87 2.73
3800 7825 1.135046 CGGCGATGAGATCACACATC 58.865 55.000 0.00 13.71 39.51 3.06
4045 8085 6.831353 CCCCCTTTTGTTCCTTTTGTATTTTT 59.169 34.615 0.00 0.00 0.00 1.94
4116 8175 4.003648 GCAGGTGGGATGCAATATACTAC 58.996 47.826 0.00 0.00 43.31 2.73
4163 8244 3.424433 GCAAAACACTAGAATTCCGGACG 60.424 47.826 1.83 0.00 0.00 4.79
4178 8259 2.571212 ACTTCGATGGAGTGCAAAACA 58.429 42.857 3.12 0.00 0.00 2.83
4310 8396 7.376335 AGAACAAGGAGTAGTAGGTCTTTTT 57.624 36.000 0.00 0.00 0.00 1.94
4311 8397 6.997942 AGAACAAGGAGTAGTAGGTCTTTT 57.002 37.500 0.00 0.00 0.00 2.27
4312 8398 6.997942 AAGAACAAGGAGTAGTAGGTCTTT 57.002 37.500 0.00 0.00 0.00 2.52
4363 8714 0.890542 AACATGACGCTGGTGTGCAT 60.891 50.000 0.00 0.00 0.00 3.96
4370 8721 1.066858 ACTAGTGGAACATGACGCTGG 60.067 52.381 0.00 6.00 44.52 4.85


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

AutoCloner maintained by Alex Coulton.