Multiple sequence alignment - TraesCS3B01G195100

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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 TraesCS3B01G195100 chr3B 100.000 5808 0 0 1 5808 220663489 220657682 0.000000e+00 10726
1 TraesCS3B01G195100 chr3B 97.960 5834 85 9 1 5807 219366061 219360235 0.000000e+00 10083
2 TraesCS3B01G195100 chr3B 94.094 2489 126 12 2438 4912 171002455 170999974 0.000000e+00 3762
3 TraesCS3B01G195100 chr3B 93.446 2487 137 14 2438 4912 219285274 219282802 0.000000e+00 3666
4 TraesCS3B01G195100 chr3B 92.451 2477 125 18 1 2441 171005681 171003231 0.000000e+00 3482
5 TraesCS3B01G195100 chr3B 90.632 1708 117 11 1 1691 130421784 130423465 0.000000e+00 2228
6 TraesCS3B01G195100 chr3B 90.893 549 35 2 2438 2971 171003197 171002649 0.000000e+00 723
7 TraesCS3B01G195100 chrUn 95.091 2485 104 10 2438 4912 70478622 70476146 0.000000e+00 3897
8 TraesCS3B01G195100 chrUn 93.399 2454 122 15 1 2441 70481082 70478656 0.000000e+00 3598
9 TraesCS3B01G195100 chrUn 93.454 2154 120 11 300 2439 233338091 233340237 0.000000e+00 3177
10 TraesCS3B01G195100 chrUn 93.454 2154 120 11 300 2439 236805254 236807400 0.000000e+00 3177
11 TraesCS3B01G195100 chrUn 95.465 904 35 6 4910 5808 70476074 70475172 0.000000e+00 1437
12 TraesCS3B01G195100 chr1D 94.819 2490 107 12 2438 4912 299672036 299674518 0.000000e+00 3864
13 TraesCS3B01G195100 chr1D 94.215 2489 128 9 2438 4912 25332736 25335222 0.000000e+00 3784
14 TraesCS3B01G195100 chr1D 93.213 2446 112 19 2 2441 25330305 25332702 0.000000e+00 3548
15 TraesCS3B01G195100 chr1D 95.460 903 37 4 4910 5808 19588691 19587789 0.000000e+00 1437
16 TraesCS3B01G195100 chr6D 94.785 2493 106 12 2438 4912 54712677 54715163 0.000000e+00 3862
17 TraesCS3B01G195100 chr6D 94.101 2458 102 15 1 2441 30391857 30389426 0.000000e+00 3696
18 TraesCS3B01G195100 chr6D 94.132 2454 103 15 1 2441 365491490 365493915 0.000000e+00 3696
19 TraesCS3B01G195100 chr6D 95.681 903 35 4 4910 5808 298948879 298949781 0.000000e+00 1448
20 TraesCS3B01G195100 chr7D 94.600 2500 105 9 2438 4912 110031866 110034360 0.000000e+00 3842
21 TraesCS3B01G195100 chr7D 95.686 904 32 7 4910 5808 69772680 69773581 0.000000e+00 1447
22 TraesCS3B01G195100 chr7D 95.455 902 38 3 4910 5808 13248367 13249268 0.000000e+00 1435
23 TraesCS3B01G195100 chr4B 94.616 2489 119 8 2438 4912 27495323 27497810 0.000000e+00 3840
24 TraesCS3B01G195100 chr4B 91.093 2470 160 23 1 2439 369718125 369715685 0.000000e+00 3288
25 TraesCS3B01G195100 chr2D 93.603 2423 116 11 1 2409 579020246 579017849 0.000000e+00 3579
26 TraesCS3B01G195100 chr2D 95.460 903 35 6 4910 5808 579014792 579013892 0.000000e+00 1435
27 TraesCS3B01G195100 chr7B 92.965 2459 138 17 1 2441 77501164 77503605 0.000000e+00 3550
28 TraesCS3B01G195100 chr7B 95.631 206 7 2 2236 2441 80435341 80435138 4.340000e-86 329
29 TraesCS3B01G195100 chr1B 92.120 2462 146 21 1 2441 619451003 619448569 0.000000e+00 3428
30 TraesCS3B01G195100 chr5A 93.466 1209 75 1 1 1209 51986053 51987257 0.000000e+00 1792
31 TraesCS3B01G195100 chr5A 92.033 1230 78 5 1 1230 701015397 701014188 0.000000e+00 1711
32 TraesCS3B01G195100 chr3A 92.007 1226 75 5 1 1209 745153509 745154728 0.000000e+00 1700
33 TraesCS3B01G195100 chr6B 91.064 1175 94 5 1 1166 650399361 650400533 0.000000e+00 1578
34 TraesCS3B01G195100 chr7A 95.686 904 31 7 4910 5808 184077447 184078347 0.000000e+00 1447
35 TraesCS3B01G195100 chr5D 95.455 902 38 3 4910 5808 21164688 21163787 0.000000e+00 1435


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 TraesCS3B01G195100 chr3B 220657682 220663489 5807 True 10726.000000 10726 100.000000 1 5808 1 chr3B.!!$R3 5807
1 TraesCS3B01G195100 chr3B 219360235 219366061 5826 True 10083.000000 10083 97.960000 1 5807 1 chr3B.!!$R2 5806
2 TraesCS3B01G195100 chr3B 219282802 219285274 2472 True 3666.000000 3666 93.446000 2438 4912 1 chr3B.!!$R1 2474
3 TraesCS3B01G195100 chr3B 170999974 171005681 5707 True 2655.666667 3762 92.479333 1 4912 3 chr3B.!!$R4 4911
4 TraesCS3B01G195100 chr3B 130421784 130423465 1681 False 2228.000000 2228 90.632000 1 1691 1 chr3B.!!$F1 1690
5 TraesCS3B01G195100 chrUn 233338091 233340237 2146 False 3177.000000 3177 93.454000 300 2439 1 chrUn.!!$F1 2139
6 TraesCS3B01G195100 chrUn 236805254 236807400 2146 False 3177.000000 3177 93.454000 300 2439 1 chrUn.!!$F2 2139
7 TraesCS3B01G195100 chrUn 70475172 70481082 5910 True 2977.333333 3897 94.651667 1 5808 3 chrUn.!!$R1 5807
8 TraesCS3B01G195100 chr1D 299672036 299674518 2482 False 3864.000000 3864 94.819000 2438 4912 1 chr1D.!!$F1 2474
9 TraesCS3B01G195100 chr1D 25330305 25335222 4917 False 3666.000000 3784 93.714000 2 4912 2 chr1D.!!$F2 4910
10 TraesCS3B01G195100 chr1D 19587789 19588691 902 True 1437.000000 1437 95.460000 4910 5808 1 chr1D.!!$R1 898
11 TraesCS3B01G195100 chr6D 54712677 54715163 2486 False 3862.000000 3862 94.785000 2438 4912 1 chr6D.!!$F1 2474
12 TraesCS3B01G195100 chr6D 30389426 30391857 2431 True 3696.000000 3696 94.101000 1 2441 1 chr6D.!!$R1 2440
13 TraesCS3B01G195100 chr6D 365491490 365493915 2425 False 3696.000000 3696 94.132000 1 2441 1 chr6D.!!$F3 2440
14 TraesCS3B01G195100 chr6D 298948879 298949781 902 False 1448.000000 1448 95.681000 4910 5808 1 chr6D.!!$F2 898
15 TraesCS3B01G195100 chr7D 110031866 110034360 2494 False 3842.000000 3842 94.600000 2438 4912 1 chr7D.!!$F3 2474
16 TraesCS3B01G195100 chr7D 69772680 69773581 901 False 1447.000000 1447 95.686000 4910 5808 1 chr7D.!!$F2 898
17 TraesCS3B01G195100 chr7D 13248367 13249268 901 False 1435.000000 1435 95.455000 4910 5808 1 chr7D.!!$F1 898
18 TraesCS3B01G195100 chr4B 27495323 27497810 2487 False 3840.000000 3840 94.616000 2438 4912 1 chr4B.!!$F1 2474
19 TraesCS3B01G195100 chr4B 369715685 369718125 2440 True 3288.000000 3288 91.093000 1 2439 1 chr4B.!!$R1 2438
20 TraesCS3B01G195100 chr2D 579013892 579020246 6354 True 2507.000000 3579 94.531500 1 5808 2 chr2D.!!$R1 5807
21 TraesCS3B01G195100 chr7B 77501164 77503605 2441 False 3550.000000 3550 92.965000 1 2441 1 chr7B.!!$F1 2440
22 TraesCS3B01G195100 chr1B 619448569 619451003 2434 True 3428.000000 3428 92.120000 1 2441 1 chr1B.!!$R1 2440
23 TraesCS3B01G195100 chr5A 51986053 51987257 1204 False 1792.000000 1792 93.466000 1 1209 1 chr5A.!!$F1 1208
24 TraesCS3B01G195100 chr5A 701014188 701015397 1209 True 1711.000000 1711 92.033000 1 1230 1 chr5A.!!$R1 1229
25 TraesCS3B01G195100 chr3A 745153509 745154728 1219 False 1700.000000 1700 92.007000 1 1209 1 chr3A.!!$F1 1208
26 TraesCS3B01G195100 chr6B 650399361 650400533 1172 False 1578.000000 1578 91.064000 1 1166 1 chr6B.!!$F1 1165
27 TraesCS3B01G195100 chr7A 184077447 184078347 900 False 1447.000000 1447 95.686000 4910 5808 1 chr7A.!!$F1 898
28 TraesCS3B01G195100 chr5D 21163787 21164688 901 True 1435.000000 1435 95.455000 4910 5808 1 chr5D.!!$R1 898

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
879 895 1.210155 GCATTTATCCCATCGCCGC 59.790 57.895 0.00 0.0 0.00 6.53 F
1685 1817 7.100458 AGTTTTTGCACTAAACTTCATGTCT 57.900 32.000 16.54 0.0 41.69 3.41 F
2050 2186 3.244840 ACAGAAGCAGAGGCAGAAGAATT 60.245 43.478 0.00 0.0 44.61 2.17 F
3137 4574 5.793030 ATATCCTAGGTTTTCTCTGGTCG 57.207 43.478 9.08 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2050 2186 4.079253 GTTGGCTTTTGAGTCCATAAGGA 58.921 43.478 0.00 0.0 43.21 3.36 R
2921 4345 5.211174 AGCTACCTGTTCCGGATTATTAC 57.789 43.478 4.15 0.0 0.00 1.89 R
3833 5279 3.056393 TGTCCCACAACTAAGTATCACCG 60.056 47.826 0.00 0.0 0.00 4.94 R
4856 6319 2.779755 TGGGATGTTACGACTGCATT 57.220 45.000 0.00 0.0 0.00 3.56 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
130 133 2.224426 ACTCAAACCATGCACCGTTAGA 60.224 45.455 0.00 0.00 0.00 2.10
240 247 1.443872 AAAGAGACACGCGGCTACG 60.444 57.895 12.47 0.00 44.63 3.51
491 498 2.899345 TATGCGCGGTTGCTGACGAT 62.899 55.000 8.83 0.00 39.65 3.73
608 615 3.506067 CCTACAAATTCAGTTGTCCCACC 59.494 47.826 0.00 0.00 40.85 4.61
615 622 4.649267 TTCAGTTGTCCCACCATATGAA 57.351 40.909 3.65 0.00 0.00 2.57
870 886 3.191371 CGCTTCCCCATTAGCATTTATCC 59.809 47.826 0.00 0.00 37.23 2.59
879 895 1.210155 GCATTTATCCCATCGCCGC 59.790 57.895 0.00 0.00 0.00 6.53
1685 1817 7.100458 AGTTTTTGCACTAAACTTCATGTCT 57.900 32.000 16.54 0.00 41.69 3.41
1950 2084 7.532571 TCATTTTCTGTCATTCATGCTTGTAG 58.467 34.615 0.00 0.00 0.00 2.74
2050 2186 3.244840 ACAGAAGCAGAGGCAGAAGAATT 60.245 43.478 0.00 0.00 44.61 2.17
3137 4574 5.793030 ATATCCTAGGTTTTCTCTGGTCG 57.207 43.478 9.08 0.00 0.00 4.79
3224 4661 6.948886 TGGTTTAAATGTTCCATAAGTGGCTA 59.051 34.615 0.00 0.00 45.63 3.93
3538 4983 7.537596 AACTTGTTGACCATCCAATATGAAA 57.462 32.000 0.00 0.00 0.00 2.69
3748 5194 9.605275 GCCATTATAGCATGTCAAGATAGATTA 57.395 33.333 0.00 0.00 0.00 1.75
3982 5432 0.324645 AGGAACATTGATGGGTGGGC 60.325 55.000 0.00 0.00 0.00 5.36
4102 5552 8.511321 CAGCTCACGAGATATTTTATCTAGTCT 58.489 37.037 7.15 1.52 32.88 3.24
4339 5792 2.281484 CCACACTTGGGTCCCACG 60.281 66.667 11.24 12.17 39.57 4.94
4387 5840 0.608035 TTCCCTTAGGCTTGCCAACG 60.608 55.000 14.54 1.18 0.00 4.10
4628 6087 9.710900 CATTATGTTTCATAGACTATGTGCCTA 57.289 33.333 19.60 6.91 37.45 3.93
4856 6319 4.679639 GCGACCTATCAAGTACCATCAACA 60.680 45.833 0.00 0.00 0.00 3.33
4866 6329 1.896220 ACCATCAACAATGCAGTCGT 58.104 45.000 0.00 0.00 33.71 4.34
4892 6355 4.038271 TCCCAAGACAGCATCAAGAATT 57.962 40.909 0.00 0.00 0.00 2.17
4893 6356 4.410099 TCCCAAGACAGCATCAAGAATTT 58.590 39.130 0.00 0.00 0.00 1.82
5791 7331 1.500396 CCGTCGTGACAGATCGTGA 59.500 57.895 0.41 0.00 0.00 4.35
5807 7347 4.796495 GACCATGGACGTGGGGGC 62.796 72.222 21.47 0.90 43.77 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
130 133 1.073284 GTATGGTGTGGGTCAACCTGT 59.927 52.381 0.00 0.00 41.11 4.00
240 247 1.468054 GGATCTCGGTGTGCAATTTGC 60.468 52.381 14.49 14.49 45.29 3.68
491 498 3.133542 TGGCAAATGGATGTGACAAAACA 59.866 39.130 0.00 0.00 26.90 2.83
608 615 9.726232 CCTCATTACACAGAACAAATTCATATG 57.274 33.333 0.00 0.00 37.29 1.78
615 622 4.702131 GCTCCCTCATTACACAGAACAAAT 59.298 41.667 0.00 0.00 0.00 2.32
1654 1786 6.518208 AGTTTAGTGCAAAAACTACACCAA 57.482 33.333 21.05 0.00 43.54 3.67
1685 1817 9.512435 GCGTGAGAGACTAGTTTTATACAAATA 57.488 33.333 0.00 0.00 0.00 1.40
2050 2186 4.079253 GTTGGCTTTTGAGTCCATAAGGA 58.921 43.478 0.00 0.00 43.21 3.36
2921 4345 5.211174 AGCTACCTGTTCCGGATTATTAC 57.789 43.478 4.15 0.00 0.00 1.89
3748 5194 7.174426 CCACTGCACATCATTATTGTGATATCT 59.826 37.037 7.93 0.00 45.83 1.98
3833 5279 3.056393 TGTCCCACAACTAAGTATCACCG 60.056 47.826 0.00 0.00 0.00 4.94
3982 5432 4.408182 AGTTTCCCCTGTTGATCGATAG 57.592 45.455 0.00 0.00 0.00 2.08
4130 5582 7.858382 CAGAGCAGTATACAGATGTACTAACAC 59.142 40.741 5.50 0.00 38.78 3.32
4131 5583 7.468768 GCAGAGCAGTATACAGATGTACTAACA 60.469 40.741 5.50 0.00 40.69 2.41
4132 5584 6.858993 GCAGAGCAGTATACAGATGTACTAAC 59.141 42.308 5.50 0.00 31.45 2.34
4387 5840 5.591099 AGTTCATCAAAATGACAACCACAC 58.409 37.500 0.00 0.00 41.62 3.82
4393 5846 8.792633 CCTAAGGTTAGTTCATCAAAATGACAA 58.207 33.333 0.00 0.00 41.62 3.18
4856 6319 2.779755 TGGGATGTTACGACTGCATT 57.220 45.000 0.00 0.00 0.00 3.56
4866 6329 3.998913 TGATGCTGTCTTGGGATGTTA 57.001 42.857 0.00 0.00 0.00 2.41
4892 6355 5.569355 TCAATTCACCCTGAAAGCATAGAA 58.431 37.500 0.00 0.00 40.12 2.10
4893 6356 5.178096 TCAATTCACCCTGAAAGCATAGA 57.822 39.130 0.00 0.00 40.12 1.98


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

AutoCloner maintained by Alex Coulton.