Multiple sequence alignment - TraesCS7A01G087000

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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 TraesCS7A01G087000 chr7A 100.000 3107 0 0 1 3107 51200709 51203815 0.000000e+00 5738.0
1 TraesCS7A01G087000 chr7A 98.136 3112 52 4 1 3107 51140730 51143840 0.000000e+00 5421.0
2 TraesCS7A01G087000 chr7A 97.259 3137 55 7 1 3107 51089873 51093008 0.000000e+00 5288.0
3 TraesCS7A01G087000 chr7A 97.222 3132 60 6 1 3107 51258502 51261631 0.000000e+00 5276.0
4 TraesCS7A01G087000 chr7D 91.053 950 73 5 1178 2126 48356370 48357308 0.000000e+00 1273.0
5 TraesCS7A01G087000 chr7D 87.451 765 58 20 2373 3107 589315078 589314322 0.000000e+00 846.0
6 TraesCS7A01G087000 chr7D 90.345 435 29 1 1 422 48355931 48356365 2.710000e-155 558.0
7 TraesCS7A01G087000 chr7D 89.278 457 20 8 2373 2828 609937196 609936768 2.110000e-151 545.0
8 TraesCS7A01G087000 chr7D 93.436 259 15 1 2851 3107 609936463 609936205 1.750000e-102 383.0
9 TraesCS7A01G087000 chr7D 94.286 105 5 1 2270 2373 48359229 48359333 3.210000e-35 159.0
10 TraesCS7A01G087000 chr7D 96.386 83 3 0 2117 2199 48359119 48359201 1.500000e-28 137.0
11 TraesCS7A01G087000 chr2D 81.312 1402 225 22 710 2083 28915484 28914092 0.000000e+00 1103.0
12 TraesCS7A01G087000 chr2D 76.150 1413 283 34 713 2084 5267265 5268664 0.000000e+00 693.0
13 TraesCS7A01G087000 chr2B 81.064 1410 223 24 709 2087 46677669 46679065 0.000000e+00 1085.0
14 TraesCS7A01G087000 chr2B 76.570 1417 273 38 713 2084 6178717 6180119 0.000000e+00 723.0
15 TraesCS7A01G087000 chr2B 91.373 255 21 1 2 256 252103488 252103235 6.380000e-92 348.0
16 TraesCS7A01G087000 chr2B 88.439 173 13 4 2931 3097 104588297 104588468 5.250000e-48 202.0
17 TraesCS7A01G087000 chr2B 74.271 377 73 14 869 1223 46688851 46689225 1.500000e-28 137.0
18 TraesCS7A01G087000 chr2B 95.455 44 2 0 3059 3102 575235349 575235392 1.550000e-08 71.3
19 TraesCS7A01G087000 chr4D 90.613 767 38 11 2374 3107 318591707 318590942 0.000000e+00 987.0
20 TraesCS7A01G087000 chr2A 75.869 1409 291 27 713 2081 3816526 3817925 0.000000e+00 673.0
21 TraesCS7A01G087000 chr1A 80.628 764 99 30 2372 3094 253315471 253316226 2.110000e-151 545.0
22 TraesCS7A01G087000 chr1A 94.231 52 3 0 310 361 490892317 490892368 2.570000e-11 80.5
23 TraesCS7A01G087000 chrUn 78.284 746 138 14 869 1592 17076865 17076122 2.820000e-125 459.0
24 TraesCS7A01G087000 chrUn 77.852 745 137 15 869 1592 327358415 327357678 1.320000e-118 436.0
25 TraesCS7A01G087000 chrUn 77.852 745 137 15 869 1592 374807230 374807967 1.320000e-118 436.0
26 TraesCS7A01G087000 chrUn 76.714 700 130 19 709 1379 370635965 370635270 2.950000e-95 359.0
27 TraesCS7A01G087000 chrUn 98.095 105 2 0 2269 2373 49504924 49505028 1.900000e-42 183.0
28 TraesCS7A01G087000 chr6D 92.969 256 18 0 1 256 395034067 395034322 1.050000e-99 374.0
29 TraesCS7A01G087000 chr6D 92.578 256 19 0 1 256 395023519 395023774 4.890000e-98 368.0
30 TraesCS7A01G087000 chr3D 92.969 256 18 0 1 256 69664903 69664648 1.050000e-99 374.0
31 TraesCS7A01G087000 chr5B 89.453 256 27 0 1 256 465869236 465869491 1.070000e-84 324.0
32 TraesCS7A01G087000 chr4B 88.119 101 12 0 3007 3107 672960422 672960522 1.510000e-23 121.0
33 TraesCS7A01G087000 chr5A 95.745 47 2 0 313 359 654159947 654159901 3.320000e-10 76.8
34 TraesCS7A01G087000 chr1B 93.878 49 3 0 309 357 295089214 295089166 1.190000e-09 75.0


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 TraesCS7A01G087000 chr7A 51200709 51203815 3106 False 5738.00 5738 100.0000 1 3107 1 chr7A.!!$F3 3106
1 TraesCS7A01G087000 chr7A 51140730 51143840 3110 False 5421.00 5421 98.1360 1 3107 1 chr7A.!!$F2 3106
2 TraesCS7A01G087000 chr7A 51089873 51093008 3135 False 5288.00 5288 97.2590 1 3107 1 chr7A.!!$F1 3106
3 TraesCS7A01G087000 chr7A 51258502 51261631 3129 False 5276.00 5276 97.2220 1 3107 1 chr7A.!!$F4 3106
4 TraesCS7A01G087000 chr7D 589314322 589315078 756 True 846.00 846 87.4510 2373 3107 1 chr7D.!!$R1 734
5 TraesCS7A01G087000 chr7D 48355931 48359333 3402 False 531.75 1273 93.0175 1 2373 4 chr7D.!!$F1 2372
6 TraesCS7A01G087000 chr7D 609936205 609937196 991 True 464.00 545 91.3570 2373 3107 2 chr7D.!!$R2 734
7 TraesCS7A01G087000 chr2D 28914092 28915484 1392 True 1103.00 1103 81.3120 710 2083 1 chr2D.!!$R1 1373
8 TraesCS7A01G087000 chr2D 5267265 5268664 1399 False 693.00 693 76.1500 713 2084 1 chr2D.!!$F1 1371
9 TraesCS7A01G087000 chr2B 46677669 46679065 1396 False 1085.00 1085 81.0640 709 2087 1 chr2B.!!$F2 1378
10 TraesCS7A01G087000 chr2B 6178717 6180119 1402 False 723.00 723 76.5700 713 2084 1 chr2B.!!$F1 1371
11 TraesCS7A01G087000 chr4D 318590942 318591707 765 True 987.00 987 90.6130 2374 3107 1 chr4D.!!$R1 733
12 TraesCS7A01G087000 chr2A 3816526 3817925 1399 False 673.00 673 75.8690 713 2081 1 chr2A.!!$F1 1368
13 TraesCS7A01G087000 chr1A 253315471 253316226 755 False 545.00 545 80.6280 2372 3094 1 chr1A.!!$F1 722
14 TraesCS7A01G087000 chrUn 17076122 17076865 743 True 459.00 459 78.2840 869 1592 1 chrUn.!!$R1 723
15 TraesCS7A01G087000 chrUn 327357678 327358415 737 True 436.00 436 77.8520 869 1592 1 chrUn.!!$R2 723
16 TraesCS7A01G087000 chrUn 374807230 374807967 737 False 436.00 436 77.8520 869 1592 1 chrUn.!!$F2 723
17 TraesCS7A01G087000 chrUn 370635270 370635965 695 True 359.00 359 76.7140 709 1379 1 chrUn.!!$R3 670

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
830 846 0.178767 CGTCATCATCAAGCCCTCCA 59.821 55.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2569 4520 1.152008 GAGGGGATCGGGAGGGATT 60.152 63.158 0.0 0.0 0.0 3.01 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
329 343 9.286946 CTGCTTTTCTTCTATCAATGAAATGAC 57.713 33.333 0.0 0.0 30.82 3.06
826 842 1.233019 CCATCGTCATCATCAAGCCC 58.767 55.000 0.0 0.0 0.00 5.19
830 846 0.178767 CGTCATCATCAAGCCCTCCA 59.821 55.000 0.0 0.0 0.00 3.86
833 849 2.106166 GTCATCATCAAGCCCTCCATCT 59.894 50.000 0.0 0.0 0.00 2.90
834 850 2.371179 TCATCATCAAGCCCTCCATCTC 59.629 50.000 0.0 0.0 0.00 2.75
836 852 1.138568 CATCAAGCCCTCCATCTCCT 58.861 55.000 0.0 0.0 0.00 3.69
837 853 1.493871 CATCAAGCCCTCCATCTCCTT 59.506 52.381 0.0 0.0 0.00 3.36
839 855 0.182299 CAAGCCCTCCATCTCCTTCC 59.818 60.000 0.0 0.0 0.00 3.46
840 856 0.253347 AAGCCCTCCATCTCCTTCCA 60.253 55.000 0.0 0.0 0.00 3.53
842 858 0.985490 GCCCTCCATCTCCTTCCACT 60.985 60.000 0.0 0.0 0.00 4.00
1373 1442 2.608988 CACACCTCCCAGCCTCCT 60.609 66.667 0.0 0.0 0.00 3.69
1682 1754 1.681666 CAGAGGGCTTCTTGGAGCA 59.318 57.895 0.0 0.0 44.49 4.26
2569 4520 2.182827 CTGAAGTCATCACCCTCCTCA 58.817 52.381 0.0 0.0 33.47 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 2.750814 TGGATAGAGGTCATGACAGCA 58.249 47.619 26.47 9.36 0.00 4.41
443 459 2.288640 GCTCACCAGCAAAGAAAGCAAT 60.289 45.455 0.00 0.00 46.06 3.56
826 842 0.179936 GGCAGTGGAAGGAGATGGAG 59.820 60.000 0.00 0.00 0.00 3.86
830 846 2.370445 CCCGGCAGTGGAAGGAGAT 61.370 63.158 0.00 0.00 0.00 2.75
836 852 3.860930 GAAAGGCCCGGCAGTGGAA 62.861 63.158 12.58 0.00 0.00 3.53
837 853 4.344865 GAAAGGCCCGGCAGTGGA 62.345 66.667 12.58 0.00 0.00 4.02
839 855 4.351054 AGGAAAGGCCCGGCAGTG 62.351 66.667 12.58 0.00 37.37 3.66
840 856 4.351054 CAGGAAAGGCCCGGCAGT 62.351 66.667 12.58 0.00 37.37 4.40
1146 1215 2.725312 GCTCCTCGCCCATGTCTCA 61.725 63.158 0.00 0.00 0.00 3.27
1195 1264 1.661498 TTTGAAGCAGTGCGTTGCCA 61.661 50.000 10.00 0.00 45.18 4.92
1373 1442 0.173481 GCAGTAGACATGAGGCGTCA 59.827 55.000 12.13 12.13 35.77 4.35
1682 1754 3.637273 GACCCGTGCCCTTGGTCT 61.637 66.667 0.00 0.00 44.17 3.85
1852 1924 4.199310 TCTTTCTCCAGGAACACTTTGTG 58.801 43.478 0.00 0.00 39.75 3.33
2569 4520 1.152008 GAGGGGATCGGGAGGGATT 60.152 63.158 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.