Multiple sequence alignment - TraesCS7A01G086800

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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 TraesCS7A01G086800 chr7A 100.000 3441 0 0 1 3441 51089563 51093003 0.000000e+00 6355.0
1 TraesCS7A01G086800 chr7A 97.966 3441 64 2 1 3441 51258192 51261626 0.000000e+00 5962.0
2 TraesCS7A01G086800 chr7A 97.298 3442 62 7 1 3441 51200399 51203810 0.000000e+00 5812.0
3 TraesCS7A01G086800 chr7A 97.037 3443 73 6 1 3441 51140420 51143835 0.000000e+00 5766.0
4 TraesCS7A01G086800 chr7A 93.478 46 2 1 16 60 470913822 470913777 2.220000e-07 67.6
5 TraesCS7A01G086800 chr7D 91.263 950 71 5 1512 2460 48356370 48357308 0.000000e+00 1284.0
6 TraesCS7A01G086800 chr7D 91.449 690 44 3 58 733 48355677 48356365 0.000000e+00 933.0
7 TraesCS7A01G086800 chr7D 87.270 762 60 20 2707 3441 589315078 589314327 0.000000e+00 835.0
8 TraesCS7A01G086800 chr7D 89.059 457 21 8 2707 3162 609937196 609936768 1.090000e-149 540.0
9 TraesCS7A01G086800 chr7D 92.520 254 15 2 3190 3441 609936461 609936210 9.080000e-96 361.0
10 TraesCS7A01G086800 chr7D 94.118 102 5 1 2604 2704 48359229 48359330 1.650000e-33 154.0
11 TraesCS7A01G086800 chr7D 96.386 83 3 0 2451 2533 48359119 48359201 1.670000e-28 137.0
12 TraesCS7A01G086800 chr7D 91.228 57 3 2 612 668 7594019 7594073 3.680000e-10 76.8
13 TraesCS7A01G086800 chr2D 82.739 1402 228 8 1021 2417 28915484 28914092 0.000000e+00 1236.0
14 TraesCS7A01G086800 chr2D 77.408 1412 290 21 1024 2418 5267265 5268664 0.000000e+00 813.0
15 TraesCS7A01G086800 chr2D 75.720 1355 308 16 1027 2377 109030766 109032103 0.000000e+00 660.0
16 TraesCS7A01G086800 chr2B 82.328 1409 230 12 1020 2421 46677669 46679065 0.000000e+00 1205.0
17 TraesCS7A01G086800 chr2B 77.825 1416 280 25 1024 2418 6178717 6180119 0.000000e+00 845.0
18 TraesCS7A01G086800 chr2B 91.736 363 29 1 204 566 252103596 252103235 1.430000e-138 503.0
19 TraesCS7A01G086800 chr2B 95.455 44 2 0 3398 3441 575235349 575235392 1.710000e-08 71.3
20 TraesCS7A01G086800 chr4D 90.314 764 41 12 2708 3441 318591707 318590947 0.000000e+00 970.0
21 TraesCS7A01G086800 chr4D 86.994 346 39 2 218 562 21872944 21872604 5.390000e-103 385.0
22 TraesCS7A01G086800 chr2A 77.076 1409 297 18 1024 2415 3816526 3817925 0.000000e+00 789.0
23 TraesCS7A01G086800 chr3D 75.973 1336 298 17 1022 2346 359630465 359631788 0.000000e+00 667.0
24 TraesCS7A01G086800 chr3D 90.566 53 4 1 620 671 389255133 389255185 6.160000e-08 69.4
25 TraesCS7A01G086800 chr3B 75.455 1373 308 20 1022 2380 465887227 465885870 2.900000e-180 641.0
26 TraesCS7A01G086800 chr3A 74.820 1247 285 20 1040 2271 479099156 479100388 1.410000e-148 536.0
27 TraesCS7A01G086800 chr6D 92.011 363 29 0 204 566 395033960 395034322 8.520000e-141 510.0
28 TraesCS7A01G086800 chr6D 91.736 363 30 0 204 566 395023412 395023774 3.960000e-139 505.0
29 TraesCS7A01G086800 chr5B 89.097 321 32 1 249 566 465869171 465869491 2.490000e-106 396.0
30 TraesCS7A01G086800 chrUn 98.039 102 2 0 2603 2704 49504924 49505025 9.810000e-41 178.0
31 TraesCS7A01G086800 chr1B 88.550 131 13 2 2707 2836 619091228 619091099 1.280000e-34 158.0
32 TraesCS7A01G086800 chr4B 91.667 60 4 1 1 60 17829549 17829607 7.910000e-12 82.4
33 TraesCS7A01G086800 chr4A 95.455 44 2 0 16 59 88756546 88756503 1.710000e-08 71.3
34 TraesCS7A01G086800 chr7B 100.000 33 0 0 620 652 408512744 408512776 1.030000e-05 62.1


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 TraesCS7A01G086800 chr7A 51089563 51093003 3440 False 6355.0 6355 100.0000 1 3441 1 chr7A.!!$F1 3440
1 TraesCS7A01G086800 chr7A 51258192 51261626 3434 False 5962.0 5962 97.9660 1 3441 1 chr7A.!!$F4 3440
2 TraesCS7A01G086800 chr7A 51200399 51203810 3411 False 5812.0 5812 97.2980 1 3441 1 chr7A.!!$F3 3440
3 TraesCS7A01G086800 chr7A 51140420 51143835 3415 False 5766.0 5766 97.0370 1 3441 1 chr7A.!!$F2 3440
4 TraesCS7A01G086800 chr7D 589314327 589315078 751 True 835.0 835 87.2700 2707 3441 1 chr7D.!!$R1 734
5 TraesCS7A01G086800 chr7D 48355677 48359330 3653 False 627.0 1284 93.3040 58 2704 4 chr7D.!!$F2 2646
6 TraesCS7A01G086800 chr7D 609936210 609937196 986 True 450.5 540 90.7895 2707 3441 2 chr7D.!!$R2 734
7 TraesCS7A01G086800 chr2D 28914092 28915484 1392 True 1236.0 1236 82.7390 1021 2417 1 chr2D.!!$R1 1396
8 TraesCS7A01G086800 chr2D 5267265 5268664 1399 False 813.0 813 77.4080 1024 2418 1 chr2D.!!$F1 1394
9 TraesCS7A01G086800 chr2D 109030766 109032103 1337 False 660.0 660 75.7200 1027 2377 1 chr2D.!!$F2 1350
10 TraesCS7A01G086800 chr2B 46677669 46679065 1396 False 1205.0 1205 82.3280 1020 2421 1 chr2B.!!$F2 1401
11 TraesCS7A01G086800 chr2B 6178717 6180119 1402 False 845.0 845 77.8250 1024 2418 1 chr2B.!!$F1 1394
12 TraesCS7A01G086800 chr4D 318590947 318591707 760 True 970.0 970 90.3140 2708 3441 1 chr4D.!!$R2 733
13 TraesCS7A01G086800 chr2A 3816526 3817925 1399 False 789.0 789 77.0760 1024 2415 1 chr2A.!!$F1 1391
14 TraesCS7A01G086800 chr3D 359630465 359631788 1323 False 667.0 667 75.9730 1022 2346 1 chr3D.!!$F1 1324
15 TraesCS7A01G086800 chr3B 465885870 465887227 1357 True 641.0 641 75.4550 1022 2380 1 chr3B.!!$R1 1358
16 TraesCS7A01G086800 chr3A 479099156 479100388 1232 False 536.0 536 74.8200 1040 2271 1 chr3A.!!$F1 1231

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
532 533 0.714180 TGCCCCTCTACTTGGGTCTA 59.286 55.0 0.00 0.0 44.2 2.59 F
1362 1391 0.601311 ACTTCTTCTGCAGTGTCGCC 60.601 55.0 14.67 0.0 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1366 1395 2.583593 GAGCTCCGTGGCGACATC 60.584 66.667 0.87 0.0 46.14 3.06 R
2874 4809 0.037326 GATGACTTCAGGTGGCGACA 60.037 55.000 0.00 0.0 38.70 4.35 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
83 84 3.636300 TCTTACAGCATGGCAAAACTTGT 59.364 39.130 0.00 0.00 43.62 3.16
127 128 5.421056 CCTATACCCTGGATTATAGCAACGA 59.579 44.000 13.13 0.00 29.98 3.85
202 203 2.528818 CCACCCACCCTCTCAAGCA 61.529 63.158 0.00 0.00 0.00 3.91
532 533 0.714180 TGCCCCTCTACTTGGGTCTA 59.286 55.000 0.00 0.00 44.20 2.59
547 548 2.305052 GGGTCTAGCTTGGTGGTTTAGT 59.695 50.000 0.00 0.00 0.00 2.24
644 658 7.338440 TCTTCTATCAATGAAATGATACGCG 57.662 36.000 3.53 3.53 40.44 6.01
662 676 1.595489 GCGAGCTTTGCGTATTCATGG 60.595 52.381 0.00 0.00 0.00 3.66
877 891 1.469079 GGTTGTGTTGCGTTGCTCTTT 60.469 47.619 0.00 0.00 0.00 2.52
936 950 3.669344 CCGCGCCACACACCAAAT 61.669 61.111 0.00 0.00 0.00 2.32
959 973 2.737180 CCGACACCACACTGCTCT 59.263 61.111 0.00 0.00 0.00 4.09
1196 1219 3.697747 CACCGCGGTCAACCCCTA 61.698 66.667 31.80 0.00 0.00 3.53
1300 1323 1.303155 GCCTCCAGTTTGCAGCTCT 60.303 57.895 0.00 0.00 0.00 4.09
1303 1326 1.602311 CTCCAGTTTGCAGCTCTGTT 58.398 50.000 11.76 0.00 0.00 3.16
1362 1391 0.601311 ACTTCTTCTGCAGTGTCGCC 60.601 55.000 14.67 0.00 0.00 5.54
1363 1392 1.621301 CTTCTTCTGCAGTGTCGCCG 61.621 60.000 14.67 0.00 0.00 6.46
1364 1393 2.356313 CTTCTGCAGTGTCGCCGT 60.356 61.111 14.67 0.00 0.00 5.68
1365 1394 2.661537 TTCTGCAGTGTCGCCGTG 60.662 61.111 14.67 0.00 0.00 4.94
1366 1395 4.662961 TCTGCAGTGTCGCCGTGG 62.663 66.667 14.67 0.00 0.00 4.94
1367 1396 4.662961 CTGCAGTGTCGCCGTGGA 62.663 66.667 5.25 0.00 0.00 4.02
1368 1397 3.939837 CTGCAGTGTCGCCGTGGAT 62.940 63.158 5.25 0.00 0.00 3.41
1369 1398 3.490759 GCAGTGTCGCCGTGGATG 61.491 66.667 0.00 0.00 0.00 3.51
1370 1399 2.048222 CAGTGTCGCCGTGGATGT 60.048 61.111 0.00 0.00 0.00 3.06
1371 1400 2.094659 CAGTGTCGCCGTGGATGTC 61.095 63.158 0.00 0.00 0.00 3.06
1372 1401 3.179265 GTGTCGCCGTGGATGTCG 61.179 66.667 0.00 0.00 0.00 4.35
1381 1410 4.451150 TGGATGTCGCCACGGAGC 62.451 66.667 0.00 0.00 31.66 4.70
1382 1411 4.148825 GGATGTCGCCACGGAGCT 62.149 66.667 0.00 0.00 0.00 4.09
2128 2184 0.824759 GGTGGAACTCCGTGCTAGAT 59.175 55.000 0.00 0.00 39.43 1.98
2704 4601 9.902684 TGGAAATTTTGGTGCAAATATTATGAT 57.097 25.926 0.00 0.00 33.19 2.45
2731 4628 0.025770 CCGATAATGCGCGTTCGTTT 59.974 50.000 19.98 2.30 38.14 3.60
2923 4858 2.393710 ATCCCTCCCGATCCCCTCAG 62.394 65.000 0.00 0.00 0.00 3.35
3385 5604 2.821546 TGATAGTGTTGCGATGTAGGC 58.178 47.619 0.00 0.00 0.00 3.93
3394 5613 2.423898 CGATGTAGGCGGTCACCCT 61.424 63.158 0.00 0.00 36.47 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 84 0.320050 TACATGAGCAGCGTGACCAA 59.680 50.000 0.00 0.00 36.97 3.67
127 128 7.524717 TCTTTTGGCAGCTTAGAAAATAAGT 57.475 32.000 0.00 0.00 0.00 2.24
202 203 1.555533 GGGTCCGAAGATGAGGAAGTT 59.444 52.381 0.00 0.00 38.41 2.66
420 421 2.839486 TCAAGAAGGTGAGCGATGTT 57.161 45.000 0.00 0.00 0.00 2.71
532 533 2.306847 CCACAACTAAACCACCAAGCT 58.693 47.619 0.00 0.00 0.00 3.74
547 548 4.199310 CAGGACAGAAGAAAAGACCACAA 58.801 43.478 0.00 0.00 0.00 3.33
644 658 4.355543 TTTCCATGAATACGCAAAGCTC 57.644 40.909 0.00 0.00 0.00 4.09
800 814 1.688311 CCTAGGCTAGCCAGTACACCA 60.688 57.143 34.70 8.56 38.92 4.17
877 891 6.497259 AGAGCCCCGACAATTTATAGATAAGA 59.503 38.462 0.00 0.00 0.00 2.10
936 950 0.813610 CAGTGTGGTGTCGGCTTTGA 60.814 55.000 0.00 0.00 0.00 2.69
959 973 2.429930 CTTGTTCAGTCCCGGCCA 59.570 61.111 2.24 0.00 0.00 5.36
1086 1100 0.240945 CGTGAGCGGCCAAGATTTTT 59.759 50.000 2.24 0.00 0.00 1.94
1196 1219 0.908198 GAGGCAGTGGAAGGAGATGT 59.092 55.000 0.00 0.00 0.00 3.06
1292 1315 1.002430 CCAGGAAGTAACAGAGCTGCA 59.998 52.381 1.02 0.00 0.00 4.41
1300 1323 1.290955 CGCCGTCCAGGAAGTAACA 59.709 57.895 1.32 0.00 45.00 2.41
1303 1326 3.766691 GGCGCCGTCCAGGAAGTA 61.767 66.667 12.58 0.00 45.00 2.24
1364 1393 4.451150 GCTCCGTGGCGACATCCA 62.451 66.667 0.00 0.00 46.14 3.41
1365 1394 4.148825 AGCTCCGTGGCGACATCC 62.149 66.667 0.00 0.00 46.14 3.51
1366 1395 2.583593 GAGCTCCGTGGCGACATC 60.584 66.667 0.87 0.00 46.14 3.06
1367 1396 4.498520 CGAGCTCCGTGGCGACAT 62.499 66.667 8.47 0.00 46.14 3.06
1373 1402 4.899239 GGATGCCGAGCTCCGTGG 62.899 72.222 8.47 4.84 36.31 4.94
1374 1403 4.899239 GGGATGCCGAGCTCCGTG 62.899 72.222 8.47 0.00 36.31 4.94
2731 4628 1.605453 GCGGACACCCTAAATCCCA 59.395 57.895 0.00 0.00 0.00 4.37
2874 4809 0.037326 GATGACTTCAGGTGGCGACA 60.037 55.000 0.00 0.00 38.70 4.35
2923 4858 1.746787 GACGGAGAGAGGAAGGAACTC 59.253 57.143 0.00 0.00 38.49 3.01
3188 5404 1.212195 GGTTCATGGGAAGGGTAGGAC 59.788 57.143 0.00 0.00 32.62 3.85


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

AutoCloner maintained by Alex Coulton.