Multiple sequence alignment - TraesCS2A01G435300

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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 TraesCS2A01G435300 chr2A 100.000 2628 0 0 1 2628 687305169 687307796 0.000000e+00 4854
1 TraesCS2A01G435300 chr2A 96.490 1282 39 6 1348 2627 214059070 214060347 0.000000e+00 2113
2 TraesCS2A01G435300 chr2A 98.374 738 11 1 1 737 713164019 713163282 0.000000e+00 1295
3 TraesCS2A01G435300 chr2A 85.981 107 14 1 1275 1381 256213338 256213233 2.140000e-21 113
4 TraesCS2A01G435300 chr2A 82.540 126 20 2 1261 1385 6477912 6477788 2.770000e-20 110
5 TraesCS2A01G435300 chr5D 97.136 1292 24 8 1340 2627 76204490 76205772 0.000000e+00 2169
6 TraesCS2A01G435300 chr5D 89.362 611 41 6 737 1346 160751456 160750869 0.000000e+00 747
7 TraesCS2A01G435300 chr3D 95.264 1288 48 6 1349 2627 141537043 141535760 0.000000e+00 2028
8 TraesCS2A01G435300 chr3D 86.134 238 28 4 2148 2384 601239365 601239132 4.340000e-63 252
9 TraesCS2A01G435300 chr3D 85.641 195 27 1 1941 2134 601240154 601239960 1.230000e-48 204
10 TraesCS2A01G435300 chr3D 80.000 175 26 8 1214 1386 301329272 301329439 1.280000e-23 121
11 TraesCS2A01G435300 chr3A 98.234 736 13 0 1 736 724287103 724287838 0.000000e+00 1288
12 TraesCS2A01G435300 chr4A 98.106 739 12 2 1 737 572696003 572695265 0.000000e+00 1286
13 TraesCS2A01G435300 chr4A 98.103 738 13 1 1 737 5689952 5690689 0.000000e+00 1284
14 TraesCS2A01G435300 chr4A 96.268 777 24 5 1 773 495805419 495804644 0.000000e+00 1269
15 TraesCS2A01G435300 chr4A 82.171 516 55 21 1287 1777 689217873 689218376 2.430000e-110 409
16 TraesCS2A01G435300 chr5B 98.100 737 14 0 1 737 24135238 24134502 0.000000e+00 1284
17 TraesCS2A01G435300 chr5B 97.965 737 15 0 1 737 52379641 52378905 0.000000e+00 1279
18 TraesCS2A01G435300 chr5B 83.130 492 51 16 1310 1777 44882982 44882499 1.120000e-113 420
19 TraesCS2A01G435300 chr1A 98.098 736 14 0 1 736 24914804 24915539 0.000000e+00 1282
20 TraesCS2A01G435300 chr5A 97.965 737 15 0 1 737 57427445 57428181 0.000000e+00 1279
21 TraesCS2A01G435300 chr5A 95.074 609 25 4 2020 2627 385252508 385251904 0.000000e+00 953
22 TraesCS2A01G435300 chr2B 94.066 573 34 0 737 1309 501011606 501011034 0.000000e+00 870
23 TraesCS2A01G435300 chr2B 92.164 587 41 2 737 1318 15507089 15506503 0.000000e+00 824
24 TraesCS2A01G435300 chrUn 92.170 613 47 1 737 1349 40194078 40193467 0.000000e+00 865
25 TraesCS2A01G435300 chr6A 91.830 612 49 1 738 1349 194460005 194459395 0.000000e+00 852
26 TraesCS2A01G435300 chr6B 91.176 544 48 0 782 1325 464513968 464513425 0.000000e+00 739
27 TraesCS2A01G435300 chr6B 88.185 584 47 4 737 1320 432519870 432519309 0.000000e+00 676
28 TraesCS2A01G435300 chr6B 84.106 151 22 2 1264 1413 560665977 560665828 7.580000e-31 145
29 TraesCS2A01G435300 chr7A 88.418 613 48 5 737 1349 417545323 417545912 0.000000e+00 717
30 TraesCS2A01G435300 chr2D 82.017 595 78 19 1349 1924 609289003 609289587 1.830000e-131 479
31 TraesCS2A01G435300 chr4D 80.906 618 76 28 1339 1924 483538129 483537522 1.430000e-122 449
32 TraesCS2A01G435300 chr4D 84.277 159 22 3 1767 1924 483567604 483567448 4.530000e-33 152
33 TraesCS2A01G435300 chr1B 94.779 249 13 0 737 985 491733873 491734121 3.170000e-104 388
34 TraesCS2A01G435300 chr1B 84.478 393 52 7 1382 1773 514359322 514358938 1.910000e-101 379
35 TraesCS2A01G435300 chr1B 87.037 162 18 3 1772 1931 514358910 514358750 2.080000e-41 180
36 TraesCS2A01G435300 chr7D 80.000 235 40 6 929 1158 504525395 504525163 1.620000e-37 167
37 TraesCS2A01G435300 chr1D 83.432 169 23 4 1217 1385 50892407 50892244 4.530000e-33 152


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 TraesCS2A01G435300 chr2A 687305169 687307796 2627 False 4854.0 4854 100.0000 1 2628 1 chr2A.!!$F2 2627
1 TraesCS2A01G435300 chr2A 214059070 214060347 1277 False 2113.0 2113 96.4900 1348 2627 1 chr2A.!!$F1 1279
2 TraesCS2A01G435300 chr2A 713163282 713164019 737 True 1295.0 1295 98.3740 1 737 1 chr2A.!!$R3 736
3 TraesCS2A01G435300 chr5D 76204490 76205772 1282 False 2169.0 2169 97.1360 1340 2627 1 chr5D.!!$F1 1287
4 TraesCS2A01G435300 chr5D 160750869 160751456 587 True 747.0 747 89.3620 737 1346 1 chr5D.!!$R1 609
5 TraesCS2A01G435300 chr3D 141535760 141537043 1283 True 2028.0 2028 95.2640 1349 2627 1 chr3D.!!$R1 1278
6 TraesCS2A01G435300 chr3D 601239132 601240154 1022 True 228.0 252 85.8875 1941 2384 2 chr3D.!!$R2 443
7 TraesCS2A01G435300 chr3A 724287103 724287838 735 False 1288.0 1288 98.2340 1 736 1 chr3A.!!$F1 735
8 TraesCS2A01G435300 chr4A 572695265 572696003 738 True 1286.0 1286 98.1060 1 737 1 chr4A.!!$R2 736
9 TraesCS2A01G435300 chr4A 5689952 5690689 737 False 1284.0 1284 98.1030 1 737 1 chr4A.!!$F1 736
10 TraesCS2A01G435300 chr4A 495804644 495805419 775 True 1269.0 1269 96.2680 1 773 1 chr4A.!!$R1 772
11 TraesCS2A01G435300 chr4A 689217873 689218376 503 False 409.0 409 82.1710 1287 1777 1 chr4A.!!$F2 490
12 TraesCS2A01G435300 chr5B 24134502 24135238 736 True 1284.0 1284 98.1000 1 737 1 chr5B.!!$R1 736
13 TraesCS2A01G435300 chr5B 52378905 52379641 736 True 1279.0 1279 97.9650 1 737 1 chr5B.!!$R3 736
14 TraesCS2A01G435300 chr1A 24914804 24915539 735 False 1282.0 1282 98.0980 1 736 1 chr1A.!!$F1 735
15 TraesCS2A01G435300 chr5A 57427445 57428181 736 False 1279.0 1279 97.9650 1 737 1 chr5A.!!$F1 736
16 TraesCS2A01G435300 chr5A 385251904 385252508 604 True 953.0 953 95.0740 2020 2627 1 chr5A.!!$R1 607
17 TraesCS2A01G435300 chr2B 501011034 501011606 572 True 870.0 870 94.0660 737 1309 1 chr2B.!!$R2 572
18 TraesCS2A01G435300 chr2B 15506503 15507089 586 True 824.0 824 92.1640 737 1318 1 chr2B.!!$R1 581
19 TraesCS2A01G435300 chrUn 40193467 40194078 611 True 865.0 865 92.1700 737 1349 1 chrUn.!!$R1 612
20 TraesCS2A01G435300 chr6A 194459395 194460005 610 True 852.0 852 91.8300 738 1349 1 chr6A.!!$R1 611
21 TraesCS2A01G435300 chr6B 464513425 464513968 543 True 739.0 739 91.1760 782 1325 1 chr6B.!!$R2 543
22 TraesCS2A01G435300 chr6B 432519309 432519870 561 True 676.0 676 88.1850 737 1320 1 chr6B.!!$R1 583
23 TraesCS2A01G435300 chr7A 417545323 417545912 589 False 717.0 717 88.4180 737 1349 1 chr7A.!!$F1 612
24 TraesCS2A01G435300 chr2D 609289003 609289587 584 False 479.0 479 82.0170 1349 1924 1 chr2D.!!$F1 575
25 TraesCS2A01G435300 chr4D 483537522 483538129 607 True 449.0 449 80.9060 1339 1924 1 chr4D.!!$R1 585
26 TraesCS2A01G435300 chr1B 514358750 514359322 572 True 279.5 379 85.7575 1382 1931 2 chr1B.!!$R1 549

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
799 811 0.541998 TCTTCCTCGCCTCACCTCAA 60.542 55.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2399 3103 1.724148 TTCCACCATTGCCCCTCACA 61.724 55.0 0.0 0.0 0.0 3.58 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
156 158 8.790718 AGTCTCTTTACTCGTTCTGTAATACAA 58.209 33.333 0.00 0.00 31.13 2.41
330 333 7.350382 TGTAATGCTCCTTTATAATCACCCAA 58.650 34.615 0.00 0.00 0.00 4.12
376 379 1.613437 CAAAGTGTTCCTCCGGCAAAT 59.387 47.619 0.00 0.00 0.00 2.32
595 599 4.582656 AGCTAGTCAAGTAGAGGCATACTG 59.417 45.833 3.52 0.14 36.14 2.74
799 811 0.541998 TCTTCCTCGCCTCACCTCAA 60.542 55.000 0.00 0.00 0.00 3.02
807 819 0.747283 GCCTCACCTCAATGCTCCTG 60.747 60.000 0.00 0.00 0.00 3.86
899 911 4.394712 GCGGCTGTACCCTGCACT 62.395 66.667 8.97 0.00 37.27 4.40
969 981 1.429299 TCTCACTTCTCTCCCTCACCA 59.571 52.381 0.00 0.00 0.00 4.17
973 985 1.229529 TTCTCTCCCTCACCACCCC 60.230 63.158 0.00 0.00 0.00 4.95
990 1002 1.304052 CCGTCCCATTTCTGCCCAA 60.304 57.895 0.00 0.00 0.00 4.12
993 1005 1.177401 GTCCCATTTCTGCCCAAGAC 58.823 55.000 0.00 0.00 33.46 3.01
995 1007 0.972471 CCCATTTCTGCCCAAGACCC 60.972 60.000 0.00 0.00 33.46 4.46
1135 1147 2.282674 CCCTGCAAGCTTCAGCCA 60.283 61.111 16.09 3.78 43.38 4.75
1136 1148 1.681327 CCCTGCAAGCTTCAGCCAT 60.681 57.895 16.09 0.00 43.38 4.40
1179 1191 1.082104 CCCAAAACGAGAGCAACGC 60.082 57.895 0.00 0.00 0.00 4.84
1180 1192 1.646540 CCAAAACGAGAGCAACGCA 59.353 52.632 0.00 0.00 0.00 5.24
1181 1193 0.028770 CCAAAACGAGAGCAACGCAA 59.971 50.000 0.00 0.00 0.00 4.85
1183 1195 0.307760 AAAACGAGAGCAACGCAAGG 59.692 50.000 0.00 0.00 46.39 3.61
1184 1196 0.814010 AAACGAGAGCAACGCAAGGT 60.814 50.000 0.00 0.00 46.39 3.50
1185 1197 0.814010 AACGAGAGCAACGCAAGGTT 60.814 50.000 0.00 0.00 46.39 3.50
1197 1209 5.508200 AACGCAAGGTTGAATACTCAAAA 57.492 34.783 0.00 0.00 41.67 2.44
1198 1210 4.855531 ACGCAAGGTTGAATACTCAAAAC 58.144 39.130 0.00 0.00 41.67 2.43
1199 1211 4.226761 CGCAAGGTTGAATACTCAAAACC 58.773 43.478 0.00 0.00 43.18 3.27
1200 1212 4.261405 CGCAAGGTTGAATACTCAAAACCA 60.261 41.667 6.23 0.00 43.18 3.67
1249 1305 6.231211 ACGTTTTCTCACAGATATCCACTTT 58.769 36.000 0.00 0.00 0.00 2.66
1285 1341 5.534407 GGGTTCAATTACCGAAAAACACAT 58.466 37.500 0.00 0.00 39.18 3.21
1431 1513 4.361783 TGATGGACCAATTGAGAGTAGGA 58.638 43.478 7.12 0.00 0.00 2.94
1660 1742 3.741249 TGAGCGTTGTTACCATGGTTAA 58.259 40.909 25.38 13.38 0.00 2.01
1773 1855 8.870116 TGATATATGTGCTGAAGTTACCTGTAT 58.130 33.333 0.00 0.00 0.00 2.29
2212 2914 3.676172 CGTAACACTCTAATTTCACGCCA 59.324 43.478 0.00 0.00 0.00 5.69
2399 3103 2.196997 TAGGCGGCAGAGGCATGTTT 62.197 55.000 13.08 0.00 43.71 2.83
2574 3278 2.351726 GCCGCGAGTTCAAAATAGACAT 59.648 45.455 8.23 0.00 0.00 3.06
2586 3290 9.241317 GTTCAAAATAGACATGAGCAAATATGG 57.759 33.333 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
156 158 3.350219 AATGAGTTAGTTGCGGGATGT 57.650 42.857 0.00 0.00 0.00 3.06
376 379 5.366477 TGACTATGAGATTATGCAACTCCCA 59.634 40.000 0.00 0.00 0.00 4.37
595 599 4.632153 ACATAGACAAACAGAGTGTCACC 58.368 43.478 7.26 0.00 46.44 4.02
722 727 3.279434 GCGGAACCTGAAGGAAATATGT 58.721 45.455 2.62 0.00 38.94 2.29
799 811 1.273269 AAGCAGGAGAGCAGGAGCAT 61.273 55.000 0.00 0.00 45.49 3.79
807 819 2.236382 CGCGATGAAGCAGGAGAGC 61.236 63.158 0.00 0.00 36.85 4.09
911 923 1.178276 GACATGAGGTCAGACGAGGT 58.822 55.000 0.00 0.00 46.19 3.85
969 981 2.355115 GCAGAAATGGGACGGGGT 59.645 61.111 0.00 0.00 0.00 4.95
973 985 0.322456 TCTTGGGCAGAAATGGGACG 60.322 55.000 0.00 0.00 0.00 4.79
979 991 1.678970 GCGGGTCTTGGGCAGAAAT 60.679 57.895 0.00 0.00 31.28 2.17
990 1002 4.552365 CATGGCATCCGCGGGTCT 62.552 66.667 27.83 7.73 39.92 3.85
993 1005 4.648626 ATCCATGGCATCCGCGGG 62.649 66.667 27.83 11.74 39.92 6.13
995 1007 3.052082 GGATCCATGGCATCCGCG 61.052 66.667 20.62 0.00 39.92 6.46
1031 1043 2.599281 TGACGACGAGGAAGGCCA 60.599 61.111 5.01 0.00 36.29 5.36
1135 1147 4.212913 ATGCAGAGCGTCGGCGAT 62.213 61.111 16.53 6.82 46.35 4.58
1136 1148 4.854784 GATGCAGAGCGTCGGCGA 62.855 66.667 16.53 4.99 46.35 5.54
1179 1191 6.142818 TGTGGTTTTGAGTATTCAACCTTG 57.857 37.500 9.69 0.00 42.79 3.61
1180 1192 6.239289 CCATGTGGTTTTGAGTATTCAACCTT 60.239 38.462 9.69 0.00 42.79 3.50
1181 1193 5.243730 CCATGTGGTTTTGAGTATTCAACCT 59.756 40.000 9.69 0.00 42.79 3.50
1182 1194 5.469479 CCATGTGGTTTTGAGTATTCAACC 58.531 41.667 0.00 1.33 42.79 3.77
1198 1210 7.812648 TCGTTTTTATAGAAAGAACCATGTGG 58.187 34.615 0.00 0.00 42.17 4.17
1199 1211 9.672086 TTTCGTTTTTATAGAAAGAACCATGTG 57.328 29.630 0.00 0.00 31.25 3.21
1200 1212 9.673454 GTTTCGTTTTTATAGAAAGAACCATGT 57.327 29.630 0.00 0.00 34.96 3.21
1249 1305 2.540265 TGAACCCGCGGTACTTTTTA 57.460 45.000 26.12 2.81 33.12 1.52
1326 1382 4.632538 AATAATAAAGCACGGGTTGAGC 57.367 40.909 0.00 0.00 0.00 4.26
1368 1424 2.094545 GTCATTTTTCTCCCGCTGCAAT 60.095 45.455 0.00 0.00 0.00 3.56
1374 1430 1.800681 CCCGTCATTTTTCTCCCGC 59.199 57.895 0.00 0.00 0.00 6.13
1660 1742 8.021396 GCTATTTCTTCAGTCGGTGTAATTTTT 58.979 33.333 0.00 0.00 0.00 1.94
2092 2213 2.629051 GGTTTCGCCTTACACATAGCT 58.371 47.619 0.00 0.00 0.00 3.32
2399 3103 1.724148 TTCCACCATTGCCCCTCACA 61.724 55.000 0.00 0.00 0.00 3.58
2574 3278 6.714810 ACACTACAAAGTTCCATATTTGCTCA 59.285 34.615 0.00 0.00 39.49 4.26


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

AutoCloner maintained by Alex Coulton.