Multiple sequence alignment - TraesCS3A01G112400

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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 TraesCS3A01G112400 chr3A 100.000 2843 0 0 1 2843 79876640 79873798 0.000000e+00 5251
1 TraesCS3A01G112400 chr3A 95.253 2865 106 18 1 2843 79803408 79800552 0.000000e+00 4510
2 TraesCS3A01G112400 chr3A 93.156 2864 131 28 1 2843 79906213 79903394 0.000000e+00 4143
3 TraesCS3A01G112400 chr3A 83.444 906 139 10 990 1889 138807347 138808247 0.000000e+00 832
4 TraesCS3A01G112400 chr3A 84.058 552 68 6 494 1040 138806813 138807349 5.430000e-142 514
5 TraesCS3A01G112400 chr3D 92.324 2879 141 30 1 2843 68038125 68035291 0.000000e+00 4019
6 TraesCS3A01G112400 chr3D 84.010 1157 167 7 990 2141 127904078 127905221 0.000000e+00 1096
7 TraesCS3A01G112400 chr3D 83.413 627 72 16 429 1040 127903471 127904080 1.150000e-153 553
8 TraesCS3A01G112400 chr3D 74.843 318 59 17 729 1028 71116344 71116030 1.070000e-24 124
9 TraesCS3A01G112400 chr3B 93.236 2395 119 20 456 2843 113983152 113985510 0.000000e+00 3485
10 TraesCS3A01G112400 chr3B 82.957 1725 258 18 429 2141 182202940 182204640 0.000000e+00 1524
11 TraesCS3A01G112400 chr3B 91.946 447 32 3 1 444 113974436 113974881 8.650000e-175 623
12 TraesCS3A01G112400 chr3B 75.079 317 60 15 729 1028 116438026 116437712 2.300000e-26 130
13 TraesCS3A01G112400 chr2A 77.831 839 168 18 1285 2110 545800752 545801585 1.180000e-138 503
14 TraesCS3A01G112400 chr2A 81.154 260 41 8 2111 2369 177658673 177658421 4.800000e-48 202
15 TraesCS3A01G112400 chr2A 77.689 251 51 4 1022 1270 545800445 545800692 6.350000e-32 148
16 TraesCS3A01G112400 chr4D 81.673 251 39 6 2111 2359 416060703 416060948 4.800000e-48 202
17 TraesCS3A01G112400 chr1A 79.845 258 46 6 2111 2368 591612989 591613240 1.740000e-42 183
18 TraesCS3A01G112400 chr7A 79.842 253 42 7 2111 2359 163128931 163129178 2.910000e-40 176
19 TraesCS3A01G112400 chr7A 79.087 263 45 8 2111 2369 163129358 163129614 3.770000e-39 172


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 TraesCS3A01G112400 chr3A 79873798 79876640 2842 True 5251.0 5251 100.0000 1 2843 1 chr3A.!!$R2 2842
1 TraesCS3A01G112400 chr3A 79800552 79803408 2856 True 4510.0 4510 95.2530 1 2843 1 chr3A.!!$R1 2842
2 TraesCS3A01G112400 chr3A 79903394 79906213 2819 True 4143.0 4143 93.1560 1 2843 1 chr3A.!!$R3 2842
3 TraesCS3A01G112400 chr3A 138806813 138808247 1434 False 673.0 832 83.7510 494 1889 2 chr3A.!!$F1 1395
4 TraesCS3A01G112400 chr3D 68035291 68038125 2834 True 4019.0 4019 92.3240 1 2843 1 chr3D.!!$R1 2842
5 TraesCS3A01G112400 chr3D 127903471 127905221 1750 False 824.5 1096 83.7115 429 2141 2 chr3D.!!$F1 1712
6 TraesCS3A01G112400 chr3B 113983152 113985510 2358 False 3485.0 3485 93.2360 456 2843 1 chr3B.!!$F2 2387
7 TraesCS3A01G112400 chr3B 182202940 182204640 1700 False 1524.0 1524 82.9570 429 2141 1 chr3B.!!$F3 1712
8 TraesCS3A01G112400 chr2A 545800445 545801585 1140 False 325.5 503 77.7600 1022 2110 2 chr2A.!!$F1 1088

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
476 480 0.253868 TCTCTCTCTCTCCCTCCCCA 60.254 60.0 0.0 0.0 0.0 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1854 2042 1.179152 CAAGCATGGGATGTCAAGCA 58.821 50.0 0.0 0.0 34.25 3.91 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
38 39 4.399303 GAGGTTTCCTTGACCATGTTATGG 59.601 45.833 6.30 6.30 45.24 2.74
166 167 1.717194 GGACGATTGGTTGAACGCTA 58.283 50.000 0.00 0.00 0.00 4.26
249 251 1.553248 AGCATCAACATTGCCAATGCT 59.447 42.857 17.14 6.24 46.06 3.79
385 389 9.542462 AATATTTCAATGATGAAGGCAATCTTG 57.458 29.630 0.00 0.00 45.82 3.02
475 479 0.478507 CTCTCTCTCTCTCCCTCCCC 59.521 65.000 0.00 0.00 0.00 4.81
476 480 0.253868 TCTCTCTCTCTCCCTCCCCA 60.254 60.000 0.00 0.00 0.00 4.96
1425 1610 5.648960 GCCAAATTCAATTGTTCATTCCCAT 59.351 36.000 5.13 0.00 0.00 4.00
1429 1614 9.005777 CAAATTCAATTGTTCATTCCCATCTTT 57.994 29.630 5.13 0.00 0.00 2.52
1837 2025 3.760684 AGCAAGGATGAAAAGCCTACAAG 59.239 43.478 0.00 0.00 33.20 3.16
1854 2042 4.118168 ACAAGGTTGATCTTCCCATGTT 57.882 40.909 0.00 0.00 0.00 2.71
2090 2287 7.668052 TGCTATTTCCCTATGTAAACAACAGTT 59.332 33.333 0.00 0.00 42.70 3.16
2135 2332 6.122964 ACTCCCTCTGTTCCAAAATATAAGC 58.877 40.000 0.00 0.00 0.00 3.09
2142 2339 7.839907 TCTGTTCCAAAATATAAGCTGCATTT 58.160 30.769 1.02 0.00 0.00 2.32
2161 2358 5.448904 GCATTTGTTTTTGTGCCAGTCAAAT 60.449 36.000 0.00 0.00 35.25 2.32
2175 2372 6.589523 TGCCAGTCAAATTTATGTACATTTGC 59.410 34.615 14.77 9.19 39.34 3.68
2177 2374 7.322664 CCAGTCAAATTTATGTACATTTGCCT 58.677 34.615 14.77 5.56 39.34 4.75
2223 2420 8.068977 TCAACATCTGCATTGCAAAAATAAAAC 58.931 29.630 13.18 0.00 38.41 2.43
2278 2475 7.862372 AGCTAATGATACAAATTTGGTATTGCG 59.138 33.333 21.74 11.75 31.84 4.85
2284 2481 9.508642 TGATACAAATTTGGTATTGCGGATATA 57.491 29.630 21.74 1.48 31.84 0.86
2392 2590 8.697507 AGACACCTTCTATTTTGAAACAGATT 57.302 30.769 0.00 0.00 30.17 2.40
2554 2752 8.288208 GTGATAATTTGCCATATGAAGAGTGAG 58.712 37.037 3.65 0.00 0.00 3.51
2557 2755 5.682234 TTTGCCATATGAAGAGTGAGAGA 57.318 39.130 3.65 0.00 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 3.103742 TCCATTATGGCCAAGGGAAAAC 58.896 45.455 10.96 0.00 35.53 2.43
166 167 0.252467 AGCTAAGGAGTCAGCAGGGT 60.252 55.000 4.00 0.00 40.36 4.34
267 269 0.779997 ACCTTGGTGCCTCCTTCATT 59.220 50.000 0.00 0.00 37.07 2.57
268 270 1.561542 CTACCTTGGTGCCTCCTTCAT 59.438 52.381 2.03 0.00 37.07 2.57
269 271 0.984230 CTACCTTGGTGCCTCCTTCA 59.016 55.000 2.03 0.00 37.07 3.02
385 389 5.034152 CCAAATATGTTGTGATGTAACCGC 58.966 41.667 0.00 0.00 0.00 5.68
475 479 4.083643 GGATCTTTGAGACACACACACATG 60.084 45.833 0.00 0.00 0.00 3.21
476 480 4.067896 GGATCTTTGAGACACACACACAT 58.932 43.478 0.00 0.00 0.00 3.21
974 1010 7.106239 AGCTACTAGCAGTATCAACAATTTGT 58.894 34.615 10.73 0.00 45.56 2.83
1329 1513 3.620374 GCATCTGATGTGACGAGTTGAAT 59.380 43.478 18.19 0.00 0.00 2.57
1521 1708 4.916183 AGGGGTGAATCTTTTGAGAAGAG 58.084 43.478 0.00 0.00 0.00 2.85
1837 2025 2.450476 AGCAACATGGGAAGATCAACC 58.550 47.619 0.00 0.00 0.00 3.77
1854 2042 1.179152 CAAGCATGGGATGTCAAGCA 58.821 50.000 0.00 0.00 34.25 3.91
2090 2287 7.364408 GGGAGTAGTACACAACCATCAAAGATA 60.364 40.741 2.52 0.00 0.00 1.98
2135 2332 2.937799 ACTGGCACAAAAACAAATGCAG 59.062 40.909 0.00 0.00 39.92 4.41
2142 2339 6.820656 ACATAAATTTGACTGGCACAAAAACA 59.179 30.769 7.27 0.00 39.95 2.83
2161 2358 8.815565 TTCAATCCTAGGCAAATGTACATAAA 57.184 30.769 9.21 0.00 0.00 1.40
2253 2450 7.114811 CCGCAATACCAAATTTGTATCATTAGC 59.885 37.037 16.73 12.87 0.00 3.09
2261 2458 7.940137 ACCTATATCCGCAATACCAAATTTGTA 59.060 33.333 16.73 9.57 0.00 2.41
2368 2566 7.809806 CCAATCTGTTTCAAAATAGAAGGTGTC 59.190 37.037 6.11 0.00 39.16 3.67
2392 2590 7.996644 GGGAAAGATAATTAACATACTCCACCA 59.003 37.037 0.00 0.00 0.00 4.17
2528 2726 8.158169 TCACTCTTCATATGGCAAATTATCAC 57.842 34.615 2.13 0.00 0.00 3.06
2662 2861 5.483231 TGCAAGTTCATGGGGAAAATTCATA 59.517 36.000 0.00 0.00 37.23 2.15
2739 2942 4.792068 AGCAGCATGGGTTAGCTTTTATA 58.208 39.130 0.00 0.00 39.50 0.98
2798 3002 7.013846 AGGGATCGAAAATTGTTTTTGAGTGTA 59.986 33.333 10.02 0.00 44.03 2.90


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

AutoCloner maintained by Alex Coulton.