Multiple sequence alignment - TraesCS5A01G424200

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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 TraesCS5A01G424200 chr5A 100.000 2651 0 0 1 2651 609823866 609821216 0.000000e+00 4896
1 TraesCS5A01G424200 chr5A 92.272 854 47 7 439 1290 688243208 688244044 0.000000e+00 1194
2 TraesCS5A01G424200 chr5A 89.630 405 34 4 1380 1777 688244181 688244584 2.350000e-140 508
3 TraesCS5A01G424200 chr5A 89.752 322 31 2 1380 1700 680364945 680365265 6.830000e-111 411
4 TraesCS5A01G424200 chr5A 86.747 249 26 4 1141 1383 680364641 680364888 1.210000e-68 270
5 TraesCS5A01G424200 chr5A 93.805 113 7 0 1724 1836 680365260 680365372 1.260000e-38 171
6 TraesCS5A01G424200 chr5A 100.000 73 0 0 2138 2210 605038938 605038866 4.600000e-28 135
7 TraesCS5A01G424200 chr3A 97.738 2652 48 4 1 2651 697520115 697522755 0.000000e+00 4554
8 TraesCS5A01G424200 chr4A 97.904 2338 43 1 1 2332 17244793 17247130 0.000000e+00 4041
9 TraesCS5A01G424200 chr4A 97.933 387 7 1 2259 2645 17247111 17247496 0.000000e+00 669
10 TraesCS5A01G424200 chr7A 97.384 2332 60 1 1 2332 672599478 672597148 0.000000e+00 3967
11 TraesCS5A01G424200 chr7A 97.170 2332 65 1 1 2332 113794924 113797254 0.000000e+00 3940
12 TraesCS5A01G424200 chr7A 96.868 1788 36 1 545 2332 674116095 674114328 0.000000e+00 2974
13 TraesCS5A01G424200 chr7A 98.011 553 11 0 1 553 674121727 674121175 0.000000e+00 961
14 TraesCS5A01G424200 chr7A 99.746 393 1 0 2259 2651 674114347 674113955 0.000000e+00 721
15 TraesCS5A01G424200 chr7A 99.743 389 1 0 2259 2647 672597167 672596779 0.000000e+00 713
16 TraesCS5A01G424200 chr7A 98.966 387 4 0 2259 2645 113797235 113797621 0.000000e+00 693
17 TraesCS5A01G424200 chr7A 93.805 113 7 0 2008 2120 613712209 613712321 1.260000e-38 171
18 TraesCS5A01G424200 chr7A 98.630 73 1 0 2138 2210 613713189 613713117 2.140000e-26 130
19 TraesCS5A01G424200 chr4B 89.502 943 76 9 439 1374 649491307 649492233 0.000000e+00 1171
20 TraesCS5A01G424200 chr4B 91.228 456 25 2 1380 1835 649492303 649492743 8.120000e-170 606
21 TraesCS5A01G424200 chr4D 86.766 937 62 27 439 1368 503669221 503670102 0.000000e+00 987
22 TraesCS5A01G424200 chr4D 87.676 641 45 12 745 1383 503639662 503640270 0.000000e+00 715
23 TraesCS5A01G424200 chr4D 88.863 431 35 6 1380 1802 503670177 503670602 3.910000e-143 518
24 TraesCS5A01G424200 chr4D 87.250 400 21 13 1436 1835 503641746 503642115 1.890000e-116 429
25 TraesCS5A01G424200 chr4D 93.805 113 7 0 2008 2120 198583169 198583281 1.260000e-38 171
26 TraesCS5A01G424200 chr4D 100.000 73 0 0 2138 2210 198584148 198584076 4.600000e-28 135
27 TraesCS5A01G424200 chr1B 93.980 598 20 4 439 1029 117290240 117289652 0.000000e+00 891
28 TraesCS5A01G424200 chr1B 97.080 411 9 2 2244 2651 117289653 117289243 0.000000e+00 689
29 TraesCS5A01G424200 chr1B 93.888 409 25 0 5 413 117290938 117290530 3.750000e-173 617
30 TraesCS5A01G424200 chr3B 92.290 441 29 4 2215 2651 742768201 742767762 2.900000e-174 621
31 TraesCS5A01G424200 chr3B 91.837 441 30 5 2215 2651 742625195 742624757 6.270000e-171 610
32 TraesCS5A01G424200 chr5D 95.868 363 11 3 2244 2603 358667910 358667549 3.800000e-163 584
33 TraesCS5A01G424200 chr5D 92.171 281 21 1 80 359 358669211 358668931 1.910000e-106 396
34 TraesCS5A01G424200 chr5D 91.538 130 11 0 1854 1983 548028003 548027874 2.100000e-41 180
35 TraesCS5A01G424200 chr5D 95.050 101 5 0 1851 1951 358668096 358667996 2.730000e-35 159
36 TraesCS5A01G424200 chr7D 94.817 328 16 1 33 359 32582892 32582565 6.550000e-141 510
37 TraesCS5A01G424200 chr5B 90.909 132 12 0 1852 1983 692215151 692215020 7.540000e-41 178
38 TraesCS5A01G424200 chr5B 92.920 113 8 0 2008 2120 386154126 386154238 5.870000e-37 165
39 TraesCS5A01G424200 chr5B 100.000 73 0 0 2138 2210 386155100 386155028 4.600000e-28 135


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 TraesCS5A01G424200 chr5A 609821216 609823866 2650 True 4896.000000 4896 100.000000 1 2651 1 chr5A.!!$R2 2650
1 TraesCS5A01G424200 chr5A 688243208 688244584 1376 False 851.000000 1194 90.951000 439 1777 2 chr5A.!!$F2 1338
2 TraesCS5A01G424200 chr5A 680364641 680365372 731 False 284.000000 411 90.101333 1141 1836 3 chr5A.!!$F1 695
3 TraesCS5A01G424200 chr3A 697520115 697522755 2640 False 4554.000000 4554 97.738000 1 2651 1 chr3A.!!$F1 2650
4 TraesCS5A01G424200 chr4A 17244793 17247496 2703 False 2355.000000 4041 97.918500 1 2645 2 chr4A.!!$F1 2644
5 TraesCS5A01G424200 chr7A 672596779 672599478 2699 True 2340.000000 3967 98.563500 1 2647 2 chr7A.!!$R3 2646
6 TraesCS5A01G424200 chr7A 113794924 113797621 2697 False 2316.500000 3940 98.068000 1 2645 2 chr7A.!!$F2 2644
7 TraesCS5A01G424200 chr7A 674113955 674116095 2140 True 1847.500000 2974 98.307000 545 2651 2 chr7A.!!$R4 2106
8 TraesCS5A01G424200 chr7A 674121175 674121727 552 True 961.000000 961 98.011000 1 553 1 chr7A.!!$R2 552
9 TraesCS5A01G424200 chr4B 649491307 649492743 1436 False 888.500000 1171 90.365000 439 1835 2 chr4B.!!$F1 1396
10 TraesCS5A01G424200 chr4D 503669221 503670602 1381 False 752.500000 987 87.814500 439 1802 2 chr4D.!!$F3 1363
11 TraesCS5A01G424200 chr4D 503639662 503642115 2453 False 572.000000 715 87.463000 745 1835 2 chr4D.!!$F2 1090
12 TraesCS5A01G424200 chr1B 117289243 117290938 1695 True 732.333333 891 94.982667 5 2651 3 chr1B.!!$R1 2646
13 TraesCS5A01G424200 chr5D 358667549 358669211 1662 True 379.666667 584 94.363000 80 2603 3 chr5D.!!$R2 2523

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
390 485 0.411848 GGGGGAATTTTGTCAGGGGA 59.588 55.0 0.0 0.0 0.00 4.81 F
1058 1475 0.593128 ATCGTGCAGCTTTTGTGGAC 59.407 50.0 0.0 0.0 33.22 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1314 1731 1.599071 GGAGGCAAAACAAAAGCTTGC 59.401 47.619 0.0 0.0 43.75 4.01 R
2216 4162 7.611467 ACTCATAAATTGCCATCACAACTCTTA 59.389 33.333 0.0 0.0 31.03 2.10 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
265 266 2.100584 ACGAGATGATGAGAAGGACAGC 59.899 50.000 0.00 0.0 0.00 4.40
390 485 0.411848 GGGGGAATTTTGTCAGGGGA 59.588 55.000 0.00 0.0 0.00 4.81
682 1077 4.823790 TTTTTCCGAGTTAAGCTTCACC 57.176 40.909 0.00 0.0 0.00 4.02
730 1131 5.934625 GTCTGTACCATCTGAAACTCACAAT 59.065 40.000 0.00 0.0 0.00 2.71
1058 1475 0.593128 ATCGTGCAGCTTTTGTGGAC 59.407 50.000 0.00 0.0 33.22 4.02
1199 1616 1.745115 GTCCATGCAGTTGCGCCTA 60.745 57.895 4.18 0.0 45.83 3.93
1890 3836 4.101430 AGTTTGTGATTTGATGGTTGGCTT 59.899 37.500 0.00 0.0 0.00 4.35
2090 4036 6.648879 TTATAGGCTTTCTTGTTGCTTGTT 57.351 33.333 0.00 0.0 0.00 2.83
2131 4077 1.194547 CACGATTTGTCTGGGTGAACG 59.805 52.381 0.00 0.0 0.00 3.95
2216 4162 5.079643 ACTGCAAACTAAATTCACCCAGAT 58.920 37.500 0.00 0.0 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
216 217 2.285368 CTCCACCACCCCCTGCTA 60.285 66.667 0.00 0.00 0.00 3.49
237 238 3.998099 TCTCATCATCTCGTTGCCTAG 57.002 47.619 0.00 0.00 0.00 3.02
682 1077 2.036992 GTCCCTGACTAGATGGCATCAG 59.963 54.545 27.93 22.75 38.65 2.90
1058 1475 1.269413 CCTGACAAGCCAAGCACAAAG 60.269 52.381 0.00 0.00 0.00 2.77
1191 1608 3.882888 CCCTTCAGATAATTTAGGCGCAA 59.117 43.478 10.83 0.00 0.00 4.85
1199 1616 5.759059 TCAGTGCATCCCTTCAGATAATTT 58.241 37.500 0.00 0.00 0.00 1.82
1314 1731 1.599071 GGAGGCAAAACAAAAGCTTGC 59.401 47.619 0.00 0.00 43.75 4.01
1890 3836 7.618019 AGCTCTGGATATAACTAAATGACCA 57.382 36.000 0.00 0.00 0.00 4.02
2131 4077 9.717942 AGGAGTATTTGCAGTTCTGAATATATC 57.282 33.333 3.84 3.67 0.00 1.63
2216 4162 7.611467 ACTCATAAATTGCCATCACAACTCTTA 59.389 33.333 0.00 0.00 31.03 2.10


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

AutoCloner maintained by Alex Coulton.