Multiple sequence alignment - TraesCS6B01G099100

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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 TraesCS6B01G099100 chr6B 100.000 2516 0 0 1 2516 76599476 76596961 0.000000e+00 4647
1 TraesCS6B01G099100 chr6B 96.694 1603 53 0 912 2514 76733990 76732388 0.000000e+00 2667
2 TraesCS6B01G099100 chr6B 87.905 2282 254 16 1 2269 118823683 118821411 0.000000e+00 2665
3 TraesCS6B01G099100 chr6B 96.408 863 28 3 1 860 76742311 76741449 0.000000e+00 1419
4 TraesCS6B01G099100 chr6D 88.356 2336 234 30 1 2316 53309093 53311410 0.000000e+00 2772
5 TraesCS6B01G099100 chr6D 87.371 2328 260 22 1 2316 51624974 51622669 0.000000e+00 2639
6 TraesCS6B01G099100 chr6A 86.958 2331 270 25 1 2316 62490030 62487719 0.000000e+00 2590
7 TraesCS6B01G099100 chr6A 88.503 1783 172 12 516 2289 42389528 42387770 0.000000e+00 2126
8 TraesCS6B01G099100 chr6A 87.942 1783 174 11 516 2289 42208617 42206867 0.000000e+00 2063
9 TraesCS6B01G099100 chr6A 91.195 477 35 5 1 473 42209088 42208615 2.110000e-180 641
10 TraesCS6B01G099100 chr6A 90.985 477 36 5 1 473 42389999 42389526 9.820000e-179 636
11 TraesCS6B01G099100 chrUn 89.210 1557 152 9 768 2316 105245674 105247222 0.000000e+00 1930
12 TraesCS6B01G099100 chrUn 91.213 569 40 4 1 566 105245112 105245673 0.000000e+00 765
13 TraesCS6B01G099100 chrUn 90.520 327 26 3 1 324 345248608 345248284 6.430000e-116 427
14 TraesCS6B01G099100 chrUn 90.625 192 17 1 2326 2516 2683402 2683211 1.160000e-63 254
15 TraesCS6B01G099100 chr2B 93.467 199 12 1 2318 2516 100323129 100323326 6.810000e-76 294
16 TraesCS6B01G099100 chr2B 90.155 193 16 3 2318 2509 486310692 486310882 5.370000e-62 248
17 TraesCS6B01G099100 chr1B 91.192 193 17 0 2323 2515 370384280 370384472 1.920000e-66 263
18 TraesCS6B01G099100 chr1B 89.500 200 20 1 2317 2515 370392549 370392748 4.150000e-63 252
19 TraesCS6B01G099100 chr5B 89.899 198 19 1 2318 2514 266806827 266806630 1.160000e-63 254
20 TraesCS6B01G099100 chr5B 89.848 197 20 0 2318 2514 450947584 450947780 1.160000e-63 254
21 TraesCS6B01G099100 chr5B 88.889 198 21 1 2318 2514 86646586 86646389 2.500000e-60 243


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 TraesCS6B01G099100 chr6B 76596961 76599476 2515 True 4647.0 4647 100.0000 1 2516 1 chr6B.!!$R1 2515
1 TraesCS6B01G099100 chr6B 76732388 76733990 1602 True 2667.0 2667 96.6940 912 2514 1 chr6B.!!$R2 1602
2 TraesCS6B01G099100 chr6B 118821411 118823683 2272 True 2665.0 2665 87.9050 1 2269 1 chr6B.!!$R4 2268
3 TraesCS6B01G099100 chr6B 76741449 76742311 862 True 1419.0 1419 96.4080 1 860 1 chr6B.!!$R3 859
4 TraesCS6B01G099100 chr6D 53309093 53311410 2317 False 2772.0 2772 88.3560 1 2316 1 chr6D.!!$F1 2315
5 TraesCS6B01G099100 chr6D 51622669 51624974 2305 True 2639.0 2639 87.3710 1 2316 1 chr6D.!!$R1 2315
6 TraesCS6B01G099100 chr6A 62487719 62490030 2311 True 2590.0 2590 86.9580 1 2316 1 chr6A.!!$R1 2315
7 TraesCS6B01G099100 chr6A 42387770 42389999 2229 True 1381.0 2126 89.7440 1 2289 2 chr6A.!!$R3 2288
8 TraesCS6B01G099100 chr6A 42206867 42209088 2221 True 1352.0 2063 89.5685 1 2289 2 chr6A.!!$R2 2288
9 TraesCS6B01G099100 chrUn 105245112 105247222 2110 False 1347.5 1930 90.2115 1 2316 2 chrUn.!!$F1 2315

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
890 900 2.431057 AGAGAACAAACGAGTGAGGTGT 59.569 45.455 0.0 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2493 2529 1.541889 GGCATGCATAGCAGCTAGTCA 60.542 52.381 21.36 8.41 43.65 3.41 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
111 118 9.685276 TTGTCATGTATGAATAAATCCAGTTCT 57.315 29.630 0.00 0.00 38.75 3.01
216 223 3.945921 TCTAGGATGGTGTGAAGTAGACG 59.054 47.826 0.00 0.00 0.00 4.18
640 650 6.633234 GTCTTGAAAAACTTTAGGAAGAAGCG 59.367 38.462 0.00 0.00 36.69 4.68
795 805 9.745018 CCAAATATATTCCAGGTCAAGTATGAT 57.255 33.333 0.00 0.00 38.01 2.45
879 889 7.011857 AGTGATCTGAAGAACAAGAGAACAAAC 59.988 37.037 0.00 0.00 0.00 2.93
890 900 2.431057 AGAGAACAAACGAGTGAGGTGT 59.569 45.455 0.00 0.00 0.00 4.16
987 998 6.992123 TCAGTTTCATACAACACATTCTGACT 59.008 34.615 0.00 0.00 0.00 3.41
1234 1248 3.496692 CCACAACAAAGATGAGGACCTCA 60.497 47.826 26.28 26.28 44.99 3.86
1356 1370 3.314080 ACGAGATACTAGAGCTTGCAGAC 59.686 47.826 0.00 0.00 0.00 3.51
1412 1426 4.177783 GAGGAAATGGAGTCGAAGAAGAC 58.822 47.826 0.00 0.00 39.69 3.01
1449 1463 1.418334 AGATGCGGCTGGAGAACTAT 58.582 50.000 0.00 0.00 0.00 2.12
1523 1537 2.159226 CGACAAGGATCTAGGGTGTGTC 60.159 54.545 0.00 0.00 0.00 3.67
1687 1710 5.571741 GCTTTCATGTGTGAATGTCTCAATG 59.428 40.000 0.00 0.00 43.49 2.82
1694 1717 7.160547 TGTGTGAATGTCTCAATGCATTATT 57.839 32.000 12.53 7.85 35.69 1.40
1814 1841 1.224965 GGAATCATCTCGCTCTTGCC 58.775 55.000 0.00 0.00 35.36 4.52
1830 1857 2.530460 TGCCACTATTGCCAAATCCT 57.470 45.000 0.00 0.00 0.00 3.24
1875 1902 7.149202 ACCCATAGTCATTGCTTAATTCCTA 57.851 36.000 0.00 0.00 0.00 2.94
1975 2002 3.713826 AATGTCGGTTGGTGGTAGATT 57.286 42.857 0.00 0.00 0.00 2.40
2301 2337 3.062639 CACGGATCATCTAGTGTTTGTGC 59.937 47.826 0.00 0.00 0.00 4.57
2316 2352 5.961843 GTGTTTGTGCGATCTCATTATTCTG 59.038 40.000 0.00 0.00 0.00 3.02
2360 2396 4.963318 GATCACATGGATCCCTTCTACA 57.037 45.455 9.90 0.00 45.58 2.74
2408 2444 1.806542 AGCATGTCCAACGATCAACAC 59.193 47.619 0.00 0.00 0.00 3.32
2409 2445 1.535028 GCATGTCCAACGATCAACACA 59.465 47.619 0.00 0.00 0.00 3.72
2460 2496 3.171528 AGAAGCGTAAAACCCTAGTCCT 58.828 45.455 0.00 0.00 0.00 3.85
2514 2550 0.250640 ACTAGCTGCTATGCATGCCC 60.251 55.000 16.68 1.38 38.13 5.36
2515 2551 0.250597 CTAGCTGCTATGCATGCCCA 60.251 55.000 16.68 6.26 38.13 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 2.992817 AATCACCACCCCAAAGCGCA 62.993 55.000 11.47 0.00 0.00 6.09
17 18 2.275380 AATCACCACCCCAAAGCGC 61.275 57.895 0.00 0.00 0.00 5.92
99 103 6.302535 TCAACCGGATTAGAACTGGATTTA 57.697 37.500 9.46 0.00 37.25 1.40
314 323 6.962686 TCTTCATCATGAACACAAGAAACAG 58.037 36.000 0.00 0.00 32.21 3.16
615 625 6.633234 CGCTTCTTCCTAAAGTTTTTCAAGAC 59.367 38.462 0.00 0.00 33.95 3.01
795 805 6.183360 CCGTTTATTAGCCTTTAATGCTTGGA 60.183 38.462 0.00 0.00 40.23 3.53
879 889 3.625897 TGCCCCACACCTCACTCG 61.626 66.667 0.00 0.00 0.00 4.18
987 998 1.131638 GGGCCATCAGATCTGTGGTA 58.868 55.000 29.25 13.18 35.57 3.25
1070 1081 3.168528 ACGACACCCCCTTGCACT 61.169 61.111 0.00 0.00 0.00 4.40
1095 1106 3.495100 CCTTGAAAGTACTCTGGTGTGCT 60.495 47.826 0.00 0.00 34.46 4.40
1234 1248 1.271379 CCCGACATGAAGAGGGTTGTT 60.271 52.381 0.00 0.00 39.05 2.83
1292 1306 2.183811 CGAGTGAGAGCAGCCAGG 59.816 66.667 0.00 0.00 0.00 4.45
1377 1391 3.118223 CCATTTCCTCCACTAGGTCCTTC 60.118 52.174 0.00 0.00 46.62 3.46
1403 1417 1.133216 TCTCCATCTGCGTCTTCTTCG 59.867 52.381 0.00 0.00 0.00 3.79
1412 1426 3.449528 TCTTCTCATTCTCCATCTGCG 57.550 47.619 0.00 0.00 0.00 5.18
1523 1537 5.389859 TGAAAAACAACCTAGATGCATGG 57.610 39.130 2.46 1.00 0.00 3.66
1744 1769 4.340666 TCTCAATGAGCTCCACAGAGTATC 59.659 45.833 12.15 0.00 42.59 2.24
1814 1841 5.066505 GTGAAGGTAGGATTTGGCAATAGTG 59.933 44.000 0.00 0.00 0.00 2.74
1830 1857 2.999928 AGAAAGAAGGGGGTGAAGGTA 58.000 47.619 0.00 0.00 0.00 3.08
1875 1902 2.040813 AGTGAGGTCAAGCAATGTGGAT 59.959 45.455 0.00 0.00 0.00 3.41
1909 1936 6.045318 CACCACAAGTATGGAGAGTAATCAG 58.955 44.000 0.00 0.00 43.02 2.90
1975 2002 5.815740 GGAGCTGAAGACATACGGAAAATTA 59.184 40.000 0.00 0.00 0.00 1.40
2254 2290 8.723311 TGTATGTGTTAATTACTACCTTTGTGC 58.277 33.333 0.00 0.00 0.00 4.57
2301 2337 4.564041 CCCTGACCAGAATAATGAGATCG 58.436 47.826 0.00 0.00 0.00 3.69
2316 2352 1.823169 TAGGTGTCGTTGCCCTGACC 61.823 60.000 0.00 0.00 34.18 4.02
2360 2396 2.685380 CCCTCTCTCCCGCCAACT 60.685 66.667 0.00 0.00 0.00 3.16
2408 2444 6.019779 TCGAACCTGGTTAAAAATCCATTG 57.980 37.500 12.96 0.00 33.01 2.82
2409 2445 5.336451 GCTCGAACCTGGTTAAAAATCCATT 60.336 40.000 12.96 0.00 33.01 3.16
2493 2529 1.541889 GGCATGCATAGCAGCTAGTCA 60.542 52.381 21.36 8.41 43.65 3.41


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

AutoCloner maintained by Alex Coulton.