Multiple sequence alignment - TraesCS1A01G092400

Loading Multiple Alignment...

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 TraesCS1A01G092400 chr1A 100.000 2754 0 0 1 2754 84817931 84820684 0.000000e+00 5086.0
1 TraesCS1A01G092400 chr1A 97.824 2757 50 8 1 2754 115062442 115065191 0.000000e+00 4750.0
2 TraesCS1A01G092400 chr1A 100.000 218 0 0 2932 3149 84820862 84821079 1.360000e-108 403.0
3 TraesCS1A01G092400 chr1A 96.789 218 7 0 2932 3149 115065568 115065785 6.420000e-97 364.0
4 TraesCS1A01G092400 chr4A 98.258 2755 45 3 1 2754 618796112 618793360 0.000000e+00 4819.0
5 TraesCS1A01G092400 chr4A 98.113 2756 47 5 1 2754 618718131 618715379 0.000000e+00 4796.0
6 TraesCS1A01G092400 chr4A 95.909 220 6 3 2932 3149 618793352 618793134 1.390000e-93 353.0
7 TraesCS1A01G092400 chr4A 95.909 220 6 3 2932 3149 618810021 618809803 1.390000e-93 353.0
8 TraesCS1A01G092400 chr4A 95.434 219 9 1 2932 3149 543519746 543519528 6.460000e-92 348.0
9 TraesCS1A01G092400 chr4A 94.545 220 9 3 2932 3149 618714558 618714340 1.400000e-88 337.0
10 TraesCS1A01G092400 chr7A 98.102 2740 41 4 1 2740 139397043 139399771 0.000000e+00 4761.0
11 TraesCS1A01G092400 chr7A 95.074 203 8 2 2948 3149 139400170 139400371 5.070000e-83 318.0
12 TraesCS1A01G092400 chr7A 93.750 112 5 2 2643 2754 139400173 139400282 1.940000e-37 167.0
13 TraesCS1A01G092400 chr7A 78.166 229 39 10 2472 2693 597618913 597619137 5.480000e-28 135.0
14 TraesCS1A01G092400 chr7A 95.652 69 2 1 2686 2754 139400170 139400237 3.320000e-20 110.0
15 TraesCS1A01G092400 chr7A 89.062 64 3 4 2682 2744 391497272 391497332 3.370000e-10 76.8
16 TraesCS1A01G092400 chr2D 94.741 2700 127 13 1 2688 264003544 264000848 0.000000e+00 4185.0
17 TraesCS1A01G092400 chr2D 93.722 223 9 3 2932 3149 264000306 264000084 2.340000e-86 329.0
18 TraesCS1A01G092400 chr1B 92.489 2796 136 52 1 2754 117797105 117799868 0.000000e+00 3932.0
19 TraesCS1A01G092400 chr1B 92.115 2790 157 43 1 2754 118418952 118416190 0.000000e+00 3875.0
20 TraesCS1A01G092400 chr2B 91.004 2790 197 41 1 2754 156049181 156046410 0.000000e+00 3712.0
21 TraesCS1A01G092400 chr3B 90.863 2791 199 41 1 2754 56691737 56688966 0.000000e+00 3690.0
22 TraesCS1A01G092400 chrUn 95.475 221 6 3 2932 3149 411827774 411827993 1.800000e-92 350.0
23 TraesCS1A01G092400 chr4D 90.367 218 18 3 2932 3146 478460238 478460455 1.850000e-72 283.0
24 TraesCS1A01G092400 chr2A 90.541 148 7 3 2546 2693 481280292 481280432 4.150000e-44 189.0
25 TraesCS1A01G092400 chr2A 86.364 132 11 5 2613 2743 297540707 297540582 1.520000e-28 137.0
26 TraesCS1A01G092400 chr3A 80.315 127 17 7 2612 2735 401944072 401944193 4.330000e-14 89.8
27 TraesCS1A01G092400 chr3A 74.667 225 40 16 2515 2733 245302588 245302801 2.010000e-12 84.2


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 TraesCS1A01G092400 chr1A 84817931 84821079 3148 False 2744.5 5086 100.0000 1 3149 2 chr1A.!!$F1 3148
1 TraesCS1A01G092400 chr1A 115062442 115065785 3343 False 2557.0 4750 97.3065 1 3149 2 chr1A.!!$F2 3148
2 TraesCS1A01G092400 chr4A 618793134 618796112 2978 True 2586.0 4819 97.0835 1 3149 2 chr4A.!!$R4 3148
3 TraesCS1A01G092400 chr4A 618714340 618718131 3791 True 2566.5 4796 96.3290 1 3149 2 chr4A.!!$R3 3148
4 TraesCS1A01G092400 chr7A 139397043 139400371 3328 False 1339.0 4761 95.6445 1 3149 4 chr7A.!!$F3 3148
5 TraesCS1A01G092400 chr2D 264000084 264003544 3460 True 2257.0 4185 94.2315 1 3149 2 chr2D.!!$R1 3148
6 TraesCS1A01G092400 chr1B 117797105 117799868 2763 False 3932.0 3932 92.4890 1 2754 1 chr1B.!!$F1 2753
7 TraesCS1A01G092400 chr1B 118416190 118418952 2762 True 3875.0 3875 92.1150 1 2754 1 chr1B.!!$R1 2753
8 TraesCS1A01G092400 chr2B 156046410 156049181 2771 True 3712.0 3712 91.0040 1 2754 1 chr2B.!!$R1 2753
9 TraesCS1A01G092400 chr3B 56688966 56691737 2771 True 3690.0 3690 90.8630 1 2754 1 chr3B.!!$R1 2753

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
761 763 0.322366 TGCCGGCAGTGAATCATTGA 60.322 50.000 29.03 0.0 0.0 2.57 F
1430 1456 3.555168 CCTTCTTATCGCCAGGTGATACC 60.555 52.174 20.63 0.0 35.2 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1589 1615 0.383231 GGAAAATCTCATGGCGCTGG 59.617 55.000 7.64 0.0 0.00 4.85 R
3013 4655 4.885907 CCATACCCTCACGAGTCTAAACTA 59.114 45.833 0.00 0.0 35.28 2.24 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
110 111 5.669904 TGTCCAGGGAAATTATCTATGGTGA 59.330 40.000 0.00 0.00 35.99 4.02
261 262 3.444742 GCATTCACCATTTCCATCTGTCA 59.555 43.478 0.00 0.00 0.00 3.58
299 300 4.039245 GGAGAAGGTCCGATTATGATGACA 59.961 45.833 0.00 0.00 34.84 3.58
333 334 1.152525 AGCCGTATCATCCCGACCT 60.153 57.895 0.00 0.00 0.00 3.85
629 630 7.838079 AGGCTTGCCAAATATGTGAATAATA 57.162 32.000 14.54 0.00 0.00 0.98
761 763 0.322366 TGCCGGCAGTGAATCATTGA 60.322 50.000 29.03 0.00 0.00 2.57
1320 1341 5.577945 CGCAGGCTGATATTTCAAACATTTT 59.422 36.000 20.86 0.00 0.00 1.82
1430 1456 3.555168 CCTTCTTATCGCCAGGTGATACC 60.555 52.174 20.63 0.00 35.20 2.73
1544 1570 4.702831 TGGATGCTATCGATTTGTTGCTA 58.297 39.130 1.71 0.00 0.00 3.49
1589 1615 4.164843 TGCCCCTACATTAACAGATTCC 57.835 45.455 0.00 0.00 0.00 3.01
2098 2124 1.722034 AGAAGTCTGAAGGAGTGGCA 58.278 50.000 0.00 0.00 0.00 4.92
2355 2391 3.712016 TTGCATGAACTAGCTTGGGTA 57.288 42.857 0.00 0.00 0.00 3.69
2573 3404 5.394883 CGTGCCCCAGTTTATACTCTTAAGA 60.395 44.000 4.81 4.81 30.26 2.10
3134 4822 3.093814 GGAATTTCCCATTTACCGGTGT 58.906 45.455 19.93 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 111 5.395324 CGTGTGGAATCCTAAACATAGTCCT 60.395 44.000 0.00 0.00 0.00 3.85
194 195 3.823304 GCCAAGTCAGAGAAATTTGAGGT 59.177 43.478 0.00 0.00 0.00 3.85
261 262 0.325296 TCTCCACGGTAGCATCCCTT 60.325 55.000 0.00 0.00 0.00 3.95
299 300 1.269206 CGGCTCAACAATGCACAAGTT 60.269 47.619 0.00 0.00 0.00 2.66
333 334 1.974265 TTTGAATTGTCGAGCCACCA 58.026 45.000 0.00 0.00 0.00 4.17
448 449 2.568623 AGTGAGGCTGTTTCGGATTT 57.431 45.000 0.00 0.00 0.00 2.17
761 763 5.045797 GTGGTAACCTCTTAAGATGTCCCTT 60.046 44.000 20.39 8.59 0.00 3.95
1320 1341 0.750546 ACCGTGCGTAGAGATAGGCA 60.751 55.000 0.00 0.00 38.34 4.75
1430 1456 3.065510 TGACGAGATTAGAAGCTCCTTCG 59.934 47.826 2.12 0.00 44.34 3.79
1589 1615 0.383231 GGAAAATCTCATGGCGCTGG 59.617 55.000 7.64 0.00 0.00 4.85
1814 1840 4.074627 CAGCATGGATGACATCTCTTCT 57.925 45.455 14.95 5.44 37.84 2.85
2098 2124 4.990526 AGAAACTCAATTGGACATGGAGT 58.009 39.130 5.42 0.00 40.33 3.85
2573 3404 5.537300 AATCATCAAGCGTACTCCATACT 57.463 39.130 0.00 0.00 0.00 2.12
3013 4655 4.885907 CCATACCCTCACGAGTCTAAACTA 59.114 45.833 0.00 0.00 35.28 2.24
3107 4795 5.889289 CCGGTAAATGGGAAATTCCTTAAGA 59.111 40.000 12.28 0.00 36.57 2.10


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

AutoCloner maintained by Alex Coulton.