Multiple sequence alignment - TraesCS6A01G117700

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 TraesCS6A01G117700 chr6A 100.000 3312 0 0 1 3312 88095242 88098553 0.000000e+00 6117.0
1 TraesCS6A01G117700 chr6A 97.865 3278 48 4 43 3312 479403924 479407187 0.000000e+00 5646.0
2 TraesCS6A01G117700 chr6A 92.308 91 4 2 41 128 479403849 479403939 3.470000e-25 126.0
3 TraesCS6A01G117700 chr5B 98.915 3226 25 3 97 3312 522908154 522904929 0.000000e+00 5755.0
4 TraesCS6A01G117700 chr5B 100.000 28 0 0 53 80 522908181 522908154 6.000000e-03 52.8
5 TraesCS6A01G117700 chr7A 98.179 3294 47 6 31 3312 671188841 671192133 0.000000e+00 5738.0
6 TraesCS6A01G117700 chr7A 96.123 619 20 1 41 659 163373937 163373323 0.000000e+00 1007.0
7 TraesCS6A01G117700 chr7D 97.504 2925 48 10 403 3312 28369167 28366253 0.000000e+00 4974.0
8 TraesCS6A01G117700 chr7D 93.872 359 16 4 44 402 28383197 28382845 1.350000e-148 536.0
9 TraesCS6A01G117700 chr7B 87.724 2346 238 26 1001 3312 133496924 133494595 0.000000e+00 2691.0
10 TraesCS6A01G117700 chr5D 88.889 2160 207 15 1167 3312 245298147 245300287 0.000000e+00 2628.0
11 TraesCS6A01G117700 chr4A 85.910 1895 214 26 1001 2860 281409988 281411864 0.000000e+00 1971.0
12 TraesCS6A01G117700 chr4A 91.828 465 30 2 2856 3312 281416891 281417355 2.790000e-180 641.0
13 TraesCS6A01G117700 chr1A 98.064 1033 12 2 2288 3312 549415506 549416538 0.000000e+00 1790.0
14 TraesCS6A01G117700 chr1A 97.990 796 12 3 40 832 549414713 549415507 0.000000e+00 1378.0
15 TraesCS6A01G117700 chr2D 80.365 932 104 45 210 1111 14462990 14463872 4.660000e-178 634.0
16 TraesCS6A01G117700 chr2D 88.060 134 10 5 48 178 14462863 14462993 1.590000e-33 154.0


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 TraesCS6A01G117700 chr6A 88095242 88098553 3311 False 6117.0 6117 100.0000 1 3312 1 chr6A.!!$F1 3311
1 TraesCS6A01G117700 chr6A 479403849 479407187 3338 False 2886.0 5646 95.0865 41 3312 2 chr6A.!!$F2 3271
2 TraesCS6A01G117700 chr5B 522904929 522908181 3252 True 2903.9 5755 99.4575 53 3312 2 chr5B.!!$R1 3259
3 TraesCS6A01G117700 chr7A 671188841 671192133 3292 False 5738.0 5738 98.1790 31 3312 1 chr7A.!!$F1 3281
4 TraesCS6A01G117700 chr7A 163373323 163373937 614 True 1007.0 1007 96.1230 41 659 1 chr7A.!!$R1 618
5 TraesCS6A01G117700 chr7D 28366253 28369167 2914 True 4974.0 4974 97.5040 403 3312 1 chr7D.!!$R1 2909
6 TraesCS6A01G117700 chr7B 133494595 133496924 2329 True 2691.0 2691 87.7240 1001 3312 1 chr7B.!!$R1 2311
7 TraesCS6A01G117700 chr5D 245298147 245300287 2140 False 2628.0 2628 88.8890 1167 3312 1 chr5D.!!$F1 2145
8 TraesCS6A01G117700 chr4A 281409988 281411864 1876 False 1971.0 1971 85.9100 1001 2860 1 chr4A.!!$F1 1859
9 TraesCS6A01G117700 chr1A 549414713 549416538 1825 False 1584.0 1790 98.0270 40 3312 2 chr1A.!!$F1 3272
10 TraesCS6A01G117700 chr2D 14462863 14463872 1009 False 394.0 634 84.2125 48 1111 2 chr2D.!!$F1 1063

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
35 36 0.400213 ACACGGCCTGGAATCAGAAA 59.600 50.000 0.0 0.0 43.49 2.52 F
36 37 0.804989 CACGGCCTGGAATCAGAAAC 59.195 55.000 0.0 0.0 43.49 2.78 F
37 38 0.400213 ACGGCCTGGAATCAGAAACA 59.600 50.000 0.0 0.0 43.49 2.83 F
38 39 1.202879 ACGGCCTGGAATCAGAAACAA 60.203 47.619 0.0 0.0 43.49 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1864 2011 2.261361 CGCATGTCCGACTCACCA 59.739 61.111 0.00 0.0 0.00 4.17 R
2101 2248 2.651642 AGGGGTCCTCTAGCTTCTTT 57.348 50.000 0.00 0.0 0.00 2.52 R
2295 2442 7.884354 ACCACAATGGCTAATTTTGATCATTTT 59.116 29.630 0.00 0.0 42.67 1.82 R
3040 3194 7.574967 CGGAAAATTTTACCTTGTAGATGCTGT 60.575 37.037 7.58 0.0 0.00 4.40 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
22 23 5.941948 AAATAGCAAAGGATATACACGGC 57.058 39.130 0.00 0.00 0.00 5.68
23 24 2.256117 AGCAAAGGATATACACGGCC 57.744 50.000 0.00 0.00 0.00 6.13
24 25 1.768870 AGCAAAGGATATACACGGCCT 59.231 47.619 0.00 0.00 0.00 5.19
25 26 1.873591 GCAAAGGATATACACGGCCTG 59.126 52.381 0.00 0.21 0.00 4.85
26 27 2.494059 CAAAGGATATACACGGCCTGG 58.506 52.381 0.00 0.00 0.00 4.45
27 28 2.097110 AAGGATATACACGGCCTGGA 57.903 50.000 0.00 0.00 0.00 3.86
28 29 2.097110 AGGATATACACGGCCTGGAA 57.903 50.000 0.00 0.00 0.00 3.53
29 30 2.621070 AGGATATACACGGCCTGGAAT 58.379 47.619 0.00 0.00 0.00 3.01
30 31 2.567615 AGGATATACACGGCCTGGAATC 59.432 50.000 0.00 3.70 0.00 2.52
31 32 2.301870 GGATATACACGGCCTGGAATCA 59.698 50.000 0.00 0.00 0.00 2.57
32 33 3.589988 GATATACACGGCCTGGAATCAG 58.410 50.000 0.00 0.00 40.59 2.90
33 34 1.496060 ATACACGGCCTGGAATCAGA 58.504 50.000 0.00 0.00 43.49 3.27
34 35 1.271856 TACACGGCCTGGAATCAGAA 58.728 50.000 0.00 0.00 43.49 3.02
35 36 0.400213 ACACGGCCTGGAATCAGAAA 59.600 50.000 0.00 0.00 43.49 2.52
36 37 0.804989 CACGGCCTGGAATCAGAAAC 59.195 55.000 0.00 0.00 43.49 2.78
37 38 0.400213 ACGGCCTGGAATCAGAAACA 59.600 50.000 0.00 0.00 43.49 2.83
38 39 1.202879 ACGGCCTGGAATCAGAAACAA 60.203 47.619 0.00 0.00 43.49 2.83
195 286 7.609532 CCATTCTCTATTTCACAGGAAAGTTCT 59.390 37.037 0.00 0.00 45.58 3.01
199 290 8.210946 TCTCTATTTCACAGGAAAGTTCTCAAA 58.789 33.333 0.00 0.00 45.58 2.69
204 295 4.640201 TCACAGGAAAGTTCTCAAAAGGTG 59.360 41.667 0.00 0.00 0.00 4.00
1319 1466 1.234615 ATGTGCCTGGTTTTCGGACG 61.235 55.000 0.00 0.00 0.00 4.79
1466 1613 5.410067 ACTGTGAAAAAGTTGTTGGATGTG 58.590 37.500 0.00 0.00 19.07 3.21
1864 2011 3.022557 TCACCTACTATGCCGGTTACT 57.977 47.619 1.90 0.00 0.00 2.24
2101 2248 1.473677 CGATTTGCTGCCATTGAGGAA 59.526 47.619 0.00 0.00 41.22 3.36
2295 2442 0.313672 GAGATTGCACGTGCCCAAAA 59.686 50.000 35.72 23.91 41.18 2.44
3040 3194 5.080337 TGGAGCCAAAAATTGTGGTGTATA 58.920 37.500 3.85 0.00 38.50 1.47
3125 3287 0.392193 ACTCTTGCATCTGAAGCCGG 60.392 55.000 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.760204 GGCCGTGTATATCCTTTGCTATTT 59.240 41.667 0.00 0.00 0.00 1.40
2 3 3.583086 AGGCCGTGTATATCCTTTGCTAT 59.417 43.478 0.00 0.00 0.00 2.97
3 4 2.969950 AGGCCGTGTATATCCTTTGCTA 59.030 45.455 0.00 0.00 0.00 3.49
5 6 1.873591 CAGGCCGTGTATATCCTTTGC 59.126 52.381 0.00 0.00 0.00 3.68
7 8 2.404559 TCCAGGCCGTGTATATCCTTT 58.595 47.619 0.00 0.00 0.00 3.11
9 10 2.097110 TTCCAGGCCGTGTATATCCT 57.903 50.000 0.00 0.00 0.00 3.24
10 11 2.301870 TGATTCCAGGCCGTGTATATCC 59.698 50.000 0.00 0.00 0.00 2.59
11 12 3.258372 TCTGATTCCAGGCCGTGTATATC 59.742 47.826 0.00 0.00 40.76 1.63
12 13 3.239449 TCTGATTCCAGGCCGTGTATAT 58.761 45.455 0.00 0.00 40.76 0.86
13 14 2.673258 TCTGATTCCAGGCCGTGTATA 58.327 47.619 0.00 0.00 40.76 1.47
14 15 1.496060 TCTGATTCCAGGCCGTGTAT 58.504 50.000 0.00 0.00 40.76 2.29
15 16 1.271856 TTCTGATTCCAGGCCGTGTA 58.728 50.000 0.00 0.00 40.76 2.90
16 17 0.400213 TTTCTGATTCCAGGCCGTGT 59.600 50.000 0.00 0.00 40.76 4.49
17 18 0.804989 GTTTCTGATTCCAGGCCGTG 59.195 55.000 0.00 0.00 40.76 4.94
18 19 0.400213 TGTTTCTGATTCCAGGCCGT 59.600 50.000 0.00 0.00 40.76 5.68
19 20 1.200020 GTTGTTTCTGATTCCAGGCCG 59.800 52.381 0.00 0.00 40.76 6.13
20 21 1.546029 GGTTGTTTCTGATTCCAGGCC 59.454 52.381 0.00 0.00 40.76 5.19
21 22 2.519013 AGGTTGTTTCTGATTCCAGGC 58.481 47.619 0.00 0.00 40.76 4.85
22 23 5.560724 TCTAAGGTTGTTTCTGATTCCAGG 58.439 41.667 0.00 0.00 40.76 4.45
23 24 5.123027 GCTCTAAGGTTGTTTCTGATTCCAG 59.877 44.000 0.00 0.00 41.74 3.86
24 25 5.003804 GCTCTAAGGTTGTTTCTGATTCCA 58.996 41.667 0.00 0.00 0.00 3.53
25 26 5.249420 AGCTCTAAGGTTGTTTCTGATTCC 58.751 41.667 0.00 0.00 0.00 3.01
26 27 5.352846 GGAGCTCTAAGGTTGTTTCTGATTC 59.647 44.000 14.64 0.00 0.00 2.52
27 28 5.013599 AGGAGCTCTAAGGTTGTTTCTGATT 59.986 40.000 14.64 0.00 0.00 2.57
28 29 4.534103 AGGAGCTCTAAGGTTGTTTCTGAT 59.466 41.667 14.64 0.00 0.00 2.90
29 30 3.904339 AGGAGCTCTAAGGTTGTTTCTGA 59.096 43.478 14.64 0.00 0.00 3.27
30 31 4.278975 AGGAGCTCTAAGGTTGTTTCTG 57.721 45.455 14.64 0.00 0.00 3.02
31 32 4.984146 AAGGAGCTCTAAGGTTGTTTCT 57.016 40.909 14.64 0.00 0.00 2.52
32 33 5.063880 TCAAAGGAGCTCTAAGGTTGTTTC 58.936 41.667 14.64 0.00 0.00 2.78
33 34 5.048846 TCAAAGGAGCTCTAAGGTTGTTT 57.951 39.130 14.64 0.00 0.00 2.83
34 35 4.706842 TCAAAGGAGCTCTAAGGTTGTT 57.293 40.909 14.64 0.00 0.00 2.83
35 36 4.917906 ATCAAAGGAGCTCTAAGGTTGT 57.082 40.909 14.64 0.73 0.00 3.32
36 37 5.248640 TGAATCAAAGGAGCTCTAAGGTTG 58.751 41.667 14.64 10.61 0.00 3.77
37 38 5.505181 TGAATCAAAGGAGCTCTAAGGTT 57.495 39.130 14.64 4.03 0.00 3.50
38 39 5.435291 CATGAATCAAAGGAGCTCTAAGGT 58.565 41.667 14.64 0.00 0.00 3.50
171 262 8.378565 TGAGAACTTTCCTGTGAAATAGAGAAT 58.621 33.333 0.00 0.00 39.65 2.40
195 286 1.270839 CCGAGAGCTTCCACCTTTTGA 60.271 52.381 0.00 0.00 0.00 2.69
199 290 1.002544 CTTTCCGAGAGCTTCCACCTT 59.997 52.381 0.00 0.00 0.00 3.50
204 295 2.556257 GGATTCTTTCCGAGAGCTTCC 58.444 52.381 0.00 0.00 35.37 3.46
392 495 2.592993 CCGAGGACCTGGGCAGAAA 61.593 63.158 9.94 0.00 0.00 2.52
941 1058 6.070653 ACAGGGCACAAATGATATTTGTTCAT 60.071 34.615 15.14 7.63 40.30 2.57
1382 1529 5.308825 ACTTGGTTGAGAGTAAATGACTGG 58.691 41.667 0.00 0.00 39.06 4.00
1466 1613 3.217626 CTTATCCCATCCAAAGCCACTC 58.782 50.000 0.00 0.00 0.00 3.51
1864 2011 2.261361 CGCATGTCCGACTCACCA 59.739 61.111 0.00 0.00 0.00 4.17
2101 2248 2.651642 AGGGGTCCTCTAGCTTCTTT 57.348 50.000 0.00 0.00 0.00 2.52
2295 2442 7.884354 ACCACAATGGCTAATTTTGATCATTTT 59.116 29.630 0.00 0.00 42.67 1.82
3040 3194 7.574967 CGGAAAATTTTACCTTGTAGATGCTGT 60.575 37.037 7.58 0.00 0.00 4.40
3125 3287 1.379044 CATGCTGGTTGGGAGGGAC 60.379 63.158 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.