AutoCloner

Multiple sequence alignment - TraesCS2D01G304500

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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	TraesCS2D01G304500	chr2D	100.000	2898	0	0	1	2898	390397144	390394247	0.000000e+00	5352
1	TraesCS2D01G304500	chr2D	86.971	307	31	6	2594	2898	529560252	529560551	1.290000e-88	337
2	TraesCS2D01G304500	chr2D	85.993	307	33	7	2594	2898	529592876	529593174	1.300000e-83	320
3	TraesCS2D01G304500	chr2D	79.435	496	55	25	1912	2373	529610194	529610676	1.010000e-79	307
4	TraesCS2D01G304500	chr2D	91.892	111	5	2	788	898	390396302	390396196	5.000000e-33	152
5	TraesCS2D01G304500	chr2D	91.892	111	5	2	843	949	390396357	390396247	5.000000e-33	152
6	TraesCS2D01G304500	chr2D	92.222	90	7	0	1336	1425	529601924	529602013	8.430000e-26	128
7	TraesCS2D01G304500	chr2B	96.585	2928	35	15	31	2898	461524858	461521936	0.000000e+00	4793
8	TraesCS2D01G304500	chr2B	89.616	443	40	6	1664	2104	629596575	629597013	2.520000e-155	558
9	TraesCS2D01G304500	chr2B	87.085	271	27	5	2629	2898	629126741	629127004	1.690000e-77	300
10	TraesCS2D01G304500	chr2B	86.940	268	32	2	2631	2898	629637243	629637507	6.070000e-77	298
11	TraesCS2D01G304500	chr2B	84.229	279	33	2	1336	1603	629596294	629596572	7.970000e-66	261
12	TraesCS2D01G304500	chr2B	77.328	494	55	34	1912	2373	629499389	629499857	3.730000e-59	239
13	TraesCS2D01G304500	chr2B	90.991	111	6	2	788	898	461524001	461523895	2.330000e-31	147
14	TraesCS2D01G304500	chr2B	90.991	111	6	2	843	949	461524056	461523946	2.330000e-31	147
15	TraesCS2D01G304500	chr2B	90.000	90	9	0	1336	1425	629441320	629441409	1.820000e-22	117
16	TraesCS2D01G304500	chr2A	93.311	2078	70	22	843	2898	526345675	526343645	0.000000e+00	3003
17	TraesCS2D01G304500	chr2A	86.235	603	40	11	254	845	526346188	526345618	5.310000e-172	614
18	TraesCS2D01G304500	chr2A	87.296	307	30	6	2594	2898	674062954	674063253	2.770000e-90	342
19	TraesCS2D01G304500	chr2A	81.818	385	46	21	2341	2713	526254268	526253896	4.690000e-78	302
20	TraesCS2D01G304500	chr2A	84.828	290	37	5	1336	1619	674089839	674090127	4.730000e-73	285
21	TraesCS2D01G304500	chr2A	85.874	269	33	4	2631	2898	674083076	674083340	6.110000e-72	281
22	TraesCS2D01G304500	chr2A	85.657	251	20	2	1664	1914	674181533	674181767	1.720000e-62	250
23	TraesCS2D01G304500	chr2A	93.333	90	5	1	1336	1425	674070911	674070999	6.520000e-27	132
24	TraesCS2D01G304500	chr2A	89.362	94	6	2	31	120	526346749	526346656	6.560000e-22	115
25	TraesCS2D01G304500	chr4B	83.898	1329	163	33	1585	2896	27656808	27655514	0.000000e+00	1221
26	TraesCS2D01G304500	chr4B	88.845	251	24	1	2645	2895	27867995	27868241	3.630000e-79	305
27	TraesCS2D01G304500	chr4D	89.494	257	22	2	2640	2895	16023917	16024169	1.300000e-83	320
28	TraesCS2D01G304500	chr1D	85.849	106	15	0	1824	1929	22340856	22340961	2.360000e-21	113

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	TraesCS2D01G304500	chr2D	390394247	390397144	2897	True	1885.333333	5352	94.594667	1	2898	3	chr2D.!!$R1	2897
1	TraesCS2D01G304500	chr2B	461521936	461524858	2922	True	1695.666667	4793	92.855667	31	2898	3	chr2B.!!$R1	2867
2	TraesCS2D01G304500	chr2B	629596294	629597013	719	False	409.500000	558	86.922500	1336	2104	2	chr2B.!!$F5	768
3	TraesCS2D01G304500	chr2A	526343645	526346749	3104	True	1244.000000	3003	89.636000	31	2898	3	chr2A.!!$R2	2867
4	TraesCS2D01G304500	chr4B	27655514	27656808	1294	True	1221.000000	1221	83.898000	1585	2896	1	chr4B.!!$R1	1311

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
19	20	0.829182	ACTGGGCAGGCAAAGGAAAG	60.829	55.0	0.00	0.0	0.0	2.62	F
1020	1372	0.911053	TGCAGCTGTATCACCATCCA	59.089	50.0	16.64	0.0	0.0	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1044	1396	0.470080	TCTCTTCCAGGGCTATCCGG	60.470	60.0	0.00	0.0	41.52	5.14	R
2808	3206	0.529378	CAAGCTGGAATTGCTGGACC	59.471	55.0	6.01	0.0	41.03	4.46	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
17	18	2.934369	ACTGGGCAGGCAAAGGAA	59.066	55.556	0.00	0.00	0.00	3.36
18	19	1.232792	ACTGGGCAGGCAAAGGAAA	59.767	52.632	0.00	0.00	0.00	3.13
19	20	0.829182	ACTGGGCAGGCAAAGGAAAG	60.829	55.000	0.00	0.00	0.00	2.62
20	21	1.533753	TGGGCAGGCAAAGGAAAGG	60.534	57.895	0.00	0.00	0.00	3.11
21	22	1.228862	GGGCAGGCAAAGGAAAGGA	60.229	57.895	0.00	0.00	0.00	3.36
22	23	1.253593	GGGCAGGCAAAGGAAAGGAG	61.254	60.000	0.00	0.00	0.00	3.69
23	24	1.253593	GGCAGGCAAAGGAAAGGAGG	61.254	60.000	0.00	0.00	0.00	4.30
24	25	1.881903	GCAGGCAAAGGAAAGGAGGC	61.882	60.000	0.00	0.00	0.00	4.70
25	26	1.303643	AGGCAAAGGAAAGGAGGCG	60.304	57.895	0.00	0.00	0.00	5.52
26	27	2.343426	GGCAAAGGAAAGGAGGCGG	61.343	63.158	0.00	0.00	0.00	6.13
27	28	1.303317	GCAAAGGAAAGGAGGCGGA	60.303	57.895	0.00	0.00	0.00	5.54
28	29	1.308783	GCAAAGGAAAGGAGGCGGAG	61.309	60.000	0.00	0.00	0.00	4.63
139	144	4.366684	CAGCACCCCCACTTCCCC	62.367	72.222	0.00	0.00	0.00	4.81
194	199	1.834822	CTCTCCGGTCTCCCATCCC	60.835	68.421	0.00	0.00	0.00	3.85
338	680	7.272731	GGCGTTAGATTTGGTTGTCTATTTTTC	59.727	37.037	0.00	0.00	0.00	2.29
371	713	5.937111	AGAAGTACTTTTGGACTAAAGGCA	58.063	37.500	10.02	0.00	39.02	4.75
448	798	4.395854	TGTTGATCCTGAATTCATGAACCG	59.604	41.667	16.03	0.79	0.00	4.44
507	857	4.213482	GCGATTTGTTCCGGCTAATATCTT	59.787	41.667	0.00	0.00	0.00	2.40
578	928	5.523369	TGCAGACGTTATGATCAGTATCTG	58.477	41.667	15.60	15.60	36.30	2.90
579	929	5.067805	TGCAGACGTTATGATCAGTATCTGT	59.932	40.000	18.68	7.22	35.76	3.41
580	930	6.262273	TGCAGACGTTATGATCAGTATCTGTA	59.738	38.462	18.68	14.59	35.76	2.74
687	1037	8.470040	AATATTGTGTGTCGTTAATTACTCGT	57.530	30.769	8.44	0.00	0.00	4.18
806	1157	8.196103	AGAGACTACTTAGTTTGAACGAACTTT	58.804	33.333	11.89	2.11	40.24	2.66
912	1263	3.002246	CACTGCAACTTAGTTTGAGCGAA	59.998	43.478	0.00	0.00	0.00	4.70
1020	1372	0.911053	TGCAGCTGTATCACCATCCA	59.089	50.000	16.64	0.00	0.00	3.41
1044	1396	1.964223	TCACTGGACAGTCAGAAGGTC	59.036	52.381	1.21	0.00	40.20	3.85
1440	1799	2.930826	ACTCACACCCCACTAAAGTG	57.069	50.000	3.02	3.02	45.23	3.16
2482	2869	4.634199	TCCGTACTTAACTGGGAAACAAG	58.366	43.478	0.00	0.00	0.00	3.16
2497	2884	6.721208	TGGGAAACAAGCTTCTTCTTAATCAT	59.279	34.615	14.50	0.00	0.00	2.45
2808	3206	7.601073	TTATACATCAGAGCTGAAACACTTG	57.399	36.000	4.06	0.08	43.58	3.16

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	0.829182	CTTTCCTTTGCCTGCCCAGT	60.829	55.000	0.00	0.00	0.00	4.00
1	2	1.538687	CCTTTCCTTTGCCTGCCCAG	61.539	60.000	0.00	0.00	0.00	4.45
2	3	1.533753	CCTTTCCTTTGCCTGCCCA	60.534	57.895	0.00	0.00	0.00	5.36
3	4	1.228862	TCCTTTCCTTTGCCTGCCC	60.229	57.895	0.00	0.00	0.00	5.36
4	5	1.253593	CCTCCTTTCCTTTGCCTGCC	61.254	60.000	0.00	0.00	0.00	4.85
5	6	1.881903	GCCTCCTTTCCTTTGCCTGC	61.882	60.000	0.00	0.00	0.00	4.85
6	7	1.589716	CGCCTCCTTTCCTTTGCCTG	61.590	60.000	0.00	0.00	0.00	4.85
7	8	1.303643	CGCCTCCTTTCCTTTGCCT	60.304	57.895	0.00	0.00	0.00	4.75
8	9	2.343426	CCGCCTCCTTTCCTTTGCC	61.343	63.158	0.00	0.00	0.00	4.52
9	10	1.303317	TCCGCCTCCTTTCCTTTGC	60.303	57.895	0.00	0.00	0.00	3.68
10	11	1.308783	GCTCCGCCTCCTTTCCTTTG	61.309	60.000	0.00	0.00	0.00	2.77
11	12	1.002011	GCTCCGCCTCCTTTCCTTT	60.002	57.895	0.00	0.00	0.00	3.11
12	13	2.671682	GCTCCGCCTCCTTTCCTT	59.328	61.111	0.00	0.00	0.00	3.36
13	14	3.775654	CGCTCCGCCTCCTTTCCT	61.776	66.667	0.00	0.00	0.00	3.36
14	15	3.724914	CTCGCTCCGCCTCCTTTCC	62.725	68.421	0.00	0.00	0.00	3.13
15	16	2.202810	CTCGCTCCGCCTCCTTTC	60.203	66.667	0.00	0.00	0.00	2.62
16	17	2.680352	TCTCGCTCCGCCTCCTTT	60.680	61.111	0.00	0.00	0.00	3.11
17	18	3.144193	CTCTCGCTCCGCCTCCTT	61.144	66.667	0.00	0.00	0.00	3.36
18	19	4.434354	ACTCTCGCTCCGCCTCCT	62.434	66.667	0.00	0.00	0.00	3.69
19	20	4.200283	CACTCTCGCTCCGCCTCC	62.200	72.222	0.00	0.00	0.00	4.30
20	21	3.134792	TCACTCTCGCTCCGCCTC	61.135	66.667	0.00	0.00	0.00	4.70
21	22	3.444805	GTCACTCTCGCTCCGCCT	61.445	66.667	0.00	0.00	0.00	5.52
22	23	3.691744	CTGTCACTCTCGCTCCGCC	62.692	68.421	0.00	0.00	0.00	6.13
23	24	2.202544	CTGTCACTCTCGCTCCGC	60.203	66.667	0.00	0.00	0.00	5.54
24	25	1.427419	CTCTGTCACTCTCGCTCCG	59.573	63.158	0.00	0.00	0.00	4.63
25	26	1.662438	CCCTCTGTCACTCTCGCTCC	61.662	65.000	0.00	0.00	0.00	4.70
26	27	0.678366	TCCCTCTGTCACTCTCGCTC	60.678	60.000	0.00	0.00	0.00	5.03
27	28	0.963355	GTCCCTCTGTCACTCTCGCT	60.963	60.000	0.00	0.00	0.00	4.93
28	29	1.244697	TGTCCCTCTGTCACTCTCGC	61.245	60.000	0.00	0.00	0.00	5.03
29	30	1.248486	TTGTCCCTCTGTCACTCTCG	58.752	55.000	0.00	0.00	0.00	4.04
76	77	2.225963	ACGTCTGAAGTGAACTACTCCG	59.774	50.000	0.00	0.00	39.18	4.63
139	144	1.134901	CTCGACGAGGAGACGGTTG	59.865	63.158	17.27	0.00	38.48	3.77
213	244	0.907230	AGAGAAGGGACTCACCTGGC	60.907	60.000	0.00	0.00	40.87	4.85
338	680	4.689345	CCAAAAGTACTTCTACGGAACCAG	59.311	45.833	8.95	0.00	0.00	4.00
371	713	2.889512	GGGGGTTTTGTCCAGAATCTT	58.110	47.619	0.00	0.00	0.00	2.40
448	798	8.579863	CAAAATATATTGACCTCCAATCTTCCC	58.420	37.037	0.00	0.00	43.96	3.97
507	857	0.800683	CAGTCGCGTTCGCCTCAATA	60.801	55.000	5.77	0.00	35.26	1.90
806	1157	3.075882	AGGGACTGTGATGGAAAAATGGA	59.924	43.478	0.00	0.00	37.18	3.41
912	1263	2.515429	ACTATGATGGGAAATGGGCAGT	59.485	45.455	0.00	0.00	0.00	4.40
1020	1372	4.780021	ACCTTCTGACTGTCCAGTGAATAT	59.220	41.667	4.35	0.00	42.66	1.28
1044	1396	0.470080	TCTCTTCCAGGGCTATCCGG	60.470	60.000	0.00	0.00	41.52	5.14
1440	1799	3.667087	TGGAGACAAATGCACGGC	58.333	55.556	0.00	0.00	37.44	5.68
2482	2869	7.981225	TGCCCATTTTAATGATTAAGAAGAAGC	59.019	33.333	4.07	0.72	38.70	3.86
2808	3206	0.529378	CAAGCTGGAATTGCTGGACC	59.471	55.000	6.01	0.00	41.03	4.46

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.