AutoCloner

Multiple sequence alignment - TraesCS7D01G383300

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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	TraesCS7D01G383300	chr7D	100.000	2906	0	0	1	2906	497047528	497044623	0.000000e+00	5367.0
1	TraesCS7D01G383300	chr7B	91.032	1260	78	9	1	1246	525027732	525026494	0.000000e+00	1668.0
2	TraesCS7D01G383300	chr7B	95.603	887	31	4	1244	2126	525026234	525025352	0.000000e+00	1415.0
3	TraesCS7D01G383300	chr7B	94.472	615	34	0	2292	2906	572029119	572029733	0.000000e+00	948.0
4	TraesCS7D01G383300	chr7B	91.870	615	36	4	2292	2906	735911776	735911176	0.000000e+00	846.0
5	TraesCS7D01G383300	chr7A	95.604	1001	25	4	1291	2275	562303588	562302591	0.000000e+00	1587.0
6	TraesCS7D01G383300	chr7A	90.345	580	35	6	2296	2856	20681028	20681605	0.000000e+00	741.0
7	TraesCS7D01G383300	chr7A	86.873	678	46	15	621	1284	562304482	562303834	0.000000e+00	719.0
8	TraesCS7D01G383300	chr7A	83.923	622	80	13	2292	2906	571694806	571694198	6.980000e-161	577.0
9	TraesCS7D01G383300	chr7A	81.967	122	13	3	410	527	562320323	562320207	8.570000e-16	95.3
10	TraesCS7D01G383300	chr3B	82.094	1385	184	36	774	2126	46469896	46468544	0.000000e+00	1125.0
11	TraesCS7D01G383300	chr3B	81.877	1385	187	35	774	2126	46614032	46612680	0.000000e+00	1109.0
12	TraesCS7D01G383300	chr5D	88.165	583	68	1	1328	1910	51686388	51686969	0.000000e+00	693.0
13	TraesCS7D01G383300	chr5D	80.515	272	36	8	896	1153	51685908	51686176	2.960000e-45	193.0
14	TraesCS7D01G383300	chr5B	88.165	583	68	1	1328	1910	54702604	54703185	0.000000e+00	693.0
15	TraesCS7D01G383300	chr5B	79.104	335	46	10	834	1153	54702070	54702395	2.930000e-50	209.0
16	TraesCS7D01G383300	chr5B	81.522	92	12	4	2651	2740	703233289	703233377	1.440000e-08	71.3
17	TraesCS7D01G383300	chr5A	87.993	583	69	1	1328	1910	40720203	40720784	0.000000e+00	688.0
18	TraesCS7D01G383300	chr5A	86.601	612	57	6	2296	2906	477583641	477583054	0.000000e+00	652.0
19	TraesCS7D01G383300	chr1A	86.134	613	51	9	2296	2906	59607455	59606875	5.280000e-177	630.0
20	TraesCS7D01G383300	chr2D	81.944	432	48	17	2296	2721	378513238	378513645	3.590000e-89	339.0
21	TraesCS7D01G383300	chr2D	80.000	140	27	1	2302	2440	323067059	323066920	5.120000e-18	102.0
22	TraesCS7D01G383300	chr3D	78.924	223	29	17	2295	2506	583231881	583232096	5.050000e-28	135.0
23	TraesCS7D01G383300	chr4A	90.625	96	9	0	2811	2906	681922866	681922961	8.450000e-26	128.0
24	TraesCS7D01G383300	chr3A	81.818	132	15	9	2311	2437	86381807	86381934	5.120000e-18	102.0
25	TraesCS7D01G383300	chr2B	85.938	64	4	4	2679	2740	95751954	95752014	2.420000e-06	63.9

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	TraesCS7D01G383300	chr7D	497044623	497047528	2905	True	5367.0	5367	100.0000	1	2906	1	chr7D.!!$R1	2905
1	TraesCS7D01G383300	chr7B	525025352	525027732	2380	True	1541.5	1668	93.3175	1	2126	2	chr7B.!!$R2	2125
2	TraesCS7D01G383300	chr7B	572029119	572029733	614	False	948.0	948	94.4720	2292	2906	1	chr7B.!!$F1	614
3	TraesCS7D01G383300	chr7B	735911176	735911776	600	True	846.0	846	91.8700	2292	2906	1	chr7B.!!$R1	614
4	TraesCS7D01G383300	chr7A	562302591	562304482	1891	True	1153.0	1587	91.2385	621	2275	2	chr7A.!!$R3	1654
5	TraesCS7D01G383300	chr7A	20681028	20681605	577	False	741.0	741	90.3450	2296	2856	1	chr7A.!!$F1	560
6	TraesCS7D01G383300	chr7A	571694198	571694806	608	True	577.0	577	83.9230	2292	2906	1	chr7A.!!$R2	614
7	TraesCS7D01G383300	chr3B	46468544	46469896	1352	True	1125.0	1125	82.0940	774	2126	1	chr3B.!!$R1	1352
8	TraesCS7D01G383300	chr3B	46612680	46614032	1352	True	1109.0	1109	81.8770	774	2126	1	chr3B.!!$R2	1352
9	TraesCS7D01G383300	chr5D	51685908	51686969	1061	False	443.0	693	84.3400	896	1910	2	chr5D.!!$F1	1014
10	TraesCS7D01G383300	chr5B	54702070	54703185	1115	False	451.0	693	83.6345	834	1910	2	chr5B.!!$F2	1076
11	TraesCS7D01G383300	chr5A	40720203	40720784	581	False	688.0	688	87.9930	1328	1910	1	chr5A.!!$F1	582
12	TraesCS7D01G383300	chr5A	477583054	477583641	587	True	652.0	652	86.6010	2296	2906	1	chr5A.!!$R1	610
13	TraesCS7D01G383300	chr1A	59606875	59607455	580	True	630.0	630	86.1340	2296	2906	1	chr1A.!!$R1	610

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
484	487	0.834612	TGCAGGATTTAGGGGTACGG	59.165	55.000	0.0	0.0	0.0	4.02	F
953	969	1.062587	GCATATCACCACACGCTGTTC	59.937	52.381	0.0	0.0	0.0	3.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1359	1936	0.463620	TTGGGTCCTTGCAAGCAAAC	59.536	50.000	21.43	16.69	35.33	2.93	R
2740	3366	1.079127	CTGACCCGAAGCCGTCAAT	60.079	57.895	0.00	0.00	38.48	2.57	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
26	27	4.577283	TGGCACATCATGATCATAACTGTG	59.423	41.667	25.49	25.49	36.48	3.66
46	47	3.684788	GTGCTCAGTCGTCCAAAATATGT	59.315	43.478	0.00	0.00	0.00	2.29
57	58	4.035675	GTCCAAAATATGTAGCTGGTCTGC	59.964	45.833	0.00	0.00	0.00	4.26
78	79	3.596214	CCACGTGCTTACATAAGGTTCT	58.404	45.455	10.91	0.00	33.95	3.01
80	81	5.172934	CCACGTGCTTACATAAGGTTCTTA	58.827	41.667	10.91	0.00	33.95	2.10
82	83	5.867716	CACGTGCTTACATAAGGTTCTTACT	59.132	40.000	0.82	0.00	33.95	2.24
186	189	7.168905	AGTATTTTCTAAGAAACTGGACCAGG	58.831	38.462	25.34	7.84	35.51	4.45
188	191	4.891992	TTCTAAGAAACTGGACCAGGAG	57.108	45.455	25.34	11.76	35.51	3.69
191	194	0.842467	AGAAACTGGACCAGGAGGGG	60.842	60.000	25.34	0.15	42.91	4.79
195	198	2.874245	TGGACCAGGAGGGGGAGA	60.874	66.667	0.00	0.00	42.91	3.71
218	221	4.602107	AGCCCCTACCGCTTTTAATTAAA	58.398	39.130	6.54	6.54	30.57	1.52
308	311	4.350620	CAACGCTGCACTCTGACT	57.649	55.556	0.00	0.00	0.00	3.41
318	321	1.306226	ACTCTGACTACTGGGGGCC	60.306	63.158	0.00	0.00	0.00	5.80
351	354	8.792633	CCCATTCACAAGTTTCAAGTATCTAAA	58.207	33.333	0.00	0.00	0.00	1.85
362	365	7.849804	TTCAAGTATCTAAACTGAGCATTCC	57.150	36.000	0.00	0.00	0.00	3.01
368	371	5.401531	TCTAAACTGAGCATTCCGTAAGT	57.598	39.130	0.00	0.00	0.00	2.24
374	377	7.448748	AACTGAGCATTCCGTAAGTTTTAAT	57.551	32.000	0.00	0.00	0.00	1.40
406	409	8.523658	AGTAAAAACTGATTTGCCTATTTCTCC	58.476	33.333	0.00	0.00	0.00	3.71
407	410	5.567138	AAACTGATTTGCCTATTTCTCCG	57.433	39.130	0.00	0.00	0.00	4.63
408	411	2.945668	ACTGATTTGCCTATTTCTCCGC	59.054	45.455	0.00	0.00	0.00	5.54
414	417	1.299926	CCTATTTCTCCGCGGGTCG	60.300	63.158	27.83	14.44	38.08	4.79
442	445	2.002586	CTTCAATATCGGGCATAGCGG	58.997	52.381	0.00	0.00	0.00	5.52
451	454	1.533273	GGCATAGCGGGAGGAGGTA	60.533	63.158	0.00	0.00	0.00	3.08
470	473	6.483640	GGAGGTAAAGATAAATGTAGTGCAGG	59.516	42.308	0.00	0.00	0.00	4.85
477	480	8.682936	AAGATAAATGTAGTGCAGGATTTAGG	57.317	34.615	0.00	0.00	0.00	2.69
478	481	7.227156	AGATAAATGTAGTGCAGGATTTAGGG	58.773	38.462	0.00	0.00	0.00	3.53
484	487	0.834612	TGCAGGATTTAGGGGTACGG	59.165	55.000	0.00	0.00	0.00	4.02
493	496	3.872459	TTAGGGGTACGGGTTCAAAAA	57.128	42.857	0.00	0.00	0.00	1.94
495	498	5.511386	TTAGGGGTACGGGTTCAAAAATA	57.489	39.130	0.00	0.00	0.00	1.40
502	505	6.183360	GGGTACGGGTTCAAAAATATCTTCTG	60.183	42.308	0.00	0.00	0.00	3.02
613	616	5.406649	TGTGAGGTCATTTGTTGTTGTTTC	58.593	37.500	0.00	0.00	0.00	2.78
632	635	2.843077	TCGCTAAGTCGTTTGTACTCG	58.157	47.619	0.00	0.00	0.00	4.18
660	663	6.485648	CCTTCTTCTATGATGATCACATGCAA	59.514	38.462	16.35	10.09	36.82	4.08
664	667	6.812879	TCTATGATGATCACATGCAATTCC	57.187	37.500	16.35	0.00	36.82	3.01
684	687	1.134907	CCCTTCATGGTTTCTGCATGC	60.135	52.381	11.82	11.82	0.00	4.06
688	691	2.516906	TCATGGTTTCTGCATGCTTCA	58.483	42.857	20.33	8.25	0.00	3.02
690	693	2.275134	TGGTTTCTGCATGCTTCAGA	57.725	45.000	20.33	10.79	38.67	3.27
736	739	2.143122	TCTGTGTCGTCCAAGAAATGC	58.857	47.619	0.00	0.00	0.00	3.56
837	840	5.826643	ACTTAAGAAGTTGGGCCATCAATA	58.173	37.500	16.58	2.81	39.04	1.90
892	896	5.988310	TGGTTGATAAGTTCCTCTCGTAA	57.012	39.130	0.00	0.00	0.00	3.18
947	963	2.032054	GGTTCATGCATATCACCACACG	59.968	50.000	13.73	0.00	0.00	4.49
953	969	1.062587	GCATATCACCACACGCTGTTC	59.937	52.381	0.00	0.00	0.00	3.18
1004	1027	3.093555	AGCACACCCATCCATGCT	58.906	55.556	0.00	0.00	43.50	3.79
1026	1049	2.622942	TCCATTGACAAAGCAACTCACC	59.377	45.455	0.00	0.00	0.00	4.02
1215	1258	8.792830	ATGTTGTAGTTAATGTTGTGATAGCT	57.207	30.769	0.00	0.00	0.00	3.32
1258	1346	8.880244	TGGAAGGTTACTACATGCTGATAATAT	58.120	33.333	0.00	0.00	0.00	1.28
1296	1873	6.072286	GCATTATTACTACATGCTCAAGCCAT	60.072	38.462	0.00	0.00	40.23	4.40
1359	1936	1.064505	CATGCAGTGCGAGTAAATGGG	59.935	52.381	11.20	0.00	0.00	4.00
2128	2727	2.550180	GCTCCTTTCTCTCGTTGCTTTT	59.450	45.455	0.00	0.00	0.00	2.27
2164	2763	5.837437	ACCTTTCTCTCGTTGCTGATATAG	58.163	41.667	0.00	0.00	0.00	1.31
2235	2834	9.772973	TGTTATTTCTAGACACAGTTTACATGT	57.227	29.630	2.69	2.69	0.00	3.21
2241	2840	7.320399	TCTAGACACAGTTTACATGTACATGG	58.680	38.462	33.32	19.69	42.91	3.66
2248	2847	6.770785	ACAGTTTACATGTACATGGAACTTGT	59.229	34.615	33.99	31.05	41.08	3.16
2254	2853	6.872920	ACATGTACATGGAACTTGTTTTTGT	58.127	32.000	33.32	11.29	42.91	2.83
2280	2879	4.718858	CAAGTGATTTGTTTACGACCGA	57.281	40.909	0.00	0.00	31.92	4.69
2281	2880	4.698276	CAAGTGATTTGTTTACGACCGAG	58.302	43.478	0.00	0.00	31.92	4.63
2282	2881	2.735134	AGTGATTTGTTTACGACCGAGC	59.265	45.455	0.00	0.00	0.00	5.03
2283	2882	2.735134	GTGATTTGTTTACGACCGAGCT	59.265	45.455	0.00	0.00	0.00	4.09
2284	2883	3.185797	GTGATTTGTTTACGACCGAGCTT	59.814	43.478	0.00	0.00	0.00	3.74
2285	2884	3.430895	TGATTTGTTTACGACCGAGCTTC	59.569	43.478	0.00	0.00	0.00	3.86
2286	2885	2.512485	TTGTTTACGACCGAGCTTCA	57.488	45.000	0.00	0.00	0.00	3.02
2287	2886	2.736144	TGTTTACGACCGAGCTTCAT	57.264	45.000	0.00	0.00	0.00	2.57
2288	2887	3.034721	TGTTTACGACCGAGCTTCATT	57.965	42.857	0.00	0.00	0.00	2.57
2289	2888	2.991190	TGTTTACGACCGAGCTTCATTC	59.009	45.455	0.00	0.00	0.00	2.67
2290	2889	3.251571	GTTTACGACCGAGCTTCATTCT	58.748	45.455	0.00	0.00	0.00	2.40
2461	3080	2.286121	CCCTCCCTTGCCCACCTA	60.286	66.667	0.00	0.00	0.00	3.08

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
4	5	5.104562	CACAGTTATGATCATGATGTGCC	57.895	43.478	24.47	0.00	31.30	5.01
26	27	4.025647	GCTACATATTTTGGACGACTGAGC	60.026	45.833	0.00	0.00	0.00	4.26
57	58	3.596214	AGAACCTTATGTAAGCACGTGG	58.404	45.455	18.88	0.00	32.02	4.94
166	167	4.041691	CCTCCTGGTCCAGTTTCTTAGAAA	59.958	45.833	17.85	2.94	0.00	2.52
169	170	2.237392	CCCTCCTGGTCCAGTTTCTTAG	59.763	54.545	17.85	0.52	0.00	2.18
170	171	2.266279	CCCTCCTGGTCCAGTTTCTTA	58.734	52.381	17.85	0.00	0.00	2.10
173	176	1.685820	CCCCTCCTGGTCCAGTTTC	59.314	63.158	17.85	0.00	0.00	2.78
179	182	1.690985	CTTCTCCCCCTCCTGGTCC	60.691	68.421	0.00	0.00	0.00	4.46
191	194	2.764547	AGCGGTAGGGGCTTCTCC	60.765	66.667	0.00	0.00	37.50	3.71
237	240	6.015434	GGTTCTAACATGGGTCTCACATTTTT	60.015	38.462	0.00	0.00	0.00	1.94
238	241	5.476945	GGTTCTAACATGGGTCTCACATTTT	59.523	40.000	0.00	0.00	0.00	1.82
243	246	2.232941	TCGGTTCTAACATGGGTCTCAC	59.767	50.000	0.00	0.00	0.00	3.51
281	284	2.082354	GCAGCGTTGCCTTCTAGTC	58.918	57.895	13.92	0.00	44.74	2.59
282	285	4.285851	GCAGCGTTGCCTTCTAGT	57.714	55.556	13.92	0.00	44.74	2.57
292	295	0.962489	AGTAGTCAGAGTGCAGCGTT	59.038	50.000	0.00	0.00	0.00	4.84
293	296	0.242286	CAGTAGTCAGAGTGCAGCGT	59.758	55.000	0.00	0.00	0.00	5.07
295	298	0.108424	CCCAGTAGTCAGAGTGCAGC	60.108	60.000	0.00	0.00	0.00	5.25
308	311	1.384082	GGCTCTTAGGCCCCCAGTA	60.384	63.158	0.00	0.00	45.92	2.74
318	321	4.761739	TGAAACTTGTGAATGGGCTCTTAG	59.238	41.667	0.00	0.00	0.00	2.18
330	333	9.261180	CTCAGTTTAGATACTTGAAACTTGTGA	57.739	33.333	0.00	0.00	40.54	3.58
351	354	8.732746	ATATTAAAACTTACGGAATGCTCAGT	57.267	30.769	0.00	0.00	34.16	3.41
388	391	2.032549	CGCGGAGAAATAGGCAAATCAG	60.033	50.000	0.00	0.00	0.00	2.90
442	445	6.706716	GCACTACATTTATCTTTACCTCCTCC	59.293	42.308	0.00	0.00	0.00	4.30
451	454	9.125026	CCTAAATCCTGCACTACATTTATCTTT	57.875	33.333	0.00	0.00	0.00	2.52
470	473	3.632643	TTGAACCCGTACCCCTAAATC	57.367	47.619	0.00	0.00	0.00	2.17
477	480	5.884232	AGAAGATATTTTTGAACCCGTACCC	59.116	40.000	0.00	0.00	0.00	3.69
478	481	6.596497	TCAGAAGATATTTTTGAACCCGTACC	59.404	38.462	0.00	0.00	0.00	3.34
495	498	9.381033	CAAATAGTTGTGAGAAGATCAGAAGAT	57.619	33.333	0.00	0.00	41.49	2.40
537	540	4.453136	AGGCAAAACACGACACGTATAAAT	59.547	37.500	0.00	0.00	38.32	1.40
542	545	2.034432	TCTAGGCAAAACACGACACGTA	59.966	45.455	0.00	0.00	38.32	3.57
570	573	8.025445	CCTCACAAACAAAAGAATATCAGAAGG	58.975	37.037	0.00	0.00	0.00	3.46
613	616	2.578495	ACGAGTACAAACGACTTAGCG	58.422	47.619	12.48	0.00	37.29	4.26
632	635	7.307870	GCATGTGATCATCATAGAAGAAGGAAC	60.308	40.741	0.00	0.00	31.15	3.62
660	663	2.225343	TGCAGAAACCATGAAGGGGAAT	60.225	45.455	0.00	0.00	43.89	3.01
664	667	1.134907	GCATGCAGAAACCATGAAGGG	60.135	52.381	14.21	0.00	41.97	3.95
703	706	2.486203	CGACACAGAGTAGAAGAGCAGT	59.514	50.000	0.00	0.00	0.00	4.40
736	739	1.730121	GCATGTGCTTGACCGACATTG	60.730	52.381	0.00	0.00	38.21	2.82
837	840	1.612726	CCTGCTGGCTGCTAGAACTTT	60.613	52.381	17.76	0.00	43.37	2.66
862	865	5.783111	AGGAACTTATCAACCAATTGCAAC	58.217	37.500	0.00	0.00	31.93	4.17
892	896	7.445945	AGCAAATAGAACAAGTCAAGTACTCT	58.554	34.615	0.00	0.00	37.50	3.24
969	989	3.273919	GCTTAAATAGCCGCAGATTGG	57.726	47.619	0.00	0.00	44.48	3.16
1004	1027	3.068024	GGTGAGTTGCTTTGTCAATGGAA	59.932	43.478	1.87	1.87	0.00	3.53
1026	1049	2.950309	CAATGAGGAAGAGGAAGCCATG	59.050	50.000	0.00	0.00	0.00	3.66
1215	1258	4.641541	CCTTCCATGTGTGATCAATGCTAA	59.358	41.667	0.00	0.00	0.00	3.09
1325	1902	4.659088	CACTGCATGCATAGAGAAAGTTG	58.341	43.478	22.97	7.24	0.00	3.16
1326	1903	4.959596	CACTGCATGCATAGAGAAAGTT	57.040	40.909	22.97	0.00	0.00	2.66
1359	1936	0.463620	TTGGGTCCTTGCAAGCAAAC	59.536	50.000	21.43	16.69	35.33	2.93
1386	1963	3.836762	GAAGAAGTCTTCCGGGGTC	57.163	57.895	9.04	0.00	44.93	4.46
1794	2371	2.214376	TCGGTGGCTTTGATCCAAAT	57.786	45.000	0.00	0.00	35.01	2.32
2047	2641	5.298527	CACCAGCACATTATGACATGAATCT	59.701	40.000	0.00	0.00	0.00	2.40
2087	2686	4.712476	AGCACCTCTGTATTCCATTCATC	58.288	43.478	0.00	0.00	0.00	2.92
2164	2763	7.137426	GCTTTGTCATTAACATCATGGATCTC	58.863	38.462	0.00	0.00	37.82	2.75
2235	2834	6.375736	TGTCAGACAAAAACAAGTTCCATGTA	59.624	34.615	0.00	0.00	0.00	2.29
2264	2863	3.430895	TGAAGCTCGGTCGTAAACAAATC	59.569	43.478	0.00	0.00	0.00	2.17
2275	2874	2.500509	ATCGAGAATGAAGCTCGGTC	57.499	50.000	12.32	0.00	45.27	4.79
2740	3366	1.079127	CTGACCCGAAGCCGTCAAT	60.079	57.895	0.00	0.00	38.48	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.