AutoCloner

Multiple sequence alignment - TraesCS6D01G313700

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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	TraesCS6D01G313700	chr6D	100.000	3055	0	0	1	3055	422214387	422217441	0.000000e+00	5642.0
1	TraesCS6D01G313700	chr6D	89.593	1989	110	43	671	2579	422600941	422602912	0.000000e+00	2436.0
2	TraesCS6D01G313700	chr6D	87.724	1955	140	42	675	2566	421661505	421663422	0.000000e+00	2189.0
3	TraesCS6D01G313700	chr6D	87.333	1950	141	45	675	2566	421679494	421681395	0.000000e+00	2135.0
4	TraesCS6D01G313700	chr6D	87.922	1805	149	34	696	2459	421468282	421466506	0.000000e+00	2061.0
5	TraesCS6D01G313700	chr6D	88.588	1516	113	27	986	2459	420970352	420968855	0.000000e+00	1786.0
6	TraesCS6D01G313700	chr6D	90.179	1395	82	19	675	2036	421688833	421690205	0.000000e+00	1766.0
7	TraesCS6D01G313700	chr6D	94.340	689	27	5	1	678	422600234	422600921	0.000000e+00	1046.0
8	TraesCS6D01G313700	chr6D	92.602	392	15	6	301	678	421688416	421688807	4.450000e-153	551.0
9	TraesCS6D01G313700	chr6D	91.837	392	18	8	301	678	421679077	421679468	4.480000e-148	534.0
10	TraesCS6D01G313700	chr6D	87.500	456	49	5	2603	3055	422602906	422603356	1.260000e-143	520.0
11	TraesCS6D01G313700	chr6D	89.205	352	23	5	191	534	420971408	420971064	2.820000e-115	425.0
12	TraesCS6D01G313700	chr6D	93.233	266	12	2	419	678	421661214	421661479	1.330000e-103	387.0
13	TraesCS6D01G313700	chr6D	92.308	247	19	0	1	247	421688173	421688419	4.850000e-93	351.0
14	TraesCS6D01G313700	chr6D	91.903	247	20	0	1	247	421651862	421652108	2.250000e-91	346.0
15	TraesCS6D01G313700	chr6D	90.283	247	24	0	1	247	421678834	421679080	1.060000e-84	324.0
16	TraesCS6D01G313700	chr6D	92.308	156	11	1	1	155	420971559	420971404	1.430000e-53	220.0
17	TraesCS6D01G313700	chr6D	87.568	185	17	5	2720	2899	421681536	421681719	3.090000e-50	209.0
18	TraesCS6D01G313700	chr6D	87.097	186	18	5	2719	2899	421695999	421696183	3.990000e-49	206.0
19	TraesCS6D01G313700	chr6D	87.027	185	19	4	2719	2899	421663562	421663745	1.440000e-48	204.0
20	TraesCS6D01G313700	chr6D	89.032	155	2	2	769	919	420970525	420970382	8.700000e-41	178.0
21	TraesCS6D01G313700	chr6D	91.339	127	3	5	301	423	421652105	421652227	1.880000e-37	167.0
22	TraesCS6D01G313700	chr6D	87.500	64	3	2	675	733	420970599	420970536	5.470000e-08	69.4
23	TraesCS6D01G313700	chr6A	90.440	1862	101	36	745	2560	565340123	565341953	0.000000e+00	2381.0
24	TraesCS6D01G313700	chr6A	88.388	1843	139	39	675	2459	564279200	564277375	0.000000e+00	2148.0
25	TraesCS6D01G313700	chr6A	92.721	577	30	7	88	656	565317229	565317801	0.000000e+00	822.0
26	TraesCS6D01G313700	chr6A	93.103	464	29	3	2595	3055	565341953	565342416	0.000000e+00	676.0
27	TraesCS6D01G313700	chr6A	88.889	549	38	9	1	530	564279820	564279276	0.000000e+00	654.0
28	TraesCS6D01G313700	chr6A	94.444	90	5	0	1	90	565316979	565317068	4.110000e-29	139.0
29	TraesCS6D01G313700	chr6B	91.137	1557	91	10	1046	2566	636746185	636747730	0.000000e+00	2067.0
30	TraesCS6D01G313700	chr6B	86.912	1658	140	32	696	2292	634504295	634502654	0.000000e+00	1788.0
31	TraesCS6D01G313700	chr6B	93.866	538	22	4	1	531	636743803	636744336	0.000000e+00	800.0
32	TraesCS6D01G313700	chr6B	89.278	457	39	6	2604	3055	636747738	636748189	5.720000e-157	564.0
33	TraesCS6D01G313700	chr6B	91.867	332	26	1	1	331	634560532	634560201	2.150000e-126	462.0
34	TraesCS6D01G313700	chr6B	82.684	231	25	5	2220	2439	634502671	634502445	1.120000e-44	191.0
35	TraesCS6D01G313700	chr6B	90.411	146	10	4	908	1051	636745142	636745285	4.020000e-44	189.0
36	TraesCS6D01G313700	chr6B	89.781	137	8	3	696	827	636744386	636744521	1.460000e-38	171.0
37	TraesCS6D01G313700	chr6B	83.696	92	13	2	2344	2435	3874391	3874480	5.430000e-13	86.1
38	TraesCS6D01G313700	chr3B	77.762	688	87	47	764	1401	70874454	70875125	2.240000e-96	363.0
39	TraesCS6D01G313700	chr3D	76.282	312	43	24	764	1054	45244889	45245190	1.480000e-28	137.0
40	TraesCS6D01G313700	chr4B	88.095	84	10	0	2458	2541	535426901	535426818	1.940000e-17	100.0

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	TraesCS6D01G313700	chr6D	422214387	422217441	3054	False	5642.000000	5642	100.000000	1	3055	1	chr6D.!!$F2	3054
1	TraesCS6D01G313700	chr6D	421466506	421468282	1776	True	2061.000000	2061	87.922000	696	2459	1	chr6D.!!$R1	1763
2	TraesCS6D01G313700	chr6D	422600234	422603356	3122	False	1334.000000	2436	90.477667	1	3055	3	chr6D.!!$F7	3054
3	TraesCS6D01G313700	chr6D	421661214	421663745	2531	False	926.666667	2189	89.328000	419	2899	3	chr6D.!!$F4	2480
4	TraesCS6D01G313700	chr6D	421688173	421690205	2032	False	889.333333	1766	91.696333	1	2036	3	chr6D.!!$F6	2035
5	TraesCS6D01G313700	chr6D	421678834	421681719	2885	False	800.500000	2135	89.255250	1	2899	4	chr6D.!!$F5	2898
6	TraesCS6D01G313700	chr6D	420968855	420971559	2704	True	535.680000	1786	89.326600	1	2459	5	chr6D.!!$R2	2458
7	TraesCS6D01G313700	chr6A	565340123	565342416	2293	False	1528.500000	2381	91.771500	745	3055	2	chr6A.!!$F2	2310
8	TraesCS6D01G313700	chr6A	564277375	564279820	2445	True	1401.000000	2148	88.638500	1	2459	2	chr6A.!!$R1	2458
9	TraesCS6D01G313700	chr6A	565316979	565317801	822	False	480.500000	822	93.582500	1	656	2	chr6A.!!$F1	655
10	TraesCS6D01G313700	chr6B	634502445	634504295	1850	True	989.500000	1788	84.798000	696	2439	2	chr6B.!!$R2	1743
11	TraesCS6D01G313700	chr6B	636743803	636748189	4386	False	758.200000	2067	90.894600	1	3055	5	chr6B.!!$F2	3054
12	TraesCS6D01G313700	chr3B	70874454	70875125	671	False	363.000000	363	77.762000	764	1401	1	chr3B.!!$F1	637

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
601	933	0.105224	TACAATACCGTCGCCCCATG	59.895	55.0	0.0	0.0	0.0	3.66	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2585	4905	0.612453	AGGTCCTCGGGTGAGTTCTC	60.612	60.0	0.0	0.0	40.85	2.87	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
197	363	5.301045	CACTTCCATGTTATCCATCTGCAAT	59.699	40.000	0.00	0.00	0.00	3.56
276	513	1.144716	GATCGTGCCCATCAGCAGA	59.855	57.895	0.00	0.00	45.14	4.26
443	708	5.360714	TCCAGAACTTGTTCTTCAAATGCTT	59.639	36.000	12.73	0.00	35.48	3.91
598	930	1.589727	CGTACAATACCGTCGCCCC	60.590	63.158	0.00	0.00	0.00	5.80
601	933	0.105224	TACAATACCGTCGCCCCATG	59.895	55.000	0.00	0.00	0.00	3.66
668	1147	2.813179	GCTATTCGCCAGGCACGTG	61.813	63.158	12.28	12.28	0.00	4.49
713	1351	5.905181	CGCACGTAATTAATGATAAACCCAC	59.095	40.000	0.00	0.00	0.00	4.61
819	1473	1.210931	CCGTACGTGTGGTGATCGT	59.789	57.895	15.21	0.00	40.78	3.73
922	2139	0.170561	CTAGCTGCAAAGCAAGGCTG	59.829	55.000	13.80	3.39	39.69	4.85
923	2140	0.250858	TAGCTGCAAAGCAAGGCTGA	60.251	50.000	13.80	0.00	39.69	4.26
953	2177	6.929049	TCGCTGGAAACATATTAGAATCGATT	59.071	34.615	11.20	11.20	41.51	3.34
983	2220	7.090953	ACAAGTTTTTGTTTTCTCCATCGTA	57.909	32.000	0.00	0.00	45.01	3.43
1062	3210	3.825014	TCGGTACATATACAGGCCTCTTC	59.175	47.826	0.00	0.00	32.40	2.87
1244	3421	5.299531	GGTTTTATCAGAAAGTATGGAGCCC	59.700	44.000	0.00	0.00	0.00	5.19
1261	3438	4.011698	GAGCCCGGAATTAAAAAGGTACA	58.988	43.478	0.73	0.00	0.00	2.90
1310	3504	0.254747	TCGCCCCCTTTGATTTCGAT	59.745	50.000	0.00	0.00	0.00	3.59
1515	3717	4.764679	TGCTACACACCAATCAAATCAC	57.235	40.909	0.00	0.00	0.00	3.06
1526	3728	9.744468	ACACCAATCAAATCACTAAAAGTTTAC	57.256	29.630	0.00	0.00	0.00	2.01
1540	3742	9.150348	ACTAAAAGTTTACATGCCATATTTTGC	57.850	29.630	0.00	0.00	0.00	3.68
1584	3794	8.063200	TCTCAAATTATTCTAGGTTCACGAGA	57.937	34.615	0.00	0.00	0.00	4.04
1740	3959	7.941919	TGTTCTCTTATCATGCGTCTACTATT	58.058	34.615	0.00	0.00	0.00	1.73
1743	3962	8.341892	TCTCTTATCATGCGTCTACTATTGAT	57.658	34.615	0.00	0.00	0.00	2.57
1752	3971	5.067021	CGTCTACTATTGATTTTGGACGC	57.933	43.478	0.00	0.00	38.67	5.19
1755	3974	3.740044	ACTATTGATTTTGGACGCGTG	57.260	42.857	20.70	0.00	0.00	5.34
1765	3984	2.676632	TGGACGCGTGTTAATATGGT	57.323	45.000	20.70	0.00	0.00	3.55
1801	4020	4.092821	TCGCTCTACCGTTTCAATTGATTG	59.907	41.667	9.40	2.18	39.10	2.67
1888	4108	2.234908	GGCCTACTGTCTTCATCAGTGT	59.765	50.000	0.00	0.00	44.41	3.55
2024	4244	2.675317	GCTGAATGGTCGAAGCACTACT	60.675	50.000	0.00	0.00	0.00	2.57
2070	4290	1.137282	TGTAACCGCGGCAGATTCATA	59.863	47.619	28.58	2.70	0.00	2.15
2109	4329	7.520451	AATGTCTTGTTAGGGGTTAAAGAAC	57.480	36.000	0.00	0.00	34.56	3.01
2170	4390	9.147732	TCATTATCATAGTCTCCACAACATAGT	57.852	33.333	0.00	0.00	0.00	2.12
2213	4433	5.278463	CCATCCGTCTTGTTGAAGTCATTTT	60.278	40.000	0.00	0.00	0.00	1.82
2601	4921	1.712056	TTTGAGAACTCACCCGAGGA	58.288	50.000	3.88	0.00	44.17	3.71
2677	5001	2.439701	CCTCCGTAGTCGCCCTCA	60.440	66.667	0.00	0.00	35.54	3.86
2732	5071	3.370953	GGGAGGCAATTCACATGTAGAGT	60.371	47.826	0.00	0.00	0.00	3.24
2750	5089	4.322567	AGAGTGGAAGAGAAGCAATTGTC	58.677	43.478	7.40	0.00	0.00	3.18
2949	5293	6.204301	GGGACACTCTTACCTTCTTTTTACAC	59.796	42.308	0.00	0.00	0.00	2.90
2950	5294	6.204301	GGACACTCTTACCTTCTTTTTACACC	59.796	42.308	0.00	0.00	0.00	4.16
2951	5295	5.756833	ACACTCTTACCTTCTTTTTACACCG	59.243	40.000	0.00	0.00	0.00	4.94
2953	5297	4.644498	TCTTACCTTCTTTTTACACCGGG	58.356	43.478	6.32	0.00	0.00	5.73
2961	5305	3.393941	TCTTTTTACACCGGGGGTAAGAA	59.606	43.478	20.40	20.32	32.11	2.52
2973	5317	8.419442	CACCGGGGGTAAGAATATATAATAGAC	58.581	40.741	6.32	0.00	32.11	2.59
2986	5330	4.696479	ATAATAGACCTGAGCTTGTGGG	57.304	45.455	0.00	0.00	0.00	4.61
2988	5333	1.729586	TAGACCTGAGCTTGTGGGTT	58.270	50.000	0.00	0.00	31.60	4.11
2992	5337	1.064017	ACCTGAGCTTGTGGGTTCAAA	60.064	47.619	0.00	0.00	0.00	2.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
276	513	0.250770	GCTCTTCCCGGTTGAGGTTT	60.251	55.000	14.59	0.00	0.00	3.27
443	708	2.104792	AGTTCAAGCACAGTTGAGCCTA	59.895	45.455	0.00	0.00	38.15	3.93
598	930	0.461339	GAGCTTGCCAAATGCCCATG	60.461	55.000	0.00	0.00	40.16	3.66
601	933	1.217244	CTGAGCTTGCCAAATGCCC	59.783	57.895	0.00	0.00	40.16	5.36
713	1351	3.730662	CGGTTTGCAACTGATTTATCCCG	60.731	47.826	0.00	0.00	40.26	5.14
922	2139	4.336532	AATATGTTTCCAGCGAACGTTC	57.663	40.909	18.47	18.47	0.00	3.95
923	2140	5.172934	TCTAATATGTTTCCAGCGAACGTT	58.827	37.500	0.00	0.00	0.00	3.99
961	2188	7.090953	TGTACGATGGAGAAAACAAAAACTT	57.909	32.000	0.00	0.00	0.00	2.66
1062	3210	3.951979	ACGCTGAAGAACACTGAAAAG	57.048	42.857	0.00	0.00	0.00	2.27
1226	3403	1.417890	CCGGGCTCCATACTTTCTGAT	59.582	52.381	0.00	0.00	0.00	2.90
1270	3462	4.261405	CGACAAACTGAAGCCCACATTTTA	60.261	41.667	0.00	0.00	0.00	1.52
1310	3504	5.481105	TGCATGCATCTATCAATATGTCGA	58.519	37.500	18.46	0.00	0.00	4.20
1515	3717	9.369904	AGCAAAATATGGCATGTAAACTTTTAG	57.630	29.630	10.98	0.00	0.00	1.85
1526	3728	3.188159	AGGCAAGCAAAATATGGCATG	57.812	42.857	10.98	0.00	41.64	4.06
1530	3732	6.746745	ATTTTCAAGGCAAGCAAAATATGG	57.253	33.333	0.00	0.00	28.78	2.74
1540	3742	9.649167	ATTTGAGAAGATTATTTTCAAGGCAAG	57.351	29.630	0.00	0.00	0.00	4.01
1584	3794	4.827835	TCGGATTTCTCCAGTATCTCGATT	59.172	41.667	0.00	0.00	42.19	3.34
1740	3959	5.447954	CCATATTAACACGCGTCCAAAATCA	60.448	40.000	9.86	0.00	0.00	2.57
1743	3962	3.752222	ACCATATTAACACGCGTCCAAAA	59.248	39.130	9.86	1.49	0.00	2.44
1765	3984	6.409704	ACGGTAGAGCGAGGTATATATACAA	58.590	40.000	21.56	0.00	34.98	2.41
1801	4020	9.372541	CACAAAAATTAACAATGCAAAGACATC	57.627	29.630	0.00	0.00	0.00	3.06
1888	4108	5.981315	GTGTGCTTGCGTACCTTATAAGATA	59.019	40.000	14.28	0.00	0.00	1.98
2170	4390	7.015292	ACGGATGGAGCTCAATTACTTCTATTA	59.985	37.037	17.19	0.00	0.00	0.98
2177	4397	3.034635	AGACGGATGGAGCTCAATTACT	58.965	45.455	17.19	5.40	0.00	2.24
2178	4398	3.460857	AGACGGATGGAGCTCAATTAC	57.539	47.619	17.19	6.37	0.00	1.89
2183	4403	0.976641	AACAAGACGGATGGAGCTCA	59.023	50.000	17.19	1.87	0.00	4.26
2213	4433	1.684450	TCTTGTCAACCGTGCTACAGA	59.316	47.619	0.00	0.00	0.00	3.41
2484	4803	3.430929	CCAACTCGTCCCTTAGATCCAAG	60.431	52.174	0.00	0.00	0.00	3.61
2580	4900	2.436542	TCCTCGGGTGAGTTCTCAAAAA	59.563	45.455	3.99	0.00	40.85	1.94
2581	4901	2.043992	TCCTCGGGTGAGTTCTCAAAA	58.956	47.619	3.99	0.00	40.85	2.44
2582	4902	1.343465	GTCCTCGGGTGAGTTCTCAAA	59.657	52.381	3.99	0.00	40.85	2.69
2583	4903	0.966920	GTCCTCGGGTGAGTTCTCAA	59.033	55.000	3.99	0.00	40.85	3.02
2584	4904	0.898789	GGTCCTCGGGTGAGTTCTCA	60.899	60.000	0.00	0.00	40.85	3.27
2585	4905	0.612453	AGGTCCTCGGGTGAGTTCTC	60.612	60.000	0.00	0.00	40.85	2.87
2586	4906	0.612453	GAGGTCCTCGGGTGAGTTCT	60.612	60.000	2.28	0.00	40.85	3.01
2587	4907	1.605971	GGAGGTCCTCGGGTGAGTTC	61.606	65.000	12.91	0.00	40.85	3.01
2588	4908	1.609794	GGAGGTCCTCGGGTGAGTT	60.610	63.158	12.91	0.00	40.85	3.01
2589	4909	2.037527	GGAGGTCCTCGGGTGAGT	59.962	66.667	12.91	0.00	40.85	3.41
2590	4910	2.360980	AGGAGGTCCTCGGGTGAG	59.639	66.667	12.91	0.00	44.77	3.51
2601	4921	0.393077	CCTCACGTGTTGAAGGAGGT	59.607	55.000	16.51	0.00	40.18	3.85
2677	5001	2.056906	AACTGCCTCTTGGGTCGCTT	62.057	55.000	0.00	0.00	37.43	4.68
2687	5011	1.339097	ACACGACCTAAACTGCCTCT	58.661	50.000	0.00	0.00	0.00	3.69
2732	5071	2.816087	GCAGACAATTGCTTCTCTTCCA	59.184	45.455	5.05	0.00	40.89	3.53
2949	5293	7.788385	AGGTCTATTATATATTCTTACCCCCGG	59.212	40.741	0.00	0.00	0.00	5.73
2950	5294	8.639761	CAGGTCTATTATATATTCTTACCCCCG	58.360	40.741	0.00	0.00	0.00	5.73
2951	5295	9.725206	TCAGGTCTATTATATATTCTTACCCCC	57.275	37.037	0.00	0.00	0.00	5.40
2961	5305	7.680310	ACCCACAAGCTCAGGTCTATTATATAT	59.320	37.037	0.00	0.00	0.00	0.86
2973	5317	1.691196	TTTGAACCCACAAGCTCAGG	58.309	50.000	0.00	0.00	0.00	3.86
2988	5333	9.958234	TCTCGTGTTTCATTAAATTCATTTTGA	57.042	25.926	0.00	0.00	0.00	2.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.