AutoCloner

Multiple sequence alignment - TraesCS5A01G001000

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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	TraesCS5A01G001000	chr5A	100.000	2354	0	0	1	2354	834966	837319	0.000000e+00	4348.0
1	TraesCS5A01G001000	chr3A	98.827	1449	13	2	1	1445	699631695	699630247	0.000000e+00	2579.0
2	TraesCS5A01G001000	chr3A	82.276	914	152	10	1446	2353	458811213	458810304	0.000000e+00	782.0
3	TraesCS5A01G001000	chr1D	97.529	1457	22	4	4	1446	281398667	281397211	0.000000e+00	2479.0
4	TraesCS5A01G001000	chr7D	96.843	1457	28	4	1	1446	52488836	52487387	0.000000e+00	2420.0
5	TraesCS5A01G001000	chr7D	83.938	909	139	7	1445	2350	612679756	612678852	0.000000e+00	863.0
6	TraesCS5A01G001000	chr7D	83.278	909	146	6	1445	2350	475457901	475458806	0.000000e+00	832.0
7	TraesCS5A01G001000	chr1B	91.828	979	47	17	1	973	687156043	687155092	0.000000e+00	1334.0
8	TraesCS5A01G001000	chr1B	88.782	731	80	2	1517	2246	321048308	321047579	0.000000e+00	894.0
9	TraesCS5A01G001000	chr1B	95.977	174	7	0	1257	1430	687155078	687154905	1.380000e-72	283.0
10	TraesCS5A01G001000	chr3D	84.013	907	142	3	1445	2350	37174545	37175449	0.000000e+00	869.0
11	TraesCS5A01G001000	chr3D	81.271	913	165	5	1446	2353	343865727	343866638	0.000000e+00	734.0
12	TraesCS5A01G001000	chr5D	86.284	802	75	10	374	1160	552440104	552440885	0.000000e+00	839.0
13	TraesCS5A01G001000	chr5D	81.465	901	160	6	1445	2344	419362119	419363013	0.000000e+00	732.0
14	TraesCS5A01G001000	chr5D	90.610	213	18	2	1233	1445	552440903	552441113	4.950000e-72	281.0
15	TraesCS5A01G001000	chr5D	90.431	209	13	3	1	203	552439828	552440035	3.860000e-68	268.0
16	TraesCS5A01G001000	chr5D	89.759	166	10	2	155	320	552439945	552440103	3.070000e-49	206.0
17	TraesCS5A01G001000	chr2B	81.498	908	163	5	1448	2353	796383984	796383080	0.000000e+00	741.0
18	TraesCS5A01G001000	chr7B	81.271	913	162	9	1445	2353	354243788	354242881	0.000000e+00	730.0
19	TraesCS5A01G001000	chr7B	83.571	140	20	3	1310	1447	588054851	588054989	6.830000e-26	128.0
20	TraesCS5A01G001000	chr2D	85.777	682	73	17	517	1184	190398083	190397412	0.000000e+00	701.0
21	TraesCS5A01G001000	chr2D	90.054	372	26	6	155	524	190399392	190399030	2.740000e-129	472.0
22	TraesCS5A01G001000	chr2D	91.388	209	11	3	1	203	190399509	190399302	1.780000e-71	279.0
23	TraesCS5A01G001000	chr2D	90.047	211	20	1	1235	1445	190397397	190397188	2.980000e-69	272.0
24	TraesCS5A01G001000	chr6A	87.631	574	51	10	625	1184	2269858	2269291	0.000000e+00	649.0
25	TraesCS5A01G001000	chr6A	88.913	460	38	4	155	614	2270356	2269910	2.640000e-154	555.0
26	TraesCS5A01G001000	chr6A	83.853	545	57	17	428	956	56405377	56405906	7.560000e-135	490.0
27	TraesCS5A01G001000	chr6A	87.097	279	26	5	155	432	56313029	56313298	8.170000e-80	307.0
28	TraesCS5A01G001000	chr6A	90.047	211	12	3	1	203	2270475	2270266	4.990000e-67	265.0
29	TraesCS5A01G001000	chr7A	86.519	497	42	7	155	651	7806051	7805580	7.450000e-145	523.0
30	TraesCS5A01G001000	chr7A	83.894	416	46	14	769	1184	7805287	7804893	6.140000e-101	377.0
31	TraesCS5A01G001000	chr7A	92.241	116	3	2	4	113	7810908	7810793	2.420000e-35	159.0
32	TraesCS5A01G001000	chr7A	92.593	108	8	0	652	759	7805487	7805380	3.130000e-34	156.0
33	TraesCS5A01G001000	chr7A	97.143	35	1	0	1410	1444	696201155	696201121	2.530000e-05	60.2
34	TraesCS5A01G001000	chr2A	88.571	70	8	0	57	126	298643513	298643582	4.170000e-13	86.1

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	TraesCS5A01G001000	chr5A	834966	837319	2353	False	4348.000000	4348	100.000000	1	2354	1	chr5A.!!$F1	2353
1	TraesCS5A01G001000	chr3A	699630247	699631695	1448	True	2579.000000	2579	98.827000	1	1445	1	chr3A.!!$R2	1444
2	TraesCS5A01G001000	chr3A	458810304	458811213	909	True	782.000000	782	82.276000	1446	2353	1	chr3A.!!$R1	907
3	TraesCS5A01G001000	chr1D	281397211	281398667	1456	True	2479.000000	2479	97.529000	4	1446	1	chr1D.!!$R1	1442
4	TraesCS5A01G001000	chr7D	52487387	52488836	1449	True	2420.000000	2420	96.843000	1	1446	1	chr7D.!!$R1	1445
5	TraesCS5A01G001000	chr7D	612678852	612679756	904	True	863.000000	863	83.938000	1445	2350	1	chr7D.!!$R2	905
6	TraesCS5A01G001000	chr7D	475457901	475458806	905	False	832.000000	832	83.278000	1445	2350	1	chr7D.!!$F1	905
7	TraesCS5A01G001000	chr1B	321047579	321048308	729	True	894.000000	894	88.782000	1517	2246	1	chr1B.!!$R1	729
8	TraesCS5A01G001000	chr1B	687154905	687156043	1138	True	808.500000	1334	93.902500	1	1430	2	chr1B.!!$R2	1429
9	TraesCS5A01G001000	chr3D	37174545	37175449	904	False	869.000000	869	84.013000	1445	2350	1	chr3D.!!$F1	905
10	TraesCS5A01G001000	chr3D	343865727	343866638	911	False	734.000000	734	81.271000	1446	2353	1	chr3D.!!$F2	907
11	TraesCS5A01G001000	chr5D	419362119	419363013	894	False	732.000000	732	81.465000	1445	2344	1	chr5D.!!$F1	899
12	TraesCS5A01G001000	chr5D	552439828	552441113	1285	False	398.500000	839	89.271000	1	1445	4	chr5D.!!$F2	1444
13	TraesCS5A01G001000	chr2B	796383080	796383984	904	True	741.000000	741	81.498000	1448	2353	1	chr2B.!!$R1	905
14	TraesCS5A01G001000	chr7B	354242881	354243788	907	True	730.000000	730	81.271000	1445	2353	1	chr7B.!!$R1	908
15	TraesCS5A01G001000	chr2D	190397188	190399509	2321	True	431.000000	701	89.316500	1	1445	4	chr2D.!!$R1	1444
16	TraesCS5A01G001000	chr6A	56405377	56405906	529	False	490.000000	490	83.853000	428	956	1	chr6A.!!$F2	528
17	TraesCS5A01G001000	chr6A	2269291	2270475	1184	True	489.666667	649	88.863667	1	1184	3	chr6A.!!$R1	1183
18	TraesCS5A01G001000	chr7A	7804893	7806051	1158	True	352.000000	523	87.668667	155	1184	3	chr7A.!!$R3	1029

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
443	589	3.316588	GCTTAGCAATTCCCTTTCTAGGC	59.683	47.826	0.0	0.0	40.5	3.93	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1693	3042	0.036875	CCAGACCACCAACCCTCTTC	59.963	60.0	0.0	0.0	0.0	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
443	589	3.316588	GCTTAGCAATTCCCTTTCTAGGC	59.683	47.826	0.00	0.00	40.50	3.93
774	2094	7.916450	AGCGAAGTACTTGACTAATTATCAGAC	59.084	37.037	14.14	0.00	37.44	3.51
1169	2513	0.753848	GGAGAGGGAGTTCTCGAGGG	60.754	65.000	13.56	0.00	43.64	4.30
1263	2608	0.749454	CAGAAGATGGCGAAAGGGGG	60.749	60.000	0.00	0.00	0.00	5.40
1323	2668	0.909623	GCTACACTTCAAGGCCCCTA	59.090	55.000	0.00	0.00	0.00	3.53
1450	2795	3.614616	GCACTGGATACGTTCTCTTCAAG	59.385	47.826	0.00	0.00	42.51	3.02
1458	2803	7.147897	TGGATACGTTCTCTTCAAGTATGTCAT	60.148	37.037	0.00	0.00	42.51	3.06
1472	2818	6.992664	AGTATGTCATGGAGAGCTCTAAAT	57.007	37.500	18.25	10.55	0.00	1.40
1473	2819	6.991938	AGTATGTCATGGAGAGCTCTAAATC	58.008	40.000	18.25	3.93	0.00	2.17
1478	2824	5.812642	GTCATGGAGAGCTCTAAATCGAAAA	59.187	40.000	18.25	0.00	0.00	2.29
1493	2839	6.894339	AATCGAAAATAAGTGGTTGGAAGT	57.106	33.333	0.00	0.00	0.00	3.01
1517	2863	3.575399	GGTTTGTCCAAAGCAGCAG	57.425	52.632	15.05	0.00	45.25	4.24
1586	2932	5.011329	ACCATGATTTGTTTTCAGCTCACAT	59.989	36.000	0.00	0.00	0.00	3.21
1620	2968	2.498078	GGAACCTGACTTCGATCTCCTT	59.502	50.000	0.00	0.00	0.00	3.36
1675	3023	4.012374	GGAAAGTGCATTGGATCTCTTGA	58.988	43.478	0.00	0.00	0.00	3.02
1714	3063	1.846124	GAGGGTTGGTGGTCTGGGA	60.846	63.158	0.00	0.00	0.00	4.37
1721	3073	2.668632	GTGGTCTGGGATTCCGCA	59.331	61.111	0.00	0.00	35.24	5.69
1726	3078	0.322546	GTCTGGGATTCCGCAAACCT	60.323	55.000	0.00	0.00	34.70	3.50
1878	3232	6.425114	CCATCTAATGCATCCTACACTTACAC	59.575	42.308	0.00	0.00	0.00	2.90
1977	3331	2.239654	ACCATGACAACTGGATTCCGAT	59.760	45.455	1.99	0.00	37.22	4.18
2053	3407	0.034476	CAGACCTGCTCACAGCTGAA	59.966	55.000	23.35	7.07	41.94	3.02
2054	3408	0.982704	AGACCTGCTCACAGCTGAAT	59.017	50.000	23.35	0.00	41.94	2.57
2164	3519	1.208052	GAGCAGGACTACTTGGCATGA	59.792	52.381	7.45	0.00	37.76	3.07
2202	3559	2.309528	TGCTTCAACGTCAAGTCTGT	57.690	45.000	8.55	0.00	0.00	3.41
2215	3572	5.007234	CGTCAAGTCTGTGTACCATTTGAAA	59.993	40.000	0.00	0.00	0.00	2.69
2223	3580	8.017946	GTCTGTGTACCATTTGAAAAGATCTTC	58.982	37.037	8.78	0.00	0.00	2.87
2229	3586	2.577606	TTGAAAAGATCTTCGGGGCA	57.422	45.000	8.78	0.39	0.00	5.36
2233	3590	2.806945	AAAGATCTTCGGGGCAATCA	57.193	45.000	8.78	0.00	0.00	2.57
2265	3622	2.110006	GGAGGCCTCTGATTCGGC	59.890	66.667	31.36	9.17	45.55	5.54
2284	3641	1.821216	CACAGACGCATAAGGGGTTT	58.179	50.000	0.00	0.00	43.60	3.27
2290	3647	1.064314	ACGCATAAGGGGTTTATGGCA	60.064	47.619	8.49	0.00	45.77	4.92
2319	3677	0.901827	TCATGTGCTCCCGCTAAAGA	59.098	50.000	0.00	0.00	36.97	2.52
2324	3682	2.552315	TGTGCTCCCGCTAAAGAAAAAG	59.448	45.455	0.00	0.00	36.97	2.27
2329	3687	4.378149	GCTCCCGCTAAAGAAAAAGTACAC	60.378	45.833	0.00	0.00	0.00	2.90
2353	3711	1.027357	GGCGCATGATCAAGAATGGT	58.973	50.000	10.83	0.00	0.00	3.55

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
443	589	4.946157	AGCTTCAGGAAGTTGATTGTATGG	59.054	41.667	10.47	0.00	40.45	2.74
774	2094	6.815641	GTGGAATATAGATGTGCTATGTCTGG	59.184	42.308	0.00	0.00	40.05	3.86
973	2301	2.357952	CTCAACGATCCGAGGTATGTGA	59.642	50.000	0.00	0.00	0.00	3.58
1169	2513	1.826487	GGCGTCTCCCTCTCCTCTC	60.826	68.421	0.00	0.00	0.00	3.20
1263	2608	3.541632	TCCAAACTCCACTTTGTGTCTC	58.458	45.455	0.00	0.00	30.33	3.36
1323	2668	1.550072	GGGTGCTGGTACATTTTGCAT	59.450	47.619	0.00	0.00	38.05	3.96
1450	2795	5.861251	CGATTTAGAGCTCTCCATGACATAC	59.139	44.000	22.17	0.00	0.00	2.39
1458	2803	7.492669	CACTTATTTTCGATTTAGAGCTCTCCA	59.507	37.037	22.17	8.52	0.00	3.86
1472	2818	4.517453	CCACTTCCAACCACTTATTTTCGA	59.483	41.667	0.00	0.00	0.00	3.71
1473	2819	4.794169	CCACTTCCAACCACTTATTTTCG	58.206	43.478	0.00	0.00	0.00	3.46
1478	2824	2.969821	TGCCACTTCCAACCACTTAT	57.030	45.000	0.00	0.00	0.00	1.73
1493	2839	0.463620	GCTTTGGACAAACCTTGCCA	59.536	50.000	0.00	0.00	39.86	4.92
1517	2863	3.944015	CCAGATTTGATCAACACCTCTCC	59.056	47.826	7.89	0.00	0.00	3.71
1586	2932	4.134563	GTCAGGTTCCAGCAAGTTTTCTA	58.865	43.478	0.00	0.00	0.00	2.10
1594	2940	0.756294	TCGAAGTCAGGTTCCAGCAA	59.244	50.000	0.00	0.00	0.00	3.91
1620	2968	0.187117	TGCACCCCACCAGAATTTCA	59.813	50.000	0.00	0.00	0.00	2.69
1693	3042	0.036875	CCAGACCACCAACCCTCTTC	59.963	60.000	0.00	0.00	0.00	2.87
1714	3063	2.040544	CGCCTCAGGTTTGCGGAAT	61.041	57.895	0.00	0.00	44.29	3.01
1721	3073	2.270352	TGATTGAACGCCTCAGGTTT	57.730	45.000	0.00	0.00	34.81	3.27
1726	3078	1.896220	AAGCTTGATTGAACGCCTCA	58.104	45.000	0.00	0.00	0.00	3.86
1755	3107	1.830279	CAGAATTCTCCAGGCTTGCA	58.170	50.000	4.57	0.00	0.00	4.08
1845	3199	4.141181	AGGATGCATTAGATGGGCAAGTAA	60.141	41.667	0.00	0.00	41.43	2.24
1878	3232	3.187227	GTCTCTGCCATGTAACACACTTG	59.813	47.826	0.00	0.00	33.20	3.16
1977	3331	4.956700	CCAGTGGTCTCATAGTTCCTCTTA	59.043	45.833	0.00	0.00	0.00	2.10
2071	3425	6.653020	ACTGAACATCTCATTTACTATGGCA	58.347	36.000	0.00	0.00	32.14	4.92
2107	3462	7.556635	CCTATTGCAATCTGATGGATATCATGT	59.443	37.037	16.86	0.00	42.19	3.21
2215	3572	2.648059	CTTGATTGCCCCGAAGATCTT	58.352	47.619	7.95	7.95	0.00	2.40
2223	3580	2.824041	CGGTCCTTGATTGCCCCG	60.824	66.667	0.00	0.00	0.00	5.73
2229	3586	1.299976	GGCTGTCCGGTCCTTGATT	59.700	57.895	0.00	0.00	0.00	2.57
2265	3622	1.821216	AAACCCCTTATGCGTCTGTG	58.179	50.000	0.00	0.00	0.00	3.66
2284	3641	2.241941	ACATGACTCCCACAATGCCATA	59.758	45.455	0.00	0.00	0.00	2.74
2290	3647	1.340405	GGAGCACATGACTCCCACAAT	60.340	52.381	21.75	0.00	46.81	2.71
2311	3669	5.851177	CCACATGTGTACTTTTTCTTTAGCG	59.149	40.000	23.79	0.00	0.00	4.26
2319	3677	1.678627	TGCGCCACATGTGTACTTTTT	59.321	42.857	23.79	0.00	0.00	1.94

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.