AutoCloner

Multiple sequence alignment - TraesCS6A01G014500

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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	TraesCS6A01G014500	chr6A	100.000	2762	0	0	1	2762	7078617	7081378	0.000000e+00	5101.0
1	TraesCS6A01G014500	chr6A	92.842	1900	119	13	873	2762	7176094	7174202	0.000000e+00	2739.0
2	TraesCS6A01G014500	chr6A	88.235	442	52	0	1	442	586803223	586803664	1.880000e-146	529.0
3	TraesCS6A01G014500	chr6A	100.000	34	0	0	823	856	7176125	7176092	2.300000e-06	63.9
4	TraesCS6A01G014500	chr6B	88.535	2041	199	20	730	2760	12886330	12888345	0.000000e+00	2440.0
5	TraesCS6A01G014500	chr6B	90.441	1768	162	7	999	2762	26861804	26863568	0.000000e+00	2322.0
6	TraesCS6A01G014500	chr6B	89.043	1798	185	8	973	2762	13653949	13652156	0.000000e+00	2218.0
7	TraesCS6A01G014500	chr6B	88.593	1201	120	11	955	2143	13704897	13703702	0.000000e+00	1443.0
8	TraesCS6A01G014500	chr6B	92.800	125	8	1	736	860	13654179	13654056	2.190000e-41	180.0
9	TraesCS6A01G014500	chr6B	80.282	142	24	4	527	666	482428158	482428297	1.350000e-18	104.0
10	TraesCS6A01G014500	chr5B	88.201	2051	200	20	716	2762	432982436	432984448	0.000000e+00	2409.0
11	TraesCS6A01G014500	chrUn	89.286	1792	187	5	973	2762	79937079	79938867	0.000000e+00	2241.0
12	TraesCS6A01G014500	chrUn	88.462	1794	197	10	973	2760	80037167	80035378	0.000000e+00	2158.0
13	TraesCS6A01G014500	chr7D	88.493	1825	199	9	942	2760	597677191	597675372	0.000000e+00	2196.0
14	TraesCS6A01G014500	chr6D	87.720	1816	212	10	952	2762	7346012	7344203	0.000000e+00	2108.0
15	TraesCS6A01G014500	chr6D	76.087	690	147	18	2	683	58486747	58487426	7.320000e-91	344.0
16	TraesCS6A01G014500	chr6D	86.957	115	9	1	691	805	7346242	7346134	1.040000e-24	124.0
17	TraesCS6A01G014500	chr6D	83.333	72	11	1	691	761	7359656	7359585	6.380000e-07	65.8
18	TraesCS6A01G014500	chr7A	89.620	684	65	4	1	683	669025625	669026303	0.000000e+00	865.0
19	TraesCS6A01G014500	chr7A	89.312	683	71	2	1	682	167166347	167167028	0.000000e+00	856.0
20	TraesCS6A01G014500	chr7A	92.308	104	8	0	568	671	19801681	19801784	6.160000e-32	148.0
21	TraesCS6A01G014500	chr2B	94.366	355	19	1	329	683	590596404	590596757	6.730000e-151	544.0
22	TraesCS6A01G014500	chr3A	91.789	341	26	2	343	683	10445817	10446155	8.950000e-130	473.0
23	TraesCS6A01G014500	chr3D	73.246	684	168	11	7	683	584473364	584474039	4.600000e-58	235.0
24	TraesCS6A01G014500	chr5D	89.231	130	14	0	553	682	451979106	451979235	2.200000e-36	163.0

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	TraesCS6A01G014500	chr6A	7078617	7081378	2761	False	5101.00	5101	100.0000	1	2762	1	chr6A.!!$F1	2761
1	TraesCS6A01G014500	chr6A	7174202	7176125	1923	True	1401.45	2739	96.4210	823	2762	2	chr6A.!!$R1	1939
2	TraesCS6A01G014500	chr6B	12886330	12888345	2015	False	2440.00	2440	88.5350	730	2760	1	chr6B.!!$F1	2030
3	TraesCS6A01G014500	chr6B	26861804	26863568	1764	False	2322.00	2322	90.4410	999	2762	1	chr6B.!!$F2	1763
4	TraesCS6A01G014500	chr6B	13703702	13704897	1195	True	1443.00	1443	88.5930	955	2143	1	chr6B.!!$R1	1188
5	TraesCS6A01G014500	chr6B	13652156	13654179	2023	True	1199.00	2218	90.9215	736	2762	2	chr6B.!!$R2	2026
6	TraesCS6A01G014500	chr5B	432982436	432984448	2012	False	2409.00	2409	88.2010	716	2762	1	chr5B.!!$F1	2046
7	TraesCS6A01G014500	chrUn	79937079	79938867	1788	False	2241.00	2241	89.2860	973	2762	1	chrUn.!!$F1	1789
8	TraesCS6A01G014500	chrUn	80035378	80037167	1789	True	2158.00	2158	88.4620	973	2760	1	chrUn.!!$R1	1787
9	TraesCS6A01G014500	chr7D	597675372	597677191	1819	True	2196.00	2196	88.4930	942	2760	1	chr7D.!!$R1	1818
10	TraesCS6A01G014500	chr6D	7344203	7346242	2039	True	1116.00	2108	87.3385	691	2762	2	chr6D.!!$R2	2071
11	TraesCS6A01G014500	chr6D	58486747	58487426	679	False	344.00	344	76.0870	2	683	1	chr6D.!!$F1	681
12	TraesCS6A01G014500	chr7A	669025625	669026303	678	False	865.00	865	89.6200	1	683	1	chr7A.!!$F3	682
13	TraesCS6A01G014500	chr7A	167166347	167167028	681	False	856.00	856	89.3120	1	682	1	chr7A.!!$F2	681
14	TraesCS6A01G014500	chr3D	584473364	584474039	675	False	235.00	235	73.2460	7	683	1	chr3D.!!$F1	676

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
210	211	0.395862	GGGAGATCCAGGACTCGTCA	60.396	60.0	0.47	0.0	37.91	4.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1964	2031	0.106419	TCGGTTTTTGGCCCAGACTT	60.106	50.0	0.0	0.0	0.0	3.01	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
53	54	1.064463	GGAGTGGATCTTTGCCATGGA	60.064	52.381	18.40	0.00	37.81	3.41
54	55	2.621407	GGAGTGGATCTTTGCCATGGAA	60.621	50.000	18.40	0.00	37.81	3.53
70	71	5.786311	CCATGGAAAAAGCTCTTTCATCAA	58.214	37.500	14.27	0.00	37.09	2.57
71	72	6.403878	CCATGGAAAAAGCTCTTTCATCAAT	58.596	36.000	14.27	0.14	37.09	2.57
92	93	1.263776	GAGTTCGTCAGATGTGCGAG	58.736	55.000	8.77	0.00	34.95	5.03
114	115	1.991230	GCTATGGGCGATATGGGGT	59.009	57.895	0.00	0.00	0.00	4.95
117	118	1.130678	TATGGGCGATATGGGGTGCA	61.131	55.000	0.00	0.00	0.00	4.57
165	166	3.502191	TTCAAAAGCCCGTATGCAATC	57.498	42.857	0.00	0.00	0.00	2.67
177	178	4.104776	CGTATGCAATCCATGGTTTTGTC	58.895	43.478	22.55	17.34	35.34	3.18
192	193	2.577606	TTGTCAACACATACCTGGGG	57.422	50.000	0.00	0.00	30.55	4.96
208	209	1.075896	GGGGAGATCCAGGACTCGT	60.076	63.158	0.47	0.00	37.91	4.18
210	211	0.395862	GGGAGATCCAGGACTCGTCA	60.396	60.000	0.47	0.00	37.91	4.35
257	258	2.504920	CCACCAGAGGCACGAGATA	58.495	57.895	0.00	0.00	0.00	1.98
319	320	2.373707	GCAGTGGGCAGAGGAGGAT	61.374	63.158	0.00	0.00	43.97	3.24
372	373	1.168714	ACGATGGCTCTTTTTCAGGC	58.831	50.000	0.00	0.00	36.96	4.85
379	380	1.068333	GCTCTTTTTCAGGCGCATCAA	60.068	47.619	10.83	0.00	0.00	2.57
442	443	2.208431	CAATGGCGATCAGAGAAGGTC	58.792	52.381	0.00	0.00	0.00	3.85
478	479	4.517285	AGAGTTGAATGTGCACCGAATAT	58.483	39.130	15.69	0.00	0.00	1.28
521	522	3.216800	GCATGGTGGCAGAGATCAAATA	58.783	45.455	0.00	0.00	0.00	1.40
549	550	2.289631	TGGATCGGCTTATGGTGCTATG	60.290	50.000	0.00	0.00	0.00	2.23
551	552	3.557054	GGATCGGCTTATGGTGCTATGAA	60.557	47.826	0.00	0.00	0.00	2.57
564	565	8.593945	ATGGTGCTATGAAAGAGGAAATTAAA	57.406	30.769	0.00	0.00	0.00	1.52
617	618	6.407202	ACGTAATTCATGAGTTTAGGAGCTT	58.593	36.000	19.00	3.15	0.00	3.74
621	622	6.749923	ATTCATGAGTTTAGGAGCTTCAAC	57.250	37.500	0.00	0.00	0.00	3.18
685	686	3.736483	GGCGTCATGTATGGCCAG	58.264	61.111	13.05	0.00	44.91	4.85
686	687	2.546494	GGCGTCATGTATGGCCAGC	61.546	63.158	13.05	6.14	44.91	4.85
687	688	2.885676	GCGTCATGTATGGCCAGCG	61.886	63.158	13.05	7.91	0.00	5.18
688	689	2.885676	CGTCATGTATGGCCAGCGC	61.886	63.158	13.05	0.00	0.00	5.92
689	690	2.588596	TCATGTATGGCCAGCGCG	60.589	61.111	13.05	0.00	35.02	6.86
709	710	2.647158	GGAGGGTCGCCTCGTCTTT	61.647	63.158	3.37	0.00	37.68	2.52
779	780	2.126463	CGCTGTGACCGTGTCGAT	60.126	61.111	0.00	0.00	34.95	3.59
805	806	2.739996	CCGGCAGCCAGATCTCCTT	61.740	63.158	13.30	0.00	0.00	3.36
806	807	1.222936	CGGCAGCCAGATCTCCTTT	59.777	57.895	13.30	0.00	0.00	3.11
819	820	6.219473	CAGATCTCCTTTAGTACATCGCATT	58.781	40.000	0.00	0.00	0.00	3.56
861	870	1.037579	TCGACGGTGAGCATCCTGAT	61.038	55.000	0.00	0.00	0.00	2.90
871	880	1.142465	AGCATCCTGATGACCATGGAC	59.858	52.381	21.47	13.94	41.20	4.02
916	925	1.134175	CAGCTCGTCCTTCTTCCTCTC	59.866	57.143	0.00	0.00	0.00	3.20
921	930	2.826725	TCGTCCTTCTTCCTCTCCTTTC	59.173	50.000	0.00	0.00	0.00	2.62
923	932	3.178046	GTCCTTCTTCCTCTCCTTTCCT	58.822	50.000	0.00	0.00	0.00	3.36
925	934	3.841255	TCCTTCTTCCTCTCCTTTCCTTC	59.159	47.826	0.00	0.00	0.00	3.46
927	936	3.569135	TCTTCCTCTCCTTTCCTTCCT	57.431	47.619	0.00	0.00	0.00	3.36
928	937	3.875571	TCTTCCTCTCCTTTCCTTCCTT	58.124	45.455	0.00	0.00	0.00	3.36
929	938	4.243643	TCTTCCTCTCCTTTCCTTCCTTT	58.756	43.478	0.00	0.00	0.00	3.11
930	939	4.665483	TCTTCCTCTCCTTTCCTTCCTTTT	59.335	41.667	0.00	0.00	0.00	2.27
931	940	5.850028	TCTTCCTCTCCTTTCCTTCCTTTTA	59.150	40.000	0.00	0.00	0.00	1.52
932	941	6.331837	TCTTCCTCTCCTTTCCTTCCTTTTAA	59.668	38.462	0.00	0.00	0.00	1.52
933	942	6.128138	TCCTCTCCTTTCCTTCCTTTTAAG	57.872	41.667	0.00	0.00	0.00	1.85
1068	1131	2.995574	AAGGCTCGGTACCACGCT	60.996	61.111	13.54	1.20	0.00	5.07
1137	1200	2.436109	GTTGCTGGGCCTTCCTCA	59.564	61.111	4.53	0.00	36.20	3.86
1142	1205	1.614824	CTGGGCCTTCCTCAGTCCT	60.615	63.158	4.53	0.00	36.20	3.85
1413	1476	3.054139	AGAAGACCAGCTATGCAATGGAA	60.054	43.478	15.16	0.00	37.54	3.53
1608	1674	5.106555	CGTACTTGATGGCTTGTTGAAAGAT	60.107	40.000	0.00	0.00	0.00	2.40
1759	1825	5.874093	AGGTTCTTCAACAGATGACTGATT	58.126	37.500	0.00	0.00	46.03	2.57
1773	1839	3.776969	TGACTGATTGAGGTATTCTGCCT	59.223	43.478	0.00	0.00	39.42	4.75
1791	1857	2.554032	GCCTGATGTTGCCACATATACC	59.446	50.000	2.94	0.00	44.22	2.73
1797	1863	4.137116	TGTTGCCACATATACCAGTCTC	57.863	45.455	0.00	0.00	0.00	3.36
1932	1998	0.465460	TTTGCAAGAGCGGAAGGTGT	60.465	50.000	0.00	0.00	46.23	4.16
1964	2031	6.772716	GCTAGGAAGATTTTGATTCCATGGTA	59.227	38.462	12.58	1.50	46.21	3.25
1968	2035	7.340487	AGGAAGATTTTGATTCCATGGTAAGTC	59.660	37.037	12.58	6.56	46.21	3.01
2178	2245	6.128849	GCATATATTTACAAAAATGCGGCAGG	60.129	38.462	9.25	0.00	36.02	4.85
2459	2529	6.271159	ACCTTTGCAAAAATGGAAGGGTTATA	59.729	34.615	19.65	0.00	44.60	0.98
2593	2663	6.316390	GGGAGGAAGTTACTTGACAATATGTG	59.684	42.308	0.93	0.00	0.00	3.21
2653	2723	8.200024	AGCATACTGATTGATGGTTACTCTAT	57.800	34.615	0.00	0.00	29.68	1.98
2668	2738	6.211785	GGTTACTCTATGAAGGGAAGGATAGG	59.788	46.154	0.00	0.00	0.00	2.57
2714	2784	5.303333	GGAAATGTTGGACAGGAAGGTTAAA	59.697	40.000	0.00	0.00	0.00	1.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
10	11	5.449588	CCTTGGCACTATCATGTTGATTGAC	60.450	44.000	6.05	0.00	38.26	3.18
21	22	1.951209	TCCACTCCTTGGCACTATCA	58.049	50.000	0.00	0.00	46.47	2.15
42	43	3.672767	AGAGCTTTTTCCATGGCAAAG	57.327	42.857	22.87	22.87	0.00	2.77
53	54	6.661304	ACTCCATTGATGAAAGAGCTTTTT	57.339	33.333	1.13	1.13	32.11	1.94
54	55	6.569226	CGAACTCCATTGATGAAAGAGCTTTT	60.569	38.462	0.00	0.00	32.11	2.27
70	71	1.737029	CGCACATCTGACGAACTCCAT	60.737	52.381	0.00	0.00	0.00	3.41
71	72	0.388520	CGCACATCTGACGAACTCCA	60.389	55.000	0.00	0.00	0.00	3.86
158	159	4.202336	TGTTGACAAAACCATGGATTGCAT	60.202	37.500	21.47	8.16	0.00	3.96
165	166	4.280677	AGGTATGTGTTGACAAAACCATGG	59.719	41.667	11.19	11.19	41.51	3.66
177	178	1.285280	TCTCCCCCAGGTATGTGTTG	58.715	55.000	0.00	0.00	0.00	3.33
192	193	0.741915	GTGACGAGTCCTGGATCTCC	59.258	60.000	15.84	7.61	0.00	3.71
208	209	1.103803	CGATTCTCCTCCTTCGGTGA	58.896	55.000	0.00	0.00	0.00	4.02
210	211	0.818296	CACGATTCTCCTCCTTCGGT	59.182	55.000	0.00	0.00	35.98	4.69
253	254	0.687757	TCCGGTGGAGCAAGCTATCT	60.688	55.000	0.00	0.00	0.00	1.98
281	282	4.422840	TGCAGCATCCACATTAATTTTCG	58.577	39.130	0.00	0.00	0.00	3.46
324	325	2.476534	AAATTGCCGCAACTGCTCCG	62.477	55.000	8.25	0.00	39.32	4.63
333	334	1.242989	TGCTTCTACAAATTGCCGCA	58.757	45.000	0.00	0.00	0.00	5.69
372	373	5.635549	TTGTGAATACTATCGTTGATGCG	57.364	39.130	0.00	0.00	0.00	4.73
379	380	4.634443	GCCTTGGTTTGTGAATACTATCGT	59.366	41.667	0.00	0.00	0.00	3.73
459	460	6.545504	AGATATATTCGGTGCACATTCAAC	57.454	37.500	20.43	0.00	0.00	3.18
478	479	1.269723	CTGGCAATCCGACGCTAGATA	59.730	52.381	0.00	0.00	38.90	1.98
502	503	4.404640	CCATATTTGATCTCTGCCACCAT	58.595	43.478	0.00	0.00	0.00	3.55
521	522	1.349026	CATAAGCCGATCCACTCCCAT	59.651	52.381	0.00	0.00	0.00	4.00
595	596	7.849804	TGAAGCTCCTAAACTCATGAATTAC	57.150	36.000	0.00	0.00	0.00	1.89
598	599	6.240894	TGTTGAAGCTCCTAAACTCATGAAT	58.759	36.000	0.00	0.00	0.00	2.57
617	618	2.373169	AGATTGTGAGCCTCCTTGTTGA	59.627	45.455	0.00	0.00	0.00	3.18
621	622	2.559440	GCTAGATTGTGAGCCTCCTTG	58.441	52.381	0.00	0.00	32.25	3.61
657	658	2.078665	ATGACGCCCAGGCCCTAAT	61.079	57.895	0.00	0.00	37.98	1.73
696	697	1.207377	GCCGATAAAGACGAGGCGAC	61.207	60.000	0.00	0.00	38.28	5.19
699	700	0.597898	GAGGCCGATAAAGACGAGGC	60.598	60.000	0.00	0.00	46.51	4.70
700	701	0.744874	TGAGGCCGATAAAGACGAGG	59.255	55.000	0.00	0.00	0.00	4.63
805	806	4.406326	TGGGAGGTAAATGCGATGTACTAA	59.594	41.667	0.00	0.00	0.00	2.24
806	807	3.962063	TGGGAGGTAAATGCGATGTACTA	59.038	43.478	0.00	0.00	0.00	1.82
819	820	1.679311	CAGCTGCTGTGGGAGGTAA	59.321	57.895	21.21	0.00	39.52	2.85
861	870	4.340617	GAGGTAAAAATGGTCCATGGTCA	58.659	43.478	12.58	12.05	0.00	4.02
871	880	3.378427	GCTGCTGTAGGAGGTAAAAATGG	59.622	47.826	2.57	0.00	33.79	3.16
916	925	7.929785	GGGTTAAAACTTAAAAGGAAGGAAAGG	59.070	37.037	0.00	0.00	0.00	3.11
921	930	6.239487	CCTGGGGTTAAAACTTAAAAGGAAGG	60.239	42.308	0.00	0.00	0.00	3.46
923	932	6.203813	ACCTGGGGTTAAAACTTAAAAGGAA	58.796	36.000	0.00	0.00	27.29	3.36
925	934	6.325545	AGAACCTGGGGTTAAAACTTAAAAGG	59.674	38.462	1.66	0.00	46.95	3.11
927	936	6.668718	ACAGAACCTGGGGTTAAAACTTAAAA	59.331	34.615	1.66	0.00	46.95	1.52
928	937	6.196434	ACAGAACCTGGGGTTAAAACTTAAA	58.804	36.000	1.66	0.00	46.95	1.52
929	938	5.768752	ACAGAACCTGGGGTTAAAACTTAA	58.231	37.500	1.66	0.00	46.95	1.85
930	939	5.391577	ACAGAACCTGGGGTTAAAACTTA	57.608	39.130	1.66	0.00	46.95	2.24
931	940	4.259933	ACAGAACCTGGGGTTAAAACTT	57.740	40.909	1.66	0.00	46.95	2.66
932	941	3.965470	ACAGAACCTGGGGTTAAAACT	57.035	42.857	1.66	0.00	46.95	2.66
933	942	4.077108	CCTACAGAACCTGGGGTTAAAAC	58.923	47.826	1.66	0.00	46.95	2.43
1068	1131	1.296392	CTCGGTGCCAATGTCTCCA	59.704	57.895	0.00	0.00	0.00	3.86
1137	1200	1.078848	GCAGTTGATGGCGAGGACT	60.079	57.895	0.00	0.00	0.00	3.85
1390	1453	2.877168	CCATTGCATAGCTGGTCTTCTC	59.123	50.000	0.00	0.00	0.00	2.87
1608	1674	4.284550	GCCTTGCCCACCTCACCA	62.285	66.667	0.00	0.00	0.00	4.17
1759	1825	3.877559	CAACATCAGGCAGAATACCTCA	58.122	45.455	0.00	0.00	34.42	3.86
1932	1998	4.910195	TCAAAATCTTCCTAGCTTCTGCA	58.090	39.130	0.00	0.00	42.74	4.41
1964	2031	0.106419	TCGGTTTTTGGCCCAGACTT	60.106	50.000	0.00	0.00	0.00	3.01
1968	2035	2.914908	CGGTCGGTTTTTGGCCCAG	61.915	63.158	0.00	0.00	0.00	4.45
2027	2094	5.810587	ACAATGCATCTCATGAAAAGATTGC	59.189	36.000	0.00	4.36	35.13	3.56
2178	2245	3.119352	GCAACATCAGGGTTCAATCCTTC	60.119	47.826	0.00	0.00	31.06	3.46
2333	2401	2.364970	CTCCCATTTGCCACAAGAACAA	59.635	45.455	0.00	0.00	0.00	2.83
2459	2529	1.118838	CGAAGAGATCCTGGGCTTCT	58.881	55.000	13.47	6.31	35.72	2.85
2653	2723	2.439507	GCATCACCTATCCTTCCCTTCA	59.560	50.000	0.00	0.00	0.00	3.02
2668	2738	4.171005	CCTGACAACAATCAATGCATCAC	58.829	43.478	0.00	0.00	0.00	3.06

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.