AutoCloner

Multiple sequence alignment - TraesCS6A01G214600

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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	TraesCS6A01G214600	chr6A	100.000	3842	0	0	1	3842	393541146	393544987	0.000000e+00	7095.0
1	TraesCS6A01G214600	chr6A	92.535	710	42	5	1	699	393520274	393520983	0.000000e+00	1007.0
2	TraesCS6A01G214600	chr6A	91.051	447	36	4	205	648	606036479	606036924	5.490000e-168	601.0
3	TraesCS6A01G214600	chr6B	96.231	3131	64	15	752	3839	436808123	436805004	0.000000e+00	5079.0
4	TraesCS6A01G214600	chr6B	92.627	434	31	1	216	648	560702988	560702555	1.170000e-174	623.0
5	TraesCS6A01G214600	chr6B	96.450	169	6	0	3671	3839	436802086	436801918	2.920000e-71	279.0
6	TraesCS6A01G214600	chr6D	97.527	2871	61	6	935	3799	274346980	274344114	0.000000e+00	4900.0
7	TraesCS6A01G214600	chr6D	89.377	273	23	3	672	943	274351204	274350937	4.750000e-89	339.0
8	TraesCS6A01G214600	chr6D	84.000	225	26	8	1	215	274351422	274351198	1.400000e-49	207.0
9	TraesCS6A01G214600	chr7B	92.081	442	32	3	210	648	588251731	588252172	1.520000e-173	619.0
10	TraesCS6A01G214600	chr2B	92.396	434	31	2	216	648	201236672	201237104	5.450000e-173	617.0
11	TraesCS6A01G214600	chr2B	91.480	446	34	2	217	662	98393778	98394219	9.130000e-171	610.0
12	TraesCS6A01G214600	chr1A	92.220	437	29	5	216	648	472948871	472948436	7.050000e-172	614.0
13	TraesCS6A01G214600	chr1A	90.749	454	37	5	199	648	492810443	492809991	5.490000e-168	601.0
14	TraesCS6A01G214600	chr4A	91.781	438	34	2	213	648	403171751	403172188	3.280000e-170	608.0
15	TraesCS6A01G214600	chr5D	94.231	52	3	0	3405	3456	479456011	479456062	3.180000e-11	80.5
16	TraesCS6A01G214600	chr5D	95.556	45	2	0	3406	3450	479455985	479455941	5.320000e-09	73.1
17	TraesCS6A01G214600	chr4D	97.826	46	1	0	3405	3450	298241437	298241392	3.180000e-11	80.5
18	TraesCS6A01G214600	chr5B	95.745	47	2	0	3405	3451	398069782	398069828	4.120000e-10	76.8
19	TraesCS6A01G214600	chr3D	97.674	43	1	0	3405	3447	426873403	426873361	1.480000e-09	75.0
20	TraesCS6A01G214600	chr3A	100.000	38	0	0	3410	3447	178256877	178256914	1.910000e-08	71.3
21	TraesCS6A01G214600	chrUn	84.848	66	5	4	3386	3450	317943216	317943277	1.150000e-05	62.1

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	TraesCS6A01G214600	chr6A	393541146	393544987	3841	False	7095.000000	7095	100.000000	1	3842	1	chr6A.!!$F2	3841
1	TraesCS6A01G214600	chr6A	393520274	393520983	709	False	1007.000000	1007	92.535000	1	699	1	chr6A.!!$F1	698
2	TraesCS6A01G214600	chr6B	436801918	436808123	6205	True	2679.000000	5079	96.340500	752	3839	2	chr6B.!!$R2	3087
3	TraesCS6A01G214600	chr6D	274344114	274351422	7308	True	1815.333333	4900	90.301333	1	3799	3	chr6D.!!$R1	3798

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	End Stability	Orientation
689	717	0.314935	CTTCCACACACCACCAATGC	59.685	55.000	3.56	F
857	886	2.043992	TGACTTCTTCCCCGTCTTCAA	58.956	47.619	2.69	F
1791	5799	2.283604	TCCGGTCTAGTGCCTGCA	60.284	61.111	4.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2681	6692	0.107312	GTCACTGAGCCAGCCATGAT	60.107	55.0	0.00	34.37	2.45	R
2736	6747	5.335583	GCTAGTCATCGTGCTGATAGAGAAT	60.336	44.0	0.00	34.83	2.40	R
3502	7521	0.176680	AGGAGCGCTTACCATGACAG	59.823	55.0	13.26	0.00	3.51	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
133	144	0.321298	TTGACAGAAACCCTAGCGCC	60.321	55.000	2.29	0.00	0.00	6.53
226	237	1.202806	GCTTCCACATATAGCTGGCCA	60.203	52.381	4.71	4.71	32.26	5.36
292	303	4.175337	GCTATGGGCCAGGCACGA	62.175	66.667	23.51	0.00	32.76	4.35
486	499	3.446873	CCCAACAGGCTAAATATGTGCAA	59.553	43.478	0.00	0.00	0.00	4.08
487	500	4.099881	CCCAACAGGCTAAATATGTGCAAT	59.900	41.667	0.00	0.00	0.00	3.56
501	514	1.226295	GCAATCCGGCGTGCTAAAC	60.226	57.895	18.74	0.00	37.78	2.01
534	547	1.306148	GGCCCGTTTACTAATCAGGC	58.694	55.000	0.00	0.00	38.21	4.85
536	549	1.578583	CCCGTTTACTAATCAGGCCG	58.421	55.000	0.00	0.00	0.00	6.13
632	645	1.066587	GAGCGAGGCACGATTAGCT	59.933	57.895	8.92	0.00	41.91	3.32
663	691	4.278513	CCCGTTTGGCCAGGTCCA	62.279	66.667	5.11	0.00	0.00	4.02
664	692	2.672996	CCGTTTGGCCAGGTCCAG	60.673	66.667	5.11	0.00	37.44	3.86
665	693	2.672996	CGTTTGGCCAGGTCCAGG	60.673	66.667	5.11	0.00	37.44	4.45
666	694	2.520968	GTTTGGCCAGGTCCAGGT	59.479	61.111	5.11	0.00	37.44	4.00
689	717	0.314935	CTTCCACACACCACCAATGC	59.685	55.000	0.00	0.00	0.00	3.56
728	756	4.503714	AACGTCTTACATTGGGATGGAT	57.496	40.909	0.00	0.00	37.60	3.41
735	763	5.851693	TCTTACATTGGGATGGATGGAGTAT	59.148	40.000	0.00	0.00	37.60	2.12
785	813	2.046411	ACATTCGCCGGTGCATCA	60.046	55.556	11.05	0.00	37.32	3.07
853	882	3.432326	GCATATTGACTTCTTCCCCGTCT	60.432	47.826	0.00	0.00	0.00	4.18
854	883	4.770795	CATATTGACTTCTTCCCCGTCTT	58.229	43.478	0.00	0.00	0.00	3.01
857	886	2.043992	TGACTTCTTCCCCGTCTTCAA	58.956	47.619	0.00	0.00	0.00	2.69
1791	5799	2.283604	TCCGGTCTAGTGCCTGCA	60.284	61.111	0.00	0.00	0.00	4.41
1836	5844	4.371417	TACCTGCGTCTCGGGGGT	62.371	66.667	0.00	0.00	45.92	4.95
2577	6588	2.666272	TGCCAACAACAGATGGGTTA	57.334	45.000	0.00	0.00	37.19	2.85
2681	6692	9.325248	AGAAGGGAAAATTTCAGGAAATAATCA	57.675	29.630	8.09	0.00	39.88	2.57
2820	6831	5.019785	AGGCTAGGAATTTCGTATTTCGT	57.980	39.130	0.00	0.00	40.80	3.85
2825	6836	3.621715	AGGAATTTCGTATTTCGTCCTGC	59.378	43.478	0.00	0.00	39.01	4.85
2913	6924	6.480651	TGTGCGAAGTTTGAGTGATTTTAGTA	59.519	34.615	0.00	0.00	0.00	1.82
2945	6956	1.745232	TGACGAAGGCAAGTTGTGTT	58.255	45.000	4.48	0.00	0.00	3.32
3120	7133	3.985925	GTCCTGTTACGGAAGTTGTACAG	59.014	47.826	0.00	0.00	46.40	2.74
3169	7183	5.030295	CCAATGAATGTTGTACGAGCAATC	58.970	41.667	0.00	0.00	0.00	2.67
3321	7336	7.812690	TTTGATTGGAGATCATTGGTCTATG	57.187	36.000	0.00	0.00	0.00	2.23
3360	7377	5.072741	AGACTTGCATTGGTTGTTCTGTAT	58.927	37.500	0.00	0.00	0.00	2.29
3413	7430	3.761897	TGGTTGCATTGGTAGTTTAGCT	58.238	40.909	0.00	0.00	0.00	3.32
3502	7521	1.092345	GGCGGCAACCATTCTCTCTC	61.092	60.000	3.07	0.00	0.00	3.20
3573	7592	3.406764	ACCACTGAGCATTTGAGAAGTC	58.593	45.455	0.00	0.00	0.00	3.01
3802	10907	1.399727	GCACACCACGGAATTTTCTCG	60.400	52.381	0.00	0.00	0.00	4.04
3839	10944	8.885494	TTTTGTAGCAAATTAGCTTTGTTCAT	57.115	26.923	0.00	0.00	43.70	2.57
3840	10945	9.973450	TTTTGTAGCAAATTAGCTTTGTTCATA	57.027	25.926	0.00	0.00	43.70	2.15
3841	10946	8.964420	TTGTAGCAAATTAGCTTTGTTCATAC	57.036	30.769	0.00	0.00	43.70	2.39

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
10	11	1.264749	ACCATGGCAGAGAACGGCTA	61.265	55.000	13.04	0.00	37.38	3.93
290	301	2.812178	CCCGTTTAGCCCGTGTCG	60.812	66.667	0.00	0.00	0.00	4.35
292	303	4.710167	GGCCCGTTTAGCCCGTGT	62.710	66.667	0.00	0.00	45.16	4.49
336	347	3.854669	CTCCAGGCCTAGGCACGG	61.855	72.222	34.09	30.30	44.11	4.94
450	463	4.086457	CCTGTTGGGCTGTTATTTAGGTT	58.914	43.478	0.00	0.00	0.00	3.50
451	464	3.697166	CCTGTTGGGCTGTTATTTAGGT	58.303	45.455	0.00	0.00	0.00	3.08
572	585	2.632136	TTAATAGCCGGGTCGTGCCG	62.632	60.000	10.79	0.00	38.44	5.69
579	592	0.745486	GGCACGTTTAATAGCCGGGT	60.745	55.000	12.58	12.58	37.41	5.28
615	628	1.066587	GAGCTAATCGTGCCTCGCT	59.933	57.895	0.00	0.00	39.67	4.93
616	629	1.211818	CTGAGCTAATCGTGCCTCGC	61.212	60.000	0.00	0.00	39.67	5.03
618	631	0.878086	GCCTGAGCTAATCGTGCCTC	60.878	60.000	0.00	0.00	35.50	4.70
661	689	1.453155	GTGTGTGGAAGCATACCTGG	58.547	55.000	0.00	0.00	0.00	4.45
662	690	1.271325	TGGTGTGTGGAAGCATACCTG	60.271	52.381	11.99	0.00	46.55	4.00
663	691	1.064003	TGGTGTGTGGAAGCATACCT	58.936	50.000	11.99	0.00	46.55	3.08
664	692	1.165270	GTGGTGTGTGGAAGCATACC	58.835	55.000	5.26	5.26	46.58	2.73
665	693	1.165270	GGTGGTGTGTGGAAGCATAC	58.835	55.000	0.00	0.00	0.00	2.39
666	694	0.767998	TGGTGGTGTGTGGAAGCATA	59.232	50.000	0.00	0.00	0.00	3.14
708	736	3.433598	CCATCCATCCCAATGTAAGACGT	60.434	47.826	0.00	0.00	0.00	4.34
709	737	3.141398	CCATCCATCCCAATGTAAGACG	58.859	50.000	0.00	0.00	0.00	4.18
710	738	4.141390	ACTCCATCCATCCCAATGTAAGAC	60.141	45.833	0.00	0.00	0.00	3.01
711	739	4.047166	ACTCCATCCATCCCAATGTAAGA	58.953	43.478	0.00	0.00	0.00	2.10
712	740	4.443978	ACTCCATCCATCCCAATGTAAG	57.556	45.455	0.00	0.00	0.00	2.34
714	742	6.529084	AAATACTCCATCCATCCCAATGTA	57.471	37.500	0.00	0.00	0.00	2.29
715	743	5.408079	AAATACTCCATCCATCCCAATGT	57.592	39.130	0.00	0.00	0.00	2.71
716	744	6.736110	AAAAATACTCCATCCATCCCAATG	57.264	37.500	0.00	0.00	0.00	2.82
747	775	2.124278	GGAGTTTCCCATCCGGCC	60.124	66.667	0.00	0.00	0.00	6.13
814	842	1.153349	GCTGGTTTCTAGAGCCGGG	60.153	63.158	19.62	12.08	0.00	5.73
822	850	6.823689	GGAAGAAGTCAATATGCTGGTTTCTA	59.176	38.462	0.00	0.00	0.00	2.10
853	882	5.565834	GCGGTAATTTGGAGGAAATGTTGAA	60.566	40.000	0.00	0.00	34.30	2.69
854	883	4.082463	GCGGTAATTTGGAGGAAATGTTGA	60.082	41.667	0.00	0.00	34.30	3.18
857	886	3.192633	GTGCGGTAATTTGGAGGAAATGT	59.807	43.478	0.00	0.00	34.30	2.71
905	947	0.459237	GGATCAGTGACACTGGAGCG	60.459	60.000	30.39	9.37	45.94	5.03
912	954	3.088532	AGAGAGAGTGGATCAGTGACAC	58.911	50.000	0.00	0.00	35.43	3.67
1836	5844	2.032860	GCGCCCCAGAGAGCTGATTA	62.033	60.000	0.00	0.00	45.17	1.75
2568	6579	2.578940	TGGGAATTTCCGTAACCCATCT	59.421	45.455	9.31	0.00	44.50	2.90
2577	6588	1.078426	CGCTCCTGGGAATTTCCGT	60.078	57.895	9.31	0.00	37.43	4.69
2681	6692	0.107312	GTCACTGAGCCAGCCATGAT	60.107	55.000	0.00	0.00	34.37	2.45
2736	6747	5.335583	GCTAGTCATCGTGCTGATAGAGAAT	60.336	44.000	0.00	0.00	34.83	2.40
2794	6805	5.367945	AATACGAAATTCCTAGCCTTGGA	57.632	39.130	0.00	0.00	0.00	3.53
2825	6836	7.147983	CCCTCTAACCTCAATATTCTATCCTCG	60.148	44.444	0.00	0.00	0.00	4.63
2913	6924	3.201290	CCTTCGTCAAGATTAGCTGCAT	58.799	45.455	1.02	0.00	0.00	3.96
2945	6956	2.799017	ACCTGATCATTCAAGCAAGCA	58.201	42.857	0.00	0.00	0.00	3.91
3120	7133	2.024414	GGCCAACACATCACCTAATCC	58.976	52.381	0.00	0.00	0.00	3.01
3148	7161	5.643348	TGAGATTGCTCGTACAACATTCATT	59.357	36.000	0.00	0.00	44.33	2.57
3169	7183	7.303182	TGGATACAGGGTATTTACATCTGAG	57.697	40.000	13.55	0.00	46.17	3.35
3267	7282	5.069251	AGACCATCAAAAGGTAGATCTACGG	59.931	44.000	23.35	18.33	40.09	4.02
3321	7336	8.934507	ATGCAAGTCTAAAGATACAGTTCTAC	57.065	34.615	0.00	0.00	0.00	2.59
3502	7521	0.176680	AGGAGCGCTTACCATGACAG	59.823	55.000	13.26	0.00	0.00	3.51
3573	7592	3.429043	GCAAATGCATGGTGGAGTG	57.571	52.632	0.00	0.00	41.59	3.51
3593	7612	9.085250	GTACAGTAAGAATCCTTAAGCTACAAC	57.915	37.037	0.00	0.00	36.69	3.32
3701	7720	1.025113	CCATGCCAGCACTGACTCAG	61.025	60.000	4.36	4.36	37.52	3.35

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.