AutoCloner

Multiple sequence alignment - TraesCS6A01G359100

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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	TraesCS6A01G359100	chr6A	100.000	2055	0	0	1	2055	590043004	590045058	0.000000e+00	3795
1	TraesCS6A01G359100	chr6A	100.000	460	0	0	2327	2786	590045330	590045789	0.000000e+00	850
2	TraesCS6A01G359100	chr6D	95.882	2064	54	15	1	2055	441524831	441526872	0.000000e+00	3312
3	TraesCS6A01G359100	chr6D	80.615	650	110	11	883	1529	441316743	441317379	3.230000e-134	488
4	TraesCS6A01G359100	chr6D	80.615	650	110	11	883	1529	441397605	441398241	3.230000e-134	488
5	TraesCS6A01G359100	chr6D	91.040	346	9	6	2463	2786	441534772	441535117	5.470000e-122	448
6	TraesCS6A01G359100	chr6D	93.590	156	3	2	2327	2475	441526939	441527094	2.790000e-55	226
7	TraesCS6A01G359100	chr6B	93.736	1836	89	13	232	2051	666773719	666775544	0.000000e+00	2730
8	TraesCS6A01G359100	chr6B	89.072	485	24	7	2327	2784	666775570	666776052	2.410000e-160	575
9	TraesCS6A01G359100	chr6B	85.169	236	27	6	1	231	666773320	666773552	4.640000e-58	235
10	TraesCS6A01G359100	chr6B	77.419	372	65	9	892	1245	666055025	666055395	1.310000e-48	204
11	TraesCS6A01G359100	chr3A	85.138	471	68	2	994	1463	552434316	552434785	5.400000e-132	481
12	TraesCS6A01G359100	chr3A	84.000	125	13	6	745	868	552434026	552434144	2.270000e-21	113
13	TraesCS6A01G359100	chr3D	80.679	471	86	3	998	1468	103820978	103820513	7.340000e-96	361
14	TraesCS6A01G359100	chr3B	80.421	475	89	1	998	1468	154451561	154451087	2.640000e-95	359
15	TraesCS6A01G359100	chr7A	80.000	270	37	12	755	1020	731292125	731291869	1.700000e-42	183

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	TraesCS6A01G359100	chr6A	590043004	590045789	2785	False	2322.5	3795	100.000000	1	2786	2	chr6A.!!$F1	2785
1	TraesCS6A01G359100	chr6D	441524831	441527094	2263	False	1769.0	3312	94.736000	1	2475	2	chr6D.!!$F4	2474
2	TraesCS6A01G359100	chr6D	441316743	441317379	636	False	488.0	488	80.615000	883	1529	1	chr6D.!!$F1	646
3	TraesCS6A01G359100	chr6D	441397605	441398241	636	False	488.0	488	80.615000	883	1529	1	chr6D.!!$F2	646
4	TraesCS6A01G359100	chr6B	666773320	666776052	2732	False	1180.0	2730	89.325667	1	2784	3	chr6B.!!$F2	2783
5	TraesCS6A01G359100	chr3A	552434026	552434785	759	False	297.0	481	84.569000	745	1463	2	chr3A.!!$F1	718

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
162	165	0.176449	GGTATGGTTACCGGCGAACT	59.824	55.0	9.3	3.94	38.69	3.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1960	2205	5.944599	ACATAGACGACCGACCTCATATAAT	59.055	40.0	0.0	0.0	0.0	1.28	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
21	22	1.899814	AGTTGCGTTGGATCAGGACTA	59.100	47.619	0.00	0.00	0.00	2.59
25	26	1.751924	GCGTTGGATCAGGACTAGACT	59.248	52.381	0.00	0.00	0.00	3.24
59	60	2.552743	GGTCAGGCAAAAGTAACCACTC	59.447	50.000	0.00	0.00	32.29	3.51
60	61	2.223377	GTCAGGCAAAAGTAACCACTCG	59.777	50.000	0.00	0.00	32.29	4.18
86	87	3.497942	GGTCACCACTTTGTCCCATAAGT	60.498	47.826	0.00	0.00	35.06	2.24
91	92	3.486383	CACTTTGTCCCATAAGTGGTGT	58.514	45.455	0.00	0.00	44.65	4.16
107	108	5.815581	AGTGGTGTGTATTGTACCAATGAT	58.184	37.500	0.00	0.00	45.30	2.45
127	128	1.271871	TGGGTCCACTAGTGCAATTGG	60.272	52.381	17.86	2.75	0.00	3.16
150	151	2.626743	ACGCTAGCGATAAAGGTATGGT	59.373	45.455	41.33	13.19	42.83	3.55
162	165	0.176449	GGTATGGTTACCGGCGAACT	59.824	55.000	9.30	3.94	38.69	3.01
171	174	4.201753	GGTTACCGGCGAACTCTATTTTTC	60.202	45.833	9.30	0.00	0.00	2.29
179	182	5.898159	CGAACTCTATTTTTCGCATGTTG	57.102	39.130	0.00	0.00	38.31	3.33
180	183	5.617609	CGAACTCTATTTTTCGCATGTTGA	58.382	37.500	0.00	0.00	38.31	3.18
181	184	6.250819	CGAACTCTATTTTTCGCATGTTGAT	58.749	36.000	0.00	0.00	38.31	2.57
182	185	7.398746	CGAACTCTATTTTTCGCATGTTGATA	58.601	34.615	0.00	0.00	38.31	2.15
183	186	7.580523	CGAACTCTATTTTTCGCATGTTGATAG	59.419	37.037	0.00	0.00	38.31	2.08
184	187	7.849804	ACTCTATTTTTCGCATGTTGATAGT	57.150	32.000	0.00	0.00	0.00	2.12
185	188	7.688372	ACTCTATTTTTCGCATGTTGATAGTG	58.312	34.615	0.00	0.00	0.00	2.74
197	202	8.274939	CGCATGTTGATAGTGAAAATTTGTTTT	58.725	29.630	0.00	0.00	0.00	2.43
234	405	4.249661	ACAAACAACGTTGATGGCTTTTT	58.750	34.783	33.66	18.26	32.59	1.94
283	454	2.310309	CTGACAGCAACAGCAACGA	58.690	52.632	0.00	0.00	0.00	3.85
325	496	7.566858	GTGAAACCACATTCAATTCACATAC	57.433	36.000	10.98	0.00	45.63	2.39
499	670	2.096069	CGAATGAGCAAATGGCCGATAG	60.096	50.000	0.00	0.00	46.50	2.08
500	671	1.242076	ATGAGCAAATGGCCGATAGC	58.758	50.000	0.00	0.00	46.50	2.97
566	737	9.791801	ATTAACTGGAAAATTAAGTTGGCAATT	57.208	25.926	1.92	0.00	35.77	2.32
616	788	7.841729	TGTTAATAAAGATGGATGGCCCTTTTA	59.158	33.333	0.00	0.00	31.06	1.52
799	976	1.586028	CACAATGAAGGCCGGGTTG	59.414	57.895	2.18	4.35	0.00	3.77
1820	2060	0.684479	TGGTGGTGAGGATCCTCTCG	60.684	60.000	35.84	0.00	43.12	4.04
2016	2261	3.072915	TCATCAGGTTCTTTGAGCCAAGA	59.927	43.478	3.47	1.67	35.33	3.02
2514	2766	1.260544	GGTGCCTTGAATTTCCTGCT	58.739	50.000	0.00	0.00	0.00	4.24
2581	2833	9.747293	GTATTAACTAGTTGAAGATGTACTCCC	57.253	37.037	18.56	0.00	0.00	4.30
2582	2834	8.611051	ATTAACTAGTTGAAGATGTACTCCCT	57.389	34.615	18.56	0.00	0.00	4.20
2584	2836	4.712337	ACTAGTTGAAGATGTACTCCCTGG	59.288	45.833	0.00	0.00	0.00	4.45
2585	2837	3.791320	AGTTGAAGATGTACTCCCTGGA	58.209	45.455	0.00	0.00	0.00	3.86
2586	2838	3.772025	AGTTGAAGATGTACTCCCTGGAG	59.228	47.826	11.68	11.68	46.91	3.86
2587	2839	2.111384	TGAAGATGTACTCCCTGGAGC	58.889	52.381	13.15	0.00	45.54	4.70
2593	2867	2.551270	TGTACTCCCTGGAGCAATCTT	58.449	47.619	13.15	0.00	45.54	2.40
2616	2890	8.980596	TCTTTGCCTGGATAATTAATGATTTGT	58.019	29.630	0.00	0.00	0.00	2.83
2704	2978	5.761165	TTACTCAAAGTTTACCACAAGCC	57.239	39.130	0.00	0.00	0.00	4.35
2730	3004	4.879295	ACAAATAGGATCATGGGGTTGA	57.121	40.909	0.00	0.00	0.00	3.18
2749	3023	2.625790	TGACTTAACCAAACATGGCACC	59.374	45.455	0.00	0.00	0.00	5.01
2750	3024	1.967779	ACTTAACCAAACATGGCACCC	59.032	47.619	0.00	0.00	0.00	4.61
2770	3044	4.192317	CCCCTGATTTAAAGACCGAGAAG	58.808	47.826	0.00	0.00	0.00	2.85
2781	3055	3.614399	CCGAGAAGACTTGGCAAGT	57.386	52.632	31.59	31.59	46.38	3.16
2783	3057	3.040147	CCGAGAAGACTTGGCAAGTAA	57.960	47.619	31.24	0.00	43.03	2.24
2784	3058	3.399330	CCGAGAAGACTTGGCAAGTAAA	58.601	45.455	31.24	0.00	43.03	2.01
2785	3059	4.003648	CCGAGAAGACTTGGCAAGTAAAT	58.996	43.478	31.24	20.05	43.03	1.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
12	13	6.897966	TCACAATCCTAAAGTCTAGTCCTGAT	59.102	38.462	0.00	0.00	0.00	2.90
15	16	5.659079	CCTCACAATCCTAAAGTCTAGTCCT	59.341	44.000	0.00	0.00	0.00	3.85
21	22	4.223923	CCTGACCTCACAATCCTAAAGTCT	59.776	45.833	0.00	0.00	0.00	3.24
25	26	2.642311	TGCCTGACCTCACAATCCTAAA	59.358	45.455	0.00	0.00	0.00	1.85
91	92	4.228438	TGGACCCATCATTGGTACAATACA	59.772	41.667	0.00	0.00	43.82	2.29
107	108	1.271871	CCAATTGCACTAGTGGACCCA	60.272	52.381	23.95	10.63	32.54	4.51
127	128	2.129823	TACCTTTATCGCTAGCGTGC	57.870	50.000	34.10	0.00	40.74	5.34
150	151	3.613737	CGAAAAATAGAGTTCGCCGGTAA	59.386	43.478	1.90	0.00	40.04	2.85
162	165	7.841915	TCACTATCAACATGCGAAAAATAGA	57.158	32.000	0.00	0.00	0.00	1.98
171	174	6.932901	ACAAATTTTCACTATCAACATGCG	57.067	33.333	0.00	0.00	0.00	4.73
181	184	9.535878	GACACCCAATAAAACAAATTTTCACTA	57.464	29.630	0.00	0.00	38.91	2.74
182	185	8.264347	AGACACCCAATAAAACAAATTTTCACT	58.736	29.630	0.00	0.00	38.91	3.41
183	186	8.334632	CAGACACCCAATAAAACAAATTTTCAC	58.665	33.333	0.00	0.00	38.91	3.18
184	187	8.043710	ACAGACACCCAATAAAACAAATTTTCA	58.956	29.630	0.00	0.00	38.91	2.69
185	188	8.432110	ACAGACACCCAATAAAACAAATTTTC	57.568	30.769	0.00	0.00	38.91	2.29
197	202	5.007823	CGTTGTTTGTAACAGACACCCAATA	59.992	40.000	0.00	0.00	43.27	1.90
283	454	6.777580	GGTTTCACATATCCAGGGTTGAATAT	59.222	38.462	0.00	0.00	0.00	1.28
325	496	6.054941	AGTAAAGTTTGGCCAAATTTTCCTG	58.945	36.000	39.20	0.00	39.69	3.86
566	737	9.173021	ACACAATGTGCTTGTTTTAGCTATATA	57.827	29.630	14.01	0.00	45.98	0.86
616	788	6.721704	AAGAAGCAATGAAAGGTTTCTCTT	57.278	33.333	4.19	1.46	34.14	2.85
1960	2205	5.944599	ACATAGACGACCGACCTCATATAAT	59.055	40.000	0.00	0.00	0.00	1.28
2421	2667	8.612619	ACACACAAACTATGCAAGTATATAAGC	58.387	33.333	0.00	0.00	37.50	3.09
2514	2766	4.873746	TTCTGGACACCAAAAACAAACA	57.126	36.364	0.00	0.00	30.80	2.83
2576	2828	2.503895	CAAAGATTGCTCCAGGGAGT	57.496	50.000	16.31	0.00	43.70	3.85
2587	2839	9.991906	AATCATTAATTATCCAGGCAAAGATTG	57.008	29.630	0.00	0.00	0.00	2.67
2593	2867	8.196771	GTCACAAATCATTAATTATCCAGGCAA	58.803	33.333	0.00	0.00	0.00	4.52
2616	2890	7.168219	ACAGCTTTCTCCATGTAATTAAGTCA	58.832	34.615	0.00	0.00	0.00	3.41
2632	2906	5.859495	AGCAGTTAACTAGAACAGCTTTCT	58.141	37.500	8.04	13.34	46.40	2.52
2675	2949	8.685838	TGTGGTAAACTTTGAGTAATAAAGCT	57.314	30.769	0.00	0.00	38.41	3.74
2704	2978	4.019321	ACCCCATGATCCTATTTGTATCCG	60.019	45.833	0.00	0.00	0.00	4.18
2730	3004	1.967779	GGGTGCCATGTTTGGTTAAGT	59.032	47.619	0.00	0.00	45.57	2.24
2749	3023	4.870991	GTCTTCTCGGTCTTTAAATCAGGG	59.129	45.833	0.00	0.00	0.00	4.45
2750	3024	5.725362	AGTCTTCTCGGTCTTTAAATCAGG	58.275	41.667	0.00	0.00	0.00	3.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.