AutoCloner

Multiple sequence alignment - TraesCS2A01G530700

Loading Multiple Alignment...

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	TraesCS2A01G530700	chr2A	100.000	2819	0	0	1	2819	748438039	748440857	0.000000e+00	5206
1	TraesCS2A01G530700	chr2A	92.617	1937	139	4	1	1937	748285630	748287562	0.000000e+00	2782
2	TraesCS2A01G530700	chr2A	93.465	1867	119	3	2	1868	746620878	746622741	0.000000e+00	2769
3	TraesCS2A01G530700	chr2A	89.327	2230	194	25	307	2504	748400736	748402953	0.000000e+00	2760
4	TraesCS2A01G530700	chr2D	94.296	2577	133	5	1	2566	617887793	617890366	0.000000e+00	3932
5	TraesCS2A01G530700	chr2D	91.406	2525	188	17	1	2504	617546940	617549456	0.000000e+00	3434
6	TraesCS2A01G530700	chr2D	90.775	2374	170	17	1	2348	617731389	617733739	0.000000e+00	3125
7	TraesCS2A01G530700	chr2D	90.531	2260	167	22	10	2228	617909285	617907032	0.000000e+00	2944
8	TraesCS2A01G530700	chr2D	94.325	1868	103	3	1	1868	617634325	617636189	0.000000e+00	2859
9	TraesCS2A01G530700	chr2D	93.951	1868	112	1	1	1868	617539325	617541191	0.000000e+00	2822
10	TraesCS2A01G530700	chr2D	93.041	1868	127	3	1	1868	617760595	617762459	0.000000e+00	2726
11	TraesCS2A01G530700	chr2D	89.815	216	21	1	2604	2819	617890367	617890581	2.770000e-70	276
12	TraesCS2A01G530700	chr2B	91.157	2307	192	9	10	2308	753808140	753805838	0.000000e+00	3120
13	TraesCS2A01G530700	chr2B	82.759	261	23	16	2383	2643	753805834	753805596	2.200000e-51	213
14	TraesCS2A01G530700	chr7B	89.068	311	27	5	2045	2348	7811067	7810757	2.050000e-101	379
15	TraesCS2A01G530700	chr7B	88.889	144	13	2	2347	2490	7810675	7810535	1.040000e-39	174

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	TraesCS2A01G530700	chr2A	748438039	748440857	2818	False	5206.0	5206	100.0000	1	2819	1	chr2A.!!$F4	2818
1	TraesCS2A01G530700	chr2A	748285630	748287562	1932	False	2782.0	2782	92.6170	1	1937	1	chr2A.!!$F2	1936
2	TraesCS2A01G530700	chr2A	746620878	746622741	1863	False	2769.0	2769	93.4650	2	1868	1	chr2A.!!$F1	1866
3	TraesCS2A01G530700	chr2A	748400736	748402953	2217	False	2760.0	2760	89.3270	307	2504	1	chr2A.!!$F3	2197
4	TraesCS2A01G530700	chr2D	617546940	617549456	2516	False	3434.0	3434	91.4060	1	2504	1	chr2D.!!$F2	2503
5	TraesCS2A01G530700	chr2D	617731389	617733739	2350	False	3125.0	3125	90.7750	1	2348	1	chr2D.!!$F4	2347
6	TraesCS2A01G530700	chr2D	617907032	617909285	2253	True	2944.0	2944	90.5310	10	2228	1	chr2D.!!$R1	2218
7	TraesCS2A01G530700	chr2D	617634325	617636189	1864	False	2859.0	2859	94.3250	1	1868	1	chr2D.!!$F3	1867
8	TraesCS2A01G530700	chr2D	617539325	617541191	1866	False	2822.0	2822	93.9510	1	1868	1	chr2D.!!$F1	1867
9	TraesCS2A01G530700	chr2D	617760595	617762459	1864	False	2726.0	2726	93.0410	1	1868	1	chr2D.!!$F5	1867
10	TraesCS2A01G530700	chr2D	617887793	617890581	2788	False	2104.0	3932	92.0555	1	2819	2	chr2D.!!$F6	2818
11	TraesCS2A01G530700	chr2B	753805596	753808140	2544	True	1666.5	3120	86.9580	10	2643	2	chr2B.!!$R1	2633
12	TraesCS2A01G530700	chr7B	7810535	7811067	532	True	276.5	379	88.9785	2045	2490	2	chr7B.!!$R1	445

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
449	450	1.810031	GCAAAGGGCCAAAAACCTGAC	60.81	52.381	6.18	0.0	37.13	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2090	2131	2.168313	CCCTGCCACAAATTTGGATACC	59.832	50.0	21.74	6.42	39.24	2.73	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
449	450	1.810031	GCAAAGGGCCAAAAACCTGAC	60.810	52.381	6.18	0.00	37.13	3.51
535	536	7.628234	ACTGATCTCTTCAATTTGATGGTACT	58.372	34.615	11.19	0.00	32.78	2.73
672	673	8.561738	AGTAAACCCAAATGTAGTTGACTATG	57.438	34.615	3.07	0.00	34.14	2.23
733	734	4.439289	GGATGCTGCTCTGGACAAATTTAC	60.439	45.833	0.00	0.00	0.00	2.01
862	863	7.624549	TCTGAAGCAATTAATAGAGGTCTGTT	58.375	34.615	0.00	0.00	0.00	3.16
902	903	8.985315	TCTTCTATCCTGTAATAAACGACCTA	57.015	34.615	0.00	0.00	0.00	3.08
1010	1011	7.292319	ACAATTCACTGATGGATGGATATTGA	58.708	34.615	0.00	0.00	0.00	2.57
1011	1012	7.447545	ACAATTCACTGATGGATGGATATTGAG	59.552	37.037	0.00	0.00	0.00	3.02
1295	1296	0.684153	GGCATACCAGTGGGCATTGT	60.684	55.000	15.21	0.00	37.90	2.71
1321	1322	8.267183	TCACATACAACATAGTTCTTCATGGAT	58.733	33.333	0.00	0.00	0.00	3.41
1376	1377	3.131396	AGCTGTTCAAGAAACTACGTGG	58.869	45.455	0.00	0.00	38.76	4.94
1608	1609	2.125753	GGCTGTGCTCCTGACTCG	60.126	66.667	0.00	0.00	0.00	4.18
1862	1863	6.184789	TGGAACTTCCTACTGAAAAACAAGT	58.815	36.000	9.31	0.00	37.46	3.16
2018	2049	5.835819	CCTGAGAGTCATATGAGTTTCCCTA	59.164	44.000	22.07	8.37	30.13	3.53
2090	2131	4.576463	GTCACACATTTAGGCCTATTCAGG	59.424	45.833	14.74	5.29	45.77	3.86
2473	2641	0.827368	GCAGTCTCCCCAGTAAGAGG	59.173	60.000	0.00	0.00	0.00	3.69
2566	2734	3.263489	ACAGAGCATGAAGGATCAGTG	57.737	47.619	0.00	0.00	39.39	3.66
2567	2735	2.570752	ACAGAGCATGAAGGATCAGTGT	59.429	45.455	0.00	0.00	39.39	3.55
2568	2736	3.008813	ACAGAGCATGAAGGATCAGTGTT	59.991	43.478	0.00	0.00	39.39	3.32
2569	2737	3.374367	CAGAGCATGAAGGATCAGTGTTG	59.626	47.826	0.00	0.00	39.39	3.33
2570	2738	3.008813	AGAGCATGAAGGATCAGTGTTGT	59.991	43.478	0.00	0.00	39.39	3.32
2571	2739	4.223700	AGAGCATGAAGGATCAGTGTTGTA	59.776	41.667	0.00	0.00	39.39	2.41
2572	2740	4.256920	AGCATGAAGGATCAGTGTTGTAC	58.743	43.478	0.00	0.00	39.39	2.90
2573	2741	3.375299	GCATGAAGGATCAGTGTTGTACC	59.625	47.826	0.00	0.00	39.39	3.34
2574	2742	3.313012	TGAAGGATCAGTGTTGTACCG	57.687	47.619	0.00	0.00	0.00	4.02
2575	2743	2.000447	GAAGGATCAGTGTTGTACCGC	59.000	52.381	0.00	0.00	0.00	5.68
2576	2744	0.249398	AGGATCAGTGTTGTACCGCC	59.751	55.000	0.00	0.00	0.00	6.13
2577	2745	1.082117	GGATCAGTGTTGTACCGCCG	61.082	60.000	0.00	0.00	0.00	6.46
2578	2746	1.693083	GATCAGTGTTGTACCGCCGC	61.693	60.000	0.00	0.00	0.00	6.53
2579	2747	2.167398	ATCAGTGTTGTACCGCCGCT	62.167	55.000	0.00	0.00	0.00	5.52
2580	2748	2.357034	AGTGTTGTACCGCCGCTG	60.357	61.111	0.00	0.00	0.00	5.18
2581	2749	3.419759	GTGTTGTACCGCCGCTGG	61.420	66.667	0.00	0.44	0.00	4.85
2582	2750	4.690719	TGTTGTACCGCCGCTGGG	62.691	66.667	6.28	0.00	0.00	4.45
2583	2751	4.382320	GTTGTACCGCCGCTGGGA	62.382	66.667	6.28	0.00	34.06	4.37
2584	2752	3.395702	TTGTACCGCCGCTGGGAT	61.396	61.111	6.28	0.00	34.06	3.85
2585	2753	2.961893	TTGTACCGCCGCTGGGATT	61.962	57.895	6.28	0.00	34.06	3.01
2586	2754	2.588034	GTACCGCCGCTGGGATTC	60.588	66.667	6.28	0.00	34.06	2.52
2587	2755	2.762459	TACCGCCGCTGGGATTCT	60.762	61.111	6.28	0.00	34.06	2.40
2588	2756	2.792947	TACCGCCGCTGGGATTCTC	61.793	63.158	6.28	0.00	34.06	2.87
2589	2757	4.161295	CCGCCGCTGGGATTCTCA	62.161	66.667	0.00	0.00	34.06	3.27
2590	2758	2.892425	CGCCGCTGGGATTCTCAC	60.892	66.667	0.00	0.00	34.06	3.51
2591	2759	2.268920	GCCGCTGGGATTCTCACA	59.731	61.111	0.00	0.00	34.06	3.58
2592	2760	2.109126	GCCGCTGGGATTCTCACAC	61.109	63.158	0.00	0.00	34.06	3.82
2593	2761	1.599047	CCGCTGGGATTCTCACACT	59.401	57.895	0.00	0.00	34.06	3.55
2594	2762	0.824109	CCGCTGGGATTCTCACACTA	59.176	55.000	0.00	0.00	34.06	2.74
2595	2763	1.471676	CCGCTGGGATTCTCACACTAC	60.472	57.143	0.00	0.00	34.06	2.73
2596	2764	1.471676	CGCTGGGATTCTCACACTACC	60.472	57.143	0.00	0.00	0.00	3.18
2597	2765	1.555075	GCTGGGATTCTCACACTACCA	59.445	52.381	0.00	0.00	0.00	3.25
2598	2766	2.419297	GCTGGGATTCTCACACTACCAG	60.419	54.545	0.00	0.00	45.11	4.00
2599	2767	3.099905	CTGGGATTCTCACACTACCAGA	58.900	50.000	0.00	0.00	45.14	3.86
2600	2768	3.515502	CTGGGATTCTCACACTACCAGAA	59.484	47.826	0.00	0.00	45.14	3.02
2601	2769	3.907474	TGGGATTCTCACACTACCAGAAA	59.093	43.478	0.00	0.00	30.07	2.52
2602	2770	4.254492	GGGATTCTCACACTACCAGAAAC	58.746	47.826	0.00	0.00	30.07	2.78
2615	2813	9.959721	ACACTACCAGAAACATTTAATACATCT	57.040	29.630	0.00	0.00	0.00	2.90
2671	2869	4.080015	GCTAGAGCTATCAGAGGGGAGATA	60.080	50.000	0.00	0.00	38.21	1.98
2675	2873	4.183116	AGCTATCAGAGGGGAGATAGAGA	58.817	47.826	12.27	0.00	44.03	3.10
2685	2883	2.292292	GGGAGATAGAGAGAGCGTGAAC	59.708	54.545	0.00	0.00	0.00	3.18
2719	2917	1.276622	ACTACTGCCGTTGGGATTCT	58.723	50.000	0.00	0.00	34.06	2.40
2736	2934	4.103153	GGATTCTCATCCCAGGAACATGTA	59.897	45.833	0.00	0.00	43.29	2.29
2738	2936	3.041211	TCTCATCCCAGGAACATGTAGG	58.959	50.000	0.00	0.00	0.00	3.18
2774	2972	1.609932	CGCTGTGCATTTGCTGTTAG	58.390	50.000	3.94	0.00	42.66	2.34
2788	2986	3.117663	TGCTGTTAGGGTTCTCCAGTTTT	60.118	43.478	0.00	0.00	38.24	2.43
2789	2987	4.103469	TGCTGTTAGGGTTCTCCAGTTTTA	59.897	41.667	0.00	0.00	38.24	1.52
2793	2991	7.519032	TGTTAGGGTTCTCCAGTTTTATTTG	57.481	36.000	0.00	0.00	38.24	2.32
2794	2992	6.492087	TGTTAGGGTTCTCCAGTTTTATTTGG	59.508	38.462	0.00	0.00	38.24	3.28
2806	3004	5.634859	CAGTTTTATTTGGGTTGCTGATGAC	59.365	40.000	0.00	0.00	0.00	3.06
2809	3007	2.655090	TTTGGGTTGCTGATGACAGA	57.345	45.000	0.00	0.00	46.03	3.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
672	673	7.843490	TGCAAAGTGAATCCATTACTACTAC	57.157	36.000	0.00	0.00	0.00	2.73
733	734	4.484537	ACTCCTTGATTGACCATCTGAG	57.515	45.455	0.00	0.00	32.94	3.35
862	863	7.872993	CAGGATAGAAGAACACACTGTTAGAAA	59.127	37.037	0.00	0.00	41.28	2.52
902	903	3.575687	CCTTCACCTTTCCTTCTTTGCAT	59.424	43.478	0.00	0.00	0.00	3.96
1295	1296	7.619965	TCCATGAAGAACTATGTTGTATGTGA	58.380	34.615	0.00	0.00	0.00	3.58
1321	1322	7.487484	TCATCAGTGCAATTGTTTCTACAAAA	58.513	30.769	7.40	0.00	46.62	2.44
1608	1609	2.924290	GACCACGTGATTTAGCAGTCTC	59.076	50.000	19.30	0.00	0.00	3.36
1804	1805	5.336213	GCATCAATTGTCAGTCCAACATCTT	60.336	40.000	5.13	0.00	0.00	2.40
1862	1863	5.046663	TGTGTCAGCTATGAGTGAATACCAA	60.047	40.000	0.00	0.00	35.66	3.67
2018	2049	4.074970	ACGCCTTCTTCATCACAGAAAAT	58.925	39.130	0.00	0.00	29.74	1.82
2090	2131	2.168313	CCCTGCCACAAATTTGGATACC	59.832	50.000	21.74	6.42	39.24	2.73
2242	2308	5.871396	AAAACACTACTGTTGAGAGAGGA	57.129	39.130	0.00	0.00	39.88	3.71
2319	2399	9.334693	GATTTTAGATGACAACACAGTTCAATC	57.665	33.333	0.00	0.00	0.00	2.67
2504	2672	4.183101	CTCTAGCTGGAGCAGAAAGAAAG	58.817	47.826	14.70	0.00	45.16	2.62
2566	2734	3.675619	ATCCCAGCGGCGGTACAAC	62.676	63.158	12.74	0.00	0.00	3.32
2567	2735	2.862674	GAATCCCAGCGGCGGTACAA	62.863	60.000	12.74	0.00	0.00	2.41
2568	2736	3.379865	GAATCCCAGCGGCGGTACA	62.380	63.158	12.74	0.00	0.00	2.90
2569	2737	2.588034	GAATCCCAGCGGCGGTAC	60.588	66.667	12.74	0.00	0.00	3.34
2570	2738	2.762459	AGAATCCCAGCGGCGGTA	60.762	61.111	12.74	0.00	0.00	4.02
2571	2739	4.162690	GAGAATCCCAGCGGCGGT	62.163	66.667	5.44	5.44	0.00	5.68
2572	2740	4.161295	TGAGAATCCCAGCGGCGG	62.161	66.667	9.78	0.00	0.00	6.13
2573	2741	2.892425	GTGAGAATCCCAGCGGCG	60.892	66.667	0.51	0.51	0.00	6.46
2574	2742	2.109126	GTGTGAGAATCCCAGCGGC	61.109	63.158	0.00	0.00	0.00	6.53
2575	2743	0.824109	TAGTGTGAGAATCCCAGCGG	59.176	55.000	0.00	0.00	0.00	5.52
2576	2744	1.471676	GGTAGTGTGAGAATCCCAGCG	60.472	57.143	0.00	0.00	0.00	5.18
2577	2745	1.555075	TGGTAGTGTGAGAATCCCAGC	59.445	52.381	0.00	0.00	0.00	4.85
2578	2746	3.099905	TCTGGTAGTGTGAGAATCCCAG	58.900	50.000	0.00	0.00	38.09	4.45
2579	2747	3.184382	TCTGGTAGTGTGAGAATCCCA	57.816	47.619	0.00	0.00	0.00	4.37
2580	2748	4.254492	GTTTCTGGTAGTGTGAGAATCCC	58.746	47.826	0.00	0.00	0.00	3.85
2581	2749	4.894784	TGTTTCTGGTAGTGTGAGAATCC	58.105	43.478	0.00	0.00	0.00	3.01
2582	2750	7.440523	AAATGTTTCTGGTAGTGTGAGAATC	57.559	36.000	0.00	0.00	0.00	2.52
2583	2751	8.918202	TTAAATGTTTCTGGTAGTGTGAGAAT	57.082	30.769	0.00	0.00	0.00	2.40
2584	2752	8.918202	ATTAAATGTTTCTGGTAGTGTGAGAA	57.082	30.769	0.00	0.00	0.00	2.87
2585	2753	9.431887	GTATTAAATGTTTCTGGTAGTGTGAGA	57.568	33.333	0.00	0.00	0.00	3.27
2586	2754	9.214957	TGTATTAAATGTTTCTGGTAGTGTGAG	57.785	33.333	0.00	0.00	0.00	3.51
2587	2755	9.733556	ATGTATTAAATGTTTCTGGTAGTGTGA	57.266	29.630	0.00	0.00	0.00	3.58
2588	2756	9.988350	GATGTATTAAATGTTTCTGGTAGTGTG	57.012	33.333	0.00	0.00	0.00	3.82
2589	2757	9.959721	AGATGTATTAAATGTTTCTGGTAGTGT	57.040	29.630	0.00	0.00	0.00	3.55
2591	2759	9.959721	ACAGATGTATTAAATGTTTCTGGTAGT	57.040	29.630	0.00	0.00	34.78	2.73
2594	2762	9.295825	TGAACAGATGTATTAAATGTTTCTGGT	57.704	29.630	0.00	0.00	34.41	4.00
2666	2864	2.867368	TCGTTCACGCTCTCTCTATCTC	59.133	50.000	0.00	0.00	39.60	2.75
2671	2869	1.400142	CTGATCGTTCACGCTCTCTCT	59.600	52.381	4.95	0.00	39.60	3.10
2675	2873	2.061773	CAAACTGATCGTTCACGCTCT	58.938	47.619	4.95	0.00	39.60	4.09
2719	2917	2.126882	CCCTACATGTTCCTGGGATGA	58.873	52.381	2.30	0.00	40.23	2.92
2728	2926	3.573491	GCGCCGCCCTACATGTTC	61.573	66.667	2.30	0.00	0.00	3.18
2757	2955	1.888512	ACCCTAACAGCAAATGCACAG	59.111	47.619	8.28	0.00	45.16	3.66
2768	2966	7.309194	CCAAATAAAACTGGAGAACCCTAACAG	60.309	40.741	0.00	0.00	34.35	3.16
2774	2972	4.157246	ACCCAAATAAAACTGGAGAACCC	58.843	43.478	0.00	0.00	34.35	4.11
2788	2986	4.299586	TCTGTCATCAGCAACCCAAATA	57.700	40.909	0.00	0.00	41.10	1.40
2789	2987	3.159213	TCTGTCATCAGCAACCCAAAT	57.841	42.857	0.00	0.00	41.10	2.32
2793	2991	1.197721	CGTTTCTGTCATCAGCAACCC	59.802	52.381	5.51	0.00	42.02	4.11
2794	2992	2.143122	TCGTTTCTGTCATCAGCAACC	58.857	47.619	5.51	0.00	42.02	3.77

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.