AutoCloner

Multiple sequence alignment - TraesCS4A01G109100

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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	TraesCS4A01G109100	chr4A	100.000	3078	0	0	1	3078	129089300	129092377	0.000000e+00	5685.0
1	TraesCS4A01G109100	chr4A	80.247	162	32	0	2676	2837	550079904	550079743	4.170000e-24	122.0
2	TraesCS4A01G109100	chr4A	88.298	94	8	1	2323	2416	129091553	129091643	3.240000e-20	110.0
3	TraesCS4A01G109100	chr4D	94.112	3125	119	20	1	3078	340087851	340084745	0.000000e+00	4691.0
4	TraesCS4A01G109100	chr4D	90.541	74	7	0	2346	2419	340085561	340085488	7.020000e-17	99.0
5	TraesCS4A01G109100	chr4B	93.975	2058	63	17	1	2027	420198768	420196741	0.000000e+00	3057.0
6	TraesCS4A01G109100	chr4B	85.106	94	10	2	2883	2973	96927262	96927170	3.270000e-15	93.5
7	TraesCS4A01G109100	chr1A	78.142	366	72	3	2477	2834	449845960	449845595	3.090000e-55	226.0
8	TraesCS4A01G109100	chr1A	91.489	47	3	1	2999	3045	58674980	58674935	2.560000e-06	63.9
9	TraesCS4A01G109100	chr1A	92.308	39	3	0	2595	2633	528074018	528074056	4.290000e-04	56.5
10	TraesCS4A01G109100	chr5D	77.049	366	62	15	2484	2837	330077046	330077401	1.130000e-44	191.0
11	TraesCS4A01G109100	chr5D	79.747	237	27	14	2080	2296	432332221	432331986	5.320000e-33	152.0
12	TraesCS4A01G109100	chr5D	100.000	33	0	0	3003	3035	431129280	431129312	9.220000e-06	62.1
13	TraesCS4A01G109100	chr2D	75.916	382	78	7	2477	2849	616500050	616500426	1.890000e-42	183.0
14	TraesCS4A01G109100	chr2D	74.419	387	77	16	2461	2836	102861347	102861722	2.470000e-31	147.0
15	TraesCS4A01G109100	chr2D	88.679	53	6	0	2593	2645	446655978	446655926	7.120000e-07	65.8
16	TraesCS4A01G109100	chr1B	91.228	114	10	0	2346	2459	633744984	633745097	4.110000e-34	156.0
17	TraesCS4A01G109100	chr6A	78.125	256	47	3	2592	2838	65660209	65659954	1.480000e-33	154.0
18	TraesCS4A01G109100	chr6A	79.755	163	30	2	2675	2837	146016343	146016184	6.970000e-22	115.0
19	TraesCS4A01G109100	chr7D	77.344	256	51	3	2592	2840	582062644	582062389	8.900000e-31	145.0
20	TraesCS4A01G109100	chr7A	92.929	99	7	0	2347	2445	35750924	35750826	8.900000e-31	145.0
21	TraesCS4A01G109100	chr1D	75.746	268	55	8	2589	2848	456173954	456174219	3.220000e-25	126.0
22	TraesCS4A01G109100	chr7B	92.771	83	6	0	2346	2428	62894718	62894800	1.500000e-23	121.0
23	TraesCS4A01G109100	chr7B	77.070	157	27	5	2484	2640	726717780	726717633	7.070000e-12	82.4
24	TraesCS4A01G109100	chr5B	84.615	78	11	1	2592	2669	703508610	703508534	3.290000e-10	76.8
25	TraesCS4A01G109100	chr3A	84.848	66	10	0	3000	3065	16154481	16154546	1.980000e-07	67.6
26	TraesCS4A01G109100	chr2B	100.000	34	0	0	3000	3033	45540020	45539987	2.560000e-06	63.9
27	TraesCS4A01G109100	chr2B	89.362	47	4	1	2990	3035	799527489	799527535	1.190000e-04	58.4
28	TraesCS4A01G109100	chr6D	93.023	43	2	1	2994	3035	82214661	82214703	9.220000e-06	62.1
29	TraesCS4A01G109100	chr3D	94.737	38	1	1	2999	3035	161718352	161718389	1.190000e-04	58.4
30	TraesCS4A01G109100	chrUn	94.444	36	2	0	3000	3035	100764556	100764591	4.290000e-04	56.5

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	TraesCS4A01G109100	chr4A	129089300	129092377	3077	False	2897.5	5685	94.1490	1	3078	2	chr4A.!!$F1	3077
1	TraesCS4A01G109100	chr4D	340084745	340087851	3106	True	2395.0	4691	92.3265	1	3078	2	chr4D.!!$R1	3077
2	TraesCS4A01G109100	chr4B	420196741	420198768	2027	True	3057.0	3057	93.9750	1	2027	1	chr4B.!!$R2	2026

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
556	572	0.666577	GTGTGGAGGTGCACGAGTAC	60.667	60.0	11.45	8.24	0.0	2.73	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2099	2134	0.034059	AGAAGCACAGAGGTCAACCG	59.966	55.0	0.0	0.0	42.08	4.44	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
25	26	5.415701	TGGCTATGTGAAGAAACCAGATTTC	59.584	40.000	0.00	0.00	46.21	2.17
82	83	1.816835	CCGACAGCAGACTTACCTGTA	59.183	52.381	0.00	0.00	39.72	2.74
126	127	5.830799	AATGCATTCCTTCCTTTCCTTTT	57.169	34.783	5.99	0.00	0.00	2.27
127	128	5.830799	ATGCATTCCTTCCTTTCCTTTTT	57.169	34.783	0.00	0.00	0.00	1.94
129	130	4.237724	GCATTCCTTCCTTTCCTTTTTCG	58.762	43.478	0.00	0.00	0.00	3.46
160	161	4.601315	GAAACGGGTTTCACGTGC	57.399	55.556	11.67	0.00	46.03	5.34
274	275	6.543430	TTTATGCAAAGGTATTGCCAGAAT	57.457	33.333	10.34	0.81	44.32	2.40
281	282	3.614092	AGGTATTGCCAGAATCACTGTG	58.386	45.455	0.17	0.17	44.40	3.66
325	327	3.077359	AGAATCGGAAAAGAAGTGCCAG	58.923	45.455	0.00	0.00	0.00	4.85
371	387	3.743911	TGTATACAAGTGAACGCCAACTG	59.256	43.478	2.20	0.00	0.00	3.16
556	572	0.666577	GTGTGGAGGTGCACGAGTAC	60.667	60.000	11.45	8.24	0.00	2.73
758	774	2.981805	GCATTGCACATGTGTTGTAGTG	59.018	45.455	26.01	16.69	36.57	2.74
822	838	5.530519	TTGATTTGTCGCAGATGTAAGAC	57.469	39.130	0.00	0.00	40.67	3.01
851	867	1.804748	GGCTGGTAGAACCGTGAAAAG	59.195	52.381	0.00	0.00	42.58	2.27
917	933	1.860950	CGTGCGATCAGGAATGTAAGG	59.139	52.381	0.00	0.00	0.00	2.69
950	966	1.403647	CGACGGTGCTGATTGAACCTA	60.404	52.381	0.00	0.00	42.49	3.08
1023	1039	4.016706	AAGGGCAAGGGGACGACG	62.017	66.667	0.00	0.00	0.00	5.12
1122	1138	3.780173	GCCGCCTGCTTCTCCTCT	61.780	66.667	0.00	0.00	36.87	3.69
1131	1147	0.249405	GCTTCTCCTCTGCATCCTCG	60.249	60.000	0.00	0.00	0.00	4.63
1140	1156	4.148825	GCATCCTCGGGCGTGTCT	62.149	66.667	0.00	0.00	0.00	3.41
1254	1279	2.300967	GGTGGAGGTCATGGGCTCA	61.301	63.158	0.00	0.00	0.00	4.26
1535	1563	8.625571	AGGCCTCAGGTAATTAGTAGACTATAT	58.374	37.037	0.00	0.00	0.00	0.86
1720	1748	1.612676	GGGGTTTTAGCAAGTCCGTT	58.387	50.000	0.00	0.00	0.00	4.44
1725	1753	2.512485	TTTAGCAAGTCCGTTGACGA	57.488	45.000	4.91	0.00	46.51	4.20
2130	2165	1.206610	TGTGCTTCTCTCTCTCATGGC	59.793	52.381	0.00	0.00	0.00	4.40
2150	2199	0.912006	ACAGAGCCCCCTTTCTCCTC	60.912	60.000	0.00	0.00	0.00	3.71
2160	2209	1.257743	CTTTCTCCTCGGTCCACAGA	58.742	55.000	0.00	0.00	0.00	3.41
2210	2262	6.038603	CAGTTCATGGAAGAAAGAACTCACAA	59.961	38.462	0.00	0.00	45.35	3.33
2211	2263	6.603201	AGTTCATGGAAGAAAGAACTCACAAA	59.397	34.615	0.00	0.00	45.35	2.83
2212	2264	7.122650	AGTTCATGGAAGAAAGAACTCACAAAA	59.877	33.333	0.00	0.00	45.35	2.44
2213	2265	6.795399	TCATGGAAGAAAGAACTCACAAAAC	58.205	36.000	0.00	0.00	0.00	2.43
2214	2266	6.603201	TCATGGAAGAAAGAACTCACAAAACT	59.397	34.615	0.00	0.00	0.00	2.66
2445	2497	6.824553	ACTATCTTTTCCGTATACTTTCCCC	58.175	40.000	0.56	0.00	0.00	4.81
2450	2502	2.455557	TCCGTATACTTTCCCCGTTCA	58.544	47.619	0.56	0.00	0.00	3.18
2482	2534	0.106519	AAGTTCACTGCAGGCACCTT	60.107	50.000	19.93	11.45	0.00	3.50
2521	2573	7.806680	TTACATATAGATTCCCATAGCACCA	57.193	36.000	0.00	0.00	0.00	4.17
2532	2584	3.371487	CCCATAGCACCAAATGACCACTA	60.371	47.826	0.00	0.00	0.00	2.74
2535	2587	1.423541	AGCACCAAATGACCACTACCA	59.576	47.619	0.00	0.00	0.00	3.25
2550	2602	0.106708	TACCATCGCCAGAATGAGCC	59.893	55.000	0.00	0.00	39.69	4.70
2552	2604	1.227350	CATCGCCAGAATGAGCCGA	60.227	57.895	0.00	0.00	39.69	5.54
2557	2609	1.493950	GCCAGAATGAGCCGATGACG	61.494	60.000	0.00	0.00	39.69	4.35
2560	2612	1.878522	GAATGAGCCGATGACGCGT	60.879	57.895	13.85	13.85	38.29	6.01
2562	2614	4.829518	TGAGCCGATGACGCGTCG	62.830	66.667	31.88	21.76	41.82	5.12
2574	2626	4.759096	GCGTCGCAATTGCCGCTT	62.759	61.111	32.87	0.00	44.35	4.68
2581	2633	1.508088	CAATTGCCGCTTCCCTGTC	59.492	57.895	0.00	0.00	0.00	3.51
2609	2661	4.641396	TGGTTTGACCTTGTCTATGACAG	58.359	43.478	0.66	0.00	38.89	3.51
2639	2691	0.676466	TTCGTGCATGTGCCCCTAAG	60.676	55.000	5.68	0.00	41.18	2.18
2705	2760	2.455674	TCACCTGACACCAAATCTCG	57.544	50.000	0.00	0.00	0.00	4.04
2738	2793	2.502142	AACCCTAATTTCACCGTCCC	57.498	50.000	0.00	0.00	0.00	4.46
2741	2796	2.290705	ACCCTAATTTCACCGTCCCAAG	60.291	50.000	0.00	0.00	0.00	3.61
2746	2801	0.685097	TTTCACCGTCCCAAGGAGAG	59.315	55.000	0.00	0.00	29.39	3.20
2761	2816	5.071519	CCAAGGAGAGGTCATGAATCTACAT	59.928	44.000	18.98	8.27	0.00	2.29
2813	2868	4.154918	ACAAACTCAATGAAGATCGAAGCC	59.845	41.667	0.00	0.00	0.00	4.35
2838	2893	5.177696	CGGAAGACAAACTCGAAGAAGAAAT	59.822	40.000	0.00	0.00	34.09	2.17
2851	2906	4.858965	AGAAGAAATGCCTTCATCCTCT	57.141	40.909	0.00	0.00	43.68	3.69
2860	2915	1.836166	CCTTCATCCTCTTGAGAGCCA	59.164	52.381	2.42	0.00	40.75	4.75
2891	2946	3.072944	GCATCAGCATCTCCAGGATTAC	58.927	50.000	0.00	0.00	41.58	1.89
2931	2996	1.880675	TCGAGCACTATAGCTACAGGC	59.119	52.381	3.66	4.32	46.75	4.85
2934	2999	3.305676	CGAGCACTATAGCTACAGGCAAT	60.306	47.826	12.92	0.00	46.75	3.56
2959	3024	2.091665	GGAATCCATCTTCACACCCCAT	60.092	50.000	0.00	0.00	0.00	4.00
2980	3045	2.365635	GCCTAGGGCCTGTCTCCA	60.366	66.667	18.53	0.00	44.06	3.86
3001	3066	2.744202	ACCGCTGCTTGTGAAGATTAAG	59.256	45.455	0.00	0.00	0.00	1.85
3025	3090	8.131847	AGAACCCTAACCTAAACTACTAACTG	57.868	38.462	0.00	0.00	0.00	3.16
3037	3102	0.542232	ACTAACTGGAGCGGAGGTGT	60.542	55.000	0.00	0.00	39.88	4.16
3038	3103	0.108615	CTAACTGGAGCGGAGGTGTG	60.109	60.000	0.00	0.00	39.88	3.82
3055	3120	2.875704	TGGGGATTGTCCTCCACAA	58.124	52.632	0.00	0.00	45.79	3.33

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
25	26	4.414852	CATCCGGACAAGTTTGCATTAAG	58.585	43.478	6.12	0.00	0.00	1.85
106	107	4.261994	CGAAAAAGGAAAGGAAGGAATGCA	60.262	41.667	0.00	0.00	0.00	3.96
117	118	8.406172	TGAATTTCAGAAACGAAAAAGGAAAG	57.594	30.769	0.00	0.00	38.33	2.62
160	161	3.325135	ACTTTGACCTGAGAACCAGTAGG	59.675	47.826	0.00	0.00	41.33	3.18
274	275	7.274603	TCATTTTGATGATGAAACACAGTGA	57.725	32.000	7.81	0.00	30.96	3.41
310	311	4.590850	ATGTTTCTGGCACTTCTTTTCC	57.409	40.909	0.00	0.00	0.00	3.13
325	327	2.663119	GCACGCTGATTTCCAATGTTTC	59.337	45.455	0.00	0.00	0.00	2.78
371	387	6.347160	GGCATTCAAATTTCAGTTCTTGCTTC	60.347	38.462	0.00	0.00	0.00	3.86
430	446	1.030488	TCCTCATCACCGAGTCCGAC	61.030	60.000	0.00	0.00	38.22	4.79
556	572	0.168348	AGTCGTCCTCGTTCACATCG	59.832	55.000	0.00	0.00	38.33	3.84
758	774	6.038985	AGCTATCATATGACACGCATGATAC	58.961	40.000	7.78	8.57	39.50	2.24
822	838	0.608035	TTCTACCAGCCGCCAAAAGG	60.608	55.000	0.00	0.00	0.00	3.11
845	861	5.394115	GGGAAGCAACTCAAAAGTCTTTTCA	60.394	40.000	7.62	0.00	33.48	2.69
851	867	1.947456	ACGGGAAGCAACTCAAAAGTC	59.053	47.619	0.00	0.00	33.48	3.01
950	966	8.997734	AGGTCTCTTATCCACTATGATTTTCTT	58.002	33.333	0.00	0.00	0.00	2.52
1023	1039	2.124983	TGCTCTGGCGATTGGCTC	60.125	61.111	8.17	0.00	42.94	4.70
1026	1042	3.197790	CCGTGCTCTGGCGATTGG	61.198	66.667	0.00	0.00	42.25	3.16
1067	1083	3.815407	ATGGCCATGGATTCCGCCC	62.815	63.158	20.04	5.55	40.87	6.13
1113	1129	0.388659	CCGAGGATGCAGAGGAGAAG	59.611	60.000	0.00	0.00	0.00	2.85
1122	1138	4.451150	GACACGCCCGAGGATGCA	62.451	66.667	0.00	0.00	0.00	3.96
1238	1263	0.979709	CTCTGAGCCCATGACCTCCA	60.980	60.000	0.00	0.00	0.00	3.86
1254	1279	2.204059	AGCAGCTGGAACCCCTCT	60.204	61.111	17.12	0.00	0.00	3.69
1535	1563	2.753055	TGTCACCGCAGCAAAGTATA	57.247	45.000	0.00	0.00	0.00	1.47
1705	1733	2.823984	TCGTCAACGGACTTGCTAAAA	58.176	42.857	2.31	0.00	42.05	1.52
1725	1753	2.185350	CCAGCTCGGCGAAGTCAT	59.815	61.111	12.13	0.00	0.00	3.06
2004	2039	7.333423	GGCTATGTAGTACAAGATGTTGACAAA	59.667	37.037	9.96	0.00	37.10	2.83
2099	2134	0.034059	AGAAGCACAGAGGTCAACCG	59.966	55.000	0.00	0.00	42.08	4.44
2130	2165	1.204113	AGGAGAAAGGGGGCTCTGTG	61.204	60.000	0.00	0.00	0.00	3.66
2140	2189	0.247736	CTGTGGACCGAGGAGAAAGG	59.752	60.000	0.00	0.00	0.00	3.11
2173	2222	1.195448	CATGAACTGTCGGCACAAGTC	59.805	52.381	0.00	0.00	29.82	3.01
2181	2230	3.664107	TCTTTCTTCCATGAACTGTCGG	58.336	45.455	0.00	0.00	0.00	4.79
2424	2476	4.162888	ACGGGGAAAGTATACGGAAAAGAT	59.837	41.667	0.00	0.00	0.00	2.40
2431	2483	2.965572	TGAACGGGGAAAGTATACGG	57.034	50.000	0.00	0.00	0.00	4.02
2438	2490	2.817258	TGTAGCAATTGAACGGGGAAAG	59.183	45.455	10.34	0.00	0.00	2.62
2445	2497	7.803189	AGTGAACTTTTATGTAGCAATTGAACG	59.197	33.333	10.34	0.00	0.00	3.95
2450	2502	6.980593	TGCAGTGAACTTTTATGTAGCAATT	58.019	32.000	0.00	0.00	0.00	2.32
2511	2563	2.726821	AGTGGTCATTTGGTGCTATGG	58.273	47.619	0.00	0.00	0.00	2.74
2516	2568	1.904287	TGGTAGTGGTCATTTGGTGC	58.096	50.000	0.00	0.00	0.00	5.01
2521	2573	1.280710	TGGCGATGGTAGTGGTCATTT	59.719	47.619	0.00	0.00	0.00	2.32
2532	2584	1.153086	GGCTCATTCTGGCGATGGT	60.153	57.895	0.00	0.00	0.00	3.55
2550	2602	1.645236	CAATTGCGACGCGTCATCG	60.645	57.895	35.71	24.96	42.55	3.84
2552	2604	2.098298	GCAATTGCGACGCGTCAT	59.902	55.556	35.71	20.90	0.00	3.06
2557	2609	4.759096	AAGCGGCAATTGCGACGC	62.759	61.111	33.04	33.04	46.75	5.19
2560	2612	3.439540	GGGAAGCGGCAATTGCGA	61.440	61.111	23.48	0.00	43.26	5.10
2562	2614	2.182537	CAGGGAAGCGGCAATTGC	59.817	61.111	22.47	22.47	41.14	3.56
2581	2633	0.179029	ACAAGGTCAAACCAGTCCCG	60.179	55.000	0.00	0.00	41.95	5.14
2590	2642	3.072330	TGGCTGTCATAGACAAGGTCAAA	59.928	43.478	1.19	0.00	42.98	2.69
2609	2661	1.089920	ATGCACGAAGACTTCATGGC	58.910	50.000	12.80	12.96	0.00	4.40
2639	2691	2.604174	CGCTCCACGGTGTTGGTTC	61.604	63.158	7.45	0.00	37.93	3.62
2662	2714	5.521906	TCAGATCTATTCTTCAACGAGGG	57.478	43.478	0.00	0.00	29.93	4.30
2705	2760	1.749258	GGGTTTCTCATCGTGGGGC	60.749	63.158	0.00	0.00	0.00	5.80
2738	2793	5.604758	TGTAGATTCATGACCTCTCCTTG	57.395	43.478	9.68	0.00	0.00	3.61
2741	2796	5.070981	TCCAATGTAGATTCATGACCTCTCC	59.929	44.000	9.68	1.24	0.00	3.71
2746	2801	5.529060	GGAGTTCCAATGTAGATTCATGACC	59.471	44.000	0.00	0.00	35.64	4.02
2791	2846	4.437930	GGGCTTCGATCTTCATTGAGTTTG	60.438	45.833	0.00	0.00	0.00	2.93
2800	2855	0.175760	CTTCCGGGCTTCGATCTTCA	59.824	55.000	0.00	0.00	42.43	3.02
2813	2868	2.433868	TCTTCGAGTTTGTCTTCCGG	57.566	50.000	0.00	0.00	0.00	5.14
2838	2893	1.209019	GCTCTCAAGAGGATGAAGGCA	59.791	52.381	9.01	0.00	42.29	4.75
2851	2906	1.811558	GCTCACAAGTGTGGCTCTCAA	60.812	52.381	11.38	0.00	45.65	3.02
2860	2915	2.082231	GATGCTGATGCTCACAAGTGT	58.918	47.619	0.00	0.00	40.48	3.55
2875	2930	0.394565	GCCGTAATCCTGGAGATGCT	59.605	55.000	1.52	0.00	34.56	3.79
2931	2996	5.163581	GGTGTGAAGATGGATTCCTTCATTG	60.164	44.000	18.05	0.00	46.89	2.82
2934	2999	3.308402	GGGTGTGAAGATGGATTCCTTCA	60.308	47.826	18.05	10.59	44.38	3.02
2980	3045	2.472695	TAATCTTCACAAGCAGCGGT	57.527	45.000	0.00	0.00	0.00	5.68
3001	3066	7.179160	TCCAGTTAGTAGTTTAGGTTAGGGTTC	59.821	40.741	0.00	0.00	0.00	3.62
3037	3102	0.404040	GTTGTGGAGGACAATCCCCA	59.596	55.000	0.00	2.06	46.34	4.96
3038	3103	0.404040	TGTTGTGGAGGACAATCCCC	59.596	55.000	0.00	0.00	46.34	4.81

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.