AutoCloner

Multiple sequence alignment - TraesCS6A01G128700

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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	TraesCS6A01G128700	chr6A	100.000	2873	0	0	1	2873	100766817	100763945	0.000000e+00	5306.0
1	TraesCS6A01G128700	chr6A	87.059	1955	153	49	585	2516	100179987	100181864	0.000000e+00	2117.0
2	TraesCS6A01G128700	chr6A	90.253	1621	111	30	366	1951	100813193	100811585	0.000000e+00	2074.0
3	TraesCS6A01G128700	chr6A	92.122	622	27	13	2256	2873	100811184	100810581	0.000000e+00	857.0
4	TraesCS6A01G128700	chr6A	89.130	276	19	4	1	275	100904968	100904703	1.650000e-87	333.0
5	TraesCS6A01G128700	chr6A	86.058	208	12	8	1864	2061	100811619	100811419	1.040000e-49	207.0
6	TraesCS6A01G128700	chr6A	88.272	162	14	2	31	187	100813688	100813527	3.780000e-44	189.0
7	TraesCS6A01G128700	chr6A	94.643	112	5	1	2762	2873	100808705	100808595	3.810000e-39	172.0
8	TraesCS6A01G128700	chr6B	88.051	2042	132	33	28	1967	159409194	159407163	0.000000e+00	2316.0
9	TraesCS6A01G128700	chr6B	89.822	1739	124	25	275	1967	159600475	159598744	0.000000e+00	2182.0
10	TraesCS6A01G128700	chr6B	88.742	1590	117	26	583	2126	158144411	158145984	0.000000e+00	1888.0
11	TraesCS6A01G128700	chr6B	92.520	254	15	2	22	275	159600766	159600517	7.570000e-96	361.0
12	TraesCS6A01G128700	chr6B	84.783	276	27	6	2367	2641	158146251	158146512	2.200000e-66	263.0
13	TraesCS6A01G128700	chr6B	88.532	218	17	4	49	265	159601588	159601378	1.020000e-64	257.0
14	TraesCS6A01G128700	chr6B	87.692	195	12	3	2532	2726	159598419	159598237	1.730000e-52	217.0
15	TraesCS6A01G128700	chr6B	86.700	203	14	8	1864	2057	159598800	159598602	2.240000e-51	213.0
16	TraesCS6A01G128700	chr6B	80.000	310	36	14	1864	2166	159407216	159406926	3.750000e-49	206.0
17	TraesCS6A01G128700	chr6B	96.429	112	3	1	2762	2873	159405221	159405111	1.760000e-42	183.0
18	TraesCS6A01G128700	chr6B	86.339	183	7	2	2449	2615	159406089	159405909	1.760000e-42	183.0
19	TraesCS6A01G128700	chr6B	89.535	86	3	4	2449	2533	159598534	159598454	1.410000e-18	104.0
20	TraesCS6A01G128700	chr6B	97.561	41	0	1	2379	2419	159406140	159406101	5.140000e-08	69.4
21	TraesCS6A01G128700	chr6D	86.922	1621	135	28	384	1967	83551576	83549996	0.000000e+00	1748.0
22	TraesCS6A01G128700	chr6D	84.472	1829	165	41	381	2126	83101176	83102968	0.000000e+00	1694.0
23	TraesCS6A01G128700	chr6D	88.728	1313	94	16	859	2126	84031816	84030513	0.000000e+00	1555.0
24	TraesCS6A01G128700	chr6D	86.792	530	32	12	328	851	84032284	84031787	8.990000e-155	556.0
25	TraesCS6A01G128700	chr6D	85.276	489	26	23	2262	2726	83103176	83103642	2.020000e-126	462.0
26	TraesCS6A01G128700	chr6D	83.694	509	35	18	2261	2726	83544839	83544336	1.220000e-118	436.0
27	TraesCS6A01G128700	chr6D	83.099	426	25	18	2260	2660	84030291	84029888	7.620000e-91	344.0
28	TraesCS6A01G128700	chr6D	92.208	231	14	2	22	252	84064978	84064752	9.930000e-85	324.0
29	TraesCS6A01G128700	chr6D	90.323	217	12	4	49	265	83552962	83552755	2.820000e-70	276.0
30	TraesCS6A01G128700	chr6D	89.401	217	16	3	49	265	84065798	84065589	1.700000e-67	267.0
31	TraesCS6A01G128700	chr6D	91.566	166	14	0	22	187	83552124	83551959	2.230000e-56	230.0
32	TraesCS6A01G128700	chr6D	86.364	176	10	9	2449	2612	83114245	83114418	2.270000e-41	180.0
33	TraesCS6A01G128700	chr6D	95.495	111	4	1	2762	2872	83104273	83104382	2.940000e-40	176.0
34	TraesCS6A01G128700	chr6D	82.840	169	9	7	2256	2424	83112705	83112853	1.800000e-27	134.0
35	TraesCS6A01G128700	chr6D	79.439	214	22	10	1864	2067	83550051	83549850	6.460000e-27	132.0
36	TraesCS6A01G128700	chr6D	86.076	79	3	4	2084	2162	83549858	83549788	8.530000e-11	78.7
37	TraesCS6A01G128700	chr6D	97.368	38	1	0	275	312	84032364	84032327	6.640000e-07	65.8
38	TraesCS6A01G128700	chr6D	94.444	36	0	2	242	275	84032440	84032405	1.000000e-03	54.7

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	TraesCS6A01G128700	chr6A	100763945	100766817	2872	True	5306.000000	5306	100.000000	1	2873	1	chr6A.!!$R1	2872
1	TraesCS6A01G128700	chr6A	100179987	100181864	1877	False	2117.000000	2117	87.059000	585	2516	1	chr6A.!!$F1	1931
2	TraesCS6A01G128700	chr6A	100808595	100813688	5093	True	699.800000	2074	90.269600	31	2873	5	chr6A.!!$R3	2842
3	TraesCS6A01G128700	chr6B	158144411	158146512	2101	False	1075.500000	1888	86.762500	583	2641	2	chr6B.!!$F1	2058
4	TraesCS6A01G128700	chr6B	159405111	159409194	4083	True	591.480000	2316	89.676000	28	2873	5	chr6B.!!$R1	2845
5	TraesCS6A01G128700	chr6B	159598237	159601588	3351	True	555.666667	2182	89.133500	22	2726	6	chr6B.!!$R2	2704
6	TraesCS6A01G128700	chr6D	83101176	83104382	3206	False	777.333333	1694	88.414333	381	2872	3	chr6D.!!$F1	2491
7	TraesCS6A01G128700	chr6D	84029888	84032440	2552	True	515.100000	1555	90.086200	242	2660	5	chr6D.!!$R3	2418
8	TraesCS6A01G128700	chr6D	83549788	83552962	3174	True	492.940000	1748	86.865200	22	2162	5	chr6D.!!$R2	2140
9	TraesCS6A01G128700	chr6D	83544336	83544839	503	True	436.000000	436	83.694000	2261	2726	1	chr6D.!!$R1	465
10	TraesCS6A01G128700	chr6D	84064752	84065798	1046	True	295.500000	324	90.804500	22	265	2	chr6D.!!$R4	243

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
494	1644	0.108138	ACTCATGCGGGTAACAGAGC	60.108	55.0	0.0	0.0	39.74	4.09	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2132	3684	0.171455	CGACTACACCTGTCCTGCTC	59.829	60.0	0.0	0.0	0.0	4.26	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
23	24	5.733676	AGAAAAGCAACCAGTCACAAATTT	58.266	33.333	0.00	0.00	0.00	1.82
24	25	5.812127	AGAAAAGCAACCAGTCACAAATTTC	59.188	36.000	0.00	0.00	0.00	2.17
25	26	4.734398	AAGCAACCAGTCACAAATTTCA	57.266	36.364	0.00	0.00	0.00	2.69
78	900	3.141398	CCGCCAAGTTACATATGCATCT	58.859	45.455	0.19	0.00	0.00	2.90
187	1016	4.253685	GCCAGCTTATTTGTCAGTGTAGA	58.746	43.478	0.00	0.00	0.00	2.59
189	1018	5.482908	CCAGCTTATTTGTCAGTGTAGACT	58.517	41.667	0.00	0.00	39.27	3.24
191	1020	6.428159	CCAGCTTATTTGTCAGTGTAGACTTT	59.572	38.462	0.00	0.00	39.27	2.66
192	1021	7.602644	CCAGCTTATTTGTCAGTGTAGACTTTA	59.397	37.037	0.00	0.00	39.27	1.85
193	1022	8.651588	CAGCTTATTTGTCAGTGTAGACTTTAG	58.348	37.037	0.00	0.00	39.27	1.85
195	1024	8.648968	GCTTATTTGTCAGTGTAGACTTTAGTC	58.351	37.037	1.59	1.59	45.08	2.59
199	1204	8.418597	TTTGTCAGTGTAGACTTTAGTCCTAT	57.581	34.615	6.28	0.00	45.85	2.57
281	1328	6.978659	TCGCTCTATTAACATTGAACTACTGG	59.021	38.462	0.00	0.00	0.00	4.00
315	1362	4.782019	TCAAATTGATTGAAAGGACCGG	57.218	40.909	0.00	0.00	44.94	5.28
316	1363	3.509575	TCAAATTGATTGAAAGGACCGGG	59.490	43.478	6.32	0.00	44.94	5.73
318	1365	0.111446	TTGATTGAAAGGACCGGGCA	59.889	50.000	11.00	0.00	0.00	5.36
319	1366	0.331278	TGATTGAAAGGACCGGGCAT	59.669	50.000	11.00	0.00	0.00	4.40
320	1367	1.025041	GATTGAAAGGACCGGGCATC	58.975	55.000	11.00	4.55	0.00	3.91
326	1406	4.554036	GGACCGGGCATCCTGCTC	62.554	72.222	11.00	0.00	44.28	4.26
368	1462	0.592247	CAAGCGCAACAACTGACCAC	60.592	55.000	11.47	0.00	0.00	4.16
416	1537	1.968540	AGCGCAGGAGGAAAGCAAC	60.969	57.895	11.47	0.00	0.00	4.17
494	1644	0.108138	ACTCATGCGGGTAACAGAGC	60.108	55.000	0.00	0.00	39.74	4.09
618	1822	3.551863	CGAAGAGGAGGAAAGATCGGATG	60.552	52.174	0.00	0.00	0.00	3.51
619	1823	3.320610	AGAGGAGGAAAGATCGGATGA	57.679	47.619	0.00	0.00	0.00	2.92
906	2155	4.367450	CTCTTTCTTCTCCGGTCATCATC	58.633	47.826	0.00	0.00	0.00	2.92
1448	2706	1.649321	AAGCCTGTGACTGAGATGGA	58.351	50.000	0.00	0.00	0.00	3.41
1450	2708	0.461693	GCCTGTGACTGAGATGGAGC	60.462	60.000	0.00	0.00	0.00	4.70
1477	2735	0.321653	GGTGGTGACATCCTTCGCTT	60.322	55.000	0.00	0.00	46.14	4.68
1483	2741	0.678048	GACATCCTTCGCTTGCCCTT	60.678	55.000	0.00	0.00	0.00	3.95
1500	2758	0.733729	CTTCTCCGTCGATCGACCTT	59.266	55.000	35.48	0.00	41.76	3.50
1544	2805	1.608717	GAGATGGTGGCAGACTCGGT	61.609	60.000	0.00	0.00	0.00	4.69
1590	2866	1.585006	GTCGGAGAAGAAGGCGACA	59.415	57.895	0.00	0.00	39.69	4.35
1662	2938	4.697756	CGGCCCGACAAGAAGCCA	62.698	66.667	0.00	0.00	46.08	4.75
1861	3146	0.658829	CTTAGTCGCTCCGATGCTCG	60.659	60.000	0.00	0.00	38.42	5.03
1870	3155	0.817654	TCCGATGCTCGTTGATCAGT	59.182	50.000	0.00	0.00	38.40	3.41
1907	3297	4.628074	TGTTTTCAGTGTGTAGCTAGGTC	58.372	43.478	0.00	0.00	0.00	3.85
1910	3300	2.082231	TCAGTGTGTAGCTAGGTCGAC	58.918	52.381	7.13	7.13	0.00	4.20
1961	3405	4.521536	TCAGTATGTAGCTAGGTGGACT	57.478	45.455	4.27	0.00	37.40	3.85
1979	3469	6.136071	GTGGACTATGCTTAATACAATTGCG	58.864	40.000	5.05	0.00	0.00	4.85
1985	3475	5.168526	TGCTTAATACAATTGCGACCATC	57.831	39.130	5.05	0.00	0.00	3.51
1986	3476	4.036262	TGCTTAATACAATTGCGACCATCC	59.964	41.667	5.05	0.00	0.00	3.51
2063	3590	5.300969	GCATTCTGCAAATAAGTGTCAGA	57.699	39.130	0.00	0.00	44.26	3.27
2064	3591	5.091431	GCATTCTGCAAATAAGTGTCAGAC	58.909	41.667	0.00	0.00	44.26	3.51
2065	3592	5.335113	GCATTCTGCAAATAAGTGTCAGACA	60.335	40.000	0.00	0.00	44.26	3.41
2066	3593	7.324354	GCATTCTGCAAATAAGTGTCAGACAC	61.324	42.308	24.13	24.13	45.41	3.67
2074	3601	3.814577	GTGTCAGACACGGCATACT	57.185	52.632	17.96	0.00	39.53	2.12
2075	3602	1.350193	GTGTCAGACACGGCATACTG	58.650	55.000	17.96	0.00	39.53	2.74
2122	3674	2.192861	CGCAAACACCTTGAGGGCA	61.193	57.895	1.54	0.00	40.27	5.36
2126	3678	1.270550	CAAACACCTTGAGGGCATGAC	59.729	52.381	0.00	0.00	40.27	3.06
2127	3679	0.251341	AACACCTTGAGGGCATGACC	60.251	55.000	10.65	10.65	40.27	4.02
2128	3680	1.746615	CACCTTGAGGGCATGACCG	60.747	63.158	13.29	0.00	40.62	4.79
2129	3681	2.825836	CCTTGAGGGCATGACCGC	60.826	66.667	15.56	15.56	40.62	5.68
2130	3682	2.046023	CTTGAGGGCATGACCGCA	60.046	61.111	21.55	21.55	40.62	5.69
2131	3683	1.452651	CTTGAGGGCATGACCGCAT	60.453	57.895	25.89	0.00	40.08	4.73
2144	3697	2.267006	CGCATGAGCAGGACAGGT	59.733	61.111	0.00	0.00	42.27	4.00
2179	3738	3.741476	GGCGGCCAAGCTCTTGTG	61.741	66.667	15.62	2.29	38.85	3.33
2184	3743	1.246737	GGCCAAGCTCTTGTGGAAGG	61.247	60.000	6.34	0.00	38.85	3.46
2239	3859	1.735920	CGCCTCGGCTGCATATCTC	60.736	63.158	6.35	0.00	39.32	2.75
2244	3864	1.202114	CTCGGCTGCATATCTCTCTCC	59.798	57.143	0.50	0.00	0.00	3.71
2246	3866	0.612744	GGCTGCATATCTCTCTCCCC	59.387	60.000	0.50	0.00	0.00	4.81
2580	5043	5.121611	CACACTAACACTGCGAAATGGAATA	59.878	40.000	0.00	0.00	0.00	1.75
2641	5143	4.165779	CAGCTTTTACGCCAACCAAATAG	58.834	43.478	0.00	0.00	0.00	1.73
2642	5144	3.824443	AGCTTTTACGCCAACCAAATAGT	59.176	39.130	0.00	0.00	0.00	2.12
2646	5148	6.403855	GCTTTTACGCCAACCAAATAGTATGA	60.404	38.462	0.00	0.00	0.00	2.15
2649	5151	3.315191	ACGCCAACCAAATAGTATGATGC	59.685	43.478	0.00	0.00	0.00	3.91
2832	7399	5.221362	ACGCTTGGGGGTTATAATTTTATGC	60.221	40.000	0.00	0.00	34.95	3.14

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	5.580297	TGAAATTTGTGACTGGTTGCTTTTC	59.420	36.000	0.00	0.00	0.00	2.29
3	4	5.083533	TGAAATTTGTGACTGGTTGCTTT	57.916	34.783	0.00	0.00	0.00	3.51
6	7	4.629200	TGTTTGAAATTTGTGACTGGTTGC	59.371	37.500	0.00	0.00	0.00	4.17
7	8	6.718454	TTGTTTGAAATTTGTGACTGGTTG	57.282	33.333	0.00	0.00	0.00	3.77
8	9	7.920160	AATTGTTTGAAATTTGTGACTGGTT	57.080	28.000	0.00	0.00	0.00	3.67
9	10	7.605691	TGAAATTGTTTGAAATTTGTGACTGGT	59.394	29.630	0.00	0.00	39.31	4.00
11	12	8.658609	ACTGAAATTGTTTGAAATTTGTGACTG	58.341	29.630	0.00	0.00	39.31	3.51
12	13	8.658609	CACTGAAATTGTTTGAAATTTGTGACT	58.341	29.630	0.00	0.00	39.31	3.41
13	14	7.904461	CCACTGAAATTGTTTGAAATTTGTGAC	59.096	33.333	0.00	0.00	39.31	3.67
14	15	7.821359	TCCACTGAAATTGTTTGAAATTTGTGA	59.179	29.630	0.00	0.00	39.31	3.58
15	16	7.972527	TCCACTGAAATTGTTTGAAATTTGTG	58.027	30.769	0.00	3.68	39.31	3.33
16	17	8.735692	ATCCACTGAAATTGTTTGAAATTTGT	57.264	26.923	0.00	0.00	39.31	2.83
78	900	7.093596	TGGTGTGCATTTGTTAATTCCATGATA	60.094	33.333	0.00	0.00	0.00	2.15
169	998	8.535690	ACTAAAGTCTACACTGACAAATAAGC	57.464	34.615	0.00	0.00	39.27	3.09
216	1221	3.994392	ACGAGTTCACCATGTGTAATCAC	59.006	43.478	0.00	0.00	44.08	3.06
281	1328	4.494350	TCAATTTGAGCAGAAGCAACTC	57.506	40.909	0.00	0.00	45.49	3.01
368	1462	3.626996	TTCCACGCTGCTCCATGGG	62.627	63.158	13.02	3.69	32.73	4.00
416	1537	4.431131	AGATGCTGGCCGGGGTTG	62.431	66.667	15.02	0.00	0.00	3.77
906	2155	4.171005	ACAATTGCGATGCTGAAATTCAG	58.829	39.130	18.02	18.02	46.90	3.02
1368	2626	0.811219	CGGAGATTGATGCCTGCGAA	60.811	55.000	0.00	0.00	45.08	4.70
1418	2676	2.550180	GTCACAGGCTTTGTCTTCTTCC	59.450	50.000	0.00	0.00	38.16	3.46
1448	2706	0.251209	TGTCACCACCGAGTCTAGCT	60.251	55.000	0.00	0.00	0.00	3.32
1450	2708	1.405821	GGATGTCACCACCGAGTCTAG	59.594	57.143	0.00	0.00	0.00	2.43
1477	2735	2.771639	CGATCGACGGAGAAGGGCA	61.772	63.158	10.26	0.00	38.46	5.36
1483	2741	0.731417	GAAAGGTCGATCGACGGAGA	59.269	55.000	34.69	4.96	45.41	3.71
1500	2758	2.982130	GGCTCTGCCTTCTCCGAA	59.018	61.111	0.73	0.00	46.69	4.30
1595	2871	1.153429	GATGCCTCCACCACGGTAC	60.153	63.158	0.00	0.00	35.57	3.34
1662	2938	2.172293	CTCCATCTTAGCCAGAGCCTTT	59.828	50.000	0.00	0.00	41.25	3.11
1752	3037	3.111853	GACATGATGAAGGTCGGCATA	57.888	47.619	0.00	0.00	0.00	3.14
1797	3082	4.101114	TGTGCTTATAGAGGAAGGTTGGA	58.899	43.478	0.00	0.00	0.00	3.53
1842	3127	3.171705	GAGCATCGGAGCGACTAAG	57.828	57.895	0.00	0.00	39.18	2.18
1861	3146	4.094146	GCTTCAAGCTCCTTACTGATCAAC	59.906	45.833	0.71	0.00	38.45	3.18
1877	3209	4.361451	ACACACTGAAAACAGCTTCAAG	57.639	40.909	0.00	0.00	34.96	3.02
1895	3227	2.879646	AGCATAGTCGACCTAGCTACAC	59.120	50.000	20.37	0.97	32.11	2.90
1961	3405	6.072728	GGATGGTCGCAATTGTATTAAGCATA	60.073	38.462	7.40	0.00	0.00	3.14
1979	3469	3.070018	CCAAGCTCGATAATGGATGGTC	58.930	50.000	4.90	0.00	34.82	4.02
1985	3475	1.600957	CAGTGCCAAGCTCGATAATGG	59.399	52.381	6.23	6.23	36.00	3.16
1986	3476	2.554142	TCAGTGCCAAGCTCGATAATG	58.446	47.619	0.00	0.00	0.00	1.90
2082	3609	3.062763	AGAATGTCGTCTCTGTTTGCAG	58.937	45.455	0.00	0.00	43.87	4.41
2122	3674	1.153289	GTCCTGCTCATGCGGTCAT	60.153	57.895	0.00	0.00	43.76	3.06
2126	3678	2.513204	CCTGTCCTGCTCATGCGG	60.513	66.667	0.00	0.00	44.81	5.69
2127	3679	2.104859	CACCTGTCCTGCTCATGCG	61.105	63.158	0.00	0.00	43.34	4.73
2128	3680	0.250234	TACACCTGTCCTGCTCATGC	59.750	55.000	0.00	0.00	40.20	4.06
2129	3681	1.552337	ACTACACCTGTCCTGCTCATG	59.448	52.381	0.00	0.00	0.00	3.07
2130	3682	1.827969	GACTACACCTGTCCTGCTCAT	59.172	52.381	0.00	0.00	0.00	2.90
2131	3683	1.257743	GACTACACCTGTCCTGCTCA	58.742	55.000	0.00	0.00	0.00	4.26
2132	3684	0.171455	CGACTACACCTGTCCTGCTC	59.829	60.000	0.00	0.00	0.00	4.26
2133	3685	1.878656	GCGACTACACCTGTCCTGCT	61.879	60.000	0.00	0.00	0.00	4.24
2580	5043	4.961438	AAATTCACCTTCCACTTGCATT	57.039	36.364	0.00	0.00	0.00	3.56
2646	5148	7.145474	TGGCCTGAATCATATATGATAGCAT	57.855	36.000	25.03	12.09	46.22	3.79
2649	5151	7.173390	CAGCATGGCCTGAATCATATATGATAG	59.827	40.741	25.03	19.39	46.22	2.08

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.