AutoCloner

Multiple sequence alignment - TraesCS6D01G107500

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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	TraesCS6D01G107500	chr6D	100.000	3002	0	0	1	3002	71134582	71137583	0.000000e+00	5544.0
1	TraesCS6D01G107500	chr6D	93.414	2065	112	10	1	2044	71142627	71144688	0.000000e+00	3038.0
2	TraesCS6D01G107500	chr6D	88.545	323	29	6	2351	2667	71145036	71145356	4.690000e-103	385.0
3	TraesCS6D01G107500	chr6D	89.789	284	23	4	2045	2327	71144771	71145049	2.850000e-95	359.0
4	TraesCS6D01G107500	chr6A	91.317	2384	146	24	1	2327	87929849	87932228	0.000000e+00	3199.0
5	TraesCS6D01G107500	chr6A	87.749	351	28	12	2351	2690	87932215	87932561	2.170000e-106	396.0
6	TraesCS6D01G107500	chr6A	89.840	187	8	5	2804	2990	87924456	87924631	2.330000e-56	230.0
7	TraesCS6D01G107500	chr3D	88.431	2161	200	29	1	2124	360333965	360336112	0.000000e+00	2560.0
8	TraesCS6D01G107500	chr3D	87.490	1295	134	13	833	2119	360558291	360559565	0.000000e+00	1469.0
9	TraesCS6D01G107500	chr3D	86.842	836	83	16	1	831	360557375	360558188	0.000000e+00	909.0
10	TraesCS6D01G107500	chr3B	88.410	2157	201	26	1	2124	466264293	466266433	0.000000e+00	2553.0
11	TraesCS6D01G107500	chr3B	87.081	836	81	16	1	831	466610096	466610909	0.000000e+00	920.0
12	TraesCS6D01G107500	chr3A	87.993	2157	206	31	1	2124	479771951	479774087	0.000000e+00	2499.0
13	TraesCS6D01G107500	chr3A	86.722	2154	234	34	1	2114	480050257	480052398	0.000000e+00	2346.0
14	TraesCS6D01G107500	chr6B	97.474	1227	31	0	1	1227	145890069	145891295	0.000000e+00	2095.0
15	TraesCS6D01G107500	chr6B	94.293	1244	64	6	807	2047	145898508	145899747	0.000000e+00	1897.0
16	TraesCS6D01G107500	chr6B	95.724	912	35	1	1224	2135	145891417	145892324	0.000000e+00	1465.0
17	TraesCS6D01G107500	chr6B	89.316	833	64	11	2171	2992	145892322	145893140	0.000000e+00	1022.0
18	TraesCS6D01G107500	chr6B	97.070	273	8	0	1	273	145898243	145898515	7.580000e-126	460.0
19	TraesCS6D01G107500	chr6B	91.197	284	20	3	2045	2327	145899814	145900093	6.070000e-102	381.0
20	TraesCS6D01G107500	chr4A	87.302	63	7	1	2731	2793	185993977	185993916	1.490000e-08	71.3

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	TraesCS6D01G107500	chr6D	71134582	71137583	3001	False	5544.000000	5544	100.000000	1	3002	1	chr6D.!!$F1	3001
1	TraesCS6D01G107500	chr6D	71142627	71145356	2729	False	1260.666667	3038	90.582667	1	2667	3	chr6D.!!$F2	2666
2	TraesCS6D01G107500	chr6A	87929849	87932561	2712	False	1797.500000	3199	89.533000	1	2690	2	chr6A.!!$F2	2689
3	TraesCS6D01G107500	chr3D	360333965	360336112	2147	False	2560.000000	2560	88.431000	1	2124	1	chr3D.!!$F1	2123
4	TraesCS6D01G107500	chr3D	360557375	360559565	2190	False	1189.000000	1469	87.166000	1	2119	2	chr3D.!!$F2	2118
5	TraesCS6D01G107500	chr3B	466264293	466266433	2140	False	2553.000000	2553	88.410000	1	2124	1	chr3B.!!$F1	2123
6	TraesCS6D01G107500	chr3B	466610096	466610909	813	False	920.000000	920	87.081000	1	831	1	chr3B.!!$F2	830
7	TraesCS6D01G107500	chr3A	479771951	479774087	2136	False	2499.000000	2499	87.993000	1	2124	1	chr3A.!!$F1	2123
8	TraesCS6D01G107500	chr3A	480050257	480052398	2141	False	2346.000000	2346	86.722000	1	2114	1	chr3A.!!$F2	2113
9	TraesCS6D01G107500	chr6B	145890069	145893140	3071	False	1527.333333	2095	94.171333	1	2992	3	chr6B.!!$F1	2991
10	TraesCS6D01G107500	chr6B	145898243	145900093	1850	False	912.666667	1897	94.186667	1	2327	3	chr6B.!!$F2	2326

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
322	336	1.086696	TCGCTTTTATGGCAGACTGC	58.913	50.000	19.55	19.55	44.08	4.40	F
689	744	1.269569	GGGCTTGGTTTTGGTTTCTCG	60.270	52.381	0.00	0.00	0.00	4.04	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1567	1856	0.179040	TTTGTCACCTCCCCGTGTTC	60.179	55.0	0.0	0.0	35.18	3.18	R
2446	2851	0.043334	AGCATCCCAGAGGTAGGTGT	59.957	55.0	0.0	0.0	0.00	4.16	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
206	220	1.142870	ACAGTGGTGCACTTGGTACAT	59.857	47.619	17.98	0.00	42.59	2.29
215	229	3.070878	TGCACTTGGTACATGACTCTCAA	59.929	43.478	0.00	0.00	39.30	3.02
276	290	3.580458	CTGGGCCTTATAGTGCAGTCTAT	59.420	47.826	4.53	0.00	35.24	1.98
304	318	5.118990	TCACTAATAGCTGGCTTTGTCATC	58.881	41.667	0.00	0.00	0.00	2.92
322	336	1.086696	TCGCTTTTATGGCAGACTGC	58.913	50.000	19.55	19.55	44.08	4.40
663	718	1.281867	AGGGCATTCGAAGTGGAATCA	59.718	47.619	3.35	0.00	34.50	2.57
689	744	1.269569	GGGCTTGGTTTTGGTTTCTCG	60.270	52.381	0.00	0.00	0.00	4.04
744	799	5.590663	TGTTTCTATGTTGGTGCACAGTTTA	59.409	36.000	20.43	0.57	0.00	2.01
752	807	3.729966	TGGTGCACAGTTTATACGTCAA	58.270	40.909	20.43	0.00	0.00	3.18
763	818	9.367444	ACAGTTTATACGTCAAGGAAAATCTAG	57.633	33.333	0.00	0.00	0.00	2.43
877	1035	4.911514	TTCCTTGTCTTAGTTTTGGCAC	57.088	40.909	0.00	0.00	0.00	5.01
937	1095	3.181482	TGCGACAAAAGCAAAGGATTCAA	60.181	39.130	0.00	0.00	42.18	2.69
951	1109	7.440856	GCAAAGGATTCAACCATTTCTGTTTTA	59.559	33.333	0.00	0.00	0.00	1.52
1044	1202	5.415701	AGGCGACATTGATTTCAGTAATGTT	59.584	36.000	0.00	0.00	43.03	2.71
1287	1575	9.770097	TCTCATATATAAGAAGCTTTCAACTGG	57.230	33.333	0.00	0.00	0.00	4.00
1363	1652	5.796502	TTCCTTCCTTTTCCAGACCATAT	57.203	39.130	0.00	0.00	0.00	1.78
1461	1750	6.912426	TGGTAGTATCTCAGTAGATGGAGTT	58.088	40.000	0.00	0.00	42.60	3.01
1506	1795	2.780010	CTGGTTAAGGGATCAGATGGGT	59.220	50.000	0.00	0.00	0.00	4.51
1567	1856	1.268335	GCGCAAACATAACATACGGGG	60.268	52.381	0.30	0.00	0.00	5.73
1833	2122	1.852633	TGGATCGAGTCATGGTGAGT	58.147	50.000	0.00	0.00	31.62	3.41
1937	2226	3.766051	GCAGAAAAGGGAAATCATGAGGT	59.234	43.478	0.09	0.00	0.00	3.85
2193	2578	6.488683	ACCAACTAAAAACTGCAGCAGTATTA	59.511	34.615	28.48	24.97	44.62	0.98
2204	2589	6.078202	TGCAGCAGTATTAGTAGTCTGATC	57.922	41.667	0.00	0.00	0.00	2.92
2227	2617	4.201970	CGAAGAAACGCCTAGAGAAGAGAT	60.202	45.833	0.00	0.00	0.00	2.75
2265	2656	8.024145	TCTGTCCCTTAGAAAAATCTAGATCC	57.976	38.462	5.51	0.00	0.00	3.36
2308	2713	1.068474	CAGGTTCTACGCAAAGGACG	58.932	55.000	0.00	0.00	0.00	4.79
2327	2732	2.188994	GCAGGCAGCAGTAGGGAG	59.811	66.667	0.00	0.00	44.79	4.30
2360	2765	1.332375	GTTTGACAACCGCAGCAGTAA	59.668	47.619	0.00	0.00	0.00	2.24
2446	2851	4.177165	TCGTCGGCTAAAGTGATAAACA	57.823	40.909	0.00	0.00	0.00	2.83
2465	2870	0.043334	ACACCTACCTCTGGGATGCT	59.957	55.000	0.00	0.00	36.25	3.79
2466	2871	1.207791	CACCTACCTCTGGGATGCTT	58.792	55.000	0.00	0.00	36.25	3.91
2487	2892	1.673920	GCGTTCTGAAACAGGGAAACA	59.326	47.619	0.00	0.00	34.93	2.83
2525	2930	8.935844	CAAATTTTATAGCATCGCATACCTCTA	58.064	33.333	0.00	0.00	0.00	2.43
2531	2936	0.251209	ATCGCATACCTCTAGGCCGA	60.251	55.000	0.00	0.00	39.32	5.54
2609	3021	2.044551	GGGCAGCCCTCTTTCTGG	60.045	66.667	24.99	0.00	41.34	3.86
2610	3022	2.759795	GGCAGCCCTCTTTCTGGT	59.240	61.111	0.00	0.00	0.00	4.00
2611	3023	1.075659	GGCAGCCCTCTTTCTGGTT	59.924	57.895	0.00	0.00	0.00	3.67
2684	3111	0.830648	CATCTCTGGCCCTAAACCGA	59.169	55.000	0.00	0.00	0.00	4.69
2686	3113	2.464796	TCTCTGGCCCTAAACCGATA	57.535	50.000	0.00	0.00	0.00	2.92
2693	3120	2.158798	GGCCCTAAACCGATAAAGAGCT	60.159	50.000	0.00	0.00	0.00	4.09
2695	3122	3.312697	GCCCTAAACCGATAAAGAGCTTG	59.687	47.826	0.00	0.00	0.00	4.01
2726	3153	0.802494	CAAATCCGACCCCTCAAACG	59.198	55.000	0.00	0.00	0.00	3.60
2728	3155	0.036671	AATCCGACCCCTCAAACGTC	60.037	55.000	0.00	0.00	0.00	4.34
2753	3180	1.752501	GCGTCCGTGGACAATGATCG	61.753	60.000	18.54	4.36	44.77	3.69
2766	3193	2.675844	CAATGATCGGTCACGCCTTAAA	59.324	45.455	0.00	0.00	40.69	1.52
2809	3236	5.998363	GGATACCTTAGGACTGCCAATAAAG	59.002	44.000	4.77	0.00	36.29	1.85
2839	3266	9.699410	ATCTAACATTCATGGGTTATCAAAAGA	57.301	29.630	0.00	0.00	0.00	2.52
2898	3325	4.278919	TCATGCATGACTTGTTGATGTTGT	59.721	37.500	25.42	0.00	0.00	3.32
2973	3400	5.224135	TGATTTGTTGATGTGACATTGCTG	58.776	37.500	0.00	0.00	0.00	4.41
2983	3410	3.208594	GTGACATTGCTGCATGGATAGA	58.791	45.455	1.84	0.00	0.00	1.98

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
206	220	6.149308	ACATTTAATGCGTCAATTGAGAGTCA	59.851	34.615	8.80	8.91	0.00	3.41
215	229	3.434637	GCCGAACATTTAATGCGTCAAT	58.565	40.909	4.68	0.00	0.00	2.57
304	318	0.804364	TGCAGTCTGCCATAAAAGCG	59.196	50.000	21.99	0.00	44.23	4.68
322	336	1.945394	GTGATAATCAGTGCAGGCCTG	59.055	52.381	29.34	29.34	0.00	4.85
327	341	4.692155	TGACACAAGTGATAATCAGTGCAG	59.308	41.667	7.28	0.00	28.97	4.41
513	568	5.609423	ACTTGCATCTTCATACATCTCCTC	58.391	41.667	0.00	0.00	0.00	3.71
547	602	3.508402	TCTGATACTACCAACAGCGTCAA	59.492	43.478	0.00	0.00	0.00	3.18
627	682	3.304829	TGCCCTGTTTCCTTAAAGCTTT	58.695	40.909	17.30	17.30	0.00	3.51
663	718	1.351076	CCAAAACCAAGCCCTCCAAT	58.649	50.000	0.00	0.00	0.00	3.16
689	744	7.516627	GCAAATGTCAAATACAACACCAAGAAC	60.517	37.037	0.00	0.00	42.70	3.01
744	799	6.035758	GCGAAACTAGATTTTCCTTGACGTAT	59.964	38.462	0.00	0.00	32.67	3.06
752	807	5.491982	ACATCTGCGAAACTAGATTTTCCT	58.508	37.500	0.00	0.00	32.67	3.36
763	818	6.910433	TCTTACTTTGAAAACATCTGCGAAAC	59.090	34.615	0.00	0.00	0.00	2.78
877	1035	1.675641	CCTGCGAAACCCCAAGAGG	60.676	63.158	0.00	0.00	0.00	3.69
951	1109	9.892130	ATTTTTGACTTCCGATCTAGAATACTT	57.108	29.630	0.00	0.00	0.00	2.24
1044	1202	3.592059	GCGTGATGGGTACTTGAAACTA	58.408	45.455	0.00	0.00	0.00	2.24
1125	1283	6.228273	TGAACAAGACTAGAAAAGATTGCG	57.772	37.500	0.00	0.00	32.26	4.85
1230	1518	2.119801	AGACCATGCATCACCTGTTC	57.880	50.000	0.00	0.00	0.00	3.18
1287	1575	9.531942	TTGCCAATCATCATATGTGAAATTAAC	57.468	29.630	1.90	0.00	38.01	2.01
1363	1652	3.527507	ACCACTCTCTCCAACTAGTGA	57.472	47.619	0.00	0.00	41.47	3.41
1461	1750	7.710044	CAGCTAATTCTCAAGCTCTTAATCTCA	59.290	37.037	0.00	0.00	45.92	3.27
1567	1856	0.179040	TTTGTCACCTCCCCGTGTTC	60.179	55.000	0.00	0.00	35.18	3.18
1635	1924	0.323178	ATCCCTGTGGCAAGCTTGAG	60.323	55.000	30.39	17.24	0.00	3.02
1707	1996	2.186903	CTTGCGATGGCTACCCGT	59.813	61.111	0.15	0.00	40.82	5.28
1937	2226	0.465705	GTCCTTGATCCGCATCAGGA	59.534	55.000	0.00	2.00	45.54	3.86
2086	2466	7.232118	TCACTTCTCAGATCACAAATCACTA	57.768	36.000	0.00	0.00	0.00	2.74
2193	2578	3.427773	GGCGTTTCTTCGATCAGACTACT	60.428	47.826	0.00	0.00	0.00	2.57
2204	2589	3.127203	TCTCTTCTCTAGGCGTTTCTTCG	59.873	47.826	0.00	0.00	0.00	3.79
2227	2617	1.120530	GGACAGAGCCCGAAATCCTA	58.879	55.000	0.00	0.00	0.00	2.94
2265	2656	4.058817	AGTTTTTGTGAAGTAGAGGCTCG	58.941	43.478	9.22	0.00	0.00	5.03
2313	2718	1.168714	CAAAACTCCCTACTGCTGCC	58.831	55.000	0.00	0.00	0.00	4.85
2379	2784	6.795098	TGTGTGTTCATAGTCATTTGGTAC	57.205	37.500	0.00	0.00	0.00	3.34
2446	2851	0.043334	AGCATCCCAGAGGTAGGTGT	59.957	55.000	0.00	0.00	0.00	4.16
2448	2853	1.207791	CAAGCATCCCAGAGGTAGGT	58.792	55.000	0.00	0.00	0.00	3.08
2465	2870	2.045561	TTCCCTGTTTCAGAACGCAA	57.954	45.000	0.00	0.00	38.65	4.85
2466	2871	1.673920	GTTTCCCTGTTTCAGAACGCA	59.326	47.619	0.00	0.00	38.65	5.24
2487	2892	7.784037	TGCTATAAAATTTGCATGGATTCTGT	58.216	30.769	0.00	0.00	0.00	3.41
2597	3009	0.315251	GCACAAACCAGAAAGAGGGC	59.685	55.000	0.00	0.00	0.00	5.19
2601	3013	1.677576	CAGCAGCACAAACCAGAAAGA	59.322	47.619	0.00	0.00	0.00	2.52
2602	3014	1.269413	CCAGCAGCACAAACCAGAAAG	60.269	52.381	0.00	0.00	0.00	2.62
2603	3015	0.746063	CCAGCAGCACAAACCAGAAA	59.254	50.000	0.00	0.00	0.00	2.52
2604	3016	1.108727	CCCAGCAGCACAAACCAGAA	61.109	55.000	0.00	0.00	0.00	3.02
2605	3017	1.529010	CCCAGCAGCACAAACCAGA	60.529	57.895	0.00	0.00	0.00	3.86
2606	3018	2.567497	CCCCAGCAGCACAAACCAG	61.567	63.158	0.00	0.00	0.00	4.00
2607	3019	2.521465	CCCCAGCAGCACAAACCA	60.521	61.111	0.00	0.00	0.00	3.67
2608	3020	2.521708	ACCCCAGCAGCACAAACC	60.522	61.111	0.00	0.00	0.00	3.27
2609	3021	2.730094	CACCCCAGCAGCACAAAC	59.270	61.111	0.00	0.00	0.00	2.93
2610	3022	2.521465	CCACCCCAGCAGCACAAA	60.521	61.111	0.00	0.00	0.00	2.83
2611	3023	4.601794	CCCACCCCAGCAGCACAA	62.602	66.667	0.00	0.00	0.00	3.33
2650	3075	2.700897	AGAGATGCCCTAAGTTATGCGT	59.299	45.455	0.27	0.27	0.00	5.24
2651	3076	3.062763	CAGAGATGCCCTAAGTTATGCG	58.937	50.000	1.50	0.00	0.00	4.73
2684	3111	3.728385	AGGTCCTTGCAAGCTCTTTAT	57.272	42.857	21.43	0.00	0.00	1.40
2686	3113	1.959282	CAAGGTCCTTGCAAGCTCTTT	59.041	47.619	21.43	14.26	34.63	2.52
2713	3140	2.431942	CGGACGTTTGAGGGGTCG	60.432	66.667	0.00	0.00	0.00	4.79
2741	3168	0.739462	GCGTGACCGATCATTGTCCA	60.739	55.000	0.00	0.00	37.14	4.02
2748	3175	2.459060	TTTTAAGGCGTGACCGATCA	57.541	45.000	0.00	0.00	46.52	2.92
2753	3180	7.033185	ACAATGAAATATTTTAAGGCGTGACC	58.967	34.615	1.43	0.00	39.61	4.02
2766	3193	9.793259	AGGTATCCGATTGTACAATGAAATATT	57.207	29.630	25.42	0.00	0.00	1.28
2785	3212	5.562298	TTATTGGCAGTCCTAAGGTATCC	57.438	43.478	0.00	0.00	0.00	2.59
2934	3361	7.975058	TCAACAAATCATGCATGTTAACCATAG	59.025	33.333	25.43	9.77	35.63	2.23
2940	3367	7.328982	GTCACATCAACAAATCATGCATGTTAA	59.671	33.333	25.43	7.83	35.63	2.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.