AutoCloner

Multiple sequence alignment - TraesCS3D01G360800

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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	TraesCS3D01G360800	chr3D	100.000	3146	0	0	1	3146	474431514	474434659	0.000000e+00	5810.0
1	TraesCS3D01G360800	chr3D	89.032	155	11	4	1815	1966	474433289	474433440	1.490000e-43	187.0
2	TraesCS3D01G360800	chr3D	89.032	155	11	4	1776	1927	474433328	474433479	1.490000e-43	187.0
3	TraesCS3D01G360800	chr3D	88.793	116	10	1	1851	1966	474433289	474433401	4.230000e-29	139.0
4	TraesCS3D01G360800	chr3D	88.793	116	10	1	1776	1888	474433364	474433479	4.230000e-29	139.0
5	TraesCS3D01G360800	chr3D	88.312	77	6	2	1890	1966	474433289	474433362	4.320000e-14	89.8
6	TraesCS3D01G360800	chr3D	88.312	77	6	2	1776	1849	474433403	474433479	4.320000e-14	89.8
7	TraesCS3D01G360800	chr3D	92.105	38	3	0	1929	1966	474433289	474433326	2.000000e-03	54.7
8	TraesCS3D01G360800	chr3D	92.105	38	3	0	1776	1813	474433442	474433479	2.000000e-03	54.7
9	TraesCS3D01G360800	chr3B	93.677	2641	96	19	1	2636	630590631	630593205	0.000000e+00	3886.0
10	TraesCS3D01G360800	chr3B	93.857	407	18	5	2698	3100	630593415	630593818	9.650000e-170	606.0
11	TraesCS3D01G360800	chr3B	84.153	183	22	6	2968	3146	630594597	630594776	1.500000e-38	171.0
12	TraesCS3D01G360800	chr3B	87.156	109	8	3	1851	1959	630592366	630592468	5.510000e-23	119.0
13	TraesCS3D01G360800	chr3B	96.364	55	2	0	2635	2689	630593287	630593341	1.200000e-14	91.6
14	TraesCS3D01G360800	chr3B	87.013	77	7	2	1776	1849	630592477	630592553	2.010000e-12	84.2
15	TraesCS3D01G360800	chr3A	92.087	1921	86	18	1	1920	616710607	616712462	0.000000e+00	2645.0
16	TraesCS3D01G360800	chr3A	94.084	862	43	6	1830	2689	616712336	616713191	0.000000e+00	1303.0
17	TraesCS3D01G360800	chr3A	90.749	454	24	7	2698	3146	616713268	616713708	9.720000e-165	590.0
18	TraesCS3D01G360800	chr3A	88.596	114	10	1	1853	1966	616712320	616712430	5.470000e-28	135.0
19	TraesCS3D01G360800	chr3A	86.667	75	7	1	1892	1966	616712320	616712391	2.600000e-11	80.5
20	TraesCS3D01G360800	chr4A	100.000	28	0	0	167	194	635598193	635598220	6.000000e-03	52.8

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	TraesCS3D01G360800	chr3D	474431514	474434659	3145	False	750.111111	5810	90.720444	1	3146	9	chr3D.!!$F1	3145
1	TraesCS3D01G360800	chr3B	630590631	630594776	4145	False	826.300000	3886	90.370000	1	3146	6	chr3B.!!$F1	3145
2	TraesCS3D01G360800	chr3A	616710607	616713708	3101	False	950.700000	2645	90.436600	1	3146	5	chr3A.!!$F1	3145

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
881	894	0.031721	CGTAGTGCGGGGATTAGGAC	59.968	60.000	0.0	0.0	36.85	3.85	F
1860	1873	1.406069	GGTGTGACTGGGCAGTATGAG	60.406	57.143	0.0	0.0	42.66	2.90	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1866	1879	0.191064	TCACACCCTCAGTCCTTCCT	59.809	55.000	0.0	0.0	0.0	3.36	R
2707	2872	3.127548	CCATGCAACGTCAATCTAGCTTT	59.872	43.478	0.0	0.0	0.0	3.51	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
121	127	4.824537	TCATGAAGTTTTCCAAATCCACGA	59.175	37.500	0.00	0.00	0.00	4.35
628	636	4.489306	TTTTTGAAACCCGGGAACATTT	57.511	36.364	32.02	17.89	0.00	2.32
629	637	4.489306	TTTTGAAACCCGGGAACATTTT	57.511	36.364	32.02	17.45	0.00	1.82
642	650	6.426328	CCGGGAACATTTTTGAAATCATGAAA	59.574	34.615	0.00	0.00	0.00	2.69
672	680	9.898152	TTTCAAATTTGGAACATTTTTAGACCT	57.102	25.926	17.90	0.00	39.30	3.85
674	682	9.898152	TCAAATTTGGAACATTTTTAGACCTTT	57.102	25.926	17.90	0.00	39.30	3.11
881	894	0.031721	CGTAGTGCGGGGATTAGGAC	59.968	60.000	0.00	0.00	36.85	3.85
935	948	1.680207	CCAGCGAGTCATCAGATCAGA	59.320	52.381	0.00	0.00	0.00	3.27
936	949	2.287728	CCAGCGAGTCATCAGATCAGAG	60.288	54.545	0.00	0.00	0.00	3.35
1044	1057	3.636231	CCTCTCCACCCGCACCAA	61.636	66.667	0.00	0.00	0.00	3.67
1096	1109	3.000819	CCCACCCGCAGTACCAGA	61.001	66.667	0.00	0.00	0.00	3.86
1704	1717	1.603456	GTCCTAGCGGGTACTACTCC	58.397	60.000	0.00	0.00	36.25	3.85
1713	1726	3.511595	TACTACTCCGCGCCACCG	61.512	66.667	0.00	0.00	37.57	4.94
1742	1755	4.008330	CCTCCTTCTCAGTACGAGTACAA	58.992	47.826	14.83	2.98	42.88	2.41
1758	1771	4.335647	AACACAGGGCCCTCTGCG	62.336	66.667	25.75	15.86	42.61	5.18
1860	1873	1.406069	GGTGTGACTGGGCAGTATGAG	60.406	57.143	0.00	0.00	42.66	2.90
1878	1891	2.224621	TGAGCCAAAAGGAAGGACTGAG	60.225	50.000	0.00	0.00	0.00	3.35
1884	1897	1.059913	AAGGAAGGACTGAGGGTGTG	58.940	55.000	0.00	0.00	0.00	3.82
1938	1951	1.406069	GGTGTGACTGGGCAGTATGAG	60.406	57.143	0.00	0.00	42.66	2.90
1956	1969	2.705658	TGAGCAAAGAGGAAGGACTGAA	59.294	45.455	0.00	0.00	0.00	3.02
2156	2169	4.895889	TCGAGAGTATTGATGGGAGTTCAT	59.104	41.667	0.00	0.00	0.00	2.57
2160	2173	4.785301	AGTATTGATGGGAGTTCATGTGG	58.215	43.478	0.00	0.00	0.00	4.17
2180	2193	1.080995	GTGAGGATGCGCTGTGAGTC	61.081	60.000	9.73	0.00	0.00	3.36
2193	2206	3.053455	CTGTGAGTCGGTTCTTCTCAAC	58.947	50.000	0.00	0.00	39.42	3.18
2229	2242	5.304101	TGGGAATAAGTTGCAGTGTGATTTT	59.696	36.000	0.00	0.00	0.00	1.82
2307	2320	1.148048	TGCTTATGGCCTGCGCATA	59.852	52.632	12.24	0.00	40.92	3.14
2308	2321	0.250858	TGCTTATGGCCTGCGCATAT	60.251	50.000	12.24	6.18	40.92	1.78
2310	2323	1.270550	GCTTATGGCCTGCGCATATTT	59.729	47.619	12.24	0.00	36.38	1.40
2362	2375	5.001232	TGTGATTACCTTTGAAGCTGTACC	58.999	41.667	0.00	0.00	0.00	3.34
2379	2392	1.237285	ACCCGCAACTTGATGTCTGC	61.237	55.000	0.00	0.00	32.96	4.26
2465	2478	0.751452	TGCTTGGCATTGCAGTGAAA	59.249	45.000	14.15	5.56	34.84	2.69
2478	2491	7.217447	GCATTGCAGTGAAATTCAATTTTATGC	59.783	33.333	14.15	15.65	36.57	3.14
2533	2547	6.942532	ACAGCGTACCAAATTTGATATGAT	57.057	33.333	19.86	8.28	0.00	2.45
2607	2621	9.651913	TTTTCTGCAATGTTTTCTAGTTTTCTT	57.348	25.926	0.00	0.00	0.00	2.52
2609	2623	8.633075	TCTGCAATGTTTTCTAGTTTTCTTTG	57.367	30.769	0.00	0.00	0.00	2.77
2637	2734	4.442706	CCTGTGAGCCAAGTATTTCGTAT	58.557	43.478	0.00	0.00	0.00	3.06
2689	2786	5.122869	GTCATGCTTCAGTTTATCTTGCAGA	59.877	40.000	0.00	0.00	31.57	4.26
2690	2787	5.706833	TCATGCTTCAGTTTATCTTGCAGAA	59.293	36.000	0.00	0.00	31.57	3.02
2692	2789	6.389830	TGCTTCAGTTTATCTTGCAGAAAA	57.610	33.333	0.00	0.00	0.00	2.29
2693	2790	6.208644	TGCTTCAGTTTATCTTGCAGAAAAC	58.791	36.000	7.01	7.01	31.52	2.43
2694	2791	6.183360	TGCTTCAGTTTATCTTGCAGAAAACA	60.183	34.615	13.95	0.46	32.64	2.83
2695	2792	6.142958	GCTTCAGTTTATCTTGCAGAAAACAC	59.857	38.462	13.95	0.00	32.64	3.32
2696	2793	6.691754	TCAGTTTATCTTGCAGAAAACACA	57.308	33.333	13.95	2.31	32.64	3.72
2707	2872	6.691754	TGCAGAAAACACAGAAAACATAGA	57.308	33.333	0.00	0.00	0.00	1.98
2727	2892	4.256920	AGAAAGCTAGATTGACGTTGCAT	58.743	39.130	0.00	0.00	0.00	3.96
2955	3125	4.343526	GGATTCTCAGAGCTTCCATGAGTA	59.656	45.833	14.82	8.94	41.01	2.59
2956	3126	5.163364	GGATTCTCAGAGCTTCCATGAGTAA	60.163	44.000	14.82	10.32	41.01	2.24
2957	3127	5.946942	TTCTCAGAGCTTCCATGAGTAAT	57.053	39.130	14.82	0.00	41.01	1.89
2993	3163	6.661805	TGTGTAGTTTCTTGAGGAACCTTTTT	59.338	34.615	0.00	0.00	33.13	1.94
3083	3253	7.084486	TGTTAAGAGCTCATATATGCTGTACG	58.916	38.462	17.77	0.00	39.91	3.67
3108	4186	9.051679	CGAAGGTGTATATTTATTGGTTGATCA	57.948	33.333	0.00	0.00	0.00	2.92

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
154	160	5.846994	CACGAATTTGAAAAATTGTGCATGG	59.153	36.000	0.00	0.00	0.00	3.66
310	317	6.761731	TTGTGTATTTCAAAAATTGCTCCG	57.238	33.333	0.00	0.00	0.00	4.63
611	619	3.031736	TCAAAAATGTTCCCGGGTTTCA	58.968	40.909	22.86	17.92	0.00	2.69
612	620	3.737032	TCAAAAATGTTCCCGGGTTTC	57.263	42.857	22.86	12.61	0.00	2.78
613	621	4.489306	TTTCAAAAATGTTCCCGGGTTT	57.511	36.364	22.86	11.00	0.00	3.27
614	622	4.101741	TGATTTCAAAAATGTTCCCGGGTT	59.898	37.500	22.86	3.85	0.00	4.11
615	623	3.643792	TGATTTCAAAAATGTTCCCGGGT	59.356	39.130	22.86	0.00	0.00	5.28
616	624	4.264460	TGATTTCAAAAATGTTCCCGGG	57.736	40.909	16.85	16.85	0.00	5.73
617	625	5.477510	TCATGATTTCAAAAATGTTCCCGG	58.522	37.500	0.00	0.00	0.00	5.73
618	626	7.418840	TTTCATGATTTCAAAAATGTTCCCG	57.581	32.000	0.00	0.00	0.00	5.14
895	908	1.219124	GAGGCGACCTGCTTGATCA	59.781	57.895	2.98	0.00	45.43	2.92
935	948	1.296715	GGGTTGGTGATGAGTCGCT	59.703	57.895	0.00	0.00	35.21	4.93
936	949	1.745489	GGGGTTGGTGATGAGTCGC	60.745	63.158	0.00	0.00	0.00	5.19
1713	1726	3.672295	CTGAGAAGGAGGCGGTGGC	62.672	68.421	0.00	0.00	38.90	5.01
1714	1727	0.970937	TACTGAGAAGGAGGCGGTGG	60.971	60.000	0.00	0.00	0.00	4.61
1758	1771	2.125512	CTGCCGTACTCCACAGGC	60.126	66.667	0.68	0.68	43.11	4.85
1860	1873	1.539157	CCTCAGTCCTTCCTTTTGGC	58.461	55.000	0.00	0.00	40.12	4.52
1863	1876	2.136026	ACACCCTCAGTCCTTCCTTTT	58.864	47.619	0.00	0.00	0.00	2.27
1865	1878	1.059913	CACACCCTCAGTCCTTCCTT	58.940	55.000	0.00	0.00	0.00	3.36
1866	1879	0.191064	TCACACCCTCAGTCCTTCCT	59.809	55.000	0.00	0.00	0.00	3.36
1867	1880	0.321996	GTCACACCCTCAGTCCTTCC	59.678	60.000	0.00	0.00	0.00	3.46
1878	1891	0.392998	CATACTGCCCAGTCACACCC	60.393	60.000	3.88	0.00	42.54	4.61
1884	1897	4.865865	GGCTCATACTGCCCAGTC	57.134	61.111	3.88	0.00	44.32	3.51
1938	1951	2.431454	CCTTCAGTCCTTCCTCTTTGC	58.569	52.381	0.00	0.00	0.00	3.68
2031	2044	2.485426	CACACCTTCATCAATCGCAAGT	59.515	45.455	0.00	0.00	39.48	3.16
2156	2169	3.321648	AGCGCATCCTCACCCACA	61.322	61.111	11.47	0.00	0.00	4.17
2160	2173	1.812922	CTCACAGCGCATCCTCACC	60.813	63.158	11.47	0.00	0.00	4.02
2180	2193	2.821991	ACAGGAGTTGAGAAGAACCG	57.178	50.000	0.00	0.00	0.00	4.44
2193	2206	6.404734	GCAACTTATTCCCACATTAACAGGAG	60.405	42.308	0.00	0.00	0.00	3.69
2362	2375	0.806868	ATGCAGACATCAAGTTGCGG	59.193	50.000	0.00	0.00	37.19	5.69
2379	2392	8.388853	CACAACTCAGATCAGAGACAAATTATG	58.611	37.037	20.82	1.37	38.98	1.90
2465	2478	9.985730	TTGACTGAAAGAAGCATAAAATTGAAT	57.014	25.926	0.00	0.00	37.43	2.57
2495	2508	4.300189	ACGCTGTTCAACAAAGCAATAA	57.700	36.364	2.97	0.00	36.73	1.40
2539	2553	6.145534	CACGTGTAGATTTGAGTTAGAAGCAA	59.854	38.462	7.58	0.00	0.00	3.91
2540	2554	5.633601	CACGTGTAGATTTGAGTTAGAAGCA	59.366	40.000	7.58	0.00	0.00	3.91
2541	2555	5.862323	TCACGTGTAGATTTGAGTTAGAAGC	59.138	40.000	16.51	0.00	0.00	3.86
2542	2556	8.467402	AATCACGTGTAGATTTGAGTTAGAAG	57.533	34.615	16.51	0.00	31.99	2.85
2543	2557	8.827177	AAATCACGTGTAGATTTGAGTTAGAA	57.173	30.769	16.51	0.00	42.39	2.10
2584	2598	8.465999	TCAAAGAAAACTAGAAAACATTGCAGA	58.534	29.630	0.00	0.00	0.00	4.26
2607	2621	0.770499	TTGGCTCACAGGGTGATCAA	59.230	50.000	0.00	5.58	41.94	2.57
2609	2623	0.326264	ACTTGGCTCACAGGGTGATC	59.674	55.000	0.00	0.00	41.94	2.92
2637	2734	8.637986	ACTCTGAACATGTTATGGCTTTTAAAA	58.362	29.630	11.95	0.00	33.60	1.52
2652	2749	4.214758	TGAAGCATGACAACTCTGAACATG	59.785	41.667	0.00	0.00	40.34	3.21
2689	2786	9.120538	TCTAGCTTTCTATGTTTTCTGTGTTTT	57.879	29.630	0.00	0.00	0.00	2.43
2690	2787	8.677148	TCTAGCTTTCTATGTTTTCTGTGTTT	57.323	30.769	0.00	0.00	0.00	2.83
2692	2789	8.725148	CAATCTAGCTTTCTATGTTTTCTGTGT	58.275	33.333	0.00	0.00	0.00	3.72
2693	2790	8.939929	TCAATCTAGCTTTCTATGTTTTCTGTG	58.060	33.333	0.00	0.00	0.00	3.66
2694	2791	8.940952	GTCAATCTAGCTTTCTATGTTTTCTGT	58.059	33.333	0.00	0.00	0.00	3.41
2695	2792	8.113062	CGTCAATCTAGCTTTCTATGTTTTCTG	58.887	37.037	0.00	0.00	0.00	3.02
2696	2793	7.819900	ACGTCAATCTAGCTTTCTATGTTTTCT	59.180	33.333	0.00	0.00	0.00	2.52
2707	2872	3.127548	CCATGCAACGTCAATCTAGCTTT	59.872	43.478	0.00	0.00	0.00	3.51
2791	2956	7.255208	GGTTCAGGTGTTTAAAATTTCGAGGTA	60.255	37.037	0.00	0.00	0.00	3.08
2797	2962	6.019075	GCACAGGTTCAGGTGTTTAAAATTTC	60.019	38.462	0.00	0.00	37.35	2.17
2871	3036	5.941647	TCCAGCAAAACAAAGGGTAGTATAC	59.058	40.000	0.00	0.00	42.04	1.47

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.