AutoCloner

Multiple sequence alignment - TraesCS2D01G470700

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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	TraesCS2D01G470700	chr2D	100.000	3086	0	0	1	3086	575158419	575161504	0.000000e+00	5699
1	TraesCS2D01G470700	chr2D	91.005	2190	129	26	6	2169	574663791	574661644	0.000000e+00	2891
2	TraesCS2D01G470700	chr2D	97.390	1073	20	2	2022	3086	575167599	575168671	0.000000e+00	1820
3	TraesCS2D01G470700	chr2D	87.014	901	114	3	1252	2151	574572064	574572962	0.000000e+00	1013
4	TraesCS2D01G470700	chr2D	87.029	902	112	5	1252	2151	574600689	574601587	0.000000e+00	1013
5	TraesCS2D01G470700	chr2D	90.050	603	59	1	1549	2151	574597059	574597660	0.000000e+00	780
6	TraesCS2D01G470700	chr2D	90.123	405	38	2	2683	3086	574657465	574657062	2.730000e-145	525
7	TraesCS2D01G470700	chr2D	84.158	404	59	3	2612	3010	574978656	574979059	1.340000e-103	387
8	TraesCS2D01G470700	chr2A	93.177	1832	94	14	350	2169	713125422	713123610	0.000000e+00	2662
9	TraesCS2D01G470700	chr2A	91.429	1925	117	18	471	2368	713189299	713191202	0.000000e+00	2597
10	TraesCS2D01G470700	chr2A	82.260	699	54	19	2401	3086	713203420	713204061	9.740000e-150	540
11	TraesCS2D01G470700	chr2A	89.367	395	41	1	2692	3086	713017251	713016858	2.140000e-136	496
12	TraesCS2D01G470700	chr2B	93.318	1751	94	12	350	2094	690942618	690940885	0.000000e+00	2564
13	TraesCS2D01G470700	chr2B	91.527	1676	113	16	431	2094	691046891	691048549	0.000000e+00	2281
14	TraesCS2D01G470700	chr2B	95.176	995	36	6	2092	3086	691048921	691049903	0.000000e+00	1561
15	TraesCS2D01G470700	chr2B	84.771	1333	190	9	902	2232	691038170	691039491	0.000000e+00	1325
16	TraesCS2D01G470700	chr2B	86.015	522	59	8	2575	3086	690931888	690931371	5.820000e-152	547

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	TraesCS2D01G470700	chr2D	575158419	575161504	3085	False	5699.0	5699	100.0000	1	3086	1	chr2D.!!$F3	3085
1	TraesCS2D01G470700	chr2D	574661644	574663791	2147	True	2891.0	2891	91.0050	6	2169	1	chr2D.!!$R2	2163
2	TraesCS2D01G470700	chr2D	575167599	575168671	1072	False	1820.0	1820	97.3900	2022	3086	1	chr2D.!!$F4	1064
3	TraesCS2D01G470700	chr2D	574572064	574572962	898	False	1013.0	1013	87.0140	1252	2151	1	chr2D.!!$F1	899
4	TraesCS2D01G470700	chr2D	574597059	574601587	4528	False	896.5	1013	88.5395	1252	2151	2	chr2D.!!$F5	899
5	TraesCS2D01G470700	chr2A	713123610	713125422	1812	True	2662.0	2662	93.1770	350	2169	1	chr2A.!!$R2	1819
6	TraesCS2D01G470700	chr2A	713189299	713191202	1903	False	2597.0	2597	91.4290	471	2368	1	chr2A.!!$F1	1897
7	TraesCS2D01G470700	chr2A	713203420	713204061	641	False	540.0	540	82.2600	2401	3086	1	chr2A.!!$F2	685
8	TraesCS2D01G470700	chr2B	690940885	690942618	1733	True	2564.0	2564	93.3180	350	2094	1	chr2B.!!$R2	1744
9	TraesCS2D01G470700	chr2B	691046891	691049903	3012	False	1921.0	2281	93.3515	431	3086	2	chr2B.!!$F2	2655
10	TraesCS2D01G470700	chr2B	691038170	691039491	1321	False	1325.0	1325	84.7710	902	2232	1	chr2B.!!$F1	1330
11	TraesCS2D01G470700	chr2B	690931371	690931888	517	True	547.0	547	86.0150	2575	3086	1	chr2B.!!$R1	511

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
812	854	0.103937	CCAAATGGTGGCGTGTTTGT	59.896	50.0	0.0	0.0	41.72	2.83	F
1905	4285	0.531974	TTGACGTGGAGACTGTTGCC	60.532	55.0	0.0	0.0	0.00	4.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1962	4348	0.174845	TCCGTGGAGCCATAAACTCG	59.825	55.0	0.0	0.0	34.87	4.18	R
2975	5772	0.043334	AGGCTGGTATGGAGGACAGT	59.957	55.0	0.0	0.0	33.62	3.55	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
95	96	4.843220	AAGAATCTTGAACCAGCTTGTG	57.157	40.909	0.00	0.00	0.00	3.33
105	106	3.040965	CAGCTTGTGGTTGGATGGT	57.959	52.632	0.00	0.00	0.00	3.55
106	107	1.331214	CAGCTTGTGGTTGGATGGTT	58.669	50.000	0.00	0.00	0.00	3.67
107	108	2.513753	CAGCTTGTGGTTGGATGGTTA	58.486	47.619	0.00	0.00	0.00	2.85
108	109	2.890311	CAGCTTGTGGTTGGATGGTTAA	59.110	45.455	0.00	0.00	0.00	2.01
112	113	3.433306	TGTGGTTGGATGGTTAAGAGG	57.567	47.619	0.00	0.00	0.00	3.69
113	114	2.983192	TGTGGTTGGATGGTTAAGAGGA	59.017	45.455	0.00	0.00	0.00	3.71
115	116	2.027561	TGGTTGGATGGTTAAGAGGACG	60.028	50.000	0.00	0.00	0.00	4.79
128	129	2.946785	AGAGGACGGTAGTATTCCCAG	58.053	52.381	0.00	0.00	0.00	4.45
146	147	1.671379	GCCCAGGACGGTTCAAGTC	60.671	63.158	0.00	0.00	37.86	3.01
155	156	2.494870	GACGGTTCAAGTCCTAGCCTTA	59.505	50.000	0.00	0.00	32.78	2.69
201	205	4.487714	TTATTTCAGGTCTTCCAGCGAT	57.512	40.909	0.00	0.00	35.89	4.58
202	206	2.859165	TTTCAGGTCTTCCAGCGATT	57.141	45.000	0.00	0.00	35.89	3.34
286	298	3.071457	CAGGGGTGAGTGTATATGCATGA	59.929	47.826	10.16	0.00	0.00	3.07
310	322	6.935741	ATGTTTGCTTCTGTACTGTGTTTA	57.064	33.333	0.00	0.00	0.00	2.01
812	854	0.103937	CCAAATGGTGGCGTGTTTGT	59.896	50.000	0.00	0.00	41.72	2.83
927	977	2.883386	AGGCTCATATTTGCTAGCTTGC	59.117	45.455	17.23	13.56	35.30	4.01
943	995	6.238184	GCTAGCTTGCAAACTGAATTTTTGTT	60.238	34.615	15.53	0.00	36.50	2.83
1041	1094	0.682209	AAGTTAGCCATGGCCAGCTG	60.682	55.000	33.14	14.01	43.17	4.24
1203	1256	4.703093	TGGTTTATCAATTTCTTCCCGGAC	59.297	41.667	0.73	0.00	0.00	4.79
1350	3730	9.793252	GCACAATTAACTAAATGTGATGAGATT	57.207	29.630	17.79	0.00	32.70	2.40
1409	3789	3.214328	ACTTCAGATTCGTTGCCAAAGT	58.786	40.909	0.00	0.00	0.00	2.66
1436	3816	0.729116	AAATCATCGTCGCAAGCCAG	59.271	50.000	0.00	0.00	37.18	4.85
1492	3872	3.071479	GTGATAAAAGAACCTCGCACCA	58.929	45.455	0.00	0.00	0.00	4.17
1696	4076	0.868406	GGAGAAGGAAACACACTGCG	59.132	55.000	0.00	0.00	0.00	5.18
1714	4094	4.095410	TGCGTCAAAATTGATGACATCC	57.905	40.909	17.32	10.49	45.90	3.51
1731	4111	4.739793	ACATCCACCCTGAAATCTTTGAA	58.260	39.130	0.00	0.00	0.00	2.69
1755	4135	7.416964	AGCTCTTCTTCACTTCATATACACT	57.583	36.000	0.00	0.00	0.00	3.55
1856	4236	7.552687	TCGATATGGATTGGATAGGTTAAATGC	59.447	37.037	0.00	0.00	0.00	3.56
1857	4237	7.336679	CGATATGGATTGGATAGGTTAAATGCA	59.663	37.037	0.00	0.00	35.30	3.96
1878	4258	5.982516	TGCAATGTGTGAAAGTAAATTGTCC	59.017	36.000	0.00	0.00	0.00	4.02
1905	4285	0.531974	TTGACGTGGAGACTGTTGCC	60.532	55.000	0.00	0.00	0.00	4.52
1908	4288	3.642755	GTGGAGACTGTTGCCACG	58.357	61.111	14.45	0.00	42.20	4.94
1962	4348	2.095053	GGATCTCAAAGAAGCTTGCGTC	59.905	50.000	2.10	0.44	0.00	5.19
2095	4859	2.419667	GCAGTGGCTAGTTCCGTTAAA	58.580	47.619	0.00	0.00	36.96	1.52
2806	5591	0.403271	AACACATGAAGCTCAGGCCT	59.597	50.000	0.00	0.00	39.73	5.19
2975	5772	1.656263	GTGCTCACGACGACGAACA	60.656	57.895	15.32	3.43	42.66	3.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
72	73	5.218139	CACAAGCTGGTTCAAGATTCTTTC	58.782	41.667	0.00	0.00	0.00	2.62
95	96	2.629051	CGTCCTCTTAACCATCCAACC	58.371	52.381	0.00	0.00	0.00	3.77
97	98	2.262637	ACCGTCCTCTTAACCATCCAA	58.737	47.619	0.00	0.00	0.00	3.53
99	100	3.029570	ACTACCGTCCTCTTAACCATCC	58.970	50.000	0.00	0.00	0.00	3.51
100	101	6.402456	AATACTACCGTCCTCTTAACCATC	57.598	41.667	0.00	0.00	0.00	3.51
101	102	5.303845	GGAATACTACCGTCCTCTTAACCAT	59.696	44.000	0.00	0.00	0.00	3.55
102	103	4.646492	GGAATACTACCGTCCTCTTAACCA	59.354	45.833	0.00	0.00	0.00	3.67
103	104	4.038522	GGGAATACTACCGTCCTCTTAACC	59.961	50.000	0.00	0.00	0.00	2.85
104	105	4.646492	TGGGAATACTACCGTCCTCTTAAC	59.354	45.833	0.00	0.00	0.00	2.01
105	106	4.870636	TGGGAATACTACCGTCCTCTTAA	58.129	43.478	0.00	0.00	0.00	1.85
106	107	4.467769	CTGGGAATACTACCGTCCTCTTA	58.532	47.826	0.00	0.00	0.00	2.10
107	108	3.297736	CTGGGAATACTACCGTCCTCTT	58.702	50.000	0.00	0.00	0.00	2.85
108	109	2.946785	CTGGGAATACTACCGTCCTCT	58.053	52.381	0.00	0.00	0.00	3.69
112	113	0.391966	GGGCTGGGAATACTACCGTC	59.608	60.000	0.00	0.00	0.00	4.79
113	114	0.325860	TGGGCTGGGAATACTACCGT	60.326	55.000	0.00	0.00	0.00	4.83
115	116	0.765510	CCTGGGCTGGGAATACTACC	59.234	60.000	0.00	0.00	0.00	3.18
128	129	1.671379	GACTTGAACCGTCCTGGGC	60.671	63.158	0.00	0.00	44.64	5.36
146	147	4.101585	TGACCATCAATGTCTAAGGCTAGG	59.898	45.833	0.00	0.00	0.00	3.02
177	178	5.253330	TCGCTGGAAGACCTGAAATAAAAT	58.747	37.500	0.00	0.00	37.31	1.82
190	194	0.796312	GAACGCAAATCGCTGGAAGA	59.204	50.000	0.00	0.00	43.23	2.87
201	205	2.045561	TTTCTCCCACTGAACGCAAA	57.954	45.000	0.00	0.00	0.00	3.68
202	206	1.673920	GTTTTCTCCCACTGAACGCAA	59.326	47.619	0.00	0.00	0.00	4.85
286	298	5.835113	AACACAGTACAGAAGCAAACATT	57.165	34.783	0.00	0.00	0.00	2.71
322	334	9.397280	GGCCTTGTTCTCTAGAAAACTATTATT	57.603	33.333	10.22	0.00	35.58	1.40
324	336	7.336396	GGGCCTTGTTCTCTAGAAAACTATTA	58.664	38.462	10.22	0.00	35.58	0.98
325	337	6.181190	GGGCCTTGTTCTCTAGAAAACTATT	58.819	40.000	10.22	0.00	35.58	1.73
328	340	3.244946	GGGGCCTTGTTCTCTAGAAAACT	60.245	47.826	10.22	0.00	35.58	2.66
374	386	4.401519	CAGTGAAATCAGCCCATGAGAAAT	59.598	41.667	0.00	0.00	42.53	2.17
458	474	3.565063	GGGACTACCTTGTCGACTAGATC	59.435	52.174	25.55	16.54	37.81	2.75
459	475	3.553904	GGGACTACCTTGTCGACTAGAT	58.446	50.000	25.55	13.66	37.81	1.98
812	854	9.676861	AATCTGATAACAATGAGATCTCAACAA	57.323	29.630	28.40	13.10	43.58	2.83
927	977	9.586435	AACTTCCTCTAACAAAAATTCAGTTTG	57.414	29.630	0.54	0.54	40.95	2.93
936	986	6.038271	GCAGACAGAACTTCCTCTAACAAAAA	59.962	38.462	0.00	0.00	0.00	1.94
943	995	3.191581	CGAAGCAGACAGAACTTCCTCTA	59.808	47.826	0.00	0.00	37.17	2.43
1041	1094	0.392998	ATGTGGACGATGTCTTGGGC	60.393	55.000	0.00	0.00	32.47	5.36
1203	1256	1.742768	GTAGTCTGCCATCCTCCCG	59.257	63.158	0.00	0.00	0.00	5.14
1350	3730	4.290711	TGCTGAGGAAAAGACATGATCA	57.709	40.909	0.00	0.00	0.00	2.92
1409	3789	3.063485	TGCGACGATGATTTCAGTTTCA	58.937	40.909	0.00	0.00	0.00	2.69
1436	3816	3.365364	GCGTATAATCAAGGAGCCATTGC	60.365	47.826	0.00	0.00	37.95	3.56
1445	3825	5.005779	GTGAGAACACAGCGTATAATCAAGG	59.994	44.000	0.00	0.00	45.32	3.61
1492	3872	5.112129	ACAACAGTGTTCCTCTTAACCTT	57.888	39.130	5.27	0.00	32.58	3.50
1539	3919	1.361204	TCCACATTTGGGAGAGCTGA	58.639	50.000	0.00	0.00	44.11	4.26
1547	3927	0.826062	GCCATCCTTCCACATTTGGG	59.174	55.000	0.00	0.00	44.11	4.12
1666	4046	4.202315	TGTTTCCTTCTCCTTCATCGAACA	60.202	41.667	0.00	0.00	0.00	3.18
1669	4049	3.323691	TGTGTTTCCTTCTCCTTCATCGA	59.676	43.478	0.00	0.00	0.00	3.59
1696	4076	4.463891	AGGGTGGATGTCATCAATTTTGAC	59.536	41.667	14.72	10.16	43.04	3.18
1714	4094	4.077822	AGAGCTTCAAAGATTTCAGGGTG	58.922	43.478	0.00	0.00	0.00	4.61
1731	4111	7.123397	TCAGTGTATATGAAGTGAAGAAGAGCT	59.877	37.037	0.00	0.00	0.00	4.09
1755	4135	3.256879	GCTCATCGACTATCAGGGAATCA	59.743	47.826	0.00	0.00	0.00	2.57
1856	4236	6.434596	TCGGACAATTTACTTTCACACATTG	58.565	36.000	0.00	0.00	0.00	2.82
1857	4237	6.262273	ACTCGGACAATTTACTTTCACACATT	59.738	34.615	0.00	0.00	0.00	2.71
1878	4258	0.388520	TCTCCACGTCAATGCACTCG	60.389	55.000	0.00	0.00	0.00	4.18
1905	4285	3.667960	GCTCTGCTAAAACCAATGTCGTG	60.668	47.826	0.00	0.00	0.00	4.35
1908	4288	4.229876	GTTGCTCTGCTAAAACCAATGTC	58.770	43.478	0.00	0.00	0.00	3.06
1962	4348	0.174845	TCCGTGGAGCCATAAACTCG	59.825	55.000	0.00	0.00	34.87	4.18
2095	4859	5.372343	TGCACATATGATACCTTGACCTT	57.628	39.130	10.38	0.00	0.00	3.50
2695	5473	4.331968	TGTTCAAGACCAAGTTGTGAACT	58.668	39.130	25.32	9.36	45.29	3.01
2806	5591	1.302192	GAAGTGGGTGGCGCTACAA	60.302	57.895	25.79	10.35	0.00	2.41
2975	5772	0.043334	AGGCTGGTATGGAGGACAGT	59.957	55.000	0.00	0.00	33.62	3.55

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.