AutoCloner

Multiple sequence alignment - TraesCS2A01G348700

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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	TraesCS2A01G348700	chr2A	100.000	5536	0	0	1	5536	587440559	587446094	0.000000e+00	10224.0
1	TraesCS2A01G348700	chr2A	94.212	311	13	4	3375	3685	210063194	210062889	2.330000e-128	470.0
2	TraesCS2A01G348700	chr2A	80.925	173	30	3	2471	2643	723642141	723641972	3.480000e-27	134.0
3	TraesCS2A01G348700	chr2A	80.952	126	18	5	42	162	542761938	542761814	1.640000e-15	95.3
4	TraesCS2A01G348700	chr2B	90.923	2578	156	36	850	3380	523262985	523265531	0.000000e+00	3393.0
5	TraesCS2A01G348700	chr2B	89.439	1231	63	25	3768	4980	523265583	523266764	0.000000e+00	1491.0
6	TraesCS2A01G348700	chr2B	85.795	176	17	3	5209	5378	523266763	523266936	4.410000e-41	180.0
7	TraesCS2A01G348700	chr2D	92.004	988	51	8	3669	4645	445188705	445189675	0.000000e+00	1362.0
8	TraesCS2A01G348700	chr2D	84.094	1446	122	44	249	1630	445185326	445186727	0.000000e+00	1297.0
9	TraesCS2A01G348700	chr2D	87.759	1062	96	18	2344	3398	445187578	445188612	0.000000e+00	1210.0
10	TraesCS2A01G348700	chr2D	92.269	401	19	5	1893	2292	445187089	445187478	4.840000e-155	558.0
11	TraesCS2A01G348700	chr2D	93.269	312	19	2	3376	3687	46936945	46936636	5.050000e-125	459.0
12	TraesCS2A01G348700	chr2D	88.426	216	23	2	1634	1849	445186882	445187095	5.500000e-65	259.0
13	TraesCS2A01G348700	chr2D	86.026	229	25	5	17	244	445185053	445185275	7.170000e-59	239.0
14	TraesCS2A01G348700	chr2D	85.333	150	6	3	5211	5355	445190428	445190566	2.080000e-29	141.0
15	TraesCS2A01G348700	chr3D	95.779	308	12	1	3378	3685	481230418	481230112	3.850000e-136	496.0
16	TraesCS2A01G348700	chr3D	94.175	309	17	1	3379	3687	472882180	472881873	2.330000e-128	470.0
17	TraesCS2A01G348700	chr3D	90.000	130	13	0	5063	5192	475870017	475869888	9.540000e-38	169.0
18	TraesCS2A01G348700	chr1D	95.114	307	14	1	3378	3684	411905198	411904893	3.000000e-132	483.0
19	TraesCS2A01G348700	chr3A	94.771	306	15	1	3379	3684	340266223	340265919	5.020000e-130	475.0
20	TraesCS2A01G348700	chr3A	91.589	107	9	0	4980	5086	647888551	647888445	1.240000e-31	148.0
21	TraesCS2A01G348700	chr3A	82.081	173	28	3	2471	2643	127086637	127086468	1.610000e-30	145.0
22	TraesCS2A01G348700	chr3A	87.778	90	10	1	2471	2560	359362409	359362497	2.730000e-18	104.0
23	TraesCS2A01G348700	chr6B	94.463	307	16	1	3379	3685	460488473	460488778	6.490000e-129	472.0
24	TraesCS2A01G348700	chr6B	89.474	133	14	0	5060	5192	6344577	6344445	9.540000e-38	169.0
25	TraesCS2A01G348700	chr1A	94.194	310	16	2	3379	3688	285590329	285590022	6.490000e-129	472.0
26	TraesCS2A01G348700	chr1A	92.913	127	9	0	5066	5192	544457933	544457807	9.470000e-43	185.0
27	TraesCS2A01G348700	chr1A	94.792	96	5	0	4976	5071	517104203	517104108	3.450000e-32	150.0
28	TraesCS2A01G348700	chr5D	94.175	309	16	2	3378	3685	478597202	478597509	2.330000e-128	470.0
29	TraesCS2A01G348700	chr5D	83.007	153	17	7	2489	2637	66297134	66296987	4.500000e-26	130.0
30	TraesCS2A01G348700	chr5D	84.722	72	6	5	15	83	324318393	324318324	3.580000e-07	67.6
31	TraesCS2A01G348700	chr7A	91.473	129	11	0	5064	5192	508643062	508642934	1.580000e-40	178.0
32	TraesCS2A01G348700	chr7A	91.339	127	11	0	5066	5192	542632877	542632751	2.050000e-39	174.0
33	TraesCS2A01G348700	chr7A	90.625	128	12	0	5065	5192	37238878	37239005	2.650000e-38	171.0
34	TraesCS2A01G348700	chr7A	93.548	93	6	0	4978	5070	66251033	66250941	7.480000e-29	139.0
35	TraesCS2A01G348700	chr1B	81.034	232	35	7	4982	5211	434748717	434748493	5.700000e-40	176.0
36	TraesCS2A01G348700	chr5A	90.000	130	13	0	5066	5195	350567627	350567498	9.540000e-38	169.0
37	TraesCS2A01G348700	chr5A	89.062	128	14	0	5065	5192	6845547	6845674	5.740000e-35	159.0
38	TraesCS2A01G348700	chr5A	91.304	115	10	0	4980	5094	428970091	428970205	2.060000e-34	158.0
39	TraesCS2A01G348700	chr5A	95.699	93	4	0	4979	5071	27736990	27736898	3.450000e-32	150.0
40	TraesCS2A01G348700	chr5A	94.737	95	5	0	4977	5071	473849426	473849520	1.240000e-31	148.0
41	TraesCS2A01G348700	chr3B	89.844	128	13	0	5065	5192	620182399	620182272	1.230000e-36	165.0
42	TraesCS2A01G348700	chr4A	96.774	93	3	0	4979	5071	570912987	570912895	7.430000e-34	156.0
43	TraesCS2A01G348700	chr6A	87.931	116	13	1	4979	5094	598156651	598156537	9.670000e-28	135.0
44	TraesCS2A01G348700	chr4D	78.916	166	30	5	17	179	385224479	385224642	2.110000e-19	108.0
45	TraesCS2A01G348700	chr4B	81.982	111	18	2	1	110	4185644	4185753	5.900000e-15	93.5

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	TraesCS2A01G348700	chr2A	587440559	587446094	5535	False	10224.000000	10224	100.000000	1	5536	1	chr2A.!!$F1	5535
1	TraesCS2A01G348700	chr2B	523262985	523266936	3951	False	1688.000000	3393	88.719000	850	5378	3	chr2B.!!$F1	4528
2	TraesCS2A01G348700	chr2D	445185053	445190566	5513	False	723.714286	1362	87.987286	17	5355	7	chr2D.!!$F1	5338

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	Hairpin	End Stability	Orientation
144	145	0.179067	TTTCGAGAGGCACAACCGTT	60.179	50.0	46.52	4.44	F
995	1092	0.649992	ATCCAATCCTCCTCTCCCCA	59.350	55.0	0.00	4.96	F
1351	1456	0.243636	CCTTCACAATTTCCGGGTGC	59.756	55.0	32.69	5.01	F
2036	2308	1.075601	AACCTCCAGATTTGGCTCCA	58.924	50.0	44.63	3.86	F
3402	3730	0.172803	CCTCCGTCCGGTAAAGAGTG	59.827	60.0	36.47	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1065	1168	0.259356	AGGACGGGAAGAGGAGTAGG	59.741	60.0	0.00	0.00	0.00	3.18	R
1817	2089	0.465460	GAATAGGCCGGCACAATCCA	60.465	55.0	30.85	4.43	0.00	3.41	R
3043	3367	0.402121	AGTCCACAAGGAGAAAGGGC	59.598	55.0	0.00	0.00	46.92	5.19	R
3495	3823	0.034089	GCACTTAGCTCATTGGGGGT	60.034	55.0	0.00	0.00	41.15	4.95	R
5360	6269	0.246086	GGCAATCATGGGTCGCAAAA	59.754	50.0	0.00	0.00	0.00	2.44	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
39	40	5.350504	TTTTTCCTTTTCATGAAGCACCA	57.649	34.783	8.41	0.00	4.17
74	75	1.615392	GAAGCAAACCTGTGCCTTCAT	59.385	47.619	0.00	46.14	2.57
141	142	1.266989	CCTTTTTCGAGAGGCACAACC	59.733	52.381	0.00	39.61	3.77
144	145	0.179067	TTTCGAGAGGCACAACCGTT	60.179	50.000	0.00	46.52	4.44
154	155	1.948104	CACAACCGTTCCTCTTGTGA	58.052	50.000	4.11	45.06	3.58
157	158	3.127895	CACAACCGTTCCTCTTGTGAAAA	59.872	43.478	4.11	45.06	2.29
162	163	4.102649	CCGTTCCTCTTGTGAAAACAAAC	58.897	43.478	0.00	0.00	2.93
164	165	4.430007	GTTCCTCTTGTGAAAACAAACCC	58.570	43.478	0.00	0.00	4.11
196	197	5.006165	CACGAGAAACAAATCTATGCCTCTC	59.994	44.000	0.00	32.22	3.20
197	198	4.509600	CGAGAAACAAATCTATGCCTCTCC	59.490	45.833	0.00	32.03	3.71
198	199	5.679601	GAGAAACAAATCTATGCCTCTCCT	58.320	41.667	0.00	30.61	3.69
200	201	5.190528	AGAAACAAATCTATGCCTCTCCTGA	59.809	40.000	0.00	0.00	3.86
201	202	5.441718	AACAAATCTATGCCTCTCCTGAA	57.558	39.130	0.00	0.00	3.02
202	203	5.441718	ACAAATCTATGCCTCTCCTGAAA	57.558	39.130	0.00	0.00	2.69
203	204	5.435291	ACAAATCTATGCCTCTCCTGAAAG	58.565	41.667	0.00	0.00	2.62
204	205	5.190528	ACAAATCTATGCCTCTCCTGAAAGA	59.809	40.000	0.00	34.07	2.52
245	246	5.349824	CTCTTTTTGAGAGGCACAACTAC	57.650	43.478	0.00	46.77	2.73
246	247	4.776349	TCTTTTTGAGAGGCACAACTACA	58.224	39.130	0.00	0.00	2.74
247	248	5.376625	TCTTTTTGAGAGGCACAACTACAT	58.623	37.500	0.00	0.00	2.29
254	301	1.134965	AGGCACAACTACATCTCTCGC	60.135	52.381	0.00	0.00	5.03
313	362	7.929941	TTTTTGTCCAAAACCTAAGCAAAAT	57.070	28.000	4.75	39.70	1.82
317	366	4.022676	GTCCAAAACCTAAGCAAAATCGGA	60.023	41.667	0.00	0.00	4.55
319	368	4.261825	CCAAAACCTAAGCAAAATCGGACA	60.262	41.667	0.00	0.00	4.02
326	375	5.402270	CCTAAGCAAAATCGGACAAAAACTG	59.598	40.000	0.00	0.00	3.16
335	384	2.857748	CGGACAAAAACTGAAAAGCCAC	59.142	45.455	0.00	0.00	5.01

Showing 1 to 25 of 581 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
38	39	1.572085	CTTCCGCAAGAGGCACAGTG	61.572	60.000	0.00	0.00	45.17	3.66
39	40	1.302033	CTTCCGCAAGAGGCACAGT	60.302	57.895	0.00	0.00	45.17	3.55
74	75	4.525874	TGAGAGACAGAGATTTGCTTCTCA	59.474	41.667	12.37	0.00	43.82	3.27
86	87	3.924918	TTTCTTCCGTGAGAGACAGAG	57.075	47.619	0.00	0.00	0.00	3.35
109	110	6.293244	CCTCTCGAAAAAGGAAAATACACGTT	60.293	38.462	2.69	0.00	34.35	3.99
110	111	5.178809	CCTCTCGAAAAAGGAAAATACACGT	59.821	40.000	2.69	0.00	34.35	4.49
111	112	5.618561	CCTCTCGAAAAAGGAAAATACACG	58.381	41.667	2.69	0.00	34.35	4.49
112	113	5.048991	TGCCTCTCGAAAAAGGAAAATACAC	60.049	40.000	11.34	0.00	34.35	2.90
113	114	5.048991	GTGCCTCTCGAAAAAGGAAAATACA	60.049	40.000	11.34	0.00	34.35	2.29
114	115	5.048991	TGTGCCTCTCGAAAAAGGAAAATAC	60.049	40.000	11.34	3.92	34.35	1.89
115	116	5.067273	TGTGCCTCTCGAAAAAGGAAAATA	58.933	37.500	11.34	0.00	34.35	1.40
116	117	3.888930	TGTGCCTCTCGAAAAAGGAAAAT	59.111	39.130	11.34	0.00	34.35	1.82
126	127	0.599204	GAACGGTTGTGCCTCTCGAA	60.599	55.000	0.00	0.00	34.25	3.71
141	142	4.102649	GGTTTGTTTTCACAAGAGGAACG	58.897	43.478	0.00	0.00	43.92	3.95
144	145	2.685897	CGGGTTTGTTTTCACAAGAGGA	59.314	45.455	0.00	0.00	43.92	3.71
154	155	0.684805	TGGAGGCACGGGTTTGTTTT	60.685	50.000	0.00	0.00	0.00	2.43
157	158	2.203294	GTGGAGGCACGGGTTTGT	60.203	61.111	0.00	0.00	0.00	2.83
180	181	5.190528	TCTTTCAGGAGAGGCATAGATTTGT	59.809	40.000	0.00	0.00	0.00	2.83
226	227	5.376625	AGATGTAGTTGTGCCTCTCAAAAA	58.623	37.500	0.00	0.00	0.00	1.94
230	231	3.435275	AGAGATGTAGTTGTGCCTCTCA	58.565	45.455	0.00	0.00	34.06	3.27
231	232	3.488384	CGAGAGATGTAGTTGTGCCTCTC	60.488	52.174	0.00	0.00	41.71	3.20
308	357	6.184706	GCTTTTCAGTTTTTGTCCGATTTTG	58.815	36.000	0.00	0.00	0.00	2.44
311	360	4.142049	TGGCTTTTCAGTTTTTGTCCGATT	60.142	37.500	0.00	0.00	0.00	3.34
313	362	2.755655	TGGCTTTTCAGTTTTTGTCCGA	59.244	40.909	0.00	0.00	0.00	4.55
317	366	2.093181	GGGGTGGCTTTTCAGTTTTTGT	60.093	45.455	0.00	0.00	0.00	2.83

Showing 1 to 25 of 599 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.