AutoCloner

Multiple sequence alignment - TraesCS3A01G030300

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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	TraesCS3A01G030300	chr3A	100.000	2734	0	0	1	2734	15998065	15995332	0.000000e+00	5049.0
1	TraesCS3A01G030300	chr3A	85.895	1028	87	34	915	1898	16072034	16073047	0.000000e+00	1042.0
2	TraesCS3A01G030300	chr3A	83.527	431	39	17	1472	1876	16265804	16265380	9.240000e-100	374.0
3	TraesCS3A01G030300	chr3A	81.585	467	67	7	1908	2355	16265323	16264857	4.300000e-98	368.0
4	TraesCS3A01G030300	chr3A	83.459	133	21	1	2224	2355	17357020	17356888	3.700000e-24	122.0
5	TraesCS3A01G030300	chr3B	88.770	1772	98	35	672	2357	12588668	12590424	0.000000e+00	2076.0
6	TraesCS3A01G030300	chr3B	92.579	822	43	13	1091	1898	13238841	13238024	0.000000e+00	1164.0
7	TraesCS3A01G030300	chr3B	83.894	1248	127	46	713	1898	13243933	13242698	0.000000e+00	1123.0
8	TraesCS3A01G030300	chr3B	92.535	777	42	11	1091	1855	13173219	13172447	0.000000e+00	1099.0
9	TraesCS3A01G030300	chr3B	91.632	478	23	7	1898	2358	13170961	13170484	0.000000e+00	645.0
10	TraesCS3A01G030300	chr3B	89.437	426	22	8	672	1084	13239288	13238873	1.450000e-142	516.0
11	TraesCS3A01G030300	chr3B	90.127	314	26	3	2422	2733	12590575	12590885	1.180000e-108	403.0
12	TraesCS3A01G030300	chr3B	86.364	374	37	7	713	1084	13443068	13443429	1.970000e-106	396.0
13	TraesCS3A01G030300	chr3B	88.502	287	29	4	2427	2710	13188035	13187750	7.250000e-91	344.0
14	TraesCS3A01G030300	chr3B	95.477	199	9	0	2159	2357	13188621	13188423	4.390000e-83	318.0
15	TraesCS3A01G030300	chr3B	83.801	321	20	8	672	978	13240446	13240144	2.680000e-70	276.0
16	TraesCS3A01G030300	chr3B	91.160	181	14	2	1	180	178980727	178980548	7.560000e-61	244.0
17	TraesCS3A01G030300	chr3B	94.309	123	7	0	2422	2544	13170264	13170142	3.590000e-44	189.0
18	TraesCS3A01G030300	chr3B	95.238	63	3	0	2247	2309	13408382	13408444	1.730000e-17	100.0
19	TraesCS3A01G030300	chr3D	92.937	1246	48	14	669	1898	5411558	5412779	0.000000e+00	1777.0
20	TraesCS3A01G030300	chr3D	82.969	1098	127	33	1091	2140	41216293	41217378	0.000000e+00	937.0
21	TraesCS3A01G030300	chr3D	85.317	647	73	14	1091	1722	41208167	41208806	0.000000e+00	649.0
22	TraesCS3A01G030300	chr3D	82.444	581	101	1	1161	1740	5387794	5387214	8.740000e-140	507.0
23	TraesCS3A01G030300	chr3D	86.093	453	38	11	1899	2328	5412811	5413261	5.330000e-127	464.0
24	TraesCS3A01G030300	chr3D	91.374	313	26	1	2422	2733	5413488	5413800	7.000000e-116	427.0
25	TraesCS3A01G030300	chr3D	91.322	242	11	4	844	1085	41207903	41208134	3.400000e-84	322.0
26	TraesCS3A01G030300	chr3D	91.220	205	10	4	874	1076	41216052	41216250	3.470000e-69	272.0
27	TraesCS3A01G030300	chr3D	80.319	376	48	14	1908	2260	5381067	5380695	7.510000e-66	261.0
28	TraesCS3A01G030300	chr3D	98.333	60	1	0	2352	2411	380271863	380271922	3.720000e-19	106.0
29	TraesCS3A01G030300	chr3D	93.939	66	3	1	1808	1872	5381195	5381130	6.230000e-17	99.0
30	TraesCS3A01G030300	chr1D	87.444	669	50	11	1	640	458444648	458445311	0.000000e+00	739.0
31	TraesCS3A01G030300	chr1D	89.960	498	41	7	175	667	160828232	160828725	3.840000e-178	634.0
32	TraesCS3A01G030300	chr4A	86.976	668	56	14	1	640	593091753	593091089	0.000000e+00	723.0
33	TraesCS3A01G030300	chr4A	86.527	668	59	14	1	640	592811492	592810828	0.000000e+00	706.0
34	TraesCS3A01G030300	chr4A	86.377	668	59	15	1	640	592525198	592524535	0.000000e+00	701.0
35	TraesCS3A01G030300	chr5A	87.029	663	57	15	1	643	619464715	619464062	0.000000e+00	721.0
36	TraesCS3A01G030300	chr5A	94.118	51	2	1	2674	2723	591368540	591368490	2.920000e-10	76.8
37	TraesCS3A01G030300	chr2A	86.686	676	56	13	1	648	629992531	629993200	0.000000e+00	719.0
38	TraesCS3A01G030300	chr6D	86.091	683	63	18	1	657	92486	93162	0.000000e+00	706.0
39	TraesCS3A01G030300	chr6D	90.812	468	36	5	175	640	438824741	438825203	1.080000e-173	619.0
40	TraesCS3A01G030300	chrUn	86.957	598	47	14	1	570	395014146	395013552	0.000000e+00	643.0
41	TraesCS3A01G030300	chrUn	81.585	467	67	8	1908	2355	296442513	296442979	4.300000e-98	368.0
42	TraesCS3A01G030300	chrUn	81.585	467	67	8	1908	2355	296447567	296448033	4.300000e-98	368.0
43	TraesCS3A01G030300	chrUn	89.925	268	24	2	713	978	36175385	36175651	2.610000e-90	342.0
44	TraesCS3A01G030300	chrUn	82.831	332	25	17	1571	1876	296442131	296442456	4.490000e-68	268.0
45	TraesCS3A01G030300	chrUn	82.831	332	25	17	1571	1876	296447185	296447510	4.490000e-68	268.0
46	TraesCS3A01G030300	chr2B	84.501	671	61	25	1	643	440523	439868	8.310000e-175	623.0
47	TraesCS3A01G030300	chr2B	84.862	436	35	9	1	408	164898427	164898859	7.050000e-111	411.0
48	TraesCS3A01G030300	chr2B	92.754	69	4	1	2344	2412	722081364	722081431	6.230000e-17	99.0
49	TraesCS3A01G030300	chr7B	89.200	500	46	6	175	673	627992652	627992160	3.870000e-173	617.0
50	TraesCS3A01G030300	chr7B	90.558	466	43	1	175	640	509850168	509850632	1.390000e-172	616.0
51	TraesCS3A01G030300	chr4D	90.773	466	38	3	175	640	404060267	404060727	3.870000e-173	617.0
52	TraesCS3A01G030300	chr4B	84.006	669	71	20	1	640	486688990	486688329	6.470000e-171	610.0
53	TraesCS3A01G030300	chr5D	88.469	503	51	6	175	673	35659085	35658586	3.900000e-168	601.0
54	TraesCS3A01G030300	chr5D	91.667	72	5	1	2343	2414	45177947	45178017	6.230000e-17	99.0
55	TraesCS3A01G030300	chr6A	96.721	61	2	0	2355	2415	199990863	199990923	4.820000e-18	102.0
56	TraesCS3A01G030300	chr6B	90.667	75	5	2	2339	2412	550782259	550782332	6.230000e-17	99.0
57	TraesCS3A01G030300	chr6B	90.541	74	5	2	2339	2411	550587857	550587929	2.240000e-16	97.1
58	TraesCS3A01G030300	chr6B	90.541	74	5	2	2339	2411	550803810	550803882	2.240000e-16	97.1
59	TraesCS3A01G030300	chr1A	90.541	74	5	2	2341	2412	117977853	117977926	2.240000e-16	97.1
60	TraesCS3A01G030300	chr7D	80.556	108	15	6	2308	2412	530766796	530766900	8.120000e-11	78.7

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	TraesCS3A01G030300	chr3A	15995332	15998065	2733	True	5049.000000	5049	100.000000	1	2734	1	chr3A.!!$R1	2733
1	TraesCS3A01G030300	chr3A	16072034	16073047	1013	False	1042.000000	1042	85.895000	915	1898	1	chr3A.!!$F1	983
2	TraesCS3A01G030300	chr3A	16264857	16265804	947	True	371.000000	374	82.556000	1472	2355	2	chr3A.!!$R3	883
3	TraesCS3A01G030300	chr3B	12588668	12590885	2217	False	1239.500000	2076	89.448500	672	2733	2	chr3B.!!$F3	2061
4	TraesCS3A01G030300	chr3B	13238024	13243933	5909	True	769.750000	1164	87.427750	672	1898	4	chr3B.!!$R4	1226
5	TraesCS3A01G030300	chr3B	13170142	13173219	3077	True	644.333333	1099	92.825333	1091	2544	3	chr3B.!!$R2	1453
6	TraesCS3A01G030300	chr3B	13187750	13188621	871	True	331.000000	344	91.989500	2159	2710	2	chr3B.!!$R3	551
7	TraesCS3A01G030300	chr3D	5411558	5413800	2242	False	889.333333	1777	90.134667	669	2733	3	chr3D.!!$F2	2064
8	TraesCS3A01G030300	chr3D	41216052	41217378	1326	False	604.500000	937	87.094500	874	2140	2	chr3D.!!$F4	1266
9	TraesCS3A01G030300	chr3D	5387214	5387794	580	True	507.000000	507	82.444000	1161	1740	1	chr3D.!!$R1	579
10	TraesCS3A01G030300	chr3D	41207903	41208806	903	False	485.500000	649	88.319500	844	1722	2	chr3D.!!$F3	878
11	TraesCS3A01G030300	chr1D	458444648	458445311	663	False	739.000000	739	87.444000	1	640	1	chr1D.!!$F2	639
12	TraesCS3A01G030300	chr4A	593091089	593091753	664	True	723.000000	723	86.976000	1	640	1	chr4A.!!$R3	639
13	TraesCS3A01G030300	chr4A	592810828	592811492	664	True	706.000000	706	86.527000	1	640	1	chr4A.!!$R2	639
14	TraesCS3A01G030300	chr4A	592524535	592525198	663	True	701.000000	701	86.377000	1	640	1	chr4A.!!$R1	639
15	TraesCS3A01G030300	chr5A	619464062	619464715	653	True	721.000000	721	87.029000	1	643	1	chr5A.!!$R2	642
16	TraesCS3A01G030300	chr2A	629992531	629993200	669	False	719.000000	719	86.686000	1	648	1	chr2A.!!$F1	647
17	TraesCS3A01G030300	chr6D	92486	93162	676	False	706.000000	706	86.091000	1	657	1	chr6D.!!$F1	656
18	TraesCS3A01G030300	chrUn	395013552	395014146	594	True	643.000000	643	86.957000	1	570	1	chrUn.!!$R1	569
19	TraesCS3A01G030300	chrUn	296442131	296442979	848	False	318.000000	368	82.208000	1571	2355	2	chrUn.!!$F2	784
20	TraesCS3A01G030300	chrUn	296447185	296448033	848	False	318.000000	368	82.208000	1571	2355	2	chrUn.!!$F3	784
21	TraesCS3A01G030300	chr2B	439868	440523	655	True	623.000000	623	84.501000	1	643	1	chr2B.!!$R1	642
22	TraesCS3A01G030300	chr4B	486688329	486688990	661	True	610.000000	610	84.006000	1	640	1	chr4B.!!$R1	639

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
721	4705	2.613026	TTTTTGTGAGACCGAGCAGA	57.387	45.0	0.0	0.0	0.0	4.26	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2418	8051	0.106708	AGCACCATAGTGGGCGTATG	59.893	55.0	0.52	0.0	43.37	2.39	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	Self end TH	Hairpin	End Stability
68	69	6.271159	TGCCATACATGTCATAGGTATTGGTA	59.729	38.462	0.00	0.00	34.25	3.25
85	86	7.226720	GGTATTGGTACCTGTTTCATCACTATG	59.773	40.741	14.36	0.00	45.78	2.23
136	138	4.546829	ATTTTTGTCATGCATGCCTCTT	57.453	36.364	22.25	0.51	0.00	2.85
237	267	8.682936	ATTTCTTTTATAGCGGACATCTCATT	57.317	30.769	0.00	0.00	0.00	2.57
252	282	7.093333	GGACATCTCATTTTTATTGGGTCCTTT	60.093	37.037	0.00	0.00	38.38	3.11
293	323	5.221244	GCATGTCCTTATTTATTGGGTGTCC	60.221	44.000	0.00	0.00	0.00	4.02
691	3508	4.934356	AGATTTTGAGATGCCCTAAACCA	58.066	39.130	0.00	0.00	0.00	3.67
721	4705	2.613026	TTTTTGTGAGACCGAGCAGA	57.387	45.000	0.00	0.00	0.00	4.26
740	4724	7.148573	CGAGCAGATTATACGCATAAAGGAAAT	60.149	37.037	0.00	0.00	30.50	2.17
885	4870	3.368116	CGAGTTCGGGTTGGACTTCTATT	60.368	47.826	0.00	0.00	35.37	1.73
1119	5175	7.208777	TCACGAATCGATCTTAGTACTACTCT	58.791	38.462	10.55	0.00	0.00	3.24
1302	5373	3.655486	ACCACATCGTTGTATCGTGAAA	58.345	40.909	0.00	0.00	33.76	2.69
1415	5486	0.387878	GCCTCACCATCGATAGCTCG	60.388	60.000	0.00	0.00	46.41	5.03
1575	5646	5.609088	CGTTAAGGAAACATCGACAAGAAG	58.391	41.667	0.00	0.00	38.03	2.85
1651	5723	2.306805	TCTTTGACACCATCCTGCAGAT	59.693	45.455	17.39	3.92	34.66	2.90
1779	5853	5.480422	TCTGTTCTAGGATTGTTGCTGACTA	59.520	40.000	0.00	0.00	0.00	2.59
1919	7482	3.907474	TCCTTCTGTGTTAGGTGGATTCA	59.093	43.478	0.00	0.00	33.15	2.57
1937	7500	1.400142	TCAGAAAACAATATGGCCGCG	59.600	47.619	0.00	0.00	0.00	6.46
1987	7550	1.238439	CTGGATTTGCTGTCAACGGT	58.762	50.000	0.00	0.00	30.75	4.83
2024	7592	8.789762	GGTTTACTTGTATGTACATTCCAAGTT	58.210	33.333	34.45	25.31	39.85	2.66
2043	7611	3.749609	AGTTATTTACCACCTTCACGCAC	59.250	43.478	0.00	0.00	0.00	5.34
2044	7612	1.153353	ATTTACCACCTTCACGCACG	58.847	50.000	0.00	0.00	0.00	5.34
2045	7613	0.179078	TTTACCACCTTCACGCACGT	60.179	50.000	0.00	0.00	0.00	4.49
2047	7615	0.672889	TACCACCTTCACGCACGTAA	59.327	50.000	0.00	0.00	0.00	3.18
2048	7616	0.034337	ACCACCTTCACGCACGTAAT	59.966	50.000	0.00	0.00	0.00	1.89

Showing 1 to 25 of 58 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
15	16	4.046286	AGTGATGAAATAGGGGCACAAA	57.954	40.909	0.00	0.00	0.00	2.83
252	282	7.669427	AGGACATGCATGACAAGAAATAAAAA	58.331	30.769	32.75	0.00	0.00	1.94
322	352	4.922206	ACACCTCAGCAAAATCAGGATTA	58.078	39.130	0.00	0.00	0.00	1.75
397	428	8.917088	ACTATTTAGGCAGCAATGTTAATCAAT	58.083	29.630	0.00	0.00	0.00	2.57
546	582	8.470805	ACCCGCAATACATATCAAATGTTTTTA	58.529	29.630	0.00	0.00	33.76	1.52
664	704	8.951243	GGTTTAGGGCATCTCAAAATCTATATC	58.049	37.037	0.00	0.00	0.00	1.63
665	705	8.448008	TGGTTTAGGGCATCTCAAAATCTATAT	58.552	33.333	0.00	0.00	0.00	0.86
666	706	7.811282	TGGTTTAGGGCATCTCAAAATCTATA	58.189	34.615	0.00	0.00	0.00	1.31
667	707	6.672593	TGGTTTAGGGCATCTCAAAATCTAT	58.327	36.000	0.00	0.00	0.00	1.98
721	4705	6.708949	ACCGACATTTCCTTTATGCGTATAAT	59.291	34.615	6.79	0.00	0.00	1.28
740	4724	0.752658	CCAGCATAGATCCACCGACA	59.247	55.000	0.00	0.00	0.00	4.35
885	4870	4.599041	AGCAAGGCTGATTGTGGTTATAA	58.401	39.130	0.00	0.00	37.57	0.98
1004	4992	4.100653	TGCTAGTCTCCTTCATCAATCCAG	59.899	45.833	0.00	0.00	0.00	3.86
1089	5140	8.928270	AGTACTAAGATCGATTCGTGAAATTT	57.072	30.769	5.89	0.00	0.00	1.82
1415	5486	8.090831	TGGATACTATGTCTGATAGTTTGCATC	58.909	37.037	0.00	0.00	36.38	3.91
1467	5538	2.088423	TGCCAAGTAAAATAGCCCACG	58.912	47.619	0.00	0.00	0.00	4.94
1575	5646	7.272037	TCAATAGTTGTTTCCTCCTTTTGTC	57.728	36.000	0.00	0.00	0.00	3.18
1651	5723	2.895404	ACTAGCCTTTTCACAGACGGTA	59.105	45.455	0.00	0.00	0.00	4.02
1788	5862	7.979786	AGGACTCTCAAGAAGGAATATGTAA	57.020	36.000	0.00	0.00	0.00	2.41
1789	5863	7.231722	GCTAGGACTCTCAAGAAGGAATATGTA	59.768	40.741	0.00	0.00	0.00	2.29
1790	5864	6.041523	GCTAGGACTCTCAAGAAGGAATATGT	59.958	42.308	0.00	0.00	0.00	2.29
1791	5865	6.041409	TGCTAGGACTCTCAAGAAGGAATATG	59.959	42.308	0.00	0.00	0.00	1.78
1793	5867	5.519808	TGCTAGGACTCTCAAGAAGGAATA	58.480	41.667	0.00	0.00	0.00	1.75
1795	5869	3.766591	CTGCTAGGACTCTCAAGAAGGAA	59.233	47.826	0.00	0.00	0.00	3.36
1796	5870	3.010696	TCTGCTAGGACTCTCAAGAAGGA	59.989	47.826	0.00	0.00	0.00	3.36

Showing 1 to 25 of 65 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.