AutoCloner

Multiple sequence alignment - TraesCS2D01G362100

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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	TraesCS2D01G362100	chr2D	100.000	5178	0	0	1	5178	468103977	468098800	0.000000e+00	9563.0
1	TraesCS2D01G362100	chr2D	81.606	386	61	8	4796	5172	591539744	591540128	1.400000e-80	311.0
2	TraesCS2D01G362100	chr2D	83.019	159	17	6	1	157	618282146	618281996	9.040000e-28	135.0
3	TraesCS2D01G362100	chr2D	84.112	107	4	3	4199	4305	467252357	467252264	1.990000e-14	91.6
4	TraesCS2D01G362100	chr2D	97.674	43	1	0	4414	4456	468099529	468099487	2.000000e-09	75.0
5	TraesCS2D01G362100	chr2D	97.674	43	1	0	4449	4491	468099564	468099522	2.000000e-09	75.0
6	TraesCS2D01G362100	chr2A	92.003	3889	192	47	490	4308	608036587	608032748	0.000000e+00	5349.0
7	TraesCS2D01G362100	chr2A	85.597	486	55	14	17	498	608037840	608037366	3.600000e-136	496.0
8	TraesCS2D01G362100	chr2A	81.118	519	87	9	4663	5172	726289157	726289673	6.240000e-109	405.0
9	TraesCS2D01G362100	chr2A	78.916	498	91	11	4683	5172	726222146	726222637	5.000000e-85	326.0
10	TraesCS2D01G362100	chr2A	84.906	159	14	6	1	157	749097841	749097691	8.980000e-33	152.0
11	TraesCS2D01G362100	chr2B	95.576	2871	104	7	874	3742	546590649	546587800	0.000000e+00	4577.0
12	TraesCS2D01G362100	chr2B	92.680	724	31	10	3742	4456	546587742	546587032	0.000000e+00	1024.0
13	TraesCS2D01G362100	chr2B	87.810	484	36	13	3	465	546591672	546591191	3.530000e-151	545.0
14	TraesCS2D01G362100	chr2B	91.237	388	34	0	4791	5178	546428321	546427934	3.550000e-146	529.0
15	TraesCS2D01G362100	chr2B	90.994	322	11	4	505	811	546590987	546590669	8.020000e-113	418.0
16	TraesCS2D01G362100	chr2B	80.228	526	80	16	4665	5172	35401045	35401564	1.760000e-99	374.0
17	TraesCS2D01G362100	chr2B	86.603	209	24	4	4443	4649	800263607	800263813	1.450000e-55	228.0
18	TraesCS2D01G362100	chr2B	77.841	176	22	9	400	562	156631991	156631820	5.520000e-15	93.5
19	TraesCS2D01G362100	chr7B	81.996	511	84	5	4669	5175	210802732	210802226	1.330000e-115	427.0
20	TraesCS2D01G362100	chr7B	79.902	204	38	2	4464	4664	210802975	210802772	4.180000e-31	147.0
21	TraesCS2D01G362100	chr4A	80.864	486	75	14	4701	5178	723493289	723492814	2.950000e-97	366.0
22	TraesCS2D01G362100	chr4A	77.622	286	45	5	4383	4665	726699337	726699068	6.940000e-34	156.0
23	TraesCS2D01G362100	chr3B	80.624	449	75	9	4728	5172	403402298	403402738	2.310000e-88	337.0
24	TraesCS2D01G362100	chr3B	79.845	129	20	4	3	128	748624182	748624057	7.140000e-14	89.8
25	TraesCS2D01G362100	chr6A	83.168	303	48	2	4804	5103	487208291	487208593	1.840000e-69	274.0
26	TraesCS2D01G362100	chr6A	83.158	95	11	4	4725	4817	305262913	305263004	1.200000e-11	82.4
27	TraesCS2D01G362100	chr5A	87.179	156	16	3	3	157	665778359	665778511	1.920000e-39	174.0
28	TraesCS2D01G362100	chr6D	87.805	123	12	3	3	125	32381959	32382078	1.940000e-29	141.0
29	TraesCS2D01G362100	chr6D	78.922	204	33	9	4464	4664	60299998	60300194	4.210000e-26	130.0
30	TraesCS2D01G362100	chr3D	85.827	127	15	3	3	129	382779301	382779178	1.170000e-26	132.0
31	TraesCS2D01G362100	chr1D	77.778	207	46	0	4458	4664	483699485	483699691	1.510000e-25	128.0
32	TraesCS2D01G362100	chr5B	80.892	157	21	9	3	157	129317695	129317844	1.180000e-21	115.0
33	TraesCS2D01G362100	chr1A	89.041	73	8	0	4465	4537	547580728	547580656	1.990000e-14	91.6
34	TraesCS2D01G362100	chr7A	85.135	74	11	0	4464	4537	215929686	215929613	5.560000e-10	76.8

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	TraesCS2D01G362100	chr2D	468098800	468103977	5177	True	9563.0	9563	100.000	1	5178	1	chr2D.!!$R2	5177
1	TraesCS2D01G362100	chr2A	608032748	608037840	5092	True	2922.5	5349	88.800	17	4308	2	chr2A.!!$R2	4291
2	TraesCS2D01G362100	chr2A	726289157	726289673	516	False	405.0	405	81.118	4663	5172	1	chr2A.!!$F2	509
3	TraesCS2D01G362100	chr2B	546587032	546591672	4640	True	1641.0	4577	91.765	3	4456	4	chr2B.!!$R3	4453
4	TraesCS2D01G362100	chr2B	35401045	35401564	519	False	374.0	374	80.228	4665	5172	1	chr2B.!!$F1	507
5	TraesCS2D01G362100	chr7B	210802226	210802975	749	True	287.0	427	80.949	4464	5175	2	chr7B.!!$R1	711

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
661	1495	0.099082	CTAGCGGCCTAGCGCTATAC	59.901	60.0	19.19	12.76	38.84	1.47	F
1456	2326	0.179094	TTAGCCATTACGGTCCAGCG	60.179	55.0	0.00	0.00	36.97	5.18	F
1681	2564	0.243907	GAGCTGCGTGTGGTTCTCTA	59.756	55.0	0.00	0.00	0.00	2.43	F
1785	2670	0.380733	TAGCTGTGCTGATCGTACGG	59.619	55.0	16.52	0.00	40.10	4.02	F
1796	2681	0.389426	ATCGTACGGCACTTCACACC	60.389	55.0	16.52	0.00	0.00	4.16	F
1938	2823	0.471971	TATCAGGGGCAGACTAGGGC	60.472	60.0	0.00	0.00	0.00	5.19	F
3855	4802	0.746659	GCAACCACCACTTCTGCTTT	59.253	50.0	0.00	0.00	0.00	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1919	2804	0.471971	GCCCTAGTCTGCCCCTGATA	60.472	60.000	0.0	0.0	0.0	2.15	R
3091	3978	0.687354	ACTCCGTTGGAAGCTCACAT	59.313	50.000	0.0	0.0	0.0	3.21	R
3584	4473	4.848299	CAGTTCGCTTCTAAATGCTGAAAC	59.152	41.667	0.0	0.0	0.0	2.78	R
3622	4511	7.162082	CCCACTCTTGAAACTACAGAACTAAT	58.838	38.462	0.0	0.0	0.0	1.73	R
3855	4802	8.021898	TCTCATGGATGTAAATATCACAGTCA	57.978	34.615	0.0	0.0	0.0	3.41	R
3983	4935	2.658325	CAGAAAGCTTACAACAATGCGC	59.342	45.455	0.0	0.0	0.0	6.09	R
4666	5650	0.037419	CCCGCCCAAAAATCAACCTG	60.037	55.000	0.0	0.0	0.0	4.00	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
85	89	6.591935	TGTGTCTACTTTGAACTTGGATCTT	58.408	36.000	0.00	0.00	0.00	2.40
195	223	4.974645	TGAGAGTATCCAAGTGGTTGTT	57.025	40.909	0.00	0.00	33.66	2.83
220	249	4.260170	AGAGCAACATGGATGAGAAGTTC	58.740	43.478	0.00	0.00	0.00	3.01
294	323	4.202080	CGAGATTACCGTTTATGAGGGTCA	60.202	45.833	0.00	0.00	42.78	4.02
317	346	1.306654	TAGCAATCCGGGGTCACCT	60.307	57.895	0.00	0.00	36.97	4.00
424	457	3.217242	GCTCAAAGCTCGTGAGGAA	57.783	52.632	22.36	0.00	42.36	3.36
426	459	2.079925	GCTCAAAGCTCGTGAGGAAAT	58.920	47.619	22.36	0.00	42.36	2.17
427	460	2.159599	GCTCAAAGCTCGTGAGGAAATG	60.160	50.000	22.36	4.35	42.36	2.32
429	462	3.329386	TCAAAGCTCGTGAGGAAATGAG	58.671	45.455	0.00	0.00	36.45	2.90
431	464	2.002127	GCTCGTGAGGAAATGAGCG	58.998	57.895	2.89	0.00	46.25	5.03
432	465	2.002127	CTCGTGAGGAAATGAGCGC	58.998	57.895	0.00	0.00	0.00	5.92
433	466	0.459237	CTCGTGAGGAAATGAGCGCT	60.459	55.000	11.27	11.27	0.00	5.92
434	467	0.815095	TCGTGAGGAAATGAGCGCTA	59.185	50.000	11.50	0.00	0.00	4.26
472	510	3.611113	GCTCGTGCTCGTAAGTTAATGAA	59.389	43.478	8.17	0.00	38.33	2.57
487	525	7.590139	AGTTAATGAACCGAGCTGATCAGCA	62.590	44.000	40.91	23.93	45.65	4.41
658	1492	1.303398	ATCTAGCGGCCTAGCGCTA	60.303	57.895	17.75	17.75	40.73	4.26
661	1495	0.099082	CTAGCGGCCTAGCGCTATAC	59.901	60.000	19.19	12.76	38.84	1.47
662	1496	0.322277	TAGCGGCCTAGCGCTATACT	60.322	55.000	19.19	12.84	43.00	2.12
671	1505	3.002348	CCTAGCGCTATACTGCCAAAAAC	59.998	47.826	19.19	0.00	0.00	2.43
675	1509	3.984633	GCGCTATACTGCCAAAAACAAAA	59.015	39.130	0.00	0.00	0.00	2.44
860	1719	1.455959	CCTCCCCGATCTCCGTTCT	60.456	63.158	0.00	0.00	36.31	3.01
1037	1897	0.257039	ATCCCAGCATCCAACTCCAC	59.743	55.000	0.00	0.00	0.00	4.02
1172	2032	0.257616	AAGAGGAGGAGGAGGAGACG	59.742	60.000	0.00	0.00	0.00	4.18
1415	2275	3.199289	AGGTTAGTTGCTACGCCCTATTT	59.801	43.478	5.06	0.00	0.00	1.40
1416	2276	3.558829	GGTTAGTTGCTACGCCCTATTTC	59.441	47.826	0.00	0.00	0.00	2.17

Showing 1 to 25 of 158 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
98	102	3.936453	TCACAACACAGGTGTCTACAAAC	59.064	43.478	5.41	0.00	44.13	2.93
180	208	4.072131	GCTCTTCAACAACCACTTGGATA	58.928	43.478	1.14	0.00	38.94	2.59
195	223	3.986996	TCTCATCCATGTTGCTCTTCA	57.013	42.857	0.00	0.00	0.00	3.02
294	323	0.392060	GACCCCGGATTGCTACGTTT	60.392	55.000	0.73	0.00	0.00	3.60
410	443	2.079925	GCTCATTTCCTCACGAGCTTT	58.920	47.619	0.00	0.00	45.86	3.51
422	455	1.202313	ACTCGAGGTAGCGCTCATTTC	60.202	52.381	16.34	7.14	0.00	2.17
424	457	0.382515	GACTCGAGGTAGCGCTCATT	59.617	55.000	16.34	0.00	0.00	2.57
426	459	2.461945	CGACTCGAGGTAGCGCTCA	61.462	63.158	16.34	0.00	0.00	4.26
427	460	1.979831	AACGACTCGAGGTAGCGCTC	61.980	60.000	16.34	5.63	0.00	5.03
429	462	1.132780	GAAACGACTCGAGGTAGCGC	61.133	60.000	18.41	0.00	0.00	5.92
430	463	0.167470	TGAAACGACTCGAGGTAGCG	59.833	55.000	18.41	16.13	0.00	4.26
431	464	1.897641	CTGAAACGACTCGAGGTAGC	58.102	55.000	18.41	2.12	0.00	3.58
432	465	1.469308	AGCTGAAACGACTCGAGGTAG	59.531	52.381	18.41	9.82	0.00	3.18
433	466	1.467734	GAGCTGAAACGACTCGAGGTA	59.532	52.381	18.41	0.00	0.00	3.08
434	467	0.241481	GAGCTGAAACGACTCGAGGT	59.759	55.000	18.41	2.55	0.00	3.85
503	1336	4.365899	TTTGCTCGAGCTCGTTAATCTA	57.634	40.909	35.27	13.31	42.66	1.98
675	1509	0.391228	GGGGTGTGGCGTGAATTTTT	59.609	50.000	0.00	0.00	0.00	1.94
840	1689	3.680920	AACGGAGATCGGGGAGGCT	62.681	63.158	0.00	0.00	44.45	4.58
849	1708	0.179108	CGGGGTTCAGAACGGAGATC	60.179	60.000	7.22	0.00	0.00	2.75
860	1719	2.993264	GTCGGGACTCGGGGTTCA	60.993	66.667	0.00	0.00	39.77	3.18
1016	1876	0.466922	GGAGTTGGATGCTGGGATGG	60.467	60.000	0.00	0.00	0.00	3.51
1404	2264	5.123227	CAGGAAATCAAGAAATAGGGCGTA	58.877	41.667	0.00	0.00	0.00	4.42
1415	2275	2.355716	CCTAACGGGCAGGAAATCAAGA	60.356	50.000	0.00	0.00	34.91	3.02
1416	2276	2.017049	CCTAACGGGCAGGAAATCAAG	58.983	52.381	0.00	0.00	34.91	3.02
1428	2288	2.476821	CGTAATGGCTAACCTAACGGG	58.523	52.381	0.00	0.00	41.89	5.28

Showing 1 to 25 of 158 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.