AutoCloner

Multiple sequence alignment - TraesCS3D01G534800

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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	TraesCS3D01G534800	chr3D	100.000	3446	0	0	1	3446	609362822	609366267	0.000000e+00	6364.0
1	TraesCS3D01G534800	chr3D	80.831	313	42	8	3023	3321	609352143	609352451	2.680000e-56	230.0
2	TraesCS3D01G534800	chr3A	94.010	2521	104	24	964	3446	742928909	742931420	0.000000e+00	3775.0
3	TraesCS3D01G534800	chr3A	91.779	961	54	9	1	936	742927950	742928910	0.000000e+00	1314.0
4	TraesCS3D01G534800	chr3A	84.684	901	104	17	996	1895	742955107	742955974	0.000000e+00	869.0
5	TraesCS3D01G534800	chr3A	87.838	222	27	0	2260	2481	742962573	742962794	9.490000e-66	261.0
6	TraesCS3D01G534800	chr3B	86.757	2371	252	29	996	3338	820178971	820176635	0.000000e+00	2582.0
7	TraesCS3D01G534800	chr3B	92.500	1480	110	1	970	2448	820185903	820184424	0.000000e+00	2117.0
8	TraesCS3D01G534800	chr3B	93.601	1422	51	12	1512	2919	820114793	820116188	0.000000e+00	2085.0
9	TraesCS3D01G534800	chr3B	88.376	1755	158	22	803	2532	819992141	819990408	0.000000e+00	2069.0
10	TraesCS3D01G534800	chr3B	86.624	1555	186	12	996	2532	820122919	820124469	0.000000e+00	1700.0
11	TraesCS3D01G534800	chr3B	94.601	815	37	3	579	1392	820113994	820114802	0.000000e+00	1254.0
12	TraesCS3D01G534800	chr3B	94.270	541	27	3	2907	3446	820116225	820116762	0.000000e+00	824.0
13	TraesCS3D01G534800	chr3B	88.889	522	50	6	72	588	820112379	820112897	1.350000e-178	636.0
14	TraesCS3D01G534800	chr3B	80.793	656	81	16	2751	3367	820217106	820216457	4.030000e-129	472.0
15	TraesCS3D01G534800	chr3B	86.495	311	38	2	3104	3414	820109396	820109702	4.260000e-89	339.0
16	TraesCS3D01G534800	chr3B	90.041	241	19	3	283	519	820175998	820175759	1.200000e-79	307.0
17	TraesCS3D01G534800	chr3B	82.353	323	28	14	2776	3071	820107207	820107527	1.590000e-63	254.0
18	TraesCS3D01G534800	chr3B	86.239	109	6	5	2676	2784	820090782	820090881	3.640000e-20	110.0
19	TraesCS3D01G534800	chr3B	78.571	154	30	2	2933	3085	525833139	525833290	7.870000e-17	99.0
20	TraesCS3D01G534800	chr3B	97.368	38	1	0	933	970	820179059	820179022	7.980000e-07	65.8
21	TraesCS3D01G534800	chr1A	86.167	1482	189	10	977	2453	578941160	578939690	0.000000e+00	1587.0
22	TraesCS3D01G534800	chr1D	84.800	1125	137	17	837	1949	482243622	482242520	0.000000e+00	1099.0
23	TraesCS3D01G534800	chr2A	78.140	215	39	8	1988	2198	763333087	763332877	2.790000e-26	130.0
24	TraesCS3D01G534800	chr2D	81.065	169	9	10	350	504	73458813	73458972	2.810000e-21	113.0
25	TraesCS3D01G534800	chr2D	78.846	156	25	8	2004	2155	568410146	568410297	7.870000e-17	99.0
26	TraesCS3D01G534800	chr2D	80.702	114	15	6	424	535	640254891	640254783	7.930000e-12	82.4
27	TraesCS3D01G534800	chr2B	82.906	117	19	1	2803	2919	546824836	546824951	1.690000e-18	104.0
28	TraesCS3D01G534800	chr2B	80.147	136	25	2	2021	2155	681218938	681219072	2.190000e-17	100.0
29	TraesCS3D01G534800	chr2B	82.075	106	14	4	426	528	404183295	404183398	6.130000e-13	86.1
30	TraesCS3D01G534800	chr7A	83.810	105	10	5	426	528	79817744	79817843	3.660000e-15	93.5
31	TraesCS3D01G534800	chr7A	78.846	156	18	12	377	528	183807520	183807664	1.320000e-14	91.6
32	TraesCS3D01G534800	chr7B	81.250	112	15	5	426	535	710677576	710677469	6.130000e-13	86.1

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	TraesCS3D01G534800	chr3D	609362822	609366267	3445	False	6364.000000	6364	100.000000	1	3446	1	chr3D.!!$F2	3445
1	TraesCS3D01G534800	chr3A	742927950	742931420	3470	False	2544.500000	3775	92.894500	1	3446	2	chr3A.!!$F3	3445
2	TraesCS3D01G534800	chr3A	742955107	742955974	867	False	869.000000	869	84.684000	996	1895	1	chr3A.!!$F1	899
3	TraesCS3D01G534800	chr3B	820184424	820185903	1479	True	2117.000000	2117	92.500000	970	2448	1	chr3B.!!$R2	1478
4	TraesCS3D01G534800	chr3B	819990408	819992141	1733	True	2069.000000	2069	88.376000	803	2532	1	chr3B.!!$R1	1729
5	TraesCS3D01G534800	chr3B	820122919	820124469	1550	False	1700.000000	1700	86.624000	996	2532	1	chr3B.!!$F3	1536
6	TraesCS3D01G534800	chr3B	820175759	820179059	3300	True	984.933333	2582	91.388667	283	3338	3	chr3B.!!$R4	3055
7	TraesCS3D01G534800	chr3B	820107207	820116762	9555	False	898.666667	2085	90.034833	72	3446	6	chr3B.!!$F4	3374
8	TraesCS3D01G534800	chr3B	820216457	820217106	649	True	472.000000	472	80.793000	2751	3367	1	chr3B.!!$R3	616
9	TraesCS3D01G534800	chr1A	578939690	578941160	1470	True	1587.000000	1587	86.167000	977	2453	1	chr1A.!!$R1	1476
10	TraesCS3D01G534800	chr1D	482242520	482243622	1102	True	1099.000000	1099	84.800000	837	1949	1	chr1D.!!$R1	1112

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
165	5266	0.320771	CACAAGCTTCACTAGGCGGT	60.321	55.0	0.0	0.0	0.0	5.68	F
975	7221	0.610232	AGTGCCACCTCCAATTCTGC	60.610	55.0	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
1635	7903	0.228742	CCAACGACTCGAACGTGTTG	59.771	55.000	15.88	13.11	43.16	3.33	R
2726	9013	1.351017	GTTCCAGTTCCATCCACCTGA	59.649	52.381	0.00	0.00	0.00	3.86	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
26	27	3.090765	CCAGGGGCTGCCTTAACT	58.909	61.111	19.68	9.10	0.00	2.24
100	5201	1.685224	GTCTCCATGCCCACCAGAA	59.315	57.895	0.00	0.00	0.00	3.02
102	5203	1.002069	TCTCCATGCCCACCAGAATT	58.998	50.000	0.00	0.00	0.00	2.17
127	5228	1.301401	CCGCCACGAGAAGAAACCA	60.301	57.895	0.00	0.00	0.00	3.67
133	5234	1.663702	CGAGAAGAAACCACGCCGT	60.664	57.895	0.00	0.00	0.00	5.68
165	5266	0.320771	CACAAGCTTCACTAGGCGGT	60.321	55.000	0.00	0.00	0.00	5.68
214	5315	4.506255	GGGAGGAATGGTGGGGCG	62.506	72.222	0.00	0.00	0.00	6.13
258	5360	3.365265	CTTGGGCAAGGCGACACC	61.365	66.667	0.00	0.00	34.87	4.16
276	5378	2.613133	CACCGGGTCGAGTTTGTTTTTA	59.387	45.455	6.32	0.00	0.00	1.52
289	5391	3.574284	TGTTTTTAGCAGCGCAATCAT	57.426	38.095	11.47	0.00	0.00	2.45
294	5396	6.422100	TGTTTTTAGCAGCGCAATCATTTTTA	59.578	30.769	11.47	0.00	0.00	1.52
297	5399	7.413475	TTTAGCAGCGCAATCATTTTTAAAA	57.587	28.000	11.47	0.00	0.00	1.52
299	5401	6.484818	AGCAGCGCAATCATTTTTAAAAAT	57.515	29.167	18.40	18.40	39.07	1.82
360	5462	8.603181	ACTTTGCTGTGTGAAATTATTTTGAAC	58.397	29.630	0.00	0.00	0.00	3.18
523	5629	5.791336	TCTCGCTGTGAGGTATTCAATAT	57.209	39.130	17.44	0.00	45.32	1.28
565	5671	5.288232	TCGCACAATGCAATAAAATGCTAAC	59.712	36.000	0.00	0.00	45.36	2.34
574	5682	7.351223	TGCAATAAAATGCTAACTTTTTGTGC	58.649	30.769	14.32	14.32	46.54	4.57
595	6809	6.098017	GTGCTAGAGTAAAACGTAGTGGATT	58.902	40.000	0.00	0.00	45.00	3.01
621	6835	3.452627	AGAAGGGATGACTTTAGCATCGT	59.547	43.478	0.00	0.00	42.32	3.73
661	6875	4.703645	TGTCGACACACAATTCCAAAAA	57.296	36.364	15.76	0.00	0.00	1.94
709	6924	4.324402	CCGCTATCAACAAAAAGATGCAAC	59.676	41.667	0.00	0.00	0.00	4.17
809	7024	0.613777	GGACAATTCACGGGAGGTCT	59.386	55.000	13.58	0.00	0.00	3.85
867	7082	2.033550	GTCCGCATATCTCTGAGTCGTT	59.966	50.000	4.32	0.00	0.00	3.85
975	7221	0.610232	AGTGCCACCTCCAATTCTGC	60.610	55.000	0.00	0.00	0.00	4.26
1434	7702	4.385405	GCCTCGTGCCTGTCAGCT	62.385	66.667	0.00	0.00	0.00	4.24
1635	7903	1.153349	GACCATGGGCGTTCTCCTC	60.153	63.158	18.09	0.00	0.00	3.71
1760	8028	2.361610	CAAGGGCGCCAAGGATGT	60.362	61.111	30.85	0.86	0.00	3.06
1968	8240	3.368427	GCCCAGAAAAATACTTGGAAGGC	60.368	47.826	0.00	0.00	0.00	4.35
2014	8286	1.628846	TCCTGCCTCAAGGGTTCTTAC	59.371	52.381	0.00	0.00	37.96	2.34
2208	8480	5.545063	TGAACAAGGTGTCTATGACAGAA	57.455	39.130	0.20	0.00	43.57	3.02
2557	8843	5.471424	TCCATCCTCTCAAGAATATGACCT	58.529	41.667	3.85	0.00	0.00	3.85
2670	8957	7.071014	TGCAGAAAAGGAAAACATCAAAAAC	57.929	32.000	0.00	0.00	0.00	2.43
2673	8960	8.020244	GCAGAAAAGGAAAACATCAAAAACAAA	58.980	29.630	0.00	0.00	0.00	2.83
2725	9012	4.032445	GCGAAGTCTGCGTTATTTATGTGA	59.968	41.667	1.31	0.00	0.00	3.58
2726	9013	5.276868	GCGAAGTCTGCGTTATTTATGTGAT	60.277	40.000	1.31	0.00	0.00	3.06
2727	9014	6.347881	CGAAGTCTGCGTTATTTATGTGATC	58.652	40.000	0.00	0.00	0.00	2.92
2806	9093	4.261614	GCGGGGGAATTTCAATAGCTTTAG	60.262	45.833	0.00	0.00	0.00	1.85
2894	9185	2.802247	CAGCTTTCAGTCACGTCAATCA	59.198	45.455	0.00	0.00	0.00	2.57
2897	9188	3.187227	GCTTTCAGTCACGTCAATCATGT	59.813	43.478	0.00	0.00	0.00	3.21
2977	9317	7.856145	ACTAACAAGCTCTCCAATTTCTATG	57.144	36.000	0.00	0.00	0.00	2.23
3021	9361	1.888436	GAGTCATGGCGAGTGGTCCA	61.888	60.000	0.00	0.00	36.70	4.02
3022	9362	1.448540	GTCATGGCGAGTGGTCCAG	60.449	63.158	0.00	0.00	35.57	3.86
3065	9405	5.639506	GGTAATCCATCTACGGAATGACATG	59.360	44.000	0.00	0.00	38.95	3.21
3073	9413	7.655732	CCATCTACGGAATGACATGTGTAAATA	59.344	37.037	1.15	0.00	0.00	1.40
3087	9427	4.263550	TGTGTAAATACCCTAAGCTTGGCA	60.264	41.667	9.86	0.00	0.00	4.92
3098	9452	0.962356	AGCTTGGCAAAGATGACCCG	60.962	55.000	4.56	0.00	35.19	5.28
3148	9502	5.468658	ACTCCTTGGTATAGCTTACTCCAT	58.531	41.667	3.20	0.00	0.00	3.41
3240	9594	3.750371	CAGTGTGGGTGTTAATCTTGGA	58.250	45.455	0.00	0.00	0.00	3.53
3286	9640	4.818863	CCATGGCCGGGCATCACA	62.819	66.667	38.25	14.55	0.00	3.58

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
26	27	4.082523	GGCAGCTGGCTGGACGTA	62.083	66.667	31.40	0.00	43.77	3.57
100	5201	2.031919	TCGTGGCGGCAACTCAAT	59.968	55.556	15.50	0.00	0.00	2.57
102	5203	3.158537	TTCTCGTGGCGGCAACTCA	62.159	57.895	15.50	0.00	0.00	3.41
183	5284	2.955246	TCCCTCCTCCTCCTGCCT	60.955	66.667	0.00	0.00	0.00	4.75
214	5315	2.184579	GCGTGACTCTACCCTGGC	59.815	66.667	0.00	0.00	0.00	4.85
215	5316	2.722201	GGGCGTGACTCTACCCTGG	61.722	68.421	0.00	0.00	39.42	4.45
258	5360	2.288458	TGCTAAAAACAAACTCGACCCG	59.712	45.455	0.00	0.00	0.00	5.28
267	5369	3.711086	TGATTGCGCTGCTAAAAACAAA	58.289	36.364	9.73	0.00	0.00	2.83
268	5370	3.361794	TGATTGCGCTGCTAAAAACAA	57.638	38.095	9.73	0.00	0.00	2.83
276	5378	5.921004	TTTTTAAAAATGATTGCGCTGCT	57.079	30.435	9.73	0.00	0.00	4.24
428	5530	6.859017	TCGTGCAACATAGTACTCATTTCTA	58.141	36.000	0.00	0.00	35.74	2.10
565	5671	7.792508	CACTACGTTTTACTCTAGCACAAAAAG	59.207	37.037	0.00	0.00	0.00	2.27
574	5682	6.628185	ACCAATCCACTACGTTTTACTCTAG	58.372	40.000	0.00	0.00	0.00	2.43
595	6809	4.101114	TGCTAAAGTCATCCCTTCTACCA	58.899	43.478	0.00	0.00	0.00	3.25
621	6835	0.981183	ATTACCTCGTGTGGGCTCAA	59.019	50.000	0.00	0.00	0.00	3.02
661	6875	1.615392	GTACCCACCTAACGTGTCACT	59.385	52.381	0.65	0.00	41.26	3.41
709	6924	4.127171	CTCCGTACAATACCCATCTTTGG	58.873	47.826	0.00	0.00	43.23	3.28
809	7024	1.153353	GGAAATTCTTCCGTGCACGA	58.847	50.000	39.10	22.39	41.89	4.35
867	7082	2.025037	AGCAGTTTGGGCATGGAATCTA	60.025	45.455	0.00	0.00	0.00	1.98
930	7146	2.983592	CACTGGCGGGGTGGAAAC	60.984	66.667	0.00	0.00	0.00	2.78
975	7221	1.922821	CCTATGGAAGGTGGGTGGG	59.077	63.158	0.00	0.00	40.94	4.61
1434	7702	1.077805	TGTCGGGAGCTGGGTTAGA	59.922	57.895	0.00	0.00	0.00	2.10
1635	7903	0.228742	CCAACGACTCGAACGTGTTG	59.771	55.000	15.88	13.11	43.16	3.33
1760	8028	5.540400	TTCGTTCCTCTCTACTTTTTCCA	57.460	39.130	0.00	0.00	0.00	3.53
1968	8240	3.259633	AAGTTCCGGCTCAGGGCAG	62.260	63.158	0.00	0.00	44.01	4.85
2014	8286	3.136123	CCTGCCATTGGTCCGCTG	61.136	66.667	4.26	0.00	0.00	5.18
2088	8360	4.874977	TGTGTCACGAACGCGCCA	62.875	61.111	5.73	0.00	41.49	5.69
2400	8672	7.972277	CCAAGATTATCAACATCCAACAGAAAG	59.028	37.037	0.00	0.00	0.00	2.62
2484	8759	3.862845	CGCAACCAAAATGTAAATAGGGC	59.137	43.478	0.00	0.00	0.00	5.19
2489	8775	4.202161	TGACCACGCAACCAAAATGTAAAT	60.202	37.500	0.00	0.00	0.00	1.40
2725	9012	1.971149	TCCAGTTCCATCCACCTGAT	58.029	50.000	0.00	0.00	0.00	2.90
2726	9013	1.351017	GTTCCAGTTCCATCCACCTGA	59.649	52.381	0.00	0.00	0.00	3.86
2727	9014	1.614317	GGTTCCAGTTCCATCCACCTG	60.614	57.143	0.00	0.00	0.00	4.00
2894	9185	4.870123	TTTGTGCCAAGCATTCTAACAT	57.130	36.364	0.00	0.00	41.91	2.71
2897	9188	9.364989	GTTAAATATTTGTGCCAAGCATTCTAA	57.635	29.630	11.05	0.00	41.91	2.10
2957	9297	7.765695	TTTTCATAGAAATTGGAGAGCTTGT	57.234	32.000	0.00	0.00	0.00	3.16
2977	9317	1.606668	TCAGTCGTGGCACCAATTTTC	59.393	47.619	12.86	0.00	0.00	2.29
3021	9361	3.181416	ACCTAGAGTTGGTGAACCTCTCT	60.181	47.826	21.75	21.75	43.92	3.10
3022	9362	3.166679	ACCTAGAGTTGGTGAACCTCTC	58.833	50.000	13.48	13.48	36.30	3.20
3065	9405	4.266714	TGCCAAGCTTAGGGTATTTACAC	58.733	43.478	14.32	0.00	0.00	2.90
3073	9413	2.041620	TCATCTTTGCCAAGCTTAGGGT	59.958	45.455	14.32	0.00	0.00	4.34
3087	9427	3.388841	AGCCGACGGGTCATCTTT	58.611	55.556	13.98	0.00	34.97	2.52
3148	9502	2.274542	TCCAGTTCATTTCTAGGGGCA	58.725	47.619	0.00	0.00	0.00	5.36
3240	9594	2.376695	TCCTCGAGACCCGGATTATT	57.623	50.000	15.71	0.00	39.14	1.40
3286	9640	1.661463	TTCCTGGACCTCATGCTCTT	58.339	50.000	0.00	0.00	0.00	2.85
3359	9713	3.803162	GCAGGAGGGGGAAGGCTC	61.803	72.222	0.00	0.00	0.00	4.70

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.