AutoCloner

Multiple sequence alignment - TraesCS4A01G060300

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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	TraesCS4A01G060300	chr4A	100.000	3503	0	0	1	3503	56512214	56508712	0.000000e+00	6469
1	TraesCS4A01G060300	chr4A	90.960	177	15	1	740	915	673027597	673027773	1.630000e-58	237
2	TraesCS4A01G060300	chr4B	93.521	3241	144	30	1	3209	492226326	492223120	0.000000e+00	4761
3	TraesCS4A01G060300	chr4B	96.774	248	7	1	3256	3503	492222785	492222539	2.520000e-111	412
4	TraesCS4A01G060300	chr4B	98.214	56	1	0	3204	3259	492222962	492222907	8.000000e-17	99
5	TraesCS4A01G060300	chr4D	93.404	3093	124	35	454	3503	399190805	399187750	0.000000e+00	4508
6	TraesCS4A01G060300	chr7A	84.337	830	79	25	106	915	60636474	60637272	0.000000e+00	765
7	TraesCS4A01G060300	chr7A	81.516	752	86	36	179	913	195481517	195482232	1.410000e-158	569
8	TraesCS4A01G060300	chr7A	90.805	87	8	0	2789	2875	190472980	190473066	2.210000e-22	117
9	TraesCS4A01G060300	chr2D	85.009	567	59	22	114	663	601986543	601987100	1.420000e-153	553
10	TraesCS4A01G060300	chr5B	83.246	573	70	21	242	800	268810018	268810578	1.450000e-138	503
11	TraesCS4A01G060300	chr7D	81.350	622	86	24	122	724	72769834	72769224	2.450000e-131	479
12	TraesCS4A01G060300	chr3D	80.687	611	82	32	114	705	95486180	95486773	3.210000e-120	442
13	TraesCS4A01G060300	chr3D	82.095	296	34	13	624	915	367306591	367306871	5.850000e-58	235
14	TraesCS4A01G060300	chr3A	80.480	625	82	29	105	705	685767144	685766536	3.210000e-120	442
15	TraesCS4A01G060300	chr6A	80.226	531	82	21	399	914	98807261	98806739	9.180000e-101	377
16	TraesCS4A01G060300	chr6A	90.698	86	8	0	2789	2874	604890750	604890665	7.950000e-22	115
17	TraesCS4A01G060300	chr5D	92.045	88	5	2	2788	2874	482103359	482103273	4.750000e-24	122
18	TraesCS4A01G060300	chr1D	90.909	88	8	0	2788	2875	326159435	326159348	6.140000e-23	119
19	TraesCS4A01G060300	chr1A	90.909	88	8	0	2788	2875	415638133	415638046	6.140000e-23	119
20	TraesCS4A01G060300	chr7B	87.500	96	10	2	2789	2883	482485036	482484942	3.700000e-20	110
21	TraesCS4A01G060300	chr1B	85.577	104	11	3	2789	2889	439444727	439444829	4.780000e-19	106

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	TraesCS4A01G060300	chr4A	56508712	56512214	3502	True	6469.000000	6469	100.000000	1	3503	1	chr4A.!!$R1	3502
1	TraesCS4A01G060300	chr4B	492222539	492226326	3787	True	1757.333333	4761	96.169667	1	3503	3	chr4B.!!$R1	3502
2	TraesCS4A01G060300	chr4D	399187750	399190805	3055	True	4508.000000	4508	93.404000	454	3503	1	chr4D.!!$R1	3049
3	TraesCS4A01G060300	chr7A	60636474	60637272	798	False	765.000000	765	84.337000	106	915	1	chr7A.!!$F1	809
4	TraesCS4A01G060300	chr7A	195481517	195482232	715	False	569.000000	569	81.516000	179	913	1	chr7A.!!$F3	734
5	TraesCS4A01G060300	chr2D	601986543	601987100	557	False	553.000000	553	85.009000	114	663	1	chr2D.!!$F1	549
6	TraesCS4A01G060300	chr5B	268810018	268810578	560	False	503.000000	503	83.246000	242	800	1	chr5B.!!$F1	558
7	TraesCS4A01G060300	chr7D	72769224	72769834	610	True	479.000000	479	81.350000	122	724	1	chr7D.!!$R1	602
8	TraesCS4A01G060300	chr3D	95486180	95486773	593	False	442.000000	442	80.687000	114	705	1	chr3D.!!$F1	591
9	TraesCS4A01G060300	chr3A	685766536	685767144	608	True	442.000000	442	80.480000	105	705	1	chr3A.!!$R1	600
10	TraesCS4A01G060300	chr6A	98806739	98807261	522	True	377.000000	377	80.226000	399	914	1	chr6A.!!$R1	515

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
100	102	0.317479	CAGGTCCTCTCGAACCGTTT	59.683	55.0	0.0	0.0	40.63	3.60	F
1260	1802	0.037326	ATTTCACGCTCTCCGCAGAA	60.037	50.0	0.0	0.0	41.76	3.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1708	2250	0.034670	GCCCAGTCCTTCAGCAATCT	60.035	55.000	0.00	0.0	0.00	2.4	R
3018	3587	2.350522	CACCAGGTGAGCTTCATGTAC	58.649	52.381	15.35	0.0	35.23	2.9	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
25	26	4.659172	TCAAGGCGGTGCAAGGGG	62.659	66.667	0.00	0.00	0.00	4.79
64	66	3.072468	CCAGGGCATGCAAGGTGG	61.072	66.667	21.36	15.37	0.00	4.61
94	96	3.068691	CGGGCAGGTCCTCTCGAA	61.069	66.667	5.03	0.00	34.39	3.71
98	100	2.637383	GCAGGTCCTCTCGAACCGT	61.637	63.158	0.00	0.00	40.63	4.83
99	101	1.965219	CAGGTCCTCTCGAACCGTT	59.035	57.895	0.00	0.00	40.63	4.44
100	102	0.317479	CAGGTCCTCTCGAACCGTTT	59.683	55.000	0.00	0.00	40.63	3.60
101	103	1.046204	AGGTCCTCTCGAACCGTTTT	58.954	50.000	0.00	0.00	40.63	2.43
102	104	1.415289	AGGTCCTCTCGAACCGTTTTT	59.585	47.619	0.00	0.00	40.63	1.94
366	448	5.283012	GTCCGAACGCTTATTCAACATTTTC	59.717	40.000	0.00	0.00	0.00	2.29
484	632	7.928706	TCAACATTTTTCAAATACCCGTTCAAT	59.071	29.630	0.00	0.00	0.00	2.57
581	919	9.906660	GGACTTATTCAACATTTGTCAAATACA	57.093	29.630	10.46	0.00	35.88	2.29
928	1461	3.146828	GCCCCATACCCATCCCACC	62.147	68.421	0.00	0.00	0.00	4.61
934	1467	1.782752	CATACCCATCCCACCAATCCT	59.217	52.381	0.00	0.00	0.00	3.24
935	1468	1.518367	TACCCATCCCACCAATCCTC	58.482	55.000	0.00	0.00	0.00	3.71
936	1469	1.289244	ACCCATCCCACCAATCCTCC	61.289	60.000	0.00	0.00	0.00	4.30
982	1515	2.490903	GTGCTGATCCAGAACTGCAAAT	59.509	45.455	10.28	0.00	37.08	2.32
1012	1545	1.696832	GACGACCATGAAGCTTCGGC	61.697	60.000	21.11	7.69	42.17	5.54
1197	1739	2.122769	TGTTCACCGGACCCCTCA	60.123	61.111	9.46	0.00	0.00	3.86
1260	1802	0.037326	ATTTCACGCTCTCCGCAGAA	60.037	50.000	0.00	0.00	41.76	3.02
1289	1831	3.056328	GCCACCGCCTCCTCAAAC	61.056	66.667	0.00	0.00	0.00	2.93
1290	1832	2.429930	CCACCGCCTCCTCAAACA	59.570	61.111	0.00	0.00	0.00	2.83
1323	1865	1.533273	TAGCCCGGATACAGCCTCC	60.533	63.158	0.73	0.00	36.17	4.30
1348	1890	0.389817	GCAAATTGCTTCCGGTTCCC	60.390	55.000	11.19	0.00	40.96	3.97
1382	1924	2.494918	CGGTGGATCCTCGTCACC	59.505	66.667	14.23	10.67	45.36	4.02
1386	1928	4.570663	GGATCCTCGTCACCGCCG	62.571	72.222	3.84	0.00	0.00	6.46
1585	2127	1.312815	GATTGGGATTCTCAAGCGGG	58.687	55.000	5.05	0.00	0.00	6.13
1608	2150	3.157252	GAGGCGGAGGATGCTGGA	61.157	66.667	0.00	0.00	0.00	3.86
1609	2151	2.447379	AGGCGGAGGATGCTGGAT	60.447	61.111	0.00	0.00	0.00	3.41
1662	2204	2.932194	TCCCTGCAGGCAGCTCTT	60.932	61.111	28.39	0.00	45.94	2.85
1758	2300	0.511221	CGGCAACACTGACCGTAAAG	59.489	55.000	0.00	0.00	37.42	1.85
1791	2333	1.450312	GCTTGTCGCCATGCTACCT	60.450	57.895	0.00	0.00	38.39	3.08
1839	2381	2.203470	TGAACTGCTCATTGATGCCA	57.797	45.000	5.89	0.00	0.00	4.92
1869	2411	3.652387	TGATGATATATGGGTGTGTGCCT	59.348	43.478	0.00	0.00	0.00	4.75
2118	2660	2.509964	AGTCTTGGAGTTTGTTCCTGGT	59.490	45.455	0.00	0.00	38.12	4.00
2245	2787	1.144936	GGTTCTGGATGGAGCGGAG	59.855	63.158	0.00	0.00	0.00	4.63
2695	3238	0.829990	TCTAGCCAACGCCATGATCA	59.170	50.000	0.00	0.00	34.57	2.92
2940	3509	9.300681	TCATCAACAAATCTTGAAATAGGACTT	57.699	29.630	0.00	0.00	33.85	3.01
2946	3515	9.014297	ACAAATCTTGAAATAGGACTTAGGTTG	57.986	33.333	0.00	0.00	0.00	3.77
3018	3587	7.951530	AAATGGCATTTAGAAAGTTGTGAAG	57.048	32.000	23.23	0.00	0.00	3.02
3200	3770	8.196802	TGATGTCAAGTTATCCTCGTTTTATG	57.803	34.615	0.00	0.00	0.00	1.90
3278	4136	5.540719	GGTACATCTCAGTAGAGGGCTATTT	59.459	44.000	0.00	0.00	42.34	1.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
5	6	2.281761	CTTGCACCGCCTTGACCT	60.282	61.111	0.00	0.00	0.00	3.85
7	8	3.365265	CCCTTGCACCGCCTTGAC	61.365	66.667	0.00	0.00	0.00	3.18
25	26	2.042831	GCACCTGCTCATGTGGGAC	61.043	63.158	7.26	0.00	38.21	4.46
53	54	2.985282	ACACGGCCACCTTGCATG	60.985	61.111	2.24	0.00	0.00	4.06
54	55	2.985282	CACACGGCCACCTTGCAT	60.985	61.111	2.24	0.00	0.00	3.96
155	178	5.961272	ACCAAAGACGAAGAAACAAAATGT	58.039	33.333	0.00	0.00	0.00	2.71
326	385	5.559225	CGTTCGGACAATGTTGAACATGTAA	60.559	40.000	22.83	2.02	37.97	2.41
396	478	9.900264	GTTGAACAAGTATTTGAAAATGTTGAC	57.100	29.630	4.81	10.48	37.73	3.18
532	869	8.827677	GTCCTAAAATTGCTGAACGAGTATTAT	58.172	33.333	0.00	0.00	0.00	1.28
761	1279	9.479278	TTTTTGCTTTATTTTTGTACTTTTCGC	57.521	25.926	0.00	0.00	0.00	4.70
920	1453	1.216064	TCAGGAGGATTGGTGGGATG	58.784	55.000	0.00	0.00	0.00	3.51
928	1461	2.037772	CGAGGGGTATTCAGGAGGATTG	59.962	54.545	0.00	0.00	0.00	2.67
934	1467	1.380785	ACGCGAGGGGTATTCAGGA	60.381	57.895	15.93	0.00	0.00	3.86
935	1468	1.067582	GACGCGAGGGGTATTCAGG	59.932	63.158	15.93	0.00	0.00	3.86
936	1469	1.299165	CGACGCGAGGGGTATTCAG	60.299	63.158	15.93	0.00	0.00	3.02
982	1515	0.768622	ATGGTCGTCTGTTGGGGAAA	59.231	50.000	0.00	0.00	0.00	3.13
1084	1626	0.250513	AGGAAGGACTTCACATCGGC	59.749	55.000	13.51	0.00	41.20	5.54
1147	1689	2.579738	GTTGAGGGAGAGGCGGAC	59.420	66.667	0.00	0.00	0.00	4.79
1180	1722	2.122769	TGAGGGGTCCGGTGAACA	60.123	61.111	0.00	0.00	0.00	3.18
1260	1802	1.156736	GCGGTGGCTGCGATAATAAT	58.843	50.000	0.00	0.00	35.83	1.28
1285	1827	1.176619	GGGTTCCGGGGAAGTGTTTG	61.177	60.000	0.00	0.00	34.49	2.93
1289	1831	1.905512	CTAGGGTTCCGGGGAAGTG	59.094	63.158	0.00	0.00	34.49	3.16
1290	1832	1.993948	GCTAGGGTTCCGGGGAAGT	60.994	63.158	0.00	0.00	34.49	3.01
1323	1865	0.526096	CGGAAGCAATTTGCCCGATG	60.526	55.000	25.57	8.12	46.41	3.84
1382	1924	2.350192	TGTATGTGTAGATTTTGCGGCG	59.650	45.455	0.51	0.51	0.00	6.46
1386	1928	4.396166	ACAGGCTGTATGTGTAGATTTTGC	59.604	41.667	20.61	0.00	0.00	3.68
1585	2127	1.670590	CATCCTCCGCCTCCATCTC	59.329	63.158	0.00	0.00	0.00	2.75
1608	2150	3.315191	GGATAACTGTACCATTTGCGCAT	59.685	43.478	12.75	0.00	0.00	4.73
1609	2151	2.680841	GGATAACTGTACCATTTGCGCA	59.319	45.455	5.66	5.66	0.00	6.09
1623	2165	2.036475	CACAGCTAGGCGATGGATAACT	59.964	50.000	0.00	0.00	32.00	2.24
1662	2204	0.674581	CAAGGAAGCCAGCATCGACA	60.675	55.000	0.00	0.00	0.00	4.35
1706	2248	1.681166	CCCAGTCCTTCAGCAATCTGG	60.681	57.143	0.00	0.00	40.69	3.86
1708	2250	0.034670	GCCCAGTCCTTCAGCAATCT	60.035	55.000	0.00	0.00	0.00	2.40
1758	2300	0.175073	CAAGCTCCGGTAGGGTGTAC	59.825	60.000	0.00	0.00	38.33	2.90
1791	2333	0.491823	TCTTCCCCTCTTCACCCTCA	59.508	55.000	0.00	0.00	0.00	3.86
1839	2381	8.980596	ACACACCCATATATCATCACAAAATTT	58.019	29.630	0.00	0.00	0.00	1.82
1869	2411	1.001764	CACTTCTGAGCATGCCCCA	60.002	57.895	15.66	12.09	0.00	4.96
1877	2419	0.096628	CAATCTGCGCACTTCTGAGC	59.903	55.000	5.66	0.00	43.14	4.26
2118	2660	2.886523	CTGAACCCTTGCAAGATCAACA	59.113	45.455	28.05	17.51	0.00	3.33
2245	2787	3.392882	CCACAAACCTTTGCTTCCAATC	58.607	45.455	0.00	0.00	41.79	2.67
3007	3576	5.822519	TGAGCTTCATGTACTTCACAACTTT	59.177	36.000	0.00	0.00	41.55	2.66
3018	3587	2.350522	CACCAGGTGAGCTTCATGTAC	58.649	52.381	15.35	0.00	35.23	2.90
3278	4136	4.980573	ACCTACATTTGCACTGACCTAAA	58.019	39.130	2.57	0.00	0.00	1.85
3419	4277	2.695666	TGCCGGGAACAATCTTTGAAAA	59.304	40.909	2.18	0.00	0.00	2.29

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.