AutoCloner

Multiple sequence alignment - TraesCS4A01G191600

Loading Multiple Alignment...

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	TraesCS4A01G191600	chr4A	100.000	2405	0	0	1	2405	471928454	471930858	0.000000e+00	4442.0
1	TraesCS4A01G191600	chr4D	93.173	1582	60	21	844	2405	103237021	103235468	0.000000e+00	2279.0
2	TraesCS4A01G191600	chr4B	90.132	1510	69	32	924	2400	147369778	147368316	0.000000e+00	1890.0
3	TraesCS4A01G191600	chr4B	98.465	847	11	2	1	845	117766229	117767075	0.000000e+00	1491.0
4	TraesCS4A01G191600	chr5B	98.462	845	12	1	1	845	439456171	439457014	0.000000e+00	1487.0
5	TraesCS4A01G191600	chr2B	95.278	593	13	2	1	578	676950156	676950748	0.000000e+00	926.0
6	TraesCS4A01G191600	chr2A	84.198	867	79	31	11	842	38884510	38883667	0.000000e+00	789.0
7	TraesCS4A01G191600	chr2A	82.280	886	79	27	10	840	726393470	726394332	0.000000e+00	695.0
8	TraesCS4A01G191600	chrUn	83.431	851	82	32	35	850	41027092	41026266	0.000000e+00	736.0
9	TraesCS4A01G191600	chrUn	83.431	851	82	32	35	850	447939055	447938229	0.000000e+00	736.0
10	TraesCS4A01G191600	chr1B	82.413	887	77	28	10	841	615382512	615383374	0.000000e+00	701.0
11	TraesCS4A01G191600	chr7B	85.827	254	24	6	595	840	145783941	145784190	2.370000e-65	259.0
12	TraesCS4A01G191600	chr7B	87.204	211	15	4	139	347	145783429	145783629	1.860000e-56	230.0
13	TraesCS4A01G191600	chr7B	93.636	110	7	0	11	120	145783227	145783336	5.320000e-37	165.0
14	TraesCS4A01G191600	chr7B	93.478	46	3	0	801	846	707842152	707842107	4.290000e-08	69.4
15	TraesCS4A01G191600	chr5D	83.978	181	18	7	1189	1369	233819170	233819001	1.910000e-36	163.0
16	TraesCS4A01G191600	chr5A	83.978	181	18	5	1189	1369	320743454	320743623	1.910000e-36	163.0
17	TraesCS4A01G191600	chr6B	100.000	39	0	0	808	846	124551197	124551159	3.320000e-09	73.1
18	TraesCS4A01G191600	chr1A	91.667	48	3	1	798	845	224099676	224099722	5.550000e-07	65.8

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	TraesCS4A01G191600	chr4A	471928454	471930858	2404	False	4442	4442	100.000	1	2405	1	chr4A.!!$F1	2404
1	TraesCS4A01G191600	chr4D	103235468	103237021	1553	True	2279	2279	93.173	844	2405	1	chr4D.!!$R1	1561
2	TraesCS4A01G191600	chr4B	147368316	147369778	1462	True	1890	1890	90.132	924	2400	1	chr4B.!!$R1	1476
3	TraesCS4A01G191600	chr4B	117766229	117767075	846	False	1491	1491	98.465	1	845	1	chr4B.!!$F1	844
4	TraesCS4A01G191600	chr5B	439456171	439457014	843	False	1487	1487	98.462	1	845	1	chr5B.!!$F1	844
5	TraesCS4A01G191600	chr2B	676950156	676950748	592	False	926	926	95.278	1	578	1	chr2B.!!$F1	577
6	TraesCS4A01G191600	chr2A	38883667	38884510	843	True	789	789	84.198	11	842	1	chr2A.!!$R1	831
7	TraesCS4A01G191600	chr2A	726393470	726394332	862	False	695	695	82.280	10	840	1	chr2A.!!$F1	830
8	TraesCS4A01G191600	chrUn	41026266	41027092	826	True	736	736	83.431	35	850	1	chrUn.!!$R1	815
9	TraesCS4A01G191600	chrUn	447938229	447939055	826	True	736	736	83.431	35	850	1	chrUn.!!$R2	815
10	TraesCS4A01G191600	chr1B	615382512	615383374	862	False	701	701	82.413	10	841	1	chr1B.!!$F1	831
11	TraesCS4A01G191600	chr7B	145783227	145784190	963	False	218	259	88.889	11	840	3	chr7B.!!$F1	829

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
902	1181	0.321122	GAGTTGCTGTCCAGTCCCTG	60.321	60.0	0.0	0.0	0.0	4.45	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2358	2679	0.759346	AGAAGCTTGACCTGGACGTT	59.241	50.0	2.1	0.0	0.0	3.99	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
380	571	4.405036	TCAGCCCATTAAAGCAATGCAATA	59.595	37.500	8.35	0.00	42.40	1.90
450	644	4.383774	TTCTCAAAATAGTGCAACGACG	57.616	40.909	0.00	0.00	45.86	5.12
871	1150	4.684703	CACCCGAAATGATCTCCGTTATAC	59.315	45.833	0.00	0.00	0.00	1.47
872	1151	4.587684	ACCCGAAATGATCTCCGTTATACT	59.412	41.667	0.00	0.00	0.00	2.12
873	1152	5.771666	ACCCGAAATGATCTCCGTTATACTA	59.228	40.000	0.00	0.00	0.00	1.82
900	1179	1.003233	GGAGTTGCTGTCCAGTCCC	60.003	63.158	0.00	0.00	33.84	4.46
901	1180	1.484444	GGAGTTGCTGTCCAGTCCCT	61.484	60.000	0.00	0.00	33.84	4.20
902	1181	0.321122	GAGTTGCTGTCCAGTCCCTG	60.321	60.000	0.00	0.00	0.00	4.45
903	1182	1.968540	GTTGCTGTCCAGTCCCTGC	60.969	63.158	0.00	0.00	0.00	4.85
905	1184	3.640407	GCTGTCCAGTCCCTGCCA	61.640	66.667	0.00	0.00	0.00	4.92
911	1190	2.520458	CAGTCCCTGCCAAACCCA	59.480	61.111	0.00	0.00	0.00	4.51
922	1201	2.503356	TGCCAAACCCAATTGTCACTTT	59.497	40.909	4.43	0.00	0.00	2.66
928	1215	2.558359	ACCCAATTGTCACTTTGCTAGC	59.442	45.455	8.10	8.10	0.00	3.42
929	1216	2.821969	CCCAATTGTCACTTTGCTAGCT	59.178	45.455	17.23	0.00	0.00	3.32
948	1235	1.413812	CTCCAAAAAGGGTGCAGCTTT	59.586	47.619	16.65	12.14	38.24	3.51
970	1257	3.852578	TGCTTATTTTCCTCTCCTTCCCT	59.147	43.478	0.00	0.00	0.00	4.20
971	1258	5.036916	TGCTTATTTTCCTCTCCTTCCCTA	58.963	41.667	0.00	0.00	0.00	3.53
972	1259	5.672194	TGCTTATTTTCCTCTCCTTCCCTAT	59.328	40.000	0.00	0.00	0.00	2.57
975	1262	7.013750	GCTTATTTTCCTCTCCTTCCCTATTTG	59.986	40.741	0.00	0.00	0.00	2.32
1036	1326	3.283751	CCGTCCAACTCTCTCATACTCT	58.716	50.000	0.00	0.00	0.00	3.24
1048	1338	3.269643	TCTCATACTCTTCCTGGTCCTCA	59.730	47.826	0.00	0.00	0.00	3.86
1050	1340	3.011821	TCATACTCTTCCTGGTCCTCACT	59.988	47.826	0.00	0.00	0.00	3.41
1061	1351	1.909302	GGTCCTCACTTCCATCCAAGA	59.091	52.381	0.00	0.00	0.00	3.02
1417	1716	0.747255	CACCTAGGGACACCGATCAG	59.253	60.000	14.81	0.00	43.47	2.90
1429	1728	2.885861	GATCAGCCTCGTCACCGT	59.114	61.111	0.00	0.00	35.01	4.83
1433	1732	1.734477	CAGCCTCGTCACCGTTCAG	60.734	63.158	0.00	0.00	35.01	3.02
1436	1735	2.338620	CTCGTCACCGTTCAGCCA	59.661	61.111	0.00	0.00	35.01	4.75
1437	1736	1.300620	CTCGTCACCGTTCAGCCAA	60.301	57.895	0.00	0.00	35.01	4.52
1474	1773	1.461127	CCTGCTAGCTGTTTTCGACAC	59.539	52.381	17.23	0.00	33.82	3.67
1544	1843	2.435437	TGGCACTGCAGATATAGCTCAA	59.565	45.455	23.35	4.07	0.00	3.02
1609	1909	8.804688	TTTTGGGTACTGTCGAAATAATTTTG	57.195	30.769	0.00	0.00	0.00	2.44
1774	2081	0.746204	TGACTCTTGCACGCACCAAA	60.746	50.000	0.00	0.00	0.00	3.28
1805	2112	2.266554	GCACTGACTATGACTGCACTC	58.733	52.381	0.00	0.00	0.00	3.51
1807	2114	3.678252	GCACTGACTATGACTGCACTCAT	60.678	47.826	12.62	12.62	35.05	2.90
1808	2115	3.864003	CACTGACTATGACTGCACTCATG	59.136	47.826	16.42	10.15	32.86	3.07
1834	2141	5.833082	CCTATACGGGCATATATGAGTCAC	58.167	45.833	17.10	0.00	0.00	3.67
1970	2281	4.653341	TCCCTCTGCTTTTTCCAATCAAAA	59.347	37.500	0.00	0.00	0.00	2.44
2093	2414	1.067776	ACGAACAAGTGATCTCCCGAC	60.068	52.381	0.00	0.00	0.00	4.79
2129	2450	6.801862	CAGATGTGCGATATATTCTTACGACA	59.198	38.462	0.00	0.00	0.00	4.35
2140	2461	4.445452	TTCTTACGACAAAGCGATACCT	57.555	40.909	0.00	0.00	34.83	3.08
2358	2679	7.884877	TCTTCCATGCTTCTATCTTTTCTTTCA	59.115	33.333	0.00	0.00	0.00	2.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
47	49	5.900865	TGCTGCTCATTCACAATATTCAA	57.099	34.783	0.00	0.00	0.00	2.69
380	571	4.120946	ACAAGAGAGGAGGTACAGAGTT	57.879	45.455	0.00	0.00	0.00	3.01
450	644	4.369182	CGTACTCATCATCTTGTTACCCC	58.631	47.826	0.00	0.00	0.00	4.95
871	1150	4.177026	GACAGCAACTCCACATGTACTAG	58.823	47.826	0.00	0.00	0.00	2.57
872	1151	3.056107	GGACAGCAACTCCACATGTACTA	60.056	47.826	0.00	0.00	0.00	1.82
873	1152	2.289694	GGACAGCAACTCCACATGTACT	60.290	50.000	0.00	0.00	0.00	2.73
900	1179	1.688197	AGTGACAATTGGGTTTGGCAG	59.312	47.619	10.83	0.00	45.05	4.85
901	1180	1.786937	AGTGACAATTGGGTTTGGCA	58.213	45.000	10.83	0.00	42.30	4.92
902	1181	2.871633	CAAAGTGACAATTGGGTTTGGC	59.128	45.455	10.83	0.00	35.06	4.52
903	1182	2.871633	GCAAAGTGACAATTGGGTTTGG	59.128	45.455	10.83	0.00	0.00	3.28
905	1184	4.501400	GCTAGCAAAGTGACAATTGGGTTT	60.501	41.667	10.63	0.98	0.00	3.27
911	1190	3.754965	TGGAGCTAGCAAAGTGACAATT	58.245	40.909	18.83	0.00	0.00	2.32
922	1201	1.909700	CACCCTTTTTGGAGCTAGCA	58.090	50.000	18.83	0.00	38.35	3.49
928	1215	1.043022	AAGCTGCACCCTTTTTGGAG	58.957	50.000	1.02	0.00	38.35	3.86
929	1216	1.138661	CAAAGCTGCACCCTTTTTGGA	59.861	47.619	1.02	0.00	38.35	3.53
948	1235	3.852578	AGGGAAGGAGAGGAAAATAAGCA	59.147	43.478	0.00	0.00	0.00	3.91
970	1257	1.411501	GGCTTGGGGAGGATGCAAATA	60.412	52.381	0.00	0.00	0.00	1.40
971	1258	0.688749	GGCTTGGGGAGGATGCAAAT	60.689	55.000	0.00	0.00	0.00	2.32
972	1259	1.305213	GGCTTGGGGAGGATGCAAA	60.305	57.895	0.00	0.00	0.00	3.68
975	1262	3.728292	CTGGGCTTGGGGAGGATGC	62.728	68.421	0.00	0.00	0.00	3.91
1036	1326	1.909302	GATGGAAGTGAGGACCAGGAA	59.091	52.381	0.00	0.00	37.12	3.36
1048	1338	0.036010	CTGCCGTCTTGGATGGAAGT	60.036	55.000	9.68	0.00	39.09	3.01
1050	1340	0.250234	CTCTGCCGTCTTGGATGGAA	59.750	55.000	9.68	0.00	40.94	3.53
1429	1728	0.108804	GAGGACGATCGTTGGCTGAA	60.109	55.000	23.63	0.00	0.00	3.02
1433	1732	0.179111	TGATGAGGACGATCGTTGGC	60.179	55.000	23.63	14.34	0.00	4.52
1436	1735	1.825474	AGGTTGATGAGGACGATCGTT	59.175	47.619	23.63	7.27	0.00	3.85
1437	1736	1.135139	CAGGTTGATGAGGACGATCGT	59.865	52.381	22.97	22.97	0.00	3.73
1474	1773	9.834628	TTCCAAATTGAAGTAAAAGTAATAGCG	57.165	29.630	0.00	0.00	0.00	4.26
1568	1867	7.942341	AGTACCCAAAAGAATTGACATCAGTAA	59.058	33.333	0.00	0.00	0.00	2.24
1609	1909	1.064952	GCCAACTCTCTAGAGACGAGC	59.935	57.143	18.76	14.40	44.74	5.03
1638	1938	2.568509	AGGGGGCAAAATGAGTCAAATG	59.431	45.455	0.00	0.00	0.00	2.32
1813	2120	4.647853	GGGTGACTCATATATGCCCGTATA	59.352	45.833	7.92	0.00	0.00	1.47
1819	2126	2.299013	TGACGGGTGACTCATATATGCC	59.701	50.000	7.92	3.05	0.00	4.40
1830	2137	2.486203	TGCACAATTATTGACGGGTGAC	59.514	45.455	12.28	0.00	0.00	3.67
1831	2138	2.784347	TGCACAATTATTGACGGGTGA	58.216	42.857	12.28	0.00	0.00	4.02
1834	2141	3.181501	ACGATTGCACAATTATTGACGGG	60.182	43.478	12.28	0.00	0.00	5.28
1889	2200	6.551975	TGATTGATGGAGATTTGGTGCATATT	59.448	34.615	0.00	0.00	0.00	1.28
2051	2362	4.824848	CGTAAGAATATATCGCACTGGC	57.175	45.455	0.00	0.00	43.02	4.85
2093	2414	1.929169	CGCACATCTGATGTAGTGGTG	59.071	52.381	21.88	12.77	42.70	4.17
2129	2450	2.766263	TCTGATGTGGAGGTATCGCTTT	59.234	45.455	0.00	0.00	0.00	3.51
2140	2461	2.912295	TCCAGTCCAAATCTGATGTGGA	59.088	45.455	22.91	22.91	39.14	4.02
2218	2539	4.158579	ACTCTTGCCTAAAATAAGCCTTGC	59.841	41.667	0.00	0.00	0.00	4.01
2246	2567	7.778470	GATGAACTCTCTAATTTTCATCCGT	57.222	36.000	13.72	0.00	44.46	4.69
2281	2602	4.202161	CGCTCTTTTCTCCTAGCCAGATAA	60.202	45.833	0.00	0.00	0.00	1.75
2358	2679	0.759346	AGAAGCTTGACCTGGACGTT	59.241	50.000	2.10	0.00	0.00	3.99

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.