AutoCloner

Multiple sequence alignment - TraesCS7A01G465300

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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	TraesCS7A01G465300	chr7A	100.000	1778	0	0	457	2234	661646532	661648309	0.000000e+00	3284.0
1	TraesCS7A01G465300	chr7A	100.000	271	0	0	1	271	661646076	661646346	3.310000e-138	501.0
2	TraesCS7A01G465300	chr7A	79.851	670	85	20	798	1443	661945119	661945762	5.660000e-121	444.0
3	TraesCS7A01G465300	chr7A	91.739	230	19	0	998	1227	647934665	647934436	9.950000e-84	320.0
4	TraesCS7A01G465300	chr7A	82.266	203	26	5	464	659	661943242	661943441	1.370000e-37	167.0
5	TraesCS7A01G465300	chr7D	88.231	1368	71	33	493	1823	572649785	572651099	0.000000e+00	1552.0
6	TraesCS7A01G465300	chr7D	87.918	389	33	4	1848	2234	572651205	572651581	1.570000e-121	446.0
7	TraesCS7A01G465300	chr7D	91.852	270	22	0	976	1245	572723680	572723949	5.820000e-101	377.0
8	TraesCS7A01G465300	chr7D	92.147	191	12	3	55	244	572649599	572649787	1.320000e-67	267.0
9	TraesCS7A01G465300	chr7D	93.846	65	1	2	1	65	572616775	572616836	6.570000e-16	95.3
10	TraesCS7A01G465300	chr7B	90.348	632	35	10	458	1065	629423785	629423156	0.000000e+00	806.0
11	TraesCS7A01G465300	chr7B	93.454	443	19	5	1085	1518	629416867	629416426	0.000000e+00	649.0
12	TraesCS7A01G465300	chr7B	85.934	391	36	7	1848	2233	629414567	629414191	1.240000e-107	399.0
13	TraesCS7A01G465300	chr7B	86.921	367	32	7	976	1326	630139051	630139417	4.470000e-107	398.0
14	TraesCS7A01G465300	chr7B	93.382	272	8	7	1	271	629424394	629424132	5.780000e-106	394.0
15	TraesCS7A01G465300	chr7B	83.270	263	33	10	1557	1812	629414973	629414715	4.800000e-57	231.0
16	TraesCS7A01G465300	chr2A	90.948	232	21	0	1001	1232	665843362	665843131	1.670000e-81	313.0
17	TraesCS7A01G465300	chr5D	90.254	236	23	0	1001	1236	92464595	92464360	2.150000e-80	309.0
18	TraesCS7A01G465300	chr1B	90.870	230	21	0	999	1228	651561289	651561060	2.150000e-80	309.0

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	TraesCS7A01G465300	chr7A	661646076	661648309	2233	False	1892.500000	3284	100.000000	1	2234	2	chr7A.!!$F1	2233
1	TraesCS7A01G465300	chr7A	661943242	661945762	2520	False	305.500000	444	81.058500	464	1443	2	chr7A.!!$F2	979
2	TraesCS7A01G465300	chr7D	572649599	572651581	1982	False	755.000000	1552	89.432000	55	2234	3	chr7D.!!$F3	2179
3	TraesCS7A01G465300	chr7B	629423156	629424394	1238	True	600.000000	806	91.865000	1	1065	2	chr7B.!!$R2	1064
4	TraesCS7A01G465300	chr7B	629414191	629416867	2676	True	426.333333	649	87.552667	1085	2233	3	chr7B.!!$R1	1148

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
264	265	0.468226	CCCCCTGATTCCGATCGAAA	59.532	55.0	18.66	1.57	34.91	3.46	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1363	3106	0.107831	ACAAAACAGAGGCCACGCTA	59.892	50.0	5.01	0.0	0.0	4.26	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
54	55	2.207988	TGGTTCTGGTGATCCCATCAT	58.792	47.619	3.70	0.00	44.15	2.45
55	56	2.173356	TGGTTCTGGTGATCCCATCATC	59.827	50.000	3.70	0.00	44.15	2.92
157	158	2.804368	GATACTCGATCGGCTGGGCG	62.804	65.000	16.41	10.25	0.00	6.13
177	178	3.530104	CGCGTGACGTAACCGAGC	61.530	66.667	6.91	0.35	37.88	5.03
178	179	3.530104	GCGTGACGTAACCGAGCG	61.530	66.667	6.91	0.00	37.88	5.03
179	180	2.174107	CGTGACGTAACCGAGCGA	59.826	61.111	0.00	0.00	37.88	4.93
180	181	2.142239	CGTGACGTAACCGAGCGAC	61.142	63.158	0.00	0.00	37.88	5.19
182	183	1.968017	TGACGTAACCGAGCGACCT	60.968	57.895	0.00	0.00	37.88	3.85
194	195	1.218316	GCGACCTTCGTTCCCATCT	59.782	57.895	0.00	0.00	42.81	2.90
217	218	1.176527	AAATTCCTGCACACCCGATG	58.823	50.000	0.00	0.00	0.00	3.84
244	245	3.486383	TCCTTCAACCAATCAACCAGAC	58.514	45.455	0.00	0.00	0.00	3.51
264	265	0.468226	CCCCCTGATTCCGATCGAAA	59.532	55.000	18.66	1.57	34.91	3.46
266	267	1.940613	CCCCTGATTCCGATCGAAAAC	59.059	52.381	18.66	1.01	34.91	2.43
267	268	2.627945	CCCTGATTCCGATCGAAAACA	58.372	47.619	18.66	6.80	34.91	2.83
268	269	3.206150	CCCTGATTCCGATCGAAAACAT	58.794	45.455	18.66	0.26	34.91	2.71
597	776	6.221659	TGTCGTAGATGAGTCGATATAGTGT	58.778	40.000	0.00	0.00	40.67	3.55
685	893	2.489329	AGGATTGTCGTTTGCAGATTGG	59.511	45.455	0.00	0.00	0.00	3.16
686	894	2.415893	GGATTGTCGTTTGCAGATTGGG	60.416	50.000	0.00	0.00	0.00	4.12
687	895	1.686355	TTGTCGTTTGCAGATTGGGT	58.314	45.000	0.00	0.00	0.00	4.51
688	896	1.686355	TGTCGTTTGCAGATTGGGTT	58.314	45.000	0.00	0.00	0.00	4.11
771	2432	4.319177	GTCAGTCCTGTTAGCACAATCTT	58.681	43.478	0.00	0.00	30.36	2.40
835	2556	1.639722	TGATCCCGTGGTTTCTCTCA	58.360	50.000	0.00	0.00	0.00	3.27
859	2580	7.013369	TCAGTAGCTGTCGAATATTGACTACAT	59.987	37.037	14.81	5.78	37.26	2.29
1363	3106	5.089970	TGAACATCTGCTGCTGTAATAGT	57.910	39.130	0.00	0.00	0.00	2.12
1371	3121	2.128035	CTGCTGTAATAGTAGCGTGGC	58.872	52.381	0.00	0.00	42.74	5.01
1413	3165	6.311690	GTGGCAGTGTAGAACTTAATCTTCTC	59.688	42.308	0.00	0.00	36.83	2.87
1438	3191	6.418819	CACTCTGTGATTGTGGTTTTCAAATC	59.581	38.462	0.00	0.00	35.23	2.17
1518	3271	3.525537	ACTATCGTTGCTGAATCTGGTG	58.474	45.455	0.00	0.00	0.00	4.17
1519	3272	1.742761	ATCGTTGCTGAATCTGGTGG	58.257	50.000	0.00	0.00	0.00	4.61
1520	3273	0.396435	TCGTTGCTGAATCTGGTGGT	59.604	50.000	0.00	0.00	0.00	4.16
1521	3274	0.798776	CGTTGCTGAATCTGGTGGTC	59.201	55.000	0.00	0.00	0.00	4.02
1570	4740	5.658849	GAGGGACTAAGAGCATCTCCAACA	61.659	50.000	0.00	0.00	44.39	3.33
1619	4790	3.299542	GCCGTTTGTGTAAATAATGCACG	59.700	43.478	0.00	0.00	46.49	5.34
1632	4803	2.634777	GCACGGTTGCGCAGTTTA	59.365	55.556	11.31	0.00	39.50	2.01
1658	4829	1.372582	GTGATGCCGAAGATTGAGCA	58.627	50.000	0.00	0.00	40.00	4.26
1687	4858	4.315803	GTGTAGCAACATAGACCACTTGT	58.684	43.478	0.00	0.00	38.08	3.16
1688	4859	5.475719	GTGTAGCAACATAGACCACTTGTA	58.524	41.667	0.00	0.00	38.08	2.41
1689	4860	5.577164	GTGTAGCAACATAGACCACTTGTAG	59.423	44.000	0.00	0.00	38.08	2.74
1690	4861	3.600388	AGCAACATAGACCACTTGTAGC	58.400	45.455	0.00	0.00	0.00	3.58
1691	4862	3.007940	AGCAACATAGACCACTTGTAGCA	59.992	43.478	0.00	0.00	0.00	3.49
1692	4863	3.751175	GCAACATAGACCACTTGTAGCAA	59.249	43.478	0.00	0.00	0.00	3.91
1694	4865	4.617253	ACATAGACCACTTGTAGCAACA	57.383	40.909	0.00	0.00	0.00	3.33
1698	4885	0.179468	ACCACTTGTAGCAACACCGT	59.821	50.000	0.00	0.00	34.61	4.83
1701	4888	2.143122	CACTTGTAGCAACACCGTGAT	58.857	47.619	5.28	0.00	38.57	3.06
1707	4894	3.124921	CAACACCGTGATCCCCGC	61.125	66.667	5.28	0.00	0.00	6.13
1775	4963	3.411517	CTCCCCACCTCGCCCAAT	61.412	66.667	0.00	0.00	0.00	3.16
1784	4972	3.074369	TCGCCCAATCTCCTCGCA	61.074	61.111	0.00	0.00	0.00	5.10
1786	4974	1.524621	CGCCCAATCTCCTCGCAAT	60.525	57.895	0.00	0.00	0.00	3.56
1823	5011	3.991536	GAAGTCGCACCGGCTCCTC	62.992	68.421	0.00	0.00	42.48	3.71
1852	5152	0.399075	TCCACCCCTTTTCCGACTTC	59.601	55.000	0.00	0.00	0.00	3.01
2140	5447	3.096495	TCCCCATACCCTGCAGGC	61.096	66.667	28.39	0.00	40.58	4.85
2180	5487	1.542375	ATGGACCTGTGCCCTCCTT	60.542	57.895	0.00	0.00	0.00	3.36

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
15	16	5.432885	ACCATCTCAACGTTTCGATTTTT	57.567	34.783	0.00	0.00	0.00	1.94
91	92	3.622826	CGGAACCTGGTCCCACGT	61.623	66.667	2.06	0.00	33.74	4.49
177	178	2.953466	TAAGATGGGAACGAAGGTCG	57.047	50.000	0.00	0.00	46.93	4.79
178	179	7.041303	GGAATTTATAAGATGGGAACGAAGGTC	60.041	40.741	0.00	0.00	0.00	3.85
179	180	6.771267	GGAATTTATAAGATGGGAACGAAGGT	59.229	38.462	0.00	0.00	0.00	3.50
180	181	6.998673	AGGAATTTATAAGATGGGAACGAAGG	59.001	38.462	0.00	0.00	0.00	3.46
182	183	6.262273	GCAGGAATTTATAAGATGGGAACGAA	59.738	38.462	0.00	0.00	0.00	3.85
194	195	4.223556	TCGGGTGTGCAGGAATTTATAA	57.776	40.909	0.00	0.00	0.00	0.98
217	218	2.178580	TGATTGGTTGAAGGATTGCCC	58.821	47.619	0.00	0.00	33.31	5.36
219	220	3.006752	TGGTTGATTGGTTGAAGGATTGC	59.993	43.478	0.00	0.00	0.00	3.56
223	224	3.486383	GTCTGGTTGATTGGTTGAAGGA	58.514	45.455	0.00	0.00	0.00	3.36
583	762	4.681942	GGATGCACAACACTATATCGACTC	59.318	45.833	0.00	0.00	0.00	3.36
597	776	3.129113	GTGCAATCTACATGGATGCACAA	59.871	43.478	24.07	0.00	42.71	3.33
685	893	4.911033	CGGAAACACGGTAAACATTAAACC	59.089	41.667	0.00	0.00	0.00	3.27
686	894	5.509771	ACGGAAACACGGTAAACATTAAAC	58.490	37.500	0.00	0.00	38.39	2.01
687	895	5.526846	AGACGGAAACACGGTAAACATTAAA	59.473	36.000	0.00	0.00	38.39	1.52
688	896	5.055812	AGACGGAAACACGGTAAACATTAA	58.944	37.500	0.00	0.00	38.39	1.40
794	2455	2.886523	TGCAACAGGAAGGTTTGATCTG	59.113	45.455	0.00	0.00	0.00	2.90
835	2556	6.694877	TGTAGTCAATATTCGACAGCTACT	57.305	37.500	15.69	0.00	35.77	2.57
894	2615	7.772332	ATTCAGTCATGTAAATCGTAAGGAC	57.228	36.000	0.00	0.00	38.47	3.85
959	2680	7.517614	TGCAATTCAGTATTAAGTCACCAAA	57.482	32.000	0.00	0.00	0.00	3.28
972	2693	6.535865	GCATCATTGGAATTTGCAATTCAGTA	59.464	34.615	12.80	0.00	36.23	2.74
1068	2792	5.076182	TGGATCTTTGCCTTAACATTGTCA	58.924	37.500	0.00	0.00	0.00	3.58
1113	2837	3.382803	GATCAGGCGCTGCTGGTCT	62.383	63.158	16.80	0.00	0.00	3.85
1137	2861	3.313524	TCCTCGAGCTGCTTGCCA	61.314	61.111	12.16	0.00	44.23	4.92
1168	2892	5.160607	TCCTTCTGAATGTTGTAATCGGT	57.839	39.130	0.00	0.00	0.00	4.69
1363	3106	0.107831	ACAAAACAGAGGCCACGCTA	59.892	50.000	5.01	0.00	0.00	4.26
1371	3121	3.119173	TGCCACTTCAAACAAAACAGAGG	60.119	43.478	0.00	0.00	0.00	3.69
1413	3165	4.898829	TGAAAACCACAATCACAGAGTG	57.101	40.909	0.00	0.00	33.62	3.51
1438	3191	2.702751	TACCATATTGGCGCCGACGG	62.703	60.000	21.40	21.61	42.67	4.79
1518	3271	0.618981	CCCAAGAAGTACCCTGGACC	59.381	60.000	0.00	0.00	0.00	4.46
1519	3272	1.652947	TCCCAAGAAGTACCCTGGAC	58.347	55.000	0.00	0.00	0.00	4.02
1520	3273	2.478292	GATCCCAAGAAGTACCCTGGA	58.522	52.381	0.00	0.00	0.00	3.86
1521	3274	1.490910	GGATCCCAAGAAGTACCCTGG	59.509	57.143	0.00	0.00	0.00	4.45
1570	4740	6.360618	CAGAAATTCTAGGTTTATGGGAGCT	58.639	40.000	0.00	0.00	0.00	4.09
1619	4790	3.047093	ACGATTTTTAAACTGCGCAACC	58.953	40.909	13.05	0.00	0.00	3.77
1632	4803	4.155826	TCAATCTTCGGCATCACGATTTTT	59.844	37.500	0.00	0.00	43.11	1.94
1658	4829	5.221843	TGGTCTATGTTGCTACACCTTTTCT	60.222	40.000	2.28	0.00	37.03	2.52
1687	4858	1.600107	GGGGATCACGGTGTTGCTA	59.400	57.895	8.17	0.00	0.00	3.49
1688	4859	2.351276	GGGGATCACGGTGTTGCT	59.649	61.111	8.17	0.00	0.00	3.91
1689	4860	3.124921	CGGGGATCACGGTGTTGC	61.125	66.667	8.17	5.08	0.00	4.17
1690	4861	3.124921	GCGGGGATCACGGTGTTG	61.125	66.667	8.17	0.00	0.00	3.33
1691	4862	4.752879	CGCGGGGATCACGGTGTT	62.753	66.667	8.17	0.00	0.00	3.32
1727	4914	2.598787	CCCAGCTACGGTTTCCCCA	61.599	63.158	0.00	0.00	0.00	4.96
1728	4915	2.271173	CCCAGCTACGGTTTCCCC	59.729	66.667	0.00	0.00	0.00	4.81
1773	4961	0.824109	TCGGTGATTGCGAGGAGATT	59.176	50.000	0.00	0.00	0.00	2.40
1775	4963	1.809869	CTCGGTGATTGCGAGGAGA	59.190	57.895	0.00	0.00	0.00	3.71
1817	5005	4.828925	GAGGCGGCACAGAGGAGC	62.829	72.222	13.08	0.00	0.00	4.70
1830	5054	2.361230	CGGAAAAGGGGTGGAGGC	60.361	66.667	0.00	0.00	0.00	4.70
1887	5187	1.227380	GCTGGCGTAGGTGGATCTG	60.227	63.158	0.00	0.00	0.00	2.90
2036	5339	0.605319	GCAACCACCGAGATGAACCA	60.605	55.000	0.00	0.00	0.00	3.67
2082	5389	3.660111	GCCACACACTCGGCCAAC	61.660	66.667	2.24	0.00	42.82	3.77
2152	5459	3.164269	AGGTCCATGGCCGCTAGG	61.164	66.667	6.96	0.00	41.62	3.02
2154	5461	2.687200	ACAGGTCCATGGCCGCTA	60.687	61.111	6.96	0.00	0.00	4.26
2155	5462	4.415150	CACAGGTCCATGGCCGCT	62.415	66.667	6.96	0.00	0.00	5.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.