AutoCloner

Multiple sequence alignment - TraesCS7D01G212400

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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	TraesCS7D01G212400	chr7D	100.000	2237	0	0	1	2237	170729591	170731827	0.000000e+00	4132.0
1	TraesCS7D01G212400	chr7D	76.384	271	59	4	1018	1287	170607641	170607907	8.330000e-30	141.0
2	TraesCS7D01G212400	chr7B	94.539	1813	59	19	1	1810	137025812	137027587	0.000000e+00	2763.0
3	TraesCS7D01G212400	chr7B	83.784	407	41	13	1793	2189	137027602	137027993	1.630000e-96	363.0
4	TraesCS7D01G212400	chr7B	77.122	271	57	4	1018	1287	136888314	136888580	3.850000e-33	152.0
5	TraesCS7D01G212400	chr7A	94.560	1728	52	15	1	1708	173637581	173639286	0.000000e+00	2632.0
6	TraesCS7D01G212400	chr7A	86.149	296	21	5	1948	2237	173639885	173640166	3.610000e-78	302.0
7	TraesCS7D01G212400	chr7A	83.981	206	18	7	1758	1961	173639284	173639476	1.360000e-42	183.0
8	TraesCS7D01G212400	chr7A	77.491	271	56	4	1018	1287	173493068	173493334	8.270000e-35	158.0
9	TraesCS7D01G212400	chr3D	78.049	287	47	15	1009	1287	327575506	327575784	1.370000e-37	167.0
10	TraesCS7D01G212400	chr3A	77.972	286	49	13	1009	1287	441570621	441570899	1.370000e-37	167.0
11	TraesCS7D01G212400	chr3B	77.273	286	51	13	1009	1287	422157812	422157534	2.970000e-34	156.0
12	TraesCS7D01G212400	chr6A	78.818	203	31	10	102	295	521649895	521649696	2.330000e-25	126.0
13	TraesCS7D01G212400	chr6A	74.884	215	43	10	109	314	162309211	162309423	1.100000e-13	87.9
14	TraesCS7D01G212400	chr6D	77.778	180	32	7	109	281	121344821	121344999	1.090000e-18	104.0
15	TraesCS7D01G212400	chr6D	76.536	179	34	7	109	280	136390567	136390390	8.510000e-15	91.6
16	TraesCS7D01G212400	chr6B	77.049	183	34	7	109	284	213468391	213468210	5.080000e-17	99.0
17	TraesCS7D01G212400	chr6B	100.000	28	0	0	1407	1434	660756552	660756525	4.000000e-03	52.8

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	TraesCS7D01G212400	chr7D	170729591	170731827	2236	False	4132	4132	100.0000	1	2237	1	chr7D.!!$F2	2236
1	TraesCS7D01G212400	chr7B	137025812	137027993	2181	False	1563	2763	89.1615	1	2189	2	chr7B.!!$F2	2188
2	TraesCS7D01G212400	chr7A	173637581	173640166	2585	False	1039	2632	88.2300	1	2237	3	chr7A.!!$F2	2236

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
855	866	2.500229	GTCGTGGAAATGTCTTTGGGA	58.5	47.619	0.0	0.0	0.0	4.37	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2068	2572	0.036164	ACCAAGGTGTCATAGCGCAA	59.964	50.0	11.47	0.0	0.0	4.85	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
39	40	3.004944	GGAATTTCCGTAACAACCAGCAA	59.995	43.478	0.00	0.00	0.00	3.91
590	601	2.506438	GTAGTGGCAGGCGACGAC	60.506	66.667	0.00	0.00	0.00	4.34
809	820	4.916249	GGTGAAGTTGTAAGACTCGTAGTG	59.084	45.833	0.00	0.00	0.00	2.74
855	866	2.500229	GTCGTGGAAATGTCTTTGGGA	58.500	47.619	0.00	0.00	0.00	4.37
866	877	2.912956	TGTCTTTGGGATACTCCAGCTT	59.087	45.455	0.00	0.00	38.64	3.74
934	946	6.535274	TCGAAATGTAGATCATGCATTCTG	57.465	37.500	10.58	0.00	42.63	3.02
935	947	6.051074	TCGAAATGTAGATCATGCATTCTGT	58.949	36.000	10.58	0.00	42.63	3.41
936	948	7.209475	TCGAAATGTAGATCATGCATTCTGTA	58.791	34.615	10.58	1.20	42.63	2.74
937	949	7.383300	TCGAAATGTAGATCATGCATTCTGTAG	59.617	37.037	10.58	0.00	42.63	2.74
938	950	7.170489	CGAAATGTAGATCATGCATTCTGTAGT	59.830	37.037	10.58	0.00	42.63	2.73
951	963	7.836842	TGCATTCTGTAGTGTAGATCAGTAAA	58.163	34.615	0.00	0.00	34.26	2.01
991	1009	9.499479	CAGTGGACTGAAATTTATATCAGCTAT	57.501	33.333	0.04	0.00	46.59	2.97
1083	1104	3.371097	GACGAAGGCCATGGAGCGA	62.371	63.158	18.40	0.00	0.00	4.93
1599	1621	2.031163	GTGCCTGGTGACGAGCTT	59.969	61.111	0.00	0.00	0.00	3.74
1603	1625	1.302033	CCTGGTGACGAGCTTGCTT	60.302	57.895	0.00	0.00	0.00	3.91
1806	1861	3.252458	GGTACGTCAGCTTTGGTTTGATT	59.748	43.478	0.00	0.00	0.00	2.57
1872	1933	4.729856	GAACCGCGCGTACTGGGT	62.730	66.667	29.95	15.43	0.00	4.51
1873	1934	3.340953	GAACCGCGCGTACTGGGTA	62.341	63.158	29.95	0.00	31.18	3.69
1874	1935	2.817470	GAACCGCGCGTACTGGGTAA	62.817	60.000	29.95	0.00	31.18	2.85
1885	1962	2.074547	ACTGGGTAAATCACGTGACG	57.925	50.000	22.71	2.24	0.00	4.35
1904	1982	2.010580	GCTTTGTCGAGCGATAATGC	57.989	50.000	18.68	18.68	38.44	3.56
1961	2039	1.519234	CAGCAGCAATGCAGCATGG	60.519	57.895	23.83	7.11	43.44	3.66
1963	2041	0.681887	AGCAGCAATGCAGCATGGTA	60.682	50.000	23.83	0.00	43.44	3.25
1964	2042	0.248907	GCAGCAATGCAGCATGGTAG	60.249	55.000	17.68	3.96	40.73	3.18
1966	2044	0.681887	AGCAATGCAGCATGGTAGCA	60.682	50.000	19.30	19.30	43.14	3.49
1967	2045	0.173935	GCAATGCAGCATGGTAGCAA	59.826	50.000	20.37	8.93	42.15	3.91
1968	2046	1.404449	GCAATGCAGCATGGTAGCAAA	60.404	47.619	20.37	4.62	42.15	3.68
1969	2047	2.931753	GCAATGCAGCATGGTAGCAAAA	60.932	45.455	20.37	4.05	42.15	2.44
1987	2486	0.476771	AACCATTCCTTCACCGTGGT	59.523	50.000	0.00	0.00	44.62	4.16
2105	2609	5.584649	CCTTGGTATCAATGTGTCACGTAAT	59.415	40.000	0.00	0.00	31.75	1.89
2153	2657	1.305297	AGGCACGATGAGAGACCCA	60.305	57.895	0.00	0.00	0.00	4.51
2154	2658	1.142748	GGCACGATGAGAGACCCAG	59.857	63.158	0.00	0.00	0.00	4.45
2155	2659	1.520342	GCACGATGAGAGACCCAGC	60.520	63.158	0.00	0.00	0.00	4.85
2156	2660	1.893062	CACGATGAGAGACCCAGCA	59.107	57.895	0.00	0.00	0.00	4.41
2181	2685	4.585526	GCGGCCGGTGATGATCGA	62.586	66.667	29.38	0.00	0.00	3.59
2189	2693	2.035193	CCGGTGATGATCGATCTGAAGT	59.965	50.000	25.02	7.17	31.55	3.01
2190	2694	3.048501	CGGTGATGATCGATCTGAAGTG	58.951	50.000	25.02	8.57	31.55	3.16
2204	2708	1.580845	GAAGTGAAGCGCATGCCACT	61.581	55.000	18.17	18.17	42.89	4.00
2232	2736	4.054825	GCCGGCATGTGGGTGTTG	62.055	66.667	24.80	0.00	0.00	3.33
2233	2737	2.597217	CCGGCATGTGGGTGTTGT	60.597	61.111	0.00	0.00	0.00	3.32
2234	2738	2.644418	CGGCATGTGGGTGTTGTG	59.356	61.111	0.00	0.00	0.00	3.33
2235	2739	2.192861	CGGCATGTGGGTGTTGTGT	61.193	57.895	0.00	0.00	0.00	3.72

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
309	320	4.742201	GAGGAGTTCGCGCAGGCA	62.742	66.667	8.75	0.00	39.92	4.75
732	743	3.352338	GAACCAGTCCGACGCCGAT	62.352	63.158	0.00	0.00	38.22	4.18
809	820	2.508526	ACCAAGAATTCAGGACACTGC	58.491	47.619	20.07	0.00	44.54	4.40
934	946	8.263940	TGCCAAAATTTACTGATCTACACTAC	57.736	34.615	0.00	0.00	0.00	2.73
935	947	8.856153	TTGCCAAAATTTACTGATCTACACTA	57.144	30.769	0.00	0.00	0.00	2.74
936	948	7.759489	TTGCCAAAATTTACTGATCTACACT	57.241	32.000	0.00	0.00	0.00	3.55
951	963	5.969423	CAGTCCACTGATTATTGCCAAAAT	58.031	37.500	0.00	0.00	46.59	1.82
991	1009	9.832445	GTCCAAGGTAATAATCATCAGTTTAGA	57.168	33.333	0.00	0.00	0.00	2.10
994	1012	8.877864	TTGTCCAAGGTAATAATCATCAGTTT	57.122	30.769	0.00	0.00	0.00	2.66
1002	1020	5.297029	GTGCCTCTTGTCCAAGGTAATAATC	59.703	44.000	7.16	0.00	38.88	1.75
1155	1176	3.826637	CGACCTCGGCTTCCTTAAA	57.173	52.632	0.00	0.00	35.37	1.52
1581	1603	2.511452	AAGCTCGTCACCAGGCACT	61.511	57.895	0.00	0.00	43.88	4.40
1582	1604	2.031163	AAGCTCGTCACCAGGCAC	59.969	61.111	0.00	0.00	0.00	5.01
1583	1605	2.031012	CAAGCTCGTCACCAGGCA	59.969	61.111	0.00	0.00	0.00	4.75
1584	1606	3.426568	GCAAGCTCGTCACCAGGC	61.427	66.667	0.00	0.00	0.00	4.85
1585	1607	1.302033	AAGCAAGCTCGTCACCAGG	60.302	57.895	0.00	0.00	0.00	4.45
1586	1608	1.864862	CAAGCAAGCTCGTCACCAG	59.135	57.895	0.00	0.00	0.00	4.00
1587	1609	2.253758	GCAAGCAAGCTCGTCACCA	61.254	57.895	0.00	0.00	0.00	4.17
1588	1610	0.670546	TAGCAAGCAAGCTCGTCACC	60.671	55.000	6.16	0.00	45.26	4.02
1647	1669	4.003788	CCCCACGACAAGCCGAGT	62.004	66.667	0.00	0.00	0.00	4.18
1872	1933	2.154198	CGACAAAGCGTCACGTGATTTA	59.846	45.455	23.12	0.00	45.70	1.40
1873	1934	1.070843	CGACAAAGCGTCACGTGATTT	60.071	47.619	23.12	15.28	45.70	2.17
1874	1935	0.506932	CGACAAAGCGTCACGTGATT	59.493	50.000	23.12	9.44	45.70	2.57
1885	1962	1.594862	AGCATTATCGCTCGACAAAGC	59.405	47.619	2.80	2.80	37.91	3.51
1909	1987	3.435327	ACAGCATTATCGCTCGACAAAAA	59.565	39.130	0.00	0.00	41.38	1.94
1910	1988	3.000041	ACAGCATTATCGCTCGACAAAA	59.000	40.909	0.00	0.00	41.38	2.44
1911	1989	2.603110	GACAGCATTATCGCTCGACAAA	59.397	45.455	0.00	0.00	41.38	2.83
1912	1990	2.193447	GACAGCATTATCGCTCGACAA	58.807	47.619	0.00	0.00	41.38	3.18
1913	1991	1.134175	TGACAGCATTATCGCTCGACA	59.866	47.619	0.00	0.00	41.38	4.35
1914	1992	1.518929	GTGACAGCATTATCGCTCGAC	59.481	52.381	0.00	0.00	41.38	4.20
1915	1993	1.405463	AGTGACAGCATTATCGCTCGA	59.595	47.619	0.00	0.00	41.38	4.04
1916	1994	1.845266	AGTGACAGCATTATCGCTCG	58.155	50.000	0.00	0.00	41.38	5.03
1917	1995	2.286294	CCAAGTGACAGCATTATCGCTC	59.714	50.000	0.00	0.00	41.38	5.03
1918	1996	2.283298	CCAAGTGACAGCATTATCGCT	58.717	47.619	0.00	0.00	45.21	4.93
1919	1997	1.331756	CCCAAGTGACAGCATTATCGC	59.668	52.381	0.00	0.00	0.00	4.58
1920	1998	1.331756	GCCCAAGTGACAGCATTATCG	59.668	52.381	0.00	0.00	0.00	2.92
1961	2039	3.365969	CGGTGAAGGAATGGTTTTGCTAC	60.366	47.826	0.00	0.00	0.00	3.58
1963	2041	1.613437	CGGTGAAGGAATGGTTTTGCT	59.387	47.619	0.00	0.00	0.00	3.91
1964	2042	1.339929	ACGGTGAAGGAATGGTTTTGC	59.660	47.619	0.00	0.00	0.00	3.68
1966	2044	1.960689	CCACGGTGAAGGAATGGTTTT	59.039	47.619	10.28	0.00	0.00	2.43
1967	2045	1.133606	ACCACGGTGAAGGAATGGTTT	60.134	47.619	10.28	0.00	40.86	3.27
1968	2046	0.476771	ACCACGGTGAAGGAATGGTT	59.523	50.000	10.28	0.00	40.86	3.67
1969	2047	0.036306	GACCACGGTGAAGGAATGGT	59.964	55.000	10.28	0.00	46.37	3.55
1975	2474	1.372997	CTCACGACCACGGTGAAGG	60.373	63.158	10.28	0.00	44.46	3.46
1999	2498	2.243407	CTACGACACTTCAGTTCTCGC	58.757	52.381	0.00	0.00	31.97	5.03
2068	2572	0.036164	ACCAAGGTGTCATAGCGCAA	59.964	50.000	11.47	0.00	0.00	4.85
2071	2575	3.452755	TGATACCAAGGTGTCATAGCG	57.547	47.619	13.78	0.00	40.43	4.26
2134	2638	1.323271	TGGGTCTCTCATCGTGCCTC	61.323	60.000	0.00	0.00	0.00	4.70
2141	2645	0.251354	TGCTTGCTGGGTCTCTCATC	59.749	55.000	0.00	0.00	0.00	2.92
2180	2684	1.267932	GCATGCGCTTCACTTCAGATC	60.268	52.381	9.73	0.00	34.30	2.75
2181	2685	0.731417	GCATGCGCTTCACTTCAGAT	59.269	50.000	9.73	0.00	34.30	2.90
2189	2693	3.057548	CCAGTGGCATGCGCTTCA	61.058	61.111	12.44	0.19	38.60	3.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.