AutoCloner

Multiple sequence alignment - TraesCS6D01G345300

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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	TraesCS6D01G345300	chr6D	100.000	3262	0	0	1	3262	445278734	445275473	0.000000e+00	6024.0
1	TraesCS6D01G345300	chr6D	95.594	2633	66	9	635	3262	387624677	387622090	0.000000e+00	4174.0
2	TraesCS6D01G345300	chr6D	97.994	947	18	1	1	947	445210747	445209802	0.000000e+00	1642.0
3	TraesCS6D01G345300	chr6D	88.267	375	34	5	265	634	445345728	445345359	1.070000e-119	440.0
4	TraesCS6D01G345300	chr3D	97.567	2630	61	3	635	3262	374010878	374008250	0.000000e+00	4499.0
5	TraesCS6D01G345300	chr3D	97.110	2630	73	3	635	3262	155675847	155678475	0.000000e+00	4433.0
6	TraesCS6D01G345300	chr3D	96.416	2232	78	2	635	2864	609771286	609769055	0.000000e+00	3677.0
7	TraesCS6D01G345300	chr3D	96.113	1904	56	2	1377	3262	580651484	580649581	0.000000e+00	3090.0
8	TraesCS6D01G345300	chr2D	97.262	2630	69	3	635	3262	535662318	535664946	0.000000e+00	4455.0
9	TraesCS6D01G345300	chr2D	95.855	2654	72	19	635	3262	77209587	77212228	0.000000e+00	4257.0
10	TraesCS6D01G345300	chr2D	94.753	2630	104	6	635	3262	633747075	633749672	0.000000e+00	4061.0
11	TraesCS6D01G345300	chr2D	97.125	1913	53	2	1350	3262	207005518	207003608	0.000000e+00	3227.0
12	TraesCS6D01G345300	chr1D	97.190	2633	70	4	634	3262	422850796	422848164	0.000000e+00	4449.0
13	TraesCS6D01G345300	chr5D	96.768	2630	81	3	635	3262	504761414	504764041	0.000000e+00	4383.0
14	TraesCS6D01G345300	chr2A	89.076	119	8	3	1	115	39602450	39602333	3.390000e-30	143.0
15	TraesCS6D01G345300	chr2B	88.235	119	9	3	1	115	60967197	60967314	1.580000e-28	137.0
16	TraesCS6D01G345300	chr2B	82.759	58	10	0	207	264	26137568	26137625	6.000000e-03	52.8
17	TraesCS6D01G345300	chr5B	91.045	67	6	0	200	266	684043262	684043196	1.250000e-14	91.6

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	TraesCS6D01G345300	chr6D	445275473	445278734	3261	True	6024	6024	100.000	1	3262	1	chr6D.!!$R3	3261
1	TraesCS6D01G345300	chr6D	387622090	387624677	2587	True	4174	4174	95.594	635	3262	1	chr6D.!!$R1	2627
2	TraesCS6D01G345300	chr6D	445209802	445210747	945	True	1642	1642	97.994	1	947	1	chr6D.!!$R2	946
3	TraesCS6D01G345300	chr3D	374008250	374010878	2628	True	4499	4499	97.567	635	3262	1	chr3D.!!$R1	2627
4	TraesCS6D01G345300	chr3D	155675847	155678475	2628	False	4433	4433	97.110	635	3262	1	chr3D.!!$F1	2627
5	TraesCS6D01G345300	chr3D	609769055	609771286	2231	True	3677	3677	96.416	635	2864	1	chr3D.!!$R3	2229
6	TraesCS6D01G345300	chr3D	580649581	580651484	1903	True	3090	3090	96.113	1377	3262	1	chr3D.!!$R2	1885
7	TraesCS6D01G345300	chr2D	535662318	535664946	2628	False	4455	4455	97.262	635	3262	1	chr2D.!!$F2	2627
8	TraesCS6D01G345300	chr2D	77209587	77212228	2641	False	4257	4257	95.855	635	3262	1	chr2D.!!$F1	2627
9	TraesCS6D01G345300	chr2D	633747075	633749672	2597	False	4061	4061	94.753	635	3262	1	chr2D.!!$F3	2627
10	TraesCS6D01G345300	chr2D	207003608	207005518	1910	True	3227	3227	97.125	1350	3262	1	chr2D.!!$R1	1912
11	TraesCS6D01G345300	chr1D	422848164	422850796	2632	True	4449	4449	97.190	634	3262	1	chr1D.!!$R1	2628
12	TraesCS6D01G345300	chr5D	504761414	504764041	2627	False	4383	4383	96.768	635	3262	1	chr5D.!!$F1	2627

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
30	31	0.615331	ACATGTGCATCGGTTCTCCT	59.385	50.0	0.00	0.0	0.00	3.69	F
1659	1666	0.917533	AGATGAGCATTGGCCAGAGT	59.082	50.0	5.11	0.0	42.56	3.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1748	1755	1.726791	GGCTGTGTGAGATTGTGTACG	59.273	52.381	0.00	0.0	0.0	3.67	R
2948	3016	0.738762	CGAGGTCGTCGTACTCTCCA	60.739	60.000	6.77	0.0	44.2	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
30	31	0.615331	ACATGTGCATCGGTTCTCCT	59.385	50.000	0.00	0.00	0.00	3.69
31	32	1.003580	ACATGTGCATCGGTTCTCCTT	59.996	47.619	0.00	0.00	0.00	3.36
167	168	2.349886	GTGAGAGTATGCTTTTGAGCCG	59.650	50.000	0.00	0.00	0.00	5.52
321	322	3.208747	TCTTATCCTGCCGAAAATCCC	57.791	47.619	0.00	0.00	0.00	3.85
597	598	2.023771	CGACTGTGCATGCGTGTCT	61.024	57.895	24.55	5.47	0.00	3.41
782	784	1.376812	GGTTGAGGGCGTTTCCGAT	60.377	57.895	0.00	0.00	35.63	4.18
978	981	2.185310	TTTGCTCCTTCCTCTCCGGC	62.185	60.000	0.00	0.00	0.00	6.13
1054	1057	2.890474	CCCGCGCACAGTACATCC	60.890	66.667	8.75	0.00	0.00	3.51
1427	1430	3.802948	AGGGTTCATAGTTACTGCTCG	57.197	47.619	0.00	0.00	0.00	5.03
1659	1666	0.917533	AGATGAGCATTGGCCAGAGT	59.082	50.000	5.11	0.00	42.56	3.24
1748	1755	1.941999	GCCTGGAGCATTCAAGCACC	61.942	60.000	0.00	0.00	44.31	5.01
1768	1775	1.726791	CGTACACAATCTCACACAGCC	59.273	52.381	0.00	0.00	0.00	4.85
2002	2009	8.019669	CACTGTCATTAGGAATTTGAAGTTCAG	58.980	37.037	5.56	0.00	0.00	3.02
2070	2098	3.432749	GGAGATTTGCTATGCTGACCTGA	60.433	47.826	0.00	0.00	0.00	3.86
2071	2099	4.194640	GAGATTTGCTATGCTGACCTGAA	58.805	43.478	0.00	0.00	0.00	3.02
2072	2100	4.197750	AGATTTGCTATGCTGACCTGAAG	58.802	43.478	0.00	0.00	0.00	3.02
2073	2101	3.701205	TTTGCTATGCTGACCTGAAGA	57.299	42.857	0.00	0.00	0.00	2.87
2074	2102	3.701205	TTGCTATGCTGACCTGAAGAA	57.299	42.857	0.00	0.00	0.00	2.52
2075	2103	3.701205	TGCTATGCTGACCTGAAGAAA	57.299	42.857	0.00	0.00	0.00	2.52
2076	2104	3.603532	TGCTATGCTGACCTGAAGAAAG	58.396	45.455	0.00	0.00	0.00	2.62
2077	2105	3.261643	TGCTATGCTGACCTGAAGAAAGA	59.738	43.478	0.00	0.00	0.00	2.52
2078	2106	3.870419	GCTATGCTGACCTGAAGAAAGAG	59.130	47.826	0.00	0.00	0.00	2.85
2079	2107	4.382470	GCTATGCTGACCTGAAGAAAGAGA	60.382	45.833	0.00	0.00	0.00	3.10
2080	2108	4.630644	ATGCTGACCTGAAGAAAGAGAA	57.369	40.909	0.00	0.00	0.00	2.87
2081	2109	4.000331	TGCTGACCTGAAGAAAGAGAAG	58.000	45.455	0.00	0.00	0.00	2.85
2082	2110	3.244353	TGCTGACCTGAAGAAAGAGAAGG	60.244	47.826	0.00	0.00	0.00	3.46
2083	2111	3.007398	GCTGACCTGAAGAAAGAGAAGGA	59.993	47.826	0.00	0.00	0.00	3.36
2084	2112	4.323409	GCTGACCTGAAGAAAGAGAAGGAT	60.323	45.833	0.00	0.00	0.00	3.24
2085	2113	5.157940	TGACCTGAAGAAAGAGAAGGATG	57.842	43.478	0.00	0.00	0.00	3.51
2086	2114	4.840680	TGACCTGAAGAAAGAGAAGGATGA	59.159	41.667	0.00	0.00	0.00	2.92
2087	2115	5.159273	ACCTGAAGAAAGAGAAGGATGAC	57.841	43.478	0.00	0.00	0.00	3.06
2088	2116	4.019771	ACCTGAAGAAAGAGAAGGATGACC	60.020	45.833	0.00	0.00	0.00	4.02
2213	2241	2.167281	GCTCAAGACAGCAGGTGATAGA	59.833	50.000	6.61	0.00	39.43	1.98
2275	2303	5.250200	TGAGGACTAAGTTGTGTTGTTGTT	58.750	37.500	0.00	0.00	0.00	2.83
2433	2461	8.791327	TCTGTTTGTGATGAATTATCAGCTTA	57.209	30.769	0.00	0.00	46.09	3.09
2531	2575	9.520515	TCATACTGCATAGATAGTCTGACATAA	57.479	33.333	10.88	0.00	28.80	1.90
2624	2691	9.988815	GATACAAATGACATAGATAGAACTGGT	57.011	33.333	0.00	0.00	0.00	4.00
2886	2954	0.260230	TTGGGTTGTTCTTCTGCCCA	59.740	50.000	0.00	0.00	46.59	5.36
2931	2999	1.818785	GAGCTGCACATCAGGCTCC	60.819	63.158	11.28	0.00	43.06	4.70
2948	3016	4.244326	CTCATCGGAGGAGTCGGT	57.756	61.111	11.33	0.00	37.51	4.69
3019	3087	2.978489	GTTTCGTCAGAGTTGTAGTCGG	59.022	50.000	0.00	0.00	0.00	4.79
3045	3113	0.323816	ACTCGGCATCAGAGTCCTCA	60.324	55.000	0.00	0.00	44.87	3.86
3181	3249	1.592743	CGGTACATCCACCAACGGA	59.407	57.895	0.00	0.00	38.61	4.69
3186	3254	3.998672	ATCCACCAACGGACGCGT	61.999	61.111	13.85	13.85	38.07	6.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
321	322	6.153000	ACAGGTGTTACTTATAGGACTGTGAG	59.847	42.308	0.00	0.00	35.56	3.51
360	361	2.857483	TGGCATCGGGGTATTGTAATG	58.143	47.619	0.00	0.00	0.00	1.90
516	517	0.240945	GTTGTTTCCATGGAGGCACG	59.759	55.000	15.53	0.00	37.29	5.34
597	598	9.444600	GTCTTGAAGTCTATTAATTAACCCACA	57.555	33.333	0.00	0.00	0.00	4.17
782	784	0.629058	GAGATTTTGGGCCCCACCTA	59.371	55.000	22.27	0.00	39.10	3.08
995	998	1.379916	CTCCAGGACACCATGGCAA	59.620	57.895	13.04	0.00	36.47	4.52
996	999	3.080641	CTCCAGGACACCATGGCA	58.919	61.111	13.04	0.00	36.47	4.92
1039	1042	2.890474	GGGGATGTACTGTGCGCG	60.890	66.667	0.00	0.00	0.00	6.86
1054	1057	4.444081	AGGGGAGTCGTCGGAGGG	62.444	72.222	0.00	0.00	0.00	4.30
1427	1430	7.166691	TCAGTAACTATGAACCCTAGAACAC	57.833	40.000	0.00	0.00	0.00	3.32
1748	1755	1.726791	GGCTGTGTGAGATTGTGTACG	59.273	52.381	0.00	0.00	0.00	3.67
1787	1794	6.732531	TCTTCAACAAGCTTCTCATATGTG	57.267	37.500	0.00	0.00	0.00	3.21
2002	2009	6.825944	ACTTTTCCTTCTCTTTAAGATGGC	57.174	37.500	0.00	0.00	45.06	4.40
2070	2098	5.545723	TCTTCAGGTCATCCTTCTCTTTCTT	59.454	40.000	0.00	0.00	43.07	2.52
2071	2099	5.090139	TCTTCAGGTCATCCTTCTCTTTCT	58.910	41.667	0.00	0.00	43.07	2.52
2072	2100	5.413309	TCTTCAGGTCATCCTTCTCTTTC	57.587	43.478	0.00	0.00	43.07	2.62
2073	2101	5.832539	TTCTTCAGGTCATCCTTCTCTTT	57.167	39.130	0.00	0.00	43.07	2.52
2074	2102	5.545723	TCTTTCTTCAGGTCATCCTTCTCTT	59.454	40.000	0.00	0.00	43.07	2.85
2075	2103	5.090139	TCTTTCTTCAGGTCATCCTTCTCT	58.910	41.667	0.00	0.00	43.07	3.10
2076	2104	5.186797	TCTCTTTCTTCAGGTCATCCTTCTC	59.813	44.000	0.00	0.00	43.07	2.87
2077	2105	5.090139	TCTCTTTCTTCAGGTCATCCTTCT	58.910	41.667	0.00	0.00	43.07	2.85
2078	2106	5.413309	TCTCTTTCTTCAGGTCATCCTTC	57.587	43.478	0.00	0.00	43.07	3.46
2079	2107	5.280419	CCTTCTCTTTCTTCAGGTCATCCTT	60.280	44.000	0.00	0.00	43.07	3.36
2080	2108	4.224818	CCTTCTCTTTCTTCAGGTCATCCT	59.775	45.833	0.00	0.00	46.37	3.24
2081	2109	4.223923	TCCTTCTCTTTCTTCAGGTCATCC	59.776	45.833	0.00	0.00	0.00	3.51
2082	2110	5.413309	TCCTTCTCTTTCTTCAGGTCATC	57.587	43.478	0.00	0.00	0.00	2.92
2083	2111	7.502060	TTATCCTTCTCTTTCTTCAGGTCAT	57.498	36.000	0.00	0.00	0.00	3.06
2084	2112	6.575254	GCTTATCCTTCTCTTTCTTCAGGTCA	60.575	42.308	0.00	0.00	0.00	4.02
2085	2113	5.815222	GCTTATCCTTCTCTTTCTTCAGGTC	59.185	44.000	0.00	0.00	0.00	3.85
2086	2114	5.487131	AGCTTATCCTTCTCTTTCTTCAGGT	59.513	40.000	0.00	0.00	0.00	4.00
2087	2115	5.816777	CAGCTTATCCTTCTCTTTCTTCAGG	59.183	44.000	0.00	0.00	0.00	3.86
2088	2116	5.816777	CCAGCTTATCCTTCTCTTTCTTCAG	59.183	44.000	0.00	0.00	0.00	3.02
2089	2117	5.485353	TCCAGCTTATCCTTCTCTTTCTTCA	59.515	40.000	0.00	0.00	0.00	3.02
2090	2118	5.983540	TCCAGCTTATCCTTCTCTTTCTTC	58.016	41.667	0.00	0.00	0.00	2.87
2213	2241	3.117888	TCTGGTGAAGCTTCCTCTTGTTT	60.118	43.478	23.42	0.00	0.00	2.83
2365	2393	4.832266	ACAATCCAAGGTTCATTGCTACAA	59.168	37.500	0.00	0.00	31.74	2.41
2531	2575	8.364142	GCCAGTTCTATCTATGTCAGTTCTATT	58.636	37.037	0.00	0.00	0.00	1.73
2624	2691	8.971321	GTTCAGTTTCGTCAGTATGTTAGTTTA	58.029	33.333	0.00	0.00	37.40	2.01
2931	2999	1.729470	CCACCGACTCCTCCGATGAG	61.729	65.000	0.00	0.00	38.42	2.90
2948	3016	0.738762	CGAGGTCGTCGTACTCTCCA	60.739	60.000	6.77	0.00	44.20	3.86
3019	3087	1.227205	CTGATGCCGAGTCCTCTGC	60.227	63.158	4.01	4.01	39.75	4.26
3045	3113	3.721172	ATGGGTCCTCGGGCCAGAT	62.721	63.158	5.89	0.00	0.00	2.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.