AutoCloner

Multiple sequence alignment - TraesCS1A01G114200

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	TraesCS1A01G114200	chr1A	100.000	3035	0	0	1	3035	118139591	118136557	0.000000e+00	5605
1	TraesCS1A01G114200	chr1A	95.066	3040	113	17	1	3035	363568062	363565055	0.000000e+00	4748
2	TraesCS1A01G114200	chr1A	94.801	2039	86	16	1	2038	548119719	548121738	0.000000e+00	3160
3	TraesCS1A01G114200	chr1A	95.181	996	45	3	2043	3035	548121910	548122905	0.000000e+00	1570
4	TraesCS1A01G114200	chr2A	95.520	3036	108	9	3	3035	53529747	53526737	0.000000e+00	4828
5	TraesCS1A01G114200	chr2A	94.847	2057	83	8	1	2038	591109617	591107565	0.000000e+00	3190
6	TraesCS1A01G114200	chr2A	94.970	994	49	1	2043	3035	591107393	591106400	0.000000e+00	1557
7	TraesCS1A01G114200	chr6A	94.565	3036	128	18	1	3035	594095333	594098332	0.000000e+00	4658
8	TraesCS1A01G114200	chr5A	95.243	2039	75	3	1	2038	689798219	689796202	0.000000e+00	3208
9	TraesCS1A01G114200	chr5A	95.573	994	42	2	2043	3035	689796030	689795038	0.000000e+00	1591
10	TraesCS1A01G114200	chr2D	94.098	2050	101	9	1	2038	26166167	26168208	0.000000e+00	3097
11	TraesCS1A01G114200	chr7D	93.294	2058	102	10	1	2033	518168744	518170790	0.000000e+00	3003
12	TraesCS1A01G114200	chr7D	92.702	1754	114	12	1	1754	166368939	166370678	0.000000e+00	2518
13	TraesCS1A01G114200	chr7D	95.149	907	34	1	1142	2038	614604586	614605492	0.000000e+00	1423
14	TraesCS1A01G114200	chr3D	95.026	1910	81	5	139	2038	516290664	516288759	0.000000e+00	2988
15	TraesCS1A01G114200	chr1D	93.262	2048	93	20	1	2038	100579674	100581686	0.000000e+00	2976
16	TraesCS1A01G114200	chr6D	92.878	2064	100	12	1	2038	411304444	411302402	0.000000e+00	2953
17	TraesCS1A01G114200	chr6D	95.171	994	47	1	2043	3035	35107386	35108379	0.000000e+00	1568
18	TraesCS1A01G114200	chr4D	94.653	1889	87	5	160	2038	482596715	482594831	0.000000e+00	2916
19	TraesCS1A01G114200	chr4D	95.070	994	48	1	2043	3035	490765398	490766391	0.000000e+00	1563
20	TraesCS1A01G114200	chr7A	95.976	994	39	1	2043	3035	500036910	500037903	0.000000e+00	1613
21	TraesCS1A01G114200	chr7A	94.340	159	8	1	1	159	500023390	500023547	3.020000e-60	243
22	TraesCS1A01G114200	chr4A	83.448	145	14	10	3	139	663096377	663096519	3.180000e-25	126

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	TraesCS1A01G114200	chr1A	118136557	118139591	3034	True	5605.0	5605	100.0000	1	3035	1	chr1A.!!$R1	3034
1	TraesCS1A01G114200	chr1A	363565055	363568062	3007	True	4748.0	4748	95.0660	1	3035	1	chr1A.!!$R2	3034
2	TraesCS1A01G114200	chr1A	548119719	548122905	3186	False	2365.0	3160	94.9910	1	3035	2	chr1A.!!$F1	3034
3	TraesCS1A01G114200	chr2A	53526737	53529747	3010	True	4828.0	4828	95.5200	3	3035	1	chr2A.!!$R1	3032
4	TraesCS1A01G114200	chr2A	591106400	591109617	3217	True	2373.5	3190	94.9085	1	3035	2	chr2A.!!$R2	3034
5	TraesCS1A01G114200	chr6A	594095333	594098332	2999	False	4658.0	4658	94.5650	1	3035	1	chr6A.!!$F1	3034
6	TraesCS1A01G114200	chr5A	689795038	689798219	3181	True	2399.5	3208	95.4080	1	3035	2	chr5A.!!$R1	3034
7	TraesCS1A01G114200	chr2D	26166167	26168208	2041	False	3097.0	3097	94.0980	1	2038	1	chr2D.!!$F1	2037
8	TraesCS1A01G114200	chr7D	518168744	518170790	2046	False	3003.0	3003	93.2940	1	2033	1	chr7D.!!$F2	2032
9	TraesCS1A01G114200	chr7D	166368939	166370678	1739	False	2518.0	2518	92.7020	1	1754	1	chr7D.!!$F1	1753
10	TraesCS1A01G114200	chr7D	614604586	614605492	906	False	1423.0	1423	95.1490	1142	2038	1	chr7D.!!$F3	896
11	TraesCS1A01G114200	chr3D	516288759	516290664	1905	True	2988.0	2988	95.0260	139	2038	1	chr3D.!!$R1	1899
12	TraesCS1A01G114200	chr1D	100579674	100581686	2012	False	2976.0	2976	93.2620	1	2038	1	chr1D.!!$F1	2037
13	TraesCS1A01G114200	chr6D	411302402	411304444	2042	True	2953.0	2953	92.8780	1	2038	1	chr6D.!!$R1	2037
14	TraesCS1A01G114200	chr6D	35107386	35108379	993	False	1568.0	1568	95.1710	2043	3035	1	chr6D.!!$F1	992
15	TraesCS1A01G114200	chr4D	482594831	482596715	1884	True	2916.0	2916	94.6530	160	2038	1	chr4D.!!$R1	1878
16	TraesCS1A01G114200	chr4D	490765398	490766391	993	False	1563.0	1563	95.0700	2043	3035	1	chr4D.!!$F1	992
17	TraesCS1A01G114200	chr7A	500036910	500037903	993	False	1613.0	1613	95.9760	2043	3035	1	chr7A.!!$F2	992

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
551	639	0.040958	CTTCGGCTGTGCTGTGAAAC	60.041	55.0	0.0	0.0	36.18	2.78	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2076	2364	0.502275	CAAAAACATTCGTGTGCGGC	59.498	50.0	0.0	0.0	38.89	6.53	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
43	44	4.653888	GTGGGGGTTGGTGGGTCG	62.654	72.222	0.00	0.00	0.00	4.79
58	59	2.125961	GTCGGGCGAGTAGGTGGAT	61.126	63.158	0.00	0.00	0.00	3.41
135	138	6.476378	GCTCTCTCACTATATCTCTTCCTCT	58.524	44.000	0.00	0.00	0.00	3.69
137	140	7.527868	GCTCTCTCACTATATCTCTTCCTCTCT	60.528	44.444	0.00	0.00	0.00	3.10
139	142	7.734865	TCTCTCACTATATCTCTTCCTCTCTCT	59.265	40.741	0.00	0.00	0.00	3.10
140	143	7.907389	TCTCACTATATCTCTTCCTCTCTCTC	58.093	42.308	0.00	0.00	0.00	3.20
141	144	7.734865	TCTCACTATATCTCTTCCTCTCTCTCT	59.265	40.741	0.00	0.00	0.00	3.10
142	145	7.907389	TCACTATATCTCTTCCTCTCTCTCTC	58.093	42.308	0.00	0.00	0.00	3.20
143	146	7.734865	TCACTATATCTCTTCCTCTCTCTCTCT	59.265	40.741	0.00	0.00	0.00	3.10
144	147	9.035890	CACTATATCTCTTCCTCTCTCTCTCTA	57.964	40.741	0.00	0.00	0.00	2.43
145	148	9.790297	ACTATATCTCTTCCTCTCTCTCTCTAT	57.210	37.037	0.00	0.00	0.00	1.98
153	156	5.970289	TCCTCTCTCTCTCTATCTCTCTCT	58.030	45.833	0.00	0.00	0.00	3.10
200	288	1.351430	CTCTCAAATTCGACGCCGCA	61.351	55.000	0.00	0.00	35.37	5.69
446	534	4.828939	ACAATGATTTCTGTGGCAAAGAGA	59.171	37.500	7.56	3.64	0.00	3.10
478	566	5.585445	TCCTCTCTACTATGTTCTTCACGAC	59.415	44.000	0.00	0.00	0.00	4.34
551	639	0.040958	CTTCGGCTGTGCTGTGAAAC	60.041	55.000	0.00	0.00	36.18	2.78
849	943	1.274728	AGTTGTCTGCAGAGGTAGCTG	59.725	52.381	18.89	0.00	38.91	4.24
850	944	1.001406	GTTGTCTGCAGAGGTAGCTGT	59.999	52.381	18.89	0.00	38.17	4.40
1045	1140	9.914131	GTGAACTTTATTATTTTCCAGAGCTTT	57.086	29.630	0.00	0.00	0.00	3.51
1104	1199	1.674359	TTTTTGTTCGCAGAGAGGCA	58.326	45.000	0.00	0.00	38.43	4.75
1259	1354	9.474313	AGGCTTAAAATGGATAATGAACAAGTA	57.526	29.630	0.00	0.00	0.00	2.24
1309	1404	6.293955	GCAGCTGTGGAAAGAACTAATGTAAA	60.294	38.462	16.64	0.00	0.00	2.01
1331	1426	3.159213	ACCATGAAGATTGACAGGCAA	57.841	42.857	0.00	0.00	41.53	4.52
1435	1530	3.624777	ACAATGGTGAGATTAAGCTGGG	58.375	45.455	0.00	0.00	0.00	4.45
1448	1543	1.298953	AGCTGGGCAGGGATTTTCTA	58.701	50.000	0.00	0.00	0.00	2.10
1470	1565	1.561542	AGGAGGAGGTGCATAAACTGG	59.438	52.381	0.00	0.00	0.00	4.00
1472	1567	2.026262	GGAGGAGGTGCATAAACTGGAA	60.026	50.000	0.00	0.00	0.00	3.53
2017	2138	6.920817	TGTACTCAGACATAAACTCGTTCAT	58.079	36.000	0.00	0.00	0.00	2.57
2038	2159	4.371855	TGGACATGCGTTTACACAAAAA	57.628	36.364	0.00	0.00	0.00	1.94
2076	2364	3.341857	TTTTTGTTTCATGGTCGACGG	57.658	42.857	9.92	1.63	0.00	4.79
2294	2583	2.353958	CCAGTGTCCAGCAGGCAT	59.646	61.111	0.00	0.00	33.74	4.40
2407	2696	3.054166	GGCGCGTTTGGAAACTTTATTT	58.946	40.909	8.43	0.00	36.77	1.40
2468	2757	1.000955	GCGTGAAGTCTGAGGGAAAGA	59.999	52.381	0.00	0.00	0.00	2.52
2498	2787	1.570979	TCCTCATGGTCTCTAGCTCCA	59.429	52.381	0.00	0.00	35.64	3.86
2508	2797	4.054671	GTCTCTAGCTCCATTGCATACAC	58.945	47.826	0.00	0.00	34.99	2.90
2572	2861	5.730550	TCATAATCTTCCAGCGTTACTGTT	58.269	37.500	0.00	0.00	45.68	3.16
2739	3028	1.306296	CATGACCCCCGTCCCAATT	59.694	57.895	0.00	0.00	38.32	2.32

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
43	44	3.139077	CAAATAATCCACCTACTCGCCC	58.861	50.000	0.00	0.00	0.00	6.13
58	59	3.446507	GTCCGGCTCGACCAAATAA	57.553	52.632	0.00	0.00	39.03	1.40
135	138	6.857848	AGAGAGAGAGAGAGATAGAGAGAGA	58.142	44.000	0.00	0.00	0.00	3.10
137	140	6.857848	AGAGAGAGAGAGAGAGATAGAGAGA	58.142	44.000	0.00	0.00	0.00	3.10
139	142	6.857848	AGAGAGAGAGAGAGAGAGATAGAGA	58.142	44.000	0.00	0.00	0.00	3.10
140	143	6.947733	AGAGAGAGAGAGAGAGAGAGATAGAG	59.052	46.154	0.00	0.00	0.00	2.43
141	144	6.857848	AGAGAGAGAGAGAGAGAGAGATAGA	58.142	44.000	0.00	0.00	0.00	1.98
142	145	6.947733	AGAGAGAGAGAGAGAGAGAGAGATAG	59.052	46.154	0.00	0.00	0.00	2.08
143	146	6.857848	AGAGAGAGAGAGAGAGAGAGAGATA	58.142	44.000	0.00	0.00	0.00	1.98
144	147	5.714863	AGAGAGAGAGAGAGAGAGAGAGAT	58.285	45.833	0.00	0.00	0.00	2.75
145	148	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
153	156	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
200	288	3.699538	TGTGAGCAGTTCCGACACTATAT	59.300	43.478	0.00	0.00	33.41	0.86
446	534	5.298989	ACATAGTAGAGAGGACAGTCGAT	57.701	43.478	0.00	0.00	0.00	3.59
478	566	4.709840	CACCTGAGAGGCTTGGTG	57.290	61.111	12.85	12.85	39.63	4.17
551	639	5.634020	ACTCGGATTTTCGAAAGTGACTAAG	59.366	40.000	10.93	6.88	38.77	2.18
849	943	9.508567	CTTTTAAGCCAGCTTGAATTAATCTAC	57.491	33.333	15.05	0.00	37.47	2.59
850	944	9.461312	TCTTTTAAGCCAGCTTGAATTAATCTA	57.539	29.630	15.05	0.00	37.47	1.98
1045	1140	6.758416	CAGAGACTATTAATACACTGCTGCAA	59.242	38.462	3.02	0.00	0.00	4.08
1104	1199	4.499865	CCATTCGACGACTCCATAGTTCAT	60.500	45.833	0.00	0.00	35.56	2.57
1259	1354	5.552178	ACAAGATTCTCGAGCTTAAGGTTT	58.448	37.500	7.81	0.00	0.00	3.27
1309	1404	4.508551	TGCCTGTCAATCTTCATGGTAT	57.491	40.909	0.00	0.00	0.00	2.73
1331	1426	1.485066	ACGATACCCATCCGCTTCTTT	59.515	47.619	0.00	0.00	0.00	2.52
1435	1530	4.203226	CTCCTCCTTTAGAAAATCCCTGC	58.797	47.826	0.00	0.00	0.00	4.85
1448	1543	3.562176	CCAGTTTATGCACCTCCTCCTTT	60.562	47.826	0.00	0.00	0.00	3.11
1470	1565	9.665719	ACTTTCCATCTTCTTTCTATTCTCTTC	57.334	33.333	0.00	0.00	0.00	2.87
1472	1567	8.601546	ACACTTTCCATCTTCTTTCTATTCTCT	58.398	33.333	0.00	0.00	0.00	3.10
1985	2106	9.209175	GAGTTTATGTCTGAGTACAAACAATCT	57.791	33.333	0.00	0.00	30.55	2.40
2017	2138	4.371855	TTTTTGTGTAAACGCATGTCCA	57.628	36.364	0.00	0.00	36.14	4.02
2076	2364	0.502275	CAAAAACATTCGTGTGCGGC	59.498	50.000	0.00	0.00	38.89	6.53
2173	2461	3.735514	GCCTTTTGCACCGTTTTGTAAGA	60.736	43.478	0.00	0.00	40.77	2.10
2210	2499	5.523552	CGCCAATCTGATTCTGTGTTATGTA	59.476	40.000	0.00	0.00	0.00	2.29
2294	2583	4.221924	TGATTTGTCAGATCCGTTCACCTA	59.778	41.667	1.14	0.00	0.00	3.08
2468	2757	6.882768	AGAGACCATGAGGATTAAGTTTCT	57.117	37.500	0.00	0.00	38.69	2.52
2498	2787	5.711506	TGAGGTTCTTCATTGTGTATGCAAT	59.288	36.000	0.00	0.00	39.42	3.56
2508	2797	5.756195	TGAGTTTGTGAGGTTCTTCATTG	57.244	39.130	0.00	0.00	0.00	2.82
2739	3028	3.947910	AGGGAAATGTTCGACGAACTA	57.052	42.857	33.51	22.92	42.39	2.24
2946	3247	2.299013	AGTGGACGTGCTCATTCACTTA	59.701	45.455	8.99	0.00	34.92	2.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.