AutoCloner

Multiple sequence alignment - TraesCS6A01G167500

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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	TraesCS6A01G167500	chr6A	100.000	3496	0	0	1	3496	171797030	171793535	0.000000e+00	6457
1	TraesCS6A01G167500	chr6A	95.976	845	17	11	2145	2982	209566638	209565804	0.000000e+00	1356
2	TraesCS6A01G167500	chr4A	96.812	1349	26	10	2152	3496	391391816	391390481	0.000000e+00	2237
3	TraesCS6A01G167500	chr4A	90.748	735	48	8	5	735	553605950	553605232	0.000000e+00	963
4	TraesCS6A01G167500	chr5A	96.796	1311	34	8	2190	3496	569641309	569640003	0.000000e+00	2182
5	TraesCS6A01G167500	chr6D	96.119	1314	38	8	814	2115	132758185	132756873	0.000000e+00	2132
6	TraesCS6A01G167500	chr6D	89.789	284	26	3	454	735	178009104	178009386	9.220000e-96	361
7	TraesCS6A01G167500	chr1A	96.729	1131	28	8	2152	3278	3764250	3763125	0.000000e+00	1875
8	TraesCS6A01G167500	chr1A	92.966	526	35	2	7	531	527173284	527173808	0.000000e+00	765
9	TraesCS6A01G167500	chr1A	89.302	215	19	2	522	735	527173830	527174041	2.070000e-67	267
10	TraesCS6A01G167500	chr2A	96.566	990	27	7	2154	3139	340539943	340540929	0.000000e+00	1633
11	TraesCS6A01G167500	chr5D	89.619	944	77	18	2152	3086	431881270	431882201	0.000000e+00	1181
12	TraesCS6A01G167500	chr7B	89.079	934	75	19	2159	3080	656927092	656928010	0.000000e+00	1134
13	TraesCS6A01G167500	chr7B	88.054	745	72	9	5	735	734423382	734422641	0.000000e+00	867
14	TraesCS6A01G167500	chr7B	94.340	106	5	1	56	160	734506149	734506044	1.000000e-35	161
15	TraesCS6A01G167500	chr1D	88.596	947	81	18	2158	3086	265670004	265669067	0.000000e+00	1125
16	TraesCS6A01G167500	chr1D	88.248	953	92	16	2148	3086	489450983	489451929	0.000000e+00	1122
17	TraesCS6A01G167500	chr2D	89.793	725	64	7	10	727	508142790	508142069	0.000000e+00	920
18	TraesCS6A01G167500	chr3B	91.039	558	47	3	74	630	449856626	449856071	0.000000e+00	750
19	TraesCS6A01G167500	chr4D	90.141	213	20	1	524	735	378487489	378487277	3.440000e-70	276
20	TraesCS6A01G167500	chr3A	90.476	210	18	2	527	735	80792593	80792385	3.440000e-70	276
21	TraesCS6A01G167500	chr6B	89.447	199	21	0	468	666	295761165	295760967	5.790000e-63	252

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	TraesCS6A01G167500	chr6A	171793535	171797030	3495	True	6457	6457	100.000	1	3496	1	chr6A.!!$R1	3495
1	TraesCS6A01G167500	chr6A	209565804	209566638	834	True	1356	1356	95.976	2145	2982	1	chr6A.!!$R2	837
2	TraesCS6A01G167500	chr4A	391390481	391391816	1335	True	2237	2237	96.812	2152	3496	1	chr4A.!!$R1	1344
3	TraesCS6A01G167500	chr4A	553605232	553605950	718	True	963	963	90.748	5	735	1	chr4A.!!$R2	730
4	TraesCS6A01G167500	chr5A	569640003	569641309	1306	True	2182	2182	96.796	2190	3496	1	chr5A.!!$R1	1306
5	TraesCS6A01G167500	chr6D	132756873	132758185	1312	True	2132	2132	96.119	814	2115	1	chr6D.!!$R1	1301
6	TraesCS6A01G167500	chr1A	3763125	3764250	1125	True	1875	1875	96.729	2152	3278	1	chr1A.!!$R1	1126
7	TraesCS6A01G167500	chr1A	527173284	527174041	757	False	516	765	91.134	7	735	2	chr1A.!!$F1	728
8	TraesCS6A01G167500	chr2A	340539943	340540929	986	False	1633	1633	96.566	2154	3139	1	chr2A.!!$F1	985
9	TraesCS6A01G167500	chr5D	431881270	431882201	931	False	1181	1181	89.619	2152	3086	1	chr5D.!!$F1	934
10	TraesCS6A01G167500	chr7B	656927092	656928010	918	False	1134	1134	89.079	2159	3080	1	chr7B.!!$F1	921
11	TraesCS6A01G167500	chr7B	734422641	734423382	741	True	867	867	88.054	5	735	1	chr7B.!!$R1	730
12	TraesCS6A01G167500	chr1D	265669067	265670004	937	True	1125	1125	88.596	2158	3086	1	chr1D.!!$R1	928
13	TraesCS6A01G167500	chr1D	489450983	489451929	946	False	1122	1122	88.248	2148	3086	1	chr1D.!!$F1	938
14	TraesCS6A01G167500	chr2D	508142069	508142790	721	True	920	920	89.793	10	727	1	chr2D.!!$R1	717
15	TraesCS6A01G167500	chr3B	449856071	449856626	555	True	750	750	91.039	74	630	1	chr3B.!!$R1	556

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
908	959	0.739561	GGCACGTAGGTAGGACTCTG	59.260	60.0	0.0	0.0	0.0	3.35	F
1239	1301	0.031721	GAACATCCGCTACTACCCCG	59.968	60.0	0.0	0.0	0.0	5.73	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1748	1810	1.642037	CCTCAGGCTGCATGTCGTTG	61.642	60.000	14.4	1.46	0.0	4.1	R
2520	2588	3.691498	GGTTCGAAAAACTGTTCACTGG	58.309	45.455	0.0	0.00	0.0	4.0	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
41	42	2.009051	CAACGCATGCTTGTCCTGATA	58.991	47.619	17.13	0.00	0.00	2.15
101	102	2.692041	CCATGAGAAGCCTTTGATTCCC	59.308	50.000	0.00	0.00	37.61	3.97
212	216	9.268268	GGTAAAATTCCGAACATGATGTATAGA	57.732	33.333	0.00	0.00	0.00	1.98
252	257	2.826128	AGCAAGTCAATCTGTCCGAGTA	59.174	45.455	0.00	0.00	0.00	2.59
264	269	4.755629	TCTGTCCGAGTACTATAGCATCAC	59.244	45.833	0.00	0.00	0.00	3.06
382	387	1.106285	GCTGGCCAGGTAATCTTTGG	58.894	55.000	33.46	5.30	35.06	3.28
416	423	3.006728	TTCGATTGCCCCGGACCT	61.007	61.111	0.73	0.00	0.00	3.85
439	446	0.886563	GAGGCTGAGTTTGCTGCATT	59.113	50.000	1.84	0.00	34.81	3.56
443	450	2.325761	GCTGAGTTTGCTGCATTTGAG	58.674	47.619	1.84	0.00	33.53	3.02
467	474	3.587506	AGGGACTTAAGTTGGCACTACAT	59.412	43.478	10.02	0.00	27.25	2.29
505	512	2.768253	TTGATGGAGACTGATTGCGT	57.232	45.000	0.00	0.00	0.00	5.24
531	538	6.489700	TGAAATCTTGTCCTTAGTGAATGCAA	59.510	34.615	0.00	0.00	0.00	4.08
600	639	4.816385	CAGAACTGTTGAAGTAGAGGCAAA	59.184	41.667	0.00	0.00	38.56	3.68
697	746	1.323412	ACGGCATGTTGGTTAGCAAA	58.677	45.000	0.00	0.00	0.00	3.68
699	748	3.085533	ACGGCATGTTGGTTAGCAAATA	58.914	40.909	0.00	0.00	0.00	1.40
707	756	6.061022	TGTTGGTTAGCAAATATCCTCAGA	57.939	37.500	0.00	0.00	0.00	3.27
764	815	8.634335	TTTTGACCAGATGAATGATTGTAAGA	57.366	30.769	0.00	0.00	0.00	2.10
765	816	8.634335	TTTGACCAGATGAATGATTGTAAGAA	57.366	30.769	0.00	0.00	0.00	2.52
766	817	7.615582	TGACCAGATGAATGATTGTAAGAAC	57.384	36.000	0.00	0.00	0.00	3.01
767	818	7.167535	TGACCAGATGAATGATTGTAAGAACA	58.832	34.615	0.00	0.00	0.00	3.18
768	819	7.830697	TGACCAGATGAATGATTGTAAGAACAT	59.169	33.333	0.00	0.00	34.97	2.71
769	820	8.585471	ACCAGATGAATGATTGTAAGAACATT	57.415	30.769	0.00	0.00	34.97	2.71
770	821	9.685276	ACCAGATGAATGATTGTAAGAACATTA	57.315	29.630	0.00	0.00	34.97	1.90
803	854	8.749354	ACTCAAGTAATGAATTGATTTTACCCC	58.251	33.333	0.00	0.00	37.67	4.95
804	855	7.767261	TCAAGTAATGAATTGATTTTACCCCG	58.233	34.615	0.00	0.00	34.30	5.73
805	856	6.144078	AGTAATGAATTGATTTTACCCCGC	57.856	37.500	0.00	0.00	0.00	6.13
806	857	5.654650	AGTAATGAATTGATTTTACCCCGCA	59.345	36.000	0.00	0.00	0.00	5.69
807	858	5.413309	AATGAATTGATTTTACCCCGCAA	57.587	34.783	0.00	0.00	0.00	4.85
808	859	4.873746	TGAATTGATTTTACCCCGCAAA	57.126	36.364	0.00	0.00	0.00	3.68
809	860	5.215252	TGAATTGATTTTACCCCGCAAAA	57.785	34.783	0.00	0.00	0.00	2.44
810	861	5.611374	TGAATTGATTTTACCCCGCAAAAA	58.389	33.333	0.00	0.00	0.00	1.94
874	925	2.125773	TACTCGGGTCCAAGAGACTC	57.874	55.000	17.42	0.00	45.54	3.36
893	944	2.076100	TCATGTGATTTGAGTCGGCAC	58.924	47.619	0.00	0.00	0.00	5.01
908	959	0.739561	GGCACGTAGGTAGGACTCTG	59.260	60.000	0.00	0.00	0.00	3.35
909	960	0.739561	GCACGTAGGTAGGACTCTGG	59.260	60.000	0.00	0.00	0.00	3.86
912	963	1.357079	ACGTAGGTAGGACTCTGGGTT	59.643	52.381	0.00	0.00	0.00	4.11
915	966	2.715763	AGGTAGGACTCTGGGTTCAA	57.284	50.000	0.00	0.00	0.00	2.69
945	996	4.695455	CCCAGTGATTGACGACATACTTTT	59.305	41.667	0.00	0.00	0.00	2.27
948	999	7.065803	CCCAGTGATTGACGACATACTTTTATT	59.934	37.037	0.00	0.00	0.00	1.40
993	1044	2.678336	CGGAATTCTGTTAGGCACTTCC	59.322	50.000	6.08	0.00	41.75	3.46
1017	1068	3.885521	AGGAGTACGCGCGTAGGC	61.886	66.667	40.07	31.68	0.00	3.93
1019	1070	3.885521	GAGTACGCGCGTAGGCCT	61.886	66.667	40.07	32.22	35.02	5.19
1025	1076	0.959372	ACGCGCGTAGGCCTATCTAT	60.959	55.000	37.08	3.77	35.02	1.98
1239	1301	0.031721	GAACATCCGCTACTACCCCG	59.968	60.000	0.00	0.00	0.00	5.73
1367	1429	4.778143	CCCTCCCTGGTTTCGCGG	62.778	72.222	6.13	0.00	0.00	6.46
1731	1793	4.785453	GCGGGCTGGGGTTCTCTG	62.785	72.222	0.00	0.00	0.00	3.35
1802	1864	7.336475	TCTCCTCTACTACATCTACATGGAT	57.664	40.000	0.00	0.00	33.82	3.41
2143	2206	9.431887	ACGTTTTGACACTACAATATAAGATGT	57.568	29.630	0.00	0.00	0.00	3.06
2418	2486	3.385577	TGCGCAAGGGAACATTTAAAAC	58.614	40.909	8.16	0.00	38.28	2.43

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	7.151308	TGCGTTGTATTTCATTCATTTCCTTT	58.849	30.769	0.00	0.00	0.00	3.11
41	42	2.112198	CCACACACGCCACAACACT	61.112	57.895	0.00	0.00	0.00	3.55
212	216	2.621338	CTCGTACACATCAATGCTGGT	58.379	47.619	0.00	0.00	0.00	4.00
252	257	0.969894	GGCTCCCGTGATGCTATAGT	59.030	55.000	0.84	0.00	0.00	2.12
264	269	2.124507	TTTTCTGGTGGAGGCTCCCG	62.125	60.000	30.03	15.64	35.03	5.14
342	347	1.153289	GGTCACGCAGGATCATGCT	60.153	57.895	27.75	13.61	44.24	3.79
382	387	1.808133	CGAAGAGCCATCTACAAGCCC	60.808	57.143	0.00	0.00	33.45	5.19
416	423	1.066573	GCAGCAAACTCAGCCTCTAGA	60.067	52.381	0.00	0.00	0.00	2.43
439	446	2.039879	GCCAACTTAAGTCCCTCCTCAA	59.960	50.000	8.95	0.00	0.00	3.02
443	450	1.351350	AGTGCCAACTTAAGTCCCTCC	59.649	52.381	8.95	0.00	30.14	4.30
486	493	2.743664	CAACGCAATCAGTCTCCATCAA	59.256	45.455	0.00	0.00	0.00	2.57
489	496	2.768253	TCAACGCAATCAGTCTCCAT	57.232	45.000	0.00	0.00	0.00	3.41
505	512	6.489700	TGCATTCACTAAGGACAAGATTTCAA	59.510	34.615	0.00	0.00	0.00	2.69
531	538	1.202582	CCTCGAACGATCAAGTGACCT	59.797	52.381	0.00	0.00	0.00	3.85
591	630	8.650143	ATTTTCCTAATTTCAGTTTGCCTCTA	57.350	30.769	0.00	0.00	0.00	2.43
600	639	9.354673	TGTTCTCTTGATTTTCCTAATTTCAGT	57.645	29.630	0.00	0.00	0.00	3.41
680	719	4.342092	AGGATATTTGCTAACCAACATGCC	59.658	41.667	0.00	0.00	31.97	4.40
681	720	5.067674	TGAGGATATTTGCTAACCAACATGC	59.932	40.000	0.00	0.00	31.97	4.06
697	746	8.891985	TGATAGTGCTAATCTTCTGAGGATAT	57.108	34.615	2.46	0.00	0.00	1.63
699	748	7.454066	TGATGATAGTGCTAATCTTCTGAGGAT	59.546	37.037	0.00	0.00	0.00	3.24
738	789	9.076781	TCTTACAATCATTCATCTGGTCAAAAA	57.923	29.630	0.00	0.00	0.00	1.94
739	790	8.634335	TCTTACAATCATTCATCTGGTCAAAA	57.366	30.769	0.00	0.00	0.00	2.44
740	791	8.514594	GTTCTTACAATCATTCATCTGGTCAAA	58.485	33.333	0.00	0.00	0.00	2.69
741	792	7.665145	TGTTCTTACAATCATTCATCTGGTCAA	59.335	33.333	0.00	0.00	0.00	3.18
742	793	7.167535	TGTTCTTACAATCATTCATCTGGTCA	58.832	34.615	0.00	0.00	0.00	4.02
743	794	7.615582	TGTTCTTACAATCATTCATCTGGTC	57.384	36.000	0.00	0.00	0.00	4.02
744	795	8.585471	AATGTTCTTACAATCATTCATCTGGT	57.415	30.769	0.00	0.00	37.91	4.00
777	828	8.749354	GGGGTAAAATCAATTCATTACTTGAGT	58.251	33.333	0.00	0.00	35.04	3.41
778	829	7.915397	CGGGGTAAAATCAATTCATTACTTGAG	59.085	37.037	0.00	0.00	35.04	3.02
779	830	7.629652	GCGGGGTAAAATCAATTCATTACTTGA	60.630	37.037	0.00	0.00	35.95	3.02
780	831	6.475402	GCGGGGTAAAATCAATTCATTACTTG	59.525	38.462	0.00	0.00	0.00	3.16
781	832	6.153680	TGCGGGGTAAAATCAATTCATTACTT	59.846	34.615	0.00	0.00	0.00	2.24
782	833	5.654650	TGCGGGGTAAAATCAATTCATTACT	59.345	36.000	0.00	0.00	0.00	2.24
783	834	5.897050	TGCGGGGTAAAATCAATTCATTAC	58.103	37.500	0.00	0.00	0.00	1.89
784	835	6.531503	TTGCGGGGTAAAATCAATTCATTA	57.468	33.333	0.00	0.00	0.00	1.90
785	836	5.413309	TTGCGGGGTAAAATCAATTCATT	57.587	34.783	0.00	0.00	0.00	2.57
786	837	5.413309	TTTGCGGGGTAAAATCAATTCAT	57.587	34.783	0.00	0.00	0.00	2.57
787	838	4.873746	TTTGCGGGGTAAAATCAATTCA	57.126	36.364	0.00	0.00	0.00	2.57
849	900	3.581332	TCTCTTGGACCCGAGTATTTTGT	59.419	43.478	3.38	0.00	0.00	2.83
874	925	1.201954	CGTGCCGACTCAAATCACATG	60.202	52.381	0.00	0.00	0.00	3.21
893	944	2.022934	GAACCCAGAGTCCTACCTACG	58.977	57.143	0.00	0.00	0.00	3.51
908	959	1.002544	CACTGGGAGACTCTTGAACCC	59.997	57.143	1.74	0.00	40.79	4.11
909	960	1.971357	TCACTGGGAGACTCTTGAACC	59.029	52.381	1.74	0.00	0.00	3.62
912	963	3.259374	GTCAATCACTGGGAGACTCTTGA	59.741	47.826	1.74	0.00	0.00	3.02
915	966	1.821753	CGTCAATCACTGGGAGACTCT	59.178	52.381	1.74	0.00	0.00	3.24
945	996	4.717233	TCGGTCCGTGCTAAACTAAATA	57.283	40.909	11.88	0.00	0.00	1.40
948	999	4.924305	ATATCGGTCCGTGCTAAACTAA	57.076	40.909	11.88	0.00	0.00	2.24
954	1005	1.536766	CCGTTATATCGGTCCGTGCTA	59.463	52.381	11.88	2.45	44.77	3.49
956	1007	2.805277	CCGTTATATCGGTCCGTGC	58.195	57.895	11.88	0.00	44.77	5.34
993	1044	1.003116	ACGCGCGTACTCCTGTATAAG	60.003	52.381	37.08	0.00	0.00	1.73
1017	1068	9.226606	GATGGATCGGATCTAGTAATAGATAGG	57.773	40.741	16.96	7.90	36.96	2.57
1025	1076	4.160439	GGCATGATGGATCGGATCTAGTAA	59.840	45.833	16.96	2.50	0.00	2.24
1239	1301	4.484872	GGGCTTCAGGTACCCGCC	62.485	72.222	18.73	18.73	39.98	6.13
1347	1409	3.702048	CGAAACCAGGGAGGGCGA	61.702	66.667	0.00	0.00	43.89	5.54
1378	1440	1.228894	AGGTCGGAGGTGAAGAGCA	60.229	57.895	0.00	0.00	35.12	4.26
1583	1645	0.393944	ACTCGTACATCCTGGCGAGA	60.394	55.000	21.92	2.01	43.96	4.04
1661	1723	3.129502	CTCATGGCCAGCACGGTG	61.130	66.667	13.05	2.97	36.97	4.94
1715	1777	4.101448	CCAGAGAACCCCAGCCCG	62.101	72.222	0.00	0.00	0.00	6.13
1748	1810	1.642037	CCTCAGGCTGCATGTCGTTG	61.642	60.000	14.40	1.46	0.00	4.10
2117	2180	9.431887	ACATCTTATATTGTAGTGTCAAAACGT	57.568	29.630	0.00	0.00	0.00	3.99
2520	2588	3.691498	GGTTCGAAAAACTGTTCACTGG	58.309	45.455	0.00	0.00	0.00	4.00

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.