AutoCloner

Multiple sequence alignment - TraesCS2A01G482900

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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	TraesCS2A01G482900	chr2A	100.000	2387	0	0	1	2387	718983451	718981065	0.000000e+00	4409
1	TraesCS2A01G482900	chr2A	84.712	556	68	9	780	1333	718944747	718945287	7.510000e-150	540
2	TraesCS2A01G482900	chr2A	90.871	241	21	1	1160	1400	718962419	718962658	2.960000e-84	322
3	TraesCS2A01G482900	chr2A	86.054	294	26	5	780	1069	718962107	718962389	3.860000e-78	302
4	TraesCS2A01G482900	chr2A	94.545	110	4	2	302	410	718943663	718943771	4.080000e-38	169
5	TraesCS2A01G482900	chr2A	83.951	162	21	3	802	962	719287233	719287390	1.480000e-32	150
6	TraesCS2A01G482900	chr7A	95.985	822	31	2	1568	2387	466209372	466210193	0.000000e+00	1334
7	TraesCS2A01G482900	chr1A	95.849	819	32	2	1570	2387	21230973	21231790	0.000000e+00	1323
8	TraesCS2A01G482900	chr1A	95.042	827	39	2	1561	2386	586359411	586360236	0.000000e+00	1299
9	TraesCS2A01G482900	chr1A	93.000	100	5	2	308	405	513859293	513859194	6.880000e-31	145
10	TraesCS2A01G482900	chr3A	95.615	821	35	1	1568	2387	36755475	36754655	0.000000e+00	1315
11	TraesCS2A01G482900	chr3A	95.604	819	34	2	1570	2387	534189028	534188211	0.000000e+00	1312
12	TraesCS2A01G482900	chr3A	95.366	820	36	2	1569	2387	7563089	7563907	0.000000e+00	1303
13	TraesCS2A01G482900	chr3A	92.929	99	5	2	308	405	557264909	557265006	2.470000e-30	143
14	TraesCS2A01G482900	chr5A	95.604	819	35	1	1570	2387	680191440	680192258	0.000000e+00	1312
15	TraesCS2A01G482900	chr5A	95.482	819	36	1	1570	2387	398979299	398980117	0.000000e+00	1306
16	TraesCS2A01G482900	chr5B	95.366	820	36	2	1569	2387	523366855	523367673	0.000000e+00	1303
17	TraesCS2A01G482900	chr2D	88.145	1105	56	13	483	1521	584891591	584890496	0.000000e+00	1245
18	TraesCS2A01G482900	chr2D	89.169	397	39	3	1	397	584892231	584891839	2.130000e-135	492
19	TraesCS2A01G482900	chr2D	92.157	102	7	1	302	403	584839493	584839593	2.470000e-30	143
20	TraesCS2A01G482900	chr2B	87.884	619	57	7	789	1400	705225318	705225925	0.000000e+00	712
21	TraesCS2A01G482900	chr2B	78.774	848	126	33	717	1555	705220435	705221237	9.780000e-144	520
22	TraesCS2A01G482900	chr2B	86.513	304	31	9	107	405	705362150	705361852	2.290000e-85	326
23	TraesCS2A01G482900	chr2B	82.641	409	30	18	408	780	705361733	705361330	8.230000e-85	324
24	TraesCS2A01G482900	chr2B	91.228	114	6	4	300	410	705051463	705051575	4.110000e-33	152
25	TraesCS2A01G482900	chr3D	93.878	98	4	2	308	404	428437316	428437220	1.910000e-31	147
26	TraesCS2A01G482900	chr1D	93.000	100	6	1	307	405	22896973	22896874	6.880000e-31	145

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	TraesCS2A01G482900	chr2A	718981065	718983451	2386	True	4409.0	4409	100.0000	1	2387	1	chr2A.!!$R1	2386
1	TraesCS2A01G482900	chr2A	718943663	718945287	1624	False	354.5	540	89.6285	302	1333	2	chr2A.!!$F2	1031
2	TraesCS2A01G482900	chr2A	718962107	718962658	551	False	312.0	322	88.4625	780	1400	2	chr2A.!!$F3	620
3	TraesCS2A01G482900	chr7A	466209372	466210193	821	False	1334.0	1334	95.9850	1568	2387	1	chr7A.!!$F1	819
4	TraesCS2A01G482900	chr1A	21230973	21231790	817	False	1323.0	1323	95.8490	1570	2387	1	chr1A.!!$F1	817
5	TraesCS2A01G482900	chr1A	586359411	586360236	825	False	1299.0	1299	95.0420	1561	2386	1	chr1A.!!$F2	825
6	TraesCS2A01G482900	chr3A	36754655	36755475	820	True	1315.0	1315	95.6150	1568	2387	1	chr3A.!!$R1	819
7	TraesCS2A01G482900	chr3A	534188211	534189028	817	True	1312.0	1312	95.6040	1570	2387	1	chr3A.!!$R2	817
8	TraesCS2A01G482900	chr3A	7563089	7563907	818	False	1303.0	1303	95.3660	1569	2387	1	chr3A.!!$F1	818
9	TraesCS2A01G482900	chr5A	680191440	680192258	818	False	1312.0	1312	95.6040	1570	2387	1	chr5A.!!$F2	817
10	TraesCS2A01G482900	chr5A	398979299	398980117	818	False	1306.0	1306	95.4820	1570	2387	1	chr5A.!!$F1	817
11	TraesCS2A01G482900	chr5B	523366855	523367673	818	False	1303.0	1303	95.3660	1569	2387	1	chr5B.!!$F1	818
12	TraesCS2A01G482900	chr2D	584890496	584892231	1735	True	868.5	1245	88.6570	1	1521	2	chr2D.!!$R1	1520
13	TraesCS2A01G482900	chr2B	705225318	705225925	607	False	712.0	712	87.8840	789	1400	1	chr2B.!!$F3	611
14	TraesCS2A01G482900	chr2B	705220435	705221237	802	False	520.0	520	78.7740	717	1555	1	chr2B.!!$F2	838
15	TraesCS2A01G482900	chr2B	705361330	705362150	820	True	325.0	326	84.5770	107	780	2	chr2B.!!$R1	673

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
654	1315	1.001974	TCAAGAGGTTGTCCATGTCCG	59.998	52.381	0.0	0.0	34.98	4.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1538	2367	0.250338	AGAACAGAACCGCAACCTCC	60.25	55.0	0.0	0.0	0.0	4.3	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
95	96	5.580691	TGGCTATTCGATAAGAACAACAGTG	59.419	40.000	0.00	0.00	42.39	3.66
221	223	3.664025	TTCTCCATGCCGTGCCTCG	62.664	63.158	0.00	0.00	39.52	4.63
287	289	5.991606	TCCCTTAAAATCGTGAGCTCATATG	59.008	40.000	21.47	13.11	0.00	1.78
288	290	5.991606	CCCTTAAAATCGTGAGCTCATATGA	59.008	40.000	21.47	17.99	0.00	2.15
448	783	6.666678	TCTTCTCTTCAGATTAATTGCCCAT	58.333	36.000	0.00	0.00	0.00	4.00
461	796	7.775053	TTAATTGCCCATAAGTGTTCTTCTT	57.225	32.000	0.00	0.00	35.36	2.52
494	1051	1.077858	CCAGCTCTTCCCTTGCTCC	60.078	63.158	0.00	0.00	34.51	4.70
495	1052	1.681666	CAGCTCTTCCCTTGCTCCA	59.318	57.895	0.00	0.00	34.51	3.86
586	1242	1.672363	CGATGACAATGTCACATGGGG	59.328	52.381	19.17	0.94	45.65	4.96
650	1311	4.899502	ACTTACTCAAGAGGTTGTCCATG	58.100	43.478	1.73	0.00	35.60	3.66
652	1313	3.409026	ACTCAAGAGGTTGTCCATGTC	57.591	47.619	1.73	0.00	34.98	3.06
653	1314	2.039084	ACTCAAGAGGTTGTCCATGTCC	59.961	50.000	1.73	0.00	34.98	4.02
654	1315	1.001974	TCAAGAGGTTGTCCATGTCCG	59.998	52.381	0.00	0.00	34.98	4.79
659	1365	1.628340	AGGTTGTCCATGTCCGAATCA	59.372	47.619	0.00	0.00	35.89	2.57
660	1366	2.039746	AGGTTGTCCATGTCCGAATCAA	59.960	45.455	0.00	0.00	35.89	2.57
863	1663	1.973281	CAAGGTGAAGCGGTGCCAT	60.973	57.895	0.00	0.00	0.00	4.40
985	1791	3.248024	TCTACACCAAGTCAGGTCCAAT	58.752	45.455	0.00	0.00	40.77	3.16
990	1796	2.711009	ACCAAGTCAGGTCCAATCAGAA	59.289	45.455	0.00	0.00	37.28	3.02
991	1797	3.138283	ACCAAGTCAGGTCCAATCAGAAA	59.862	43.478	0.00	0.00	37.28	2.52
992	1798	3.755378	CCAAGTCAGGTCCAATCAGAAAG	59.245	47.826	0.00	0.00	0.00	2.62
993	1799	4.505566	CCAAGTCAGGTCCAATCAGAAAGA	60.506	45.833	0.00	0.00	0.00	2.52
994	1800	5.251764	CAAGTCAGGTCCAATCAGAAAGAT	58.748	41.667	0.00	0.00	39.09	2.40
995	1801	5.096443	AGTCAGGTCCAATCAGAAAGATC	57.904	43.478	0.00	0.00	35.39	2.75
996	1802	4.533707	AGTCAGGTCCAATCAGAAAGATCA	59.466	41.667	0.00	0.00	35.39	2.92
1049	1855	1.840650	CCATCCTCTCCAGCCGGAT	60.841	63.158	5.05	0.00	41.79	4.18
1197	2003	1.209019	GAGGCTGCAGAGGAATTCTCA	59.791	52.381	20.43	0.00	44.81	3.27
1209	2015	4.756084	GGAATTCTCAATATTCCAGGCG	57.244	45.455	5.23	0.00	46.72	5.52
1215	2021	1.024271	CAATATTCCAGGCGTGGGTG	58.976	55.000	24.54	11.48	45.11	4.61
1284	2090	2.430367	GCTCACCGGGAACAGGTT	59.570	61.111	6.32	0.00	40.59	3.50
1293	2099	0.250338	GGGAACAGGTTCGAGCTTGT	60.250	55.000	11.24	11.24	40.37	3.16
1441	2248	2.735134	ACCGCAAGTTCTAAGTTTAGCG	59.265	45.455	0.00	0.00	43.13	4.26
1465	2272	7.077605	CGATGTGTTTCTGTTGTCATGTTAAT	58.922	34.615	0.00	0.00	0.00	1.40
1537	2366	7.399191	TCACTATGTATACCAGTCAGTTTTCCT	59.601	37.037	0.00	0.00	0.00	3.36
1538	2367	7.492669	CACTATGTATACCAGTCAGTTTTCCTG	59.507	40.741	0.00	0.00	42.97	3.86
1543	2372	2.938956	CAGTCAGTTTTCCTGGAGGT	57.061	50.000	0.00	0.00	41.83	3.85
1555	2384	0.535102	CTGGAGGTTGCGGTTCTGTT	60.535	55.000	0.00	0.00	0.00	3.16
1556	2385	0.534203	TGGAGGTTGCGGTTCTGTTC	60.534	55.000	0.00	0.00	0.00	3.18
1557	2386	0.250338	GGAGGTTGCGGTTCTGTTCT	60.250	55.000	0.00	0.00	0.00	3.01
1558	2387	1.594331	GAGGTTGCGGTTCTGTTCTT	58.406	50.000	0.00	0.00	0.00	2.52
1559	2388	2.549349	GGAGGTTGCGGTTCTGTTCTTA	60.549	50.000	0.00	0.00	0.00	2.10
1560	2389	2.479275	GAGGTTGCGGTTCTGTTCTTAC	59.521	50.000	0.00	0.00	0.00	2.34
1561	2390	2.158871	AGGTTGCGGTTCTGTTCTTACA	60.159	45.455	0.00	0.00	0.00	2.41
1562	2391	2.812011	GGTTGCGGTTCTGTTCTTACAT	59.188	45.455	0.00	0.00	32.86	2.29
1563	2392	3.252458	GGTTGCGGTTCTGTTCTTACATT	59.748	43.478	0.00	0.00	32.86	2.71
1564	2393	4.261447	GGTTGCGGTTCTGTTCTTACATTT	60.261	41.667	0.00	0.00	32.86	2.32
1565	2394	4.481930	TGCGGTTCTGTTCTTACATTTG	57.518	40.909	0.00	0.00	32.86	2.32
1566	2395	3.234386	GCGGTTCTGTTCTTACATTTGC	58.766	45.455	0.00	0.00	32.86	3.68
1742	2571	1.926426	ATGAAGGGGTGCTACCTGGC	61.926	60.000	0.00	0.00	38.63	4.85
1815	2644	2.504519	GAGCCACATACCGGGTCC	59.495	66.667	6.32	0.00	43.78	4.46
1828	2657	1.688269	CGGGTCCGGGGCATAAACTA	61.688	60.000	0.00	0.00	35.56	2.24
1838	2667	1.852895	GGCATAAACTAGTCTGACGCG	59.147	52.381	3.53	3.53	0.00	6.01
1875	2704	1.685224	GCCATCTTCCACAGGTCCA	59.315	57.895	0.00	0.00	0.00	4.02
1955	2785	1.045407	TGACGCCAGACAACTACCTT	58.955	50.000	0.00	0.00	0.00	3.50
2002	2832	3.138798	GGCGCCGAGTCTCCACTA	61.139	66.667	12.58	0.00	30.63	2.74
2091	2921	1.152819	CTGGTCCCTCGATCCCGTA	60.153	63.158	0.00	0.00	37.05	4.02
2206	3036	4.394729	CGGATAGAGGTCTAGAGCTTCTT	58.605	47.826	24.54	15.54	39.57	2.52
2313	3143	0.175989	GGATCCGCTCGAAGAACCTT	59.824	55.000	0.00	0.00	34.09	3.50
2335	3165	2.523179	CACGTATTGTGTGCACGGA	58.477	52.632	13.13	0.23	43.88	4.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
20	21	5.597594	AGCAACTCAACTAGGTATACCCTAC	59.402	44.000	18.65	0.00	43.87	3.18
44	45	2.174685	TGTGGAGGATTGCTAGGCTA	57.825	50.000	0.00	0.00	0.00	3.93
45	46	1.142465	CATGTGGAGGATTGCTAGGCT	59.858	52.381	0.00	0.00	0.00	4.58
74	75	7.812309	TGACACTGTTGTTCTTATCGAATAG	57.188	36.000	0.00	0.00	35.47	1.73
95	96	5.270083	TCGACAATCAATGTTGTTGTTGAC	58.730	37.500	17.49	10.61	44.12	3.18
185	187	7.938140	TGGAGAAAATTAATCCGACAATTCT	57.062	32.000	0.00	0.00	35.78	2.40
186	188	7.168135	GCATGGAGAAAATTAATCCGACAATTC	59.832	37.037	0.00	0.00	35.78	2.17
193	195	3.315191	ACGGCATGGAGAAAATTAATCCG	59.685	43.478	0.00	0.00	35.78	4.18
229	231	4.549458	CACGAATCTGAGGTGCAATTTTT	58.451	39.130	0.00	0.00	0.00	1.94
231	233	2.489329	CCACGAATCTGAGGTGCAATTT	59.511	45.455	0.00	0.00	0.00	1.82
232	234	2.086869	CCACGAATCTGAGGTGCAATT	58.913	47.619	0.00	0.00	0.00	2.32
233	235	1.003580	ACCACGAATCTGAGGTGCAAT	59.996	47.619	0.00	0.00	31.19	3.56
261	263	4.442706	TGAGCTCACGATTTTAAGGGATC	58.557	43.478	13.74	0.00	0.00	3.36
298	300	9.190858	CTTGTTGGAATTAATTTCGAAATCACA	57.809	29.630	22.93	10.81	34.37	3.58
299	301	9.191995	ACTTGTTGGAATTAATTTCGAAATCAC	57.808	29.630	22.93	12.29	34.37	3.06
332	334	3.319972	GCGGGAATACTCACCACTATACA	59.680	47.826	0.00	0.00	0.00	2.29
416	555	2.969990	TCTGAAGAGAAGATGCACAGC	58.030	47.619	0.00	0.00	0.00	4.40
448	783	6.323996	TCAGAGGAACAGAAGAAGAACACTTA	59.676	38.462	0.00	0.00	0.00	2.24
461	796	2.499289	GAGCTGGATTCAGAGGAACAGA	59.501	50.000	4.75	0.00	43.49	3.41
494	1051	4.362470	TGGCCCATTCATAAGAGAGATG	57.638	45.455	0.00	0.00	0.00	2.90
495	1052	4.414846	AGTTGGCCCATTCATAAGAGAGAT	59.585	41.667	0.00	0.00	0.00	2.75
586	1242	7.463961	TCCTACTTATATCGTTCAAGGGATC	57.536	40.000	0.00	0.00	0.00	3.36
650	1311	2.260481	GAGTCGGAGTTTGATTCGGAC	58.740	52.381	5.20	5.20	42.11	4.79
652	1313	1.641577	GGAGTCGGAGTTTGATTCGG	58.358	55.000	0.00	0.00	0.00	4.30
653	1314	1.135489	TCGGAGTCGGAGTTTGATTCG	60.135	52.381	0.00	0.00	36.95	3.34
654	1315	2.094649	AGTCGGAGTCGGAGTTTGATTC	60.095	50.000	0.00	0.00	36.95	2.52
659	1365	1.166989	GAGAGTCGGAGTCGGAGTTT	58.833	55.000	9.22	4.11	36.95	2.66
660	1366	0.325602	AGAGAGTCGGAGTCGGAGTT	59.674	55.000	9.22	0.00	36.95	3.01
969	1775	2.338809	TCTGATTGGACCTGACTTGGT	58.661	47.619	0.00	0.00	44.10	3.67
985	1791	4.186926	CGCCTCATCTTTGATCTTTCTGA	58.813	43.478	0.00	0.00	0.00	3.27
990	1796	1.211457	AGCCGCCTCATCTTTGATCTT	59.789	47.619	0.00	0.00	0.00	2.40
991	1797	0.835941	AGCCGCCTCATCTTTGATCT	59.164	50.000	0.00	0.00	0.00	2.75
992	1798	0.942962	CAGCCGCCTCATCTTTGATC	59.057	55.000	0.00	0.00	0.00	2.92
993	1799	1.099879	GCAGCCGCCTCATCTTTGAT	61.100	55.000	0.00	0.00	0.00	2.57
994	1800	1.746615	GCAGCCGCCTCATCTTTGA	60.747	57.895	0.00	0.00	0.00	2.69
995	1801	2.796651	GCAGCCGCCTCATCTTTG	59.203	61.111	0.00	0.00	0.00	2.77
1073	1879	2.787915	GCTTCAGCGCCTTGTAGC	59.212	61.111	11.46	11.46	34.96	3.58
1197	2003	0.751643	GCACCCACGCCTGGAATATT	60.752	55.000	2.94	0.00	40.55	1.28
1209	2015	3.755628	TACTCGCTCCGCACCCAC	61.756	66.667	0.00	0.00	0.00	4.61
1273	2079	1.004918	AAGCTCGAACCTGTTCCCG	60.005	57.895	4.54	0.00	36.27	5.14
1284	2090	1.264557	GCTCTATCGCTACAAGCTCGA	59.735	52.381	0.00	0.00	39.60	4.04
1379	2185	3.559069	CAATATGGATGGGTTCAGTGCT	58.441	45.455	0.00	0.00	0.00	4.40
1432	2239	5.065988	ACAACAGAAACACATCGCTAAACTT	59.934	36.000	0.00	0.00	0.00	2.66
1441	2248	8.693504	CAATTAACATGACAACAGAAACACATC	58.306	33.333	0.00	0.00	0.00	3.06
1534	2363	1.841556	AGAACCGCAACCTCCAGGA	60.842	57.895	0.00	0.00	38.94	3.86
1537	2366	0.534203	GAACAGAACCGCAACCTCCA	60.534	55.000	0.00	0.00	0.00	3.86
1538	2367	0.250338	AGAACAGAACCGCAACCTCC	60.250	55.000	0.00	0.00	0.00	4.30
1543	2372	4.791411	GCAAATGTAAGAACAGAACCGCAA	60.791	41.667	0.00	0.00	39.49	4.85
1742	2571	1.038280	GAGTAGACCGGGTATGTGGG	58.962	60.000	6.32	0.00	0.00	4.61
1815	2644	2.798499	CGTCAGACTAGTTTATGCCCCG	60.798	54.545	0.00	0.00	0.00	5.73
1828	2657	1.445066	CATGTGAGCGCGTCAGACT	60.445	57.895	8.43	0.00	35.13	3.24
1838	2667	2.730672	GGCGACGACACATGTGAGC	61.731	63.158	31.94	23.81	0.00	4.26
1875	2704	4.594062	AGCCTCAATATCTGCTCTGAAGAT	59.406	41.667	0.00	0.00	38.03	2.40
1955	2785	3.356639	GATGGACTCGCGCAGGTGA	62.357	63.158	8.75	0.00	0.00	4.02
2002	2832	0.392998	GGATCTCAACGGCATGGTGT	60.393	55.000	0.00	0.00	0.00	4.16
2091	2921	1.806623	GCGTCATTCTTGGAGGCGTAT	60.807	52.381	0.00	0.00	36.58	3.06
2335	3165	4.654412	GCTCAGATCGGCGGCGAT	62.654	66.667	41.91	41.91	0.00	4.58

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.