AutoCloner

Multiple sequence alignment - TraesCS6A01G250600

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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	TraesCS6A01G250600	chr6A	100.000	3185	0	0	1	3185	464692028	464688844	0.000000e+00	5882.0
1	TraesCS6A01G250600	chr6A	86.325	351	45	1	1306	1656	12367546	12367199	2.320000e-101	379.0
2	TraesCS6A01G250600	chr6D	94.786	1611	48	12	743	2337	325821752	325820162	0.000000e+00	2477.0
3	TraesCS6A01G250600	chr6D	93.457	810	17	9	2378	3182	325820065	325819287	0.000000e+00	1170.0
4	TraesCS6A01G250600	chr6D	87.731	432	52	1	1225	1656	10810276	10809846	1.320000e-138	503.0
5	TraesCS6A01G250600	chr6B	93.621	1646	60	10	705	2335	496986200	496987815	0.000000e+00	2416.0
6	TraesCS6A01G250600	chr6B	95.643	459	15	3	2717	3171	496988418	496988875	0.000000e+00	732.0
7	TraesCS6A01G250600	chr6B	91.944	360	6	4	2378	2736	496987913	496988250	1.720000e-132	483.0
8	TraesCS6A01G250600	chr3A	99.579	712	3	0	1	712	534175217	534174506	0.000000e+00	1299.0
9	TraesCS6A01G250600	chr3A	86.634	606	56	9	1226	1822	648104212	648104801	0.000000e+00	647.0
10	TraesCS6A01G250600	chr2A	98.872	709	7	1	1	708	52551381	52550673	0.000000e+00	1264.0
11	TraesCS6A01G250600	chr2A	86.926	849	111	0	1234	2082	671712475	671711627	0.000000e+00	953.0
12	TraesCS6A01G250600	chr2A	88.361	610	62	3	1227	1828	535218087	535217479	0.000000e+00	725.0
13	TraesCS6A01G250600	chr2A	82.075	106	17	2	2744	2848	671704443	671704339	4.380000e-14	89.8
14	TraesCS6A01G250600	chr2D	97.021	705	20	1	1	705	178351192	178350489	0.000000e+00	1184.0
15	TraesCS6A01G250600	chr2D	87.279	849	108	0	1234	2082	526526865	526526017	0.000000e+00	970.0
16	TraesCS6A01G250600	chr2D	86.076	79	11	0	2744	2822	526516562	526516484	5.660000e-13	86.1
17	TraesCS6A01G250600	chr2B	87.044	849	110	0	1234	2082	622922682	622921834	0.000000e+00	959.0
18	TraesCS6A01G250600	chr2B	85.281	462	60	4	1511	1972	572269045	572268592	1.340000e-128	470.0
19	TraesCS6A01G250600	chr2B	83.871	93	15	0	2744	2836	622914438	622914346	4.380000e-14	89.8
20	TraesCS6A01G250600	chr5B	87.740	416	40	4	1245	1649	690230581	690230996	2.870000e-130	475.0
21	TraesCS6A01G250600	chr5B	87.209	344	38	1	1498	1835	579515052	579515395	1.390000e-103	387.0
22	TraesCS6A01G250600	chr1B	85.459	392	50	3	1511	1901	625757440	625757055	4.950000e-108	401.0
23	TraesCS6A01G250600	chr1B	93.443	61	4	0	1913	1973	625723714	625723654	1.220000e-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	TraesCS6A01G250600	chr6A	464688844	464692028	3184	True	5882.000000	5882	100.0000	1	3185	1	chr6A.!!$R2	3184
1	TraesCS6A01G250600	chr6D	325819287	325821752	2465	True	1823.500000	2477	94.1215	743	3182	2	chr6D.!!$R2	2439
2	TraesCS6A01G250600	chr6B	496986200	496988875	2675	False	1210.333333	2416	93.7360	705	3171	3	chr6B.!!$F1	2466
3	TraesCS6A01G250600	chr3A	534174506	534175217	711	True	1299.000000	1299	99.5790	1	712	1	chr3A.!!$R1	711
4	TraesCS6A01G250600	chr3A	648104212	648104801	589	False	647.000000	647	86.6340	1226	1822	1	chr3A.!!$F1	596
5	TraesCS6A01G250600	chr2A	52550673	52551381	708	True	1264.000000	1264	98.8720	1	708	1	chr2A.!!$R1	707
6	TraesCS6A01G250600	chr2A	671711627	671712475	848	True	953.000000	953	86.9260	1234	2082	1	chr2A.!!$R4	848
7	TraesCS6A01G250600	chr2A	535217479	535218087	608	True	725.000000	725	88.3610	1227	1828	1	chr2A.!!$R2	601
8	TraesCS6A01G250600	chr2D	178350489	178351192	703	True	1184.000000	1184	97.0210	1	705	1	chr2D.!!$R1	704
9	TraesCS6A01G250600	chr2D	526526017	526526865	848	True	970.000000	970	87.2790	1234	2082	1	chr2D.!!$R3	848
10	TraesCS6A01G250600	chr2B	622921834	622922682	848	True	959.000000	959	87.0440	1234	2082	1	chr2B.!!$R3	848

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
832	844	0.238553	GAACGCCTTTCTGCAAGTCC	59.761	55.0	0.0	0.0	33.76	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2457	2546	0.103208	GTAGGACATCACAGGCCTCG	59.897	60.0	0.0	0.52	32.04	4.63	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
713	714	1.014804	AGTTGGCCCCCATTTATCCA	58.985	50.000	0.00	0.00	31.53	3.41
761	762	5.295950	AGAGATCTGTATCAATTTGCTCGG	58.704	41.667	0.00	0.00	34.28	4.63
832	844	0.238553	GAACGCCTTTCTGCAAGTCC	59.761	55.000	0.00	0.00	33.76	3.85
846	858	3.130340	TGCAAGTCCTTGACCAAAGAAAC	59.870	43.478	11.12	0.00	42.93	2.78
1125	1142	1.543429	CGCATCCCTCCCAAATCCTAC	60.543	57.143	0.00	0.00	0.00	3.18
1375	1395	3.432051	GATCCGCGACCTGGTCCTG	62.432	68.421	20.68	12.85	0.00	3.86
1864	1893	3.214845	ATACTCGCGGACCGGGAC	61.215	66.667	27.89	4.68	43.39	4.46
1906	1935	2.871427	GATTGACATCGCCGGCGTC	61.871	63.158	44.16	34.52	40.74	5.19
2108	2139	9.153952	GAAACTTGTTTGTTTGTTGTTTCTTTC	57.846	29.630	3.27	0.00	39.86	2.62
2152	2185	2.564947	GTGGGTTGGATGGTTTTGCATA	59.435	45.455	0.00	0.00	0.00	3.14
2258	2291	3.848272	TCGTGGCAAGATTTTCCAATC	57.152	42.857	0.00	0.00	39.45	2.67
2259	2292	3.153130	TCGTGGCAAGATTTTCCAATCA	58.847	40.909	0.00	0.00	41.37	2.57
2260	2293	3.571828	TCGTGGCAAGATTTTCCAATCAA	59.428	39.130	0.00	0.00	41.37	2.57
2261	2294	4.038522	TCGTGGCAAGATTTTCCAATCAAA	59.961	37.500	0.00	0.00	41.37	2.69
2262	2295	4.749099	CGTGGCAAGATTTTCCAATCAAAA	59.251	37.500	0.00	0.00	41.37	2.44
2263	2296	5.409214	CGTGGCAAGATTTTCCAATCAAAAT	59.591	36.000	0.00	0.00	41.37	1.82
2264	2297	6.401367	CGTGGCAAGATTTTCCAATCAAAATC	60.401	38.462	9.64	9.64	46.58	2.17
2270	2303	6.413018	GATTTTCCAATCAAAATCTGCCAC	57.587	37.500	10.18	0.00	44.38	5.01
2271	2304	5.549742	TTTTCCAATCAAAATCTGCCACT	57.450	34.783	0.00	0.00	0.00	4.00
2272	2305	4.524316	TTCCAATCAAAATCTGCCACTG	57.476	40.909	0.00	0.00	0.00	3.66
2273	2306	2.827322	TCCAATCAAAATCTGCCACTGG	59.173	45.455	0.00	0.00	0.00	4.00
2274	2307	2.827322	CCAATCAAAATCTGCCACTGGA	59.173	45.455	0.00	0.00	0.00	3.86
2275	2308	3.367703	CCAATCAAAATCTGCCACTGGAC	60.368	47.826	0.00	0.00	0.00	4.02
2276	2309	2.957402	TCAAAATCTGCCACTGGACT	57.043	45.000	0.00	0.00	0.00	3.85
2277	2310	3.228188	TCAAAATCTGCCACTGGACTT	57.772	42.857	0.00	0.00	0.00	3.01
2282	2315	2.260844	TCTGCCACTGGACTTTCTTG	57.739	50.000	0.00	0.00	0.00	3.02
2300	2333	8.481314	ACTTTCTTGTCAGCATTCTATCTATCA	58.519	33.333	0.00	0.00	0.00	2.15
2346	2404	4.098055	TCAAGCTCTACAAGACACGATC	57.902	45.455	0.00	0.00	0.00	3.69
2350	2408	3.119316	AGCTCTACAAGACACGATCAAGG	60.119	47.826	0.00	0.00	0.00	3.61
2358	2416	0.541863	ACACGATCAAGGATCCCCAC	59.458	55.000	8.55	0.00	35.83	4.61
2368	2427	2.348472	AGGATCCCCACTGACTTTCAA	58.652	47.619	8.55	0.00	33.88	2.69
2374	2433	5.255397	TCCCCACTGACTTTCAATTACAT	57.745	39.130	0.00	0.00	0.00	2.29
2376	2435	6.969043	TCCCCACTGACTTTCAATTACATAT	58.031	36.000	0.00	0.00	0.00	1.78
2418	2507	6.770785	GGTCAAATGATTACAGCCCAGTAATA	59.229	38.462	6.75	0.00	42.93	0.98
2419	2508	7.448469	GGTCAAATGATTACAGCCCAGTAATAT	59.552	37.037	6.75	1.27	42.93	1.28
2420	2509	9.502091	GTCAAATGATTACAGCCCAGTAATATA	57.498	33.333	6.75	1.91	42.93	0.86
2446	2535	4.804608	TCAATGTACAAGTTTCGTGTGG	57.195	40.909	0.00	0.00	0.00	4.17
2447	2536	4.443621	TCAATGTACAAGTTTCGTGTGGA	58.556	39.130	0.00	0.00	0.00	4.02
2448	2537	5.060506	TCAATGTACAAGTTTCGTGTGGAT	58.939	37.500	0.00	0.00	0.00	3.41
2449	2538	5.049749	TCAATGTACAAGTTTCGTGTGGATG	60.050	40.000	0.00	0.00	0.00	3.51
2450	2539	3.799366	TGTACAAGTTTCGTGTGGATGT	58.201	40.909	0.00	0.00	0.00	3.06
2451	2540	4.946445	TGTACAAGTTTCGTGTGGATGTA	58.054	39.130	0.00	0.00	0.00	2.29
2452	2541	5.358090	TGTACAAGTTTCGTGTGGATGTAA	58.642	37.500	0.00	0.00	0.00	2.41
2453	2542	5.816258	TGTACAAGTTTCGTGTGGATGTAAA	59.184	36.000	0.00	0.00	0.00	2.01
2454	2543	6.483974	TGTACAAGTTTCGTGTGGATGTAAAT	59.516	34.615	0.00	0.00	0.00	1.40
2455	2544	5.997385	ACAAGTTTCGTGTGGATGTAAATC	58.003	37.500	0.00	0.00	0.00	2.17
2456	2545	4.921470	AGTTTCGTGTGGATGTAAATCG	57.079	40.909	0.00	0.00	0.00	3.34
2457	2546	3.124636	AGTTTCGTGTGGATGTAAATCGC	59.875	43.478	0.00	0.00	0.00	4.58
2458	2547	1.273688	TCGTGTGGATGTAAATCGCG	58.726	50.000	0.00	0.00	0.00	5.87
2459	2548	1.135344	TCGTGTGGATGTAAATCGCGA	60.135	47.619	13.09	13.09	38.39	5.87
2460	2549	1.255342	CGTGTGGATGTAAATCGCGAG	59.745	52.381	16.66	0.00	34.64	5.03
2461	2550	1.593006	GTGTGGATGTAAATCGCGAGG	59.407	52.381	16.66	0.00	0.00	4.63
2489	2578	1.593933	TGTCCTACAAAACGTGTTCGC	59.406	47.619	0.00	0.00	41.98	4.70
2605	2694	7.073265	TGCAAGCTTAAACATTTAACTACGAC	58.927	34.615	0.00	0.00	0.00	4.34
2639	2728	2.491693	CCACACCGGCAATGTAAATTCT	59.508	45.455	0.00	0.00	0.00	2.40
2781	3057	1.429463	CTCACTTGGTACGAGCAACC	58.571	55.000	0.00	0.00	37.53	3.77
3060	3339	7.222805	GCATGTATGTATACCCAGACGATAATG	59.777	40.741	0.00	0.00	32.33	1.90
3159	3439	4.759953	ACTACTGTTCTAGGGGGAAAAGA	58.240	43.478	1.97	0.00	34.95	2.52
3160	3440	4.531339	ACTACTGTTCTAGGGGGAAAAGAC	59.469	45.833	1.97	0.00	34.95	3.01
3162	3442	2.913617	CTGTTCTAGGGGGAAAAGACCT	59.086	50.000	0.00	0.00	33.60	3.85
3172	3452	4.098155	GGGGAAAAGACCTCTCTTCTAGT	58.902	47.826	0.00	0.00	35.52	2.57
3182	3462	7.662897	AGACCTCTCTTCTAGTAAACAAACAG	58.337	38.462	0.00	0.00	0.00	3.16
3183	3463	7.506261	AGACCTCTCTTCTAGTAAACAAACAGA	59.494	37.037	0.00	0.00	0.00	3.41
3184	3464	8.019656	ACCTCTCTTCTAGTAAACAAACAGAA	57.980	34.615	0.00	0.00	0.00	3.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
75	76	0.250252	TGTGCTTCATGCTCACCGAA	60.250	50.000	8.59	0.00	39.83	4.30
351	352	6.459298	GCAAGAAATCCAGACATATTGGTGAG	60.459	42.308	0.00	0.00	37.02	3.51
713	714	1.301479	GAGCGTTTCCAACCGGACT	60.301	57.895	9.46	0.00	42.67	3.85
727	728	1.944024	ACAGATCTCTTACTCGGAGCG	59.056	52.381	4.58	0.00	0.00	5.03
810	822	1.956477	ACTTGCAGAAAGGCGTTCATT	59.044	42.857	15.39	0.00	40.51	2.57
832	844	3.119637	ACGTGGTTGTTTCTTTGGTCAAG	60.120	43.478	0.00	0.00	0.00	3.02
937	949	3.946558	AGAGACGGTACTTGTAGATGGAC	59.053	47.826	0.00	0.00	0.00	4.02
993	1010	4.280019	ACGGAAGGGGTTGGTGGC	62.280	66.667	0.00	0.00	0.00	5.01
1034	1051	1.672356	CCGAGGAGCCTTGGTGTTG	60.672	63.158	13.81	0.00	41.59	3.33
2131	2164	0.755686	TGCAAAACCATCCAACCCAC	59.244	50.000	0.00	0.00	0.00	4.61
2152	2185	4.164843	ACACAGTTACCACAAATGAGGT	57.835	40.909	7.66	7.66	41.80	3.85
2258	2291	3.571401	AGAAAGTCCAGTGGCAGATTTTG	59.429	43.478	3.51	0.00	0.00	2.44
2259	2292	3.837355	AGAAAGTCCAGTGGCAGATTTT	58.163	40.909	3.51	0.00	0.00	1.82
2260	2293	3.515602	AGAAAGTCCAGTGGCAGATTT	57.484	42.857	3.51	2.42	0.00	2.17
2261	2294	3.152341	CAAGAAAGTCCAGTGGCAGATT	58.848	45.455	3.51	0.00	0.00	2.40
2262	2295	2.107204	ACAAGAAAGTCCAGTGGCAGAT	59.893	45.455	3.51	0.00	0.00	2.90
2263	2296	1.490490	ACAAGAAAGTCCAGTGGCAGA	59.510	47.619	3.51	0.00	0.00	4.26
2264	2297	1.876156	GACAAGAAAGTCCAGTGGCAG	59.124	52.381	3.51	0.00	32.36	4.85
2265	2298	1.211703	TGACAAGAAAGTCCAGTGGCA	59.788	47.619	3.51	0.00	37.73	4.92
2266	2299	1.876156	CTGACAAGAAAGTCCAGTGGC	59.124	52.381	3.51	0.00	37.73	5.01
2267	2300	1.876156	GCTGACAAGAAAGTCCAGTGG	59.124	52.381	1.40	1.40	37.73	4.00
2268	2301	2.564771	TGCTGACAAGAAAGTCCAGTG	58.435	47.619	0.00	0.00	37.73	3.66
2269	2302	3.498774	ATGCTGACAAGAAAGTCCAGT	57.501	42.857	0.00	0.00	37.73	4.00
2270	2303	4.070716	AGAATGCTGACAAGAAAGTCCAG	58.929	43.478	0.00	0.00	37.73	3.86
2271	2304	4.090761	AGAATGCTGACAAGAAAGTCCA	57.909	40.909	0.00	0.00	37.73	4.02
2272	2305	6.112058	AGATAGAATGCTGACAAGAAAGTCC	58.888	40.000	0.00	0.00	37.73	3.85
2273	2306	8.885494	ATAGATAGAATGCTGACAAGAAAGTC	57.115	34.615	0.00	0.00	38.99	3.01
2274	2307	8.481314	TGATAGATAGAATGCTGACAAGAAAGT	58.519	33.333	0.00	0.00	0.00	2.66
2275	2308	8.883954	TGATAGATAGAATGCTGACAAGAAAG	57.116	34.615	0.00	0.00	0.00	2.62
2276	2309	9.486497	GATGATAGATAGAATGCTGACAAGAAA	57.514	33.333	0.00	0.00	0.00	2.52
2277	2310	8.868103	AGATGATAGATAGAATGCTGACAAGAA	58.132	33.333	0.00	0.00	0.00	2.52
2282	2315	8.924691	GTTTCAGATGATAGATAGAATGCTGAC	58.075	37.037	0.00	0.00	30.49	3.51
2300	2333	1.469940	CGCCAGCGAGTAGTTTCAGAT	60.470	52.381	6.06	0.00	42.83	2.90
2337	2370	1.123928	GGGGATCCTTGATCGTGTCT	58.876	55.000	12.58	0.00	39.72	3.41
2346	2404	2.040278	TGAAAGTCAGTGGGGATCCTTG	59.960	50.000	12.58	5.79	0.00	3.61
2350	2408	5.253330	TGTAATTGAAAGTCAGTGGGGATC	58.747	41.667	0.00	0.00	0.00	3.36
2376	2435	8.253810	TCATTTGACCATGAAACTGTTGTAAAA	58.746	29.630	0.00	0.00	29.81	1.52
2418	2507	8.564574	ACACGAAACTTGTACATTGATTGTTAT	58.435	29.630	0.00	0.00	39.87	1.89
2419	2508	7.853437	CACACGAAACTTGTACATTGATTGTTA	59.147	33.333	0.00	0.00	39.87	2.41
2420	2509	6.690957	CACACGAAACTTGTACATTGATTGTT	59.309	34.615	0.00	0.00	39.87	2.83
2421	2510	6.198687	CACACGAAACTTGTACATTGATTGT	58.801	36.000	0.00	0.00	42.62	2.71
2422	2511	5.624900	CCACACGAAACTTGTACATTGATTG	59.375	40.000	0.00	0.00	0.00	2.67
2446	2535	0.861837	CAGGCCTCGCGATTTACATC	59.138	55.000	10.36	0.00	0.00	3.06
2447	2536	0.178068	ACAGGCCTCGCGATTTACAT	59.822	50.000	10.36	0.00	0.00	2.29
2448	2537	0.739462	CACAGGCCTCGCGATTTACA	60.739	55.000	10.36	0.00	0.00	2.41
2449	2538	0.459585	TCACAGGCCTCGCGATTTAC	60.460	55.000	10.36	0.02	0.00	2.01
2450	2539	0.464036	ATCACAGGCCTCGCGATTTA	59.536	50.000	10.36	0.00	0.00	1.40
2451	2540	1.091771	CATCACAGGCCTCGCGATTT	61.092	55.000	10.36	0.00	0.00	2.17
2452	2541	1.522355	CATCACAGGCCTCGCGATT	60.522	57.895	10.36	0.00	0.00	3.34
2453	2542	2.107750	CATCACAGGCCTCGCGAT	59.892	61.111	10.36	1.61	0.00	4.58
2454	2543	3.356639	GACATCACAGGCCTCGCGA	62.357	63.158	9.26	9.26	0.00	5.87
2455	2544	2.887568	GACATCACAGGCCTCGCG	60.888	66.667	0.00	0.00	0.00	5.87
2456	2545	1.676678	TAGGACATCACAGGCCTCGC	61.677	60.000	0.00	0.00	32.04	5.03
2457	2546	0.103208	GTAGGACATCACAGGCCTCG	59.897	60.000	0.00	0.52	32.04	4.63
2458	2547	1.195115	TGTAGGACATCACAGGCCTC	58.805	55.000	0.00	0.00	32.04	4.70
2459	2548	1.656587	TTGTAGGACATCACAGGCCT	58.343	50.000	0.00	0.00	34.56	5.19
2460	2549	2.488153	GTTTTGTAGGACATCACAGGCC	59.512	50.000	0.00	0.00	0.00	5.19
2461	2550	2.159627	CGTTTTGTAGGACATCACAGGC	59.840	50.000	0.00	0.00	0.00	4.85
2489	2578	4.022589	AGTGTGGTGATTGCAAGATTTCTG	60.023	41.667	4.94	0.00	0.00	3.02
2639	2728	1.408969	GACTTGGTTTGAAAGGCCCA	58.591	50.000	0.00	0.00	0.00	5.36
2781	3057	2.444624	CGTCTTCATCGTGGTGGCG	61.445	63.158	0.00	0.00	0.00	5.69
3159	3439	7.598759	TCTGTTTGTTTACTAGAAGAGAGGT	57.401	36.000	0.00	0.00	0.00	3.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.