AutoCloner

Multiple sequence alignment - TraesCS3D01G514300

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	TraesCS3D01G514300	chr3D	100.000	3182	0	0	1	3182	598050225	598047044	0.000000e+00	5877
1	TraesCS3D01G514300	chr3D	86.318	1586	165	35	638	2186	598060504	598062074	0.000000e+00	1679
2	TraesCS3D01G514300	chr3D	79.672	305	16	16	638	937	598057947	598057684	9.070000e-41	178
3	TraesCS3D01G514300	chr3A	94.987	1855	69	11	495	2341	729690163	729692001	0.000000e+00	2889
4	TraesCS3D01G514300	chr3A	94.836	1859	68	12	495	2341	728019107	728017265	0.000000e+00	2876
5	TraesCS3D01G514300	chr3A	97.449	1215	31	0	1127	2341	728033570	728032356	0.000000e+00	2073
6	TraesCS3D01G514300	chr3A	90.372	1236	115	3	953	2186	728056540	728057773	0.000000e+00	1620
7	TraesCS3D01G514300	chr3A	88.089	1209	128	12	993	2186	728384615	728385822	0.000000e+00	1421
8	TraesCS3D01G514300	chr3A	85.299	1204	163	7	996	2186	728458187	728456985	0.000000e+00	1230
9	TraesCS3D01G514300	chr3A	88.914	442	39	9	1	438	728019543	728019108	1.300000e-148	536
10	TraesCS3D01G514300	chr3A	88.889	432	39	8	1	429	729689728	729690153	1.010000e-144	523
11	TraesCS3D01G514300	chr3A	96.129	155	5	1	2388	2542	728017273	728017120	5.270000e-63	252
12	TraesCS3D01G514300	chr3A	96.129	155	5	1	2388	2542	728032364	728032211	5.270000e-63	252
13	TraesCS3D01G514300	chr3A	95.570	158	6	1	2385	2542	729691990	729692146	5.270000e-63	252
14	TraesCS3D01G514300	chr3A	82.661	248	20	12	701	937	728049338	728049103	6.960000e-47	198
15	TraesCS3D01G514300	chr3B	95.522	1608	59	7	586	2184	805005071	805003468	0.000000e+00	2558
16	TraesCS3D01G514300	chr3B	85.809	1205	157	10	995	2186	805425854	805424651	0.000000e+00	1266
17	TraesCS3D01G514300	chr3B	87.328	363	29	3	2178	2537	805003318	805002970	1.780000e-107	399
18	TraesCS3D01G514300	chr3B	78.363	342	37	21	2839	3169	796008912	796009227	1.510000e-43	187
19	TraesCS3D01G514300	chr3B	88.722	133	15	0	327	459	805005214	805005082	2.540000e-36	163
20	TraesCS3D01G514300	chr6B	90.658	653	38	8	2540	3182	5280041	5280680	0.000000e+00	846
21	TraesCS3D01G514300	chr7A	89.602	654	41	15	2539	3182	580379389	580380025	0.000000e+00	806
22	TraesCS3D01G514300	chr1A	89.660	648	43	10	2543	3182	186481443	186480812	0.000000e+00	804
23	TraesCS3D01G514300	chrUn	86.577	447	47	10	989	1423	42058267	42057822	6.170000e-132	481

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	TraesCS3D01G514300	chr3D	598047044	598050225	3181	True	5877.000000	5877	100.000000	1	3182	1	chr3D.!!$R1	3181
1	TraesCS3D01G514300	chr3D	598060504	598062074	1570	False	1679.000000	1679	86.318000	638	2186	1	chr3D.!!$F1	1548
2	TraesCS3D01G514300	chr3A	728056540	728057773	1233	False	1620.000000	1620	90.372000	953	2186	1	chr3A.!!$F1	1233
3	TraesCS3D01G514300	chr3A	728384615	728385822	1207	False	1421.000000	1421	88.089000	993	2186	1	chr3A.!!$F2	1193
4	TraesCS3D01G514300	chr3A	728456985	728458187	1202	True	1230.000000	1230	85.299000	996	2186	1	chr3A.!!$R2	1190
5	TraesCS3D01G514300	chr3A	728017120	728019543	2423	True	1221.333333	2876	93.293000	1	2542	3	chr3A.!!$R3	2541
6	TraesCS3D01G514300	chr3A	729689728	729692146	2418	False	1221.333333	2889	93.148667	1	2542	3	chr3A.!!$F3	2541
7	TraesCS3D01G514300	chr3A	728032211	728033570	1359	True	1162.500000	2073	96.789000	1127	2542	2	chr3A.!!$R4	1415
8	TraesCS3D01G514300	chr3B	805424651	805425854	1203	True	1266.000000	1266	85.809000	995	2186	1	chr3B.!!$R1	1191
9	TraesCS3D01G514300	chr3B	805002970	805005214	2244	True	1040.000000	2558	90.524000	327	2537	3	chr3B.!!$R2	2210
10	TraesCS3D01G514300	chr6B	5280041	5280680	639	False	846.000000	846	90.658000	2540	3182	1	chr6B.!!$F1	642
11	TraesCS3D01G514300	chr7A	580379389	580380025	636	False	806.000000	806	89.602000	2539	3182	1	chr7A.!!$F1	643
12	TraesCS3D01G514300	chr1A	186480812	186481443	631	True	804.000000	804	89.660000	2543	3182	1	chr1A.!!$R1	639

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
746	754	0.321671	AGCAGTCCAACACGTAGCAT	59.678	50.0	0.0	0.0	0.0	3.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2578	2826	0.250553	TTTCGGCCATCTCGTTTGGT	60.251	50.0	2.24	0.0	36.57	3.67	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
184	188	9.918630	AATCATCGAATTGAAGAAAAAGTTCAT	57.081	25.926	0.00	0.00	36.09	2.57
224	228	5.179368	TCATCGAGCCAGTAAGAACAAAAAG	59.821	40.000	0.00	0.00	0.00	2.27
233	237	7.544217	GCCAGTAAGAACAAAAAGAAAGAAACA	59.456	33.333	0.00	0.00	0.00	2.83
245	249	8.620533	AAAAGAAAGAAACAGAAGATGAAACG	57.379	30.769	0.00	0.00	0.00	3.60
248	252	5.931441	AAGAAACAGAAGATGAAACGGAG	57.069	39.130	0.00	0.00	0.00	4.63
249	253	5.215252	AGAAACAGAAGATGAAACGGAGA	57.785	39.130	0.00	0.00	0.00	3.71
253	257	5.931441	ACAGAAGATGAAACGGAGAAAAG	57.069	39.130	0.00	0.00	0.00	2.27
254	258	5.611374	ACAGAAGATGAAACGGAGAAAAGA	58.389	37.500	0.00	0.00	0.00	2.52
292	296	9.078990	AGGAAAAGGACGAATAAAAGAAGAAAT	57.921	29.630	0.00	0.00	0.00	2.17
318	322	3.274288	GAAAGCTAACAGATCCTGGTGG	58.726	50.000	0.00	0.00	35.51	4.61
319	323	1.207791	AGCTAACAGATCCTGGTGGG	58.792	55.000	0.00	0.00	35.51	4.61
361	365	4.577693	TGCTACCTCGACGACAATAGTAAT	59.422	41.667	0.00	0.00	0.00	1.89
403	407	1.535444	TCTGCCTTCCGTTCCTCCA	60.535	57.895	0.00	0.00	0.00	3.86
404	408	1.376037	CTGCCTTCCGTTCCTCCAC	60.376	63.158	0.00	0.00	0.00	4.02
413	417	1.761174	GTTCCTCCACTGGAAGGCA	59.239	57.895	0.00	0.00	45.62	4.75
414	418	0.329596	GTTCCTCCACTGGAAGGCAT	59.670	55.000	0.00	0.00	45.62	4.40
459	463	3.260740	ACAAGTGTGACGTTCGGTAAAA	58.739	40.909	0.00	0.00	0.00	1.52
487	491	2.194056	CCGACCCGGGCTAGACTA	59.806	66.667	24.08	0.00	44.15	2.59
488	492	1.897615	CCGACCCGGGCTAGACTAG	60.898	68.421	24.08	5.03	44.15	2.57
542	546	2.644992	CACCAAACGCTCAAGCCC	59.355	61.111	0.00	0.00	37.91	5.19
544	548	1.228552	ACCAAACGCTCAAGCCCAT	60.229	52.632	0.00	0.00	37.91	4.00
561	565	3.624707	GCCCATACTTGAATTCTGGTGGA	60.625	47.826	7.05	0.00	0.00	4.02
564	568	5.256474	CCATACTTGAATTCTGGTGGACTT	58.744	41.667	7.05	0.00	0.00	3.01
565	569	5.124457	CCATACTTGAATTCTGGTGGACTTG	59.876	44.000	7.05	1.86	0.00	3.16
566	570	4.437682	ACTTGAATTCTGGTGGACTTGA	57.562	40.909	7.05	0.00	0.00	3.02
569	573	3.754965	TGAATTCTGGTGGACTTGAAGG	58.245	45.455	7.05	0.00	0.00	3.46
570	574	3.394274	TGAATTCTGGTGGACTTGAAGGA	59.606	43.478	7.05	0.00	0.00	3.36
572	576	2.930826	TCTGGTGGACTTGAAGGAAC	57.069	50.000	0.00	0.00	0.00	3.62
574	578	2.368875	TCTGGTGGACTTGAAGGAACTC	59.631	50.000	0.00	0.00	38.49	3.01
575	579	1.420138	TGGTGGACTTGAAGGAACTCC	59.580	52.381	0.00	0.00	38.49	3.85
578	582	0.328592	GGACTTGAAGGAACTCCCCC	59.671	60.000	0.00	0.00	38.49	5.40
579	583	1.064825	GACTTGAAGGAACTCCCCCA	58.935	55.000	0.00	0.00	38.49	4.96
591	596	5.103643	AGGAACTCCCCCACCTTATTTTATC	60.104	44.000	0.00	0.00	36.42	1.75
716	723	1.490693	CGCATACACATCGAGCCACC	61.491	60.000	0.00	0.00	0.00	4.61
746	754	0.321671	AGCAGTCCAACACGTAGCAT	59.678	50.000	0.00	0.00	0.00	3.79
841	873	1.372087	CCTTCTTCCAGATGCCACGC	61.372	60.000	0.00	0.00	0.00	5.34
1134	1211	0.179100	CCTCGCTGGTGGACATACTG	60.179	60.000	0.00	0.00	0.00	2.74
1923	2011	1.846007	CGGGATATGAGGGAGAGGAG	58.154	60.000	0.00	0.00	0.00	3.69
2304	2549	9.219603	CCAGAATAACATATGACGACCAAATAT	57.780	33.333	10.38	0.00	0.00	1.28
2312	2557	5.723672	ATGACGACCAAATATATCTCCGT	57.276	39.130	0.00	0.00	0.00	4.69
2354	2599	5.033326	TCATCATGTGTTCACAACGATTG	57.967	39.130	9.68	3.83	0.00	2.67
2379	2626	6.146021	GTGAGCGTCAAAATCATTTTTCCATT	59.854	34.615	0.00	0.00	32.72	3.16
2419	2666	4.267349	AGGCACTAATACTCGTGTTTGT	57.733	40.909	0.00	0.00	36.02	2.83
2481	2728	0.679640	CCCAAAAGCCGGCACATCTA	60.680	55.000	31.54	0.00	0.00	1.98
2516	2763	5.601583	AATTGATTGCTGATGTTGGCATA	57.398	34.783	0.00	0.00	38.30	3.14
2703	2951	1.591504	GGCCGAAATTCAGCCGGAAA	61.592	55.000	5.05	0.00	45.58	3.13
2747	2995	5.941948	AAGTATAGCAGTTGAACAACACC	57.058	39.130	17.85	9.19	43.47	4.16
2874	3127	1.490490	AGGTGTTGCAGAGTTGAGGAA	59.510	47.619	0.00	0.00	0.00	3.36
2899	3152	1.378882	GCCGATGGATTCAGCTGCAA	61.379	55.000	9.47	4.90	38.93	4.08
2920	3173	2.033141	GCAGCCAGCAGAGGTCAA	59.967	61.111	0.00	0.00	44.79	3.18
2938	3191	3.130340	GTCAACAAAAAGGAGTCTTGCCA	59.870	43.478	0.00	0.00	32.75	4.92
2953	3206	2.125147	CCATCAGGAAGGCGCGAA	60.125	61.111	12.10	0.00	36.89	4.70
3086	3342	1.804396	TTCGGGTGTTCGGTTCGCTA	61.804	55.000	0.00	0.00	0.00	4.26
3163	3420	3.118592	ACTGTTCAAAATGGGCCGAAAAA	60.119	39.130	0.00	0.00	0.00	1.94

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
24	25	6.935167	TCTTTTTCCAAAACTTCAAAGAGCT	58.065	32.000	0.00	0.00	0.00	4.09
26	27	8.931385	TGATCTTTTTCCAAAACTTCAAAGAG	57.069	30.769	0.00	0.00	34.59	2.85
125	127	9.883142	ACTTGATAAACTTTTCCAAATTTGTGA	57.117	25.926	16.73	10.66	0.00	3.58
184	188	6.237996	GGCTCGATGAATTGTTCGTAAATACA	60.238	38.462	6.53	0.00	36.74	2.29
193	197	4.870426	TCTTACTGGCTCGATGAATTGTTC	59.130	41.667	0.00	0.00	0.00	3.18
224	228	6.202954	TCTCCGTTTCATCTTCTGTTTCTTTC	59.797	38.462	0.00	0.00	0.00	2.62
233	237	7.568199	TTTTCTTTTCTCCGTTTCATCTTCT	57.432	32.000	0.00	0.00	0.00	2.85
264	268	9.563748	TTCTTCTTTTATTCGTCCTTTTCCTTA	57.436	29.630	0.00	0.00	0.00	2.69
292	296	5.248477	ACCAGGATCTGTTAGCTTTCACTTA	59.752	40.000	0.00	0.00	0.00	2.24
295	299	3.686726	CACCAGGATCTGTTAGCTTTCAC	59.313	47.826	0.00	0.00	0.00	3.18
318	322	1.840224	TAGTTAACCACCACGCCCCC	61.840	60.000	0.88	0.00	0.00	5.40
319	323	0.253894	ATAGTTAACCACCACGCCCC	59.746	55.000	0.88	0.00	0.00	5.80
361	365	2.410322	ATTTGACGCTCCAGGCACCA	62.410	55.000	0.00	0.00	41.91	4.17
403	407	2.359900	GAACGAATCATGCCTTCCAGT	58.640	47.619	0.00	0.00	0.00	4.00
404	408	1.672881	GGAACGAATCATGCCTTCCAG	59.327	52.381	0.00	0.00	32.16	3.86
413	417	1.846439	ACCCCAGATGGAACGAATCAT	59.154	47.619	0.00	0.00	37.39	2.45
414	418	1.285280	ACCCCAGATGGAACGAATCA	58.715	50.000	0.00	0.00	37.39	2.57
461	465	1.529152	GCCCGGGTCGGTTTCATTTT	61.529	55.000	24.63	0.00	46.80	1.82
462	466	1.974875	GCCCGGGTCGGTTTCATTT	60.975	57.895	24.63	0.00	46.80	2.32
463	467	1.555477	TAGCCCGGGTCGGTTTCATT	61.555	55.000	24.63	0.00	46.80	2.57
464	468	1.968050	CTAGCCCGGGTCGGTTTCAT	61.968	60.000	24.63	0.00	46.80	2.57
465	469	2.604079	TAGCCCGGGTCGGTTTCA	60.604	61.111	24.63	0.00	46.80	2.69
466	470	2.186125	CTAGCCCGGGTCGGTTTC	59.814	66.667	24.63	2.54	46.80	2.78
467	471	2.284112	TCTAGCCCGGGTCGGTTT	60.284	61.111	24.63	3.69	46.80	3.27
468	472	2.215451	TAGTCTAGCCCGGGTCGGTT	62.215	60.000	24.63	6.56	46.80	4.44
469	473	2.621517	CTAGTCTAGCCCGGGTCGGT	62.622	65.000	24.63	7.21	46.80	4.69
471	475	2.553727	GCTAGTCTAGCCCGGGTCG	61.554	68.421	24.63	11.00	45.95	4.79
472	476	3.445888	GCTAGTCTAGCCCGGGTC	58.554	66.667	24.63	14.90	45.95	4.46
518	522	1.164411	TGAGCGTTTGGTGCTTATGG	58.836	50.000	0.00	0.00	44.18	2.74
542	546	5.939883	TCAAGTCCACCAGAATTCAAGTATG	59.060	40.000	8.44	0.00	28.05	2.39
544	548	5.560722	TCAAGTCCACCAGAATTCAAGTA	57.439	39.130	8.44	0.00	28.05	2.24
550	554	4.141158	AGTTCCTTCAAGTCCACCAGAATT	60.141	41.667	0.00	0.00	31.58	2.17
553	557	2.368875	GAGTTCCTTCAAGTCCACCAGA	59.631	50.000	0.00	0.00	0.00	3.86
561	565	0.771755	GTGGGGGAGTTCCTTCAAGT	59.228	55.000	0.00	0.00	35.95	3.16
564	568	0.402861	AAGGTGGGGGAGTTCCTTCA	60.403	55.000	0.00	0.00	35.70	3.02
565	569	1.665137	TAAGGTGGGGGAGTTCCTTC	58.335	55.000	0.00	0.00	40.26	3.46
566	570	2.378308	ATAAGGTGGGGGAGTTCCTT	57.622	50.000	0.00	0.00	42.10	3.36
569	573	4.820173	CGATAAAATAAGGTGGGGGAGTTC	59.180	45.833	0.00	0.00	0.00	3.01
570	574	4.788679	CGATAAAATAAGGTGGGGGAGTT	58.211	43.478	0.00	0.00	0.00	3.01
572	576	3.146847	GCGATAAAATAAGGTGGGGGAG	58.853	50.000	0.00	0.00	0.00	4.30
573	577	2.781174	AGCGATAAAATAAGGTGGGGGA	59.219	45.455	0.00	0.00	0.00	4.81
574	578	3.223674	AGCGATAAAATAAGGTGGGGG	57.776	47.619	0.00	0.00	0.00	5.40
575	579	5.240844	CCTTAAGCGATAAAATAAGGTGGGG	59.759	44.000	0.00	0.00	31.87	4.96
591	596	6.582437	TTTCTTTTGAAAAAGCCTTAAGCG	57.418	33.333	10.10	0.00	45.30	4.68
716	723	0.249868	TGGACTGCTTTCGTGGTCAG	60.250	55.000	0.00	0.00	0.00	3.51
746	754	2.163412	GGCAGCATTATTCAACGACCAA	59.837	45.455	0.00	0.00	0.00	3.67
2287	2532	7.220875	CACGGAGATATATTTGGTCGTCATATG	59.779	40.741	0.00	0.00	0.00	1.78
2288	2533	7.093902	ACACGGAGATATATTTGGTCGTCATAT	60.094	37.037	0.00	0.00	0.00	1.78
2304	2549	7.061566	TGGATAATTCATTCACACGGAGATA	57.938	36.000	0.00	0.00	0.00	1.98
2312	2557	6.773685	TGATGAGCATGGATAATTCATTCACA	59.226	34.615	0.00	0.00	0.00	3.58
2347	2592	3.249799	TGATTTTGACGCTCACAATCGTT	59.750	39.130	15.57	0.00	43.08	3.85
2354	2599	4.981674	TGGAAAAATGATTTTGACGCTCAC	59.018	37.500	3.62	0.00	38.83	3.51
2379	2626	6.265196	AGTGCCTTACAAGAATGAACAATTGA	59.735	34.615	13.59	0.00	0.00	2.57
2419	2666	4.340666	TCAAAAGCAACAGACCAGCAATAA	59.659	37.500	0.00	0.00	0.00	1.40
2481	2728	8.114331	TCAGCAATCAATTAGAACAATCAACT	57.886	30.769	0.00	0.00	0.00	3.16
2516	2763	9.174166	GTACCCAACTAGTGATATTTGTCAAAT	57.826	33.333	14.98	14.98	34.90	2.32
2532	2779	3.472283	TCAAAACGCAGTACCCAACTA	57.528	42.857	0.00	0.00	45.00	2.24
2578	2826	0.250553	TTTCGGCCATCTCGTTTGGT	60.251	50.000	2.24	0.00	36.57	3.67
2618	2866	6.164876	TGTAATTTCGTCCGAGATTTTACCA	58.835	36.000	10.19	2.12	32.36	3.25
2695	2943	3.559655	GCTTGTTTTCAAATTTTCCGGCT	59.440	39.130	0.00	0.00	39.47	5.52
2700	2948	7.538303	TTCCTCTGCTTGTTTTCAAATTTTC	57.462	32.000	0.00	0.00	39.47	2.29
2703	2951	7.105588	ACTTTTCCTCTGCTTGTTTTCAAATT	58.894	30.769	0.00	0.00	39.47	1.82
2747	2995	8.534778	GGTAAACATTTATTTACGTACTCCTCG	58.465	37.037	0.00	0.00	43.22	4.63
2859	3112	3.329386	CGATTCTTCCTCAACTCTGCAA	58.671	45.455	0.00	0.00	0.00	4.08
2874	3127	2.160822	CTGAATCCATCGGCGATTCT	57.839	50.000	21.54	4.65	43.94	2.40
2920	3173	3.565307	TGATGGCAAGACTCCTTTTTGT	58.435	40.909	0.00	0.00	0.00	2.83
2938	3191	2.509336	CGTTCGCGCCTTCCTGAT	60.509	61.111	0.00	0.00	0.00	2.90
2987	3242	1.989966	GATCTTCCACTCGTCGCCGA	61.990	60.000	0.00	0.00	41.73	5.54
3054	3310	2.705127	ACACCCGAACCCTAAACAACTA	59.295	45.455	0.00	0.00	0.00	2.24
3086	3342	5.063880	CCTTGTCTGCCTAAGTTTAACAGT	58.936	41.667	0.00	0.00	0.00	3.55
3143	3400	3.543680	TTTTTCGGCCCATTTTGAACA	57.456	38.095	0.00	0.00	0.00	3.18
3151	3408	3.549412	GCCAAATTTTTCGGCCCAT	57.451	47.368	6.74	0.00	40.07	4.00
3163	3420	1.304381	ATGTCTGTGCCGGCCAAAT	60.304	52.632	26.77	11.87	0.00	2.32

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.