AutoCloner

Multiple sequence alignment - TraesCS5D01G134800

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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	TraesCS5D01G134800	chr5D	100.000	3151	0	0	1	3151	215245893	215242743	0.000000e+00	5819.0
1	TraesCS5D01G134800	chr5D	91.781	292	12	4	2872	3151	215197312	215197021	2.280000e-106	396.0
2	TraesCS5D01G134800	chr5A	91.739	2312	95	43	4	2279	283015341	283013090	0.000000e+00	3123.0
3	TraesCS5D01G134800	chr5A	89.811	265	17	5	2281	2535	283004330	283004066	6.510000e-87	331.0
4	TraesCS5D01G134800	chr5A	92.208	77	4	2	2872	2947	167147511	167147436	1.200000e-19	108.0
5	TraesCS5D01G134800	chr5B	92.406	1172	38	18	1152	2277	230427894	230426728	0.000000e+00	1624.0
6	TraesCS5D01G134800	chr5B	95.388	1019	35	10	140	1156	230434245	230433237	0.000000e+00	1611.0
7	TraesCS5D01G134800	chr5B	92.138	636	27	6	2533	3151	230425513	230424884	0.000000e+00	876.0
8	TraesCS5D01G134800	chr5B	93.750	256	14	2	2281	2535	230425808	230425554	1.770000e-102	383.0
9	TraesCS5D01G134800	chr5B	94.118	221	13	0	2931	3151	230369831	230369611	1.400000e-88	337.0
10	TraesCS5D01G134800	chr5B	84.437	302	15	10	2870	3151	280645510	280645221	5.180000e-68	268.0
11	TraesCS5D01G134800	chr5B	93.204	103	7	0	5	107	230434346	230434244	5.440000e-33	152.0
12	TraesCS5D01G134800	chr4D	79.553	626	86	29	2281	2870	11001306	11001925	2.930000e-110	409.0
13	TraesCS5D01G134800	chr4D	82.659	346	51	4	2535	2871	424475567	424475912	6.610000e-77	298.0
14	TraesCS5D01G134800	chr4D	86.466	266	20	4	2286	2535	51606855	51606590	8.610000e-71	278.0
15	TraesCS5D01G134800	chr2B	89.437	284	26	4	2870	3151	185894680	185894399	3.870000e-94	355.0
16	TraesCS5D01G134800	chr2B	85.759	323	12	13	2862	3151	468741722	468741401	8.490000e-81	311.0
17	TraesCS5D01G134800	chr3A	95.434	219	6	3	2933	3151	323562969	323562755	2.330000e-91	346.0
18	TraesCS5D01G134800	chr3A	88.235	85	8	2	2872	2956	667790636	667790554	2.000000e-17	100.0
19	TraesCS5D01G134800	chr7D	95.045	222	6	4	2933	3151	498060962	498061181	8.370000e-91	344.0
20	TraesCS5D01G134800	chr7D	84.733	262	24	7	2286	2531	539699407	539699668	6.750000e-62	248.0
21	TraesCS5D01G134800	chr7D	86.585	82	7	4	2876	2956	259374877	259374799	1.560000e-13	87.9
22	TraesCS5D01G134800	chr2A	94.222	225	9	4	2927	3151	455634197	455633977	1.080000e-89	340.0
23	TraesCS5D01G134800	chr2A	85.763	295	28	11	2866	3151	311471065	311471354	1.840000e-77	300.0
24	TraesCS5D01G134800	chr2A	93.506	77	2	3	2866	2941	320464130	320464056	9.240000e-21	111.0
25	TraesCS5D01G134800	chr1D	93.805	226	11	3	2927	3151	162825049	162824826	1.400000e-88	337.0
26	TraesCS5D01G134800	chr1D	83.668	349	53	4	2534	2878	283613898	283614246	3.030000e-85	326.0
27	TraesCS5D01G134800	chr1D	84.838	277	20	9	2281	2535	182045592	182045316	3.120000e-65	259.0
28	TraesCS5D01G134800	chr1D	83.146	267	29	5	2281	2531	465396850	465397116	2.440000e-56	230.0
29	TraesCS5D01G134800	chr1D	83.459	266	22	5	2281	2524	223179874	223180139	8.790000e-56	228.0
30	TraesCS5D01G134800	chr1D	87.209	172	9	5	2376	2534	338745890	338745719	1.930000e-42	183.0
31	TraesCS5D01G134800	chr1D	86.713	143	9	2	2392	2524	473796142	473796284	1.960000e-32	150.0
32	TraesCS5D01G134800	chr3D	84.524	336	48	4	2534	2866	124540769	124540435	2.340000e-86	329.0
33	TraesCS5D01G134800	chr3D	82.405	341	55	5	2535	2871	560879942	560880281	3.070000e-75	292.0
34	TraesCS5D01G134800	chr3D	82.803	314	22	15	2864	3151	234333038	234332731	5.220000e-63	252.0
35	TraesCS5D01G134800	chr3D	86.364	88	8	4	2870	2956	296857417	296857333	3.350000e-15	93.5
36	TraesCS5D01G134800	chr2D	83.382	343	50	5	2534	2871	450233224	450233564	8.490000e-81	311.0
37	TraesCS5D01G134800	chr2D	86.770	257	20	3	2281	2523	450232914	450233170	1.110000e-69	274.0
38	TraesCS5D01G134800	chr2D	83.260	227	19	5	2308	2524	474657946	474657729	1.150000e-44	191.0
39	TraesCS5D01G134800	chr2D	84.706	85	10	3	2872	2956	274825169	274825088	7.240000e-12	82.4
40	TraesCS5D01G134800	chr1A	83.284	341	49	7	2535	2871	119563320	119563656	1.100000e-79	307.0
41	TraesCS5D01G134800	chr1A	87.075	147	9	2	2392	2528	148747254	148747400	1.170000e-34	158.0
42	TraesCS5D01G134800	chr6A	88.462	260	20	2	2281	2530	503731325	503731584	3.950000e-79	305.0
43	TraesCS5D01G134800	chr6A	85.000	160	13	3	2373	2522	448641454	448641296	5.440000e-33	152.0
44	TraesCS5D01G134800	chr6B	87.547	265	23	2	2281	2535	549190003	549189739	6.610000e-77	298.0
45	TraesCS5D01G134800	chrUn	82.319	345	52	7	2535	2871	8094397	8094740	1.110000e-74	291.0
46	TraesCS5D01G134800	chr4B	85.609	271	22	5	2281	2535	339259736	339259467	5.180000e-68	268.0
47	TraesCS5D01G134800	chr4B	86.154	260	20	5	2281	2524	36004944	36005203	1.860000e-67	267.0
48	TraesCS5D01G134800	chr6D	80.586	273	29	9	2287	2535	437632958	437632686	4.150000e-44	189.0
49	TraesCS5D01G134800	chr6D	81.452	248	27	8	2286	2523	312058594	312058356	5.370000e-43	185.0
50	TraesCS5D01G134800	chr6D	92.105	76	6	0	2866	2941	147685584	147685659	1.200000e-19	108.0
51	TraesCS5D01G134800	chr1B	85.621	153	12	2	2392	2534	196059098	196058946	5.440000e-33	152.0
52	TraesCS5D01G134800	chr4A	86.014	143	9	3	2392	2524	468211160	468211301	3.280000e-30	143.0
53	TraesCS5D01G134800	chr7B	90.141	71	5	2	2872	2941	296383518	296383587	1.200000e-14	91.6
54	TraesCS5D01G134800	chr7A	86.047	86	11	1	2872	2956	711167145	711167060	1.200000e-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	TraesCS5D01G134800	chr5D	215242743	215245893	3150	True	5819.0	5819	100.000000	1	3151	1	chr5D.!!$R2	3150
1	TraesCS5D01G134800	chr5A	283013090	283015341	2251	True	3123.0	3123	91.739000	4	2279	1	chr5A.!!$R3	2275
2	TraesCS5D01G134800	chr5B	230424884	230427894	3010	True	961.0	1624	92.764667	1152	3151	3	chr5B.!!$R3	1999
3	TraesCS5D01G134800	chr5B	230433237	230434346	1109	True	881.5	1611	94.296000	5	1156	2	chr5B.!!$R4	1151
4	TraesCS5D01G134800	chr4D	11001306	11001925	619	False	409.0	409	79.553000	2281	2870	1	chr4D.!!$F1	589
5	TraesCS5D01G134800	chr2D	450232914	450233564	650	False	292.5	311	85.076000	2281	2871	2	chr2D.!!$F1	590

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
886	891	0.179124	GAGTTAGAGAGCCAGCCACG	60.179	60.0	0.0	0.0	0.0	4.94	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2662	3699	1.480954	CTTAGTCCAGTACGCCATGGT	59.519	52.381	14.67	0.0	37.84	3.55	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
49	50	4.436998	GAGAGGTGGTGGCGTCGG	62.437	72.222	0.00	0.00	0.00	4.79
109	110	3.376078	CGCCATGGCCTGCTGTTT	61.376	61.111	30.79	0.00	37.98	2.83
260	261	2.224426	TGACTTTTAGTGCCACGTGGAT	60.224	45.455	38.30	23.55	37.39	3.41
292	293	4.702831	GGGCTTTTCCTGTCAAAAATTGA	58.297	39.130	0.00	0.00	34.23	2.57
362	363	8.229253	AGTAAGAAAACCGGTAGATTTTTGTT	57.771	30.769	8.00	11.79	32.39	2.83
376	377	6.899089	AGATTTTTGTTGGGTCCAAAGAATT	58.101	32.000	3.74	0.00	37.70	2.17
378	379	6.993786	TTTTTGTTGGGTCCAAAGAATTTC	57.006	33.333	3.74	0.00	35.03	2.17
423	424	5.677319	TCAAATGTGGTGGTTTTTGGTTA	57.323	34.783	0.00	0.00	31.57	2.85
492	494	6.650120	TGGTAGTTCAAACTTCAGACTTTCT	58.350	36.000	0.00	0.00	40.37	2.52
535	537	7.508687	TGATAGATGGTTTTGCAGATAGCTAA	58.491	34.615	0.00	0.00	45.94	3.09
659	662	2.239751	TACAAATGATTGCGTGCGTG	57.760	45.000	0.00	0.00	40.34	5.34
660	663	1.003262	ACAAATGATTGCGTGCGTGC	61.003	50.000	0.00	0.00	40.34	5.34
661	664	1.797143	AAATGATTGCGTGCGTGCG	60.797	52.632	0.00	0.00	37.81	5.34
884	889	1.272704	TGAGAGTTAGAGAGCCAGCCA	60.273	52.381	0.00	0.00	0.00	4.75
885	890	1.136110	GAGAGTTAGAGAGCCAGCCAC	59.864	57.143	0.00	0.00	0.00	5.01
886	891	0.179124	GAGTTAGAGAGCCAGCCACG	60.179	60.000	0.00	0.00	0.00	4.94
887	892	0.900647	AGTTAGAGAGCCAGCCACGT	60.901	55.000	0.00	0.00	0.00	4.49
937	943	6.070366	GGGTTTAGTGGACTAACTAGGTTGAT	60.070	42.308	0.00	0.00	38.09	2.57
947	953	6.937392	ACTAACTAGGTTGATTTCTCACTCC	58.063	40.000	0.00	0.00	0.00	3.85
995	1001	1.129811	GATTTCCCGCACCGTTTACAG	59.870	52.381	0.00	0.00	0.00	2.74
1030	1036	1.439365	GCTGCACGCAAACTTCTCG	60.439	57.895	0.00	0.00	38.92	4.04
1063	1069	7.239271	TCTGCTGTATATATTTACGTCGCTAC	58.761	38.462	0.00	0.00	0.00	3.58
1097	1103	0.861866	AACTCGCGATGATGACGACG	60.862	55.000	10.36	0.00	34.08	5.12
1132	1138	1.227263	CCGGTGGCGATCTGTTAGG	60.227	63.158	0.00	0.00	0.00	2.69
1277	1283	2.469765	CCACCACCCTTCCCACCTT	61.470	63.158	0.00	0.00	0.00	3.50
1301	1307	3.365220	GCTGTAAGTTCATCGTGTCAGTC	59.635	47.826	0.00	0.00	35.30	3.51
1302	1308	3.909430	TGTAAGTTCATCGTGTCAGTCC	58.091	45.455	0.00	0.00	0.00	3.85
1303	1309	3.319689	TGTAAGTTCATCGTGTCAGTCCA	59.680	43.478	0.00	0.00	0.00	4.02
1311	1335	1.302752	GTGTCAGTCCAGGCATGCA	60.303	57.895	21.36	0.00	0.00	3.96
1347	1372	0.172578	TGAACTCGCCTGACCATACG	59.827	55.000	0.00	0.00	0.00	3.06
1629	1660	1.069513	ACCACGTGGAAGATGAACGAA	59.930	47.619	40.21	0.00	39.64	3.85
1746	1777	5.236047	ACTTAATCGCTGATTTGATGCTCTC	59.764	40.000	8.65	0.00	33.95	3.20
1759	1790	4.582869	TGATGCTCTCCATGCCATAATAC	58.417	43.478	0.00	0.00	33.29	1.89
1764	1795	5.065914	GCTCTCCATGCCATAATACTTTGA	58.934	41.667	0.00	0.00	0.00	2.69
1868	1899	1.133792	CCCCTCAATACTTCCGGCAAT	60.134	52.381	0.00	0.00	0.00	3.56
2036	2067	5.011635	TCAACTGTAGTATTCTTGGAGCACA	59.988	40.000	0.00	0.00	0.00	4.57
2178	2211	7.425577	AGTCGCCTAAAATTTACTTTTACGT	57.574	32.000	0.00	0.00	38.09	3.57
2263	2320	1.452108	GTCCTACCTGCATGTGCCC	60.452	63.158	4.73	0.00	41.18	5.36
2279	2336	0.317770	GCCCGTGTTGTGTGTGATTG	60.318	55.000	0.00	0.00	0.00	2.67
2359	3332	4.916041	TTCACAACATCTCCTCTTCCAT	57.084	40.909	0.00	0.00	0.00	3.41
2588	3624	1.224592	GTCGGGCCATGAATCAGGT	59.775	57.895	4.39	0.00	0.00	4.00
2662	3699	2.181777	CGCCTCAAGACTAGCGCA	59.818	61.111	11.47	0.00	42.31	6.09
2701	3738	1.403972	GACGTTCATGTCGTCGGAGC	61.404	60.000	21.98	7.73	45.64	4.70
2703	3740	0.802222	CGTTCATGTCGTCGGAGCAT	60.802	55.000	0.00	0.00	0.00	3.79
2793	3830	6.401394	TCTTGACGAAGATGATGACAAAGAT	58.599	36.000	0.00	0.00	32.98	2.40
2907	3951	0.249489	CTAGGGGCCGATCTTTCACG	60.249	60.000	0.00	0.00	0.00	4.35
2916	3960	3.521560	CCGATCTTTCACGAAATGGAGA	58.478	45.455	0.00	0.00	0.00	3.71
2919	3963	3.334583	TCTTTCACGAAATGGAGAGGG	57.665	47.619	0.00	0.00	0.00	4.30
2944	4000	2.636519	GCGAAGAACACGAGGAAAAAC	58.363	47.619	0.00	0.00	0.00	2.43
2979	4035	3.189287	GTCCAATCACACATCCACAAGAC	59.811	47.826	0.00	0.00	0.00	3.01
3057	4113	5.358160	GGTAGAGTTCATCCCAAATCCAAAG	59.642	44.000	0.00	0.00	0.00	2.77
3099	4155	2.826488	AGATAGATCCTTCCCCGATGG	58.174	52.381	0.00	0.00	0.00	3.51
3114	4170	1.279271	CGATGGGGGTCTTGATATCCC	59.721	57.143	0.00	0.00	40.41	3.85
3116	4172	2.118403	TGGGGGTCTTGATATCCCTC	57.882	55.000	0.00	0.00	41.93	4.30

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	2.430244	TGGCGCTCTTTCGTCGTC	60.430	61.111	7.64	0.00	36.78	4.20
1	2	2.430921	CTGGCGCTCTTTCGTCGT	60.431	61.111	7.64	0.00	36.78	4.34
2	3	2.126463	TCTGGCGCTCTTTCGTCG	60.126	61.111	7.64	0.00	36.78	5.12
53	54	1.450312	CCACCAACGAGCTGGATCC	60.450	63.158	4.20	4.20	38.96	3.36
55	56	2.045926	GCCACCAACGAGCTGGAT	60.046	61.111	1.44	0.00	38.96	3.41
197	198	2.933287	TTGGATGTGGGACCCGCT	60.933	61.111	24.48	10.43	34.70	5.52
260	261	1.460273	GGAAAAGCCCGCTGGTCAAA	61.460	55.000	0.00	0.00	0.00	2.69
292	293	6.855763	TGACTGATTTGGAGCCAATTATTT	57.144	33.333	2.29	0.00	35.70	1.40
362	363	3.078837	GCTACGAAATTCTTTGGACCCA	58.921	45.455	0.00	0.00	0.00	4.51
376	377	7.266922	AGTTTAATTTCAGGTTTGCTACGAA	57.733	32.000	0.00	0.00	0.00	3.85
378	379	7.136119	TGAAGTTTAATTTCAGGTTTGCTACG	58.864	34.615	0.00	0.00	31.35	3.51
429	430	7.397476	TGAATTACATAAAACCAGCCCACAATA	59.603	33.333	0.00	0.00	0.00	1.90
659	662	0.110147	CCGGATCTCTACATCGACGC	60.110	60.000	0.00	0.00	0.00	5.19
660	663	1.194997	GTCCGGATCTCTACATCGACG	59.805	57.143	7.81	0.00	0.00	5.12
661	664	2.496111	AGTCCGGATCTCTACATCGAC	58.504	52.381	7.81	0.00	0.00	4.20
760	765	0.734942	CGTACACACTTACAGGGGCG	60.735	60.000	0.00	0.00	0.00	6.13
884	889	0.872881	GGCAACAGTGACACGTACGT	60.873	55.000	16.72	16.72	30.49	3.57
885	890	0.596600	AGGCAACAGTGACACGTACG	60.597	55.000	15.01	15.01	33.83	3.67
886	891	2.056577	GTAGGCAACAGTGACACGTAC	58.943	52.381	0.00	0.00	33.83	3.67
887	892	1.335233	CGTAGGCAACAGTGACACGTA	60.335	52.381	0.00	0.00	33.83	3.57
937	943	0.687354	GACCAGCTGGGAGTGAGAAA	59.313	55.000	35.42	0.00	41.15	2.52
947	953	4.680237	TTGACGCGGACCAGCTGG	62.680	66.667	31.60	31.60	42.17	4.85
995	1001	2.165301	GCCGTACTGGTCGTGCATC	61.165	63.158	0.00	0.00	41.21	3.91
1030	1036	0.969894	ATATACAGCAGAGGCCGGTC	59.030	55.000	0.00	0.00	42.56	4.79
1063	1069	1.463034	CGAGTTTGATCAGCTGCAACG	60.463	52.381	9.47	5.15	0.00	4.10
1302	1308	4.175489	GAGCGTGCTGCATGCCTG	62.175	66.667	35.68	9.38	46.38	4.85
1303	1309	3.914579	AAGAGCGTGCTGCATGCCT	62.915	57.895	35.68	28.92	46.38	4.75
1311	1335	3.946201	AGGCCACAAGAGCGTGCT	61.946	61.111	5.01	0.00	35.47	4.40
1347	1372	4.152625	GCGCGTGCACCAGATGTC	62.153	66.667	17.66	0.00	42.15	3.06
1398	1423	2.808202	GCAGAAGAAGAACCACTGCTCA	60.808	50.000	0.00	0.00	46.66	4.26
1759	1790	7.120285	TCCTCAGCTGAACAATAAAGATCAAAG	59.880	37.037	18.85	0.00	0.00	2.77
1764	1795	5.352569	CGTTCCTCAGCTGAACAATAAAGAT	59.647	40.000	18.85	0.00	41.70	2.40
2205	2258	5.581126	ACACACACAAAATCTGACACATT	57.419	34.783	0.00	0.00	0.00	2.71
2263	2320	4.025750	GTGTTACAATCACACACAACACG	58.974	43.478	0.00	0.00	43.52	4.49
2279	2336	7.789026	AGTGTGGGTAAATATAGGAGTGTTAC	58.211	38.462	0.00	0.00	0.00	2.50
2359	3332	4.282496	GGAGAGGTGGTGAAATAGAGAGA	58.718	47.826	0.00	0.00	0.00	3.10
2604	3640	2.159085	GGTCCATCTTTCCCTCTGTACG	60.159	54.545	0.00	0.00	0.00	3.67
2606	3642	3.199442	TGGTCCATCTTTCCCTCTGTA	57.801	47.619	0.00	0.00	0.00	2.74
2662	3699	1.480954	CTTAGTCCAGTACGCCATGGT	59.519	52.381	14.67	0.00	37.84	3.55
2701	3738	2.469847	CACCGCGTCGTTGTCATG	59.530	61.111	4.92	0.00	0.00	3.07
2907	3951	1.153147	GCGGGACCCTCTCCATTTC	60.153	63.158	9.41	0.00	41.63	2.17
2916	3960	2.920912	TGTTCTTCGCGGGACCCT	60.921	61.111	9.41	0.00	0.00	4.34
2939	3983	5.975693	TGGACTTGTTCTTGAGTGTTTTT	57.024	34.783	0.00	0.00	0.00	1.94
2944	4000	4.576053	TGTGATTGGACTTGTTCTTGAGTG	59.424	41.667	0.00	0.00	0.00	3.51
2979	4035	5.185668	TGTGGATCTTGTGTGTTTGATTG	57.814	39.130	0.00	0.00	0.00	2.67
3057	4113	0.776176	ATCATCAAGCCCCCATCTCC	59.224	55.000	0.00	0.00	0.00	3.71
3099	4155	0.977395	CCGAGGGATATCAAGACCCC	59.023	60.000	4.83	0.00	44.21	4.95

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.