AutoCloner

Multiple sequence alignment - TraesCS5B01G199900

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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	TraesCS5B01G199900	chr5B	100.000	2768	0	0	1	2768	360860638	360863405	0.000000e+00	5112.0
1	TraesCS5B01G199900	chr5B	91.855	442	29	4	1337	1776	360922588	360922152	6.550000e-171	610.0
2	TraesCS5B01G199900	chr5B	86.667	330	41	1	4	333	360925331	360925005	2.030000e-96	363.0
3	TraesCS5B01G199900	chr5B	80.892	314	42	9	2473	2768	38632921	38633234	5.960000e-57	231.0
4	TraesCS5B01G199900	chr5B	80.442	317	40	11	2473	2768	37660572	37660257	3.590000e-54	222.0
5	TraesCS5B01G199900	chr5A	91.628	2401	135	25	1	2380	407124624	407126979	0.000000e+00	3260.0
6	TraesCS5B01G199900	chr5A	94.418	1039	56	1	739	1775	407154564	407153526	0.000000e+00	1596.0
7	TraesCS5B01G199900	chr5A	85.000	640	65	15	4	624	407157138	407156511	3.030000e-174	621.0
8	TraesCS5B01G199900	chr5A	92.857	56	3	1	2397	2452	407126963	407127017	2.290000e-11	80.5
9	TraesCS5B01G199900	chr5A	88.060	67	7	1	2703	2768	414418864	414418798	8.220000e-11	78.7
10	TraesCS5B01G199900	chr5D	90.211	1798	103	24	4	1772	313333724	313331971	0.000000e+00	2278.0
11	TraesCS5B01G199900	chr5D	91.110	1676	94	30	728	2381	313151965	313153607	0.000000e+00	2218.0
12	TraesCS5B01G199900	chr5D	87.903	496	54	5	5	497	313151167	313151659	1.850000e-161	579.0
13	TraesCS5B01G199900	chr5D	88.451	381	22	6	2397	2768	313153591	313153958	9.100000e-120	440.0
14	TraesCS5B01G199900	chr1D	78.692	535	84	18	2255	2768	212076346	212076871	2.060000e-86	329.0
15	TraesCS5B01G199900	chr4D	82.450	302	37	9	2482	2768	42096702	42096402	1.650000e-62	250.0
16	TraesCS5B01G199900	chr4D	90.226	133	12	1	2247	2378	52771411	52771279	3.670000e-39	172.0
17	TraesCS5B01G199900	chr4D	88.172	93	10	1	2281	2373	42096833	42096742	2.910000e-20	110.0
18	TraesCS5B01G199900	chr1A	78.329	383	43	23	2401	2768	37469980	37469623	7.770000e-51	211.0
19	TraesCS5B01G199900	chrUn	77.926	376	49	26	2413	2768	144752212	144751851	1.300000e-48	204.0
20	TraesCS5B01G199900	chr2D	86.301	146	20	0	2233	2378	484078296	484078151	2.850000e-35	159.0
21	TraesCS5B01G199900	chr1B	83.178	107	16	1	2255	2361	304387484	304387380	2.270000e-16	97.1
22	TraesCS5B01G199900	chr1B	85.057	87	13	0	2286	2372	303226919	303226833	3.800000e-14	89.8
23	TraesCS5B01G199900	chr7D	93.333	60	4	0	2707	2766	153662813	153662754	3.800000e-14	89.8
24	TraesCS5B01G199900	chr6B	93.103	58	3	1	2699	2755	521074701	521074644	1.770000e-12	84.2
25	TraesCS5B01G199900	chr4A	89.552	67	6	1	2703	2768	139550009	139549943	1.770000e-12	84.2
26	TraesCS5B01G199900	chr3A	89.130	46	5	0	2137	2182	55213491	55213446	1.070000e-04	58.4

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	TraesCS5B01G199900	chr5B	360860638	360863405	2767	False	5112.00	5112	100.000000	1	2768	1	chr5B.!!$F2	2767
1	TraesCS5B01G199900	chr5B	360922152	360925331	3179	True	486.50	610	89.261000	4	1776	2	chr5B.!!$R2	1772
2	TraesCS5B01G199900	chr5A	407124624	407127017	2393	False	1670.25	3260	92.242500	1	2452	2	chr5A.!!$F1	2451
3	TraesCS5B01G199900	chr5A	407153526	407157138	3612	True	1108.50	1596	89.709000	4	1775	2	chr5A.!!$R2	1771
4	TraesCS5B01G199900	chr5D	313331971	313333724	1753	True	2278.00	2278	90.211000	4	1772	1	chr5D.!!$R1	1768
5	TraesCS5B01G199900	chr5D	313151167	313153958	2791	False	1079.00	2218	89.154667	5	2768	3	chr5D.!!$F1	2763
6	TraesCS5B01G199900	chr1D	212076346	212076871	525	False	329.00	329	78.692000	2255	2768	1	chr1D.!!$F1	513

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
496	2757	0.397957	TCTCCCCTATAGCCGCACAA	60.398	55.0	0.0	0.0	0.0	3.33	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2237	6525	0.383949	GGAGAAGTGCGCAAAAACCA	59.616	50.0	14.0	0.0	0.0	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
20	21	1.226435	GCCGTCGTTGTTTTGCACA	60.226	52.632	0.00	0.00	0.00	4.57
262	266	5.931441	ATCTCGAAGTTTTTCTGGAAGTG	57.069	39.130	0.00	0.00	33.76	3.16
342	1680	2.332362	GATCCACGCCGCGTAGAAGA	62.332	60.000	19.71	13.17	38.32	2.87
434	2687	2.971330	CAGGATCAGGATAAGCAGGTCT	59.029	50.000	0.00	0.00	0.00	3.85
495	2756	0.827925	CTCTCCCCTATAGCCGCACA	60.828	60.000	0.00	0.00	0.00	4.57
496	2757	0.397957	TCTCCCCTATAGCCGCACAA	60.398	55.000	0.00	0.00	0.00	3.33
497	2758	0.687354	CTCCCCTATAGCCGCACAAT	59.313	55.000	0.00	0.00	0.00	2.71
498	2759	1.899814	CTCCCCTATAGCCGCACAATA	59.100	52.381	0.00	0.00	0.00	1.90
563	2904	4.025015	TCGAGCTTTACCTTTACGCTAG	57.975	45.455	0.00	0.00	0.00	3.42
632	2978	2.636893	CCATCCCTAGTAGAAGCAGCAT	59.363	50.000	0.00	0.00	0.00	3.79
633	2979	3.834813	CCATCCCTAGTAGAAGCAGCATA	59.165	47.826	0.00	0.00	0.00	3.14
634	2980	4.469227	CCATCCCTAGTAGAAGCAGCATAT	59.531	45.833	0.00	0.00	0.00	1.78
656	3011	3.921119	TGTCACGTACGTACAATCCTT	57.079	42.857	22.34	0.00	0.00	3.36
701	3068	3.215568	CCGTGTGGGCAACAGCAA	61.216	61.111	0.00	0.00	40.26	3.91
702	3069	2.026014	CGTGTGGGCAACAGCAAC	59.974	61.111	0.00	0.00	40.26	4.17
703	3070	2.417097	GTGTGGGCAACAGCAACC	59.583	61.111	0.00	0.00	40.26	3.77
840	5093	0.905357	CGTTTCCTCTGGATCCAGGT	59.095	55.000	35.95	0.00	43.75	4.00
887	5155	2.034879	AACATGACGGCGAGGCAAG	61.035	57.895	16.62	8.33	44.01	4.01
1038	5306	3.416156	GCACAACTCTTTCCTCTGGAAT	58.584	45.455	0.00	0.00	41.71	3.01
1050	5318	4.107072	TCCTCTGGAATCCATCAACTCTT	58.893	43.478	0.87	0.00	30.82	2.85
1389	5659	1.604755	CAACAACGTTTCCCAATCGGA	59.395	47.619	0.00	0.00	39.68	4.55
1627	5897	1.273327	TCGGTCTAAGAAAACGGGACC	59.727	52.381	0.00	0.00	41.92	4.46
1716	5986	1.380302	GCACAATCCTGGACCCAGT	59.620	57.895	14.38	0.00	42.15	4.00
1722	5992	0.978146	ATCCTGGACCCAGTCTTCGG	60.978	60.000	14.38	0.00	42.15	4.30
1857	6127	7.605691	AGTCTTGAGAACAATCTATTCCACTTG	59.394	37.037	0.00	0.00	35.54	3.16
1940	6211	9.834628	TTTCTTTATTAAAGCAAGTATCCAACG	57.165	29.630	10.71	0.00	38.39	4.10
2111	6386	4.209307	TGTTGTGTGTCAGTTTAGTCCA	57.791	40.909	0.00	0.00	0.00	4.02
2176	6454	9.975218	AAAGGTGTGTCATTTTAGTCCTATAAT	57.025	29.630	0.00	0.00	0.00	1.28
2202	6490	3.504375	ACTGTAGTTTTAGGTCCGGAGT	58.496	45.455	3.06	0.00	0.00	3.85
2204	6492	5.079643	ACTGTAGTTTTAGGTCCGGAGTTA	58.920	41.667	3.06	0.00	0.00	2.24
2208	6496	5.494390	AGTTTTAGGTCCGGAGTTATGTT	57.506	39.130	3.06	0.00	0.00	2.71
2217	6505	6.212187	AGGTCCGGAGTTATGTTAGTTTAGTT	59.788	38.462	3.06	0.00	0.00	2.24
2252	6540	2.159114	ACTTCATGGTTTTTGCGCACTT	60.159	40.909	11.12	0.00	0.00	3.16
2356	6664	1.303236	CAAGGATGTCGGGGCAACA	60.303	57.895	0.00	0.00	39.74	3.33
2363	6671	0.753479	TGTCGGGGCAACAACAATGT	60.753	50.000	0.00	0.00	43.14	2.71
2364	6672	0.039527	GTCGGGGCAACAACAATGTC	60.040	55.000	0.00	0.00	39.40	3.06
2365	6673	0.466372	TCGGGGCAACAACAATGTCA	60.466	50.000	0.00	0.00	39.40	3.58
2366	6674	0.602562	CGGGGCAACAACAATGTCAT	59.397	50.000	0.00	0.00	39.40	3.06
2367	6675	1.669502	CGGGGCAACAACAATGTCATG	60.670	52.381	0.00	0.00	39.40	3.07
2368	6676	1.617850	GGGGCAACAACAATGTCATGA	59.382	47.619	0.00	0.00	39.40	3.07
2369	6677	2.353011	GGGGCAACAACAATGTCATGAG	60.353	50.000	0.00	0.00	39.40	2.90
2370	6678	2.557924	GGGCAACAACAATGTCATGAGA	59.442	45.455	0.00	0.00	39.40	3.27
2371	6679	3.366679	GGGCAACAACAATGTCATGAGAG	60.367	47.826	0.00	0.00	39.40	3.20
2372	6680	3.503363	GGCAACAACAATGTCATGAGAGA	59.497	43.478	0.00	0.00	39.40	3.10
2373	6681	4.022935	GGCAACAACAATGTCATGAGAGAA	60.023	41.667	0.00	0.00	39.40	2.87
2374	6682	5.507817	GGCAACAACAATGTCATGAGAGAAA	60.508	40.000	0.00	0.00	39.40	2.52
2375	6683	5.628193	GCAACAACAATGTCATGAGAGAAAG	59.372	40.000	0.00	0.00	39.40	2.62
2376	6684	6.513884	GCAACAACAATGTCATGAGAGAAAGA	60.514	38.462	0.00	0.00	39.40	2.52
2377	6685	6.798315	ACAACAATGTCATGAGAGAAAGAG	57.202	37.500	0.00	0.00	33.41	2.85
2378	6686	6.294473	ACAACAATGTCATGAGAGAAAGAGT	58.706	36.000	0.00	0.00	33.41	3.24
2379	6687	6.769822	ACAACAATGTCATGAGAGAAAGAGTT	59.230	34.615	0.00	0.00	33.41	3.01
2380	6688	7.284034	ACAACAATGTCATGAGAGAAAGAGTTT	59.716	33.333	0.00	0.00	33.41	2.66
2381	6689	7.814264	ACAATGTCATGAGAGAAAGAGTTTT	57.186	32.000	0.00	0.00	0.00	2.43
2382	6690	8.230472	ACAATGTCATGAGAGAAAGAGTTTTT	57.770	30.769	0.00	0.00	0.00	1.94
2479	6794	0.105039	CGCCAAGGTAGAGGGATGTC	59.895	60.000	0.00	0.00	0.00	3.06
2510	6826	2.041265	AATGGCTCGGGTCTCCCT	59.959	61.111	3.25	0.00	42.67	4.20
2560	6877	0.465097	GCACTGTAGCTCATGGCCAT	60.465	55.000	14.09	14.09	43.05	4.40
2601	6918	2.521771	GCAACACACTGCGACGTGA	61.522	57.895	10.86	0.00	38.27	4.35
2620	6938	4.614993	CGTGAAAGCGTATGGACCATTTTT	60.615	41.667	13.40	8.68	0.00	1.94
2647	6965	6.262496	GGAAGTAAACACATATAAAGGGCTCC	59.738	42.308	0.00	0.00	0.00	4.70
2675	6998	2.742428	ATGCACCATAGATGCTGGTT	57.258	45.000	0.00	0.00	44.67	3.67
2740	7072	7.307751	CCAAAACTGCAGTTTCGAAGTTATAGA	60.308	37.037	37.59	0.00	46.47	1.98

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
20	21	2.549754	CGCTCAAGAGATTGGTTGTTGT	59.450	45.455	0.32	0.00	0.00	3.32
262	266	0.682209	TGTCCGCTACTACAGTCCCC	60.682	60.000	0.00	0.00	0.00	4.81
334	338	1.868251	GCCGTGTCGCTCTTCTACG	60.868	63.158	0.00	0.00	34.78	3.51
434	2687	2.025226	AGATTGGTCGTCTCTCCCAGTA	60.025	50.000	0.00	0.00	0.00	2.74
495	2756	5.129815	TCTCCGCTATTACCACCTGTTTATT	59.870	40.000	0.00	0.00	0.00	1.40
496	2757	4.652421	TCTCCGCTATTACCACCTGTTTAT	59.348	41.667	0.00	0.00	0.00	1.40
497	2758	4.025360	TCTCCGCTATTACCACCTGTTTA	58.975	43.478	0.00	0.00	0.00	2.01
498	2759	2.835764	TCTCCGCTATTACCACCTGTTT	59.164	45.455	0.00	0.00	0.00	2.83
579	2920	3.591527	TGGGCTCCAAGAGAGGAAATTTA	59.408	43.478	0.00	0.00	43.46	1.40
581	2922	1.995542	TGGGCTCCAAGAGAGGAAATT	59.004	47.619	0.00	0.00	43.46	1.82
582	2923	1.673767	TGGGCTCCAAGAGAGGAAAT	58.326	50.000	0.00	0.00	43.46	2.17
618	2959	6.206829	ACGTGACATATATGCTGCTTCTACTA	59.793	38.462	12.79	0.00	0.00	1.82
632	2978	6.866010	AGGATTGTACGTACGTGACATATA	57.134	37.500	30.25	14.78	0.00	0.86
633	2979	5.762825	AGGATTGTACGTACGTGACATAT	57.237	39.130	30.25	20.76	0.00	1.78
634	2980	5.334319	CAAGGATTGTACGTACGTGACATA	58.666	41.667	30.25	17.96	42.34	2.29
656	3011	1.047002	TTTAGGTTTCGGGTCGGACA	58.953	50.000	10.76	0.00	0.00	4.02
761	5014	1.846648	CGCGTATCCATCTTGTCGC	59.153	57.895	0.00	0.00	40.19	5.19
766	5019	4.033894	GCAGCGCGTATCCATCTT	57.966	55.556	8.43	0.00	0.00	2.40
1038	5306	5.163364	GCTAATCCTCTCAAGAGTTGATGGA	60.163	44.000	6.30	11.49	42.33	3.41
1050	5318	4.079154	TCTGGAGGTAAGCTAATCCTCTCA	60.079	45.833	22.36	18.39	44.85	3.27
1059	5327	3.011369	TCTCTTGGTCTGGAGGTAAGCTA	59.989	47.826	0.00	0.00	0.00	3.32
1361	5631	1.199624	GAAACGTTGTTGCAGCAAGG	58.800	50.000	27.44	27.44	39.35	3.61
1389	5659	2.884639	GCCGCAATGAAACCTGGTATAT	59.115	45.455	0.00	0.00	0.00	0.86
1627	5897	7.795734	GTCATCAGACATCAAAAAGTATATGCG	59.204	37.037	0.00	0.00	44.34	4.73
1716	5986	3.700038	GAGGTACAAGAGAATCCCGAAGA	59.300	47.826	0.00	0.00	33.66	2.87
1722	5992	8.794335	ATAAAAACTGAGGTACAAGAGAATCC	57.206	34.615	0.00	0.00	33.66	3.01
1837	6107	7.913674	AAGACAAGTGGAATAGATTGTTCTC	57.086	36.000	0.00	0.00	36.08	2.87
1957	6228	2.294233	CACGGCCATATCATGAAAAGGG	59.706	50.000	2.24	3.45	0.00	3.95
1974	6245	2.098443	GGCAAAATACATACCCACACGG	59.902	50.000	0.00	0.00	37.81	4.94
2150	6425	9.975218	ATTATAGGACTAAAATGACACACCTTT	57.025	29.630	0.00	0.00	0.00	3.11
2151	6426	9.975218	AATTATAGGACTAAAATGACACACCTT	57.025	29.630	0.00	0.00	0.00	3.50
2176	6454	5.058490	CCGGACCTAAAACTACAGTCAAAA	58.942	41.667	0.00	0.00	0.00	2.44
2236	6524	1.000274	GGAGAAGTGCGCAAAAACCAT	60.000	47.619	14.00	0.00	0.00	3.55
2237	6525	0.383949	GGAGAAGTGCGCAAAAACCA	59.616	50.000	14.00	0.00	0.00	3.67
2356	6664	7.814264	AAACTCTTTCTCTCATGACATTGTT	57.186	32.000	0.00	0.00	0.00	2.83
2384	6692	5.850557	TTCTCTCATGAGGTTTGCAAAAA	57.149	34.783	22.42	0.35	40.58	1.94
2385	6693	5.593909	TCTTTCTCTCATGAGGTTTGCAAAA	59.406	36.000	22.42	10.90	40.58	2.44
2386	6694	5.132502	TCTTTCTCTCATGAGGTTTGCAAA	58.867	37.500	22.42	8.05	40.58	3.68
2387	6695	4.717877	TCTTTCTCTCATGAGGTTTGCAA	58.282	39.130	22.42	0.00	40.58	4.08
2388	6696	4.202398	ACTCTTTCTCTCATGAGGTTTGCA	60.202	41.667	22.42	1.03	40.58	4.08
2389	6697	4.322567	ACTCTTTCTCTCATGAGGTTTGC	58.677	43.478	22.42	0.00	40.58	3.68
2390	6698	5.180868	CCAACTCTTTCTCTCATGAGGTTTG	59.819	44.000	22.42	12.60	40.58	2.93
2391	6699	5.312079	CCAACTCTTTCTCTCATGAGGTTT	58.688	41.667	22.42	2.29	40.58	3.27
2392	6700	4.263243	CCCAACTCTTTCTCTCATGAGGTT	60.263	45.833	22.42	13.15	40.58	3.50
2393	6701	3.262915	CCCAACTCTTTCTCTCATGAGGT	59.737	47.826	22.42	7.73	40.58	3.85
2394	6702	3.517100	TCCCAACTCTTTCTCTCATGAGG	59.483	47.826	22.42	13.07	40.58	3.86
2395	6703	4.815533	TCCCAACTCTTTCTCTCATGAG	57.184	45.455	17.07	17.07	41.51	2.90
2464	6779	1.777941	GGACGACATCCCTCTACCTT	58.222	55.000	0.00	0.00	42.46	3.50
2479	6794	3.723172	CATTCGGCATGGAGGACG	58.277	61.111	0.00	0.00	41.81	4.79
2510	6826	0.531974	GAGGTTTGGCACAGTCGTCA	60.532	55.000	0.00	0.00	42.39	4.35
2566	6883	1.964373	GCAACCTACACACCCACCG	60.964	63.158	0.00	0.00	0.00	4.94
2569	6886	0.256177	TGTTGCAACCTACACACCCA	59.744	50.000	26.14	0.84	0.00	4.51
2601	6918	3.056179	CCCAAAAATGGTCCATACGCTTT	60.056	43.478	4.33	0.00	0.00	3.51
2620	6938	5.889289	GCCCTTTATATGTGTTTACTTCCCA	59.111	40.000	0.00	0.00	0.00	4.37
2675	6998	5.500234	AGTTTCATGTCCTAAGCTTGCATA	58.500	37.500	9.86	0.00	0.00	3.14

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.