AutoCloner

Multiple sequence alignment - TraesCS1A01G040300

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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	TraesCS1A01G040300	chr1A	100.000	2570	0	0	1	2570	22283979	22281410	0.000000e+00	4747.0
1	TraesCS1A01G040300	chr1A	76.603	889	133	46	997	1836	22271964	22271102	1.100000e-113	420.0
2	TraesCS1A01G040300	chr1A	78.000	400	53	24	1152	1547	22074513	22074145	4.310000e-53	219.0
3	TraesCS1A01G040300	chr1A	82.171	129	13	7	1030	1156	22076859	22076739	4.520000e-18	102.0
4	TraesCS1A01G040300	chr1D	90.525	2132	156	24	462	2569	20184478	20186587	0.000000e+00	2776.0
5	TraesCS1A01G040300	chr1D	85.096	2402	232	55	1	2320	20060891	20063248	0.000000e+00	2337.0
6	TraesCS1A01G040300	chr1D	84.504	484	49	14	1	468	20182495	20182968	3.010000e-124	455.0
7	TraesCS1A01G040300	chr1D	77.744	665	95	29	998	1636	20193407	20194044	2.430000e-95	359.0
8	TraesCS1A01G040300	chr1B	90.765	2014	132	30	1	1983	33922556	33920566	0.000000e+00	2639.0
9	TraesCS1A01G040300	chr1B	86.435	2101	175	39	1	2032	33947770	33945711	0.000000e+00	2200.0
10	TraesCS1A01G040300	chr1B	90.909	583	46	4	1991	2569	33918984	33918405	0.000000e+00	776.0
11	TraesCS1A01G040300	chr1B	75.940	931	142	47	996	1892	33857392	33856510	1.110000e-108	403.0
12	TraesCS1A01G040300	chr1B	89.950	199	10	3	446	641	33963061	33962870	5.490000e-62	248.0
13	TraesCS1A01G040300	chr1B	86.893	206	19	7	640	844	33962776	33962578	9.250000e-55	224.0
14	TraesCS1A01G040300	chr1B	87.218	133	10	4	4	136	33963197	33963072	7.410000e-31	145.0
15	TraesCS1A01G040300	chr1B	90.698	86	8	0	841	926	33962299	33962214	5.810000e-22	115.0
16	TraesCS1A01G040300	chr7A	90.141	71	6	1	357	427	662119345	662119414	9.790000e-15	91.6
17	TraesCS1A01G040300	chr5B	90.000	70	7	0	1126	1195	659604788	659604857	9.790000e-15	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	TraesCS1A01G040300	chr1A	22281410	22283979	2569	True	4747.0	4747	100.0000	1	2570	1	chr1A.!!$R2	2569
1	TraesCS1A01G040300	chr1A	22271102	22271964	862	True	420.0	420	76.6030	997	1836	1	chr1A.!!$R1	839
2	TraesCS1A01G040300	chr1D	20060891	20063248	2357	False	2337.0	2337	85.0960	1	2320	1	chr1D.!!$F1	2319
3	TraesCS1A01G040300	chr1D	20182495	20186587	4092	False	1615.5	2776	87.5145	1	2569	2	chr1D.!!$F3	2568
4	TraesCS1A01G040300	chr1D	20193407	20194044	637	False	359.0	359	77.7440	998	1636	1	chr1D.!!$F2	638
5	TraesCS1A01G040300	chr1B	33945711	33947770	2059	True	2200.0	2200	86.4350	1	2032	1	chr1B.!!$R2	2031
6	TraesCS1A01G040300	chr1B	33918405	33922556	4151	True	1707.5	2639	90.8370	1	2569	2	chr1B.!!$R3	2568
7	TraesCS1A01G040300	chr1B	33856510	33857392	882	True	403.0	403	75.9400	996	1892	1	chr1B.!!$R1	896

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
137	139	0.031857	CAGGCGATCTTCAGCGATCT	59.968	55.0	0.0	0.0	38.09	2.75	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1936	3632	0.186873	GGGAAGATGACATGGGGCAT	59.813	55.0	0.0	0.0	0.0	4.4	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
131	133	3.461061	TCATTAAGCAGGCGATCTTCAG	58.539	45.455	0.00	0.00	0.00	3.02
137	139	0.031857	CAGGCGATCTTCAGCGATCT	59.968	55.000	0.00	0.00	38.09	2.75
192	195	1.421268	TGCCATACCAATCAGCCTAGG	59.579	52.381	3.67	3.67	0.00	3.02
199	202	2.766828	ACCAATCAGCCTAGGTAGTCAC	59.233	50.000	11.31	0.00	31.32	3.67
223	236	2.816087	CCAAAACTGATGGGACTGACAG	59.184	50.000	0.00	0.00	34.15	3.51
249	262	1.649321	ACTCTGCAGGATTCAGTGGA	58.351	50.000	15.13	0.00	29.10	4.02
427	456	7.922837	TGATATGAAGTGCACTTGTTGATATG	58.077	34.615	35.67	0.00	36.11	1.78
435	464	4.818005	TGCACTTGTTGATATGCTATCCTG	59.182	41.667	0.00	0.00	38.90	3.86
457	486	4.766373	TGCCACATTTCAAAGATTCTGCTA	59.234	37.500	0.00	0.00	0.00	3.49
493	2038	3.454447	TCTCTCCAAAACAAGACAGGACA	59.546	43.478	0.00	0.00	0.00	4.02
675	2230	0.035725	CAAGGGATGCACTGAGCTCA	60.036	55.000	17.19	17.19	45.94	4.26
687	2242	4.942481	AGCTCACGACGCGTTGCA	62.942	61.111	26.19	12.20	38.32	4.08
690	2245	2.355244	TCACGACGCGTTGCATGA	60.355	55.556	26.19	19.53	38.32	3.07
706	2261	1.761784	CATGAGGCTCTAGAGTGGCTT	59.238	52.381	20.75	4.17	43.08	4.35
732	2287	1.200716	CGAACCACTTGCATTGCATCT	59.799	47.619	12.95	0.00	38.76	2.90
737	2292	1.816835	CACTTGCATTGCATCTGAGGT	59.183	47.619	12.95	2.67	38.76	3.85
745	2309	2.172372	GCATCTGAGGTGAGCAGCG	61.172	63.158	0.00	0.00	33.45	5.18
746	2310	1.521010	CATCTGAGGTGAGCAGCGG	60.521	63.158	0.00	0.00	33.45	5.52
747	2311	3.382803	ATCTGAGGTGAGCAGCGGC	62.383	63.158	0.00	0.00	41.61	6.53
872	2439	2.035632	CTGCCTAGCTACTACTGGCTT	58.964	52.381	18.64	0.00	43.57	4.35
951	2518	6.046290	TCTTCATCAGCTTCTTCATCTTCA	57.954	37.500	0.00	0.00	0.00	3.02
991	2582	7.173722	AGAGTTTCAGAGATTGATCAATTGGT	58.826	34.615	21.57	10.05	35.27	3.67
992	2583	7.336427	AGAGTTTCAGAGATTGATCAATTGGTC	59.664	37.037	21.57	17.23	35.27	4.02
1013	2605	3.582647	TCCAGAGCAATGACAAAGAGGTA	59.417	43.478	0.00	0.00	0.00	3.08
1020	2612	5.244626	AGCAATGACAAAGAGGTATGCTTTT	59.755	36.000	0.00	0.00	39.69	2.27
1237	2847	1.531602	GGCAACCTCAAGCCCAAGT	60.532	57.895	0.00	0.00	45.18	3.16
1278	2888	2.892640	CTGGAGTTCGCCATCGGA	59.107	61.111	0.00	0.00	37.30	4.55
1323	2933	4.769063	CACCGTGCCATGGCCGTA	62.769	66.667	33.44	13.18	41.09	4.02
1347	2963	4.722700	GGTGGTGGCGTCATGGCT	62.723	66.667	0.00	0.00	45.14	4.75
1465	3096	1.153647	CCTTGCGATGAGTACGGCA	60.154	57.895	0.00	0.00	0.00	5.69
1553	3184	1.690985	TGGATACCGGCACCATGGA	60.691	57.895	21.47	0.00	0.00	3.41
1838	3509	5.956642	TCAGGTTTTCCGGTTATTATTTGC	58.043	37.500	0.00	0.00	46.35	3.68
1936	3632	9.948964	ATATGGATCTCGTGATTTATCAATTCA	57.051	29.630	0.87	0.00	38.75	2.57
2044	5319	3.479505	TTATCGTGCGTTCCAAATTGG	57.520	42.857	5.48	5.48	39.43	3.16
2066	5341	1.359848	CGTGACCTATGCAACTGTCC	58.640	55.000	9.50	2.52	0.00	4.02
2087	5387	4.342665	TCCACCACATTAAACCCAGAAAAC	59.657	41.667	0.00	0.00	0.00	2.43
2132	5432	6.249951	ACTCAGACCTAGTATTGAAGAGTGT	58.750	40.000	0.00	0.00	33.06	3.55
2151	5451	4.523943	AGTGTCTTGCATTTGAGGCATTTA	59.476	37.500	0.00	0.00	41.58	1.40
2154	5454	6.202570	GTGTCTTGCATTTGAGGCATTTAAAA	59.797	34.615	0.00	0.00	41.58	1.52
2178	5479	6.635030	AAAGGCGAAAGGTTCCATATATTC	57.365	37.500	0.00	0.00	0.00	1.75
2189	5490	7.497925	GGTTCCATATATTCAGGAAACACTC	57.502	40.000	11.65	0.00	46.07	3.51
2258	5559	6.335471	TGTCATGTGAAGCAATCAAGAAAT	57.665	33.333	0.00	0.00	40.50	2.17
2264	5565	8.552865	CATGTGAAGCAATCAAGAAATTTTCAA	58.447	29.630	11.53	0.00	40.50	2.69
2321	5623	8.685427	TGGAACACAAATGATCATATTAGTTGG	58.315	33.333	9.04	6.37	29.58	3.77
2325	5627	9.023962	ACACAAATGATCATATTAGTTGGTTGT	57.976	29.630	9.04	9.43	29.58	3.32
2540	5845	7.082602	GCCATAGCACATAAATCATCTCTTTG	58.917	38.462	0.00	0.00	39.53	2.77
2541	5846	7.040892	GCCATAGCACATAAATCATCTCTTTGA	60.041	37.037	0.00	0.00	39.53	2.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
131	133	2.493713	AGTATCACACCGAAGATCGC	57.506	50.000	0.00	0.00	38.82	4.58
137	139	8.270080	TGCAATTAAATTAGTATCACACCGAA	57.730	30.769	0.00	0.00	0.00	4.30
167	170	2.422803	GGCTGATTGGTATGGCAACCTA	60.423	50.000	16.26	11.17	40.44	3.08
176	179	4.589374	GTGACTACCTAGGCTGATTGGTAT	59.411	45.833	9.30	0.00	34.93	2.73
192	195	3.432252	CCATCAGTTTTGGTCGTGACTAC	59.568	47.826	0.00	0.00	0.00	2.73
199	202	1.806542	CAGTCCCATCAGTTTTGGTCG	59.193	52.381	0.00	0.00	31.99	4.79
223	236	5.121454	CACTGAATCCTGCAGAGTTTACTTC	59.879	44.000	17.39	7.45	36.86	3.01
249	262	4.777366	CCTTTTCCTGGGATAAATTGTGGT	59.223	41.667	0.00	0.00	0.00	4.16
353	371	6.930164	AGAACTGAGATGAGATTATGACATGC	59.070	38.462	0.00	0.00	0.00	4.06
395	416	5.426689	AGTGCACTTCATATCAGAAAGGA	57.573	39.130	15.25	0.00	0.00	3.36
396	417	5.413833	ACAAGTGCACTTCATATCAGAAAGG	59.586	40.000	28.97	14.99	33.11	3.11
427	456	3.696051	TCTTTGAAATGTGGCAGGATAGC	59.304	43.478	0.00	0.00	0.00	2.97
435	464	4.184079	AGCAGAATCTTTGAAATGTGGC	57.816	40.909	0.00	0.00	0.00	5.01
457	486	8.477256	TGTTTTGGAGAGACTGAAAATTTCAAT	58.523	29.630	9.85	0.00	39.58	2.57
493	2038	3.579151	GGTCAACTGTTTCCTCCTCTAGT	59.421	47.826	0.00	0.00	0.00	2.57
675	2230	3.112075	CCTCATGCAACGCGTCGT	61.112	61.111	14.44	0.00	43.97	4.34
687	2242	1.761784	CAAGCCACTCTAGAGCCTCAT	59.238	52.381	19.97	0.94	0.00	2.90
690	2245	2.173126	ATCAAGCCACTCTAGAGCCT	57.827	50.000	19.97	10.60	0.00	4.58
706	2261	3.856638	GCAATGCAAGTGGTTCGAAATCA	60.857	43.478	0.00	0.00	28.90	2.57
751	2315	1.159098	ACGGCGTCGAGTATCTCCTC	61.159	60.000	20.03	0.00	40.11	3.71
752	2316	0.747283	AACGGCGTCGAGTATCTCCT	60.747	55.000	20.03	0.00	40.11	3.69
753	2317	0.591741	CAACGGCGTCGAGTATCTCC	60.592	60.000	20.03	0.00	40.11	3.71
754	2318	1.201098	GCAACGGCGTCGAGTATCTC	61.201	60.000	20.03	0.00	40.11	2.75
755	2319	1.226603	GCAACGGCGTCGAGTATCT	60.227	57.895	20.03	0.00	40.11	1.98
872	2439	5.645497	GGCCATTTGCACCATAAAACAAATA	59.355	36.000	0.00	0.00	39.92	1.40
922	2489	5.862845	TGAAGAAGCTGATGAAGAAGAAGT	58.137	37.500	0.00	0.00	0.00	3.01
923	2490	6.819649	AGATGAAGAAGCTGATGAAGAAGAAG	59.180	38.462	0.00	0.00	0.00	2.85
951	2518	9.767228	CTCTGAAACTCTAAAGATGATGATGAT	57.233	33.333	0.00	0.00	0.00	2.45
980	2571	3.438216	TTGCTCTGGACCAATTGATCA	57.562	42.857	7.12	0.00	0.00	2.92
991	2582	2.373169	ACCTCTTTGTCATTGCTCTGGA	59.627	45.455	0.00	0.00	0.00	3.86
992	2583	2.787994	ACCTCTTTGTCATTGCTCTGG	58.212	47.619	0.00	0.00	0.00	3.86
1005	2597	5.505181	TCTCCTCAAAAGCATACCTCTTT	57.495	39.130	0.00	0.00	35.47	2.52
1013	2605	4.525024	CATCTCCTTCTCCTCAAAAGCAT	58.475	43.478	0.00	0.00	0.00	3.79
1020	2612	1.680522	GCGCCATCTCCTTCTCCTCA	61.681	60.000	0.00	0.00	0.00	3.86
1222	2832	0.396974	TGCAACTTGGGCTTGAGGTT	60.397	50.000	0.00	0.00	0.00	3.50
1332	2942	0.833949	TAATAGCCATGACGCCACCA	59.166	50.000	0.00	0.00	0.00	4.17
1347	2963	2.278989	GCTGTCGGCGGCGTAATA	60.279	61.111	31.06	9.09	37.24	0.98
1465	3096	4.427661	GTCGCTCTCGCTGCTGGT	62.428	66.667	0.00	0.00	35.26	4.00
1511	3142	2.739671	GGTGGAACGTGTACCCGC	60.740	66.667	0.00	0.00	38.12	6.13
1666	3316	7.935210	GGATTTATCCATGCATGAAAAAGGAAT	59.065	33.333	28.31	16.14	46.38	3.01
1711	3372	2.328099	GCCTTTCACTGGGCACTCG	61.328	63.158	0.00	0.00	46.84	4.18
1917	3613	5.239306	GGGCATGAATTGATAAATCACGAGA	59.761	40.000	0.00	0.00	36.36	4.04
1920	3616	4.037803	TGGGGCATGAATTGATAAATCACG	59.962	41.667	0.00	0.00	36.36	4.35
1935	3631	1.325355	GGAAGATGACATGGGGCATG	58.675	55.000	0.00	0.00	46.18	4.06
1936	3632	0.186873	GGGAAGATGACATGGGGCAT	59.813	55.000	0.00	0.00	0.00	4.40
2009	5282	5.171337	CGCACGATAATTTATGGTTCAAAGC	59.829	40.000	1.73	2.26	0.00	3.51
2044	5319	1.337823	ACAGTTGCATAGGTCACGGTC	60.338	52.381	0.00	0.00	0.00	4.79
2052	5327	1.271325	TGTGGTGGACAGTTGCATAGG	60.271	52.381	0.00	0.00	0.00	2.57
2066	5341	5.301805	AGAGTTTTCTGGGTTTAATGTGGTG	59.698	40.000	0.00	0.00	30.72	4.17
2087	5387	9.831737	CTGAGTTCATGTTAAATGGTTTTAGAG	57.168	33.333	0.00	0.00	0.00	2.43
2154	5454	6.605594	TGAATATATGGAACCTTTCGCCTTTT	59.394	34.615	0.00	0.00	0.00	2.27
2165	5466	7.227512	CAGAGTGTTTCCTGAATATATGGAACC	59.772	40.741	3.14	0.00	39.29	3.62
2178	5479	3.797039	TGTCAAGTCAGAGTGTTTCCTG	58.203	45.455	0.00	0.00	0.00	3.86
2203	5504	6.586082	GTCATATTTTTGGACGAATTTGTGCT	59.414	34.615	17.21	0.73	0.00	4.40
2264	5565	8.685838	ACACACAACTAAACACAATAGGTAAT	57.314	30.769	0.00	0.00	0.00	1.89
2358	5660	7.881775	AAGTGGAAAGTAATTTAGGGCATAG	57.118	36.000	0.00	0.00	0.00	2.23
2372	5674	9.508642	CTAAAAGAGATCCTAAAAGTGGAAAGT	57.491	33.333	0.00	0.00	37.13	2.66
2516	5821	8.387190	TCAAAGAGATGATTTATGTGCTATGG	57.613	34.615	0.00	0.00	0.00	2.74

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.