AutoCloner

Multiple sequence alignment - TraesCS3B01G205800

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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	TraesCS3B01G205800	chr3B	100.000	3095	0	0	1	3095	240533130	240530036	0.000000e+00	5716.0
1	TraesCS3B01G205800	chr3D	96.414	1924	55	9	1	1916	164548006	164546089	0.000000e+00	3158.0
2	TraesCS3B01G205800	chr3A	97.436	1053	25	2	1	1053	196763414	196762364	0.000000e+00	1794.0
3	TraesCS3B01G205800	chr3A	94.712	832	32	7	1093	1916	196762379	196761552	0.000000e+00	1282.0
4	TraesCS3B01G205800	chr3A	83.333	330	46	6	2769	3093	129489092	129489417	2.330000e-76	296.0
5	TraesCS3B01G205800	chr2B	91.913	915	47	18	1941	2834	541891820	541892728	0.000000e+00	1254.0
6	TraesCS3B01G205800	chr2B	79.765	850	121	30	2287	3093	110829768	110830609	1.250000e-158	569.0
7	TraesCS3B01G205800	chr2B	91.867	332	23	4	2763	3093	541892708	541893036	7.820000e-126	460.0
8	TraesCS3B01G205800	chr2B	81.875	160	25	4	1347	1504	100024867	100025024	6.960000e-27	132.0
9	TraesCS3B01G205800	chr2D	82.253	879	104	27	1953	2790	395109444	395110311	0.000000e+00	712.0
10	TraesCS3B01G205800	chr2D	79.781	183	35	2	1347	1528	64011106	64011287	6.960000e-27	132.0
11	TraesCS3B01G205800	chr7D	76.000	1200	186	47	1947	3091	168493931	168492779	7.600000e-146	527.0
12	TraesCS3B01G205800	chr7D	76.376	1054	165	41	2110	3093	379776452	379775413	9.970000e-135	490.0
13	TraesCS3B01G205800	chr7D	78.442	552	75	24	2279	2791	560991016	560991562	1.380000e-83	320.0
14	TraesCS3B01G205800	chr7D	72.911	395	79	20	2710	3093	560908736	560909113	9.070000e-21	111.0
15	TraesCS3B01G205800	chrUn	89.286	308	33	0	1220	1527	296339372	296339679	1.350000e-103	387.0
16	TraesCS3B01G205800	chr1B	88.854	314	35	0	1223	1536	21383951	21383638	1.350000e-103	387.0
17	TraesCS3B01G205800	chr1B	88.854	314	35	0	1223	1536	21390741	21390428	1.350000e-103	387.0
18	TraesCS3B01G205800	chr1B	88.217	314	37	0	1223	1536	21409318	21409005	2.910000e-100	375.0
19	TraesCS3B01G205800	chr1A	87.037	162	18	1	1378	1536	16093936	16094097	2.450000e-41	180.0
20	TraesCS3B01G205800	chr6A	74.185	399	79	16	2713	3094	186481275	186480884	8.950000e-31	145.0
21	TraesCS3B01G205800	chr5B	75.194	258	51	11	2842	3093	589993933	589994183	3.260000e-20	110.0
22	TraesCS3B01G205800	chr4B	74.419	258	53	10	2842	3093	643647718	643647468	7.060000e-17	99.0
23	TraesCS3B01G205800	chr2A	100.000	28	0	0	2969	2996	76370766	76370793	6.000000e-03	52.8

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	TraesCS3B01G205800	chr3B	240530036	240533130	3094	True	5716	5716	100.000	1	3095	1	chr3B.!!$R1	3094
1	TraesCS3B01G205800	chr3D	164546089	164548006	1917	True	3158	3158	96.414	1	1916	1	chr3D.!!$R1	1915
2	TraesCS3B01G205800	chr3A	196761552	196763414	1862	True	1538	1794	96.074	1	1916	2	chr3A.!!$R1	1915
3	TraesCS3B01G205800	chr2B	541891820	541893036	1216	False	857	1254	91.890	1941	3093	2	chr2B.!!$F3	1152
4	TraesCS3B01G205800	chr2B	110829768	110830609	841	False	569	569	79.765	2287	3093	1	chr2B.!!$F2	806
5	TraesCS3B01G205800	chr2D	395109444	395110311	867	False	712	712	82.253	1953	2790	1	chr2D.!!$F2	837
6	TraesCS3B01G205800	chr7D	168492779	168493931	1152	True	527	527	76.000	1947	3091	1	chr7D.!!$R1	1144
7	TraesCS3B01G205800	chr7D	379775413	379776452	1039	True	490	490	76.376	2110	3093	1	chr7D.!!$R2	983
8	TraesCS3B01G205800	chr7D	560991016	560991562	546	False	320	320	78.442	2279	2791	1	chr7D.!!$F2	512

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
372	374	2.365293	CCTTTCAGGAAAAAGGTGGGTG	59.635	50.0	7.16	0.0	46.81	4.61	F
1101	1104	0.458543	CTGAACTCCACATCGTCCCG	60.459	60.0	0.00	0.0	0.00	5.14	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1614	1620	0.106521	AACAACAAACCCTGCATGGC	59.893	50.0	8.09	0.0	0.0	4.40	R
3030	3263	0.184933	CCCCAGTTGAAAGTCCACCA	59.815	55.0	0.00	0.0	0.0	4.17	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
177	179	4.656041	GAGAGCATCAATTTTGTTCTCGG	58.344	43.478	13.05	0.00	40.19	4.63
372	374	2.365293	CCTTTCAGGAAAAAGGTGGGTG	59.635	50.000	7.16	0.00	46.81	4.61
467	469	6.421485	GCATGAATTATATGTGGATCTCCCT	58.579	40.000	0.00	0.00	35.38	4.20
607	610	9.729023	CGTAATTCTGGAAAATAACAATATGCA	57.271	29.630	0.00	0.00	0.00	3.96
827	830	4.794334	TCTTCCTGACCTAACCTAGCTAG	58.206	47.826	14.20	14.20	0.00	3.42
905	908	4.923264	TCACTAGCAGTATAGTATCGCG	57.077	45.455	0.00	0.00	34.21	5.87
1016	1019	5.850278	TCCACCTCTATATATACCCCCTTG	58.150	45.833	0.00	0.00	0.00	3.61
1101	1104	0.458543	CTGAACTCCACATCGTCCCG	60.459	60.000	0.00	0.00	0.00	5.14
1176	1179	2.691011	GCCGATAGAGAGGTGAGAGTTT	59.309	50.000	0.00	0.00	39.76	2.66
1338	1341	4.699522	GGGCAGGTGGTGTCGTCC	62.700	72.222	0.00	0.00	0.00	4.79
1407	1410	3.537874	GAGGACCCGGCGCTGTAT	61.538	66.667	16.49	1.68	0.00	2.29
1536	1539	3.807538	GTCGTCGACGCCTAGCCA	61.808	66.667	32.19	11.25	39.60	4.75
1574	1577	1.521006	CAGTCTCTCGATCTCGTCTCG	59.479	57.143	0.00	0.00	40.80	4.04
1614	1620	6.000891	TCTTCCATCGTTTGACTTGATTTG	57.999	37.500	0.00	0.00	0.00	2.32
1615	1621	4.159377	TCCATCGTTTGACTTGATTTGC	57.841	40.909	0.00	0.00	0.00	3.68
1641	1650	3.364964	GCAGGGTTTGTTGTTAGTGATCG	60.365	47.826	0.00	0.00	0.00	3.69
1644	1653	3.404899	GGTTTGTTGTTAGTGATCGGGA	58.595	45.455	0.00	0.00	0.00	5.14
1654	1663	9.136952	GTTGTTAGTGATCGGGATGTTATATAC	57.863	37.037	0.00	0.00	0.00	1.47
1669	1678	6.818233	TGTTATATACGATTGGTTGTGCCTA	58.182	36.000	0.00	0.00	38.35	3.93
1746	1755	3.680620	ATATGTGCGCGTGGTGCCT	62.681	57.895	8.43	0.00	42.08	4.75
1795	1804	3.802139	GTGTGTATATGTATGCGTGCTGT	59.198	43.478	0.00	0.00	0.00	4.40
1837	1846	6.375377	TGTTTTGATGTAAATTAGTGTCCGC	58.625	36.000	0.00	0.00	0.00	5.54
1856	1867	4.887655	TCCGCGTGATGACTATATATCCAT	59.112	41.667	4.92	0.00	0.00	3.41
1908	1919	3.212275	GCATGATGCATGGCACCA	58.788	55.556	13.36	0.00	43.04	4.17
1920	1931	2.352422	GCACCAGCCATGTCCTGA	59.648	61.111	11.10	0.00	32.03	3.86
1921	1932	1.303561	GCACCAGCCATGTCCTGAA	60.304	57.895	11.10	0.00	32.03	3.02
1922	1933	1.589716	GCACCAGCCATGTCCTGAAC	61.590	60.000	11.10	0.00	32.03	3.18
1923	1934	0.037303	CACCAGCCATGTCCTGAACT	59.963	55.000	11.10	0.00	32.03	3.01
1924	1935	0.773644	ACCAGCCATGTCCTGAACTT	59.226	50.000	11.10	0.00	32.03	2.66
1925	1936	1.171308	CCAGCCATGTCCTGAACTTG	58.829	55.000	11.10	0.00	33.81	3.16
1926	1937	1.546323	CCAGCCATGTCCTGAACTTGT	60.546	52.381	11.10	0.00	32.49	3.16
1927	1938	2.233271	CAGCCATGTCCTGAACTTGTT	58.767	47.619	4.99	0.00	32.49	2.83
1928	1939	2.030540	CAGCCATGTCCTGAACTTGTTG	60.031	50.000	4.99	0.00	32.49	3.33
1929	1940	1.336240	GCCATGTCCTGAACTTGTTGC	60.336	52.381	0.00	0.00	32.49	4.17
1930	1941	1.955778	CCATGTCCTGAACTTGTTGCA	59.044	47.619	0.00	0.00	32.49	4.08
1931	1942	2.559668	CCATGTCCTGAACTTGTTGCAT	59.440	45.455	0.00	0.00	32.49	3.96
1932	1943	3.571571	CATGTCCTGAACTTGTTGCATG	58.428	45.455	0.00	0.00	0.00	4.06
1933	1944	1.337703	TGTCCTGAACTTGTTGCATGC	59.662	47.619	11.82	11.82	0.00	4.06
1934	1945	1.337703	GTCCTGAACTTGTTGCATGCA	59.662	47.619	18.46	18.46	0.00	3.96
1935	1946	2.029649	GTCCTGAACTTGTTGCATGCAT	60.030	45.455	23.37	4.78	0.00	3.96
1936	1947	3.191162	GTCCTGAACTTGTTGCATGCATA	59.809	43.478	23.37	11.29	0.00	3.14
1937	1948	4.018490	TCCTGAACTTGTTGCATGCATAT	58.982	39.130	23.37	4.15	0.00	1.78
1938	1949	5.066375	GTCCTGAACTTGTTGCATGCATATA	59.934	40.000	23.37	3.27	0.00	0.86
1939	1950	5.829391	TCCTGAACTTGTTGCATGCATATAT	59.171	36.000	23.37	6.06	0.00	0.86
2154	2171	2.604614	CGCATGCACGCTACTGTAGATA	60.605	50.000	19.57	0.04	0.00	1.98
2178	2195	0.457035	CAAGGTGCTTGCTTGTGTGT	59.543	50.000	0.00	0.00	34.63	3.72
2368	2416	9.323963	CTTTGAAAAACGCAAACATTTTTAACT	57.676	25.926	0.00	0.00	37.96	2.24
2545	2647	3.882888	CCTCACTTGCAACTAGGACAAAA	59.117	43.478	10.24	0.00	0.00	2.44
2690	2801	0.310854	GGACAAACTTGCAACTCGGG	59.689	55.000	0.00	0.00	0.00	5.14
2698	2809	2.293399	ACTTGCAACTCGGGAAAATCAC	59.707	45.455	0.00	0.00	0.00	3.06
2885	3058	0.757561	TCGTGAGTTGAGGGTGGACA	60.758	55.000	0.00	0.00	0.00	4.02
2930	3103	2.485426	TCGTGTCCTAGTTACAAGTCGG	59.515	50.000	7.80	0.00	0.00	4.79
2933	3106	1.134877	GTCCTAGTTACAAGTCGGGGC	60.135	57.143	0.00	0.00	0.00	5.80
2996	3171	0.038166	TCAAGGATGGACTGGCAACC	59.962	55.000	3.80	3.80	0.00	3.77
3030	3263	1.282157	GGGCCCTAGTTGTGAGTTGAT	59.718	52.381	17.04	0.00	0.00	2.57
3040	3273	3.576078	TGTGAGTTGATGGTGGACTTT	57.424	42.857	0.00	0.00	0.00	2.66
3046	3279	3.885297	AGTTGATGGTGGACTTTCAACTG	59.115	43.478	18.65	0.00	43.83	3.16
3073	3306	2.101640	AAAGATTTGGCCCCACTTGT	57.898	45.000	0.00	0.00	0.00	3.16
3084	3317	1.185618	CCCACTTGTGAGTCGAGGGA	61.186	60.000	1.89	0.00	38.37	4.20
3093	3326	0.968393	GAGTCGAGGGAGGACTTGCT	60.968	60.000	0.00	0.00	44.41	3.91
3094	3327	1.216710	GTCGAGGGAGGACTTGCTG	59.783	63.158	0.00	0.00	0.00	4.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
160	162	4.386652	CCTTTGCCGAGAACAAAATTGATG	59.613	41.667	0.00	0.00	36.63	3.07
177	179	0.869730	CAAGCCAATGTTGCCTTTGC	59.130	50.000	0.00	0.00	38.26	3.68
243	245	0.933796	GAGCTATCTTTGCGCACCTC	59.066	55.000	11.12	3.75	35.28	3.85
372	374	1.017387	GATGTTGTGCGAGGAATCCC	58.983	55.000	0.00	0.00	0.00	3.85
458	460	4.767409	GGTTAATTGCCAATAGGGAGATCC	59.233	45.833	0.00	0.00	40.01	3.36
467	469	3.512033	GGCGTTGGTTAATTGCCAATA	57.488	42.857	16.05	0.00	46.25	1.90
827	830	3.927854	AGAGAAGGGCGTCTTTAGTTTC	58.072	45.455	0.00	0.00	35.50	2.78
905	908	5.406780	CAGGACATAGATTTCTTATGCGACC	59.593	44.000	0.00	0.00	0.00	4.79
1016	1019	2.110006	GCAAGGGAGGGCGAGATC	59.890	66.667	0.00	0.00	0.00	2.75
1101	1104	1.009829	CAATTGGTCGAGCTAGCACC	58.990	55.000	18.83	16.26	0.00	5.01
1407	1410	2.664851	CCGCGCTTGTGGAACTGA	60.665	61.111	5.56	0.00	46.68	3.41
1534	1537	2.370445	ATGGACGGAAGAGGGCTGG	61.370	63.158	0.00	0.00	0.00	4.85
1536	1539	3.036429	GCATGGACGGAAGAGGGCT	62.036	63.158	0.00	0.00	0.00	5.19
1614	1620	0.106521	AACAACAAACCCTGCATGGC	59.893	50.000	8.09	0.00	0.00	4.40
1615	1621	2.627699	ACTAACAACAAACCCTGCATGG	59.372	45.455	6.46	6.46	0.00	3.66
1641	1650	6.348213	GCACAACCAATCGTATATAACATCCC	60.348	42.308	0.00	0.00	0.00	3.85
1644	1653	6.296026	AGGCACAACCAATCGTATATAACAT	58.704	36.000	0.00	0.00	43.14	2.71
1654	1663	3.056891	ACCAAATTAGGCACAACCAATCG	60.057	43.478	0.00	0.00	43.14	3.34
1669	1678	4.340950	CACACTACACTTCCCAACCAAATT	59.659	41.667	0.00	0.00	0.00	1.82
1737	1746	1.202521	TGCATATACTCAGGCACCACG	60.203	52.381	0.00	0.00	0.00	4.94
1746	1755	7.011016	CACAACGAAAACCTATGCATATACTCA	59.989	37.037	6.92	0.00	0.00	3.41
1795	1804	2.902608	ACAGAGATCTTACACACCCCA	58.097	47.619	0.00	0.00	0.00	4.96
1837	1846	9.569167	AACGTAAATGGATATATAGTCATCACG	57.431	33.333	19.56	19.56	0.00	4.35
1903	1914	1.303561	TTCAGGACATGGCTGGTGC	60.304	57.895	0.00	0.00	38.76	5.01
1908	1919	2.233271	CAACAAGTTCAGGACATGGCT	58.767	47.619	0.00	0.00	31.38	4.75
1916	1927	2.736144	ATGCATGCAACAAGTTCAGG	57.264	45.000	26.68	0.00	0.00	3.86
1917	1928	5.918576	CCATATATGCATGCAACAAGTTCAG	59.081	40.000	26.68	8.45	0.00	3.02
1918	1929	5.221283	CCCATATATGCATGCAACAAGTTCA	60.221	40.000	26.68	4.58	0.00	3.18
1919	1930	5.221303	ACCCATATATGCATGCAACAAGTTC	60.221	40.000	26.68	0.00	0.00	3.01
1920	1931	4.650588	ACCCATATATGCATGCAACAAGTT	59.349	37.500	26.68	9.68	0.00	2.66
1921	1932	4.217510	ACCCATATATGCATGCAACAAGT	58.782	39.130	26.68	10.51	0.00	3.16
1922	1933	4.859304	ACCCATATATGCATGCAACAAG	57.141	40.909	26.68	13.40	0.00	3.16
1923	1934	6.008960	TCATACCCATATATGCATGCAACAA	58.991	36.000	26.68	13.80	33.31	2.83
1924	1935	5.415389	GTCATACCCATATATGCATGCAACA	59.585	40.000	26.68	16.20	33.31	3.33
1925	1936	5.649395	AGTCATACCCATATATGCATGCAAC	59.351	40.000	26.68	13.15	33.31	4.17
1926	1937	5.818887	AGTCATACCCATATATGCATGCAA	58.181	37.500	26.68	14.46	33.31	4.08
1927	1938	5.440207	AGTCATACCCATATATGCATGCA	57.560	39.130	25.04	25.04	33.31	3.96
1928	1939	6.994496	ACATAGTCATACCCATATATGCATGC	59.006	38.462	11.82	11.82	33.31	4.06
1929	1940	8.206189	TGACATAGTCATACCCATATATGCATG	58.794	37.037	10.16	9.75	37.67	4.06
1930	1941	8.206867	GTGACATAGTCATACCCATATATGCAT	58.793	37.037	3.79	3.79	44.63	3.96
1931	1942	7.180051	TGTGACATAGTCATACCCATATATGCA	59.820	37.037	7.24	0.00	44.63	3.96
1932	1943	7.555965	TGTGACATAGTCATACCCATATATGC	58.444	38.462	7.24	0.00	44.63	3.14
1933	1944	9.755804	GATGTGACATAGTCATACCCATATATG	57.244	37.037	5.68	5.68	44.63	1.78
1934	1945	9.720874	AGATGTGACATAGTCATACCCATATAT	57.279	33.333	0.00	0.00	44.63	0.86
1936	1947	9.194972	CTAGATGTGACATAGTCATACCCATAT	57.805	37.037	0.00	2.75	44.63	1.78
1937	1948	8.390921	TCTAGATGTGACATAGTCATACCCATA	58.609	37.037	0.00	0.00	44.63	2.74
1938	1949	7.241628	TCTAGATGTGACATAGTCATACCCAT	58.758	38.462	0.00	2.37	44.63	4.00
1939	1950	6.610830	TCTAGATGTGACATAGTCATACCCA	58.389	40.000	0.00	0.00	44.63	4.51
2154	2171	3.118665	ACACAAGCAAGCACCTTGATTTT	60.119	39.130	15.12	0.00	45.87	1.82
2178	2195	2.035832	GCAAAGCTAGCCTCAAACCAAA	59.964	45.455	12.13	0.00	0.00	3.28
2450	2504	9.288576	TCAGAAAGTCACAAATGTTCAATATCT	57.711	29.630	0.00	0.00	0.00	1.98
2454	2537	9.434420	TTTTTCAGAAAGTCACAAATGTTCAAT	57.566	25.926	0.00	0.00	0.00	2.57
2457	2540	8.687824	TCTTTTTCAGAAAGTCACAAATGTTC	57.312	30.769	0.00	0.00	0.00	3.18
2561	2665	2.169832	AATCCACAACCGACTCACAG	57.830	50.000	0.00	0.00	0.00	3.66
2655	2764	3.328382	TGTCCTTGACTCGTAATTGGG	57.672	47.619	0.00	0.00	33.15	4.12
2690	2801	2.833943	AGGGCCCTTGATTGTGATTTTC	59.166	45.455	22.28	0.00	0.00	2.29
2698	2809	1.186917	TGCAACAGGGCCCTTGATTG	61.187	55.000	26.10	26.19	0.00	2.67
2885	3058	5.543790	ACCTTTTAGTTTCTCCCAATTGCAT	59.456	36.000	0.00	0.00	0.00	3.96
2930	3103	2.353610	CCAGTTGCAATCCCAGCCC	61.354	63.158	0.59	0.00	0.00	5.19
2933	3106	0.251297	TGTCCCAGTTGCAATCCCAG	60.251	55.000	0.59	0.00	0.00	4.45
2958	3131	3.551496	CTCGCAACTGGGGCCTGAA	62.551	63.158	0.84	0.00	0.00	3.02
2961	3136	4.021925	GACTCGCAACTGGGGCCT	62.022	66.667	0.84	0.00	0.00	5.19
2996	3171	1.079197	GGCCCGCCCATTCTTTTTG	60.079	57.895	0.00	0.00	0.00	2.44
3022	3255	3.855255	TGAAAGTCCACCATCAACTCA	57.145	42.857	0.00	0.00	0.00	3.41
3030	3263	0.184933	CCCCAGTTGAAAGTCCACCA	59.815	55.000	0.00	0.00	0.00	4.17
3060	3293	1.150536	GACTCACAAGTGGGGCCAA	59.849	57.895	4.39	0.00	31.17	4.52
3061	3294	2.836154	GACTCACAAGTGGGGCCA	59.164	61.111	4.39	0.00	31.17	5.36
3069	3302	0.528470	GTCCTCCCTCGACTCACAAG	59.472	60.000	0.00	0.00	0.00	3.16
3073	3306	1.251527	GCAAGTCCTCCCTCGACTCA	61.252	60.000	0.00	0.00	39.69	3.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.