AutoCloner

Multiple sequence alignment - TraesCS1A01G366600

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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	TraesCS1A01G366600	chr1A	100.000	2639	0	0	1	2639	545473753	545476391	0.000000e+00	4874
1	TraesCS1A01G366600	chr1A	89.750	1961	170	17	1	1957	528297613	528295680	0.000000e+00	2479
2	TraesCS1A01G366600	chr1A	85.782	211	28	2	3	213	528297192	528296984	3.420000e-54	222
3	TraesCS1A01G366600	chr7D	91.403	2466	174	12	181	2639	616459554	616457120	0.000000e+00	3345
4	TraesCS1A01G366600	chr7D	89.312	683	71	2	1957	2639	463028589	463029269	0.000000e+00	856
5	TraesCS1A01G366600	chr7D	94.709	189	7	1	1	189	616460146	616459961	9.240000e-75	291
6	TraesCS1A01G366600	chr7D	89.623	212	20	1	3	214	616459312	616459103	4.330000e-68	268
7	TraesCS1A01G366600	chr7D	86.705	173	17	5	717	885	616459519	616459349	1.250000e-43	187
8	TraesCS1A01G366600	chr1B	88.957	1965	185	16	1	1958	617087426	617089365	0.000000e+00	2398
9	TraesCS1A01G366600	chr1B	90.429	606	44	6	1	601	617283601	617284197	0.000000e+00	785
10	TraesCS1A01G366600	chr1B	81.928	415	44	16	1	386	617284012	617284424	3.280000e-84	322
11	TraesCS1A01G366600	chr1B	90.295	237	19	1	657	889	617284192	617284428	9.180000e-80	307
12	TraesCS1A01G366600	chr1B	88.341	223	25	1	831	1053	617284438	617284659	1.560000e-67	267
13	TraesCS1A01G366600	chr1D	91.529	909	60	10	1	903	450203013	450203910	0.000000e+00	1236
14	TraesCS1A01G366600	chr1D	89.513	677	64	4	1963	2639	292109229	292109898	0.000000e+00	850
15	TraesCS1A01G366600	chr1D	88.971	680	69	3	1963	2639	293056507	293057183	0.000000e+00	835
16	TraesCS1A01G366600	chr2B	88.741	675	76	0	1965	2639	154646238	154645564	0.000000e+00	826
17	TraesCS1A01G366600	chr2D	88.450	684	77	2	1957	2639	323069426	323070108	0.000000e+00	824
18	TraesCS1A01G366600	chr4D	88.529	680	72	3	1963	2639	145490638	145489962	0.000000e+00	819
19	TraesCS1A01G366600	chr4D	88.365	679	75	4	1963	2639	152922280	152922956	0.000000e+00	813
20	TraesCS1A01G366600	chr5D	88.372	688	69	6	1956	2639	214928562	214929242	0.000000e+00	817
21	TraesCS1A01G366600	chr4A	84.071	113	15	3	246	356	725589095	725588984	3.590000e-19	106

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	TraesCS1A01G366600	chr1A	545473753	545476391	2638	False	4874.00	4874	100.00000	1	2639	1	chr1A.!!$F1	2638
1	TraesCS1A01G366600	chr1A	528295680	528297613	1933	True	1350.50	2479	87.76600	1	1957	2	chr1A.!!$R1	1956
2	TraesCS1A01G366600	chr7D	616457120	616460146	3026	True	1022.75	3345	90.61000	1	2639	4	chr7D.!!$R1	2638
3	TraesCS1A01G366600	chr7D	463028589	463029269	680	False	856.00	856	89.31200	1957	2639	1	chr7D.!!$F1	682
4	TraesCS1A01G366600	chr1B	617087426	617089365	1939	False	2398.00	2398	88.95700	1	1958	1	chr1B.!!$F1	1957
5	TraesCS1A01G366600	chr1B	617283601	617284659	1058	False	420.25	785	87.74825	1	1053	4	chr1B.!!$F2	1052
6	TraesCS1A01G366600	chr1D	450203013	450203910	897	False	1236.00	1236	91.52900	1	903	1	chr1D.!!$F3	902
7	TraesCS1A01G366600	chr1D	292109229	292109898	669	False	850.00	850	89.51300	1963	2639	1	chr1D.!!$F1	676
8	TraesCS1A01G366600	chr1D	293056507	293057183	676	False	835.00	835	88.97100	1963	2639	1	chr1D.!!$F2	676
9	TraesCS1A01G366600	chr2B	154645564	154646238	674	True	826.00	826	88.74100	1965	2639	1	chr2B.!!$R1	674
10	TraesCS1A01G366600	chr2D	323069426	323070108	682	False	824.00	824	88.45000	1957	2639	1	chr2D.!!$F1	682
11	TraesCS1A01G366600	chr4D	145489962	145490638	676	True	819.00	819	88.52900	1963	2639	1	chr4D.!!$R1	676
12	TraesCS1A01G366600	chr4D	152922280	152922956	676	False	813.00	813	88.36500	1963	2639	1	chr4D.!!$F1	676
13	TraesCS1A01G366600	chr5D	214928562	214929242	680	False	817.00	817	88.37200	1956	2639	1	chr5D.!!$F1	683

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
913	1406	3.140707	AGCCATCCAACCATCCATTCATA	59.859	43.478	0.0	0.0	0.0	2.15	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1726	2220	0.179059	ACATCTTCACACCGTGCACA	60.179	50.0	18.64	0.0	32.98	4.57	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
93	94	9.658799	ACATTAATACGAGGATATCTGAAATGG	57.341	33.333	2.05	0.00	0.00	3.16
214	630	3.949586	TGATATCCAAAGTGGGCATCA	57.050	42.857	0.00	7.31	38.32	3.07
425	841	3.792401	CATCCACGTACCTATGCAAAGA	58.208	45.455	0.00	0.00	0.00	2.52
483	904	9.995003	GGATCAATATTTGTGAATAGAGAGAGT	57.005	33.333	0.00	0.00	31.58	3.24
632	1053	3.949586	TGATATCCAAAGTGGGCATCA	57.050	42.857	0.00	7.31	38.32	3.07
673	1094	8.640063	ACCAATACATATATGCACACATTGAT	57.360	30.769	12.79	0.23	37.74	2.57
726	1151	6.001460	GCTATGTTACATTAATGGGCCTACA	58.999	40.000	19.37	14.16	0.00	2.74
913	1406	3.140707	AGCCATCCAACCATCCATTCATA	59.859	43.478	0.00	0.00	0.00	2.15
928	1421	9.305555	CATCCATTCATATCTCCCTTTAACATT	57.694	33.333	0.00	0.00	0.00	2.71
951	1444	7.969690	TTGTTTCATATACAATTGTCCCCAT	57.030	32.000	15.85	5.56	30.96	4.00
961	1454	3.567478	ATTGTCCCCATCACTCTTAGC	57.433	47.619	0.00	0.00	0.00	3.09
1016	1509	2.299013	CAGCAATGGCAATAGCATGGAT	59.701	45.455	10.95	0.00	44.61	3.41
1036	1529	3.688049	TGACCACCATCATCTCCTCTA	57.312	47.619	0.00	0.00	0.00	2.43
1091	1584	1.295792	GCTCAGACCAACAACGACAA	58.704	50.000	0.00	0.00	0.00	3.18
1101	1594	1.107114	ACAACGACAATGGTGGCAAA	58.893	45.000	0.00	0.00	30.49	3.68
1117	1610	1.827245	GCAAACCCAAGAGGACCCATT	60.827	52.381	0.00	0.00	39.89	3.16
1164	1658	6.656902	TGCTTCAATCAACTCCTCTGAATAT	58.343	36.000	0.00	0.00	0.00	1.28
1166	1660	6.073873	GCTTCAATCAACTCCTCTGAATATCG	60.074	42.308	0.00	0.00	0.00	2.92
1171	1665	3.972950	ACTCCTCTGAATATCGTCACG	57.027	47.619	0.00	0.00	0.00	4.35
1177	1671	4.412207	CTCTGAATATCGTCACGTCACAA	58.588	43.478	0.00	0.00	0.00	3.33
1195	1689	2.480419	ACAAAAGAATTCTGCGTCTCGG	59.520	45.455	9.17	0.00	0.00	4.63
1269	1763	3.446161	CCCTCGTTGGTGTAGACATTCTA	59.554	47.826	0.00	0.00	0.00	2.10
1347	1841	2.804549	TGGCACATCAACAGCACAA	58.195	47.368	0.00	0.00	0.00	3.33
1356	1850	1.146041	AACAGCACAACGCCTCAGA	59.854	52.632	0.00	0.00	44.04	3.27
1362	1856	1.229428	CACAACGCCTCAGATTGTGT	58.771	50.000	7.92	0.00	45.24	3.72
1366	1860	0.969149	ACGCCTCAGATTGTGTGAGA	59.031	50.000	5.76	0.00	43.65	3.27
1377	1871	6.325804	TCAGATTGTGTGAGATGGACTATGAT	59.674	38.462	0.00	0.00	0.00	2.45
1398	1892	1.375396	CGCGGTGACCATCCTCAAA	60.375	57.895	1.11	0.00	0.00	2.69
1408	1902	1.815003	CCATCCTCAAAGTCTGCAACC	59.185	52.381	0.00	0.00	0.00	3.77
1451	1945	2.764010	GTCCCAAAGGTGGTGAAAAAGT	59.236	45.455	0.00	0.00	44.30	2.66
1461	1955	2.291930	TGGTGAAAAAGTTGGACCACCT	60.292	45.455	0.00	0.00	43.15	4.00
1487	1981	4.620589	TTTATTTACCCGACTGTGTGGA	57.379	40.909	0.00	0.00	0.00	4.02
1565	2059	4.919754	GCAGGAAGCATTGTACAAAGAAAG	59.080	41.667	13.23	2.07	44.79	2.62
1609	2103	1.547372	ACCTCAATGTTGCCTTGATGC	59.453	47.619	0.00	0.00	32.50	3.91
1610	2104	1.546923	CCTCAATGTTGCCTTGATGCA	59.453	47.619	0.00	0.00	40.07	3.96
1626	2120	5.954153	TGATGCAACCATATTGGGATTTT	57.046	34.783	0.00	0.00	43.37	1.82
1753	2247	2.420547	CGGTGTGAAGATGTCCCATCAT	60.421	50.000	6.96	0.00	0.00	2.45
1754	2248	2.947652	GGTGTGAAGATGTCCCATCATG	59.052	50.000	6.96	0.00	0.00	3.07
1755	2249	2.357009	GTGTGAAGATGTCCCATCATGC	59.643	50.000	6.96	0.00	0.00	4.06
1756	2250	1.952296	GTGAAGATGTCCCATCATGCC	59.048	52.381	6.96	0.00	0.00	4.40
1758	2252	0.928505	AAGATGTCCCATCATGCCCA	59.071	50.000	6.96	0.00	0.00	5.36
1759	2253	0.184451	AGATGTCCCATCATGCCCAC	59.816	55.000	6.96	0.00	0.00	4.61
1761	2255	0.184451	ATGTCCCATCATGCCCACTC	59.816	55.000	0.00	0.00	0.00	3.51
1762	2256	0.915872	TGTCCCATCATGCCCACTCT	60.916	55.000	0.00	0.00	0.00	3.24
1789	2284	4.556233	ACGCGCTCATTGTATATGTACAT	58.444	39.130	13.93	13.93	40.35	2.29
1797	2292	8.285394	GCTCATTGTATATGTACATGTTTCCAG	58.715	37.037	18.81	6.00	40.35	3.86
1808	2303	2.489938	TGTTTCCAGATGGCACCTAC	57.510	50.000	0.00	0.00	34.44	3.18
1850	2345	2.438021	GACATGGGTGCCAAGTAGGATA	59.562	50.000	0.00	0.00	35.48	2.59
1855	2350	2.438021	GGGTGCCAAGTAGGATATGACA	59.562	50.000	0.00	0.00	41.22	3.58
1862	2357	2.990195	AGTAGGATATGACATGGCCCA	58.010	47.619	0.00	0.00	0.00	5.36
1888	2383	4.348168	CAGTATGGGTAGTTTAGATGGGCT	59.652	45.833	0.00	0.00	0.00	5.19
1925	2420	9.933723	AATTTTGGCCATTTAGCTCAATATATC	57.066	29.630	6.09	0.00	0.00	1.63
1929	2424	6.183347	GGCCATTTAGCTCAATATATCTGGT	58.817	40.000	0.00	0.00	0.00	4.00
1984	2479	9.383519	CAGTTGTAGGATTGAAAGTATGTGTAT	57.616	33.333	0.00	0.00	0.00	2.29
1989	2489	7.079451	AGGATTGAAAGTATGTGTATAGGGG	57.921	40.000	0.00	0.00	0.00	4.79
2034	2543	8.983789	TGACCAAATAAAAACTTACCCTTTTCT	58.016	29.630	0.00	0.00	0.00	2.52
2086	2595	2.901839	TCTACCAAGTCAAGTACACCCC	59.098	50.000	0.00	0.00	0.00	4.95
2125	2634	5.564550	AGAGTTGAGCAGTGGAATGTAAAT	58.435	37.500	0.00	0.00	0.00	1.40
2268	2777	2.363680	CACAAAGGGTAATGGTTGTGCA	59.636	45.455	2.77	0.00	42.94	4.57
2317	2826	2.893489	GGTCCATGAAGAAGCAACCTTT	59.107	45.455	0.00	0.00	0.00	3.11
2339	2848	3.980022	TCCTATTCCACCATGGCTTATGA	59.020	43.478	13.04	0.00	39.21	2.15
2385	2894	3.633065	GGTAGATCTTCACGAAGTAGGCT	59.367	47.826	0.00	0.00	41.61	4.58
2421	2930	4.236527	ACAAACTCCTTGGTTCAACTCT	57.763	40.909	0.00	0.00	39.56	3.24
2495	3009	7.402071	ACTCTCCAAAAGGTAATAGATGGTGTA	59.598	37.037	0.00	0.00	0.00	2.90
2509	3023	2.892374	TGGTGTAGCTGATGATGAACG	58.108	47.619	0.00	0.00	0.00	3.95
2528	3042	0.886563	GCCTTGCTCTTGTGCTTCAT	59.113	50.000	0.00	0.00	0.00	2.57
2593	3107	1.893315	TTGGTAGGAGAGGGGATTGG	58.107	55.000	0.00	0.00	0.00	3.16

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
67	68	9.658799	CCATTTCAGATATCCTCGTATTAATGT	57.341	33.333	0.00	0.00	0.00	2.71
93	94	6.882610	TCTATGCACAAATATGTTGATCCC	57.117	37.500	0.00	0.00	37.82	3.85
214	630	4.127566	ACGTTTACTACATACGCCCATT	57.872	40.909	0.00	0.00	38.77	3.16
551	972	3.513662	CAACACAACCATGCCATATGTG	58.486	45.455	12.99	12.99	45.18	3.21
755	1180	9.729281	ATATGTACATATGTTGATGCTCATTGA	57.271	29.630	24.39	0.00	33.05	2.57
756	1181	9.983804	GATATGTACATATGTTGATGCTCATTG	57.016	33.333	28.82	0.00	34.36	2.82
951	1444	8.846943	TTGAATTGTATTGAAGCTAAGAGTGA	57.153	30.769	0.00	0.00	0.00	3.41
961	1454	8.273780	ACTAGAAGCCTTGAATTGTATTGAAG	57.726	34.615	0.00	0.00	0.00	3.02
1016	1509	2.557555	AGAGGAGATGATGGTGGTCA	57.442	50.000	0.00	0.00	0.00	4.02
1031	1524	6.297080	AGAGCATGATGATTATGGTAGAGG	57.703	41.667	1.74	0.00	36.49	3.69
1036	1529	6.371278	AGGAAAAGAGCATGATGATTATGGT	58.629	36.000	1.31	1.31	38.82	3.55
1101	1594	1.455822	TGAAATGGGTCCTCTTGGGT	58.544	50.000	0.00	0.00	36.25	4.51
1117	1610	6.431278	CATTTTTGCATGCTTCAACAATGAA	58.569	32.000	20.33	0.00	40.92	2.57
1164	1658	4.026062	CAGAATTCTTTTGTGACGTGACGA	60.026	41.667	13.70	0.00	0.00	4.20
1166	1660	3.968724	GCAGAATTCTTTTGTGACGTGAC	59.031	43.478	4.86	0.00	0.00	3.67
1171	1665	4.458708	GAGACGCAGAATTCTTTTGTGAC	58.541	43.478	4.86	3.39	0.00	3.67
1177	1671	1.079503	GCCGAGACGCAGAATTCTTT	58.920	50.000	4.86	0.00	0.00	2.52
1202	1696	1.548357	ATCACTCCGCTTGTCCTGCT	61.548	55.000	0.00	0.00	0.00	4.24
1269	1763	1.956477	GCGGCAATGATATGTCCCTTT	59.044	47.619	0.00	0.00	0.00	3.11
1347	1841	0.969149	TCTCACACAATCTGAGGCGT	59.031	50.000	0.00	0.00	36.55	5.68
1356	1850	5.061853	GCATCATAGTCCATCTCACACAAT	58.938	41.667	0.00	0.00	0.00	2.71
1362	1856	1.001293	GCGGCATCATAGTCCATCTCA	59.999	52.381	0.00	0.00	0.00	3.27
1366	1860	1.004560	CCGCGGCATCATAGTCCAT	60.005	57.895	14.67	0.00	0.00	3.41
1398	1892	1.001641	GAGCATGGGGTTGCAGACT	60.002	57.895	0.00	0.00	45.23	3.24
1408	1902	0.179073	CGGTAGTCCTTGAGCATGGG	60.179	60.000	0.00	0.00	0.00	4.00
1451	1945	5.776208	GGTAAATAAAAGGAAGGTGGTCCAA	59.224	40.000	0.00	0.00	40.48	3.53
1461	1955	5.470777	CACACAGTCGGGTAAATAAAAGGAA	59.529	40.000	0.00	0.00	0.00	3.36
1487	1981	1.064758	TGACAAAGCCGGATGCCTTAT	60.065	47.619	5.05	0.00	42.71	1.73
1548	2042	7.175641	AGCTCAATACTTTCTTTGTACAATGCT	59.824	33.333	9.56	0.00	0.00	3.79
1551	2045	7.148407	CCGAGCTCAATACTTTCTTTGTACAAT	60.148	37.037	15.40	0.00	0.00	2.71
1726	2220	0.179059	ACATCTTCACACCGTGCACA	60.179	50.000	18.64	0.00	32.98	4.57
1753	2247	4.373116	GCGTCCGAAGAGTGGGCA	62.373	66.667	0.00	0.00	0.00	5.36
1756	2250	4.421479	AGCGCGTCCGAAGAGTGG	62.421	66.667	8.43	0.00	36.29	4.00
1758	2252	2.214181	AATGAGCGCGTCCGAAGAGT	62.214	55.000	8.43	0.00	36.29	3.24
1759	2253	1.517257	AATGAGCGCGTCCGAAGAG	60.517	57.895	8.43	0.00	36.29	2.85
1761	2255	0.800683	TACAATGAGCGCGTCCGAAG	60.801	55.000	8.43	0.00	36.29	3.79
1762	2256	0.179121	ATACAATGAGCGCGTCCGAA	60.179	50.000	8.43	0.00	36.29	4.30
1789	2284	1.004277	GGTAGGTGCCATCTGGAAACA	59.996	52.381	0.00	0.00	30.59	2.83
1797	2292	2.224606	CATGTCATGGTAGGTGCCATC	58.775	52.381	4.78	0.00	45.47	3.51
1836	2331	4.067896	CCATGTCATATCCTACTTGGCAC	58.932	47.826	0.00	0.00	35.09	5.01
1850	2345	3.493334	CATACTGATTGGGCCATGTCAT	58.507	45.455	18.82	5.43	0.00	3.06
1862	2357	6.465894	GCCCATCTAAACTACCCATACTGATT	60.466	42.308	0.00	0.00	0.00	2.57
1925	2420	4.213564	ACTAGCTTTTGAGATGGACCAG	57.786	45.455	0.00	0.00	0.00	4.00
1989	2489	2.957006	TCAAGTAGTCTAATCGCCTCCC	59.043	50.000	0.00	0.00	0.00	4.30
1992	2492	3.362706	TGGTCAAGTAGTCTAATCGCCT	58.637	45.455	0.00	0.00	0.00	5.52
2026	2535	6.223120	CCCACAAGTAAAATTGAGAAAAGGG	58.777	40.000	0.00	0.00	34.20	3.95
2086	2595	3.325293	ACTCTTAGACCTGCATGTGTG	57.675	47.619	0.00	0.00	0.00	3.82
2125	2634	7.990886	CCCTCCTTTACTTACATATGCAAAGTA	59.009	37.037	19.77	19.77	35.23	2.24
2210	2719	2.309528	ATGTGGACGTACGATTGCAT	57.690	45.000	24.41	16.50	0.00	3.96
2214	2723	3.118920	TCCATCAATGTGGACGTACGATT	60.119	43.478	24.41	7.83	43.20	3.34
2265	2774	4.329545	GCCCTCCGTGGACTTGCA	62.330	66.667	0.00	0.00	38.35	4.08
2268	2777	3.003763	GGAGCCCTCCGTGGACTT	61.004	66.667	0.00	0.00	40.36	3.01
2317	2826	3.980022	TCATAAGCCATGGTGGAATAGGA	59.020	43.478	14.67	4.39	40.96	2.94
2385	2894	4.261801	GAGTTTGTAAGGGCAAGCAGATA	58.738	43.478	0.00	0.00	33.01	1.98
2421	2930	1.965414	TTGGGAGCCTCCAAGATGTA	58.035	50.000	13.90	0.00	41.44	2.29
2495	3009	1.376543	CAAGGCGTTCATCATCAGCT	58.623	50.000	0.00	0.00	0.00	4.24
2509	3023	0.886563	ATGAAGCACAAGAGCAAGGC	59.113	50.000	0.00	0.00	36.85	4.35
2528	3042	4.878968	TGAGTGTTGGGGAGACTATCATA	58.121	43.478	0.00	0.00	30.90	2.15
2593	3107	1.821216	TCCCCAAGTTGCTTTCGATC	58.179	50.000	0.00	0.00	0.00	3.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.