AutoCloner

Multiple sequence alignment - TraesCS4B01G382400

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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	TraesCS4B01G382400	chr4B	100.000	3440	0	0	1	3440	661683247	661679808	0.000000e+00	6353
1	TraesCS4B01G382400	chr4B	94.765	1872	82	9	1538	3393	661495189	661497060	0.000000e+00	2900
2	TraesCS4B01G382400	chr4B	92.908	1551	110	0	1	1551	661493610	661495160	0.000000e+00	2255
3	TraesCS4B01G382400	chr4D	90.356	2416	198	14	1	2412	505991996	505989612	0.000000e+00	3138
4	TraesCS4B01G382400	chr4D	90.909	528	22	2	2606	3133	505989616	505989115	0.000000e+00	686
5	TraesCS4B01G382400	chr4D	91.159	328	10	5	3131	3440	505989063	505988737	8.820000e-116	427
6	TraesCS4B01G382400	chr5A	89.387	2318	204	14	1	2311	702140924	702138642	0.000000e+00	2880
7	TraesCS4B01G382400	chr5A	90.833	1200	60	15	2284	3440	702138629	702137437	0.000000e+00	1561
8	TraesCS4B01G382400	chrUn	78.282	1409	244	45	892	2273	88950109	88951482	0.000000e+00	850
9	TraesCS4B01G382400	chrUn	78.282	1409	244	45	892	2273	269543288	269541915	0.000000e+00	850
10	TraesCS4B01G382400	chrUn	77.999	1409	248	46	892	2273	88958458	88959831	0.000000e+00	828
11	TraesCS4B01G382400	chr7B	78.236	1406	240	39	1703	3067	746551792	746550412	0.000000e+00	841
12	TraesCS4B01G382400	chr7B	78.293	1336	242	26	823	2129	746601411	746600095	0.000000e+00	817
13	TraesCS4B01G382400	chr7B	78.219	1336	243	26	823	2129	746573103	746571787	0.000000e+00	811
14	TraesCS4B01G382400	chr7B	81.293	882	153	10	1732	2605	746223791	746224668	0.000000e+00	704
15	TraesCS4B01G382400	chr7B	81.330	857	151	9	1732	2582	746568813	746567960	0.000000e+00	688
16	TraesCS4B01G382400	chr7B	81.330	857	151	9	1732	2582	746597141	746596288	0.000000e+00	688
17	TraesCS4B01G382400	chr7B	81.235	858	152	8	1732	2582	744679438	744678583	0.000000e+00	684
18	TraesCS4B01G382400	chr7B	77.778	279	48	13	2706	2975	746228644	746228917	3.550000e-35	159
19	TraesCS4B01G382400	chr7B	78.919	185	31	5	3251	3434	746215743	746215920	6.030000e-23	119
20	TraesCS4B01G382400	chr7A	77.861	1328	239	40	1709	3006	735061301	735059999	0.000000e+00	773
21	TraesCS4B01G382400	chr7A	77.312	1406	255	37	1703	3067	735058398	735057016	0.000000e+00	771
22	TraesCS4B01G382400	chr7A	80.208	192	31	4	3239	3429	735053566	735053381	1.660000e-28	137

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	TraesCS4B01G382400	chr4B	661679808	661683247	3439	True	6353.000000	6353	100.000000	1	3440	1	chr4B.!!$R1	3439
1	TraesCS4B01G382400	chr4B	661493610	661497060	3450	False	2577.500000	2900	93.836500	1	3393	2	chr4B.!!$F1	3392
2	TraesCS4B01G382400	chr4D	505988737	505991996	3259	True	1417.000000	3138	90.808000	1	3440	3	chr4D.!!$R1	3439
3	TraesCS4B01G382400	chr5A	702137437	702140924	3487	True	2220.500000	2880	90.110000	1	3440	2	chr5A.!!$R1	3439
4	TraesCS4B01G382400	chrUn	88950109	88951482	1373	False	850.000000	850	78.282000	892	2273	1	chrUn.!!$F1	1381
5	TraesCS4B01G382400	chrUn	269541915	269543288	1373	True	850.000000	850	78.282000	892	2273	1	chrUn.!!$R1	1381
6	TraesCS4B01G382400	chrUn	88958458	88959831	1373	False	828.000000	828	77.999000	892	2273	1	chrUn.!!$F2	1381
7	TraesCS4B01G382400	chr7B	746550412	746551792	1380	True	841.000000	841	78.236000	1703	3067	1	chr7B.!!$R2	1364
8	TraesCS4B01G382400	chr7B	746596288	746601411	5123	True	752.500000	817	79.811500	823	2582	2	chr7B.!!$R4	1759
9	TraesCS4B01G382400	chr7B	746567960	746573103	5143	True	749.500000	811	79.774500	823	2582	2	chr7B.!!$R3	1759
10	TraesCS4B01G382400	chr7B	744678583	744679438	855	True	684.000000	684	81.235000	1732	2582	1	chr7B.!!$R1	850
11	TraesCS4B01G382400	chr7B	746223791	746228917	5126	False	431.500000	704	79.535500	1732	2975	2	chr7B.!!$F2	1243
12	TraesCS4B01G382400	chr7A	735053381	735061301	7920	True	560.333333	773	78.460333	1703	3429	3	chr7A.!!$R1	1726

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
687	688	0.242825	CGACCGACTACCTCTTTGCA	59.757	55.0	0.0	0.0	0.00	4.08	F
1977	2069	0.031178	GCAGCCAAAGTGGAACAGTG	59.969	55.0	0.0	0.0	43.84	3.66	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2202	5671	0.321298	TTCCTTGCAGCCCGAAGTAC	60.321	55.0	0.0	0.0	0.00	2.73	R
3100	16368	0.105039	GTCATAGGACCAAGAGCCGG	59.895	60.0	0.0	0.0	38.12	6.13	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
46	47	3.247173	GGCTAATGTGCTCTCATCGAAAG	59.753	47.826	0.00	0.00	0.00	2.62
90	91	3.818787	GCCATCAGCGCCAACCAG	61.819	66.667	2.29	0.00	0.00	4.00
118	119	1.935873	CATCATCAATGCCGTCGTTCT	59.064	47.619	0.00	0.00	0.00	3.01
174	175	2.288763	TGTGTGCATCGTTAAGAGCTCA	60.289	45.455	17.77	0.00	0.00	4.26
213	214	3.957586	CTCCAGGCCACACCAGCA	61.958	66.667	5.01	0.00	43.14	4.41
283	284	0.253044	TATCTCCAACCAGCTGCCAC	59.747	55.000	8.66	0.00	0.00	5.01
286	287	4.954970	CCAACCAGCTGCCACGGT	62.955	66.667	8.66	0.00	33.32	4.83
287	288	3.357079	CAACCAGCTGCCACGGTC	61.357	66.667	8.66	0.00	30.91	4.79
328	329	2.516227	AGACCACTCCTTCTCATCGA	57.484	50.000	0.00	0.00	0.00	3.59
333	334	1.064803	CACTCCTTCTCATCGACCTCG	59.935	57.143	0.00	0.00	41.45	4.63
342	343	2.422479	CTCATCGACCTCGTCCTTTGTA	59.578	50.000	0.00	0.00	40.80	2.41
349	350	4.320788	CGACCTCGTCCTTTGTAAGTAACT	60.321	45.833	0.00	0.00	34.11	2.24
373	374	4.285517	AGGACAGTGTTTCTCATCTCATGT	59.714	41.667	0.00	0.00	0.00	3.21
378	379	6.017605	ACAGTGTTTCTCATCTCATGTTTGAC	60.018	38.462	0.00	0.00	0.00	3.18
474	475	0.899717	ATTTCAGGGTGCCACGCAAT	60.900	50.000	14.73	2.61	41.47	3.56
491	492	3.244215	CGCAATAGCCTCCTATCAAAGGA	60.244	47.826	0.00	0.00	45.04	3.36
572	573	0.940126	GATAATGTGCAGTGGGCTCG	59.060	55.000	0.00	0.00	45.15	5.03
659	660	3.454375	GGATTTATGACGGCTTCTTCGA	58.546	45.455	0.00	0.00	0.00	3.71
687	688	0.242825	CGACCGACTACCTCTTTGCA	59.757	55.000	0.00	0.00	0.00	4.08
735	736	1.118965	TCAAGGGTGTGCTCTCGGAA	61.119	55.000	0.00	0.00	0.00	4.30
741	742	1.197721	GGTGTGCTCTCGGAAAACATG	59.802	52.381	0.00	0.00	0.00	3.21
742	743	2.143122	GTGTGCTCTCGGAAAACATGA	58.857	47.619	0.00	0.00	0.00	3.07
760	761	0.445436	GAAGTGCAATGAGCCGACAG	59.555	55.000	0.00	0.00	44.83	3.51
801	802	1.213678	TCCCTGAATGGAGGCAATCAG	59.786	52.381	0.00	0.00	39.16	2.90
844	845	2.939261	GCGAAGAGGGGTCGGACAA	61.939	63.158	10.76	0.00	38.93	3.18
882	883	1.217057	ATTCTGCCATGTCTGGGGGT	61.217	55.000	0.00	0.00	43.36	4.95
959	960	2.807676	GGAGGAGGCATTTTTCAAGGA	58.192	47.619	0.00	0.00	0.00	3.36
1045	1046	3.665675	ATGAAGGGCGAGGACGTGC	62.666	63.158	0.00	0.00	41.98	5.34
1057	1058	3.457234	GAGGACGTGCATGTGATGAATA	58.543	45.455	18.17	0.00	0.00	1.75
1122	1123	5.465390	CGATCTTAATAACATCCTCGGCAAA	59.535	40.000	0.00	0.00	0.00	3.68
1186	1227	1.121407	TGGCCTACAGTCTGTGCAGT	61.121	55.000	16.03	0.00	0.00	4.40
1191	1232	3.668447	CCTACAGTCTGTGCAGTTCAAT	58.332	45.455	16.03	0.00	0.00	2.57
1311	1352	1.272092	TGTGCTTCTTGGAATCTGGGG	60.272	52.381	0.00	0.00	0.00	4.96
1335	1376	5.011227	GGATACAGGAGGTAAAGAGGATCAC	59.989	48.000	0.00	0.00	34.15	3.06
1336	1377	3.791320	ACAGGAGGTAAAGAGGATCACA	58.209	45.455	0.00	0.00	37.82	3.58
1338	1379	3.772025	CAGGAGGTAAAGAGGATCACAGT	59.228	47.826	0.00	0.00	37.82	3.55
1347	1391	7.064728	GGTAAAGAGGATCACAGTTGAACATAC	59.935	40.741	0.00	0.00	37.82	2.39
1360	1404	5.007039	AGTTGAACATACTGATAGCAATGCG	59.993	40.000	0.00	0.00	0.00	4.73
1449	1495	3.531262	GGTACACACCAATCAAACGAC	57.469	47.619	0.00	0.00	45.04	4.34
1475	1521	5.129320	TCTCTTTTCTACTCCAGCATGCATA	59.871	40.000	21.98	3.30	31.97	3.14
1755	1846	4.917385	ACAATAGTGTTGTTCCTGCCATA	58.083	39.130	0.00	0.00	32.58	2.74
1925	2017	5.863965	TCCTGAAATGTCAATCTACACACA	58.136	37.500	0.00	0.00	31.88	3.72
1977	2069	0.031178	GCAGCCAAAGTGGAACAGTG	59.969	55.000	0.00	0.00	43.84	3.66
2052	5521	0.914644	CATCCCATCACTCCACCACT	59.085	55.000	0.00	0.00	0.00	4.00
2095	5564	2.519377	TTCCTAGTGTTGTCGTGTGG	57.481	50.000	0.00	0.00	0.00	4.17
2223	5692	1.302832	CTTCGGGCTGCAAGGAAGT	60.303	57.895	14.51	0.00	33.07	3.01
2282	5752	1.334869	CCTGTCTGCACAAACCAGTTC	59.665	52.381	0.00	0.00	29.82	3.01
2311	9699	2.839975	TGTTCGTAACTTCACATGCCA	58.160	42.857	0.00	0.00	0.00	4.92
2313	9701	3.628032	TGTTCGTAACTTCACATGCCAAA	59.372	39.130	0.00	0.00	0.00	3.28
2362	9750	3.200605	ACTGCTCAACATATCCCATGACA	59.799	43.478	0.00	0.00	0.00	3.58
2431	9819	2.457759	GGGAGGATGTGGAGATCCC	58.542	63.158	0.00	0.00	42.81	3.85
2487	9876	4.160439	TGTCCTCGCTTCATAGAGTTTCAT	59.840	41.667	0.00	0.00	32.88	2.57
2616	10006	1.678101	AGCAGGACTTTCAAAGCACAC	59.322	47.619	0.00	0.00	0.00	3.82
2835	16077	6.079424	TGTTATGTTTGTTCCTTTGCCTAC	57.921	37.500	0.00	0.00	0.00	3.18
2875	16117	5.968528	ATATTCCAGTACTAGAAGCCGAG	57.031	43.478	9.60	0.00	0.00	4.63
3085	16353	8.719596	TGGTATAAATATAAAAGCCTCCTCACA	58.280	33.333	0.00	0.00	0.00	3.58
3100	16368	4.199310	TCCTCACATTCGGAAATCCAATC	58.801	43.478	0.00	0.00	35.14	2.67
3214	16931	5.804944	ATTCACCATTTCCATGTTGTTCA	57.195	34.783	0.00	0.00	0.00	3.18
3349	17074	9.646427	GCCATACAATAACCAGACATTTTTAAA	57.354	29.630	0.00	0.00	0.00	1.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
46	47	3.198872	CGGATAAAGAGAAGAAGGGTGC	58.801	50.000	0.00	0.00	0.00	5.01
90	91	1.068748	GGCATTGATGATGATGTCGCC	60.069	52.381	0.00	0.00	38.03	5.54
118	119	3.018856	CCATCAACTCATTAAGCAGGCA	58.981	45.455	0.00	0.00	0.00	4.75
174	175	3.446570	GCAGCGGCAAAGGAGCAT	61.447	61.111	3.18	0.00	40.72	3.79
256	257	3.900601	AGCTGGTTGGAGATAGTGGATAG	59.099	47.826	0.00	0.00	0.00	2.08
283	284	2.511600	GGACATGAAGGCCGACCG	60.512	66.667	0.00	0.00	42.76	4.79
328	329	5.184671	CCTAGTTACTTACAAAGGACGAGGT	59.815	44.000	12.30	0.00	37.09	3.85
342	343	6.726490	TGAGAAACACTGTCCTAGTTACTT	57.274	37.500	0.00	0.00	37.60	2.24
349	350	5.481824	ACATGAGATGAGAAACACTGTCCTA	59.518	40.000	0.00	0.00	0.00	2.94
373	374	4.858680	TGTGGCGCCGTGGTCAAA	62.859	61.111	23.90	0.00	0.00	2.69
443	444	0.539051	CCTGAAATCGAGCCTGGAGT	59.461	55.000	0.00	0.00	0.00	3.85
543	544	1.498865	GCACATTATCGCTCGGTGGG	61.499	60.000	0.00	0.00	0.00	4.61
594	595	0.036010	CTGAGACCGCCACTTGGAAT	60.036	55.000	0.00	0.00	37.39	3.01
600	601	1.680651	CTCCTCTGAGACCGCCACT	60.681	63.158	6.17	0.00	41.42	4.00
659	660	0.669077	GTAGTCGGTCGCATCTGGAT	59.331	55.000	0.00	0.00	0.00	3.41
735	736	2.352030	CGGCTCATTGCACTTCATGTTT	60.352	45.455	0.00	0.00	45.15	2.83
741	742	0.445436	CTGTCGGCTCATTGCACTTC	59.555	55.000	0.00	0.00	45.15	3.01
742	743	1.580845	GCTGTCGGCTCATTGCACTT	61.581	55.000	0.00	0.00	45.15	3.16
760	761	5.298026	GGGAAAAGAGATGATTAGAAGTGGC	59.702	44.000	0.00	0.00	0.00	5.01
801	802	3.743886	CTTACGTTCAAATTTCGGGCTC	58.256	45.455	0.00	0.00	0.00	4.70
808	809	1.400500	CGCCGGCTTACGTTCAAATTT	60.400	47.619	26.68	0.00	42.24	1.82
844	845	3.721087	ATTGTCCTTCTCCGGATGTTT	57.279	42.857	3.57	0.00	35.11	2.83
882	883	0.616395	TCTGGTGTATCTTCGGGCCA	60.616	55.000	4.39	0.00	0.00	5.36
890	891	2.761208	CCGAGGACTTTCTGGTGTATCT	59.239	50.000	0.00	0.00	0.00	1.98
959	960	2.604686	TCGCACCCTCCTCTGCTT	60.605	61.111	0.00	0.00	0.00	3.91
1045	1046	3.999001	CTGTCCCCGATATTCATCACATG	59.001	47.826	0.00	0.00	0.00	3.21
1057	1058	2.697761	CGACACGACTGTCCCCGAT	61.698	63.158	1.55	0.00	43.64	4.18
1122	1123	0.674895	GCAGATCCTTCGGTGTTGCT	60.675	55.000	0.00	0.00	0.00	3.91
1186	1227	6.942005	ACAGAGGTATTGTGTTCATCATTGAA	59.058	34.615	0.00	0.00	39.54	2.69
1191	1232	5.863965	TCAACAGAGGTATTGTGTTCATCA	58.136	37.500	0.00	0.00	40.96	3.07
1311	1352	5.011227	GTGATCCTCTTTACCTCCTGTATCC	59.989	48.000	0.00	0.00	0.00	2.59
1335	1376	6.197276	GCATTGCTATCAGTATGTTCAACTG	58.803	40.000	0.16	0.00	44.66	3.16
1336	1377	5.007039	CGCATTGCTATCAGTATGTTCAACT	59.993	40.000	7.12	0.00	37.40	3.16
1338	1379	5.115480	TCGCATTGCTATCAGTATGTTCAA	58.885	37.500	7.12	0.00	37.40	2.69
1347	1391	3.124806	GTGGATGATCGCATTGCTATCAG	59.875	47.826	24.48	3.52	42.37	2.90
1360	1404	0.461548	TCACTCTGCCGTGGATGATC	59.538	55.000	0.00	0.00	35.63	2.92
1447	1493	3.057456	TGCTGGAGTAGAAAAGAGACGTC	60.057	47.826	7.70	7.70	0.00	4.34
1449	1495	3.577649	TGCTGGAGTAGAAAAGAGACG	57.422	47.619	0.00	0.00	0.00	4.18
1475	1521	1.278985	TGGTCGGAGATGTGCTTGAAT	59.721	47.619	0.00	0.00	40.67	2.57
1755	1846	8.137437	CAGTTTTTAGGTTCTTCATCAACATGT	58.863	33.333	0.00	0.00	0.00	3.21
1819	1910	6.647334	TCACAGTTTCAATGGCTTTCATAA	57.353	33.333	0.00	0.00	34.44	1.90
1925	2017	7.850935	AAATGAGCATCCCTTGAATTATCAT	57.149	32.000	0.00	0.00	34.96	2.45
1977	2069	3.460103	TCTTGAAGGACGGTAACAACAC	58.540	45.455	0.00	0.00	0.00	3.32
2029	2122	1.616725	GGTGGAGTGATGGGATGCAAA	60.617	52.381	0.00	0.00	0.00	3.68
2073	5542	3.186409	CCACACGACAACACTAGGAATTG	59.814	47.826	0.00	0.00	0.00	2.32
2075	5544	2.870435	GCCACACGACAACACTAGGAAT	60.870	50.000	0.00	0.00	0.00	3.01
2095	5564	3.060602	GTGAAATACTGATAGAGCCCGC	58.939	50.000	0.00	0.00	0.00	6.13
2202	5671	0.321298	TTCCTTGCAGCCCGAAGTAC	60.321	55.000	0.00	0.00	0.00	2.73
2282	5752	7.962934	TGTGAAGTTACGAACAATTTCAAAG	57.037	32.000	0.00	0.00	36.35	2.77
2362	9750	4.111577	TCATCATGGTACCTCCTCCTTTT	58.888	43.478	14.36	0.00	37.07	2.27
2398	9786	1.765314	CCTCCCCTTGAACGAGATCAT	59.235	52.381	0.00	0.00	0.00	2.45
2431	9819	2.014128	CCAACACTATGCCTAAACGGG	58.986	52.381	0.00	0.00	0.00	5.28
2487	9876	2.370519	TGCTCACTAGGCAACCAACTTA	59.629	45.455	0.00	0.00	36.71	2.24
2616	10006	0.667993	AGGTTGTTGTTCATGGTGCG	59.332	50.000	0.00	0.00	0.00	5.34
2762	15997	2.601240	TCTTTCCATCACCATTGCCA	57.399	45.000	0.00	0.00	0.00	4.92
2835	16077	5.349817	GGAATATAGCAATCTCGGTCATGTG	59.650	44.000	0.00	0.00	0.00	3.21
2875	16117	3.885521	GGCGCAGAGAAGCATGCC	61.886	66.667	15.66	0.00	39.30	4.40
3100	16368	0.105039	GTCATAGGACCAAGAGCCGG	59.895	60.000	0.00	0.00	38.12	6.13
3172	16494	5.366477	TGAATACAGAGTTCTGGATATGGCA	59.634	40.000	13.30	0.00	46.43	4.92

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.