AutoCloner

Multiple sequence alignment - TraesCS7A01G023600

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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	TraesCS7A01G023600	chr7A	100.000	2771	0	0	1	2771	9363144	9365914	0.000000e+00	5118
1	TraesCS7A01G023600	chr7A	91.885	1528	84	16	673	2166	9683680	9682159	0.000000e+00	2098
2	TraesCS7A01G023600	chr7A	93.935	676	40	1	1	675	711925199	711924524	0.000000e+00	1020
3	TraesCS7A01G023600	chr7A	91.888	678	32	4	1	675	169967426	169968083	0.000000e+00	926
4	TraesCS7A01G023600	chr7A	93.727	542	25	3	1	540	61568358	61567824	0.000000e+00	804
5	TraesCS7A01G023600	chr7A	91.169	385	26	2	2149	2532	9682145	9681768	1.470000e-142	516
6	TraesCS7A01G023600	chr7A	91.561	237	20	0	2535	2771	9681733	9681497	7.400000e-86	327
7	TraesCS7A01G023600	chr7A	96.992	133	4	0	2639	2771	9378403	9378535	9.990000e-55	224
8	TraesCS7A01G023600	chr4A	87.901	1901	151	26	671	2532	729152243	729154103	0.000000e+00	2163
9	TraesCS7A01G023600	chr4A	90.495	1536	111	12	673	2181	729654194	729655721	0.000000e+00	1995
10	TraesCS7A01G023600	chr4A	91.014	1380	109	8	673	2042	729798552	729799926	0.000000e+00	1847
11	TraesCS7A01G023600	chr4A	89.984	1278	96	15	1242	2503	729120520	729119259	0.000000e+00	1622
12	TraesCS7A01G023600	chr4A	90.488	1209	98	15	673	1874	729213244	729214442	0.000000e+00	1580
13	TraesCS7A01G023600	chr4A	87.509	1345	105	22	1457	2763	729921293	729922612	0.000000e+00	1495
14	TraesCS7A01G023600	chr4A	85.853	926	83	20	1867	2769	729214771	729215671	0.000000e+00	941
15	TraesCS7A01G023600	chr4A	89.911	674	50	9	673	1328	729857252	729857925	0.000000e+00	852
16	TraesCS7A01G023600	chr4A	84.772	591	58	9	673	1247	730007200	730006626	5.180000e-157	564
17	TraesCS7A01G023600	chr4A	84.630	540	40	15	678	1179	729920388	729920922	5.330000e-137	497
18	TraesCS7A01G023600	chr4A	88.283	367	34	4	2168	2532	729657063	729657422	5.480000e-117	431
19	TraesCS7A01G023600	chr4A	89.873	237	20	1	2535	2771	729154138	729154370	4.490000e-78	302
20	TraesCS7A01G023600	chr4A	80.201	298	39	10	1763	2048	728834112	728834401	3.620000e-49	206
21	TraesCS7A01G023600	chr4A	84.259	216	19	1	947	1147	729023459	729023244	2.180000e-46	196
22	TraesCS7A01G023600	chr7D	90.217	1615	94	17	673	2269	10056718	10058286	0.000000e+00	2049
23	TraesCS7A01G023600	chr7D	97.041	676	19	1	1	675	22089255	22089930	0.000000e+00	1136
24	TraesCS7A01G023600	chr2D	96.746	676	21	1	1	675	577713473	577714148	0.000000e+00	1125
25	TraesCS7A01G023600	chr2D	81.356	944	146	20	832	1757	564438276	564439207	0.000000e+00	741
26	TraesCS7A01G023600	chr2D	80.810	839	141	13	931	1757	564476237	564477067	8.370000e-180	640
27	TraesCS7A01G023600	chr6B	95.562	676	29	1	1	675	679325020	679325695	0.000000e+00	1081
28	TraesCS7A01G023600	chr6B	95.741	540	23	0	1	540	679290341	679289802	0.000000e+00	870
29	TraesCS7A01G023600	chr3A	94.222	675	38	1	1	675	594646297	594645624	0.000000e+00	1029
30	TraesCS7A01G023600	chr3B	93.074	592	35	4	89	675	829507552	829508142	0.000000e+00	861
31	TraesCS7A01G023600	chr3B	92.593	594	34	7	92	680	434416929	434416341	0.000000e+00	845
32	TraesCS7A01G023600	chrUn	89.623	106	7	2	1	106	183983495	183983596	6.230000e-27	132

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	TraesCS7A01G023600	chr7A	9363144	9365914	2770	False	5118.000000	5118	100.000000	1	2771	1	chr7A.!!$F1	2770
1	TraesCS7A01G023600	chr7A	711924524	711925199	675	True	1020.000000	1020	93.935000	1	675	1	chr7A.!!$R2	674
2	TraesCS7A01G023600	chr7A	9681497	9683680	2183	True	980.333333	2098	91.538333	673	2771	3	chr7A.!!$R3	2098
3	TraesCS7A01G023600	chr7A	169967426	169968083	657	False	926.000000	926	91.888000	1	675	1	chr7A.!!$F3	674
4	TraesCS7A01G023600	chr7A	61567824	61568358	534	True	804.000000	804	93.727000	1	540	1	chr7A.!!$R1	539
5	TraesCS7A01G023600	chr4A	729798552	729799926	1374	False	1847.000000	1847	91.014000	673	2042	1	chr4A.!!$F2	1369
6	TraesCS7A01G023600	chr4A	729119259	729120520	1261	True	1622.000000	1622	89.984000	1242	2503	1	chr4A.!!$R2	1261
7	TraesCS7A01G023600	chr4A	729213244	729215671	2427	False	1260.500000	1580	88.170500	673	2769	2	chr4A.!!$F5	2096
8	TraesCS7A01G023600	chr4A	729152243	729154370	2127	False	1232.500000	2163	88.887000	671	2771	2	chr4A.!!$F4	2100
9	TraesCS7A01G023600	chr4A	729654194	729657422	3228	False	1213.000000	1995	89.389000	673	2532	2	chr4A.!!$F6	1859
10	TraesCS7A01G023600	chr4A	729920388	729922612	2224	False	996.000000	1495	86.069500	678	2763	2	chr4A.!!$F7	2085
11	TraesCS7A01G023600	chr4A	729857252	729857925	673	False	852.000000	852	89.911000	673	1328	1	chr4A.!!$F3	655
12	TraesCS7A01G023600	chr4A	730006626	730007200	574	True	564.000000	564	84.772000	673	1247	1	chr4A.!!$R3	574
13	TraesCS7A01G023600	chr7D	10056718	10058286	1568	False	2049.000000	2049	90.217000	673	2269	1	chr7D.!!$F1	1596
14	TraesCS7A01G023600	chr7D	22089255	22089930	675	False	1136.000000	1136	97.041000	1	675	1	chr7D.!!$F2	674
15	TraesCS7A01G023600	chr2D	577713473	577714148	675	False	1125.000000	1125	96.746000	1	675	1	chr2D.!!$F3	674
16	TraesCS7A01G023600	chr2D	564438276	564439207	931	False	741.000000	741	81.356000	832	1757	1	chr2D.!!$F1	925
17	TraesCS7A01G023600	chr2D	564476237	564477067	830	False	640.000000	640	80.810000	931	1757	1	chr2D.!!$F2	826
18	TraesCS7A01G023600	chr6B	679325020	679325695	675	False	1081.000000	1081	95.562000	1	675	1	chr6B.!!$F1	674
19	TraesCS7A01G023600	chr6B	679289802	679290341	539	True	870.000000	870	95.741000	1	540	1	chr6B.!!$R1	539
20	TraesCS7A01G023600	chr3A	594645624	594646297	673	True	1029.000000	1029	94.222000	1	675	1	chr3A.!!$R1	674
21	TraesCS7A01G023600	chr3B	829507552	829508142	590	False	861.000000	861	93.074000	89	675	1	chr3B.!!$F1	586
22	TraesCS7A01G023600	chr3B	434416341	434416929	588	True	845.000000	845	92.593000	92	680	1	chr3B.!!$R1	588

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
267	269	0.030101	TGGCGGAAAAAGCTTCAACG	59.970	50.000	0.00	3.89	34.52	4.10	F
1436	1685	1.001706	TGTCGAGTTTGACACGAGGAG	60.002	52.381	1.03	0.00	43.62	3.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1709	1958	1.110442	CAGTTGGGTGAAGTTGGCAA	58.890	50.0	0.0	0.0	0.0	4.52	R
2446	4450	0.603569	ACTCATTTCCGACGACAGCT	59.396	50.0	0.0	0.0	0.0	4.24	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
201	203	3.127533	GGCGCCGATGCTTCAACT	61.128	61.111	12.58	0.00	34.43	3.16
267	269	0.030101	TGGCGGAAAAAGCTTCAACG	59.970	50.000	0.00	3.89	34.52	4.10
303	305	3.250617	AGCTTCAACCCCCATGAAAAAT	58.749	40.909	0.00	0.00	36.43	1.82
447	456	4.640690	AGAGGACGGGGGTGCTGT	62.641	66.667	0.00	0.00	0.00	4.40
554	564	1.617947	GGATCTGAAGCGTGGGGAGT	61.618	60.000	0.00	0.00	0.00	3.85
577	588	6.097554	AGTGAGGAAGAAGATGATATGACGTT	59.902	38.462	0.00	0.00	0.00	3.99
655	667	2.739784	CAAATTTGGGCCGGTGCA	59.260	55.556	10.49	0.00	40.13	4.57
683	696	3.016736	CGTATCACTGCCCCTTTTCATT	58.983	45.455	0.00	0.00	0.00	2.57
736	751	5.449041	CGCATAGTCAAACATATTGCTGGTT	60.449	40.000	0.00	0.00	0.00	3.67
762	777	4.488518	GCATATGTCACAACATTTTGCG	57.511	40.909	4.29	0.00	43.74	4.85
803	834	1.614903	CATTGGGCTGTTTCTCTGCAA	59.385	47.619	0.00	0.00	41.72	4.08
951	998	4.714308	ACTCCTCTATCTTGAGAAGGTTGG	59.286	45.833	0.00	0.00	36.23	3.77
1005	1059	3.636300	TGCCCAATACCAATAGCATGTTC	59.364	43.478	0.00	0.00	0.00	3.18
1092	1174	2.293122	TCCCAACTTCAACGCAATCAAG	59.707	45.455	0.00	0.00	0.00	3.02
1347	1596	1.626686	ATCCATCGTTGCCCAACAAA	58.373	45.000	11.27	0.00	40.82	2.83
1436	1685	1.001706	TGTCGAGTTTGACACGAGGAG	60.002	52.381	1.03	0.00	43.62	3.69
1534	1783	5.760253	CCGCTTAGTAATGTTTCCATCATCT	59.240	40.000	0.00	0.00	0.00	2.90
1620	1869	6.476378	AGTATTTCTAGTCCAACACAGCATT	58.524	36.000	0.00	0.00	0.00	3.56
1632	1881	2.173669	CAGCATTCGTGGGCGGTAG	61.174	63.158	0.00	0.00	38.89	3.18
1635	1884	1.813753	CATTCGTGGGCGGTAGGTG	60.814	63.158	0.00	0.00	38.89	4.00
1709	1958	3.737559	TCTGGTATTTGCAGGTTCCAT	57.262	42.857	3.87	0.00	0.00	3.41
1712	1961	2.233431	TGGTATTTGCAGGTTCCATTGC	59.767	45.455	0.00	0.00	40.67	3.56
1878	2464	2.292267	ACACAACAGTTTCTGCTCCAG	58.708	47.619	0.00	0.00	34.37	3.86
2069	2659	3.525199	AGGACCTATCAAACCAATGCTCT	59.475	43.478	0.00	0.00	0.00	4.09
2072	2672	4.265073	ACCTATCAAACCAATGCTCTGAC	58.735	43.478	0.00	0.00	0.00	3.51
2202	4191	9.713740	GATTGCTTGTTGATCTACATTAAGAAG	57.286	33.333	10.81	5.59	33.98	2.85
2273	4263	2.927004	ACGAAACATCGTGTGCCAT	58.073	47.368	2.72	0.00	45.30	4.40
2274	4264	1.234821	ACGAAACATCGTGTGCCATT	58.765	45.000	2.72	0.00	45.30	3.16
2275	4265	1.196808	ACGAAACATCGTGTGCCATTC	59.803	47.619	2.72	0.00	45.30	2.67
2276	4266	1.196581	CGAAACATCGTGTGCCATTCA	59.803	47.619	0.00	0.00	0.00	2.57
2277	4267	2.350293	CGAAACATCGTGTGCCATTCAA	60.350	45.455	0.00	0.00	0.00	2.69
2278	4268	2.704725	AACATCGTGTGCCATTCAAC	57.295	45.000	0.00	0.00	0.00	3.18
2279	4269	1.896220	ACATCGTGTGCCATTCAACT	58.104	45.000	0.00	0.00	0.00	3.16
2307	4298	7.704472	TCAACTAAAAATTGTTGGTCATGACAC	59.296	33.333	26.47	17.29	42.48	3.67
2435	4439	2.803030	TCTAGCTTACCGACCTGTCT	57.197	50.000	0.00	0.00	0.00	3.41
2446	4450	4.533815	ACCGACCTGTCTGAATCTATGTA	58.466	43.478	0.00	0.00	0.00	2.29
2478	4483	4.322567	GGAAATGAGTGAAGCTTCTGACT	58.677	43.478	26.09	21.28	0.00	3.41
2504	4509	4.336713	ACCTGAAGTCTGAAGCTTTTCAAC	59.663	41.667	10.78	3.76	0.00	3.18
2508	4513	5.357878	TGAAGTCTGAAGCTTTTCAACACAT	59.642	36.000	0.00	0.00	0.00	3.21
2597	4634	2.696707	ACTTACTGACTTGTCCGAACCA	59.303	45.455	0.00	0.00	0.00	3.67
2659	4696	3.497884	GACACCCAACCTGCCAGCT	62.498	63.158	0.00	0.00	0.00	4.24
2684	4721	3.138625	CACCACCACACCGTCTCT	58.861	61.111	0.00	0.00	0.00	3.10
2698	4735	3.000727	CCGTCTCTACACAATTTCACCC	58.999	50.000	0.00	0.00	0.00	4.61
2700	4737	3.306780	CGTCTCTACACAATTTCACCCCT	60.307	47.826	0.00	0.00	0.00	4.79
2709	4746	0.609131	ATTTCACCCCTGCTTCACCG	60.609	55.000	0.00	0.00	0.00	4.94
2732	4769	3.287445	GCCATGCCAACCAATCGT	58.713	55.556	0.00	0.00	0.00	3.73

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
16	17	4.201970	CGGTTGTAGCAAAAAGAAACTCCA	60.202	41.667	0.00	0.00	0.00	3.86
48	49	1.339055	GCACTGCCAGTTCTACCATCA	60.339	52.381	0.00	0.00	0.00	3.07
53	54	0.319555	TGTCGCACTGCCAGTTCTAC	60.320	55.000	0.00	0.00	0.00	2.59
125	127	1.204704	GTAGCAAAAACAGGATGGGGC	59.795	52.381	0.00	0.00	43.62	5.80
128	130	2.231235	GGTGGTAGCAAAAACAGGATGG	59.769	50.000	0.00	0.00	43.62	3.51
267	269	2.825532	TGAAGCTTTTTCCACTATGCCC	59.174	45.455	0.00	0.00	0.00	5.36
303	305	1.611491	GCATTTTTCCACGGGTGAAGA	59.389	47.619	0.00	0.00	0.00	2.87
447	456	4.043100	TCCTCTCCCTCGCCGTCA	62.043	66.667	0.00	0.00	0.00	4.35
532	542	0.816825	CCCCACGCTTCAGATCCATG	60.817	60.000	0.00	0.00	0.00	3.66
554	564	6.276091	CAACGTCATATCATCTTCTTCCTCA	58.724	40.000	0.00	0.00	0.00	3.86
683	696	4.408921	TCACCTTCTTTTCACAAGAGAGGA	59.591	41.667	14.54	0.00	33.14	3.71
736	751	7.471721	GCAAAATGTTGTGACATATGCTACTA	58.528	34.615	16.48	0.00	45.58	1.82
803	834	5.149976	AGCCTGGGATAATATTTGTGCAAT	58.850	37.500	0.00	0.00	0.00	3.56
936	981	3.308046	GCTTCCTCCAACCTTCTCAAGAT	60.308	47.826	0.00	0.00	0.00	2.40
951	998	5.935206	GCTAAATGGTTCCTATAGCTTCCTC	59.065	44.000	0.00	0.00	36.81	3.71
1005	1059	3.125316	GGACGACAATACAGGAAAAGCTG	59.875	47.826	0.00	0.00	0.00	4.24
1046	1128	2.781945	AAACTGCAAGCAACTACAGC	57.218	45.000	0.00	0.00	37.60	4.40
1092	1174	3.317430	GGCTGAAGGTGAAATCATCCATC	59.683	47.826	0.00	0.00	33.18	3.51
1395	1644	3.381908	CAGCTACTACTGGATCCGTCTTT	59.618	47.826	7.39	0.00	33.85	2.52
1404	1653	2.783609	ACTCGACAGCTACTACTGGA	57.216	50.000	0.00	0.00	42.21	3.86
1436	1685	2.968574	TCAAGGTCATCCTCATAGCTCC	59.031	50.000	0.00	0.00	44.35	4.70
1460	1709	3.605013	TCGATGCCGATATGGTTGG	57.395	52.632	0.00	0.00	40.30	3.77
1534	1783	4.080919	CCATACATCAGACCCACTTGAGAA	60.081	45.833	0.00	0.00	0.00	2.87
1620	1869	2.035469	TACACCTACCGCCCACGA	59.965	61.111	0.00	0.00	43.93	4.35
1632	1881	6.919775	ATGTAGATATCTCCTTGGTACACC	57.080	41.667	8.95	0.00	39.29	4.16
1635	1884	9.030452	AGATCAATGTAGATATCTCCTTGGTAC	57.970	37.037	8.95	0.36	0.00	3.34
1709	1958	1.110442	CAGTTGGGTGAAGTTGGCAA	58.890	50.000	0.00	0.00	0.00	4.52
1712	1961	1.681264	GGTTCAGTTGGGTGAAGTTGG	59.319	52.381	0.00	0.00	37.12	3.77
1878	2464	2.962421	CTCATGAGGGAAGTAGAGGTCC	59.038	54.545	15.38	0.00	0.00	4.46
2069	2659	4.471904	AGGACATGCTAAGAAATCGTCA	57.528	40.909	0.00	0.00	0.00	4.35
2173	2807	6.690194	AATGTAGATCAACAAGCAATCTCC	57.310	37.500	0.00	0.00	32.25	3.71
2202	4191	6.763355	TGTCTAGAATCCTATTGCAATCTCC	58.237	40.000	16.86	0.95	0.00	3.71
2273	4263	9.495572	ACCAACAATTTTTAGTTGAAAGTTGAA	57.504	25.926	11.01	0.00	46.01	2.69
2274	4264	9.145865	GACCAACAATTTTTAGTTGAAAGTTGA	57.854	29.630	11.01	0.00	46.01	3.18
2275	4265	8.930760	TGACCAACAATTTTTAGTTGAAAGTTG	58.069	29.630	7.71	0.00	46.01	3.16
2276	4266	9.665719	ATGACCAACAATTTTTAGTTGAAAGTT	57.334	25.926	7.71	0.00	46.01	2.66
2277	4267	9.097257	CATGACCAACAATTTTTAGTTGAAAGT	57.903	29.630	7.71	0.00	46.01	2.66
2278	4268	9.311916	TCATGACCAACAATTTTTAGTTGAAAG	57.688	29.630	7.71	0.00	46.01	2.62
2279	4269	9.092876	GTCATGACCAACAATTTTTAGTTGAAA	57.907	29.630	15.31	0.00	46.01	2.69
2297	4287	5.138125	ACAAATTGAATGGTGTCATGACC	57.862	39.130	22.85	13.66	36.43	4.02
2307	4298	3.899734	TCGAGCACAACAAATTGAATGG	58.100	40.909	0.00	0.00	39.30	3.16
2417	4421	2.366533	TCAGACAGGTCGGTAAGCTAG	58.633	52.381	0.00	0.00	33.36	3.42
2435	4439	3.003378	CCGACGACAGCTACATAGATTCA	59.997	47.826	0.00	0.00	0.00	2.57
2446	4450	0.603569	ACTCATTTCCGACGACAGCT	59.396	50.000	0.00	0.00	0.00	4.24
2478	4483	4.689612	AAAGCTTCAGACTTCAGGTACA	57.310	40.909	0.00	0.00	0.00	2.90
2504	4509	5.909621	AGGAATTGAAGATGTTGGATGTG	57.090	39.130	0.00	0.00	0.00	3.21
2532	4537	9.289303	CTGGTATTTCTCGAACCATTTATTTTG	57.711	33.333	6.38	0.00	42.23	2.44
2533	4538	7.973944	GCTGGTATTTCTCGAACCATTTATTTT	59.026	33.333	6.38	0.00	42.23	1.82
2541	4578	3.334691	CAAGCTGGTATTTCTCGAACCA	58.665	45.455	5.81	5.81	40.94	3.67
2597	4634	2.238646	TGACCTATTTCCAGCGACCATT	59.761	45.455	0.00	0.00	0.00	3.16
2640	4677	2.839098	CTGGCAGGTTGGGTGTCT	59.161	61.111	6.61	0.00	0.00	3.41
2684	4721	2.969821	AGCAGGGGTGAAATTGTGTA	57.030	45.000	0.00	0.00	0.00	2.90
2698	4735	2.956987	CCAAAGCGGTGAAGCAGG	59.043	61.111	0.00	0.00	40.15	4.85
2700	4737	3.294493	GGCCAAAGCGGTGAAGCA	61.294	61.111	0.00	0.00	41.24	3.91

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.