AutoCloner

Multiple sequence alignment - TraesCS1A01G132000

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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	TraesCS1A01G132000	chr1A	100.000	3437	0	0	1	3437	177482768	177486204	0.000000e+00	6348
1	TraesCS1A01G132000	chr2A	94.163	3118	164	13	77	3182	133569940	133566829	0.000000e+00	4734
2	TraesCS1A01G132000	chr2A	88.889	261	24	1	3182	3437	133566761	133566501	1.990000e-82	316
3	TraesCS1A01G132000	chr2A	93.902	82	5	0	1	82	133570113	133570032	1.300000e-24	124
4	TraesCS1A01G132000	chr3A	93.175	3121	193	13	77	3182	98497564	98494449	0.000000e+00	4566
5	TraesCS1A01G132000	chr3A	96.156	2107	71	7	1085	3182	637987637	637989742	0.000000e+00	3434
6	TraesCS1A01G132000	chr3A	95.562	1014	39	5	77	1089	637968964	637969972	0.000000e+00	1618
7	TraesCS1A01G132000	chr3A	92.130	953	73	2	1806	2757	685704569	685705520	0.000000e+00	1343
8	TraesCS1A01G132000	chr3A	90.106	283	27	1	994	1276	685702064	685702345	1.950000e-97	366
9	TraesCS1A01G132000	chr3A	92.460	252	14	1	3191	3437	637989810	637990061	4.220000e-94	355
10	TraesCS1A01G132000	chr3A	89.961	259	21	1	3182	3435	98494381	98494123	2.560000e-86	329
11	TraesCS1A01G132000	chr3A	97.183	71	2	0	1	71	637968789	637968859	1.680000e-23	121
12	TraesCS1A01G132000	chr1B	90.672	1072	88	5	1546	2611	489899007	489897942	0.000000e+00	1415
13	TraesCS1A01G132000	chrUn	88.418	1062	112	6	1546	2597	333635356	333634296	0.000000e+00	1269
14	TraesCS1A01G132000	chrUn	88.418	1062	112	6	1546	2597	333654697	333653637	0.000000e+00	1269
15	TraesCS1A01G132000	chrUn	88.806	670	70	2	1932	2597	357107335	357106667	0.000000e+00	817
16	TraesCS1A01G132000	chr5A	90.839	906	67	9	1543	2442	246895013	246895908	0.000000e+00	1199
17	TraesCS1A01G132000	chr5A	90.618	437	39	2	840	1276	246893650	246894084	2.300000e-161	579
18	TraesCS1A01G132000	chr5A	90.698	172	16	0	358	529	246862782	246862611	2.670000e-56	230
19	TraesCS1A01G132000	chr5A	93.289	149	9	1	77	224	246862925	246862777	5.780000e-53	219
20	TraesCS1A01G132000	chr5A	88.953	172	19	0	358	529	246892691	246892862	2.690000e-51	213
21	TraesCS1A01G132000	chr5A	87.349	166	10	2	521	675	246862448	246862283	2.730000e-41	180
22	TraesCS1A01G132000	chr5A	96.117	103	3	1	123	224	246892594	246892696	2.120000e-37	167
23	TraesCS1A01G132000	chr5A	89.744	78	7	1	1	78	246863068	246862992	7.850000e-17	99
24	TraesCS1A01G132000	chr2B	93.217	575	38	1	1912	2486	795733135	795733708	0.000000e+00	845
25	TraesCS1A01G132000	chr2B	91.786	280	20	3	2491	2768	795737979	795738257	1.500000e-103	387
26	TraesCS1A01G132000	chr2B	89.394	264	20	3	3182	3437	795738917	795739180	3.310000e-85	326
27	TraesCS1A01G132000	chr2B	90.678	118	7	3	1243	1357	795732439	795732555	1.650000e-33	154
28	TraesCS1A01G132000	chr3B	87.874	602	63	8	1550	2144	684978292	684977694	0.000000e+00	699
29	TraesCS1A01G132000	chr7B	81.865	193	30	4	3176	3364	415332643	415332834	1.280000e-34	158

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	TraesCS1A01G132000	chr1A	177482768	177486204	3436	False	6348.000000	6348	100.00000	1	3437	1	chr1A.!!$F1	3436
1	TraesCS1A01G132000	chr2A	133566501	133570113	3612	True	1724.666667	4734	92.31800	1	3437	3	chr2A.!!$R1	3436
2	TraesCS1A01G132000	chr3A	98494123	98497564	3441	True	2447.500000	4566	91.56800	77	3435	2	chr3A.!!$R1	3358
3	TraesCS1A01G132000	chr3A	637987637	637990061	2424	False	1894.500000	3434	94.30800	1085	3437	2	chr3A.!!$F2	2352
4	TraesCS1A01G132000	chr3A	637968789	637969972	1183	False	869.500000	1618	96.37250	1	1089	2	chr3A.!!$F1	1088
5	TraesCS1A01G132000	chr3A	685702064	685705520	3456	False	854.500000	1343	91.11800	994	2757	2	chr3A.!!$F3	1763
6	TraesCS1A01G132000	chr1B	489897942	489899007	1065	True	1415.000000	1415	90.67200	1546	2611	1	chr1B.!!$R1	1065
7	TraesCS1A01G132000	chrUn	333634296	333635356	1060	True	1269.000000	1269	88.41800	1546	2597	1	chrUn.!!$R1	1051
8	TraesCS1A01G132000	chrUn	333653637	333654697	1060	True	1269.000000	1269	88.41800	1546	2597	1	chrUn.!!$R2	1051
9	TraesCS1A01G132000	chrUn	357106667	357107335	668	True	817.000000	817	88.80600	1932	2597	1	chrUn.!!$R3	665
10	TraesCS1A01G132000	chr5A	246892594	246895908	3314	False	539.500000	1199	91.63175	123	2442	4	chr5A.!!$F1	2319
11	TraesCS1A01G132000	chr2B	795732439	795733708	1269	False	499.500000	845	91.94750	1243	2486	2	chr2B.!!$F1	1243
12	TraesCS1A01G132000	chr2B	795737979	795739180	1201	False	356.500000	387	90.59000	2491	3437	2	chr2B.!!$F2	946
13	TraesCS1A01G132000	chr3B	684977694	684978292	598	True	699.000000	699	87.87400	1550	2144	1	chr3B.!!$R1	594

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
414	515	1.083401	GTGACAAACTCACGCGCTG	60.083	57.895	5.73	3.89	40.14	5.18	F
827	1124	1.307430	AAGGCCTCTTCTCCCTCCC	60.307	63.158	5.23	0.00	0.00	4.30	F
1186	1767	2.695147	ACCAGCCTCCAAGAAAACAAAG	59.305	45.455	0.00	0.00	0.00	2.77	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1960	4470	0.033504	ACCGTCACACGATTCTTGCT	59.966	50.000	46.05	3.91	R
2220	4730	1.345063	AGTACCACCCTTTGCGTAGT	58.655	50.000	0.00	2.73	R
3138	5940	1.523095	CTGCTCCTATTTTACTCGCGC	59.477	52.381	0.00	6.86	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
74	75	5.319043	ACAAGGTGGATTAAAGTTCCAGA	57.681	39.130	0.00	0.00	43.78	3.86
399	500	1.792367	CAGTCGACAAGCAAATCGTGA	59.208	47.619	19.50	0.00	39.38	4.35
414	515	1.083401	GTGACAAACTCACGCGCTG	60.083	57.895	5.73	3.89	40.14	5.18
419	520	1.871039	ACAAACTCACGCGCTGTTATT	59.129	42.857	5.73	0.00	0.00	1.40
477	578	3.631250	TGAAATCAATAGCCAACCTCCC	58.369	45.455	0.00	0.00	0.00	4.30
496	597	6.331307	ACCTCCCTATAGAAAGCAGATCAAAT	59.669	38.462	0.00	0.00	0.00	2.32
767	1064	2.043852	GCCTCCTCGGTCCTCTCA	60.044	66.667	0.00	0.00	34.25	3.27
795	1092	2.989824	ACCCACTCCCACTCGTCG	60.990	66.667	0.00	0.00	0.00	5.12
800	1097	3.062466	CTCCCACTCGTCGCCTCA	61.062	66.667	0.00	0.00	0.00	3.86
801	1098	3.057547	CTCCCACTCGTCGCCTCAG	62.058	68.421	0.00	0.00	0.00	3.35
827	1124	1.307430	AAGGCCTCTTCTCCCTCCC	60.307	63.158	5.23	0.00	0.00	4.30
968	1549	4.508405	CCACTTTCCCCTCACCTCAATTTA	60.508	45.833	0.00	0.00	0.00	1.40
1080	1661	3.744530	CGAGGAAAAGAACACCTGAACCT	60.745	47.826	0.00	0.00	33.89	3.50
1081	1662	3.555966	AGGAAAAGAACACCTGAACCTG	58.444	45.455	0.00	0.00	32.39	4.00
1094	1675	3.521937	CCTGAACCTGGGGTAACATTCTA	59.478	47.826	0.00	0.00	33.12	2.10
1186	1767	2.695147	ACCAGCCTCCAAGAAAACAAAG	59.305	45.455	0.00	0.00	0.00	2.77
1240	1821	6.564873	GCATGTTCTATATCTTTCGGAAGTGC	60.565	42.308	2.72	0.00	34.41	4.40
1311	3527	5.192176	TGTGCCACTTTAATATCTGATGCA	58.808	37.500	0.00	0.00	0.00	3.96
1326	3543	3.678289	TGATGCAGCTCTGTTACACATT	58.322	40.909	2.53	0.00	0.00	2.71
1433	3816	5.645497	CCACTCTTTATTCCCTTTCTCTGTG	59.355	44.000	0.00	0.00	0.00	3.66
1461	3844	9.606631	CTAAAGCCTTACTGAGAATGTTTAGAT	57.393	33.333	0.00	0.00	30.06	1.98
1538	3921	5.635280	GTCATCCGGACATAATAGTGACATG	59.365	44.000	20.38	5.78	46.19	3.21
1760	4270	9.663904	AAATATACTGCACTATATTTTGCGTTG	57.336	29.630	18.29	0.00	41.96	4.10
1927	4437	3.243873	GCTAAAAGCTTTGAAGTTGCCCT	60.244	43.478	13.54	0.00	38.45	5.19
1960	4470	4.655649	ACTATCACAAGATATGTCCAGGCA	59.344	41.667	0.00	0.00	41.46	4.75
1996	4506	4.084223	TGACGGTTACTTTCAATTCTTCGC	60.084	41.667	0.00	0.00	0.00	4.70
2552	5062	8.413899	CTTTTGGAGCACTCTAAGTAAGATAC	57.586	38.462	3.40	0.00	32.41	2.24
2553	5063	7.476540	TTTGGAGCACTCTAAGTAAGATACA	57.523	36.000	0.00	0.00	32.41	2.29
2671	5186	8.335356	TCGCTTGTTCTCTATGTAAATAATTGC	58.665	33.333	0.00	0.00	0.00	3.56
2696	5211	6.656693	CCTTTCTCCTGCTATTTTCAGAAGAA	59.343	38.462	0.00	0.00	33.54	2.52
2794	5574	2.026301	GTAGCCCACGAGCTAGCG	59.974	66.667	9.55	0.00	45.74	4.26
2803	5583	2.927477	CCACGAGCTAGCGAACAAAATA	59.073	45.455	9.55	0.00	34.83	1.40
2839	5619	3.393800	ACGCCATGTACTATGAATGCTC	58.606	45.455	6.81	0.00	0.00	4.26
2874	5654	9.784531	AATCTCTGTCAAGAACAATCTAAGAAA	57.215	29.630	0.00	0.00	37.45	2.52
3014	5797	9.442047	CTAAACTAAGAACAACTCATCCATTCT	57.558	33.333	0.00	0.00	0.00	2.40
3088	5871	4.280436	TCCATTCGAAACATGGTAGTGT	57.720	40.909	14.37	0.00	41.90	3.55
3138	5940	1.374947	CCCATATACACCGGCCCAG	59.625	63.158	0.00	0.00	0.00	4.45
3161	5963	3.733988	CGCGAGTAAAATAGGAGCAGACA	60.734	47.826	0.00	0.00	0.00	3.41
3299	6169	0.034574	ACACCTTGTCAAGCACCACA	60.035	50.000	7.09	0.00	0.00	4.17
3319	6189	1.437573	CTACGCAGATCCAAGCCGA	59.562	57.895	0.00	0.00	0.00	5.54
3320	6190	0.032678	CTACGCAGATCCAAGCCGAT	59.967	55.000	0.00	0.00	0.00	4.18
3364	6237	2.353109	CCAGTCATCGTCTTCTTCTGCA	60.353	50.000	0.00	0.00	0.00	4.41
3369	6242	1.502231	TCGTCTTCTTCTGCAGCAAC	58.498	50.000	9.47	0.00	0.00	4.17
3381	6254	1.970917	GCAGCAACGACCCAATCTCG	61.971	60.000	0.00	0.00	37.17	4.04
3382	6255	0.670546	CAGCAACGACCCAATCTCGT	60.671	55.000	0.00	0.00	46.20	4.18
3386	6259	2.126071	CGACCCAATCTCGTGCGT	60.126	61.111	0.00	0.00	0.00	5.24
3390	6263	2.047274	CCAATCTCGTGCGTGGGT	60.047	61.111	0.00	0.00	0.00	4.51

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
41	42	9.736023	CTTTAATCCACCTTGTTAATAGCAATC	57.264	33.333	0.00	0.00	0.00	2.67
48	49	7.947890	TCTGGAACTTTAATCCACCTTGTTAAT	59.052	33.333	0.00	0.00	41.98	1.40
339	440	5.359194	TTGAGAGCCTAAACCTTAGGATG	57.641	43.478	15.23	0.00	36.85	3.51
399	500	1.508632	ATAACAGCGCGTGAGTTTGT	58.491	45.000	8.43	3.41	0.00	2.83
419	520	6.274672	AGGGCCATACCTAGCTAAATTTCATA	59.725	38.462	6.18	0.00	39.65	2.15
619	903	2.040464	GAGATGAGGGGGAGGCCA	60.040	66.667	5.01	0.00	0.00	5.36
725	1022	0.962489	CATCTTATCCTCTCGCCGGT	59.038	55.000	1.90	0.00	0.00	5.28
767	1064	2.448542	AGTGGGTGGAGCAGGTGT	60.449	61.111	0.00	0.00	0.00	4.16
795	1092	4.120755	CCTTGGAGGGGCTGAGGC	62.121	72.222	0.00	0.00	37.82	4.70
968	1549	4.263639	TGTTGGATCTGAGCTGGAAGAAAT	60.264	41.667	0.00	0.00	34.07	2.17
1064	1645	1.133482	CCCCAGGTTCAGGTGTTCTTT	60.133	52.381	0.00	0.00	0.00	2.52
1080	1661	7.091720	ACAATAGGGATTTAGAATGTTACCCCA	60.092	37.037	0.00	0.00	36.84	4.96
1081	1662	7.295340	ACAATAGGGATTTAGAATGTTACCCC	58.705	38.462	0.00	0.00	36.84	4.95
1094	1675	9.401058	CTGAGAAATGAGTTACAATAGGGATTT	57.599	33.333	0.00	0.00	0.00	2.17
1186	1767	8.845942	TTTGTGATGTACGTATGTAGATGTAC	57.154	34.615	9.34	8.71	40.69	2.90
1240	1821	0.037303	AGTGTGATCAAGTGGCCTGG	59.963	55.000	3.32	0.00	0.00	4.45
1326	3543	7.921041	AATCTGACATCTCTAGGACCAAATA	57.079	36.000	0.00	0.00	0.00	1.40
1381	3764	8.862325	TGACCAGTACATTCAAAATGTAGAAT	57.138	30.769	11.70	1.15	35.43	2.40
1461	3844	6.942532	AAGTGCTACAGAGTGAAAAATCAA	57.057	33.333	0.00	0.00	0.00	2.57
1474	3857	5.521735	GTCTCACATGGAATAAGTGCTACAG	59.478	44.000	0.00	0.00	33.44	2.74
1534	3917	8.190784	CCTTTCAAGTTTCTTTAGTTGACATGT	58.809	33.333	0.00	0.00	37.24	3.21
1538	3921	6.972901	CACCCTTTCAAGTTTCTTTAGTTGAC	59.027	38.462	0.00	0.00	37.24	3.18
1623	4127	4.656112	TCCTAAAGGATAAGAGAGGGCAAG	59.344	45.833	0.00	0.00	39.78	4.01
1627	4131	7.142995	ACATTTCCTAAAGGATAAGAGAGGG	57.857	40.000	0.00	0.00	44.98	4.30
1741	4251	7.269084	GCATATACAACGCAAAATATAGTGCAG	59.731	37.037	10.27	6.25	40.94	4.41
1836	4346	6.121776	TCTTCCTGTGGAGCAAAAGTAATA	57.878	37.500	0.00	0.00	31.21	0.98
1846	4356	0.833287	TAGGCATCTTCCTGTGGAGC	59.167	55.000	0.00	0.00	37.01	4.70
1927	4437	8.478066	ACATATCTTGTGATAGTAACTTGCAGA	58.522	33.333	0.00	0.00	38.42	4.26
1960	4470	0.033504	ACCGTCACACGATTCTTGCT	59.966	50.000	0.00	0.00	46.05	3.91
1996	4506	4.250464	AGCAAACCATCAATCAATTGCAG	58.750	39.130	10.45	0.00	44.08	4.41
2122	4632	6.070995	TGGGTGTAGTGGTAGTCTCTTATTTG	60.071	42.308	0.00	0.00	0.00	2.32
2220	4730	1.345063	AGTACCACCCTTTGCGTAGT	58.655	50.000	0.00	0.00	0.00	2.73
2526	5036	5.877564	ATCTTACTTAGAGTGCTCCAAAAGC	59.122	40.000	0.00	0.00	43.33	3.51
2552	5062	4.558095	GCAGCAATGGAAGGCTACAATATG	60.558	45.833	0.00	0.00	38.56	1.78
2553	5063	3.571401	GCAGCAATGGAAGGCTACAATAT	59.429	43.478	0.00	0.00	38.56	1.28
2612	5127	8.529476	AGTGAGTTTAACCGTAGAGATAACAAT	58.471	33.333	0.00	0.00	0.00	2.71
2671	5186	6.176183	TCTTCTGAAAATAGCAGGAGAAAGG	58.824	40.000	0.00	0.00	43.29	3.11
2696	5211	9.886132	CAGTAAAGAGGTGGTTTAACTATGTAT	57.114	33.333	0.00	0.00	0.00	2.29
2803	5583	5.437060	ACATGGCGTTGATATAGAAAAGGT	58.563	37.500	0.00	0.00	0.00	3.50
2874	5654	9.660180	TTTGTAAGCCATGTTTTTCTTTTAAGT	57.340	25.926	0.00	0.00	0.00	2.24
3014	5797	6.715264	GGAGGAGGTATTTTTCTTCTTGTGAA	59.285	38.462	0.00	0.00	0.00	3.18
3088	5871	4.624364	CGGTGCAGCAGTGGGTGA	62.624	66.667	17.33	0.00	45.29	4.02
3138	5940	1.523095	CTGCTCCTATTTTACTCGCGC	59.477	52.381	0.00	0.00	0.00	6.86
3188	6058	0.611896	AATGGGGAGAAGGGCGTTTG	60.612	55.000	0.00	0.00	0.00	2.93
3319	6189	3.315142	ATGACTGGGTGCGCGACAT	62.315	57.895	12.10	0.00	0.00	3.06
3320	6190	3.932580	GATGACTGGGTGCGCGACA	62.933	63.158	12.10	4.31	0.00	4.35
3364	6237	4.598257	CGAGATTGGGTCGTTGCT	57.402	55.556	0.00	0.00	32.62	3.91
3369	6242	2.126071	ACGCACGAGATTGGGTCG	60.126	61.111	0.00	0.00	38.17	4.79
3381	6254	3.986006	TCGACTCCACCCACGCAC	61.986	66.667	0.00	0.00	0.00	5.34
3382	6255	3.986006	GTCGACTCCACCCACGCA	61.986	66.667	8.70	0.00	0.00	5.24
3386	6259	2.741092	GCTTGTCGACTCCACCCA	59.259	61.111	17.92	0.00	0.00	4.51
3390	6263	4.717629	CGGCGCTTGTCGACTCCA	62.718	66.667	17.92	0.00	45.47	3.86
3408	6286	2.475487	CCGTCGTTGAGGAAGAAGAAAC	59.525	50.000	0.00	0.00	0.00	2.78

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.