AutoCloner

Multiple sequence alignment - TraesCS2D01G125500

Loading Multiple Alignment...

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	TraesCS2D01G125500	chr2D	100.000	2554	0	0	1	2554	73210055	73212608	0.000000e+00	4717.0
1	TraesCS2D01G125500	chr2D	80.097	824	110	20	767	1553	73191221	73192027	4.770000e-157	564.0
2	TraesCS2D01G125500	chr2D	79.692	650	86	24	795	1421	73219674	73220300	6.530000e-116	427.0
3	TraesCS2D01G125500	chr2D	83.562	365	55	5	1198	1558	73143075	73143438	1.130000e-88	337.0
4	TraesCS2D01G125500	chr2D	82.671	277	41	7	1	273	391657666	391657939	3.280000e-59	239.0
5	TraesCS2D01G125500	chr2D	100.000	28	0	0	1126	1153	73189926	73189953	5.000000e-03	52.8
6	TraesCS2D01G125500	chr2B	93.917	1874	79	14	690	2554	110818105	110819952	0.000000e+00	2796.0
7	TraesCS2D01G125500	chr2B	84.590	597	76	8	977	1557	110763461	110764057	1.700000e-161	579.0
8	TraesCS2D01G125500	chr2B	87.702	309	33	4	1306	1614	110676106	110676409	3.130000e-94	355.0
9	TraesCS2D01G125500	chr2B	91.489	47	4	0	2243	2289	110684510	110684556	5.900000e-07	65.8
10	TraesCS2D01G125500	chr2A	89.394	1914	120	37	1	1850	72516646	72518540	0.000000e+00	2333.0
11	TraesCS2D01G125500	chr2A	82.474	582	91	11	983	1556	72512202	72512780	1.360000e-137	499.0
12	TraesCS2D01G125500	chr2A	83.607	366	57	3	1196	1558	72388969	72389334	8.750000e-90	340.0
13	TraesCS2D01G125500	chr2A	82.310	277	44	5	1	273	144499884	144500159	4.250000e-58	235.0
14	TraesCS2D01G125500	chr2A	100.000	29	0	0	1125	1153	72393183	72393211	1.000000e-03	54.7
15	TraesCS2D01G125500	chr5D	83.448	290	36	9	12	297	360915099	360914818	2.520000e-65	259.0
16	TraesCS2D01G125500	chr5D	81.272	283	50	3	4	283	168715511	168715229	2.560000e-55	226.0
17	TraesCS2D01G125500	chr4D	82.105	285	46	4	4	285	384387818	384387536	3.280000e-59	239.0
18	TraesCS2D01G125500	chr5B	82.246	276	46	3	4	276	330440911	330440636	4.250000e-58	235.0
19	TraesCS2D01G125500	chr7D	82.482	274	41	7	4	273	317484599	317484329	1.530000e-57	233.0
20	TraesCS2D01G125500	chr6B	81.495	281	47	5	1	277	426448475	426448754	2.560000e-55	226.0
21	TraesCS2D01G125500	chr4B	89.831	59	6	0	1494	1552	623347456	623347398	2.720000e-10	76.8

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	TraesCS2D01G125500	chr2D	73210055	73212608	2553	False	4717.0	4717	100.0000	1	2554	1	chr2D.!!$F2	2553
1	TraesCS2D01G125500	chr2D	73219674	73220300	626	False	427.0	427	79.6920	795	1421	1	chr2D.!!$F3	626
2	TraesCS2D01G125500	chr2D	73189926	73192027	2101	False	308.4	564	90.0485	767	1553	2	chr2D.!!$F5	786
3	TraesCS2D01G125500	chr2B	110818105	110819952	1847	False	2796.0	2796	93.9170	690	2554	1	chr2B.!!$F4	1864
4	TraesCS2D01G125500	chr2B	110763461	110764057	596	False	579.0	579	84.5900	977	1557	1	chr2B.!!$F3	580
5	TraesCS2D01G125500	chr2A	72512202	72518540	6338	False	1416.0	2333	85.9340	1	1850	2	chr2A.!!$F3	1849

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
361	4806	0.106149	GGCAGGGTGGACTATTACCG	59.894	60.0	0.0	0.0	37.85	4.02	F
965	5496	0.107848	CCACACCCACCCTATCGTTC	60.108	60.0	0.0	0.0	0.00	3.95	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1200	5757	0.609131	GTCCACCACATCAACCTGGG	60.609	60.0	0.00	0.00	0.0	4.45	R
2388	6963	0.730265	GTATCATGAACGGCGCCAAA	59.270	50.0	28.98	8.68	0.0	3.28	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
36	4481	9.798994	ATCATTCTTAAAATGATTCTGACAAGC	57.201	29.630	14.74	0.00	42.85	4.01
61	4506	6.661304	TGACTCATCTATGCACATAGTGAT	57.339	37.500	15.44	2.87	41.12	3.06
69	4514	2.989909	TGCACATAGTGATGGTCTTGG	58.010	47.619	0.58	0.00	37.39	3.61
70	4515	2.305635	TGCACATAGTGATGGTCTTGGT	59.694	45.455	0.58	0.00	37.39	3.67
85	4530	6.598503	TGGTCTTGGTACTAGAATCTATCGA	58.401	40.000	0.00	0.00	0.00	3.59
86	4531	6.485984	TGGTCTTGGTACTAGAATCTATCGAC	59.514	42.308	0.00	0.00	0.00	4.20
118	4563	7.995488	CCTGGATCAAGTTGTTAGATTCCTTAT	59.005	37.037	2.11	0.00	0.00	1.73
134	4579	4.196193	TCCTTATATGTTTTCGTGCCTGG	58.804	43.478	0.00	0.00	0.00	4.45
150	4595	3.711190	TGCCTGGAGAAGCTATACATCAA	59.289	43.478	0.00	0.00	0.00	2.57
212	4657	9.859692	CGAAGTTAAATTTCTCGTACTTTTTCT	57.140	29.630	0.00	0.00	0.00	2.52
214	4659	9.859692	AAGTTAAATTTCTCGTACTTTTTCTCG	57.140	29.630	0.00	0.00	0.00	4.04
236	4681	7.707464	TCTCGAGTTTACAAAGACAAATGTACA	59.293	33.333	13.13	0.00	32.07	2.90
361	4806	0.106149	GGCAGGGTGGACTATTACCG	59.894	60.000	0.00	0.00	37.85	4.02
369	4814	3.306919	GGTGGACTATTACCGTGGTCAAA	60.307	47.826	0.00	0.00	31.88	2.69
371	4816	3.324268	TGGACTATTACCGTGGTCAAACA	59.676	43.478	0.00	0.00	31.88	2.83
416	4861	3.059868	ACGTGTGTTTTAGCAACGAGATG	60.060	43.478	0.00	0.00	0.00	2.90
417	4862	3.183574	CGTGTGTTTTAGCAACGAGATGA	59.816	43.478	0.00	0.00	0.00	2.92
431	4876	3.130516	ACGAGATGAGATTAGGCGTGAAA	59.869	43.478	0.00	0.00	0.00	2.69
436	4881	3.334691	TGAGATTAGGCGTGAAACCAAG	58.665	45.455	0.00	0.00	0.00	3.61
485	4937	6.146216	TCAAATGTTTCGTATCGCAAATGTT	58.854	32.000	0.00	0.00	0.00	2.71
541	4993	6.985645	TCCATGGCTTCAAACAAATATTATGC	59.014	34.615	6.96	0.00	0.00	3.14
547	4999	8.720562	GGCTTCAAACAAATATTATGCAGTTTT	58.279	29.630	0.00	0.00	0.00	2.43
604	5056	4.486125	AAAAAGGGTTTCAAGCATGTGT	57.514	36.364	0.00	0.00	0.00	3.72
615	5067	0.604780	AGCATGTGTGTGAGACTGCC	60.605	55.000	0.00	0.00	0.00	4.85
635	5087	2.026822	CCCTGCAGTCCATGTTTCTACT	60.027	50.000	13.81	0.00	0.00	2.57
649	5101	8.391106	CCATGTTTCTACTAGTATGAAGTTTGC	58.609	37.037	2.33	1.52	0.00	3.68
656	5108	3.611766	AGTATGAAGTTTGCGCCTACT	57.388	42.857	4.18	5.14	0.00	2.57
659	5111	0.533978	TGAAGTTTGCGCCTACTGCA	60.534	50.000	13.93	13.93	41.33	4.41
688	5140	0.673644	CTTACCACGTCCAAGCTGGG	60.674	60.000	0.00	0.00	38.32	4.45
702	5154	2.042464	AGCTGGGACATGTACATCGAT	58.958	47.619	10.99	0.00	38.20	3.59
836	5346	1.980765	TGAAAGCATCCAGGACTGACT	59.019	47.619	0.00	0.00	0.00	3.41
849	5359	0.528470	ACTGACTCGGCTAAGCTGTC	59.472	55.000	0.00	0.00	36.18	3.51
850	5364	0.179124	CTGACTCGGCTAAGCTGTCC	60.179	60.000	0.00	0.00	36.18	4.02
922	5444	5.390991	GGAGTTCATCTTTTTCCATGACGAC	60.391	44.000	0.00	0.00	0.00	4.34
965	5496	0.107848	CCACACCCACCCTATCGTTC	60.108	60.000	0.00	0.00	0.00	3.95
979	5510	2.273179	CGTTCGAGACAGACCCCCA	61.273	63.158	0.00	0.00	0.00	4.96
1098	5629	0.324368	TCGTCTGTATCCTGGCTGGT	60.324	55.000	10.44	0.93	37.07	4.00
1175	5721	2.733956	TGTTAATCCCATCCCTGCAAC	58.266	47.619	0.00	0.00	0.00	4.17
1200	5757	6.404074	CCTTTCTCTGATGGTATCACTTTTGC	60.404	42.308	0.00	0.00	35.06	3.68
1398	5958	4.907034	CCGTCGACCATCTCGCCG	62.907	72.222	10.58	0.00	43.26	6.46
1412	5972	0.892755	TCGCCGTCCAGAACAACTAT	59.107	50.000	0.00	0.00	0.00	2.12
1424	5984	2.513897	AACTATTGCGGCCCGAGC	60.514	61.111	7.68	0.00	38.76	5.03
1614	6174	0.547712	AGAGCCCAGGGAAGCACTAA	60.548	55.000	10.89	0.00	0.00	2.24
1615	6175	0.107459	GAGCCCAGGGAAGCACTAAG	60.107	60.000	10.89	0.00	0.00	2.18
1616	6176	1.750780	GCCCAGGGAAGCACTAAGC	60.751	63.158	10.89	0.00	46.19	3.09
1702	6262	3.645884	TCAGTTACGTGGCTTGTAGAAC	58.354	45.455	0.00	0.00	0.00	3.01
2004	6579	1.079256	CCTCCAGTCCTCCTCCACA	59.921	63.158	0.00	0.00	0.00	4.17
2046	6621	1.284982	CGGCGCTGGGAAATATCTCG	61.285	60.000	8.83	0.00	0.00	4.04
2101	6676	4.753877	CCGAGAGCGCGTTCACGA	62.754	66.667	35.30	0.00	41.87	4.35
2131	6706	2.803155	GATGACGGTGGCCTTGCAGA	62.803	60.000	3.32	0.00	0.00	4.26
2152	6727	2.882876	CGTTCGTGAGGATCGGGT	59.117	61.111	0.00	0.00	38.61	5.28
2381	6956	2.799916	GTCCTGCACGTCGTCGAC	60.800	66.667	15.51	15.51	40.62	4.20
2401	6976	3.342627	CGACTTTGGCGCCGTTCA	61.343	61.111	23.90	0.00	0.00	3.18
2409	6984	0.529773	TGGCGCCGTTCATGATACTC	60.530	55.000	23.90	0.00	0.00	2.59
2415	6990	0.248907	CGTTCATGATACTCCGCCGT	60.249	55.000	0.00	0.00	0.00	5.68
2416	6991	1.488527	GTTCATGATACTCCGCCGTC	58.511	55.000	0.00	0.00	0.00	4.79
2417	6992	0.030235	TTCATGATACTCCGCCGTCG	59.970	55.000	0.00	0.00	0.00	5.12
2418	6993	1.099295	TCATGATACTCCGCCGTCGT	61.099	55.000	0.00	0.00	0.00	4.34
2419	6994	0.660595	CATGATACTCCGCCGTCGTC	60.661	60.000	0.00	0.00	0.00	4.20
2420	6995	2.052414	GATACTCCGCCGTCGTCG	60.052	66.667	0.00	0.00	0.00	5.12
2421	6996	4.247612	ATACTCCGCCGTCGTCGC	62.248	66.667	0.00	0.00	35.54	5.19
2471	7046	3.916359	TGGACACAACTTTACCACTCA	57.084	42.857	0.00	0.00	0.00	3.41
2485	7060	3.157087	ACCACTCATGTTGGCCTTTAAG	58.843	45.455	3.32	0.00	0.00	1.85
2496	7071	2.046285	CCTTTAAGCCACGGCCAGG	61.046	63.158	2.24	4.95	43.17	4.45

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
10	4455	9.798994	GCTTGTCAGAATCATTTTAAGAATGAT	57.201	29.630	14.74	14.74	40.60	2.45
18	4463	7.445096	TGAGTCAAGCTTGTCAGAATCATTTTA	59.555	33.333	25.19	0.00	31.18	1.52
23	4468	4.341366	TGAGTCAAGCTTGTCAGAATCA	57.659	40.909	25.19	17.34	33.37	2.57
24	4469	5.177326	AGATGAGTCAAGCTTGTCAGAATC	58.823	41.667	25.19	20.34	0.00	2.52
36	4481	6.510536	TCACTATGTGCATAGATGAGTCAAG	58.489	40.000	21.81	0.00	42.55	3.02
61	4506	6.598503	TCGATAGATTCTAGTACCAAGACCA	58.401	40.000	0.00	0.00	42.67	4.02
85	4530	0.840722	AACTTGATCCAGGTCGGGGT	60.841	55.000	0.00	0.00	34.36	4.95
86	4531	0.392998	CAACTTGATCCAGGTCGGGG	60.393	60.000	0.00	0.00	34.36	5.73
118	4563	3.334691	CTTCTCCAGGCACGAAAACATA	58.665	45.455	0.00	0.00	0.00	2.29
150	4595	1.366319	ACAGGAAAGGAGCATCACCT	58.634	50.000	0.00	0.00	39.69	4.00
162	4607	6.508777	GTTGTGGTTAGCATTTAACAGGAAA	58.491	36.000	0.00	0.00	0.00	3.13
206	4651	9.284594	CATTTGTCTTTGTAAACTCGAGAAAAA	57.715	29.630	21.68	10.34	30.58	1.94
212	4657	7.773864	TGTACATTTGTCTTTGTAAACTCGA	57.226	32.000	0.00	0.00	30.59	4.04
214	4659	8.617809	TCCTTGTACATTTGTCTTTGTAAACTC	58.382	33.333	0.00	0.00	30.59	3.01
236	4681	9.379770	TCCTTCAAAATTCCTTTAGAAATCCTT	57.620	29.630	0.00	0.00	38.21	3.36
351	4796	4.933400	ACATGTTTGACCACGGTAATAGTC	59.067	41.667	0.00	0.00	0.00	2.59
361	4806	6.128172	CCTTCTCATAAGACATGTTTGACCAC	60.128	42.308	0.00	0.00	0.00	4.16
369	4814	5.503927	ACAATGCCTTCTCATAAGACATGT	58.496	37.500	0.00	0.00	0.00	3.21
371	4816	5.587844	GTGACAATGCCTTCTCATAAGACAT	59.412	40.000	0.00	0.00	0.00	3.06
416	4861	2.678336	CCTTGGTTTCACGCCTAATCTC	59.322	50.000	0.00	0.00	0.00	2.75
417	4862	2.618045	CCCTTGGTTTCACGCCTAATCT	60.618	50.000	0.00	0.00	0.00	2.40
496	4948	6.395780	TGGAATTGGACCAAACTTATAGGA	57.604	37.500	11.82	0.00	34.25	2.94
498	4950	6.461509	GCCATGGAATTGGACCAAACTTATAG	60.462	42.308	18.40	0.07	40.93	1.31
499	4951	5.362430	GCCATGGAATTGGACCAAACTTATA	59.638	40.000	18.40	0.00	40.93	0.98
500	4952	4.162131	GCCATGGAATTGGACCAAACTTAT	59.838	41.667	18.40	1.51	40.93	1.73
501	4953	3.513515	GCCATGGAATTGGACCAAACTTA	59.486	43.478	18.40	0.00	40.93	2.24
502	4954	2.302733	GCCATGGAATTGGACCAAACTT	59.697	45.455	18.40	1.34	40.93	2.66
503	4955	1.901833	GCCATGGAATTGGACCAAACT	59.098	47.619	18.40	0.97	40.93	2.66
504	4956	1.901833	AGCCATGGAATTGGACCAAAC	59.098	47.619	18.40	8.50	40.93	2.93
505	4957	2.323999	AGCCATGGAATTGGACCAAA	57.676	45.000	18.40	0.00	40.93	3.28
512	4964	7.852971	ATATTTGTTTGAAGCCATGGAATTG	57.147	32.000	18.40	0.00	0.00	2.32
584	5036	3.197549	ACACACATGCTTGAAACCCTTTT	59.802	39.130	6.60	0.00	0.00	2.27
615	5067	3.340814	AGTAGAAACATGGACTGCAGG	57.659	47.619	19.93	1.54	0.00	4.85
635	5087	4.430007	CAGTAGGCGCAAACTTCATACTA	58.570	43.478	10.83	0.00	0.00	1.82
656	5108	0.835971	TGGTAAGCCTGACTCCTGCA	60.836	55.000	0.00	0.00	35.27	4.41
659	5111	0.542232	ACGTGGTAAGCCTGACTCCT	60.542	55.000	0.00	0.00	35.27	3.69
688	5140	3.349488	TCCACGATCGATGTACATGTC	57.651	47.619	24.34	7.65	0.00	3.06
692	5144	2.734175	GCACTTCCACGATCGATGTACA	60.734	50.000	24.34	0.00	0.00	2.90
702	5154	3.334751	CGTTGCGCACTTCCACGA	61.335	61.111	23.24	0.00	0.00	4.35
756	5218	2.540515	CCTGCTGTAGTAATGACCGTG	58.459	52.381	0.00	0.00	0.00	4.94
849	5359	0.660300	GTTTCCACAAAAGCTCGCGG	60.660	55.000	6.13	0.00	0.00	6.46
850	5364	0.991770	CGTTTCCACAAAAGCTCGCG	60.992	55.000	0.00	0.00	0.00	5.87
877	5391	1.228552	CACCCACCACCCCTTTGAG	60.229	63.158	0.00	0.00	0.00	3.02
965	5496	3.775654	GGCTGGGGGTCTGTCTCG	61.776	72.222	0.00	0.00	0.00	4.04
1007	5538	2.516460	GCTCCAGCATCCTGCCTG	60.516	66.667	0.00	0.00	46.52	4.85
1098	5629	2.951642	CCTAAACGTCGGGTAGTATGGA	59.048	50.000	0.00	0.00	0.00	3.41
1175	5721	6.404074	GCAAAAGTGATACCATCAGAGAAAGG	60.404	42.308	0.00	0.00	40.53	3.11
1200	5757	0.609131	GTCCACCACATCAACCTGGG	60.609	60.000	0.00	0.00	0.00	4.45
1398	5958	1.130561	GCCGCAATAGTTGTTCTGGAC	59.869	52.381	0.00	0.00	0.00	4.02
1702	6262	8.542132	CAGTTTCATTTTGTAATTGAACACCAG	58.458	33.333	0.00	0.00	0.00	4.00
2033	6608	3.260884	GTCTATGGCCGAGATATTTCCCA	59.739	47.826	10.19	0.00	0.00	4.37
2046	6621	2.513897	GGTGCGGTGTCTATGGCC	60.514	66.667	0.00	0.00	0.00	5.36
2131	6706	1.298413	CGATCCTCACGAACGCGAT	60.298	57.895	15.93	0.00	41.64	4.58
2166	6741	2.587753	ACCAGCGTCGTTGGTGTG	60.588	61.111	29.94	7.20	45.08	3.82
2388	6963	0.730265	GTATCATGAACGGCGCCAAA	59.270	50.000	28.98	8.68	0.00	3.28
2401	6976	1.653115	GACGACGGCGGAGTATCAT	59.347	57.895	18.49	0.00	43.17	2.45
2415	6990	4.492160	GCATCGACAGGGCGACGA	62.492	66.667	0.00	0.00	45.45	4.20
2421	6996	4.147449	TGAGCGGCATCGACAGGG	62.147	66.667	1.45	0.00	39.00	4.45
2446	7021	3.252458	GTGGTAAAGTTGTGTCCATCACC	59.748	47.826	0.00	0.00	45.61	4.02
2456	7031	3.317993	GCCAACATGAGTGGTAAAGTTGT	59.682	43.478	17.68	0.00	35.75	3.32

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.