AutoCloner

Multiple sequence alignment - TraesCS2D01G460900

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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	TraesCS2D01G460900	chr2D	100.000	3032	0	0	1	3032	567476279	567479310	0.000000e+00	5600.0
1	TraesCS2D01G460900	chr2D	97.059	34	1	0	2598	2631	567478907	567478940	1.170000e-04	58.4
2	TraesCS2D01G460900	chr2B	92.328	2711	110	33	1	2664	680192949	680195608	0.000000e+00	3764.0
3	TraesCS2D01G460900	chr2B	93.933	445	17	6	2598	3032	680195573	680196017	0.000000e+00	664.0
4	TraesCS2D01G460900	chr2A	94.311	2338	86	21	712	3032	706994904	706997211	0.000000e+00	3537.0
5	TraesCS2D01G460900	chr2A	92.991	428	21	6	295	714	706994352	706994778	1.540000e-172	616.0
6	TraesCS2D01G460900	chr2A	87.059	340	16	7	1	333	706994037	706994355	2.870000e-95	359.0
7	TraesCS2D01G460900	chr5A	87.634	3073	198	63	1	3032	282588883	282585952	0.000000e+00	3402.0
8	TraesCS2D01G460900	chr5A	100.000	40	0	0	2604	2643	282586332	282586293	1.170000e-09	75.0
9	TraesCS2D01G460900	chr5D	87.578	3059	214	76	1	3032	214920617	214917698	0.000000e+00	3391.0
10	TraesCS2D01G460900	chr5B	89.005	2683	173	52	1	2662	230249464	230246883	0.000000e+00	3208.0
11	TraesCS2D01G460900	chr5B	92.478	226	17	0	2807	3032	230246703	230246478	1.050000e-84	324.0
12	TraesCS2D01G460900	chr5B	97.826	46	1	0	2598	2643	230246916	230246871	2.510000e-11	80.5
13	TraesCS2D01G460900	chr4B	82.333	600	73	23	840	1431	135211258	135211832	9.770000e-135	490.0
14	TraesCS2D01G460900	chr4B	87.234	141	13	5	510	646	135210867	135211006	4.050000e-34	156.0
15	TraesCS2D01G460900	chr4B	97.297	74	2	0	573	646	211593400	211593327	3.170000e-25	126.0
16	TraesCS2D01G460900	chr4D	81.924	603	77	25	840	1431	95780935	95781516	5.880000e-132	481.0
17	TraesCS2D01G460900	chr4D	87.234	141	13	5	510	646	95780563	95780702	4.050000e-34	156.0
18	TraesCS2D01G460900	chr4A	81.653	605	80	21	840	1431	483951562	483950976	9.840000e-130	473.0
19	TraesCS2D01G460900	chr4A	86.861	137	12	6	515	646	483951949	483951814	6.770000e-32	148.0
20	TraesCS2D01G460900	chrUn	92.478	226	17	0	2807	3032	476965542	476965767	1.050000e-84	324.0
21	TraesCS2D01G460900	chr3D	81.377	247	41	4	1097	1339	362069952	362069707	2.380000e-46	196.0

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	TraesCS2D01G460900	chr2D	567476279	567479310	3031	False	2829.200000	5600	98.529500	1	3032	2	chr2D.!!$F1	3031
1	TraesCS2D01G460900	chr2B	680192949	680196017	3068	False	2214.000000	3764	93.130500	1	3032	2	chr2B.!!$F1	3031
2	TraesCS2D01G460900	chr2A	706994037	706997211	3174	False	1504.000000	3537	91.453667	1	3032	3	chr2A.!!$F1	3031
3	TraesCS2D01G460900	chr5A	282585952	282588883	2931	True	1738.500000	3402	93.817000	1	3032	2	chr5A.!!$R1	3031
4	TraesCS2D01G460900	chr5D	214917698	214920617	2919	True	3391.000000	3391	87.578000	1	3032	1	chr5D.!!$R1	3031
5	TraesCS2D01G460900	chr5B	230246478	230249464	2986	True	1204.166667	3208	93.103000	1	3032	3	chr5B.!!$R1	3031
6	TraesCS2D01G460900	chr4B	135210867	135211832	965	False	323.000000	490	84.783500	510	1431	2	chr4B.!!$F1	921
7	TraesCS2D01G460900	chr4D	95780563	95781516	953	False	318.500000	481	84.579000	510	1431	2	chr4D.!!$F1	921
8	TraesCS2D01G460900	chr4A	483950976	483951949	973	True	310.500000	473	84.257000	515	1431	2	chr4A.!!$R1	916

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
920	1203	0.683973	CATCCTATTCCTGCCTCGCT	59.316	55.0	0.0	0.0	0.0	4.93	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2460	2838	3.309296	TGTTTCTTGAGGAGACTGGAGT	58.691	45.455	0.0	0.0	44.43	3.85	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
100	102	8.217131	TGATTGTGTTGAATCTGATATCAAGG	57.783	34.615	6.90	0.00	36.31	3.61
136	138	4.308899	AGCGTACTCCATAGTGAATGAC	57.691	45.455	0.00	0.00	37.86	3.06
179	181	4.080975	TGCACCTCACATGTCATATCTCAA	60.081	41.667	0.00	0.00	0.00	3.02
180	182	4.877823	GCACCTCACATGTCATATCTCAAA	59.122	41.667	0.00	0.00	0.00	2.69
181	183	5.007430	GCACCTCACATGTCATATCTCAAAG	59.993	44.000	0.00	0.00	0.00	2.77
182	184	6.343703	CACCTCACATGTCATATCTCAAAGA	58.656	40.000	0.00	0.00	0.00	2.52
183	185	6.479331	CACCTCACATGTCATATCTCAAAGAG	59.521	42.308	0.00	0.00	0.00	2.85
184	186	6.382282	ACCTCACATGTCATATCTCAAAGAGA	59.618	38.462	0.00	0.00	43.20	3.10
186	188	7.599621	CCTCACATGTCATATCTCAAAGAGATC	59.400	40.741	12.41	0.54	45.03	2.75
187	189	8.247666	TCACATGTCATATCTCAAAGAGATCT	57.752	34.615	12.41	0.00	45.03	2.75
188	190	8.358895	TCACATGTCATATCTCAAAGAGATCTC	58.641	37.037	15.29	15.29	45.03	2.75
189	191	8.361889	CACATGTCATATCTCAAAGAGATCTCT	58.638	37.037	19.92	19.92	45.03	3.10
190	192	9.585369	ACATGTCATATCTCAAAGAGATCTCTA	57.415	33.333	25.37	10.10	45.03	2.43
291	305	4.425772	ACCAATCTATATCATCGGTCCCA	58.574	43.478	0.00	0.00	0.00	4.37
338	388	2.450476	ACAAATGGGATGGACTCTTGC	58.550	47.619	0.00	0.00	0.00	4.01
359	409	6.409524	TGCTGGAAATTGAGTTTCTGAATT	57.590	33.333	0.50	0.00	44.54	2.17
363	413	7.867403	GCTGGAAATTGAGTTTCTGAATTAACA	59.133	33.333	0.50	0.00	44.54	2.41
427	486	3.279116	GTCCAACACAGCGCTGCA	61.279	61.111	36.28	11.24	0.00	4.41
428	487	2.974148	TCCAACACAGCGCTGCAG	60.974	61.111	36.28	29.44	0.00	4.41
429	488	4.695231	CCAACACAGCGCTGCAGC	62.695	66.667	36.28	29.12	37.78	5.25
559	622	1.998530	CAATGGTGAGGCCTACCCA	59.001	57.895	21.83	21.83	37.40	4.51
676	752	7.686434	TGGAACCATATATTCTAACCTTAGCC	58.314	38.462	0.00	0.00	0.00	3.93
686	818	4.172807	TCTAACCTTAGCCCCTTTGAAGA	58.827	43.478	0.00	0.00	0.00	2.87
777	1060	4.092968	GCACAAGTCCTCCTTACGTAAATG	59.907	45.833	9.68	3.95	0.00	2.32
793	1076	6.205784	ACGTAAATGCCAATACATTATGTGC	58.794	36.000	8.26	3.33	39.32	4.57
797	1080	3.630168	TGCCAATACATTATGTGCAGGT	58.370	40.909	8.26	0.00	0.00	4.00
798	1081	3.380954	TGCCAATACATTATGTGCAGGTG	59.619	43.478	8.26	0.00	0.00	4.00
799	1082	3.796504	GCCAATACATTATGTGCAGGTGC	60.797	47.826	8.26	0.00	42.50	5.01
853	1136	7.567622	TGTAAAGTTCTACTTGGGAGGCTATAT	59.432	37.037	0.00	0.00	38.66	0.86
918	1201	1.051812	ACCATCCTATTCCTGCCTCG	58.948	55.000	0.00	0.00	0.00	4.63
920	1203	0.683973	CATCCTATTCCTGCCTCGCT	59.316	55.000	0.00	0.00	0.00	4.93
965	1265	3.056607	CCCAACTTTTGCCATAGACAAGG	60.057	47.826	0.00	0.00	0.00	3.61
1012	1324	3.014085	GCAGCAATGGCCATGCACT	62.014	57.895	29.62	20.80	46.22	4.40
1083	1398	2.304761	CACCAACCTACACTACCACCAT	59.695	50.000	0.00	0.00	0.00	3.55
1087	1402	1.831736	ACCTACACTACCACCATCAGC	59.168	52.381	0.00	0.00	0.00	4.26
1218	1533	2.144078	TGACTCCCCTGGCGACAAA	61.144	57.895	0.00	0.00	42.06	2.83
1350	1665	2.734673	GGAGAAGCAGCTTGACGCG	61.735	63.158	13.91	3.53	45.59	6.01
1377	1692	0.607217	TCGTGCACTTCGAGAGGGTA	60.607	55.000	16.19	0.00	33.38	3.69
1556	1871	3.953775	CCCTGCCAACTCCCACGT	61.954	66.667	0.00	0.00	0.00	4.49
1639	1954	2.615912	AGCACTCAAGAACAAAGCACTC	59.384	45.455	0.00	0.00	0.00	3.51
1655	1970	3.064408	AGCACTCGATAACATGCAACATG	59.936	43.478	6.03	6.03	40.63	3.21
1694	2016	8.119226	GTGCTGAAAATCACATATCTCTTACAC	58.881	37.037	0.00	0.00	33.63	2.90
1728	2050	1.016130	ATTCTTGCAGGTGACTCGCG	61.016	55.000	0.00	0.00	40.21	5.87
1858	2180	3.146783	GCCAATGTACGGCTACACA	57.853	52.632	3.25	0.00	46.56	3.72
1864	2186	0.032403	TGTACGGCTACACACACCAC	59.968	55.000	0.00	0.00	0.00	4.16
1925	2247	6.360370	ACTGGTGAGTACTGTAAACATCAT	57.640	37.500	0.00	0.00	0.00	2.45
2108	2458	2.544844	ACTACCAGCCAGCCTACTAA	57.455	50.000	0.00	0.00	0.00	2.24
2118	2468	3.556999	CCAGCCTACTAAGCTACTCTGA	58.443	50.000	0.00	0.00	38.95	3.27
2460	2838	8.862325	AACAAACTATGAAGTTGATGTATCCA	57.138	30.769	0.00	0.00	45.37	3.41
2467	2845	4.532126	TGAAGTTGATGTATCCACTCCAGT	59.468	41.667	0.00	0.00	32.29	4.00
2484	2862	5.163152	ACTCCAGTCTCCTCAAGAAACAAAT	60.163	40.000	0.00	0.00	35.21	2.32
2551	2938	4.223032	CCTTCTTGCCTCTTCCAGTACTAA	59.777	45.833	0.00	0.00	0.00	2.24
2939	3462	2.945668	AGAAGTTTGAGGTGTGCAAGTC	59.054	45.455	0.00	0.00	0.00	3.01
2984	3507	3.258123	TGCAAAGGAAAAGGATGGCTAAC	59.742	43.478	0.00	0.00	0.00	2.34
2996	3522	0.106569	TGGCTAACATGATGGCCTGG	60.107	55.000	26.73	0.00	44.36	4.45

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
136	138	1.825090	TGGGCTGTGTGCTCTTATTG	58.175	50.000	0.00	0.00	44.09	1.90
157	159	4.063998	TGAGATATGACATGTGAGGTGC	57.936	45.455	1.15	0.00	0.00	5.01
182	184	5.787327	AGGGGTCTTTTGAGATAGAGATCT	58.213	41.667	0.00	0.00	45.59	2.75
183	185	6.780522	AGTAGGGGTCTTTTGAGATAGAGATC	59.219	42.308	0.00	0.00	0.00	2.75
184	186	6.553100	CAGTAGGGGTCTTTTGAGATAGAGAT	59.447	42.308	0.00	0.00	0.00	2.75
185	187	5.894393	CAGTAGGGGTCTTTTGAGATAGAGA	59.106	44.000	0.00	0.00	0.00	3.10
186	188	5.452636	GCAGTAGGGGTCTTTTGAGATAGAG	60.453	48.000	0.00	0.00	0.00	2.43
187	189	4.406003	GCAGTAGGGGTCTTTTGAGATAGA	59.594	45.833	0.00	0.00	0.00	1.98
188	190	4.443598	GGCAGTAGGGGTCTTTTGAGATAG	60.444	50.000	0.00	0.00	0.00	2.08
189	191	3.454812	GGCAGTAGGGGTCTTTTGAGATA	59.545	47.826	0.00	0.00	0.00	1.98
190	192	2.239907	GGCAGTAGGGGTCTTTTGAGAT	59.760	50.000	0.00	0.00	0.00	2.75
191	193	1.628846	GGCAGTAGGGGTCTTTTGAGA	59.371	52.381	0.00	0.00	0.00	3.27
192	194	1.340114	GGGCAGTAGGGGTCTTTTGAG	60.340	57.143	0.00	0.00	0.00	3.02
193	195	0.696501	GGGCAGTAGGGGTCTTTTGA	59.303	55.000	0.00	0.00	0.00	2.69
194	196	0.698818	AGGGCAGTAGGGGTCTTTTG	59.301	55.000	0.00	0.00	0.00	2.44
195	197	0.698818	CAGGGCAGTAGGGGTCTTTT	59.301	55.000	0.00	0.00	0.00	2.27
291	305	1.686236	ATGGACATGGAGGTTCCCTT	58.314	50.000	0.00	0.00	35.03	3.95
308	322	6.603201	AGTCCATCCCATTTGTAACTTGTATG	59.397	38.462	0.00	0.00	0.00	2.39
338	388	9.748708	TTGTTAATTCAGAAACTCAATTTCCAG	57.251	29.630	0.00	0.00	46.94	3.86
359	409	2.289547	GCAAGAAAGTCGTGGCTTGTTA	59.710	45.455	0.00	0.00	39.79	2.41
363	413	0.663153	GTGCAAGAAAGTCGTGGCTT	59.337	50.000	0.00	0.00	0.00	4.35
427	486	3.944476	CAGGTTTCTGGTGCTAGCT	57.056	52.632	17.23	0.00	37.36	3.32
455	514	7.809880	AACTCCTCATTTTAACCTACCTACT	57.190	36.000	0.00	0.00	0.00	2.57
676	752	4.644685	TCAAAGTGAAAGGTCTTCAAAGGG	59.355	41.667	0.00	0.00	0.00	3.95
686	818	6.830838	AGACAAGAAGAATCAAAGTGAAAGGT	59.169	34.615	0.00	0.00	0.00	3.50
777	1060	3.796504	GCACCTGCACATAATGTATTGGC	60.797	47.826	0.00	0.00	41.59	4.52
797	1080	0.532573	GTGTCTAGCTAGTGCCTGCA	59.467	55.000	20.10	8.29	40.80	4.41
798	1081	0.179097	GGTGTCTAGCTAGTGCCTGC	60.179	60.000	20.10	6.36	40.80	4.85
799	1082	1.407258	GAGGTGTCTAGCTAGTGCCTG	59.593	57.143	26.15	4.16	40.80	4.85
800	1083	1.686741	GGAGGTGTCTAGCTAGTGCCT	60.687	57.143	23.36	23.36	40.80	4.75
801	1084	0.747852	GGAGGTGTCTAGCTAGTGCC	59.252	60.000	20.10	18.38	40.80	5.01
802	1085	1.475403	TGGAGGTGTCTAGCTAGTGC	58.525	55.000	20.10	14.31	34.13	4.40
853	1136	5.937975	TGCATATGTCATAGCTAGGCATA	57.062	39.130	18.18	18.18	0.00	3.14
918	1201	3.096092	TGGAGAGAAGAGAAGAGGAAGC	58.904	50.000	0.00	0.00	0.00	3.86
920	1203	4.085733	CAGTGGAGAGAAGAGAAGAGGAA	58.914	47.826	0.00	0.00	0.00	3.36
1012	1324	2.039624	GTGCCCCTGGGAGAGAGA	59.960	66.667	16.20	0.00	37.50	3.10
1083	1398	2.283173	TGCTCCCTCTCGTGCTGA	60.283	61.111	0.00	0.00	0.00	4.26
1087	1402	1.821061	AACAGGTGCTCCCTCTCGTG	61.821	60.000	0.00	0.00	43.86	4.35
1200	1515	2.111999	CTTTGTCGCCAGGGGAGTCA	62.112	60.000	6.42	0.00	0.00	3.41
1218	1533	0.605589	CGAAAGACAGGAGCAGGTCT	59.394	55.000	0.00	0.00	45.85	3.85
1350	1665	1.626654	CGAAGTGCACGATGTGTCCC	61.627	60.000	12.01	0.00	35.75	4.46
1354	1669	0.987715	CTCTCGAAGTGCACGATGTG	59.012	55.000	12.01	6.13	39.02	3.21
1556	1871	3.592814	CCACGGAGCGGCGATAGA	61.593	66.667	12.98	0.00	39.76	1.98
1609	1924	9.261180	GCTTTGTTCTTGAGTGCTGTATATATA	57.739	33.333	0.00	0.00	0.00	0.86
1610	1925	7.770433	TGCTTTGTTCTTGAGTGCTGTATATAT	59.230	33.333	0.00	0.00	0.00	0.86
1611	1926	7.064609	GTGCTTTGTTCTTGAGTGCTGTATATA	59.935	37.037	0.00	0.00	0.00	0.86
1612	1927	5.939883	TGCTTTGTTCTTGAGTGCTGTATAT	59.060	36.000	0.00	0.00	0.00	0.86
1613	1928	5.179368	GTGCTTTGTTCTTGAGTGCTGTATA	59.821	40.000	0.00	0.00	0.00	1.47
1614	1929	4.023707	GTGCTTTGTTCTTGAGTGCTGTAT	60.024	41.667	0.00	0.00	0.00	2.29
1615	1930	3.312421	GTGCTTTGTTCTTGAGTGCTGTA	59.688	43.478	0.00	0.00	0.00	2.74
1639	1954	6.588348	TCTAAGTCATGTTGCATGTTATCG	57.412	37.500	8.68	0.00	0.00	2.92
1655	1970	2.680312	TCAGCACCTGCATCTAAGTC	57.320	50.000	0.00	0.00	45.16	3.01
1694	2016	2.684881	CAAGAATTCACCGGAGAATGGG	59.315	50.000	25.10	12.55	38.21	4.00
1858	2180	4.016706	GCGTAGGGGCTGTGGTGT	62.017	66.667	0.00	0.00	0.00	4.16
1925	2247	6.475504	ACAGATGTGTATGAATGGAACTTGA	58.524	36.000	0.00	0.00	34.05	3.02
2108	2458	3.491342	TGTCACTCAGTTCAGAGTAGCT	58.509	45.455	0.00	0.00	46.65	3.32
2118	2468	3.498774	ATTCAAGCCTGTCACTCAGTT	57.501	42.857	0.00	0.00	42.19	3.16
2460	2838	3.309296	TGTTTCTTGAGGAGACTGGAGT	58.691	45.455	0.00	0.00	44.43	3.85
2467	2845	7.557719	GGGATATGAATTTGTTTCTTGAGGAGA	59.442	37.037	0.00	0.00	35.23	3.71
2602	2990	4.943705	TGAGAAGGTAAGGTGAATGCATTC	59.056	41.667	28.83	28.83	37.31	2.67
2939	3462	3.574396	TCCTATTAGGGCAGATTGAGACG	59.426	47.826	9.88	0.00	35.59	4.18
2996	3522	0.108585	TGTGTCTGGAACTTGCCTCC	59.891	55.000	0.00	0.00	0.00	4.30

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.