AutoCloner

Multiple sequence alignment - TraesCS5B01G408900

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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	TraesCS5B01G408900	chr5B	100.000	2367	0	0	1	2367	584274196	584276562	0.000000e+00	4372.0
1	TraesCS5B01G408900	chr5B	90.879	1491	112	12	899	2367	320484386	320482898	0.000000e+00	1978.0
2	TraesCS5B01G408900	chr5B	83.799	537	72	15	37	565	88345788	88345259	1.630000e-136	496.0
3	TraesCS5B01G408900	chr5B	98.113	53	1	0	1	53	584274268	584274320	2.500000e-15	93.5
4	TraesCS5B01G408900	chr1B	91.207	1831	138	13	557	2367	308913174	308915001	0.000000e+00	2468.0
5	TraesCS5B01G408900	chr1B	85.066	529	66	10	46	565	373632108	373632632	5.790000e-146	527.0
6	TraesCS5B01G408900	chr1B	85.825	388	38	9	37	414	596261400	596261780	1.700000e-106	396.0
7	TraesCS5B01G408900	chr1B	88.679	53	6	0	1	53	670572738	670572790	5.460000e-07	65.8
8	TraesCS5B01G408900	chr5D	91.852	1755	115	18	562	2298	247315565	247313821	0.000000e+00	2423.0
9	TraesCS5B01G408900	chr5D	80.996	542	75	17	37	565	452554509	452553983	2.830000e-109	405.0
10	TraesCS5B01G408900	chr3B	90.879	1820	133	16	566	2367	120409061	120407257	0.000000e+00	2410.0
11	TraesCS5B01G408900	chr3B	90.164	1830	141	18	565	2367	161796529	161794712	0.000000e+00	2346.0
12	TraesCS5B01G408900	chr3B	81.437	501	72	16	73	565	36381233	36380746	7.930000e-105	390.0
13	TraesCS5B01G408900	chr3D	90.616	1833	142	15	562	2367	126392960	126394789	0.000000e+00	2405.0
14	TraesCS5B01G408900	chr3D	88.679	53	6	0	1	53	374581300	374581352	5.460000e-07	65.8
15	TraesCS5B01G408900	chrUn	90.799	1815	132	16	562	2358	218123472	218121675	0.000000e+00	2394.0
16	TraesCS5B01G408900	chrUn	91.330	1511	110	11	562	2053	366980020	366978512	0.000000e+00	2045.0
17	TraesCS5B01G408900	chrUn	83.613	537	62	14	46	565	61035745	61035218	4.580000e-132	481.0
18	TraesCS5B01G408900	chr4A	90.445	1821	143	18	567	2363	712562596	712560783	0.000000e+00	2370.0
19	TraesCS5B01G408900	chr4A	89.989	1828	137	11	562	2367	701567035	701565232	0.000000e+00	2320.0
20	TraesCS5B01G408900	chr2B	90.400	1823	146	11	562	2363	625913163	625914977	0.000000e+00	2370.0
21	TraesCS5B01G408900	chr2B	89.989	1828	138	21	562	2367	733144233	733146037	0.000000e+00	2320.0
22	TraesCS5B01G408900	chr4B	90.268	1829	145	19	562	2367	71568851	71567033	0.000000e+00	2361.0
23	TraesCS5B01G408900	chr4B	90.149	1817	146	11	566	2363	221186826	221185024	0.000000e+00	2333.0
24	TraesCS5B01G408900	chr7D	87.486	1846	199	19	545	2367	182612304	182610468	0.000000e+00	2100.0
25	TraesCS5B01G408900	chr6B	92.774	941	51	6	1439	2363	651405457	651406396	0.000000e+00	1345.0
26	TraesCS5B01G408900	chr6B	80.157	509	77	17	60	565	202591428	202590941	2.240000e-95	359.0
27	TraesCS5B01G408900	chr2D	83.738	535	76	9	37	565	505534419	505533890	1.630000e-136	496.0
28	TraesCS5B01G408900	chr2D	83.577	548	67	12	37	565	460867494	460866951	2.110000e-135	492.0
29	TraesCS5B01G408900	chr2D	83.425	543	62	17	46	560	306627378	306626836	1.650000e-131	479.0
30	TraesCS5B01G408900	chr3A	82.474	485	71	9	85	558	588840665	588841146	1.690000e-111	412.0
31	TraesCS5B01G408900	chr5A	78.700	554	84	21	37	565	363873185	363873729	2.910000e-89	339.0
32	TraesCS5B01G408900	chr1A	100.000	29	0	0	13	41	266901593	266901565	1.000000e-03	54.7

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	TraesCS5B01G408900	chr5B	584274196	584276562	2366	False	2232.75	4372	99.0565	1	2367	2	chr5B.!!$F1	2366
1	TraesCS5B01G408900	chr5B	320482898	320484386	1488	True	1978.00	1978	90.8790	899	2367	1	chr5B.!!$R2	1468
2	TraesCS5B01G408900	chr5B	88345259	88345788	529	True	496.00	496	83.7990	37	565	1	chr5B.!!$R1	528
3	TraesCS5B01G408900	chr1B	308913174	308915001	1827	False	2468.00	2468	91.2070	557	2367	1	chr1B.!!$F1	1810
4	TraesCS5B01G408900	chr1B	373632108	373632632	524	False	527.00	527	85.0660	46	565	1	chr1B.!!$F2	519
5	TraesCS5B01G408900	chr5D	247313821	247315565	1744	True	2423.00	2423	91.8520	562	2298	1	chr5D.!!$R1	1736
6	TraesCS5B01G408900	chr5D	452553983	452554509	526	True	405.00	405	80.9960	37	565	1	chr5D.!!$R2	528
7	TraesCS5B01G408900	chr3B	120407257	120409061	1804	True	2410.00	2410	90.8790	566	2367	1	chr3B.!!$R2	1801
8	TraesCS5B01G408900	chr3B	161794712	161796529	1817	True	2346.00	2346	90.1640	565	2367	1	chr3B.!!$R3	1802
9	TraesCS5B01G408900	chr3D	126392960	126394789	1829	False	2405.00	2405	90.6160	562	2367	1	chr3D.!!$F1	1805
10	TraesCS5B01G408900	chrUn	218121675	218123472	1797	True	2394.00	2394	90.7990	562	2358	1	chrUn.!!$R2	1796
11	TraesCS5B01G408900	chrUn	366978512	366980020	1508	True	2045.00	2045	91.3300	562	2053	1	chrUn.!!$R3	1491
12	TraesCS5B01G408900	chrUn	61035218	61035745	527	True	481.00	481	83.6130	46	565	1	chrUn.!!$R1	519
13	TraesCS5B01G408900	chr4A	712560783	712562596	1813	True	2370.00	2370	90.4450	567	2363	1	chr4A.!!$R2	1796
14	TraesCS5B01G408900	chr4A	701565232	701567035	1803	True	2320.00	2320	89.9890	562	2367	1	chr4A.!!$R1	1805
15	TraesCS5B01G408900	chr2B	625913163	625914977	1814	False	2370.00	2370	90.4000	562	2363	1	chr2B.!!$F1	1801
16	TraesCS5B01G408900	chr2B	733144233	733146037	1804	False	2320.00	2320	89.9890	562	2367	1	chr2B.!!$F2	1805
17	TraesCS5B01G408900	chr4B	71567033	71568851	1818	True	2361.00	2361	90.2680	562	2367	1	chr4B.!!$R1	1805
18	TraesCS5B01G408900	chr4B	221185024	221186826	1802	True	2333.00	2333	90.1490	566	2363	1	chr4B.!!$R2	1797
19	TraesCS5B01G408900	chr7D	182610468	182612304	1836	True	2100.00	2100	87.4860	545	2367	1	chr7D.!!$R1	1822
20	TraesCS5B01G408900	chr6B	651405457	651406396	939	False	1345.00	1345	92.7740	1439	2363	1	chr6B.!!$F1	924
21	TraesCS5B01G408900	chr2D	505533890	505534419	529	True	496.00	496	83.7380	37	565	1	chr2D.!!$R3	528
22	TraesCS5B01G408900	chr2D	460866951	460867494	543	True	492.00	492	83.5770	37	565	1	chr2D.!!$R2	528
23	TraesCS5B01G408900	chr2D	306626836	306627378	542	True	479.00	479	83.4250	46	560	1	chr2D.!!$R1	514
24	TraesCS5B01G408900	chr5A	363873185	363873729	544	False	339.00	339	78.7000	37	565	1	chr5A.!!$F1	528

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
930	1024	0.179073	CTGGCTTCGATCCCGACAAT	60.179	55.0	2.26	0.0	45.5	2.71	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2067	2192	0.108804	GCATCTTCTCGAACCACGGA	60.109	55.0	0.0	0.0	42.82	4.69	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
17	18	2.254051	AAATGTCGGCCAAACGCG	59.746	55.556	3.53	3.53	38.94	6.01
18	19	3.889831	AAATGTCGGCCAAACGCGC	62.890	57.895	5.73	0.00	38.94	6.86
26	27	3.427425	CCAAACGCGCCGATCCAA	61.427	61.111	5.73	0.00	0.00	3.53
27	28	2.558821	CAAACGCGCCGATCCAAA	59.441	55.556	5.73	0.00	0.00	3.28
28	29	1.795962	CAAACGCGCCGATCCAAAC	60.796	57.895	5.73	0.00	0.00	2.93
29	30	3.303397	AAACGCGCCGATCCAAACG	62.303	57.895	5.73	0.00	0.00	3.60
36	37	2.776072	CGATCCAAACGGACGCAC	59.224	61.111	0.00	0.00	34.62	5.34
37	38	2.776072	GATCCAAACGGACGCACG	59.224	61.111	0.00	0.00	34.62	5.34
55	56	2.029964	TCCACTTGGCGTCCGTTC	59.970	61.111	0.00	0.00	34.44	3.95
64	65	4.351938	CGTCCGTTCAGGTCGGCA	62.352	66.667	0.00	0.00	45.53	5.69
172	174	4.557942	GCAGGATTTGCGTTGGTG	57.442	55.556	0.00	0.00	44.09	4.17
173	175	1.956043	GCAGGATTTGCGTTGGTGA	59.044	52.632	0.00	0.00	44.09	4.02
176	178	0.400213	AGGATTTGCGTTGGTGAGGA	59.600	50.000	0.00	0.00	0.00	3.71
210	221	4.459089	GCGCGCCTTCTCCTCCTT	62.459	66.667	23.24	0.00	0.00	3.36
218	230	4.798682	TCTCCTCCTTCGGGCCCC	62.799	72.222	18.66	0.00	34.44	5.80
319	359	1.725557	CCATGGACGACGACCTCGAT	61.726	60.000	16.98	0.16	46.14	3.59
321	361	1.725557	ATGGACGACGACCTCGATGG	61.726	60.000	16.98	0.00	46.14	3.51
325	365	4.194720	GACGACCTCGATGGCGCT	62.195	66.667	16.30	3.34	43.02	5.92
390	439	4.785453	CAAGCCTCACGCCCCCTC	62.785	72.222	0.00	0.00	38.78	4.30
420	475	2.047179	GCCGAAGCCGAAGAAGGT	60.047	61.111	0.00	0.00	38.22	3.50
424	479	1.337447	CCGAAGCCGAAGAAGGTGTTA	60.337	52.381	0.00	0.00	38.22	2.41
457	512	1.463674	GGGCAAATGAGTCGACCAAT	58.536	50.000	13.01	3.07	0.00	3.16
591	647	2.735772	GCTCATCCGCCTTCCCTCA	61.736	63.158	0.00	0.00	0.00	3.86
608	664	2.029073	AGACGGTGTTGCCTGACG	59.971	61.111	0.00	0.00	34.25	4.35
656	713	2.642254	CCGGCTTCCACGTCTACCA	61.642	63.158	0.00	0.00	0.00	3.25
658	715	1.874345	CGGCTTCCACGTCTACCAGT	61.874	60.000	0.00	0.00	0.00	4.00
792	869	4.736896	GGAGGCGCGAGGAAACGT	62.737	66.667	12.10	0.00	35.59	3.99
930	1024	0.179073	CTGGCTTCGATCCCGACAAT	60.179	55.000	2.26	0.00	45.50	2.71
1090	1192	0.681564	AGGAAGAGGACGAGTGCGAT	60.682	55.000	0.00	0.00	41.64	4.58
1170	1272	0.959372	AAGCGCAAGAGCAAGCAGAT	60.959	50.000	11.47	0.00	42.27	2.90
1260	1365	4.717629	GGGCGCCGAACAAAAGCC	62.718	66.667	22.54	0.00	46.51	4.35
1270	1375	4.735283	GCCGAACAAAAGCCTTCAACTTTA	60.735	41.667	0.00	0.00	36.35	1.85
1366	1472	1.999735	GTGTCCATTTCGAAGCGATGA	59.000	47.619	9.40	0.00	35.23	2.92
1386	1492	3.138283	TGAAGGGTGATCCAACAAGAGTT	59.862	43.478	0.00	0.00	38.88	3.01
1412	1518	1.678101	AGTTTTGTGCCACTCTTGAGC	59.322	47.619	0.00	0.00	0.00	4.26
1448	1555	2.110967	GTGAGCAGCATCGGCATGT	61.111	57.895	0.00	0.00	44.61	3.21
1482	1590	2.941415	GCTAGCAAGCTGCCCTCTTTTA	60.941	50.000	10.63	0.00	46.52	1.52
1666	1777	3.347216	AGAAGTTCAAGGCGCAATATGT	58.653	40.909	10.83	0.00	0.00	2.29
1679	1790	2.213499	CAATATGTCGCCCTCAAGTCC	58.787	52.381	0.00	0.00	0.00	3.85
1770	1895	4.934797	TCCAAGAAGGAGGACATCAATT	57.065	40.909	0.00	0.00	43.07	2.32
1873	1998	1.212616	GAACGCCTTCATGGAGATCG	58.787	55.000	1.24	8.27	39.07	3.69
1891	2016	0.742635	CGAAAGGAGGAGGCTTGAGC	60.743	60.000	0.00	0.00	41.14	4.26
2004	2129	0.667487	CGAAAGAAGTGGCTCTCGCA	60.667	55.000	0.00	0.00	38.10	5.10
2014	2139	1.647629	GCTCTCGCAAGCATGATGG	59.352	57.895	0.00	0.00	42.05	3.51
2041	2166	3.117738	GGTGGAGATCATGAAGGTGGATT	60.118	47.826	0.00	0.00	0.00	3.01
2053	2178	0.039527	GGTGGATTTCAACACCGTGC	60.040	55.000	0.00	0.00	46.61	5.34
2061	2186	4.868116	AACACCGTGCCGCCAAGT	62.868	61.111	0.00	0.00	0.00	3.16
2062	2187	4.868116	ACACCGTGCCGCCAAGTT	62.868	61.111	0.00	0.00	0.00	2.66
2067	2192	1.374252	CGTGCCGCCAAGTTAGAGT	60.374	57.895	0.00	0.00	0.00	3.24
2125	2251	1.260825	TCGACGACGAGTGATCTATGC	59.739	52.381	5.75	0.00	43.81	3.14
2179	2308	3.127533	GCTGACATGACCACGGGC	61.128	66.667	0.00	0.00	0.00	6.13
2304	2444	0.392461	AAGCCGACATTGTATGCCGT	60.392	50.000	6.44	0.00	34.18	5.68

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	2.254051	CGCGTTTGGCCGACATTT	59.746	55.556	0.00	0.00	38.94	2.32
1	2	4.398598	GCGCGTTTGGCCGACATT	62.399	61.111	8.43	0.00	38.94	2.71
9	10	2.972144	TTTGGATCGGCGCGTTTGG	61.972	57.895	8.43	0.00	0.00	3.28
10	11	1.795962	GTTTGGATCGGCGCGTTTG	60.796	57.895	8.43	0.00	0.00	2.93
11	12	2.559330	GTTTGGATCGGCGCGTTT	59.441	55.556	8.43	0.00	0.00	3.60
12	13	3.784412	CGTTTGGATCGGCGCGTT	61.784	61.111	8.43	0.00	0.00	4.84
22	23	2.659244	GACGTGCGTCCGTTTGGA	60.659	61.111	13.11	0.00	41.98	3.53
30	31	3.712881	GCCAAGTGGACGTGCGTC	61.713	66.667	15.44	15.44	43.87	5.19
33	34	3.712881	GACGCCAAGTGGACGTGC	61.713	66.667	19.62	0.00	43.88	5.34
34	35	3.041940	GGACGCCAAGTGGACGTG	61.042	66.667	19.62	2.19	43.88	4.49
35	36	4.657824	CGGACGCCAAGTGGACGT	62.658	66.667	16.19	16.19	45.49	4.34
36	37	4.657824	ACGGACGCCAAGTGGACG	62.658	66.667	0.18	7.04	39.44	4.79
37	38	2.280592	AACGGACGCCAAGTGGAC	60.281	61.111	0.18	0.00	37.39	4.02
38	39	2.029964	GAACGGACGCCAAGTGGA	59.970	61.111	0.18	0.00	37.39	4.02
39	40	2.280524	TGAACGGACGCCAAGTGG	60.281	61.111	0.00	0.00	38.53	4.00
40	41	2.317609	CCTGAACGGACGCCAAGTG	61.318	63.158	0.00	0.00	33.16	3.16
41	42	2.030562	CCTGAACGGACGCCAAGT	59.969	61.111	0.00	0.00	33.16	3.16
42	43	2.027625	GACCTGAACGGACGCCAAG	61.028	63.158	0.00	0.00	36.31	3.61
43	44	2.029964	GACCTGAACGGACGCCAA	59.970	61.111	0.00	0.00	36.31	4.52
55	56	3.800685	TTGTGTCCGTGCCGACCTG	62.801	63.158	0.00	0.00	31.35	4.00
64	65	1.964373	GGCCGACATTTGTGTCCGT	60.964	57.895	3.24	0.00	35.52	4.69
157	159	0.400213	TCCTCACCAACGCAAATCCT	59.600	50.000	0.00	0.00	0.00	3.24
169	171	4.436998	CCGCCTCGTGTCCTCACC	62.437	72.222	0.00	0.00	41.09	4.02
170	172	3.371063	TCCGCCTCGTGTCCTCAC	61.371	66.667	0.00	0.00	40.79	3.51
171	173	3.371063	GTCCGCCTCGTGTCCTCA	61.371	66.667	0.00	0.00	0.00	3.86
172	174	4.477975	CGTCCGCCTCGTGTCCTC	62.478	72.222	0.00	0.00	0.00	3.71
367	416	2.669569	GCGTGAGGCTTGCCTTCA	60.670	61.111	15.92	11.75	39.11	3.02
420	475	2.311701	CGCTGTTCGGGCGTTAACA	61.312	57.895	6.39	0.00	46.37	2.41
457	512	1.684734	GTGCCTCCGGTCCTTCCTA	60.685	63.158	0.00	0.00	0.00	2.94
485	540	1.742146	CGATGGCTTCATCCCTCGA	59.258	57.895	2.09	0.00	43.80	4.04
591	647	2.029073	CGTCAGGCAACACCGTCT	59.971	61.111	0.00	0.00	46.52	4.18
870	958	5.592054	TCGAAGATCATGTTCTGGATGTAC	58.408	41.667	7.06	0.00	0.00	2.90
968	1062	2.168313	TGATCTTCATTGTAGCCAGCGA	59.832	45.455	0.00	0.00	0.00	4.93
1170	1272	2.125310	CCGCCGTGTATGCCTTGA	60.125	61.111	0.00	0.00	0.00	3.02
1260	1365	5.411361	TGGACACGAATCCATAAAGTTGAAG	59.589	40.000	8.11	0.00	44.14	3.02
1285	1390	1.446099	GCGCTCATGGAACTCACGA	60.446	57.895	0.00	0.00	0.00	4.35
1366	1472	3.138283	TGAACTCTTGTTGGATCACCCTT	59.862	43.478	0.00	0.00	36.39	3.95
1386	1492	3.088532	AGAGTGGCACAAAACTTGTTGA	58.911	40.909	21.41	0.00	44.16	3.18
1425	1532	4.147449	CGATGCTGCTCACGGGGA	62.147	66.667	0.00	0.00	0.00	4.81
1448	1555	4.380531	GCTTGCTAGCATACCATGTCTTA	58.619	43.478	20.13	0.00	46.95	2.10
1666	1777	3.691342	CACGGGACTTGAGGGCGA	61.691	66.667	0.00	0.00	0.00	5.54
1679	1790	3.365265	GCTTGCTTCCCACCACGG	61.365	66.667	0.00	0.00	0.00	4.94
1770	1895	2.031919	ACGGTTGCGATCAAGGCA	59.968	55.556	0.00	0.00	38.93	4.75
1873	1998	0.617935	AGCTCAAGCCTCCTCCTTTC	59.382	55.000	0.00	0.00	43.38	2.62
1891	2016	1.712977	GCTTGCTTCTCCGCATCCAG	61.713	60.000	0.00	0.00	40.04	3.86
2004	2129	3.743017	ACCCCGGCCATCATGCTT	61.743	61.111	2.24	0.00	0.00	3.91
2014	2139	1.983119	TTCATGATCTCCACCCCGGC	61.983	60.000	0.00	0.00	33.14	6.13
2053	2178	0.736325	CACGGACTCTAACTTGGCGG	60.736	60.000	0.00	0.00	0.00	6.13
2061	2186	2.189594	TCTCGAACCACGGACTCTAA	57.810	50.000	0.00	0.00	42.82	2.10
2062	2187	2.082231	CTTCTCGAACCACGGACTCTA	58.918	52.381	0.00	0.00	42.82	2.43
2067	2192	0.108804	GCATCTTCTCGAACCACGGA	60.109	55.000	0.00	0.00	42.82	4.69
2304	2444	3.690280	TCGACACCATGCCAGCGA	61.690	61.111	0.00	0.00	0.00	4.93
2318	2458	1.141665	CGGCCATGTCTCATGTCGA	59.858	57.895	2.24	0.00	0.00	4.20

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.