AutoCloner

Multiple sequence alignment - TraesCS5B01G302600

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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	TraesCS5B01G302600	chr5B	100.000	3098	0	0	1	3098	487246744	487249841	0.000000e+00	5722.0
1	TraesCS5B01G302600	chr5B	100.000	84	0	0	2823	2906	487249532	487249615	4.140000e-34	156.0
2	TraesCS5B01G302600	chr5B	100.000	84	0	0	2789	2872	487249566	487249649	4.140000e-34	156.0
3	TraesCS5B01G302600	chr5B	100.000	50	0	0	2857	2906	487249532	487249581	3.290000e-15	93.5
4	TraesCS5B01G302600	chr5B	100.000	50	0	0	2789	2838	487249600	487249649	3.290000e-15	93.5
5	TraesCS5B01G302600	chr5A	92.405	2857	140	23	1	2838	511962000	511964798	0.000000e+00	4002.0
6	TraesCS5B01G302600	chr5A	97.980	99	2	0	2871	2969	511964763	511964861	4.110000e-39	172.0
7	TraesCS5B01G302600	chr5A	88.660	97	5	2	2905	3001	512024562	512024652	2.520000e-21	113.0
8	TraesCS5B01G302600	chr5A	90.244	82	5	2	2725	2803	511964798	511964879	1.520000e-18	104.0
9	TraesCS5B01G302600	chr5A	100.000	36	0	0	2837	2872	511964763	511964798	1.990000e-07	67.6
10	TraesCS5B01G302600	chr5D	96.580	2105	66	5	739	2838	406350017	406352120	0.000000e+00	3483.0
11	TraesCS5B01G302600	chr5D	90.305	753	63	6	1	747	406345543	406346291	0.000000e+00	977.0
12	TraesCS5B01G302600	chr5D	95.062	243	11	1	2857	3098	406352070	406352312	6.270000e-102	381.0
13	TraesCS5B01G302600	chr5D	79.602	201	27	9	92	281	423223640	423223837	6.970000e-27	132.0
14	TraesCS5B01G302600	chr2A	85.258	1723	201	26	1109	2799	21193206	21191505	0.000000e+00	1725.0
15	TraesCS5B01G302600	chr2A	85.194	1675	194	24	1100	2729	21005058	21006723	0.000000e+00	1670.0
16	TraesCS5B01G302600	chr2A	84.316	1696	219	18	1099	2757	21178968	21177283	0.000000e+00	1615.0
17	TraesCS5B01G302600	chr2A	85.183	1586	196	14	1099	2657	21149813	21148240	0.000000e+00	1591.0
18	TraesCS5B01G302600	chr2A	83.427	531	82	3	1099	1629	21180892	21180368	3.590000e-134	488.0
19	TraesCS5B01G302600	chr2A	86.813	182	20	2	970	1150	10550454	10550276	1.880000e-47	200.0
20	TraesCS5B01G302600	chr2B	85.767	1637	189	20	1093	2696	33729953	33728328	0.000000e+00	1692.0
21	TraesCS5B01G302600	chr2B	84.360	1688	219	18	1104	2756	33664633	33662956	0.000000e+00	1613.0
22	TraesCS5B01G302600	chr2B	85.874	538	69	3	1093	1629	33578463	33578994	1.610000e-157	566.0
23	TraesCS5B01G302600	chr2D	84.229	1674	214	18	1099	2734	20323133	20324794	0.000000e+00	1583.0
24	TraesCS5B01G302600	chr2D	87.349	1328	129	14	1060	2355	10314886	10313566	0.000000e+00	1485.0
25	TraesCS5B01G302600	chr2D	86.988	1099	139	3	1634	2729	20382124	20381027	0.000000e+00	1234.0
26	TraesCS5B01G302600	chr2D	85.299	551	72	5	1093	1642	20382687	20382145	7.500000e-156	560.0
27	TraesCS5B01G302600	chr2D	85.932	526	68	1	1104	1629	20314919	20315438	9.700000e-155	556.0
28	TraesCS5B01G302600	chr3D	80.226	177	24	5	127	297	497513454	497513283	4.200000e-24	122.0
29	TraesCS5B01G302600	chr7B	76.847	203	44	3	432	631	728629161	728629363	9.080000e-21	111.0
30	TraesCS5B01G302600	chr7D	71.935	310	69	13	329	631	627354558	627354260	1.190000e-09	75.0

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	TraesCS5B01G302600	chr5B	487246744	487249841	3097	False	1244.200000	5722	100.000000	1	3098	5	chr5B.!!$F1	3097
1	TraesCS5B01G302600	chr5A	511962000	511964879	2879	False	1086.400000	4002	95.157250	1	2969	4	chr5A.!!$F2	2968
2	TraesCS5B01G302600	chr5D	406345543	406352312	6769	False	1613.666667	3483	93.982333	1	3098	3	chr5D.!!$F2	3097
3	TraesCS5B01G302600	chr2A	21191505	21193206	1701	True	1725.000000	1725	85.258000	1109	2799	1	chr2A.!!$R3	1690
4	TraesCS5B01G302600	chr2A	21005058	21006723	1665	False	1670.000000	1670	85.194000	1100	2729	1	chr2A.!!$F1	1629
5	TraesCS5B01G302600	chr2A	21148240	21149813	1573	True	1591.000000	1591	85.183000	1099	2657	1	chr2A.!!$R2	1558
6	TraesCS5B01G302600	chr2A	21177283	21180892	3609	True	1051.500000	1615	83.871500	1099	2757	2	chr2A.!!$R4	1658
7	TraesCS5B01G302600	chr2B	33728328	33729953	1625	True	1692.000000	1692	85.767000	1093	2696	1	chr2B.!!$R2	1603
8	TraesCS5B01G302600	chr2B	33662956	33664633	1677	True	1613.000000	1613	84.360000	1104	2756	1	chr2B.!!$R1	1652
9	TraesCS5B01G302600	chr2B	33578463	33578994	531	False	566.000000	566	85.874000	1093	1629	1	chr2B.!!$F1	536
10	TraesCS5B01G302600	chr2D	20323133	20324794	1661	False	1583.000000	1583	84.229000	1099	2734	1	chr2D.!!$F2	1635
11	TraesCS5B01G302600	chr2D	10313566	10314886	1320	True	1485.000000	1485	87.349000	1060	2355	1	chr2D.!!$R1	1295
12	TraesCS5B01G302600	chr2D	20381027	20382687	1660	True	897.000000	1234	86.143500	1093	2729	2	chr2D.!!$R2	1636
13	TraesCS5B01G302600	chr2D	20314919	20315438	519	False	556.000000	556	85.932000	1104	1629	1	chr2D.!!$F1	525

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
545	553	1.207329	GCCACCACCTAGTCGATTTCT	59.793	52.381	0.0	0.0	0.0	2.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2568	8298	1.402456	CCTCCAACTACACCGACTTCG	60.402	57.143	0.0	0.0	39.44	3.79	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
125	128	5.763876	AAGCCGAAGATAAGCCCTAATAT	57.236	39.130	0.00	0.00	0.00	1.28
297	305	3.192633	CCCGAAAAATGTCCAGGTTTAGG	59.807	47.826	0.00	0.00	0.00	2.69
350	358	5.455392	CAGAAGATGTTGAAATTGTCGCTT	58.545	37.500	0.00	0.00	0.00	4.68
363	371	2.179018	CGCTTCAATGGCCAACCG	59.821	61.111	10.96	0.21	39.70	4.44
390	398	3.571590	TCTTTGTAAAGGGCACACCAAT	58.428	40.909	4.67	0.00	43.89	3.16
419	427	5.794894	AGATCTGAAACGTGTCAATAGGTT	58.205	37.500	10.22	0.00	0.00	3.50
542	550	1.515954	CGCCACCACCTAGTCGATT	59.484	57.895	0.00	0.00	0.00	3.34
545	553	1.207329	GCCACCACCTAGTCGATTTCT	59.793	52.381	0.00	0.00	0.00	2.52
548	556	3.181485	CCACCACCTAGTCGATTTCTCTC	60.181	52.174	0.00	0.00	0.00	3.20
591	603	1.698874	AAAAGGATGGATGGGTCCCT	58.301	50.000	10.00	0.00	44.41	4.20
646	658	3.069318	GAGAAGGGGGAGCGACGT	61.069	66.667	0.00	0.00	0.00	4.34
687	699	2.740826	CGACGACGGCCATGGTTT	60.741	61.111	14.67	0.00	35.72	3.27
694	706	1.207329	GACGGCCATGGTTTAGAGAGT	59.793	52.381	14.67	2.18	0.00	3.24
840	4586	3.431673	TGGCTATTGTCATCACCAACA	57.568	42.857	0.00	0.00	0.00	3.33
945	4691	8.348285	TGAAAACAGAAATCATTAGTTAGGGG	57.652	34.615	0.00	0.00	0.00	4.79
1243	4992	0.107831	TGCCACTTTGGTAGCTCGTT	59.892	50.000	0.00	0.00	40.46	3.85
1407	5156	1.283793	CTTTGCCGTTCCAGTGCTG	59.716	57.895	0.00	0.00	0.00	4.41
1575	7249	0.034896	TCGTTGGTGAGGGCTTTCTC	59.965	55.000	0.00	0.00	0.00	2.87
1775	7476	0.175989	GAGGTACAGGGCTTCGAAGG	59.824	60.000	25.77	11.96	0.00	3.46
1954	7678	3.842126	CACGACAGCACGATGCCG	61.842	66.667	6.39	6.12	46.52	5.69
1955	7679	4.050934	ACGACAGCACGATGCCGA	62.051	61.111	0.00	0.00	46.52	5.54
1956	7680	2.809174	CGACAGCACGATGCCGAA	60.809	61.111	6.39	0.00	46.52	4.30
1957	7681	2.379634	CGACAGCACGATGCCGAAA	61.380	57.895	6.39	0.00	46.52	3.46
1958	7682	1.695893	CGACAGCACGATGCCGAAAT	61.696	55.000	6.39	0.00	46.52	2.17
1959	7683	0.447801	GACAGCACGATGCCGAAATT	59.552	50.000	6.39	0.00	46.52	1.82
1960	7684	0.168788	ACAGCACGATGCCGAAATTG	59.831	50.000	6.39	1.22	46.52	2.32
1961	7685	1.135699	CAGCACGATGCCGAAATTGC	61.136	55.000	6.39	0.00	46.52	3.56
1962	7686	1.873572	GCACGATGCCGAAATTGCC	60.874	57.895	0.00	0.00	37.42	4.52
1963	7687	1.583451	CACGATGCCGAAATTGCCG	60.583	57.895	0.00	0.00	39.50	5.69
1964	7688	2.651863	CGATGCCGAAATTGCCGC	60.652	61.111	0.00	0.00	38.22	6.53
1965	7689	2.278792	GATGCCGAAATTGCCGCC	60.279	61.111	0.00	0.00	0.00	6.13
1966	7690	4.191950	ATGCCGAAATTGCCGCCG	62.192	61.111	0.00	0.00	0.00	6.46
2022	7746	2.282180	GGCCTTCTTGTCCGCCAA	60.282	61.111	0.00	0.00	41.25	4.52
2284	8014	1.153549	GAGCTTGGCGAGGTCGATT	60.154	57.895	17.52	0.00	42.45	3.34
2314	8044	3.241530	TCGCTGTTGGGGCAGACT	61.242	61.111	0.00	0.00	38.70	3.24
2443	8173	1.520120	CATCACGATGCAGAGCGGT	60.520	57.895	10.49	0.00	34.48	5.68
2568	8298	2.887568	CGTGGAGATGCAGCGGAC	60.888	66.667	0.00	0.00	0.00	4.79
2589	8322	1.617357	GAAGTCGGTGTAGTTGGAGGT	59.383	52.381	0.00	0.00	0.00	3.85
2965	8713	7.238486	TGGTTAATTACATGCATGGAAGTTT	57.762	32.000	27.96	20.18	33.38	2.66
3045	8793	2.621055	GGCCGGTTAATTACATGCATGA	59.379	45.455	32.75	12.33	0.00	3.07
3061	8809	4.692228	TGCATGAAAGTTTCTTCCCAAAC	58.308	39.130	16.33	0.00	36.64	2.93
3078	8826	5.729229	TCCCAAACCAAGTAGGAGATGAATA	59.271	40.000	0.00	0.00	41.22	1.75
3086	8834	6.373774	CCAAGTAGGAGATGAATATGATTGGC	59.626	42.308	0.00	0.00	41.22	4.52
3087	8835	6.059787	AGTAGGAGATGAATATGATTGGCC	57.940	41.667	0.00	0.00	0.00	5.36
3090	8838	3.307691	GGAGATGAATATGATTGGCCGGA	60.308	47.826	5.05	0.00	0.00	5.14

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
17	18	2.391130	TGGGGTGTTGCTCCAACCT	61.391	57.895	9.65	0.00	46.79	3.50
50	51	3.903714	TCTATCCGATGGTGATGGACAAT	59.096	43.478	0.00	0.00	33.91	2.71
206	213	2.430332	CCGGCCCAAAACACATGAATAT	59.570	45.455	0.00	0.00	0.00	1.28
208	215	0.607620	CCGGCCCAAAACACATGAAT	59.392	50.000	0.00	0.00	0.00	2.57
273	280	0.898326	ACCTGGACATTTTTCGGGCC	60.898	55.000	0.00	0.00	0.00	5.80
275	282	3.192633	CCTAAACCTGGACATTTTTCGGG	59.807	47.826	0.00	0.00	0.00	5.14
281	289	3.562176	CCTCTGCCTAAACCTGGACATTT	60.562	47.826	0.00	0.00	0.00	2.32
319	327	5.833406	TTTCAACATCTTCTGCAACTTGA	57.167	34.783	0.00	0.00	0.00	3.02
322	330	6.152932	ACAATTTCAACATCTTCTGCAACT	57.847	33.333	0.00	0.00	0.00	3.16
350	358	2.569354	GCAACCGGTTGGCCATTGA	61.569	57.895	40.34	0.00	40.74	2.57
363	371	1.960689	TGCCCTTTACAAAGAGCAACC	59.039	47.619	8.26	0.00	45.01	3.77
390	398	7.905604	ATTGACACGTTTCAGATCTTGATAA	57.094	32.000	4.36	0.00	35.27	1.75
419	427	7.121463	GTGAGAGTTTGTGTCTCTAGATCCTAA	59.879	40.741	0.00	0.00	41.58	2.69
463	471	1.955080	ACCTCTACGATGTTCGATCCC	59.045	52.381	3.62	0.00	43.74	3.85
468	476	3.875727	TCTTCCTACCTCTACGATGTTCG	59.124	47.826	0.00	0.00	46.93	3.95
483	491	1.341778	GGTCCCTTCGGTCTCTTCCTA	60.342	57.143	0.00	0.00	0.00	2.94
487	495	2.617840	TAAGGTCCCTTCGGTCTCTT	57.382	50.000	0.89	0.00	37.47	2.85
542	550	3.570912	AGGTTTTGTTTCCCGAGAGAA	57.429	42.857	0.00	0.00	0.00	2.87
545	553	2.039348	CCCTAGGTTTTGTTTCCCGAGA	59.961	50.000	8.29	0.00	0.00	4.04
548	556	2.039348	TCTCCCTAGGTTTTGTTTCCCG	59.961	50.000	8.29	0.00	0.00	5.14
583	595	1.694693	GGCAAGGATAGTAGGGACCCA	60.695	57.143	14.60	0.00	0.00	4.51
591	603	1.038681	TGTCGGCGGCAAGGATAGTA	61.039	55.000	13.70	0.00	0.00	1.82
646	658	2.758207	TTTCTTCCCCACACCGCCA	61.758	57.895	0.00	0.00	0.00	5.69
682	694	3.510360	GGTAGCACAGACTCTCTAAACCA	59.490	47.826	0.00	0.00	0.00	3.67
687	699	4.302559	TCTTGGTAGCACAGACTCTCTA	57.697	45.455	0.00	0.00	0.00	2.43
694	706	2.723273	TCTCGATCTTGGTAGCACAGA	58.277	47.619	0.00	1.74	0.00	3.41
945	4691	2.159379	GCCAACATAGCTGCAAAGGTAC	60.159	50.000	1.02	0.00	0.00	3.34
1407	5156	3.179830	CTCTACAACATCCAGTACGTGC	58.820	50.000	0.00	0.00	0.00	5.34
1775	7476	1.659098	CGTAGAAAATCGTCAGGCCAC	59.341	52.381	5.01	0.00	0.00	5.01
1974	7698	4.161295	TCTTCTGGGCCATCCGCG	62.161	66.667	6.72	0.00	38.94	6.46
1975	7699	2.203126	CTCTTCTGGGCCATCCGC	60.203	66.667	6.72	0.00	38.76	5.54
1976	7700	2.317149	GACCTCTTCTGGGCCATCCG	62.317	65.000	6.72	0.00	38.76	4.18
2022	7746	1.814527	GACGCCTACGGGAATCTGT	59.185	57.895	0.00	0.00	46.04	3.41
2314	8044	2.043248	GGCCTCTCCTACCGGTCA	60.043	66.667	12.40	0.00	0.00	4.02
2426	8156	1.520120	CACCGCTCTGCATCGTGAT	60.520	57.895	0.00	0.00	0.00	3.06
2568	8298	1.402456	CCTCCAACTACACCGACTTCG	60.402	57.143	0.00	0.00	39.44	3.79
2580	8313	1.006102	CTTGCGTCGACCTCCAACT	60.006	57.895	10.58	0.00	0.00	3.16
2613	8346	4.284746	TGGTTTGTTTCTTGGGTTTGTTCT	59.715	37.500	0.00	0.00	0.00	3.01
2617	8350	4.764172	TCATGGTTTGTTTCTTGGGTTTG	58.236	39.130	0.00	0.00	0.00	2.93
2820	8568	6.600882	ACGGACTTCTCCTACTTGATTTTA	57.399	37.500	0.00	0.00	33.79	1.52
2822	8570	5.485209	AACGGACTTCTCCTACTTGATTT	57.515	39.130	0.00	0.00	33.79	2.17
2823	8571	5.480205	GAAACGGACTTCTCCTACTTGATT	58.520	41.667	0.00	0.00	33.79	2.57
2824	8572	4.380655	CGAAACGGACTTCTCCTACTTGAT	60.381	45.833	0.00	0.00	33.79	2.57
2825	8573	3.057736	CGAAACGGACTTCTCCTACTTGA	60.058	47.826	0.00	0.00	33.79	3.02
2826	8574	3.057736	TCGAAACGGACTTCTCCTACTTG	60.058	47.826	0.00	0.00	33.79	3.16
2827	8575	3.152341	TCGAAACGGACTTCTCCTACTT	58.848	45.455	0.00	0.00	33.79	2.24
2828	8576	2.787994	TCGAAACGGACTTCTCCTACT	58.212	47.619	0.00	0.00	33.79	2.57
2829	8577	3.565905	TTCGAAACGGACTTCTCCTAC	57.434	47.619	0.00	0.00	33.79	3.18
2830	8578	4.589216	TTTTCGAAACGGACTTCTCCTA	57.411	40.909	10.79	0.00	33.79	2.94
2831	8579	3.464111	TTTTCGAAACGGACTTCTCCT	57.536	42.857	10.79	0.00	33.79	3.69
2850	8598	8.947115	CGGACTTCTCCTACTTGATTTTATTTT	58.053	33.333	0.00	0.00	33.79	1.82
2851	8599	8.101419	ACGGACTTCTCCTACTTGATTTTATTT	58.899	33.333	0.00	0.00	33.79	1.40
2852	8600	7.621796	ACGGACTTCTCCTACTTGATTTTATT	58.378	34.615	0.00	0.00	33.79	1.40
2853	8601	7.184067	ACGGACTTCTCCTACTTGATTTTAT	57.816	36.000	0.00	0.00	33.79	1.40
2854	8602	6.600882	ACGGACTTCTCCTACTTGATTTTA	57.399	37.500	0.00	0.00	33.79	1.52
2855	8603	5.485209	ACGGACTTCTCCTACTTGATTTT	57.515	39.130	0.00	0.00	33.79	1.82
2856	8604	5.485209	AACGGACTTCTCCTACTTGATTT	57.515	39.130	0.00	0.00	33.79	2.17
2857	8605	5.480205	GAAACGGACTTCTCCTACTTGATT	58.520	41.667	0.00	0.00	33.79	2.57
2858	8606	4.380655	CGAAACGGACTTCTCCTACTTGAT	60.381	45.833	0.00	0.00	33.79	2.57
2859	8607	3.057736	CGAAACGGACTTCTCCTACTTGA	60.058	47.826	0.00	0.00	33.79	3.02
2860	8608	3.057736	TCGAAACGGACTTCTCCTACTTG	60.058	47.826	0.00	0.00	33.79	3.16
2861	8609	3.152341	TCGAAACGGACTTCTCCTACTT	58.848	45.455	0.00	0.00	33.79	2.24
2862	8610	2.787994	TCGAAACGGACTTCTCCTACT	58.212	47.619	0.00	0.00	33.79	2.57
2863	8611	3.565905	TTCGAAACGGACTTCTCCTAC	57.434	47.619	0.00	0.00	33.79	3.18
2864	8612	4.589216	TTTTCGAAACGGACTTCTCCTA	57.411	40.909	10.79	0.00	33.79	2.94
2865	8613	3.464111	TTTTCGAAACGGACTTCTCCT	57.536	42.857	10.79	0.00	33.79	3.69
2945	8693	7.178274	ACCAAGAAACTTCCATGCATGTAATTA	59.822	33.333	24.58	4.86	0.00	1.40
2965	8713	4.518970	GGTGAATTAGAACAAGCACCAAGA	59.481	41.667	0.00	0.00	43.87	3.02
3045	8793	5.362717	CCTACTTGGTTTGGGAAGAAACTTT	59.637	40.000	0.00	0.00	36.30	2.66
3061	8809	6.373774	GCCAATCATATTCATCTCCTACTTGG	59.626	42.308	0.00	0.00	33.17	3.61
3078	8826	0.987294	CCTCCTATCCGGCCAATCAT	59.013	55.000	2.24	0.00	0.00	2.45

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.