AutoCloner

Multiple sequence alignment - TraesCS7A01G449700

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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	TraesCS7A01G449700	chr7A	100.000	2309	0	0	1	2309	643609197	643611505	0.000000e+00	4265.0
1	TraesCS7A01G449700	chr7A	93.313	2333	91	23	1	2309	699322969	699320678	0.000000e+00	3384.0
2	TraesCS7A01G449700	chr7A	96.627	1779	60	0	1	1779	134595897	134597675	0.000000e+00	2953.0
3	TraesCS7A01G449700	chr7A	96.290	1779	65	1	1	1779	192624629	192626406	0.000000e+00	2918.0
4	TraesCS7A01G449700	chr7A	96.284	1184	38	2	728	1911	130557908	130559085	0.000000e+00	1938.0
5	TraesCS7A01G449700	chr7A	96.774	837	27	0	1	837	16878286	16877450	0.000000e+00	1397.0
6	TraesCS7A01G449700	chr7A	96.530	807	22	3	1	801	124062108	124061302	0.000000e+00	1330.0
7	TraesCS7A01G449700	chr7A	82.927	533	34	20	1807	2309	38739008	38739513	5.900000e-116	427.0
8	TraesCS7A01G449700	chr7A	88.814	295	24	5	2015	2309	124060206	124059921	1.010000e-93	353.0
9	TraesCS7A01G449700	chr7A	92.531	241	18	0	2015	2255	38739358	38739598	1.700000e-91	346.0
10	TraesCS7A01G449700	chr7A	87.713	293	27	5	2017	2309	192627531	192627814	1.320000e-87	333.0
11	TraesCS7A01G449700	chr7A	85.443	316	18	6	1953	2255	192627599	192627899	1.040000e-78	303.0
12	TraesCS7A01G449700	chr7A	85.714	266	19	5	1950	2201	192627338	192627598	1.760000e-66	263.0
13	TraesCS7A01G449700	chr7A	94.611	167	9	0	1717	1883	7463043	7462877	2.280000e-65	259.0
14	TraesCS7A01G449700	chr7A	87.440	207	10	4	1953	2158	134597939	134598130	8.300000e-55	224.0
15	TraesCS7A01G449700	chr7A	80.531	226	11	7	1953	2164	38739428	38739634	2.390000e-30	143.0
16	TraesCS7A01G449700	chr7A	91.489	47	4	0	2257	2303	192627889	192627935	5.320000e-07	65.8
17	TraesCS7A01G449700	chr5A	93.603	2126	74	14	1	2110	288269153	288267074	0.000000e+00	3116.0
18	TraesCS7A01G449700	chr5A	90.635	299	16	7	2015	2309	606689923	606690213	1.000000e-103	387.0
19	TraesCS7A01G449700	chr5A	84.543	317	16	6	1953	2251	606689993	606690294	1.350000e-72	283.0
20	TraesCS7A01G449700	chr7D	94.681	1899	67	17	1	1883	16799695	16797815	0.000000e+00	2916.0
21	TraesCS7A01G449700	chr4A	94.368	1900	77	15	1	1883	514407628	514405742	0.000000e+00	2889.0
22	TraesCS7A01G449700	chr4A	97.378	801	21	0	1	801	637837276	637836476	0.000000e+00	1363.0
23	TraesCS7A01G449700	chr4A	85.843	445	30	14	1810	2254	637835558	637835147	2.110000e-120	442.0
24	TraesCS7A01G449700	chr2A	94.125	1532	57	17	409	1908	677899071	677897541	0.000000e+00	2300.0
25	TraesCS7A01G449700	chr2A	95.579	837	25	4	1	837	778395525	778396349	0.000000e+00	1330.0
26	TraesCS7A01G449700	chr2A	91.356	509	23	2	1801	2309	677897573	677897086	0.000000e+00	676.0
27	TraesCS7A01G449700	chr6A	92.535	1621	78	14	648	2251	516297513	516295919	0.000000e+00	2283.0
28	TraesCS7A01G449700	chr6A	95.143	1256	43	7	648	1903	79831454	79830217	0.000000e+00	1965.0
29	TraesCS7A01G449700	chr1A	96.305	1272	46	1	618	1889	480958750	480960020	0.000000e+00	2087.0
30	TraesCS7A01G449700	chr1A	96.655	837	27	1	1	837	559589398	559590233	0.000000e+00	1389.0
31	TraesCS7A01G449700	chr3A	88.927	289	20	1	2015	2303	635314181	635314457	1.700000e-91	346.0

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	TraesCS7A01G449700	chr7A	643609197	643611505	2308	False	4265.000000	4265	100.000000	1	2309	1	chr7A.!!$F2	2308
1	TraesCS7A01G449700	chr7A	699320678	699322969	2291	True	3384.000000	3384	93.313000	1	2309	1	chr7A.!!$R3	2308
2	TraesCS7A01G449700	chr7A	130557908	130559085	1177	False	1938.000000	1938	96.284000	728	1911	1	chr7A.!!$F1	1183
3	TraesCS7A01G449700	chr7A	134595897	134598130	2233	False	1588.500000	2953	92.033500	1	2158	2	chr7A.!!$F4	2157
4	TraesCS7A01G449700	chr7A	16877450	16878286	836	True	1397.000000	1397	96.774000	1	837	1	chr7A.!!$R2	836
5	TraesCS7A01G449700	chr7A	124059921	124062108	2187	True	841.500000	1330	92.672000	1	2309	2	chr7A.!!$R4	2308
6	TraesCS7A01G449700	chr7A	192624629	192627935	3306	False	776.560000	2918	89.329800	1	2309	5	chr7A.!!$F5	2308
7	TraesCS7A01G449700	chr7A	38739008	38739634	626	False	305.333333	427	85.329667	1807	2309	3	chr7A.!!$F3	502
8	TraesCS7A01G449700	chr5A	288267074	288269153	2079	True	3116.000000	3116	93.603000	1	2110	1	chr5A.!!$R1	2109
9	TraesCS7A01G449700	chr7D	16797815	16799695	1880	True	2916.000000	2916	94.681000	1	1883	1	chr7D.!!$R1	1882
10	TraesCS7A01G449700	chr4A	514405742	514407628	1886	True	2889.000000	2889	94.368000	1	1883	1	chr4A.!!$R1	1882
11	TraesCS7A01G449700	chr4A	637835147	637837276	2129	True	902.500000	1363	91.610500	1	2254	2	chr4A.!!$R2	2253
12	TraesCS7A01G449700	chr2A	677897086	677899071	1985	True	1488.000000	2300	92.740500	409	2309	2	chr2A.!!$R1	1900
13	TraesCS7A01G449700	chr2A	778395525	778396349	824	False	1330.000000	1330	95.579000	1	837	1	chr2A.!!$F1	836
14	TraesCS7A01G449700	chr6A	516295919	516297513	1594	True	2283.000000	2283	92.535000	648	2251	1	chr6A.!!$R2	1603
15	TraesCS7A01G449700	chr6A	79830217	79831454	1237	True	1965.000000	1965	95.143000	648	1903	1	chr6A.!!$R1	1255
16	TraesCS7A01G449700	chr1A	480958750	480960020	1270	False	2087.000000	2087	96.305000	618	1889	1	chr1A.!!$F1	1271
17	TraesCS7A01G449700	chr1A	559589398	559590233	835	False	1389.000000	1389	96.655000	1	837	1	chr1A.!!$F2	836

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
482	483	0.32121	CAACTGTGGGATGTGCGGTA	60.321	55.0	0.0	0.0	0.0	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2009	3378	0.034059	CTTGGCGTCTGGTCTTGTCT	59.966	55.0	0.0	0.0	0.0	3.41	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
106	107	0.877071	CTGCATTTGAGGTGCGTCTT	59.123	50.000	0.00	0.00	45.37	3.01
151	152	5.241949	CGAGAGGCCTAGTAAGTATCATTGT	59.758	44.000	4.42	0.00	0.00	2.71
160	161	6.239217	AGTAAGTATCATTGTCCATGCTCA	57.761	37.500	0.00	0.00	32.13	4.26
276	277	1.678970	GGGCGCCAAGATTTCACCT	60.679	57.895	30.85	0.00	0.00	4.00
280	281	2.547855	GGCGCCAAGATTTCACCTTTTT	60.548	45.455	24.80	0.00	0.00	1.94
400	401	3.143933	TCAGGGGTGATATGGATGACCTA	59.856	47.826	0.00	0.00	39.21	3.08
473	474	2.567169	CCTGACACTATCAACTGTGGGA	59.433	50.000	0.00	0.00	36.69	4.37
482	483	0.321210	CAACTGTGGGATGTGCGGTA	60.321	55.000	0.00	0.00	0.00	4.02
1161	1373	2.841044	AAGGTGTCCACGGACCGT	60.841	61.111	15.37	15.37	43.97	4.83
1201	1413	4.520179	AGGTAGAAGGTTTTTCGTGTGTT	58.480	39.130	0.00	0.00	0.00	3.32
1338	1551	9.520515	AAACATGATTTTTATGTAGTCACCTCT	57.479	29.630	0.00	0.00	37.77	3.69
1380	1593	6.136155	TCACTTGGATAGATCATGAGGTACA	58.864	40.000	0.09	0.00	0.00	2.90
1527	1741	1.242076	CAAGAGAGGGCACACAAAGG	58.758	55.000	0.00	0.00	0.00	3.11
1780	2048	5.694910	TGTGAACTTGTTATTCGAGACCTTC	59.305	40.000	0.00	0.00	0.00	3.46
1903	3085	7.331440	TGCAACCTATTTGAAATTATGTGCAAG	59.669	33.333	13.13	0.00	37.39	4.01
2010	3379	4.065321	GTCCATATCCAGACCAGACAAG	57.935	50.000	0.00	0.00	0.00	3.16
2011	3380	3.706594	GTCCATATCCAGACCAGACAAGA	59.293	47.826	0.00	0.00	0.00	3.02
2012	3381	3.706594	TCCATATCCAGACCAGACAAGAC	59.293	47.826	0.00	0.00	0.00	3.01
2013	3382	3.452264	CCATATCCAGACCAGACAAGACA	59.548	47.826	0.00	0.00	0.00	3.41
2014	3383	4.080919	CCATATCCAGACCAGACAAGACAA	60.081	45.833	0.00	0.00	0.00	3.18
2015	3384	3.692257	ATCCAGACCAGACAAGACAAG	57.308	47.619	0.00	0.00	0.00	3.16
2016	3385	2.677914	TCCAGACCAGACAAGACAAGA	58.322	47.619	0.00	0.00	0.00	3.02
2017	3386	2.365617	TCCAGACCAGACAAGACAAGAC	59.634	50.000	0.00	0.00	0.00	3.01
2044	3413	4.640690	AGGTCCCTGGCGTCTGGT	62.641	66.667	12.29	0.00	0.00	4.00
2057	3426	1.260561	CGTCTGGTTCGTTTTGGTCAG	59.739	52.381	0.00	0.00	0.00	3.51
2104	3486	2.659016	CAGAGAGCCAGACGCCAA	59.341	61.111	0.00	0.00	38.78	4.52
2142	3524	1.043816	CCATATCCAGACCAGACGCT	58.956	55.000	0.00	0.00	0.00	5.07
2230	4011	1.039785	CCGATCCAGAGAGCCAGACA	61.040	60.000	0.00	0.00	0.00	3.41
2255	4036	2.115266	CCCTGGCGTTTGGGTCTT	59.885	61.111	0.00	0.00	38.65	3.01
2256	4037	1.971695	CCCTGGCGTTTGGGTCTTC	60.972	63.158	0.00	0.00	38.65	2.87
2257	4038	2.325082	CCTGGCGTTTGGGTCTTCG	61.325	63.158	0.00	0.00	0.00	3.79
2260	4041	1.301479	GGCGTTTGGGTCTTCGTCT	60.301	57.895	0.00	0.00	0.00	4.18
2261	4042	1.566018	GGCGTTTGGGTCTTCGTCTG	61.566	60.000	0.00	0.00	0.00	3.51
2262	4043	1.566018	GCGTTTGGGTCTTCGTCTGG	61.566	60.000	0.00	0.00	0.00	3.86
2263	4044	0.949105	CGTTTGGGTCTTCGTCTGGG	60.949	60.000	0.00	0.00	0.00	4.45
2264	4045	0.108019	GTTTGGGTCTTCGTCTGGGT	59.892	55.000	0.00	0.00	0.00	4.51
2265	4046	0.395312	TTTGGGTCTTCGTCTGGGTC	59.605	55.000	0.00	0.00	0.00	4.46

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
106	107	0.830444	ACTGGCACCACCGAGTCTTA	60.830	55.000	0.00	0.00	43.94	2.10
151	152	3.627123	CCGTTATCAAATGTGAGCATGGA	59.373	43.478	0.00	0.00	37.14	3.41
160	161	0.741574	TCGCCGCCGTTATCAAATGT	60.742	50.000	0.00	0.00	35.54	2.71
280	281	1.327303	GCCACTGTGATTGGTCCAAA	58.673	50.000	8.75	0.00	36.40	3.28
400	401	1.206878	TCATGCCAGTGTATCCAGCT	58.793	50.000	0.00	0.00	0.00	4.24
473	474	1.301954	GTCCCCCTTTACCGCACAT	59.698	57.895	0.00	0.00	0.00	3.21
482	483	0.609131	CGCTCATTGTGTCCCCCTTT	60.609	55.000	0.00	0.00	0.00	3.11
566	574	1.185618	CCGTCACCTCTTCCACCTCA	61.186	60.000	0.00	0.00	0.00	3.86
784	958	0.832135	TGCTTCCTCTCCGACCACTT	60.832	55.000	0.00	0.00	0.00	3.16
785	959	1.228894	TGCTTCCTCTCCGACCACT	60.229	57.895	0.00	0.00	0.00	4.00
1161	1373	6.253758	TCTACCTTCTGTCCATGACTTCTTA	58.746	40.000	0.00	0.00	33.15	2.10
1201	1413	3.457234	GACGATCATGTGCATAGTTGGA	58.543	45.455	0.00	0.00	0.00	3.53
1372	1585	5.935945	TCTTGGACATCTTTTTGTACCTCA	58.064	37.500	0.00	0.00	28.61	3.86
1432	1646	1.673033	CGTGCAAAGGACTCCTCGAAT	60.673	52.381	0.00	0.00	30.89	3.34
1527	1741	0.608640	TTCTTGACGAGCCTCCTTCC	59.391	55.000	0.00	0.00	0.00	3.46
1639	1853	0.038343	CCGGTGCCTTTCCATTTGTG	60.038	55.000	0.00	0.00	0.00	3.33
1780	2048	6.536224	TGCACATAAGTAGTTCATGATCACAG	59.464	38.462	0.00	0.00	0.00	3.66
1903	3085	3.567585	GGGAAAAATGCTCTCTGGATAGC	59.432	47.826	1.74	1.74	39.25	2.97
1922	3104	4.977739	ACATAATTTCCTCTCTGGATGGGA	59.022	41.667	0.00	0.00	45.68	4.37
2009	3378	0.034059	CTTGGCGTCTGGTCTTGTCT	59.966	55.000	0.00	0.00	0.00	3.41
2010	3379	0.951040	CCTTGGCGTCTGGTCTTGTC	60.951	60.000	0.00	0.00	0.00	3.18
2011	3380	1.071471	CCTTGGCGTCTGGTCTTGT	59.929	57.895	0.00	0.00	0.00	3.16
2012	3381	0.951040	GACCTTGGCGTCTGGTCTTG	60.951	60.000	20.16	0.00	44.84	3.02
2013	3382	1.371558	GACCTTGGCGTCTGGTCTT	59.628	57.895	20.16	0.00	44.84	3.01
2014	3383	2.584391	GGACCTTGGCGTCTGGTCT	61.584	63.158	24.17	0.00	46.76	3.85
2015	3384	2.047179	GGACCTTGGCGTCTGGTC	60.047	66.667	19.56	19.56	46.83	4.02
2016	3385	3.637273	GGGACCTTGGCGTCTGGT	61.637	66.667	5.03	5.03	36.70	4.00
2017	3386	3.322466	AGGGACCTTGGCGTCTGG	61.322	66.667	0.00	0.00	33.07	3.86
2044	3413	0.181587	TCCTGCCTGACCAAAACGAA	59.818	50.000	0.00	0.00	0.00	3.85
2057	3426	4.083862	GGTGTCCGGTCTCCTGCC	62.084	72.222	11.86	0.00	0.00	4.85
2068	3437	1.833630	TGGATGATCAGACAGGTGTCC	59.166	52.381	6.50	0.92	45.85	4.02
2142	3524	1.987855	CCAGACGCCAGGGACCTTA	60.988	63.158	0.00	0.00	0.00	2.69
2247	4028	0.471211	AGACCCAGACGAAGACCCAA	60.471	55.000	0.00	0.00	0.00	4.12
2263	4044	2.574399	GCGTCTGGGTCTGGAGAC	59.426	66.667	0.00	0.00	44.04	3.36
2264	4045	2.680352	GGCGTCTGGGTCTGGAGA	60.680	66.667	0.00	0.00	0.00	3.71
2265	4046	2.111999	TTTGGCGTCTGGGTCTGGAG	62.112	60.000	0.00	0.00	0.00	3.86
2290	4071	2.668550	AAAACGAGCCAGACGCCC	60.669	61.111	0.00	0.00	38.78	6.13

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.