AutoCloner

Multiple sequence alignment - TraesCS7D01G005600

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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	TraesCS7D01G005600	chr7D	100.000	2839	0	0	1	2839	2689736	2686898	0.000000e+00	5243.0
1	TraesCS7D01G005600	chr7D	84.874	595	52	17	2275	2839	3551805	3551219	1.480000e-157	566.0
2	TraesCS7D01G005600	chr7D	86.290	496	38	18	2273	2754	2904077	2903598	1.950000e-141	512.0
3	TraesCS7D01G005600	chr7D	86.441	118	11	2	2002	2114	2905184	2905067	1.070000e-24	124.0
4	TraesCS7D01G005600	chr7D	100.000	28	0	0	2241	2268	3552760	3552733	5.000000e-03	52.8
5	TraesCS7D01G005600	chr7A	96.150	2000	76	1	1	1999	225701948	225699949	0.000000e+00	3265.0
6	TraesCS7D01G005600	chr7A	82.292	576	53	16	2273	2839	3155181	3154646	1.200000e-123	453.0
7	TraesCS7D01G005600	chr7A	87.978	366	35	4	2381	2744	2687442	2687084	9.400000e-115	424.0
8	TraesCS7D01G005600	chr7A	89.873	237	23	1	2002	2237	2688904	2688668	1.280000e-78	303.0
9	TraesCS7D01G005600	chr7A	91.250	160	12	2	2002	2161	3156313	3156156	1.710000e-52	217.0
10	TraesCS7D01G005600	chr7A	92.727	110	8	0	2273	2382	2687586	2687477	2.930000e-35	159.0
11	TraesCS7D01G005600	chr5D	93.270	2006	121	8	1	2003	545108231	545110225	0.000000e+00	2944.0
12	TraesCS7D01G005600	chr3D	88.487	1824	197	7	106	1926	55979218	55977405	0.000000e+00	2193.0
13	TraesCS7D01G005600	chr5A	95.311	789	36	1	1212	1999	609826028	609825240	0.000000e+00	1251.0
14	TraesCS7D01G005600	chr5A	70.000	1270	353	25	515	1769	367847211	367848467	2.870000e-50	209.0
15	TraesCS7D01G005600	chr5A	74.771	218	48	7	1355	1569	433167393	433167180	1.080000e-14	91.6
16	TraesCS7D01G005600	chr2A	96.040	606	21	3	1397	2001	51016808	51017411	0.000000e+00	983.0
17	TraesCS7D01G005600	chr5B	95.833	432	13	3	1568	1998	27315697	27315270	0.000000e+00	693.0
18	TraesCS7D01G005600	chr3A	96.642	268	9	0	1732	1999	587908785	587909052	2.010000e-121	446.0
19	TraesCS7D01G005600	chr4A	89.219	269	20	3	2273	2539	740852777	740853038	7.580000e-86	327.0
20	TraesCS7D01G005600	chr3B	94.811	212	7	3	1694	1905	68408017	68408224	7.580000e-86	327.0
21	TraesCS7D01G005600	chr1B	77.083	144	31	2	1355	1497	473239520	473239378	6.520000e-12	82.4
22	TraesCS7D01G005600	chr1A	81.707	82	15	0	1674	1755	266896536	266896455	5.080000e-08	69.4

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	TraesCS7D01G005600	chr7D	2686898	2689736	2838	True	5243.000000	5243	100.000000	1	2839	1	chr7D.!!$R1	2838
1	TraesCS7D01G005600	chr7D	2903598	2905184	1586	True	318.000000	512	86.365500	2002	2754	2	chr7D.!!$R2	752
2	TraesCS7D01G005600	chr7D	3551219	3552760	1541	True	309.400000	566	92.437000	2241	2839	2	chr7D.!!$R3	598
3	TraesCS7D01G005600	chr7A	225699949	225701948	1999	True	3265.000000	3265	96.150000	1	1999	1	chr7A.!!$R1	1998
4	TraesCS7D01G005600	chr7A	3154646	3156313	1667	True	335.000000	453	86.771000	2002	2839	2	chr7A.!!$R3	837
5	TraesCS7D01G005600	chr7A	2687084	2688904	1820	True	295.333333	424	90.192667	2002	2744	3	chr7A.!!$R2	742
6	TraesCS7D01G005600	chr5D	545108231	545110225	1994	False	2944.000000	2944	93.270000	1	2003	1	chr5D.!!$F1	2002
7	TraesCS7D01G005600	chr3D	55977405	55979218	1813	True	2193.000000	2193	88.487000	106	1926	1	chr3D.!!$R1	1820
8	TraesCS7D01G005600	chr5A	609825240	609826028	788	True	1251.000000	1251	95.311000	1212	1999	1	chr5A.!!$R2	787
9	TraesCS7D01G005600	chr5A	367847211	367848467	1256	False	209.000000	209	70.000000	515	1769	1	chr5A.!!$F1	1254
10	TraesCS7D01G005600	chr2A	51016808	51017411	603	False	983.000000	983	96.040000	1397	2001	1	chr2A.!!$F1	604

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
169	170	1.168714	GTTGTCAACTGCATCCTCCC	58.831	55.0	8.53	0.0	0.0	4.3	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2131	2143	0.592637	TGCACTTTTCCTGCGATGTG	59.407	50.0	0.0	0.0	37.46	3.21	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
33	34	1.359833	CCAGAAACGCAAGCAAGCA	59.640	52.632	1.32	0.00	45.62	3.91
93	94	6.003950	CACTTTGTCTTGGGAATTCCTTCTA	58.996	40.000	23.63	4.73	36.20	2.10
101	102	3.017442	GGGAATTCCTTCTACAAGTGCC	58.983	50.000	23.63	0.00	35.95	5.01
141	142	1.211457	AGAAGGTGGTGCTCATGGATC	59.789	52.381	0.00	0.00	0.00	3.36
165	166	2.557924	TGGATTGTTGTCAACTGCATCC	59.442	45.455	22.71	22.71	36.33	3.51
169	170	1.168714	GTTGTCAACTGCATCCTCCC	58.831	55.000	8.53	0.00	0.00	4.30
189	190	4.349048	TCCCCTATTCTCATGAATGGAGTG	59.651	45.833	0.00	0.00	41.75	3.51
362	363	1.620323	GCCAAGAGCCTCCATTTTTGT	59.380	47.619	0.00	0.00	34.35	2.83
434	435	7.978975	GTCCATATCTAGTATTCTGAATCTGCC	59.021	40.741	6.10	0.00	0.00	4.85
996	998	5.768164	GGACACTAATGAAAAGGAGGTTCAA	59.232	40.000	0.00	0.00	38.44	2.69
1215	1217	0.036448	CTCTCATAGCCATGGCCCAG	59.964	60.000	33.14	21.79	43.17	4.45
1311	1313	3.119029	TCACGCATGATCATCAGTTCTCA	60.119	43.478	4.86	0.00	0.00	3.27
1312	1314	3.619929	CACGCATGATCATCAGTTCTCAA	59.380	43.478	4.86	0.00	0.00	3.02
1335	1337	3.093574	CAAGAGCGCGTATCAATTGTTG	58.906	45.455	8.43	3.28	0.00	3.33
1438	1440	1.202758	TGGCAGTTCACGGAAGATGTT	60.203	47.619	0.00	0.00	0.00	2.71
1481	1483	0.400213	AGGAACTGGCCGTCAAATGA	59.600	50.000	0.00	0.00	37.18	2.57
1730	1733	3.575630	GATTTGGAAGGAAAGAAACGCC	58.424	45.455	0.00	0.00	0.00	5.68
1831	1834	3.021695	CAGGATGCATTTGTGACCTGAT	58.978	45.455	20.08	0.00	45.02	2.90
1841	1844	2.687370	TGTGACCTGATGACGTGATTG	58.313	47.619	0.00	0.00	0.00	2.67
2006	2013	1.672881	CAATGGCCCTTCGTGAAGATC	59.327	52.381	11.11	2.51	40.79	2.75
2022	2033	6.199154	CGTGAAGATCTGCGTTATATGTTCTT	59.801	38.462	0.00	0.00	0.00	2.52
2063	2075	5.412594	GCAAATCGGATTCATTCCTATAGCA	59.587	40.000	3.28	0.00	42.99	3.49
2105	2117	4.025647	GCTGCTGATTTTGATAGGTCGTAC	60.026	45.833	0.00	0.00	0.00	3.67
2124	2136	6.195983	GTCGTACGGTAGTGATTTAGATGTTG	59.804	42.308	16.52	0.00	0.00	3.33
2131	2143	7.254455	CGGTAGTGATTTAGATGTTGAATGGTC	60.254	40.741	0.00	0.00	0.00	4.02
2146	2158	1.522668	TGGTCACATCGCAGGAAAAG	58.477	50.000	0.00	0.00	0.00	2.27
2269	2317	2.366640	TCGAGTAGCTGGCTTATCCT	57.633	50.000	0.00	0.00	35.26	3.24
2270	2318	3.503800	TCGAGTAGCTGGCTTATCCTA	57.496	47.619	0.00	0.00	35.26	2.94
2282	3340	4.588951	TGGCTTATCCTACAGAGGTACATG	59.411	45.833	0.00	0.00	44.19	3.21
2324	3382	9.220906	TCATATAGTTCAAGTAGTAAATGGGGT	57.779	33.333	0.00	0.00	0.00	4.95
2336	3394	4.526650	AGTAAATGGGGTGTTGGATGAAAC	59.473	41.667	0.00	0.00	0.00	2.78
2346	3404	2.677836	GTTGGATGAAACGCAGCTGATA	59.322	45.455	20.43	0.00	32.29	2.15
2437	3531	0.370273	GCAAAGATAGCGTCACACCG	59.630	55.000	0.00	0.00	0.00	4.94
2449	3543	0.250124	TCACACCGGCGAAGAAATGT	60.250	50.000	9.30	0.00	0.00	2.71
2455	3549	1.062587	CCGGCGAAGAAATGTGTGATC	59.937	52.381	9.30	0.00	0.00	2.92
2456	3550	1.731709	CGGCGAAGAAATGTGTGATCA	59.268	47.619	0.00	0.00	0.00	2.92
2457	3551	2.159430	CGGCGAAGAAATGTGTGATCAA	59.841	45.455	0.00	0.00	0.00	2.57
2458	3552	3.181507	CGGCGAAGAAATGTGTGATCAAT	60.182	43.478	0.00	0.00	0.00	2.57
2459	3553	4.346129	GGCGAAGAAATGTGTGATCAATC	58.654	43.478	0.00	0.00	0.00	2.67
2460	3554	4.346129	GCGAAGAAATGTGTGATCAATCC	58.654	43.478	0.00	0.00	0.00	3.01
2461	3555	4.731773	GCGAAGAAATGTGTGATCAATCCC	60.732	45.833	0.00	0.00	0.00	3.85
2462	3556	4.201950	CGAAGAAATGTGTGATCAATCCCC	60.202	45.833	0.00	0.00	0.00	4.81
2501	3596	6.099845	ACATCTCTTATACAAGGGTTCGGATT	59.900	38.462	0.00	0.00	33.59	3.01
2502	3597	6.555463	TCTCTTATACAAGGGTTCGGATTT	57.445	37.500	0.00	0.00	33.59	2.17
2509	3604	4.196971	ACAAGGGTTCGGATTTACTATGC	58.803	43.478	0.00	0.00	0.00	3.14
2713	3824	6.324819	AGTATCTGGATTGCGAAATTTTGTG	58.675	36.000	7.27	0.00	0.00	3.33
2737	3848	8.185505	GTGAATCAGAAATAGACTTCTCGTAGT	58.814	37.037	0.00	0.00	33.25	2.73
2747	3860	6.011476	AGACTTCTCGTAGTTAAACTGGAC	57.989	41.667	0.00	0.00	0.00	4.02
2749	3884	3.207474	TCTCGTAGTTAAACTGGACGC	57.793	47.619	0.00	0.00	32.07	5.19
2757	3892	1.919240	TAAACTGGACGCCTCTCTCA	58.081	50.000	0.00	0.00	0.00	3.27
2765	3900	0.033011	ACGCCTCTCTCATGTACCCT	60.033	55.000	0.00	0.00	0.00	4.34
2768	3903	2.111384	GCCTCTCTCATGTACCCTTCA	58.889	52.381	0.00	0.00	0.00	3.02
2769	3904	2.703007	GCCTCTCTCATGTACCCTTCAT	59.297	50.000	0.00	0.00	0.00	2.57
2772	3907	5.363939	CCTCTCTCATGTACCCTTCATTTC	58.636	45.833	0.00	0.00	0.00	2.17
2773	3908	5.130145	CCTCTCTCATGTACCCTTCATTTCT	59.870	44.000	0.00	0.00	0.00	2.52
2776	3911	8.146053	TCTCTCATGTACCCTTCATTTCTTTA	57.854	34.615	0.00	0.00	0.00	1.85
2777	3912	8.772250	TCTCTCATGTACCCTTCATTTCTTTAT	58.228	33.333	0.00	0.00	0.00	1.40
2805	3945	4.706035	TGCCAACTTTAGACCTTAACGAA	58.294	39.130	0.00	0.00	0.00	3.85
2806	3946	4.512571	TGCCAACTTTAGACCTTAACGAAC	59.487	41.667	0.00	0.00	0.00	3.95
2812	3952	5.069516	ACTTTAGACCTTAACGAACTGGTGA	59.930	40.000	0.00	0.00	32.30	4.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
33	34	5.879223	GGAGATGTCAATCTTCATCAACACT	59.121	40.000	7.68	0.00	43.48	3.55
93	94	0.605589	CTCTCTTCCTCGGCACTTGT	59.394	55.000	0.00	0.00	0.00	3.16
101	102	3.449018	TCTTCCAAATCCTCTCTTCCTCG	59.551	47.826	0.00	0.00	0.00	4.63
141	142	2.358582	TGCAGTTGACAACAATCCACAG	59.641	45.455	20.08	1.47	38.32	3.66
165	166	4.596643	ACTCCATTCATGAGAATAGGGGAG	59.403	45.833	15.76	15.76	46.85	4.30
169	170	5.061853	CACCACTCCATTCATGAGAATAGG	58.938	45.833	0.00	0.00	42.46	2.57
189	190	2.425592	GCAAAAGGTTGGCCCACC	59.574	61.111	18.48	18.48	35.10	4.61
312	313	3.499918	AGTTGCAAGCAATATCCGATAGC	59.500	43.478	11.00	0.00	38.28	2.97
362	363	5.486735	AAAGAACAAAATGGCATCATCCA	57.513	34.783	0.00	0.00	40.97	3.41
1215	1217	8.370940	TGAACAATATCCCAGATCTTCAGATAC	58.629	37.037	0.00	0.00	34.37	2.24
1311	1313	3.623060	ACAATTGATACGCGCTCTTGATT	59.377	39.130	13.59	3.54	0.00	2.57
1312	1314	3.198068	ACAATTGATACGCGCTCTTGAT	58.802	40.909	13.59	0.00	0.00	2.57
1438	1440	3.018856	TCTCTAAGTTATCCGCCGTCAA	58.981	45.455	0.00	0.00	0.00	3.18
1481	1483	0.620030	TGAGCATAGTGGGCATGTGT	59.380	50.000	0.00	0.00	0.00	3.72
1730	1733	6.017605	AGCTAGCGACATTATCAAAAATCCTG	60.018	38.462	9.55	0.00	0.00	3.86
1831	1834	1.375908	GGCCAGCTCAATCACGTCA	60.376	57.895	0.00	0.00	0.00	4.35
1841	1844	1.743252	CGACCAAGAAGGCCAGCTC	60.743	63.158	5.01	0.00	43.14	4.09
1939	1942	5.011586	AGAGAGAGTACAAGGTTACAGTCC	58.988	45.833	0.00	0.00	0.00	3.85
2006	2013	4.025396	CAGCCTGAAGAACATATAACGCAG	60.025	45.833	0.00	0.00	0.00	5.18
2022	2033	6.294120	CCGATTTGCATATTTTATCAGCCTGA	60.294	38.462	0.00	0.00	0.00	3.86
2105	2117	6.538742	ACCATTCAACATCTAAATCACTACCG	59.461	38.462	0.00	0.00	0.00	4.02
2124	2136	1.737838	TTCCTGCGATGTGACCATTC	58.262	50.000	0.00	0.00	0.00	2.67
2131	2143	0.592637	TGCACTTTTCCTGCGATGTG	59.407	50.000	0.00	0.00	37.46	3.21
2146	2158	5.982465	TTTGTTAGAAAAATTGCCTGCAC	57.018	34.783	0.00	0.00	0.00	4.57
2201	2213	4.822036	TTTGTGTGCACGCTATTTAAGT	57.178	36.364	29.04	0.00	0.00	2.24
2237	2249	3.056107	AGCTACTCGAATTTGTGTGGCTA	60.056	43.478	27.57	3.26	44.68	3.93
2238	2250	2.076863	GCTACTCGAATTTGTGTGGCT	58.923	47.619	22.11	0.00	37.03	4.75
2269	2317	7.626999	AAATAATAGGGCATGTACCTCTGTA	57.373	36.000	13.40	6.39	39.54	2.74
2270	2318	6.515512	AAATAATAGGGCATGTACCTCTGT	57.484	37.500	13.40	4.69	39.54	3.41
2324	3382	0.592637	CAGCTGCGTTTCATCCAACA	59.407	50.000	0.00	0.00	0.00	3.33
2336	3394	4.802999	TCATAGTTCATCTATCAGCTGCG	58.197	43.478	9.47	0.00	37.26	5.18
2415	3509	2.076863	GTGTGACGCTATCTTTGCCTT	58.923	47.619	0.00	0.00	0.00	4.35
2416	3510	1.676014	GGTGTGACGCTATCTTTGCCT	60.676	52.381	0.00	0.00	0.00	4.75
2437	3531	3.829886	TTGATCACACATTTCTTCGCC	57.170	42.857	0.00	0.00	0.00	5.54
2449	3543	6.666980	TCAAACATAATTGGGGATTGATCACA	59.333	34.615	0.00	0.00	0.00	3.58
2455	3549	6.528537	TGTCTCAAACATAATTGGGGATTG	57.471	37.500	0.00	0.00	31.46	2.67
2488	3583	4.451900	AGCATAGTAAATCCGAACCCTTG	58.548	43.478	0.00	0.00	0.00	3.61
2577	3687	5.710099	CCAACCCAAAGTATAGCAAAGAAGA	59.290	40.000	0.00	0.00	0.00	2.87
2613	3723	6.899393	ATATATGAACATGGGCGAACATTT	57.101	33.333	0.00	0.00	0.00	2.32
2737	3848	2.244695	TGAGAGAGGCGTCCAGTTTAA	58.755	47.619	2.06	0.00	0.00	1.52
2747	3860	1.067821	GAAGGGTACATGAGAGAGGCG	59.932	57.143	0.00	0.00	0.00	5.52
2749	3884	5.130145	AGAAATGAAGGGTACATGAGAGAGG	59.870	44.000	0.00	0.00	0.00	3.69
2777	3912	8.885722	CGTTAAGGTCTAAAGTTGGCATTATAA	58.114	33.333	0.00	0.00	0.00	0.98
2805	3945	2.224597	TGCATGAATGTCAGTCACCAGT	60.225	45.455	4.88	0.00	0.00	4.00
2806	3946	2.429478	TGCATGAATGTCAGTCACCAG	58.571	47.619	4.88	0.32	0.00	4.00
2812	3952	3.928005	AGAGGATGCATGAATGTCAGT	57.072	42.857	2.46	0.00	0.00	3.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.