AutoCloner

Multiple sequence alignment - TraesCS3A01G116600

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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	TraesCS3A01G116600	chr3A	100.000	3269	0	0	1	3269	85370496	85373764	0.000000e+00	6037.0
1	TraesCS3A01G116600	chr3A	93.008	2274	78	25	896	3149	85270590	85272802	0.000000e+00	3243.0
2	TraesCS3A01G116600	chr3A	90.982	1863	112	19	1	1840	85532585	85534414	0.000000e+00	2459.0
3	TraesCS3A01G116600	chr3A	90.929	1863	113	20	1	1840	85463322	85465151	0.000000e+00	2453.0
4	TraesCS3A01G116600	chr3A	97.834	785	17	0	2365	3149	85475520	85476304	0.000000e+00	1356.0
5	TraesCS3A01G116600	chr3A	97.707	785	18	0	2365	3149	85544390	85545174	0.000000e+00	1351.0
6	TraesCS3A01G116600	chr3A	90.556	953	60	13	898	1825	84649206	84650153	0.000000e+00	1234.0
7	TraesCS3A01G116600	chr3A	90.553	561	42	6	1834	2390	84650234	84650787	0.000000e+00	732.0
8	TraesCS3A01G116600	chr3A	93.287	432	26	3	1835	2266	85475095	85475523	4.600000e-178	634.0
9	TraesCS3A01G116600	chr3A	91.667	432	33	1	1835	2266	85543965	85544393	2.170000e-166	595.0
10	TraesCS3A01G116600	chr3A	85.155	613	52	22	2385	2973	84650821	84651418	2.810000e-165	592.0
11	TraesCS3A01G116600	chr3B	92.942	1346	63	8	1822	3149	118252146	118253477	0.000000e+00	1930.0
12	TraesCS3A01G116600	chr3B	89.315	964	58	21	898	1818	118136523	118137484	0.000000e+00	1168.0
13	TraesCS3A01G116600	chr3B	96.410	585	17	4	898	1480	118251207	118251789	0.000000e+00	961.0
14	TraesCS3A01G116600	chr3B	89.539	564	45	6	1834	2390	118137572	118138128	0.000000e+00	702.0
15	TraesCS3A01G116600	chr3B	96.677	331	10	1	1499	1829	118251778	118252107	1.710000e-152	549.0
16	TraesCS3A01G116600	chr3B	84.961	512	44	16	2385	2868	118138162	118138668	3.790000e-134	488.0
17	TraesCS3A01G116600	chr3B	89.831	118	10	2	3152	3269	800993398	800993513	2.030000e-32	150.0
18	TraesCS3A01G116600	chr3B	89.873	79	8	0	776	854	93221432	93221354	5.770000e-18	102.0
19	TraesCS3A01G116600	chr3D	95.052	1152	43	3	2012	3149	72649823	72650974	0.000000e+00	1799.0
20	TraesCS3A01G116600	chr3D	96.371	937	30	3	896	1829	72648728	72649663	0.000000e+00	1539.0
21	TraesCS3A01G116600	chr3D	90.221	951	57	21	909	1825	72251923	72252871	0.000000e+00	1208.0
22	TraesCS3A01G116600	chr3D	89.322	693	69	5	1	690	477550802	477550112	0.000000e+00	865.0
23	TraesCS3A01G116600	chr3D	89.539	564	42	8	1834	2390	72252952	72253505	0.000000e+00	699.0
24	TraesCS3A01G116600	chr3D	86.386	617	42	22	2385	2973	72253539	72254141	1.280000e-178	636.0
25	TraesCS3A01G116600	chr3D	100.000	118	0	0	1834	1951	72649702	72649819	5.490000e-53	219.0
26	TraesCS3A01G116600	chr3D	92.105	76	6	0	776	851	282648081	282648006	1.240000e-19	108.0
27	TraesCS3A01G116600	chr3D	89.873	79	7	1	776	854	383968494	383968417	2.080000e-17	100.0
28	TraesCS3A01G116600	chr3D	96.000	50	2	0	853	902	72648665	72648714	7.520000e-12	82.4
29	TraesCS3A01G116600	chr5A	91.775	693	54	3	1	690	285969462	285970154	0.000000e+00	961.0
30	TraesCS3A01G116600	chr6D	89.884	692	66	4	1	690	158473804	158473115	0.000000e+00	887.0
31	TraesCS3A01G116600	chr6D	89.017	692	72	4	1	689	141202337	141201647	0.000000e+00	854.0
32	TraesCS3A01G116600	chr6D	89.017	692	68	4	1	690	243316452	243315767	0.000000e+00	850.0
33	TraesCS3A01G116600	chr6D	92.105	76	6	0	776	851	338232584	338232659	1.240000e-19	108.0
34	TraesCS3A01G116600	chr4D	89.451	692	71	2	1	690	325847834	325847143	0.000000e+00	872.0
35	TraesCS3A01G116600	chr4D	90.135	669	64	2	8	674	102350823	102351491	0.000000e+00	869.0
36	TraesCS3A01G116600	chr4D	88.043	92	10	1	763	854	298704493	298704403	1.240000e-19	108.0
37	TraesCS3A01G116600	chr7A	99.167	120	1	0	3150	3269	617699746	617699865	1.980000e-52	217.0
38	TraesCS3A01G116600	chr7A	98.347	121	2	0	3149	3269	617699233	617699353	2.560000e-51	213.0
39	TraesCS3A01G116600	chr7A	98.319	119	1	1	3151	3269	707633057	707632940	1.190000e-49	207.0
40	TraesCS3A01G116600	chr7B	98.305	118	1	1	3152	3269	151156157	151156273	4.280000e-49	206.0
41	TraesCS3A01G116600	chr6B	93.443	122	7	1	3148	3269	26399628	26399748	2.590000e-41	180.0
42	TraesCS3A01G116600	chr4A	93.548	124	2	2	3151	3269	46416255	46416133	2.590000e-41	180.0
43	TraesCS3A01G116600	chr2D	97.101	69	1	1	686	754	145972274	145972207	7.410000e-22	115.0
44	TraesCS3A01G116600	chr5B	93.151	73	5	0	686	758	324432623	324432695	1.240000e-19	108.0
45	TraesCS3A01G116600	chr6A	90.789	76	7	0	776	851	236731018	236731093	5.770000e-18	102.0
46	TraesCS3A01G116600	chr2B	91.892	74	4	2	686	759	206182461	206182390	5.770000e-18	102.0
47	TraesCS3A01G116600	chr2A	90.789	76	7	0	776	851	573074434	573074509	5.770000e-18	102.0
48	TraesCS3A01G116600	chr1D	91.667	72	5	1	688	759	174611171	174611241	7.460000e-17	99.0

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	TraesCS3A01G116600	chr3A	85370496	85373764	3268	False	6037.000000	6037	100.000000	1	3269	1	chr3A.!!$F2	3268
1	TraesCS3A01G116600	chr3A	85270590	85272802	2212	False	3243.000000	3243	93.008000	896	3149	1	chr3A.!!$F1	2253
2	TraesCS3A01G116600	chr3A	85532585	85534414	1829	False	2459.000000	2459	90.982000	1	1840	1	chr3A.!!$F4	1839
3	TraesCS3A01G116600	chr3A	85463322	85465151	1829	False	2453.000000	2453	90.929000	1	1840	1	chr3A.!!$F3	1839
4	TraesCS3A01G116600	chr3A	85475095	85476304	1209	False	995.000000	1356	95.560500	1835	3149	2	chr3A.!!$F6	1314
5	TraesCS3A01G116600	chr3A	85543965	85545174	1209	False	973.000000	1351	94.687000	1835	3149	2	chr3A.!!$F7	1314
6	TraesCS3A01G116600	chr3A	84649206	84651418	2212	False	852.666667	1234	88.754667	898	2973	3	chr3A.!!$F5	2075
7	TraesCS3A01G116600	chr3B	118251207	118253477	2270	False	1146.666667	1930	95.343000	898	3149	3	chr3B.!!$F3	2251
8	TraesCS3A01G116600	chr3B	118136523	118138668	2145	False	786.000000	1168	87.938333	898	2868	3	chr3B.!!$F2	1970
9	TraesCS3A01G116600	chr3D	72648665	72650974	2309	False	909.850000	1799	96.855750	853	3149	4	chr3D.!!$F2	2296
10	TraesCS3A01G116600	chr3D	477550112	477550802	690	True	865.000000	865	89.322000	1	690	1	chr3D.!!$R3	689
11	TraesCS3A01G116600	chr3D	72251923	72254141	2218	False	847.666667	1208	88.715333	909	2973	3	chr3D.!!$F1	2064
12	TraesCS3A01G116600	chr5A	285969462	285970154	692	False	961.000000	961	91.775000	1	690	1	chr5A.!!$F1	689
13	TraesCS3A01G116600	chr6D	158473115	158473804	689	True	887.000000	887	89.884000	1	690	1	chr6D.!!$R2	689
14	TraesCS3A01G116600	chr6D	141201647	141202337	690	True	854.000000	854	89.017000	1	689	1	chr6D.!!$R1	688
15	TraesCS3A01G116600	chr6D	243315767	243316452	685	True	850.000000	850	89.017000	1	690	1	chr6D.!!$R3	689
16	TraesCS3A01G116600	chr4D	325847143	325847834	691	True	872.000000	872	89.451000	1	690	1	chr4D.!!$R2	689
17	TraesCS3A01G116600	chr4D	102350823	102351491	668	False	869.000000	869	90.135000	8	674	1	chr4D.!!$F1	666
18	TraesCS3A01G116600	chr7A	617699233	617699865	632	False	215.000000	217	98.757000	3149	3269	2	chr7A.!!$F1	120

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
811	816	0.743097	GCTAAAGCAAGCCCCATGAG	59.257	55.0	0.0	0.0	41.59	2.9	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2274	2476	0.040204	CCTCCTTGGTGGCCTTGAAT	59.96	55.0	3.32	0.0	35.26	2.57	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
218	219	3.444742	TGAAAGTGGCAATGATCATCACC	59.555	43.478	17.81	17.18	0.00	4.02
233	234	8.070034	TGATCATCACCAAGAAAATGCTTATT	57.930	30.769	0.00	0.00	0.00	1.40
376	379	5.716228	TGTTTCATTGGCAGAACCTATCAAT	59.284	36.000	0.00	0.00	40.22	2.57
504	507	3.544684	AGAAGCACAATATCATCGGCAA	58.455	40.909	0.00	0.00	0.00	4.52
608	612	6.070995	ACACAGGTAGAAGGTATTGATTTCGA	60.071	38.462	0.00	0.00	0.00	3.71
658	663	3.258872	TGGGCAATTCACATTCTTCTTGG	59.741	43.478	0.00	0.00	0.00	3.61
703	708	2.091541	GCTTTATGTTAGGCAGCCACA	58.908	47.619	15.80	10.95	0.00	4.17
717	722	1.069049	AGCCACATTGCTTTGAACACC	59.931	47.619	0.00	0.00	38.85	4.16
755	760	4.292977	AGTTTTCAGGTTGAAGAAAGCG	57.707	40.909	0.00	0.00	41.32	4.68
756	761	3.694566	AGTTTTCAGGTTGAAGAAAGCGT	59.305	39.130	0.00	0.00	41.32	5.07
757	762	4.157840	AGTTTTCAGGTTGAAGAAAGCGTT	59.842	37.500	0.00	0.00	41.32	4.84
758	763	4.712122	TTTCAGGTTGAAGAAAGCGTTT	57.288	36.364	0.00	0.00	41.32	3.60
759	764	4.712122	TTCAGGTTGAAGAAAGCGTTTT	57.288	36.364	0.00	0.00	41.32	2.43
760	765	4.287238	TCAGGTTGAAGAAAGCGTTTTC	57.713	40.909	16.03	16.03	42.44	2.29
782	787	2.217429	TTTTGCGGGTGAAAGAAAGC	57.783	45.000	0.00	0.00	0.00	3.51
807	812	2.826674	ATTAGCTAAAGCAAGCCCCA	57.173	45.000	10.85	0.00	43.86	4.96
808	813	2.826674	TTAGCTAAAGCAAGCCCCAT	57.173	45.000	2.97	0.00	43.86	4.00
811	816	0.743097	GCTAAAGCAAGCCCCATGAG	59.257	55.000	0.00	0.00	41.59	2.90
816	821	1.755395	GCAAGCCCCATGAGCATGA	60.755	57.895	11.84	0.00	41.20	3.07
827	832	4.263639	CCCATGAGCATGATATAACACCCT	60.264	45.833	11.84	0.00	41.20	4.34
1568	1680	1.073923	GGTGGAGAAAGGCTTCAAGGA	59.926	52.381	0.00	0.00	32.68	3.36
1569	1681	2.291217	GGTGGAGAAAGGCTTCAAGGAT	60.291	50.000	0.00	0.00	32.68	3.24
1613	1725	1.668751	GTTCAACGACCTCAACAAGCA	59.331	47.619	0.00	0.00	0.00	3.91
1982	2178	4.678269	CGGCCGCGTCGACGATAT	62.678	66.667	39.74	0.00	43.02	1.63
2084	2283	0.036294	GGGGAAGAGAACGGGAACAG	60.036	60.000	0.00	0.00	0.00	3.16
2268	2470	1.891919	GAAGCACCGCCACAAGTGA	60.892	57.895	0.94	0.00	36.01	3.41
2270	2472	3.357079	GCACCGCCACAAGTGAGG	61.357	66.667	0.94	7.37	36.01	3.86
2293	2495	0.040204	ATTCAAGGCCACCAAGGAGG	59.960	55.000	5.01	0.00	41.22	4.30
2383	2585	1.686587	TCAAGCAGAAGGAGTTCGACA	59.313	47.619	0.00	0.00	37.79	4.35
2584	2835	1.280710	TCCTTTTCCTTCGCCAGCATA	59.719	47.619	0.00	0.00	0.00	3.14
2671	2928	4.502087	GCCTGCCTTGAATTGAGAAGTTTT	60.502	41.667	0.00	0.00	0.00	2.43
2793	3070	1.121407	CCATGGGCATCTCCGAGGTA	61.121	60.000	2.85	0.00	34.94	3.08
2915	3201	1.036707	GCAGTGGCTCTACCTAGGAG	58.963	60.000	17.98	8.82	40.22	3.69
3022	3310	9.653287	TCGGGTCTTTAATTAGCTATATCAATG	57.347	33.333	0.00	0.00	0.00	2.82
3099	3397	3.981211	TCCTTTTCTGCTGTTTGAATGC	58.019	40.909	0.00	0.00	0.00	3.56

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
201	202	3.018856	TCTTGGTGATGATCATTGCCAC	58.981	45.455	23.45	19.24	0.00	5.01
218	219	5.796935	CCACACGAGAATAAGCATTTTCTTG	59.203	40.000	7.56	7.56	38.69	3.02
376	379	8.654094	TCTGGATCATTCATAGCTTCTTCATTA	58.346	33.333	0.00	0.00	0.00	1.90
504	507	5.936956	TGCTTATTGCGGAAAATCCATTTTT	59.063	32.000	0.00	0.00	46.63	1.94
608	612	7.992608	TGTATGCAACAGGAGTATATGTTTCAT	59.007	33.333	7.97	7.97	42.89	2.57
658	663	9.173939	GCAGAATATCATTGTAGTTTGCATAAC	57.826	33.333	0.00	0.00	0.00	1.89
690	695	0.890683	AAGCAATGTGGCTGCCTAAC	59.109	50.000	21.03	11.26	45.07	2.34
695	700	1.142474	GTTCAAAGCAATGTGGCTGC	58.858	50.000	0.00	0.00	45.07	5.25
699	704	1.688197	AGGGTGTTCAAAGCAATGTGG	59.312	47.619	0.00	0.00	0.00	4.17
703	708	2.949447	ACTCAGGGTGTTCAAAGCAAT	58.051	42.857	0.00	0.00	0.00	3.56
717	722	7.702348	CCTGAAAACTTTGTTAAGAAACTCAGG	59.298	37.037	17.39	17.39	38.92	3.86
762	767	2.167487	AGCTTTCTTTCACCCGCAAAAA	59.833	40.909	0.00	0.00	0.00	1.94
763	768	1.754226	AGCTTTCTTTCACCCGCAAAA	59.246	42.857	0.00	0.00	0.00	2.44
764	769	1.398692	AGCTTTCTTTCACCCGCAAA	58.601	45.000	0.00	0.00	0.00	3.68
765	770	1.398692	AAGCTTTCTTTCACCCGCAA	58.601	45.000	0.00	0.00	0.00	4.85
766	771	1.398692	AAAGCTTTCTTTCACCCGCA	58.601	45.000	5.69	0.00	38.03	5.69
767	772	3.850122	ATAAAGCTTTCTTTCACCCGC	57.150	42.857	16.57	0.00	41.34	6.13
768	773	7.132863	GCTAATATAAAGCTTTCTTTCACCCG	58.867	38.462	16.57	0.00	41.34	5.28
782	787	6.490040	TGGGGCTTGCTTTAGCTAATATAAAG	59.510	38.462	7.08	9.96	41.25	1.85
803	808	4.012374	GGTGTTATATCATGCTCATGGGG	58.988	47.826	9.69	0.00	39.24	4.96
807	812	5.830799	TCAGGGTGTTATATCATGCTCAT	57.169	39.130	0.00	0.00	0.00	2.90
808	813	5.366477	TCTTCAGGGTGTTATATCATGCTCA	59.634	40.000	0.00	0.00	0.00	4.26
811	816	6.058183	ACTTCTTCAGGGTGTTATATCATGC	58.942	40.000	0.00	0.00	0.00	4.06
816	821	7.451566	AGCAAAAACTTCTTCAGGGTGTTATAT	59.548	33.333	0.00	0.00	0.00	0.86
827	832	4.955925	TTGTCGAGCAAAAACTTCTTCA	57.044	36.364	0.00	0.00	33.53	3.02
902	927	3.449227	CGCTGGCCCGTGTAGAGA	61.449	66.667	0.00	0.00	0.00	3.10
961	992	3.467803	CGGTCTCTGGTTTCAACTCTTT	58.532	45.455	0.00	0.00	0.00	2.52
963	994	1.344763	CCGGTCTCTGGTTTCAACTCT	59.655	52.381	0.00	0.00	0.00	3.24
964	995	1.070289	ACCGGTCTCTGGTTTCAACTC	59.930	52.381	0.00	0.00	35.82	3.01
965	996	1.129058	ACCGGTCTCTGGTTTCAACT	58.871	50.000	0.00	0.00	35.82	3.16
967	998	0.107831	CCACCGGTCTCTGGTTTCAA	59.892	55.000	2.59	0.00	37.72	2.69
968	999	1.052124	ACCACCGGTCTCTGGTTTCA	61.052	55.000	2.59	0.00	37.51	2.69
969	1000	1.752833	ACCACCGGTCTCTGGTTTC	59.247	57.895	2.59	0.00	37.51	2.78
970	1001	3.981313	ACCACCGGTCTCTGGTTT	58.019	55.556	2.59	0.00	37.51	3.27
1354	1433	2.125912	GAGCAGACGCACCATCGT	60.126	61.111	0.00	0.00	46.38	3.73
1613	1725	0.165511	GTCGACGACTCGCTTGTAGT	59.834	55.000	20.52	0.00	39.96	2.73
1830	2008	1.991230	CGTGGAGGAATTCACCCCT	59.009	57.895	7.93	0.00	35.02	4.79
1832	2019	2.106683	CGCGTGGAGGAATTCACCC	61.107	63.158	7.93	8.00	0.00	4.61
1980	2176	4.188462	CGTAGTTGTGGAAGCCATTGATA	58.812	43.478	0.00	0.00	35.28	2.15
1982	2178	2.422597	CGTAGTTGTGGAAGCCATTGA	58.577	47.619	0.00	0.00	35.28	2.57
2059	2255	0.320697	CCGTTCTCTTCCCCGTCTTT	59.679	55.000	0.00	0.00	0.00	2.52
2274	2476	0.040204	CCTCCTTGGTGGCCTTGAAT	59.960	55.000	3.32	0.00	35.26	2.57
2293	2495	2.187946	CTCGTGCTCCATGTCCCC	59.812	66.667	0.00	0.00	0.00	4.81
2671	2928	8.774546	AAGAGACCATAGACATCTGAATTCTA	57.225	34.615	7.05	2.22	0.00	2.10
2793	3070	3.946201	AGTTGCAGAGCGCCAGGT	61.946	61.111	2.29	0.00	41.33	4.00
2858	3144	4.664677	GTGCGCAGTGGACCTCGT	62.665	66.667	12.22	0.00	31.75	4.18
3099	3397	2.377810	TGCTGGCCTGATACCTGGG	61.378	63.158	14.77	0.00	32.58	4.45

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.