AutoCloner

Multiple sequence alignment - TraesCS3A01G534300

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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	TraesCS3A01G534300	chr3A	100.000	2461	0	0	1	2461	746294688	746292228	0.000000e+00	4545.0
1	TraesCS3A01G534300	chr3A	82.032	1447	199	28	232	1624	746275640	746274201	0.000000e+00	1175.0
2	TraesCS3A01G534300	chr3A	83.319	1199	156	19	451	1625	746213013	746211835	0.000000e+00	1066.0
3	TraesCS3A01G534300	chr3A	82.143	784	115	17	395	1164	746208623	746207851	0.000000e+00	649.0
4	TraesCS3A01G534300	chr3A	92.262	168	11	2	232	398	746208818	746208652	1.140000e-58	237.0
5	TraesCS3A01G534300	chr3A	90.419	167	15	1	233	398	746278973	746278807	4.120000e-53	219.0
6	TraesCS3A01G534300	chr3A	88.550	131	10	5	395	522	746216370	746216242	1.180000e-33	154.0
7	TraesCS3A01G534300	chr3D	92.923	2275	112	23	213	2461	611505106	611502855	0.000000e+00	3264.0
8	TraesCS3A01G534300	chr3D	83.766	1386	178	28	395	1743	611369234	611367859	0.000000e+00	1269.0
9	TraesCS3A01G534300	chr3D	82.072	1255	161	26	395	1624	611364614	611363399	0.000000e+00	1013.0
10	TraesCS3A01G534300	chr3D	83.805	883	92	17	908	1743	611416601	611415723	0.000000e+00	791.0
11	TraesCS3A01G534300	chr3D	85.057	783	91	9	787	1552	611362221	611361448	0.000000e+00	774.0
12	TraesCS3A01G534300	chr3D	90.708	226	16	4	1	222	611526551	611526327	1.850000e-76	296.0
13	TraesCS3A01G534300	chr3D	91.250	160	10	4	232	390	611369427	611369271	5.330000e-52	215.0
14	TraesCS3A01G534300	chr3D	89.655	145	9	4	395	537	611419839	611419699	1.940000e-41	180.0
15	TraesCS3A01G534300	chr3D	88.742	151	10	6	395	541	611417249	611417102	6.990000e-41	178.0
16	TraesCS3A01G534300	chr3D	81.019	216	32	3	575	787	611422063	611421854	1.960000e-36	163.0
17	TraesCS3A01G534300	chr3D	95.833	96	4	0	1823	1918	611415346	611415251	3.280000e-34	156.0
18	TraesCS3A01G534300	chr3D	90.517	116	9	2	395	508	611422373	611422258	4.240000e-33	152.0
19	TraesCS3A01G534300	chr3D	78.409	176	24	5	1569	1734	611494606	611494435	4.330000e-18	102.0
20	TraesCS3A01G534300	chr3D	96.774	31	1	0	1823	1853	611370686	611370656	4.000000e-03	52.8
21	TraesCS3A01G534300	chr3B	92.998	2085	117	12	1	2061	829245552	829243473	0.000000e+00	3014.0
22	TraesCS3A01G534300	chr3B	84.663	815	113	8	682	1492	829062948	829062142	0.000000e+00	802.0
23	TraesCS3A01G534300	chr3B	77.943	943	147	36	232	1134	829067634	829066713	1.300000e-147	532.0
24	TraesCS3A01G534300	chr3B	93.902	164	9	1	233	395	829143952	829143789	1.890000e-61	246.0
25	TraesCS3A01G534300	chr3B	93.293	164	10	1	233	395	829150632	829150469	8.790000e-60	241.0
26	TraesCS3A01G534300	chr3B	92.216	167	12	1	233	398	829140388	829140222	4.090000e-58	235.0
27	TraesCS3A01G534300	chr3B	92.169	166	5	2	2059	2216	829235448	829235283	6.850000e-56	228.0
28	TraesCS3A01G534300	chr3B	91.667	96	8	0	1823	1918	829133732	829133637	1.540000e-27	134.0
29	TraesCS3A01G534300	chr3B	94.444	36	2	0	1823	1858	829063621	829063586	3.420000e-04	56.5
30	TraesCS3A01G534300	chr7D	87.347	245	26	5	2218	2459	117531451	117531209	2.410000e-70	276.0
31	TraesCS3A01G534300	chr7D	86.864	236	27	4	2226	2461	563605757	563605526	6.750000e-66	261.0
32	TraesCS3A01G534300	chr7D	86.425	221	28	2	2238	2458	503687570	503687788	8.790000e-60	241.0
33	TraesCS3A01G534300	chr2A	89.302	215	22	1	2247	2461	384989934	384989721	4.030000e-68	268.0
34	TraesCS3A01G534300	chr7B	86.076	237	29	4	2223	2458	135031046	135031279	4.060000e-63	252.0
35	TraesCS3A01G534300	chr6D	85.833	240	30	4	2223	2461	103039393	103039157	4.060000e-63	252.0
36	TraesCS3A01G534300	chr6D	85.217	230	32	2	2230	2458	45814189	45814417	4.090000e-58	235.0
37	TraesCS3A01G534300	chr2D	85.294	238	32	3	2225	2461	650719189	650718954	2.450000e-60	243.0

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	TraesCS3A01G534300	chr3A	746292228	746294688	2460	True	4545.00	4545	100.000000	1	2461	1	chr3A.!!$R1	2460
1	TraesCS3A01G534300	chr3A	746274201	746278973	4772	True	697.00	1175	86.225500	232	1624	2	chr3A.!!$R3	1392
2	TraesCS3A01G534300	chr3A	746207851	746216370	8519	True	526.50	1066	86.568500	232	1625	4	chr3A.!!$R2	1393
3	TraesCS3A01G534300	chr3D	611502855	611505106	2251	True	3264.00	3264	92.923000	213	2461	1	chr3D.!!$R2	2248
4	TraesCS3A01G534300	chr3D	611361448	611370686	9238	True	664.76	1269	87.783800	232	1853	5	chr3D.!!$R4	1621
5	TraesCS3A01G534300	chr3D	611415251	611422373	7122	True	270.00	791	88.261833	395	1918	6	chr3D.!!$R5	1523
6	TraesCS3A01G534300	chr3B	829243473	829245552	2079	True	3014.00	3014	92.998000	1	2061	1	chr3B.!!$R4	2060
7	TraesCS3A01G534300	chr3B	829062142	829067634	5492	True	463.50	802	85.683333	232	1858	3	chr3B.!!$R5	1626
8	TraesCS3A01G534300	chr3B	829140222	829143952	3730	True	240.50	246	93.059000	233	398	2	chr3B.!!$R6	165

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
997	11330	0.037605	GTTCGCCGAAGAAGAAGGGA	60.038	55.0	0.0	0.0	0.0	4.2	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1980	18268	1.032794	ATCGACGGCTTGATCTGCTA	58.967	50.0	10.22	0.0	0.0	3.49	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
49	50	5.523552	GGCATATTGGAAAATGTAACCAAGC	59.476	40.000	0.00	0.00	44.95	4.01
107	108	6.419484	TCTGAGTACCTTCAATGAAGAACA	57.581	37.500	23.32	13.48	41.71	3.18
112	113	7.226720	TGAGTACCTTCAATGAAGAACAGTTTC	59.773	37.037	23.32	13.63	41.71	2.78
125	126	9.248291	TGAAGAACAGTTTCATAGAATTTTTGC	57.752	29.630	0.00	0.00	33.72	3.68
127	128	7.955918	AGAACAGTTTCATAGAATTTTTGCCT	58.044	30.769	0.00	0.00	33.72	4.75
130	135	5.801947	CAGTTTCATAGAATTTTTGCCTCCG	59.198	40.000	0.00	0.00	0.00	4.63
141	146	1.868713	TTGCCTCCGGGTGAGTAATA	58.131	50.000	0.00	0.00	39.65	0.98
145	150	3.201266	TGCCTCCGGGTGAGTAATATTTT	59.799	43.478	0.00	0.00	39.65	1.82
188	193	8.400186	GGCAAAAGTTTTAACTACTCACACTTA	58.600	33.333	0.00	0.00	38.57	2.24
394	1425	7.389053	CCCCTAGATGCTTATGTATTTTGAGAC	59.611	40.741	0.00	0.00	0.00	3.36
395	1426	8.153550	CCCTAGATGCTTATGTATTTTGAGACT	58.846	37.037	0.00	0.00	0.00	3.24
396	1427	9.553064	CCTAGATGCTTATGTATTTTGAGACTT	57.447	33.333	0.00	0.00	0.00	3.01
453	2595	4.836125	TCTTTGGTGTGAGAAATGCTTC	57.164	40.909	0.00	0.00	0.00	3.86
626	10692	3.665190	GACAAAAGATTCTCGTGTCCCT	58.335	45.455	14.49	0.00	33.95	4.20
731	10800	2.202743	ACACGGATCGCACCATCG	60.203	61.111	0.00	0.00	0.00	3.84
769	10838	0.459411	CGCACCATACACATCCGACA	60.459	55.000	0.00	0.00	0.00	4.35
778	10847	1.902508	ACACATCCGACAGTGGAGAAT	59.097	47.619	0.00	0.00	42.45	2.40
864	10938	1.892862	CTCCTAGATCCGACGGCGT	60.893	63.158	14.65	14.65	35.23	5.68
890	10966	2.809601	GTCACGTGAATCGCGCCT	60.810	61.111	21.95	0.00	44.19	5.52
891	10967	2.809174	TCACGTGAATCGCGCCTG	60.809	61.111	17.62	8.24	44.19	4.85
949	11279	0.647410	CTCGCGTTCACATCCATCAC	59.353	55.000	5.77	0.00	0.00	3.06
955	11286	2.125147	CACATCCATCACCGCCGT	60.125	61.111	0.00	0.00	0.00	5.68
986	11319	0.524414	TCGAGATTCAAGTTCGCCGA	59.476	50.000	0.00	0.00	34.52	5.54
997	11330	0.037605	GTTCGCCGAAGAAGAAGGGA	60.038	55.000	0.00	0.00	0.00	4.20
1003	11336	2.093447	GCCGAAGAAGAAGGGAAGATGA	60.093	50.000	0.00	0.00	0.00	2.92
1210	13606	1.954382	CACCGATCTCGTCCATTCCTA	59.046	52.381	0.00	0.00	37.74	2.94
1218	13614	4.601084	TCTCGTCCATTCCTACTCTTCTT	58.399	43.478	0.00	0.00	0.00	2.52
1224	13620	3.937706	CCATTCCTACTCTTCTTGTGCTG	59.062	47.826	0.00	0.00	0.00	4.41
1246	13642	2.832129	GACTGGGTGGTAACTGATCTCA	59.168	50.000	0.00	0.00	37.61	3.27
1259	13655	2.620585	CTGATCTCATCTCGGTGTGCTA	59.379	50.000	0.00	0.00	0.00	3.49
1275	13671	4.216257	GTGTGCTATTTGAACCACAGATGT	59.784	41.667	0.00	0.00	38.70	3.06
1453	17368	1.609072	GTTCTCCAAGAAGGCCAACAC	59.391	52.381	5.01	0.00	34.42	3.32
1640	17604	4.207165	ACCCGGGATTAATTCTTCACATG	58.793	43.478	32.02	0.00	0.00	3.21
1659	17623	6.032717	CACATGTTGTGTTGTGTAATGACAA	58.967	36.000	0.00	0.00	43.08	3.18
1671	17635	5.247337	TGTGTAATGACAATGGTCTACTGGA	59.753	40.000	1.02	0.00	44.61	3.86
1672	17636	6.070251	TGTGTAATGACAATGGTCTACTGGAT	60.070	38.462	1.02	0.00	44.61	3.41
1673	17637	6.480320	GTGTAATGACAATGGTCTACTGGATC	59.520	42.308	1.02	0.00	44.61	3.36
1676	17640	7.379059	AATGACAATGGTCTACTGGATCATA	57.621	36.000	1.02	0.00	44.28	2.15
1717	17682	6.381420	CCCCTTCCCATATACATCTAGTACAG	59.619	46.154	0.00	0.00	35.05	2.74
1770	17771	6.728200	TCGCTGGAAAATGAATGTAATCATC	58.272	36.000	0.00	0.00	39.08	2.92
1799	17863	1.607628	AGATGCCGTATACCGACAGAC	59.392	52.381	0.00	0.00	39.56	3.51
1980	18268	3.130516	TCTGTCCGATTTTAGCACGATCT	59.869	43.478	0.00	0.00	0.00	2.75
2235	22374	2.040359	CTTCCCCCTCCTCCTCCC	60.040	72.222	0.00	0.00	0.00	4.30
2236	22375	3.707189	TTCCCCCTCCTCCTCCCC	61.707	72.222	0.00	0.00	0.00	4.81
2237	22376	4.761304	TCCCCCTCCTCCTCCCCT	62.761	72.222	0.00	0.00	0.00	4.79
2238	22377	4.179599	CCCCCTCCTCCTCCCCTC	62.180	77.778	0.00	0.00	0.00	4.30
2239	22378	4.548513	CCCCTCCTCCTCCCCTCG	62.549	77.778	0.00	0.00	0.00	4.63
2242	22381	4.824515	CTCCTCCTCCCCTCGCGT	62.825	72.222	5.77	0.00	0.00	6.01
2243	22382	4.816984	TCCTCCTCCCCTCGCGTC	62.817	72.222	5.77	0.00	0.00	5.19
2291	22430	4.162690	GATCCCGAGCCGCCAGTT	62.163	66.667	0.00	0.00	0.00	3.16
2432	22571	3.474570	GTCTCATGCGGGGAGGCT	61.475	66.667	0.00	0.00	34.23	4.58

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
49	50	3.870723	TTTAGTGTGTTTGCTAGCACG	57.129	42.857	19.17	0.00	38.36	5.34
107	108	5.105756	CCGGAGGCAAAAATTCTATGAAACT	60.106	40.000	0.00	0.00	46.14	2.66
127	128	3.942748	GCACAAAATATTACTCACCCGGA	59.057	43.478	0.73	0.00	0.00	5.14
130	135	5.048364	TGTGTGCACAAAATATTACTCACCC	60.048	40.000	23.59	3.43	38.56	4.61
141	146	5.418524	TGCCTCTAATATGTGTGCACAAAAT	59.581	36.000	23.59	19.94	45.41	1.82
145	150	3.625649	TGCCTCTAATATGTGTGCACA	57.374	42.857	17.42	17.42	46.44	4.57
188	193	5.365605	TGATGTCCTCCACGGTATTTAAGAT	59.634	40.000	0.00	0.00	0.00	2.40
396	1427	5.321959	TGTCATGAAGCACTCAACAAAAA	57.678	34.783	0.00	0.00	37.67	1.94
397	1428	4.979943	TGTCATGAAGCACTCAACAAAA	57.020	36.364	0.00	0.00	37.67	2.44
462	5906	6.426633	CCTTTTTGTTTTGGTATGATTGACCC	59.573	38.462	0.00	0.00	35.99	4.46
749	10818	1.142965	TCGGATGTGTATGGTGCGG	59.857	57.895	0.00	0.00	0.00	5.69
756	10825	2.735151	TCTCCACTGTCGGATGTGTAT	58.265	47.619	11.30	0.00	33.56	2.29
758	10827	1.338107	TTCTCCACTGTCGGATGTGT	58.662	50.000	11.30	0.00	33.56	3.72
761	10830	2.674852	CAACATTCTCCACTGTCGGATG	59.325	50.000	0.52	0.28	33.56	3.51
769	10838	2.806745	CGTGTGACCAACATTCTCCACT	60.807	50.000	0.00	0.00	41.97	4.00
778	10847	0.466124	TGTGATCCGTGTGACCAACA	59.534	50.000	0.00	0.00	36.04	3.33
890	10966	2.745037	GGGTGCTCCGTGGTAACA	59.255	61.111	0.00	0.00	38.58	2.41
891	10967	2.046604	GGGGTGCTCCGTGGTAAC	60.047	66.667	0.00	0.00	36.01	2.50
949	11279	4.715523	ATTGTGGGTGGACGGCGG	62.716	66.667	13.24	0.00	0.00	6.13
955	11286	2.304470	TGAATCTCGAATTGTGGGTGGA	59.696	45.455	0.00	0.00	0.00	4.02
986	11319	2.237392	CCGGTCATCTTCCCTTCTTCTT	59.763	50.000	0.00	0.00	0.00	2.52
997	11330	1.490574	CTCTTCCTCCCGGTCATCTT	58.509	55.000	0.00	0.00	0.00	2.40
1210	13606	1.071385	CCAGTCCAGCACAAGAAGAGT	59.929	52.381	0.00	0.00	0.00	3.24
1218	13614	1.057275	TTACCACCCAGTCCAGCACA	61.057	55.000	0.00	0.00	0.00	4.57
1224	13620	2.168728	GAGATCAGTTACCACCCAGTCC	59.831	54.545	0.00	0.00	0.00	3.85
1246	13642	3.270877	GGTTCAAATAGCACACCGAGAT	58.729	45.455	0.00	0.00	0.00	2.75
1259	13655	4.473444	ACTCCAACATCTGTGGTTCAAAT	58.527	39.130	0.00	0.00	0.00	2.32
1275	13671	2.117206	ATTGCCCGCCAACTCCAA	59.883	55.556	0.00	0.00	35.99	3.53
1453	17368	2.814269	TGAAGTTGCTATGCTAGAGCG	58.186	47.619	0.00	0.00	45.83	5.03
1640	17604	5.587289	ACCATTGTCATTACACAACACAAC	58.413	37.500	0.00	0.00	39.09	3.32
1659	17623	7.921304	TGCATTATTATGATCCAGTAGACCAT	58.079	34.615	0.00	0.00	33.37	3.55
1672	17636	9.466497	GAAGGGGATATTTCTGCATTATTATGA	57.534	33.333	0.00	0.00	33.37	2.15
1673	17637	8.689972	GGAAGGGGATATTTCTGCATTATTATG	58.310	37.037	0.00	0.00	34.76	1.90
1676	17640	6.019108	GGGAAGGGGATATTTCTGCATTATT	58.981	40.000	0.00	0.00	0.00	1.40
1693	17657	6.954684	ACTGTACTAGATGTATATGGGAAGGG	59.045	42.308	0.00	0.00	33.23	3.95
1736	17701	5.924356	TCATTTTCCAGCGAGTAATATGGA	58.076	37.500	0.00	0.00	40.04	3.41
1751	17752	8.078596	GCAGGTAGATGATTACATTCATTTTCC	58.921	37.037	0.00	0.00	36.48	3.13
1815	17880	4.423732	ACAAACTGCAACAACATCTGTTC	58.576	39.130	0.00	0.00	45.50	3.18
1980	18268	1.032794	ATCGACGGCTTGATCTGCTA	58.967	50.000	10.22	0.00	0.00	3.49
2079	18371	7.500720	TGTCAGAATCTATAACATGCCATTG	57.499	36.000	0.00	0.00	0.00	2.82
2084	18376	8.158169	TCCAAATGTCAGAATCTATAACATGC	57.842	34.615	0.00	0.00	31.29	4.06
2140	18473	7.332557	TCCTTATTGCGGTTCTTGTCTATTTA	58.667	34.615	0.00	0.00	0.00	1.40
2154	18497	1.202687	TCAGCCATCTCCTTATTGCGG	60.203	52.381	0.00	0.00	0.00	5.69
2236	22375	3.827898	GAGGGGAGTGGACGCGAG	61.828	72.222	15.93	0.00	0.00	5.03
2290	22429	2.041265	GGAGCAGAGGGGAGGGAA	59.959	66.667	0.00	0.00	0.00	3.97
2291	22430	2.880612	TTGGAGCAGAGGGGAGGGA	61.881	63.158	0.00	0.00	0.00	4.20
2294	22433	2.674220	GGGTTGGAGCAGAGGGGAG	61.674	68.421	0.00	0.00	0.00	4.30
2295	22434	2.610859	GGGTTGGAGCAGAGGGGA	60.611	66.667	0.00	0.00	0.00	4.81
2300	22439	3.650950	GGCTGGGGTTGGAGCAGA	61.651	66.667	0.00	0.00	36.90	4.26

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.