AutoCloner

Multiple sequence alignment - TraesCS3B01G071600

Loading Multiple Alignment...

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	TraesCS3B01G071600	chr3B	100.000	2339	0	0	1	2339	43255536	43257874	0.000000e+00	4320.0
1	TraesCS3B01G071600	chrUn	96.247	1359	49	1	969	2327	57104111	57102755	0.000000e+00	2226.0
2	TraesCS3B01G071600	chrUn	96.247	1359	49	1	969	2327	294653146	294654502	0.000000e+00	2226.0
3	TraesCS3B01G071600	chrUn	95.812	955	33	6	22	972	57108760	57107809	0.000000e+00	1535.0
4	TraesCS3B01G071600	chrUn	95.812	955	33	6	22	972	309514244	309515195	0.000000e+00	1535.0
5	TraesCS3B01G071600	chr4B	95.143	1359	46	4	969	2327	642269727	642271065	0.000000e+00	2126.0
6	TraesCS3B01G071600	chr4B	95.807	954	33	6	22	972	642265089	642266038	0.000000e+00	1533.0
7	TraesCS3B01G071600	chr4B	85.393	712	60	18	272	945	611614904	611614199	0.000000e+00	699.0
8	TraesCS3B01G071600	chr1D	93.167	1361	71	10	969	2327	419054236	419055576	0.000000e+00	1978.0
9	TraesCS3B01G071600	chr1D	92.053	1359	86	11	971	2327	34230403	34231741	0.000000e+00	1892.0
10	TraesCS3B01G071600	chr1D	90.775	271	24	1	20	289	487345822	487346092	6.140000e-96	361.0
11	TraesCS3B01G071600	chr5B	93.230	1359	55	14	969	2327	705458615	705459936	0.000000e+00	1965.0
12	TraesCS3B01G071600	chr5B	95.046	545	24	3	24	566	705452032	705452575	0.000000e+00	854.0
13	TraesCS3B01G071600	chr5B	93.154	409	25	2	565	972	705454212	705454618	4.300000e-167	597.0
14	TraesCS3B01G071600	chr5B	90.775	271	22	3	20	289	519154409	519154677	2.210000e-95	359.0
15	TraesCS3B01G071600	chr7D	91.183	1361	80	18	969	2327	61668398	61667076	0.000000e+00	1812.0
16	TraesCS3B01G071600	chr2A	88.788	1320	94	28	1024	2327	218576610	218577891	0.000000e+00	1568.0
17	TraesCS3B01G071600	chr2A	86.628	344	23	8	265	585	685511612	685511269	2.210000e-95	359.0
18	TraesCS3B01G071600	chr2A	100.000	28	0	0	1	28	569995283	569995310	4.000000e-03	52.8
19	TraesCS3B01G071600	chr2D	93.478	1012	58	6	969	1978	459634256	459633251	0.000000e+00	1496.0
20	TraesCS3B01G071600	chr5A	92.829	1018	66	6	969	1984	338457916	338456904	0.000000e+00	1469.0
21	TraesCS3B01G071600	chr5A	85.649	655	46	18	359	972	338462232	338461585	0.000000e+00	645.0
22	TraesCS3B01G071600	chr1A	92.815	1016	64	7	969	1982	48228986	48227978	0.000000e+00	1463.0
23	TraesCS3B01G071600	chr1A	92.197	346	27	0	1982	2327	48228033	48227688	7.510000e-135	490.0
24	TraesCS3B01G071600	chr4A	88.432	925	64	19	20	921	228120685	228121589	0.000000e+00	1075.0
25	TraesCS3B01G071600	chr4A	87.862	552	46	11	425	965	601696007	601695466	1.530000e-176	628.0
26	TraesCS3B01G071600	chr4A	87.943	282	26	5	20	299	170809222	170808947	2.240000e-85	326.0
27	TraesCS3B01G071600	chr4A	100.000	29	0	0	1	29	691059867	691059895	1.000000e-03	54.7
28	TraesCS3B01G071600	chr3A	88.225	552	43	7	422	962	717426176	717426716	7.050000e-180	640.0
29	TraesCS3B01G071600	chr6B	85.072	556	58	16	422	958	430912335	430912884	5.680000e-151	544.0
30	TraesCS3B01G071600	chr2B	91.513	271	21	2	20	289	513262156	513261887	2.840000e-99	372.0
31	TraesCS3B01G071600	chr2B	91.463	164	6	2	810	972	83719421	83719577	3.910000e-53	219.0

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	TraesCS3B01G071600	chr3B	43255536	43257874	2338	False	4320.000000	4320	100.0000	1	2339	1	chr3B.!!$F1	2338
1	TraesCS3B01G071600	chrUn	294653146	294654502	1356	False	2226.000000	2226	96.2470	969	2327	1	chrUn.!!$F1	1358
2	TraesCS3B01G071600	chrUn	57102755	57108760	6005	True	1880.500000	2226	96.0295	22	2327	2	chrUn.!!$R1	2305
3	TraesCS3B01G071600	chrUn	309514244	309515195	951	False	1535.000000	1535	95.8120	22	972	1	chrUn.!!$F2	950
4	TraesCS3B01G071600	chr4B	642265089	642271065	5976	False	1829.500000	2126	95.4750	22	2327	2	chr4B.!!$F1	2305
5	TraesCS3B01G071600	chr4B	611614199	611614904	705	True	699.000000	699	85.3930	272	945	1	chr4B.!!$R1	673
6	TraesCS3B01G071600	chr1D	419054236	419055576	1340	False	1978.000000	1978	93.1670	969	2327	1	chr1D.!!$F2	1358
7	TraesCS3B01G071600	chr1D	34230403	34231741	1338	False	1892.000000	1892	92.0530	971	2327	1	chr1D.!!$F1	1356
8	TraesCS3B01G071600	chr5B	705452032	705459936	7904	False	1138.666667	1965	93.8100	24	2327	3	chr5B.!!$F2	2303
9	TraesCS3B01G071600	chr7D	61667076	61668398	1322	True	1812.000000	1812	91.1830	969	2327	1	chr7D.!!$R1	1358
10	TraesCS3B01G071600	chr2A	218576610	218577891	1281	False	1568.000000	1568	88.7880	1024	2327	1	chr2A.!!$F1	1303
11	TraesCS3B01G071600	chr2D	459633251	459634256	1005	True	1496.000000	1496	93.4780	969	1978	1	chr2D.!!$R1	1009
12	TraesCS3B01G071600	chr5A	338456904	338462232	5328	True	1057.000000	1469	89.2390	359	1984	2	chr5A.!!$R1	1625
13	TraesCS3B01G071600	chr1A	48227688	48228986	1298	True	976.500000	1463	92.5060	969	2327	2	chr1A.!!$R1	1358
14	TraesCS3B01G071600	chr4A	228120685	228121589	904	False	1075.000000	1075	88.4320	20	921	1	chr4A.!!$F1	901
15	TraesCS3B01G071600	chr4A	601695466	601696007	541	True	628.000000	628	87.8620	425	965	1	chr4A.!!$R2	540
16	TraesCS3B01G071600	chr3A	717426176	717426716	540	False	640.000000	640	88.2250	422	962	1	chr3A.!!$F1	540
17	TraesCS3B01G071600	chr6B	430912335	430912884	549	False	544.000000	544	85.0720	422	958	1	chr6B.!!$F1	536

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
752	2432	0.528901	CCCCGCGTATCGTCAAATCA	60.529	55.0	4.92	0.0	36.19	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2041	7862	1.076024	ACAAGTCCCATGTGGCATCTT	59.924	47.619	0.0	0.0	0.0	2.4	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
206	209	0.898789	TCTCCGGCGAGTTCTTCCTT	60.899	55.000	9.30	0.00	37.40	3.36
212	215	1.276705	GGCGAGTTCTTCCTTCCTCTT	59.723	52.381	0.00	0.00	0.00	2.85
313	316	7.980662	TGAATAACTAAACCGATAATCGAACCA	59.019	33.333	0.00	0.00	43.74	3.67
319	322	4.996788	ACCGATAATCGAACCAGTAAGT	57.003	40.909	0.00	0.00	43.74	2.24
322	325	5.357878	ACCGATAATCGAACCAGTAAGTACA	59.642	40.000	0.00	0.00	43.74	2.90
349	352	7.616313	TGGTTCAAATTTTTACCAGTCAAACT	58.384	30.769	14.34	0.00	35.82	2.66
710	2389	3.411517	CCTTCCTCCCCCGCATGT	61.412	66.667	0.00	0.00	0.00	3.21
711	2390	2.124570	CTTCCTCCCCCGCATGTG	60.125	66.667	0.00	0.00	0.00	3.21
752	2432	0.528901	CCCCGCGTATCGTCAAATCA	60.529	55.000	4.92	0.00	36.19	2.57
808	2489	1.613630	ACGGCTTCACCTCCTCCAT	60.614	57.895	0.00	0.00	35.61	3.41
945	2645	3.838903	CCTCACCAAACCCTAGAGTAAGT	59.161	47.826	0.00	0.00	0.00	2.24
1084	6822	2.847327	AGCTGAAGTGCTTGCTAAGA	57.153	45.000	0.00	0.00	40.93	2.10
1102	6840	2.784347	AGAACACTAAGAAGCCAAGGC	58.216	47.619	2.02	2.02	42.33	4.35
1317	7055	0.255033	AGCAAGCTGAGATGGATGCA	59.745	50.000	5.62	0.00	36.30	3.96
1318	7056	1.100510	GCAAGCTGAGATGGATGCAA	58.899	50.000	0.00	0.00	34.10	4.08
1568	7306	6.708502	TGTAAGCTCAATGTTACTGTGCTTTA	59.291	34.615	15.39	6.59	46.16	1.85
1618	7356	3.326006	TGATGGATCTGGAGATGTAAGCC	59.674	47.826	0.00	0.00	34.37	4.35
1646	7396	3.552068	GCTTGGAAACCCATGTTGTGTAC	60.552	47.826	0.00	0.00	34.13	2.90
1681	7431	1.612950	TGCGTCGGGTAGAGTAAACAA	59.387	47.619	0.00	0.00	0.00	2.83
1736	7488	5.118286	CACTTTCTGGCCAAAAAGAAACAT	58.882	37.500	33.22	11.66	37.46	2.71
1744	7496	4.376146	GCCAAAAAGAAACATAAGTGCCA	58.624	39.130	0.00	0.00	0.00	4.92
1794	7546	3.140141	CGCGTGGAAATGGGCCAT	61.140	61.111	14.78	14.78	37.81	4.40
1940	7695	2.042831	GGTGCCATGTCAGCTCCAC	61.043	63.158	0.00	0.00	42.23	4.02
1992	7791	1.281287	ACATCAGCTCCACATCAGCTT	59.719	47.619	0.00	0.00	45.34	3.74
2041	7862	4.492160	GCCACGTCAGATCGCGGA	62.492	66.667	6.13	0.00	35.38	5.54
2243	8064	6.757010	GCGATATACATGACGGATTTTAGGAT	59.243	38.462	0.00	0.00	0.00	3.24
2327	8148	7.381408	CACAGATTAACGACTTTCTTGTAGTGA	59.619	37.037	0.00	0.00	0.00	3.41
2328	8149	8.088981	ACAGATTAACGACTTTCTTGTAGTGAT	58.911	33.333	0.00	0.00	0.00	3.06
2329	8150	8.587950	CAGATTAACGACTTTCTTGTAGTGATC	58.412	37.037	0.00	0.00	0.00	2.92
2330	8151	6.922980	TTAACGACTTTCTTGTAGTGATCG	57.077	37.500	0.00	0.00	0.00	3.69
2331	8152	4.761235	ACGACTTTCTTGTAGTGATCGA	57.239	40.909	0.00	0.00	0.00	3.59
2332	8153	5.117355	ACGACTTTCTTGTAGTGATCGAA	57.883	39.130	0.00	0.00	0.00	3.71
2333	8154	5.526115	ACGACTTTCTTGTAGTGATCGAAA	58.474	37.500	0.00	0.00	0.00	3.46
2334	8155	5.401674	ACGACTTTCTTGTAGTGATCGAAAC	59.598	40.000	0.00	0.00	0.00	2.78
2335	8156	5.164080	CGACTTTCTTGTAGTGATCGAAACC	60.164	44.000	0.00	0.00	0.00	3.27
2336	8157	5.855045	ACTTTCTTGTAGTGATCGAAACCT	58.145	37.500	0.00	0.00	0.00	3.50
2337	8158	6.289064	ACTTTCTTGTAGTGATCGAAACCTT	58.711	36.000	0.00	0.00	0.00	3.50
2338	8159	6.766467	ACTTTCTTGTAGTGATCGAAACCTTT	59.234	34.615	0.00	0.00	0.00	3.11

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	5.041191	ACACTGAAGGAAATATGCCCTAG	57.959	43.478	0.00	0.00	31.36	3.02
1	2	5.192927	CAACACTGAAGGAAATATGCCCTA	58.807	41.667	0.00	0.00	31.36	3.53
2	3	4.019174	CAACACTGAAGGAAATATGCCCT	58.981	43.478	0.00	0.00	0.00	5.19
3	4	3.429410	GCAACACTGAAGGAAATATGCCC	60.429	47.826	0.00	0.00	0.00	5.36
4	5	3.429410	GGCAACACTGAAGGAAATATGCC	60.429	47.826	0.00	0.00	43.31	4.40
206	209	0.608640	GGAGAAACAGCCGAAGAGGA	59.391	55.000	0.00	0.00	45.00	3.71
212	215	2.151202	GTTCAATGGAGAAACAGCCGA	58.849	47.619	0.00	0.00	0.00	5.54
319	322	8.696374	TGACTGGTAAAAATTTGAACCAATGTA	58.304	29.630	19.87	8.90	41.30	2.29
322	325	8.888716	GTTTGACTGGTAAAAATTTGAACCAAT	58.111	29.630	19.87	13.61	41.30	3.16
710	2389	0.039618	GAAGGGGATTTGGCTGGTCA	59.960	55.000	0.00	0.00	0.00	4.02
711	2390	0.684479	GGAAGGGGATTTGGCTGGTC	60.684	60.000	0.00	0.00	0.00	4.02
752	2432	2.368878	GGGGAATGGGAGGGAGCT	60.369	66.667	0.00	0.00	0.00	4.09
808	2489	4.388499	GGAAGTTGGGCTCGGCGA	62.388	66.667	10.14	10.14	0.00	5.54
962	2664	1.664333	CAACAAACATGGTGGCGGC	60.664	57.895	0.00	0.00	0.00	6.53
1084	6822	2.959465	AGCCTTGGCTTCTTAGTGTT	57.041	45.000	8.56	0.00	0.00	3.32
1102	6840	2.295885	GATCCCCACATGCTGAAGAAG	58.704	52.381	0.00	0.00	0.00	2.85
1646	7396	1.264288	GACGCAACCCTTCTCTGTTTG	59.736	52.381	0.00	0.00	0.00	2.93
1681	7431	3.496331	CCCACTTTATTCGGCCCATTAT	58.504	45.455	0.00	0.00	0.00	1.28
1736	7488	6.382570	AGCCCATTAAAATTATGTGGCACTTA	59.617	34.615	19.83	14.10	40.08	2.24
1744	7496	6.127111	TGCACATCAGCCCATTAAAATTATGT	60.127	34.615	0.00	0.00	0.00	2.29
1794	7546	4.093998	GTCCGTAGTCATTTACACTCTCGA	59.906	45.833	0.00	0.00	0.00	4.04
2041	7862	1.076024	ACAAGTCCCATGTGGCATCTT	59.924	47.619	0.00	0.00	0.00	2.40
2140	7961	2.265904	CGGTCTGTCTCCGTCACCA	61.266	63.158	0.00	0.00	42.62	4.17
2243	8064	2.499205	GATGGTCGGGCATGACGA	59.501	61.111	8.58	8.58	39.83	4.20

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.