AutoCloner

Multiple sequence alignment - TraesCS6A01G372600

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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	TraesCS6A01G372600	chr6A	100.000	3049	0	0	1	3049	596420256	596423304	0.000000e+00	5631
1	TraesCS6A01G372600	chr6A	97.433	779	16	3	1	776	585146487	585145710	0.000000e+00	1325
2	TraesCS6A01G372600	chr6A	88.477	512	37	8	1900	2401	554454103	554453604	1.560000e-167	599
3	TraesCS6A01G372600	chr6A	86.792	477	43	6	1353	1829	554454564	554454108	5.830000e-142	514
4	TraesCS6A01G372600	chr6A	87.705	122	12	2	2852	2972	554453602	554453483	4.100000e-29	139
5	TraesCS6A01G372600	chr6B	90.986	1664	81	25	1407	3049	684504214	684505829	0.000000e+00	2178
6	TraesCS6A01G372600	chr6B	96.658	778	20	5	1	774	239323633	239324408	0.000000e+00	1288
7	TraesCS6A01G372600	chr6B	96.628	771	23	2	1	770	205540813	205541581	0.000000e+00	1277
8	TraesCS6A01G372600	chr6B	91.472	727	40	8	2166	2874	613105323	613104601	0.000000e+00	979
9	TraesCS6A01G372600	chr6B	90.355	394	25	8	900	1292	684503798	684504179	3.510000e-139	505
10	TraesCS6A01G372600	chr6B	84.774	243	20	5	1900	2134	613105555	613105322	8.500000e-56	228
11	TraesCS6A01G372600	chr6B	89.167	120	11	1	2861	2980	613104363	613104246	6.810000e-32	148
12	TraesCS6A01G372600	chr6D	85.674	1752	127	38	1341	3049	408645070	408643400	0.000000e+00	1731
13	TraesCS6A01G372600	chr6D	89.545	1320	90	22	771	2076	450826523	450827808	0.000000e+00	1629
14	TraesCS6A01G372600	chr6D	95.143	947	28	5	2117	3049	450827816	450828758	0.000000e+00	1478
15	TraesCS6A01G372600	chr7A	97.671	773	14	3	1	770	442161458	442162229	0.000000e+00	1325
16	TraesCS6A01G372600	chr7A	96.774	775	19	4	1	771	556772224	556771452	0.000000e+00	1288
17	TraesCS6A01G372600	chr1A	96.899	774	20	3	1	770	48733697	48732924	0.000000e+00	1293
18	TraesCS6A01G372600	chr5A	96.887	771	21	3	1	770	647524410	647523642	0.000000e+00	1288
19	TraesCS6A01G372600	chr3A	96.774	775	18	4	1	770	457507354	457506582	0.000000e+00	1286
20	TraesCS6A01G372600	chr1B	96.061	787	24	6	1	781	632965688	632964903	0.000000e+00	1275
21	TraesCS6A01G372600	chr4D	91.445	339	16	4	999	1330	20108554	20108886	1.290000e-123	453

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	TraesCS6A01G372600	chr6A	596420256	596423304	3048	False	5631.000000	5631	100.0000	1	3049	1	chr6A.!!$F1	3048
1	TraesCS6A01G372600	chr6A	585145710	585146487	777	True	1325.000000	1325	97.4330	1	776	1	chr6A.!!$R1	775
2	TraesCS6A01G372600	chr6A	554453483	554454564	1081	True	417.333333	599	87.6580	1353	2972	3	chr6A.!!$R2	1619
3	TraesCS6A01G372600	chr6B	684503798	684505829	2031	False	1341.500000	2178	90.6705	900	3049	2	chr6B.!!$F3	2149
4	TraesCS6A01G372600	chr6B	239323633	239324408	775	False	1288.000000	1288	96.6580	1	774	1	chr6B.!!$F2	773
5	TraesCS6A01G372600	chr6B	205540813	205541581	768	False	1277.000000	1277	96.6280	1	770	1	chr6B.!!$F1	769
6	TraesCS6A01G372600	chr6B	613104246	613105555	1309	True	451.666667	979	88.4710	1900	2980	3	chr6B.!!$R1	1080
7	TraesCS6A01G372600	chr6D	408643400	408645070	1670	True	1731.000000	1731	85.6740	1341	3049	1	chr6D.!!$R1	1708
8	TraesCS6A01G372600	chr6D	450826523	450828758	2235	False	1553.500000	1629	92.3440	771	3049	2	chr6D.!!$F1	2278
9	TraesCS6A01G372600	chr7A	442161458	442162229	771	False	1325.000000	1325	97.6710	1	770	1	chr7A.!!$F1	769
10	TraesCS6A01G372600	chr7A	556771452	556772224	772	True	1288.000000	1288	96.7740	1	771	1	chr7A.!!$R1	770
11	TraesCS6A01G372600	chr1A	48732924	48733697	773	True	1293.000000	1293	96.8990	1	770	1	chr1A.!!$R1	769
12	TraesCS6A01G372600	chr5A	647523642	647524410	768	True	1288.000000	1288	96.8870	1	770	1	chr5A.!!$R1	769
13	TraesCS6A01G372600	chr3A	457506582	457507354	772	True	1286.000000	1286	96.7740	1	770	1	chr3A.!!$R1	769
14	TraesCS6A01G372600	chr1B	632964903	632965688	785	True	1275.000000	1275	96.0610	1	781	1	chr1B.!!$R1	780

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
498	500	0.042131	CCACCCCCACCACTAGACTA	59.958	60.0	0.0	0.0	0.0	2.59	F
789	798	0.246360	GACCCCTCGGCAAAAATTGG	59.754	55.0	0.0	0.0	0.0	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1664	1692	0.170561	GTCTTGCTAGGCGTCTCGAA	59.829	55.000	0.0	0.0	0.00	3.71	R
2735	2789	1.875963	CGGAACATTGCTGTGTCCC	59.124	57.895	0.0	0.0	35.22	4.46	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
211	212	1.077501	CATGAAGCGTGGGGTCCAT	60.078	57.895	0.00	0.00	35.28	3.41
298	299	2.612972	CCACTCGACCAAGCAACATACT	60.613	50.000	0.00	0.00	0.00	2.12
333	334	1.542492	AGTTCACCACTCGACCGTAT	58.458	50.000	0.00	0.00	0.00	3.06
498	500	0.042131	CCACCCCCACCACTAGACTA	59.958	60.000	0.00	0.00	0.00	2.59
648	657	3.588336	GGAGCACGAGACGTAGGT	58.412	61.111	0.00	0.00	38.32	3.08
789	798	0.246360	GACCCCTCGGCAAAAATTGG	59.754	55.000	0.00	0.00	0.00	3.16
853	866	1.648467	GCGTGGGGCAGAAGATCAAC	61.648	60.000	0.00	0.00	42.87	3.18
854	867	1.026718	CGTGGGGCAGAAGATCAACC	61.027	60.000	0.00	0.00	0.00	3.77
855	868	0.681243	GTGGGGCAGAAGATCAACCC	60.681	60.000	0.00	0.00	40.05	4.11
872	885	3.830698	CCCCCTAGTTTTCCGGGT	58.169	61.111	0.00	0.00	36.18	5.28
873	886	3.010627	CCCCCTAGTTTTCCGGGTA	57.989	57.895	0.00	0.00	36.18	3.69
874	887	0.543277	CCCCCTAGTTTTCCGGGTAC	59.457	60.000	0.00	0.00	36.18	3.34
877	890	2.355412	CCCCTAGTTTTCCGGGTACTTG	60.355	54.545	0.00	3.93	36.18	3.16
897	910	2.875317	TGTACGAAAACTGCATGCTCAA	59.125	40.909	20.33	0.00	0.00	3.02
918	931	7.328277	TCAATCTCACGGAAAAGAAAAGAAA	57.672	32.000	0.00	0.00	0.00	2.52
919	932	7.767261	TCAATCTCACGGAAAAGAAAAGAAAA	58.233	30.769	0.00	0.00	0.00	2.29
920	933	7.915397	TCAATCTCACGGAAAAGAAAAGAAAAG	59.085	33.333	0.00	0.00	0.00	2.27
924	937	6.926313	TCACGGAAAAGAAAAGAAAAGGAAA	58.074	32.000	0.00	0.00	0.00	3.13
1015	1029	2.125350	CCCGTCTCTGCTTCCTGC	60.125	66.667	0.00	0.00	43.25	4.85
1249	1263	2.284995	AGTGCTCCTCCTCCCCAC	60.285	66.667	0.00	0.00	0.00	4.61
1255	1269	3.721706	CCTCCTCCCCACACTGCC	61.722	72.222	0.00	0.00	0.00	4.85
1270	1284	3.242936	ACACTGCCGTAACAAATGTGTTC	60.243	43.478	4.02	0.00	45.00	3.18
1279	1293	5.277297	CGTAACAAATGTGTTCTGCTCAGAA	60.277	40.000	4.02	8.14	45.00	3.02
1280	1294	5.779529	AACAAATGTGTTCTGCTCAGAAT	57.220	34.783	14.54	0.00	45.00	2.40
1281	1295	5.766222	AACAAATGTGTTCTGCTCAGAATC	58.234	37.500	14.54	11.46	45.00	2.52
1282	1296	5.533903	AACAAATGTGTTCTGCTCAGAATCT	59.466	36.000	14.54	0.00	45.00	2.40
1283	1297	6.040166	AACAAATGTGTTCTGCTCAGAATCTT	59.960	34.615	14.54	7.59	45.00	2.40
1284	1298	7.417116	AACAAATGTGTTCTGCTCAGAATCTTT	60.417	33.333	14.54	11.81	45.00	2.52
1302	1316	3.260884	TCTTTATCTTCAGGTTCGGCAGT	59.739	43.478	0.00	0.00	0.00	4.40
1336	1350	3.933332	GGAACACTGGTAGCACTACATTC	59.067	47.826	9.87	5.27	37.78	2.67
1337	1351	4.562757	GGAACACTGGTAGCACTACATTCA	60.563	45.833	9.87	0.00	37.78	2.57
1340	1354	4.020218	ACACTGGTAGCACTACATTCACAT	60.020	41.667	9.87	0.00	37.78	3.21
1346	1360	8.245195	TGGTAGCACTACATTCACATAATCTA	57.755	34.615	9.87	0.00	37.78	1.98
1373	1390	5.812127	ACTGAAATTTGCTTGGTTTCTGAAC	59.188	36.000	0.00	0.00	35.82	3.18
1393	1412	2.235016	CCGATTTCCCTTTGGTTCACA	58.765	47.619	0.00	0.00	0.00	3.58
1535	1554	2.894387	GAGGCGCTGCTCATGGTC	60.894	66.667	7.64	0.00	0.00	4.02
1612	1640	1.900486	ACAGGACTAGGCCTTGTACAC	59.100	52.381	28.30	17.40	35.66	2.90
1617	1645	1.907255	ACTAGGCCTTGTACACCCTTC	59.093	52.381	18.82	0.00	0.00	3.46
1618	1646	1.906574	CTAGGCCTTGTACACCCTTCA	59.093	52.381	12.58	0.00	0.00	3.02
1631	1659	4.137543	ACACCCTTCAAAGTTCAGATGAC	58.862	43.478	0.00	0.00	0.00	3.06
1667	1695	2.940147	TCGGTTCCATTTTGCAATTCG	58.060	42.857	0.00	0.00	0.00	3.34
1676	1704	2.087501	TTTGCAATTCGAGACGCCTA	57.912	45.000	0.00	0.00	0.00	3.93
1678	1706	0.806102	TGCAATTCGAGACGCCTAGC	60.806	55.000	0.00	0.00	0.00	3.42
1849	1881	2.771089	CACAGCCTGATGTTGTACTGT	58.229	47.619	0.00	0.00	38.84	3.55
1850	1882	2.481568	CACAGCCTGATGTTGTACTGTG	59.518	50.000	0.00	6.56	46.10	3.66
1870	1902	5.989477	TGTGAGATGATCTACCGGAAAAAT	58.011	37.500	9.46	0.00	0.00	1.82
1964	2009	7.182817	ACTGTTACATGCTCTAGGAAATACA	57.817	36.000	0.00	0.00	0.00	2.29
2163	2213	7.703621	CGATTAATTGAAGAATTGCAGATTGGT	59.296	33.333	0.00	0.00	33.63	3.67
2346	2398	2.523015	CAATTGATTGCAGAACCGAGC	58.477	47.619	0.00	0.00	0.00	5.03
2436	2489	6.618287	ACATCGACAAATCTTTTCAGACAA	57.382	33.333	0.00	0.00	0.00	3.18
2437	2490	6.430451	ACATCGACAAATCTTTTCAGACAAC	58.570	36.000	0.00	0.00	0.00	3.32
2438	2491	6.038161	ACATCGACAAATCTTTTCAGACAACA	59.962	34.615	0.00	0.00	0.00	3.33
2457	2510	8.886719	AGACAACATGTAACAACATATGATCAG	58.113	33.333	10.38	0.00	0.00	2.90
2552	2606	6.195244	GCATTGCAGTATAACGAAATCAAGTG	59.805	38.462	3.15	0.00	0.00	3.16
2735	2789	2.032550	CCCTTATCAAGCAGCAACGATG	59.967	50.000	0.00	0.00	0.00	3.84
2770	2832	1.208535	TCCGCTGGTAACGATCCAAAT	59.791	47.619	0.00	0.00	42.51	2.32

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
211	212	1.349688	GACCTGGACCCACATGTTGTA	59.650	52.381	0.00	0.00	0.00	2.41
298	299	9.977260	AGTGGTGAACTATCATCCGAGTGGATA	62.977	44.444	0.00	0.00	45.31	2.59
313	314	2.183478	TACGGTCGAGTGGTGAACTA	57.817	50.000	0.00	0.00	40.07	2.24
333	334	4.510711	GTCTTCGTATATCCGAGTGAGTCA	59.489	45.833	0.00	0.00	38.23	3.41
498	500	4.678743	GTGGAAGCCGCCCCCTTT	62.679	66.667	1.00	0.00	0.00	3.11
648	657	3.056107	CCTCTCACGGTGGAGATAACAAA	60.056	47.826	20.96	0.00	42.69	2.83
789	798	0.752743	TTCATGCCATAGTGCCCTGC	60.753	55.000	0.00	0.00	0.00	4.85
816	829	0.463620	GCTTGTTGGAACTTTGGGCA	59.536	50.000	0.00	0.00	0.00	5.36
868	881	2.156310	GCAGTTTTCGTACAAGTACCCG	59.844	50.000	4.89	0.00	32.61	5.28
871	884	4.084013	AGCATGCAGTTTTCGTACAAGTAC	60.084	41.667	21.98	0.29	0.00	2.73
872	885	4.062293	AGCATGCAGTTTTCGTACAAGTA	58.938	39.130	21.98	0.00	0.00	2.24
873	886	2.878406	AGCATGCAGTTTTCGTACAAGT	59.122	40.909	21.98	0.00	0.00	3.16
874	887	3.058983	TGAGCATGCAGTTTTCGTACAAG	60.059	43.478	21.98	0.00	0.00	3.16
877	890	3.536158	TTGAGCATGCAGTTTTCGTAC	57.464	42.857	21.98	0.00	0.00	3.67
897	910	6.546034	TCCTTTTCTTTTCTTTTCCGTGAGAT	59.454	34.615	0.00	0.00	0.00	2.75
1015	1029	4.849329	GACACGAGTAGGGCGCGG	62.849	72.222	8.83	0.00	44.64	6.46
1023	1037	2.717044	CCCGCCATGGACACGAGTA	61.717	63.158	18.40	0.00	42.00	2.59
1024	1038	4.082523	CCCGCCATGGACACGAGT	62.083	66.667	18.40	0.00	42.00	4.18
1198	1212	4.020617	CCCTTGCTGTCCGGCTCA	62.021	66.667	0.00	0.00	0.00	4.26
1249	1263	3.003275	AGAACACATTTGTTACGGCAGTG	59.997	43.478	0.00	0.00	46.43	3.66
1255	1269	4.211164	TCTGAGCAGAACACATTTGTTACG	59.789	41.667	0.00	0.00	46.43	3.18
1270	1284	6.347696	ACCTGAAGATAAAGATTCTGAGCAG	58.652	40.000	0.00	0.00	0.00	4.24
1279	1293	4.080863	ACTGCCGAACCTGAAGATAAAGAT	60.081	41.667	0.00	0.00	0.00	2.40
1280	1294	3.260884	ACTGCCGAACCTGAAGATAAAGA	59.739	43.478	0.00	0.00	0.00	2.52
1281	1295	3.600388	ACTGCCGAACCTGAAGATAAAG	58.400	45.455	0.00	0.00	0.00	1.85
1282	1296	3.007506	TGACTGCCGAACCTGAAGATAAA	59.992	43.478	0.00	0.00	0.00	1.40
1283	1297	2.565391	TGACTGCCGAACCTGAAGATAA	59.435	45.455	0.00	0.00	0.00	1.75
1284	1298	2.176045	TGACTGCCGAACCTGAAGATA	58.824	47.619	0.00	0.00	0.00	1.98
1346	1360	7.725251	TCAGAAACCAAGCAAATTTCAGTTAT	58.275	30.769	0.00	0.00	35.26	1.89
1373	1390	2.235016	TGTGAACCAAAGGGAAATCGG	58.765	47.619	0.00	0.00	38.05	4.18
1393	1412	3.569701	GTCATCCTGGTTGAACAACACAT	59.430	43.478	17.43	3.10	42.85	3.21
1496	1515	1.522806	GATGTTGGGCCGCGTGATA	60.523	57.895	4.92	0.00	0.00	2.15
1517	1536	4.827087	ACCATGAGCAGCGCCTCG	62.827	66.667	2.29	0.00	34.56	4.63
1603	1628	4.204012	TGAACTTTGAAGGGTGTACAAGG	58.796	43.478	0.00	0.00	0.00	3.61
1612	1640	5.005740	TGATGTCATCTGAACTTTGAAGGG	58.994	41.667	13.90	0.00	0.00	3.95
1617	1645	6.250344	ACACATGATGTCATCTGAACTTTG	57.750	37.500	13.90	6.41	36.54	2.77
1645	1673	3.738282	CGAATTGCAAAATGGAACCGAAA	59.262	39.130	1.71	0.00	32.17	3.46
1649	1677	3.920412	GTCTCGAATTGCAAAATGGAACC	59.080	43.478	1.71	0.00	28.29	3.62
1650	1678	3.603770	CGTCTCGAATTGCAAAATGGAAC	59.396	43.478	1.71	0.00	28.29	3.62
1653	1681	1.913403	GCGTCTCGAATTGCAAAATGG	59.087	47.619	1.71	0.00	0.00	3.16
1664	1692	0.170561	GTCTTGCTAGGCGTCTCGAA	59.829	55.000	0.00	0.00	0.00	3.71
1667	1695	4.386245	CGTCTTGCTAGGCGTCTC	57.614	61.111	14.09	0.00	44.27	3.36
1676	1704	3.179443	TCTGTTCTTGTTCGTCTTGCT	57.821	42.857	0.00	0.00	0.00	3.91
1678	1706	6.017933	GCATATTCTGTTCTTGTTCGTCTTG	58.982	40.000	0.00	0.00	0.00	3.02
1723	1751	4.419522	ACACAAGATTTGCGGACATAAC	57.580	40.909	0.00	0.00	0.00	1.89
1726	1754	3.149196	AGAACACAAGATTTGCGGACAT	58.851	40.909	0.00	0.00	0.00	3.06
1891	1925	9.935241	ATCGATGAAGCTACATTCTATGTAAAT	57.065	29.630	0.00	0.00	44.44	1.40
1892	1926	9.764363	AATCGATGAAGCTACATTCTATGTAAA	57.236	29.630	0.00	0.00	44.44	2.01
1898	1932	8.893219	ATTGAAATCGATGAAGCTACATTCTA	57.107	30.769	0.00	0.00	0.00	2.10
1901	1935	9.499479	AGATATTGAAATCGATGAAGCTACATT	57.501	29.630	0.00	0.00	0.00	2.71
1964	2009	3.563808	TGAATTTTGCTGTAGTCGCACTT	59.436	39.130	0.00	0.00	37.07	3.16
2141	2191	9.638239	GTTAACCAATCTGCAATTCTTCAATTA	57.362	29.630	0.00	0.00	30.51	1.40
2280	2332	3.118075	TGTCCTCATGTTGACCAAGTTGA	60.118	43.478	3.87	0.00	0.00	3.18
2393	2446	6.536582	CGATGTAGAAATTCATGTCCAGTTCT	59.463	38.462	0.00	9.03	0.00	3.01
2400	2453	8.607459	AGATTTGTCGATGTAGAAATTCATGTC	58.393	33.333	0.00	0.00	0.00	3.06
2436	2489	8.260114	TCTCACTGATCATATGTTGTTACATGT	58.740	33.333	2.69	2.69	44.56	3.21
2437	2490	8.652810	TCTCACTGATCATATGTTGTTACATG	57.347	34.615	1.90	0.00	44.56	3.21
2438	2491	9.842775	ATTCTCACTGATCATATGTTGTTACAT	57.157	29.630	1.90	0.00	46.49	2.29
2457	2510	9.810545	GCCTTATATCCTTCAGTATATTCTCAC	57.189	37.037	0.00	0.00	0.00	3.51
2552	2606	2.453983	TTGCTGGGTAAAAATGCTGC	57.546	45.000	0.00	0.00	0.00	5.25
2735	2789	1.875963	CGGAACATTGCTGTGTCCC	59.124	57.895	0.00	0.00	35.22	4.46
2770	2832	5.759506	TGTCAGCGGAAAGTTCATTTTAA	57.240	34.783	0.00	0.00	0.00	1.52
2982	3310	3.591527	TCCCCTCTTGAGCCTTTTTATGA	59.408	43.478	0.00	0.00	0.00	2.15
2983	3311	3.968265	TCCCCTCTTGAGCCTTTTTATG	58.032	45.455	0.00	0.00	0.00	1.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.