AutoCloner

Multiple sequence alignment - TraesCS1B01G164400

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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	TraesCS1B01G164400	chr1B	100.000	2727	0	0	1	2727	286757446	286760172	0.000000e+00	5036.0
1	TraesCS1B01G164400	chr1B	93.511	940	40	9	1	925	6041063	6040130	0.000000e+00	1378.0
2	TraesCS1B01G164400	chr1B	94.595	592	25	3	2137	2727	38111954	38112539	0.000000e+00	909.0
3	TraesCS1B01G164400	chr1B	93.802	597	27	7	1133	1726	38110864	38111453	0.000000e+00	889.0
4	TraesCS1B01G164400	chr1B	95.115	348	17	0	1728	2075	38111495	38111842	1.430000e-152	549.0
5	TraesCS1B01G164400	chr1B	80.000	480	51	25	2251	2727	661145295	661145732	2.040000e-81	313.0
6	TraesCS1B01G164400	chr1B	85.590	229	27	6	1155	1379	661136775	661137001	4.540000e-58	235.0
7	TraesCS1B01G164400	chr1B	84.018	219	22	8	1938	2143	661137211	661137429	5.960000e-47	198.0
8	TraesCS1B01G164400	chr1B	90.984	122	10	1	957	1077	38110733	38110854	2.170000e-36	163.0
9	TraesCS1B01G164400	chr1B	83.974	156	21	3	2201	2354	661148030	661148183	2.190000e-31	147.0
10	TraesCS1B01G164400	chr1B	86.813	91	12	0	1548	1638	661137071	661137161	4.800000e-18	102.0
11	TraesCS1B01G164400	chr1B	73.958	192	40	9	956	1142	621026541	621026355	4.870000e-08	69.4
12	TraesCS1B01G164400	chr1B	96.875	32	1	0	957	988	58375975	58375944	1.000000e-03	54.7
13	TraesCS1B01G164400	chr5B	94.094	1016	39	8	1728	2727	16284253	16285263	0.000000e+00	1524.0
14	TraesCS1B01G164400	chr5B	91.970	934	55	7	1	921	74368470	74369396	0.000000e+00	1291.0
15	TraesCS1B01G164400	chr5B	91.578	938	53	9	1	924	107926985	107926060	0.000000e+00	1271.0
16	TraesCS1B01G164400	chr5B	95.775	284	10	2	1452	1733	16283939	16284222	8.900000e-125	457.0
17	TraesCS1B01G164400	chr3B	94.112	1002	50	5	1728	2727	575447443	575446449	0.000000e+00	1515.0
18	TraesCS1B01G164400	chr3B	94.776	938	32	5	1	921	792144476	792145413	0.000000e+00	1445.0
19	TraesCS1B01G164400	chr3B	92.439	939	52	7	1	925	792030481	792031414	0.000000e+00	1323.0
20	TraesCS1B01G164400	chr3B	91.782	937	53	10	1	921	763431628	763430700	0.000000e+00	1282.0
21	TraesCS1B01G164400	chr3B	92.061	781	48	6	957	1733	575448245	575447475	0.000000e+00	1086.0
22	TraesCS1B01G164400	chr3B	82.336	702	83	25	1888	2585	470523237	470523901	3.050000e-159	571.0
23	TraesCS1B01G164400	chr7B	94.540	934	27	12	1	923	5335057	5335977	0.000000e+00	1421.0
24	TraesCS1B01G164400	chr7B	79.430	807	81	44	1794	2588	611603829	611604562	2.440000e-135	492.0
25	TraesCS1B01G164400	chr2B	93.390	938	42	7	1	925	797532420	797531490	0.000000e+00	1371.0
26	TraesCS1B01G164400	chr6B	92.706	946	46	9	1	930	45664239	45663301	0.000000e+00	1343.0
27	TraesCS1B01G164400	chr6B	90.792	934	40	19	1	921	239386948	239386048	0.000000e+00	1206.0
28	TraesCS1B01G164400	chr4B	92.365	943	42	9	8	921	20586213	20587154	0.000000e+00	1315.0
29	TraesCS1B01G164400	chr4B	91.141	824	65	6	1908	2727	120577255	120578074	0.000000e+00	1110.0
30	TraesCS1B01G164400	chr4B	87.225	681	61	11	955	1633	120511566	120512222	0.000000e+00	752.0
31	TraesCS1B01G164400	chr4B	87.681	138	9	1	1749	1886	120577144	120577273	1.310000e-33	154.0
32	TraesCS1B01G164400	chr6A	87.321	560	61	9	2032	2585	147978708	147978153	1.380000e-177	632.0
33	TraesCS1B01G164400	chr1D	86.087	230	19	7	2007	2223	475240784	475241013	4.540000e-58	235.0
34	TraesCS1B01G164400	chr1D	77.219	338	55	12	954	1271	475238471	475238806	7.760000e-41	178.0
35	TraesCS1B01G164400	chr1D	86.813	91	12	0	1548	1638	475239258	475239348	4.800000e-18	102.0
36	TraesCS1B01G164400	chrUn	89.894	188	5	2	1	175	279001421	279001607	2.110000e-56	230.0
37	TraesCS1B01G164400	chrUn	89.894	188	5	2	1	175	470255079	470255265	2.110000e-56	230.0
38	TraesCS1B01G164400	chr4A	88.571	175	20	0	2411	2585	607632595	607632421	2.130000e-51	213.0
39	TraesCS1B01G164400	chr4A	74.603	189	44	4	957	1142	725872020	725871833	2.250000e-11	80.5

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	TraesCS1B01G164400	chr1B	286757446	286760172	2726	False	5036.0	5036	100.0000	1	2727	1	chr1B.!!$F1	2726
1	TraesCS1B01G164400	chr1B	6040130	6041063	933	True	1378.0	1378	93.5110	1	925	1	chr1B.!!$R1	924
2	TraesCS1B01G164400	chr1B	38110733	38112539	1806	False	627.5	909	93.6240	957	2727	4	chr1B.!!$F2	1770
3	TraesCS1B01G164400	chr1B	661145295	661148183	2888	False	230.0	313	81.9870	2201	2727	2	chr1B.!!$F4	526
4	TraesCS1B01G164400	chr5B	74368470	74369396	926	False	1291.0	1291	91.9700	1	921	1	chr5B.!!$F1	920
5	TraesCS1B01G164400	chr5B	107926060	107926985	925	True	1271.0	1271	91.5780	1	924	1	chr5B.!!$R1	923
6	TraesCS1B01G164400	chr5B	16283939	16285263	1324	False	990.5	1524	94.9345	1452	2727	2	chr5B.!!$F2	1275
7	TraesCS1B01G164400	chr3B	792144476	792145413	937	False	1445.0	1445	94.7760	1	921	1	chr3B.!!$F3	920
8	TraesCS1B01G164400	chr3B	792030481	792031414	933	False	1323.0	1323	92.4390	1	925	1	chr3B.!!$F2	924
9	TraesCS1B01G164400	chr3B	575446449	575448245	1796	True	1300.5	1515	93.0865	957	2727	2	chr3B.!!$R2	1770
10	TraesCS1B01G164400	chr3B	763430700	763431628	928	True	1282.0	1282	91.7820	1	921	1	chr3B.!!$R1	920
11	TraesCS1B01G164400	chr3B	470523237	470523901	664	False	571.0	571	82.3360	1888	2585	1	chr3B.!!$F1	697
12	TraesCS1B01G164400	chr7B	5335057	5335977	920	False	1421.0	1421	94.5400	1	923	1	chr7B.!!$F1	922
13	TraesCS1B01G164400	chr7B	611603829	611604562	733	False	492.0	492	79.4300	1794	2588	1	chr7B.!!$F2	794
14	TraesCS1B01G164400	chr2B	797531490	797532420	930	True	1371.0	1371	93.3900	1	925	1	chr2B.!!$R1	924
15	TraesCS1B01G164400	chr6B	45663301	45664239	938	True	1343.0	1343	92.7060	1	930	1	chr6B.!!$R1	929
16	TraesCS1B01G164400	chr6B	239386048	239386948	900	True	1206.0	1206	90.7920	1	921	1	chr6B.!!$R2	920
17	TraesCS1B01G164400	chr4B	20586213	20587154	941	False	1315.0	1315	92.3650	8	921	1	chr4B.!!$F1	913
18	TraesCS1B01G164400	chr4B	120511566	120512222	656	False	752.0	752	87.2250	955	1633	1	chr4B.!!$F2	678
19	TraesCS1B01G164400	chr4B	120577144	120578074	930	False	632.0	1110	89.4110	1749	2727	2	chr4B.!!$F3	978
20	TraesCS1B01G164400	chr6A	147978153	147978708	555	True	632.0	632	87.3210	2032	2585	1	chr6A.!!$R1	553

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
934	988	1.125633	TGCCCTAAGATACGAACCCC	58.874	55.0	0.0	0.0	0.0	4.95	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2492	2698	0.175073	ATACTCCTTTCCGACACGCC	59.825	55.0	0.0	0.0	0.0	5.68	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
618	650	1.990060	TCAAGGAGGAGAAGGCCGG	60.990	63.158	0.00	0.00	0.00	6.13
894	947	2.046700	CGCTTTTAGACGCCCCCA	60.047	61.111	0.00	0.00	0.00	4.96
926	980	2.260822	GGCTGGAGATGCCCTAAGATA	58.739	52.381	0.00	0.00	44.32	1.98
927	981	2.027653	GGCTGGAGATGCCCTAAGATAC	60.028	54.545	0.00	0.00	44.32	2.24
928	982	2.353208	GCTGGAGATGCCCTAAGATACG	60.353	54.545	0.00	0.00	34.97	3.06
929	983	3.157881	CTGGAGATGCCCTAAGATACGA	58.842	50.000	0.00	0.00	34.97	3.43
930	984	3.572642	TGGAGATGCCCTAAGATACGAA	58.427	45.455	0.00	0.00	34.97	3.85
931	985	3.321111	TGGAGATGCCCTAAGATACGAAC	59.679	47.826	0.00	0.00	34.97	3.95
932	986	3.306156	GGAGATGCCCTAAGATACGAACC	60.306	52.174	0.00	0.00	0.00	3.62
933	987	2.633481	AGATGCCCTAAGATACGAACCC	59.367	50.000	0.00	0.00	0.00	4.11
934	988	1.125633	TGCCCTAAGATACGAACCCC	58.874	55.000	0.00	0.00	0.00	4.95
935	989	1.125633	GCCCTAAGATACGAACCCCA	58.874	55.000	0.00	0.00	0.00	4.96
936	990	1.697982	GCCCTAAGATACGAACCCCAT	59.302	52.381	0.00	0.00	0.00	4.00
937	991	2.289506	GCCCTAAGATACGAACCCCATC	60.290	54.545	0.00	0.00	0.00	3.51
938	992	3.240302	CCCTAAGATACGAACCCCATCT	58.760	50.000	0.00	0.00	0.00	2.90
939	993	3.646637	CCCTAAGATACGAACCCCATCTT	59.353	47.826	0.00	0.00	40.96	2.40
940	994	4.836736	CCCTAAGATACGAACCCCATCTTA	59.163	45.833	0.00	0.00	39.24	2.10
941	995	5.484290	CCCTAAGATACGAACCCCATCTTAT	59.516	44.000	0.00	0.00	39.38	1.73
942	996	6.398918	CCTAAGATACGAACCCCATCTTATG	58.601	44.000	0.00	0.00	39.38	1.90
943	997	4.273148	AGATACGAACCCCATCTTATGC	57.727	45.455	0.00	0.00	0.00	3.14
944	998	3.904339	AGATACGAACCCCATCTTATGCT	59.096	43.478	0.00	0.00	0.00	3.79
945	999	4.348168	AGATACGAACCCCATCTTATGCTT	59.652	41.667	0.00	0.00	0.00	3.91
946	1000	2.919228	ACGAACCCCATCTTATGCTTC	58.081	47.619	0.00	0.00	0.00	3.86
947	1001	2.238646	ACGAACCCCATCTTATGCTTCA	59.761	45.455	0.00	0.00	0.00	3.02
948	1002	3.278574	CGAACCCCATCTTATGCTTCAA	58.721	45.455	0.00	0.00	0.00	2.69
949	1003	3.065371	CGAACCCCATCTTATGCTTCAAC	59.935	47.826	0.00	0.00	0.00	3.18
950	1004	2.643551	ACCCCATCTTATGCTTCAACG	58.356	47.619	0.00	0.00	0.00	4.10
951	1005	2.238646	ACCCCATCTTATGCTTCAACGA	59.761	45.455	0.00	0.00	0.00	3.85
952	1006	3.278574	CCCCATCTTATGCTTCAACGAA	58.721	45.455	0.00	0.00	0.00	3.85
953	1007	3.885297	CCCCATCTTATGCTTCAACGAAT	59.115	43.478	0.00	0.00	0.00	3.34
954	1008	5.063204	CCCCATCTTATGCTTCAACGAATA	58.937	41.667	0.00	0.00	0.00	1.75
955	1009	5.707298	CCCCATCTTATGCTTCAACGAATAT	59.293	40.000	0.00	0.00	0.00	1.28
1002	1056	7.254455	GCGAACATATTCATAACTAAGTGCACT	60.254	37.037	15.25	15.25	34.14	4.40
1005	1059	9.448438	AACATATTCATAACTAAGTGCACTCAA	57.552	29.630	21.95	10.78	0.00	3.02
1006	1060	9.618890	ACATATTCATAACTAAGTGCACTCAAT	57.381	29.630	21.95	7.37	0.00	2.57
1055	1110	4.679373	ATAACAGCCTCACGATCAGATT	57.321	40.909	0.00	0.00	0.00	2.40
1125	1181	3.276882	CGTTTAGCAATTTTGACGGGT	57.723	42.857	0.00	0.00	0.00	5.28
1143	1199	1.523758	GTGGACGAAAACTCTGCCAT	58.476	50.000	0.00	0.00	0.00	4.40
1173	1229	4.690719	CCCACGCCCGCACAAGTA	62.691	66.667	0.00	0.00	0.00	2.24
1174	1230	3.118454	CCACGCCCGCACAAGTAG	61.118	66.667	0.00	0.00	0.00	2.57
1446	1502	2.439701	CCTCGCCGACCTGGACTA	60.440	66.667	0.00	0.00	42.00	2.59
1665	1723	1.589461	CACCGTGACGTCAAACCGA	60.589	57.895	21.95	0.00	0.00	4.69
1693	1751	4.253257	CCTCGACGCCTAGGACGC	62.253	72.222	14.75	10.67	34.58	5.19
1788	1888	2.369257	ATTGGATCGAGCGACCGCAT	62.369	55.000	16.97	1.24	44.88	4.73
1850	1950	2.890311	TGAAATCCAATCACCGCAACTT	59.110	40.909	0.00	0.00	0.00	2.66
2054	2163	4.724602	TGCTCGACGCTGGTGCTC	62.725	66.667	8.07	0.00	40.11	4.26
2416	2622	0.041839	CGGCGCATCACATTTAGCTC	60.042	55.000	10.83	0.00	0.00	4.09
2430	2636	5.046304	ACATTTAGCTCAGTTGGCTCTCTAA	60.046	40.000	0.00	0.00	40.74	2.10
2680	2893	2.688446	CTGGACAATCATGCTTGATGCT	59.312	45.455	15.86	4.24	41.83	3.79
2686	2899	5.434408	ACAATCATGCTTGATGCTAAGAGA	58.566	37.500	15.86	0.00	41.83	3.10

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
107	109	1.458588	AGGATCGGGAGGAGGAAGC	60.459	63.158	0.00	0.00	0.00	3.86
520	549	3.601685	TCGCTGTCGCACAGGACA	61.602	61.111	15.16	5.44	46.01	4.02
685	724	9.260002	GCCAAATTCGTCCATTTTCATTATTAT	57.740	29.630	0.00	0.00	0.00	1.28
686	725	7.708752	GGCCAAATTCGTCCATTTTCATTATTA	59.291	33.333	0.00	0.00	0.00	0.98
688	727	6.048509	GGCCAAATTCGTCCATTTTCATTAT	58.951	36.000	0.00	0.00	0.00	1.28
926	980	2.238646	TGAAGCATAAGATGGGGTTCGT	59.761	45.455	0.00	0.00	40.79	3.85
927	981	2.917933	TGAAGCATAAGATGGGGTTCG	58.082	47.619	0.00	0.00	40.79	3.95
928	982	3.065371	CGTTGAAGCATAAGATGGGGTTC	59.935	47.826	0.00	0.00	38.97	3.62
929	983	3.016736	CGTTGAAGCATAAGATGGGGTT	58.983	45.455	0.00	0.00	0.00	4.11
930	984	2.238646	TCGTTGAAGCATAAGATGGGGT	59.761	45.455	0.00	0.00	0.00	4.95
931	985	2.917933	TCGTTGAAGCATAAGATGGGG	58.082	47.619	0.00	0.00	0.00	4.96
932	986	6.808008	ATATTCGTTGAAGCATAAGATGGG	57.192	37.500	0.00	0.00	0.00	4.00
933	987	8.092521	AGAATATTCGTTGAAGCATAAGATGG	57.907	34.615	9.78	0.00	0.00	3.51
934	988	8.986847	AGAGAATATTCGTTGAAGCATAAGATG	58.013	33.333	9.78	0.00	0.00	2.90
936	990	9.464714	GTAGAGAATATTCGTTGAAGCATAAGA	57.535	33.333	9.78	0.00	0.00	2.10
937	991	9.469807	AGTAGAGAATATTCGTTGAAGCATAAG	57.530	33.333	9.78	0.00	0.00	1.73
939	993	9.894783	GTAGTAGAGAATATTCGTTGAAGCATA	57.105	33.333	9.78	0.00	0.00	3.14
940	994	8.634444	AGTAGTAGAGAATATTCGTTGAAGCAT	58.366	33.333	9.78	0.00	0.00	3.79
941	995	7.997482	AGTAGTAGAGAATATTCGTTGAAGCA	58.003	34.615	9.78	0.00	0.00	3.91
955	1009	9.565213	GTTCGCTTGTTTAATAGTAGTAGAGAA	57.435	33.333	0.00	0.00	0.00	2.87
990	1044	4.223923	AGCCTAGATTGAGTGCACTTAGTT	59.776	41.667	22.65	8.34	0.00	2.24
1002	1056	4.040461	GCTGTTATGGGTAGCCTAGATTGA	59.960	45.833	13.11	0.00	0.00	2.57
1005	1059	3.325135	GTGCTGTTATGGGTAGCCTAGAT	59.675	47.826	13.11	0.00	36.64	1.98
1006	1060	2.698797	GTGCTGTTATGGGTAGCCTAGA	59.301	50.000	13.11	0.00	36.64	2.43
1009	1063	0.178068	CGTGCTGTTATGGGTAGCCT	59.822	55.000	13.11	0.26	36.64	4.58
1087	1143	0.250553	CGCAGTTTGGGTTGAGGGTA	60.251	55.000	0.00	0.00	0.00	3.69
1125	1181	2.301870	ACTATGGCAGAGTTTTCGTCCA	59.698	45.455	9.36	0.00	35.26	4.02
1143	1199	3.424703	GGGCGTGGGATATGTACTACTA	58.575	50.000	0.00	0.00	0.00	1.82
1174	1230	9.315525	GGAGATGTTTGTTTCCTATTCTACTAC	57.684	37.037	0.00	0.00	0.00	2.73
1665	1723	1.291877	GCGTCGAGGAGCACATTGTT	61.292	55.000	9.75	0.00	0.00	2.83
1746	1846	2.684881	CCATGACATGTTCAACCTAGGC	59.315	50.000	9.30	0.00	37.92	3.93
1752	1852	3.763360	TCCAATCCCATGACATGTTCAAC	59.237	43.478	14.26	0.00	37.92	3.18
1831	1931	2.095263	CGAAGTTGCGGTGATTGGATTT	60.095	45.455	0.00	0.00	0.00	2.17
1987	2094	2.192861	CGCAACAGGAAGTGCCCAA	61.193	57.895	0.00	0.00	37.37	4.12
2222	2417	5.722021	AAAAACACTGCCCTATTTGTAGG	57.278	39.130	0.00	0.00	36.98	3.18
2315	2521	9.196552	CTAAAAGCATCAATACATCGATACTGA	57.803	33.333	0.00	0.00	0.00	3.41
2416	2622	3.128242	CCAAGCAATTAGAGAGCCAACTG	59.872	47.826	0.00	0.00	0.00	3.16
2430	2636	5.716228	TCAATCTACAACCAATCCAAGCAAT	59.284	36.000	0.00	0.00	0.00	3.56
2492	2698	0.175073	ATACTCCTTTCCGACACGCC	59.825	55.000	0.00	0.00	0.00	5.68
2680	2893	8.618677	CGTAGTCAAGTAACACCATATCTCTTA	58.381	37.037	0.00	0.00	0.00	2.10
2686	2899	5.333299	TGCGTAGTCAAGTAACACCATAT	57.667	39.130	0.00	0.00	0.00	1.78

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.