AutoCloner

Multiple sequence alignment - TraesCS7D01G054200

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	TraesCS7D01G054200	chr7D	100.000	2705	0	0	1	2705	28690209	28692913	0.000000e+00	4996.0
1	TraesCS7D01G054200	chr7D	88.421	475	47	2	649	1121	28668465	28668933	1.410000e-157	566.0
2	TraesCS7D01G054200	chr7D	91.803	305	18	5	1463	1761	28668934	28669237	4.170000e-113	418.0
3	TraesCS7D01G054200	chr7D	86.957	230	26	2	1537	1762	28598538	28598309	3.460000e-64	255.0
4	TraesCS7D01G054200	chr7D	86.957	230	26	2	1537	1762	28602744	28602515	3.460000e-64	255.0
5	TraesCS7D01G054200	chr7D	86.695	233	27	2	1534	1762	28648270	28648502	3.460000e-64	255.0
6	TraesCS7D01G054200	chr7D	80.488	205	26	7	278	471	28620774	28620573	7.810000e-31	145.0
7	TraesCS7D01G054200	chr7D	80.488	205	26	7	278	471	28626228	28626429	7.810000e-31	145.0
8	TraesCS7D01G054200	chr7A	92.135	2403	122	25	1	2378	29104357	29106717	0.000000e+00	3328.0
9	TraesCS7D01G054200	chr7A	94.294	333	18	1	2373	2705	29106749	29107080	2.400000e-140	508.0
10	TraesCS7D01G054200	chr7A	89.439	303	28	1	1463	1761	29022523	29022825	1.970000e-101	379.0
11	TraesCS7D01G054200	chr7A	85.761	309	34	4	813	1121	29022218	29022516	4.350000e-83	318.0
12	TraesCS7D01G054200	chr7A	81.493	335	42	10	2079	2408	29022883	29023202	9.610000e-65	257.0
13	TraesCS7D01G054200	chr7A	92.361	144	10	1	649	792	29022015	29022157	1.270000e-48	204.0
14	TraesCS7D01G054200	chr7A	89.041	73	8	0	1	73	29011010	29011082	1.030000e-14	91.6
15	TraesCS7D01G054200	chr4A	93.022	1691	109	5	29	1713	702392507	702394194	0.000000e+00	2460.0
16	TraesCS7D01G054200	chr4A	92.066	605	46	2	1129	1733	702331741	702331139	0.000000e+00	850.0
17	TraesCS7D01G054200	chr4A	88.729	417	38	4	649	1063	702375422	702375831	4.020000e-138	501.0
18	TraesCS7D01G054200	chr4A	90.625	288	23	1	1478	1761	702375834	702376121	1.970000e-101	379.0
19	TraesCS7D01G054200	chr4A	85.603	257	26	6	786	1039	702332006	702331758	2.670000e-65	259.0
20	TraesCS7D01G054200	chr4A	81.579	304	42	9	2108	2408	702394601	702394893	3.480000e-59	239.0
21	TraesCS7D01G054200	chr4A	92.857	70	5	0	2010	2079	704436845	704436776	4.760000e-18	102.0
22	TraesCS7D01G054200	chrUn	80.488	205	26	7	278	471	356611967	356612168	7.810000e-31	145.0
23	TraesCS7D01G054200	chr5A	94.366	71	4	0	2009	2079	544438899	544438969	2.850000e-20	110.0
24	TraesCS7D01G054200	chr1A	80.405	148	21	7	204	343	32106767	32106620	3.680000e-19	106.0
25	TraesCS7D01G054200	chr7B	94.118	68	4	0	2011	2078	741995363	741995296	1.320000e-18	104.0
26	TraesCS7D01G054200	chr7B	92.754	69	5	0	2011	2079	479529496	479529564	1.710000e-17	100.0
27	TraesCS7D01G054200	chr4B	92.000	75	5	1	2010	2084	418517454	418517381	1.320000e-18	104.0
28	TraesCS7D01G054200	chr4B	90.541	74	7	0	2011	2084	346926478	346926405	6.160000e-17	99.0
29	TraesCS7D01G054200	chr2B	92.857	70	5	0	2010	2079	35046352	35046283	4.760000e-18	102.0
30	TraesCS7D01G054200	chr4D	89.873	79	7	1	2011	2088	47533250	47533172	1.710000e-17	100.0

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	TraesCS7D01G054200	chr7D	28690209	28692913	2704	False	4996.0	4996	100.0000	1	2705	1	chr7D.!!$F3	2704
1	TraesCS7D01G054200	chr7D	28668465	28669237	772	False	492.0	566	90.1120	649	1761	2	chr7D.!!$F4	1112
2	TraesCS7D01G054200	chr7D	28598309	28602744	4435	True	255.0	255	86.9570	1537	1762	2	chr7D.!!$R2	225
3	TraesCS7D01G054200	chr7A	29104357	29107080	2723	False	1918.0	3328	93.2145	1	2705	2	chr7A.!!$F3	2704
4	TraesCS7D01G054200	chr7A	29022015	29023202	1187	False	289.5	379	87.2635	649	2408	4	chr7A.!!$F2	1759
5	TraesCS7D01G054200	chr4A	702392507	702394893	2386	False	1349.5	2460	87.3005	29	2408	2	chr4A.!!$F2	2379
6	TraesCS7D01G054200	chr4A	702331139	702332006	867	True	554.5	850	88.8345	786	1733	2	chr4A.!!$R2	947
7	TraesCS7D01G054200	chr4A	702375422	702376121	699	False	440.0	501	89.6770	649	1761	2	chr4A.!!$F1	1112

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
647	653	0.321653	ATTCTTGTGCAGGTCCCGTC	60.322	55.0	0.00	0.00	0.00	4.79	F
1218	1288	0.750850	GCACCTTCATAGGCGTCCTA	59.249	55.0	7.86	7.86	46.22	2.94	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1535	1605	1.226746	GAAGACACCCGTTCCACTTG	58.773	55.0	0.0	0.0	0.0	3.16	R
2678	7250	1.227999	CGAGCGGAAGAGTTTGGCAA	61.228	55.0	0.0	0.0	0.0	4.52	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
31	32	1.234615	ATTTGTTGGGTGAGCGTCGG	61.235	55.000	0.00	0.00	0.00	4.79
156	157	2.799871	TGTATACGTATGCACACACGG	58.200	47.619	20.58	0.00	42.35	4.94
170	171	4.772434	CACACACGGTTGTTATCAAGAAG	58.228	43.478	0.00	0.00	31.66	2.85
180	181	7.967854	CGGTTGTTATCAAGAAGCATATTTTCA	59.032	33.333	0.00	0.00	32.34	2.69
190	191	7.081526	AGAAGCATATTTTCACAGTCATGAC	57.918	36.000	18.47	18.47	0.00	3.06
270	271	7.039784	TCAGGATAATTAAGCTGCAACAACTTT	60.040	33.333	1.02	0.00	0.00	2.66
337	338	8.645487	GTTGCTGTACATTGTAGTTAAGTAGAC	58.355	37.037	0.00	0.00	0.00	2.59
382	384	5.994054	GGAATCTGCAGTATTTAGAGCATCA	59.006	40.000	14.67	0.00	37.82	3.07
384	386	7.174599	GGAATCTGCAGTATTTAGAGCATCAAT	59.825	37.037	14.67	0.00	37.82	2.57
387	389	9.736414	ATCTGCAGTATTTAGAGCATCAATAAT	57.264	29.630	14.67	0.00	37.82	1.28
439	441	2.354188	CGACGCGTCTGTGACCAA	60.354	61.111	33.94	0.00	0.00	3.67
444	446	2.320587	GCGTCTGTGACCAAGCAGG	61.321	63.158	0.00	0.00	45.67	4.85
482	488	2.746904	CCACAACTACGCCATTTGATCA	59.253	45.455	0.00	0.00	0.00	2.92
538	544	2.160205	CCTCCTAATCTCGTCGCCATA	58.840	52.381	0.00	0.00	0.00	2.74
565	571	1.689813	TCACCGCTAGACAAAGGTTGA	59.310	47.619	0.00	0.00	34.25	3.18
612	618	1.814586	CCTCCGTCGTCGCTCTAGT	60.815	63.158	0.00	0.00	35.54	2.57
633	639	2.042831	GCGGCTGTGGCAGATTCTT	61.043	57.895	0.00	0.00	40.87	2.52
647	653	0.321653	ATTCTTGTGCAGGTCCCGTC	60.322	55.000	0.00	0.00	0.00	4.79
741	747	7.938563	ACTCTCTTCGATCTGTATTAATTGC	57.061	36.000	0.00	0.00	0.00	3.56
771	777	9.838975	TGATTTAGTACAATTATTTGCACAGTG	57.161	29.630	0.00	0.00	36.22	3.66
920	979	2.039084	AGAGCCTTGAAGGTTTCGTCAT	59.961	45.455	13.58	0.00	37.80	3.06
961	1026	2.141517	CACATCGATGGGATCAGCTTC	58.858	52.381	28.09	0.00	31.22	3.86
994	1059	6.647067	GGCAACCACTACTATATCTGTCAATC	59.353	42.308	0.00	0.00	0.00	2.67
1006	1076	4.639078	TCTGTCAATCCCTTCATGTCAA	57.361	40.909	0.00	0.00	0.00	3.18
1218	1288	0.750850	GCACCTTCATAGGCGTCCTA	59.249	55.000	7.86	7.86	46.22	2.94
1532	1602	2.413765	CCGGATACTTCGATAACGCGAT	60.414	50.000	15.93	2.34	40.35	4.58
1535	1605	1.762419	TACTTCGATAACGCGATGGC	58.238	50.000	15.93	0.00	40.35	4.40
1558	1628	2.222013	GGAACGGGTGTCTTCCCCT	61.222	63.158	0.00	0.00	44.32	4.79
1614	1684	3.112709	GGCGAGCTGACGACAACC	61.113	66.667	0.00	0.00	41.34	3.77
1759	6283	6.455647	CAGGTGTTCTGTACTCATCTGTAAA	58.544	40.000	10.61	0.00	38.64	2.01
1760	6284	6.929049	CAGGTGTTCTGTACTCATCTGTAAAA	59.071	38.462	10.61	0.00	38.64	1.52
1761	6285	7.116948	CAGGTGTTCTGTACTCATCTGTAAAAG	59.883	40.741	10.61	0.00	38.64	2.27
1762	6286	6.369065	GGTGTTCTGTACTCATCTGTAAAAGG	59.631	42.308	0.00	0.00	0.00	3.11
1763	6287	7.152645	GTGTTCTGTACTCATCTGTAAAAGGA	58.847	38.462	0.00	0.00	0.00	3.36
1764	6288	7.819900	GTGTTCTGTACTCATCTGTAAAAGGAT	59.180	37.037	0.00	0.00	0.00	3.24
1765	6289	7.819415	TGTTCTGTACTCATCTGTAAAAGGATG	59.181	37.037	0.00	0.00	40.23	3.51
1766	6290	6.341316	TCTGTACTCATCTGTAAAAGGATGC	58.659	40.000	0.00	0.00	39.14	3.91
1767	6291	6.048732	TGTACTCATCTGTAAAAGGATGCA	57.951	37.500	0.00	0.00	39.14	3.96
1768	6292	6.472016	TGTACTCATCTGTAAAAGGATGCAA	58.528	36.000	0.00	0.00	39.14	4.08
1769	6293	6.595326	TGTACTCATCTGTAAAAGGATGCAAG	59.405	38.462	0.00	0.00	39.14	4.01
1770	6294	4.397417	ACTCATCTGTAAAAGGATGCAAGC	59.603	41.667	0.00	0.00	39.14	4.01
1771	6295	3.374988	TCATCTGTAAAAGGATGCAAGCG	59.625	43.478	0.00	0.00	39.14	4.68
1772	6296	1.468520	TCTGTAAAAGGATGCAAGCGC	59.531	47.619	0.00	0.00	39.24	5.92
1773	6297	0.525761	TGTAAAAGGATGCAAGCGCC	59.474	50.000	2.29	0.00	37.32	6.53
1774	6298	0.525761	GTAAAAGGATGCAAGCGCCA	59.474	50.000	2.29	0.00	37.32	5.69
1775	6299	0.810648	TAAAAGGATGCAAGCGCCAG	59.189	50.000	2.29	0.00	37.32	4.85
1776	6300	1.181098	AAAAGGATGCAAGCGCCAGT	61.181	50.000	2.29	0.00	37.32	4.00
1777	6301	1.870055	AAAGGATGCAAGCGCCAGTG	61.870	55.000	2.29	0.41	37.32	3.66
1778	6302	3.818787	GGATGCAAGCGCCAGTGG	61.819	66.667	2.29	4.20	37.32	4.00
1779	6303	4.487412	GATGCAAGCGCCAGTGGC	62.487	66.667	25.07	25.07	46.75	5.01
1989	6515	5.005394	GCTCCAAGTTTTTCTTTTTCGGTTC	59.995	40.000	0.00	0.00	33.63	3.62
2006	6532	9.615295	TTTTCGGTTCATAATTAGTAGCAAAAC	57.385	29.630	0.00	0.00	0.00	2.43
2127	6659	4.142038	TCTAACTCCTGCGCTATGTGATA	58.858	43.478	9.73	0.00	0.00	2.15
2133	6665	1.615883	CTGCGCTATGTGATAGACCCT	59.384	52.381	9.73	0.00	34.77	4.34
2134	6666	2.036475	CTGCGCTATGTGATAGACCCTT	59.964	50.000	9.73	0.00	34.77	3.95
2192	6727	8.755696	TGGTTAGTCATTTCAATAAAACATGC	57.244	30.769	0.00	0.00	0.00	4.06
2227	6762	3.196685	AGACAGGAATAGAGAGCCAACAC	59.803	47.826	0.00	0.00	0.00	3.32
2237	6772	1.425066	AGAGCCAACACAATCTCCCAA	59.575	47.619	0.00	0.00	0.00	4.12
2440	7012	2.295909	TCTGGAAAACGCCTTCAATTGG	59.704	45.455	5.42	0.00	0.00	3.16
2491	7063	0.179163	GCGCACTTAGCAATTCCACC	60.179	55.000	0.30	0.00	46.13	4.61
2493	7065	1.812571	CGCACTTAGCAATTCCACCTT	59.187	47.619	0.00	0.00	46.13	3.50
2498	7070	4.524328	CACTTAGCAATTCCACCTTTTCCT	59.476	41.667	0.00	0.00	0.00	3.36
2523	7095	4.724074	ATGTGCACCTACCAATGATTTG	57.276	40.909	15.69	0.00	0.00	2.32
2587	7159	7.009907	GCATAGAGAAGGAACAATTTTGATTGC	59.990	37.037	0.00	0.00	35.04	3.56
2605	7177	5.873164	TGATTGCATCATGCTATAGTGCTAG	59.127	40.000	11.84	0.00	45.31	3.42
2639	7211	3.365820	TCGCTCGTTAGAATTTCCGTTTC	59.634	43.478	0.00	0.00	0.00	2.78
2642	7214	4.151867	GCTCGTTAGAATTTCCGTTTCACT	59.848	41.667	0.00	0.00	0.00	3.41
2673	7245	6.084925	GGACTGACTATATAATGACCGTTCG	58.915	44.000	0.00	0.00	0.00	3.95
2678	7250	6.152932	ACTATATAATGACCGTTCGGTTGT	57.847	37.500	17.90	7.39	38.85	3.32
2680	7252	5.728351	ATATAATGACCGTTCGGTTGTTG	57.272	39.130	17.90	0.00	38.85	3.33
2685	7257	1.313812	ACCGTTCGGTTGTTGCCAAA	61.314	50.000	11.27	0.00	34.35	3.28
2690	7262	1.757682	TCGGTTGTTGCCAAACTCTT	58.242	45.000	0.00	0.00	36.06	2.85
2692	7264	1.269051	CGGTTGTTGCCAAACTCTTCC	60.269	52.381	0.00	0.00	36.06	3.46

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
31	32	5.123344	ACAAAATATTTGTACAGCTCCCGTC	59.877	40.000	6.68	0.00	0.00	4.79
156	157	9.624697	TGTGAAAATATGCTTCTTGATAACAAC	57.375	29.630	0.00	0.00	32.27	3.32
170	171	7.872163	TTTTGTCATGACTGTGAAAATATGC	57.128	32.000	25.55	0.00	0.00	3.14
202	203	8.249638	TGTCACTGAAAAAGATTGACAAAATCA	58.750	29.630	0.34	0.00	32.79	2.57
270	271	5.497635	TGGTATACGTGCATTACTTCGTA	57.502	39.130	7.35	7.35	41.64	3.43
359	361	7.488187	TTGATGCTCTAAATACTGCAGATTC	57.512	36.000	23.35	4.50	38.87	2.52
382	384	6.983890	GCCGGATTTTGGTGTTTATGATTATT	59.016	34.615	5.05	0.00	0.00	1.40
384	386	5.163499	GGCCGGATTTTGGTGTTTATGATTA	60.163	40.000	5.05	0.00	0.00	1.75
387	389	2.494073	GGCCGGATTTTGGTGTTTATGA	59.506	45.455	5.05	0.00	0.00	2.15
422	424	2.354188	TTGGTCACAGACGCGTCG	60.354	61.111	31.56	26.74	32.65	5.12
428	430	0.106708	TGTCCTGCTTGGTCACAGAC	59.893	55.000	0.00	0.00	35.90	3.51
620	626	1.241165	CTGCACAAGAATCTGCCACA	58.759	50.000	0.00	0.00	31.97	4.17
633	639	2.107041	AAATCGACGGGACCTGCACA	62.107	55.000	0.00	0.00	0.00	4.57
647	653	3.191162	TCAAATTGGGCAGTCAGAAATCG	59.809	43.478	0.00	0.00	0.00	3.34
730	736	9.163899	TGTACTAAATCAACGGCAATTAATACA	57.836	29.630	0.00	0.00	0.00	2.29
731	737	9.991388	TTGTACTAAATCAACGGCAATTAATAC	57.009	29.630	0.00	0.00	0.00	1.89
741	747	8.794406	GTGCAAATAATTGTACTAAATCAACGG	58.206	33.333	4.67	0.00	45.38	4.44
771	777	2.162408	GCAAACAAGGACTGATGCTACC	59.838	50.000	0.00	0.00	37.96	3.18
936	997	3.393800	CTGATCCCATCGATGTGGTAAC	58.606	50.000	23.27	16.96	37.57	2.50
961	1026	0.872388	GTAGTGGTTGCCCTTGTTCG	59.128	55.000	0.00	0.00	0.00	3.95
994	1059	2.430465	CAGGTGACTTGACATGAAGGG	58.570	52.381	0.00	0.00	40.21	3.95
1006	1076	1.606889	GGAGACGACCCAGGTGACT	60.607	63.158	0.00	0.00	46.44	3.41
1101	1171	1.688772	GATCAGGAGCGTACTGGGTA	58.311	55.000	5.69	0.00	36.62	3.69
1107	1177	0.530870	GGCTTGGATCAGGAGCGTAC	60.531	60.000	0.00	0.00	37.29	3.67
1218	1288	0.267054	TGAGCCAGATGAGGAGGGAT	59.733	55.000	0.00	0.00	0.00	3.85
1532	1602	2.203280	CACCCGTTCCACTTGCCA	60.203	61.111	0.00	0.00	0.00	4.92
1535	1605	1.226746	GAAGACACCCGTTCCACTTG	58.773	55.000	0.00	0.00	0.00	3.16
1759	6283	2.034687	ACTGGCGCTTGCATCCTT	59.965	55.556	7.64	0.00	41.71	3.36
1760	6284	2.749044	CACTGGCGCTTGCATCCT	60.749	61.111	7.64	0.00	41.71	3.24
1761	6285	3.818787	CCACTGGCGCTTGCATCC	61.819	66.667	7.64	0.00	41.71	3.51
1762	6286	4.487412	GCCACTGGCGCTTGCATC	62.487	66.667	7.64	0.00	39.62	3.91
1779	6303	1.771073	TTTCACCAACAGCGTGCTCG	61.771	55.000	3.31	3.31	40.37	5.03
2006	6532	9.046296	AGTGATCTTAACGCTCTTATATTTTGG	57.954	33.333	0.00	0.00	0.00	3.28
2069	6595	8.859090	CAATTCTCATCTAGATGGTACTCTCTT	58.141	37.037	28.30	11.40	39.24	2.85
2072	6598	7.782168	TGTCAATTCTCATCTAGATGGTACTCT	59.218	37.037	28.30	9.81	39.24	3.24
2192	6727	8.335532	TCTATTCCTGTCTACAAAAACCATTG	57.664	34.615	0.00	0.00	36.37	2.82
2320	6855	5.353123	TCAAAATTAGATTCCACGTGGCTAC	59.647	40.000	30.25	20.66	34.44	3.58
2418	6990	3.568538	CAATTGAAGGCGTTTTCCAGAG	58.431	45.455	0.00	0.00	0.00	3.35
2491	7063	4.156008	GGTAGGTGCACATACAAGGAAAAG	59.844	45.833	34.61	0.00	35.06	2.27
2493	7065	3.073209	TGGTAGGTGCACATACAAGGAAA	59.927	43.478	34.61	15.21	35.06	3.13
2498	7070	4.293662	TCATTGGTAGGTGCACATACAA	57.706	40.909	34.61	26.00	35.06	2.41
2523	7095	3.747099	ACTATGCTTGACATGCGAAAC	57.253	42.857	8.61	0.00	40.06	2.78
2587	7159	9.866798	TTAGAATTCTAGCACTATAGCATGATG	57.133	33.333	14.63	0.00	36.85	3.07
2639	7211	5.860941	ATATAGTCAGTCCACTCCAAGTG	57.139	43.478	0.01	0.01	45.53	3.16
2642	7214	7.015292	GGTCATTATATAGTCAGTCCACTCCAA	59.985	40.741	0.00	0.00	0.00	3.53
2678	7250	1.227999	CGAGCGGAAGAGTTTGGCAA	61.228	55.000	0.00	0.00	0.00	4.52
2680	7252	1.355066	CTCGAGCGGAAGAGTTTGGC	61.355	60.000	0.00	0.00	0.00	4.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.