AutoCloner

Multiple sequence alignment - TraesCS7D01G528100

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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	TraesCS7D01G528100	chr7D	100.000	2327	0	0	1	2327	623352205	623354531	0.000000e+00	4298.0
1	TraesCS7D01G528100	chr7D	85.039	254	31	4	930	1182	622993405	622993652	3.840000e-63	252.0
2	TraesCS7D01G528100	chr7D	83.142	261	41	3	108	365	459742874	459743134	3.870000e-58	235.0
3	TraesCS7D01G528100	chr7A	93.390	1407	83	7	925	2325	718271318	718269916	0.000000e+00	2074.0
4	TraesCS7D01G528100	chr7A	92.237	1301	83	9	711	1998	718354809	718353514	0.000000e+00	1827.0
5	TraesCS7D01G528100	chr7A	89.462	446	22	8	1	434	718271801	718271369	7.320000e-150	540.0
6	TraesCS7D01G528100	chr7A	89.349	338	31	5	63	395	718357010	718356673	9.940000e-114	420.0
7	TraesCS7D01G528100	chr7A	93.359	256	16	1	386	640	718356045	718355790	6.070000e-101	377.0
8	TraesCS7D01G528100	chr7A	93.548	124	8	0	1998	2121	3407839	3407716	3.950000e-43	185.0
9	TraesCS7D01G528100	chr7A	92.208	77	6	0	638	714	718355230	718355154	2.440000e-20	110.0
10	TraesCS7D01G528100	chr7B	86.537	1077	111	13	926	1997	720888067	720887020	0.000000e+00	1155.0
11	TraesCS7D01G528100	chr7B	86.456	1078	111	14	926	1997	720843805	720842757	0.000000e+00	1149.0
12	TraesCS7D01G528100	chr7B	89.757	781	61	10	9	771	720891646	720890867	0.000000e+00	981.0
13	TraesCS7D01G528100	chr7B	89.916	238	24	0	526	763	720845948	720845711	8.080000e-80	307.0
14	TraesCS7D01G528100	chr7B	86.010	193	21	4	2122	2310	720938947	720938757	3.920000e-48	202.0
15	TraesCS7D01G528100	chr7B	95.413	109	5	0	801	909	720890873	720890765	8.550000e-40	174.0
16	TraesCS7D01G528100	chr7B	94.118	102	5	1	1898	1998	720939039	720938938	1.110000e-33	154.0
17	TraesCS7D01G528100	chr7B	91.765	85	7	0	770	854	720940762	720940678	4.060000e-23	119.0
18	TraesCS7D01G528100	chrUn	89.349	338	31	5	63	395	263832157	263831820	9.940000e-114	420.0
19	TraesCS7D01G528100	chrUn	93.333	195	12	1	386	579	263831192	263830998	1.050000e-73	287.0
20	TraesCS7D01G528100	chrUn	91.463	82	6	1	2023	2104	87112850	87112770	6.800000e-21	111.0
21	TraesCS7D01G528100	chr3D	85.039	254	35	3	108	358	454000934	454000681	2.970000e-64	255.0
22	TraesCS7D01G528100	chr3D	83.643	269	42	2	103	369	481916470	481916202	3.840000e-63	252.0
23	TraesCS7D01G528100	chr6A	82.847	274	43	4	95	365	129765221	129764949	2.310000e-60	243.0
24	TraesCS7D01G528100	chr5B	83.462	260	41	2	108	365	27825299	27825040	8.310000e-60	241.0
25	TraesCS7D01G528100	chr1D	90.551	127	11	1	1996	2121	482101229	482101103	1.430000e-37	167.0
26	TraesCS7D01G528100	chr3A	87.778	90	11	0	2010	2099	709067015	709067104	3.160000e-19	106.0
27	TraesCS7D01G528100	chr5D	97.297	37	1	0	2078	2114	378209629	378209593	1.930000e-06	63.9

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	TraesCS7D01G528100	chr7D	623352205	623354531	2326	False	4298.0	4298	100.00000	1	2327	1	chr7D.!!$F3	2326
1	TraesCS7D01G528100	chr7A	718269916	718271801	1885	True	1307.0	2074	91.42600	1	2325	2	chr7A.!!$R2	2324
2	TraesCS7D01G528100	chr7A	718353514	718357010	3496	True	683.5	1827	91.78825	63	1998	4	chr7A.!!$R3	1935
3	TraesCS7D01G528100	chr7B	720887020	720891646	4626	True	770.0	1155	90.56900	9	1997	3	chr7B.!!$R2	1988
4	TraesCS7D01G528100	chr7B	720842757	720845948	3191	True	728.0	1149	88.18600	526	1997	2	chr7B.!!$R1	1471
5	TraesCS7D01G528100	chrUn	263830998	263832157	1159	True	353.5	420	91.34100	63	579	2	chrUn.!!$R2	516

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
38	39	0.237498	GTCGTGTAAGCAAGCCCAAC	59.763	55.0	0.00	0.0	0.0	3.77	F
776	2385	0.478072	ATGGGAGCATATGGCCGAAA	59.522	50.0	4.56	0.0	46.5	3.46	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1103	6284	0.736325	GCGGTCACAATAGACGCACT	60.736	55.0	0.00	0.00	39.42	4.40	R
2038	7226	0.846015	TTCTGGGCCCACATATCAGG	59.154	55.0	24.45	9.02	0.00	3.86	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
38	39	0.237498	GTCGTGTAAGCAAGCCCAAC	59.763	55.000	0.00	0.00	0.00	3.77
65	72	1.700186	GGGAGATTAGTTAGGGGCCAG	59.300	57.143	4.39	0.00	0.00	4.85
79	86	2.241430	GGGGCCAGGTAACAGAGTATTT	59.759	50.000	4.39	0.00	41.41	1.40
260	270	4.135747	TGACGCATCCAGTGATATTGAA	57.864	40.909	0.00	0.00	0.00	2.69
457	1108	7.605691	AGTGTCTTCTTTCTGATAAGAACATGG	59.394	37.037	0.00	3.71	38.78	3.66
459	1110	8.324306	TGTCTTCTTTCTGATAAGAACATGGAT	58.676	33.333	0.00	0.00	38.78	3.41
692	1911	4.260194	CAACGCGTGGATCTGACA	57.740	55.556	14.98	0.00	0.00	3.58
741	2308	4.038282	TCGTTACTCCTGCAGTCAAGTTTA	59.962	41.667	13.81	2.93	36.43	2.01
776	2385	0.478072	ATGGGAGCATATGGCCGAAA	59.522	50.000	4.56	0.00	46.50	3.46
778	2387	0.954452	GGGAGCATATGGCCGAAAAG	59.046	55.000	4.56	0.00	46.50	2.27
785	2394	3.149196	CATATGGCCGAAAAGCTACCAT	58.851	45.455	0.00	0.00	43.42	3.55
786	2395	1.680338	ATGGCCGAAAAGCTACCATC	58.320	50.000	0.00	0.00	36.36	3.51
787	2396	0.618458	TGGCCGAAAAGCTACCATCT	59.382	50.000	0.00	0.00	0.00	2.90
788	2397	1.300481	GGCCGAAAAGCTACCATCTC	58.700	55.000	0.00	0.00	0.00	2.75
789	2398	0.931005	GCCGAAAAGCTACCATCTCG	59.069	55.000	0.00	0.00	0.00	4.04
790	2399	1.571919	CCGAAAAGCTACCATCTCGG	58.428	55.000	0.00	0.00	39.79	4.63
791	2400	0.931005	CGAAAAGCTACCATCTCGGC	59.069	55.000	0.00	0.00	39.03	5.54
792	2401	0.931005	GAAAAGCTACCATCTCGGCG	59.069	55.000	0.00	0.00	39.03	6.46
793	2402	1.090052	AAAAGCTACCATCTCGGCGC	61.090	55.000	0.00	0.00	39.03	6.53
794	2403	2.925162	AAAGCTACCATCTCGGCGCC	62.925	60.000	19.07	19.07	39.03	6.53
795	2404	4.221422	GCTACCATCTCGGCGCCA	62.221	66.667	28.98	12.94	39.03	5.69
796	2405	2.499205	CTACCATCTCGGCGCCAA	59.501	61.111	28.98	7.25	39.03	4.52
797	2406	1.069765	CTACCATCTCGGCGCCAAT	59.930	57.895	28.98	13.86	39.03	3.16
798	2407	1.224069	CTACCATCTCGGCGCCAATG	61.224	60.000	28.98	24.08	39.03	2.82
799	2408	3.957535	CCATCTCGGCGCCAATGC	61.958	66.667	28.98	0.00	0.00	3.56
902	2549	2.758089	CCGTACGTCGTCCTCCCAG	61.758	68.421	15.21	0.00	37.94	4.45
1057	6238	3.672295	CTCGAGCTCACCCTTGCCC	62.672	68.421	15.40	0.00	0.00	5.36
1063	6244	4.659172	TCACCCTTGCCCTTGCCG	62.659	66.667	0.00	0.00	36.33	5.69
1113	6294	1.134670	GGCTTCTTCCAGTGCGTCTAT	60.135	52.381	0.00	0.00	0.00	1.98
1129	6310	2.415512	GTCTATTGTGACCGCAAGTTCC	59.584	50.000	2.41	0.00	0.00	3.62
1134	6315	1.599518	TGACCGCAAGTTCCGCAAT	60.600	52.632	0.00	0.00	0.00	3.56
1318	6499	1.173043	CGAGCTGGACTTGTCTCTCT	58.827	55.000	0.00	0.00	0.00	3.10
1343	6524	0.174845	TAACCGGTTGCCAGATCGAG	59.825	55.000	30.08	0.00	0.00	4.04
1397	6578	4.202326	CCTTTCCGGTGCTAGGTATGTTAT	60.202	45.833	0.00	0.00	0.00	1.89
1459	6640	1.078709	CGTTGGATTCATGTCAGCGT	58.921	50.000	0.00	0.00	32.10	5.07
1581	6762	1.423845	CGGCTAATGACGTTGCCAC	59.576	57.895	16.22	0.00	45.13	5.01
1627	6808	3.190327	TGAATGTTCACTTTACGGGCATG	59.810	43.478	0.00	0.00	31.01	4.06
1631	6812	2.676342	GTTCACTTTACGGGCATGTAGG	59.324	50.000	0.00	0.00	0.00	3.18
1693	6874	4.345257	TGATAAGTGCTCCTTCTATCCCAC	59.655	45.833	0.00	0.00	34.46	4.61
1740	6921	8.115490	ACAACTTTACACGGAGTACTAGTTAT	57.885	34.615	0.00	0.00	41.61	1.89
1750	6931	7.228108	CACGGAGTACTAGTTATCTTCCATACA	59.772	40.741	0.00	0.00	41.61	2.29
1784	6965	6.490721	CGGACTACTATCCCTTTAAGACATCT	59.509	42.308	0.00	0.00	35.03	2.90
1785	6966	7.308710	CGGACTACTATCCCTTTAAGACATCTC	60.309	44.444	0.00	0.00	35.03	2.75
1786	6967	7.726738	GGACTACTATCCCTTTAAGACATCTCT	59.273	40.741	0.00	0.00	31.94	3.10
1787	6968	8.472007	ACTACTATCCCTTTAAGACATCTCTG	57.528	38.462	0.00	0.00	0.00	3.35
1788	6969	8.282982	ACTACTATCCCTTTAAGACATCTCTGA	58.717	37.037	0.00	0.00	0.00	3.27
1793	6974	6.837312	TCCCTTTAAGACATCTCTGAAAACA	58.163	36.000	0.00	0.00	27.80	2.83
1809	6990	8.781067	TCTGAAAACAAATGTACGAATTTCTG	57.219	30.769	0.00	7.96	0.00	3.02
1816	6997	9.607285	AACAAATGTACGAATTTCTGTGTATTC	57.393	29.630	0.00	0.00	0.00	1.75
1998	7186	6.900189	ACATGTCGAAGTATAGATAACTCGG	58.100	40.000	0.00	0.00	0.00	4.63
2005	7193	5.226194	AGTATAGATAACTCGGACGAGGT	57.774	43.478	23.63	20.51	45.88	3.85
2015	7203	1.507174	GGACGAGGTTCCTCTGACG	59.493	63.158	15.60	6.70	32.24	4.35
2018	7206	2.015587	GACGAGGTTCCTCTGACGTAT	58.984	52.381	15.60	0.00	34.26	3.06
2021	7209	2.163815	CGAGGTTCCTCTGACGTATTGT	59.836	50.000	15.60	0.00	0.00	2.71
2038	7226	3.015145	TAGGGAGCAGTTGGGCCC	61.015	66.667	17.59	17.59	41.00	5.80
2041	7229	4.748144	GGAGCAGTTGGGCCCCTG	62.748	72.222	22.27	21.29	0.00	4.45
2042	7230	3.650950	GAGCAGTTGGGCCCCTGA	61.651	66.667	27.10	8.77	0.00	3.86
2066	7254	1.303282	GGGCCCAGAAGTAGGTTGG	59.697	63.158	19.95	0.00	0.00	3.77
2084	7272	2.348998	CCCACCTGTCAGTGAGCC	59.651	66.667	0.00	0.00	40.34	4.70
2108	7296	1.738099	CACCCTGCAGTACGTCAGC	60.738	63.158	13.81	0.00	0.00	4.26
2147	7335	0.388520	TCGTCTTCCACACGATGCAG	60.389	55.000	0.00	0.00	41.27	4.41
2150	7338	1.728971	GTCTTCCACACGATGCAGAAG	59.271	52.381	0.00	0.00	33.56	2.85
2157	7345	1.070758	ACACGATGCAGAAGACACCTT	59.929	47.619	0.00	0.00	34.81	3.50
2171	7359	4.694339	AGACACCTTGAACTTGACTGTAC	58.306	43.478	0.00	0.00	0.00	2.90
2179	7367	6.462487	CCTTGAACTTGACTGTACACCTTAGA	60.462	42.308	0.00	0.00	0.00	2.10
2199	7387	9.832445	CCTTAGAACTATTGCAAAGATAGGTAA	57.168	33.333	1.71	1.19	32.57	2.85
2293	7482	4.882671	AACATCATCGTTGGCATTACTC	57.117	40.909	0.00	0.00	0.00	2.59
2299	7488	1.295357	CGTTGGCATTACTCGGTGCA	61.295	55.000	0.00	0.00	43.00	4.57
2303	7492	0.179045	GGCATTACTCGGTGCATCCT	60.179	55.000	0.00	0.00	43.00	3.24
2326	7515	8.134895	TCCTTTTTGGATAAATATCGTTCATGC	58.865	33.333	0.00	0.00	40.56	4.06

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
38	39	5.564550	CCCCTAACTAATCTCCCATCATTG	58.435	45.833	0.00	0.00	0.00	2.82
86	96	8.957466	GGCAGTTGAATACTCTTTTATTTAGGT	58.043	33.333	0.00	0.00	33.85	3.08
320	331	6.877236	ACCCTGCATATAAATTTGTCCAAAG	58.123	36.000	0.00	0.00	33.32	2.77
322	333	7.962995	TTACCCTGCATATAAATTTGTCCAA	57.037	32.000	0.00	0.00	0.00	3.53
324	335	9.830975	ATTTTTACCCTGCATATAAATTTGTCC	57.169	29.630	0.00	0.00	0.00	4.02
332	343	5.533154	CCGGTCATTTTTACCCTGCATATAA	59.467	40.000	0.00	0.00	33.10	0.98
351	364	4.576879	ACTTCTTTTTACTCCATCCGGTC	58.423	43.478	0.00	0.00	0.00	4.79
457	1108	9.114952	CTTCTCACCTCCCTTATTTTTCTTATC	57.885	37.037	0.00	0.00	0.00	1.75
459	1110	7.985589	ACTTCTCACCTCCCTTATTTTTCTTA	58.014	34.615	0.00	0.00	0.00	2.10
576	1233	9.444600	ACACAAGGATAACTTACGTATCAAAAT	57.555	29.630	0.00	0.00	37.29	1.82
692	1911	4.788679	CCTAAATTATTTCCTGGGGTCGT	58.211	43.478	0.00	0.00	0.00	4.34
741	2308	1.220529	CCATTCATATCGTGCGTGCT	58.779	50.000	0.00	0.00	0.00	4.40
776	2385	2.107141	GCGCCGAGATGGTAGCTT	59.893	61.111	0.00	0.00	41.21	3.74
778	2387	2.996168	ATTGGCGCCGAGATGGTAGC	62.996	60.000	23.38	0.00	41.21	3.58
794	2403	1.885388	CATGGCCCAATGCGCATTG	60.885	57.895	42.43	42.43	45.77	2.82
795	2404	2.502093	CATGGCCCAATGCGCATT	59.498	55.556	29.36	29.36	42.61	3.56
796	2405	4.230002	GCATGGCCCAATGCGCAT	62.230	61.111	19.28	19.28	43.22	4.73
819	2465	1.497278	CTGATTGGCGACCAACGTG	59.503	57.895	12.53	3.74	46.95	4.49
902	2549	2.046314	CCGGGGTGTGGTGATGAC	60.046	66.667	0.00	0.00	0.00	3.06
1020	6201	1.680522	GGCTGAGATCCTCCTTCGCA	61.681	60.000	0.00	0.00	0.00	5.10
1092	6273	2.357517	ACGCACTGGAAGAAGCCG	60.358	61.111	0.00	0.00	37.43	5.52
1103	6284	0.736325	GCGGTCACAATAGACGCACT	60.736	55.000	0.00	0.00	39.42	4.40
1113	6294	2.539338	GCGGAACTTGCGGTCACAA	61.539	57.895	4.76	0.00	0.00	3.33
1155	6336	3.735208	GCTCTAGCTTATGTGCGTTCTGA	60.735	47.826	0.00	0.00	38.21	3.27
1164	6345	1.300233	GGCGCGCTCTAGCTTATGT	60.300	57.895	32.29	0.00	39.32	2.29
1318	6499	2.281900	GGCAACCGGTTACAGCCA	60.282	61.111	31.79	0.00	44.59	4.75
1343	6524	3.131046	CCATGGATACTGAAAGGGTTTGC	59.869	47.826	5.56	0.00	39.30	3.68
1627	6808	6.590677	GTCCTTAGTTTCACAATGTCTCCTAC	59.409	42.308	0.00	0.00	0.00	3.18
1631	6812	7.301054	CAATGTCCTTAGTTTCACAATGTCTC	58.699	38.462	0.00	0.00	0.00	3.36
1693	6874	4.322101	ACTAAAACAGCGACGCTTATTG	57.678	40.909	21.97	12.63	36.40	1.90
1784	6965	8.402472	ACAGAAATTCGTACATTTGTTTTCAGA	58.598	29.630	0.00	0.00	0.00	3.27
1785	6966	8.471457	CACAGAAATTCGTACATTTGTTTTCAG	58.529	33.333	0.00	3.19	0.00	3.02
1786	6967	7.971168	ACACAGAAATTCGTACATTTGTTTTCA	59.029	29.630	0.00	0.00	0.00	2.69
1787	6968	8.335256	ACACAGAAATTCGTACATTTGTTTTC	57.665	30.769	0.00	0.00	0.00	2.29
1788	6969	9.959749	ATACACAGAAATTCGTACATTTGTTTT	57.040	25.926	0.00	0.00	0.00	2.43
1793	6974	8.561738	AGGAATACACAGAAATTCGTACATTT	57.438	30.769	0.00	0.00	33.72	2.32
1998	7186	1.446907	TACGTCAGAGGAACCTCGTC	58.553	55.000	14.13	8.46	46.90	4.20
2005	7193	3.952323	CTCCCTACAATACGTCAGAGGAA	59.048	47.826	0.00	0.00	0.00	3.36
2015	7203	2.919228	CCCAACTGCTCCCTACAATAC	58.081	52.381	0.00	0.00	0.00	1.89
2018	7206	1.378762	GCCCAACTGCTCCCTACAA	59.621	57.895	0.00	0.00	0.00	2.41
2021	7209	3.015145	GGGCCCAACTGCTCCCTA	61.015	66.667	19.95	0.00	35.87	3.53
2038	7226	0.846015	TTCTGGGCCCACATATCAGG	59.154	55.000	24.45	9.02	0.00	3.86
2041	7229	2.039084	CCTACTTCTGGGCCCACATATC	59.961	54.545	24.45	0.00	0.00	1.63
2042	7230	2.057922	CCTACTTCTGGGCCCACATAT	58.942	52.381	24.45	9.92	0.00	1.78
2074	7262	1.510480	GGTGCAGTTGGCTCACTGAC	61.510	60.000	18.16	13.14	46.29	3.51
2108	7296	2.028130	AGTTATCTGGACTCAGCTCCG	58.972	52.381	0.00	0.00	40.69	4.63
2147	7335	4.192317	ACAGTCAAGTTCAAGGTGTCTTC	58.808	43.478	0.00	0.00	0.00	2.87
2150	7338	4.270325	GTGTACAGTCAAGTTCAAGGTGTC	59.730	45.833	0.00	0.00	0.00	3.67
2157	7345	6.097839	AGTTCTAAGGTGTACAGTCAAGTTCA	59.902	38.462	0.00	0.00	0.00	3.18
2171	7359	7.770897	ACCTATCTTTGCAATAGTTCTAAGGTG	59.229	37.037	0.00	0.00	30.24	4.00
2179	7367	9.338622	GGTATGTTACCTATCTTTGCAATAGTT	57.661	33.333	0.00	0.00	45.52	2.24
2199	7387	9.344772	TCTTGTTTATTATTAATGCGGGTATGT	57.655	29.630	0.00	0.00	0.00	2.29
2285	7474	1.668419	AAGGATGCACCGAGTAATGC	58.332	50.000	0.00	0.00	44.74	3.56

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.