AutoCloner

Multiple sequence alignment - TraesCS6B01G022900

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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	TraesCS6B01G022900	chr6B	100.000	3167	0	0	1	3167	14302291	14305457	0.000000e+00	5849.0
1	TraesCS6B01G022900	chr6B	85.773	1448	180	12	940	2368	54422326	54420886	0.000000e+00	1509.0
2	TraesCS6B01G022900	chr6B	87.129	1282	139	16	905	2172	14323425	14324694	0.000000e+00	1430.0
3	TraesCS6B01G022900	chr6B	87.295	1220	141	11	964	2175	14311083	14312296	0.000000e+00	1382.0
4	TraesCS6B01G022900	chr6B	85.703	1280	168	14	905	2175	39310976	39312249	0.000000e+00	1336.0
5	TraesCS6B01G022900	chr6B	86.382	1219	153	9	964	2175	13934121	13932909	0.000000e+00	1319.0
6	TraesCS6B01G022900	chr6B	85.714	1225	158	15	959	2175	14455074	14453859	0.000000e+00	1277.0
7	TraesCS6B01G022900	chr6B	88.124	741	54	14	2449	3167	54420671	54419943	0.000000e+00	850.0
8	TraesCS6B01G022900	chr6B	88.116	690	39	20	2511	3167	39327866	39328545	0.000000e+00	780.0
9	TraesCS6B01G022900	chr6B	77.391	1234	230	36	971	2170	26841998	26840780	0.000000e+00	688.0
10	TraesCS6B01G022900	chr6B	77.262	1227	233	32	964	2173	15751037	15749840	0.000000e+00	678.0
11	TraesCS6B01G022900	chr6D	93.210	2209	103	13	963	3167	7678756	7680921	0.000000e+00	3205.0
12	TraesCS6B01G022900	chr6D	85.609	1216	150	16	965	2175	7885716	7886911	0.000000e+00	1253.0
13	TraesCS6B01G022900	chr6D	91.388	836	37	12	2361	3167	7654173	7655002	0.000000e+00	1112.0
14	TraesCS6B01G022900	chr6D	90.588	340	24	7	2511	2846	24253310	24253645	8.060000e-121	444.0
15	TraesCS6B01G022900	chr4A	85.612	2238	251	36	964	3167	667425295	667427495	0.000000e+00	2283.0
16	TraesCS6B01G022900	chr4A	85.022	2270	240	40	964	3167	667380012	667382247	0.000000e+00	2217.0
17	TraesCS6B01G022900	chr4A	94.643	56	0	1	1	56	291741094	291741146	2.020000e-12	84.2
18	TraesCS6B01G022900	chr6A	84.568	2294	260	45	941	3166	7977673	7979940	0.000000e+00	2189.0
19	TraesCS6B01G022900	chr6A	84.119	2248	248	47	941	3117	12420327	12422536	0.000000e+00	2073.0
20	TraesCS6B01G022900	chr6A	100.000	55	0	0	2	56	78093694	78093748	5.590000e-18	102.0
21	TraesCS6B01G022900	chr6A	96.364	55	0	1	1	55	74387500	74387552	4.350000e-14	89.8
22	TraesCS6B01G022900	chr3B	91.825	844	56	8	55	889	50778548	50777709	0.000000e+00	1164.0
23	TraesCS6B01G022900	chr3B	91.627	836	57	8	55	889	125621955	125622778	0.000000e+00	1144.0
24	TraesCS6B01G022900	chr3B	87.622	614	54	8	254	863	41114773	41115368	0.000000e+00	693.0
25	TraesCS6B01G022900	chr3D	91.726	846	55	6	55	889	49610802	49611643	0.000000e+00	1160.0
26	TraesCS6B01G022900	chr5B	88.849	843	83	6	54	889	433321333	433320495	0.000000e+00	1026.0
27	TraesCS6B01G022900	chr1B	87.957	847	73	16	55	889	41350875	41351704	0.000000e+00	972.0
28	TraesCS6B01G022900	chr1B	93.453	611	39	1	60	670	4041942	4041333	0.000000e+00	905.0
29	TraesCS6B01G022900	chr1B	89.503	181	15	3	710	889	4041330	4041153	3.180000e-55	226.0
30	TraesCS6B01G022900	chrUn	87.540	618	54	9	254	866	258182431	258181832	0.000000e+00	693.0
31	TraesCS6B01G022900	chrUn	87.379	618	55	8	254	866	253396007	253395408	0.000000e+00	688.0
32	TraesCS6B01G022900	chr4B	93.410	349	22	1	55	402	580035799	580036147	1.680000e-142	516.0
33	TraesCS6B01G022900	chr2A	84.286	350	43	10	54	396	711671269	711671613	6.550000e-87	331.0
34	TraesCS6B01G022900	chr2A	83.590	195	24	8	54	243	95210811	95210620	3.250000e-40	176.0
35	TraesCS6B01G022900	chr2A	98.305	59	0	1	2	59	252221134	252221192	5.590000e-18	102.0
36	TraesCS6B01G022900	chr2A	98.182	55	0	1	1	55	21553853	21553800	9.350000e-16	95.3
37	TraesCS6B01G022900	chr2A	94.545	55	1	1	1	55	640549232	640549180	2.020000e-12	84.2
38	TraesCS6B01G022900	chr7B	88.519	270	23	3	2707	2968	639999346	639999615	1.420000e-83	320.0
39	TraesCS6B01G022900	chr7A	98.182	55	0	1	1	55	438988313	438988366	9.350000e-16	95.3
40	TraesCS6B01G022900	chr5A	96.364	55	0	1	2	56	567547124	567547176	4.350000e-14	89.8
41	TraesCS6B01G022900	chr5A	100.000	47	0	0	9	55	55054130	55054084	1.560000e-13	87.9

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	TraesCS6B01G022900	chr6B	14302291	14305457	3166	False	5849.0	5849	100.0000	1	3167	1	chr6B.!!$F1	3166
1	TraesCS6B01G022900	chr6B	14323425	14324694	1269	False	1430.0	1430	87.1290	905	2172	1	chr6B.!!$F3	1267
2	TraesCS6B01G022900	chr6B	14311083	14312296	1213	False	1382.0	1382	87.2950	964	2175	1	chr6B.!!$F2	1211
3	TraesCS6B01G022900	chr6B	39310976	39312249	1273	False	1336.0	1336	85.7030	905	2175	1	chr6B.!!$F4	1270
4	TraesCS6B01G022900	chr6B	13932909	13934121	1212	True	1319.0	1319	86.3820	964	2175	1	chr6B.!!$R1	1211
5	TraesCS6B01G022900	chr6B	14453859	14455074	1215	True	1277.0	1277	85.7140	959	2175	1	chr6B.!!$R2	1216
6	TraesCS6B01G022900	chr6B	54419943	54422326	2383	True	1179.5	1509	86.9485	940	3167	2	chr6B.!!$R5	2227
7	TraesCS6B01G022900	chr6B	39327866	39328545	679	False	780.0	780	88.1160	2511	3167	1	chr6B.!!$F5	656
8	TraesCS6B01G022900	chr6B	26840780	26841998	1218	True	688.0	688	77.3910	971	2170	1	chr6B.!!$R4	1199
9	TraesCS6B01G022900	chr6B	15749840	15751037	1197	True	678.0	678	77.2620	964	2173	1	chr6B.!!$R3	1209
10	TraesCS6B01G022900	chr6D	7678756	7680921	2165	False	3205.0	3205	93.2100	963	3167	1	chr6D.!!$F2	2204
11	TraesCS6B01G022900	chr6D	7885716	7886911	1195	False	1253.0	1253	85.6090	965	2175	1	chr6D.!!$F3	1210
12	TraesCS6B01G022900	chr6D	7654173	7655002	829	False	1112.0	1112	91.3880	2361	3167	1	chr6D.!!$F1	806
13	TraesCS6B01G022900	chr4A	667425295	667427495	2200	False	2283.0	2283	85.6120	964	3167	1	chr4A.!!$F3	2203
14	TraesCS6B01G022900	chr4A	667380012	667382247	2235	False	2217.0	2217	85.0220	964	3167	1	chr4A.!!$F2	2203
15	TraesCS6B01G022900	chr6A	7977673	7979940	2267	False	2189.0	2189	84.5680	941	3166	1	chr6A.!!$F1	2225
16	TraesCS6B01G022900	chr6A	12420327	12422536	2209	False	2073.0	2073	84.1190	941	3117	1	chr6A.!!$F2	2176
17	TraesCS6B01G022900	chr3B	50777709	50778548	839	True	1164.0	1164	91.8250	55	889	1	chr3B.!!$R1	834
18	TraesCS6B01G022900	chr3B	125621955	125622778	823	False	1144.0	1144	91.6270	55	889	1	chr3B.!!$F2	834
19	TraesCS6B01G022900	chr3B	41114773	41115368	595	False	693.0	693	87.6220	254	863	1	chr3B.!!$F1	609
20	TraesCS6B01G022900	chr3D	49610802	49611643	841	False	1160.0	1160	91.7260	55	889	1	chr3D.!!$F1	834
21	TraesCS6B01G022900	chr5B	433320495	433321333	838	True	1026.0	1026	88.8490	54	889	1	chr5B.!!$R1	835
22	TraesCS6B01G022900	chr1B	41350875	41351704	829	False	972.0	972	87.9570	55	889	1	chr1B.!!$F1	834
23	TraesCS6B01G022900	chr1B	4041153	4041942	789	True	565.5	905	91.4780	60	889	2	chr1B.!!$R1	829
24	TraesCS6B01G022900	chrUn	258181832	258182431	599	True	693.0	693	87.5400	254	866	1	chrUn.!!$R2	612
25	TraesCS6B01G022900	chrUn	253395408	253396007	599	True	688.0	688	87.3790	254	866	1	chrUn.!!$R1	612

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
873	894	0.881118	ATACTTTGGCACGGCTGTTG	59.119	50.000	0.00	0.0	0.0	3.33	F
1399	1477	1.475751	CCCCTTCTGATATTGTGCGCT	60.476	52.381	9.73	0.0	0.0	5.92	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1965	2043	3.640029	ACCTCATAACATAGTACCGTGGG	59.36	47.826	0.0	0.0	0.0	4.61	R
3066	3384	3.490348	AGGCTGTCAACAAAATGCTACT	58.51	40.909	0.0	0.0	0.0	2.57	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
225	226	1.227031	AAGTTGCGTCACGTTCGGA	60.227	52.632	0.00	6.10	0.00	4.55
308	310	2.315176	ACAACTTTGCATGGTGCCTTA	58.685	42.857	5.33	0.00	44.23	2.69
325	327	6.811665	GGTGCCTTAAATTTGTCATAGAAACC	59.188	38.462	0.00	0.00	0.00	3.27
370	373	9.793252	CATTTGAAGGATGTCGAGAAAAATAAT	57.207	29.630	0.00	0.00	0.00	1.28
442	445	2.601666	AGCAGCACAGGGAGACGA	60.602	61.111	0.00	0.00	0.00	4.20
540	543	4.099266	CGACTTCTCTCAAGGATCCAGATT	59.901	45.833	15.82	0.00	0.00	2.40
608	611	3.383505	AGTTGGAAAAACCTAGTGTTGCC	59.616	43.478	0.00	0.00	37.23	4.52
670	673	4.087892	CTGCGGTCCTCCAGGTGG	62.088	72.222	0.39	0.39	36.34	4.61
686	689	6.812998	TCCAGGTGGTCTATATAGTTTTTCG	58.187	40.000	9.58	0.00	36.34	3.46
719	722	7.436933	AGGTCTGCAAATTAAGAAAAGGAAAG	58.563	34.615	0.00	0.00	0.00	2.62
867	888	4.379082	GGAAACAAGTATACTTTGGCACGG	60.379	45.833	15.60	5.47	33.11	4.94
873	894	0.881118	ATACTTTGGCACGGCTGTTG	59.119	50.000	0.00	0.00	0.00	3.33
884	905	2.036475	CACGGCTGTTGAGCTATCCTAT	59.964	50.000	0.00	0.00	45.44	2.57
889	910	4.061596	GCTGTTGAGCTATCCTATTGGTC	58.938	47.826	0.00	0.00	42.52	4.02
890	911	4.202305	GCTGTTGAGCTATCCTATTGGTCT	60.202	45.833	0.00	0.00	42.52	3.85
891	912	5.282055	TGTTGAGCTATCCTATTGGTCTG	57.718	43.478	0.00	0.00	34.44	3.51
892	913	4.716784	TGTTGAGCTATCCTATTGGTCTGT	59.283	41.667	0.00	0.00	34.44	3.41
893	914	5.163405	TGTTGAGCTATCCTATTGGTCTGTC	60.163	44.000	0.00	0.00	34.44	3.51
894	915	3.898123	TGAGCTATCCTATTGGTCTGTCC	59.102	47.826	0.00	0.00	34.44	4.02
895	916	3.898123	GAGCTATCCTATTGGTCTGTCCA	59.102	47.826	0.00	0.00	45.60	4.02
906	927	3.651645	CTGTCCAGCACAGCACAG	58.348	61.111	0.00	0.00	46.30	3.66
924	945	2.355837	CACACCACCGGAGACACG	60.356	66.667	9.46	0.00	0.00	4.49
925	946	2.520020	ACACCACCGGAGACACGA	60.520	61.111	9.46	0.00	35.47	4.35
926	947	2.129146	ACACCACCGGAGACACGAA	61.129	57.895	9.46	0.00	35.47	3.85
927	948	1.663702	CACCACCGGAGACACGAAC	60.664	63.158	9.46	0.00	35.47	3.95
928	949	2.129146	ACCACCGGAGACACGAACA	61.129	57.895	9.46	0.00	35.47	3.18
929	950	1.663702	CCACCGGAGACACGAACAC	60.664	63.158	9.46	0.00	35.47	3.32
930	951	2.014554	CACCGGAGACACGAACACG	61.015	63.158	9.46	0.00	35.47	4.49
931	952	3.103911	CCGGAGACACGAACACGC	61.104	66.667	0.00	0.00	35.47	5.34
932	953	3.103911	CGGAGACACGAACACGCC	61.104	66.667	0.00	0.00	35.47	5.68
933	954	3.103911	GGAGACACGAACACGCCG	61.104	66.667	0.00	0.00	0.00	6.46
1284	1362	2.490148	CCTCTCCGGCGCTGATGTA	61.490	63.158	20.25	0.00	0.00	2.29
1394	1472	4.528596	CGGTCTATCCCCTTCTGATATTGT	59.471	45.833	0.00	0.00	0.00	2.71
1399	1477	1.475751	CCCCTTCTGATATTGTGCGCT	60.476	52.381	9.73	0.00	0.00	5.92
1651	1729	4.065110	GCTCCAAACCAGAGCGTT	57.935	55.556	0.00	0.00	46.58	4.84
2309	2410	0.693049	CCACTTGTAGGGGAAGTGCT	59.307	55.000	0.00	0.00	43.10	4.40
2335	2436	7.092137	TCTAATTTGAGATTTGCATGACCAG	57.908	36.000	0.00	0.00	0.00	4.00
2446	2563	7.667557	TGTTGGTTATCTGCTATAGTATGTCC	58.332	38.462	0.84	2.32	0.00	4.02
2538	2780	6.228616	TGTCCATTACATCATTCGGTAGAA	57.771	37.500	0.00	0.00	35.30	2.10
2613	2857	7.558081	TCATGCATACTAGAACTAAGAGAGTGT	59.442	37.037	0.00	0.00	38.87	3.55
2614	2858	7.089770	TGCATACTAGAACTAAGAGAGTGTG	57.910	40.000	0.00	0.00	38.87	3.82
2914	3204	2.100605	AACTCGTCATTCTTCCTGCC	57.899	50.000	0.00	0.00	0.00	4.85
2960	3250	4.460263	ACTGTTGTGAAAGCAGGTCATTA	58.540	39.130	0.00	0.00	34.79	1.90
3090	3409	3.221771	AGCATTTTGTTGACAGCCTACA	58.778	40.909	0.00	0.00	0.00	2.74
3147	3467	4.505191	CCTTGTATTTGTACCGGATACACG	59.495	45.833	9.46	9.01	43.71	4.49

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
48	49	2.747855	CCGTTTGAGAGCAGGGGC	60.748	66.667	0.00	0.0	41.61	5.80
49	50	1.376037	GTCCGTTTGAGAGCAGGGG	60.376	63.158	0.00	0.0	0.00	4.79
50	51	1.376037	GGTCCGTTTGAGAGCAGGG	60.376	63.158	0.00	0.0	0.00	4.45
51	52	1.376037	GGGTCCGTTTGAGAGCAGG	60.376	63.158	0.00	0.0	33.37	4.85
52	53	0.035458	AAGGGTCCGTTTGAGAGCAG	59.965	55.000	0.00	0.0	33.37	4.24
162	163	1.825105	ACCAGATATGGATGCCCACT	58.175	50.000	14.70	0.0	46.98	4.00
225	226	7.935210	ACCCGGTGAAAAATAGTCGATAAATAT	59.065	33.333	0.00	0.0	0.00	1.28
308	310	5.074115	TCCACCGGTTTCTATGACAAATTT	58.926	37.500	2.97	0.0	0.00	1.82
338	340	2.428171	CGACATCCTTCAAATGGCCAAT	59.572	45.455	10.96	0.0	0.00	3.16
442	445	1.110442	CTCAAGCTCCATCGAGTCCT	58.890	55.000	0.00	0.0	38.49	3.85
458	461	1.972198	CACGGCTCCAACTACCTCA	59.028	57.895	0.00	0.0	0.00	3.86
591	594	1.335597	GCCGGCAACACTAGGTTTTTC	60.336	52.381	24.80	0.0	37.72	2.29
793	812	2.988010	AAGCATGCGTCTCCAATCTA	57.012	45.000	13.01	0.0	0.00	1.98
867	888	4.061596	GACCAATAGGATAGCTCAACAGC	58.938	47.826	0.00	0.0	41.68	4.40
873	894	3.898123	TGGACAGACCAATAGGATAGCTC	59.102	47.826	0.00	0.0	46.75	4.09
890	911	2.592574	GCTGTGCTGTGCTGGACA	60.593	61.111	1.10	1.1	36.83	4.02
891	912	2.592574	TGCTGTGCTGTGCTGGAC	60.593	61.111	0.00	0.0	0.00	4.02
892	913	2.592574	GTGCTGTGCTGTGCTGGA	60.593	61.111	0.00	0.0	0.00	3.86
893	914	2.903350	TGTGCTGTGCTGTGCTGG	60.903	61.111	0.00	0.0	0.00	4.85
894	915	2.330393	GTGTGCTGTGCTGTGCTG	59.670	61.111	0.00	0.0	0.00	4.41
895	916	2.903855	GGTGTGCTGTGCTGTGCT	60.904	61.111	0.00	0.0	0.00	4.40
896	917	3.211245	TGGTGTGCTGTGCTGTGC	61.211	61.111	0.00	0.0	0.00	4.57
897	918	2.717485	GTGGTGTGCTGTGCTGTG	59.283	61.111	0.00	0.0	0.00	3.66
898	919	2.516930	GGTGGTGTGCTGTGCTGT	60.517	61.111	0.00	0.0	0.00	4.40
899	920	3.653009	CGGTGGTGTGCTGTGCTG	61.653	66.667	0.00	0.0	0.00	4.41
900	921	4.935495	CCGGTGGTGTGCTGTGCT	62.935	66.667	0.00	0.0	0.00	4.40
901	922	4.927782	TCCGGTGGTGTGCTGTGC	62.928	66.667	0.00	0.0	0.00	4.57
902	923	2.666190	CTCCGGTGGTGTGCTGTG	60.666	66.667	0.00	0.0	0.00	3.66
903	924	2.842462	TCTCCGGTGGTGTGCTGT	60.842	61.111	0.00	0.0	0.00	4.40
906	927	2.665185	GTGTCTCCGGTGGTGTGC	60.665	66.667	0.00	0.0	0.00	4.57
937	958	4.619227	AGTGGCGTCGGTTGTGGG	62.619	66.667	0.00	0.0	0.00	4.61
943	964	1.445582	GAATTCGAGTGGCGTCGGT	60.446	57.895	8.94	0.0	40.49	4.69
1394	1472	3.105782	CGAGCAAGACGAAGCGCA	61.106	61.111	11.47	0.0	35.48	6.09
1399	1477	2.654877	GGGGACGAGCAAGACGAA	59.345	61.111	0.00	0.0	34.70	3.85
1557	1635	1.824230	CACTCTGCTAGGAGCTTGACT	59.176	52.381	6.35	0.0	42.97	3.41
1965	2043	3.640029	ACCTCATAACATAGTACCGTGGG	59.360	47.826	0.00	0.0	0.00	4.61
2309	2410	7.894708	TGGTCATGCAAATCTCAAATTAGAAA	58.105	30.769	0.00	0.0	0.00	2.52
2335	2436	3.805207	ACCAATTCTCATAGCCCGTTAC	58.195	45.455	0.00	0.0	0.00	2.50
2446	2563	4.491924	GCGACACTGAATTAACATGTACCG	60.492	45.833	0.00	0.0	0.00	4.02
3063	3381	5.182001	AGGCTGTCAACAAAATGCTACTTAG	59.818	40.000	0.00	0.0	0.00	2.18
3064	3382	5.070001	AGGCTGTCAACAAAATGCTACTTA	58.930	37.500	0.00	0.0	0.00	2.24
3065	3383	3.891366	AGGCTGTCAACAAAATGCTACTT	59.109	39.130	0.00	0.0	0.00	2.24
3066	3384	3.490348	AGGCTGTCAACAAAATGCTACT	58.510	40.909	0.00	0.0	0.00	2.57
3090	3409	4.439305	TCCGTTACGTAGTGCTAAATGT	57.561	40.909	3.52	0.0	45.73	2.71

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.