AutoCloner

Multiple sequence alignment - TraesCS1A01G032100

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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	TraesCS1A01G032100	chr1A	100.000	3188	0	0	1	3188	14792908	14789721	0.000000e+00	5888
1	TraesCS1A01G032100	chr1A	90.298	1845	149	17	586	2414	14840302	14838472	0.000000e+00	2388
2	TraesCS1A01G032100	chr1A	94.271	576	30	3	1	573	376743776	376743201	0.000000e+00	878
3	TraesCS1A01G032100	chr1A	83.056	360	37	10	2613	2949	14836634	14836276	4.000000e-79	305
4	TraesCS1A01G032100	chr1B	91.770	2673	163	28	570	3187	19620417	19617747	0.000000e+00	3664
5	TraesCS1A01G032100	chr1B	91.732	2673	165	26	570	3187	19951847	19949176	0.000000e+00	3661
6	TraesCS1A01G032100	chr1B	91.582	2673	169	27	570	3187	19839971	19837300	0.000000e+00	3639
7	TraesCS1A01G032100	chr1B	91.180	2687	166	33	570	3187	19720377	19717693	0.000000e+00	3583
8	TraesCS1A01G032100	chr1B	90.947	2673	176	28	570	3187	19780997	19778336	0.000000e+00	3535
9	TraesCS1A01G032100	chr1B	91.946	2297	129	26	946	3187	19892022	19889727	0.000000e+00	3166
10	TraesCS1A01G032100	chr1B	90.961	2279	134	28	587	2812	20048190	20045931	0.000000e+00	3001
11	TraesCS1A01G032100	chr1B	93.057	1858	100	14	570	2415	20554842	20556682	0.000000e+00	2689
12	TraesCS1A01G032100	chr1B	93.648	614	36	3	2576	3188	20556788	20557399	0.000000e+00	915
13	TraesCS1A01G032100	chr1B	94.957	575	27	2	1	573	491719547	491720121	0.000000e+00	900
14	TraesCS1A01G032100	chr1B	94.444	576	29	3	1	573	12741584	12742159	0.000000e+00	883
15	TraesCS1A01G032100	chr1B	93.629	361	18	5	2830	3188	20045942	20045585	4.680000e-148	534
16	TraesCS1A01G032100	chr1D	93.554	2296	94	6	570	2812	13818094	13815800	0.000000e+00	3371
17	TraesCS1A01G032100	chr1D	93.423	2296	97	7	570	2812	13728945	13726651	0.000000e+00	3354
18	TraesCS1A01G032100	chr1D	91.924	1003	50	16	1562	2534	13722788	13721787	0.000000e+00	1375
19	TraesCS1A01G032100	chr1D	91.326	1003	55	14	1562	2534	13811546	13810546	0.000000e+00	1341
20	TraesCS1A01G032100	chr1D	93.511	601	37	2	2588	3188	13810549	13809951	0.000000e+00	893
21	TraesCS1A01G032100	chr1D	93.012	601	40	2	2588	3188	13721790	13721192	0.000000e+00	876
22	TraesCS1A01G032100	chr1D	92.737	358	23	2	2830	3185	13726662	13726306	6.100000e-142	514
23	TraesCS1A01G032100	chr1D	92.835	321	20	2	2830	3148	13815811	13815492	2.240000e-126	462
24	TraesCS1A01G032100	chrUn	94.444	576	29	3	1	573	304340649	304341224	0.000000e+00	883
25	TraesCS1A01G032100	chr7D	94.444	576	29	3	1	573	101487233	101486658	0.000000e+00	883
26	TraesCS1A01G032100	chr6A	94.444	576	29	3	1	573	169950448	169949873	0.000000e+00	883
27	TraesCS1A01G032100	chr6A	93.414	577	33	5	1	574	80518717	80518143	0.000000e+00	850
28	TraesCS1A01G032100	chr3A	94.444	576	29	3	1	573	459062199	459061624	0.000000e+00	883
29	TraesCS1A01G032100	chr4A	93.391	575	30	5	1	570	601346006	601345435	0.000000e+00	845

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	TraesCS1A01G032100	chr1A	14789721	14792908	3187	True	5888.00	5888	100.0000	1	3188	1	chr1A.!!$R1	3187
1	TraesCS1A01G032100	chr1A	14836276	14840302	4026	True	1346.50	2388	86.6770	586	2949	2	chr1A.!!$R3	2363
2	TraesCS1A01G032100	chr1A	376743201	376743776	575	True	878.00	878	94.2710	1	573	1	chr1A.!!$R2	572
3	TraesCS1A01G032100	chr1B	19617747	19620417	2670	True	3664.00	3664	91.7700	570	3187	1	chr1B.!!$R1	2617
4	TraesCS1A01G032100	chr1B	19949176	19951847	2671	True	3661.00	3661	91.7320	570	3187	1	chr1B.!!$R6	2617
5	TraesCS1A01G032100	chr1B	19837300	19839971	2671	True	3639.00	3639	91.5820	570	3187	1	chr1B.!!$R4	2617
6	TraesCS1A01G032100	chr1B	19717693	19720377	2684	True	3583.00	3583	91.1800	570	3187	1	chr1B.!!$R2	2617
7	TraesCS1A01G032100	chr1B	19778336	19780997	2661	True	3535.00	3535	90.9470	570	3187	1	chr1B.!!$R3	2617
8	TraesCS1A01G032100	chr1B	19889727	19892022	2295	True	3166.00	3166	91.9460	946	3187	1	chr1B.!!$R5	2241
9	TraesCS1A01G032100	chr1B	20554842	20557399	2557	False	1802.00	2689	93.3525	570	3188	2	chr1B.!!$F3	2618
10	TraesCS1A01G032100	chr1B	20045585	20048190	2605	True	1767.50	3001	92.2950	587	3188	2	chr1B.!!$R7	2601
11	TraesCS1A01G032100	chr1B	491719547	491720121	574	False	900.00	900	94.9570	1	573	1	chr1B.!!$F2	572
12	TraesCS1A01G032100	chr1B	12741584	12742159	575	False	883.00	883	94.4440	1	573	1	chr1B.!!$F1	572
13	TraesCS1A01G032100	chr1D	13721192	13728945	7753	True	1529.75	3354	92.7740	570	3188	4	chr1D.!!$R1	2618
14	TraesCS1A01G032100	chr1D	13809951	13818094	8143	True	1516.75	3371	92.8065	570	3188	4	chr1D.!!$R2	2618
15	TraesCS1A01G032100	chrUn	304340649	304341224	575	False	883.00	883	94.4440	1	573	1	chrUn.!!$F1	572
16	TraesCS1A01G032100	chr7D	101486658	101487233	575	True	883.00	883	94.4440	1	573	1	chr7D.!!$R1	572
17	TraesCS1A01G032100	chr6A	169949873	169950448	575	True	883.00	883	94.4440	1	573	1	chr6A.!!$R2	572
18	TraesCS1A01G032100	chr6A	80518143	80518717	574	True	850.00	850	93.4140	1	574	1	chr6A.!!$R1	573
19	TraesCS1A01G032100	chr3A	459061624	459062199	575	True	883.00	883	94.4440	1	573	1	chr3A.!!$R1	572
20	TraesCS1A01G032100	chr4A	601345435	601346006	571	True	845.00	845	93.3910	1	570	1	chr4A.!!$R1	569

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
749	761	0.107703	CCATGCTCCTTAAGACGGCA	60.108	55.0	15.38	15.38	37.32	5.69	F
1708	1755	0.038159	CGACGAGCCCTTTGAGAAGT	60.038	55.0	0.00	0.00	0.00	3.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1998	2045	0.535335	ACATGTTGCCGTACTCCGAT	59.465	50.00	0.0	0.0	39.56	4.18	R
3088	15387	5.633830	AAAGTGCATGGATTCAGTACTTG	57.366	39.13	0.0	0.0	30.30	3.16	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
143	145	0.179100	CGGCTCGTCTCCATGACAAT	60.179	55.000	0.00	0.00	45.60	2.71
148	150	1.349627	GTCTCCATGACAATGCGCG	59.650	57.895	0.00	0.00	44.73	6.86
181	183	2.594303	CAACAACAGCGAGGGCCA	60.594	61.111	6.18	0.00	41.24	5.36
443	447	6.438259	TGTTAAAATTTGGACGAACTGTGA	57.562	33.333	0.00	0.00	0.00	3.58
453	457	1.666011	GAACTGTGAGGGCGTCTGA	59.334	57.895	8.82	0.00	0.00	3.27
601	608	2.981859	ATCTTAACGATTGCCGACCT	57.018	45.000	0.00	0.00	41.76	3.85
603	610	1.274167	TCTTAACGATTGCCGACCTGT	59.726	47.619	0.00	0.00	41.76	4.00
623	630	2.260869	CCAGCCGTGTCCTGTTTGG	61.261	63.158	0.00	0.00	37.10	3.28
627	634	4.025401	CGTGTCCTGTTTGGCGCC	62.025	66.667	22.73	22.73	35.26	6.53
672	679	4.518970	TGGCAGAGTTGTTTTATGGTTCTC	59.481	41.667	0.00	0.00	0.00	2.87
749	761	0.107703	CCATGCTCCTTAAGACGGCA	60.108	55.000	15.38	15.38	37.32	5.69
824	842	1.007271	AAGCTCAGTCGTCGGTGTG	60.007	57.895	0.00	0.00	0.00	3.82
844	864	4.141892	TGTGTTCAACTCCGGTAGAGAAAA	60.142	41.667	0.00	1.30	46.50	2.29
938	958	7.809331	TGAGAAATACAATCTTACGTTACGTGT	59.191	33.333	21.22	10.88	41.39	4.49
1444	1491	1.874345	CGACTACCAGTTGGCGAGGT	61.874	60.000	0.99	0.00	39.11	3.85
1587	1634	0.323816	TGGTCTGCTCGGAGATCACT	60.324	55.000	9.69	0.00	33.89	3.41
1708	1755	0.038159	CGACGAGCCCTTTGAGAAGT	60.038	55.000	0.00	0.00	0.00	3.01
1833	1880	3.474570	GTGCCCGGGCTCATCTCT	61.475	66.667	43.34	0.00	42.51	3.10
1920	1967	1.075482	CTGGATTGCACACCCTGGT	59.925	57.895	5.98	0.00	0.00	4.00
2046	2093	1.096416	GTGTCCTCTTCGTCCTCGAT	58.904	55.000	0.00	0.00	45.65	3.59
2149	2196	2.649034	GCCTCACCGTCGAGACAA	59.351	61.111	4.02	0.00	34.79	3.18
2186	2233	0.179076	CCGATCACAGCCACTGCATA	60.179	55.000	0.00	0.00	41.13	3.14
2265	2312	0.038526	ACAAGTGGTTACGAGAGCGG	60.039	55.000	0.00	0.00	43.17	5.52
2268	2315	3.766691	TGGTTACGAGAGCGGCCC	61.767	66.667	0.00	0.00	43.17	5.80
2300	2347	4.918588	TGTTCTGAGTTTCCTTTATCCCC	58.081	43.478	0.00	0.00	0.00	4.81
2303	2350	1.562475	TGAGTTTCCTTTATCCCCGGG	59.438	52.381	15.80	15.80	0.00	5.73
2341	2394	9.013229	TGTTTTCTGCTGTAAGAATTGATATGT	57.987	29.630	0.00	0.00	36.12	2.29
2393	2447	4.793353	GCTCCTGATGTACCTCGTGTATTC	60.793	50.000	0.00	0.00	0.00	1.75
2555	3939	7.629222	GCATAATCCATATGTTTGGGATGCTAC	60.629	40.741	1.24	0.00	42.89	3.58
2565	3949	2.407562	TGGGATGCTACAGCCATCTAA	58.592	47.619	4.05	0.00	42.36	2.10
2632	9422	6.864165	TGGTGTTTTCGGTTTTCAAATATAGC	59.136	34.615	0.00	0.00	0.00	2.97
2742	15012	4.382457	CCATTTGTGATTGTACTGTTTGCG	59.618	41.667	0.00	0.00	0.00	4.85
2790	15068	5.361427	TCGAGACACAACTATTTTTCACCA	58.639	37.500	0.00	0.00	0.00	4.17
2791	15069	5.465390	TCGAGACACAACTATTTTTCACCAG	59.535	40.000	0.00	0.00	0.00	4.00
2811	15108	9.667107	TCACCAGAGGAACTTTATGTTTATAAG	57.333	33.333	0.00	0.00	41.55	1.73
2965	15263	4.910195	TGGTTTAGAGATGTTGAGCATGT	58.090	39.130	0.00	0.00	38.06	3.21
2966	15264	4.937620	TGGTTTAGAGATGTTGAGCATGTC	59.062	41.667	0.00	0.00	45.21	3.06
2970	15268	2.836372	AGAGATGTTGAGCATGTCCTCA	59.164	45.455	2.90	0.00	45.79	3.86
3068	15366	5.145564	GTTCTATAGGGAGTACATGTGGGA	58.854	45.833	9.11	0.00	0.00	4.37
3094	15393	6.303903	TCATTTCCCCCTAGTAACAAGTAC	57.696	41.667	0.00	0.00	0.00	2.73
3118	15417	7.844009	ACTGAATCCATGCACTTTATTCATTT	58.156	30.769	13.05	4.69	36.33	2.32
3126	15425	6.403866	TGCACTTTATTCATTTTGTCTGGT	57.596	33.333	0.00	0.00	0.00	4.00
3134	15433	9.770097	TTTATTCATTTTGTCTGGTAAAATGCA	57.230	25.926	14.88	7.76	46.97	3.96

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
382	386	1.405821	ACAAACACGGCCAAATTTCGA	59.594	42.857	2.24	0.00	0.00	3.71
601	608	1.978455	AACAGGACACGGCTGGAACA	61.978	55.000	0.00	0.00	0.00	3.18
603	610	0.817634	CAAACAGGACACGGCTGGAA	60.818	55.000	0.00	0.00	0.00	3.53
627	634	2.126502	GTTTGCCATGTTCCGCCG	60.127	61.111	0.00	0.00	0.00	6.46
637	644	0.535780	CTCTGCCAGTGAGTTTGCCA	60.536	55.000	0.00	0.00	0.00	4.92
672	679	5.850653	GGCAATGTTTCCAATTTTAAAAGCG	59.149	36.000	6.79	0.02	0.00	4.68
725	733	0.181114	TCTTAAGGAGCATGGCGCAT	59.819	50.000	10.83	0.00	46.13	4.73
749	761	7.713073	GCAGCTTAGAGAAACTCTACCATAATT	59.287	37.037	7.83	0.00	41.99	1.40
844	864	5.047377	ACATGGTTTGCTAACGGATTCATTT	60.047	36.000	4.95	0.00	35.00	2.32
863	883	3.947196	TGCTGCCACTTTATAGAACATGG	59.053	43.478	0.00	0.00	0.00	3.66
934	954	1.877443	CAAGGGTTTGGAAGGTACACG	59.123	52.381	0.00	0.00	0.00	4.49
938	958	2.290705	GCTAGCAAGGGTTTGGAAGGTA	60.291	50.000	10.63	0.00	34.79	3.08
1708	1755	2.762887	CTGATACCAGCTGGAAGAGTGA	59.237	50.000	39.19	14.25	38.94	3.41
1833	1880	2.221169	AGCGCTTGTTCAATGTTCTCA	58.779	42.857	2.64	0.00	0.00	3.27
1920	1967	2.940467	TCCAGGATTGCTGGCCCA	60.940	61.111	18.72	0.00	41.53	5.36
1998	2045	0.535335	ACATGTTGCCGTACTCCGAT	59.465	50.000	0.00	0.00	39.56	4.18
2046	2093	2.094182	GGAAGAGGTCTTACGCATCACA	60.094	50.000	0.00	0.00	36.11	3.58
2149	2196	2.492090	GACGCTGCAGAGGACGAT	59.508	61.111	20.43	0.00	0.00	3.73
2186	2233	2.783135	AGTGTGGTTTGCTGATCGATT	58.217	42.857	0.00	0.00	0.00	3.34
2268	2315	2.469274	ACTCAGAACAGCCATCACAG	57.531	50.000	0.00	0.00	0.00	3.66
2300	2347	5.670094	GCAGAAAACAAAAAGTGAAAACCCG	60.670	40.000	0.00	0.00	0.00	5.28
2303	2350	6.887368	ACAGCAGAAAACAAAAAGTGAAAAC	58.113	32.000	0.00	0.00	0.00	2.43
2341	2394	0.938192	AGGGTTTGGGGAGGAAAACA	59.062	50.000	0.00	0.00	37.89	2.83
2393	2447	8.761497	CCCATACATAATGTTGAACGTTACTAG	58.239	37.037	11.79	8.02	32.94	2.57
2555	3939	9.770097	TTAAGAACATTCTATCTTAGATGGCTG	57.230	33.333	4.78	5.84	38.84	4.85
2632	9422	6.313658	TGATCAAAATAGTGTCCTGAATGTCG	59.686	38.462	0.00	0.00	0.00	4.35
2742	15012	7.681939	TTGATGGTTGGAAAAGAGTATACAC	57.318	36.000	5.50	0.00	0.00	2.90
3068	15366	6.800890	ACTTGTTACTAGGGGGAAATGAATT	58.199	36.000	0.00	0.00	0.00	2.17
3083	15382	5.643777	GTGCATGGATTCAGTACTTGTTACT	59.356	40.000	0.00	0.00	42.23	2.24
3088	15387	5.633830	AAAGTGCATGGATTCAGTACTTG	57.366	39.130	0.00	0.00	30.30	3.16
3094	15393	8.600625	CAAAATGAATAAAGTGCATGGATTCAG	58.399	33.333	16.36	5.14	39.26	3.02
3118	15417	9.202273	GTTTCAATATTGCATTTTACCAGACAA	57.798	29.630	10.76	0.00	0.00	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.