AutoCloner

Multiple sequence alignment - TraesCS7B01G019200

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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	TraesCS7B01G019200	chr7B	100.000	3448	0	0	1	3448	16514035	16517482	0.000000e+00	6368
1	TraesCS7B01G019200	chr7B	92.475	3362	206	17	107	3448	16706684	16710018	0.000000e+00	4763
2	TraesCS7B01G019200	chr7B	92.982	114	8	0	1	114	16682640	16682753	2.130000e-37	167
3	TraesCS7B01G019200	chr7D	93.840	3458	194	12	2	3448	73621860	73618411	0.000000e+00	5188
4	TraesCS7B01G019200	chr7D	92.691	3448	212	11	1	3439	73545259	73548675	0.000000e+00	4935
5	TraesCS7B01G019200	chr7D	93.396	3301	192	11	115	3405	73362459	73365743	0.000000e+00	4865
6	TraesCS7B01G019200	chr7D	81.753	1962	287	54	745	2674	64830798	64828876	0.000000e+00	1574
7	TraesCS7B01G019200	chr7D	84.000	850	102	21	1850	2675	64808780	64807941	0.000000e+00	785
8	TraesCS7B01G019200	chr7D	89.323	384	27	7	3072	3448	73365789	73366165	1.450000e-128	470
9	TraesCS7B01G019200	chr7A	93.295	3460	203	16	2	3448	78143454	78140011	0.000000e+00	5077
10	TraesCS7B01G019200	chr7A	92.283	3382	214	23	1	3374	77876406	77879748	0.000000e+00	4756
11	TraesCS7B01G019200	chr7A	91.604	3466	224	33	1	3448	77998029	78001445	0.000000e+00	4726
12	TraesCS7B01G019200	chr7A	82.959	1068	157	20	750	1804	68916776	68915721	0.000000e+00	941
13	TraesCS7B01G019200	chr7A	90.429	303	27	2	3072	3374	77879832	77880132	6.930000e-107	398

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	TraesCS7B01G019200	chr7B	16514035	16517482	3447	False	6368.0	6368	100.0000	1	3448	1	chr7B.!!$F1	3447
1	TraesCS7B01G019200	chr7B	16706684	16710018	3334	False	4763.0	4763	92.4750	107	3448	1	chr7B.!!$F3	3341
2	TraesCS7B01G019200	chr7D	73618411	73621860	3449	True	5188.0	5188	93.8400	2	3448	1	chr7D.!!$R3	3446
3	TraesCS7B01G019200	chr7D	73545259	73548675	3416	False	4935.0	4935	92.6910	1	3439	1	chr7D.!!$F1	3438
4	TraesCS7B01G019200	chr7D	73362459	73366165	3706	False	2667.5	4865	91.3595	115	3448	2	chr7D.!!$F2	3333
5	TraesCS7B01G019200	chr7D	64828876	64830798	1922	True	1574.0	1574	81.7530	745	2674	1	chr7D.!!$R2	1929
6	TraesCS7B01G019200	chr7D	64807941	64808780	839	True	785.0	785	84.0000	1850	2675	1	chr7D.!!$R1	825
7	TraesCS7B01G019200	chr7A	78140011	78143454	3443	True	5077.0	5077	93.2950	2	3448	1	chr7A.!!$R2	3446
8	TraesCS7B01G019200	chr7A	77998029	78001445	3416	False	4726.0	4726	91.6040	1	3448	1	chr7A.!!$F1	3447
9	TraesCS7B01G019200	chr7A	77876406	77880132	3726	False	2577.0	4756	91.3560	1	3374	2	chr7A.!!$F2	3373
10	TraesCS7B01G019200	chr7A	68915721	68916776	1055	True	941.0	941	82.9590	750	1804	1	chr7A.!!$R1	1054

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
553	563	3.309961	TCAAGACTCTGATGTCAGTGC	57.69	47.619	9.65	4.72	44.12	4.4	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2518	2586	2.616524	AGTTCACTAACCCCTACTGCA	58.383	47.619	0.0	0.0	36.15	4.41	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
71	72	7.375808	CGATCATGGTGGTTATGTAATTTTTCG	59.624	37.037	0.00	0.00	0.00	3.46
225	228	6.491714	TTTGTTTGGGAATCAAGGAAATCA	57.508	33.333	0.00	0.00	36.62	2.57
245	248	7.545362	AATCAGTACGAAATTTGAGAGATGG	57.455	36.000	0.00	0.00	0.00	3.51
553	563	3.309961	TCAAGACTCTGATGTCAGTGC	57.690	47.619	9.65	4.72	44.12	4.40
583	595	6.406961	CCTTCTACACTATCACATGGCAAGTA	60.407	42.308	0.00	0.00	0.00	2.24
747	762	9.878599	CCACCGAAACTATATTGACAATAAATC	57.121	33.333	11.80	5.76	0.00	2.17
820	835	7.616313	TCCATACAACACATACATGTCACTAA	58.384	34.615	0.00	0.00	39.39	2.24
861	877	6.373005	TCATGTTTTACCATCAGAGAAGGA	57.627	37.500	0.00	0.00	0.00	3.36
929	946	5.546499	ACCCTCTCCATACAAACACTCTTTA	59.454	40.000	0.00	0.00	0.00	1.85
933	950	6.464222	TCTCCATACAAACACTCTTTAGGTG	58.536	40.000	0.00	0.00	40.19	4.00
1016	1037	5.705397	TCCTCCATGAATCAAAGAGTCAT	57.295	39.130	4.32	4.32	46.12	3.06
1087	1108	5.762825	TCGTCTCAACAACTACTACAACT	57.237	39.130	0.00	0.00	0.00	3.16
1088	1109	5.516996	TCGTCTCAACAACTACTACAACTG	58.483	41.667	0.00	0.00	0.00	3.16
1102	1123	1.151221	AACTGTGATGGCACCAGCA	59.849	52.632	2.92	2.92	44.51	4.41
1131	1152	6.820656	AGAAGAACAAGAAGCATGATATCGTT	59.179	34.615	0.00	0.00	0.00	3.85
1157	1178	4.591321	ATCTCAAAGCATGGTTCCCTAA	57.409	40.909	11.16	0.00	0.00	2.69
1321	1343	2.496899	TGGATTGCAAGAGGAGGTTC	57.503	50.000	4.94	0.00	0.00	3.62
1326	1348	1.965414	TGCAAGAGGAGGTTCCCATA	58.035	50.000	0.00	0.00	37.19	2.74
1352	1374	5.151454	AGGAATGGGTATTTTGTTTGGTCA	58.849	37.500	0.00	0.00	0.00	4.02
1376	1398	6.061022	TCCATTAGAGAGTATGCAAACCAA	57.939	37.500	0.00	0.00	0.00	3.67
1404	1426	2.289945	ACAAGAAGAGGTGCAGATGGTC	60.290	50.000	0.00	0.00	0.00	4.02
1413	1435	1.137872	GTGCAGATGGTCGAGGAGAAT	59.862	52.381	0.00	0.00	0.00	2.40
1579	1604	5.022282	TGATTATTCGCTTGGAGATGTCA	57.978	39.130	0.00	0.00	0.00	3.58
1622	1653	9.449719	AAGCATACTATAAACTATTATGTGGGC	57.550	33.333	0.00	0.00	33.75	5.36
1640	1672	5.892686	TGTGGGCTTTCATTATCATGAATCA	59.107	36.000	0.00	0.00	46.68	2.57
1737	1770	8.780846	TGTATATATTTTGTTTGTGGACGACT	57.219	30.769	0.00	0.00	0.00	4.18
1746	1779	4.748102	TGTTTGTGGACGACTGACTTTATC	59.252	41.667	0.00	0.00	0.00	1.75
1761	1794	9.890629	ACTGACTTTATCTCATTATTGTGCTTA	57.109	29.630	0.00	0.00	0.00	3.09
1791	1824	0.249676	TTAATACCACCGGCGCTTGA	59.750	50.000	7.64	0.00	0.00	3.02
1804	1837	1.400242	GCGCTTGACCTTGCAACTAAG	60.400	52.381	0.00	0.00	0.00	2.18
1999	2045	8.079211	AGATAGATGTCCTTTACTAGCACAAA	57.921	34.615	0.00	0.00	0.00	2.83
2013	2059	6.863275	ACTAGCACAAAGGTTAATATTTGGC	58.137	36.000	15.60	14.81	40.05	4.52
2309	2372	1.046204	TGGAGCTCGATGATGCTGAT	58.954	50.000	7.83	0.00	39.91	2.90
2315	2378	1.732809	CTCGATGATGCTGATCCATGC	59.267	52.381	0.00	0.00	0.00	4.06
2358	2421	2.669569	GGCAAGCACTCGCCTTGA	60.670	61.111	5.41	0.00	45.29	3.02
2397	2460	8.547894	GTGTTGATAACCAAAATCCAAGTTTTC	58.452	33.333	0.00	0.00	36.36	2.29
2500	2568	8.829612	GGAGTTAGTAGTAGTATCTTGTGAGAC	58.170	40.741	0.00	0.00	33.99	3.36
2518	2586	7.320399	TGTGAGACTTATATGATGTTGTCGTT	58.680	34.615	0.00	0.00	0.00	3.85
2529	2598	0.250166	GTTGTCGTTGCAGTAGGGGT	60.250	55.000	0.00	0.00	0.00	4.95
2560	2629	8.999220	AACTTTGTTCCTACTAGTATACAAGC	57.001	34.615	17.52	4.84	0.00	4.01
2701	2770	9.585099	CTATGGTTGTTGTATAAACATTGCAAT	57.415	29.630	5.99	5.99	36.82	3.56
2721	2790	6.377712	TGCAATTGAGATTGATGTGGTATTGA	59.622	34.615	10.34	0.00	44.37	2.57
2832	2901	3.695830	AGCCTCATTAGTGAAAACCGA	57.304	42.857	0.00	0.00	33.05	4.69
2842	2911	3.486383	AGTGAAAACCGATGTCAACCAT	58.514	40.909	0.00	0.00	36.13	3.55
2847	2916	0.392998	ACCGATGTCAACCATGCTCC	60.393	55.000	0.00	0.00	32.56	4.70
2876	2945	4.811555	TTCTTGAACGGATTGACAAGTG	57.188	40.909	0.00	0.00	40.07	3.16
2877	2946	2.548057	TCTTGAACGGATTGACAAGTGC	59.452	45.455	0.00	0.00	40.07	4.40
2900	2969	6.147985	TGCGATGTGTGCATTAACTAGTTTTA	59.852	34.615	14.49	2.95	37.44	1.52
2972	3041	9.543018	GAACTAATCTCAATTGGAAACGTTTAG	57.457	33.333	14.65	5.95	0.00	1.85
3053	3123	2.622452	CCAACTCCATGGAGGCTTCAAT	60.622	50.000	38.54	18.30	45.88	2.57
3090	3160	6.153510	AGGCTAAAGAGAAGCTTTATTTTGGG	59.846	38.462	0.00	1.83	45.39	4.12
3148	3599	6.065976	ACATGATTCAATTCTACTGGACCA	57.934	37.500	0.00	0.00	0.00	4.02
3205	3656	1.229951	AGAGGCCAACTGGATCCCA	60.230	57.895	9.90	0.00	37.39	4.37
3209	3660	0.681243	GGCCAACTGGATCCCAAGAC	60.681	60.000	9.90	0.00	37.39	3.01
3305	3761	7.827729	TCTTAAGTTCTTATTGGTCTTTAGGGC	59.172	37.037	1.63	0.00	0.00	5.19
3358	3814	3.177997	ACTCACCAACACCAAAAATGC	57.822	42.857	0.00	0.00	0.00	3.56
3359	3815	2.158971	ACTCACCAACACCAAAAATGCC	60.159	45.455	0.00	0.00	0.00	4.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
8	9	1.962807	CATTGCTCACAACTTCCCCAA	59.037	47.619	0.00	0.0	38.99	4.12
71	72	7.497595	AGGTTGGATAGGTTTTCAAAAGAAAC	58.502	34.615	0.00	0.0	36.51	2.78
225	228	6.037786	TGACCATCTCTCAAATTTCGTACT	57.962	37.500	0.00	0.0	0.00	2.73
335	339	4.082026	GCAAGAAAGTTAAGTCATGGGCAT	60.082	41.667	0.00	0.0	0.00	4.40
553	563	6.045318	CCATGTGATAGTGTAGAAGGTCAAG	58.955	44.000	0.00	0.0	0.00	3.02
583	595	7.277098	AGTCGTGATATTACGCACACTATTTTT	59.723	33.333	14.67	0.0	43.40	1.94
747	762	9.800433	ATATCGAGACTAGCAATTTCATATCTG	57.200	33.333	0.00	0.0	0.00	2.90
796	811	7.333174	TGTTAGTGACATGTATGTGTTGTATGG	59.667	37.037	0.00	0.0	41.95	2.74
856	872	8.053026	AGCATCATCATATAGCAAATTCCTTC	57.947	34.615	0.00	0.0	0.00	3.46
933	950	9.262358	GTTGGATAAAACTATGAGAGGTATGAC	57.738	37.037	0.00	0.0	0.00	3.06
1087	1108	0.251253	TCATTGCTGGTGCCATCACA	60.251	50.000	0.00	0.0	44.87	3.58
1088	1109	0.454600	CTCATTGCTGGTGCCATCAC	59.545	55.000	0.00	0.0	42.40	3.06
1102	1123	8.749026	ATATCATGCTTCTTGTTCTTCTCATT	57.251	30.769	0.00	0.0	0.00	2.57
1131	1152	1.927487	ACCATGCTTTGAGATTGGCA	58.073	45.000	0.00	0.0	39.06	4.92
1157	1178	3.181445	TGTTACCTGTTGCATGGTCTTCT	60.181	43.478	9.40	0.0	37.74	2.85
1326	1348	5.843969	ACCAAACAAAATACCCATTCCTTCT	59.156	36.000	0.00	0.0	0.00	2.85
1352	1374	6.252599	TGGTTTGCATACTCTCTAATGGAT	57.747	37.500	7.25	0.0	0.00	3.41
1376	1398	3.445008	TGCACCTCTTCTTGTATCTCCT	58.555	45.455	0.00	0.0	0.00	3.69
1404	1426	3.262420	CAACACCACCTTATTCTCCTCG	58.738	50.000	0.00	0.0	0.00	4.63
1413	1435	6.012858	ACATCTTATTCTCCAACACCACCTTA	60.013	38.462	0.00	0.0	0.00	2.69
1607	1638	9.420118	TGATAATGAAAGCCCACATAATAGTTT	57.580	29.630	0.00	0.0	0.00	2.66
1677	1710	9.912634	CTATTGTTTCTGGTAAATGTGAAATGT	57.087	29.630	0.00	0.0	32.22	2.71
1731	1764	8.535592	CACAATAATGAGATAAAGTCAGTCGTC	58.464	37.037	0.00	0.0	0.00	4.20
1737	1770	9.665719	TGTAAGCACAATAATGAGATAAAGTCA	57.334	29.630	0.00	0.0	0.00	3.41
1761	1794	6.203338	CGCCGGTGGTATTAACTTATTAATGT	59.797	38.462	7.26	0.0	40.51	2.71
1791	1824	2.644798	ACTCCATCCTTAGTTGCAAGGT	59.355	45.455	0.00	0.0	44.68	3.50
1846	1880	7.129457	AGACCATGATAAGACTTGCAATAGA	57.871	36.000	0.00	0.0	0.00	1.98
2309	2372	4.539726	AGCTATTCTCCATTTTGCATGGA	58.460	39.130	7.30	7.3	45.24	3.41
2358	2421	8.415950	TGGTTATCAACACCAATTGTAGATTT	57.584	30.769	4.43	0.0	41.58	2.17
2397	2460	4.202141	TGGACTTGAAGGAGTTTGCAAATG	60.202	41.667	16.21	0.0	0.00	2.32
2491	2559	7.489435	ACGACAACATCATATAAGTCTCACAAG	59.511	37.037	0.00	0.0	0.00	3.16
2500	2568	6.349973	ACTGCAACGACAACATCATATAAG	57.650	37.500	0.00	0.0	0.00	1.73
2518	2586	2.616524	AGTTCACTAACCCCTACTGCA	58.383	47.619	0.00	0.0	36.15	4.41
2627	2696	5.534278	TGACTCTCCAAACACATATGCAAAA	59.466	36.000	1.58	0.0	0.00	2.44
2701	2770	9.850198	TTCATATCAATACCACATCAATCTCAA	57.150	29.630	0.00	0.0	0.00	3.02
2721	2790	8.061304	ACCCAGAGAAAAATGGTATGTTCATAT	58.939	33.333	0.00	0.0	34.58	1.78
2832	2901	0.548031	ATCCGGAGCATGGTTGACAT	59.452	50.000	11.34	0.0	41.57	3.06
2842	2911	3.009723	GTTCAAGAATCAATCCGGAGCA	58.990	45.455	11.34	0.0	0.00	4.26
2847	2916	4.332543	TCAATCCGTTCAAGAATCAATCCG	59.667	41.667	0.00	0.0	0.00	4.18
2876	2945	4.600012	AACTAGTTAATGCACACATCGC	57.400	40.909	6.26	0.0	34.62	4.58
2877	2946	9.849607	CTATAAAACTAGTTAATGCACACATCG	57.150	33.333	8.92	0.0	34.62	3.84
2900	2969	5.413833	CACTTTGCTCTCAACCATGAACTAT	59.586	40.000	0.00	0.0	34.49	2.12
3090	3160	1.154035	CAAAATGCCCGCTTCGTCC	60.154	57.895	0.00	0.0	0.00	4.79
3141	3592	5.147330	TGTGTTTACACTCTATGGTCCAG	57.853	43.478	13.61	0.0	46.55	3.86
3205	3656	2.689646	GCAAACTTCTCGCTAGGTCTT	58.310	47.619	0.00	0.0	0.00	3.01
3209	3660	1.710339	GCGCAAACTTCTCGCTAGG	59.290	57.895	0.30	0.0	44.79	3.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.