AutoCloner

Multiple sequence alignment - TraesCS4A01G374300

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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	TraesCS4A01G374300	chr4A	100.000	3662	0	0	1	3662	649144365	649148026	0.000000e+00	6763
1	TraesCS4A01G374300	chr4A	92.988	3665	234	15	2	3662	657366534	657370179	0.000000e+00	5323
2	TraesCS4A01G374300	chr4A	92.882	3667	236	15	2	3662	657306839	657310486	0.000000e+00	5302
3	TraesCS4A01G374300	chr4A	93.425	2099	123	7	2	2094	649173840	649175929	0.000000e+00	3097
4	TraesCS4A01G374300	chr7B	93.724	3665	214	15	2	3662	2564614	2560962	0.000000e+00	5480
5	TraesCS4A01G374300	chr7A	93.096	3476	211	13	204	3662	41625898	41629361	0.000000e+00	5062
6	TraesCS4A01G374300	chr7A	89.481	3565	284	40	45	3547	41618777	41622312	0.000000e+00	4421
7	TraesCS4A01G374300	chr7A	91.543	2637	186	19	596	3215	41716217	41718833	0.000000e+00	3600
8	TraesCS4A01G374300	chr7A	92.526	2462	154	19	457	2914	655037917	655040352	0.000000e+00	3500
9	TraesCS4A01G374300	chr7A	87.640	445	28	10	3232	3661	41791230	41791662	3.290000e-135	492
10	TraesCS4A01G374300	chr7D	91.522	3633	250	31	2	3590	42212189	42215807	0.000000e+00	4950
11	TraesCS4A01G374300	chr7D	93.872	3117	147	15	555	3662	42246216	42249297	0.000000e+00	4658
12	TraesCS4A01G374300	chr7D	92.482	3259	204	24	2	3240	42084834	42081597	0.000000e+00	4623
13	TraesCS4A01G374300	chr7D	92.095	3112	208	21	2	3096	41917444	41914354	0.000000e+00	4349
14	TraesCS4A01G374300	chr7D	91.839	2463	168	13	457	2914	567986933	567989367	0.000000e+00	3404
15	TraesCS4A01G374300	chr7D	90.405	469	44	1	2	469	42245569	42246037	1.870000e-172	616
16	TraesCS4A01G374300	chr7D	89.367	442	32	6	3232	3661	42435549	42435987	3.220000e-150	542
17	TraesCS4A01G374300	chr7D	85.955	534	40	8	3094	3594	41875289	41874758	4.160000e-149	538
18	TraesCS4A01G374300	chr2B	90.639	1111	88	9	2038	3135	784373849	784374956	0.000000e+00	1461
19	TraesCS4A01G374300	chrUn	83.271	269	28	9	3405	3661	250930294	250930031	7.910000e-57	231
20	TraesCS4A01G374300	chrUn	83.271	269	28	9	3405	3661	283093499	283093762	7.910000e-57	231

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	TraesCS4A01G374300	chr4A	649144365	649148026	3661	False	6763.0	6763	100.0000	1	3662	1	chr4A.!!$F1	3661
1	TraesCS4A01G374300	chr4A	657366534	657370179	3645	False	5323.0	5323	92.9880	2	3662	1	chr4A.!!$F4	3660
2	TraesCS4A01G374300	chr4A	657306839	657310486	3647	False	5302.0	5302	92.8820	2	3662	1	chr4A.!!$F3	3660
3	TraesCS4A01G374300	chr4A	649173840	649175929	2089	False	3097.0	3097	93.4250	2	2094	1	chr4A.!!$F2	2092
4	TraesCS4A01G374300	chr7B	2560962	2564614	3652	True	5480.0	5480	93.7240	2	3662	1	chr7B.!!$R1	3660
5	TraesCS4A01G374300	chr7A	41618777	41629361	10584	False	4741.5	5062	91.2885	45	3662	2	chr7A.!!$F4	3617
6	TraesCS4A01G374300	chr7A	41716217	41718833	2616	False	3600.0	3600	91.5430	596	3215	1	chr7A.!!$F1	2619
7	TraesCS4A01G374300	chr7A	655037917	655040352	2435	False	3500.0	3500	92.5260	457	2914	1	chr7A.!!$F3	2457
8	TraesCS4A01G374300	chr7D	42212189	42215807	3618	False	4950.0	4950	91.5220	2	3590	1	chr7D.!!$F1	3588
9	TraesCS4A01G374300	chr7D	42081597	42084834	3237	True	4623.0	4623	92.4820	2	3240	1	chr7D.!!$R3	3238
10	TraesCS4A01G374300	chr7D	41914354	41917444	3090	True	4349.0	4349	92.0950	2	3096	1	chr7D.!!$R2	3094
11	TraesCS4A01G374300	chr7D	567986933	567989367	2434	False	3404.0	3404	91.8390	457	2914	1	chr7D.!!$F3	2457
12	TraesCS4A01G374300	chr7D	42245569	42249297	3728	False	2637.0	4658	92.1385	2	3662	2	chr7D.!!$F4	3660
13	TraesCS4A01G374300	chr7D	41874758	41875289	531	True	538.0	538	85.9550	3094	3594	1	chr7D.!!$R1	500
14	TraesCS4A01G374300	chr2B	784373849	784374956	1107	False	1461.0	1461	90.6390	2038	3135	1	chr2B.!!$F1	1097

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
169	172	0.181587	ACCATGTTGACAACGACCCA	59.818	50.0	13.46	0.0	0.00	4.51	F
783	909	0.320683	TCAGGACATGCTTCCACACG	60.321	55.0	5.24	0.0	38.25	4.49	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1347	8447	0.528924	TGCTCTTTGCCATGTCATGC	59.471	50.0	7.35	4.05	42.0	4.06	R
2741	9869	0.827925	CTACCCTAGCCCTGCATCGA	60.828	60.0	0.00	0.00	0.0	3.59	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
42	43	4.189231	CAAACTAGGTTCCAATAGGACCG	58.811	47.826	0.00	0.00	45.73	4.79
43	44	3.111741	ACTAGGTTCCAATAGGACCGT	57.888	47.619	0.00	0.00	45.73	4.83
68	70	5.620206	TCTCAAAACAAGATGAGGTAGCAA	58.380	37.500	3.23	0.00	42.62	3.91
104	107	1.634702	TTTTTCACGGCAGCACAAAC	58.365	45.000	0.00	0.00	0.00	2.93
169	172	0.181587	ACCATGTTGACAACGACCCA	59.818	50.000	13.46	0.00	0.00	4.51
196	199	3.861689	GCTTATGCTCAAAACATGCCTTC	59.138	43.478	0.00	0.00	36.03	3.46
202	205	1.010419	CAAAACATGCCTTCCTGCGC	61.010	55.000	0.00	0.00	0.00	6.09
278	281	1.562575	GGTACAAGTGCAACCCGACG	61.563	60.000	0.00	0.00	37.80	5.12
319	322	4.074970	CCTTGCTCAATCAGTACTTTGGT	58.925	43.478	7.32	0.00	0.00	3.67
342	345	1.067821	CGATAGCCCAGAAGACACCTC	59.932	57.143	0.00	0.00	0.00	3.85
502	509	2.250921	TACAATTACTCCCCCGTCCA	57.749	50.000	0.00	0.00	0.00	4.02
503	510	1.364269	ACAATTACTCCCCCGTCCAA	58.636	50.000	0.00	0.00	0.00	3.53
518	584	3.124636	CCGTCCAAAATTACGTCCTGAAG	59.875	47.826	0.00	0.00	37.40	3.02
745	871	5.012664	TCAAGAGTGTGTTTCCTGCCTATTA	59.987	40.000	0.00	0.00	0.00	0.98
777	903	6.820656	CCCTATAATGTATCAGGACATGCTTC	59.179	42.308	0.00	0.00	39.99	3.86
783	909	0.320683	TCAGGACATGCTTCCACACG	60.321	55.000	5.24	0.00	38.25	4.49
787	913	1.225855	GACATGCTTCCACACGAACA	58.774	50.000	0.00	0.00	0.00	3.18
885	1014	9.591792	TCACTCTAAATAGATTGACACATGAAG	57.408	33.333	0.00	0.00	37.17	3.02
936	1065	5.105106	TGCATCCAAAGATTCATCAAGCAAT	60.105	36.000	0.00	0.00	0.00	3.56
1347	8447	1.105457	AATGTTGGTCCATCATGGCG	58.895	50.000	14.88	0.00	37.47	5.69
1428	8528	6.518208	AGTGGTGAGAATAGTGTAGAGAAC	57.482	41.667	0.00	0.00	0.00	3.01
1547	8647	1.609061	CGTTGGATCTGGCAACTCTGT	60.609	52.381	10.38	0.00	37.61	3.41
1821	8933	7.057402	CGATAGACTGTTTTATAACATGCACG	58.943	38.462	0.00	0.00	40.43	5.34
1850	8962	8.757789	CAACTAAACAATTAGACGAACTACACA	58.242	33.333	2.80	0.00	40.90	3.72
2035	9149	1.779061	AACCTCCTTGTGATGGCGGT	61.779	55.000	0.00	0.00	43.79	5.68
2145	9261	3.373748	CGCTGTTATTGATGTTGGCACTA	59.626	43.478	0.00	0.00	0.00	2.74
2270	9386	6.613153	ATTCATCTCCTATAGGTACAAGGC	57.387	41.667	18.51	0.00	36.34	4.35
2308	9424	5.408299	TCATGGGCGATATAGTTGAATTTCG	59.592	40.000	0.00	0.00	34.64	3.46
2434	9550	5.083533	TGAGTTTGTTTTCTTGGTGCAAT	57.916	34.783	0.00	0.00	0.00	3.56
2469	9586	3.004629	TGCTAACAAGCTCCATGTTGTTG	59.995	43.478	17.73	11.06	44.60	3.33
2601	9720	0.947244	GAGGATTGGCTGGTATTGCG	59.053	55.000	0.00	0.00	0.00	4.85
2728	9856	1.133823	TGCTTGGCTCCTCAACAAGAA	60.134	47.619	7.73	0.00	43.13	2.52
2741	9869	5.709164	CCTCAACAAGAACAAGGATGAGATT	59.291	40.000	0.00	0.00	35.91	2.40
2758	9886	1.056700	ATTCGATGCAGGGCTAGGGT	61.057	55.000	0.00	0.00	0.00	4.34
2799	9927	0.770499	TGTTCTGCACCAATCCTGGA	59.230	50.000	0.00	0.00	46.92	3.86
2878	10007	3.959535	TTCCCATCCTTTCAATGCAAC	57.040	42.857	0.00	0.00	0.00	4.17
2959	10093	1.747355	GGCTAGTGTGCTAGACGGTTA	59.253	52.381	5.89	0.00	45.77	2.85
2984	10118	8.517062	AATTCTTTGAGAAATCTATCCACTGG	57.483	34.615	0.00	0.00	37.82	4.00
2999	10133	4.030216	TCCACTGGCACATGTCTATCTAA	58.970	43.478	0.00	0.00	38.20	2.10
3000	10134	4.469586	TCCACTGGCACATGTCTATCTAAA	59.530	41.667	0.00	0.00	38.20	1.85
3046	10190	9.791820	TGTTTATTTCAAGATTCATATGTGCTG	57.208	29.630	1.90	0.00	0.00	4.41
3325	10476	6.071503	ACGAGTAATTGTAGTAGCTTCCAAGT	60.072	38.462	0.00	0.00	0.00	3.16
3457	10636	2.574006	TCAGCACCAATCTTCAAGCT	57.426	45.000	0.00	0.00	0.00	3.74
3523	10716	3.097614	AGTTTAGTCTACCACCGAGCAT	58.902	45.455	0.00	0.00	0.00	3.79
3604	10797	5.649831	AGTTTAGACATTCTCTGGCATTTCC	59.350	40.000	0.00	0.00	34.10	3.13
3614	10807	3.189606	TCTGGCATTTCCTCCCTTTCTA	58.810	45.455	0.00	0.00	35.26	2.10
3623	10816	2.122768	CCTCCCTTTCTACAGAGGCAT	58.877	52.381	0.00	0.00	39.54	4.40
3640	10833	5.843421	AGAGGCATGGAGAATGAAGTATACT	59.157	40.000	0.00	0.00	38.72	2.12

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
42	43	6.818644	TGCTACCTCATCTTGTTTTGAGATAC	59.181	38.462	1.63	0.00	41.53	2.24
43	44	6.946340	TGCTACCTCATCTTGTTTTGAGATA	58.054	36.000	1.63	0.00	41.53	1.98
196	199	1.134699	TCTAGAAACTCCATGCGCAGG	60.135	52.381	18.32	17.38	0.00	4.85
202	205	5.059833	GGTTGGCTATCTAGAAACTCCATG	58.940	45.833	0.00	0.00	0.00	3.66
278	281	1.134371	GGATGGCCTTACACTCTGGTC	60.134	57.143	3.32	0.00	0.00	4.02
299	302	4.460263	ACACCAAAGTACTGATTGAGCAA	58.540	39.130	8.58	0.00	0.00	3.91
305	308	5.109903	GCTATCGACACCAAAGTACTGATT	58.890	41.667	0.00	0.00	0.00	2.57
319	322	1.476891	GTGTCTTCTGGGCTATCGACA	59.523	52.381	0.00	0.00	0.00	4.35
342	345	1.615883	CCGTATGGAGATGGACTCTGG	59.384	57.143	0.00	0.00	44.37	3.86
488	495	3.619487	CGTAATTTTGGACGGGGGAGTAA	60.619	47.826	0.00	0.00	35.43	2.24
502	509	6.180472	ACATCCATCTTCAGGACGTAATTTT	58.820	36.000	0.00	0.00	38.13	1.82
503	510	5.745227	ACATCCATCTTCAGGACGTAATTT	58.255	37.500	0.00	0.00	38.13	1.82
542	618	6.419116	CACAGAATTGGATGTATCTAGACGTG	59.581	42.308	0.00	0.00	0.00	4.49
668	789	6.710744	CCGGCTTTGGATATGTTTAGACTAAT	59.289	38.462	0.00	0.00	0.00	1.73
745	871	8.129001	TGTCCTGATACATTATAGGGGATACAT	58.871	37.037	0.00	0.00	39.74	2.29
777	903	7.359262	TCTAAATATTGAACTGTTCGTGTGG	57.641	36.000	15.18	0.48	0.00	4.17
862	991	8.429493	TGCTTCATGTGTCAATCTATTTAGAG	57.571	34.615	0.00	0.00	35.50	2.43
885	1014	6.826668	TGTGGGCATATATATACTGGTATGC	58.173	40.000	13.98	13.98	45.29	3.14
936	1065	0.183492	AGGCTGGAGTGTTTGCTTGA	59.817	50.000	0.00	0.00	0.00	3.02
1347	8447	0.528924	TGCTCTTTGCCATGTCATGC	59.471	50.000	7.35	4.05	42.00	4.06
1428	8528	1.143684	AGTCCGGGGATCATTGGAATG	59.856	52.381	0.00	0.00	37.75	2.67
1547	8647	6.572519	GCAAGGTCATAAGCAATTTCCATTA	58.427	36.000	0.00	0.00	0.00	1.90
1636	8736	6.007703	CCCTAGTGTTTCCAGGTCAAAAATA	58.992	40.000	0.00	0.00	0.00	1.40
1637	8737	4.832823	CCCTAGTGTTTCCAGGTCAAAAAT	59.167	41.667	0.00	0.00	0.00	1.82
1781	8893	6.661377	ACAGTCTATCGCTCTATACCATGAAT	59.339	38.462	0.00	0.00	0.00	2.57
1821	8933	7.417496	AGTTCGTCTAATTGTTTAGTTGTCC	57.583	36.000	0.00	0.00	36.87	4.02
2090	9206	5.358160	GGTTTCTGACTTAAGGATCATTGGG	59.642	44.000	7.53	0.00	0.00	4.12
2215	9331	8.523915	TTGATAACTTGGCATATGAAGACAAT	57.476	30.769	6.97	0.00	0.00	2.71
2270	9386	3.434641	CGCCCATGATCTTACTAATGCTG	59.565	47.826	0.00	0.00	0.00	4.41
2469	9586	8.561738	TGTTCTCACCATTCTAGGATAAAAAC	57.438	34.615	0.00	0.00	0.00	2.43
2611	9730	5.929697	TTGATGTCATTGGCGATATTCTC	57.070	39.130	0.00	0.00	0.00	2.87
2712	9840	2.575532	CTTGTTCTTGTTGAGGAGCCA	58.424	47.619	0.00	0.00	0.00	4.75
2728	9856	3.464907	CTGCATCGAATCTCATCCTTGT	58.535	45.455	0.00	0.00	0.00	3.16
2741	9869	0.827925	CTACCCTAGCCCTGCATCGA	60.828	60.000	0.00	0.00	0.00	3.59
2799	9927	8.540388	AGTACATCATACAACTAAGTGGACATT	58.460	33.333	0.00	0.00	0.00	2.71
2959	10093	7.067981	GCCAGTGGATAGATTTCTCAAAGAATT	59.932	37.037	15.20	0.00	33.67	2.17
3033	10177	4.747931	GCTTACTCCCCAGCACATATGAAT	60.748	45.833	10.38	0.00	35.95	2.57
3223	10374	7.823310	CCATTTGTTGTTCATGATTTGGGATTA	59.177	33.333	0.00	0.00	0.00	1.75
3416	10595	7.916977	GCTGAATCATGTACATATCAAGCAAAA	59.083	33.333	8.32	0.00	0.00	2.44
3523	10716	7.599998	GTGGTTCTGAGAAGGTAATTACGTTTA	59.400	37.037	21.02	11.90	34.79	2.01
3604	10797	2.158842	CCATGCCTCTGTAGAAAGGGAG	60.159	54.545	0.00	0.00	36.36	4.30
3614	10807	2.575279	ACTTCATTCTCCATGCCTCTGT	59.425	45.455	0.00	0.00	32.13	3.41
3623	10816	7.962995	AACTGAGAGTATACTTCATTCTCCA	57.037	36.000	6.88	0.41	32.82	3.86
3640	10833	4.404507	GATAACAAAGCGCAAACTGAGA	57.595	40.909	11.47	0.00	0.00	3.27

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.