AutoCloner

Multiple sequence alignment - TraesCS7A01G114900

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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	TraesCS7A01G114900	chr7A	100.000	3200	0	0	1	3200	71046313	71049512	0.000000e+00	5910.0
1	TraesCS7A01G114900	chr7A	92.607	1772	106	8	806	2572	58641490	58643241	0.000000e+00	2523.0
2	TraesCS7A01G114900	chr7A	85.714	574	79	2	1399	1970	58643532	58644104	1.270000e-168	603.0
3	TraesCS7A01G114900	chr7A	90.957	376	31	1	2825	3200	58804494	58804866	1.330000e-138	503.0
4	TraesCS7A01G114900	chr7A	82.241	580	82	12	812	1370	58376031	58376610	6.210000e-132	481.0
5	TraesCS7A01G114900	chr7A	89.589	365	38	0	2826	3190	58375971	58376335	6.250000e-127	464.0
6	TraesCS7A01G114900	chr7A	84.034	357	47	7	812	1163	58804555	58804906	5.110000e-88	335.0
7	TraesCS7A01G114900	chr7A	79.661	295	47	11	2058	2348	125104289	125104574	1.950000e-47	200.0
8	TraesCS7A01G114900	chr7A	94.783	115	6	0	670	784	58641209	58641323	2.540000e-41	180.0
9	TraesCS7A01G114900	chr7B	95.451	2396	45	9	806	3200	8364085	8366417	0.000000e+00	3762.0
10	TraesCS7A01G114900	chr7B	96.497	571	13	4	219	784	8363350	8363918	0.000000e+00	937.0
11	TraesCS7A01G114900	chr7B	96.537	231	8	0	1	231	8361375	8361605	1.800000e-102	383.0
12	TraesCS7A01G114900	chr7D	93.377	1389	91	1	806	2194	54721829	54720442	0.000000e+00	2054.0
13	TraesCS7A01G114900	chr7D	91.026	1014	48	11	2193	3200	54719389	54718413	0.000000e+00	1328.0
14	TraesCS7A01G114900	chr7D	83.445	598	80	11	815	1394	54598158	54597562	3.630000e-149	538.0
15	TraesCS7A01G114900	chr7D	92.021	376	30	0	2825	3200	55088155	55087780	2.190000e-146	529.0
16	TraesCS7A01G114900	chr7D	82.130	554	93	4	1508	2060	54597502	54596954	1.340000e-128	470.0
17	TraesCS7A01G114900	chr7D	86.957	368	48	0	2826	3193	54598221	54597854	6.390000e-112	414.0
18	TraesCS7A01G114900	chr7D	81.909	503	75	7	1535	2023	55087341	55086841	8.260000e-111	411.0
19	TraesCS7A01G114900	chr7D	83.862	347	53	2	811	1154	54718728	54718382	8.560000e-86	327.0
20	TraesCS7A01G114900	chr7D	83.380	355	54	4	811	1161	55088095	55087742	1.110000e-84	324.0
21	TraesCS7A01G114900	chr7D	94.737	76	4	0	709	784	54722071	54721996	5.610000e-23	119.0
22	TraesCS7A01G114900	chr7D	95.918	49	2	0	670	718	54732878	54732830	2.650000e-11	80.5
23	TraesCS7A01G114900	chr2A	81.295	278	39	11	2066	2338	675390259	675390528	2.500000e-51	213.0
24	TraesCS7A01G114900	chr1A	78.750	320	58	9	2032	2348	297046828	297047140	4.180000e-49	206.0
25	TraesCS7A01G114900	chr6A	80.070	286	45	12	2066	2344	85564875	85565155	5.410000e-48	202.0
26	TraesCS7A01G114900	chr4D	80.451	266	45	6	2083	2348	399220198	399219940	2.520000e-46	196.0
27	TraesCS7A01G114900	chr2D	96.429	112	4	0	14	125	571459679	571459568	5.450000e-43	185.0
28	TraesCS7A01G114900	chr2D	92.857	112	8	0	14	125	107128880	107128991	2.550000e-36	163.0
29	TraesCS7A01G114900	chr2D	94.175	103	5	1	22	124	68692204	68692305	4.270000e-34	156.0
30	TraesCS7A01G114900	chr1D	78.930	299	44	14	2066	2355	125746762	125746474	5.450000e-43	185.0
31	TraesCS7A01G114900	chr3D	92.793	111	7	1	14	124	416560347	416560456	3.300000e-35	159.0
32	TraesCS7A01G114900	chr3D	91.000	100	9	0	25	124	596639115	596639016	5.570000e-28	135.0
33	TraesCS7A01G114900	chr2B	89.320	103	11	0	22	124	26953929	26954031	2.590000e-26	130.0
34	TraesCS7A01G114900	chr2B	89.320	103	11	0	22	124	628397079	628397181	2.590000e-26	130.0
35	TraesCS7A01G114900	chr1B	89.109	101	11	0	25	125	483883018	483882918	3.350000e-25	126.0
36	TraesCS7A01G114900	chr5B	100.000	28	0	0	829	856	540734641	540734668	6.000000e-03	52.8

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	TraesCS7A01G114900	chr7A	71046313	71049512	3199	False	5910.000000	5910	100.000000	1	3200	1	chr7A.!!$F1	3199
1	TraesCS7A01G114900	chr7A	58641209	58644104	2895	False	1102.000000	2523	91.034667	670	2572	3	chr7A.!!$F4	1902
2	TraesCS7A01G114900	chr7A	58375971	58376610	639	False	472.500000	481	85.915000	812	3190	2	chr7A.!!$F3	2378
3	TraesCS7A01G114900	chr7B	8361375	8366417	5042	False	1694.000000	3762	96.161667	1	3200	3	chr7B.!!$F1	3199
4	TraesCS7A01G114900	chr7D	54718382	54722071	3689	True	957.000000	2054	90.750500	709	3200	4	chr7D.!!$R3	2491
5	TraesCS7A01G114900	chr7D	54596954	54598221	1267	True	474.000000	538	84.177333	815	3193	3	chr7D.!!$R2	2378
6	TraesCS7A01G114900	chr7D	55086841	55088155	1314	True	421.333333	529	85.770000	811	3200	3	chr7D.!!$R4	2389

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
800	2561	0.257039	GGTCTCAGTGGGCCATGAAT	59.743	55.0	10.7	0.0	0.0	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2740	5834	0.98124	CGCGCGTGCACAATTATTTT	59.019	45.0	24.19	0.0	42.97	1.82	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
47	48	2.435059	GACTTGAGCTGGGCCGTC	60.435	66.667	0.00	0.00	0.00	4.79
74	75	2.207229	CCCATCTATGCCGACGGGA	61.207	63.158	17.22	14.58	38.70	5.14
99	100	2.469516	GGCATAGGTTTGGCCGTCG	61.470	63.158	0.00	0.00	43.70	5.12
116	117	4.456806	GGCATCGCCGGTTATTCT	57.543	55.556	1.90	0.00	39.62	2.40
260	2016	2.104170	GGGGGAAAACAACTTGTGACA	58.896	47.619	0.00	0.00	0.00	3.58
274	2030	4.396166	ACTTGTGACAGAAAACCTTCACAG	59.604	41.667	3.71	2.26	46.69	3.66
278	2034	4.394920	GTGACAGAAAACCTTCACAGAACA	59.605	41.667	0.00	0.00	38.60	3.18
324	2080	5.452078	TTCATCACAAGGGTTTTCATCAC	57.548	39.130	0.00	0.00	0.00	3.06
429	2185	3.374042	TCTTTGTTTGTGAGGGGAACA	57.626	42.857	0.00	0.00	0.00	3.18
436	2192	1.961793	TGTGAGGGGAACAAACGAAG	58.038	50.000	0.00	0.00	0.00	3.79
578	2335	6.667414	AGGGGTTGTATAAATGCAAATTCTGA	59.333	34.615	0.00	0.00	34.26	3.27
744	2505	9.453572	AGATTTGAGCACACAAGATAAATAGAA	57.546	29.630	0.00	0.00	0.00	2.10
790	2551	3.181367	GCAATGGCGGTCTCAGTG	58.819	61.111	0.00	0.00	33.90	3.66
791	2552	2.401766	GCAATGGCGGTCTCAGTGG	61.402	63.158	0.00	0.00	31.76	4.00
793	2554	3.628646	AATGGCGGTCTCAGTGGGC	62.629	63.158	0.00	0.00	0.00	5.36
796	2557	4.101448	GCGGTCTCAGTGGGCCAT	62.101	66.667	10.70	0.00	0.00	4.40
797	2558	2.124983	CGGTCTCAGTGGGCCATG	60.125	66.667	10.70	9.60	0.00	3.66
800	2561	0.257039	GGTCTCAGTGGGCCATGAAT	59.743	55.000	10.70	0.00	0.00	2.57
801	2562	1.490490	GGTCTCAGTGGGCCATGAATA	59.510	52.381	10.70	3.37	0.00	1.75
802	2563	2.107204	GGTCTCAGTGGGCCATGAATAT	59.893	50.000	10.70	0.00	0.00	1.28
804	2565	4.202461	GGTCTCAGTGGGCCATGAATATAA	60.202	45.833	10.70	0.00	0.00	0.98
953	2859	4.015406	CCTGCACCCGCACTACCA	62.015	66.667	0.00	0.00	45.36	3.25
957	2863	2.652095	GCACCCGCACTACCACCTA	61.652	63.158	0.00	0.00	38.36	3.08
958	2864	1.976898	CACCCGCACTACCACCTAA	59.023	57.895	0.00	0.00	0.00	2.69
1103	3009	1.299541	GCTGCTATGTTGCGGTATGT	58.700	50.000	0.00	0.00	41.12	2.29
1111	3017	1.346395	TGTTGCGGTATGTCAACCTCT	59.654	47.619	0.00	0.00	41.21	3.69
1429	3422	1.281656	CCTGGCGTCGAACCAAAAC	59.718	57.895	9.53	0.00	36.56	2.43
1650	3661	3.715628	AGAAGAACGTTTTGCTTGCAT	57.284	38.095	0.46	0.00	0.00	3.96
1685	3696	2.125350	GAGCGAAGGCCAGTGGAG	60.125	66.667	15.20	0.00	41.24	3.86
2033	4054	3.130633	GCTTGTCCAATGGTCCAAAAAC	58.869	45.455	0.00	0.00	0.00	2.43
2149	4171	4.749598	CCTGCACATACTAATGCGATTGTA	59.250	41.667	0.00	0.00	45.13	2.41
2297	5374	3.696548	GGAAGGTTGGATGAAAGGATGAC	59.303	47.826	0.00	0.00	0.00	3.06
2490	5584	2.027625	GCACGTCCCTCCAGTTTCG	61.028	63.158	0.00	0.00	0.00	3.46
2740	5834	0.586319	CTTGCTCCGAGCGAAAACAA	59.414	50.000	15.58	2.47	46.26	2.83
2857	5951	1.619827	CCAGATGATCTCCTGCTCCTC	59.380	57.143	0.00	0.00	0.00	3.71
3053	6147	3.000819	TCCCCGACGATTGCTGGT	61.001	61.111	0.00	0.00	0.00	4.00
3133	6227	0.894184	TCTTGAACGCTCTCTCCGGT	60.894	55.000	0.00	0.00	0.00	5.28

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
12	13	0.445043	TCGTCGGCGTATATCCATCG	59.555	55.000	10.18	0.00	39.49	3.84
99	100	1.507141	CCAGAATAACCGGCGATGCC	61.507	60.000	9.30	0.00	46.75	4.40
116	117	1.746322	TTCGACGGGTTGCACTACCA	61.746	55.000	9.74	0.00	40.09	3.25
205	206	0.238289	GGTGCATTGGTGACGTTCTG	59.762	55.000	0.00	0.00	0.00	3.02
238	1994	2.698274	GTCACAAGTTGTTTTCCCCCAT	59.302	45.455	5.57	0.00	0.00	4.00
260	2016	5.946377	AGAACTTGTTCTGTGAAGGTTTTCT	59.054	36.000	14.36	0.00	34.31	2.52
305	2061	4.728772	TCTGTGATGAAAACCCTTGTGAT	58.271	39.130	0.00	0.00	0.00	3.06
324	2080	5.961843	CACTACAAAAATCTGCGCTAATCTG	59.038	40.000	9.73	0.00	0.00	2.90
436	2192	0.595310	GCCACGCCGAAGATCTAGTC	60.595	60.000	0.00	0.00	0.00	2.59
478	2235	3.498774	ATATTCATGGCCCACTGAGAC	57.501	47.619	0.00	0.00	0.00	3.36
578	2335	5.726980	TCTTGAAGCTACATGGCAAAATT	57.273	34.783	0.00	0.00	34.17	1.82
636	2397	1.134401	AGGTGATTGTATGCCCAGACG	60.134	52.381	0.00	0.00	0.00	4.18
744	2505	8.050930	TCCTTTTTAAACAAGTCTACCTGTCTT	58.949	33.333	0.00	0.00	0.00	3.01
784	2545	4.978099	AGTTATATTCATGGCCCACTGAG	58.022	43.478	0.00	0.00	0.00	3.35
786	2547	4.978099	AGAGTTATATTCATGGCCCACTG	58.022	43.478	0.00	0.00	0.00	3.66
788	2549	4.520492	CCAAGAGTTATATTCATGGCCCAC	59.480	45.833	0.00	0.00	0.00	4.61
789	2550	4.415179	TCCAAGAGTTATATTCATGGCCCA	59.585	41.667	0.00	0.00	34.32	5.36
790	2551	4.762251	GTCCAAGAGTTATATTCATGGCCC	59.238	45.833	0.00	0.00	34.32	5.80
791	2552	4.762251	GGTCCAAGAGTTATATTCATGGCC	59.238	45.833	0.00	0.00	34.32	5.36
793	2554	4.452455	GCGGTCCAAGAGTTATATTCATGG	59.548	45.833	0.00	3.74	35.33	3.66
795	2556	4.202223	ACGCGGTCCAAGAGTTATATTCAT	60.202	41.667	12.47	0.00	0.00	2.57
796	2557	3.131577	ACGCGGTCCAAGAGTTATATTCA	59.868	43.478	12.47	0.00	0.00	2.57
797	2558	3.714391	ACGCGGTCCAAGAGTTATATTC	58.286	45.455	12.47	0.00	0.00	1.75
800	2561	2.857592	GACGCGGTCCAAGAGTTATA	57.142	50.000	12.47	0.00	0.00	0.98
801	2562	3.735181	GACGCGGTCCAAGAGTTAT	57.265	52.632	12.47	0.00	0.00	1.89
953	2859	1.288335	AGTCATCGGGGAGACTTAGGT	59.712	52.381	0.00	0.00	42.12	3.08
957	2863	0.616111	AGCAGTCATCGGGGAGACTT	60.616	55.000	0.00	0.00	42.87	3.01
958	2864	1.000993	AGCAGTCATCGGGGAGACT	59.999	57.895	0.00	0.00	45.46	3.24
1103	3009	0.250295	CTTTCGGTGCCAGAGGTTGA	60.250	55.000	0.00	0.00	0.00	3.18
1429	3422	0.802494	AAATCTAAACCGCACCGCAG	59.198	50.000	0.00	0.00	0.00	5.18
1641	3652	1.180456	CCTCCCACACATGCAAGCAA	61.180	55.000	0.00	0.00	0.00	3.91
1650	3661	1.126948	TCATGTCTGCCTCCCACACA	61.127	55.000	0.00	0.00	0.00	3.72
1685	3696	2.180159	TAGGCTGCCGTCCAACTTCC	62.180	60.000	13.96	0.00	0.00	3.46
1987	4003	8.947115	GCAATTAGGAATACAACTACTTGAACT	58.053	33.333	0.00	0.00	33.96	3.01
2108	4130	3.727970	GCAGGTAAATCACAAGCTAACGC	60.728	47.826	0.00	0.00	0.00	4.84
2297	5374	5.611796	TCCATGTTTCATTGTTCTTCTCG	57.388	39.130	0.00	0.00	0.00	4.04
2440	5530	5.970140	TTACTGAAACGAAACACATCGAA	57.030	34.783	3.47	0.00	45.48	3.71
2490	5584	7.849804	TTCTAACAAAATGAGTCCAGCTATC	57.150	36.000	0.00	0.00	0.00	2.08
2740	5834	0.981240	CGCGCGTGCACAATTATTTT	59.019	45.000	24.19	0.00	42.97	1.82

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.