AutoCloner

Multiple sequence alignment - TraesCS7D01G110100

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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	TraesCS7D01G110100	chr7D	100.000	2315	0	0	1	2315	66512516	66514830	0.000000e+00	4276.0
1	TraesCS7D01G110100	chr7D	92.584	445	22	5	1871	2315	68804538	68804105	1.510000e-176	628.0
2	TraesCS7D01G110100	chr7D	84.307	599	56	12	1666	2259	68923016	68922451	3.360000e-153	551.0
3	TraesCS7D01G110100	chr7D	80.168	832	70	39	971	1746	66484759	66485551	3.390000e-148	534.0
4	TraesCS7D01G110100	chr7D	85.316	538	41	12	971	1487	68935168	68934648	2.640000e-144	521.0
5	TraesCS7D01G110100	chr7D	82.406	557	45	22	872	1411	68806091	68805571	9.820000e-119	436.0
6	TraesCS7D01G110100	chr7D	89.851	335	23	7	998	1325	68914053	68913723	9.890000e-114	420.0
7	TraesCS7D01G110100	chr7D	83.795	469	41	22	815	1253	68924369	68923906	1.660000e-111	412.0
8	TraesCS7D01G110100	chr7D	84.588	279	36	5	1666	1940	68911531	68911256	1.050000e-68	270.0
9	TraesCS7D01G110100	chr7D	92.784	97	7	0	776	872	66484525	66484621	8.620000e-30	141.0
10	TraesCS7D01G110100	chr5D	94.987	758	27	5	2	752	36487307	36488060	0.000000e+00	1179.0
11	TraesCS7D01G110100	chr2B	94.875	761	28	4	2	755	25740812	25740056	0.000000e+00	1179.0
12	TraesCS7D01G110100	chr1B	94.980	757	28	3	2	751	490456513	490455760	0.000000e+00	1179.0
13	TraesCS7D01G110100	chr1B	94.612	761	31	3	2	755	185229021	185228264	0.000000e+00	1170.0
14	TraesCS7D01G110100	chr1B	94.591	758	28	3	2	752	636032783	636032032	0.000000e+00	1160.0
15	TraesCS7D01G110100	chr1B	80.847	1086	79	57	998	2046	678112521	678113514	0.000000e+00	734.0
16	TraesCS7D01G110100	chr1B	94.737	57	3	0	816	872	678107525	678107581	3.170000e-14	89.8
17	TraesCS7D01G110100	chr4A	94.641	765	30	4	2	759	583935072	583935832	0.000000e+00	1175.0
18	TraesCS7D01G110100	chr5B	94.730	759	30	3	2	753	115906169	115905414	0.000000e+00	1171.0
19	TraesCS7D01G110100	chr3B	94.848	757	28	5	2	751	537418991	537418239	0.000000e+00	1171.0
20	TraesCS7D01G110100	chr2D	94.481	761	31	6	2	754	621668631	621667874	0.000000e+00	1162.0
21	TraesCS7D01G110100	chr1D	80.547	1316	109	62	816	2061	486922273	486923511	0.000000e+00	876.0
22	TraesCS7D01G110100	chr7A	90.862	580	38	7	1739	2315	74604477	74603910	0.000000e+00	763.0
23	TraesCS7D01G110100	chr7A	85.940	633	39	18	971	1578	74610798	74610191	4.200000e-177	630.0
24	TraesCS7D01G110100	chr7A	84.743	662	40	26	815	1434	70893990	70894632	7.070000e-170	606.0
25	TraesCS7D01G110100	chr7A	89.452	493	35	9	1700	2190	71119723	71120200	7.070000e-170	606.0
26	TraesCS7D01G110100	chr7A	84.601	526	52	15	810	1319	71118517	71119029	1.600000e-136	496.0
27	TraesCS7D01G110100	chr7A	88.378	370	21	5	971	1325	74596500	74596138	2.130000e-115	425.0
28	TraesCS7D01G110100	chr7A	82.294	497	40	18	996	1483	71110261	71110718	1.000000e-103	387.0
29	TraesCS7D01G110100	chr7A	95.480	177	8	0	1665	1841	74608659	74608483	1.350000e-72	283.0
30	TraesCS7D01G110100	chr7A	84.733	262	30	7	1666	1920	74595412	74595154	1.060000e-63	254.0
31	TraesCS7D01G110100	chr7B	91.051	514	33	5	1806	2315	9814629	9814125	0.000000e+00	682.0
32	TraesCS7D01G110100	chr7B	84.946	651	50	14	1666	2315	10104874	10104271	1.180000e-172	616.0
33	TraesCS7D01G110100	chr7B	85.045	448	45	16	971	1408	7727881	7728316	9.820000e-119	436.0
34	TraesCS7D01G110100	chr7B	86.579	380	38	7	952	1325	10174975	10174603	7.700000e-110	407.0
35	TraesCS7D01G110100	chr7B	90.000	300	24	2	971	1270	10241548	10241255	1.300000e-102	383.0
36	TraesCS7D01G110100	chr7B	85.028	354	42	8	1690	2035	7558545	7558895	1.320000e-92	350.0
37	TraesCS7D01G110100	chr7B	94.350	177	10	0	1665	1841	10240919	10240743	2.930000e-69	272.0
38	TraesCS7D01G110100	chr7B	92.784	97	5	1	776	872	10235062	10234968	3.100000e-29	139.0
39	TraesCS7D01G110100	chr7B	76.412	301	25	23	1368	1667	10241197	10240942	1.120000e-23	121.0
40	TraesCS7D01G110100	chr7B	93.548	62	4	0	811	872	10241776	10241715	2.450000e-15	93.5
41	TraesCS7D01G110100	chr7B	94.828	58	3	0	815	872	8445979	8446036	8.810000e-15	91.6
42	TraesCS7D01G110100	chr7B	93.750	48	3	0	824	871	10190834	10190787	3.190000e-09	73.1

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	TraesCS7D01G110100	chr7D	66512516	66514830	2314	False	4276.000	4276	100.0000	1	2315	1	chr7D.!!$F1	2314
1	TraesCS7D01G110100	chr7D	68804105	68806091	1986	True	532.000	628	87.4950	872	2315	2	chr7D.!!$R2	1443
2	TraesCS7D01G110100	chr7D	68934648	68935168	520	True	521.000	521	85.3160	971	1487	1	chr7D.!!$R1	516
3	TraesCS7D01G110100	chr7D	68922451	68924369	1918	True	481.500	551	84.0510	815	2259	2	chr7D.!!$R4	1444
4	TraesCS7D01G110100	chr7D	68911256	68914053	2797	True	345.000	420	87.2195	998	1940	2	chr7D.!!$R3	942
5	TraesCS7D01G110100	chr7D	66484525	66485551	1026	False	337.500	534	86.4760	776	1746	2	chr7D.!!$F2	970
6	TraesCS7D01G110100	chr5D	36487307	36488060	753	False	1179.000	1179	94.9870	2	752	1	chr5D.!!$F1	750
7	TraesCS7D01G110100	chr2B	25740056	25740812	756	True	1179.000	1179	94.8750	2	755	1	chr2B.!!$R1	753
8	TraesCS7D01G110100	chr1B	490455760	490456513	753	True	1179.000	1179	94.9800	2	751	1	chr1B.!!$R2	749
9	TraesCS7D01G110100	chr1B	185228264	185229021	757	True	1170.000	1170	94.6120	2	755	1	chr1B.!!$R1	753
10	TraesCS7D01G110100	chr1B	636032032	636032783	751	True	1160.000	1160	94.5910	2	752	1	chr1B.!!$R3	750
11	TraesCS7D01G110100	chr1B	678112521	678113514	993	False	734.000	734	80.8470	998	2046	1	chr1B.!!$F2	1048
12	TraesCS7D01G110100	chr4A	583935072	583935832	760	False	1175.000	1175	94.6410	2	759	1	chr4A.!!$F1	757
13	TraesCS7D01G110100	chr5B	115905414	115906169	755	True	1171.000	1171	94.7300	2	753	1	chr5B.!!$R1	751
14	TraesCS7D01G110100	chr3B	537418239	537418991	752	True	1171.000	1171	94.8480	2	751	1	chr3B.!!$R1	749
15	TraesCS7D01G110100	chr2D	621667874	621668631	757	True	1162.000	1162	94.4810	2	754	1	chr2D.!!$R1	752
16	TraesCS7D01G110100	chr1D	486922273	486923511	1238	False	876.000	876	80.5470	816	2061	1	chr1D.!!$F1	1245
17	TraesCS7D01G110100	chr7A	74603910	74604477	567	True	763.000	763	90.8620	1739	2315	1	chr7A.!!$R1	576
18	TraesCS7D01G110100	chr7A	70893990	70894632	642	False	606.000	606	84.7430	815	1434	1	chr7A.!!$F1	619
19	TraesCS7D01G110100	chr7A	71118517	71120200	1683	False	551.000	606	87.0265	810	2190	2	chr7A.!!$F3	1380
20	TraesCS7D01G110100	chr7A	74608483	74610798	2315	True	456.500	630	90.7100	971	1841	2	chr7A.!!$R3	870
21	TraesCS7D01G110100	chr7A	74595154	74596500	1346	True	339.500	425	86.5555	971	1920	2	chr7A.!!$R2	949
22	TraesCS7D01G110100	chr7B	9814125	9814629	504	True	682.000	682	91.0510	1806	2315	1	chr7B.!!$R1	509
23	TraesCS7D01G110100	chr7B	10104271	10104874	603	True	616.000	616	84.9460	1666	2315	1	chr7B.!!$R2	649
24	TraesCS7D01G110100	chr7B	10240743	10241776	1033	True	217.375	383	88.5775	811	1841	4	chr7B.!!$R6	1030

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
866	877	0.29782	CGACTCGTTAATGGCTTCGC	59.702	55.0	0.0	0.0	0.0	4.7	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1861	5757	2.969238	CCGGATGTCGATGCAGCC	60.969	66.667	0.0	0.39	42.43	4.85	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
47	48	2.266055	GGTTGAGGGAGACGCTGG	59.734	66.667	0.00	0.00	0.00	4.85
173	174	2.328639	GATCTCGTCGAGGTCGCC	59.671	66.667	19.18	0.00	39.60	5.54
478	486	4.478371	CATGCCCTCTCAGCGCCA	62.478	66.667	2.29	0.00	0.00	5.69
619	627	1.613630	ACACAGGGCTCCGGAGATT	60.614	57.895	35.69	15.95	0.00	2.40
647	655	6.436738	TGTGTTATGGTTGTCTTAGGGTAA	57.563	37.500	0.00	0.00	0.00	2.85
671	679	4.841813	TCTAGGTGTTCATGGTCCTTTGTA	59.158	41.667	0.00	0.00	0.00	2.41
699	707	4.034048	CGTTTCAGTGTGCTTGTAAGAGTT	59.966	41.667	0.00	0.00	0.00	3.01
701	709	6.073765	CGTTTCAGTGTGCTTGTAAGAGTTAT	60.074	38.462	0.00	0.00	0.00	1.89
702	710	7.518370	CGTTTCAGTGTGCTTGTAAGAGTTATT	60.518	37.037	0.00	0.00	0.00	1.40
703	711	8.770828	GTTTCAGTGTGCTTGTAAGAGTTATTA	58.229	33.333	0.00	0.00	0.00	0.98
704	712	8.896320	TTCAGTGTGCTTGTAAGAGTTATTAA	57.104	30.769	0.00	0.00	0.00	1.40
791	802	3.492102	AAATCAGCCACCTATGCGTAT	57.508	42.857	0.00	0.00	0.00	3.06
866	877	0.297820	CGACTCGTTAATGGCTTCGC	59.702	55.000	0.00	0.00	0.00	4.70
890	919	2.992114	AAGAGGAGCCGCAGTCGT	60.992	61.111	0.00	0.00	0.00	4.34
895	924	2.881352	GAGCCGCAGTCGTAGTGC	60.881	66.667	0.00	5.04	41.02	4.40
896	925	4.436998	AGCCGCAGTCGTAGTGCC	62.437	66.667	8.47	0.00	41.38	5.01
897	926	4.436998	GCCGCAGTCGTAGTGCCT	62.437	66.667	8.47	0.00	41.38	4.75
900	932	2.202623	GCAGTCGTAGTGCCTCGG	60.203	66.667	4.03	0.00	38.58	4.63
953	993	1.268113	CCAACACACATCGCGTTTGC	61.268	55.000	5.77	0.00	37.91	3.68
958	998	1.163420	ACACATCGCGTTTGCCTGAA	61.163	50.000	5.77	0.00	38.08	3.02
969	1039	1.826340	TTGCCTGAACCTAGCTGCGA	61.826	55.000	0.00	0.00	0.00	5.10
986	1056	2.046892	ACTGCGATCTGGTGGTGC	60.047	61.111	0.00	0.00	0.00	5.01
991	1081	1.226802	CGATCTGGTGGTGCTCGAG	60.227	63.158	8.45	8.45	0.00	4.04
992	1082	1.657751	CGATCTGGTGGTGCTCGAGA	61.658	60.000	18.75	0.00	0.00	4.04
994	1084	1.137872	GATCTGGTGGTGCTCGAGAAT	59.862	52.381	18.75	0.00	0.00	2.40

Showing 1 to 25 of 57 entries

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Show entries

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Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
12	13	0.248289	CCCTAACCCTACCACACACG	59.752	60.000	0.00	0.00	4.49
173	174	1.153168	CCTCCAACCACCATAGCCG	60.153	63.158	0.00	0.00	5.52
208	209	1.202855	CGCCCATCTGAGGATCCAAAT	60.203	52.381	15.82	0.00	2.32
477	485	2.810852	GCTTCCTCCTTTCTTGACACTG	59.189	50.000	0.00	0.00	3.66
478	486	2.439507	TGCTTCCTCCTTTCTTGACACT	59.560	45.455	0.00	0.00	3.55
619	627	6.488683	CCCTAAGACAACCATAACACAAGAAA	59.511	38.462	0.00	0.00	2.52
647	655	4.289672	ACAAAGGACCATGAACACCTAGAT	59.710	41.667	0.00	32.06	1.98
671	679	2.159254	ACAAGCACACTGAAACGCAAAT	60.159	40.909	0.00	0.00	2.32
701	709	9.701098	AATCACGAATCAGTACAAAGTAGTTAA	57.299	29.630	0.00	0.00	2.01
702	710	9.701098	AAATCACGAATCAGTACAAAGTAGTTA	57.299	29.630	0.00	0.00	2.24
703	711	8.495949	CAAATCACGAATCAGTACAAAGTAGTT	58.504	33.333	0.00	0.00	2.24
704	712	7.870954	TCAAATCACGAATCAGTACAAAGTAGT	59.129	33.333	0.00	0.00	2.73
769	780	2.446435	ACGCATAGGTGGCTGATTTTT	58.554	42.857	0.00	0.00	1.94
770	781	2.128771	ACGCATAGGTGGCTGATTTT	57.871	45.000	0.00	0.00	1.82
771	782	3.403038	GATACGCATAGGTGGCTGATTT	58.597	45.455	0.00	0.00	2.17
772	783	2.289694	GGATACGCATAGGTGGCTGATT	60.290	50.000	0.00	0.00	2.57
773	784	1.276421	GGATACGCATAGGTGGCTGAT	59.724	52.381	0.00	0.00	2.90
774	785	0.679505	GGATACGCATAGGTGGCTGA	59.320	55.000	0.00	0.00	4.26
781	792	1.079819	CGCCTGGGATACGCATAGG	60.080	63.158	0.00	37.60	2.57
783	794	1.532078	TCCGCCTGGGATACGCATA	60.532	57.895	0.00	40.94	3.14
791	802	1.152735	CTAGCTAGTCCGCCTGGGA	60.153	63.158	12.92	44.68	4.37
866	877	2.507992	CGGCTCCTCTTCGTGCAG	60.508	66.667	0.00	0.00	4.41
890	919	1.640917	AAAGGTTCTCCGAGGCACTA	58.359	50.000	0.00	41.55	2.74
895	924	4.120589	GTGCTTATAAAGGTTCTCCGAGG	58.879	47.826	0.00	39.05	4.63
896	925	3.797256	CGTGCTTATAAAGGTTCTCCGAG	59.203	47.826	0.00	39.05	4.63

Showing 1 to 25 of 73 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.