AutoCloner

Multiple sequence alignment - TraesCS7D01G381500

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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	TraesCS7D01G381500	chr7D	100.000	2675	0	0	1	2675	495705552	495702878	0.000000e+00	4940.0
1	TraesCS7D01G381500	chr7D	95.996	974	37	2	1704	2675	7942658	7943631	0.000000e+00	1581.0
2	TraesCS7D01G381500	chr7D	93.452	733	39	9	1948	2675	25387739	25388467	0.000000e+00	1079.0
3	TraesCS7D01G381500	chr7D	93.296	179	4	5	1747	1924	434903968	434903797	9.500000e-65	257.0
4	TraesCS7D01G381500	chr7D	77.570	107	20	3	1025	1129	412184393	412184497	8.000000e-06	62.1
5	TraesCS7D01G381500	chr7B	94.022	987	36	15	719	1696	524037238	524036266	0.000000e+00	1474.0
6	TraesCS7D01G381500	chr7B	88.191	398	15	13	235	622	524037760	524037385	1.890000e-121	446.0
7	TraesCS7D01G381500	chr7B	92.181	243	10	2	4	237	524038060	524037818	4.270000e-88	335.0
8	TraesCS7D01G381500	chr7B	97.436	39	1	0	1091	1129	636630293	636630255	1.720000e-07	67.6
9	TraesCS7D01G381500	chr7B	79.121	91	15	4	1178	1266	600965070	600964982	2.880000e-05	60.2
10	TraesCS7D01G381500	chr6D	91.122	980	69	8	1707	2672	466654682	466655657	0.000000e+00	1312.0
11	TraesCS7D01G381500	chr6D	93.296	179	8	3	1747	1924	5419045	5419220	7.350000e-66	261.0
12	TraesCS7D01G381500	chr6B	90.216	971	74	6	1707	2660	711883519	711884485	0.000000e+00	1247.0
13	TraesCS7D01G381500	chr6B	93.304	224	13	1	1707	1928	2218983	2218760	1.990000e-86	329.0
14	TraesCS7D01G381500	chr1D	89.397	962	71	13	1736	2675	408557894	408558846	0.000000e+00	1182.0
15	TraesCS7D01G381500	chr1D	90.769	195	11	7	1736	1925	408565972	408566164	1.230000e-63	254.0
16	TraesCS7D01G381500	chr2D	94.521	730	35	5	1948	2674	108919625	108918898	0.000000e+00	1122.0
17	TraesCS7D01G381500	chr7A	89.422	917	44	14	805	1706	561584148	561583270	0.000000e+00	1107.0
18	TraesCS7D01G381500	chr7A	86.355	557	43	18	235	770	561584693	561584149	6.420000e-161	577.0
19	TraesCS7D01G381500	chr7A	89.714	175	8	5	73	237	561584898	561584724	5.800000e-52	215.0
20	TraesCS7D01G381500	chr7A	78.022	91	16	4	1178	1266	640550634	640550546	1.000000e-03	54.7
21	TraesCS7D01G381500	chr5A	93.793	725	40	5	1953	2675	603388414	603389135	0.000000e+00	1085.0
22	TraesCS7D01G381500	chr5A	93.443	732	39	8	1948	2675	265330596	265329870	0.000000e+00	1077.0
23	TraesCS7D01G381500	chr5A	87.008	508	44	8	1736	2223	24128638	24128133	1.080000e-153	553.0
24	TraesCS7D01G381500	chr5A	80.597	335	55	3	1195	1528	526396179	526396504	1.590000e-62	250.0
25	TraesCS7D01G381500	chr3D	93.141	729	48	2	1948	2675	477633912	477634639	0.000000e+00	1068.0
26	TraesCS7D01G381500	chr3D	92.916	734	46	5	1948	2675	66881649	66882382	0.000000e+00	1062.0
27	TraesCS7D01G381500	chr5B	93.194	720	45	4	1958	2675	375232192	375231475	0.000000e+00	1055.0
28	TraesCS7D01G381500	chr5B	81.194	335	53	5	1195	1528	498882503	498882828	7.350000e-66	261.0
29	TraesCS7D01G381500	chr5B	86.979	192	19	5	1010	1198	498879053	498879241	7.500000e-51	211.0
30	TraesCS7D01G381500	chr5B	97.436	39	1	0	1091	1129	112256864	112256826	1.720000e-07	67.6
31	TraesCS7D01G381500	chr5D	79.701	335	58	5	1195	1528	413700643	413700968	1.600000e-57	233.0
32	TraesCS7D01G381500	chr5D	86.979	192	19	5	1010	1198	413698368	413698556	7.500000e-51	211.0
33	TraesCS7D01G381500	chr2B	97.436	39	1	0	1091	1129	39749180	39749142	1.720000e-07	67.6
34	TraesCS7D01G381500	chr1B	97.436	39	1	0	1091	1129	322471446	322471408	1.720000e-07	67.6

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	TraesCS7D01G381500	chr7D	495702878	495705552	2674	True	4940.000000	4940	100.000000	1	2675	1	chr7D.!!$R2	2674
1	TraesCS7D01G381500	chr7D	7942658	7943631	973	False	1581.000000	1581	95.996000	1704	2675	1	chr7D.!!$F1	971
2	TraesCS7D01G381500	chr7D	25387739	25388467	728	False	1079.000000	1079	93.452000	1948	2675	1	chr7D.!!$F2	727
3	TraesCS7D01G381500	chr7B	524036266	524038060	1794	True	751.666667	1474	91.464667	4	1696	3	chr7B.!!$R3	1692
4	TraesCS7D01G381500	chr6D	466654682	466655657	975	False	1312.000000	1312	91.122000	1707	2672	1	chr6D.!!$F2	965
5	TraesCS7D01G381500	chr6B	711883519	711884485	966	False	1247.000000	1247	90.216000	1707	2660	1	chr6B.!!$F1	953
6	TraesCS7D01G381500	chr1D	408557894	408558846	952	False	1182.000000	1182	89.397000	1736	2675	1	chr1D.!!$F1	939
7	TraesCS7D01G381500	chr2D	108918898	108919625	727	True	1122.000000	1122	94.521000	1948	2674	1	chr2D.!!$R1	726
8	TraesCS7D01G381500	chr7A	561583270	561584898	1628	True	633.000000	1107	88.497000	73	1706	3	chr7A.!!$R2	1633
9	TraesCS7D01G381500	chr5A	603388414	603389135	721	False	1085.000000	1085	93.793000	1953	2675	1	chr5A.!!$F2	722
10	TraesCS7D01G381500	chr5A	265329870	265330596	726	True	1077.000000	1077	93.443000	1948	2675	1	chr5A.!!$R2	727
11	TraesCS7D01G381500	chr5A	24128133	24128638	505	True	553.000000	553	87.008000	1736	2223	1	chr5A.!!$R1	487
12	TraesCS7D01G381500	chr3D	477633912	477634639	727	False	1068.000000	1068	93.141000	1948	2675	1	chr3D.!!$F2	727
13	TraesCS7D01G381500	chr3D	66881649	66882382	733	False	1062.000000	1062	92.916000	1948	2675	1	chr3D.!!$F1	727
14	TraesCS7D01G381500	chr5B	375231475	375232192	717	True	1055.000000	1055	93.194000	1958	2675	1	chr5B.!!$R2	717
15	TraesCS7D01G381500	chr5B	498879053	498882828	3775	False	236.000000	261	84.086500	1010	1528	2	chr5B.!!$F1	518
16	TraesCS7D01G381500	chr5D	413698368	413700968	2600	False	222.000000	233	83.340000	1010	1528	2	chr5D.!!$F1	518

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
781	943	0.318441	TATAGTGGGAGCAGCGATGC	59.682	55.0	19.88	19.88	0.0	3.91	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2017	5682	1.151908	CCCACCGGGTTTGAAGGAA	59.848	57.895	6.32	0.0	38.25	3.36	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
24	25	0.664166	GTTGTGGCTTGGACGCAATG	60.664	55.000	2.67	0.00	43.17	2.82
147	166	3.576861	AGACGTAATCCATCCATCTCCA	58.423	45.455	0.00	0.00	0.00	3.86
257	343	0.981183	TAATCCTCAACTGCCGTGGT	59.019	50.000	0.00	0.00	0.00	4.16
272	358	5.538118	TGCCGTGGTTCTATATATTCTGTG	58.462	41.667	0.00	0.00	0.00	3.66
330	420	2.815503	TCACCGTCGATTCTTCTGTGTA	59.184	45.455	0.00	0.00	0.00	2.90
331	421	3.253921	TCACCGTCGATTCTTCTGTGTAA	59.746	43.478	0.00	0.00	0.00	2.41
332	422	3.608506	CACCGTCGATTCTTCTGTGTAAG	59.391	47.826	0.00	0.00	0.00	2.34
333	423	3.255149	ACCGTCGATTCTTCTGTGTAAGT	59.745	43.478	0.00	0.00	0.00	2.24
336	426	5.512082	CCGTCGATTCTTCTGTGTAAGTAAG	59.488	44.000	0.00	0.00	0.00	2.34
338	428	5.288952	GTCGATTCTTCTGTGTAAGTAAGGC	59.711	44.000	0.00	0.00	0.00	4.35
355	449	3.939740	AGGCATGATGAACACATAGGT	57.060	42.857	0.00	0.00	0.00	3.08
356	450	4.240881	AGGCATGATGAACACATAGGTT	57.759	40.909	0.00	0.00	0.00	3.50
376	470	2.100631	GGAATGGAGTGGACACGCG	61.101	63.158	3.53	3.53	36.20	6.01
394	488	1.976474	GCGGATGGCCTTTTGTGGA	60.976	57.895	3.32	0.00	34.80	4.02
401	495	2.402564	TGGCCTTTTGTGGATTTGGAA	58.597	42.857	3.32	0.00	0.00	3.53
402	496	2.978278	TGGCCTTTTGTGGATTTGGAAT	59.022	40.909	3.32	0.00	0.00	3.01
403	497	4.163427	TGGCCTTTTGTGGATTTGGAATA	58.837	39.130	3.32	0.00	0.00	1.75
404	498	4.782156	TGGCCTTTTGTGGATTTGGAATAT	59.218	37.500	3.32	0.00	0.00	1.28
408	502	8.646900	GGCCTTTTGTGGATTTGGAATATATAA	58.353	33.333	0.00	0.00	0.00	0.98
458	552	2.853003	GACGATCGACTTTCTGCCTAAC	59.147	50.000	24.34	0.00	0.00	2.34
580	677	2.113243	AAAGAGAAAGGCGCCGGAGT	62.113	55.000	23.20	7.56	0.00	3.85
591	688	2.575993	CCGGAGTCAGGCAGTCAG	59.424	66.667	0.00	0.00	0.00	3.51
592	689	2.125753	CGGAGTCAGGCAGTCAGC	60.126	66.667	0.00	0.00	44.65	4.26
634	754	2.565834	ACCTGTACGTAAGCAGTTGGAT	59.434	45.455	11.09	0.00	45.62	3.41
642	762	5.833082	ACGTAAGCAGTTGGATATCACTAG	58.167	41.667	4.83	0.00	45.62	2.57
643	763	4.681942	CGTAAGCAGTTGGATATCACTAGC	59.318	45.833	4.83	7.14	0.00	3.42
667	787	5.448632	CGGCTATAATGAACCAAGAACAACC	60.449	44.000	0.00	0.00	0.00	3.77
676	805	2.884639	ACCAAGAACAACCCTTTGATCG	59.115	45.455	0.00	0.00	39.05	3.69
695	824	4.746535	TCGTGTAGAATTGGCAGGATAA	57.253	40.909	0.00	0.00	0.00	1.75
696	825	4.693283	TCGTGTAGAATTGGCAGGATAAG	58.307	43.478	0.00	0.00	0.00	1.73
758	920	6.100279	TCAAATACTAGAAGCACCTCCATCAT	59.900	38.462	0.00	0.00	0.00	2.45
759	921	5.736951	ATACTAGAAGCACCTCCATCATC	57.263	43.478	0.00	0.00	0.00	2.92
769	931	4.562347	GCACCTCCATCATCACTATAGTGG	60.562	50.000	28.33	15.94	45.65	4.00
781	943	0.318441	TATAGTGGGAGCAGCGATGC	59.682	55.000	19.88	19.88	0.00	3.91
782	944	1.689243	ATAGTGGGAGCAGCGATGCA	61.689	55.000	29.24	5.05	37.25	3.96
783	945	2.302199	TAGTGGGAGCAGCGATGCAG	62.302	60.000	29.24	0.00	37.25	4.41
784	946	4.478371	TGGGAGCAGCGATGCAGG	62.478	66.667	29.24	0.00	37.25	4.85
785	947	4.479993	GGGAGCAGCGATGCAGGT	62.480	66.667	29.24	7.08	37.25	4.00
786	948	3.200593	GGAGCAGCGATGCAGGTG	61.201	66.667	29.24	0.00	42.04	4.00
986	1165	2.103042	GCTTGCGCTCAGACCGATT	61.103	57.895	9.73	0.00	0.00	3.34
991	1170	2.184322	GCTCAGACCGATTGCCGA	59.816	61.111	0.00	0.00	41.76	5.54
992	1171	2.167861	GCTCAGACCGATTGCCGAC	61.168	63.158	0.00	0.00	41.76	4.79
993	1172	1.519455	CTCAGACCGATTGCCGACC	60.519	63.158	0.00	0.00	41.76	4.79
1452	5092	1.135333	CAGGGGCTCTTCTTCTACGAC	59.865	57.143	0.00	0.00	0.00	4.34
1563	5203	2.125512	GCGAGAGGCAACGGTGAT	60.126	61.111	3.55	0.00	46.39	3.06
1614	5254	3.618150	GCATTTCTCTGTCTCAAGAGCTC	59.382	47.826	5.27	5.27	42.95	4.09
1668	5308	1.375098	GCAGGTGCTCTTCATGCTCC	61.375	60.000	0.00	0.00	42.44	4.70
1669	5309	2.694260	AGGTGCTCTTCATGCTCCT	58.306	52.632	3.85	3.85	45.88	3.69
1742	5383	4.734398	ACAAGAGAATAGGCACAGAGAG	57.266	45.455	0.00	0.00	0.00	3.20
1761	5405	6.866770	CAGAGAGGTAAATGAACAGTCGTTTA	59.133	38.462	0.00	0.00	41.99	2.01
1814	5460	0.918983	TTTGAGGGGATGCCACTAGG	59.081	55.000	5.30	0.00	37.42	3.02
2016	5681	8.677300	AGTATAGTGTTTGATATGTTGCCAAAG	58.323	33.333	0.00	0.00	31.40	2.77
2017	5682	5.789643	AGTGTTTGATATGTTGCCAAAGT	57.210	34.783	0.00	0.00	31.40	2.66
2202	5872	9.547753	GACATATGGTCTTGTGTTGATATTACT	57.452	33.333	7.80	0.00	43.46	2.24
2379	6052	5.778241	TGGAACATAGAAGTTGGTAGAGACA	59.222	40.000	0.00	0.00	0.00	3.41
2506	6180	4.640201	CGTTGAGATAATGGTTGGTGGATT	59.360	41.667	0.00	0.00	0.00	3.01
2597	6271	4.135306	GTCTACGATCTGACATAGTGGGA	58.865	47.826	0.00	0.00	33.75	4.37

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
3	4	1.444119	TTGCGTCCAAGCCACAACTC	61.444	55.000	0.00	0.00	36.02	3.01
4	5	0.823356	ATTGCGTCCAAGCCACAACT	60.823	50.000	0.00	0.00	33.80	3.16
7	8	0.608856	ATCATTGCGTCCAAGCCACA	60.609	50.000	0.00	0.00	33.80	4.17
8	9	0.099436	GATCATTGCGTCCAAGCCAC	59.901	55.000	0.00	0.00	33.80	5.01
9	10	1.368345	CGATCATTGCGTCCAAGCCA	61.368	55.000	0.00	0.00	33.80	4.75
57	62	4.394920	GCTATGCTTTACAACAAGGCAGTA	59.605	41.667	0.46	0.00	36.35	2.74
58	63	3.191371	GCTATGCTTTACAACAAGGCAGT	59.809	43.478	0.46	0.00	36.35	4.40
162	181	0.948623	TCACGTTGATTGGTCGGCTG	60.949	55.000	0.00	0.00	0.00	4.85
257	343	7.078249	ACATGTGGCCACAGAATATATAGAA	57.922	36.000	39.29	15.05	45.48	2.10
330	420	5.824624	CCTATGTGTTCATCATGCCTTACTT	59.175	40.000	0.00	0.00	35.70	2.24
331	421	5.104360	ACCTATGTGTTCATCATGCCTTACT	60.104	40.000	0.00	0.00	35.70	2.24
332	422	5.126067	ACCTATGTGTTCATCATGCCTTAC	58.874	41.667	0.00	0.00	35.70	2.34
333	423	5.372343	ACCTATGTGTTCATCATGCCTTA	57.628	39.130	0.00	0.00	35.70	2.69
336	426	4.516698	CCTAACCTATGTGTTCATCATGCC	59.483	45.833	0.00	0.00	35.70	4.40
338	428	7.040892	CCATTCCTAACCTATGTGTTCATCATG	60.041	40.741	0.00	0.00	35.70	3.07
355	449	1.066430	GCGTGTCCACTCCATTCCTAA	60.066	52.381	0.00	0.00	0.00	2.69
356	450	0.535335	GCGTGTCCACTCCATTCCTA	59.465	55.000	0.00	0.00	0.00	2.94
376	470	1.322538	ATCCACAAAAGGCCATCCGC	61.323	55.000	5.01	0.00	37.47	5.54
408	502	8.251026	GCATGATCATTCATCCATTCATACATT	58.749	33.333	5.16	0.00	40.70	2.71
412	506	7.613801	TCATGCATGATCATTCATCCATTCATA	59.386	33.333	25.42	0.00	37.44	2.15
458	552	3.081804	AGTATTTCCTCCGCAAAGTTGG	58.918	45.455	0.00	0.00	0.00	3.77
585	682	1.446792	CGTACTGCCTGGCTGACTG	60.447	63.158	29.14	14.81	0.00	3.51
586	683	0.611062	TACGTACTGCCTGGCTGACT	60.611	55.000	29.14	12.47	0.00	3.41
587	684	0.458025	GTACGTACTGCCTGGCTGAC	60.458	60.000	29.14	20.34	0.00	3.51
588	685	1.601419	GGTACGTACTGCCTGGCTGA	61.601	60.000	29.14	12.08	0.00	4.26
589	686	1.153628	GGTACGTACTGCCTGGCTG	60.154	63.158	24.07	22.17	0.00	4.85
590	687	2.356780	GGGTACGTACTGCCTGGCT	61.357	63.158	24.07	2.51	0.00	4.75
591	688	2.186125	GGGTACGTACTGCCTGGC	59.814	66.667	24.07	12.87	0.00	4.85
592	689	2.493030	CGGGTACGTACTGCCTGG	59.507	66.667	24.07	4.00	34.81	4.45
634	754	5.479027	TGGTTCATTATAGCCGCTAGTGATA	59.521	40.000	4.44	0.00	0.00	2.15
642	762	3.625764	TGTTCTTGGTTCATTATAGCCGC	59.374	43.478	0.00	0.00	0.00	6.53
643	763	5.448632	GGTTGTTCTTGGTTCATTATAGCCG	60.449	44.000	0.00	0.00	0.00	5.52
667	787	3.689161	TGCCAATTCTACACGATCAAAGG	59.311	43.478	0.00	0.00	0.00	3.11
676	805	9.555727	TTATTACTTATCCTGCCAATTCTACAC	57.444	33.333	0.00	0.00	0.00	2.90
730	889	7.432148	TGGAGGTGCTTCTAGTATTTGATTA	57.568	36.000	0.00	0.00	0.00	1.75
744	906	4.904251	ACTATAGTGATGATGGAGGTGCTT	59.096	41.667	4.10	0.00	0.00	3.91
759	921	1.032794	TCGCTGCTCCCACTATAGTG	58.967	55.000	23.58	23.58	45.23	2.74
781	943	1.656441	GGTTGCTCACTTGCACCTG	59.344	57.895	0.00	0.00	43.20	4.00
782	944	1.529244	GGGTTGCTCACTTGCACCT	60.529	57.895	0.00	0.00	43.20	4.00
783	945	2.564721	GGGGTTGCTCACTTGCACC	61.565	63.158	0.00	0.00	43.20	5.01
784	946	2.564721	GGGGGTTGCTCACTTGCAC	61.565	63.158	0.00	0.00	43.20	4.57
785	947	2.203480	GGGGGTTGCTCACTTGCA	60.203	61.111	0.00	0.00	41.65	4.08
786	948	1.973812	GAGGGGGTTGCTCACTTGC	60.974	63.158	0.00	0.00	0.00	4.01
892	1060	1.153489	CACTGGCTAGCTCATGCGT	60.153	57.895	15.72	3.07	45.42	5.24
969	1141	1.712081	CAATCGGTCTGAGCGCAAG	59.288	57.895	23.09	7.03	39.21	4.01
973	1152	3.257561	CGGCAATCGGTCTGAGCG	61.258	66.667	22.05	22.05	40.97	5.03
975	1154	1.519455	GGTCGGCAATCGGTCTGAG	60.519	63.158	0.00	0.00	39.77	3.35
991	1170	2.765807	CTCCTCCATGGCTCCGGT	60.766	66.667	6.96	0.00	35.26	5.28
992	1171	3.554342	CCTCCTCCATGGCTCCGG	61.554	72.222	6.96	0.00	35.26	5.14
993	1172	2.444706	TCCTCCTCCATGGCTCCG	60.445	66.667	6.96	0.00	35.26	4.63
995	1174	1.044611	GTAGTCCTCCTCCATGGCTC	58.955	60.000	6.96	0.00	35.26	4.70
1548	5188	2.109126	GCCATCACCGTTGCCTCTC	61.109	63.158	0.00	0.00	0.00	3.20
1733	5374	4.319177	ACTGTTCATTTACCTCTCTGTGC	58.681	43.478	0.00	0.00	0.00	4.57
1814	5460	2.750712	GTCTCTCTGTACAGACACCTCC	59.249	54.545	21.74	4.39	39.17	4.30
1927	5573	9.747898	TTCAAGAAATAAAGCAGTAATTAGGGA	57.252	29.630	0.00	0.00	0.00	4.20
2016	5681	1.176619	CCCACCGGGTTTGAAGGAAC	61.177	60.000	6.32	0.00	38.25	3.62
2017	5682	1.151908	CCCACCGGGTTTGAAGGAA	59.848	57.895	6.32	0.00	38.25	3.36
2379	6052	2.503331	TGCGACTGATTTGTTCACCAT	58.497	42.857	0.00	0.00	0.00	3.55
2506	6180	3.096852	TCGAAAGAGACCTCATGGCTAA	58.903	45.455	0.00	0.00	33.91	3.09

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.