AutoCloner

Multiple sequence alignment - TraesCS5B01G192200

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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	TraesCS5B01G192200	chr5B	100.000	2345	0	0	1	2345	345855919	345853575	0.000000e+00	4331
1	TraesCS5B01G192200	chr5B	98.727	707	3	2	770	1476	344537092	344536392	0.000000e+00	1251
2	TraesCS5B01G192200	chr5B	87.799	877	79	13	1470	2328	26452574	26451708	0.000000e+00	1002
3	TraesCS5B01G192200	chr5B	88.889	558	33	5	200	730	344538076	344537521	0.000000e+00	660
4	TraesCS5B01G192200	chr5B	83.333	156	16	4	60	207	344550885	344550732	4.060000e-28	135
5	TraesCS5B01G192200	chr5A	92.222	900	37	10	581	1476	398410869	398411739	0.000000e+00	1243
6	TraesCS5B01G192200	chr5A	79.728	661	79	26	740	1360	395886408	395885763	5.990000e-116	427
7	TraesCS5B01G192200	chr5A	82.178	202	31	4	183	383	398392708	398392905	4.010000e-38	169
8	TraesCS5B01G192200	chr5D	89.780	910	40	15	582	1476	301488395	301487524	0.000000e+00	1116
9	TraesCS5B01G192200	chr5D	89.779	587	52	5	1	582	301489007	301488424	0.000000e+00	745
10	TraesCS5B01G192200	chr2D	88.182	880	76	15	1476	2340	6382527	6381661	0.000000e+00	1024
11	TraesCS5B01G192200	chr3B	87.528	882	85	16	1478	2345	742104407	742105277	0.000000e+00	996
12	TraesCS5B01G192200	chr6D	86.761	846	86	19	1476	2306	348547267	348546433	0.000000e+00	918
13	TraesCS5B01G192200	chr3D	87.940	796	68	12	1546	2332	86149890	86150666	0.000000e+00	913
14	TraesCS5B01G192200	chr1D	85.552	879	87	27	1466	2326	475329730	475330586	0.000000e+00	883
15	TraesCS5B01G192200	chr1A	85.783	830	88	22	1465	2276	502509244	502510061	0.000000e+00	852
16	TraesCS5B01G192200	chr7B	84.935	843	104	19	1478	2306	669922287	669923120	0.000000e+00	832
17	TraesCS5B01G192200	chr7B	87.184	554	54	12	1805	2345	586237663	586238212	4.280000e-172	614
18	TraesCS5B01G192200	chr2B	84.852	845	93	22	1478	2306	152755284	152756109	0.000000e+00	819
19	TraesCS5B01G192200	chrUn	87.980	599	61	8	1751	2340	101959365	101958769	0.000000e+00	697
20	TraesCS5B01G192200	chr6B	88.211	475	44	8	1484	1956	366783875	366783411	7.320000e-155	556

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	TraesCS5B01G192200	chr5B	345853575	345855919	2344	True	4331.0	4331	100.0000	1	2345	1	chr5B.!!$R3	2344
1	TraesCS5B01G192200	chr5B	26451708	26452574	866	True	1002.0	1002	87.7990	1470	2328	1	chr5B.!!$R1	858
2	TraesCS5B01G192200	chr5B	344536392	344538076	1684	True	955.5	1251	93.8080	200	1476	2	chr5B.!!$R4	1276
3	TraesCS5B01G192200	chr5A	398410869	398411739	870	False	1243.0	1243	92.2220	581	1476	1	chr5A.!!$F2	895
4	TraesCS5B01G192200	chr5A	395885763	395886408	645	True	427.0	427	79.7280	740	1360	1	chr5A.!!$R1	620
5	TraesCS5B01G192200	chr5D	301487524	301489007	1483	True	930.5	1116	89.7795	1	1476	2	chr5D.!!$R1	1475
6	TraesCS5B01G192200	chr2D	6381661	6382527	866	True	1024.0	1024	88.1820	1476	2340	1	chr2D.!!$R1	864
7	TraesCS5B01G192200	chr3B	742104407	742105277	870	False	996.0	996	87.5280	1478	2345	1	chr3B.!!$F1	867
8	TraesCS5B01G192200	chr6D	348546433	348547267	834	True	918.0	918	86.7610	1476	2306	1	chr6D.!!$R1	830
9	TraesCS5B01G192200	chr3D	86149890	86150666	776	False	913.0	913	87.9400	1546	2332	1	chr3D.!!$F1	786
10	TraesCS5B01G192200	chr1D	475329730	475330586	856	False	883.0	883	85.5520	1466	2326	1	chr1D.!!$F1	860
11	TraesCS5B01G192200	chr1A	502509244	502510061	817	False	852.0	852	85.7830	1465	2276	1	chr1A.!!$F1	811
12	TraesCS5B01G192200	chr7B	669922287	669923120	833	False	832.0	832	84.9350	1478	2306	1	chr7B.!!$F2	828
13	TraesCS5B01G192200	chr7B	586237663	586238212	549	False	614.0	614	87.1840	1805	2345	1	chr7B.!!$F1	540
14	TraesCS5B01G192200	chr2B	152755284	152756109	825	False	819.0	819	84.8520	1478	2306	1	chr2B.!!$F1	828
15	TraesCS5B01G192200	chrUn	101958769	101959365	596	True	697.0	697	87.9800	1751	2340	1	chrUn.!!$R1	589

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
481	487	1.282248	GCAAGACGCGACAACAGCTA	61.282	55.0	15.93	0.0	0.0	3.32	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2082	2623	0.973632	TGCTAAGTTGAAGGAGGCGA	59.026	50.0	0.0	0.0	0.0	5.54	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
36	37	2.424956	CTCTGGTTGCCCTAGATTTTGC	59.575	50.000	0.00	0.00	0.00	3.68
64	65	2.310779	AAGTCTAGGTGTCTGGCTGA	57.689	50.000	0.00	0.00	0.00	4.26
77	78	2.358615	GCTGACGGTGGTGATGCA	60.359	61.111	0.00	0.00	0.00	3.96
95	96	3.574284	GCAATGGCACTATCAACAACA	57.426	42.857	0.00	0.00	40.72	3.33
106	107	6.183360	GCACTATCAACAACAAGGGATAAGAC	60.183	42.308	0.00	0.00	0.00	3.01
108	109	4.993705	TCAACAACAAGGGATAAGACCT	57.006	40.909	0.00	0.00	40.96	3.85
110	111	3.611766	ACAACAAGGGATAAGACCTCG	57.388	47.619	0.00	0.00	37.35	4.63
141	146	2.225491	CGATCCGACAATGTTGTTTGGT	59.775	45.455	14.03	1.22	42.43	3.67
158	163	4.724602	TGTCGGCTGAGAGCGTGC	62.725	66.667	0.00	0.00	43.62	5.34
177	182	1.709147	CGGAGCTTCAATGAAGGCCG	61.709	60.000	22.73	11.60	39.76	6.13
179	184	1.379044	AGCTTCAATGAAGGCCGGG	60.379	57.895	22.73	0.00	39.76	5.73
181	186	1.678635	CTTCAATGAAGGCCGGGCA	60.679	57.895	31.59	10.35	36.16	5.36
191	196	2.830370	GCCGGGCATGAAGGAAGG	60.830	66.667	15.62	0.00	0.00	3.46
198	203	2.107901	GGGCATGAAGGAAGGAGATGAT	59.892	50.000	0.00	0.00	0.00	2.45
207	212	4.560739	AGGAAGGAGATGATGTCATGGTA	58.439	43.478	0.00	0.00	36.57	3.25
228	233	7.488322	TGGTATGTTCTTTTCTTCTTTGGTTG	58.512	34.615	0.00	0.00	0.00	3.77
332	337	5.509498	CCAGAGTTGGGATTATCTTTTGGA	58.491	41.667	0.00	0.00	41.05	3.53
343	348	6.488344	GGATTATCTTTTGGACCTCCTTGATC	59.512	42.308	0.00	0.00	36.82	2.92
377	382	1.538204	GGCGGCGTTCTATCAAGATCA	60.538	52.381	9.37	0.00	0.00	2.92
388	393	7.869937	CGTTCTATCAAGATCATGATTGTAGGT	59.130	37.037	17.85	0.00	40.44	3.08
397	402	7.170965	AGATCATGATTGTAGGTGTCTTTTGT	58.829	34.615	10.14	0.00	0.00	2.83
400	405	6.998074	TCATGATTGTAGGTGTCTTTTGTTCT	59.002	34.615	0.00	0.00	0.00	3.01
406	411	6.822442	TGTAGGTGTCTTTTGTTCTACATCA	58.178	36.000	0.00	0.00	34.19	3.07
449	455	7.543947	CTTTTTCAAGCTCCTTTGTTTCAAT	57.456	32.000	0.00	0.00	0.00	2.57
481	487	1.282248	GCAAGACGCGACAACAGCTA	61.282	55.000	15.93	0.00	0.00	3.32
721	758	1.757682	AACAGACGGGTTGCAAAAGA	58.242	45.000	0.00	0.00	0.00	2.52
722	759	1.757682	ACAGACGGGTTGCAAAAGAA	58.242	45.000	0.00	0.00	0.00	2.52
723	760	2.096248	ACAGACGGGTTGCAAAAGAAA	58.904	42.857	0.00	0.00	0.00	2.52
724	761	2.099098	ACAGACGGGTTGCAAAAGAAAG	59.901	45.455	0.00	0.00	0.00	2.62
725	762	2.357637	CAGACGGGTTGCAAAAGAAAGA	59.642	45.455	0.00	0.00	0.00	2.52
726	763	3.020984	AGACGGGTTGCAAAAGAAAGAA	58.979	40.909	0.00	0.00	0.00	2.52
727	764	3.445805	AGACGGGTTGCAAAAGAAAGAAA	59.554	39.130	0.00	0.00	0.00	2.52
728	765	4.099419	AGACGGGTTGCAAAAGAAAGAAAT	59.901	37.500	0.00	0.00	0.00	2.17
729	766	4.368315	ACGGGTTGCAAAAGAAAGAAATC	58.632	39.130	0.00	0.00	0.00	2.17
730	767	4.142049	ACGGGTTGCAAAAGAAAGAAATCA	60.142	37.500	0.00	0.00	0.00	2.57
731	768	4.808364	CGGGTTGCAAAAGAAAGAAATCAA	59.192	37.500	0.00	0.00	0.00	2.57
732	769	5.293079	CGGGTTGCAAAAGAAAGAAATCAAA	59.707	36.000	0.00	0.00	0.00	2.69
733	770	6.183360	CGGGTTGCAAAAGAAAGAAATCAAAA	60.183	34.615	0.00	0.00	0.00	2.44
734	771	7.534282	GGGTTGCAAAAGAAAGAAATCAAAAA	58.466	30.769	0.00	0.00	0.00	1.94
1429	1912	5.530915	TGTGTTGATCGAGTGAAATTTTCCT	59.469	36.000	6.68	3.71	0.00	3.36
1430	1913	6.039270	TGTGTTGATCGAGTGAAATTTTCCTT	59.961	34.615	6.68	0.00	0.00	3.36
1431	1914	6.918022	GTGTTGATCGAGTGAAATTTTCCTTT	59.082	34.615	6.68	0.00	0.00	3.11
1462	1948	5.704053	TCCTTGTATCGACGATGCTATCTTA	59.296	40.000	23.45	2.81	0.00	2.10
1467	1953	8.433421	TGTATCGACGATGCTATCTTATGATA	57.567	34.615	23.45	0.00	34.32	2.15
1618	2109	7.189512	ACACTATTATCGCTTTTTGAAGCATC	58.810	34.615	11.22	0.00	45.75	3.91
1658	2150	4.273318	AGCCACCTTAATGTCTTTCATCC	58.727	43.478	0.00	0.00	35.48	3.51
1663	2155	5.817296	CACCTTAATGTCTTTCATCCGATGA	59.183	40.000	7.00	7.00	35.48	2.92
1678	2170	1.920574	CGATGAAAGAGTAGTGGTGCG	59.079	52.381	0.00	0.00	0.00	5.34
2011	2546	0.032952	ACACACGGTGTCTGCGTTAT	59.967	50.000	11.54	0.00	43.92	1.89
2015	2551	1.126113	CACGGTGTCTGCGTTATGAAC	59.874	52.381	0.00	0.00	0.00	3.18
2081	2622	3.326880	AGTTGTAGGGATGTCCTTCGTTT	59.673	43.478	0.00	0.00	45.47	3.60
2082	2623	4.070009	GTTGTAGGGATGTCCTTCGTTTT	58.930	43.478	0.00	0.00	45.47	2.43
2176	2721	4.449068	GGTCGAACTCATTTGCATCGATAT	59.551	41.667	9.28	0.00	43.42	1.63
2192	2737	3.622612	TCGATATCGAGACGTTTGTGGTA	59.377	43.478	23.48	0.00	44.22	3.25
2217	2762	2.990066	ATCAATCTGAAGACCCGTCC	57.010	50.000	0.00	0.00	0.00	4.79
2219	2764	0.246635	CAATCTGAAGACCCGTCCGT	59.753	55.000	0.00	0.00	0.00	4.69
2225	2770	0.033090	GAAGACCCGTCCGTTGAGTT	59.967	55.000	0.00	0.00	0.00	3.01
2233	2778	2.228343	CCGTCCGTTGAGTTTCTCTAGT	59.772	50.000	0.00	0.00	0.00	2.57
2332	2877	5.703978	ATGCTACAATTTAATGCGCCATA	57.296	34.783	4.18	0.00	0.00	2.74
2341	2886	0.248580	AATGCGCCATACGTTGCATG	60.249	50.000	4.18	0.00	46.60	4.06
2342	2887	1.094650	ATGCGCCATACGTTGCATGA	61.095	50.000	4.18	0.00	45.64	3.07

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
36	37	4.645588	CAGACACCTAGACTTAACCCCTAG	59.354	50.000	0.00	0.00	0.00	3.02
64	65	2.342650	GCCATTGCATCACCACCGT	61.343	57.895	0.00	0.00	37.47	4.83
77	78	3.511146	CCCTTGTTGTTGATAGTGCCATT	59.489	43.478	0.00	0.00	0.00	3.16
89	90	3.326880	ACGAGGTCTTATCCCTTGTTGTT	59.673	43.478	0.00	0.00	42.93	2.83
106	107	1.465387	CGGATCGAGGATAAGACGAGG	59.535	57.143	0.00	0.00	39.31	4.63
108	109	2.141517	GTCGGATCGAGGATAAGACGA	58.858	52.381	0.00	0.00	36.23	4.20
110	111	3.984508	TTGTCGGATCGAGGATAAGAC	57.015	47.619	0.00	0.00	36.23	3.01
115	120	2.168521	ACAACATTGTCGGATCGAGGAT	59.831	45.455	0.00	0.00	36.50	3.24
118	123	3.424829	CCAAACAACATTGTCGGATCGAG	60.425	47.826	7.17	0.00	41.31	4.04
141	146	4.724602	GCACGCTCTCAGCCGACA	62.725	66.667	0.00	0.00	38.18	4.35
158	163	1.709147	CGGCCTTCATTGAAGCTCCG	61.709	60.000	27.86	27.86	42.57	4.63
168	173	1.454479	CTTCATGCCCGGCCTTCAT	60.454	57.895	7.03	0.00	0.00	2.57
170	175	2.830370	CCTTCATGCCCGGCCTTC	60.830	66.667	7.03	0.00	0.00	3.46
177	182	1.492176	TCATCTCCTTCCTTCATGCCC	59.508	52.381	0.00	0.00	0.00	5.36
179	184	3.814283	GACATCATCTCCTTCCTTCATGC	59.186	47.826	0.00	0.00	0.00	4.06
181	186	5.456330	CCATGACATCATCTCCTTCCTTCAT	60.456	44.000	0.00	0.00	33.61	2.57
191	196	7.798596	AAAGAACATACCATGACATCATCTC	57.201	36.000	0.00	0.00	33.61	2.75
198	203	8.352201	CAAAGAAGAAAAGAACATACCATGACA	58.648	33.333	0.00	0.00	0.00	3.58
207	212	6.225981	AGCAACCAAAGAAGAAAAGAACAT	57.774	33.333	0.00	0.00	0.00	2.71
332	337	0.827368	GAAGCTCGGATCAAGGAGGT	59.173	55.000	6.56	6.56	42.36	3.85
365	370	8.255111	ACACCTACAATCATGATCTTGATAGA	57.745	34.615	20.86	10.60	35.29	1.98
377	382	7.936847	TGTAGAACAAAAGACACCTACAATCAT	59.063	33.333	0.00	0.00	35.13	2.45
388	393	6.046593	AGTCGTTGATGTAGAACAAAAGACA	58.953	36.000	16.10	0.00	37.84	3.41
440	445	3.254657	CCGGAGCAACCTTATTGAAACAA	59.745	43.478	0.00	0.00	36.31	2.83
464	470	1.726791	CAATAGCTGTTGTCGCGTCTT	59.273	47.619	14.56	0.00	0.00	3.01
497	503	0.532573	TCCTTCTGCATCAGTCGACC	59.467	55.000	13.01	0.00	32.61	4.79
498	504	2.094494	TCTTCCTTCTGCATCAGTCGAC	60.094	50.000	7.70	7.70	32.61	4.20
696	733	1.890041	CAACCCGTCTGTTTCGCCA	60.890	57.895	0.00	0.00	0.00	5.69
733	770	9.578439	CAGTTCTGAGTTGATTTCTTTCTTTTT	57.422	29.630	0.00	0.00	0.00	1.94
734	771	7.704047	GCAGTTCTGAGTTGATTTCTTTCTTTT	59.296	33.333	3.84	0.00	0.00	2.27
735	772	7.199078	GCAGTTCTGAGTTGATTTCTTTCTTT	58.801	34.615	3.84	0.00	0.00	2.52
736	773	6.238869	GGCAGTTCTGAGTTGATTTCTTTCTT	60.239	38.462	3.84	0.00	0.00	2.52
737	774	5.240403	GGCAGTTCTGAGTTGATTTCTTTCT	59.760	40.000	3.84	0.00	0.00	2.52
738	775	5.456265	GGCAGTTCTGAGTTGATTTCTTTC	58.544	41.667	3.84	0.00	0.00	2.62
748	785	1.604278	GAAAAGCGGCAGTTCTGAGTT	59.396	47.619	1.45	0.00	0.00	3.01
1618	2109	2.450160	GCTTTTTCACGTCCACACTTG	58.550	47.619	0.00	0.00	0.00	3.16
1658	2150	1.920574	CGCACCACTACTCTTTCATCG	59.079	52.381	0.00	0.00	0.00	3.84
1663	2155	2.902705	TTCACGCACCACTACTCTTT	57.097	45.000	0.00	0.00	0.00	2.52
1678	2170	6.481954	AAACCGATTGACAGACTATTTCAC	57.518	37.500	0.00	0.00	0.00	3.18
1798	2298	8.273780	TCATGTGTTAAAAATGTTTGCCTTTT	57.726	26.923	0.00	0.00	0.00	2.27
1799	2299	7.856145	TCATGTGTTAAAAATGTTTGCCTTT	57.144	28.000	0.00	0.00	0.00	3.11
1939	2451	5.982890	TTCCCTTTCAAGAAATCCACATC	57.017	39.130	0.00	0.00	0.00	3.06
1950	2462	7.962373	GTGTTTCAATTTGTTTTCCCTTTCAAG	59.038	33.333	0.00	0.00	0.00	3.02
2011	2546	4.023279	CGGACACCATCAATCTTTTGTTCA	60.023	41.667	0.00	0.00	34.32	3.18
2015	2551	2.228582	TGCGGACACCATCAATCTTTTG	59.771	45.455	0.00	0.00	0.00	2.44
2081	2622	1.346395	TGCTAAGTTGAAGGAGGCGAA	59.654	47.619	0.00	0.00	0.00	4.70
2082	2623	0.973632	TGCTAAGTTGAAGGAGGCGA	59.026	50.000	0.00	0.00	0.00	5.54
2176	2721	3.441496	AAGTTACCACAAACGTCTCGA	57.559	42.857	0.00	0.00	34.46	4.04
2192	2737	5.805728	ACGGGTCTTCAGATTGATAAAGTT	58.194	37.500	0.00	0.00	0.00	2.66
2217	2762	4.677378	CACTCACACTAGAGAAACTCAACG	59.323	45.833	0.00	0.00	38.98	4.10
2219	2764	5.127194	ACACACTCACACTAGAGAAACTCAA	59.873	40.000	0.00	0.00	38.98	3.02
2225	2770	7.393515	ACATACATACACACTCACACTAGAGAA	59.606	37.037	0.00	0.00	38.98	2.87
2233	2778	6.284459	TCACAAACATACATACACACTCACA	58.716	36.000	0.00	0.00	0.00	3.58

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.