AutoCloner

Multiple sequence alignment - TraesCS3B01G138400

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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	TraesCS3B01G138400	chr3B	100.000	2934	0	0	1	2934	124121326	124118393	0.000000e+00	5419
1	TraesCS3B01G138400	chr3D	88.579	2977	287	26	2	2934	78096024	78098991	0.000000e+00	3565
2	TraesCS3B01G138400	chr3D	88.445	2977	291	25	1	2934	77998330	78001296	0.000000e+00	3542
3	TraesCS3B01G138400	chr7A	88.777	2281	205	26	1	2233	181013988	181016265	0.000000e+00	2747
4	TraesCS3B01G138400	chr7A	88.248	2272	224	22	1	2233	180842937	180845204	0.000000e+00	2676
5	TraesCS3B01G138400	chr7A	87.752	2286	225	22	1	2233	181168061	181170344	0.000000e+00	2619
6	TraesCS3B01G138400	chr7A	87.385	2283	232	31	1	2233	180983966	180986242	0.000000e+00	2569
7	TraesCS3B01G138400	chr7A	87.248	2282	239	26	1	2233	181049550	181051828	0.000000e+00	2555
8	TraesCS3B01G138400	chr7A	95.266	169	8	0	2766	2934	180845196	180845364	4.820000e-68	268
9	TraesCS3B01G138400	chr7A	95.266	169	8	0	2766	2934	180986234	180986402	4.820000e-68	268
10	TraesCS3B01G138400	chr7A	94.675	169	9	0	2766	2934	181016257	181016425	2.240000e-66	263
11	TraesCS3B01G138400	chr7A	93.491	169	11	0	2766	2934	181051820	181051988	4.850000e-63	252
12	TraesCS3B01G138400	chr7A	93.491	169	11	0	2766	2934	181170336	181170504	4.850000e-63	252
13	TraesCS3B01G138400	chr3A	89.280	2015	155	21	957	2934	91285685	91283695	0.000000e+00	2468
14	TraesCS3B01G138400	chr3A	83.109	965	132	16	4	961	91289089	91288149	0.000000e+00	850
15	TraesCS3B01G138400	chr4B	87.556	1792	177	26	948	2699	476571577	476569792	0.000000e+00	2032
16	TraesCS3B01G138400	chr4B	79.809	941	148	30	4	919	476573028	476572105	0.000000e+00	647
17	TraesCS3B01G138400	chr7D	90.642	1432	99	15	837	2233	177169042	177170473	0.000000e+00	1869
18	TraesCS3B01G138400	chr7D	90.533	169	6	6	2766	2934	177170465	177170623	6.370000e-52	215
19	TraesCS3B01G138400	chr4D	87.524	1563	151	15	948	2469	388250875	388249316	0.000000e+00	1766
20	TraesCS3B01G138400	chr4D	83.843	229	36	1	2473	2700	388249009	388248781	1.770000e-52	217
21	TraesCS3B01G138400	chr4A	86.901	1565	159	15	948	2469	69511148	69509587	0.000000e+00	1712
22	TraesCS3B01G138400	chr4A	86.198	1565	170	23	948	2469	69523850	69522289	0.000000e+00	1652
23	TraesCS3B01G138400	chr4A	78.655	937	157	30	3	913	69525341	69524422	1.520000e-162	582
24	TraesCS3B01G138400	chr4A	85.535	159	23	0	2472	2630	69509281	69509123	1.810000e-37	167

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	TraesCS3B01G138400	chr3B	124118393	124121326	2933	True	5419.0	5419	100.0000	1	2934	1	chr3B.!!$R1	2933
1	TraesCS3B01G138400	chr3D	78096024	78098991	2967	False	3565.0	3565	88.5790	2	2934	1	chr3D.!!$F2	2932
2	TraesCS3B01G138400	chr3D	77998330	78001296	2966	False	3542.0	3542	88.4450	1	2934	1	chr3D.!!$F1	2933
3	TraesCS3B01G138400	chr7A	181013988	181016425	2437	False	1505.0	2747	91.7260	1	2934	2	chr7A.!!$F3	2933
4	TraesCS3B01G138400	chr7A	180842937	180845364	2427	False	1472.0	2676	91.7570	1	2934	2	chr7A.!!$F1	2933
5	TraesCS3B01G138400	chr7A	181168061	181170504	2443	False	1435.5	2619	90.6215	1	2934	2	chr7A.!!$F5	2933
6	TraesCS3B01G138400	chr7A	180983966	180986402	2436	False	1418.5	2569	91.3255	1	2934	2	chr7A.!!$F2	2933
7	TraesCS3B01G138400	chr7A	181049550	181051988	2438	False	1403.5	2555	90.3695	1	2934	2	chr7A.!!$F4	2933
8	TraesCS3B01G138400	chr3A	91283695	91289089	5394	True	1659.0	2468	86.1945	4	2934	2	chr3A.!!$R1	2930
9	TraesCS3B01G138400	chr4B	476569792	476573028	3236	True	1339.5	2032	83.6825	4	2699	2	chr4B.!!$R1	2695
10	TraesCS3B01G138400	chr7D	177169042	177170623	1581	False	1042.0	1869	90.5875	837	2934	2	chr7D.!!$F1	2097
11	TraesCS3B01G138400	chr4D	388248781	388250875	2094	True	991.5	1766	85.6835	948	2700	2	chr4D.!!$R1	1752
12	TraesCS3B01G138400	chr4A	69522289	69525341	3052	True	1117.0	1652	82.4265	3	2469	2	chr4A.!!$R2	2466
13	TraesCS3B01G138400	chr4A	69509123	69511148	2025	True	939.5	1712	86.2180	948	2630	2	chr4A.!!$R1	1682

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
823	874	0.442699	GGCGACGAGGTTGATTCAAC	59.557	55.0	19.17	19.17	42.89	3.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2601	6024	0.187117	TTGGGTTGTGCTCCATGGAA	59.813	50.0	17.0	0.0	32.48	3.53	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
22	23	5.266733	TCGTGTACTTTTTCACCTACTGT	57.733	39.130	0.00	0.00	0.00	3.55
104	105	6.619801	AATGTTTATAGGAAGCGAACATCC	57.380	37.500	0.00	0.00	39.31	3.51
147	148	3.229293	TCGAGACTCGAGAGTAGGGATA	58.771	50.000	23.27	0.00	44.82	2.59
204	209	2.203938	ACCCCACCAGGTGATCGT	60.204	61.111	22.37	10.50	39.24	3.73
239	260	1.077005	CTCCCCATCCTCCTCTCCTAG	59.923	61.905	0.00	0.00	0.00	3.02
266	288	4.954118	AGCGTGGTCCACCTGGGA	62.954	66.667	16.60	0.00	45.89	4.37
341	373	0.606673	GGTTCCTTCTGGTGGCAGTC	60.607	60.000	0.00	0.00	34.23	3.51
381	413	2.722201	GGATCGGCGAGGTGGTTCT	61.722	63.158	17.22	0.00	0.00	3.01
458	493	2.125552	TGCGAGAACATGGCCGAG	60.126	61.111	0.00	0.00	0.00	4.63
539	574	1.565305	GATCTCTGCACGGTAGCAAG	58.435	55.000	6.69	7.23	45.13	4.01
543	579	1.672356	CTGCACGGTAGCAAGGCTT	60.672	57.895	0.00	0.00	45.13	4.35
578	620	4.083862	GGCCACGGTGGTCTCCTC	62.084	72.222	26.86	10.04	39.55	3.71
611	656	1.476074	CAACCGACATGTTGCAACAC	58.524	50.000	33.29	19.89	42.51	3.32
736	783	2.757124	CCCCTCCCGCTTGGCTAAT	61.757	63.158	0.00	0.00	0.00	1.73
781	832	1.576272	TCCCTCTTCCTTCCTCTAGGG	59.424	57.143	0.00	0.00	44.29	3.53
785	836	1.933765	TCTTCCTTCCTCTAGGGCTCT	59.066	52.381	0.00	0.00	35.90	4.09
799	850	1.527370	GCTCTTATCGGTGGCCCTT	59.473	57.895	0.00	0.00	0.00	3.95
823	874	0.442699	GGCGACGAGGTTGATTCAAC	59.557	55.000	19.17	19.17	42.89	3.18
943	1522	4.613866	GTCCTTTTATGTGCGGTTTTAACG	59.386	41.667	0.00	0.00	0.00	3.18
1011	4068	8.219868	TGATAACAGATTACCATGGATGAACAT	58.780	33.333	21.47	0.00	0.00	2.71
1029	4086	5.709631	TGAACATTACAATAGTGGTGTGCAT	59.290	36.000	0.00	0.00	31.22	3.96
1038	4095	6.127925	ACAATAGTGGTGTGCATAATGAGTTG	60.128	38.462	0.00	0.00	0.00	3.16
1051	4108	4.647564	AATGAGTTGGACCTCTTCATGT	57.352	40.909	0.00	0.00	32.50	3.21
1107	4164	3.897657	AATGATGAGATGGATGGCCTT	57.102	42.857	3.32	0.00	34.31	4.35
1157	4214	5.301551	ACACTAATGATGCCAAAGTTGTTGA	59.698	36.000	0.00	0.00	0.00	3.18

Showing 1 to 25 of 81 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
22	23	6.705302	TCAGTAGTCGTCTTCCTTAGAACTA	58.295	40.000	0.00	33.81	2.24
91	92	1.745489	AAGCCGGATGTTCGCTTCC	60.745	57.895	5.05	37.89	3.46
104	105	2.125552	TCCGTCTCATGCAAGCCG	60.126	61.111	0.00	0.00	5.52
169	171	2.125512	GAGCGAGCGAACATGGGT	60.126	61.111	0.00	0.00	4.51
202	207	2.253403	GAGGGGGCTAGGGTTTGACG	62.253	65.000	0.00	0.00	4.35
204	209	1.618447	GGAGGGGGCTAGGGTTTGA	60.618	63.158	0.00	0.00	2.69
301	324	2.677228	CCGAGTGCCTGGGGAAAT	59.323	61.111	0.00	0.00	2.17
324	356	0.397941	CAGACTGCCACCAGAAGGAA	59.602	55.000	0.00	41.77	3.36
359	391	2.502492	CCACCTCGCCGATCCAGAT	61.502	63.158	0.00	0.00	2.90
511	546	2.124983	GCAGAGATCCGCAAGCCA	60.125	61.111	0.00	0.00	4.75
515	550	1.600511	TACCGTGCAGAGATCCGCAA	61.601	55.000	3.83	40.44	4.85
539	574	2.674220	CCTCCACCTCCAGGAAGCC	61.674	68.421	0.00	38.94	4.35
543	579	2.122729	CCACCTCCACCTCCAGGA	59.877	66.667	0.00	38.94	3.86
564	606	4.778415	CGCGAGGAGACCACCGTG	62.778	72.222	0.00	34.73	4.94
582	627	3.587933	GTCGGTTGCCAACGCCAA	61.588	61.111	0.74	0.00	4.52
611	656	1.664321	CTCGTGAAGTCCCCCTACCG	61.664	65.000	0.00	0.00	4.02
756	803	3.327439	AGAGGAAGGAAGAGGGAACAAA	58.673	45.455	0.00	0.00	2.83
781	832	0.815615	CAAGGGCCACCGATAAGAGC	60.816	60.000	6.18	43.47	4.09
785	836	1.540267	CAAACAAGGGCCACCGATAA	58.460	50.000	6.18	43.47	1.75
799	850	0.250124	ATCAACCTCGTCGCCAAACA	60.250	50.000	0.00	0.00	2.83
835	887	1.379443	CTGCCATCCACCAGCATGT	60.379	57.895	0.00	35.64	3.21
883	935	1.591504	CGACCCAAAAATCCCCACCG	61.592	60.000	0.00	0.00	4.94
920	1499	4.613866	CGTTAAAACCGCACATAAAAGGAC	59.386	41.667	0.00	0.00	3.85
943	1522	5.011840	CCCCTATGTAGAACTAAAGGTAGCC	59.988	48.000	0.00	0.00	3.93
952	1543	9.670442	AGAATGTTATTCCCCTATGTAGAACTA	57.330	33.333	0.00	0.00	2.24

Showing 1 to 25 of 81 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.