AutoCloner

Multiple sequence alignment - TraesCS5A01G362400

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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	TraesCS5A01G362400	chr5A	100.000	3536	0	0	1	3536	563443023	563439488	0.000000e+00	6530.0
1	TraesCS5A01G362400	chr5A	98.356	2190	34	2	448	2635	563538575	563536386	0.000000e+00	3843.0
2	TraesCS5A01G362400	chr5A	94.118	459	20	4	1	459	563540711	563540260	0.000000e+00	691.0
3	TraesCS5A01G362400	chr5A	97.059	340	9	1	1	339	563562870	563562531	3.960000e-159	571.0
4	TraesCS5A01G362400	chr5A	78.116	690	147	4	1852	2539	562892450	562891763	5.420000e-118	435.0
5	TraesCS5A01G362400	chr5A	96.863	255	0	2	2625	2879	563533866	563533620	1.520000e-113	420.0
6	TraesCS5A01G362400	chr5A	90.813	283	22	3	3253	3535	468572463	468572185	3.330000e-100	375.0
7	TraesCS5A01G362400	chr5A	89.552	67	6	1	807	872	380178796	380178862	2.260000e-12	84.2
8	TraesCS5A01G362400	chr5A	100.000	37	0	0	3210	3246	563440021	563439985	6.330000e-08	69.4
9	TraesCS5A01G362400	chr7A	95.976	671	12	1	2881	3536	638490600	638489930	0.000000e+00	1075.0
10	TraesCS5A01G362400	chr7A	78.355	231	40	7	2881	3106	275698590	275698365	1.320000e-29	141.0
11	TraesCS5A01G362400	chr7A	97.561	41	0	1	3207	3246	638490482	638490442	6.330000e-08	69.4
12	TraesCS5A01G362400	chr7D	77.718	1499	322	12	1061	2553	14422313	14420821	0.000000e+00	907.0
13	TraesCS5A01G362400	chr7D	80.717	223	39	4	2879	3099	69223575	69223355	1.690000e-38	171.0
14	TraesCS5A01G362400	chr7D	79.487	234	44	3	2880	3112	150501016	150500786	2.820000e-36	163.0
15	TraesCS5A01G362400	chr7D	78.099	242	43	7	2881	3113	255798240	255798000	1.020000e-30	145.0
16	TraesCS5A01G362400	chr7D	84.615	117	18	0	2882	2998	633183398	633183514	2.230000e-22	117.0
17	TraesCS5A01G362400	chr4B	78.254	1306	276	8	1256	2557	6084046	6085347	0.000000e+00	832.0
18	TraesCS5A01G362400	chr4B	95.305	213	10	0	1	213	182286601	182286389	4.370000e-89	339.0
19	TraesCS5A01G362400	chrUn	78.063	1363	261	29	1022	2367	15760435	15759094	0.000000e+00	826.0
20	TraesCS5A01G362400	chrUn	76.331	1521	344	13	1022	2531	15603993	15605508	0.000000e+00	800.0
21	TraesCS5A01G362400	chrUn	76.269	729	169	4	1805	2531	357124600	357125326	5.540000e-103	385.0
22	TraesCS5A01G362400	chrUn	92.857	70	3	2	805	872	89528252	89528321	2.250000e-17	100.0
23	TraesCS5A01G362400	chr4A	77.634	1310	269	18	1256	2551	601338032	601339331	0.000000e+00	774.0
24	TraesCS5A01G362400	chr4A	95.305	213	10	0	1	213	196705565	196705777	4.370000e-89	339.0
25	TraesCS5A01G362400	chr4A	87.636	275	34	0	3253	3527	113964092	113963818	1.580000e-83	320.0
26	TraesCS5A01G362400	chr4A	81.548	168	28	2	2885	3052	21241106	21241270	6.160000e-28	135.0
27	TraesCS5A01G362400	chr4A	87.805	82	7	3	793	871	724617376	724617295	3.760000e-15	93.5
28	TraesCS5A01G362400	chr2A	74.495	1584	352	39	977	2527	778631108	778632672	1.070000e-179	640.0
29	TraesCS5A01G362400	chr2A	78.415	593	114	12	1039	1624	2219363	2218778	1.200000e-99	374.0
30	TraesCS5A01G362400	chr2A	80.814	172	32	1	2881	3052	138107981	138107811	2.210000e-27	134.0
31	TraesCS5A01G362400	chr2A	83.636	110	17	1	3339	3448	2663856	2663748	6.240000e-18	102.0
32	TraesCS5A01G362400	chr2B	73.757	1448	337	34	1081	2501	777964492	777963061	2.420000e-146	529.0
33	TraesCS5A01G362400	chr2B	95.775	213	9	0	1	213	30702490	30702702	9.400000e-91	344.0
34	TraesCS5A01G362400	chr2B	80.000	105	16	4	772	871	655518053	655517949	4.900000e-09	73.1
35	TraesCS5A01G362400	chr3A	89.399	283	26	3	3253	3535	503708914	503708636	1.560000e-93	353.0
36	TraesCS5A01G362400	chr4D	95.775	213	8	1	1	213	5664988	5664777	3.380000e-90	342.0
37	TraesCS5A01G362400	chr4D	88.768	276	29	2	3253	3527	351371313	351371587	1.570000e-88	337.0
38	TraesCS5A01G362400	chr4D	88.158	228	24	2	2881	3106	351370849	351371075	5.820000e-68	268.0
39	TraesCS5A01G362400	chr4D	90.909	44	2	2	3207	3249	351370966	351371008	1.370000e-04	58.4
40	TraesCS5A01G362400	chr7B	95.305	213	10	0	1	213	89908649	89908861	4.370000e-89	339.0
41	TraesCS5A01G362400	chr7B	86.207	87	6	6	790	871	97972091	97972176	4.860000e-14	89.8
42	TraesCS5A01G362400	chr3B	94.836	213	11	0	1	213	562456002	562455790	2.030000e-87	333.0
43	TraesCS5A01G362400	chr1B	94.836	213	11	0	1	213	611790736	611790948	2.030000e-87	333.0
44	TraesCS5A01G362400	chr6A	88.339	283	21	5	3253	3535	586834357	586834627	2.630000e-86	329.0
45	TraesCS5A01G362400	chr6A	92.361	144	10	1	3392	3535	14356559	14356701	1.660000e-48	204.0
46	TraesCS5A01G362400	chr6A	92.982	57	4	0	814	870	578072068	578072012	2.260000e-12	84.2
47	TraesCS5A01G362400	chr5B	91.667	108	7	2	3403	3509	124631599	124631705	7.910000e-32	148.0
48	TraesCS5A01G362400	chr5B	90.278	72	6	1	802	872	275309972	275310043	3.760000e-15	93.5
49	TraesCS5A01G362400	chr3D	91.549	71	2	4	804	870	437473374	437473444	1.040000e-15	95.3

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	TraesCS5A01G362400	chr5A	563439488	563443023	3535	True	3299.700000	6530	100.000000	1	3536	2	chr5A.!!$R4	3535
1	TraesCS5A01G362400	chr5A	563533620	563540711	7091	True	1651.333333	3843	96.445667	1	2879	3	chr5A.!!$R5	2878
2	TraesCS5A01G362400	chr5A	562891763	562892450	687	True	435.000000	435	78.116000	1852	2539	1	chr5A.!!$R2	687
3	TraesCS5A01G362400	chr7A	638489930	638490600	670	True	572.200000	1075	96.768500	2881	3536	2	chr7A.!!$R2	655
4	TraesCS5A01G362400	chr7D	14420821	14422313	1492	True	907.000000	907	77.718000	1061	2553	1	chr7D.!!$R1	1492
5	TraesCS5A01G362400	chr4B	6084046	6085347	1301	False	832.000000	832	78.254000	1256	2557	1	chr4B.!!$F1	1301
6	TraesCS5A01G362400	chrUn	15759094	15760435	1341	True	826.000000	826	78.063000	1022	2367	1	chrUn.!!$R1	1345
7	TraesCS5A01G362400	chrUn	15603993	15605508	1515	False	800.000000	800	76.331000	1022	2531	1	chrUn.!!$F1	1509
8	TraesCS5A01G362400	chrUn	357124600	357125326	726	False	385.000000	385	76.269000	1805	2531	1	chrUn.!!$F3	726
9	TraesCS5A01G362400	chr4A	601338032	601339331	1299	False	774.000000	774	77.634000	1256	2551	1	chr4A.!!$F3	1295
10	TraesCS5A01G362400	chr2A	778631108	778632672	1564	False	640.000000	640	74.495000	977	2527	1	chr2A.!!$F1	1550
11	TraesCS5A01G362400	chr2A	2218778	2219363	585	True	374.000000	374	78.415000	1039	1624	1	chr2A.!!$R1	585
12	TraesCS5A01G362400	chr2B	777963061	777964492	1431	True	529.000000	529	73.757000	1081	2501	1	chr2B.!!$R2	1420
13	TraesCS5A01G362400	chr4D	351370849	351371587	738	False	221.133333	337	89.278333	2881	3527	3	chr4D.!!$F1	646

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
926	2625	1.493772	CACACGACCAACGAGCTTAA	58.506	50.0	0.0	0.0	45.77	1.85	F
1201	2909	0.320073	CTTGGTTCTCGCCGGTAACA	60.320	55.0	1.9	0.0	0.00	2.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2249	3974	0.472471	ACAATTCTCACCCCACACGT	59.528	50.000	0.0	0.0	0.0	4.49	R
2716	6972	3.933332	GCATACGGTTCTTTCTGTTAGCT	59.067	43.478	0.0	0.0	0.0	3.32	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
82	83	7.512992	AGAGGCTAATAAAGTAGCACATGAAT	58.487	34.615	11.13	0.00	46.98	2.57
163	164	9.063739	GTGAAATTGTAACGTTTCTTACAAACA	57.936	29.630	15.98	13.44	45.34	2.83
179	180	9.632807	TCTTACAAACAATGTATTGGTTATTGC	57.367	29.630	7.50	0.00	45.25	3.56
279	280	2.227089	CTTCTTCGCCTGCTACCGGT	62.227	60.000	13.98	13.98	0.00	5.28
302	303	8.948631	GGTACACGATCATGATGGATATAAAT	57.051	34.615	22.78	0.00	0.00	1.40
312	313	9.410556	TCATGATGGATATAAATATATGTCGCG	57.589	33.333	0.00	0.00	32.15	5.87
328	329	2.915463	GTCGCGATAAGATAATCGGTGG	59.085	50.000	14.06	0.00	46.89	4.61
345	346	7.843490	ATCGGTGGAAATAAATATGGATACG	57.157	36.000	0.00	0.00	42.51	3.06
658	2355	4.327680	GAAAAGAGTGGTTGGCTACTGAT	58.672	43.478	0.00	0.00	36.53	2.90
683	2380	8.806429	TCAACTGCTAATTAAGGATGATTTGA	57.194	30.769	0.00	0.00	0.00	2.69
872	2571	4.678743	GCCAAAACGCCCCTCCCT	62.679	66.667	0.00	0.00	0.00	4.20
926	2625	1.493772	CACACGACCAACGAGCTTAA	58.506	50.000	0.00	0.00	45.77	1.85
1050	2755	1.166129	TCTCCACACTCGTGCTACTC	58.834	55.000	0.00	0.00	42.17	2.59
1201	2909	0.320073	CTTGGTTCTCGCCGGTAACA	60.320	55.000	1.90	0.00	0.00	2.41
1513	3221	1.372004	CACATGGCAAGCACCAACG	60.372	57.895	0.00	0.00	44.65	4.10
2249	3974	2.285275	TCCATGGGAAGAATGAGGGA	57.715	50.000	13.02	0.00	0.00	4.20
2263	3989	2.920912	GGGACGTGTGGGGTGAGA	60.921	66.667	0.00	0.00	0.00	3.27
2611	4337	3.313526	CGAGGTTCAGGGCTTCAATATTG	59.686	47.826	9.29	9.29	0.00	1.90
2716	6972	5.638596	TTGTCTCAACTCGCACTATCTTA	57.361	39.130	0.00	0.00	0.00	2.10
2717	6973	5.236655	TGTCTCAACTCGCACTATCTTAG	57.763	43.478	0.00	0.00	0.00	2.18
2718	6974	4.039032	GTCTCAACTCGCACTATCTTAGC	58.961	47.826	0.00	0.00	0.00	3.09
2719	6975	3.948473	TCTCAACTCGCACTATCTTAGCT	59.052	43.478	0.00	0.00	0.00	3.32
2720	6976	5.007823	GTCTCAACTCGCACTATCTTAGCTA	59.992	44.000	0.00	0.00	0.00	3.32
2721	6977	5.589050	TCTCAACTCGCACTATCTTAGCTAA	59.411	40.000	5.94	5.94	0.00	3.09
2722	6978	5.579718	TCAACTCGCACTATCTTAGCTAAC	58.420	41.667	0.86	0.00	0.00	2.34
2930	7186	4.704540	ACTTGTGTTGGATGTTCAGTTTGA	59.295	37.500	0.00	0.00	0.00	2.69
2936	7192	5.534278	TGTTGGATGTTCAGTTTGATGCTAA	59.466	36.000	0.00	0.00	0.00	3.09
2939	7195	6.446318	TGGATGTTCAGTTTGATGCTAAAAC	58.554	36.000	2.47	2.47	37.71	2.43
2999	7255	3.250744	ACATTCAGATACGGTCACAACG	58.749	45.455	0.00	0.00	37.36	4.10
3121	7532	1.809567	AACACTACGACCCGTCACCC	61.810	60.000	0.00	0.00	41.54	4.61

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
55	56	5.932619	TGTGCTACTTTATTAGCCTCTCA	57.067	39.130	0.00	0.00	43.43	3.27
106	107	3.258872	TCCTTAAACCAATCCGAAGTCGA	59.741	43.478	1.43	0.00	43.02	4.20
107	108	3.592059	TCCTTAAACCAATCCGAAGTCG	58.408	45.455	0.00	0.00	39.44	4.18
108	109	3.374367	GCTCCTTAAACCAATCCGAAGTC	59.626	47.826	0.00	0.00	0.00	3.01
109	110	3.344515	GCTCCTTAAACCAATCCGAAGT	58.655	45.455	0.00	0.00	0.00	3.01
110	111	2.683362	GGCTCCTTAAACCAATCCGAAG	59.317	50.000	0.00	0.00	0.00	3.79
112	113	1.913419	AGGCTCCTTAAACCAATCCGA	59.087	47.619	0.00	0.00	0.00	4.55
113	114	2.420058	AGGCTCCTTAAACCAATCCG	57.580	50.000	0.00	0.00	0.00	4.18
114	115	6.486993	CACTAATAGGCTCCTTAAACCAATCC	59.513	42.308	0.00	0.00	0.00	3.01
115	116	7.280356	TCACTAATAGGCTCCTTAAACCAATC	58.720	38.462	0.00	0.00	0.00	2.67
208	209	5.742838	GCCATCCTTCCTTGTGAATGTTTTT	60.743	40.000	0.00	0.00	31.06	1.94
301	302	7.803659	CACCGATTATCTTATCGCGACATATAT	59.196	37.037	12.93	4.41	44.55	0.86
302	303	7.130269	CACCGATTATCTTATCGCGACATATA	58.870	38.462	12.93	4.50	44.55	0.86
303	304	5.971792	CACCGATTATCTTATCGCGACATAT	59.028	40.000	12.93	5.59	44.55	1.78
304	305	5.329493	CACCGATTATCTTATCGCGACATA	58.671	41.667	12.93	0.00	44.55	2.29
341	342	5.373222	TGCCACTTATTAGCCATTTCGTAT	58.627	37.500	0.00	0.00	0.00	3.06
345	346	5.105756	ACTGTTGCCACTTATTAGCCATTTC	60.106	40.000	0.00	0.00	0.00	2.17
658	2355	8.806429	TCAAATCATCCTTAATTAGCAGTTGA	57.194	30.769	0.00	0.00	0.00	3.18
683	2380	4.281182	AGAGTTCTACAGTCGACCAATGTT	59.719	41.667	13.01	0.00	0.00	2.71
744	2441	5.258051	TGGACCAACCAATCATTAACCTAC	58.742	41.667	0.00	0.00	46.75	3.18
819	2518	5.692115	TGCTCCTGGATGAACAGTAAATA	57.308	39.130	0.00	0.00	36.75	1.40
872	2571	4.644498	CATCATGTACTGCATATGGACCA	58.356	43.478	4.56	0.00	35.74	4.02
926	2625	7.815383	TCATTTATAGACATGACCCCTCAATT	58.185	34.615	0.00	0.00	0.00	2.32
1050	2755	5.579511	CCTAAAGTACAAGTACATGGGAACG	59.420	44.000	12.43	0.00	38.48	3.95
1201	2909	2.281761	CGCCCTGAAGTTGTGGCT	60.282	61.111	0.00	0.00	41.80	4.75
1229	2937	0.326927	GAACCTCATTCCGGTCCCAA	59.673	55.000	0.00	0.00	32.46	4.12
1513	3221	3.944015	AGTTCCTGCATGTCAAATAGAGC	59.056	43.478	0.00	0.00	0.00	4.09
2249	3974	0.472471	ACAATTCTCACCCCACACGT	59.528	50.000	0.00	0.00	0.00	4.49
2263	3989	5.497474	GTGTGGGTTATAGTCCAGACAATT	58.503	41.667	14.61	0.00	43.99	2.32
2716	6972	3.933332	GCATACGGTTCTTTCTGTTAGCT	59.067	43.478	0.00	0.00	0.00	3.32
2717	6973	3.933332	AGCATACGGTTCTTTCTGTTAGC	59.067	43.478	0.00	0.00	0.00	3.09
2718	6974	5.637810	TCAAGCATACGGTTCTTTCTGTTAG	59.362	40.000	0.00	0.00	0.00	2.34
2719	6975	5.543714	TCAAGCATACGGTTCTTTCTGTTA	58.456	37.500	0.00	0.00	0.00	2.41
2720	6976	4.385825	TCAAGCATACGGTTCTTTCTGTT	58.614	39.130	0.00	0.00	0.00	3.16
2721	6977	4.002906	TCAAGCATACGGTTCTTTCTGT	57.997	40.909	0.00	0.00	0.00	3.41
2722	6978	5.551760	AATCAAGCATACGGTTCTTTCTG	57.448	39.130	0.00	0.00	0.00	3.02
2878	7134	9.031537	TGTGACTTTCAGTGATATTACCTCTAA	57.968	33.333	0.00	0.00	0.00	2.10
2879	7135	8.589701	TGTGACTTTCAGTGATATTACCTCTA	57.410	34.615	0.00	0.00	0.00	2.43
2930	7186	9.705290	AAATCCGTATTTTCAAAGTTTTAGCAT	57.295	25.926	0.00	0.00	30.98	3.79
2936	7192	7.269316	ACCACAAATCCGTATTTTCAAAGTTT	58.731	30.769	0.00	0.00	32.87	2.66
2939	7195	6.442952	TGACCACAAATCCGTATTTTCAAAG	58.557	36.000	0.00	0.00	32.87	2.77
3121	7532	8.405531	TGGTCTGTCTTTCTCACAAATAAAAAG	58.594	33.333	0.00	0.00	0.00	2.27
3301	7713	2.143122	CAACGTGAATGGTGTAGCAGT	58.857	47.619	0.00	0.00	0.00	4.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.