AutoCloner

Multiple sequence alignment - TraesCS1A01G131400

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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	TraesCS1A01G131400	chr1A	100.000	3018	0	0	1	3018	174434668	174437685	0.000000e+00	5574
1	TraesCS1A01G131400	chr1A	92.248	1677	118	4	1	1675	174442433	174444099	0.000000e+00	2366
2	TraesCS1A01G131400	chr1A	93.126	1353	90	3	1669	3018	174444126	174445478	0.000000e+00	1980
3	TraesCS1A01G131400	chr1A	89.710	690	69	2	1669	2356	315047931	315048620	0.000000e+00	880
4	TraesCS1A01G131400	chr3A	87.741	1713	153	34	2	1675	694888932	694890626	0.000000e+00	1947
5	TraesCS1A01G131400	chr3A	86.217	1705	185	39	1	1676	509030957	509029274	0.000000e+00	1801
6	TraesCS1A01G131400	chr3A	85.875	1692	181	36	1	1675	713015810	713014160	0.000000e+00	1748
7	TraesCS1A01G131400	chr3A	85.512	1698	181	37	1	1675	713056281	713054626	0.000000e+00	1712
8	TraesCS1A01G131400	chr3A	86.334	1361	144	35	2	1335	316660606	316659261	0.000000e+00	1445
9	TraesCS1A01G131400	chr3A	95.062	648	28	4	2375	3018	279011618	279010971	0.000000e+00	1016
10	TraesCS1A01G131400	chr3A	93.856	651	35	5	2372	3018	279005805	279005156	0.000000e+00	976
11	TraesCS1A01G131400	chr3A	89.209	556	57	3	1671	2224	713054597	713054043	0.000000e+00	691
12	TraesCS1A01G131400	chr4A	86.913	1704	179	34	2	1676	148641019	148642707	0.000000e+00	1871
13	TraesCS1A01G131400	chr4A	84.402	1731	193	52	2	1676	389345403	389343694	0.000000e+00	1629
14	TraesCS1A01G131400	chr4A	88.360	1323	126	22	2	1315	384886073	384887376	0.000000e+00	1565
15	TraesCS1A01G131400	chr4A	88.774	1256	112	19	2	1244	75117501	75116262	0.000000e+00	1511
16	TraesCS1A01G131400	chrUn	85.816	1692	182	34	1	1675	312324218	312322568	0.000000e+00	1742
17	TraesCS1A01G131400	chrUn	85.816	1692	182	34	1	1675	312328054	312326404	0.000000e+00	1742
18	TraesCS1A01G131400	chrUn	88.909	559	59	3	1669	2225	312322541	312321984	0.000000e+00	686
19	TraesCS1A01G131400	chrUn	88.909	559	59	3	1669	2225	312326377	312325820	0.000000e+00	686
20	TraesCS1A01G131400	chrUn	88.909	559	59	3	1669	2225	331808880	331809437	0.000000e+00	686
21	TraesCS1A01G131400	chr6A	89.590	1268	115	15	3	1264	546613330	546612074	0.000000e+00	1594
22	TraesCS1A01G131400	chr6A	88.166	1276	125	22	2	1265	94725063	94726324	0.000000e+00	1496
23	TraesCS1A01G131400	chr6A	95.545	651	25	4	2372	3018	429349447	429350097	0.000000e+00	1038
24	TraesCS1A01G131400	chr6A	94.281	647	32	5	2375	3018	429355691	429356335	0.000000e+00	985
25	TraesCS1A01G131400	chr2A	87.754	1331	129	27	2	1315	57643706	57645019	0.000000e+00	1524
26	TraesCS1A01G131400	chr2A	88.277	853	89	10	829	1675	471486540	471487387	0.000000e+00	1011
27	TraesCS1A01G131400	chr2A	90.000	690	67	2	1669	2356	471480496	471481185	0.000000e+00	891
28	TraesCS1A01G131400	chr2A	89.643	560	55	3	1754	2311	412802705	412802147	0.000000e+00	710
29	TraesCS1A01G131400	chr2A	89.267	559	49	7	1754	2301	412744632	412744074	0.000000e+00	689
30	TraesCS1A01G131400	chr2A	91.232	422	36	1	1936	2356	471443870	471443449	9.380000e-160	573
31	TraesCS1A01G131400	chr2A	94.667	75	4	0	2209	2283	444358598	444358672	1.900000e-22	117
32	TraesCS1A01G131400	chr7A	87.519	1314	139	21	2	1300	308595806	308594503	0.000000e+00	1495
33	TraesCS1A01G131400	chr7A	94.579	701	29	8	2324	3018	496470625	496469928	0.000000e+00	1075
34	TraesCS1A01G131400	chr7A	94.302	702	30	7	2324	3018	496462957	496462259	0.000000e+00	1066
35	TraesCS1A01G131400	chr7A	94.931	651	29	4	2372	3018	325557359	325558009	0.000000e+00	1016
36	TraesCS1A01G131400	chr7A	94.172	652	30	6	2372	3018	325545208	325544560	0.000000e+00	987
37	TraesCS1A01G131400	chr7D	87.663	1305	122	33	1	1285	309568162	309569447	0.000000e+00	1482
38	TraesCS1A01G131400	chr5B	89.292	551	52	5	1754	2301	684564967	684565513	0.000000e+00	684
39	TraesCS1A01G131400	chr5B	89.292	551	52	5	1754	2301	684572578	684573124	0.000000e+00	684

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	TraesCS1A01G131400	chr1A	174434668	174437685	3017	False	5574.0	5574	100.0000	1	3018	1	chr1A.!!$F1	3017
1	TraesCS1A01G131400	chr1A	174442433	174445478	3045	False	2173.0	2366	92.6870	1	3018	2	chr1A.!!$F3	3017
2	TraesCS1A01G131400	chr1A	315047931	315048620	689	False	880.0	880	89.7100	1669	2356	1	chr1A.!!$F2	687
3	TraesCS1A01G131400	chr3A	694888932	694890626	1694	False	1947.0	1947	87.7410	2	1675	1	chr3A.!!$F1	1673
4	TraesCS1A01G131400	chr3A	509029274	509030957	1683	True	1801.0	1801	86.2170	1	1676	1	chr3A.!!$R4	1675
5	TraesCS1A01G131400	chr3A	713014160	713015810	1650	True	1748.0	1748	85.8750	1	1675	1	chr3A.!!$R5	1674
6	TraesCS1A01G131400	chr3A	316659261	316660606	1345	True	1445.0	1445	86.3340	2	1335	1	chr3A.!!$R3	1333
7	TraesCS1A01G131400	chr3A	713054043	713056281	2238	True	1201.5	1712	87.3605	1	2224	2	chr3A.!!$R6	2223
8	TraesCS1A01G131400	chr3A	279010971	279011618	647	True	1016.0	1016	95.0620	2375	3018	1	chr3A.!!$R2	643
9	TraesCS1A01G131400	chr3A	279005156	279005805	649	True	976.0	976	93.8560	2372	3018	1	chr3A.!!$R1	646
10	TraesCS1A01G131400	chr4A	148641019	148642707	1688	False	1871.0	1871	86.9130	2	1676	1	chr4A.!!$F1	1674
11	TraesCS1A01G131400	chr4A	389343694	389345403	1709	True	1629.0	1629	84.4020	2	1676	1	chr4A.!!$R2	1674
12	TraesCS1A01G131400	chr4A	384886073	384887376	1303	False	1565.0	1565	88.3600	2	1315	1	chr4A.!!$F2	1313
13	TraesCS1A01G131400	chr4A	75116262	75117501	1239	True	1511.0	1511	88.7740	2	1244	1	chr4A.!!$R1	1242
14	TraesCS1A01G131400	chrUn	312321984	312328054	6070	True	1214.0	1742	87.3625	1	2225	4	chrUn.!!$R1	2224
15	TraesCS1A01G131400	chrUn	331808880	331809437	557	False	686.0	686	88.9090	1669	2225	1	chrUn.!!$F1	556
16	TraesCS1A01G131400	chr6A	546612074	546613330	1256	True	1594.0	1594	89.5900	3	1264	1	chr6A.!!$R1	1261
17	TraesCS1A01G131400	chr6A	94725063	94726324	1261	False	1496.0	1496	88.1660	2	1265	1	chr6A.!!$F1	1263
18	TraesCS1A01G131400	chr6A	429349447	429350097	650	False	1038.0	1038	95.5450	2372	3018	1	chr6A.!!$F2	646
19	TraesCS1A01G131400	chr6A	429355691	429356335	644	False	985.0	985	94.2810	2375	3018	1	chr6A.!!$F3	643
20	TraesCS1A01G131400	chr2A	57643706	57645019	1313	False	1524.0	1524	87.7540	2	1315	1	chr2A.!!$F1	1313
21	TraesCS1A01G131400	chr2A	471486540	471487387	847	False	1011.0	1011	88.2770	829	1675	1	chr2A.!!$F4	846
22	TraesCS1A01G131400	chr2A	471480496	471481185	689	False	891.0	891	90.0000	1669	2356	1	chr2A.!!$F3	687
23	TraesCS1A01G131400	chr2A	412802147	412802705	558	True	710.0	710	89.6430	1754	2311	1	chr2A.!!$R2	557
24	TraesCS1A01G131400	chr2A	412744074	412744632	558	True	689.0	689	89.2670	1754	2301	1	chr2A.!!$R1	547
25	TraesCS1A01G131400	chr7A	308594503	308595806	1303	True	1495.0	1495	87.5190	2	1300	1	chr7A.!!$R1	1298
26	TraesCS1A01G131400	chr7A	496469928	496470625	697	True	1075.0	1075	94.5790	2324	3018	1	chr7A.!!$R4	694
27	TraesCS1A01G131400	chr7A	496462259	496462957	698	True	1066.0	1066	94.3020	2324	3018	1	chr7A.!!$R3	694
28	TraesCS1A01G131400	chr7A	325557359	325558009	650	False	1016.0	1016	94.9310	2372	3018	1	chr7A.!!$F1	646
29	TraesCS1A01G131400	chr7A	325544560	325545208	648	True	987.0	987	94.1720	2372	3018	1	chr7A.!!$R2	646
30	TraesCS1A01G131400	chr7D	309568162	309569447	1285	False	1482.0	1482	87.6630	1	1285	1	chr7D.!!$F1	1284
31	TraesCS1A01G131400	chr5B	684564967	684565513	546	False	684.0	684	89.2920	1754	2301	1	chr5B.!!$F1	547
32	TraesCS1A01G131400	chr5B	684572578	684573124	546	False	684.0	684	89.2920	1754	2301	1	chr5B.!!$F2	547

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
55	56	0.974010	ATGACGGAAACTAGGGCGGA	60.974	55.0	0.00	0.0	0.0	5.54	F
1135	5088	0.108992	TTCGCGACAAGGCTAACGAT	60.109	50.0	9.15	0.0	0.0	3.73	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1866	5861	0.674581	CCGCTGCTCCTGTTCATCAA	60.675	55.0	0.0	0.0	0.0	2.57	R
2301	6310	0.902531	CCTCCTTCCACCTAGCGAAA	59.097	55.0	0.0	0.0	0.0	3.46	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
55	56	0.974010	ATGACGGAAACTAGGGCGGA	60.974	55.000	0.00	0.00	0.00	5.54
76	77	4.081917	GGAAAGAGTGGAACAAAACACCAA	60.082	41.667	0.00	0.00	44.16	3.67
77	78	5.395214	GGAAAGAGTGGAACAAAACACCAAT	60.395	40.000	0.00	0.00	44.16	3.16
78	79	5.675684	AAGAGTGGAACAAAACACCAATT	57.324	34.783	0.00	0.00	44.16	2.32
87	88	6.426646	AACAAAACACCAATTATAAGGCCA	57.573	33.333	5.01	0.00	0.00	5.36
103	104	1.820010	GCCAAGCCTTCCACCCTTTG	61.820	60.000	0.00	0.00	0.00	2.77
118	119	6.102615	TCCACCCTTTGCCAAGTATATAGATT	59.897	38.462	0.00	0.00	0.00	2.40
267	311	3.181434	ACAATGGTTTGCTAGGAAGGTGA	60.181	43.478	0.00	0.00	36.22	4.02
286	330	1.210478	GAGTTAGAGGCTTGGCATGGA	59.790	52.381	2.33	0.00	0.00	3.41
320	364	5.308825	GCATGATATAGCAAGTGGTAGGTT	58.691	41.667	0.00	0.00	0.00	3.50
391	442	4.837093	TTTCGAGGGTATGGTCATCTTT	57.163	40.909	0.00	0.00	0.00	2.52
466	517	6.262273	ACGTAGTTGAACAAATCCTCACAAAT	59.738	34.615	0.00	0.00	37.78	2.32
752	830	2.490903	ACATGGCAAGAGATGAAGCAAC	59.509	45.455	0.00	0.00	0.00	4.17
787	867	7.494922	ACAATCTAAGCAATTTAAATGGGGT	57.505	32.000	0.39	0.40	0.00	4.95
1135	5088	0.108992	TTCGCGACAAGGCTAACGAT	60.109	50.000	9.15	0.00	0.00	3.73
1254	5213	0.591236	GAAGCGTGCGTTTTGAAGCA	60.591	50.000	0.00	0.00	41.55	3.91
1315	5275	4.632153	GCCATGTTCATAGTGGTAGTAGG	58.368	47.826	0.00	0.00	35.44	3.18
1376	5336	3.955551	TGGTAGTGGTACATAGCAATCGA	59.044	43.478	0.00	0.00	44.52	3.59
1471	5431	1.294138	GGCGGCAGTAGTGGTACAA	59.706	57.895	3.07	0.00	44.16	2.41
1483	5443	2.158871	AGTGGTACAAGTTTCGAAGGCA	60.159	45.455	0.00	0.00	44.16	4.75
1487	5447	3.500680	GGTACAAGTTTCGAAGGCATTCA	59.499	43.478	12.16	0.00	34.94	2.57
1518	5478	2.915869	AGAGGTACTTGGTGAATCCCA	58.084	47.619	0.00	0.00	41.55	4.37
1538	5498	2.270352	AAATGGTCTTGGCGTCTTCA	57.730	45.000	0.00	0.00	0.00	3.02
1636	5596	1.067565	AGTCGTGCACTTGTCATCGAT	60.068	47.619	16.19	0.00	26.56	3.59
1738	5733	2.049063	GCCGTGCAGAAGACGACT	60.049	61.111	0.00	0.00	39.21	4.18
1747	5742	2.360844	CAGAAGACGACTGAGCTCCTA	58.639	52.381	12.15	0.00	37.54	2.94
1752	5747	3.887352	AGACGACTGAGCTCCTATTACA	58.113	45.455	12.15	0.00	0.00	2.41
1768	5763	4.410400	CAGGGAGGGTTCGTGGCC	62.410	72.222	0.00	0.00	0.00	5.36
1866	5861	0.600557	CTGTCTGCCTCGTCAACTCT	59.399	55.000	0.00	0.00	0.00	3.24
1870	5865	1.895798	TCTGCCTCGTCAACTCTTGAT	59.104	47.619	0.00	0.00	42.47	2.57
2097	6104	2.527951	GAAGACAGGCGCCCACATCT	62.528	60.000	26.15	17.86	0.00	2.90
2100	6107	2.360350	CAGGCGCCCACATCTTGT	60.360	61.111	26.15	0.00	0.00	3.16
2109	6116	2.422597	CCCACATCTTGTACGAAGCAA	58.577	47.619	0.00	0.00	0.00	3.91
2128	6135	4.752879	GGACTTGGCGCGGCTACA	62.753	66.667	33.23	16.17	0.00	2.74
2140	6147	1.599542	GCGGCTACAATGATGAGGAAC	59.400	52.381	0.00	0.00	0.00	3.62
2146	6153	2.711542	ACAATGATGAGGAACCGAACC	58.288	47.619	0.00	0.00	0.00	3.62
2169	6176	2.443394	GGTCGGGGATGAGGCATCA	61.443	63.158	2.36	2.36	42.13	3.07
2269	6278	2.359967	GGGAACGAGGAGGTGGAGG	61.360	68.421	0.00	0.00	0.00	4.30
2401	6413	2.204319	GGATCGAGGGGATGGGGA	59.796	66.667	0.00	0.00	34.82	4.81
2432	6444	2.103432	GCTAGGTTAAAGGAGGAGGAGC	59.897	54.545	0.00	0.00	0.00	4.70
2649	6666	9.171877	AGGAATTTTAGAGAGAATAAAGTGCAG	57.828	33.333	0.00	0.00	0.00	4.41
2958	6977	9.424319	TGAGCAACTAAATTAAACAAACACAAA	57.576	25.926	0.00	0.00	0.00	2.83

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
55	56	5.675684	ATTGGTGTTTTGTTCCACTCTTT	57.324	34.783	0.00	0.00	0.00	2.52
87	88	1.533994	GGCAAAGGGTGGAAGGCTT	60.534	57.895	0.00	0.00	0.00	4.35
267	311	1.289160	TCCATGCCAAGCCTCTAACT	58.711	50.000	0.00	0.00	0.00	2.24
286	330	6.331577	TGCTATATCATGCCTCCCATATTT	57.668	37.500	0.00	0.00	31.47	1.40
320	364	3.058501	TCGATCTATTGCTATGTCGCGAA	60.059	43.478	12.06	1.13	0.00	4.70
391	442	0.617535	TTCCTTGCGGGATCTCAGGA	60.618	55.000	0.00	0.00	44.66	3.86
448	499	3.567585	TCGCATTTGTGAGGATTTGTTCA	59.432	39.130	0.00	0.00	0.00	3.18
631	696	4.679373	ACTCGTTGCATATTGATCTCCT	57.321	40.909	0.00	0.00	0.00	3.69
787	867	5.285651	GGAATTGTTGTTTGATGTTTCCGA	58.714	37.500	0.00	0.00	0.00	4.55
1135	5088	2.083774	GGATTGATCCTTGCACGTTCA	58.916	47.619	2.72	0.00	43.73	3.18
1254	5213	5.339008	TCTACTTTGCACCGAACTGATAT	57.661	39.130	0.00	0.00	0.00	1.63
1315	5275	1.475280	TCCACTACGGCATGAGTACAC	59.525	52.381	0.00	0.00	33.14	2.90
1376	5336	2.162608	CGATGACTCTCAAGTTCGTCCT	59.837	50.000	0.00	0.00	35.28	3.85
1390	5350	5.064558	ACCTATGAACGTCTATCGATGACT	58.935	41.667	8.54	0.00	42.86	3.41
1410	5370	1.056660	ACAACCATCACCGAAGACCT	58.943	50.000	0.00	0.00	0.00	3.85
1471	5431	2.997485	GCTTGAATGCCTTCGAAACT	57.003	45.000	0.00	0.00	33.86	2.66
1483	5443	7.275920	CAAGTACCTCTACTTATGGCTTGAAT	58.724	38.462	0.00	0.00	40.64	2.57
1487	5447	5.030820	ACCAAGTACCTCTACTTATGGCTT	58.969	41.667	0.00	0.00	40.64	4.35
1518	5478	2.293399	GTGAAGACGCCAAGACCATTTT	59.707	45.455	0.00	0.00	0.00	1.82
1538	5498	3.010413	GCCAAGTACCCCTACGCGT	62.010	63.158	19.17	19.17	0.00	6.01
1587	5547	1.202710	TGTGCCAAGTACCACGATGTT	60.203	47.619	0.00	0.00	34.77	2.71
1636	5596	2.206900	TCAAGACCCTCCAGCCCA	59.793	61.111	0.00	0.00	0.00	5.36
1728	5723	2.791347	TAGGAGCTCAGTCGTCTTCT	57.209	50.000	17.19	2.24	0.00	2.85
1747	5742	0.909623	CCACGAACCCTCCCTGTAAT	59.090	55.000	0.00	0.00	0.00	1.89
1752	5747	4.974438	TGGCCACGAACCCTCCCT	62.974	66.667	0.00	0.00	0.00	4.20
1768	5763	1.284982	CTCCTTTGCGTCCTGTCGTG	61.285	60.000	0.00	0.00	0.00	4.35
1781	5776	4.729918	CAGCTGCCGCCCTCCTTT	62.730	66.667	0.00	0.00	36.60	3.11
1866	5861	0.674581	CCGCTGCTCCTGTTCATCAA	60.675	55.000	0.00	0.00	0.00	2.57
1870	5865	2.031012	CACCGCTGCTCCTGTTCA	59.969	61.111	0.00	0.00	0.00	3.18
2097	6104	2.875933	CCAAGTCCTTTGCTTCGTACAA	59.124	45.455	0.00	0.00	35.37	2.41
2100	6107	1.519408	GCCAAGTCCTTTGCTTCGTA	58.481	50.000	0.00	0.00	35.37	3.43
2109	6116	3.702048	TAGCCGCGCCAAGTCCTT	61.702	61.111	0.00	0.00	0.00	3.36
2128	6135	2.356125	CCTGGTTCGGTTCCTCATCATT	60.356	50.000	0.00	0.00	0.00	2.57
2146	6153	2.136878	CCTCATCCCCGACCTCCTG	61.137	68.421	0.00	0.00	0.00	3.86
2169	6176	1.762460	CTGTACAGGATCCGGCCCT	60.762	63.158	15.49	9.15	0.00	5.19
2296	6305	2.093447	CCTTCCACCTAGCGAAATCACT	60.093	50.000	0.00	0.00	0.00	3.41
2301	6310	0.902531	CCTCCTTCCACCTAGCGAAA	59.097	55.000	0.00	0.00	0.00	3.46
2302	6311	0.976073	CCCTCCTTCCACCTAGCGAA	60.976	60.000	0.00	0.00	0.00	4.70
2401	6413	1.789523	TTAACCTAGCGCCAGGAGAT	58.210	50.000	29.19	15.58	39.18	2.75
2475	6487	1.380302	GGGAGAAGAGCAAGCCCAA	59.620	57.895	0.00	0.00	38.68	4.12
2483	6495	2.849294	AACTCAAGTGGGAGAAGAGC	57.151	50.000	0.00	0.00	38.30	4.09
2701	6719	2.936553	GCCCATTTGGATTCAGTTTGGC	60.937	50.000	0.00	0.00	37.39	4.52
2958	6977	5.698104	TCATGCATCTTCTCCATACCATTT	58.302	37.500	0.00	0.00	0.00	2.32

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.