AutoCloner

Multiple sequence alignment - TraesCS4B01G284500

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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	TraesCS4B01G284500	chr4B	100.000	3202	0	0	1	3202	568338895	568342096	0.000000e+00	5914.0
1	TraesCS4B01G284500	chr4B	98.857	875	8	2	2329	3202	5372869	5373742	0.000000e+00	1559.0
2	TraesCS4B01G284500	chr4B	98.857	875	8	2	2329	3202	90723724	90724597	0.000000e+00	1559.0
3	TraesCS4B01G284500	chr4B	98.743	875	9	2	2329	3202	187177281	187176408	0.000000e+00	1554.0
4	TraesCS4B01G284500	chr4B	82.940	1653	216	31	554	2161	568409898	568411529	0.000000e+00	1430.0
5	TraesCS4B01G284500	chr4B	81.998	1672	233	37	592	2218	568405614	568407262	0.000000e+00	1358.0
6	TraesCS4B01G284500	chr4B	83.238	1044	154	11	647	1688	568369364	568370388	0.000000e+00	939.0
7	TraesCS4B01G284500	chr4D	94.932	2052	82	12	285	2329	455253708	455255744	0.000000e+00	3193.0
8	TraesCS4B01G284500	chr4D	82.706	1116	157	19	592	1688	455289300	455290398	0.000000e+00	959.0
9	TraesCS4B01G284500	chr4D	84.256	921	108	14	1268	2160	455319208	455320119	0.000000e+00	863.0
10	TraesCS4B01G284500	chr4D	90.152	132	7	4	7	138	455253425	455253550	1.980000e-37	167.0
11	TraesCS4B01G284500	chr4D	77.381	336	36	17	1960	2280	455290891	455291201	2.560000e-36	163.0
12	TraesCS4B01G284500	chr4D	78.545	275	38	9	1704	1957	455290529	455290803	9.190000e-36	161.0
13	TraesCS4B01G284500	chr4D	92.500	80	6	0	2138	2217	455320121	455320200	7.260000e-22	115.0
14	TraesCS4B01G284500	chr4D	94.000	50	3	0	156	205	455253595	455253644	3.430000e-10	76.8
15	TraesCS4B01G284500	chr4A	93.139	2055	82	24	249	2294	12679266	12677262	0.000000e+00	2959.0
16	TraesCS4B01G284500	chr4A	83.231	1628	223	32	623	2227	12645821	12644221	0.000000e+00	1448.0
17	TraesCS4B01G284500	chr4A	85.357	799	88	8	1460	2229	12626588	12625790	0.000000e+00	800.0
18	TraesCS4B01G284500	chr4A	84.056	715	95	15	748	1453	12641299	12640595	0.000000e+00	671.0
19	TraesCS4B01G284500	chr4A	84.881	463	59	6	1229	1691	12658681	12658230	1.050000e-124	457.0
20	TraesCS4B01G284500	chr4A	80.435	460	59	17	1704	2132	12658102	12657643	3.980000e-84	322.0
21	TraesCS4B01G284500	chr4A	89.677	155	9	5	7	157	12679646	12679495	1.170000e-44	191.0
22	TraesCS4B01G284500	chr4A	81.053	190	16	13	2135	2307	12657664	12657478	2.000000e-27	134.0
23	TraesCS4B01G284500	chr3A	98.970	874	8	1	2329	3202	11468112	11467240	0.000000e+00	1563.0
24	TraesCS4B01G284500	chr3A	98.744	876	9	2	2328	3202	544482399	544481525	0.000000e+00	1555.0
25	TraesCS4B01G284500	chr7B	98.747	878	9	2	2326	3202	457408149	457407273	0.000000e+00	1559.0
26	TraesCS4B01G284500	chr1B	98.857	875	8	2	2329	3202	655769509	655770382	0.000000e+00	1559.0
27	TraesCS4B01G284500	chr6B	98.744	876	9	2	2328	3202	339383037	339383911	0.000000e+00	1555.0
28	TraesCS4B01G284500	chr6B	80.059	1018	176	16	766	1770	236571655	236572658	0.000000e+00	730.0
29	TraesCS4B01G284500	chr6B	80.488	943	159	14	757	1693	236477409	236478332	0.000000e+00	699.0
30	TraesCS4B01G284500	chr6B	85.377	212	25	6	1919	2126	236478930	236479139	6.960000e-52	215.0
31	TraesCS4B01G284500	chr2A	98.416	884	12	2	2320	3202	671337707	671338589	0.000000e+00	1554.0
32	TraesCS4B01G284500	chr6D	81.703	869	145	11	762	1626	137146097	137146955	0.000000e+00	712.0

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	TraesCS4B01G284500	chr4B	568338895	568342096	3201	False	5914.000000	5914	100.0000	1	3202	1	chr4B.!!$F3	3201
1	TraesCS4B01G284500	chr4B	5372869	5373742	873	False	1559.000000	1559	98.8570	2329	3202	1	chr4B.!!$F1	873
2	TraesCS4B01G284500	chr4B	90723724	90724597	873	False	1559.000000	1559	98.8570	2329	3202	1	chr4B.!!$F2	873
3	TraesCS4B01G284500	chr4B	187176408	187177281	873	True	1554.000000	1554	98.7430	2329	3202	1	chr4B.!!$R1	873
4	TraesCS4B01G284500	chr4B	568405614	568411529	5915	False	1394.000000	1430	82.4690	554	2218	2	chr4B.!!$F5	1664
5	TraesCS4B01G284500	chr4B	568369364	568370388	1024	False	939.000000	939	83.2380	647	1688	1	chr4B.!!$F4	1041
6	TraesCS4B01G284500	chr4D	455253425	455255744	2319	False	1145.600000	3193	93.0280	7	2329	3	chr4D.!!$F1	2322
7	TraesCS4B01G284500	chr4D	455319208	455320200	992	False	489.000000	863	88.3780	1268	2217	2	chr4D.!!$F3	949
8	TraesCS4B01G284500	chr4D	455289300	455291201	1901	False	427.666667	959	79.5440	592	2280	3	chr4D.!!$F2	1688
9	TraesCS4B01G284500	chr4A	12677262	12679646	2384	True	1575.000000	2959	91.4080	7	2294	2	chr4A.!!$R4	2287
10	TraesCS4B01G284500	chr4A	12640595	12645821	5226	True	1059.500000	1448	83.6435	623	2227	2	chr4A.!!$R2	1604
11	TraesCS4B01G284500	chr4A	12625790	12626588	798	True	800.000000	800	85.3570	1460	2229	1	chr4A.!!$R1	769
12	TraesCS4B01G284500	chr4A	12657478	12658681	1203	True	304.333333	457	82.1230	1229	2307	3	chr4A.!!$R3	1078
13	TraesCS4B01G284500	chr3A	11467240	11468112	872	True	1563.000000	1563	98.9700	2329	3202	1	chr3A.!!$R1	873
14	TraesCS4B01G284500	chr3A	544481525	544482399	874	True	1555.000000	1555	98.7440	2328	3202	1	chr3A.!!$R2	874
15	TraesCS4B01G284500	chr7B	457407273	457408149	876	True	1559.000000	1559	98.7470	2326	3202	1	chr7B.!!$R1	876
16	TraesCS4B01G284500	chr1B	655769509	655770382	873	False	1559.000000	1559	98.8570	2329	3202	1	chr1B.!!$F1	873
17	TraesCS4B01G284500	chr6B	339383037	339383911	874	False	1555.000000	1555	98.7440	2328	3202	1	chr6B.!!$F2	874
18	TraesCS4B01G284500	chr6B	236571655	236572658	1003	False	730.000000	730	80.0590	766	1770	1	chr6B.!!$F1	1004
19	TraesCS4B01G284500	chr6B	236477409	236479139	1730	False	457.000000	699	82.9325	757	2126	2	chr6B.!!$F3	1369
20	TraesCS4B01G284500	chr2A	671337707	671338589	882	False	1554.000000	1554	98.4160	2320	3202	1	chr2A.!!$F1	882
21	TraesCS4B01G284500	chr6D	137146097	137146955	858	False	712.000000	712	81.7030	762	1626	1	chr6D.!!$F1	864

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
279	425	0.183492	ACTGTCCCTCAAGCAAGCAA	59.817	50.0	0.00	0.0	0.00	3.91	F
565	719	0.544697	TCTATTCCTCCCGGCAAACC	59.455	55.0	0.00	0.0	0.00	3.27	F
957	1131	0.893447	GGAGCTTGCAAGAAGCCAAT	59.107	50.0	30.39	5.7	44.01	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1788	6704	1.877443	ACATTTCCGTAACTGGTGCAC	59.123	47.619	8.80	8.8	0.00	4.57	R
2076	7161	2.224113	CCAAAACAGCAGGCATTCTTGT	60.224	45.455	0.00	0.0	0.00	3.16	R
2496	8080	2.314071	TGGGAGGAGTCCGTTAAGAA	57.686	50.000	2.76	0.0	45.05	2.52	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
30	31	2.434359	CGTCTCCCCACGAAAGCC	60.434	66.667	0.00	0.00	42.69	4.35
42	43	0.391263	CGAAAGCCCTCTTTACGCCT	60.391	55.000	0.00	0.00	42.24	5.52
46	47	2.202892	CCCTCTTTACGCCTCCGC	60.203	66.667	0.00	0.00	38.22	5.54
181	225	2.485795	GGTGCAAACGTGGAAGCCA	61.486	57.895	0.00	0.00	0.00	4.75
213	276	3.194062	GAGGCTCTGCAGTATGAACTTC	58.806	50.000	14.67	0.77	39.69	3.01
229	292	1.134965	ACTTCATCCCTTTCTCGCTCG	60.135	52.381	0.00	0.00	0.00	5.03
276	422	1.239968	GCCACTGTCCCTCAAGCAAG	61.240	60.000	0.00	0.00	0.00	4.01
277	423	1.239968	CCACTGTCCCTCAAGCAAGC	61.240	60.000	0.00	0.00	0.00	4.01
278	424	0.535780	CACTGTCCCTCAAGCAAGCA	60.536	55.000	0.00	0.00	0.00	3.91
279	425	0.183492	ACTGTCCCTCAAGCAAGCAA	59.817	50.000	0.00	0.00	0.00	3.91
282	428	1.251251	GTCCCTCAAGCAAGCAACAT	58.749	50.000	0.00	0.00	0.00	2.71
317	463	2.611518	CACCTCGTCTTCACTTCCATC	58.388	52.381	0.00	0.00	0.00	3.51
381	527	6.381498	TCCAAACTTAACCATGATCCACTA	57.619	37.500	0.00	0.00	0.00	2.74
385	533	6.808321	AACTTAACCATGATCCACTAGCTA	57.192	37.500	0.00	0.00	0.00	3.32
386	534	6.412362	ACTTAACCATGATCCACTAGCTAG	57.588	41.667	19.44	19.44	0.00	3.42
387	535	3.760580	AACCATGATCCACTAGCTAGC	57.239	47.619	20.91	6.62	0.00	3.42
388	536	2.969628	ACCATGATCCACTAGCTAGCT	58.030	47.619	23.12	23.12	0.00	3.32
389	537	3.312890	ACCATGATCCACTAGCTAGCTT	58.687	45.455	24.88	2.63	0.00	3.74
390	538	3.713764	ACCATGATCCACTAGCTAGCTTT	59.286	43.478	24.88	7.72	0.00	3.51
391	539	4.202305	ACCATGATCCACTAGCTAGCTTTC	60.202	45.833	24.88	12.51	0.00	2.62
392	540	3.717400	TGATCCACTAGCTAGCTTTCG	57.283	47.619	24.88	14.11	0.00	3.46
393	541	3.288092	TGATCCACTAGCTAGCTTTCGA	58.712	45.455	24.88	13.62	0.00	3.71
394	542	3.891977	TGATCCACTAGCTAGCTTTCGAT	59.108	43.478	24.88	17.58	0.00	3.59
450	598	4.994852	TGCCGGTTGCTATATTATTCAGTC	59.005	41.667	1.90	0.00	42.00	3.51
547	701	1.266718	TCCAGCATCTGCAAAAACGTC	59.733	47.619	4.79	0.00	45.16	4.34
565	719	0.544697	TCTATTCCTCCCGGCAAACC	59.455	55.000	0.00	0.00	0.00	3.27
616	770	3.960102	TGTTCCTCTTGCTCCATTGTTTT	59.040	39.130	0.00	0.00	0.00	2.43
617	771	4.037923	TGTTCCTCTTGCTCCATTGTTTTC	59.962	41.667	0.00	0.00	0.00	2.29
957	1131	0.893447	GGAGCTTGCAAGAAGCCAAT	59.107	50.000	30.39	5.70	44.01	3.16
1116	1312	2.202810	GCTTTCGGAGGCGGAGAG	60.203	66.667	0.00	0.00	0.00	3.20
1330	5825	9.173939	GCTGTGTTAATTGTCTTATATTCATGC	57.826	33.333	0.00	0.00	0.00	4.06
1646	6145	1.324435	CATACGGTTCGTGCTCACATG	59.676	52.381	3.03	0.00	41.39	3.21
1668	6167	7.391554	ACATGTATATGGTAGATGTCATTTGGC	59.608	37.037	0.00	0.00	38.66	4.52
1788	6704	0.976641	TCTAAGGCCGATGCTATGGG	59.023	55.000	0.00	0.00	37.74	4.00
1791	6707	2.965716	AAGGCCGATGCTATGGGTGC	62.966	60.000	0.00	0.00	37.74	5.01
1794	6710	1.893808	CCGATGCTATGGGTGCACC	60.894	63.158	28.57	28.57	43.59	5.01
1825	6741	5.047377	GGAAATGTTGATTTGAAGCACCCTA	60.047	40.000	0.00	0.00	31.58	3.53
2014	7082	9.492973	GGTTGGTACTTGTCAGTAATTTTACTA	57.507	33.333	2.79	0.00	41.82	1.82
2076	7161	2.498644	TGTGGCAAAATCGGATGGTA	57.501	45.000	0.00	0.00	0.00	3.25
2238	7376	8.954834	ATCCCCTTATGCATATGTTTGATTTA	57.045	30.769	7.36	0.00	0.00	1.40
2239	7377	8.954834	TCCCCTTATGCATATGTTTGATTTAT	57.045	30.769	7.36	0.00	0.00	1.40
2240	7378	9.378504	TCCCCTTATGCATATGTTTGATTTATT	57.621	29.630	7.36	0.00	0.00	1.40
2283	7432	7.012421	GTGCAAGACTATAATTCCTAAACCCTG	59.988	40.741	0.00	0.00	0.00	4.45
2474	8058	3.769300	TGTCCATAGCTAGCTCTTTGTCA	59.231	43.478	23.26	14.52	0.00	3.58
2496	8080	5.488919	TCAATACTCCAATCCTTCAGGTCTT	59.511	40.000	0.00	0.00	36.34	3.01
2666	8250	0.395724	CCTCAATTGGTGCTACCCCC	60.396	60.000	5.42	0.00	37.50	5.40
2951	10262	3.367280	TCATCAATACCCCCATCCTCT	57.633	47.619	0.00	0.00	0.00	3.69
3105	10587	4.585879	CCTAAACCCTTTCGATTCCAAGA	58.414	43.478	0.00	0.00	0.00	3.02
3179	10661	0.243365	GCACCACATCATCCGCAAAA	59.757	50.000	0.00	0.00	0.00	2.44

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	1.726533	GGAGACGAGGGGAAGCTACG	61.727	65.000	0.00	0.00	0.00	3.51
1	2	1.393487	GGGAGACGAGGGGAAGCTAC	61.393	65.000	0.00	0.00	0.00	3.58
2	3	1.076192	GGGAGACGAGGGGAAGCTA	60.076	63.158	0.00	0.00	0.00	3.32
3	4	2.364448	GGGAGACGAGGGGAAGCT	60.364	66.667	0.00	0.00	0.00	3.74
5	6	2.038975	TGGGGAGACGAGGGGAAG	59.961	66.667	0.00	0.00	0.00	3.46
134	135	4.227134	CGGGAGGCATGACCGGAG	62.227	72.222	9.46	0.00	46.52	4.63
162	206	2.335011	GCTTCCACGTTTGCACCC	59.665	61.111	0.00	0.00	0.00	4.61
199	243	4.574674	AAGGGATGAAGTTCATACTGCA	57.425	40.909	24.22	0.00	44.13	4.41
213	276	0.873743	GAGCGAGCGAGAAAGGGATG	60.874	60.000	0.00	0.00	0.00	3.51
229	292	3.731717	CGTAGAAAAATAGAGGAGCGAGC	59.268	47.826	0.00	0.00	0.00	5.03
276	422	1.070038	CACGAATTTGGCCATGTTGC	58.930	50.000	6.09	0.00	0.00	4.17
277	423	1.712401	CCACGAATTTGGCCATGTTG	58.288	50.000	6.09	0.87	0.00	3.33
317	463	5.241506	ACATTTCCTTTGTGTAGATGTGGTG	59.758	40.000	0.00	0.00	0.00	4.17
344	490	7.939588	GGTTAAGTTTGGATATAGCTGAGGATT	59.060	37.037	0.00	0.00	0.00	3.01
391	539	2.407361	ACGCAACAACTAGTCGAAATCG	59.593	45.455	7.80	0.00	41.45	3.34
392	540	3.673809	AGACGCAACAACTAGTCGAAATC	59.326	43.478	7.80	0.00	38.53	2.17
393	541	3.428870	CAGACGCAACAACTAGTCGAAAT	59.571	43.478	7.80	0.00	38.53	2.17
394	542	2.792674	CAGACGCAACAACTAGTCGAAA	59.207	45.455	7.80	0.00	38.53	3.46
399	547	2.296471	AGTAGCAGACGCAACAACTAGT	59.704	45.455	0.00	0.00	42.27	2.57
403	551	1.457303	CAGAGTAGCAGACGCAACAAC	59.543	52.381	0.00	0.00	42.27	3.32
407	555	1.173913	TAGCAGAGTAGCAGACGCAA	58.826	50.000	0.00	0.00	42.27	4.85
410	558	1.601663	GGCATAGCAGAGTAGCAGACG	60.602	57.143	0.00	0.00	36.85	4.18
450	598	7.974675	ACAACTTATTCATCAACTAACCATCG	58.025	34.615	0.00	0.00	0.00	3.84
530	684	4.142600	GGAATAGACGTTTTTGCAGATGCT	60.143	41.667	6.35	0.00	42.66	3.79
597	751	3.831323	TGAAAACAATGGAGCAAGAGGA	58.169	40.909	0.00	0.00	0.00	3.71
661	817	8.142551	TCAGAAGGTTAGTAGACAAGAAAGTTC	58.857	37.037	0.00	0.00	0.00	3.01
798	972	2.444624	CGTTGGCGAGACGTCATGG	61.445	63.158	19.50	7.24	42.26	3.66
957	1131	1.071228	AGATGGCTCGCAATAGCATCA	59.929	47.619	0.00	0.00	44.64	3.07
1330	5825	4.268644	CACGGATTGTATCAGCAACTAGTG	59.731	45.833	0.00	0.00	0.00	2.74
1351	5846	2.751806	CAAGATCCTGAAAAGGAGGCAC	59.248	50.000	0.39	0.00	41.88	5.01
1477	5972	3.680490	TGCCACCGTGAAAATTATCAGA	58.320	40.909	0.00	0.00	0.00	3.27
1483	5978	2.363680	TGTTGATGCCACCGTGAAAATT	59.636	40.909	0.00	0.00	0.00	1.82
1646	6145	6.128172	GCAGCCAAATGACATCTACCATATAC	60.128	42.308	0.00	0.00	0.00	1.47
1668	6167	2.496899	AAACATGACACTAGGGGCAG	57.503	50.000	6.70	0.70	0.00	4.85
1788	6704	1.877443	ACATTTCCGTAACTGGTGCAC	59.123	47.619	8.80	8.80	0.00	4.57
1791	6707	5.371115	AATCAACATTTCCGTAACTGGTG	57.629	39.130	0.00	0.00	0.00	4.17
1794	6710	6.088085	GCTTCAAATCAACATTTCCGTAACTG	59.912	38.462	0.00	0.00	28.97	3.16
1825	6741	9.918630	GCAACCTTTATATTTATGAGCATTGAT	57.081	29.630	0.00	0.00	0.00	2.57
1834	6750	7.576236	CGAGAGTGGCAACCTTTATATTTATG	58.424	38.462	0.00	0.00	0.00	1.90
1849	6770	4.314440	GTGTGGGCGAGAGTGGCA	62.314	66.667	0.00	0.00	35.84	4.92
2014	7082	8.082242	GGCACTGAAACAGAATAATAACACTTT	58.918	33.333	5.76	0.00	35.18	2.66
2076	7161	2.224113	CCAAAACAGCAGGCATTCTTGT	60.224	45.455	0.00	0.00	0.00	3.16
2238	7376	9.762933	TCTTGCACTTTCTTAGCAAAAATAAAT	57.237	25.926	0.00	0.00	46.30	1.40
2239	7377	9.030301	GTCTTGCACTTTCTTAGCAAAAATAAA	57.970	29.630	0.00	0.00	46.30	1.40
2240	7378	8.413229	AGTCTTGCACTTTCTTAGCAAAAATAA	58.587	29.630	0.00	0.00	46.30	1.40
2241	7379	7.940850	AGTCTTGCACTTTCTTAGCAAAAATA	58.059	30.769	0.00	0.00	46.30	1.40
2312	7650	9.953697	GTTGTTGTTGTACATTTTCATAAGGTA	57.046	29.630	0.00	0.00	0.00	3.08
2313	7651	8.470805	TGTTGTTGTTGTACATTTTCATAAGGT	58.529	29.630	0.00	0.00	0.00	3.50
2425	8009	2.806745	GCGTGGAAGCTTGCTATCCATA	60.807	50.000	19.34	0.00	44.55	2.74
2474	8058	6.216456	AGAAAGACCTGAAGGATTGGAGTATT	59.784	38.462	2.62	0.00	38.94	1.89
2496	8080	2.314071	TGGGAGGAGTCCGTTAAGAA	57.686	50.000	2.76	0.00	45.05	2.52
2666	8250	9.729023	GGAATGATGATATACGAGATAGAGTTG	57.271	37.037	0.00	0.00	0.00	3.16
2951	10262	3.007398	GGTATTTGGGGTCAATGTTGCAA	59.993	43.478	0.00	0.00	32.28	4.08
3179	10661	5.171339	GAGATATCCCATGGTGTATGCTT	57.829	43.478	11.73	0.00	35.37	3.91

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.