AutoCloner

Multiple sequence alignment - TraesCS2B01G106800

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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	TraesCS2B01G106800	chr2B	100.000	2468	0	0	1	2468	67914273	67916740	0.000000e+00	4558
1	TraesCS2B01G106800	chr2B	83.479	799	113	14	1000	1789	67909124	67909912	0.000000e+00	726
2	TraesCS2B01G106800	chr2B	83.190	464	47	12	301	739	123271277	123270820	1.780000e-106	396
3	TraesCS2B01G106800	chrUn	91.748	921	48	14	894	1811	305992624	305993519	0.000000e+00	1254
4	TraesCS2B01G106800	chrUn	92.812	640	28	9	1172	1811	314907192	314906571	0.000000e+00	911
5	TraesCS2B01G106800	chrUn	92.812	640	28	9	1172	1811	382173246	382172625	0.000000e+00	911
6	TraesCS2B01G106800	chrUn	82.819	745	76	19	180	893	87331579	87332302	9.700000e-174	619
7	TraesCS2B01G106800	chrUn	84.416	462	63	8	1334	1791	305990389	305990845	1.740000e-121	446
8	TraesCS2B01G106800	chrUn	84.416	462	63	8	1334	1791	338084242	338084698	1.740000e-121	446
9	TraesCS2B01G106800	chrUn	89.606	279	19	5	894	1169	338086477	338086748	1.820000e-91	346
10	TraesCS2B01G106800	chrUn	81.928	332	53	6	1003	1329	332241867	332241538	8.700000e-70	274
11	TraesCS2B01G106800	chrUn	86.345	249	28	2	8	256	357363472	357363714	1.460000e-67	267
12	TraesCS2B01G106800	chrUn	82.960	223	35	3	1	221	87331125	87331346	5.380000e-47	198
13	TraesCS2B01G106800	chr2D	91.342	924	57	10	894	1809	43235628	43236536	0.000000e+00	1242
14	TraesCS2B01G106800	chr2D	85.593	590	81	4	1042	1629	43232160	43231573	1.250000e-172	616
15	TraesCS2B01G106800	chr2D	85.042	595	78	7	1042	1632	43230959	43231546	1.630000e-166	595
16	TraesCS2B01G106800	chr2D	78.306	484	96	4	995	1469	38798677	38799160	1.110000e-78	303
17	TraesCS2B01G106800	chr2D	76.744	387	77	11	515	893	19896317	19896698	1.160000e-48	204
18	TraesCS2B01G106800	chr2D	84.177	158	22	2	995	1149	40917359	40917516	1.530000e-32	150
19	TraesCS2B01G106800	chr1B	86.645	906	89	17	8	893	3114234	3113341	0.000000e+00	974
20	TraesCS2B01G106800	chr1B	86.747	249	27	2	8	256	59999083	59999325	3.130000e-69	272
21	TraesCS2B01G106800	chr1B	89.855	207	18	2	690	893	162230073	162230279	1.880000e-66	263
22	TraesCS2B01G106800	chr3B	93.897	639	38	1	1830	2468	26597175	26596538	0.000000e+00	963
23	TraesCS2B01G106800	chr3B	93.195	529	32	3	1	527	755461834	755462360	0.000000e+00	774
24	TraesCS2B01G106800	chr3B	83.578	816	101	22	92	896	47161857	47161064	0.000000e+00	734
25	TraesCS2B01G106800	chr6B	93.631	628	40	0	1841	2468	494477108	494476481	0.000000e+00	939
26	TraesCS2B01G106800	chr4B	92.801	639	43	3	1830	2468	69123897	69124532	0.000000e+00	922
27	TraesCS2B01G106800	chr4D	92.308	650	47	3	1819	2468	494043158	494043804	0.000000e+00	920
28	TraesCS2B01G106800	chr4D	91.692	650	47	4	1819	2468	8142031	8141389	0.000000e+00	894
29	TraesCS2B01G106800	chr4D	87.270	707	65	13	1	687	6354678	6355379	0.000000e+00	784
30	TraesCS2B01G106800	chr1D	92.645	639	45	2	1830	2468	267590	266954	0.000000e+00	918
31	TraesCS2B01G106800	chr1D	91.549	639	52	2	1830	2468	300665717	300665081	0.000000e+00	880
32	TraesCS2B01G106800	chr7A	92.236	644	48	2	1825	2468	736318202	736317561	0.000000e+00	911
33	TraesCS2B01G106800	chr5A	91.943	633	50	1	1836	2468	70675725	70675094	0.000000e+00	885
34	TraesCS2B01G106800	chr7D	84.123	718	69	15	200	893	590953618	590952922	0.000000e+00	652
35	TraesCS2B01G106800	chr7D	90.385	156	15	0	1	156	590954251	590954096	3.220000e-49	206
36	TraesCS2B01G106800	chr3A	84.314	663	56	18	257	893	697713493	697712853	2.710000e-169	604
37	TraesCS2B01G106800	chr7B	89.305	374	34	5	524	893	651993733	651994104	4.810000e-127	464
38	TraesCS2B01G106800	chr2A	81.791	335	54	6	1000	1329	44762845	44763177	8.700000e-70	274
39	TraesCS2B01G106800	chr2A	84.898	245	27	8	653	893	483381776	483382014	3.170000e-59	239
40	TraesCS2B01G106800	chr3D	78.342	374	68	12	528	893	259106217	259106585	1.910000e-56	230
41	TraesCS2B01G106800	chr3D	79.118	340	59	10	528	859	259104064	259104399	8.880000e-55	224

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	TraesCS2B01G106800	chr2B	67914273	67916740	2467	False	4558.0	4558	100.0000	1	2468	1	chr2B.!!$F2	2467
1	TraesCS2B01G106800	chr2B	67909124	67909912	788	False	726.0	726	83.4790	1000	1789	1	chr2B.!!$F1	789
2	TraesCS2B01G106800	chrUn	314906571	314907192	621	True	911.0	911	92.8120	1172	1811	1	chrUn.!!$R1	639
3	TraesCS2B01G106800	chrUn	382172625	382173246	621	True	911.0	911	92.8120	1172	1811	1	chrUn.!!$R3	639
4	TraesCS2B01G106800	chrUn	305990389	305993519	3130	False	850.0	1254	88.0820	894	1811	2	chrUn.!!$F3	917
5	TraesCS2B01G106800	chrUn	87331125	87332302	1177	False	408.5	619	82.8895	1	893	2	chrUn.!!$F2	892
6	TraesCS2B01G106800	chrUn	338084242	338086748	2506	False	396.0	446	87.0110	894	1791	2	chrUn.!!$F4	897
7	TraesCS2B01G106800	chr2D	43235628	43236536	908	False	1242.0	1242	91.3420	894	1809	1	chr2D.!!$F5	915
8	TraesCS2B01G106800	chr2D	43231573	43232160	587	True	616.0	616	85.5930	1042	1629	1	chr2D.!!$R1	587
9	TraesCS2B01G106800	chr2D	43230959	43231546	587	False	595.0	595	85.0420	1042	1632	1	chr2D.!!$F4	590
10	TraesCS2B01G106800	chr1B	3113341	3114234	893	True	974.0	974	86.6450	8	893	1	chr1B.!!$R1	885
11	TraesCS2B01G106800	chr3B	26596538	26597175	637	True	963.0	963	93.8970	1830	2468	1	chr3B.!!$R1	638
12	TraesCS2B01G106800	chr3B	755461834	755462360	526	False	774.0	774	93.1950	1	527	1	chr3B.!!$F1	526
13	TraesCS2B01G106800	chr3B	47161064	47161857	793	True	734.0	734	83.5780	92	896	1	chr3B.!!$R2	804
14	TraesCS2B01G106800	chr6B	494476481	494477108	627	True	939.0	939	93.6310	1841	2468	1	chr6B.!!$R1	627
15	TraesCS2B01G106800	chr4B	69123897	69124532	635	False	922.0	922	92.8010	1830	2468	1	chr4B.!!$F1	638
16	TraesCS2B01G106800	chr4D	494043158	494043804	646	False	920.0	920	92.3080	1819	2468	1	chr4D.!!$F2	649
17	TraesCS2B01G106800	chr4D	8141389	8142031	642	True	894.0	894	91.6920	1819	2468	1	chr4D.!!$R1	649
18	TraesCS2B01G106800	chr4D	6354678	6355379	701	False	784.0	784	87.2700	1	687	1	chr4D.!!$F1	686
19	TraesCS2B01G106800	chr1D	266954	267590	636	True	918.0	918	92.6450	1830	2468	1	chr1D.!!$R1	638
20	TraesCS2B01G106800	chr1D	300665081	300665717	636	True	880.0	880	91.5490	1830	2468	1	chr1D.!!$R2	638
21	TraesCS2B01G106800	chr7A	736317561	736318202	641	True	911.0	911	92.2360	1825	2468	1	chr7A.!!$R1	643
22	TraesCS2B01G106800	chr5A	70675094	70675725	631	True	885.0	885	91.9430	1836	2468	1	chr5A.!!$R1	632
23	TraesCS2B01G106800	chr7D	590952922	590954251	1329	True	429.0	652	87.2540	1	893	2	chr7D.!!$R1	892
24	TraesCS2B01G106800	chr3A	697712853	697713493	640	True	604.0	604	84.3140	257	893	1	chr3A.!!$R1	636
25	TraesCS2B01G106800	chr3D	259104064	259106585	2521	False	227.0	230	78.7300	528	893	2	chr3D.!!$F1	365

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
743	2381	0.032952	AAGCGTCTTTGCCGTCTGTA	59.967	50.0	0.0	0.0	34.65	2.74	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2205	5643	1.139734	CATGTCGCGTGCCTAGTCT	59.86	57.895	5.77	0.0	0.0	3.24	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
244	955	2.038659	GATCTGGAGGACAAGAGGGAG	58.961	57.143	0.00	0.00	0.00	4.30
380	1108	1.337118	GGCCTTCTCTGGATCGAGAT	58.663	55.000	7.98	0.00	39.60	2.75
417	1155	2.808567	CGGAGAGAGAGATCGTGATGGA	60.809	54.545	0.00	0.00	0.00	3.41
487	1249	2.761160	GAAATGGGACGTGGGGGT	59.239	61.111	0.00	0.00	0.00	4.95
615	2245	3.328382	TTACAGACGGCAAAGTAGCAT	57.672	42.857	0.00	0.00	35.83	3.79
625	2255	2.595386	CAAAGTAGCATTTTGCCGTCC	58.405	47.619	0.00	0.00	46.52	4.79
627	2257	0.036765	AGTAGCATTTTGCCGTCCGA	60.037	50.000	0.00	0.00	46.52	4.55
680	2315	0.528017	TGCGGTTTTGTTTGCAGACA	59.472	45.000	5.87	5.87	32.73	3.41
743	2381	0.032952	AAGCGTCTTTGCCGTCTGTA	59.967	50.000	0.00	0.00	34.65	2.74
799	2439	1.160137	AGCCATTCTTTGTCGTCAGC	58.840	50.000	0.00	0.00	0.00	4.26
807	2447	4.251543	TCTTTGTCGTCAGCAACTGATA	57.748	40.909	0.00	0.00	42.73	2.15
826	2466	1.484038	AGCAAAAGTGGTCTTTGCCA	58.516	45.000	14.76	0.00	42.26	4.92
835	2475	0.038166	GGTCTTTGCCATCTGTCCCA	59.962	55.000	0.00	0.00	0.00	4.37
860	2500	0.536006	AAGCTGACGGCAAAGAGCTT	60.536	50.000	9.51	9.51	44.95	3.74
864	2504	2.358737	ACGGCAAAGAGCTTCCCG	60.359	61.111	15.99	15.99	44.79	5.14
870	2510	2.214920	AAAGAGCTTCCCGGACGGT	61.215	57.895	0.73	0.00	0.00	4.83
907	2547	7.414222	TCCCGTAGTGTTATCTCAAGTATTT	57.586	36.000	0.00	0.00	0.00	1.40
932	2572	3.570926	GACACTGTGTCCGTAATCTGA	57.429	47.619	26.50	0.00	41.37	3.27
985	2630	0.792640	CACTTTTGCACTCGCTCGAT	59.207	50.000	0.00	0.00	39.64	3.59
1122	2770	1.073923	GACCTGGACTGGTGGTTTCAT	59.926	52.381	0.00	0.00	41.00	2.57
1130	2778	2.988684	GTGGTTTCATGGGCCGCA	60.989	61.111	0.00	0.00	33.35	5.69
1158	2806	2.106131	CACATGCGGCGCCTACTA	59.894	61.111	30.82	10.91	0.00	1.82
1159	2807	1.951130	CACATGCGGCGCCTACTAG	60.951	63.158	30.82	14.40	0.00	2.57
1169	2817	2.783288	GCCTACTAGCCGGCGAAGT	61.783	63.158	31.38	31.38	36.45	3.01
1331	2980	0.955428	GGCGTCATCACCAGCTTTCA	60.955	55.000	0.00	0.00	0.00	2.69
1373	3022	1.079405	CGGTTCGAAAGCTAGGCCA	60.079	57.895	5.01	0.00	0.00	5.36
1419	3068	1.857965	CCATCTGGGAGAGTCAGTCA	58.142	55.000	0.00	0.00	40.01	3.41
1473	3122	0.035534	TGCTTGCCATATGACACCGT	60.036	50.000	3.65	0.00	0.00	4.83
1648	3301	4.098349	AGCATGTGTGTTTTGAATGAGTGT	59.902	37.500	0.00	0.00	0.00	3.55
1651	3304	5.233957	TGTGTGTTTTGAATGAGTGTGAG	57.766	39.130	0.00	0.00	0.00	3.51
1657	3310	5.525012	TGTTTTGAATGAGTGTGAGTCTCAG	59.475	40.000	1.75	0.00	43.66	3.35
1663	3316	0.965439	AGTGTGAGTCTCAGGCAGTC	59.035	55.000	1.75	0.00	0.00	3.51
1720	3375	2.635915	AGAGGTCCCGTTTTATGACACA	59.364	45.455	0.00	0.00	0.00	3.72
1811	3466	3.056749	CAGGGTATACGGCATTAGGAGAC	60.057	52.174	0.00	0.00	0.00	3.36
1814	3469	3.193056	GGTATACGGCATTAGGAGACCTC	59.807	52.174	0.00	0.00	34.61	3.85
1839	4108	3.083997	GCCCCCACGTGATCTCCT	61.084	66.667	19.30	0.00	0.00	3.69
1900	4169	4.465446	CGGGCCTCCCTCTCCTCA	62.465	72.222	0.84	0.00	42.67	3.86
1924	4254	4.779733	GGCGTCCCTCTCCTCCCA	62.780	72.222	0.00	0.00	0.00	4.37
2031	5469	4.217159	GCGGCGACCTAATCCGGT	62.217	66.667	12.98	0.00	43.11	5.28
2122	5560	2.758327	TCGGCGGCTATGGTGTCT	60.758	61.111	7.21	0.00	0.00	3.41
2130	5568	1.765314	GGCTATGGTGTCTGATCTGGT	59.235	52.381	0.00	0.00	0.00	4.00
2159	5597	1.566231	GGATCTGGATGGTGGTTCCTT	59.434	52.381	0.00	0.00	37.07	3.36
2320	5758	2.787473	TGGATTTTCGCATCCAGTCT	57.213	45.000	6.69	0.00	46.67	3.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
380	1108	0.322648	TCCGTCTCGTACCTCTGTGA	59.677	55.000	0.00	0.00	0.00	3.58
417	1155	3.252284	CTGACAGCCCACCCACCT	61.252	66.667	0.00	0.00	0.00	4.00
487	1249	0.523519	TGCAACGCAAAACACACTCA	59.476	45.000	0.00	0.00	34.76	3.41
643	2277	2.095853	CGCAGACGGCAAATATCTTTGT	59.904	45.455	5.57	0.00	45.17	2.83
674	2309	1.601759	TGCTCCCTTTGCTGTCTGC	60.602	57.895	0.00	0.00	43.25	4.26
687	2322	0.320421	TACAGACGGCAAAGTGCTCC	60.320	55.000	0.00	0.00	44.28	4.70
718	2356	3.099574	GCAAAGACGCTTTGCCGC	61.100	61.111	30.35	16.37	46.51	6.53
799	2439	5.695851	AAGACCACTTTTGCTATCAGTTG	57.304	39.130	0.00	0.00	31.71	3.16
807	2447	1.484038	TGGCAAAGACCACTTTTGCT	58.516	45.000	18.54	0.00	43.41	3.91
826	2466	3.760684	GTCAGCTTTTCATTGGGACAGAT	59.239	43.478	0.00	0.00	42.39	2.90
835	2475	2.622942	TCTTTGCCGTCAGCTTTTCATT	59.377	40.909	0.00	0.00	44.23	2.57
860	2500	1.137479	CAGCTAATTTACCGTCCGGGA	59.863	52.381	10.91	0.00	39.97	5.14
864	2504	3.813724	GGGAATCAGCTAATTTACCGTCC	59.186	47.826	0.00	0.00	0.00	4.79
870	2510	6.229936	ACACTACGGGAATCAGCTAATTTA	57.770	37.500	0.00	0.00	0.00	1.40
932	2572	8.688151	CAAATTGAGTAGGCTAGTACTCTAGTT	58.312	37.037	17.04	13.39	46.32	2.24
979	2624	6.128172	CCCATAGTTAAATTGGATGATCGAGC	60.128	42.308	0.00	0.00	31.94	5.03
985	2630	5.010922	GCATGCCCATAGTTAAATTGGATGA	59.989	40.000	6.36	0.00	31.94	2.92
1130	2778	1.820906	CGCATGTGCTGGCACCTAT	60.821	57.895	20.80	7.80	45.63	2.57
1158	2806	4.394712	CCCTTCACTTCGCCGGCT	62.395	66.667	26.68	1.35	0.00	5.52
1245	2894	4.047125	CCTTCCGCCACCACCCAT	62.047	66.667	0.00	0.00	0.00	4.00
1331	2980	4.037565	TGACAGACGTGTTGAAGTACTCAT	59.962	41.667	0.00	0.00	36.88	2.90
1373	3022	1.305381	ACGTCCTCCTTAGCTGGCT	60.305	57.895	0.00	0.00	0.00	4.75
1419	3068	4.798682	CGGCCCCTGGGTCTAGGT	62.799	72.222	12.71	0.00	37.84	3.08
1522	3174	7.668525	ACTTTCCCGTTATCAGAGTAAAAAG	57.331	36.000	0.00	0.00	0.00	2.27
1535	3187	3.006003	GGCCAAAATCAACTTTCCCGTTA	59.994	43.478	0.00	0.00	0.00	3.18
1589	3241	7.118422	AGACTAATTCTCGAAAGAAAAACCG	57.882	36.000	0.00	0.00	44.49	4.44
1601	3254	7.166804	GCTAGCAAGTAAGAAGACTAATTCTCG	59.833	40.741	10.63	0.00	38.59	4.04
1648	3301	3.093057	AGTATGACTGCCTGAGACTCA	57.907	47.619	4.78	4.78	0.00	3.41
1651	3304	4.993029	AACTAGTATGACTGCCTGAGAC	57.007	45.455	0.00	0.00	0.00	3.36
1657	3310	5.287992	GTGACGTAAAACTAGTATGACTGCC	59.712	44.000	0.00	0.00	0.00	4.85
1663	3316	9.953825	GAAGAAATGTGACGTAAAACTAGTATG	57.046	33.333	0.00	0.00	0.00	2.39
1728	3383	3.929610	CAGACCTCTCGGAGAAAATGAAC	59.070	47.826	9.32	0.00	34.09	3.18
1729	3384	3.578716	ACAGACCTCTCGGAGAAAATGAA	59.421	43.478	9.32	0.00	34.09	2.57
1730	3385	3.165875	ACAGACCTCTCGGAGAAAATGA	58.834	45.455	9.32	0.00	34.09	2.57
1820	3475	4.530857	GAGATCACGTGGGGGCGG	62.531	72.222	17.00	0.00	35.98	6.13
1821	3476	4.530857	GGAGATCACGTGGGGGCG	62.531	72.222	17.00	0.00	37.94	6.13
1822	3477	2.595009	GAAGGAGATCACGTGGGGGC	62.595	65.000	17.00	3.32	0.00	5.80
1823	3478	1.522569	GAAGGAGATCACGTGGGGG	59.477	63.158	17.00	0.00	0.00	5.40
1824	3479	1.522569	GGAAGGAGATCACGTGGGG	59.477	63.158	17.00	0.00	0.00	4.96
1826	3481	1.522569	GGGGAAGGAGATCACGTGG	59.477	63.158	17.00	0.00	0.00	4.94
1827	3482	1.522569	GGGGGAAGGAGATCACGTG	59.477	63.158	9.94	9.94	0.00	4.49
1910	4240	2.760385	CGGTGGGAGGAGAGGGAC	60.760	72.222	0.00	0.00	0.00	4.46
2025	5463	1.146263	GCCCTTGAATCGACCGGAT	59.854	57.895	9.46	0.00	36.78	4.18
2031	5469	1.523711	GCCATCGCCCTTGAATCGA	60.524	57.895	0.00	0.00	36.63	3.59
2205	5643	1.139734	CATGTCGCGTGCCTAGTCT	59.860	57.895	5.77	0.00	0.00	3.24
2250	5688	2.532715	ATGGCCACCACCTCCACT	60.533	61.111	8.16	0.00	35.80	4.00
2287	5725	3.737559	AAATCCACAACCATCTAGCCA	57.262	42.857	0.00	0.00	0.00	4.75
2320	5758	2.363795	CTCCCCACTCTACGCCCA	60.364	66.667	0.00	0.00	0.00	5.36
2450	5888	4.383861	TCACCCAGAGCAGCGCAG	62.384	66.667	11.47	1.31	0.00	5.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.