AutoCloner

Multiple sequence alignment - TraesCS3A01G020200

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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	TraesCS3A01G020200	chr3A	100.000	3077	0	0	1	3077	11919649	11922725	0.000000e+00	5683
1	TraesCS3A01G020200	chr3A	98.854	1134	3	2	1	1133	11932257	11933381	0.000000e+00	2013
2	TraesCS3A01G020200	chr3A	91.086	1492	99	16	971	2453	12118232	12116766	0.000000e+00	1988
3	TraesCS3A01G020200	chr3A	100.000	576	0	0	231	806	11873948	11873373	0.000000e+00	1064
4	TraesCS3A01G020200	chr3A	100.000	520	0	0	936	1455	11873362	11872843	0.000000e+00	961
5	TraesCS3A01G020200	chr3A	87.605	597	56	8	1484	2077	11872790	11872209	0.000000e+00	676
6	TraesCS3A01G020200	chr3A	99.367	158	1	0	766	923	11915389	11915546	1.400000e-73	287
7	TraesCS3A01G020200	chr3A	82.927	205	18	14	2536	2737	12116748	12116558	5.280000e-38	169
8	TraesCS3A01G020200	chr3D	91.793	987	49	9	2113	3077	9066194	9065218	0.000000e+00	1345
9	TraesCS3A01G020200	chr3D	87.943	1128	102	18	971	2091	9067473	9066373	0.000000e+00	1299
10	TraesCS3A01G020200	chr3D	81.456	1305	158	42	836	2077	9121805	9123088	0.000000e+00	992
11	TraesCS3A01G020200	chr3B	88.081	990	95	12	1109	2091	11114657	11113684	0.000000e+00	1153
12	TraesCS3A01G020200	chr3B	91.346	624	51	2	1	621	819359888	819359265	0.000000e+00	850
13	TraesCS3A01G020200	chr3B	87.793	598	62	8	1481	2077	31983778	31984365	0.000000e+00	689
14	TraesCS3A01G020200	chr3B	87.124	598	66	8	1481	2077	11470081	11470668	0.000000e+00	667
15	TraesCS3A01G020200	chr3B	83.190	464	54	9	831	1279	11469404	11469858	1.330000e-108	403
16	TraesCS3A01G020200	chr3B	82.241	473	53	11	836	1279	31983085	31983555	2.240000e-101	379
17	TraesCS3A01G020200	chr2D	94.023	619	35	1	1	617	14858740	14859358	0.000000e+00	937
18	TraesCS3A01G020200	chr1D	93.900	623	35	2	1	621	487969520	487970141	0.000000e+00	937
19	TraesCS3A01G020200	chr2B	91.974	623	47	2	1	621	138748495	138749116	0.000000e+00	870
20	TraesCS3A01G020200	chr2B	86.364	132	18	0	1043	1174	763449602	763449471	8.890000e-31	145
21	TraesCS3A01G020200	chr2B	83.217	143	24	0	1032	1174	762957759	762957617	6.920000e-27	132
22	TraesCS3A01G020200	chr7D	90.792	619	54	2	1	617	627289963	627290580	0.000000e+00	824
23	TraesCS3A01G020200	chr4B	90.065	614	56	3	9	617	574692637	574693250	0.000000e+00	791
24	TraesCS3A01G020200	chrUn	91.111	585	49	3	1	584	419550571	419551153	0.000000e+00	789
25	TraesCS3A01G020200	chr2A	76.512	562	110	16	1468	2027	608920978	608920437	1.400000e-73	287
26	TraesCS3A01G020200	chr1A	77.350	468	84	18	1617	2076	97793401	97793854	1.090000e-64	257
27	TraesCS3A01G020200	chr4A	82.877	146	21	4	2934	3077	414123973	414123830	8.960000e-26	128
28	TraesCS3A01G020200	chr4A	82.313	147	15	6	2933	3077	493430647	493430784	1.940000e-22	117
29	TraesCS3A01G020200	chr7B	80.000	165	31	2	1021	1184	690904484	690904647	1.500000e-23	121
30	TraesCS3A01G020200	chr6A	90.000	80	8	0	2930	3009	110904056	110903977	1.510000e-18	104

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	TraesCS3A01G020200	chr3A	11919649	11922725	3076	False	5683.000000	5683	100.000000	1	3077	1	chr3A.!!$F2	3076
1	TraesCS3A01G020200	chr3A	11932257	11933381	1124	False	2013.000000	2013	98.854000	1	1133	1	chr3A.!!$F3	1132
2	TraesCS3A01G020200	chr3A	12116558	12118232	1674	True	1078.500000	1988	87.006500	971	2737	2	chr3A.!!$R2	1766
3	TraesCS3A01G020200	chr3A	11872209	11873948	1739	True	900.333333	1064	95.868333	231	2077	3	chr3A.!!$R1	1846
4	TraesCS3A01G020200	chr3D	9065218	9067473	2255	True	1322.000000	1345	89.868000	971	3077	2	chr3D.!!$R1	2106
5	TraesCS3A01G020200	chr3D	9121805	9123088	1283	False	992.000000	992	81.456000	836	2077	1	chr3D.!!$F1	1241
6	TraesCS3A01G020200	chr3B	11113684	11114657	973	True	1153.000000	1153	88.081000	1109	2091	1	chr3B.!!$R1	982
7	TraesCS3A01G020200	chr3B	819359265	819359888	623	True	850.000000	850	91.346000	1	621	1	chr3B.!!$R2	620
8	TraesCS3A01G020200	chr3B	11469404	11470668	1264	False	535.000000	667	85.157000	831	2077	2	chr3B.!!$F1	1246
9	TraesCS3A01G020200	chr3B	31983085	31984365	1280	False	534.000000	689	85.017000	836	2077	2	chr3B.!!$F2	1241
10	TraesCS3A01G020200	chr2D	14858740	14859358	618	False	937.000000	937	94.023000	1	617	1	chr2D.!!$F1	616
11	TraesCS3A01G020200	chr1D	487969520	487970141	621	False	937.000000	937	93.900000	1	621	1	chr1D.!!$F1	620
12	TraesCS3A01G020200	chr2B	138748495	138749116	621	False	870.000000	870	91.974000	1	621	1	chr2B.!!$F1	620
13	TraesCS3A01G020200	chr7D	627289963	627290580	617	False	824.000000	824	90.792000	1	617	1	chr7D.!!$F1	616
14	TraesCS3A01G020200	chr4B	574692637	574693250	613	False	791.000000	791	90.065000	9	617	1	chr4B.!!$F1	608
15	TraesCS3A01G020200	chrUn	419550571	419551153	582	False	789.000000	789	91.111000	1	584	1	chrUn.!!$F1	583
16	TraesCS3A01G020200	chr2A	608920437	608920978	541	True	287.000000	287	76.512000	1468	2027	1	chr2A.!!$R1	559

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
1460	1535	6.93973	TGTGAAGTCAAGGTTATCAATGCTAA	59.06	34.615	0.0	0.0	0.0	3.09	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2289	2560	0.03601	AAAGGTGACTGCATCGGGAG	60.036	55.0	0.0	0.0	42.68	4.3	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
1460	1535	6.939730	TGTGAAGTCAAGGTTATCAATGCTAA	59.060	34.615	0.00	0.00	0.00	3.09
1545	1653	0.540923	ATGGCAAGAGAGGAGCAGAC	59.459	55.000	0.00	0.00	0.00	3.51
1580	1688	0.799393	GAAGGCGAGGTTTTCTCTGC	59.201	55.000	0.00	0.00	40.30	4.26
1581	1689	0.398318	AAGGCGAGGTTTTCTCTGCT	59.602	50.000	0.00	0.00	40.30	4.24
1582	1690	0.036858	AGGCGAGGTTTTCTCTGCTC	60.037	55.000	0.00	0.00	40.30	4.26
1583	1691	0.320771	GGCGAGGTTTTCTCTGCTCA	60.321	55.000	0.00	0.00	40.30	4.26
1584	1692	0.793250	GCGAGGTTTTCTCTGCTCAC	59.207	55.000	0.00	0.00	40.30	3.51
1585	1693	1.873903	GCGAGGTTTTCTCTGCTCACA	60.874	52.381	0.00	0.00	40.30	3.58
1586	1694	2.483876	CGAGGTTTTCTCTGCTCACAA	58.516	47.619	0.00	0.00	40.30	3.33
1606	1714	3.533606	ACTCACAAGATTATGCTCGCT	57.466	42.857	0.00	0.00	0.00	4.93
1994	2108	1.812686	AATGCTGTGGTGGCAAGCAG	61.813	55.000	15.89	12.34	43.14	4.24
1997	2111	1.071987	CTGTGGTGGCAAGCAGAGA	59.928	57.895	11.94	0.00	45.49	3.10
2288	2559	1.303888	AGCTTGGTCGACGTCCCTA	60.304	57.895	10.58	2.39	0.00	3.53
2289	2560	1.153881	GCTTGGTCGACGTCCCTAC	60.154	63.158	10.58	5.90	0.00	3.18
2290	2561	1.593296	GCTTGGTCGACGTCCCTACT	61.593	60.000	10.58	0.00	0.00	2.57
2291	2562	0.450983	CTTGGTCGACGTCCCTACTC	59.549	60.000	10.58	1.77	0.00	2.59
2292	2563	0.962356	TTGGTCGACGTCCCTACTCC	60.962	60.000	10.58	4.41	0.00	3.85
2293	2564	2.117779	GGTCGACGTCCCTACTCCC	61.118	68.421	10.58	0.00	0.00	4.30
2309	2580	0.036388	TCCCGATGCAGTCACCTTTC	60.036	55.000	0.00	0.00	0.00	2.62
2348	2621	2.876550	AGCAACTAAACCGAACAAGTCC	59.123	45.455	0.00	0.00	0.00	3.85
2366	2640	3.957497	AGTCCTCTGCTCCACTTACATAG	59.043	47.826	0.00	0.00	0.00	2.23
2367	2641	3.702045	GTCCTCTGCTCCACTTACATAGT	59.298	47.826	0.00	0.00	37.68	2.12
2392	2666	9.900710	GTATATTAGCATATCCTAATCCAGTCG	57.099	37.037	2.03	0.00	38.56	4.18
2397	2671	5.046529	GCATATCCTAATCCAGTCGCATAG	58.953	45.833	0.00	0.00	0.00	2.23
2479	2755	3.387397	ACTCCCGACTAAACAAGTTTCG	58.613	45.455	0.81	0.33	39.07	3.46
2523	2799	1.216710	GCTCACTGGTCTCCCTTCG	59.783	63.158	0.00	0.00	0.00	3.79
2545	2821	1.344942	GCGTCCATGTCACTCACGTC	61.345	60.000	0.00	0.00	0.00	4.34
2685	2963	9.819267	AATGAACTAGTTTATGGCTAGTAAGAC	57.181	33.333	13.14	0.00	45.78	3.01
2688	2966	4.667519	AGTTTATGGCTAGTAAGACGGG	57.332	45.455	0.00	0.00	30.84	5.28
2754	3037	2.627863	TCGGCAAAATGGATGAAACG	57.372	45.000	0.00	0.00	0.00	3.60
2804	3087	3.790126	AGGAAACCTGGTTTTATGCCAT	58.210	40.909	24.55	7.67	35.77	4.40
2805	3088	3.515104	AGGAAACCTGGTTTTATGCCATG	59.485	43.478	24.55	0.00	35.77	3.66
2818	3119	0.935942	TGCCATGGGAGGGAAATCAT	59.064	50.000	15.13	0.00	0.00	2.45
2824	3125	4.476297	CATGGGAGGGAAATCATCATGAA	58.524	43.478	0.00	0.00	35.88	2.57
2832	3133	8.355913	GGAGGGAAATCATCATGAAGTTAAATC	58.644	37.037	0.00	0.00	0.00	2.17
2860	3161	2.939103	AGAAGACATGCATAAAGACCGC	59.061	45.455	0.00	0.00	0.00	5.68
2878	3179	4.658071	ACCGCGTGAAATATGAAATCAAC	58.342	39.130	4.92	0.00	0.00	3.18
2902	3203	1.393196	TGAAATCTGTGCGCACATACG	59.607	47.619	40.50	29.22	41.01	3.06
2910	3211	2.224314	TGTGCGCACATACGAATTCAAA	59.776	40.909	37.86	11.82	36.21	2.69
2937	3238	1.006086	TAAATCTGTGCGCCGACATG	58.994	50.000	4.18	0.00	0.00	3.21
2945	3246	4.794439	CGCCGACATGGAGCGTCA	62.794	66.667	15.49	0.00	44.65	4.35
2950	3251	1.657751	CGACATGGAGCGTCAGGAGA	61.658	60.000	0.00	0.00	32.72	3.71
2951	3252	0.749649	GACATGGAGCGTCAGGAGAT	59.250	55.000	0.00	0.00	33.43	2.75
2971	3272	3.792053	GATAGGTGGAGTGGCGGCG	62.792	68.421	0.51	0.51	0.00	6.46
2987	3288	3.443045	CGGCTGATGGTTGGCACC	61.443	66.667	0.00	0.00	44.56	5.01
3034	3335	0.981183	TTAGGCTGGTGTGGAATCGT	59.019	50.000	0.00	0.00	0.00	3.73
3052	3353	2.026636	TCGTAGTTAAATGGGCTGGCTT	60.027	45.455	0.00	0.00	0.00	4.35

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1460	1535	3.096092	TCCTGCACCTCAGTTTTTGTTT	58.904	40.909	0.00	0.00	41.25	2.83
1545	1653	2.287009	GCCTTCAACCTCAAAAGTCACG	60.287	50.000	0.00	0.00	0.00	4.35
1580	1688	5.220359	CGAGCATAATCTTGTGAGTTGTGAG	60.220	44.000	0.00	0.00	0.00	3.51
1581	1689	4.627035	CGAGCATAATCTTGTGAGTTGTGA	59.373	41.667	0.00	0.00	0.00	3.58
1582	1690	4.726021	GCGAGCATAATCTTGTGAGTTGTG	60.726	45.833	0.00	0.00	0.00	3.33
1583	1691	3.372206	GCGAGCATAATCTTGTGAGTTGT	59.628	43.478	0.00	0.00	0.00	3.32
1584	1692	3.620374	AGCGAGCATAATCTTGTGAGTTG	59.380	43.478	0.00	0.00	0.00	3.16
1585	1693	3.866651	AGCGAGCATAATCTTGTGAGTT	58.133	40.909	0.00	0.00	0.00	3.01
1586	1694	3.533606	AGCGAGCATAATCTTGTGAGT	57.466	42.857	0.00	0.00	0.00	3.41
1994	2108	2.433868	TTTGAGGTGTGCGTACTCTC	57.566	50.000	16.03	16.03	32.58	3.20
1997	2111	2.902705	TCTTTTGAGGTGTGCGTACT	57.097	45.000	4.97	0.00	0.00	2.73
2289	2560	0.036010	AAAGGTGACTGCATCGGGAG	60.036	55.000	0.00	0.00	42.68	4.30
2290	2561	0.036388	GAAAGGTGACTGCATCGGGA	60.036	55.000	0.00	0.00	42.68	5.14
2291	2562	0.036010	AGAAAGGTGACTGCATCGGG	60.036	55.000	0.00	0.00	42.68	5.14
2292	2563	1.466167	CAAGAAAGGTGACTGCATCGG	59.534	52.381	0.00	0.00	42.68	4.18
2293	2564	2.146342	ACAAGAAAGGTGACTGCATCG	58.854	47.619	0.00	0.00	42.68	3.84
2309	2580	7.020914	AGTTGCTTCTTCTTCTGTTAACAAG	57.979	36.000	10.03	5.37	0.00	3.16
2366	2640	9.900710	CGACTGGATTAGGATATGCTAATATAC	57.099	37.037	24.45	18.49	30.48	1.47
2367	2641	8.577296	GCGACTGGATTAGGATATGCTAATATA	58.423	37.037	24.45	16.64	0.00	0.86
2479	2755	1.656652	TTCTTTCGCAGCTGATAGCC	58.343	50.000	20.43	0.00	43.77	3.93
2523	2799	3.188786	GAGTGACATGGACGCCGC	61.189	66.667	0.00	0.00	0.00	6.53
2538	2814	2.188524	CTTGGATGATGTCGACGTGAG	58.811	52.381	16.54	0.00	0.00	3.51
2545	2821	1.411977	AGAGGAGCTTGGATGATGTCG	59.588	52.381	0.00	0.00	0.00	4.35
2685	2963	6.698380	AGTGCCTTATAATAGTTGATACCCG	58.302	40.000	0.00	0.00	0.00	5.28
2754	3037	4.081087	TGGAGAAGTTTGTGATACCTAGGC	60.081	45.833	9.30	0.00	0.00	3.93
2804	3087	3.528905	ACTTCATGATGATTTCCCTCCCA	59.471	43.478	15.03	0.00	0.00	4.37
2805	3088	4.176120	ACTTCATGATGATTTCCCTCCC	57.824	45.455	15.03	0.00	0.00	4.30
2824	3125	9.453572	TGCATGTCTTCTGATTTAGATTTAACT	57.546	29.630	0.00	0.00	34.80	2.24
2832	3133	8.341173	GGTCTTTATGCATGTCTTCTGATTTAG	58.659	37.037	10.16	0.00	0.00	1.85
2860	3161	4.730042	CAGCCGTTGATTTCATATTTCACG	59.270	41.667	0.00	0.00	0.00	4.35
2878	3179	2.099062	GCGCACAGATTTCAGCCG	59.901	61.111	0.30	0.00	0.00	5.52
2902	3203	8.650714	GCACAGATTTAAACATCCTTTGAATTC	58.349	33.333	0.00	0.00	0.00	2.17
2910	3211	2.423538	GGCGCACAGATTTAAACATCCT	59.576	45.455	10.83	0.00	0.00	3.24
2937	3238	1.543802	CTATCCATCTCCTGACGCTCC	59.456	57.143	0.00	0.00	0.00	4.70
2941	3242	1.615883	CCACCTATCCATCTCCTGACG	59.384	57.143	0.00	0.00	0.00	4.35
2945	3246	2.427002	CCACTCCACCTATCCATCTCCT	60.427	54.545	0.00	0.00	0.00	3.69
2950	3251	1.410850	CCGCCACTCCACCTATCCAT	61.411	60.000	0.00	0.00	0.00	3.41
2951	3252	2.063979	CCGCCACTCCACCTATCCA	61.064	63.158	0.00	0.00	0.00	3.41
2984	3285	0.687757	TTCTCCCATCTCCTCCGGTG	60.688	60.000	0.00	0.00	0.00	4.94
2987	3288	1.118356	CCCTTCTCCCATCTCCTCCG	61.118	65.000	0.00	0.00	0.00	4.63
3034	3335	3.730215	TCAAGCCAGCCCATTTAACTA	57.270	42.857	0.00	0.00	0.00	2.24
3052	3353	1.612199	CCCGGGGAGTCGAAATTTTCA	60.612	52.381	14.71	0.00	0.00	2.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.