AutoCloner

Multiple sequence alignment - TraesCS3D01G537400

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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	TraesCS3D01G537400	chr3D	100.000	3459	0	0	1	3459	610542535	610545993	0.000000e+00	6388.0
1	TraesCS3D01G537400	chr3D	77.378	1388	190	66	855	2217	610697890	610696602	0.000000e+00	710.0
2	TraesCS3D01G537400	chr3D	78.624	1221	125	57	1025	2190	613806607	613805468	0.000000e+00	684.0
3	TraesCS3D01G537400	chr3D	77.680	681	126	18	1700	2378	610685057	610684401	3.240000e-105	392.0
4	TraesCS3D01G537400	chr3D	88.298	94	11	0	1022	1115	610629374	610629281	2.820000e-21	113.0
5	TraesCS3D01G537400	chr3D	83.721	129	9	6	833	958	610629492	610629373	1.010000e-20	111.0
6	TraesCS3D01G537400	chr3D	77.251	211	28	13	1022	1217	610686083	610685878	4.720000e-19	106.0
7	TraesCS3D01G537400	chr3D	86.000	100	8	2	859	958	610597833	610597740	6.110000e-18	102.0
8	TraesCS3D01G537400	chr3D	89.610	77	8	0	1038	1114	610597725	610597649	7.900000e-17	99.0
9	TraesCS3D01G537400	chr3B	94.986	3291	125	17	166	3440	828110100	828113366	0.000000e+00	5127.0
10	TraesCS3D01G537400	chr3B	78.165	1090	190	33	1298	2378	828254038	828252988	0.000000e+00	651.0
11	TraesCS3D01G537400	chr3B	77.873	931	101	47	888	1750	823130598	823129705	6.710000e-132	481.0
12	TraesCS3D01G537400	chr3B	91.489	141	7	1	1	136	828109958	828110098	4.560000e-44	189.0
13	TraesCS3D01G537400	chr3B	91.489	94	8	0	1022	1115	828332816	828332723	2.800000e-26	130.0
14	TraesCS3D01G537400	chr3B	85.149	101	9	3	865	959	827864139	827864239	7.900000e-17	99.0
15	TraesCS3D01G537400	chr3A	93.413	2854	105	31	48	2867	744878058	744880862	0.000000e+00	4152.0
16	TraesCS3D01G537400	chr3A	86.894	557	56	8	2896	3440	744880860	744881411	2.950000e-170	608.0
17	TraesCS3D01G537400	chr3A	79.469	867	88	38	1507	2370	750298761	750297982	1.830000e-147	532.0
18	TraesCS3D01G537400	chr3A	90.426	94	9	0	1022	1115	745299372	745299279	1.300000e-24	124.0
19	TraesCS3D01G537400	chr3A	85.263	95	5	4	864	958	744941595	744941510	4.750000e-14	89.8
20	TraesCS3D01G537400	chr3A	85.263	95	5	4	864	958	745014522	745014437	4.750000e-14	89.8
21	TraesCS3D01G537400	chr3A	85.263	95	5	4	864	958	745081331	745081246	4.750000e-14	89.8
22	TraesCS3D01G537400	chr3A	85.263	95	5	4	864	958	745194533	745194448	4.750000e-14	89.8
23	TraesCS3D01G537400	chr3A	95.652	46	2	0	914	959	744792707	744792662	1.330000e-09	75.0
24	TraesCS3D01G537400	chr1D	92.181	243	16	3	1507	1749	17169115	17168876	1.190000e-89	340.0
25	TraesCS3D01G537400	chr1A	92.181	243	16	3	1507	1749	18461769	18461530	1.190000e-89	340.0

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	TraesCS3D01G537400	chr3D	610542535	610545993	3458	False	6388	6388	100.0000	1	3459	1	chr3D.!!$F1	3458
1	TraesCS3D01G537400	chr3D	610696602	610697890	1288	True	710	710	77.3780	855	2217	1	chr3D.!!$R1	1362
2	TraesCS3D01G537400	chr3D	613805468	613806607	1139	True	684	684	78.6240	1025	2190	1	chr3D.!!$R2	1165
3	TraesCS3D01G537400	chr3D	610684401	610686083	1682	True	249	392	77.4655	1022	2378	2	chr3D.!!$R5	1356
4	TraesCS3D01G537400	chr3B	828109958	828113366	3408	False	2658	5127	93.2375	1	3440	2	chr3B.!!$F2	3439
5	TraesCS3D01G537400	chr3B	828252988	828254038	1050	True	651	651	78.1650	1298	2378	1	chr3B.!!$R2	1080
6	TraesCS3D01G537400	chr3B	823129705	823130598	893	True	481	481	77.8730	888	1750	1	chr3B.!!$R1	862
7	TraesCS3D01G537400	chr3A	744878058	744881411	3353	False	2380	4152	90.1535	48	3440	2	chr3A.!!$F1	3392
8	TraesCS3D01G537400	chr3A	750297982	750298761	779	True	532	532	79.4690	1507	2370	1	chr3A.!!$R7	863

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	Hairpin	End Stability	Orientation
616	650	0.032267	GTAGCATGGGTAGCCGTCTC	59.968	60.0	1.68	0.00	3.36	F
703	737	0.041833	TGTCCTCTCCCTCCTCCAAG	59.958	60.0	0.00	0.00	3.61	F
720	754	0.390472	AAGTCGCCACAAGCTAGAGC	60.390	55.0	0.00	40.39	4.09	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1501	2006	0.247814	CATCGACATCGGCTTGTTGC	60.248	55.0	0.73	40.29	4.17	R
2201	2712	0.461870	TTCCTCCATCGTCGCCATTG	60.462	55.0	0.00	0.00	2.82	R
2563	3101	6.949352	ACAAATTAAGGCCATAGTGATCAG	57.051	37.5	5.01	0.00	2.90	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
139	145	1.066716	TGGAACCGTGGGATTACGAAG	60.067	52.381	0.00	0.00	46.46	3.79
143	149	1.067354	ACCGTGGGATTACGAAGACAC	60.067	52.381	0.00	0.00	46.46	3.67
164	170	5.354234	ACACGGAAATAGGAAAGCACATAAG	59.646	40.000	0.00	0.00	0.00	1.73
291	300	8.404107	TCCTCCAAACTACTAGGAAAAATTTG	57.596	34.615	0.00	0.00	35.20	2.32
310	319	9.665719	AAAATTTGAAAGCTGAGGTTTTCTTTA	57.334	25.926	11.24	0.00	41.25	1.85
337	346	7.332430	CGTGTAATCCAAGTATCCAAAGTGTAA	59.668	37.037	0.00	0.00	0.00	2.41
385	408	0.251564	TCCACCATTGTTCCCGCAAT	60.252	50.000	0.00	0.00	39.42	3.56
398	423	2.691011	TCCCGCAATAAACCTTATTGGC	59.309	45.455	16.80	10.35	40.22	4.52
425	450	1.239347	GTTGGCTGAACTTGGAGTCC	58.761	55.000	0.73	0.73	0.00	3.85
444	469	4.157840	AGTCCCAAAACAAAGTGAGTGAAC	59.842	41.667	0.00	0.00	0.00	3.18
612	646	0.532862	CAAGGTAGCATGGGTAGCCG	60.533	60.000	6.45	0.00	35.04	5.52
613	647	0.981277	AAGGTAGCATGGGTAGCCGT	60.981	55.000	6.45	2.44	35.04	5.68
614	648	1.069258	GGTAGCATGGGTAGCCGTC	59.931	63.158	1.68	0.00	0.00	4.79
615	649	1.400530	GGTAGCATGGGTAGCCGTCT	61.401	60.000	1.68	6.55	0.00	4.18
616	650	0.032267	GTAGCATGGGTAGCCGTCTC	59.968	60.000	1.68	0.00	0.00	3.36
617	651	0.396556	TAGCATGGGTAGCCGTCTCA	60.397	55.000	1.68	0.00	0.00	3.27
618	652	1.227380	GCATGGGTAGCCGTCTCAG	60.227	63.158	1.68	0.00	0.00	3.35
619	653	1.227380	CATGGGTAGCCGTCTCAGC	60.227	63.158	1.68	0.00	0.00	4.26
620	654	2.435693	ATGGGTAGCCGTCTCAGCC	61.436	63.158	6.45	0.00	0.00	4.85
703	737	0.041833	TGTCCTCTCCCTCCTCCAAG	59.958	60.000	0.00	0.00	0.00	3.61
720	754	0.390472	AAGTCGCCACAAGCTAGAGC	60.390	55.000	0.00	0.00	40.39	4.09
968	1005	2.110899	TCTCTTCTCTCCAACCTCCAGT	59.889	50.000	0.00	0.00	0.00	4.00
1361	1857	2.674380	CCTTCACCTGCTGGCCAC	60.674	66.667	0.00	0.00	36.63	5.01
1416	1912	0.615331	TCATGGTCAGCAGGAAGGAC	59.385	55.000	0.00	0.00	0.00	3.85
1964	2469	3.726144	GCCAGGCTGCTCTTCCCT	61.726	66.667	9.56	0.00	0.00	4.20
2013	2521	3.807538	CGCAGCAGCACCACCATC	61.808	66.667	0.82	0.00	42.27	3.51
2445	2983	0.702316	GGGGCCGGGGATGTATAAAT	59.298	55.000	2.18	0.00	0.00	1.40
2483	3021	7.277981	ACAATATGTGTTACAAGAACTCGATCC	59.722	37.037	0.00	0.00	37.01	3.36
2563	3101	4.965119	AACCTTTTGTCTGTTGAGTGTC	57.035	40.909	0.00	0.00	0.00	3.67
2641	3179	4.866508	AGCAGCTAAGTGTAGTGTGTTA	57.133	40.909	0.00	0.00	0.00	2.41
2643	3181	3.368236	GCAGCTAAGTGTAGTGTGTTAGC	59.632	47.826	5.05	5.05	45.11	3.09
2759	3300	5.062809	GCTTCTACACTGTGCTAGTTTCATC	59.937	44.000	7.90	0.00	37.60	2.92
2839	3381	4.328712	GTGTTTGCGTGAAGGTTTTTCATT	59.671	37.500	0.00	0.00	0.00	2.57
2849	3391	9.418045	CGTGAAGGTTTTTCATTATGGTTTTAT	57.582	29.630	0.00	0.00	0.00	1.40
2883	3425	6.808704	GGATGACTGGTCTTTTTCAATTAAGC	59.191	38.462	2.38	0.00	0.00	3.09
2888	3430	4.580995	TGGTCTTTTTCAATTAAGCCACGA	59.419	37.500	0.00	0.00	0.00	4.35
2904	3446	3.254060	CCACGATCGACACTGAGAATTT	58.746	45.455	24.34	0.00	0.00	1.82
2925	3467	7.876936	ATTTTCAATATGACTGTGAGATGCT	57.123	32.000	0.00	0.00	0.00	3.79
2944	3486	7.854534	AGATGCTTGCAAAACTTAACATTTTC	58.145	30.769	0.00	0.00	0.00	2.29
2971	3513	6.774170	TGGCTATGAGAATAAACAATGCATCT	59.226	34.615	0.00	0.00	0.00	2.90
3063	3611	8.974060	TGTAAAACAGGTTGAGACTTAAGAAT	57.026	30.769	10.09	0.00	0.00	2.40
3086	3634	0.250124	TCATTTGGCTGTCGACCGTT	60.250	50.000	14.12	0.00	0.00	4.44
3099	3647	4.397103	TGTCGACCGTTGTCTTAGATGTAT	59.603	41.667	14.12	0.00	39.47	2.29
3189	3738	5.886715	TCATTGTTTTGTCTGAAAATGCG	57.113	34.783	0.00	0.00	0.00	4.73
3276	3828	8.293699	TGGATGTATCGTGTATATGCTAAGAT	57.706	34.615	0.00	0.00	0.00	2.40
3301	3854	9.921637	ATCATCTCTAACGATCTCCTAAAATTC	57.078	33.333	0.00	0.00	0.00	2.17
3317	3870	2.240493	ATTCAAAGGAGGATACGGCG	57.760	50.000	4.80	4.80	46.39	6.46
3322	3875	0.184451	AAGGAGGATACGGCGGAGTA	59.816	55.000	13.24	0.00	46.39	2.59
3323	3876	0.404812	AGGAGGATACGGCGGAGTAT	59.595	55.000	13.24	0.00	46.39	2.12
3333	3886	1.269621	CGGCGGAGTATCGATCCTTTT	60.270	52.381	0.00	0.00	34.45	2.27
3382	3935	5.927281	AGTGCCGTTTCTAACCTATCTAA	57.073	39.130	0.00	0.00	0.00	2.10
3434	3990	6.420604	CACAAATTCGGTGCAAATTTAGACTT	59.579	34.615	7.15	0.00	35.20	3.01
3440	3996	5.705441	TCGGTGCAAATTTAGACTTGATTCT	59.295	36.000	0.00	0.00	0.00	2.40
3441	3997	5.796935	CGGTGCAAATTTAGACTTGATTCTG	59.203	40.000	0.00	0.00	0.00	3.02
3442	3998	6.568462	CGGTGCAAATTTAGACTTGATTCTGT	60.568	38.462	0.00	0.00	0.00	3.41
3443	3999	7.360861	CGGTGCAAATTTAGACTTGATTCTGTA	60.361	37.037	0.00	0.00	0.00	2.74
3444	4000	7.750903	GGTGCAAATTTAGACTTGATTCTGTAC	59.249	37.037	0.00	0.00	0.00	2.90
3445	4001	8.289618	GTGCAAATTTAGACTTGATTCTGTACA	58.710	33.333	0.00	0.00	0.00	2.90
3446	4002	8.845227	TGCAAATTTAGACTTGATTCTGTACAA	58.155	29.630	0.00	0.00	0.00	2.41
3447	4003	9.677567	GCAAATTTAGACTTGATTCTGTACAAA	57.322	29.630	0.00	0.00	0.00	2.83
3456	4012	8.955061	ACTTGATTCTGTACAAAATTGATTCG	57.045	30.769	0.00	0.00	0.00	3.34
3457	4013	8.783093	ACTTGATTCTGTACAAAATTGATTCGA	58.217	29.630	0.00	0.00	0.00	3.71
3458	4014	9.611284	CTTGATTCTGTACAAAATTGATTCGAA	57.389	29.630	0.00	0.00	0.00	3.71

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
41	42	5.774498	AGGAAAAAGAGACCATGACAAAC	57.226	39.130	0.00	0.00	0.00	2.93
139	145	3.071479	TGTGCTTTCCTATTTCCGTGTC	58.929	45.455	0.00	0.00	0.00	3.67
143	149	6.677781	TTCTTATGTGCTTTCCTATTTCCG	57.322	37.500	0.00	0.00	0.00	4.30
291	300	5.205565	CACGTAAAGAAAACCTCAGCTTTC	58.794	41.667	0.00	0.00	33.16	2.62
310	319	5.642063	CACTTTGGATACTTGGATTACACGT	59.358	40.000	0.00	0.00	35.52	4.49
357	380	1.167851	ACAATGGTGGATTGCAGTCG	58.832	50.000	2.84	0.00	44.85	4.18
398	423	4.340950	TCCAAGTTCAGCCAACCTTAAAAG	59.659	41.667	0.00	0.00	35.28	2.27
425	450	4.448537	TGGTTCACTCACTTTGTTTTGG	57.551	40.909	0.00	0.00	0.00	3.28
480	505	7.882791	CACATAATAGTCAATACCAGGCCATAA	59.117	37.037	5.01	0.00	0.00	1.90
486	511	5.702670	CAGCCACATAATAGTCAATACCAGG	59.297	44.000	0.00	0.00	0.00	4.45
612	646	1.451028	GTGCTGATGGGGCTGAGAC	60.451	63.158	0.00	0.00	0.00	3.36
613	647	1.614525	AGTGCTGATGGGGCTGAGA	60.615	57.895	0.00	0.00	0.00	3.27
614	648	1.153208	GAGTGCTGATGGGGCTGAG	60.153	63.158	0.00	0.00	0.00	3.35
615	649	1.919816	TGAGTGCTGATGGGGCTGA	60.920	57.895	0.00	0.00	0.00	4.26
616	650	1.748122	GTGAGTGCTGATGGGGCTG	60.748	63.158	0.00	0.00	0.00	4.85
617	651	2.673523	GTGAGTGCTGATGGGGCT	59.326	61.111	0.00	0.00	0.00	5.19
618	652	2.439156	GGTGAGTGCTGATGGGGC	60.439	66.667	0.00	0.00	0.00	5.80
619	653	0.750546	CATGGTGAGTGCTGATGGGG	60.751	60.000	0.00	0.00	0.00	4.96
620	654	0.750546	CCATGGTGAGTGCTGATGGG	60.751	60.000	2.57	0.00	31.56	4.00
720	754	2.170607	AGAAGGGTCTCTCTCTCTCTCG	59.829	54.545	0.00	0.00	0.00	4.04
1361	1857	1.075970	TCCTCCATCTCCAGGACCG	60.076	63.158	0.00	0.00	33.57	4.79
1501	2006	0.247814	CATCGACATCGGCTTGTTGC	60.248	55.000	0.73	0.00	40.29	4.17
2011	2519	2.602676	CCGTTCCCCTGGTGGTGAT	61.603	63.158	0.00	0.00	0.00	3.06
2012	2520	3.246112	CCGTTCCCCTGGTGGTGA	61.246	66.667	0.00	0.00	0.00	4.02
2013	2521	4.344865	CCCGTTCCCCTGGTGGTG	62.345	72.222	0.00	0.00	0.00	4.17
2201	2712	0.461870	TTCCTCCATCGTCGCCATTG	60.462	55.000	0.00	0.00	0.00	2.82
2445	2983	9.936759	TGTAACACATATTGTAGTGATGAAGAA	57.063	29.630	0.00	0.00	37.51	2.52
2563	3101	6.949352	ACAAATTAAGGCCATAGTGATCAG	57.051	37.500	5.01	0.00	0.00	2.90
2601	3139	7.978982	AGCTGCTAAGTATATGAAACAACAAG	58.021	34.615	0.00	0.00	0.00	3.16
2735	3276	4.307432	TGAAACTAGCACAGTGTAGAAGC	58.693	43.478	13.84	0.00	37.63	3.86
2787	3328	9.308318	GAAGTAGATCCTTGATACAAAGAGAAC	57.692	37.037	0.00	0.00	0.00	3.01
2802	3344	2.607187	CAAACACGCGAAGTAGATCCT	58.393	47.619	15.93	0.00	0.00	3.24
2839	3381	6.984474	GTCATCCGAGACTCAATAAAACCATA	59.016	38.462	2.82	0.00	35.65	2.74
2849	3391	1.819288	GACCAGTCATCCGAGACTCAA	59.181	52.381	2.82	0.00	45.35	3.02
2883	3425	2.568696	ATTCTCAGTGTCGATCGTGG	57.431	50.000	15.94	1.71	0.00	4.94
2888	3430	8.607459	GTCATATTGAAAATTCTCAGTGTCGAT	58.393	33.333	0.00	0.00	0.00	3.59
2904	3446	5.065602	GCAAGCATCTCACAGTCATATTGAA	59.934	40.000	0.00	0.00	0.00	2.69
2925	3467	6.597280	AGCCAAGAAAATGTTAAGTTTTGCAA	59.403	30.769	0.00	0.00	0.00	4.08
2944	3486	6.798482	TGCATTGTTTATTCTCATAGCCAAG	58.202	36.000	0.00	0.00	0.00	3.61
2983	3530	6.071896	TCACTGTGTTGTGGTTTTTGTTCATA	60.072	34.615	7.79	0.00	38.40	2.15
3063	3611	2.481276	CGGTCGACAGCCAAATGAGATA	60.481	50.000	18.91	0.00	0.00	1.98
3099	3647	8.601546	AGCCCACAAAATTAAATATGAAAAGGA	58.398	29.630	0.00	0.00	0.00	3.36
3112	3660	5.163405	TGCAACAAACTAGCCCACAAAATTA	60.163	36.000	0.00	0.00	0.00	1.40
3123	3672	6.035975	ACAACTTTTGATTGCAACAAACTAGC	59.964	34.615	19.81	0.00	37.05	3.42
3189	3738	9.745880	ATACATAAGTATATATGTACGCCTTGC	57.254	33.333	8.80	0.00	46.18	4.01
3276	3828	8.914011	TGAATTTTAGGAGATCGTTAGAGATGA	58.086	33.333	0.00	0.00	0.00	2.92
3301	3854	0.249489	CTCCGCCGTATCCTCCTTTG	60.249	60.000	0.00	0.00	0.00	2.77
3317	3870	4.099573	TCTCCACAAAAGGATCGATACTCC	59.900	45.833	11.46	2.49	36.99	3.85
3322	3875	7.469181	GCAAATATTCTCCACAAAAGGATCGAT	60.469	37.037	0.00	0.00	36.99	3.59
3323	3876	6.183360	GCAAATATTCTCCACAAAAGGATCGA	60.183	38.462	0.00	0.00	36.99	3.59
3324	3877	5.973565	GCAAATATTCTCCACAAAAGGATCG	59.026	40.000	0.00	0.00	36.99	3.69
3325	3878	7.105241	AGCAAATATTCTCCACAAAAGGATC	57.895	36.000	0.00	0.00	36.99	3.36

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.