AutoCloner

Multiple sequence alignment - TraesCS4D01G129200

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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	TraesCS4D01G129200	chr4D	100.000	3269	0	0	1	3269	115044915	115048183	0.000000e+00	6037.0
1	TraesCS4D01G129200	chr4D	82.635	167	23	5	267	430	179858592	179858429	3.400000e-30	143.0
2	TraesCS4D01G129200	chr4A	97.519	2822	55	7	1	2817	462222655	462219844	0.000000e+00	4809.0
3	TraesCS4D01G129200	chr4A	94.152	342	6	7	2931	3269	462219514	462219184	2.910000e-140	508.0
4	TraesCS4D01G129200	chr4B	94.089	2504	110	15	3	2491	175473371	175475851	0.000000e+00	3770.0
5	TraesCS4D01G129200	chr4B	92.899	338	8	7	2935	3269	175536733	175537057	8.210000e-131	477.0
6	TraesCS4D01G129200	chr4B	87.879	297	21	5	2592	2884	175475947	175476232	5.230000e-88	335.0
7	TraesCS4D01G129200	chr4B	96.226	53	2	0	2518	2570	175475850	175475902	1.620000e-13	87.9
8	TraesCS4D01G129200	chr6D	85.000	1880	215	35	436	2303	158075685	158073861	0.000000e+00	1847.0
9	TraesCS4D01G129200	chr6B	85.000	1880	212	40	436	2303	288793126	288794947	0.000000e+00	1845.0
10	TraesCS4D01G129200	chr6B	95.918	49	2	0	3221	3269	76227831	76227783	2.700000e-11	80.5
11	TraesCS4D01G129200	chr6A	84.848	1881	214	41	436	2303	213148502	213150324	0.000000e+00	1829.0
12	TraesCS4D01G129200	chr2B	94.079	152	9	0	3118	3269	275457918	275457767	7.050000e-57	231.0
13	TraesCS4D01G129200	chr5B	84.524	168	26	0	267	434	669487931	669487764	2.020000e-37	167.0
14	TraesCS4D01G129200	chr5B	79.042	167	31	3	267	431	367508397	367508233	9.590000e-21	111.0
15	TraesCS4D01G129200	chr5B	95.918	49	2	0	3221	3269	25482881	25482929	2.700000e-11	80.5
16	TraesCS4D01G129200	chr5B	95.918	49	2	0	3221	3269	661259593	661259641	2.700000e-11	80.5
17	TraesCS4D01G129200	chr5B	95.918	49	2	0	3221	3269	661274805	661274853	2.700000e-11	80.5
18	TraesCS4D01G129200	chr5B	100.000	38	0	0	3118	3155	25482844	25482881	1.630000e-08	71.3
19	TraesCS4D01G129200	chr3B	84.615	169	23	3	267	434	738296596	738296430	7.260000e-37	165.0
20	TraesCS4D01G129200	chr3B	82.692	156	21	4	271	425	65236340	65236490	2.050000e-27	134.0
21	TraesCS4D01G129200	chr3B	95.918	49	2	0	3221	3269	748485473	748485521	2.700000e-11	80.5
22	TraesCS4D01G129200	chr3B	100.000	38	0	0	3118	3155	748485436	748485473	1.630000e-08	71.3
23	TraesCS4D01G129200	chr1B	81.657	169	28	3	267	434	553013629	553013463	1.580000e-28	137.0
24	TraesCS4D01G129200	chr5A	77.011	174	33	5	267	435	28599463	28599634	3.470000e-15	93.5
25	TraesCS4D01G129200	chr3A	95.918	49	2	0	3221	3269	42410562	42410514	2.700000e-11	80.5

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	TraesCS4D01G129200	chr4D	115044915	115048183	3268	False	6037.000000	6037	100.000000	1	3269	1	chr4D.!!$F1	3268
1	TraesCS4D01G129200	chr4A	462219184	462222655	3471	True	2658.500000	4809	95.835500	1	3269	2	chr4A.!!$R1	3268
2	TraesCS4D01G129200	chr4B	175473371	175476232	2861	False	1397.633333	3770	92.731333	3	2884	3	chr4B.!!$F2	2881
3	TraesCS4D01G129200	chr6D	158073861	158075685	1824	True	1847.000000	1847	85.000000	436	2303	1	chr6D.!!$R1	1867
4	TraesCS4D01G129200	chr6B	288793126	288794947	1821	False	1845.000000	1845	85.000000	436	2303	1	chr6B.!!$F1	1867
5	TraesCS4D01G129200	chr6A	213148502	213150324	1822	False	1829.000000	1829	84.848000	436	2303	1	chr6A.!!$F1	1867

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
381	385	3.188048	CGCTGCTCTTGACTGAAATCTTT	59.812	43.478	0.0	0.0	0.00	2.52	F
562	568	4.102524	TCTTGACTCCTTAAAGGTCAGCAA	59.897	41.667	0.0	0.0	40.38	3.91	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1434	1450	0.534873	TCCGATGTTTCGCCTCATCA	59.465	50.0	11.68	0.0	44.12	3.07	R
2314	2331	2.032550	CAGATGCAACTAAATGAGCCCG	59.967	50.0	0.00	0.0	0.00	6.13	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
192	196	4.399004	AGGATATGTGACAGTGAAGCTC	57.601	45.455	0.00	0.00	0.00	4.09
381	385	3.188048	CGCTGCTCTTGACTGAAATCTTT	59.812	43.478	0.00	0.00	0.00	2.52
512	518	7.241042	AGCTTCTTGTACTTATAGTTCCACA	57.759	36.000	0.00	0.00	0.00	4.17
562	568	4.102524	TCTTGACTCCTTAAAGGTCAGCAA	59.897	41.667	0.00	0.00	40.38	3.91
736	746	7.445096	TCTGTTGTTCAAGCTTGAGATTATGAA	59.555	33.333	27.02	9.06	38.61	2.57
797	807	5.765182	AGAGCATGCTGTAGTTTACTTTGTT	59.235	36.000	28.27	0.00	0.00	2.83
917	933	6.177610	TGTCCTGTAAATTATGACCTGAACC	58.822	40.000	0.00	0.00	0.00	3.62
1434	1450	5.799827	TTACCCTTTTACAGCAGCAAATT	57.200	34.783	0.00	0.00	0.00	1.82
1575	1591	5.476599	ACCAAGTTTATTTACATCTGCTGCA	59.523	36.000	0.88	0.88	0.00	4.41
2058	2074	1.137404	GTTATTGCACAGGCTGGCG	59.863	57.895	20.34	10.65	41.91	5.69
2244	2260	0.625316	TACAGGCCCGAGTGTACCTA	59.375	55.000	0.00	0.00	0.00	3.08
2314	2331	1.138266	TCAGGGCGTATTAGTTCCTGC	59.862	52.381	0.00	0.00	43.30	4.85
2513	2541	8.005759	GATGTAATCCTGTCCAGTGTTTGGTG	62.006	46.154	0.00	0.00	42.08	4.17
2707	2764	8.592155	GTGTAAATTTTGAGGTTTCACAGTTTC	58.408	33.333	0.00	0.00	29.39	2.78
2740	2797	5.473504	ACGCAAAAATTCTGTGTATCTTCCT	59.526	36.000	5.20	0.00	35.80	3.36
2782	2842	9.650539	CTGTGTATCTTCCCATTGATATAGAAG	57.349	37.037	0.00	0.00	36.19	2.85
2814	2874	4.259356	GGAGGTTTACACACTTGGGATAC	58.741	47.826	0.00	0.00	0.00	2.24
2819	2906	5.229423	GTTTACACACTTGGGATACGTACA	58.771	41.667	0.00	0.00	37.60	2.90
2864	2951	4.925054	TGAATCGTTTTAGAAGTACACGGG	59.075	41.667	0.00	0.00	0.00	5.28
2898	2985	0.804989	CCTCAAAGCATCAACGTCCC	59.195	55.000	0.00	0.00	0.00	4.46
2899	2986	1.522668	CTCAAAGCATCAACGTCCCA	58.477	50.000	0.00	0.00	0.00	4.37
2900	2987	1.466167	CTCAAAGCATCAACGTCCCAG	59.534	52.381	0.00	0.00	0.00	4.45
2901	2988	1.202758	TCAAAGCATCAACGTCCCAGT	60.203	47.619	0.00	0.00	0.00	4.00
2902	2989	1.069022	CAAAGCATCAACGTCCCAGTG	60.069	52.381	0.00	0.00	0.00	3.66
2903	2990	0.396435	AAGCATCAACGTCCCAGTGA	59.604	50.000	0.00	0.00	0.00	3.41
2904	2991	0.615331	AGCATCAACGTCCCAGTGAT	59.385	50.000	0.00	0.00	0.00	3.06
2907	2994	0.984230	ATCAACGTCCCAGTGATGGT	59.016	50.000	0.00	0.00	34.03	3.55
2908	2995	0.320374	TCAACGTCCCAGTGATGGTC	59.680	55.000	0.00	0.00	34.03	4.02
2909	2996	0.673644	CAACGTCCCAGTGATGGTCC	60.674	60.000	0.00	0.00	34.03	4.46
2911	2998	1.219124	CGTCCCAGTGATGGTCCTG	59.781	63.158	0.00	0.00	0.00	3.86
2912	2999	1.604378	GTCCCAGTGATGGTCCTGG	59.396	63.158	0.00	0.00	46.43	4.45
2917	3004	1.614317	CCAGTGATGGTCCTGGTTTCC	60.614	57.143	0.00	0.00	42.72	3.13
2918	3005	0.698818	AGTGATGGTCCTGGTTTCCC	59.301	55.000	0.00	0.00	0.00	3.97
2919	3006	0.404040	GTGATGGTCCTGGTTTCCCA	59.596	55.000	0.00	0.00	38.87	4.37
2921	3008	1.203001	TGATGGTCCTGGTTTCCCAAC	60.203	52.381	0.00	0.00	41.27	3.77
2922	3009	0.856982	ATGGTCCTGGTTTCCCAACA	59.143	50.000	0.00	0.00	41.27	3.33
2923	3010	0.184933	TGGTCCTGGTTTCCCAACAG	59.815	55.000	0.00	0.00	41.27	3.16
2924	3011	0.185175	GGTCCTGGTTTCCCAACAGT	59.815	55.000	0.00	0.00	41.27	3.55
2925	3012	1.411074	GGTCCTGGTTTCCCAACAGTT	60.411	52.381	0.00	0.00	41.27	3.16
2926	3013	1.681264	GTCCTGGTTTCCCAACAGTTG	59.319	52.381	6.28	6.28	41.27	3.16
2927	3014	0.389025	CCTGGTTTCCCAACAGTTGC	59.611	55.000	7.88	0.00	41.27	4.17
2928	3015	0.030638	CTGGTTTCCCAACAGTTGCG	59.969	55.000	7.88	0.00	41.27	4.85
2929	3016	0.681564	TGGTTTCCCAACAGTTGCGT	60.682	50.000	7.88	0.00	37.98	5.24
2971	3287	1.281419	TCTAACTGAATGGGCCCGAA	58.719	50.000	19.37	0.00	0.00	4.30
2976	3292	1.001393	TGAATGGGCCCGAACCTTC	60.001	57.895	19.37	14.56	0.00	3.46
3031	3347	3.262151	GGGCTTCTTCTCTTCTACCAACT	59.738	47.826	0.00	0.00	0.00	3.16
3032	3348	4.500127	GGCTTCTTCTCTTCTACCAACTC	58.500	47.826	0.00	0.00	0.00	3.01
3033	3349	4.500127	GCTTCTTCTCTTCTACCAACTCC	58.500	47.826	0.00	0.00	0.00	3.85
3034	3350	4.221924	GCTTCTTCTCTTCTACCAACTCCT	59.778	45.833	0.00	0.00	0.00	3.69
3054	3370	2.677228	CCCATCCGTTCTGGGCTT	59.323	61.111	1.67	0.00	46.62	4.35
3055	3371	1.452108	CCCATCCGTTCTGGGCTTC	60.452	63.158	1.67	0.00	46.62	3.86
3056	3372	1.604378	CCATCCGTTCTGGGCTTCT	59.396	57.895	0.00	0.00	38.76	2.85
3057	3373	0.745845	CCATCCGTTCTGGGCTTCTG	60.746	60.000	0.00	0.00	38.76	3.02
3058	3374	0.745845	CATCCGTTCTGGGCTTCTGG	60.746	60.000	0.00	0.00	38.76	3.86
3107	3423	1.450491	CGAGAGCAGAGGAGACGGA	60.450	63.158	0.00	0.00	0.00	4.69
3125	3444	2.418976	CGGAGGTTTGCTAGGTTTTAGC	59.581	50.000	0.00	0.00	40.76	3.09

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
192	196	3.372206	CAGGTCGCTGAACCAGATTAAAG	59.628	47.826	0.00	0.00	42.12	1.85
307	311	5.869649	AATGGTATTTGTTAATCTGGCCC	57.130	39.130	0.00	0.00	0.00	5.80
340	344	0.821301	GCTGAATCTGGGCCCTAAGC	60.821	60.000	25.70	13.26	42.60	3.09
512	518	9.118300	GAAGATTCATTTCAAGTCATATGGTCT	57.882	33.333	2.13	0.00	0.00	3.85
562	568	1.338389	ACCGCATTTTACGCACTAGGT	60.338	47.619	0.00	0.00	0.00	3.08
567	573	2.325509	AAGAACCGCATTTTACGCAC	57.674	45.000	0.00	0.00	0.00	5.34
736	746	6.213600	AGACAGAGATTAATACAACCACACCT	59.786	38.462	0.00	0.00	0.00	4.00
917	933	1.956477	ACCTGCAAAAGCAACTACTGG	59.044	47.619	0.00	0.00	0.00	4.00
1434	1450	0.534873	TCCGATGTTTCGCCTCATCA	59.465	50.000	11.68	0.00	44.12	3.07
1575	1591	7.877612	TCGTGTATTGATTGGTATGCATTATCT	59.122	33.333	3.54	0.00	0.00	1.98
2244	2260	6.589135	TCAGTCAGCATATTTGACATCTGAT	58.411	36.000	15.80	0.00	45.72	2.90
2314	2331	2.032550	CAGATGCAACTAAATGAGCCCG	59.967	50.000	0.00	0.00	0.00	6.13
2472	2500	2.408050	ACATCACGCAACAGAGAGAAC	58.592	47.619	0.00	0.00	0.00	3.01
2657	2714	6.207810	ACAGTACAGAACACAAACAAAAGGAA	59.792	34.615	0.00	0.00	0.00	3.36
2658	2715	5.708230	ACAGTACAGAACACAAACAAAAGGA	59.292	36.000	0.00	0.00	0.00	3.36
2659	2716	5.799936	CACAGTACAGAACACAAACAAAAGG	59.200	40.000	0.00	0.00	0.00	3.11
2660	2717	6.378582	ACACAGTACAGAACACAAACAAAAG	58.621	36.000	0.00	0.00	0.00	2.27
2747	2807	4.471025	TGGGAAGATACACAGTGATGTCAT	59.529	41.667	7.81	0.00	33.85	3.06
2782	2842	1.897802	TGTAAACCTCCGAACCTCTCC	59.102	52.381	0.00	0.00	0.00	3.71
2855	2942	0.407139	ACTGTACCTCCCCGTGTACT	59.593	55.000	0.00	0.00	38.48	2.73
2864	2951	4.570930	CTTTGAGGAGAAACTGTACCTCC	58.429	47.826	16.24	16.24	45.61	4.30
2898	2985	1.826385	GGAAACCAGGACCATCACTG	58.174	55.000	0.00	0.00	34.54	3.66
2912	2999	0.030235	GGACGCAACTGTTGGGAAAC	59.970	55.000	34.78	24.93	45.47	2.78
2917	3004	2.908073	GCCAGGACGCAACTGTTGG	61.908	63.158	21.01	13.53	34.16	3.77
2918	3005	1.845809	GAGCCAGGACGCAACTGTTG	61.846	60.000	15.98	15.98	34.16	3.33
2919	3006	1.598130	GAGCCAGGACGCAACTGTT	60.598	57.895	0.00	0.00	34.16	3.16
2921	3008	3.114616	CGAGCCAGGACGCAACTG	61.115	66.667	0.00	0.00	35.74	3.16
2922	3009	3.165160	AACGAGCCAGGACGCAACT	62.165	57.895	6.42	0.00	0.00	3.16
2923	3010	2.665185	AACGAGCCAGGACGCAAC	60.665	61.111	6.42	0.00	0.00	4.17
2924	3011	2.664851	CAACGAGCCAGGACGCAA	60.665	61.111	6.42	0.00	0.00	4.85
2925	3012	4.680237	CCAACGAGCCAGGACGCA	62.680	66.667	6.42	0.00	0.00	5.24
2928	3015	2.579684	CTAGCCCAACGAGCCAGGAC	62.580	65.000	0.00	0.00	0.00	3.85
2929	3016	2.284331	TAGCCCAACGAGCCAGGA	60.284	61.111	0.00	0.00	0.00	3.86
3031	3347	1.689233	CAGAACGGATGGGGGAGGA	60.689	63.158	0.00	0.00	0.00	3.71
3032	3348	2.746375	CCAGAACGGATGGGGGAGG	61.746	68.421	0.00	0.00	36.56	4.30
3033	3349	2.911143	CCAGAACGGATGGGGGAG	59.089	66.667	0.00	0.00	36.56	4.30
3051	3367	2.617774	GAGAATGAGATTGGCCAGAAGC	59.382	50.000	5.11	0.00	42.60	3.86
3052	3368	2.871022	CGAGAATGAGATTGGCCAGAAG	59.129	50.000	5.11	0.00	0.00	2.85
3053	3369	2.910199	CGAGAATGAGATTGGCCAGAA	58.090	47.619	5.11	0.00	0.00	3.02
3054	3370	1.473965	GCGAGAATGAGATTGGCCAGA	60.474	52.381	5.11	0.00	0.00	3.86
3055	3371	0.942962	GCGAGAATGAGATTGGCCAG	59.057	55.000	5.11	0.00	0.00	4.85
3056	3372	0.464373	GGCGAGAATGAGATTGGCCA	60.464	55.000	0.00	0.00	38.88	5.36
3057	3373	1.502163	CGGCGAGAATGAGATTGGCC	61.502	60.000	0.00	0.00	35.78	5.36
3058	3374	1.502163	CCGGCGAGAATGAGATTGGC	61.502	60.000	9.30	0.00	0.00	4.52
3107	3423	1.810755	GCGCTAAAACCTAGCAAACCT	59.189	47.619	0.00	0.00	40.39	3.50

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.