AutoCloner

Multiple sequence alignment - TraesCS2D01G332800

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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	TraesCS2D01G332800	chr2D	100.000	3572	0	0	1	3572	426435942	426432371	0.000000e+00	6597.0
1	TraesCS2D01G332800	chr2D	100.000	48	0	0	2633	2680	426433262	426433215	4.910000e-14	89.8
2	TraesCS2D01G332800	chr2D	100.000	48	0	0	2681	2728	426433310	426433263	4.910000e-14	89.8
3	TraesCS2D01G332800	chr2A	97.282	2833	61	8	749	3572	562507769	562510594	0.000000e+00	4791.0
4	TraesCS2D01G332800	chr2A	88.766	721	58	19	1	710	562507069	562507777	0.000000e+00	861.0
5	TraesCS2D01G332800	chr2A	100.000	48	0	0	2681	2728	562509649	562509696	4.910000e-14	89.8
6	TraesCS2D01G332800	chr2B	97.476	2694	60	5	885	3572	503454163	503451472	0.000000e+00	4591.0
7	TraesCS2D01G332800	chr2B	89.903	515	44	8	4	515	503460626	503460117	0.000000e+00	656.0
8	TraesCS2D01G332800	chr2B	83.333	378	38	13	514	883	503460022	503459662	3.440000e-85	326.0
9	TraesCS2D01G332800	chr2B	100.000	48	0	0	2681	2728	503452415	503452368	4.910000e-14	89.8
10	TraesCS2D01G332800	chr2B	97.917	48	1	0	2633	2680	503452367	503452320	2.290000e-12	84.2
11	TraesCS2D01G332800	chr4B	81.926	592	92	6	2063	2653	1767396	1766819	1.490000e-133	486.0
12	TraesCS2D01G332800	chr4B	80.867	392	65	4	1384	1766	1767928	1767538	2.080000e-77	300.0
13	TraesCS2D01G332800	chrUn	79.747	711	108	27	1960	2654	43078989	43079679	1.930000e-132	483.0
14	TraesCS2D01G332800	chr3B	79.577	710	110	25	1960	2654	825499950	825499261	3.230000e-130	475.0
15	TraesCS2D01G332800	chr3B	80.303	594	107	7	1960	2548	825290313	825290901	1.180000e-119	440.0
16	TraesCS2D01G332800	chr3B	83.188	458	73	4	1960	2413	823976843	823977300	1.980000e-112	416.0
17	TraesCS2D01G332800	chr3B	84.264	394	60	2	1367	1759	825289858	825290250	2.010000e-102	383.0
18	TraesCS2D01G332800	chr3B	81.279	219	35	4	1542	1759	823976567	823976780	4.740000e-39	172.0
19	TraesCS2D01G332800	chr5D	81.143	525	89	8	1961	2479	61347477	61347997	2.570000e-111	412.0
20	TraesCS2D01G332800	chr5B	80.755	530	92	8	1964	2487	69306962	69306437	4.290000e-109	405.0
21	TraesCS2D01G332800	chr5B	73.107	647	121	36	1121	1737	619190909	619191532	7.880000e-42	182.0
22	TraesCS2D01G332800	chr5B	84.884	86	11	2	1193	1277	619106962	619107046	6.350000e-13	86.1
23	TraesCS2D01G332800	chr4A	81.170	393	62	6	1384	1766	603468903	603469293	4.480000e-79	305.0
24	TraesCS2D01G332800	chr4A	80.916	393	63	5	1384	1766	603390111	603389721	2.080000e-77	300.0
25	TraesCS2D01G332800	chr4D	81.197	234	30	8	1544	1766	1311738	1311508	3.670000e-40	176.0

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	TraesCS2D01G332800	chr2D	426432371	426435942	3571	True	2258.866667	6597	100.000000	1	3572	3	chr2D.!!$R1	3571
1	TraesCS2D01G332800	chr2A	562507069	562510594	3525	False	1913.933333	4791	95.349333	1	3572	3	chr2A.!!$F1	3571
2	TraesCS2D01G332800	chr2B	503451472	503454163	2691	True	1588.333333	4591	98.464333	885	3572	3	chr2B.!!$R1	2687
3	TraesCS2D01G332800	chr2B	503459662	503460626	964	True	491.000000	656	86.618000	4	883	2	chr2B.!!$R2	879
4	TraesCS2D01G332800	chr4B	1766819	1767928	1109	True	393.000000	486	81.396500	1384	2653	2	chr4B.!!$R1	1269
5	TraesCS2D01G332800	chrUn	43078989	43079679	690	False	483.000000	483	79.747000	1960	2654	1	chrUn.!!$F1	694
6	TraesCS2D01G332800	chr3B	825499261	825499950	689	True	475.000000	475	79.577000	1960	2654	1	chr3B.!!$R1	694
7	TraesCS2D01G332800	chr3B	825289858	825290901	1043	False	411.500000	440	82.283500	1367	2548	2	chr3B.!!$F2	1181
8	TraesCS2D01G332800	chr3B	823976567	823977300	733	False	294.000000	416	82.233500	1542	2413	2	chr3B.!!$F1	871
9	TraesCS2D01G332800	chr5D	61347477	61347997	520	False	412.000000	412	81.143000	1961	2479	1	chr5D.!!$F1	518
10	TraesCS2D01G332800	chr5B	69306437	69306962	525	True	405.000000	405	80.755000	1964	2487	1	chr5B.!!$R1	523

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
883	1009	0.389817	CAACGGCGTGGAGATGAGAA	60.390	55.0	15.7	0.0	0.00	2.87	F
1962	2097	0.687757	TTCCTCCTGGATCTGTCGGG	60.688	60.0	0.0	0.0	42.81	5.14	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2022	2163	2.436417	GCAAAACAGGTAGCAGGATCA	58.564	47.619	0.00	0.0	0.0	2.92	R
3257	3416	0.108329	GCTCCAGGCGCTGTAGTTTA	60.108	55.000	7.64	0.0	0.0	2.01	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
39	40	4.666512	ACCTCCAACATTGCTTAGACAAT	58.333	39.130	0.00	0.00	40.90	2.71
69	70	9.943163	GCAAGATTAAAAGAGTAAAGATCCATC	57.057	33.333	0.00	0.00	0.00	3.51
101	102	5.420409	ACCTCCTTCACTTTTAAGATAGCG	58.580	41.667	0.00	0.00	0.00	4.26
114	115	2.973945	AGATAGCGAAGTTTCCACCAC	58.026	47.619	0.00	0.00	0.00	4.16
183	184	7.013274	TCACCAAAACTAGGCAATTATATCAGC	59.987	37.037	0.00	0.00	0.00	4.26
194	195	7.229506	AGGCAATTATATCAGCAACCTCTTTAC	59.770	37.037	0.00	0.00	0.00	2.01
216	217	4.714308	ACAAATTCCCTTGGACAGACAAAA	59.286	37.500	0.00	0.00	0.00	2.44
235	236	6.035843	ACAAAAACACTGACATAGCAAACAG	58.964	36.000	0.00	0.00	36.58	3.16
250	251	3.016736	CAAACAGTGGTATAGCTTGGGG	58.983	50.000	3.20	0.00	0.00	4.96
251	252	1.966845	ACAGTGGTATAGCTTGGGGT	58.033	50.000	3.20	0.00	0.00	4.95
284	285	5.494390	ACCTCCAGTAGATAACGGTTTTT	57.506	39.130	0.00	0.00	0.00	1.94
302	303	6.475504	GGTTTTTCCATCCATCCTTGAATTT	58.524	36.000	0.00	0.00	35.97	1.82
344	347	2.146342	AGTGCCTGAAACAATCACTCG	58.854	47.619	0.00	0.00	33.16	4.18
351	354	4.988540	CCTGAAACAATCACTCGTGTCTAA	59.011	41.667	0.00	0.00	33.47	2.10
362	365	1.972075	TCGTGTCTAAACCCACCATGA	59.028	47.619	0.00	0.00	0.00	3.07
384	387	2.489329	CAGGCAACCCAAGATACTTGTG	59.511	50.000	9.99	2.25	37.17	3.33
427	430	8.862074	TCAATATGCAAAATTTGACAAATCTCG	58.138	29.630	13.68	6.49	0.00	4.04
432	435	6.095377	GCAAAATTTGACAAATCTCGGATCT	58.905	36.000	13.68	0.00	0.00	2.75
433	436	6.034256	GCAAAATTTGACAAATCTCGGATCTG	59.966	38.462	13.68	0.00	0.00	2.90
462	465	7.873505	AGTAGCAGAAGTGTTAGGACTAAAAAG	59.126	37.037	0.00	0.00	0.00	2.27
479	482	9.744468	GACTAAAAAGAACTAGATTTTGCCAAA	57.256	29.630	0.00	0.00	0.00	3.28
486	491	8.232913	AGAACTAGATTTTGCCAAACTAACAA	57.767	30.769	0.00	0.00	0.00	2.83
500	505	3.279434	ACTAACAATGGCCCGAATTCTC	58.721	45.455	0.00	0.00	0.00	2.87
501	506	1.094785	AACAATGGCCCGAATTCTCG	58.905	50.000	0.00	0.00	45.02	4.04
503	508	1.077787	AATGGCCCGAATTCTCGCA	60.078	52.632	0.00	3.32	44.04	5.10
506	511	2.464459	GGCCCGAATTCTCGCAGTG	61.464	63.158	13.60	0.00	44.04	3.66
640	744	0.874390	TTCTTGAGCGAATGCACACC	59.126	50.000	0.00	0.00	46.23	4.16
689	795	2.680312	TAGCAATCTCTCACTGTGGC	57.320	50.000	8.11	1.41	0.00	5.01
701	807	0.814010	ACTGTGGCGACAACAACTCC	60.814	55.000	2.34	0.00	46.06	3.85
702	808	0.532862	CTGTGGCGACAACAACTCCT	60.533	55.000	2.34	0.00	46.06	3.69
704	810	1.346395	TGTGGCGACAACAACTCCTAT	59.654	47.619	0.00	0.00	46.06	2.57
705	811	2.000447	GTGGCGACAACAACTCCTATC	59.000	52.381	0.00	0.00	46.06	2.08
706	812	1.278238	GGCGACAACAACTCCTATCG	58.722	55.000	0.00	0.00	0.00	2.92
707	813	0.645868	GCGACAACAACTCCTATCGC	59.354	55.000	0.29	0.29	46.68	4.58
708	814	1.990799	CGACAACAACTCCTATCGCA	58.009	50.000	0.00	0.00	0.00	5.10
709	815	2.333926	CGACAACAACTCCTATCGCAA	58.666	47.619	0.00	0.00	0.00	4.85
710	816	2.734606	CGACAACAACTCCTATCGCAAA	59.265	45.455	0.00	0.00	0.00	3.68
711	817	3.185594	CGACAACAACTCCTATCGCAAAA	59.814	43.478	0.00	0.00	0.00	2.44
712	818	4.319190	CGACAACAACTCCTATCGCAAAAA	60.319	41.667	0.00	0.00	0.00	1.94
713	819	5.108385	ACAACAACTCCTATCGCAAAAAG	57.892	39.130	0.00	0.00	0.00	2.27
714	820	4.819630	ACAACAACTCCTATCGCAAAAAGA	59.180	37.500	0.00	0.00	0.00	2.52
715	821	5.298276	ACAACAACTCCTATCGCAAAAAGAA	59.702	36.000	0.00	0.00	0.00	2.52
716	822	6.183360	ACAACAACTCCTATCGCAAAAAGAAA	60.183	34.615	0.00	0.00	0.00	2.52
717	823	6.385649	ACAACTCCTATCGCAAAAAGAAAA	57.614	33.333	0.00	0.00	0.00	2.29
718	824	6.801575	ACAACTCCTATCGCAAAAAGAAAAA	58.198	32.000	0.00	0.00	0.00	1.94
830	954	1.987807	ATGGCGAGCTGGGCTGTATT	61.988	55.000	22.43	0.82	39.88	1.89
833	957	0.533755	GCGAGCTGGGCTGTATTGAT	60.534	55.000	0.00	0.00	39.88	2.57
834	958	1.506493	CGAGCTGGGCTGTATTGATC	58.494	55.000	0.00	0.00	39.88	2.92
838	964	1.506493	CTGGGCTGTATTGATCGAGC	58.494	55.000	0.00	0.00	0.00	5.03
880	1006	0.669318	GAACAACGGCGTGGAGATGA	60.669	55.000	23.33	0.00	0.00	2.92
881	1007	0.670546	AACAACGGCGTGGAGATGAG	60.671	55.000	23.33	3.13	0.00	2.90
882	1008	1.215382	CAACGGCGTGGAGATGAGA	59.785	57.895	15.70	0.00	0.00	3.27
883	1009	0.389817	CAACGGCGTGGAGATGAGAA	60.390	55.000	15.70	0.00	0.00	2.87
891	1017	3.005684	GCGTGGAGATGAGAATGAGATCT	59.994	47.826	0.00	0.00	0.00	2.75
1962	2097	0.687757	TTCCTCCTGGATCTGTCGGG	60.688	60.000	0.00	0.00	42.81	5.14
2022	2163	1.414919	TCTGAGTGCAACCTACCGTTT	59.585	47.619	0.00	0.00	37.80	3.60
2759	2912	5.126067	AGTGTAATTGCCTATTGTAGCCAG	58.874	41.667	0.00	0.00	0.00	4.85
2765	2918	4.402056	TGCCTATTGTAGCCAGTAGTTC	57.598	45.455	0.00	0.00	30.94	3.01
2872	3026	8.504005	GTTTATGTCCTGTAATGGAATAATCGG	58.496	37.037	0.00	0.00	37.93	4.18
3017	3176	3.873952	ACTTCAAAACTGCTCACTGACTC	59.126	43.478	0.00	0.00	0.00	3.36
3032	3191	3.057876	ACTGACTCGTTCTACTGAAGCTG	60.058	47.826	0.00	0.00	32.15	4.24
3098	3257	6.653320	TCACACAGGCGTCTTATTTCTATTTT	59.347	34.615	0.00	0.00	0.00	1.82
3200	3359	4.036027	ACATCACAAACTGAAGTGCTTCTG	59.964	41.667	14.48	14.48	42.09	3.02
3228	3387	6.148480	GTCAAAGATCACATAGCAACTTCAGT	59.852	38.462	0.00	0.00	0.00	3.41
3257	3416	2.093128	GGTGTCCGTGGATGAAAGGTAT	60.093	50.000	0.00	0.00	0.00	2.73
3273	3432	2.102588	AGGTATAAACTACAGCGCCTGG	59.897	50.000	2.29	0.00	35.51	4.45
3332	3491	3.414700	CTTCACCGACGTGCAGCC	61.415	66.667	0.00	0.00	40.04	4.85
3546	3705	3.031660	GACGTCCATGAGGTTCGTC	57.968	57.895	3.51	14.53	46.22	4.20
3550	3709	1.608336	TCCATGAGGTTCGTCGGGT	60.608	57.895	0.00	0.00	35.89	5.28

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
69	70	5.896073	AAAGTGAAGGAGGTATGGGATAG	57.104	43.478	0.00	0.00	0.00	2.08
101	102	3.404899	TGGTATTCGTGGTGGAAACTTC	58.595	45.455	0.00	0.00	0.00	3.01
183	184	5.538433	TCCAAGGGAATTTGTAAAGAGGTTG	59.462	40.000	0.00	0.00	0.00	3.77
194	195	4.935352	TTTGTCTGTCCAAGGGAATTTG	57.065	40.909	0.00	0.00	31.38	2.32
216	217	4.818534	CACTGTTTGCTATGTCAGTGTT	57.181	40.909	13.68	0.00	46.92	3.32
235	236	3.918294	TTGTACCCCAAGCTATACCAC	57.082	47.619	0.00	0.00	0.00	4.16
237	238	4.062991	CGAATTGTACCCCAAGCTATACC	58.937	47.826	0.00	0.00	36.25	2.73
250	251	6.199937	TCTACTGGAGGTAACGAATTGTAC	57.800	41.667	0.00	0.00	46.39	2.90
251	252	8.408601	GTTATCTACTGGAGGTAACGAATTGTA	58.591	37.037	7.27	0.00	40.96	2.41
284	285	5.582953	ACAGAAAATTCAAGGATGGATGGA	58.417	37.500	0.00	0.00	0.00	3.41
344	347	3.074412	CTGTCATGGTGGGTTTAGACAC	58.926	50.000	0.00	0.00	36.89	3.67
351	354	0.827507	GTTGCCTGTCATGGTGGGTT	60.828	55.000	0.00	0.00	0.00	4.11
362	365	2.108250	ACAAGTATCTTGGGTTGCCTGT	59.892	45.455	12.95	0.00	0.00	4.00
384	387	3.883830	TTGATGGTGAAGCTCTCTCTC	57.116	47.619	0.00	0.00	0.00	3.20
427	430	1.484240	ACTTCTGCTACTGCCAGATCC	59.516	52.381	0.00	0.00	38.71	3.36
432	435	2.028112	CCTAACACTTCTGCTACTGCCA	60.028	50.000	0.00	0.00	38.71	4.92
433	436	2.233922	TCCTAACACTTCTGCTACTGCC	59.766	50.000	0.00	0.00	38.71	4.85
462	465	8.915654	CATTGTTAGTTTGGCAAAATCTAGTTC	58.084	33.333	16.93	8.65	0.00	3.01
479	482	3.279434	GAGAATTCGGGCCATTGTTAGT	58.721	45.455	4.39	0.00	0.00	2.24
486	491	1.524621	CTGCGAGAATTCGGGCCAT	60.525	57.895	17.41	0.00	46.76	4.40
500	505	3.802948	AAGTTCTAGATACCCACTGCG	57.197	47.619	0.00	0.00	0.00	5.18
501	506	6.583562	ACATAAAGTTCTAGATACCCACTGC	58.416	40.000	0.00	0.00	0.00	4.40
503	508	8.925338	CCTTACATAAAGTTCTAGATACCCACT	58.075	37.037	0.00	0.00	32.89	4.00
506	511	9.984190	CTTCCTTACATAAAGTTCTAGATACCC	57.016	37.037	0.00	0.00	32.89	3.69
664	768	6.577103	CCACAGTGAGAGATTGCTAATAGAA	58.423	40.000	0.62	0.00	0.00	2.10
666	770	4.749099	GCCACAGTGAGAGATTGCTAATAG	59.251	45.833	0.62	0.00	0.00	1.73
669	773	2.675032	CGCCACAGTGAGAGATTGCTAA	60.675	50.000	0.62	0.00	0.00	3.09
670	774	1.134995	CGCCACAGTGAGAGATTGCTA	60.135	52.381	0.62	0.00	0.00	3.49
671	775	0.390866	CGCCACAGTGAGAGATTGCT	60.391	55.000	0.62	0.00	0.00	3.91
683	789	0.532862	AGGAGTTGTTGTCGCCACAG	60.533	55.000	0.00	0.00	32.71	3.66
689	795	1.990799	TGCGATAGGAGTTGTTGTCG	58.009	50.000	0.00	0.00	0.00	4.35
715	821	3.982576	AAAGTTGCGATCGGAGTTTTT	57.017	38.095	18.30	12.34	0.00	1.94
716	822	3.982576	AAAAGTTGCGATCGGAGTTTT	57.017	38.095	18.30	18.94	0.00	2.43
717	823	3.982576	AAAAAGTTGCGATCGGAGTTT	57.017	38.095	18.30	14.32	0.00	2.66
740	846	4.081365	TCAATATGTTGCGTCCTCACCTAA	60.081	41.667	0.00	0.00	35.26	2.69
742	848	2.236146	TCAATATGTTGCGTCCTCACCT	59.764	45.455	0.00	0.00	35.26	4.00
743	849	2.609459	CTCAATATGTTGCGTCCTCACC	59.391	50.000	0.00	0.00	35.26	4.02
744	850	2.030946	GCTCAATATGTTGCGTCCTCAC	59.969	50.000	0.00	0.00	35.26	3.51
746	852	1.599542	GGCTCAATATGTTGCGTCCTC	59.400	52.381	0.00	0.00	35.26	3.71
747	853	1.210478	AGGCTCAATATGTTGCGTCCT	59.790	47.619	0.00	0.56	35.26	3.85
748	854	1.599542	GAGGCTCAATATGTTGCGTCC	59.400	52.381	10.25	0.00	35.22	4.79
749	855	1.258982	CGAGGCTCAATATGTTGCGTC	59.741	52.381	15.95	0.00	37.09	5.19
750	856	1.290203	CGAGGCTCAATATGTTGCGT	58.710	50.000	15.95	0.00	35.26	5.24
873	999	3.324268	TGCCAGATCTCATTCTCATCTCC	59.676	47.826	0.00	0.00	0.00	3.71
880	1006	2.093075	CACACCTGCCAGATCTCATTCT	60.093	50.000	0.00	0.00	0.00	2.40
881	1007	2.286872	CACACCTGCCAGATCTCATTC	58.713	52.381	0.00	0.00	0.00	2.67
882	1008	1.064906	CCACACCTGCCAGATCTCATT	60.065	52.381	0.00	0.00	0.00	2.57
883	1009	0.545171	CCACACCTGCCAGATCTCAT	59.455	55.000	0.00	0.00	0.00	2.90
891	1017	2.197324	GGTTTCCCACACCTGCCA	59.803	61.111	0.00	0.00	0.00	4.92
1962	2097	2.469516	CGGTGCATTTAGGTCCGGC	61.470	63.158	0.00	0.00	37.92	6.13
2022	2163	2.436417	GCAAAACAGGTAGCAGGATCA	58.564	47.619	0.00	0.00	0.00	2.92
2451	2593	5.724328	CTGAGAAAGTACCAGCAGATTGTA	58.276	41.667	0.00	0.00	0.00	2.41
2759	2912	9.326339	GGAAACAGATGAATTAAAACGAACTAC	57.674	33.333	0.00	0.00	0.00	2.73
2919	3078	7.599998	ACAATTCCAACTTGCAAATATCTGAAC	59.400	33.333	0.00	0.00	0.00	3.18
3017	3176	4.963953	CACAAAAACAGCTTCAGTAGAACG	59.036	41.667	0.00	0.00	0.00	3.95
3200	3359	4.394300	AGTTGCTATGTGATCTTTGACTGC	59.606	41.667	0.00	0.00	0.00	4.40
3228	3387	0.832559	TCCACGGACACCACCATACA	60.833	55.000	0.00	0.00	0.00	2.29
3257	3416	0.108329	GCTCCAGGCGCTGTAGTTTA	60.108	55.000	7.64	0.00	0.00	2.01
3273	3432	2.086054	ATGAAGTTGTGAGGTCGCTC	57.914	50.000	0.00	0.00	0.00	5.03
3546	3705	2.857748	GCAAAACTTCACAAAGAACCCG	59.142	45.455	0.00	0.00	36.30	5.28

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.