AutoCloner

Multiple sequence alignment - TraesCS2D01G050100

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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	TraesCS2D01G050100	chr2D	100.000	3124	0	0	1	3124	18372687	18375810	0.000000e+00	5770.0
1	TraesCS2D01G050100	chr2D	81.620	1148	168	26	1428	2563	18612236	18613352	0.000000e+00	911.0
2	TraesCS2D01G050100	chr2D	89.323	665	41	10	783	1423	18611540	18612198	0.000000e+00	808.0
3	TraesCS2D01G050100	chr2D	74.259	540	92	28	2608	3124	18613439	18613954	1.910000e-42	183.0
4	TraesCS2D01G050100	chr2A	97.325	2505	43	3	644	3124	19566501	19569005	0.000000e+00	4233.0
5	TraesCS2D01G050100	chr2A	81.369	1154	165	32	1428	2563	19587565	19588686	0.000000e+00	894.0
6	TraesCS2D01G050100	chr2A	94.757	534	26	2	1	533	19538675	19539207	0.000000e+00	830.0
7	TraesCS2D01G050100	chr2A	87.500	560	56	6	878	1423	19586968	19587527	4.400000e-178	634.0
8	TraesCS2D01G050100	chr2A	79.934	304	23	12	550	838	19586189	19586469	4.110000e-44	189.0
9	TraesCS2D01G050100	chr2A	72.461	581	106	34	2573	3124	19588733	19589288	1.510000e-28	137.0
10	TraesCS2D01G050100	chr2A	94.805	77	4	0	472	548	19576948	19577024	1.520000e-23	121.0
11	TraesCS2D01G050100	chr2A	97.059	34	1	0	595	628	19539203	19539236	1.210000e-04	58.4
12	TraesCS2D01G050100	chr2B	84.474	1417	157	28	1169	2563	30468097	30469472	0.000000e+00	1339.0
13	TraesCS2D01G050100	chr7D	81.783	516	78	15	921	1423	621172817	621173329	4.820000e-113	418.0

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	TraesCS2D01G050100	chr2D	18372687	18375810	3123	False	5770.0	5770	100.000	1	3124	1	chr2D.!!$F1	3123
1	TraesCS2D01G050100	chr2D	18611540	18613954	2414	False	634.0	911	81.734	783	3124	3	chr2D.!!$F2	2341
2	TraesCS2D01G050100	chr2A	19566501	19569005	2504	False	4233.0	4233	97.325	644	3124	1	chr2A.!!$F1	2480
3	TraesCS2D01G050100	chr2A	19586189	19589288	3099	False	463.5	894	80.316	550	3124	4	chr2A.!!$F4	2574
4	TraesCS2D01G050100	chr2A	19538675	19539236	561	False	444.2	830	95.908	1	628	2	chr2A.!!$F3	627
5	TraesCS2D01G050100	chr2B	30468097	30469472	1375	False	1339.0	1339	84.474	1169	2563	1	chr2B.!!$F1	1394
6	TraesCS2D01G050100	chr7D	621172817	621173329	512	False	418.0	418	81.783	921	1423	1	chr7D.!!$F1	502

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
557	559	0.107456	AGTTGTAGCACTGCAGCACT	59.893	50.0	15.27	13.99	36.85	4.4	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2404	3002	3.954258	CAGAGTTTGTTCCCAGAAAACCT	59.046	43.478	0.0	0.0	34.96	3.5	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
305	306	0.167470	GGGCGCGTCTTTCTTTTACC	59.833	55.000	11.94	0.00	0.00	2.85
348	349	6.452242	TGAAAATGACTACGTGAGAAAGCTA	58.548	36.000	0.00	0.00	0.00	3.32
349	350	6.365247	TGAAAATGACTACGTGAGAAAGCTAC	59.635	38.462	0.00	0.00	0.00	3.58
407	408	6.121776	TCATTTAAGAGAGGCAAGTTGGTA	57.878	37.500	4.75	0.00	0.00	3.25
436	437	4.134563	GTGAAAGAGAGGCAAGTTGGTAA	58.865	43.478	4.75	0.00	0.00	2.85
470	472	2.095212	CCGCAAGAAAAAGGTAAGGAGC	60.095	50.000	0.00	0.00	43.02	4.70
489	491	4.346129	GAGCGACCATCATTCATTTCAAC	58.654	43.478	0.00	0.00	0.00	3.18
492	494	3.438360	GACCATCATTCATTTCAACGGC	58.562	45.455	0.00	0.00	0.00	5.68
546	548	3.246619	GAGCAGTACTCACAGTTGTAGC	58.753	50.000	0.00	0.00	45.49	3.58
547	549	2.628178	AGCAGTACTCACAGTTGTAGCA	59.372	45.455	0.00	0.00	0.00	3.49
548	550	2.731976	GCAGTACTCACAGTTGTAGCAC	59.268	50.000	0.00	0.00	0.00	4.40
549	551	3.553096	GCAGTACTCACAGTTGTAGCACT	60.553	47.826	0.00	0.00	0.00	4.40
555	557	2.620562	CAGTTGTAGCACTGCAGCA	58.379	52.632	15.27	0.00	37.96	4.41
556	558	0.236711	CAGTTGTAGCACTGCAGCAC	59.763	55.000	15.27	5.98	37.96	4.40
557	559	0.107456	AGTTGTAGCACTGCAGCACT	59.893	50.000	15.27	13.99	36.85	4.40
558	560	1.344438	AGTTGTAGCACTGCAGCACTA	59.656	47.619	15.27	12.88	36.85	2.74
559	561	1.728971	GTTGTAGCACTGCAGCACTAG	59.271	52.381	15.27	0.00	36.85	2.57
587	589	3.030291	TGTTCTTGCCTTTTCACACCAT	58.970	40.909	0.00	0.00	0.00	3.55
600	602	3.843422	TCACACCATGTTTCCCAGAAAT	58.157	40.909	0.00	0.00	0.00	2.17
611	613	9.927668	CATGTTTCCCAGAAATAATGTAAACTT	57.072	29.630	0.00	0.00	0.00	2.66
775	792	1.269988	ACACACACAGAGCAGTAGCAG	60.270	52.381	0.00	0.00	45.49	4.24
863	904	4.918583	GCCTCATACGCATTACTCTTACTC	59.081	45.833	0.00	0.00	0.00	2.59
1042	1589	5.877012	GCAAGTTCAAGAATCCTACTGATGA	59.123	40.000	0.00	0.00	32.68	2.92
1058	1605	0.465097	ATGACCTGTGCTAGCCATGC	60.465	55.000	13.29	0.42	0.00	4.06
1164	1714	3.671971	CGAGTAGTTGTGAGGAAGAGCTG	60.672	52.174	0.00	0.00	0.00	4.24
1352	1902	2.230660	GCATATCCAGGCTACCCAAAC	58.769	52.381	0.00	0.00	0.00	2.93
1481	2064	8.764558	TCACTTTTCCTAATTATAGCTACACCA	58.235	33.333	0.00	0.00	0.00	4.17
1570	2153	0.105760	TTGTGGGTGGCACTGGAAAT	60.106	50.000	18.45	0.00	0.00	2.17
1809	2400	9.645059	ACGTAATCATATCTATTGATGTCAAGG	57.355	33.333	0.00	0.00	39.47	3.61
2168	2765	4.404715	TGTGTCTTCCCTTATGGCTAGTAC	59.595	45.833	0.00	0.00	0.00	2.73
2404	3002	9.283768	ACCTTTTTCATATTCGATGCATATACA	57.716	29.630	0.00	0.00	0.00	2.29
2487	3085	7.491372	CACAAGACATGACTTACCACGTATATT	59.509	37.037	10.09	0.00	0.00	1.28
2571	3206	7.841956	TCCTTTATTGAAACTCTAGGAGACAG	58.158	38.462	1.31	0.00	33.32	3.51
2692	3390	9.099454	AGTTCATCTCGAGGTGTAAAATTAATC	57.901	33.333	24.47	3.05	0.00	1.75
2952	3662	5.759506	ATCCAGATTACGAGACTGTACAG	57.240	43.478	21.44	21.44	0.00	2.74
2996	3707	6.094719	TGAAAATATGAAATGCTCTGTGTGC	58.905	36.000	0.00	0.00	0.00	4.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
7	8	2.038329	CCGACCTCCAGTGGGGTA	59.962	66.667	19.00	0.00	40.55	3.69
348	349	2.705821	CGCCTCTCGAGAAGCCTGT	61.706	63.158	26.24	0.00	41.67	4.00
349	350	2.103934	CGCCTCTCGAGAAGCCTG	59.896	66.667	26.24	12.46	41.67	4.85
407	408	3.845781	TGCCTCTCTTTCACACTTCTT	57.154	42.857	0.00	0.00	0.00	2.52
436	437	1.134220	TCTTGCGGGAAACACACTTCT	60.134	47.619	0.00	0.00	0.00	2.85
470	472	3.683989	CCGTTGAAATGAATGATGGTCG	58.316	45.455	0.00	0.00	0.00	4.79
489	491	2.066262	CCCGCAAATATAGTACAGCCG	58.934	52.381	0.00	0.00	0.00	5.52
492	494	3.576982	TCCTCCCCGCAAATATAGTACAG	59.423	47.826	0.00	0.00	0.00	2.74
523	525	1.000163	ACAACTGTGAGTACTGCTCCG	60.000	52.381	0.00	0.00	43.48	4.63
524	526	2.821991	ACAACTGTGAGTACTGCTCC	57.178	50.000	0.00	0.00	43.48	4.70
529	531	4.244425	CAGTGCTACAACTGTGAGTACT	57.756	45.455	0.00	0.00	42.21	2.73
538	540	0.107456	AGTGCTGCAGTGCTACAACT	59.893	50.000	17.60	11.50	0.00	3.16
539	541	1.728971	CTAGTGCTGCAGTGCTACAAC	59.271	52.381	19.81	9.40	0.00	3.32
540	542	1.344438	ACTAGTGCTGCAGTGCTACAA	59.656	47.619	19.81	0.00	0.00	2.41
541	543	0.969149	ACTAGTGCTGCAGTGCTACA	59.031	50.000	19.81	11.53	0.00	2.74
542	544	2.164624	ACTACTAGTGCTGCAGTGCTAC	59.835	50.000	19.81	12.50	0.00	3.58
543	545	2.164422	CACTACTAGTGCTGCAGTGCTA	59.836	50.000	19.81	15.76	39.62	3.49
544	546	1.067283	CACTACTAGTGCTGCAGTGCT	60.067	52.381	19.81	15.47	39.62	4.40
545	547	1.354040	CACTACTAGTGCTGCAGTGC	58.646	55.000	19.81	8.58	39.62	4.40
546	548	1.273606	ACCACTACTAGTGCTGCAGTG	59.726	52.381	19.81	14.21	44.63	3.66
547	549	1.273606	CACCACTACTAGTGCTGCAGT	59.726	52.381	16.64	15.20	44.63	4.40
548	550	1.273606	ACACCACTACTAGTGCTGCAG	59.726	52.381	10.11	10.11	44.63	4.41
549	551	1.338107	ACACCACTACTAGTGCTGCA	58.662	50.000	5.39	0.00	44.63	4.41
550	552	2.028930	AGAACACCACTACTAGTGCTGC	60.029	50.000	5.39	0.00	44.63	5.25
551	553	3.944055	AGAACACCACTACTAGTGCTG	57.056	47.619	5.39	9.74	44.63	4.41
552	554	3.555168	GCAAGAACACCACTACTAGTGCT	60.555	47.826	5.39	0.03	44.63	4.40
553	555	2.737252	GCAAGAACACCACTACTAGTGC	59.263	50.000	5.39	0.00	44.63	4.40
554	556	3.006967	AGGCAAGAACACCACTACTAGTG	59.993	47.826	5.39	9.02	45.53	2.74
555	557	3.240302	AGGCAAGAACACCACTACTAGT	58.760	45.455	0.00	0.00	0.00	2.57
556	558	3.963428	AGGCAAGAACACCACTACTAG	57.037	47.619	0.00	0.00	0.00	2.57
557	559	4.699925	AAAGGCAAGAACACCACTACTA	57.300	40.909	0.00	0.00	0.00	1.82
558	560	3.577805	AAAGGCAAGAACACCACTACT	57.422	42.857	0.00	0.00	0.00	2.57
559	561	3.630312	TGAAAAGGCAAGAACACCACTAC	59.370	43.478	0.00	0.00	0.00	2.73
587	589	9.757227	CAAAGTTTACATTATTTCTGGGAAACA	57.243	29.630	0.00	0.00	31.34	2.83
611	613	4.573201	CCAAGTCGTAAAAAGAGTCCACAA	59.427	41.667	0.00	0.00	0.00	3.33
775	792	1.202770	ACCACTTGTTCTGTAGGGCAC	60.203	52.381	0.00	0.00	0.00	5.01
863	904	4.583489	AGTAGATCACGGGTATACAAGTGG	59.417	45.833	21.82	9.82	35.50	4.00
1042	1589	2.273449	GGCATGGCTAGCACAGGT	59.727	61.111	18.24	0.00	0.00	4.00
1058	1605	2.924290	GAGAAGACGAGGAAAATCACGG	59.076	50.000	0.00	0.00	0.00	4.94
1142	1692	2.490115	AGCTCTTCCTCACAACTACTCG	59.510	50.000	0.00	0.00	0.00	4.18
1164	1714	5.428253	TGGTGCAGGTACAAAGATAGATTC	58.572	41.667	0.00	0.00	0.00	2.52
1570	2153	4.758251	CCACGCGCCATGGACAGA	62.758	66.667	18.40	0.00	39.87	3.41
1723	2314	8.421249	TGATTTCCCAACTTGACATAAATTCT	57.579	30.769	0.00	0.00	0.00	2.40
2168	2765	8.906693	CGACATTCATATTACAACAGCTAGTAG	58.093	37.037	0.00	0.00	0.00	2.57
2214	2812	6.806249	CACGCCACAAACATCTACATTATTTT	59.194	34.615	0.00	0.00	0.00	1.82
2404	3002	3.954258	CAGAGTTTGTTCCCAGAAAACCT	59.046	43.478	0.00	0.00	34.96	3.50
2571	3206	6.313164	CCCCTAATTGTCTTTCTTAAGTCGAC	59.687	42.308	7.70	7.70	32.98	4.20
2692	3390	1.318491	GTTTACGGCTACAAGCGTACG	59.682	52.381	11.84	11.84	43.62	3.67
2952	3662	3.738282	TCATGCCGTACATTTGTTTTTGC	59.262	39.130	0.00	0.00	36.64	3.68

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.