AutoCloner

Multiple sequence alignment - TraesCS7A01G322900

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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	TraesCS7A01G322900	chr7A	100.000	3587	0	0	1	3587	468831099	468834685	0.000000e+00	6625
1	TraesCS7A01G322900	chr7A	86.726	113	14	1	3132	3244	222578224	222578113	1.350000e-24	124
2	TraesCS7A01G322900	chr7B	94.212	3611	146	21	1	3568	423138361	423141951	0.000000e+00	5452
3	TraesCS7A01G322900	chr7D	94.682	3253	139	19	291	3511	408717649	408720899	0.000000e+00	5018
4	TraesCS7A01G322900	chr7D	97.342	301	5	2	1	301	408717332	408717629	3.200000e-140	508
5	TraesCS7A01G322900	chr7D	98.750	80	1	0	3508	3587	408721017	408721096	3.730000e-30	143
6	TraesCS7A01G322900	chr4B	85.025	601	75	8	1531	2118	671813893	671814491	6.630000e-167	597
7	TraesCS7A01G322900	chr4B	81.919	542	61	17	658	1189	671734187	671733673	1.190000e-114	424
8	TraesCS7A01G322900	chr4B	88.841	233	24	1	1897	2127	671732611	671732379	5.860000e-73	285
9	TraesCS7A01G322900	chrUn	84.095	503	63	8	1638	2127	30346827	30346329	1.510000e-128	470
10	TraesCS7A01G322900	chrUn	82.267	547	64	23	658	1189	30347546	30347018	3.290000e-120	442
11	TraesCS7A01G322900	chrUn	82.081	346	47	11	1897	2235	30340870	30340533	7.580000e-72	281
12	TraesCS7A01G322900	chrUn	77.754	463	72	16	753	1189	30342335	30341878	4.600000e-64	255
13	TraesCS7A01G322900	chrUn	87.047	193	25	0	2256	2448	30344848	30344656	6.030000e-53	219
14	TraesCS7A01G322900	chrUn	85.366	123	18	0	3119	3241	472409320	472409442	1.050000e-25	128
15	TraesCS7A01G322900	chr5A	83.968	499	62	9	1638	2118	659186291	659186789	2.520000e-126	462
16	TraesCS7A01G322900	chr5A	82.440	541	64	18	658	1188	659184788	659185307	9.140000e-121	444
17	TraesCS7A01G322900	chr5A	81.937	537	64	20	1635	2158	659185498	659186014	1.190000e-114	424
18	TraesCS7A01G322900	chr5A	82.235	349	47	11	1894	2235	659202405	659202745	1.630000e-73	287
19	TraesCS7A01G322900	chr5A	86.010	193	27	0	2256	2448	659187093	659187285	1.310000e-49	207
20	TraesCS7A01G322900	chr5A	88.356	146	17	0	1723	1868	709732256	709732111	3.680000e-40	176
21	TraesCS7A01G322900	chr5A	93.069	101	4	2	2353	2452	709723645	709723547	1.040000e-30	145
22	TraesCS7A01G322900	chr5A	85.714	105	12	2	1088	1189	659201296	659201400	1.360000e-19	108
23	TraesCS7A01G322900	chr4A	87.611	113	13	1	3132	3244	736230828	736230717	2.910000e-26	130
24	TraesCS7A01G322900	chr3B	87.611	113	13	1	3132	3244	814646920	814646809	2.910000e-26	130
25	TraesCS7A01G322900	chr5D	83.478	115	19	0	1578	1692	503148865	503148979	1.360000e-19	108

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	TraesCS7A01G322900	chr7A	468831099	468834685	3586	False	6625.000000	6625	100.000000	1	3587	1	chr7A.!!$F1	3586
1	TraesCS7A01G322900	chr7B	423138361	423141951	3590	False	5452.000000	5452	94.212000	1	3568	1	chr7B.!!$F1	3567
2	TraesCS7A01G322900	chr7D	408717332	408721096	3764	False	1889.666667	5018	96.924667	1	3587	3	chr7D.!!$F1	3586
3	TraesCS7A01G322900	chr4B	671813893	671814491	598	False	597.000000	597	85.025000	1531	2118	1	chr4B.!!$F1	587
4	TraesCS7A01G322900	chr4B	671732379	671734187	1808	True	354.500000	424	85.380000	658	2127	2	chr4B.!!$R1	1469
5	TraesCS7A01G322900	chrUn	30340533	30347546	7013	True	333.400000	470	82.648800	658	2448	5	chrUn.!!$R1	1790
6	TraesCS7A01G322900	chr5A	659184788	659187285	2497	False	384.250000	462	83.588750	658	2448	4	chr5A.!!$F1	1790

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
589	621	0.044161	GCGCGAATTACTAGCACACG	60.044	55.0	12.10	0.0	0.0	4.49	F
1047	1094	1.194781	TGGAGAGGGGCAAGTCTGAC	61.195	60.0	0.00	0.0	0.0	3.51	F
2230	4966	0.247695	GTTCACGCGGCAAATCTAGC	60.248	55.0	12.47	0.0	0.0	3.42	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1768	2621	0.242825	AGAATCGCCGTCAAAGTCGA	59.757	50.000	0.00	0.0	35.34	4.20	R
2236	4972	1.238439	CCAACCGATGACTGCAACTT	58.762	50.000	0.00	0.0	0.00	2.66	R
3329	7072	3.108881	AGATCGATGAACGTCAATGTCG	58.891	45.455	0.54	0.0	43.13	4.35	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
153	154	6.183347	AGATGATGACATGCATGATGATCAT	58.817	36.000	30.80	30.80	37.34	2.45
183	184	6.842437	AGCAGAACACAAGTAATCTCTCTA	57.158	37.500	0.00	0.00	0.00	2.43
301	302	4.633565	GCAGGAGAAATGAACACCTCTTAG	59.366	45.833	0.00	0.00	0.00	2.18
306	337	9.268282	AGGAGAAATGAACACCTCTTAGTAATA	57.732	33.333	0.00	0.00	0.00	0.98
349	380	6.681777	AGATACAGCTGCAAAAAGGTTTAAG	58.318	36.000	15.27	0.00	0.00	1.85
391	422	0.814457	TGCACGCACTCAAGGTTTTT	59.186	45.000	0.00	0.00	0.00	1.94
453	485	5.245301	TCGAAATGGGTTCTTTCTAGTCAGA	59.755	40.000	0.00	0.00	33.70	3.27
539	571	3.181493	GCATGCCTTGTAATGGTCTCAAG	60.181	47.826	6.36	0.00	38.45	3.02
540	572	3.788227	TGCCTTGTAATGGTCTCAAGT	57.212	42.857	0.00	0.00	37.45	3.16
542	574	5.235850	TGCCTTGTAATGGTCTCAAGTTA	57.764	39.130	0.00	0.00	37.45	2.24
571	603	8.237267	AGAACACAAGTTGCTATTTACATAAGC	58.763	33.333	1.81	0.00	38.30	3.09
584	616	5.817616	TTACATAAGCGCGAATTACTAGC	57.182	39.130	12.10	0.00	0.00	3.42
586	618	3.489785	ACATAAGCGCGAATTACTAGCAC	59.510	43.478	12.10	0.00	0.00	4.40
589	621	0.044161	GCGCGAATTACTAGCACACG	60.044	55.000	12.10	0.00	0.00	4.49
677	709	3.823873	TGGCCAATGGTTTAAGTACACTG	59.176	43.478	0.61	0.00	0.00	3.66
696	728	2.548057	CTGCAAGAAGTACAAGGCGAAA	59.452	45.455	0.00	0.00	34.07	3.46
733	765	2.119801	AGTCCATGACAACTGCATCC	57.880	50.000	0.00	0.00	34.60	3.51
962	1009	7.234782	TGTGTGTATATAACTAGGGGATTGAGG	59.765	40.741	0.00	0.00	0.00	3.86
1047	1094	1.194781	TGGAGAGGGGCAAGTCTGAC	61.195	60.000	0.00	0.00	0.00	3.51
1575	2413	2.763448	ACTAGTCCTCAGGCAAGACATC	59.237	50.000	0.00	0.00	32.82	3.06
1696	2539	4.824289	AGCATGCCAAATCCTTGTTTTAG	58.176	39.130	15.66	0.00	0.00	1.85
1699	2542	6.014669	AGCATGCCAAATCCTTGTTTTAGTTA	60.015	34.615	15.66	0.00	0.00	2.24
1768	2621	6.259608	CCATGCAAGAGACTCTTCGAAATATT	59.740	38.462	14.99	0.00	33.78	1.28
1786	2639	1.065358	TTCGACTTTGACGGCGATTC	58.935	50.000	16.62	1.19	32.38	2.52
2199	4935	9.078990	ACATGACTATACAAGCTACTAGCAATA	57.921	33.333	10.73	0.43	45.56	1.90
2230	4966	0.247695	GTTCACGCGGCAAATCTAGC	60.248	55.000	12.47	0.00	0.00	3.42
2236	4972	1.586422	GCGGCAAATCTAGCTCATCA	58.414	50.000	0.00	0.00	0.00	3.07
2250	5011	2.222976	GCTCATCAAGTTGCAGTCATCG	60.223	50.000	0.00	0.00	0.00	3.84
2271	5092	3.733684	CGGTTGGTTTGAGTTGTTTCCAG	60.734	47.826	0.00	0.00	0.00	3.86
2375	5196	0.920763	ATGGGGAACTGCCAGGATCA	60.921	55.000	0.00	0.00	38.95	2.92
2509	5331	2.951457	TCAGTCATTGCATTGCATGG	57.049	45.000	12.95	7.89	38.76	3.66
2510	5332	2.448453	TCAGTCATTGCATTGCATGGA	58.552	42.857	12.95	10.18	38.76	3.41
2537	5359	2.290367	TGTGTTTTCTGATGCCGTTCAG	59.710	45.455	2.81	2.81	43.70	3.02
2545	5367	3.452990	TCTGATGCCGTTCAGGGTTAATA	59.547	43.478	8.13	0.00	42.78	0.98
2658	5480	4.630069	ACTGCACAAGCTAATTAACCTACG	59.370	41.667	0.00	0.00	42.74	3.51
2703	5526	2.361119	GGACTTCTTTGTTGGTGGGTTC	59.639	50.000	0.00	0.00	0.00	3.62
2813	5638	8.148437	TGTAGTTTTAGTGGGTTGGATGTATA	57.852	34.615	0.00	0.00	0.00	1.47
2814	5639	8.042515	TGTAGTTTTAGTGGGTTGGATGTATAC	58.957	37.037	0.00	0.00	0.00	1.47
3044	6737	9.956720	GTTTCATCCCAGTTTGATTTATCATAG	57.043	33.333	0.00	0.00	36.56	2.23
3329	7072	7.081349	CGTACCTGATATCTTGAGATGAAGAC	58.919	42.308	3.98	0.00	34.79	3.01
3351	7094	3.547868	CGACATTGACGTTCATCGATCTT	59.452	43.478	0.00	0.00	42.86	2.40
3437	7192	4.539870	CTGTTTGCTTCATCGTTTCACAT	58.460	39.130	0.00	0.00	0.00	3.21

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
22	23	6.948309	CCACCTATTAGCAGGGCTTAATTAAT	59.052	38.462	0.00	0.00	40.44	1.40
232	233	2.265904	TCACCCCTCGTGAGTGACG	61.266	63.158	0.00	0.00	46.80	4.35
349	380	1.581934	TCTTATGCATACGCCAGTGC	58.418	50.000	5.74	0.00	41.61	4.40
453	485	1.133853	GGCTGCTCCCTGAGAAATCAT	60.134	52.381	0.00	0.00	0.00	2.45
571	603	1.541475	TCGTGTGCTAGTAATTCGCG	58.459	50.000	0.00	0.00	0.00	5.87
584	616	7.555639	TTTTATTTTAGCGGAAATTCGTGTG	57.444	32.000	5.80	0.00	31.96	3.82
586	618	8.442605	TCTTTTTATTTTAGCGGAAATTCGTG	57.557	30.769	5.80	0.00	31.96	4.35
619	651	5.633601	GCCACTCCAGCTTGTAAAAATAAAC	59.366	40.000	0.00	0.00	0.00	2.01
621	653	4.083003	CGCCACTCCAGCTTGTAAAAATAA	60.083	41.667	0.00	0.00	0.00	1.40
637	669	1.933853	CCATTAAGCTACACGCCACTC	59.066	52.381	0.00	0.00	40.39	3.51
677	709	3.492313	CATTTCGCCTTGTACTTCTTGC	58.508	45.455	0.00	0.00	0.00	4.01
696	728	7.504238	TCATGGACTTGTTTAACAGTTAACCAT	59.496	33.333	13.97	13.97	34.26	3.55
882	924	3.828451	ACAAATGATGGGGTCAACTTCTG	59.172	43.478	0.00	0.00	40.97	3.02
962	1009	2.092914	ACTACCTTAGGTTGGCATCTGC	60.093	50.000	10.01	0.00	37.09	4.26
973	1020	8.204903	TCTCCTAGATAGTGTACTACCTTAGG	57.795	42.308	0.00	0.00	34.16	2.69
1018	1065	1.118356	CCCCTCTCCATCTTCTCCCG	61.118	65.000	0.00	0.00	0.00	5.14
1047	1094	3.016971	TCCATGGCCACCCTCAGG	61.017	66.667	8.16	3.47	40.04	3.86
1095	1142	0.321475	GCTGCTGCTCCTGTTCTTCT	60.321	55.000	8.53	0.00	36.03	2.85
1233	1283	9.273016	CTTCCATTCTTACTGAACAAAAGAGTA	57.727	33.333	0.00	0.00	37.52	2.59
1575	2413	4.389687	GCAATTACCTGAACATTTTGCTGG	59.610	41.667	0.00	0.00	36.10	4.85
1768	2621	0.242825	AGAATCGCCGTCAAAGTCGA	59.757	50.000	0.00	0.00	35.34	4.20
1786	2639	3.640967	CCTTCCTCCACTTCCTCTATCAG	59.359	52.174	0.00	0.00	0.00	2.90
1940	3398	5.363517	CGTTTTGCGACACTTAAGAACTAG	58.636	41.667	10.09	0.00	44.77	2.57
2199	4935	3.564511	CCGCGTGAACAATCTTCAAATT	58.435	40.909	4.92	0.00	0.00	1.82
2230	4966	2.350804	CCGATGACTGCAACTTGATGAG	59.649	50.000	0.00	0.00	0.00	2.90
2236	4972	1.238439	CCAACCGATGACTGCAACTT	58.762	50.000	0.00	0.00	0.00	2.66
2250	5011	3.194755	ACTGGAAACAACTCAAACCAACC	59.805	43.478	0.00	0.00	42.06	3.77
2271	5092	5.665459	ACTATGCTCAACAGATTAGGTCAC	58.335	41.667	0.00	0.00	0.00	3.67
2375	5196	4.476113	TGACATCTCCTCCAAAATCCTCAT	59.524	41.667	0.00	0.00	0.00	2.90
2509	5331	5.065218	ACGGCATCAGAAAACACATATCTTC	59.935	40.000	0.00	0.00	0.00	2.87
2510	5332	4.943705	ACGGCATCAGAAAACACATATCTT	59.056	37.500	0.00	0.00	0.00	2.40
2537	5359	6.181908	TGGTGTTTGACCTGTATATTAACCC	58.818	40.000	0.00	0.00	46.32	4.11
2545	5367	2.553028	CCAGCTGGTGTTTGACCTGTAT	60.553	50.000	25.53	0.00	46.32	2.29
2658	5480	7.806014	TCCTTAATCTTCATTTTACAACGCAAC	59.194	33.333	0.00	0.00	0.00	4.17
3044	6737	8.215926	ACTATGTGAGAGAGTAAGTGTATGAC	57.784	38.462	0.00	0.00	0.00	3.06
3298	7041	5.079689	TCAAGATATCAGGTACGTGCAAA	57.920	39.130	10.71	0.00	0.00	3.68
3329	7072	3.108881	AGATCGATGAACGTCAATGTCG	58.891	45.455	0.54	0.00	43.13	4.35
3351	7094	3.617143	ATCGCAAGCAGCTGAGCCA	62.617	57.895	20.43	6.96	42.61	4.75
3425	7180	8.955061	AAAAATAACTCTGATGTGAAACGATG	57.045	30.769	0.00	0.00	42.39	3.84

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.