AutoCloner

Multiple sequence alignment - TraesCS4A01G303800

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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	TraesCS4A01G303800	chr4A	100.000	2416	0	0	1	2416	599589347	599586932	0.000000e+00	4462.0
1	TraesCS4A01G303800	chr3D	95.763	2431	76	13	4	2416	589281297	589278876	0.000000e+00	3893.0
2	TraesCS4A01G303800	chr1A	95.600	2432	74	13	4	2416	554510499	554512916	0.000000e+00	3868.0
3	TraesCS4A01G303800	chr5D	95.189	2432	91	11	4	2416	6187184	6189608	0.000000e+00	3819.0
4	TraesCS4A01G303800	chr5D	95.105	2431	94	11	4	2416	503279981	503277558	0.000000e+00	3807.0
5	TraesCS4A01G303800	chr5D	95.996	2123	70	10	303	2416	503216770	503218886	0.000000e+00	3435.0
6	TraesCS4A01G303800	chr1D	94.901	2432	99	12	4	2416	254399866	254397441	0.000000e+00	3781.0
7	TraesCS4A01G303800	chr2A	94.392	2425	104	18	4	2416	335836892	335839296	0.000000e+00	3696.0
8	TraesCS4A01G303800	chr6D	96.045	2124	68	12	303	2416	168253477	168255594	0.000000e+00	3443.0
9	TraesCS4A01G303800	chr6D	93.984	1230	51	9	4	1216	45517814	45519037	0.000000e+00	1840.0
10	TraesCS4A01G303800	chrUn	95.951	2124	69	12	303	2416	93411079	93408963	0.000000e+00	3430.0
11	TraesCS4A01G303800	chrUn	94.803	558	20	1	4	552	239346020	239345463	0.000000e+00	861.0
12	TraesCS4A01G303800	chr3B	95.857	2124	71	12	303	2416	201525576	201527692	0.000000e+00	3419.0
13	TraesCS4A01G303800	chr2D	95.810	2124	73	10	303	2416	272795342	272793225	0.000000e+00	3415.0
14	TraesCS4A01G303800	chr6B	96.899	258	8	0	4	261	450081072	450080815	1.330000e-117	433.0
15	TraesCS4A01G303800	chr2B	92.664	259	10	1	67	316	755374313	755374055	4.910000e-97	364.0
16	TraesCS4A01G303800	chr2B	93.333	60	3	1	252	310	58105386	58105327	1.190000e-13	87.9
17	TraesCS4A01G303800	chr3A	98.529	68	1	0	252	319	336825500	336825433	1.170000e-23	121.0

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	TraesCS4A01G303800	chr4A	599586932	599589347	2415	True	4462	4462	100.000	1	2416	1	chr4A.!!$R1	2415
1	TraesCS4A01G303800	chr3D	589278876	589281297	2421	True	3893	3893	95.763	4	2416	1	chr3D.!!$R1	2412
2	TraesCS4A01G303800	chr1A	554510499	554512916	2417	False	3868	3868	95.600	4	2416	1	chr1A.!!$F1	2412
3	TraesCS4A01G303800	chr5D	6187184	6189608	2424	False	3819	3819	95.189	4	2416	1	chr5D.!!$F1	2412
4	TraesCS4A01G303800	chr5D	503277558	503279981	2423	True	3807	3807	95.105	4	2416	1	chr5D.!!$R1	2412
5	TraesCS4A01G303800	chr5D	503216770	503218886	2116	False	3435	3435	95.996	303	2416	1	chr5D.!!$F2	2113
6	TraesCS4A01G303800	chr1D	254397441	254399866	2425	True	3781	3781	94.901	4	2416	1	chr1D.!!$R1	2412
7	TraesCS4A01G303800	chr2A	335836892	335839296	2404	False	3696	3696	94.392	4	2416	1	chr2A.!!$F1	2412
8	TraesCS4A01G303800	chr6D	168253477	168255594	2117	False	3443	3443	96.045	303	2416	1	chr6D.!!$F2	2113
9	TraesCS4A01G303800	chr6D	45517814	45519037	1223	False	1840	1840	93.984	4	1216	1	chr6D.!!$F1	1212
10	TraesCS4A01G303800	chrUn	93408963	93411079	2116	True	3430	3430	95.951	303	2416	1	chrUn.!!$R1	2113
11	TraesCS4A01G303800	chrUn	239345463	239346020	557	True	861	861	94.803	4	552	1	chrUn.!!$R2	548
12	TraesCS4A01G303800	chr3B	201525576	201527692	2116	False	3419	3419	95.857	303	2416	1	chr3B.!!$F1	2113
13	TraesCS4A01G303800	chr2D	272793225	272795342	2117	True	3415	3415	95.810	303	2416	1	chr2D.!!$R1	2113

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
505	517	0.817013	CGCAATTGTATGGCCAACCT	59.183	50.0	10.96	0.0	36.63	3.50	F
511	523	0.965439	TGTATGGCCAACCTTTGTGC	59.035	50.0	10.96	0.0	36.63	4.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1316	1337	1.899814	TCTACTTCAACCGATGTGCCT	59.100	47.619	0.0	0.00	32.23	4.75	R
2271	2295	2.004583	TTTGATCCGTGGACGACATC	57.995	50.000	0.0	2.87	43.02	3.06	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
125	126	4.785346	ACTTGGGCTGATATCATCAACT	57.215	40.909	5.72	0.00	39.11	3.16
158	159	4.776349	TGGTATGGAAGTAATGCACGAAT	58.224	39.130	0.00	0.00	29.34	3.34
160	161	4.814234	GGTATGGAAGTAATGCACGAATGA	59.186	41.667	0.00	0.00	29.34	2.57
489	501	4.946772	TGTTCCTTTCCATTATGAATCGCA	59.053	37.500	0.00	0.00	0.00	5.10
505	517	0.817013	CGCAATTGTATGGCCAACCT	59.183	50.000	10.96	0.00	36.63	3.50
511	523	0.965439	TGTATGGCCAACCTTTGTGC	59.035	50.000	10.96	0.00	36.63	4.57
531	543	1.269723	CGTAGAATGCTAGATGCCCGA	59.730	52.381	0.00	0.00	42.00	5.14
560	572	8.388103	CCACGTTACTATTGTTTATTTCTCCTG	58.612	37.037	0.00	0.00	0.00	3.86
566	578	8.273780	ACTATTGTTTATTTCTCCTGCTTCAG	57.726	34.615	0.00	0.00	0.00	3.02
589	601	5.355350	AGATTGACCTTTTCTATCTTTGCCG	59.645	40.000	0.00	0.00	42.22	5.69
610	622	6.094742	TGCCGATAAATGATGAGCTACAAAAA	59.905	34.615	0.00	0.00	0.00	1.94
679	693	8.306761	CCTTTTTAAAGAGTGGCATTCTATGTT	58.693	33.333	13.26	6.78	38.28	2.71
775	790	1.597742	CTGAATAAGGGGCGGATGTG	58.402	55.000	0.00	0.00	0.00	3.21
831	846	3.059386	GCGCGGGTTCAATTCCCA	61.059	61.111	8.83	0.00	44.81	4.37
834	849	1.029408	CGCGGGTTCAATTCCCATCA	61.029	55.000	0.00	0.00	44.81	3.07
838	853	2.362077	CGGGTTCAATTCCCATCATTCC	59.638	50.000	1.89	0.00	44.81	3.01
905	920	6.818644	ACTCCTAGTGACGTATTTACTTACGA	59.181	38.462	10.61	0.00	46.02	3.43
961	977	6.704056	TCCTTTCCTAGTTCTTCTTCCAAT	57.296	37.500	0.00	0.00	0.00	3.16
1024	1043	2.757077	CTTTCCCTTCACCGCCCT	59.243	61.111	0.00	0.00	0.00	5.19
1038	1057	3.716195	CCCTCATGGCGGTGGTCA	61.716	66.667	0.00	0.00	0.00	4.02
1067	1086	6.267242	GGGTTCATAACTACCCCTCTTACTAG	59.733	46.154	0.00	0.00	46.91	2.57
1068	1087	6.239261	GGTTCATAACTACCCCTCTTACTAGC	60.239	46.154	0.00	0.00	0.00	3.42
1069	1088	6.277064	TCATAACTACCCCTCTTACTAGCT	57.723	41.667	0.00	0.00	0.00	3.32
1070	1089	7.398289	TCATAACTACCCCTCTTACTAGCTA	57.602	40.000	0.00	0.00	0.00	3.32
1118	1137	1.941377	TCCGGCTCTACCCAAACTTA	58.059	50.000	0.00	0.00	33.26	2.24
1308	1329	6.827762	TGTGATTTCTATGTTATGCATGGTCA	59.172	34.615	10.16	6.12	38.47	4.02
1579	1601	6.433766	GCTTATGTTCTTCATGTAGCATTCC	58.566	40.000	0.00	0.00	41.17	3.01
1656	1678	3.056832	GGAGACATCCCTATTTTCCCCT	58.943	50.000	0.00	0.00	40.03	4.79
1763	1785	0.838987	AAGGGGTGCTTCCGGTTCTA	60.839	55.000	0.00	0.00	37.00	2.10
2000	2024	3.815809	TCAAACCACACTCAAAGGTAGG	58.184	45.455	0.00	0.00	34.63	3.18
2001	2025	2.884639	CAAACCACACTCAAAGGTAGGG	59.115	50.000	0.00	0.00	34.63	3.53
2152	2176	8.118976	TGATTAGGGTCGTATTCTATGGTTAG	57.881	38.462	0.00	0.00	0.00	2.34
2271	2295	7.745717	TCCTATGGAATTATGACCTTTACCAG	58.254	38.462	0.00	0.00	0.00	4.00
2275	2303	6.969043	TGGAATTATGACCTTTACCAGATGT	58.031	36.000	0.00	0.00	0.00	3.06
2282	2310	2.028385	ACCTTTACCAGATGTCGTCCAC	60.028	50.000	0.00	0.00	0.00	4.02
2325	2353	4.574674	TGGATTTCACTTGCCTGTCTAT	57.425	40.909	0.00	0.00	0.00	1.98
2352	2380	1.600511	TTGCGTGTGCTCGGGATAGA	61.601	55.000	0.00	0.00	43.34	1.98

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
125	126	3.329520	ACTTCCATACCAAGGTTAGCACA	59.670	43.478	0.00	0.00	0.00	4.57
158	159	3.149196	GAGGGAAGTTGTGAGCATTTCA	58.851	45.455	0.00	0.00	0.00	2.69
160	161	3.515602	AGAGGGAAGTTGTGAGCATTT	57.484	42.857	0.00	0.00	0.00	2.32
339	351	5.391449	TCTCGTCGTTAACTGAATTCTGAG	58.609	41.667	18.13	5.37	0.00	3.35
489	501	3.556843	GCACAAAGGTTGGCCATACAATT	60.557	43.478	6.09	4.30	37.19	2.32
505	517	3.309682	GCATCTAGCATTCTACGCACAAA	59.690	43.478	0.00	0.00	44.79	2.83
531	543	9.148104	GAGAAATAAACAATAGTAACGTGGTCT	57.852	33.333	0.00	0.00	0.00	3.85
560	572	7.622893	AAGATAGAAAAGGTCAATCTGAAGC	57.377	36.000	0.00	0.00	0.00	3.86
566	578	5.354234	TCGGCAAAGATAGAAAAGGTCAATC	59.646	40.000	0.00	0.00	0.00	2.67
627	639	5.690464	AAAGGAGTAATCAGCTGTGAGAT	57.310	39.130	14.67	0.00	35.66	2.75
679	693	4.992951	TCCGTACTTCGATCGAGATATTGA	59.007	41.667	18.54	9.71	42.86	2.57
759	774	1.152756	GCCACATCCGCCCCTTATT	60.153	57.895	0.00	0.00	0.00	1.40
775	790	3.521796	GCCTTGATCCGCTTGGCC	61.522	66.667	0.00	0.00	37.81	5.36
782	797	1.019673	CAATCCACTGCCTTGATCCG	58.980	55.000	0.00	0.00	0.00	4.18
831	846	3.744940	ATAATGCGATGGGGGAATGAT	57.255	42.857	0.00	0.00	0.00	2.45
834	849	1.895131	GCAATAATGCGATGGGGGAAT	59.105	47.619	0.00	0.00	43.83	3.01
868	883	6.106673	CGTCACTAGGAGTATGGAAAATTGT	58.893	40.000	0.00	0.00	0.00	2.71
881	896	7.122550	GTCGTAAGTAAATACGTCACTAGGAG	58.877	42.308	0.00	0.00	46.57	3.69
889	904	4.565229	TCGTCGTCGTAAGTAAATACGTC	58.435	43.478	0.00	1.26	46.57	4.34
905	920	5.338365	AGCGATAGTTTTATTCTTCGTCGT	58.662	37.500	0.00	0.00	39.35	4.34
938	954	6.574465	CGATTGGAAGAAGAACTAGGAAAGGA	60.574	42.308	0.00	0.00	0.00	3.36
940	956	5.064071	GCGATTGGAAGAAGAACTAGGAAAG	59.936	44.000	0.00	0.00	0.00	2.62
961	977	1.632018	CCCTTGGGGTTATCCTGCGA	61.632	60.000	0.00	0.00	38.25	5.10
1024	1043	1.302431	CTGTTGACCACCGCCATGA	60.302	57.895	0.00	0.00	0.00	3.07
1030	1049	0.250727	ATGAACCCTGTTGACCACCG	60.251	55.000	0.00	0.00	0.00	4.94
1067	1086	1.876837	GCTAGGTAAACGCCCCATAGC	60.877	57.143	0.00	0.00	0.00	2.97
1068	1087	1.270678	GGCTAGGTAAACGCCCCATAG	60.271	57.143	0.00	0.00	37.86	2.23
1069	1088	0.760572	GGCTAGGTAAACGCCCCATA	59.239	55.000	0.00	0.00	37.86	2.74
1070	1089	1.276140	TGGCTAGGTAAACGCCCCAT	61.276	55.000	0.00	0.00	43.12	4.00
1316	1337	1.899814	TCTACTTCAACCGATGTGCCT	59.100	47.619	0.00	0.00	32.23	4.75
1358	1380	4.215109	AGCTTGTACAGTTTGGGAATGTT	58.785	39.130	0.00	0.00	0.00	2.71
1359	1381	3.832527	AGCTTGTACAGTTTGGGAATGT	58.167	40.909	0.00	0.00	0.00	2.71
1361	1383	4.729868	AGAAGCTTGTACAGTTTGGGAAT	58.270	39.130	2.10	0.00	0.00	3.01
1579	1601	7.323895	ACGTAATTTCATAGAGTCATTCGATCG	59.676	37.037	9.36	9.36	0.00	3.69
1656	1678	2.025699	GCAGTGGTAATTAAGACCCCCA	60.026	50.000	6.83	0.00	35.99	4.96
1724	1746	4.444876	CCTTGTTTCAAAGAGAGGAGGACA	60.445	45.833	0.00	0.00	0.00	4.02
1763	1785	3.870419	ACAAAATTGTTTGAAGCACGCAT	59.130	34.783	6.21	0.00	45.99	4.73
1831	1853	6.017605	CAGCAAGTGATTGAGTTCAGTAGTTT	60.018	38.462	0.00	0.00	0.00	2.66
2082	2106	5.161135	ACACTATGGGGATGATGAGAAGAT	58.839	41.667	0.00	0.00	0.00	2.40
2091	2115	4.814967	TGTCTCATACACTATGGGGATGA	58.185	43.478	0.00	0.00	37.26	2.92
2199	2223	2.486982	GAGGTCATAAGCGCCTATACGA	59.513	50.000	2.29	0.00	34.06	3.43
2200	2224	2.415625	GGAGGTCATAAGCGCCTATACG	60.416	54.545	2.29	0.00	39.49	3.06
2259	2283	2.232941	GGACGACATCTGGTAAAGGTCA	59.767	50.000	0.00	0.00	0.00	4.02
2271	2295	2.004583	TTTGATCCGTGGACGACATC	57.995	50.000	0.00	2.87	43.02	3.06
2275	2303	4.269123	CGAAATAATTTGATCCGTGGACGA	59.731	41.667	0.00	0.00	43.02	4.20
2282	2310	5.914635	CCAATCCACGAAATAATTTGATCCG	59.085	40.000	0.00	0.00	0.00	4.18
2352	2380	7.954788	ACGGCAAAACATTTATACAAAACAT	57.045	28.000	0.00	0.00	0.00	2.71

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.