AutoCloner

Multiple sequence alignment - TraesCS7D01G496100

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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	TraesCS7D01G496100	chr7D	100.000	5045	0	0	1	5045	602899407	602904451	0.000000e+00	9317.0
1	TraesCS7D01G496100	chr7A	97.526	5052	113	6	1	5045	694543644	694548690	0.000000e+00	8626.0
2	TraesCS7D01G496100	chr7B	96.677	5055	125	13	1	5045	683510829	683515850	0.000000e+00	8364.0
3	TraesCS7D01G496100	chr6D	86.373	477	51	11	4575	5045	232768565	232768097	4.510000e-140	508.0
4	TraesCS7D01G496100	chr6D	97.872	47	1	0	47	93	410398329	410398375	1.160000e-11	82.4
5	TraesCS7D01G496100	chr4B	87.234	94	6	4	47	134	92547270	92547363	8.940000e-18	102.0
6	TraesCS7D01G496100	chr3D	86.957	92	5	2	47	131	365519313	365519222	4.160000e-16	97.1
7	TraesCS7D01G496100	chr5D	83.962	106	5	7	45	138	559421181	559421076	1.930000e-14	91.6
8	TraesCS7D01G496100	chr4A	97.959	49	1	0	45	93	612429075	612429027	9.000000e-13	86.1
9	TraesCS7D01G496100	chr1B	88.571	70	5	3	45	111	492788197	492788266	1.160000e-11	82.4
10	TraesCS7D01G496100	chr1A	97.872	47	1	0	47	93	361357516	361357470	1.160000e-11	82.4

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	TraesCS7D01G496100	chr7D	602899407	602904451	5044	False	9317	9317	100.000	1	5045	1	chr7D.!!$F1	5044
1	TraesCS7D01G496100	chr7A	694543644	694548690	5046	False	8626	8626	97.526	1	5045	1	chr7A.!!$F1	5044
2	TraesCS7D01G496100	chr7B	683510829	683515850	5021	False	8364	8364	96.677	1	5045	1	chr7B.!!$F1	5044

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	Hairpin	End Stability	Orientation
20	21	0.828022	ACTGGTGTTTCGGTCAGTCA	59.172	50.000	0.00	35.83	3.41	F
497	508	2.037121	TCTTTGCGAGACAGGATCAACA	59.963	45.455	0.00	0.00	3.33	F
1114	1130	0.179000	ATAGCAGAGCTGGTTTCCGG	59.821	55.000	7.56	40.10	5.14	F
2057	2073	0.535780	CCTTTGCAGCAGGTCAGTCA	60.536	55.000	5.95	0.00	3.41	F
3419	3435	1.860641	TCGGCTATCCTTCTCAACCA	58.139	50.000	0.00	0.00	3.67	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1112	1128	1.208052	TCTCTCAGCTTTTGGATCCCG	59.792	52.381	9.9	0.00	5.14	R
2234	2250	1.352017	TCTGCTGCCTTTGAGGAATCA	59.648	47.619	0.0	37.67	2.57	R
2915	2931	1.871080	AGGCTGTTGAAAGTGACTCG	58.129	50.000	0.0	0.00	4.18	R
3882	3898	2.789213	TCTTCCATTTTCCATGTGCGA	58.211	42.857	0.0	0.00	5.10	R
4804	4821	3.188460	GCGGATCACTTTGCTTTGACTAA	59.812	43.478	0.0	0.00	2.24	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
20	21	0.828022	ACTGGTGTTTCGGTCAGTCA	59.172	50.000	0.00	0.00	35.83	3.41
80	84	7.441836	ACTGATATGAGTGAACAAACACACTA	58.558	34.615	0.00	0.00	45.54	2.74
183	188	6.379417	TGCTGTTTGAATTTCCCCAAAAATTT	59.621	30.769	0.00	0.00	38.59	1.82
303	308	3.630892	AGAACAGCAGCTGATTCTCAT	57.369	42.857	29.70	9.99	31.50	2.90
479	490	2.307686	TGGAAAATAGCCGGGAAGTCTT	59.692	45.455	2.18	0.00	0.00	3.01
497	508	2.037121	TCTTTGCGAGACAGGATCAACA	59.963	45.455	0.00	0.00	0.00	3.33
626	637	6.018751	TCGAGCAGAATTAACATCAGCATAAC	60.019	38.462	9.26	0.34	32.34	1.89
676	687	4.878397	AGCATGGAGTGAAACAATAGTAGC	59.122	41.667	0.00	0.00	41.43	3.58
943	959	7.291416	TCTGTTGACCACCCTGCTTTATATATA	59.709	37.037	0.00	0.00	0.00	0.86
944	960	7.984475	TGTTGACCACCCTGCTTTATATATAT	58.016	34.615	0.00	0.00	0.00	0.86
1112	1128	3.274095	AGAATAGCAGAGCTGGTTTCC	57.726	47.619	7.56	0.00	40.10	3.13
1114	1130	0.179000	ATAGCAGAGCTGGTTTCCGG	59.821	55.000	7.56	0.00	40.10	5.14
1671	1687	2.089980	CTTTGCAGGATCTGTCCCTTG	58.910	52.381	0.00	0.00	46.34	3.61
1678	1694	4.701765	CAGGATCTGTCCCTTGTCAATAG	58.298	47.826	0.00	0.00	46.34	1.73
1699	1715	4.708177	AGTAACACAGACATGACAAAGCT	58.292	39.130	0.00	0.00	0.00	3.74
1790	1806	2.475155	TCATCTCTTGCATCTCAGGGT	58.525	47.619	0.00	0.00	0.00	4.34
1922	1938	6.821665	GGCATGTTACTCAAGTAATAGGTTCA	59.178	38.462	11.27	3.31	41.85	3.18
1979	1995	8.354711	ACTCAGAGAACTCATTTGACAGTATA	57.645	34.615	3.79	0.00	0.00	1.47
2057	2073	0.535780	CCTTTGCAGCAGGTCAGTCA	60.536	55.000	5.95	0.00	0.00	3.41
2222	2238	2.542020	TTTGGTTGACGAGATCTGCA	57.458	45.000	0.00	0.00	0.00	4.41
2291	2307	3.566322	CAGTAGAGGGAGATAAGTCACCG	59.434	52.174	0.00	0.00	36.10	4.94
2564	2580	2.012237	CATCACAGATGACAGCGGC	58.988	57.895	0.77	0.00	37.79	6.53
2573	2589	2.143925	GATGACAGCGGCCCTATTAAC	58.856	52.381	0.00	0.00	0.00	2.01
2915	2931	6.620678	TGAAAGTGAAAATACTATTGCTGGC	58.379	36.000	0.00	0.00	0.00	4.85
3419	3435	1.860641	TCGGCTATCCTTCTCAACCA	58.139	50.000	0.00	0.00	0.00	3.67
3624	3640	5.668471	TGGATTTCAACTATGCTCTCTCAG	58.332	41.667	0.00	0.00	0.00	3.35
3651	3667	2.032528	CACGAAGGGAAGCTGGCA	59.967	61.111	0.00	0.00	0.00	4.92
3799	3815	2.531483	ATCTACCCCCGGCACTGAGT	62.531	60.000	0.00	0.00	0.00	3.41
3999	4015	4.634443	ACAACATGTAGATTTAGTTCCCGC	59.366	41.667	0.00	0.00	0.00	6.13
4456	4473	4.574013	CCTTGAGATCAGGTCAGCAATAAC	59.426	45.833	0.00	0.00	0.00	1.89
4517	4534	6.008331	AGACTACGCATATGTACAATCCCTA	58.992	40.000	0.00	0.00	0.00	3.53
4549	4566	8.889849	ATGTACTGTACAAAATATCAAAACGC	57.110	30.769	23.03	0.00	42.76	4.84
4565	4582	2.491621	GCTGAGCGAAATTGCCCC	59.508	61.111	0.00	0.00	34.65	5.80
4639	4656	6.414987	GCACACACTTAAACAAATGAGAAGAC	59.585	38.462	0.00	0.00	0.00	3.01
4713	4730	7.995463	TTTTGGAAAGACGAACCTAATTTTG	57.005	32.000	0.00	0.00	0.00	2.44
4949	4966	9.853177	TTCTTGGCCCTTAAATTTAATTGAAAA	57.147	25.926	10.97	3.95	0.00	2.29

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
183	188	0.036732	AATTCGAAGCACCTGCCTGA	59.963	50.000	3.35	0.0	43.38	3.86
411	422	5.748630	TCGTTCTGTATGCACAATATCAGAC	59.251	40.000	0.00	0.0	32.94	3.51
479	490	2.768253	ATGTTGATCCTGTCTCGCAA	57.232	45.000	0.00	0.0	0.00	4.85
497	508	5.163963	GCGCTTAAAATACTGCAAGCAAAAT	60.164	36.000	0.00	0.0	42.77	1.82
626	637	6.369065	GCTAATCCTCCGTATTGATTTACAGG	59.631	42.308	0.00	0.0	31.55	4.00
676	687	5.168569	TGCATGGTAAGAACTAAGAAGACG	58.831	41.667	0.00	0.0	0.00	4.18
802	813	6.987386	AGCATCCAAGACATCACTAGTATAC	58.013	40.000	0.00	0.0	0.00	1.47
943	959	7.032598	TCAGAGTTCCTAATTTCCCTGAAAT	57.967	36.000	0.00	0.0	43.07	2.17
944	960	6.448369	TCAGAGTTCCTAATTTCCCTGAAA	57.552	37.500	0.00	0.0	35.94	2.69
1112	1128	1.208052	TCTCTCAGCTTTTGGATCCCG	59.792	52.381	9.90	0.0	0.00	5.14
1114	1130	2.617774	GCATCTCTCAGCTTTTGGATCC	59.382	50.000	4.20	4.2	0.00	3.36
1212	1228	5.464389	GCTGAACAAAATGCTGAAGACATTT	59.536	36.000	0.00	0.0	46.85	2.32
1671	1687	7.652300	TTGTCATGTCTGTGTTACTATTGAC	57.348	36.000	0.00	0.0	0.00	3.18
1678	1694	4.776743	CAGCTTTGTCATGTCTGTGTTAC	58.223	43.478	0.00	0.0	0.00	2.50
1699	1715	1.755395	GATGCTGGCATTGGAGGCA	60.755	57.895	9.52	0.0	42.25	4.75
1790	1806	2.185867	GACGCATTCGGTAGGCCA	59.814	61.111	5.01	0.0	40.69	5.36
1893	1909	2.496899	ACTTGAGTAACATGCCCAGG	57.503	50.000	0.00	0.0	0.00	4.45
1922	1938	4.225942	TCAAGAGACTTGGCATCTATGGTT	59.774	41.667	10.84	0.0	0.00	3.67
2057	2073	7.813148	GCTTCAATTGCATTATTATCAGAGCAT	59.187	33.333	0.00	0.0	0.00	3.79
2222	2238	4.104383	TGAGGAATCACCAAAGCTCTTT	57.896	40.909	0.00	0.0	42.04	2.52
2234	2250	1.352017	TCTGCTGCCTTTGAGGAATCA	59.648	47.619	0.00	0.0	37.67	2.57
2291	2307	3.650070	TCATCATACTCTGTCGATGGC	57.350	47.619	0.00	0.0	36.68	4.40
2564	2580	7.876068	TGTGTGTTCTTTCTACTGTTAATAGGG	59.124	37.037	4.12	0.0	0.00	3.53
2573	2589	3.809832	CACCCTGTGTGTTCTTTCTACTG	59.190	47.826	0.00	0.0	40.26	2.74
2915	2931	1.871080	AGGCTGTTGAAAGTGACTCG	58.129	50.000	0.00	0.0	0.00	4.18
3419	3435	3.690745	GGCAAAGACATGGCAGCT	58.309	55.556	0.00	0.0	44.66	4.24
3624	3640	3.793144	CCTTCGTGCGCCTTCAGC	61.793	66.667	4.18	0.0	38.52	4.26
3799	3815	3.951037	ACAACTGCAACTAACATTGGACA	59.049	39.130	0.00	0.0	0.00	4.02
3882	3898	2.789213	TCTTCCATTTTCCATGTGCGA	58.211	42.857	0.00	0.0	0.00	5.10
3999	4015	5.229260	GGTTAACAAAAAGAAGTTGTGCTCG	59.771	40.000	8.10	0.0	39.14	5.03
4199	4215	5.952347	AGGGAGGAAAGTTATAGCAAAAAGG	59.048	40.000	0.00	0.0	0.00	3.11
4200	4216	7.039714	ACAAGGGAGGAAAGTTATAGCAAAAAG	60.040	37.037	0.00	0.0	0.00	2.27
4281	4297	4.750098	AGAGTAAACCATGTGAACAACTCG	59.250	41.667	0.00	0.0	37.71	4.18
4549	4566	3.200522	GGGGGCAATTTCGCTCAG	58.799	61.111	0.00	0.0	32.33	3.35
4606	4623	8.976471	CATTTGTTTAAGTGTGTGCATTTGATA	58.024	29.630	0.00	0.0	0.00	2.15
4713	4730	5.927115	AGTCGACAACTATTCTGAAAGGTTC	59.073	40.000	19.50	0.0	36.07	3.62
4804	4821	3.188460	GCGGATCACTTTGCTTTGACTAA	59.812	43.478	0.00	0.0	0.00	2.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.