AutoCloner

Multiple sequence alignment - TraesCS1A01G348500

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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	TraesCS1A01G348500	chr1A	100.000	3197	0	0	1	3197	533734767	533731571	0.000000e+00	5904.0
1	TraesCS1A01G348500	chr1A	97.847	418	5	1	384	801	30919295	30919708	0.000000e+00	719.0
2	TraesCS1A01G348500	chr1D	93.566	2782	84	21	477	3197	436654793	436652046	0.000000e+00	4058.0
3	TraesCS1A01G348500	chr1D	80.713	477	25	18	1	431	436655266	436654811	3.100000e-80	309.0
4	TraesCS1A01G348500	chr1B	87.283	3169	209	89	1	3043	591452914	591449814	0.000000e+00	3441.0
5	TraesCS1A01G348500	chr1B	88.571	175	3	7	3039	3197	591449748	591449575	2.520000e-46	196.0
6	TraesCS1A01G348500	chr7D	88.595	1473	136	15	969	2437	496785497	496786941	0.000000e+00	1760.0
7	TraesCS1A01G348500	chr7A	88.522	1455	138	10	969	2419	562215664	562217093	0.000000e+00	1735.0
8	TraesCS1A01G348500	chr7B	88.340	1458	145	13	963	2419	524919263	524920696	0.000000e+00	1727.0
9	TraesCS1A01G348500	chr7B	81.275	737	114	18	567	1298	194924975	194925692	2.770000e-160	575.0
10	TraesCS1A01G348500	chr2A	97.795	771	13	1	31	801	643979028	643979794	0.000000e+00	1327.0
11	TraesCS1A01G348500	chr4A	97.147	771	18	1	31	801	119349526	119348760	0.000000e+00	1299.0
12	TraesCS1A01G348500	chr6A	96.757	771	19	2	31	801	30404573	30403809	0.000000e+00	1280.0
13	TraesCS1A01G348500	chr6A	90.698	43	3	1	3151	3192	454629049	454629007	4.460000e-04	56.5
14	TraesCS1A01G348500	chr5A	96.667	750	19	3	31	780	555367344	555366601	0.000000e+00	1242.0

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	TraesCS1A01G348500	chr1A	533731571	533734767	3196	True	5904.0	5904	100.0000	1	3197	1	chr1A.!!$R1	3196
1	TraesCS1A01G348500	chr1D	436652046	436655266	3220	True	2183.5	4058	87.1395	1	3197	2	chr1D.!!$R1	3196
2	TraesCS1A01G348500	chr1B	591449575	591452914	3339	True	1818.5	3441	87.9270	1	3197	2	chr1B.!!$R1	3196
3	TraesCS1A01G348500	chr7D	496785497	496786941	1444	False	1760.0	1760	88.5950	969	2437	1	chr7D.!!$F1	1468
4	TraesCS1A01G348500	chr7A	562215664	562217093	1429	False	1735.0	1735	88.5220	969	2419	1	chr7A.!!$F1	1450
5	TraesCS1A01G348500	chr7B	524919263	524920696	1433	False	1727.0	1727	88.3400	963	2419	1	chr7B.!!$F2	1456
6	TraesCS1A01G348500	chr7B	194924975	194925692	717	False	575.0	575	81.2750	567	1298	1	chr7B.!!$F1	731
7	TraesCS1A01G348500	chr2A	643979028	643979794	766	False	1327.0	1327	97.7950	31	801	1	chr2A.!!$F1	770
8	TraesCS1A01G348500	chr4A	119348760	119349526	766	True	1299.0	1299	97.1470	31	801	1	chr4A.!!$R1	770
9	TraesCS1A01G348500	chr6A	30403809	30404573	764	True	1280.0	1280	96.7570	31	801	1	chr6A.!!$R1	770
10	TraesCS1A01G348500	chr5A	555366601	555367344	743	True	1242.0	1242	96.6670	31	780	1	chr5A.!!$R1	749

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
316	376	1.428912	AGGGGCCTTCACAATTTCAGA	59.571	47.619	0.84	0.0	0.0	3.27	F
1410	1523	0.326264	ACTTTACTGGCCCTGCTGAG	59.674	55.000	0.00	0.0	0.0	3.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2010	2123	1.072331	ACTCTGGACGCAAAGAATGGT	59.928	47.619	0.0	0.0	0.00	3.55	R
2329	2453	0.666913	ATCATAGGAACCGACCGACG	59.333	55.000	0.0	0.0	42.18	5.12	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
188	221	2.363147	GCTCTCTCCACCCCGTCT	60.363	66.667	0.00	0.00	0.00	4.18
316	376	1.428912	AGGGGCCTTCACAATTTCAGA	59.571	47.619	0.84	0.00	0.00	3.27
821	932	4.215399	TCAAGTGCCCTTGTTTTATTCTCG	59.785	41.667	8.84	0.00	46.70	4.04
826	937	5.049267	GTGCCCTTGTTTTATTCTCGTTACA	60.049	40.000	0.00	0.00	0.00	2.41
907	1020	5.291905	ACCACTGTATTGGGCTATTAGTC	57.708	43.478	0.00	0.00	41.49	2.59
908	1021	4.102681	ACCACTGTATTGGGCTATTAGTCC	59.897	45.833	7.42	7.42	41.40	3.85
1407	1520	1.133809	TGGACTTTACTGGCCCTGCT	61.134	55.000	0.00	0.00	0.00	4.24
1410	1523	0.326264	ACTTTACTGGCCCTGCTGAG	59.674	55.000	0.00	0.00	0.00	3.35
1671	1784	1.880027	CTTTTCGGAGTTTCCACCCTG	59.120	52.381	0.00	0.00	35.91	4.45
1686	1799	0.742281	CCCTGGATGTTGTCAGAGCG	60.742	60.000	0.00	0.00	33.11	5.03
1692	1805	1.125021	GATGTTGTCAGAGCGAACACG	59.875	52.381	0.00	0.00	32.62	4.49
1788	1901	4.104102	ACAATCCTACCTCTGTTGTCCAAA	59.896	41.667	0.00	0.00	0.00	3.28
1806	1919	3.560025	CCAAAACTAGGCCATCTGTCACT	60.560	47.826	5.01	0.00	0.00	3.41
2112	2225	1.841302	ATGAGGCCAAGGCACTCGAA	61.841	55.000	13.87	3.31	38.49	3.71
2170	2283	0.512518	CATCGAGTTTGCGCACAAGA	59.487	50.000	11.12	6.11	37.04	3.02
2206	2319	1.337823	CGTCCGTTTGAGGTGAAGGAT	60.338	52.381	0.00	0.00	0.00	3.24
2234	2350	6.791299	CGATAACTCCGTACGAAGAGAATAAG	59.209	42.308	22.95	10.66	34.13	1.73
2326	2450	3.062763	CCTGGAGCAGCTATATTTGTCG	58.937	50.000	0.00	0.00	0.00	4.35
2329	2453	3.060602	GGAGCAGCTATATTTGTCGGTC	58.939	50.000	0.00	0.00	0.00	4.79
2341	2465	3.726517	TCGGTCGTCGGTCGGTTC	61.727	66.667	7.93	0.00	40.32	3.62
2430	2558	4.216042	TGTTTGACACATTACATCTGCTGG	59.784	41.667	0.00	0.00	0.00	4.85
2458	2586	1.947456	GCTTCCGAAGTTGACAAACCT	59.053	47.619	9.87	0.00	36.94	3.50
2531	2662	5.350640	GTGGGAACTTGTACTACTATGTTGC	59.649	44.000	0.00	0.00	0.00	4.17
2544	2675	0.036732	ATGTTGCGGTCACCATCAGT	59.963	50.000	0.00	0.00	0.00	3.41
2601	2764	3.394674	TGATTGGCGAGTTTACACAGA	57.605	42.857	0.00	0.00	0.00	3.41
2647	2810	3.988819	TCGATGTGAACAATGTGTCTGA	58.011	40.909	0.00	0.00	0.00	3.27
2671	2834	0.036388	GTGAGATGGACGGCTGGAAA	60.036	55.000	0.00	0.00	0.00	3.13
2705	2878	8.787852	TGGTACAATTTTGGCATTTTTAAATCC	58.212	29.630	0.00	0.00	31.92	3.01
2706	2879	9.008965	GGTACAATTTTGGCATTTTTAAATCCT	57.991	29.630	0.00	0.00	0.00	3.24
2842	3018	7.279615	TCATCCATATCACGAGGTAATTGTTT	58.720	34.615	0.00	0.00	0.00	2.83
2843	3019	6.918892	TCCATATCACGAGGTAATTGTTTG	57.081	37.500	0.00	0.00	0.00	2.93
2844	3020	6.411376	TCCATATCACGAGGTAATTGTTTGT	58.589	36.000	0.00	0.00	0.00	2.83
2845	3021	6.882140	TCCATATCACGAGGTAATTGTTTGTT	59.118	34.615	0.00	0.00	0.00	2.83
2938	3114	4.142902	CGATTTAGATTGGTTCAAGTGCGT	60.143	41.667	0.00	0.00	0.00	5.24
2962	3138	0.827507	GGAGGCCTTTGCTGGTCAAA	60.828	55.000	6.77	0.00	42.01	2.69
2964	3140	1.115326	AGGCCTTTGCTGGTCAAACC	61.115	55.000	0.00	0.00	39.58	3.27
2965	3141	1.007387	GCCTTTGCTGGTCAAACCG	60.007	57.895	0.00	0.00	42.58	4.44
3098	3347	9.691362	GACTATTTGTTCAATGTGTTTAATGGT	57.309	29.630	0.00	0.00	0.00	3.55
3120	3385	8.319057	TGGTAAATATGGAGTTGTATGAGTCT	57.681	34.615	0.00	0.00	0.00	3.24
3124	3389	7.423844	AATATGGAGTTGTATGAGTCTGTGA	57.576	36.000	0.00	0.00	0.00	3.58

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
802	912	4.499037	AACGAGAATAAAACAAGGGCAC	57.501	40.909	0.00	0.00	0.00	5.01
804	915	5.616488	TGTAACGAGAATAAAACAAGGGC	57.384	39.130	0.00	0.00	0.00	5.19
821	932	9.750882	GTAGGAACACTCGAAATAAATTGTAAC	57.249	33.333	0.00	0.00	0.00	2.50
926	1039	7.615582	TGCAGAGTCTAATTACAAATTCCAG	57.384	36.000	0.00	0.00	0.00	3.86
1098	1211	5.466819	TCAAAGTTAACTGATGACGACGAT	58.533	37.500	9.34	0.00	0.00	3.73
1671	1784	1.461127	GTGTTCGCTCTGACAACATCC	59.539	52.381	0.00	0.00	32.80	3.51
1686	1799	4.049186	TCTTCTGAGCTACAAACGTGTTC	58.951	43.478	0.00	0.00	39.30	3.18
1692	1805	3.997681	GGTCCTTCTTCTGAGCTACAAAC	59.002	47.826	0.00	0.00	0.00	2.93
1788	1901	3.327757	TGAAAGTGACAGATGGCCTAGTT	59.672	43.478	3.32	0.00	0.00	2.24
1806	1919	3.762407	TCAGTTTCCTCATCCGTGAAA	57.238	42.857	0.00	0.00	33.05	2.69
1893	2006	2.203070	GCCATGGACAGGGTAGCG	60.203	66.667	18.40	0.00	34.16	4.26
2010	2123	1.072331	ACTCTGGACGCAAAGAATGGT	59.928	47.619	0.00	0.00	0.00	3.55
2206	2319	5.109210	TCTCTTCGTACGGAGTTATCGTTA	58.891	41.667	22.64	0.32	37.78	3.18
2234	2350	2.827921	ACAGGGACAATCATTTTGCCTC	59.172	45.455	0.00	0.00	0.00	4.70
2326	2450	1.379642	ATAGGAACCGACCGACGACC	61.380	60.000	0.00	4.77	45.77	4.79
2329	2453	0.666913	ATCATAGGAACCGACCGACG	59.333	55.000	0.00	0.00	42.18	5.12
2341	2465	6.114089	CCCTCATGCAATCTAGAATCATAGG	58.886	44.000	0.00	8.09	0.00	2.57
2430	2558	3.429207	GTCAACTTCGGAAGCTACAAGAC	59.571	47.826	17.37	11.77	0.00	3.01
2475	2604	6.315393	GGTTCCGAGCAACTATCAAAGAAATA	59.685	38.462	0.00	0.00	0.00	1.40
2531	2662	3.543680	ATAGGAAACTGATGGTGACCG	57.456	47.619	0.00	0.00	43.88	4.79
2601	2764	6.877611	AATAACAAGACTGACAACGGAATT	57.122	33.333	0.00	0.00	0.00	2.17
2647	2810	2.573869	CCGTCCATCTCACACGCT	59.426	61.111	0.00	0.00	32.03	5.07
2671	2834	8.916628	AATGCCAAAATTGTACCAAAATACTT	57.083	26.923	0.00	0.00	0.00	2.24
2694	2867	3.445096	AGAGCAGCGCAGGATTTAAAAAT	59.555	39.130	11.47	0.00	0.00	1.82
2701	2874	2.404995	GCAAGAGCAGCGCAGGATT	61.405	57.895	11.47	0.00	41.58	3.01
2702	2875	2.823147	GCAAGAGCAGCGCAGGAT	60.823	61.111	11.47	0.00	41.58	3.24
2843	3019	6.968131	TTCATCTGCTGTTGAGTATACAAC	57.032	37.500	5.50	2.57	46.83	3.32
2844	3020	7.559486	AGATTCATCTGCTGTTGAGTATACAA	58.441	34.615	5.50	0.00	35.42	2.41
2845	3021	7.069208	AGAGATTCATCTGCTGTTGAGTATACA	59.931	37.037	5.50	0.00	37.25	2.29
2928	3104	1.371183	CTCCCTCCACGCACTTGAA	59.629	57.895	0.00	0.00	0.00	2.69
2938	3114	2.532715	AGCAAAGGCCTCCCTCCA	60.533	61.111	5.23	0.00	41.90	3.86
2964	3140	4.742201	CAGCCTCCACGACACCCG	62.742	72.222	0.00	0.00	45.44	5.28
2965	3141	4.394712	CCAGCCTCCACGACACCC	62.395	72.222	0.00	0.00	0.00	4.61
3098	3347	8.977412	TCACAGACTCATACAACTCCATATTTA	58.023	33.333	0.00	0.00	0.00	1.40
3124	3389	5.010516	TGTTGCCATAGTAAACAGTGCAATT	59.989	36.000	0.00	0.00	39.17	2.32

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.