AutoCloner

Multiple sequence alignment - TraesCS5A01G283600

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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	TraesCS5A01G283600	chr5A	100.000	2901	0	0	1	2901	491710026	491712926	0.000000e+00	5358
1	TraesCS5A01G283600	chr5A	94.303	1650	88	3	286	1931	493018147	493019794	0.000000e+00	2521
2	TraesCS5A01G283600	chr5A	84.615	429	30	10	2227	2624	493019823	493020246	7.530000e-106	394
3	TraesCS5A01G283600	chr5A	91.216	148	10	3	1	146	493017125	493017271	6.340000e-47	198
4	TraesCS5A01G283600	chr5A	90.164	122	8	3	175	292	493017269	493017390	3.870000e-34	156
5	TraesCS5A01G283600	chr5A	88.430	121	13	1	2723	2842	493024871	493024991	8.380000e-31	145
6	TraesCS5A01G283600	chr5D	94.289	1961	88	12	1	1946	389696425	389698376	0.000000e+00	2979
7	TraesCS5A01G283600	chr5D	93.575	1712	81	8	5	1706	388814117	388812425	0.000000e+00	2525
8	TraesCS5A01G283600	chr5D	96.516	287	10	0	2338	2624	388810414	388810128	2.620000e-130	475
9	TraesCS5A01G283600	chr5D	93.478	322	18	2	1968	2286	388810751	388810430	2.620000e-130	475
10	TraesCS5A01G283600	chr5D	85.480	427	26	10	2227	2622	389698419	389698840	2.080000e-111	412
11	TraesCS5A01G283600	chr5D	91.379	232	16	3	1728	1958	388812431	388812203	6.030000e-82	315
12	TraesCS5A01G283600	chr5D	88.186	237	20	3	2660	2896	388810136	388809908	2.850000e-70	276
13	TraesCS5A01G283600	chr5D	89.167	120	11	1	2726	2845	389699682	389699799	6.480000e-32	148
14	TraesCS5A01G283600	chr5B	93.728	1945	96	16	1	1931	469972704	469974636	0.000000e+00	2892
15	TraesCS5A01G283600	chr5B	93.428	1552	77	9	1	1544	467166679	467165145	0.000000e+00	2278
16	TraesCS5A01G283600	chr5B	90.486	946	49	22	1570	2490	467165147	467164218	0.000000e+00	1210
17	TraesCS5A01G283600	chr5B	85.781	429	25	16	2227	2624	469974704	469975127	3.460000e-114	422
18	TraesCS5A01G283600	chr5B	87.967	241	21	3	2661	2901	467161502	467161270	7.920000e-71	278
19	TraesCS5A01G283600	chr5B	88.194	144	11	4	2485	2626	467161634	467161495	1.790000e-37	167
20	TraesCS5A01G283600	chr5B	90.517	116	9	1	2730	2845	469975976	469976089	5.010000e-33	152
21	TraesCS5A01G283600	chr3D	74.497	298	70	5	1276	1570	513621303	513621009	1.090000e-24	124

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	TraesCS5A01G283600	chr5A	491710026	491712926	2900	False	5358.000000	5358	100.000000	1	2901	1	chr5A.!!$F1	2900
1	TraesCS5A01G283600	chr5A	493017125	493020246	3121	False	817.250000	2521	90.074500	1	2624	4	chr5A.!!$F3	2623
2	TraesCS5A01G283600	chr5D	389696425	389699799	3374	False	1179.666667	2979	89.645333	1	2845	3	chr5D.!!$F1	2844
3	TraesCS5A01G283600	chr5D	388809908	388814117	4209	True	813.200000	2525	92.626800	5	2896	5	chr5D.!!$R1	2891
4	TraesCS5A01G283600	chr5B	469972704	469976089	3385	False	1155.333333	2892	90.008667	1	2845	3	chr5B.!!$F1	2844
5	TraesCS5A01G283600	chr5B	467161270	467166679	5409	True	983.250000	2278	90.018750	1	2901	4	chr5B.!!$R1	2900

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
156	161	0.174845	CAAGGCATCGTCGGTTCCTA	59.825	55.0	0.0	0.0	0.0	2.94	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2130	4410	2.155924	GCTTTGCGCTACTATCCGAATC	59.844	50.0	9.73	0.0	35.14	2.52	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
77	81	8.055279	TGGATTTCAATCTGGTGTTAAAGATC	57.945	34.615	0.00	0.00	35.73	2.75
104	108	0.623723	GATTTGCTACACCCTCCCCA	59.376	55.000	0.00	0.00	0.00	4.96
156	161	0.174845	CAAGGCATCGTCGGTTCCTA	59.825	55.000	0.00	0.00	0.00	2.94
171	176	1.756950	CCTAGCTCCGCCACTGGTA	60.757	63.158	0.00	0.00	0.00	3.25
210	215	4.097741	GTCATGCCCATATAGCAACAAACA	59.902	41.667	3.90	0.00	44.83	2.83
267	274	5.860716	GCTCAATCAACTCCTTAGCAAAAAG	59.139	40.000	0.00	0.00	0.00	2.27
280	289	3.609853	AGCAAAAAGACGCCATATCTCA	58.390	40.909	0.00	0.00	0.00	3.27
356	1129	3.396685	AGAGGACTGATTGACCTAGCT	57.603	47.619	0.00	0.00	40.76	3.32
488	1261	2.095059	GCGATTGCAAGATTCCACAACT	60.095	45.455	4.94	0.00	42.15	3.16
532	1305	6.207417	TGTTCCTTGATTGATCCACTCTTTTC	59.793	38.462	0.00	0.00	0.00	2.29
536	1309	4.641396	TGATTGATCCACTCTTTTCACGT	58.359	39.130	0.00	0.00	0.00	4.49
544	1317	4.024387	TCCACTCTTTTCACGTAATGCAAC	60.024	41.667	0.00	0.00	0.00	4.17
545	1318	4.219033	CACTCTTTTCACGTAATGCAACC	58.781	43.478	0.00	0.00	0.00	3.77
660	1435	3.670627	GCTCTGGCGGATTAACAACAAAG	60.671	47.826	0.00	0.00	0.00	2.77
710	1488	2.066700	TTGCCATGCAGTGAGACCCA	62.067	55.000	0.00	0.00	40.61	4.51
883	1661	9.554395	TTGACAAAGAGTGTGAGTATTTTCATA	57.446	29.630	0.00	0.00	41.96	2.15
1005	1785	1.014352	GTCCGCGGCTTAACATGATT	58.986	50.000	23.51	0.00	0.00	2.57
1021	1801	5.984725	ACATGATTCCTTCACCAATACGTA	58.015	37.500	0.00	0.00	37.11	3.57
1190	1970	1.553690	CCCCAACTCATCACCTCGGT	61.554	60.000	0.00	0.00	0.00	4.69
1237	2029	7.290061	TCTTTTCCTATGCTTATGTATGGCTT	58.710	34.615	0.00	0.00	0.00	4.35
1408	2200	5.302568	TGAAGATTTCAGCAAAGGTGTGATT	59.697	36.000	0.00	0.00	34.08	2.57
1468	2260	4.783227	ACCATGGGTGTGAGTCTAAATAGT	59.217	41.667	18.09	0.00	32.98	2.12
1671	2469	2.342279	CGTTCCCTTGAGTCGGCA	59.658	61.111	0.00	0.00	0.00	5.69
1776	2574	3.355378	TCGTACCTTTAGGACGATCCAA	58.645	45.455	14.94	0.13	40.27	3.53
1941	2777	2.691409	TGGATGGAAATCGACACCTC	57.309	50.000	0.00	0.00	0.00	3.85
1961	2798	6.477033	CACCTCGAAAGTATTCTGTATTCTGG	59.523	42.308	0.00	0.00	33.17	3.86
1963	2800	7.093465	ACCTCGAAAGTATTCTGTATTCTGGAA	60.093	37.037	0.00	0.00	33.17	3.53
2061	4341	8.718102	TTGATTTACTACTCTGTTATTCCTGC	57.282	34.615	0.00	0.00	0.00	4.85
2100	4380	7.496529	TTTAATGGATGGAAATCGACATCTC	57.503	36.000	12.01	5.10	42.34	2.75
2286	4607	6.900194	AGGATGTATACAGGCAAAATGTACT	58.100	36.000	11.91	0.00	36.04	2.73
2287	4608	6.767902	AGGATGTATACAGGCAAAATGTACTG	59.232	38.462	11.91	0.00	36.04	2.74
2420	4770	2.596862	GTGCAAACAGAACGTTTTGGAC	59.403	45.455	21.34	18.46	45.79	4.02
2590	7530	6.071952	ACCAACATTAGCAAGTACAAATGGAG	60.072	38.462	0.00	0.00	34.38	3.86
2607	7547	2.816087	TGGAGCAGAAATTTGAGAGCAC	59.184	45.455	0.00	0.00	0.00	4.40
2700	7641	5.103000	CACGAGAATCAAGTATTTCGGACT	58.897	41.667	0.00	0.00	34.87	3.85
2704	7645	6.075519	CGAGAATCAAGTATTTCGGACTTACG	60.076	42.308	0.00	0.00	35.36	3.18
2705	7646	6.860080	AGAATCAAGTATTTCGGACTTACGA	58.140	36.000	0.00	0.00	41.76	3.43
2706	7647	6.750963	AGAATCAAGTATTTCGGACTTACGAC	59.249	38.462	0.00	0.00	43.37	4.34
2707	7648	4.737054	TCAAGTATTTCGGACTTACGACC	58.263	43.478	0.00	0.00	43.37	4.79
2708	7649	4.460382	TCAAGTATTTCGGACTTACGACCT	59.540	41.667	0.00	0.00	43.37	3.85
2709	7650	4.629251	AGTATTTCGGACTTACGACCTC	57.371	45.455	0.00	0.00	43.37	3.85
2710	7651	2.955477	ATTTCGGACTTACGACCTCC	57.045	50.000	0.00	0.00	43.37	4.30
2711	7652	1.915141	TTTCGGACTTACGACCTCCT	58.085	50.000	0.00	0.00	43.37	3.69
2714	7655	0.172803	CGGACTTACGACCTCCTTGG	59.827	60.000	0.00	0.00	42.93	3.61
2737	7678	4.065789	CTCCTTCAACAACAGGAAGTACC	58.934	47.826	0.00	0.00	38.80	3.34
2774	8520	4.260456	GGCAAAAATGATGATTGGCATTCG	60.260	41.667	10.70	0.00	45.70	3.34
2776	8522	2.806608	AATGATGATTGGCATTCGGC	57.193	45.000	5.05	0.75	37.34	5.54
2788	8534	1.934589	CATTCGGCGGTTCACATAGA	58.065	50.000	7.21	0.00	0.00	1.98
2863	8609	4.805219	GGTACACCACCTTTGCTAAAATG	58.195	43.478	0.00	0.00	44.79	2.32
2868	8614	5.221244	ACACCACCTTTGCTAAAATGAAGTC	60.221	40.000	0.00	0.00	0.00	3.01
2887	8633	4.215109	AGTCTAAGTTGGGTGTTTGCAAT	58.785	39.130	0.00	0.00	0.00	3.56

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
3	4	9.702253	TGACATAAGTTCCTCTCTACTATTCTT	57.298	33.333	0.00	0.00	0.00	2.52
77	81	5.049405	GGAGGGTGTAGCAAATCGATTTATG	60.049	44.000	22.33	13.59	0.00	1.90
171	176	8.328055	TGGGCATGACTCATATCATAGATAAT	57.672	34.615	0.00	0.00	37.20	1.28
191	196	3.696045	ACTGTTTGTTGCTATATGGGCA	58.304	40.909	1.81	1.81	37.97	5.36
267	274	6.551385	AAGAAATGAATGAGATATGGCGTC	57.449	37.500	0.00	0.00	0.00	5.19
280	289	9.933723	AGTAATGCAAAGCTTAAAGAAATGAAT	57.066	25.926	0.00	0.00	0.00	2.57
356	1129	5.932619	TCTTACTAGCAATAGTCTGGCAA	57.067	39.130	0.00	0.00	0.00	4.52
488	1261	2.288579	ACATACCTTGTCGCTCGAACAA	60.289	45.455	1.50	1.50	30.89	2.83
518	1291	4.391830	GCATTACGTGAAAAGAGTGGATCA	59.608	41.667	0.00	0.00	0.00	2.92
532	1305	3.071479	AGTGGTAAGGTTGCATTACGTG	58.929	45.455	0.00	0.00	34.58	4.49
536	1309	7.343574	TGACTCTATAGTGGTAAGGTTGCATTA	59.656	37.037	6.75	0.00	35.56	1.90
572	1345	6.448207	TTGATGTCACAATGAAACAAGTCA	57.552	33.333	0.00	0.00	0.00	3.41
660	1435	1.342174	TCCACAACACGAGGGTAAGAC	59.658	52.381	0.00	0.00	0.00	3.01
710	1488	5.627499	TTCGAGCTCTTGCATTAAACATT	57.373	34.783	12.85	0.00	42.74	2.71
795	1573	2.028748	GGTGTAAGCGTTGACCTTAGGA	60.029	50.000	4.77	0.00	0.00	2.94
915	1695	5.653330	ACCAACATGTATGCTCATCAAATGA	59.347	36.000	0.00	0.00	37.76	2.57
925	1705	6.424509	CACAAATCAAAACCAACATGTATGCT	59.575	34.615	0.00	0.00	0.00	3.79
1005	1785	3.758023	TCGAGTTACGTATTGGTGAAGGA	59.242	43.478	0.00	0.00	43.13	3.36
1021	1801	3.632604	ACACATGATCCTACGATCGAGTT	59.367	43.478	24.34	1.27	46.89	3.01
1190	1970	4.308526	TTGGAGGCACAAATACATACCA	57.691	40.909	0.00	0.00	0.00	3.25
1237	2029	9.270640	CCAAAATAATCTTTCCATGTGTTTTGA	57.729	29.630	11.30	0.00	36.60	2.69
1468	2260	4.942944	TCACTTCCACCCTACTCAGATAA	58.057	43.478	0.00	0.00	0.00	1.75
1671	2469	2.553028	CCAAGTGGGACAGCTACAACAT	60.553	50.000	0.00	0.00	41.80	2.71
1758	2556	5.205821	TCTCATTGGATCGTCCTAAAGGTA	58.794	41.667	5.77	0.00	37.46	3.08
1912	2748	5.297776	GTCGATTTCCATCCATCAAACAGAT	59.702	40.000	0.00	0.00	37.48	2.90
1941	2777	8.480643	ACTTTCCAGAATACAGAATACTTTCG	57.519	34.615	0.00	0.00	36.93	3.46
1963	2800	7.224949	GCCGTCTGCTAGAAAATAAAGATACTT	59.775	37.037	0.00	0.00	36.87	2.24
2130	4410	2.155924	GCTTTGCGCTACTATCCGAATC	59.844	50.000	9.73	0.00	35.14	2.52
2247	4568	7.609918	TGTATACATCCTATGCAACTGTTTTGT	59.390	33.333	0.08	0.00	0.00	2.83
2293	4616	2.180017	CACTTTGCGCTGCCCATC	59.820	61.111	9.73	0.00	0.00	3.51
2296	4619	1.748879	TATCCACTTTGCGCTGCCC	60.749	57.895	9.73	0.00	0.00	5.36
2420	4770	4.630644	ATGATGTAGTAGAATGGCTGGG	57.369	45.455	0.00	0.00	0.00	4.45
2590	7530	4.698583	ATCTGTGCTCTCAAATTTCTGC	57.301	40.909	0.00	0.00	0.00	4.26
2679	7620	6.075519	CGTAAGTCCGAAATACTTGATTCTCG	60.076	42.308	0.00	0.00	37.71	4.04
2700	7641	0.252103	AGGAGCCAAGGAGGTCGTAA	60.252	55.000	0.00	0.00	40.61	3.18
2704	7645	0.693049	TTGAAGGAGCCAAGGAGGTC	59.307	55.000	0.00	0.00	40.61	3.85
2705	7646	0.402121	GTTGAAGGAGCCAAGGAGGT	59.598	55.000	0.00	0.00	40.61	3.85
2706	7647	0.401738	TGTTGAAGGAGCCAAGGAGG	59.598	55.000	0.00	0.00	41.84	4.30
2707	7648	1.882623	GTTGTTGAAGGAGCCAAGGAG	59.117	52.381	0.00	0.00	0.00	3.69
2708	7649	1.214175	TGTTGTTGAAGGAGCCAAGGA	59.786	47.619	0.00	0.00	0.00	3.36
2709	7650	1.610522	CTGTTGTTGAAGGAGCCAAGG	59.389	52.381	0.00	0.00	0.00	3.61
2710	7651	1.610522	CCTGTTGTTGAAGGAGCCAAG	59.389	52.381	0.00	0.00	35.40	3.61
2711	7652	1.214175	TCCTGTTGTTGAAGGAGCCAA	59.786	47.619	0.00	0.00	37.68	4.52
2714	7655	2.576615	ACTTCCTGTTGTTGAAGGAGC	58.423	47.619	0.00	0.00	43.40	4.70
2774	8520	3.500680	TCAGTTTTTCTATGTGAACCGCC	59.499	43.478	0.00	0.00	33.88	6.13
2776	8522	5.619607	CGTTTCAGTTTTTCTATGTGAACCG	59.380	40.000	0.00	0.00	33.88	4.44
2788	8534	8.710835	ATTGTGAAAATACCGTTTCAGTTTTT	57.289	26.923	0.76	0.00	45.65	1.94
2862	8608	3.630312	GCAAACACCCAACTTAGACTTCA	59.370	43.478	0.00	0.00	0.00	3.02
2863	8609	3.630312	TGCAAACACCCAACTTAGACTTC	59.370	43.478	0.00	0.00	0.00	3.01
2868	8614	3.059166	GCATTGCAAACACCCAACTTAG	58.941	45.455	1.71	0.00	0.00	2.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.