AutoCloner

Multiple sequence alignment - TraesCS5B01G344700

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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	TraesCS5B01G344700	chr5B	100.000	2601	0	0	1	2601	527602373	527599773	0.000000e+00	4804.0
1	TraesCS5B01G344700	chr5B	91.003	1545	116	11	705	2244	527769663	527768137	0.000000e+00	2061.0
2	TraesCS5B01G344700	chr5B	84.753	892	93	18	815	1679	527492249	527491374	0.000000e+00	854.0
3	TraesCS5B01G344700	chr5B	82.952	393	27	17	2247	2599	527764841	527764449	4.180000e-83	318.0
4	TraesCS5B01G344700	chr5B	80.000	240	46	2	1222	1460	528566857	528566619	2.660000e-40	176.0
5	TraesCS5B01G344700	chr5D	92.956	1959	91	9	595	2514	434567451	434565501	0.000000e+00	2809.0
6	TraesCS5B01G344700	chr5D	87.118	1933	148	43	724	2599	434688364	434690252	0.000000e+00	2097.0
7	TraesCS5B01G344700	chr5D	85.564	949	107	11	715	1654	434600558	434599631	0.000000e+00	966.0
8	TraesCS5B01G344700	chr5D	81.807	786	88	22	790	1541	434548939	434548175	2.210000e-170	608.0
9	TraesCS5B01G344700	chr5D	85.971	556	59	13	818	1366	434666557	434667100	6.240000e-161	577.0
10	TraesCS5B01G344700	chr5D	87.941	340	38	3	1087	1425	434675699	434676036	5.220000e-107	398.0
11	TraesCS5B01G344700	chr5D	76.860	484	80	14	1074	1550	434679286	434678828	7.190000e-61	244.0
12	TraesCS5B01G344700	chr5D	80.364	275	36	12	1915	2186	434599619	434599360	2.640000e-45	193.0
13	TraesCS5B01G344700	chr5D	97.087	103	2	1	2498	2599	434565327	434565225	3.440000e-39	172.0
14	TraesCS5B01G344700	chr5D	86.170	94	7	2	1451	1538	434676032	434676125	2.130000e-16	97.1
15	TraesCS5B01G344700	chr5A	89.572	911	84	6	803	1707	548658120	548657215	0.000000e+00	1146.0
16	TraesCS5B01G344700	chr5A	80.235	1022	129	40	711	1707	548503565	548504538	0.000000e+00	701.0
17	TraesCS5B01G344700	chr5A	94.231	156	9	0	607	762	548658268	548658113	3.350000e-59	239.0
18	TraesCS5B01G344700	chr7D	97.963	540	11	0	1	540	395352287	395351748	0.000000e+00	937.0
19	TraesCS5B01G344700	chr7D	97.606	543	13	0	1	543	612277885	612277343	0.000000e+00	931.0
20	TraesCS5B01G344700	chr7D	97.403	539	14	0	1	539	484344994	484344456	0.000000e+00	918.0
21	TraesCS5B01G344700	chr7D	84.956	113	15	2	2378	2488	127768014	127768126	2.120000e-21	113.0
22	TraesCS5B01G344700	chr3D	97.952	537	10	1	1	537	253666903	253667438	0.000000e+00	929.0
23	TraesCS5B01G344700	chr3D	86.869	99	12	1	2390	2487	98566283	98566185	2.740000e-20	110.0
24	TraesCS5B01G344700	chr3D	95.455	66	3	0	543	608	25199411	25199346	3.540000e-19	106.0
25	TraesCS5B01G344700	chr3D	91.304	69	6	0	540	608	300568712	300568780	7.660000e-16	95.3
26	TraesCS5B01G344700	chr6D	97.043	541	15	1	1	540	58529925	58530465	0.000000e+00	909.0
27	TraesCS5B01G344700	chr2D	97.037	540	14	2	1	540	31037651	31038188	0.000000e+00	907.0
28	TraesCS5B01G344700	chr2D	96.858	541	16	1	1	541	599113392	599112853	0.000000e+00	904.0
29	TraesCS5B01G344700	chr1D	96.685	543	17	1	1	543	420603585	420604126	0.000000e+00	902.0
30	TraesCS5B01G344700	chr1D	95.588	68	3	0	543	610	474138142	474138075	2.740000e-20	110.0
31	TraesCS5B01G344700	chr2A	95.556	540	24	0	1	540	513846599	513847138	0.000000e+00	865.0
32	TraesCS5B01G344700	chr7B	87.156	109	11	3	2378	2484	610269195	610269302	1.260000e-23	121.0
33	TraesCS5B01G344700	chr7B	95.385	65	3	0	543	607	534826520	534826456	1.270000e-18	104.0
34	TraesCS5B01G344700	chr6A	86.842	114	8	5	2378	2487	54121654	54121764	1.260000e-23	121.0
35	TraesCS5B01G344700	chr3B	88.000	100	10	2	2390	2487	149103608	149103509	1.640000e-22	117.0
36	TraesCS5B01G344700	chr3B	93.846	65	4	0	543	607	642815912	642815848	5.920000e-17	99.0
37	TraesCS5B01G344700	chr3A	87.736	106	6	6	2378	2479	57269448	57269550	1.640000e-22	117.0
38	TraesCS5B01G344700	chr1A	85.345	116	12	4	2375	2487	150726975	150726862	5.880000e-22	115.0
39	TraesCS5B01G344700	chr1B	95.652	69	3	0	540	608	631232694	631232762	7.610000e-21	111.0
40	TraesCS5B01G344700	chr1B	91.429	70	6	0	543	612	415738367	415738298	2.130000e-16	97.1
41	TraesCS5B01G344700	chr6B	94.286	70	4	0	538	607	718384587	718384656	9.840000e-20	108.0
42	TraesCS5B01G344700	chr4B	94.203	69	3	1	540	607	295701934	295702002	1.270000e-18	104.0

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	TraesCS5B01G344700	chr5B	527599773	527602373	2600	True	4804.0	4804	100.0000	1	2601	1	chr5B.!!$R2	2600
1	TraesCS5B01G344700	chr5B	527764449	527769663	5214	True	1189.5	2061	86.9775	705	2599	2	chr5B.!!$R4	1894
2	TraesCS5B01G344700	chr5B	527491374	527492249	875	True	854.0	854	84.7530	815	1679	1	chr5B.!!$R1	864
3	TraesCS5B01G344700	chr5D	434688364	434690252	1888	False	2097.0	2097	87.1180	724	2599	1	chr5D.!!$F2	1875
4	TraesCS5B01G344700	chr5D	434565225	434567451	2226	True	1490.5	2809	95.0215	595	2599	2	chr5D.!!$R3	2004
5	TraesCS5B01G344700	chr5D	434548175	434548939	764	True	608.0	608	81.8070	790	1541	1	chr5D.!!$R1	751
6	TraesCS5B01G344700	chr5D	434599360	434600558	1198	True	579.5	966	82.9640	715	2186	2	chr5D.!!$R4	1471
7	TraesCS5B01G344700	chr5D	434666557	434667100	543	False	577.0	577	85.9710	818	1366	1	chr5D.!!$F1	548
8	TraesCS5B01G344700	chr5A	548503565	548504538	973	False	701.0	701	80.2350	711	1707	1	chr5A.!!$F1	996
9	TraesCS5B01G344700	chr5A	548657215	548658268	1053	True	692.5	1146	91.9015	607	1707	2	chr5A.!!$R1	1100
10	TraesCS5B01G344700	chr7D	395351748	395352287	539	True	937.0	937	97.9630	1	540	1	chr7D.!!$R1	539
11	TraesCS5B01G344700	chr7D	612277343	612277885	542	True	931.0	931	97.6060	1	543	1	chr7D.!!$R3	542
12	TraesCS5B01G344700	chr7D	484344456	484344994	538	True	918.0	918	97.4030	1	539	1	chr7D.!!$R2	538
13	TraesCS5B01G344700	chr3D	253666903	253667438	535	False	929.0	929	97.9520	1	537	1	chr3D.!!$F1	536
14	TraesCS5B01G344700	chr6D	58529925	58530465	540	False	909.0	909	97.0430	1	540	1	chr6D.!!$F1	539
15	TraesCS5B01G344700	chr2D	31037651	31038188	537	False	907.0	907	97.0370	1	540	1	chr2D.!!$F1	539
16	TraesCS5B01G344700	chr2D	599112853	599113392	539	True	904.0	904	96.8580	1	541	1	chr2D.!!$R1	540
17	TraesCS5B01G344700	chr1D	420603585	420604126	541	False	902.0	902	96.6850	1	543	1	chr1D.!!$F1	542
18	TraesCS5B01G344700	chr2A	513846599	513847138	539	False	865.0	865	95.5560	1	540	1	chr2A.!!$F1	539

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
126	127	0.618968	CCTAGAGGAGGTGCAGGGTT	60.619	60.000	0.0	0.0	40.98	4.11	F
784	788	3.320826	GCACACCCAAAAAGAACTATGGT	59.679	43.478	0.0	0.0	0.00	3.55	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1032	1068	1.003580	TCTTTCTTGGCTAGGTGCAGG	59.996	52.381	0.0	0.0	45.15	4.85	R
2245	5625	0.597637	ACGACTCTGACTTTGCCGTG	60.598	55.000	0.0	0.0	0.00	4.94	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
126	127	0.618968	CCTAGAGGAGGTGCAGGGTT	60.619	60.000	0.00	0.00	40.98	4.11
239	241	3.695060	CGACTTCCTAGCTCTTCAAGGTA	59.305	47.826	0.00	0.00	36.91	3.08
459	461	4.400884	TGTGTTGGTTGCTTTCTGTTGTAT	59.599	37.500	0.00	0.00	0.00	2.29
719	721	7.015292	ACGGTCTCCATCTGCTTCTTATATTTA	59.985	37.037	0.00	0.00	0.00	1.40
781	785	4.039124	CCAAGCACACCCAAAAAGAACTAT	59.961	41.667	0.00	0.00	0.00	2.12
782	786	4.853924	AGCACACCCAAAAAGAACTATG	57.146	40.909	0.00	0.00	0.00	2.23
783	787	3.573967	AGCACACCCAAAAAGAACTATGG	59.426	43.478	0.00	0.00	0.00	2.74
784	788	3.320826	GCACACCCAAAAAGAACTATGGT	59.679	43.478	0.00	0.00	0.00	3.55
785	789	4.521256	GCACACCCAAAAAGAACTATGGTA	59.479	41.667	0.00	0.00	0.00	3.25
857	861	9.419297	CAGACAAATCAAATCAAGATCACATTT	57.581	29.630	0.00	0.00	0.00	2.32
1032	1068	3.648339	TCAGAAACCAAAGCAGCATTC	57.352	42.857	0.00	0.00	0.00	2.67
1035	1071	2.298163	AGAAACCAAAGCAGCATTCCTG	59.702	45.455	0.00	0.00	44.67	3.86
1159	1203	0.779997	AAGAGGCTCACCCAAACCAT	59.220	50.000	18.26	0.00	36.11	3.55
1211	1264	0.804364	GATGTGCAACTTCGCCATCA	59.196	50.000	6.39	0.00	38.44	3.07
1235	1288	0.883833	CAATGAAGGGCCACTGTGTC	59.116	55.000	6.18	0.00	0.00	3.67
1562	1634	1.107114	TGCAGCTGTAGAGGAGCTAC	58.893	55.000	16.64	0.00	45.24	3.58
1589	1661	3.571401	AGCCCTGCTATGTTAATTGCATC	59.429	43.478	0.00	0.00	42.41	3.91
1625	1699	7.268586	ACAGTATAGCAAGTTGTAGATTGGAG	58.731	38.462	4.48	0.00	0.00	3.86
1688	1762	8.472007	TGGTGAACTTTTGTAACTCCAATAAT	57.528	30.769	0.00	0.00	33.33	1.28
1728	1810	4.552355	ACACCAAAGTTTTAAATAGCCGC	58.448	39.130	0.00	0.00	0.00	6.53
1793	1875	7.719871	ACGTAAGGCTATAGGATTCATGTAT	57.280	36.000	1.04	0.00	46.39	2.29
1822	1904	4.616953	TCGAAAAAGTTCTGAAATTGCCC	58.383	39.130	3.65	0.00	0.00	5.36
1831	1913	2.104792	TCTGAAATTGCCCGCTATAGCT	59.895	45.455	21.98	0.66	39.32	3.32
1834	1916	2.938956	AATTGCCCGCTATAGCTTCT	57.061	45.000	21.98	0.00	39.32	2.85
2149	2236	5.939296	TGATGATAGTTGAATGCTGACACAA	59.061	36.000	0.00	0.00	0.00	3.33
2205	2293	2.611518	GCGCGGATCTTCATATAGCTT	58.388	47.619	8.83	0.00	0.00	3.74
2224	2312	0.616395	TCATTGGGCCTCTACGGTGA	60.616	55.000	4.53	0.00	34.25	4.02
2245	5625	1.340114	GGGTTGAGTCAAGGATCACCC	60.340	57.143	11.77	11.77	36.73	4.61
2395	5810	6.057321	TGTCACCGGGTTTTCTCTAATTAT	57.943	37.500	6.32	0.00	0.00	1.28
2532	6141	7.309177	TGAAGAAGAGTCTAATGAAAGTCTCG	58.691	38.462	0.00	0.00	36.94	4.04
2536	6145	6.431198	AGAGTCTAATGAAAGTCTCGTCTC	57.569	41.667	0.00	0.00	36.94	3.36
2592	6202	8.512138	ACTTGGTTATACTAGACACATTTTTGC	58.488	33.333	0.00	0.00	0.00	3.68
2593	6203	8.630054	TTGGTTATACTAGACACATTTTTGCT	57.370	30.769	0.00	0.00	0.00	3.91
2595	6205	8.726988	TGGTTATACTAGACACATTTTTGCTTC	58.273	33.333	0.00	0.00	0.00	3.86
2596	6206	8.947115	GGTTATACTAGACACATTTTTGCTTCT	58.053	33.333	0.00	0.00	0.00	2.85
2597	6207	9.974750	GTTATACTAGACACATTTTTGCTTCTC	57.025	33.333	0.00	0.00	0.00	2.87
2599	6209	5.376625	ACTAGACACATTTTTGCTTCTCCA	58.623	37.500	0.00	0.00	0.00	3.86
2600	6210	4.574599	AGACACATTTTTGCTTCTCCAC	57.425	40.909	0.00	0.00	0.00	4.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
126	127	1.234821	GCAATGTTCCACCGAGACAA	58.765	50.000	0.00	0.00	0.00	3.18
205	207	0.531974	GGAAGTCGCAACCACTGTCA	60.532	55.000	0.00	0.00	0.00	3.58
239	241	2.236223	CTGCCCTGCGATCACTCTGT	62.236	60.000	0.00	0.00	0.00	3.41
574	576	4.153475	CGTCCCATGATGTAAGACGTTTTT	59.847	41.667	16.69	0.00	43.89	1.94
575	577	3.682858	CGTCCCATGATGTAAGACGTTTT	59.317	43.478	16.69	0.00	43.89	2.43
576	578	3.259064	CGTCCCATGATGTAAGACGTTT	58.741	45.455	16.69	0.00	43.89	3.60
577	579	2.418197	CCGTCCCATGATGTAAGACGTT	60.418	50.000	20.64	0.00	46.62	3.99
578	580	1.136305	CCGTCCCATGATGTAAGACGT	59.864	52.381	20.64	0.00	46.62	4.34
580	582	2.224066	CCTCCGTCCCATGATGTAAGAC	60.224	54.545	0.00	0.00	0.00	3.01
581	583	2.039418	CCTCCGTCCCATGATGTAAGA	58.961	52.381	0.00	0.00	0.00	2.10
582	584	1.070758	CCCTCCGTCCCATGATGTAAG	59.929	57.143	0.00	0.00	0.00	2.34
583	585	1.128200	CCCTCCGTCCCATGATGTAA	58.872	55.000	0.00	0.00	0.00	2.41
584	586	0.263468	TCCCTCCGTCCCATGATGTA	59.737	55.000	0.00	0.00	0.00	2.29
585	587	1.002921	TCCCTCCGTCCCATGATGT	59.997	57.895	0.00	0.00	0.00	3.06
586	588	1.050988	ACTCCCTCCGTCCCATGATG	61.051	60.000	0.00	0.00	0.00	3.07
587	589	0.561184	TACTCCCTCCGTCCCATGAT	59.439	55.000	0.00	0.00	0.00	2.45
588	590	0.106167	CTACTCCCTCCGTCCCATGA	60.106	60.000	0.00	0.00	0.00	3.07
589	591	0.106167	TCTACTCCCTCCGTCCCATG	60.106	60.000	0.00	0.00	0.00	3.66
590	592	0.861155	ATCTACTCCCTCCGTCCCAT	59.139	55.000	0.00	0.00	0.00	4.00
591	593	0.185416	GATCTACTCCCTCCGTCCCA	59.815	60.000	0.00	0.00	0.00	4.37
592	594	0.185416	TGATCTACTCCCTCCGTCCC	59.815	60.000	0.00	0.00	0.00	4.46
593	595	1.320507	GTGATCTACTCCCTCCGTCC	58.679	60.000	0.00	0.00	0.00	4.79
719	721	5.186198	GCCATACTCATCTGTTTTAGTGGT	58.814	41.667	0.00	0.00	0.00	4.16
781	785	5.127519	ACATAACTAGCGGTGTACAATACCA	59.872	40.000	0.00	0.00	38.11	3.25
782	786	5.594926	ACATAACTAGCGGTGTACAATACC	58.405	41.667	0.00	0.00	34.81	2.73
783	787	5.689068	GGACATAACTAGCGGTGTACAATAC	59.311	44.000	0.00	0.00	0.00	1.89
784	788	5.360429	TGGACATAACTAGCGGTGTACAATA	59.640	40.000	0.00	0.00	32.76	1.90
785	789	4.160814	TGGACATAACTAGCGGTGTACAAT	59.839	41.667	0.00	0.00	32.76	2.71
1032	1068	1.003580	TCTTTCTTGGCTAGGTGCAGG	59.996	52.381	0.00	0.00	45.15	4.85
1035	1071	4.700213	TGTATTTCTTTCTTGGCTAGGTGC	59.300	41.667	0.00	0.00	41.94	5.01
1159	1203	1.153168	GCTCCTTTGGCCGCTGATA	60.153	57.895	0.00	0.00	0.00	2.15
1235	1288	2.803670	CTGTCGGCGGTGTACACG	60.804	66.667	19.41	15.15	0.00	4.49
1427	1483	2.768253	TGAATGCCATCACGACTTCT	57.232	45.000	0.00	0.00	0.00	2.85
1562	1634	5.922544	GCAATTAACATAGCAGGGCTAAATG	59.077	40.000	1.63	1.08	44.62	2.32
1606	1680	5.483937	TCCTTCTCCAATCTACAACTTGCTA	59.516	40.000	0.00	0.00	0.00	3.49
1607	1681	4.287067	TCCTTCTCCAATCTACAACTTGCT	59.713	41.667	0.00	0.00	0.00	3.91
1625	1699	9.521503	GCAAGGTAATCTTCATAAATTTCCTTC	57.478	33.333	0.00	0.00	39.32	3.46
1688	1762	6.390048	TGGTGTATATACCCAAGGTTTTCA	57.610	37.500	15.39	0.00	40.09	2.69
1707	1789	3.924073	GGCGGCTATTTAAAACTTTGGTG	59.076	43.478	0.00	0.00	0.00	4.17
1709	1791	4.450082	AGGCGGCTATTTAAAACTTTGG	57.550	40.909	11.03	0.00	0.00	3.28
1800	1882	4.616953	GGGCAATTTCAGAACTTTTTCGA	58.383	39.130	0.00	0.00	36.78	3.71
1831	1913	5.003804	GCTCCTCCAAATCACTACAAAGAA	58.996	41.667	0.00	0.00	0.00	2.52
1834	1916	3.334691	CGCTCCTCCAAATCACTACAAA	58.665	45.455	0.00	0.00	0.00	2.83
2205	2293	0.616395	TCACCGTAGAGGCCCAATGA	60.616	55.000	0.00	0.00	46.52	2.57
2224	2312	1.630878	GGTGATCCTTGACTCAACCCT	59.369	52.381	0.00	0.00	0.00	4.34
2245	5625	0.597637	ACGACTCTGACTTTGCCGTG	60.598	55.000	0.00	0.00	0.00	4.94
2320	5719	1.608717	ATTCCGAAGAGTGCCTCGCT	61.609	55.000	0.00	0.00	35.36	4.93
2395	5810	0.960364	GCGAAACCAGATTGCCCAGA	60.960	55.000	0.00	0.00	0.00	3.86
2532	6141	8.134895	CAGACTAGATTCTTGTATCAAGGAGAC	58.865	40.741	0.00	1.19	0.00	3.36
2536	6145	7.776107	TGACAGACTAGATTCTTGTATCAAGG	58.224	38.462	0.00	0.00	0.00	3.61

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.