AutoCloner

Multiple sequence alignment - TraesCS1A01G318600

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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	TraesCS1A01G318600	chr1A	100.000	3151	0	0	1	3151	509850420	509847270	0.000000e+00	5819.0
1	TraesCS1A01G318600	chr1A	96.868	2267	68	3	59	2325	509720836	509718573	0.000000e+00	3790.0
2	TraesCS1A01G318600	chr1A	96.637	2260	72	4	66	2325	509794208	509791953	0.000000e+00	3749.0
3	TraesCS1A01G318600	chr1A	95.824	1820	53	9	646	2444	509915152	509913335	0.000000e+00	2918.0
4	TraesCS1A01G318600	chr1A	100.000	30	0	0	1	30	509720959	509720930	4.390000e-04	56.5
5	TraesCS1A01G318600	chr1A	100.000	30	0	0	1	30	509794430	509794401	4.390000e-04	56.5
6	TraesCS1A01G318600	chr1D	94.323	1973	85	9	498	2444	412641710	412643681	0.000000e+00	2998.0
7	TraesCS1A01G318600	chr1D	94.323	1973	85	9	498	2444	412745688	412747659	0.000000e+00	2998.0
8	TraesCS1A01G318600	chr1D	94.323	1973	85	9	498	2444	412762851	412764822	0.000000e+00	2998.0
9	TraesCS1A01G318600	chr1D	91.147	2214	104	38	79	2263	412785974	412788124	0.000000e+00	2918.0
10	TraesCS1A01G318600	chr1D	94.240	1823	86	8	456	2263	412659937	412661755	0.000000e+00	2767.0
11	TraesCS1A01G318600	chr1D	89.941	1193	53	33	87	1272	412854091	412855223	0.000000e+00	1476.0
12	TraesCS1A01G318600	chr1D	92.765	387	24	3	58	441	412659570	412659955	9.870000e-155	556.0
13	TraesCS1A01G318600	chr1B	92.008	1977	118	20	498	2444	556662624	556664590	0.000000e+00	2739.0
14	TraesCS1A01G318600	chr1B	90.294	1834	133	21	498	2313	556064794	556062988	0.000000e+00	2359.0
15	TraesCS1A01G318600	chr1B	91.926	1251	81	11	1199	2444	556834311	556835546	0.000000e+00	1733.0
16	TraesCS1A01G318600	chr1B	91.926	1251	81	11	1199	2444	556862732	556863967	0.000000e+00	1733.0
17	TraesCS1A01G318600	chr1B	89.126	1030	78	18	711	1719	556969113	556970129	0.000000e+00	1251.0
18	TraesCS1A01G318600	chr1B	91.787	621	45	5	91	708	556263487	556264104	0.000000e+00	859.0
19	TraesCS1A01G318600	chr1B	91.593	452	35	2	58	506	556662032	556662483	3.450000e-174	621.0
20	TraesCS1A01G318600	chr1B	95.082	61	3	0	2444	2504	494234813	494234873	2.590000e-16	97.1
21	TraesCS1A01G318600	chr4B	89.814	1934	159	20	495	2411	633465585	633467497	0.000000e+00	2446.0
22	TraesCS1A01G318600	chr4B	89.572	1937	161	21	495	2411	633398453	633400368	0.000000e+00	2420.0
23	TraesCS1A01G318600	chr3A	91.144	734	18	18	2435	3151	40850576	40851279	0.000000e+00	952.0
24	TraesCS1A01G318600	chr5B	82.171	129	18	5	2447	2573	11764668	11764793	4.300000e-19	106.0
25	TraesCS1A01G318600	chr5A	84.112	107	13	4	2454	2558	600058981	600058877	2.000000e-17	100.0
26	TraesCS1A01G318600	chr2B	89.744	78	6	2	2437	2514	764141763	764141838	7.190000e-17	99.0
27	TraesCS1A01G318600	chr4D	90.411	73	7	0	2442	2514	84999556	84999484	2.590000e-16	97.1
28	TraesCS1A01G318600	chr2A	81.967	122	14	7	2444	2561	757826217	757826334	2.590000e-16	97.1
29	TraesCS1A01G318600	chr2D	87.654	81	10	0	2434	2514	52224343	52224423	9.300000e-16	95.3
30	TraesCS1A01G318600	chr2D	80.952	126	16	7	2445	2566	534410658	534410537	3.350000e-15	93.5

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	TraesCS1A01G318600	chr1A	509847270	509850420	3150	True	5819.00	5819	100.0000	1	3151	1	chr1A.!!$R1	3150
1	TraesCS1A01G318600	chr1A	509913335	509915152	1817	True	2918.00	2918	95.8240	646	2444	1	chr1A.!!$R2	1798
2	TraesCS1A01G318600	chr1A	509718573	509720959	2386	True	1923.25	3790	98.4340	1	2325	2	chr1A.!!$R3	2324
3	TraesCS1A01G318600	chr1A	509791953	509794430	2477	True	1902.75	3749	98.3185	1	2325	2	chr1A.!!$R4	2324
4	TraesCS1A01G318600	chr1D	412641710	412643681	1971	False	2998.00	2998	94.3230	498	2444	1	chr1D.!!$F1	1946
5	TraesCS1A01G318600	chr1D	412745688	412747659	1971	False	2998.00	2998	94.3230	498	2444	1	chr1D.!!$F2	1946
6	TraesCS1A01G318600	chr1D	412762851	412764822	1971	False	2998.00	2998	94.3230	498	2444	1	chr1D.!!$F3	1946
7	TraesCS1A01G318600	chr1D	412785974	412788124	2150	False	2918.00	2918	91.1470	79	2263	1	chr1D.!!$F4	2184
8	TraesCS1A01G318600	chr1D	412659570	412661755	2185	False	1661.50	2767	93.5025	58	2263	2	chr1D.!!$F6	2205
9	TraesCS1A01G318600	chr1D	412854091	412855223	1132	False	1476.00	1476	89.9410	87	1272	1	chr1D.!!$F5	1185
10	TraesCS1A01G318600	chr1B	556062988	556064794	1806	True	2359.00	2359	90.2940	498	2313	1	chr1B.!!$R1	1815
11	TraesCS1A01G318600	chr1B	556834311	556835546	1235	False	1733.00	1733	91.9260	1199	2444	1	chr1B.!!$F3	1245
12	TraesCS1A01G318600	chr1B	556862732	556863967	1235	False	1733.00	1733	91.9260	1199	2444	1	chr1B.!!$F4	1245
13	TraesCS1A01G318600	chr1B	556662032	556664590	2558	False	1680.00	2739	91.8005	58	2444	2	chr1B.!!$F6	2386
14	TraesCS1A01G318600	chr1B	556969113	556970129	1016	False	1251.00	1251	89.1260	711	1719	1	chr1B.!!$F5	1008
15	TraesCS1A01G318600	chr1B	556263487	556264104	617	False	859.00	859	91.7870	91	708	1	chr1B.!!$F2	617
16	TraesCS1A01G318600	chr4B	633465585	633467497	1912	False	2446.00	2446	89.8140	495	2411	1	chr4B.!!$F2	1916
17	TraesCS1A01G318600	chr4B	633398453	633400368	1915	False	2420.00	2420	89.5720	495	2411	1	chr4B.!!$F1	1916
18	TraesCS1A01G318600	chr3A	40850576	40851279	703	False	952.00	952	91.1440	2435	3151	1	chr3A.!!$F1	716

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
34	35	0.250553	TACTTGCCTCAAACACCCCG	60.251	55.0	0.0	0.0	0.0	5.73	F
1013	1390	0.105039	GAGAAGATGGCGTGTAGGGG	59.895	60.0	0.0	0.0	0.0	4.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1231	1614	0.538057	CGGGGTACGGGCAGATACTA	60.538	60.0	0.0	0.0	39.42	1.82	R
2646	3098	0.034574	CCCACCGTCCATCCATTTGA	60.035	55.0	0.0	0.0	0.00	2.69	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
30	31	4.229876	GCAGAATTACTTGCCTCAAACAC	58.770	43.478	0.00	0.00	0.00	3.32
31	32	4.798574	CAGAATTACTTGCCTCAAACACC	58.201	43.478	0.00	0.00	0.00	4.16
32	33	3.826729	AGAATTACTTGCCTCAAACACCC	59.173	43.478	0.00	0.00	0.00	4.61
33	34	1.989706	TTACTTGCCTCAAACACCCC	58.010	50.000	0.00	0.00	0.00	4.95
34	35	0.250553	TACTTGCCTCAAACACCCCG	60.251	55.000	0.00	0.00	0.00	5.73
35	36	2.203422	TTGCCTCAAACACCCCGG	60.203	61.111	0.00	0.00	0.00	5.73
36	37	2.690653	CTTGCCTCAAACACCCCGGA	62.691	60.000	0.73	0.00	0.00	5.14
37	38	2.671963	GCCTCAAACACCCCGGAC	60.672	66.667	0.73	0.00	0.00	4.79
38	39	2.833227	CCTCAAACACCCCGGACA	59.167	61.111	0.73	0.00	0.00	4.02
39	40	1.302511	CCTCAAACACCCCGGACAG	60.303	63.158	0.73	0.00	0.00	3.51
40	41	1.302511	CTCAAACACCCCGGACAGG	60.303	63.158	0.73	0.00	40.63	4.00
404	564	7.955918	AGTTTGTAAATCTGGCTCAAAATTCT	58.044	30.769	0.00	0.00	31.45	2.40
405	565	9.077885	AGTTTGTAAATCTGGCTCAAAATTCTA	57.922	29.630	0.00	0.00	31.45	2.10
452	612	2.774007	GAAATTGCACGGATCTTCACG	58.226	47.619	0.00	0.00	0.00	4.35
490	684	2.886081	AGCATTGACTGAGACTTAGCG	58.114	47.619	0.00	0.00	0.00	4.26
512	855	0.801251	GCTGATTCGGGATAGCATGC	59.199	55.000	10.51	10.51	36.24	4.06
938	1310	4.183101	CTCAAGCTTCTCCTGATCAACTC	58.817	47.826	0.00	0.00	0.00	3.01
1013	1390	0.105039	GAGAAGATGGCGTGTAGGGG	59.895	60.000	0.00	0.00	0.00	4.79
1017	1394	3.323758	GATGGCGTGTAGGGGTGCA	62.324	63.158	0.00	0.00	0.00	4.57
1381	1780	1.627550	GAGGCTTCGGCTTTGTCGAC	61.628	60.000	9.11	9.11	40.10	4.20
1640	2043	1.642037	CCAACGAGACCGACGCTCTA	61.642	60.000	0.00	0.00	39.50	2.43
1724	2127	1.705873	AGGACCTTGTCGTCTTGTCT	58.294	50.000	0.00	0.00	32.65	3.41
1736	2139	3.832237	CTTGTCTGCCGGGCACACT	62.832	63.158	24.68	0.00	33.79	3.55
1766	2169	0.246086	CGCACTGCTTCTCCTTCTCT	59.754	55.000	0.00	0.00	0.00	3.10
2378	2813	7.096884	AGATTCATGTCACGCTTACTAGTTA	57.903	36.000	0.00	0.00	0.00	2.24
2411	2848	9.581099	AGTTGTCTTGTTTTATTTTAGGTTGTG	57.419	29.630	0.00	0.00	0.00	3.33
2452	2889	5.661056	TGTGATTTTTGTTTGGGTGTGTA	57.339	34.783	0.00	0.00	0.00	2.90
2507	2944	6.707608	GTCACATCTAAATATGACATCAGCCA	59.292	38.462	0.00	0.00	40.95	4.75
2622	3074	1.677217	GCTTCGCTTCCTCCATGTCTT	60.677	52.381	0.00	0.00	0.00	3.01
2625	3077	1.478510	TCGCTTCCTCCATGTCTTCTC	59.521	52.381	0.00	0.00	0.00	2.87
2640	3092	3.432933	GTCTTCTCTTTTCTGCTGCTCAG	59.567	47.826	0.00	0.88	44.21	3.35
2655	3107	5.769484	CTGCTCAGCTTTATCAAATGGAT	57.231	39.130	0.00	0.00	40.14	3.41
2656	3108	5.509716	TGCTCAGCTTTATCAAATGGATG	57.490	39.130	0.00	0.00	36.72	3.51
2657	3109	4.340097	TGCTCAGCTTTATCAAATGGATGG	59.660	41.667	0.00	0.00	36.72	3.51
2658	3110	4.581824	GCTCAGCTTTATCAAATGGATGGA	59.418	41.667	0.00	0.00	36.72	3.41
2659	3111	5.506982	GCTCAGCTTTATCAAATGGATGGAC	60.507	44.000	0.00	0.00	36.72	4.02
2660	3112	4.576053	TCAGCTTTATCAAATGGATGGACG	59.424	41.667	0.00	0.00	36.72	4.79
2661	3113	3.885297	AGCTTTATCAAATGGATGGACGG	59.115	43.478	0.00	0.00	36.72	4.79
2662	3114	3.632145	GCTTTATCAAATGGATGGACGGT	59.368	43.478	0.00	0.00	36.72	4.83
2663	3115	4.498009	GCTTTATCAAATGGATGGACGGTG	60.498	45.833	0.00	0.00	36.72	4.94
2664	3116	2.057137	ATCAAATGGATGGACGGTGG	57.943	50.000	0.00	0.00	34.06	4.61
2665	3117	0.034574	TCAAATGGATGGACGGTGGG	60.035	55.000	0.00	0.00	0.00	4.61
2666	3118	1.379843	AAATGGATGGACGGTGGGC	60.380	57.895	0.00	0.00	0.00	5.36
2667	3119	3.697439	AATGGATGGACGGTGGGCG	62.697	63.158	0.00	0.00	0.00	6.13
2734	3186	0.527817	ACGCCGATTGCTACTGCTAC	60.528	55.000	0.00	0.00	40.48	3.58
2771	3223	4.853924	AAGTGGCTCCTTGTGTATTTTG	57.146	40.909	0.00	0.00	0.00	2.44
2778	3230	5.240844	GGCTCCTTGTGTATTTTGTAGTTGT	59.759	40.000	0.00	0.00	0.00	3.32
2807	3259	9.961265	CAGATAGATAAATCAACCTAACGTACA	57.039	33.333	0.00	0.00	0.00	2.90
2814	3266	5.743636	ATCAACCTAACGTACAACCCTTA	57.256	39.130	0.00	0.00	0.00	2.69
2931	3383	5.523552	CACATTTACATGGTCGCTCATTCTA	59.476	40.000	0.00	0.00	34.27	2.10

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
50	51	2.565391	ACGAAAAACCAATGGGAATCCC	59.435	45.455	12.39	12.39	45.71	3.85
51	52	3.257127	TCACGAAAAACCAATGGGAATCC	59.743	43.478	3.55	0.00	38.05	3.01
52	53	4.513198	TCACGAAAAACCAATGGGAATC	57.487	40.909	3.55	0.00	38.05	2.52
53	54	4.946478	TTCACGAAAAACCAATGGGAAT	57.054	36.364	3.55	0.00	38.05	3.01
54	55	4.946478	ATTCACGAAAAACCAATGGGAA	57.054	36.364	3.55	0.00	38.05	3.97
55	56	4.827835	TGTATTCACGAAAAACCAATGGGA	59.172	37.500	3.55	0.00	38.05	4.37
56	57	5.127693	TGTATTCACGAAAAACCAATGGG	57.872	39.130	3.55	0.00	41.29	4.00
404	564	7.728148	TGTGGTCTGAAATACTTGTAACACTA	58.272	34.615	0.00	0.00	0.00	2.74
405	565	6.588204	TGTGGTCTGAAATACTTGTAACACT	58.412	36.000	0.00	0.00	0.00	3.55
452	612	4.997905	TGCTATATTCGCTTGATCTTGC	57.002	40.909	0.00	0.00	0.00	4.01
462	656	5.226396	AGTCTCAGTCAATGCTATATTCGC	58.774	41.667	0.00	0.00	0.00	4.70
490	684	2.533266	TGCTATCCCGAATCAGCTTC	57.467	50.000	0.00	0.00	35.05	3.86
512	855	6.759356	TGATCCGTATATTTATATTGGCACCG	59.241	38.462	0.00	0.00	0.00	4.94
938	1310	2.279517	GACGATGGCTAGGTGGCG	60.280	66.667	0.00	0.00	45.14	5.69
1013	1390	4.759096	GCGCCACCATCGTTGCAC	62.759	66.667	0.00	0.00	30.01	4.57
1017	1394	4.704833	AGCAGCGCCACCATCGTT	62.705	61.111	2.29	0.00	0.00	3.85
1231	1614	0.538057	CGGGGTACGGGCAGATACTA	60.538	60.000	0.00	0.00	39.42	1.82
1528	1931	6.148315	CCATGATCGAGCAGCATTAGAATTTA	59.852	38.462	10.08	0.00	0.00	1.40
1640	2043	4.585216	TTGGAGGTCGGGGGTGGT	62.585	66.667	0.00	0.00	0.00	4.16
1724	2127	4.155733	CCGATAGTGTGCCCGGCA	62.156	66.667	8.43	8.43	35.29	5.69
1736	2139	2.795973	CAGTGCGACGTCCCGATA	59.204	61.111	10.58	0.00	0.00	2.92
1766	2169	1.000506	GTGAAGTTGTAGAGCCGGTCA	59.999	52.381	1.90	0.00	0.00	4.02
2419	2856	9.623350	CCAAACAAAAATCACAACAAATCTTTT	57.377	25.926	0.00	0.00	0.00	2.27
2424	2861	6.432472	ACACCCAAACAAAAATCACAACAAAT	59.568	30.769	0.00	0.00	0.00	2.32
2434	2871	6.780522	AGTCCTATACACACCCAAACAAAAAT	59.219	34.615	0.00	0.00	0.00	1.82
2452	2889	9.019656	GTTATGTCACATCTAGATGAGTCCTAT	57.980	37.037	34.16	21.42	41.20	2.57
2493	2930	3.200605	TGTGAGGTTGGCTGATGTCATAT	59.799	43.478	0.00	0.00	0.00	1.78
2507	2944	2.365293	GGGCTGTTTTCAATGTGAGGTT	59.635	45.455	0.00	0.00	0.00	3.50
2570	3020	5.072741	AGTTTAAGATGAGCTGGCTTTGAA	58.927	37.500	0.00	0.00	0.00	2.69
2572	3022	4.436584	CGAGTTTAAGATGAGCTGGCTTTG	60.437	45.833	0.00	0.00	0.00	2.77
2573	3023	3.686726	CGAGTTTAAGATGAGCTGGCTTT	59.313	43.478	0.00	0.00	0.00	3.51
2574	3024	3.055819	TCGAGTTTAAGATGAGCTGGCTT	60.056	43.478	0.00	0.00	0.00	4.35
2575	3025	2.497675	TCGAGTTTAAGATGAGCTGGCT	59.502	45.455	0.00	0.00	0.00	4.75
2640	3092	3.632145	ACCGTCCATCCATTTGATAAAGC	59.368	43.478	0.00	0.00	30.56	3.51
2641	3093	4.036734	CCACCGTCCATCCATTTGATAAAG	59.963	45.833	0.00	0.00	30.56	1.85
2642	3094	3.951037	CCACCGTCCATCCATTTGATAAA	59.049	43.478	0.00	0.00	30.56	1.40
2643	3095	3.550820	CCACCGTCCATCCATTTGATAA	58.449	45.455	0.00	0.00	30.56	1.75
2644	3096	2.158682	CCCACCGTCCATCCATTTGATA	60.159	50.000	0.00	0.00	30.56	2.15
2645	3097	1.410083	CCCACCGTCCATCCATTTGAT	60.410	52.381	0.00	0.00	0.00	2.57
2646	3098	0.034574	CCCACCGTCCATCCATTTGA	60.035	55.000	0.00	0.00	0.00	2.69
2647	3099	1.666209	GCCCACCGTCCATCCATTTG	61.666	60.000	0.00	0.00	0.00	2.32
2648	3100	1.379843	GCCCACCGTCCATCCATTT	60.380	57.895	0.00	0.00	0.00	2.32
2649	3101	2.275418	GCCCACCGTCCATCCATT	59.725	61.111	0.00	0.00	0.00	3.16
2650	3102	4.175337	CGCCCACCGTCCATCCAT	62.175	66.667	0.00	0.00	0.00	3.41
2660	3112	3.670377	GTGACAAAGCCGCCCACC	61.670	66.667	0.00	0.00	0.00	4.61
2661	3113	2.268076	ATGTGACAAAGCCGCCCAC	61.268	57.895	0.00	0.00	0.00	4.61
2662	3114	2.115052	ATGTGACAAAGCCGCCCA	59.885	55.556	0.00	0.00	0.00	5.36
2663	3115	2.568090	CATGTGACAAAGCCGCCC	59.432	61.111	0.00	0.00	0.00	6.13
2664	3116	2.126346	GCATGTGACAAAGCCGCC	60.126	61.111	2.43	0.00	0.00	6.13
2665	3117	0.597118	TTTGCATGTGACAAAGCCGC	60.597	50.000	10.22	0.22	33.30	6.53
2666	3118	1.411394	CTTTGCATGTGACAAAGCCG	58.589	50.000	10.22	0.00	45.23	5.52
2734	3186	2.476686	CCACTTAGCAATGCATCACACG	60.477	50.000	8.35	0.00	0.00	4.49
2786	3238	6.820152	GGGTTGTACGTTAGGTTGATTTATCT	59.180	38.462	0.00	0.00	0.00	1.98
2807	3259	4.248058	CCGTCAACGAAATAGTAAGGGTT	58.752	43.478	3.71	0.00	43.02	4.11
2814	3266	3.176708	CGATCACCGTCAACGAAATAGT	58.823	45.455	3.71	0.00	43.02	2.12
2931	3383	3.769739	TGCGTGGATAAGCTATTGGAT	57.230	42.857	0.00	0.00	32.19	3.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.