AutoCloner

Multiple sequence alignment - TraesCS6A01G066300

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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	TraesCS6A01G066300	chr6A	100.000	2336	0	0	1	2336	35542452	35544787	0.000000e+00	4314.0
1	TraesCS6A01G066300	chr6A	91.740	1368	101	10	1	1360	371337482	371338845	0.000000e+00	1890.0
2	TraesCS6A01G066300	chr5A	96.774	1364	39	4	4	1363	635794530	635793168	0.000000e+00	2270.0
3	TraesCS6A01G066300	chr5A	88.119	101	12	0	2232	2332	702048463	702048363	1.130000e-23	121.0
4	TraesCS6A01G066300	chr7D	96.334	1364	43	6	1	1359	232924947	232926308	0.000000e+00	2235.0
5	TraesCS6A01G066300	chr7D	96.123	1367	46	6	4	1365	149106975	149105611	0.000000e+00	2224.0
6	TraesCS6A01G066300	chr7D	95.885	1361	50	4	4	1359	497912480	497911121	0.000000e+00	2198.0
7	TraesCS6A01G066300	chr2D	96.264	1365	44	6	1	1359	273017911	273019274	0.000000e+00	2231.0
8	TraesCS6A01G066300	chr3D	96.171	1358	47	4	6	1359	87390041	87391397	0.000000e+00	2215.0
9	TraesCS6A01G066300	chr3D	88.119	101	12	0	2232	2332	440212541	440212441	1.130000e-23	121.0
10	TraesCS6A01G066300	chr3D	88.889	90	8	2	1629	1718	30771958	30772045	2.450000e-20	110.0
11	TraesCS6A01G066300	chr3D	97.143	35	1	0	1716	1750	30773706	30773740	2.510000e-05	60.2
12	TraesCS6A01G066300	chr2A	95.891	1363	46	9	4	1359	742309304	742307945	0.000000e+00	2198.0
13	TraesCS6A01G066300	chr2A	89.109	101	11	0	2232	2332	416626613	416626513	2.440000e-25	126.0
14	TraesCS6A01G066300	chr3B	92.047	1358	95	9	4	1355	418735709	418734359	0.000000e+00	1897.0
15	TraesCS6A01G066300	chr3B	90.099	101	10	0	2232	2332	56461345	56461245	5.240000e-27	132.0
16	TraesCS6A01G066300	chr6B	87.800	1000	87	19	1359	2336	64966129	64967115	0.000000e+00	1138.0
17	TraesCS6A01G066300	chrUn	85.489	1013	98	27	1359	2336	101365107	101364109	0.000000e+00	1011.0
18	TraesCS6A01G066300	chr6D	91.089	101	9	0	2232	2332	133887166	133887066	1.130000e-28	137.0
19	TraesCS6A01G066300	chr6D	94.444	36	2	0	1714	1749	133887307	133887272	3.240000e-04	56.5
20	TraesCS6A01G066300	chr1A	88.889	99	11	0	2232	2330	536835061	536834963	3.150000e-24	122.0
21	TraesCS6A01G066300	chr1A	97.297	37	1	0	1714	1750	536835201	536835165	1.940000e-06	63.9
22	TraesCS6A01G066300	chr4B	88.119	101	12	0	2232	2332	604276988	604277088	1.130000e-23	121.0
23	TraesCS6A01G066300	chr4B	97.059	34	1	0	1717	1750	604276851	604276884	9.020000e-05	58.4
24	TraesCS6A01G066300	chr5D	87.129	101	13	0	2232	2332	12363534	12363634	5.280000e-22	115.0
25	TraesCS6A01G066300	chr2B	97.143	35	1	0	1716	1750	625470116	625470082	2.510000e-05	60.2

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	TraesCS6A01G066300	chr6A	35542452	35544787	2335	False	4314	4314	100.000	1	2336	1	chr6A.!!$F1	2335
1	TraesCS6A01G066300	chr6A	371337482	371338845	1363	False	1890	1890	91.740	1	1360	1	chr6A.!!$F2	1359
2	TraesCS6A01G066300	chr5A	635793168	635794530	1362	True	2270	2270	96.774	4	1363	1	chr5A.!!$R1	1359
3	TraesCS6A01G066300	chr7D	232924947	232926308	1361	False	2235	2235	96.334	1	1359	1	chr7D.!!$F1	1358
4	TraesCS6A01G066300	chr7D	149105611	149106975	1364	True	2224	2224	96.123	4	1365	1	chr7D.!!$R1	1361
5	TraesCS6A01G066300	chr7D	497911121	497912480	1359	True	2198	2198	95.885	4	1359	1	chr7D.!!$R2	1355
6	TraesCS6A01G066300	chr2D	273017911	273019274	1363	False	2231	2231	96.264	1	1359	1	chr2D.!!$F1	1358
7	TraesCS6A01G066300	chr3D	87390041	87391397	1356	False	2215	2215	96.171	6	1359	1	chr3D.!!$F1	1353
8	TraesCS6A01G066300	chr2A	742307945	742309304	1359	True	2198	2198	95.891	4	1359	1	chr2A.!!$R2	1355
9	TraesCS6A01G066300	chr3B	418734359	418735709	1350	True	1897	1897	92.047	4	1355	1	chr3B.!!$R2	1351
10	TraesCS6A01G066300	chr6B	64966129	64967115	986	False	1138	1138	87.800	1359	2336	1	chr6B.!!$F1	977
11	TraesCS6A01G066300	chrUn	101364109	101365107	998	True	1011	1011	85.489	1359	2336	1	chrUn.!!$R1	977

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
623	627	0.913934	TGCTGGGGAGGCAATACTGA	60.914	55.0	0.0	0.0	36.71	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1923	1962	0.038251	ATCTCAGCAGCGAACGTGAA	60.038	50.0	0.0	0.0	0.0	3.18	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
39	40	7.988937	AGTATCAATATTTGGGAAGATGCCTA	58.011	34.615	0.00	0.00	0.00	3.93
320	324	9.474313	TCAGTATGGGAGCAAACTAAAATATTT	57.526	29.630	0.00	0.00	36.16	1.40
375	379	7.821359	CCTATATGGTGTCAGATATGGAAGTTG	59.179	40.741	0.00	0.00	0.00	3.16
553	557	5.120399	TGTAGAAAAGCGAAAGAGGTTTGA	58.880	37.500	0.00	0.00	41.03	2.69
565	569	4.724279	AGAGGTTTGAAAAAGGCTAGGA	57.276	40.909	0.00	0.00	0.00	2.94
623	627	0.913934	TGCTGGGGAGGCAATACTGA	60.914	55.000	0.00	0.00	36.71	3.41
701	705	6.771267	TGTTCGAGAAATGGTAGCTATCTCTA	59.229	38.462	15.78	5.83	35.50	2.43
915	922	1.751927	CCATGACTTGCTGGAGGGC	60.752	63.158	0.00	0.00	34.24	5.19
925	933	4.731853	TGGAGGGCACGATGGGGA	62.732	66.667	0.00	0.00	0.00	4.81
952	960	1.544691	TGAGAGACGACAAAGGTAGGC	59.455	52.381	0.00	0.00	0.00	3.93
981	989	4.141390	GCAGGAGGGAATGGAAAGATAGAA	60.141	45.833	0.00	0.00	0.00	2.10
1248	1256	7.278868	GCACATGAACTTGTTAGATTAGCTAGT	59.721	37.037	0.00	0.00	0.00	2.57
1300	1311	9.297037	AGCCTATTAGTGAAATTGTAACACTTT	57.703	29.630	0.00	0.00	43.27	2.66
1457	1475	1.741770	CCGAGAAGGCGACCCAAAG	60.742	63.158	0.00	0.00	0.00	2.77
1466	1484	2.680913	CGACCCAAAGAGGCAAGCG	61.681	63.158	0.00	0.00	35.39	4.68
1518	1536	2.308866	TCAATCCTTTCCCCTCCAGAAC	59.691	50.000	0.00	0.00	0.00	3.01
1519	1537	1.299939	ATCCTTTCCCCTCCAGAACC	58.700	55.000	0.00	0.00	0.00	3.62
1520	1538	0.845102	TCCTTTCCCCTCCAGAACCC	60.845	60.000	0.00	0.00	0.00	4.11
1521	1539	0.846870	CCTTTCCCCTCCAGAACCCT	60.847	60.000	0.00	0.00	0.00	4.34
1651	1681	0.526524	CACCCGCTTCAGATCTCGAC	60.527	60.000	3.30	0.00	0.00	4.20
1780	1819	0.983481	GTTCGTTTTTGCGACGGACG	60.983	55.000	0.00	0.00	39.00	4.79
1782	1821	1.154908	CGTTTTTGCGACGGACGAG	60.155	57.895	3.67	0.00	45.77	4.18
1794	1833	1.867919	CGGACGAGCCTCACTTGAGT	61.868	60.000	5.53	0.00	40.48	3.41
1815	1854	1.949631	CCGAATCTTAGGCGTCGGC	60.950	63.158	11.43	11.43	45.74	5.54
1923	1962	1.423845	GATTGCGCGTGAAATCGGT	59.576	52.632	13.77	0.00	30.50	4.69
1973	2012	0.836606	TAGGATTCTGGGCGCAATCA	59.163	50.000	10.83	3.16	31.58	2.57
1975	2014	0.595095	GGATTCTGGGCGCAATCATC	59.405	55.000	10.83	11.23	31.58	2.92
2006	2047	4.648307	TGGGTTTTTGGTATTTGTACGGTT	59.352	37.500	0.00	0.00	0.00	4.44
2007	2048	5.221204	TGGGTTTTTGGTATTTGTACGGTTC	60.221	40.000	0.00	0.00	0.00	3.62
2009	2050	6.448852	GGTTTTTGGTATTTGTACGGTTCAT	58.551	36.000	0.00	0.00	0.00	2.57
2018	2059	7.113825	GGTATTTGTACGGTTCATTTGTTTGTC	59.886	37.037	0.00	0.00	0.00	3.18
2021	2062	3.078594	ACGGTTCATTTGTTTGTCAGC	57.921	42.857	0.00	0.00	0.00	4.26
2022	2063	2.223711	ACGGTTCATTTGTTTGTCAGCC	60.224	45.455	0.00	0.00	0.00	4.85
2024	2065	2.547855	GGTTCATTTGTTTGTCAGCCCC	60.548	50.000	0.00	0.00	0.00	5.80
2030	2071	1.303317	GTTTGTCAGCCCCGTGGAT	60.303	57.895	0.00	0.00	0.00	3.41
2076	2126	2.005606	TTTTCTGAGCCCTGGCACCA	62.006	55.000	11.38	6.99	44.88	4.17
2077	2127	2.005606	TTTCTGAGCCCTGGCACCAA	62.006	55.000	11.38	0.00	44.88	3.67
2097	2147	1.407979	ACCGTAATCAGTTAGCCCTCG	59.592	52.381	0.00	0.00	0.00	4.63
2117	2167	2.096909	CGGCGTGTTTCTGTTTCAGTAG	60.097	50.000	0.00	0.00	32.61	2.57
2119	2169	4.053295	GGCGTGTTTCTGTTTCAGTAGTA	58.947	43.478	0.00	0.00	32.61	1.82
2129	2185	8.638685	TTCTGTTTCAGTAGTAACAGTGTAAC	57.361	34.615	12.93	0.00	46.80	2.50
2173	2229	7.661040	AGTATTTTGTGCTGCTTTTATCTGTT	58.339	30.769	0.00	0.00	0.00	3.16
2197	2253	6.225981	GGGTAATTTAGAAGACCCGTAGAA	57.774	41.667	0.00	0.00	42.16	2.10
2213	2269	2.597578	AGAACATTTAGGGCGGGTTT	57.402	45.000	0.00	0.00	0.00	3.27
2221	2277	5.070714	ACATTTAGGGCGGGTTTTTACTTTT	59.929	36.000	0.00	0.00	0.00	2.27
2222	2278	4.852134	TTAGGGCGGGTTTTTACTTTTC	57.148	40.909	0.00	0.00	0.00	2.29
2223	2279	2.668625	AGGGCGGGTTTTTACTTTTCA	58.331	42.857	0.00	0.00	0.00	2.69
2225	2281	4.409187	AGGGCGGGTTTTTACTTTTCATA	58.591	39.130	0.00	0.00	0.00	2.15
2276	2333	3.959573	CAACTATGCTTGCTTAGAGCC	57.040	47.619	18.29	0.00	41.51	4.70
2284	2341	2.514824	GCTTAGAGCCGCCCTTGG	60.515	66.667	0.00	0.00	34.48	3.61
2311	2368	3.207265	ACATTATTGCGATGGCCTGTA	57.793	42.857	3.32	0.00	38.85	2.74

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	8.331740	CCAAATATTGATACTATGTCCATCCCT	58.668	37.037	0.00	0.00	0.00	4.20
15	16	8.103305	TCTAGGCATCTTCCCAAATATTGATAC	58.897	37.037	0.00	0.00	0.00	2.24
39	40	3.266772	TCCTAGTGGCACAATTTGGATCT	59.733	43.478	21.41	0.00	44.16	2.75
320	324	2.284039	TCCGTCCCATCCCGTTGA	60.284	61.111	0.00	0.00	0.00	3.18
525	529	5.187186	ACCTCTTTCGCTTTTCTACATAGGA	59.813	40.000	0.00	0.00	0.00	2.94
565	569	9.451002	CAAGCTCTCTCAATAATCATATCCAAT	57.549	33.333	0.00	0.00	0.00	3.16
701	705	5.036916	TCTTTCCCACCATAGATACCAAGT	58.963	41.667	0.00	0.00	0.00	3.16
838	845	1.384191	GAGGACATTGCCAACCCCT	59.616	57.895	0.00	0.00	0.00	4.79
915	922	2.430694	TCTCAATACTGTCCCCATCGTG	59.569	50.000	0.00	0.00	0.00	4.35
925	933	4.281182	ACCTTTGTCGTCTCTCAATACTGT	59.719	41.667	0.00	0.00	0.00	3.55
952	960	3.582998	TCCATTCCCTCCTGCAATAAG	57.417	47.619	0.00	0.00	0.00	1.73
981	989	0.885879	TGAGAACGTCCGCACAGTAT	59.114	50.000	0.00	0.00	0.00	2.12
1009	1017	2.428530	GGCCAAATTTGAGAGCTAAGGG	59.571	50.000	19.86	0.00	0.00	3.95
1134	1142	1.135717	CAGTCATCGAAAATTGCCGCA	60.136	47.619	0.00	0.00	0.00	5.69
1259	1270	0.555769	AGGCTCCTCAAACCAAACCA	59.444	50.000	0.00	0.00	0.00	3.67
1300	1311	6.804295	GCAATAACCAATACATCGTTTGTGAA	59.196	34.615	4.39	0.00	39.48	3.18
1766	1805	2.600475	GGCTCGTCCGTCGCAAAAA	61.600	57.895	0.00	0.00	39.67	1.94
1782	1821	2.765250	TTCGGCGACTCAAGTGAGGC	62.765	60.000	10.16	8.67	46.66	4.70
1787	1826	2.159226	CCTAAGATTCGGCGACTCAAGT	60.159	50.000	25.82	14.44	0.00	3.16
1878	1917	3.701241	GCCCGAAATTTGCGATTATGAA	58.299	40.909	0.00	0.00	0.00	2.57
1889	1928	1.933115	AATCGCAGCGCCCGAAATTT	61.933	50.000	21.88	11.12	38.31	1.82
1917	1956	1.897398	GCAGCGAACGTGAACCGATT	61.897	55.000	0.00	0.00	40.70	3.34
1923	1962	0.038251	ATCTCAGCAGCGAACGTGAA	60.038	50.000	0.00	0.00	0.00	3.18
1973	2012	6.950860	ATACCAAAAACCCAAATTCCTGAT	57.049	33.333	0.00	0.00	0.00	2.90
1975	2014	6.770303	ACAAATACCAAAAACCCAAATTCCTG	59.230	34.615	0.00	0.00	0.00	3.86
2006	2047	0.958091	CGGGGCTGACAAACAAATGA	59.042	50.000	0.00	0.00	0.00	2.57
2007	2048	0.673437	ACGGGGCTGACAAACAAATG	59.327	50.000	0.00	0.00	0.00	2.32
2009	2050	1.388065	CCACGGGGCTGACAAACAAA	61.388	55.000	0.00	0.00	0.00	2.83
2018	2059	1.450312	GAACTGATCCACGGGGCTG	60.450	63.158	0.00	0.00	0.00	4.85
2030	2071	4.704833	GCCTGCGCCTGGAACTGA	62.705	66.667	18.93	0.00	0.00	3.41
2050	2100	2.420022	CCAGGGCTCAGAAAACAATACG	59.580	50.000	0.00	0.00	0.00	3.06
2053	2103	1.260544	GCCAGGGCTCAGAAAACAAT	58.739	50.000	2.30	0.00	38.26	2.71
2076	2126	2.159142	CGAGGGCTAACTGATTACGGTT	60.159	50.000	0.00	0.00	45.93	4.44
2077	2127	1.407979	CGAGGGCTAACTGATTACGGT	59.592	52.381	0.00	0.00	37.19	4.83
2097	2147	2.870411	ACTACTGAAACAGAAACACGCC	59.130	45.455	5.76	0.00	35.18	5.68
2129	2185	2.096909	ACTTGACGAAAGCACGAAATCG	60.097	45.455	0.48	0.48	41.63	3.34
2143	2199	3.542712	AGCAGCACAAAATACTTGACG	57.457	42.857	0.00	0.00	0.00	4.35
2146	2202	7.596248	ACAGATAAAAGCAGCACAAAATACTTG	59.404	33.333	0.00	0.00	0.00	3.16
2191	2247	1.134610	ACCCGCCCTAAATGTTCTACG	60.135	52.381	0.00	0.00	0.00	3.51
2197	2253	3.770046	AGTAAAAACCCGCCCTAAATGT	58.230	40.909	0.00	0.00	0.00	2.71
2225	2281	9.555727	TGCAAATTTTACAGTCTAGTTTCTACT	57.444	29.630	0.00	0.00	38.44	2.57
2284	2341	3.853307	GCCATCGCAATAATGTAACCTGC	60.853	47.826	0.00	0.00	34.03	4.85
2311	2368	4.682778	TTGTAGCACACCTAAGAACAGT	57.317	40.909	0.00	0.00	0.00	3.55

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.