AutoCloner

Multiple sequence alignment - TraesCS6B01G302800

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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	TraesCS6B01G302800	chr6B	100.000	2378	0	0	1	2378	542367708	542370085	0.000000e+00	4392.0
1	TraesCS6B01G302800	chr6D	95.275	2074	72	12	1	2051	360816605	360818675	0.000000e+00	3264.0
2	TraesCS6B01G302800	chr6D	91.104	326	26	2	1	323	414239686	414239361	2.810000e-119	438.0
3	TraesCS6B01G302800	chr6D	89.222	167	16	2	2149	2314	360818989	360819154	8.610000e-50	207.0
4	TraesCS6B01G302800	chr6D	91.667	120	7	3	2033	2150	360818825	360818943	1.890000e-36	163.0
5	TraesCS6B01G302800	chr6A	92.607	1542	57	20	636	2141	501887078	501888598	0.000000e+00	2163.0
6	TraesCS6B01G302800	chr6A	86.147	231	28	4	2151	2378	501888655	501888884	1.830000e-61	246.0
7	TraesCS6B01G302800	chr6A	95.425	153	6	1	326	477	501886387	501886539	2.360000e-60	243.0
8	TraesCS6B01G302800	chr6A	98.276	58	1	0	513	570	501886540	501886597	4.180000e-18	102.0
9	TraesCS6B01G302800	chr7D	91.411	326	24	3	1	323	411596032	411596356	6.030000e-121	444.0
10	TraesCS6B01G302800	chr4A	91.641	323	24	2	4	323	669379198	669378876	6.030000e-121	444.0
11	TraesCS6B01G302800	chr5D	91.104	326	26	2	1	323	257127700	257127375	2.810000e-119	438.0
12	TraesCS6B01G302800	chr5D	90.491	326	28	2	1	323	275986587	275986262	6.070000e-116	427.0
13	TraesCS6B01G302800	chr2D	91.104	326	26	2	1	323	114822816	114822491	2.810000e-119	438.0
14	TraesCS6B01G302800	chr7B	90.798	326	27	2	1	323	62774954	62775279	1.310000e-117	433.0
15	TraesCS6B01G302800	chr7B	90.385	52	2	1	327	375	687685332	687685281	5.490000e-07	65.8
16	TraesCS6B01G302800	chr7B	91.667	48	1	1	328	372	687242980	687243027	1.970000e-06	63.9
17	TraesCS6B01G302800	chr1D	90.491	326	28	2	1	323	30590161	30590486	6.070000e-116	427.0
18	TraesCS6B01G302800	chr5A	91.667	48	1	1	328	372	277726041	277726088	1.970000e-06	63.9
19	TraesCS6B01G302800	chr5A	91.111	45	1	1	327	368	482796104	482796060	9.180000e-05	58.4
20	TraesCS6B01G302800	chr5A	89.362	47	2	2	329	372	544253316	544253362	3.300000e-04	56.5
21	TraesCS6B01G302800	chr3A	89.796	49	2	1	327	372	561287739	561287787	2.550000e-05	60.2
22	TraesCS6B01G302800	chr4D	100.000	28	0	0	328	355	449889480	449889507	4.000000e-03	52.8

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	TraesCS6B01G302800	chr6B	542367708	542370085	2377	False	4392.000000	4392	100.000000	1	2378	1	chr6B.!!$F1	2377
1	TraesCS6B01G302800	chr6D	360816605	360819154	2549	False	1211.333333	3264	92.054667	1	2314	3	chr6D.!!$F1	2313
2	TraesCS6B01G302800	chr6A	501886387	501888884	2497	False	688.500000	2163	93.113750	326	2378	4	chr6A.!!$F1	2052

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
315	319	0.482446	AGGGTTTTCACCAGGCATGA	59.518	50.0	0.0	0.0	46.43	3.07	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2103	2742	0.17691	TGCAATAGATCCGACGGCAA	59.823	50.0	9.66	0.0	0.0	4.52	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
25	26	1.337071	GCCCGATCTAACTGTCATCGA	59.663	52.381	14.69	0.00	41.61	3.59
26	27	2.859032	GCCCGATCTAACTGTCATCGAC	60.859	54.545	14.69	6.31	41.61	4.20
131	132	1.810030	GAGACCCGCCATTGTCGAC	60.810	63.158	9.11	9.11	36.61	4.20
146	147	3.490759	GACGTGCCAGATGCCACG	61.491	66.667	14.00	14.00	44.51	4.94
171	172	1.440938	CCTCCGACGCAAAACACCAA	61.441	55.000	0.00	0.00	0.00	3.67
198	201	1.457831	ACTAGTCATCCCCTCCGCC	60.458	63.158	0.00	0.00	0.00	6.13
206	209	4.351054	CCCCTCCGCCTGCAGTTT	62.351	66.667	13.81	0.00	0.00	2.66
233	236	4.531426	AGCACCCAAACGGCCCAA	62.531	61.111	0.00	0.00	33.26	4.12
252	255	2.970639	CGGCGTCTCCAAGAAGGA	59.029	61.111	0.00	0.00	46.75	3.36
268	271	1.456296	AGGATACGACACACGCAGTA	58.544	50.000	0.00	0.00	46.94	2.74
272	275	2.784957	TACGACACACGCAGTACCGC	62.785	60.000	0.00	0.00	41.61	5.68
274	277	3.569049	GACACACGCAGTACCGCCT	62.569	63.158	0.00	0.00	41.61	5.52
289	292	1.830145	GCCTCCGCCCAATCTAAGA	59.170	57.895	0.00	0.00	0.00	2.10
315	319	0.482446	AGGGTTTTCACCAGGCATGA	59.518	50.000	0.00	0.00	46.43	3.07
387	406	6.315642	GGAGGGAGTAACTTTTTCTTTATCCG	59.684	42.308	0.00	0.00	0.00	4.18
456	475	5.654603	TGGTACATACAAGGTACAGTCAG	57.345	43.478	4.51	0.00	42.21	3.51
573	592	4.332819	AGAAGACTTTGTTCAGTGTTTCCG	59.667	41.667	0.00	0.00	30.64	4.30
658	1092	3.428532	ACGTAACATGGAGGTGACTACT	58.571	45.455	0.00	0.00	44.03	2.57
978	1423	3.202690	CTGTTCTATCGCGCGCTGC	62.203	63.158	30.48	10.17	41.47	5.25
1460	1905	3.192001	TCCGGTTAGCACAGTAAGTAGTG	59.808	47.826	0.00	0.00	38.74	2.74
1461	1906	3.057033	CCGGTTAGCACAGTAAGTAGTGT	60.057	47.826	0.00	0.00	40.31	3.55
1494	1954	5.238868	AGTGTATCTACGCCAGTACTACATG	59.761	44.000	0.00	0.00	37.41	3.21
1509	1969	0.320771	ACATGGTTGTGCTCTCCGTC	60.321	55.000	0.00	0.00	33.85	4.79
1553	2013	7.710907	TGATAGATTTATGTCCTCGTTCCTTTG	59.289	37.037	0.00	0.00	0.00	2.77
1554	2014	5.805728	AGATTTATGTCCTCGTTCCTTTGT	58.194	37.500	0.00	0.00	0.00	2.83
1555	2015	6.942976	AGATTTATGTCCTCGTTCCTTTGTA	58.057	36.000	0.00	0.00	0.00	2.41
1616	2076	6.837048	ACTACCAACATTCCCTTGTTAAACTT	59.163	34.615	0.00	0.00	37.73	2.66
1637	2097	3.972276	GCCGGCGGTTCTTTTGCA	61.972	61.111	28.82	0.00	0.00	4.08
1769	2229	2.711009	TGGATATGGGAGGATTGTCCAC	59.289	50.000	0.00	0.00	39.61	4.02
1801	2261	0.110486	CCACTACCACCAACCAAGCT	59.890	55.000	0.00	0.00	0.00	3.74
1832	2298	3.688185	CCATATCTTGCCGATCTTCCATG	59.312	47.826	0.00	0.00	33.48	3.66
1866	2332	1.570813	TTAGAGCAATCATCACGGCG	58.429	50.000	4.80	4.80	0.00	6.46
1871	2337	0.247814	GCAATCATCACGGCGTTCAG	60.248	55.000	11.19	2.42	0.00	3.02
1933	2399	3.334691	TCCGAAATGGAATGTGTGACTC	58.665	45.455	0.00	0.00	46.38	3.36
1948	2414	6.632909	TGTGTGACTCTCTAGTACTCTAGTC	58.367	44.000	0.00	9.00	42.88	2.59
2042	2679	3.124297	CAGGCGAGAGTGACATTTTTCTC	59.876	47.826	0.00	0.00	34.21	2.87
2053	2690	6.015095	AGTGACATTTTTCTCCTTTGGGAATC	60.015	38.462	0.00	0.00	41.69	2.52
2141	2780	1.448540	CTGATCTTGAAGCGGGCGT	60.449	57.895	0.00	0.00	0.00	5.68
2142	2781	1.003839	TGATCTTGAAGCGGGCGTT	60.004	52.632	0.00	0.00	0.00	4.84
2176	2862	1.569548	TCCCTCCTCGTGTTATCCTCT	59.430	52.381	0.00	0.00	0.00	3.69
2206	2892	1.048601	GCGACATATCCTCTTCCCCA	58.951	55.000	0.00	0.00	0.00	4.96
2214	2900	1.538876	CCTCTTCCCCACTCCCACA	60.539	63.158	0.00	0.00	0.00	4.17
2215	2901	1.679898	CTCTTCCCCACTCCCACAC	59.320	63.158	0.00	0.00	0.00	3.82
2234	2921	1.127567	CCCTCTGTTCCTGGTGGTGA	61.128	60.000	0.00	0.00	34.23	4.02
2238	2925	0.250858	CTGTTCCTGGTGGTGATGCA	60.251	55.000	0.00	0.00	34.23	3.96
2241	2928	2.034532	CCTGGTGGTGATGCAGCA	59.965	61.111	0.00	0.00	39.63	4.41
2254	2941	0.537143	TGCAGCAACATTCCCGACTT	60.537	50.000	0.00	0.00	0.00	3.01
2255	2942	0.598065	GCAGCAACATTCCCGACTTT	59.402	50.000	0.00	0.00	0.00	2.66
2328	3016	1.375551	GGGTATTTGACGTGCGGAAT	58.624	50.000	0.00	0.00	0.00	3.01
2339	3027	3.737172	GCGGAATGCGTTGTGGCT	61.737	61.111	0.00	0.00	0.00	4.75
2340	3028	2.480555	CGGAATGCGTTGTGGCTC	59.519	61.111	0.00	0.00	0.00	4.70
2358	3047	2.242926	CTCGGAATAGAGGAGCCATGA	58.757	52.381	0.00	0.00	34.74	3.07

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
10	11	1.749063	TGGCGTCGATGACAGTTAGAT	59.251	47.619	9.73	0.00	32.09	1.98
123	124	1.361668	GCATCTGGCACGTCGACAAT	61.362	55.000	17.16	0.00	43.97	2.71
148	149	2.358247	TTTTGCGTCGGAGGAGCC	60.358	61.111	1.18	0.00	0.00	4.70
162	163	0.175531	GTGGCAGCAGTTGGTGTTTT	59.824	50.000	12.33	0.00	44.70	2.43
171	172	0.539051	GGATGACTAGTGGCAGCAGT	59.461	55.000	0.00	0.73	0.00	4.40
233	236	2.262915	CTTCTTGGAGACGCCGCT	59.737	61.111	0.00	0.00	40.66	5.52
240	243	6.158639	CGTGTGTCGTATCCTTCTTGGAGA	62.159	50.000	0.00	0.00	40.56	3.71
252	255	0.179181	CGGTACTGCGTGTGTCGTAT	60.179	55.000	0.00	0.00	42.13	3.06
272	275	1.762957	TCTTCTTAGATTGGGCGGAGG	59.237	52.381	0.00	0.00	0.00	4.30
289	292	3.832490	GCCTGGTGAAAACCCTAAATCTT	59.168	43.478	0.00	0.00	0.00	2.40
387	406	1.009829	GAGGTTGTGATGCATCGGAC	58.990	55.000	21.34	17.62	0.00	4.79
573	592	2.483491	GAGAGGGATATACACGGACGAC	59.517	54.545	0.00	0.00	0.00	4.34
658	1092	2.289274	CGCAAAGTGTGTGTGATGGTTA	59.711	45.455	0.00	0.00	32.74	2.85
746	1180	1.850755	GAAGAAGGGTGGGTGGGGA	60.851	63.158	0.00	0.00	0.00	4.81
979	1424	1.812922	CTGTCGCATCCAGGTGAGC	60.813	63.158	0.00	0.00	0.00	4.26
1047	1492	3.735037	GAGGAACATCGCCGGGGAC	62.735	68.421	25.09	10.90	0.00	4.46
1338	1783	3.699894	ACAGCAGGCACCTCCTCG	61.700	66.667	0.00	0.00	45.52	4.63
1406	1851	1.302033	AAGAACACGCCAGCAGGAG	60.302	57.895	0.00	0.00	41.02	3.69
1460	1905	4.278058	GCGTAGATACACTAAGACGGAAC	58.722	47.826	0.00	0.00	33.55	3.62
1461	1906	3.313526	GGCGTAGATACACTAAGACGGAA	59.686	47.826	0.00	0.00	33.55	4.30
1494	1954	2.047179	GGGACGGAGAGCACAACC	60.047	66.667	0.00	0.00	0.00	3.77
1509	1969	6.367983	TCTATCAAGAAAATCCTCCAATGGG	58.632	40.000	0.00	0.00	0.00	4.00
1592	2052	6.894339	AGTTTAACAAGGGAATGTTGGTAG	57.106	37.500	0.00	0.00	43.13	3.18
1637	2097	4.920662	CGTTGCAACGCATGAAGT	57.079	50.000	35.89	0.00	46.06	3.01
1757	2217	2.232941	TGGTAGTTCGTGGACAATCCTC	59.767	50.000	0.00	0.00	37.46	3.71
1769	2229	1.403780	GGTAGTGGCAGTGGTAGTTCG	60.404	57.143	4.76	0.00	0.00	3.95
1832	2298	3.057315	TGCTCTAATTGGCTTTCAGCAAC	60.057	43.478	0.47	0.00	44.75	4.17
1866	2332	3.057734	CGTGAAAGGGACACTACTGAAC	58.942	50.000	0.00	0.00	36.29	3.18
2066	2703	5.571741	TCGAGAGTGCTTAAAATCTAACGTG	59.428	40.000	0.00	0.00	0.00	4.49
2103	2742	0.176910	TGCAATAGATCCGACGGCAA	59.823	50.000	9.66	0.00	0.00	4.52
2141	2780	2.510613	GAGGGAAAAATCGTCACCCAA	58.489	47.619	0.00	0.00	42.62	4.12
2142	2781	1.271707	GGAGGGAAAAATCGTCACCCA	60.272	52.381	0.00	0.00	42.62	4.51
2176	2862	1.391933	ATATGTCGCAGTCTCCCGCA	61.392	55.000	0.00	0.00	0.00	5.69
2206	2892	1.128188	GGAACAGAGGGTGTGGGAGT	61.128	60.000	0.00	0.00	40.26	3.85
2214	2900	1.073706	ACCACCAGGAACAGAGGGT	60.074	57.895	0.00	0.00	38.69	4.34
2215	2901	1.127567	TCACCACCAGGAACAGAGGG	61.128	60.000	0.00	0.00	38.69	4.30
2234	2921	0.322816	AGTCGGGAATGTTGCTGCAT	60.323	50.000	1.84	0.00	0.00	3.96
2238	2925	1.247567	CCAAAGTCGGGAATGTTGCT	58.752	50.000	0.00	0.00	0.00	3.91
2241	2928	0.250553	TCGCCAAAGTCGGGAATGTT	60.251	50.000	0.00	0.00	0.00	2.71
2264	2951	4.554036	GCCTCCTCATCCCACGGC	62.554	72.222	0.00	0.00	0.00	5.68
2321	3009	4.036804	GCCACAACGCATTCCGCA	62.037	61.111	0.00	0.00	42.60	5.69
2328	3016	0.739462	CTATTCCGAGCCACAACGCA	60.739	55.000	0.00	0.00	0.00	5.24
2331	3019	1.480954	TCCTCTATTCCGAGCCACAAC	59.519	52.381	0.00	0.00	0.00	3.32
2339	3027	1.964223	GTCATGGCTCCTCTATTCCGA	59.036	52.381	0.00	0.00	0.00	4.55
2340	3028	1.336332	CGTCATGGCTCCTCTATTCCG	60.336	57.143	0.00	0.00	0.00	4.30

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.