AutoCloner

Multiple sequence alignment - TraesCS6A01G023800

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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	TraesCS6A01G023800	chr6A	100.000	3179	0	0	1	3179	11842583	11839405	0.000000e+00	5871.0
1	TraesCS6A01G023800	chr6A	93.524	2486	149	6	696	3179	11886500	11884025	0.000000e+00	3688.0
2	TraesCS6A01G023800	chr6A	92.648	1741	99	18	694	2431	11854540	11852826	0.000000e+00	2479.0
3	TraesCS6A01G023800	chr6A	90.573	838	61	6	2344	3179	11852819	11851998	0.000000e+00	1094.0
4	TraesCS6A01G023800	chr6A	86.905	84	11	0	388	471	3205596	3205679	9.390000e-16	95.3
5	TraesCS6A01G023800	chr6A	85.714	84	12	0	388	471	3237409	3237492	4.370000e-14	89.8
6	TraesCS6A01G023800	chr6D	94.330	3192	162	15	1	3179	10338645	10335460	0.000000e+00	4874.0
7	TraesCS6A01G023800	chr6D	94.331	2487	139	2	694	3179	10373408	10370923	0.000000e+00	3810.0
8	TraesCS6A01G023800	chr6D	94.056	2490	122	13	694	3179	10345957	10343490	0.000000e+00	3755.0
9	TraesCS6A01G023800	chr6B	93.534	2490	149	10	694	3179	19119086	19121567	0.000000e+00	3696.0
10	TraesCS6A01G023800	chr6B	93.012	2490	165	8	694	3179	18944604	18942120	0.000000e+00	3626.0
11	TraesCS6A01G023800	chr7D	91.011	89	7	1	388	475	81911036	81910948	5.570000e-23	119.0
12	TraesCS6A01G023800	chr1A	91.667	84	7	0	388	471	267144873	267144790	2.000000e-22	117.0
13	TraesCS6A01G023800	chr7A	82.906	117	18	2	2078	2192	728088775	728088659	1.560000e-18	104.0
14	TraesCS6A01G023800	chr1B	88.372	86	10	0	388	473	512679035	512678950	1.560000e-18	104.0
15	TraesCS6A01G023800	chr7B	87.640	89	10	1	382	470	581390017	581390104	5.610000e-18	102.0
16	TraesCS6A01G023800	chr2A	87.912	91	6	3	382	470	78335727	78335814	5.610000e-18	102.0
17	TraesCS6A01G023800	chr2D	85.263	95	8	3	388	476	635627183	635627089	3.380000e-15	93.5
18	TraesCS6A01G023800	chr5A	85.915	71	9	1	2082	2151	706322634	706322704	1.220000e-09	75.0

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	TraesCS6A01G023800	chr6A	11839405	11842583	3178	True	5871.0	5871	100.0000	1	3179	1	chr6A.!!$R1	3178
1	TraesCS6A01G023800	chr6A	11884025	11886500	2475	True	3688.0	3688	93.5240	696	3179	1	chr6A.!!$R2	2483
2	TraesCS6A01G023800	chr6A	11851998	11854540	2542	True	1786.5	2479	91.6105	694	3179	2	chr6A.!!$R3	2485
3	TraesCS6A01G023800	chr6D	10335460	10338645	3185	True	4874.0	4874	94.3300	1	3179	1	chr6D.!!$R1	3178
4	TraesCS6A01G023800	chr6D	10370923	10373408	2485	True	3810.0	3810	94.3310	694	3179	1	chr6D.!!$R3	2485
5	TraesCS6A01G023800	chr6D	10343490	10345957	2467	True	3755.0	3755	94.0560	694	3179	1	chr6D.!!$R2	2485
6	TraesCS6A01G023800	chr6B	19119086	19121567	2481	False	3696.0	3696	93.5340	694	3179	1	chr6B.!!$F1	2485
7	TraesCS6A01G023800	chr6B	18942120	18944604	2484	True	3626.0	3626	93.0120	694	3179	1	chr6B.!!$R1	2485

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
983	997	0.322187	CCCTAACCCCAGTTTGACCG	60.322	60.0	0.00	0.0	37.42	4.79	F
1802	1816	0.324614	TCACAGGCCGATGATGTTGT	59.675	50.0	7.82	0.0	0.00	3.32	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1890	1904	0.179181	CAGCAAACATCTCGCGCAAT	60.179	50.0	8.75	0.0	0.00	3.56	R
2841	2933	0.586319	CACAAGTGTGCCGGTGTAAG	59.414	55.0	1.90	0.0	39.39	2.34	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
31	32	1.468520	CACTTTTGCCTATGTGTCGGG	59.531	52.381	0.00	0.00	0.00	5.14
48	49	4.041198	TGTCGGGGAGAGACAAGTAAAAAT	59.959	41.667	0.00	0.00	44.56	1.82
55	56	6.710744	GGGAGAGACAAGTAAAAATGTGAAGA	59.289	38.462	0.00	0.00	0.00	2.87
59	60	9.832445	AGAGACAAGTAAAAATGTGAAGAAGTA	57.168	29.630	0.00	0.00	0.00	2.24
61	62	9.832445	AGACAAGTAAAAATGTGAAGAAGTAGA	57.168	29.630	0.00	0.00	0.00	2.59
72	73	6.853720	TGTGAAGAAGTAGACACTATAGCAC	58.146	40.000	0.00	0.00	33.48	4.40
103	104	7.774694	TTTTTAGAACCCCCTCTAATCCATA	57.225	36.000	0.00	0.00	37.66	2.74
108	109	7.331089	AGAACCCCCTCTAATCCATATTAAC	57.669	40.000	0.00	0.00	0.00	2.01
176	177	8.369218	CAGGAGTGCTTATTTTGTTTTCATTT	57.631	30.769	0.00	0.00	0.00	2.32
191	192	9.691362	TTGTTTTCATTTAGCCTACTGAAAATC	57.309	29.630	17.64	13.63	44.64	2.17
192	193	8.855110	TGTTTTCATTTAGCCTACTGAAAATCA	58.145	29.630	17.64	15.08	44.64	2.57
193	194	9.129209	GTTTTCATTTAGCCTACTGAAAATCAC	57.871	33.333	17.64	8.15	44.64	3.06
194	195	7.994425	TTCATTTAGCCTACTGAAAATCACA	57.006	32.000	0.00	0.00	0.00	3.58
321	323	6.749923	TTTTGAAAGGTGAACATTTTTGGG	57.250	33.333	0.00	0.00	29.27	4.12
322	324	5.683876	TTGAAAGGTGAACATTTTTGGGA	57.316	34.783	0.00	0.00	29.27	4.37
323	325	5.885449	TGAAAGGTGAACATTTTTGGGAT	57.115	34.783	0.00	0.00	29.27	3.85
401	410	3.611025	AAATGTTCCCTCTGTCCCAAA	57.389	42.857	0.00	0.00	0.00	3.28
402	411	2.586648	ATGTTCCCTCTGTCCCAAAC	57.413	50.000	0.00	0.00	0.00	2.93
456	465	6.198966	GTGCAAAGTTGAGTCACTTATTTTGG	59.801	38.462	11.16	0.00	35.87	3.28
464	473	2.161609	GTCACTTATTTTGGGACGCAGG	59.838	50.000	0.00	0.00	0.00	4.85
584	594	9.528018	CCATTAAAAATAGCGAAAACATACCAT	57.472	29.630	0.00	0.00	0.00	3.55
639	650	1.228533	TCCGTACAAAACCTTTCGGC	58.771	50.000	0.00	0.00	38.18	5.54
643	654	2.223745	GTACAAAACCTTTCGGCAGGA	58.776	47.619	7.72	0.00	37.39	3.86
651	662	0.740868	CTTTCGGCAGGATCGCTCAA	60.741	55.000	0.00	0.00	0.00	3.02
692	703	2.473365	GGCCATGCCCCTCCCTATT	61.473	63.158	0.00	0.00	44.06	1.73
739	750	2.353839	GCAAGCAACACACGCCAG	60.354	61.111	0.00	0.00	0.00	4.85
755	766	1.613270	CCAGCGCAATAAAACGGAAC	58.387	50.000	11.47	0.00	0.00	3.62
843	856	3.371898	GCTGGCTGGTCATTTATTTTTGC	59.628	43.478	0.00	0.00	0.00	3.68
844	857	4.824289	CTGGCTGGTCATTTATTTTTGCT	58.176	39.130	0.00	0.00	0.00	3.91
983	997	0.322187	CCCTAACCCCAGTTTGACCG	60.322	60.000	0.00	0.00	37.42	4.79
1131	1145	4.740822	GCCCATGCCTCCAACCGT	62.741	66.667	0.00	0.00	0.00	4.83
1145	1159	3.691342	CCGTGCCTTCCTCCGTCA	61.691	66.667	0.00	0.00	0.00	4.35
1276	1290	2.126071	GTCGCGCAACCTCTAGCA	60.126	61.111	8.75	0.00	0.00	3.49
1387	1401	2.026014	CCACGTTTGCAGTGCACC	59.974	61.111	19.58	10.65	38.71	5.01
1543	1557	1.745653	TGTTGATGCACCAAACAACGA	59.254	42.857	0.00	0.00	43.39	3.85
1618	1632	7.414208	GCATGAATCATAGCTTGATCATACAGG	60.414	40.741	0.00	10.76	44.51	4.00
1711	1725	6.422333	TGGAGCAACATTATTGTCTTGGATA	58.578	36.000	0.00	0.00	34.06	2.59
1802	1816	0.324614	TCACAGGCCGATGATGTTGT	59.675	50.000	7.82	0.00	0.00	3.32
1839	1853	9.219603	CTTATCCATGTCAAGAAGTTTCAACTA	57.780	33.333	0.00	0.00	38.57	2.24
1855	1869	1.589993	CTACGCATCTGGCTCCACG	60.590	63.158	0.00	0.00	41.67	4.94
1877	1891	1.165270	GGGTACACATGGTTGCTGAC	58.835	55.000	0.00	0.00	0.00	3.51
1889	1903	1.336755	GTTGCTGACGGACACCATTTT	59.663	47.619	0.00	0.00	0.00	1.82
1890	1904	2.550606	GTTGCTGACGGACACCATTTTA	59.449	45.455	0.00	0.00	0.00	1.52
1896	1910	1.135517	ACGGACACCATTTTATTGCGC	60.136	47.619	0.00	0.00	0.00	6.09
2072	2086	8.857694	AAGGAAGACGGTGATAAATTTTTCTA	57.142	30.769	9.59	0.00	0.00	2.10
2251	2265	1.543358	TGCTTTGTCTTGTTGTGTGCA	59.457	42.857	0.00	0.00	0.00	4.57
2252	2266	2.029560	TGCTTTGTCTTGTTGTGTGCAA	60.030	40.909	0.00	0.00	0.00	4.08
2295	2311	8.654997	AGCTTAGATCAATACACCAACATATCT	58.345	33.333	0.00	0.00	0.00	1.98
2499	2589	7.379529	AGCATGATTTATAAACGCTACAATTGC	59.620	33.333	5.05	4.93	0.00	3.56
2501	2591	8.895845	CATGATTTATAAACGCTACAATTGCTC	58.104	33.333	5.05	0.00	0.00	4.26
2549	2639	9.961264	TGTTGTTGTTGTCTTGGGTTATATATA	57.039	29.630	0.00	0.00	0.00	0.86
2558	2648	8.316214	TGTCTTGGGTTATATATACGGGAAATC	58.684	37.037	0.00	0.00	0.00	2.17
2582	2672	3.126453	AGGGAGGGATTAGCAGTTGAAT	58.874	45.455	0.00	0.00	0.00	2.57
2590	2680	7.300658	AGGGATTAGCAGTTGAATAATGGAAT	58.699	34.615	0.00	0.00	0.00	3.01
2604	2694	9.752961	TGAATAATGGAATTTCATGTATTGCAG	57.247	29.630	17.15	0.00	36.88	4.41
2663	2753	7.618019	ATGAATTCTTATCACCAGTAGGCTA	57.382	36.000	7.05	0.00	39.06	3.93
2668	2758	4.585162	TCTTATCACCAGTAGGCTAAGCTC	59.415	45.833	0.00	0.00	39.06	4.09
2816	2908	8.570488	TCTATTTAAGCATGCCATTATTCACAG	58.430	33.333	15.66	0.00	0.00	3.66
2825	2917	6.000246	TGCCATTATTCACAGACCTATCAA	58.000	37.500	0.00	0.00	0.00	2.57
2835	2927	7.675161	TCACAGACCTATCAATTCTGGATAA	57.325	36.000	3.09	0.00	41.00	1.75
2841	2933	8.317679	AGACCTATCAATTCTGGATAACATAGC	58.682	37.037	0.00	0.00	0.00	2.97
2882	2974	9.604626	TTGTGTTGTTGAATGTTTTTCAATTTC	57.395	25.926	4.28	0.36	40.12	2.17
2931	3023	7.256190	GCCCTACATGTCAAGTGTATAATCCTA	60.256	40.741	0.00	0.00	32.13	2.94
2946	3038	9.455144	TGTATAATCCTATCTAAAAACTCCCCA	57.545	33.333	0.00	0.00	0.00	4.96
3087	3181	5.518848	TTCTGCATTTTGAGTGACACATT	57.481	34.783	8.59	0.00	0.00	2.71
3121	3215	5.163509	TGTTGTTGCACAATTACTTGCCTTA	60.164	36.000	5.26	0.00	40.59	2.69
3145	3239	6.279513	TCAATTTGTCTTGTTCCACTTGTT	57.720	33.333	0.00	0.00	0.00	2.83

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
19	20	1.033574	GTCTCTCCCCGACACATAGG	58.966	60.000	0.00	0.00	0.00	2.57
23	24	0.469331	ACTTGTCTCTCCCCGACACA	60.469	55.000	0.00	0.00	40.78	3.72
28	29	4.154195	CACATTTTTACTTGTCTCTCCCCG	59.846	45.833	0.00	0.00	0.00	5.73
31	32	7.730364	TCTTCACATTTTTACTTGTCTCTCC	57.270	36.000	0.00	0.00	0.00	3.71
48	49	6.127703	GGTGCTATAGTGTCTACTTCTTCACA	60.128	42.308	0.84	0.00	38.36	3.58
55	56	5.017490	AGTGTGGTGCTATAGTGTCTACTT	58.983	41.667	0.84	0.00	38.36	2.24
59	60	4.891992	AAAGTGTGGTGCTATAGTGTCT	57.108	40.909	0.84	0.00	0.00	3.41
89	90	6.176183	CAGCAGTTAATATGGATTAGAGGGG	58.824	44.000	0.00	0.00	0.00	4.79
103	104	8.612619	CGACTTAATAAATCCACAGCAGTTAAT	58.387	33.333	0.00	0.00	0.00	1.40
108	109	4.260784	GCCGACTTAATAAATCCACAGCAG	60.261	45.833	0.00	0.00	0.00	4.24
122	123	6.207928	TCGATATTAATTGTCGCCGACTTAA	58.792	36.000	19.12	15.15	35.48	1.85
692	703	2.270257	CCACACCGGTCCACTACGA	61.270	63.158	2.59	0.00	0.00	3.43
739	750	5.720164	GCTTTTATGTTCCGTTTTATTGCGC	60.720	40.000	0.00	0.00	0.00	6.09
755	766	2.489329	CTGTGGTCCACCTGCTTTTATG	59.511	50.000	19.57	0.00	36.82	1.90
843	856	1.448540	CGGCTTCTGGCACCTACAG	60.449	63.158	0.00	0.00	44.01	2.74
844	857	1.764571	AACGGCTTCTGGCACCTACA	61.765	55.000	0.00	0.00	44.01	2.74
983	997	0.173255	CATTGATGTTGGGGAACGCC	59.827	55.000	0.85	0.85	42.25	5.68
1041	1055	0.324738	TGCGGAGGAGGATCTCACTT	60.325	55.000	0.00	0.00	35.58	3.16
1131	1145	1.821216	GAAATTGACGGAGGAAGGCA	58.179	50.000	0.00	0.00	0.00	4.75
1145	1159	2.012051	GCGGGTGGATCTCACGAAATT	61.012	52.381	14.91	0.00	46.96	1.82
1276	1290	2.485966	ACTCTCTGATAGGTGCCCAT	57.514	50.000	0.00	0.00	0.00	4.00
1326	1340	6.057533	CCTAATGAGTATGTTGCCATTCTGA	58.942	40.000	0.00	0.00	29.80	3.27
1328	1342	4.823989	GCCTAATGAGTATGTTGCCATTCT	59.176	41.667	0.00	0.00	32.05	2.40
1339	1353	5.494390	TCATCATGCTGCCTAATGAGTAT	57.506	39.130	7.16	0.00	36.31	2.12
1341	1355	3.851458	TCATCATGCTGCCTAATGAGT	57.149	42.857	7.16	0.00	36.31	3.41
1387	1401	1.688735	TCTCTCAGGACACACCACTTG	59.311	52.381	0.00	0.00	42.04	3.16
1618	1632	3.866582	CCATGGACGAGGGGGCTC	61.867	72.222	5.56	0.00	0.00	4.70
1711	1725	0.678048	GAGAAACTTGAGGCCGCCAT	60.678	55.000	13.15	0.00	0.00	4.40
1802	1816	8.933653	TCTTGACATGGATAAGATATACACCAA	58.066	33.333	0.00	0.00	0.00	3.67
1855	1869	1.745087	CAGCAACCATGTGTACCCATC	59.255	52.381	0.00	0.00	0.00	3.51
1877	1891	1.544686	GCGCAATAAAATGGTGTCCG	58.455	50.000	0.30	0.00	0.00	4.79
1889	1903	1.062440	CAGCAAACATCTCGCGCAATA	59.938	47.619	8.75	0.00	0.00	1.90
1890	1904	0.179181	CAGCAAACATCTCGCGCAAT	60.179	50.000	8.75	0.00	0.00	3.56
1896	1910	4.083643	ACACTCAAATCAGCAAACATCTCG	60.084	41.667	0.00	0.00	0.00	4.04
2072	2086	8.837737	AGATCATCATAAGAGGATGGATTTCAT	58.162	33.333	0.00	0.00	44.62	2.57
2227	2241	4.422840	CACACAACAAGACAAAGCAATGA	58.577	39.130	0.00	0.00	0.00	2.57
2228	2242	3.000523	GCACACAACAAGACAAAGCAATG	59.999	43.478	0.00	0.00	0.00	2.82
2229	2243	3.189285	GCACACAACAAGACAAAGCAAT	58.811	40.909	0.00	0.00	0.00	3.56
2295	2311	3.758023	CCATTCATTCTGCAACTACACCA	59.242	43.478	0.00	0.00	0.00	4.17
2368	2458	6.499106	TCCATGAATGTACTACACCATGAT	57.501	37.500	22.71	1.81	41.22	2.45
2465	2555	7.385205	AGCGTTTATAAATCATGCTACAGGTAG	59.615	37.037	12.56	2.07	36.29	3.18
2499	2589	4.386049	GTCATGACCACGTAGACAAAAGAG	59.614	45.833	15.31	0.00	0.00	2.85
2501	2591	4.150627	CAGTCATGACCACGTAGACAAAAG	59.849	45.833	22.21	0.00	0.00	2.27
2549	2639	0.983378	CCCTCCCTCTGATTTCCCGT	60.983	60.000	0.00	0.00	0.00	5.28
2558	2648	1.799933	ACTGCTAATCCCTCCCTCTG	58.200	55.000	0.00	0.00	0.00	3.35
2582	2672	7.350744	AGCTGCAATACATGAAATTCCATTA	57.649	32.000	0.00	0.00	0.00	1.90
2590	2680	5.963176	TGAAGAAGCTGCAATACATGAAA	57.037	34.783	0.00	0.00	0.00	2.69
2663	2753	1.347707	TGAGGTTCACCATTCGAGCTT	59.652	47.619	0.00	0.00	38.89	3.74
2735	2827	5.080068	CGTATCCTTTCTCGCAAAAAGAAC	58.920	41.667	4.51	0.85	36.09	3.01
2816	2908	8.317679	AGCTATGTTATCCAGAATTGATAGGTC	58.682	37.037	0.00	0.00	0.00	3.85
2825	2917	6.223852	CGGTGTAAGCTATGTTATCCAGAAT	58.776	40.000	0.00	0.00	0.00	2.40
2835	2927	0.611200	TGTGCCGGTGTAAGCTATGT	59.389	50.000	1.90	0.00	0.00	2.29
2841	2933	0.586319	CACAAGTGTGCCGGTGTAAG	59.414	55.000	1.90	0.00	39.39	2.34
2882	2974	7.180079	GGCGAAAATATCATTGTGGTATATCG	58.820	38.462	11.10	11.10	36.66	2.92
2893	2985	6.061441	TGACATGTAGGGCGAAAATATCATT	58.939	36.000	0.00	0.00	0.00	2.57
2931	3023	5.016831	GTCACCAATGGGGAGTTTTTAGAT	58.983	41.667	3.51	0.00	34.84	1.98
2946	3038	5.476945	GTCAATGAGGGTAAAAGTCACCAAT	59.523	40.000	0.00	0.00	37.84	3.16
2991	3085	6.017770	CGTGGTGTATTTTTCCTTCTACAACA	60.018	38.462	0.00	0.00	38.96	3.33
3121	3215	6.469782	ACAAGTGGAACAAGACAAATTGAT	57.530	33.333	0.00	0.00	44.16	2.57
3145	3239	5.011125	GGATCAGGGATGAAGACGATTAAGA	59.989	44.000	0.00	0.00	0.00	2.10

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.