AutoCloner

Multiple sequence alignment - TraesCS1B01G203400

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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	TraesCS1B01G203400	chr1B	100.000	2804	0	0	1	2804	365688472	365691275	0.000000e+00	5179.0
1	TraesCS1B01G203400	chr1D	93.873	2236	68	25	611	2804	230675972	230673764	0.000000e+00	3306.0
2	TraesCS1B01G203400	chr1A	94.408	1520	36	19	614	2109	319077545	319079039	0.000000e+00	2290.0
3	TraesCS1B01G203400	chr1A	82.353	544	53	27	2285	2804	319079141	319079665	1.540000e-117	433.0
4	TraesCS1B01G203400	chr1A	97.059	34	1	0	2247	2280	319079141	319079174	1.080000e-04	58.4
5	TraesCS1B01G203400	chr3B	97.585	621	10	4	1	620	653925680	653926296	0.000000e+00	1059.0
6	TraesCS1B01G203400	chr2B	97.712	612	6	5	1	611	650824145	650823541	0.000000e+00	1046.0
7	TraesCS1B01G203400	chr2B	97.381	611	6	6	1	610	650833156	650832555	0.000000e+00	1031.0
8	TraesCS1B01G203400	chr7A	97.236	615	8	6	1	612	417115059	417114451	0.000000e+00	1033.0
9	TraesCS1B01G203400	chr4B	97.227	613	10	4	1	610	639567833	639567225	0.000000e+00	1031.0
10	TraesCS1B01G203400	chr4B	97.059	612	11	5	1	610	639576857	639576251	0.000000e+00	1024.0
11	TraesCS1B01G203400	chr3A	97.231	614	7	6	1	610	673028288	673028895	0.000000e+00	1031.0
12	TraesCS1B01G203400	chrUn	96.737	613	12	5	1	612	350503336	350503941	0.000000e+00	1014.0
13	TraesCS1B01G203400	chr7B	96.737	613	11	7	1	611	359561205	359561810	0.000000e+00	1013.0
14	TraesCS1B01G203400	chr7B	78.526	624	104	20	1097	1714	56924264	56924863	1.580000e-102	383.0

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	TraesCS1B01G203400	chr1B	365688472	365691275	2803	False	5179.000000	5179	100.000000	1	2804	1	chr1B.!!$F1	2803
1	TraesCS1B01G203400	chr1D	230673764	230675972	2208	True	3306.000000	3306	93.873000	611	2804	1	chr1D.!!$R1	2193
2	TraesCS1B01G203400	chr1A	319077545	319079665	2120	False	927.133333	2290	91.273333	614	2804	3	chr1A.!!$F1	2190
3	TraesCS1B01G203400	chr3B	653925680	653926296	616	False	1059.000000	1059	97.585000	1	620	1	chr3B.!!$F1	619
4	TraesCS1B01G203400	chr2B	650823541	650824145	604	True	1046.000000	1046	97.712000	1	611	1	chr2B.!!$R1	610
5	TraesCS1B01G203400	chr2B	650832555	650833156	601	True	1031.000000	1031	97.381000	1	610	1	chr2B.!!$R2	609
6	TraesCS1B01G203400	chr7A	417114451	417115059	608	True	1033.000000	1033	97.236000	1	612	1	chr7A.!!$R1	611
7	TraesCS1B01G203400	chr4B	639567225	639567833	608	True	1031.000000	1031	97.227000	1	610	1	chr4B.!!$R1	609
8	TraesCS1B01G203400	chr4B	639576251	639576857	606	True	1024.000000	1024	97.059000	1	610	1	chr4B.!!$R2	609
9	TraesCS1B01G203400	chr3A	673028288	673028895	607	False	1031.000000	1031	97.231000	1	610	1	chr3A.!!$F1	609
10	TraesCS1B01G203400	chrUn	350503336	350503941	605	False	1014.000000	1014	96.737000	1	612	1	chrUn.!!$F1	611
11	TraesCS1B01G203400	chr7B	359561205	359561810	605	False	1013.000000	1013	96.737000	1	611	1	chr7B.!!$F2	610
12	TraesCS1B01G203400	chr7B	56924264	56924863	599	False	383.000000	383	78.526000	1097	1714	1	chr7B.!!$F1	617

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
617	626	0.178891	AGGGATGTGACAGGACACCT	60.179	55.0	0.0	0.0	39.69	4.0	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2317	2366	0.248843	CTCTCACAAGACTCCCAGCC	59.751	60.0	0.0	0.0	0.0	4.85	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
175	178	8.797438	CAGGTAAGCTTCTCCTTCTTTTATTTT	58.203	33.333	17.17	0.00	0.00	1.82
176	179	9.368416	AGGTAAGCTTCTCCTTCTTTTATTTTT	57.632	29.630	14.87	0.00	0.00	1.94
299	306	3.499918	CCAGAGCTCCTTTATAAATGGCG	59.500	47.826	10.93	0.00	0.00	5.69
464	473	4.859304	AGCAACATGAGCATTTTCTTGA	57.141	36.364	15.23	0.00	0.00	3.02
617	626	0.178891	AGGGATGTGACAGGACACCT	60.179	55.000	0.00	0.00	39.69	4.00
770	792	2.354805	CGACGAAAGGAAAATCCCCTCT	60.355	50.000	0.00	0.00	37.19	3.69
772	794	2.913617	ACGAAAGGAAAATCCCCTCTCT	59.086	45.455	0.00	0.00	37.19	3.10
773	795	3.055021	ACGAAAGGAAAATCCCCTCTCTC	60.055	47.826	0.00	0.00	37.19	3.20
774	796	3.198853	CGAAAGGAAAATCCCCTCTCTCT	59.801	47.826	0.00	0.00	37.19	3.10
786	808	1.616725	CCTCTCTCTGTCTCACTGCCT	60.617	57.143	0.00	0.00	0.00	4.75
830	853	0.896019	CCTGTCAGTCCCTCGTGTCT	60.896	60.000	0.00	0.00	0.00	3.41
931	961	2.765807	CACCTCGCCTCCCTCCAT	60.766	66.667	0.00	0.00	0.00	3.41
932	962	2.444895	ACCTCGCCTCCCTCCATC	60.445	66.667	0.00	0.00	0.00	3.51
933	963	3.237741	CCTCGCCTCCCTCCATCC	61.238	72.222	0.00	0.00	0.00	3.51
1080	1110	2.341101	CGAGGCCTACGAGGTGTGT	61.341	63.158	4.42	0.00	37.80	3.72
1194	1224	1.557269	GGGGTCACATGGAGAGCACT	61.557	60.000	17.58	0.00	34.24	4.40
1749	1785	1.893786	GGAGAAGGAGAAGCGCAGA	59.106	57.895	11.47	0.00	0.00	4.26
1830	1867	3.680786	GGGCCGGCCAACAAGTTC	61.681	66.667	44.46	22.62	37.98	3.01
1925	1967	2.252012	TAGGTGGTAGGGGAGGCCAG	62.252	65.000	5.01	0.00	32.31	4.85
1926	1968	2.040606	GTGGTAGGGGAGGCCAGA	59.959	66.667	5.01	0.00	32.31	3.86
1928	1970	2.369001	GGTAGGGGAGGCCAGAGT	59.631	66.667	5.01	0.00	0.00	3.24
1929	1971	1.226104	TGGTAGGGGAGGCCAGAGTA	61.226	60.000	5.01	0.00	0.00	2.59
1930	1972	0.470268	GGTAGGGGAGGCCAGAGTAG	60.470	65.000	5.01	0.00	0.00	2.57
1931	1973	0.556747	GTAGGGGAGGCCAGAGTAGA	59.443	60.000	5.01	0.00	0.00	2.59
1968	2010	5.940192	TTGGTTTAGTATGCTCTTGTGTG	57.060	39.130	0.00	0.00	0.00	3.82
2074	2116	4.937620	GCTCTTGTTTCTGATCACACCATA	59.062	41.667	0.00	0.00	0.00	2.74
2100	2142	7.779798	ACTTGCTGAATTAATAATCCTTGGCTA	59.220	33.333	0.00	0.00	0.00	3.93
2109	2151	2.634815	ATCCTTGGCTAGCTGATGTG	57.365	50.000	15.72	0.00	0.00	3.21
2110	2152	1.571955	TCCTTGGCTAGCTGATGTGA	58.428	50.000	15.72	1.57	0.00	3.58
2111	2153	2.121948	TCCTTGGCTAGCTGATGTGAT	58.878	47.619	15.72	0.00	0.00	3.06
2112	2154	2.158856	TCCTTGGCTAGCTGATGTGATG	60.159	50.000	15.72	0.00	0.00	3.07
2113	2155	1.602851	CTTGGCTAGCTGATGTGATGC	59.397	52.381	15.72	0.00	0.00	3.91
2225	2274	4.098807	GGTTGTGTTGGTCATTTGGTTAGT	59.901	41.667	0.00	0.00	0.00	2.24
2284	2333	2.023673	TCTTTGTGTTCCTTGGCACTG	58.976	47.619	0.00	0.00	36.63	3.66
2286	2335	0.682532	TTGTGTTCCTTGGCACTGCA	60.683	50.000	2.82	0.00	36.63	4.41
2317	2366	1.142870	TGTCTTCTTGTGTTCCTGGGG	59.857	52.381	0.00	0.00	0.00	4.96
2326	2375	4.285790	TTCCTGGGGGCTGGGAGT	62.286	66.667	0.00	0.00	0.00	3.85
2600	2666	2.691011	GACCAGACAGGGAGATCTGTAC	59.309	54.545	0.00	0.00	46.76	2.90
2665	2731	5.251601	ACCAATCGTTCTAGACTTCTAGC	57.748	43.478	8.23	0.00	44.24	3.42
2736	2807	0.463833	GCTACGCATACCTTTGGGCT	60.464	55.000	0.00	0.00	35.63	5.19
2759	2830	7.255977	GGCTAGAGAATCCAATGTCTGTATGTA	60.256	40.741	0.00	0.00	33.66	2.29
2763	2834	6.049149	AGAATCCAATGTCTGTATGTAACCG	58.951	40.000	0.00	0.00	0.00	4.44
2773	2851	1.134788	GTATGTAACCGCTGCTCACCT	60.135	52.381	0.00	0.00	0.00	4.00
2790	2868	1.963515	ACCTGTTTGACAAATCCAGGC	59.036	47.619	26.19	7.10	45.26	4.85
2793	2871	1.962807	TGTTTGACAAATCCAGGCCAG	59.037	47.619	5.01	0.00	0.00	4.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
442	451	5.204409	TCAAGAAAATGCTCATGTTGCTT	57.796	34.783	12.86	5.78	0.00	3.91
464	473	9.130661	CCAAATAAAAATTTCTCCAAAAGGGTT	57.869	29.630	0.00	0.00	38.11	4.11
617	626	2.435938	GCCGCGTGGAAATCAGGA	60.436	61.111	21.76	0.00	37.49	3.86
770	792	1.252175	GTGAGGCAGTGAGACAGAGA	58.748	55.000	0.00	0.00	0.00	3.10
772	794	1.959848	CGTGAGGCAGTGAGACAGA	59.040	57.895	0.00	0.00	0.00	3.41
773	795	4.567435	CGTGAGGCAGTGAGACAG	57.433	61.111	0.00	0.00	0.00	3.51
830	853	1.492599	TGATCCTGGTGTGTGTTTGGA	59.507	47.619	0.00	0.00	0.00	3.53
924	954	0.103930	TAATGGAGGGGGATGGAGGG	60.104	60.000	0.00	0.00	0.00	4.30
925	955	1.833187	TTAATGGAGGGGGATGGAGG	58.167	55.000	0.00	0.00	0.00	4.30
926	956	2.489802	GCTTTAATGGAGGGGGATGGAG	60.490	54.545	0.00	0.00	0.00	3.86
927	957	1.499007	GCTTTAATGGAGGGGGATGGA	59.501	52.381	0.00	0.00	0.00	3.41
928	958	1.481242	GGCTTTAATGGAGGGGGATGG	60.481	57.143	0.00	0.00	0.00	3.51
929	959	1.481242	GGGCTTTAATGGAGGGGGATG	60.481	57.143	0.00	0.00	0.00	3.51
930	960	0.860457	GGGCTTTAATGGAGGGGGAT	59.140	55.000	0.00	0.00	0.00	3.85
931	961	1.641552	CGGGCTTTAATGGAGGGGGA	61.642	60.000	0.00	0.00	0.00	4.81
932	962	1.152756	CGGGCTTTAATGGAGGGGG	60.153	63.158	0.00	0.00	0.00	5.40
933	963	1.828224	GCGGGCTTTAATGGAGGGG	60.828	63.158	0.00	0.00	0.00	4.79
1068	1098	2.202440	CGGCGACACACCTCGTAG	60.202	66.667	0.00	0.00	35.99	3.51
1179	1209	1.637338	ACTCAGTGCTCTCCATGTGA	58.363	50.000	0.00	0.00	0.00	3.58
1194	1224	0.832135	AGCGGGTGAAGGAGAACTCA	60.832	55.000	4.23	0.00	0.00	3.41
1925	1967	8.271312	ACCAATATACTCGAGCTATTCTACTC	57.729	38.462	13.61	0.00	0.00	2.59
1926	1968	8.638629	AACCAATATACTCGAGCTATTCTACT	57.361	34.615	13.61	0.00	0.00	2.57
1929	1971	9.080097	ACTAAACCAATATACTCGAGCTATTCT	57.920	33.333	13.61	0.00	0.00	2.40
1968	2010	4.179926	TCATAGATCGATTGCAGCTACC	57.820	45.455	0.00	0.00	0.00	3.18
2074	2116	6.608808	AGCCAAGGATTATTAATTCAGCAAGT	59.391	34.615	0.00	0.00	0.00	3.16
2100	2142	1.747709	GTTCCAGCATCACATCAGCT	58.252	50.000	0.00	0.00	39.63	4.24
2109	2151	1.372582	TGCTCATTCGTTCCAGCATC	58.627	50.000	0.00	0.00	36.96	3.91
2110	2152	1.825090	TTGCTCATTCGTTCCAGCAT	58.175	45.000	0.00	0.00	41.44	3.79
2111	2153	1.739466	GATTGCTCATTCGTTCCAGCA	59.261	47.619	0.00	0.00	40.13	4.41
2112	2154	2.012673	AGATTGCTCATTCGTTCCAGC	58.987	47.619	0.00	0.00	0.00	4.85
2113	2155	2.353889	CCAGATTGCTCATTCGTTCCAG	59.646	50.000	0.00	0.00	0.00	3.86
2225	2274	3.066621	GCGGTGCCATGAAATTTCATCTA	59.933	43.478	27.08	15.15	45.62	1.98
2286	2335	2.961062	ACAAGAAGACAGCCATTTTGCT	59.039	40.909	0.00	0.00	44.00	3.91
2299	2348	0.771127	CCCCCAGGAACACAAGAAGA	59.229	55.000	0.00	0.00	33.47	2.87
2317	2366	0.248843	CTCTCACAAGACTCCCAGCC	59.751	60.000	0.00	0.00	0.00	4.85
2326	2375	3.197766	ACCAACACAAGACTCTCACAAGA	59.802	43.478	0.00	0.00	0.00	3.02
2448	2497	2.270986	CCAAGGAACACAGGCAGGC	61.271	63.158	0.00	0.00	0.00	4.85
2600	2666	5.444613	CCATTGTTAACACGTGATTCGAGAG	60.445	44.000	25.01	6.17	42.86	3.20
2665	2731	1.343478	ACTGATGGGTCCAGGGTAGAG	60.343	57.143	0.00	0.00	36.03	2.43
2736	2807	8.421784	GGTTACATACAGACATTGGATTCTCTA	58.578	37.037	0.00	0.00	0.00	2.43
2759	2830	1.152963	AAACAGGTGAGCAGCGGTT	60.153	52.632	11.38	11.38	46.05	4.44
2763	2834	1.024271	TTGTCAAACAGGTGAGCAGC	58.976	50.000	0.00	0.00	0.00	5.25
2773	2851	1.962807	CTGGCCTGGATTTGTCAAACA	59.037	47.619	3.32	0.00	0.00	2.83

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.