AutoCloner

Multiple sequence alignment - TraesCS6B01G214700

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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	TraesCS6B01G214700	chr6B	100.000	3602	0	0	1	3602	290212802	290216403	0.000000e+00	6652.0
1	TraesCS6B01G214700	chr6B	96.314	1628	55	5	1	1626	290234181	290232557	0.000000e+00	2669.0
2	TraesCS6B01G214700	chr6B	90.669	718	64	3	2026	2743	290224691	290223977	0.000000e+00	952.0
3	TraesCS6B01G214700	chr6B	97.534	446	11	0	2292	2737	290226828	290226383	0.000000e+00	763.0
4	TraesCS6B01G214700	chr6B	94.815	405	21	0	1899	2303	290230396	290229992	1.820000e-177	632.0
5	TraesCS6B01G214700	chr6B	97.436	156	4	0	1752	1907	290230718	290230563	2.130000e-67	267.0
6	TraesCS6B01G214700	chr6B	89.252	214	9	5	472	683	290203633	290203834	4.620000e-64	255.0
7	TraesCS6B01G214700	chr6B	90.116	172	12	3	5	171	290187074	290187245	6.060000e-53	219.0
8	TraesCS6B01G214700	chr6B	86.667	75	10	0	3431	3505	522487035	522487109	2.300000e-12	84.2
9	TraesCS6B01G214700	chr6A	94.828	2494	110	10	277	2755	218799396	218801885	0.000000e+00	3873.0
10	TraesCS6B01G214700	chr6A	86.494	770	85	11	1985	2753	218813325	218814076	0.000000e+00	828.0
11	TraesCS6B01G214700	chr6A	89.228	622	40	4	1	595	218907141	218906520	0.000000e+00	752.0
12	TraesCS6B01G214700	chr6A	92.821	195	11	3	5	196	218799120	218799314	2.740000e-71	279.0
13	TraesCS6B01G214700	chr6D	94.487	2340	106	10	427	2755	159713882	159716209	0.000000e+00	3585.0
14	TraesCS6B01G214700	chr6D	96.203	1633	51	5	732	2353	159792774	159791142	0.000000e+00	2662.0
15	TraesCS6B01G214700	chr6D	94.266	593	32	2	149	740	159797201	159796610	0.000000e+00	905.0
16	TraesCS6B01G214700	chr6D	86.736	769	85	6	1985	2753	159788320	159787569	0.000000e+00	839.0
17	TraesCS6B01G214700	chr6D	87.671	584	55	9	2170	2753	159779763	159780329	0.000000e+00	664.0
18	TraesCS6B01G214700	chr6D	93.048	187	7	4	5	186	159712188	159712373	5.930000e-68	268.0
19	TraesCS6B01G214700	chr6D	89.674	184	18	1	1985	2168	159717765	159717947	2.160000e-57	233.0
20	TraesCS6B01G214700	chrUn	95.302	894	40	2	1862	2755	244767578	244766687	0.000000e+00	1417.0
21	TraesCS6B01G214700	chrUn	95.190	894	42	1	1862	2755	244756833	244755941	0.000000e+00	1411.0
22	TraesCS6B01G214700	chrUn	93.552	822	27	11	429	1239	244758751	244757945	0.000000e+00	1201.0
23	TraesCS6B01G214700	chrUn	87.256	769	80	10	1985	2753	244765063	244764313	0.000000e+00	861.0
24	TraesCS6B01G214700	chrUn	93.011	186	9	2	5	186	244760574	244760389	5.930000e-68	268.0
25	TraesCS6B01G214700	chr4A	95.470	861	35	3	2746	3602	686770162	686769302	0.000000e+00	1371.0
26	TraesCS6B01G214700	chr7D	90.647	417	35	3	3137	3551	608724012	608723598	5.260000e-153	551.0
27	TraesCS6B01G214700	chr7D	90.647	417	35	3	3137	3551	608733531	608733117	5.260000e-153	551.0
28	TraesCS6B01G214700	chr7B	92.339	248	18	1	3308	3555	610347203	610346957	5.720000e-93	351.0
29	TraesCS6B01G214700	chr5B	82.031	256	39	5	3295	3550	480407166	480407414	1.010000e-50	211.0
30	TraesCS6B01G214700	chr3D	81.683	202	37	0	1399	1600	107042416	107042617	6.190000e-38	169.0
31	TraesCS6B01G214700	chr5A	87.179	117	15	0	3434	3550	506111320	506111436	2.260000e-27	134.0

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	TraesCS6B01G214700	chr6B	290212802	290216403	3601	False	6652.000000	6652	100.000000	1	3602	1	chr6B.!!$F3	3601
1	TraesCS6B01G214700	chr6B	290223977	290234181	10204	True	1056.600000	2669	95.353600	1	2743	5	chr6B.!!$R1	2742
2	TraesCS6B01G214700	chr6A	218799120	218801885	2765	False	2076.000000	3873	93.824500	5	2755	2	chr6A.!!$F2	2750
3	TraesCS6B01G214700	chr6A	218813325	218814076	751	False	828.000000	828	86.494000	1985	2753	1	chr6A.!!$F1	768
4	TraesCS6B01G214700	chr6A	218906520	218907141	621	True	752.000000	752	89.228000	1	595	1	chr6A.!!$R1	594
5	TraesCS6B01G214700	chr6D	159787569	159797201	9632	True	1468.666667	2662	92.401667	149	2753	3	chr6D.!!$R1	2604
6	TraesCS6B01G214700	chr6D	159712188	159717947	5759	False	1362.000000	3585	92.403000	5	2755	3	chr6D.!!$F2	2750
7	TraesCS6B01G214700	chr6D	159779763	159780329	566	False	664.000000	664	87.671000	2170	2753	1	chr6D.!!$F1	583
8	TraesCS6B01G214700	chrUn	244755941	244767578	11637	True	1031.600000	1417	92.862200	5	2755	5	chrUn.!!$R1	2750
9	TraesCS6B01G214700	chr4A	686769302	686770162	860	True	1371.000000	1371	95.470000	2746	3602	1	chr4A.!!$R1	856

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
987	13424	0.670546	CGTCAGTCCCAAATCAGCGT	60.671	55.0	0.0	0.0	0.0	5.07	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2779	23463	0.034896	ACGACACAGATTTCGGCCTT	59.965	50.0	0.0	0.0	39.63	4.35	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
36	7037	6.018994	GTGGCTTGTTTATAGTTACATCTCCG	60.019	42.308	0.00	0.00	0.00	4.63
164	7170	7.122055	ACATCAACAAACCAGAAAGTCAACTTA	59.878	33.333	0.00	0.00	34.61	2.24
223	8673	1.209261	TGACGCCAAGCCTGATTGATA	59.791	47.619	0.00	0.00	31.55	2.15
258	8708	5.713389	CCATGCCAATCAATCCTACATACAT	59.287	40.000	0.00	0.00	0.00	2.29
454	9025	6.314784	CCTCTGAAATTACCGTCAAATTCAC	58.685	40.000	0.00	0.00	0.00	3.18
632	9212	3.381908	GGAGCTCCGAGTCAAATCTAAGA	59.618	47.826	19.06	0.00	0.00	2.10
975	13412	4.106197	CCAGTAGCTTACAATCGTCAGTC	58.894	47.826	0.00	0.00	0.00	3.51
987	13424	0.670546	CGTCAGTCCCAAATCAGCGT	60.671	55.000	0.00	0.00	0.00	5.07
1290	13735	2.753701	CCATTCCCCGTGTCACCA	59.246	61.111	0.00	0.00	0.00	4.17
1335	13780	4.200283	CAGTCTCTCGCTCCGGGC	62.200	72.222	0.00	2.69	37.64	6.13
1407	13852	2.512286	TCCGCGGACTACGTCGAT	60.512	61.111	27.28	0.00	46.52	3.59
1650	14095	1.014564	GGAAGGACCTGTTCTTCGCG	61.015	60.000	11.28	0.00	40.00	5.87
1653	14098	3.479269	GACCTGTTCTTCGCGGCG	61.479	66.667	17.70	17.70	0.00	6.46
1686	14131	1.141053	GGCCAGTTCGGGATCATAACT	59.859	52.381	0.00	0.00	33.82	2.24
1749	14194	1.255667	GGGTCCGACTTGCCTACTCA	61.256	60.000	0.00	0.00	0.00	3.41
1851	16009	4.611961	GTCCAGCTTAACCGGACC	57.388	61.111	9.46	0.00	42.87	4.46
2040	16373	0.605860	CTCAGCTGAGCTTTGTGCCT	60.606	55.000	29.79	0.00	44.23	4.75
2117	16450	2.125350	GGAGGCTGAGCTTCGGTG	60.125	66.667	10.53	0.00	35.44	4.94
2196	16529	0.319555	TTCTCGACTTTGACGCTGGG	60.320	55.000	0.00	0.00	0.00	4.45
2235	16568	3.144285	GGTGACAACCCAGTCGGA	58.856	61.111	0.00	0.00	41.04	4.55
2743	23427	9.860898	CCAGAATTTTGAAAATAGGAGGTAAAG	57.139	33.333	3.26	0.00	0.00	1.85
2762	23446	2.327568	AGATTGCGAAAATGCCGTTTG	58.672	42.857	0.00	0.00	0.00	2.93
2794	23478	1.402968	CCATGAAGGCCGAAATCTGTG	59.597	52.381	0.00	0.00	0.00	3.66
2803	23760	1.670087	CCGAAATCTGTGTCGTCTGCT	60.670	52.381	0.00	0.00	35.48	4.24
2804	23761	1.388093	CGAAATCTGTGTCGTCTGCTG	59.612	52.381	0.00	0.00	32.61	4.41
2872	23836	3.937079	CGTCACACCCTTTTTACTATCCC	59.063	47.826	0.00	0.00	0.00	3.85
2904	23868	5.779922	AGTAAATAAACAGACGACAGCTCA	58.220	37.500	0.00	0.00	0.00	4.26
2909	23873	2.929531	ACAGACGACAGCTCATGTAG	57.070	50.000	0.00	0.00	44.17	2.74
2917	23881	3.487544	CGACAGCTCATGTAGACGAATCA	60.488	47.826	0.00	0.00	44.17	2.57
2946	23911	0.393808	GGCCGCATAGTTCAAAGGGA	60.394	55.000	0.00	0.00	0.00	4.20
2959	23924	0.473117	AAAGGGAAGGAGTCACGGGA	60.473	55.000	0.00	0.00	33.41	5.14
2982	23947	6.038714	GGAAAGTACATGGGATTGATTCAGTC	59.961	42.308	0.00	0.73	0.00	3.51
2987	23952	3.912496	TGGGATTGATTCAGTCGTCAT	57.088	42.857	3.42	0.00	0.00	3.06
3032	23997	1.723003	GCCGTTTTAGTCGATCGTTGT	59.277	47.619	15.94	3.47	0.00	3.32
3039	24004	6.459330	GTTTTAGTCGATCGTTGTGAGAATC	58.541	40.000	15.94	0.00	0.00	2.52
3040	24005	3.152261	AGTCGATCGTTGTGAGAATCC	57.848	47.619	15.94	0.00	0.00	3.01
3053	24018	0.539438	AGAATCCTGCCGTTGCCAAA	60.539	50.000	0.00	0.00	36.33	3.28
3152	24117	0.456221	GCGTCTTCCTCTTCATCGGA	59.544	55.000	0.00	0.00	0.00	4.55
3167	25769	1.195115	TCGGAAGGATCCAGGAACAG	58.805	55.000	15.82	1.41	46.97	3.16
3211	25813	1.954258	GCCCAGATTGCAGAGAAGCTT	60.954	52.381	0.00	0.00	34.99	3.74
3230	25832	0.388520	TGCGTCGAGACCAACATCAG	60.389	55.000	0.00	0.00	0.00	2.90
3472	26076	6.947733	TGACAATATGATTCAGAAACAAGGGT	59.052	34.615	0.00	0.00	0.00	4.34
3542	26146	1.860326	GCAACACCACAATTTCAGTGC	59.140	47.619	0.00	0.00	35.69	4.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
36	7037	1.741528	TAAAAATTCCCGAGACGGCC	58.258	50.000	4.57	0.00	46.86	6.13
164	7170	9.691362	GACCAAGTTTTGTTTATCATGTATGTT	57.309	29.630	0.00	0.00	0.00	2.71
297	8785	4.782019	TTCTAACGCCATTTGCTTTGAT	57.218	36.364	0.00	0.00	38.05	2.57
322	8854	6.762661	TGCCGTTAAACTAGAAACTAACACTT	59.237	34.615	0.00	0.00	0.00	3.16
504	9076	2.569404	ACTGTCCCAATTCTCACTCTCC	59.431	50.000	0.00	0.00	0.00	3.71
809	13238	5.277828	GGTCGTGCAGAGTTCTTGTATTTTT	60.278	40.000	0.00	0.00	0.00	1.94
987	13424	0.817229	TTGCCATGTCGTTGCAGTGA	60.817	50.000	0.00	0.00	36.21	3.41
1096	13541	0.909610	AGGGCAAAGAGATCACCGGA	60.910	55.000	9.46	0.00	0.00	5.14
1269	13714	2.351276	GACACGGGGAATGGCACT	59.649	61.111	0.00	0.00	0.00	4.40
1335	13780	1.772882	CATGTTGACGACGACACCG	59.227	57.895	10.16	1.56	42.33	4.94
1348	13793	4.041917	CCCAAGCGTGCGCATGTT	62.042	61.111	29.00	22.04	44.88	2.71
1370	13815	1.667830	ACGTTGATGCGGTGGTGAG	60.668	57.895	0.00	0.00	35.98	3.51
1662	14107	4.115199	ATCCCGAACTGGCCCAGC	62.115	66.667	11.63	0.00	34.37	4.85
1686	14131	4.877619	AGAGCGATCCGAGCCCGA	62.878	66.667	0.00	0.00	38.22	5.14
1749	14194	0.179032	TGGTGAACGCAACCACATCT	60.179	50.000	0.58	0.00	35.13	2.90
1851	16009	3.012722	TTGGGGCCCTCGGTTAGG	61.013	66.667	25.93	0.00	46.09	2.69
2040	16373	0.464735	CCTTGGTGAACACGAACCCA	60.465	55.000	0.00	0.00	35.44	4.51
2235	16568	5.079998	TCATAGGGTACATGAGGATGAGT	57.920	43.478	0.00	0.00	33.36	3.41
2743	23427	1.389784	CCAAACGGCATTTTCGCAATC	59.610	47.619	0.00	0.00	0.00	2.67
2779	23463	0.034896	ACGACACAGATTTCGGCCTT	59.965	50.000	0.00	0.00	39.63	4.35
2794	23478	1.852942	TCAAGACAACAGCAGACGAC	58.147	50.000	0.00	0.00	0.00	4.34
2803	23760	0.250252	TGGCGCTCATCAAGACAACA	60.250	50.000	7.64	0.00	0.00	3.33
2804	23761	0.166814	GTGGCGCTCATCAAGACAAC	59.833	55.000	7.64	0.00	0.00	3.32
2872	23836	8.257841	GTCGTCTGTTTATTTACTAGCAATACG	58.742	37.037	0.00	0.00	0.00	3.06
2904	23868	2.760650	TGCTGTCCTGATTCGTCTACAT	59.239	45.455	0.00	0.00	0.00	2.29
2909	23873	0.460987	CCCTGCTGTCCTGATTCGTC	60.461	60.000	0.00	0.00	0.00	4.20
2934	23899	3.006537	CGTGACTCCTTCCCTTTGAACTA	59.993	47.826	0.00	0.00	0.00	2.24
2946	23911	2.322658	TGTACTTTCCCGTGACTCCTT	58.677	47.619	0.00	0.00	0.00	3.36
2959	23924	5.586243	CGACTGAATCAATCCCATGTACTTT	59.414	40.000	0.00	0.00	0.00	2.66
2982	23947	1.359848	GCACAGGTAGGAACATGACG	58.640	55.000	0.00	0.00	39.79	4.35
2987	23952	0.320421	GCTTCGCACAGGTAGGAACA	60.320	55.000	0.00	0.00	0.00	3.18
3032	23997	1.377202	GGCAACGGCAGGATTCTCA	60.377	57.895	0.00	0.00	43.71	3.27
3053	24018	5.047377	GCTGCTATAGATAGAAGAACTGCCT	60.047	44.000	8.52	0.00	38.14	4.75
3068	24033	1.323412	AGACAGGGTCGCTGCTATAG	58.677	55.000	16.35	0.00	37.67	1.31
3100	24065	1.501170	TGGGTTTGAGTTGGGAATGGA	59.499	47.619	0.00	0.00	0.00	3.41
3152	24117	1.201429	ACGCCTGTTCCTGGATCCTT	61.201	55.000	14.23	0.00	0.00	3.36
3180	25782	1.337071	CAATCTGGGCACATGATGAGC	59.663	52.381	6.29	6.29	33.11	4.26
3211	25813	0.388520	CTGATGTTGGTCTCGACGCA	60.389	55.000	0.00	0.00	0.00	5.24
3230	25832	1.526464	CACGCCAATTTTCTTTGCCAC	59.474	47.619	0.00	0.00	0.00	5.01
3300	25904	7.271223	GTCGTCATTGTTTTCTGAATATTGTGG	59.729	37.037	0.00	0.00	0.00	4.17

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.