AutoCloner

Multiple sequence alignment - TraesCS6D01G203500

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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	TraesCS6D01G203500	chr6D	100.000	4219	0	0	1	4219	288465658	288469876	0.000000e+00	7792.0
1	TraesCS6D01G203500	chr6D	100.000	30	0	0	767	796	18512305	18512276	5.890000e-04	56.5
2	TraesCS6D01G203500	chr5D	99.280	1944	10	4	1350	3290	462795911	462793969	0.000000e+00	3509.0
3	TraesCS6D01G203500	chr5D	98.891	1353	14	1	1	1352	462797316	462795964	0.000000e+00	2414.0
4	TraesCS6D01G203500	chr5D	98.551	69	1	0	3289	3357	462793855	462793787	5.730000e-24	122.0
5	TraesCS6D01G203500	chr5D	88.889	81	7	2	3354	3433	109098259	109098180	9.650000e-17	99.0
6	TraesCS6D01G203500	chr2B	93.576	2008	91	13	1350	3355	645133401	645131430	0.000000e+00	2959.0
7	TraesCS6D01G203500	chr2B	91.654	1354	92	3	1	1352	645134788	645133454	0.000000e+00	1855.0
8	TraesCS6D01G203500	chr2B	81.490	443	72	6	2735	3175	253263485	253263919	5.190000e-94	355.0
9	TraesCS6D01G203500	chr2B	81.250	192	30	5	604	791	398574432	398574621	2.630000e-32	150.0
10	TraesCS6D01G203500	chr3D	96.814	1695	44	6	1665	3357	283965217	283963531	0.000000e+00	2822.0
11	TraesCS6D01G203500	chr3D	94.782	1648	56	6	1	1642	283967562	283965939	0.000000e+00	2540.0
12	TraesCS6D01G203500	chr3D	92.105	38	1	2	759	796	596435515	596435550	8.000000e-03	52.8
13	TraesCS6D01G203500	chr2A	91.961	1219	86	7	1734	2949	453508537	453507328	0.000000e+00	1698.0
14	TraesCS6D01G203500	chr2A	80.891	539	80	16	2753	3276	211908158	211908688	1.830000e-108	403.0
15	TraesCS6D01G203500	chr2A	89.776	313	17	3	3057	3357	191885275	191885584	1.840000e-103	387.0
16	TraesCS6D01G203500	chr2A	88.660	194	8	2	3175	3357	453507304	453507114	1.530000e-54	224.0
17	TraesCS6D01G203500	chr2A	95.588	68	3	0	3354	3421	256799833	256799766	4.460000e-20	110.0
18	TraesCS6D01G203500	chr4A	91.027	1237	90	13	1725	2944	18745888	18747120	0.000000e+00	1650.0
19	TraesCS6D01G203500	chr4A	90.667	450	40	2	905	1352	705180484	705180035	7.810000e-167	597.0
20	TraesCS6D01G203500	chr4A	88.601	386	33	10	1350	1727	705179982	705179600	3.840000e-125	459.0
21	TraesCS6D01G203500	chr4A	77.528	445	59	25	2280	2695	12652279	12651847	3.280000e-56	230.0
22	TraesCS6D01G203500	chr4A	86.432	199	12	2	3170	3357	18747146	18747340	1.990000e-48	204.0
23	TraesCS6D01G203500	chr4A	91.176	68	6	0	3354	3421	75329938	75330005	4.490000e-15	93.5
24	TraesCS6D01G203500	chr5A	90.946	1237	94	11	1731	2953	4799394	4800626	0.000000e+00	1648.0
25	TraesCS6D01G203500	chr5A	91.083	942	55	10	2424	3341	554339457	554338521	0.000000e+00	1247.0
26	TraesCS6D01G203500	chr5A	89.922	893	59	12	3354	4219	430254111	430253223	0.000000e+00	1122.0
27	TraesCS6D01G203500	chr5A	93.621	486	28	2	1900	2385	554339940	554339458	0.000000e+00	723.0
28	TraesCS6D01G203500	chr5A	87.437	199	10	3	3170	3357	4800642	4800836	9.190000e-52	215.0
29	TraesCS6D01G203500	chr3A	90.632	950	62	12	2424	3358	454088646	454089583	0.000000e+00	1236.0
30	TraesCS6D01G203500	chr3A	88.603	895	69	20	3353	4219	158789572	158788683	0.000000e+00	1057.0
31	TraesCS6D01G203500	chr3A	91.304	667	53	4	1720	2385	454087983	454088645	0.000000e+00	905.0
32	TraesCS6D01G203500	chr1B	88.098	899	65	22	3352	4219	488510676	488509789	0.000000e+00	1029.0
33	TraesCS6D01G203500	chr1A	92.000	625	42	2	3374	3995	58548637	58549256	0.000000e+00	870.0
34	TraesCS6D01G203500	chr1A	92.611	203	13	2	4018	4219	58549307	58549508	1.480000e-74	291.0
35	TraesCS6D01G203500	chr7D	91.289	551	46	2	804	1352	22530289	22529739	0.000000e+00	750.0
36	TraesCS6D01G203500	chr7D	88.144	388	35	7	1350	1727	22529686	22529300	6.430000e-123	451.0
37	TraesCS6D01G203500	chr7A	89.876	563	52	3	795	1352	22920191	22919629	0.000000e+00	719.0
38	TraesCS6D01G203500	chr7A	90.886	395	19	2	1350	1727	22919576	22919182	8.090000e-142	514.0
39	TraesCS6D01G203500	chr2D	82.883	444	64	8	2735	3175	196345574	196346008	5.120000e-104	388.0
40	TraesCS6D01G203500	chr2D	83.582	201	20	10	604	796	330453726	330453921	4.340000e-40	176.0
41	TraesCS6D01G203500	chr4B	90.545	275	22	3	3354	3626	330289820	330290092	1.120000e-95	361.0
42	TraesCS6D01G203500	chr7B	83.553	304	44	6	2874	3173	355675501	355675802	3.210000e-71	279.0
43	TraesCS6D01G203500	chr7B	85.000	100	13	2	3354	3452	211942117	211942019	2.680000e-17	100.0
44	TraesCS6D01G203500	chrUn	100.000	28	0	0	769	796	321348738	321348711	8.000000e-03	52.8
45	TraesCS6D01G203500	chrUn	100.000	28	0	0	769	796	321352042	321352015	8.000000e-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	TraesCS6D01G203500	chr6D	288465658	288469876	4218	False	7792.0	7792	100.000000	1	4219	1	chr6D.!!$F1	4218
1	TraesCS6D01G203500	chr5D	462793787	462797316	3529	True	2015.0	3509	98.907333	1	3357	3	chr5D.!!$R2	3356
2	TraesCS6D01G203500	chr2B	645131430	645134788	3358	True	2407.0	2959	92.615000	1	3355	2	chr2B.!!$R1	3354
3	TraesCS6D01G203500	chr3D	283963531	283967562	4031	True	2681.0	2822	95.798000	1	3357	2	chr3D.!!$R1	3356
4	TraesCS6D01G203500	chr2A	453507114	453508537	1423	True	961.0	1698	90.310500	1734	3357	2	chr2A.!!$R2	1623
5	TraesCS6D01G203500	chr2A	211908158	211908688	530	False	403.0	403	80.891000	2753	3276	1	chr2A.!!$F2	523
6	TraesCS6D01G203500	chr4A	18745888	18747340	1452	False	927.0	1650	88.729500	1725	3357	2	chr4A.!!$F2	1632
7	TraesCS6D01G203500	chr4A	705179600	705180484	884	True	528.0	597	89.634000	905	1727	2	chr4A.!!$R2	822
8	TraesCS6D01G203500	chr5A	430253223	430254111	888	True	1122.0	1122	89.922000	3354	4219	1	chr5A.!!$R1	865
9	TraesCS6D01G203500	chr5A	554338521	554339940	1419	True	985.0	1247	92.352000	1900	3341	2	chr5A.!!$R2	1441
10	TraesCS6D01G203500	chr5A	4799394	4800836	1442	False	931.5	1648	89.191500	1731	3357	2	chr5A.!!$F1	1626
11	TraesCS6D01G203500	chr3A	454087983	454089583	1600	False	1070.5	1236	90.968000	1720	3358	2	chr3A.!!$F1	1638
12	TraesCS6D01G203500	chr3A	158788683	158789572	889	True	1057.0	1057	88.603000	3353	4219	1	chr3A.!!$R1	866
13	TraesCS6D01G203500	chr1B	488509789	488510676	887	True	1029.0	1029	88.098000	3352	4219	1	chr1B.!!$R1	867
14	TraesCS6D01G203500	chr1A	58548637	58549508	871	False	580.5	870	92.305500	3374	4219	2	chr1A.!!$F1	845
15	TraesCS6D01G203500	chr7D	22529300	22530289	989	True	600.5	750	89.716500	804	1727	2	chr7D.!!$R1	923
16	TraesCS6D01G203500	chr7A	22919182	22920191	1009	True	616.5	719	90.381000	795	1727	2	chr7A.!!$R1	932

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
21	22	1.132453	CGAGGATTCTGTAGACGCACA	59.868	52.381	0.0	0.0	0.0	4.57	F
1372	1438	3.895656	AGCCGCTACCATAAGTCTATCAA	59.104	43.478	0.0	0.0	0.0	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1997	2795	2.307496	AATGAAGCACCAACCATCCA	57.693	45.000	0.0	0.0	0.0	3.41	R
3367	4352	1.763770	CTGGGAGGGTGCTCAGTTT	59.236	57.895	0.0	0.0	0.0	2.66	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
21	22	1.132453	CGAGGATTCTGTAGACGCACA	59.868	52.381	0.00	0.00	0.00	4.57
583	587	8.089597	TGTAATTTATACTTGTGTTCCAGTCGA	58.910	33.333	0.00	0.00	0.00	4.20
902	911	7.837863	TCTCTGGAACTACCTTTAGTACATTG	58.162	38.462	0.00	0.00	37.59	2.82
1135	1144	5.477984	TCATTTTCTTCTGCTTTGCCTGTAT	59.522	36.000	0.00	0.00	0.00	2.29
1215	1226	6.761731	TTCCTTGACAATTTGCGTTATTTG	57.238	33.333	0.00	0.00	0.00	2.32
1372	1438	3.895656	AGCCGCTACCATAAGTCTATCAA	59.104	43.478	0.00	0.00	0.00	2.57
1766	2562	6.530120	TGACCATGTTTACAAGCTCTTAGAA	58.470	36.000	0.00	0.00	0.00	2.10
2740	3551	5.726729	GCTCCTGCTTTCTGAAACTATAC	57.273	43.478	0.00	0.00	36.03	1.47
3381	4366	9.998106	TTAGATATATTAAAACTGAGCACCCTC	57.002	33.333	0.00	0.00	38.62	4.30
3458	4443	5.163530	TGTTTATGACCATTGGATGTGATGC	60.164	40.000	10.37	0.00	0.00	3.91
3509	4494	2.134287	GTCGCTGGATGGGCTAGGA	61.134	63.158	0.00	0.00	0.00	2.94
3641	4630	0.390472	GAGTGGCCCGACAGAGAAAG	60.390	60.000	0.00	0.00	0.00	2.62
3643	4632	1.841556	TGGCCCGACAGAGAAAGGT	60.842	57.895	0.00	0.00	0.00	3.50
3644	4633	1.376037	GGCCCGACAGAGAAAGGTG	60.376	63.158	0.00	0.00	0.00	4.00
3754	4743	7.432350	TTTGTGGAAATAAATTGTCATTGCC	57.568	32.000	0.00	0.00	31.25	4.52
3805	4794	1.355210	CGCCGGCCAATTATGTCAC	59.645	57.895	23.46	0.00	0.00	3.67
3821	4810	2.104253	CACGACGGTTACCATGCCC	61.104	63.158	1.13	0.00	0.00	5.36
3834	4823	2.181975	CCATGCCCCTTCATGTTCTTT	58.818	47.619	0.00	0.00	41.60	2.52
3970	4962	1.235281	GCGACGCCTTTCCTTCCTTT	61.235	55.000	9.14	0.00	0.00	3.11
3997	4989	8.942338	TGAATTCGTGATATAGTAGCAAAGTT	57.058	30.769	0.04	0.00	0.00	2.66
3998	4990	9.378551	TGAATTCGTGATATAGTAGCAAAGTTT	57.621	29.630	0.04	0.00	0.00	2.66
4001	4993	7.751047	TCGTGATATAGTAGCAAAGTTTGAC	57.249	36.000	19.82	9.35	0.00	3.18
4002	4994	6.755141	TCGTGATATAGTAGCAAAGTTTGACC	59.245	38.462	19.82	5.73	0.00	4.02
4003	4995	6.533723	CGTGATATAGTAGCAAAGTTTGACCA	59.466	38.462	19.82	0.00	0.00	4.02
4004	4996	7.224753	CGTGATATAGTAGCAAAGTTTGACCAT	59.775	37.037	19.82	6.68	0.00	3.55
4005	4997	8.338259	GTGATATAGTAGCAAAGTTTGACCATG	58.662	37.037	19.82	0.00	0.00	3.66
4011	5003	7.221450	AGTAGCAAAGTTTGACCATGTACTAA	58.779	34.615	19.82	0.00	0.00	2.24
4012	5004	7.883311	AGTAGCAAAGTTTGACCATGTACTAAT	59.117	33.333	19.82	5.02	0.00	1.73
4013	5005	7.524717	AGCAAAGTTTGACCATGTACTAATT	57.475	32.000	19.82	0.00	0.00	1.40
4014	5006	7.370383	AGCAAAGTTTGACCATGTACTAATTG	58.630	34.615	19.82	0.00	0.00	2.32
4015	5007	7.230510	AGCAAAGTTTGACCATGTACTAATTGA	59.769	33.333	19.82	0.00	0.00	2.57
4016	5008	8.028938	GCAAAGTTTGACCATGTACTAATTGAT	58.971	33.333	19.82	0.00	0.00	2.57
4017	5009	9.912634	CAAAGTTTGACCATGTACTAATTGATT	57.087	29.630	10.19	0.00	0.00	2.57
4019	5011	8.281212	AGTTTGACCATGTACTAATTGATTCC	57.719	34.615	0.00	0.00	0.00	3.01
4020	5012	7.888021	AGTTTGACCATGTACTAATTGATTCCA	59.112	33.333	0.00	0.00	0.00	3.53
4137	5157	1.374125	TTGGCGACTGTCGTCCATG	60.374	57.895	31.51	9.64	45.07	3.66
4141	5161	2.348104	CGACTGTCGTCCATGGGGA	61.348	63.158	21.30	7.13	42.29	4.81
4176	5196	2.671177	CGCAGGCAAAGAGGACGTG	61.671	63.158	0.00	0.00	0.00	4.49

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
21	22	7.537596	TGAACCACATAAGTTCCAATTCAAT	57.462	32.000	1.53	0.00	42.41	2.57
583	587	1.236628	ACTGCGTCTACGACTCTTGT	58.763	50.000	6.71	0.00	43.02	3.16
660	666	9.366216	GAGTGATAACAAATAAATGAAAACCCC	57.634	33.333	0.00	0.00	0.00	4.95
902	911	3.316308	AGGAAACCAAATAGATGCATCGC	59.684	43.478	20.67	0.00	0.00	4.58
1135	1144	6.095580	ACGACATAAGAAGCAGATCTTACAGA	59.904	38.462	8.30	0.00	42.88	3.41
1997	2795	2.307496	AATGAAGCACCAACCATCCA	57.693	45.000	0.00	0.00	0.00	3.41
3360	4345	5.430417	TGGGAGGGTGCTCAGTTTTAATATA	59.570	40.000	0.00	0.00	0.00	0.86
3362	4347	3.589735	TGGGAGGGTGCTCAGTTTTAATA	59.410	43.478	0.00	0.00	0.00	0.98
3367	4352	1.763770	CTGGGAGGGTGCTCAGTTT	59.236	57.895	0.00	0.00	0.00	2.66
3378	4363	2.284921	TCTGTGAGGGCTGGGAGG	60.285	66.667	0.00	0.00	0.00	4.30
3381	4366	2.262774	GATGGTCTGTGAGGGCTGGG	62.263	65.000	0.00	0.00	0.00	4.45
3509	4494	0.533308	TTTTGTTACGGGAGCAGCGT	60.533	50.000	0.00	0.00	0.00	5.07
3641	4630	1.002624	TCCCAATCGGTTCTGCACC	60.003	57.895	0.00	0.00	43.16	5.01
3643	4632	0.036388	GTCTCCCAATCGGTTCTGCA	60.036	55.000	0.00	0.00	0.00	4.41
3644	4633	0.744771	GGTCTCCCAATCGGTTCTGC	60.745	60.000	0.00	0.00	0.00	4.26
3754	4743	5.389859	TTGATTGCCATTAAAGACCTGTG	57.610	39.130	0.00	0.00	0.00	3.66
3805	4794	2.512974	GGGGCATGGTAACCGTCG	60.513	66.667	0.00	0.00	0.00	5.12
3834	4823	3.587933	GCGTGCGTGGGGTGAAAA	61.588	61.111	0.00	0.00	0.00	2.29
3996	4988	8.106462	TCTGGAATCAATTAGTACATGGTCAAA	58.894	33.333	0.00	0.00	0.00	2.69
3997	4989	7.552687	GTCTGGAATCAATTAGTACATGGTCAA	59.447	37.037	0.00	0.00	0.00	3.18
3998	4990	7.047891	GTCTGGAATCAATTAGTACATGGTCA	58.952	38.462	0.00	0.00	0.00	4.02
4001	4993	6.708054	GGAGTCTGGAATCAATTAGTACATGG	59.292	42.308	0.00	0.00	0.00	3.66
4002	4994	7.275183	TGGAGTCTGGAATCAATTAGTACATG	58.725	38.462	0.00	0.00	0.00	3.21
4003	4995	7.437713	TGGAGTCTGGAATCAATTAGTACAT	57.562	36.000	0.00	0.00	0.00	2.29
4004	4996	6.867519	TGGAGTCTGGAATCAATTAGTACA	57.132	37.500	0.00	0.00	0.00	2.90
4005	4997	7.331791	AGTTGGAGTCTGGAATCAATTAGTAC	58.668	38.462	0.69	0.00	0.00	2.73
4011	5003	4.288105	AGTGAGTTGGAGTCTGGAATCAAT	59.712	41.667	0.69	0.00	0.00	2.57
4012	5004	3.648067	AGTGAGTTGGAGTCTGGAATCAA	59.352	43.478	0.69	0.00	0.00	2.57
4013	5005	3.007290	CAGTGAGTTGGAGTCTGGAATCA	59.993	47.826	0.69	0.00	0.00	2.57
4014	5006	3.594134	CAGTGAGTTGGAGTCTGGAATC	58.406	50.000	0.00	0.00	0.00	2.52
4015	5007	2.289945	GCAGTGAGTTGGAGTCTGGAAT	60.290	50.000	0.00	0.00	0.00	3.01
4016	5008	1.070758	GCAGTGAGTTGGAGTCTGGAA	59.929	52.381	0.00	0.00	0.00	3.53
4017	5009	0.681733	GCAGTGAGTTGGAGTCTGGA	59.318	55.000	0.00	0.00	0.00	3.86
4018	5010	0.668706	CGCAGTGAGTTGGAGTCTGG	60.669	60.000	0.00	0.00	0.00	3.86
4019	5011	1.287730	GCGCAGTGAGTTGGAGTCTG	61.288	60.000	0.30	0.00	0.00	3.51
4020	5012	1.005630	GCGCAGTGAGTTGGAGTCT	60.006	57.895	0.30	0.00	0.00	3.24
4049	5068	1.002624	GGACAGGGAAACGATGGCA	60.003	57.895	0.00	0.00	0.00	4.92
4116	5136	3.231501	GACGACAGTCGCCAACAC	58.768	61.111	23.09	4.28	45.12	3.32
4141	5161	3.003763	GCCACCGGGAGTTCCTCT	61.004	66.667	6.32	0.00	35.59	3.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.