AutoCloner

Multiple sequence alignment - TraesCS4B01G167600

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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	TraesCS4B01G167600	chr4B	100.000	3744	0	0	1	3744	365621306	365625049	0.000000e+00	6914
1	TraesCS4B01G167600	chr4B	97.685	907	6	2	1	894	314792020	314791116	0.000000e+00	1544
2	TraesCS4B01G167600	chr4B	89.317	908	64	14	1	895	65640114	65641001	0.000000e+00	1109
3	TraesCS4B01G167600	chr4D	97.765	2729	41	7	916	3634	294702433	294699715	0.000000e+00	4684
4	TraesCS4B01G167600	chr4D	92.800	125	9	0	3620	3744	96899442	96899566	8.260000e-42	182
5	TraesCS4B01G167600	chr4A	97.591	2740	55	10	895	3631	214311642	214314373	0.000000e+00	4684
6	TraesCS4B01G167600	chrUn	99.776	893	2	0	1	893	117390422	117389530	0.000000e+00	1639
7	TraesCS4B01G167600	chr6D	96.009	902	23	5	1	893	460311737	460310840	0.000000e+00	1454
8	TraesCS4B01G167600	chr6D	82.460	496	61	20	109	584	80007938	80007449	9.680000e-111	411
9	TraesCS4B01G167600	chr6D	97.321	112	3	0	3633	3744	404877856	404877745	1.370000e-44	191
10	TraesCS4B01G167600	chr1D	92.239	902	28	11	1	893	389795942	389795074	0.000000e+00	1240
11	TraesCS4B01G167600	chr1D	92.188	128	8	2	3617	3744	178466484	178466359	2.970000e-41	180
12	TraesCS4B01G167600	chr7D	91.285	918	33	8	1	893	608084597	608083702	0.000000e+00	1208
13	TraesCS4B01G167600	chr7D	79.021	715	110	23	172	871	43233697	43233008	1.590000e-123	453
14	TraesCS4B01G167600	chr7D	90.780	141	10	2	3605	3744	39001476	39001338	6.390000e-43	185
15	TraesCS4B01G167600	chr3D	88.606	904	71	12	1	893	564637356	564636474	0.000000e+00	1070
16	TraesCS4B01G167600	chr3D	97.321	112	3	0	3633	3744	496739962	496740073	1.370000e-44	191
17	TraesCS4B01G167600	chr2B	87.805	902	75	17	1	890	313759968	313760846	0.000000e+00	1024
18	TraesCS4B01G167600	chr2B	89.663	445	35	9	1	437	24895963	24895522	1.170000e-154	556
19	TraesCS4B01G167600	chr2B	97.368	114	3	0	3631	3744	681350867	681350980	1.060000e-45	195
20	TraesCS4B01G167600	chr7B	88.816	456	41	8	1	450	640171397	640170946	5.470000e-153	551
21	TraesCS4B01G167600	chr5B	95.000	120	6	0	3625	3744	241189406	241189287	4.940000e-44	189
22	TraesCS4B01G167600	chr3B	94.215	121	6	1	3625	3744	796354464	796354344	2.300000e-42	183
23	TraesCS4B01G167600	chr5A	89.474	133	12	2	3614	3744	19669255	19669123	2.310000e-37	167

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	TraesCS4B01G167600	chr4B	365621306	365625049	3743	False	6914	6914	100.000	1	3744	1	chr4B.!!$F2	3743
1	TraesCS4B01G167600	chr4B	314791116	314792020	904	True	1544	1544	97.685	1	894	1	chr4B.!!$R1	893
2	TraesCS4B01G167600	chr4B	65640114	65641001	887	False	1109	1109	89.317	1	895	1	chr4B.!!$F1	894
3	TraesCS4B01G167600	chr4D	294699715	294702433	2718	True	4684	4684	97.765	916	3634	1	chr4D.!!$R1	2718
4	TraesCS4B01G167600	chr4A	214311642	214314373	2731	False	4684	4684	97.591	895	3631	1	chr4A.!!$F1	2736
5	TraesCS4B01G167600	chrUn	117389530	117390422	892	True	1639	1639	99.776	1	893	1	chrUn.!!$R1	892
6	TraesCS4B01G167600	chr6D	460310840	460311737	897	True	1454	1454	96.009	1	893	1	chr6D.!!$R3	892
7	TraesCS4B01G167600	chr1D	389795074	389795942	868	True	1240	1240	92.239	1	893	1	chr1D.!!$R2	892
8	TraesCS4B01G167600	chr7D	608083702	608084597	895	True	1208	1208	91.285	1	893	1	chr7D.!!$R3	892
9	TraesCS4B01G167600	chr7D	43233008	43233697	689	True	453	453	79.021	172	871	1	chr7D.!!$R2	699
10	TraesCS4B01G167600	chr3D	564636474	564637356	882	True	1070	1070	88.606	1	893	1	chr3D.!!$R1	892
11	TraesCS4B01G167600	chr2B	313759968	313760846	878	False	1024	1024	87.805	1	890	1	chr2B.!!$F1	889

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
896	949	1.141881	CGCCTATCACTCGCCTTGT	59.858	57.895	0.0	0.0	0.0	3.16	F
1878	1931	1.697982	AGTAGTTTCCAGAAAGCCGGT	59.302	47.619	1.9	0.0	0.0	5.28	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2331	2384	0.035152	TGTACTCGCCGACCTCCTTA	60.035	55.000	0.00	0.0	0.0	2.69	R
3032	3097	1.066430	TGTTCCCAGAACCTATGTCGC	60.066	52.381	5.09	0.0	0.0	5.19	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
119	120	2.063015	ATGTCGGGTGCTGGAACCAA	62.063	55.000	3.56	0.00	42.47	3.67
896	949	1.141881	CGCCTATCACTCGCCTTGT	59.858	57.895	0.00	0.00	0.00	3.16
906	959	4.306471	CGCCTTGTTTCACGCGCA	62.306	61.111	5.73	0.00	37.97	6.09
1033	1086	7.382218	CGAAGCACCAGAAAAGAACAAAAATAT	59.618	33.333	0.00	0.00	0.00	1.28
1878	1931	1.697982	AGTAGTTTCCAGAAAGCCGGT	59.302	47.619	1.90	0.00	0.00	5.28
2166	2219	2.124445	GGATTACCGCCACCACCC	60.124	66.667	0.00	0.00	0.00	4.61
2331	2384	1.051812	CATCAAGGGCCTCGTCCTAT	58.948	55.000	6.46	0.00	36.17	2.57
2641	2694	2.558359	GGGATGTTTGTCAAGTTCCCTG	59.442	50.000	16.64	0.00	38.92	4.45
2877	2940	6.966066	TGTGTTTGTAACATCATGATATTGCG	59.034	34.615	9.52	0.00	44.35	4.85
2943	3008	5.623169	TGCATAGATGGTGATGCTATTTCA	58.377	37.500	8.20	0.00	46.98	2.69
3034	3099	6.788766	TTTTATGCTTAATCACAATTCGCG	57.211	33.333	0.00	0.00	0.00	5.87
3046	3111	2.930040	ACAATTCGCGACATAGGTTCTG	59.070	45.455	9.15	2.93	0.00	3.02
3246	3312	2.766345	TGAGAAATGCAAATTGCCCC	57.234	45.000	15.98	2.00	44.23	5.80
3270	3336	8.081025	CCCCACAATGTGAAATTTTTATTTTGG	58.919	33.333	15.91	14.72	35.23	3.28
3271	3337	8.081025	CCCACAATGTGAAATTTTTATTTTGGG	58.919	33.333	15.91	20.66	40.39	4.12
3641	3707	4.820894	ACAAGTTACATGTACTCCCTCC	57.179	45.455	4.68	0.00	0.00	4.30
3642	3708	3.194968	ACAAGTTACATGTACTCCCTCCG	59.805	47.826	4.68	0.00	0.00	4.63
3643	3709	3.097342	AGTTACATGTACTCCCTCCGT	57.903	47.619	4.68	0.00	0.00	4.69
3644	3710	3.438183	AGTTACATGTACTCCCTCCGTT	58.562	45.455	4.68	0.00	0.00	4.44
3645	3711	3.446516	AGTTACATGTACTCCCTCCGTTC	59.553	47.826	4.68	0.00	0.00	3.95
3646	3712	1.192428	ACATGTACTCCCTCCGTTCC	58.808	55.000	0.00	0.00	0.00	3.62
3647	3713	1.273098	ACATGTACTCCCTCCGTTCCT	60.273	52.381	0.00	0.00	0.00	3.36
3648	3714	2.024655	ACATGTACTCCCTCCGTTCCTA	60.025	50.000	0.00	0.00	0.00	2.94
3649	3715	2.905415	TGTACTCCCTCCGTTCCTAA	57.095	50.000	0.00	0.00	0.00	2.69
3650	3716	3.173953	TGTACTCCCTCCGTTCCTAAA	57.826	47.619	0.00	0.00	0.00	1.85
3651	3717	3.716431	TGTACTCCCTCCGTTCCTAAAT	58.284	45.455	0.00	0.00	0.00	1.40
3652	3718	4.870636	TGTACTCCCTCCGTTCCTAAATA	58.129	43.478	0.00	0.00	0.00	1.40
3653	3719	5.461327	TGTACTCCCTCCGTTCCTAAATAT	58.539	41.667	0.00	0.00	0.00	1.28
3654	3720	5.901276	TGTACTCCCTCCGTTCCTAAATATT	59.099	40.000	0.00	0.00	0.00	1.28
3655	3721	5.970501	ACTCCCTCCGTTCCTAAATATTT	57.029	39.130	5.89	5.89	0.00	1.40
3656	3722	5.681639	ACTCCCTCCGTTCCTAAATATTTG	58.318	41.667	11.05	1.40	0.00	2.32
3657	3723	5.191124	ACTCCCTCCGTTCCTAAATATTTGT	59.809	40.000	11.05	0.00	0.00	2.83
3658	3724	5.677567	TCCCTCCGTTCCTAAATATTTGTC	58.322	41.667	11.05	0.00	0.00	3.18
3659	3725	5.427481	TCCCTCCGTTCCTAAATATTTGTCT	59.573	40.000	11.05	0.00	0.00	3.41
3660	3726	6.069847	TCCCTCCGTTCCTAAATATTTGTCTT	60.070	38.462	11.05	0.00	0.00	3.01
3661	3727	6.602009	CCCTCCGTTCCTAAATATTTGTCTTT	59.398	38.462	11.05	0.00	0.00	2.52
3662	3728	7.201705	CCCTCCGTTCCTAAATATTTGTCTTTC	60.202	40.741	11.05	0.00	0.00	2.62
3663	3729	7.553044	CCTCCGTTCCTAAATATTTGTCTTTCT	59.447	37.037	11.05	0.00	0.00	2.52
3664	3730	9.595823	CTCCGTTCCTAAATATTTGTCTTTCTA	57.404	33.333	11.05	0.00	0.00	2.10
3665	3731	9.595823	TCCGTTCCTAAATATTTGTCTTTCTAG	57.404	33.333	11.05	0.00	0.00	2.43
3666	3732	9.595823	CCGTTCCTAAATATTTGTCTTTCTAGA	57.404	33.333	11.05	0.00	0.00	2.43
3700	3766	9.935682	ATAAATGACTACATACGAAGCAAAATG	57.064	29.630	0.00	0.00	35.50	2.32
3701	3767	7.609760	AATGACTACATACGAAGCAAAATGA	57.390	32.000	0.00	0.00	35.50	2.57
3702	3768	6.403333	TGACTACATACGAAGCAAAATGAC	57.597	37.500	0.00	0.00	0.00	3.06
3703	3769	6.163476	TGACTACATACGAAGCAAAATGACT	58.837	36.000	0.00	0.00	0.00	3.41
3704	3770	6.090763	TGACTACATACGAAGCAAAATGACTG	59.909	38.462	0.00	0.00	0.00	3.51
3705	3771	6.163476	ACTACATACGAAGCAAAATGACTGA	58.837	36.000	0.00	0.00	0.00	3.41
3706	3772	5.940192	ACATACGAAGCAAAATGACTGAA	57.060	34.783	0.00	0.00	0.00	3.02
3707	3773	6.500684	ACATACGAAGCAAAATGACTGAAT	57.499	33.333	0.00	0.00	0.00	2.57
3708	3774	6.546395	ACATACGAAGCAAAATGACTGAATC	58.454	36.000	0.00	0.00	0.00	2.52
3709	3775	6.372659	ACATACGAAGCAAAATGACTGAATCT	59.627	34.615	0.00	0.00	0.00	2.40
3710	3776	7.549134	ACATACGAAGCAAAATGACTGAATCTA	59.451	33.333	0.00	0.00	0.00	1.98
3711	3777	6.170675	ACGAAGCAAAATGACTGAATCTAC	57.829	37.500	0.00	0.00	0.00	2.59
3712	3778	5.700832	ACGAAGCAAAATGACTGAATCTACA	59.299	36.000	0.00	0.00	0.00	2.74
3713	3779	6.017933	CGAAGCAAAATGACTGAATCTACAC	58.982	40.000	0.00	0.00	0.00	2.90
3714	3780	6.128445	CGAAGCAAAATGACTGAATCTACACT	60.128	38.462	0.00	0.00	0.00	3.55
3715	3781	6.734104	AGCAAAATGACTGAATCTACACTC	57.266	37.500	0.00	0.00	0.00	3.51
3716	3782	6.471146	AGCAAAATGACTGAATCTACACTCT	58.529	36.000	0.00	0.00	0.00	3.24
3717	3783	7.615403	AGCAAAATGACTGAATCTACACTCTA	58.385	34.615	0.00	0.00	0.00	2.43
3718	3784	8.097038	AGCAAAATGACTGAATCTACACTCTAA	58.903	33.333	0.00	0.00	0.00	2.10
3719	3785	8.721478	GCAAAATGACTGAATCTACACTCTAAA	58.279	33.333	0.00	0.00	0.00	1.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
896	949	2.690786	AGGTAGTTAATGCGCGTGAAA	58.309	42.857	8.43	0.00	0.00	2.69
1709	1762	1.884926	GGATCCTTCTTCTGCGCCG	60.885	63.158	4.18	0.00	0.00	6.46
2166	2219	0.742281	CAGATGCCGTCAACCCAGAG	60.742	60.000	0.00	0.00	0.00	3.35
2331	2384	0.035152	TGTACTCGCCGACCTCCTTA	60.035	55.000	0.00	0.00	0.00	2.69
2641	2694	6.299141	AGGATGATTACAATGGTGGTACATC	58.701	40.000	0.00	0.00	44.52	3.06
2911	2976	6.669278	CATCACCATCTATGCAAAAGATCTG	58.331	40.000	11.03	9.75	31.22	2.90
2912	2977	5.241064	GCATCACCATCTATGCAAAAGATCT	59.759	40.000	11.03	0.00	46.19	2.75
2943	3008	7.724305	ACTAATGAACATTACGTCAAAGTGT	57.276	32.000	0.00	0.00	32.50	3.55
3032	3097	1.066430	TGTTCCCAGAACCTATGTCGC	60.066	52.381	5.09	0.00	0.00	5.19
3034	3099	3.118738	ACGATGTTCCCAGAACCTATGTC	60.119	47.826	5.09	0.00	0.00	3.06
3046	3111	2.758423	AGGCCAAAAATACGATGTTCCC	59.242	45.455	5.01	0.00	0.00	3.97
3246	3312	7.594386	GCCCAAAATAAAAATTTCACATTGTGG	59.406	33.333	16.46	15.42	34.87	4.17
3573	3639	5.353394	AATGGATAGGTACGTCAACACAT	57.647	39.130	0.00	0.00	0.00	3.21
3634	3700	5.681639	ACAAATATTTAGGAACGGAGGGAG	58.318	41.667	0.00	0.00	0.00	4.30
3635	3701	5.427481	AGACAAATATTTAGGAACGGAGGGA	59.573	40.000	0.00	0.00	0.00	4.20
3636	3702	5.681639	AGACAAATATTTAGGAACGGAGGG	58.318	41.667	0.00	0.00	0.00	4.30
3637	3703	7.553044	AGAAAGACAAATATTTAGGAACGGAGG	59.447	37.037	0.00	0.00	0.00	4.30
3638	3704	8.494016	AGAAAGACAAATATTTAGGAACGGAG	57.506	34.615	0.00	0.00	0.00	4.63
3639	3705	9.595823	CTAGAAAGACAAATATTTAGGAACGGA	57.404	33.333	0.00	0.00	0.00	4.69
3640	3706	9.595823	TCTAGAAAGACAAATATTTAGGAACGG	57.404	33.333	0.00	0.00	0.00	4.44
3674	3740	9.935682	CATTTTGCTTCGTATGTAGTCATTTAT	57.064	29.630	0.00	0.00	35.70	1.40
3675	3741	9.157104	TCATTTTGCTTCGTATGTAGTCATTTA	57.843	29.630	0.00	0.00	35.70	1.40
3676	3742	7.962918	GTCATTTTGCTTCGTATGTAGTCATTT	59.037	33.333	0.00	0.00	35.70	2.32
3677	3743	7.334421	AGTCATTTTGCTTCGTATGTAGTCATT	59.666	33.333	0.00	0.00	35.70	2.57
3678	3744	6.818644	AGTCATTTTGCTTCGTATGTAGTCAT	59.181	34.615	0.00	0.00	38.00	3.06
3679	3745	6.090763	CAGTCATTTTGCTTCGTATGTAGTCA	59.909	38.462	0.00	0.00	0.00	3.41
3680	3746	6.310467	TCAGTCATTTTGCTTCGTATGTAGTC	59.690	38.462	0.00	0.00	0.00	2.59
3681	3747	6.163476	TCAGTCATTTTGCTTCGTATGTAGT	58.837	36.000	0.00	0.00	0.00	2.73
3682	3748	6.647212	TCAGTCATTTTGCTTCGTATGTAG	57.353	37.500	0.00	0.00	0.00	2.74
3683	3749	7.549134	AGATTCAGTCATTTTGCTTCGTATGTA	59.451	33.333	0.00	0.00	0.00	2.29
3684	3750	5.940192	TTCAGTCATTTTGCTTCGTATGT	57.060	34.783	0.00	0.00	0.00	2.29
3685	3751	6.779117	AGATTCAGTCATTTTGCTTCGTATG	58.221	36.000	0.00	0.00	0.00	2.39
3686	3752	6.992063	AGATTCAGTCATTTTGCTTCGTAT	57.008	33.333	0.00	0.00	0.00	3.06
3687	3753	6.871492	TGTAGATTCAGTCATTTTGCTTCGTA	59.129	34.615	0.00	0.00	0.00	3.43
3688	3754	5.700832	TGTAGATTCAGTCATTTTGCTTCGT	59.299	36.000	0.00	0.00	0.00	3.85
3689	3755	6.017933	GTGTAGATTCAGTCATTTTGCTTCG	58.982	40.000	0.00	0.00	0.00	3.79
3690	3756	7.118971	AGAGTGTAGATTCAGTCATTTTGCTTC	59.881	37.037	0.00	0.00	39.44	3.86
3691	3757	6.939163	AGAGTGTAGATTCAGTCATTTTGCTT	59.061	34.615	0.00	0.00	39.44	3.91
3692	3758	6.471146	AGAGTGTAGATTCAGTCATTTTGCT	58.529	36.000	0.00	0.00	39.44	3.91
3693	3759	6.734104	AGAGTGTAGATTCAGTCATTTTGC	57.266	37.500	0.00	0.00	39.44	3.68

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.