AutoCloner

Multiple sequence alignment - TraesCS4A01G007500

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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	TraesCS4A01G007500	chr4A	100.000	3488	0	0	1	3488	4798468	4794981	0.000000e+00	6442
1	TraesCS4A01G007500	chr4D	93.297	2939	130	26	611	3488	465761061	465763993	0.000000e+00	4274
2	TraesCS4A01G007500	chr4D	91.486	552	22	9	1	532	127923785	127923239	0.000000e+00	736
3	TraesCS4A01G007500	chr4B	91.415	2947	107	32	611	3488	582827538	582830407	0.000000e+00	3906
4	TraesCS4A01G007500	chrUn	92.077	568	9	8	1	532	197753108	197753675	0.000000e+00	767
5	TraesCS4A01G007500	chrUn	96.386	83	3	0	529	611	197753713	197753795	1.690000e-28	137
6	TraesCS4A01G007500	chr3D	91.091	550	31	6	1	532	614586158	614585609	0.000000e+00	728
7	TraesCS4A01G007500	chr3D	90.244	82	8	0	529	610	614585571	614585490	1.320000e-19	108
8	TraesCS4A01G007500	chr7B	86.221	479	15	14	75	529	137459593	137460044	4.080000e-129	472
9	TraesCS4A01G007500	chr7B	94.845	97	5	0	1	97	137459493	137459589	6.030000e-33	152
10	TraesCS4A01G007500	chr7B	95.122	82	4	0	529	610	137460085	137460166	2.830000e-26	130
11	TraesCS4A01G007500	chr6A	97.590	83	2	0	529	611	24919184	24919266	3.630000e-30	143

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	TraesCS4A01G007500	chr4A	4794981	4798468	3487	True	6442.000000	6442	100.000000	1	3488	1	chr4A.!!$R1	3487
1	TraesCS4A01G007500	chr4D	465761061	465763993	2932	False	4274.000000	4274	93.297000	611	3488	1	chr4D.!!$F1	2877
2	TraesCS4A01G007500	chr4D	127923239	127923785	546	True	736.000000	736	91.486000	1	532	1	chr4D.!!$R1	531
3	TraesCS4A01G007500	chr4B	582827538	582830407	2869	False	3906.000000	3906	91.415000	611	3488	1	chr4B.!!$F1	2877
4	TraesCS4A01G007500	chrUn	197753108	197753795	687	False	452.000000	767	94.231500	1	611	2	chrUn.!!$F1	610
5	TraesCS4A01G007500	chr3D	614585490	614586158	668	True	418.000000	728	90.667500	1	610	2	chr3D.!!$R1	609
6	TraesCS4A01G007500	chr7B	137459493	137460166	673	False	251.333333	472	92.062667	1	610	3	chr7B.!!$F1	609

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
726	849	0.178973	ACTGGGCCGGCTAAAAAGTT	60.179	50.0	28.56	0.0	0.0	2.66	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2654	2807	0.251354	ATGAGATCCTGCAGCGTTGT	59.749	50.0	8.66	0.0	0.0	3.32	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
50	51	3.932710	AGCTGATGTACGTACATGTTTGG	59.067	43.478	38.47	24.07	46.20	3.28
231	259	3.498082	ACTTTTGTTGCTTGTGAACGAC	58.502	40.909	0.00	0.00	0.00	4.34
637	760	4.647615	CGGCTATGCGACGGGGAG	62.648	72.222	0.00	0.00	0.00	4.30
726	849	0.178973	ACTGGGCCGGCTAAAAAGTT	60.179	50.000	28.56	0.00	0.00	2.66
767	892	1.453015	GTTCATATGGGCCGGTGCA	60.453	57.895	1.90	0.00	40.13	4.57
788	913	1.209747	GTCCGTTCTGGGCCTTTATCT	59.790	52.381	4.53	0.00	35.79	1.98
820	945	1.379176	TCACTCTCTCGCCCTGGAG	60.379	63.158	0.00	0.00	35.32	3.86
821	946	2.757917	ACTCTCTCGCCCTGGAGC	60.758	66.667	0.00	0.00	33.98	4.70
823	948	2.441164	TCTCTCGCCCTGGAGCTC	60.441	66.667	4.71	4.71	33.98	4.09
824	949	2.441901	CTCTCGCCCTGGAGCTCT	60.442	66.667	14.64	0.00	33.98	4.09
946	1096	1.271840	CCAATCCTCCTCCGGGTGAA	61.272	60.000	0.00	0.00	0.00	3.18
974	1124	1.479323	CATCGTTTTACCCCTCTCCGA	59.521	52.381	0.00	0.00	0.00	4.55
975	1125	1.856629	TCGTTTTACCCCTCTCCGAT	58.143	50.000	0.00	0.00	0.00	4.18
1706	1856	1.743623	CTGGTAACGCCGATGCCAA	60.744	57.895	5.61	0.00	41.21	4.52
1718	1868	2.287788	CCGATGCCAATTCCAATGCTAC	60.288	50.000	0.00	0.00	0.00	3.58
1989	2139	2.480555	CACCTGACGCATTTCCGC	59.519	61.111	0.00	0.00	0.00	5.54
2258	2408	0.376152	GCGAGCTCATCAACATGTGG	59.624	55.000	15.40	0.00	0.00	4.17
2304	2454	8.803397	ATGATGCTGATACTATATTGCATGTT	57.197	30.769	12.05	1.94	40.58	2.71
2372	2522	3.782656	TGATGGTGAGATGGATGATGG	57.217	47.619	0.00	0.00	0.00	3.51
2488	2639	4.629200	CAGAGTCAGTGAAATCCAGTTAGC	59.371	45.833	0.00	0.00	0.00	3.09
2508	2659	3.829601	AGCAGCCTACTAGCCTAACATAG	59.170	47.826	0.00	0.00	0.00	2.23
2518	2669	6.631962	ACTAGCCTAACATAGTGAACACTTC	58.368	40.000	12.66	0.00	42.54	3.01
2528	2680	4.616181	AGTGAACACTTCTGTTTTTCCG	57.384	40.909	1.32	0.00	40.93	4.30
2593	2745	2.487762	TGCGAGCTTGTTTAGGGATTTG	59.512	45.455	2.14	0.00	0.00	2.32
2596	2748	4.558697	GCGAGCTTGTTTAGGGATTTGTTT	60.559	41.667	2.14	0.00	0.00	2.83
2642	2795	1.838112	TGATCCAAACATGGCTGGAC	58.162	50.000	17.56	12.74	44.42	4.02
2654	2807	0.620556	GGCTGGACATCCTGGAAAGA	59.379	55.000	0.00	0.00	35.73	2.52
2727	2881	4.154195	GTGATGCTGTTGTTTACTACCTGG	59.846	45.833	0.00	0.00	0.00	4.45
2738	2892	1.713297	ACTACCTGGTGTCGAAGGTT	58.287	50.000	11.63	0.00	44.63	3.50
2754	2908	5.095490	CGAAGGTTGACTTTGAATATTGGC	58.905	41.667	0.00	0.00	42.27	4.52
2892	3071	5.544176	TGGATATCTGGGGCTTACTCTTTAG	59.456	44.000	2.05	0.00	0.00	1.85
2897	3076	5.030147	TCTGGGGCTTACTCTTTAGAATGA	58.970	41.667	0.00	0.00	0.00	2.57
2905	3084	4.273148	ACTCTTTAGAATGACGGTGCTT	57.727	40.909	0.00	0.00	0.00	3.91
2944	3123	5.836898	TCTTAGTCCTTTAGTTGACCAGTCA	59.163	40.000	0.00	0.00	37.91	3.41
2991	3170	2.364632	TGACGTATTTGGGCTGGAATG	58.635	47.619	0.00	0.00	0.00	2.67
3128	3308	3.247006	ACAGACGTAAGGTTAGCCATG	57.753	47.619	0.00	0.00	46.39	3.66
3131	3311	2.159282	AGACGTAAGGTTAGCCATGTCG	60.159	50.000	0.00	0.03	46.39	4.35
3226	3406	4.709886	TGGCAGACACTAATGCTAAGTCTA	59.290	41.667	0.00	0.00	42.19	2.59
3227	3407	5.186992	TGGCAGACACTAATGCTAAGTCTAA	59.813	40.000	0.00	0.00	42.19	2.10
3289	3469	4.717233	ATCCACGCTTGCAAAATATTCA	57.283	36.364	0.00	0.00	0.00	2.57
3329	3509	6.115446	TGCTACAGCTGAGCATAATACTTTT	58.885	36.000	26.66	3.41	44.89	2.27
3347	3528	3.434940	TTTCTTACTTTCCCCTCTGCC	57.565	47.619	0.00	0.00	0.00	4.85
3382	3563	2.093128	CGTTGTGCCCTTATACCTCCTT	60.093	50.000	0.00	0.00	0.00	3.36
3404	3585	7.896496	TCCTTAAATTTACAGAAGGGGCATTTA	59.104	33.333	14.65	0.00	39.20	1.40
3414	3608	6.100134	ACAGAAGGGGCATTTATTAATTGCAT	59.900	34.615	19.43	7.12	0.00	3.96
3480	3674	1.304381	CAAGGCAAGCCCCTAAGCA	60.304	57.895	7.62	0.00	33.97	3.91

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
50	51	4.321750	CCATGAATTCATAGCCCAGCATTC	60.322	45.833	20.32	0.00	34.26	2.67
231	259	9.442047	AGAGTTGTATGTTTCTAGAAATTCAGG	57.558	33.333	20.41	0.00	32.36	3.86
549	672	4.543590	ATCTCCATCGTGAACTCACTTT	57.456	40.909	8.16	0.00	44.34	2.66
592	715	2.872038	GCCGGAAAGTGATGTTCTGAGT	60.872	50.000	5.05	0.00	33.89	3.41
652	775	1.531423	GTGACTCGACTGTACCAGGA	58.469	55.000	0.00	0.00	35.51	3.86
653	776	0.526662	GGTGACTCGACTGTACCAGG	59.473	60.000	0.00	0.00	35.51	4.45
655	778	1.239296	CCGGTGACTCGACTGTACCA	61.239	60.000	0.00	0.00	0.00	3.25
656	779	1.505353	CCGGTGACTCGACTGTACC	59.495	63.158	0.00	0.00	0.00	3.34
658	781	1.601477	TGCCGGTGACTCGACTGTA	60.601	57.895	1.90	0.00	0.00	2.74
659	782	2.910479	TGCCGGTGACTCGACTGT	60.910	61.111	1.90	0.00	0.00	3.55
660	783	2.430921	GTGCCGGTGACTCGACTG	60.431	66.667	1.90	0.00	0.00	3.51
661	784	4.039357	CGTGCCGGTGACTCGACT	62.039	66.667	1.90	0.00	0.00	4.18
738	861	2.171237	CCCATATGAACTCAGCTGGACA	59.829	50.000	15.13	9.43	34.87	4.02
767	892	1.209747	GATAAAGGCCCAGAACGGACT	59.790	52.381	0.00	0.00	46.38	3.85
772	897	2.166459	GGCAAAGATAAAGGCCCAGAAC	59.834	50.000	0.00	0.00	40.55	3.01
773	898	2.456577	GGCAAAGATAAAGGCCCAGAA	58.543	47.619	0.00	0.00	40.55	3.02
788	913	1.833787	GAGTGACGGGGTAGGGCAAA	61.834	60.000	0.00	0.00	0.00	3.68
946	1096	3.778629	AGGGGTAAAACGATGGTATGAGT	59.221	43.478	0.00	0.00	0.00	3.41
974	1124	1.296056	CGGTGCCGACGGAAAAGAAT	61.296	55.000	20.50	0.00	42.83	2.40
975	1125	1.957186	CGGTGCCGACGGAAAAGAA	60.957	57.895	20.50	0.00	42.83	2.52
1689	1839	0.678366	AATTGGCATCGGCGTTACCA	60.678	50.000	6.85	6.26	42.47	3.25
1696	1846	0.877213	GCATTGGAATTGGCATCGGC	60.877	55.000	0.00	0.00	40.13	5.54
1699	1849	4.580167	TGTAGTAGCATTGGAATTGGCATC	59.420	41.667	0.00	0.00	0.00	3.91
1706	1856	3.780294	TCCTGGTGTAGTAGCATTGGAAT	59.220	43.478	0.00	0.00	35.99	3.01
1718	1868	1.748493	GTGAGAGCTCTCCTGGTGTAG	59.252	57.143	35.07	0.00	42.20	2.74
1989	2139	1.876799	TGTGGCATAACAAACTCACGG	59.123	47.619	0.00	0.00	0.00	4.94
2258	2408	1.084370	GTCATCACTGCTACCACCGC	61.084	60.000	0.00	0.00	0.00	5.68
2304	2454	8.859236	AGAAATCATCTGAATCTTCACTTTCA	57.141	30.769	0.00	0.00	36.88	2.69
2372	2522	3.443099	TCTGACCATCATCGATGTCAC	57.557	47.619	24.09	12.81	38.28	3.67
2379	2529	3.672767	TCATCCATCTGACCATCATCG	57.327	47.619	0.00	0.00	0.00	3.84
2508	2659	4.351131	ACGGAAAAACAGAAGTGTTCAC	57.649	40.909	0.00	0.00	46.68	3.18
2518	2669	4.364415	TGTTCAGGAAACGGAAAAACAG	57.636	40.909	0.00	0.00	46.06	3.16
2528	2680	5.689383	TGTGAGCTTAATGTTCAGGAAAC	57.311	39.130	0.00	0.00	36.59	2.78
2593	2745	6.474427	CCACAATATCATCAACATCAGCAAAC	59.526	38.462	0.00	0.00	0.00	2.93
2596	2748	5.195185	ACCACAATATCATCAACATCAGCA	58.805	37.500	0.00	0.00	0.00	4.41
2642	2795	1.466167	CAGCGTTGTCTTTCCAGGATG	59.534	52.381	0.00	0.00	0.00	3.51
2654	2807	0.251354	ATGAGATCCTGCAGCGTTGT	59.749	50.000	8.66	0.00	0.00	3.32
2727	2881	4.813296	ATTCAAAGTCAACCTTCGACAC	57.187	40.909	0.00	0.00	35.77	3.67
2738	2892	5.412640	CATGCTTGCCAATATTCAAAGTCA	58.587	37.500	0.00	0.00	0.00	3.41
2750	2904	1.483004	CCAATCATCCATGCTTGCCAA	59.517	47.619	0.00	0.00	33.77	4.52
2751	2905	1.116308	CCAATCATCCATGCTTGCCA	58.884	50.000	0.00	0.00	33.77	4.92
2754	2908	3.130633	CAATGCCAATCATCCATGCTTG	58.869	45.455	0.00	0.00	33.40	4.01
2892	3071	2.271800	CTCCTACAAGCACCGTCATTC	58.728	52.381	0.00	0.00	0.00	2.67
2897	3076	1.004918	GCACTCCTACAAGCACCGT	60.005	57.895	0.00	0.00	0.00	4.83
2905	3084	2.103373	CTAAGAGCAGGCACTCCTACA	58.897	52.381	4.16	0.00	41.93	2.74
2991	3170	1.917303	CACAAACGGTGCAGAACAAAC	59.083	47.619	0.00	0.00	41.36	2.93
3012	3192	2.293677	CCACCGCTAGTAGATGAACGAT	59.706	50.000	0.00	0.00	0.00	3.73
3069	3249	8.173775	GGTTGAGATCAAATTATCATAGATGCG	58.826	37.037	0.00	0.00	37.63	4.73
3074	3254	9.775854	AGTCTGGTTGAGATCAAATTATCATAG	57.224	33.333	0.00	0.00	37.63	2.23
3102	3282	5.128171	TGGCTAACCTTACGTCTGTTATGAT	59.872	40.000	0.00	0.00	36.63	2.45
3128	3308	3.435671	AGGCAGTTTTACAGCAATACGAC	59.564	43.478	0.00	0.00	31.72	4.34
3131	3311	3.057596	TGCAGGCAGTTTTACAGCAATAC	60.058	43.478	0.00	0.00	31.72	1.89
3262	3442	5.637006	ATTTTGCAAGCGTGGATAAAGTA	57.363	34.783	0.00	0.00	0.00	2.24
3289	3469	5.409826	GCTGTAGCAGAAAAGAACTGTATGT	59.590	40.000	0.00	0.00	41.59	2.29
3329	3509	2.038863	TGGCAGAGGGGAAAGTAAGA	57.961	50.000	0.00	0.00	0.00	2.10
3347	3528	2.192624	CACAACGAGTTGCCCTTTTTG	58.807	47.619	15.09	1.69	44.03	2.44
3439	3633	6.187682	TGTCTGAGACACATAAGAGATACCA	58.812	40.000	11.93	0.00	37.67	3.25

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.