AutoCloner

Multiple sequence alignment - TraesCS4B01G280700

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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	TraesCS4B01G280700	chr4B	100.000	3849	0	0	1	3849	563630115	563626267	0.000000e+00	7108.0
1	TraesCS4B01G280700	chr4D	94.505	3312	133	16	2	3304	450333742	450330471	0.000000e+00	5062.0
2	TraesCS4B01G280700	chr4D	95.021	241	9	2	3354	3592	450330471	450330232	3.630000e-100	375.0
3	TraesCS4B01G280700	chr4D	77.990	418	56	25	1709	2099	93069536	93069944	2.990000e-56	230.0
4	TraesCS4B01G280700	chr4D	96.377	138	4	1	3713	3849	450329902	450329765	3.870000e-55	226.0
5	TraesCS4B01G280700	chr4D	89.655	58	0	1	3612	3669	450329957	450329906	6.900000e-08	69.4
6	TraesCS4B01G280700	chr4A	95.321	3035	98	17	338	3350	16246031	16249043	0.000000e+00	4778.0
7	TraesCS4B01G280700	chr4A	96.218	238	9	0	3612	3849	16249375	16249612	1.300000e-104	390.0
8	TraesCS4B01G280700	chr4A	90.301	299	24	2	31	325	16245651	16245948	1.680000e-103	387.0
9	TraesCS4B01G280700	chr4A	77.083	432	61	27	1696	2099	489434634	489434213	8.380000e-52	215.0
10	TraesCS4B01G280700	chr7B	90.155	711	33	10	101	798	703006376	703005690	0.000000e+00	891.0
11	TraesCS4B01G280700	chr7B	92.391	92	6	1	374	464	37373163	37373072	3.120000e-26	130.0
12	TraesCS4B01G280700	chr7B	86.408	103	14	0	3261	3363	61566630	61566732	3.140000e-21	113.0
13	TraesCS4B01G280700	chr1B	89.494	514	21	10	54	564	67348756	67349239	1.520000e-173	619.0
14	TraesCS4B01G280700	chrUn	89.916	119	6	3	371	483	75656701	75656819	8.620000e-32	148.0
15	TraesCS4B01G280700	chrUn	89.076	119	7	3	371	483	75683560	75683678	4.010000e-30	143.0
16	TraesCS4B01G280700	chrUn	92.857	98	4	1	470	564	38529758	38529661	5.190000e-29	139.0
17	TraesCS4B01G280700	chrUn	92.079	101	5	1	467	564	239264796	239264896	5.190000e-29	139.0
18	TraesCS4B01G280700	chr6B	89.076	119	7	3	371	483	674318504	674318622	4.010000e-30	143.0
19	TraesCS4B01G280700	chr6B	82.143	112	14	5	3253	3362	701427976	701427869	1.470000e-14	91.6
20	TraesCS4B01G280700	chr2B	89.076	119	7	3	371	483	118306617	118306735	4.010000e-30	143.0
21	TraesCS4B01G280700	chr3B	92.857	98	4	1	470	564	34599843	34599746	5.190000e-29	139.0
22	TraesCS4B01G280700	chr3B	86.957	69	9	0	2234	2302	624317596	624317528	1.150000e-10	78.7
23	TraesCS4B01G280700	chr1A	85.321	109	15	1	3255	3363	6706856	6706963	1.130000e-20	111.0
24	TraesCS4B01G280700	chr7A	90.244	82	8	0	2016	2097	8916186	8916267	1.460000e-19	108.0
25	TraesCS4B01G280700	chr7A	80.909	110	20	1	3253	3362	47558450	47558558	6.850000e-13	86.1
26	TraesCS4B01G280700	chr3A	84.685	111	12	4	3254	3362	61311267	61311374	5.260000e-19	106.0
27	TraesCS4B01G280700	chr3A	86.957	69	9	0	2234	2302	612524275	612524207	1.150000e-10	78.7
28	TraesCS4B01G280700	chr7D	90.000	80	8	0	2018	2097	8479815	8479894	1.890000e-18	104.0
29	TraesCS4B01G280700	chr7D	87.692	65	8	0	2231	2295	477932148	477932212	4.120000e-10	76.8
30	TraesCS4B01G280700	chr3D	91.549	71	5	1	3254	3324	28747637	28747706	3.170000e-16	97.1
31	TraesCS4B01G280700	chr3D	88.406	69	8	0	2234	2302	470487153	470487085	2.460000e-12	84.2
32	TraesCS4B01G280700	chr1D	91.429	70	5	1	3255	3324	406839822	406839754	1.140000e-15	95.3
33	TraesCS4B01G280700	chr1D	83.696	92	15	0	3255	3346	364767601	364767510	1.900000e-13	87.9
34	TraesCS4B01G280700	chr2A	86.364	66	9	0	2231	2296	138533219	138533284	5.330000e-09	73.1
35	TraesCS4B01G280700	chr5A	84.058	69	11	0	2234	2302	582919043	582918975	2.480000e-07	67.6
36	TraesCS4B01G280700	chr5A	84.058	69	11	0	2234	2302	616764482	616764414	2.480000e-07	67.6

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	TraesCS4B01G280700	chr4B	563626267	563630115	3848	True	7108.000000	7108	100.000000	1	3849	1	chr4B.!!$R1	3848
1	TraesCS4B01G280700	chr4D	450329765	450333742	3977	True	1433.100000	5062	93.889500	2	3849	4	chr4D.!!$R1	3847
2	TraesCS4B01G280700	chr4A	16245651	16249612	3961	False	1851.666667	4778	93.946667	31	3849	3	chr4A.!!$F1	3818
3	TraesCS4B01G280700	chr7B	703005690	703006376	686	True	891.000000	891	90.155000	101	798	1	chr7B.!!$R2	697

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
866	957	0.731417	CCTTCTGGCAATTCTGAGCG	59.269	55.000	0.0	0.0	0.0	5.03	F
1692	1792	1.227823	CCAGAACAAGGTGACGGCA	60.228	57.895	0.0	0.0	0.0	5.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1723	1823	0.178915	TGGTGGTAGTGCCTGTACCT	60.179	55.0	6.77	0.0	40.70	3.08	R
3498	3625	0.249398	ACCGCTCCCACACTAATGTC	59.751	55.0	0.00	0.0	36.72	3.06	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
24	25	4.874966	CAGATAGCACCCAAGAAGAAGAAG	59.125	45.833	0.00	0.00	0.00	2.85
25	26	1.902938	AGCACCCAAGAAGAAGAAGC	58.097	50.000	0.00	0.00	0.00	3.86
26	27	1.423161	AGCACCCAAGAAGAAGAAGCT	59.577	47.619	0.00	0.00	0.00	3.74
27	28	1.809547	GCACCCAAGAAGAAGAAGCTC	59.190	52.381	0.00	0.00	0.00	4.09
28	29	2.551938	GCACCCAAGAAGAAGAAGCTCT	60.552	50.000	0.00	0.00	0.00	4.09
29	30	3.749226	CACCCAAGAAGAAGAAGCTCTT	58.251	45.455	0.00	0.00	39.87	2.85
87	92	8.007742	AGAGGTATGTGTAGAGGTTCATCTTAT	58.992	37.037	0.00	0.00	0.00	1.73
166	171	4.643334	AGGTTTCTGTTAGGTGTTTTGGTC	59.357	41.667	0.00	0.00	0.00	4.02
170	175	6.488769	TTCTGTTAGGTGTTTTGGTCTCTA	57.511	37.500	0.00	0.00	0.00	2.43
187	192	6.386927	TGGTCTCTATATGGATTCTTGGTGTT	59.613	38.462	0.00	0.00	0.00	3.32
228	233	4.431416	TGAGCTTTCTGTTCCTGGTTAA	57.569	40.909	0.00	0.00	0.00	2.01
244	249	3.117813	TGGTTAACTACTTGTGGTTGGCT	60.118	43.478	11.80	0.00	0.00	4.75
387	462	3.425162	AGTTTCTCCCAAGTCATGTCC	57.575	47.619	0.00	0.00	0.00	4.02
474	557	3.049708	CTGGTTTCATCAGCTGAGTGA	57.950	47.619	22.96	20.49	34.68	3.41
537	620	4.949856	AGAAGATTGAGGTGTTGTGTGTTT	59.050	37.500	0.00	0.00	0.00	2.83
562	645	5.409826	GGGAAGTACAGTGATCTGAAGTTTG	59.590	44.000	0.00	0.00	43.76	2.93
652	735	4.670221	CGCTTGCAGTAGAATTCTTTCACC	60.670	45.833	14.36	0.00	34.08	4.02
714	805	6.939622	TGCCTAGTCCACTCATATCATAATG	58.060	40.000	0.00	0.00	0.00	1.90
810	901	6.663093	TCCTTTGCTCCAAATCTTGCTATTTA	59.337	34.615	0.00	0.00	32.70	1.40
866	957	0.731417	CCTTCTGGCAATTCTGAGCG	59.269	55.000	0.00	0.00	0.00	5.03
879	970	1.480954	TCTGAGCGGGATTTACTGACC	59.519	52.381	0.00	0.00	0.00	4.02
913	1006	5.802956	CCTCTATTTCTTCAGTTCGACACTC	59.197	44.000	0.00	0.00	30.92	3.51
926	1020	4.857871	TCGACACTCAAGACAAAACTTG	57.142	40.909	0.00	0.00	45.73	3.16
974	1068	6.712998	ACAGTAGTACGCTTCTGATGATAGAT	59.287	38.462	13.40	0.00	41.01	1.98
1121	1218	1.681793	CCAATACCCAGACTCGTCGAT	59.318	52.381	0.00	0.00	34.09	3.59
1317	1417	4.320456	CAGCGCAGTCACCAGGGT	62.320	66.667	11.47	0.00	0.00	4.34
1692	1792	1.227823	CCAGAACAAGGTGACGGCA	60.228	57.895	0.00	0.00	0.00	5.69
1719	1819	1.377725	CATGCTGGACCAGGTGGAC	60.378	63.158	23.09	6.38	38.94	4.02
1758	1858	1.134310	CACCAGCAGATGCAGATGGTA	60.134	52.381	13.33	0.00	42.78	3.25
2182	2286	0.687354	ATGATCGATGCAGGTACCCC	59.313	55.000	8.74	0.05	0.00	4.95
2281	2385	2.280186	GTCCGCCTATGGAAGCCG	60.280	66.667	0.00	0.00	40.44	5.52
2569	2676	4.643387	AGCCTGAACCACCACGGC	62.643	66.667	0.00	0.00	39.03	5.68
2603	2710	4.373116	TCCTGCAGGACGCGTTCC	62.373	66.667	32.00	16.33	46.97	3.62
2853	2966	1.423395	GACTTCGTCACTTGAGCTGG	58.577	55.000	0.00	0.00	32.09	4.85
2949	3062	3.653009	CGCCGCCAGTATGCATGG	61.653	66.667	10.16	4.72	41.04	3.66
3151	3264	4.929808	AGATTGGTGTACTTCATTGACGAC	59.070	41.667	0.00	0.00	0.00	4.34
3244	3360	2.604969	TTTTCGCGTTTGCCATCTAC	57.395	45.000	5.77	0.00	38.08	2.59
3251	3367	2.544267	GCGTTTGCCATCTACATCTACC	59.456	50.000	0.00	0.00	33.98	3.18
3267	3383	0.251354	TACCAGTACTCGCTCCGTCT	59.749	55.000	0.00	0.00	0.00	4.18
3399	3526	5.771153	TTTTCCGGGTTTAAGTCGATTTT	57.229	34.783	0.00	0.00	0.00	1.82
3404	3531	6.171921	TCCGGGTTTAAGTCGATTTTGATAA	58.828	36.000	0.00	0.00	0.00	1.75
3434	3561	3.618855	AAGTAGGGGAGGAGCGGCA	62.619	63.158	1.45	0.00	0.00	5.69
3455	3582	1.050988	AGAGGGGACGGGATGACATG	61.051	60.000	0.00	0.00	0.00	3.21
3523	3650	0.681564	AGTGTGGGAGCGGTAGAGAG	60.682	60.000	0.00	0.00	0.00	3.20
3535	3662	3.254060	CGGTAGAGAGTTGACATGTTGG	58.746	50.000	0.00	0.00	0.00	3.77
3604	3751	2.034048	GCGGAGGAGATGAAGGGACC	62.034	65.000	0.00	0.00	0.00	4.46
3680	4070	0.913924	TCATCAGATTCAGGCAGCCA	59.086	50.000	15.80	0.00	0.00	4.75
3682	4072	1.404391	CATCAGATTCAGGCAGCCAAC	59.596	52.381	15.80	0.00	0.00	3.77
3690	4080	1.065926	TCAGGCAGCCAACACATAGAG	60.066	52.381	15.80	0.00	0.00	2.43
3699	4089	3.877559	CCAACACATAGAGAATGGCTCA	58.122	45.455	0.00	0.00	46.45	4.26
3817	4208	7.719633	AGCAAAAGTTGAACTGAAACCTAGATA	59.280	33.333	0.00	0.00	0.00	1.98
3826	4217	7.334421	TGAACTGAAACCTAGATAACTTGCATC	59.666	37.037	0.00	0.00	0.00	3.91

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	4.096681	TCTTCTTCTTGGGTGCTATCTGA	58.903	43.478	0.00	0.00	0.00	3.27
24	25	1.212229	GCCAAGCAAGAGCAAGAGC	59.788	57.895	0.00	0.00	45.49	4.09
25	26	0.608582	AGGCCAAGCAAGAGCAAGAG	60.609	55.000	5.01	0.00	45.49	2.85
26	27	0.607489	GAGGCCAAGCAAGAGCAAGA	60.607	55.000	5.01	0.00	45.49	3.02
27	28	0.892358	TGAGGCCAAGCAAGAGCAAG	60.892	55.000	5.01	0.00	45.49	4.01
28	29	0.467844	TTGAGGCCAAGCAAGAGCAA	60.468	50.000	5.01	0.00	45.49	3.91
29	30	0.467844	TTTGAGGCCAAGCAAGAGCA	60.468	50.000	5.01	0.00	45.49	4.26
87	92	1.338973	CAAAGAGCAAGGCAAGCTTGA	59.661	47.619	30.39	0.00	43.58	3.02
166	171	7.554118	ACAACAACACCAAGAATCCATATAGAG	59.446	37.037	0.00	0.00	0.00	2.43
170	175	5.185635	CCACAACAACACCAAGAATCCATAT	59.814	40.000	0.00	0.00	0.00	1.78
213	218	6.053005	CACAAGTAGTTAACCAGGAACAGAA	58.947	40.000	0.88	0.00	0.00	3.02
228	233	0.843984	ACCAGCCAACCACAAGTAGT	59.156	50.000	0.00	0.00	0.00	2.73
372	447	2.867109	AACTGGACATGACTTGGGAG	57.133	50.000	0.00	0.00	0.00	4.30
375	450	2.359900	GCCTAACTGGACATGACTTGG	58.640	52.381	0.00	0.00	38.35	3.61
387	462	3.283020	GGGGGAAAAGGCCTAACTG	57.717	57.895	5.16	0.00	0.00	3.16
474	557	4.827692	ACAAAAAGAAACCGAAGCCTTTT	58.172	34.783	0.00	0.00	39.62	2.27
537	620	4.160329	ACTTCAGATCACTGTACTTCCCA	58.840	43.478	0.00	0.00	43.81	4.37
562	645	6.492087	GCATCTATATATCTACCTGGGAGGAC	59.508	46.154	5.98	0.00	37.67	3.85
652	735	9.933723	AAATTCATTCAGAAAATTACAAGAGGG	57.066	29.630	0.00	0.00	40.22	4.30
680	763	5.955959	TGAGTGGACTAGGCAAGAATAACTA	59.044	40.000	0.00	0.00	0.00	2.24
757	848	3.685756	GGTAAAAACATGGTGCGCTAGTA	59.314	43.478	9.73	0.00	0.00	1.82
810	901	9.515226	TTGCTCCTAAATTCAAATTACAGTAGT	57.485	29.630	0.00	0.00	0.00	2.73
854	945	2.945668	AGTAAATCCCGCTCAGAATTGC	59.054	45.455	0.00	0.00	0.00	3.56
866	957	3.062122	TGGAAACGGTCAGTAAATCCC	57.938	47.619	0.00	0.00	32.43	3.85
879	970	6.595716	ACTGAAGAAATAGAGGATTGGAAACG	59.404	38.462	0.00	0.00	0.00	3.60
913	1006	6.202516	TGGTAAGGTTCAAGTTTTGTCTTG	57.797	37.500	0.00	0.00	44.08	3.02
926	1020	1.066136	GTCGACGCTTGGTAAGGTTC	58.934	55.000	0.00	0.00	0.00	3.62
933	1027	0.039437	CTGTACTGTCGACGCTTGGT	60.039	55.000	11.62	7.06	0.00	3.67
959	1053	5.629849	GCAAATGCAATCTATCATCAGAAGC	59.370	40.000	0.00	0.00	41.59	3.86
1059	1156	2.046411	AATGACATGTCGCCGGCA	60.046	55.556	28.98	11.20	0.00	5.69
1061	1158	1.449423	TGGAATGACATGTCGCCGG	60.449	57.895	20.54	0.00	0.00	6.13
1719	1819	1.673808	GGTAGTGCCTGTACCTCCGG	61.674	65.000	0.00	0.00	37.54	5.14
1723	1823	0.178915	TGGTGGTAGTGCCTGTACCT	60.179	55.000	6.77	0.00	40.70	3.08
1935	2035	3.135457	TCGATGTACCGCAGCCGA	61.135	61.111	0.00	0.00	36.29	5.54
2182	2286	3.257393	CATCACCTTCTCCGAGTCTTTG	58.743	50.000	0.00	0.00	0.00	2.77
2228	2332	3.637273	GTTCGACACCTGCCCCCT	61.637	66.667	0.00	0.00	0.00	4.79
2281	2385	3.181461	CCTTGTACATCTCCTCCACCATC	60.181	52.174	0.00	0.00	0.00	3.51
2366	2470	4.379243	CGCCTCGTCCACCTTGCT	62.379	66.667	0.00	0.00	0.00	3.91
2407	2511	1.797933	CGTGCTCTGGAACTCGTCG	60.798	63.158	0.00	0.00	0.00	5.12
2868	2981	2.935849	CGTTATTCAGTGCCATGCTGTA	59.064	45.455	0.00	0.00	35.60	2.74
2939	3052	2.295885	GCTTGCTTCTCCATGCATACT	58.704	47.619	0.00	0.00	39.07	2.12
3151	3264	8.405418	ACAAATCATCAATATCCTGAATCCAG	57.595	34.615	0.00	0.00	40.09	3.86
3238	3354	4.757657	AGCGAGTACTGGTAGATGTAGATG	59.242	45.833	0.00	0.00	0.00	2.90
3239	3355	4.975631	AGCGAGTACTGGTAGATGTAGAT	58.024	43.478	0.00	0.00	0.00	1.98
3240	3356	4.378774	GAGCGAGTACTGGTAGATGTAGA	58.621	47.826	0.00	0.00	0.00	2.59
3241	3357	3.499157	GGAGCGAGTACTGGTAGATGTAG	59.501	52.174	0.00	0.00	0.00	2.74
3242	3358	3.474600	GGAGCGAGTACTGGTAGATGTA	58.525	50.000	0.00	0.00	0.00	2.29
3243	3359	2.299521	GGAGCGAGTACTGGTAGATGT	58.700	52.381	0.00	0.00	0.00	3.06
3244	3360	1.264557	CGGAGCGAGTACTGGTAGATG	59.735	57.143	0.00	0.00	0.00	2.90
3251	3367	1.025113	TCCAGACGGAGCGAGTACTG	61.025	60.000	0.00	0.00	35.91	2.74
3267	3383	7.815840	TTCATTTCTGTGACAAGTAATTCCA	57.184	32.000	0.00	0.00	0.00	3.53
3335	3460	8.375493	ACTCACTCCATCCTAAATTACTTGTA	57.625	34.615	0.00	0.00	0.00	2.41
3350	3475	4.159693	TCAGTTGCGTTATACTCACTCCAT	59.840	41.667	0.00	0.00	0.00	3.41
3351	3476	3.508402	TCAGTTGCGTTATACTCACTCCA	59.492	43.478	0.00	0.00	0.00	3.86
3381	3506	4.957759	ATCAAAATCGACTTAAACCCGG	57.042	40.909	0.00	0.00	0.00	5.73
3399	3526	7.236847	TCCCCTACTTCTTCAGTTCTTTTATCA	59.763	37.037	0.00	0.00	36.88	2.15
3404	3531	4.287326	CCTCCCCTACTTCTTCAGTTCTTT	59.713	45.833	0.00	0.00	36.88	2.52
3434	3561	1.686110	GTCATCCCGTCCCCTCTGT	60.686	63.158	0.00	0.00	0.00	3.41
3497	3624	0.806102	CCGCTCCCACACTAATGTCG	60.806	60.000	0.00	0.00	36.72	4.35
3498	3625	0.249398	ACCGCTCCCACACTAATGTC	59.751	55.000	0.00	0.00	36.72	3.06
3499	3626	1.480954	CTACCGCTCCCACACTAATGT	59.519	52.381	0.00	0.00	40.80	2.71
3500	3627	1.754803	TCTACCGCTCCCACACTAATG	59.245	52.381	0.00	0.00	0.00	1.90
3501	3628	2.032620	CTCTACCGCTCCCACACTAAT	58.967	52.381	0.00	0.00	0.00	1.73
3503	3630	0.622136	TCTCTACCGCTCCCACACTA	59.378	55.000	0.00	0.00	0.00	2.74
3504	3631	0.681564	CTCTCTACCGCTCCCACACT	60.682	60.000	0.00	0.00	0.00	3.55
3505	3632	0.966370	ACTCTCTACCGCTCCCACAC	60.966	60.000	0.00	0.00	0.00	3.82
3506	3633	0.251653	AACTCTCTACCGCTCCCACA	60.252	55.000	0.00	0.00	0.00	4.17
3523	3650	1.586154	CTCCCGCCCAACATGTCAAC	61.586	60.000	0.00	0.00	0.00	3.18
3680	4070	5.121811	GTCATGAGCCATTCTCTATGTGTT	58.878	41.667	0.00	0.00	42.38	3.32
3682	4072	4.700700	TGTCATGAGCCATTCTCTATGTG	58.299	43.478	0.00	0.00	42.38	3.21
3690	4080	3.878778	ACCTTACTGTCATGAGCCATTC	58.121	45.455	0.00	0.00	0.00	2.67
3817	4208	5.237344	GCTAATGACTATTCCGATGCAAGTT	59.763	40.000	0.00	0.00	0.00	2.66
3826	4217	5.196341	TGGTACTGCTAATGACTATTCCG	57.804	43.478	0.00	0.00	0.00	4.30

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.