AutoCloner

Multiple sequence alignment - TraesCS7D01G420000

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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	TraesCS7D01G420000	chr7D	100.000	3206	0	0	1	3206	539485866	539489071	0.000000e+00	5921.0
1	TraesCS7D01G420000	chr7D	92.971	441	21	3	1185	1620	603142787	603142352	4.510000e-178	634.0
2	TraesCS7D01G420000	chr7B	93.537	3203	124	33	1	3147	582278268	582281443	0.000000e+00	4691.0
3	TraesCS7D01G420000	chr7B	95.238	63	2	1	3144	3206	147573553	147573614	7.320000e-17	99.0
4	TraesCS7D01G420000	chr7B	92.754	69	3	2	3138	3206	605109068	605109134	7.320000e-17	99.0
5	TraesCS7D01G420000	chrUn	92.598	3229	120	38	1	3178	82944765	82947925	0.000000e+00	4529.0
6	TraesCS7D01G420000	chr4D	92.584	445	24	3	1185	1620	62468580	62468136	5.840000e-177	630.0
7	TraesCS7D01G420000	chr1A	89.796	441	31	6	1185	1620	558476037	558476468	1.300000e-153	553.0
8	TraesCS7D01G420000	chr1A	95.238	63	2	1	3144	3206	571781752	571781691	7.320000e-17	99.0
9	TraesCS7D01G420000	chr2A	95.509	334	15	0	1185	1518	773369888	773369555	4.710000e-148	534.0
10	TraesCS7D01G420000	chr2A	90.769	130	4	5	1514	1638	773355391	773355265	1.980000e-37	167.0
11	TraesCS7D01G420000	chr2B	87.939	456	24	2	1165	1620	602256438	602256862	2.850000e-140	508.0
12	TraesCS7D01G420000	chr6B	95.238	63	2	1	3144	3206	89204309	89204370	7.320000e-17	99.0
13	TraesCS7D01G420000	chr6B	95.238	63	2	1	3144	3206	711511073	711511012	7.320000e-17	99.0
14	TraesCS7D01G420000	chr4A	95.238	63	2	1	3144	3206	631641394	631641333	7.320000e-17	99.0
15	TraesCS7D01G420000	chr3B	95.238	63	2	1	3144	3206	738127455	738127516	7.320000e-17	99.0
16	TraesCS7D01G420000	chr5D	90.411	73	4	3	3135	3206	256266865	256266795	3.410000e-15	93.5

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	TraesCS7D01G420000	chr7D	539485866	539489071	3205	False	5921	5921	100.000	1	3206	1	chr7D.!!$F1	3205
1	TraesCS7D01G420000	chr7B	582278268	582281443	3175	False	4691	4691	93.537	1	3147	1	chr7B.!!$F2	3146
2	TraesCS7D01G420000	chrUn	82944765	82947925	3160	False	4529	4529	92.598	1	3178	1	chrUn.!!$F1	3177

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
447	463	0.249398	ACAGTAATCTCGCCCGCTTT	59.751	50.0	0.0	0.0	0.0	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2295	2335	0.108585	TGAACCCACTGGAGTGCTTC	59.891	55.0	0.91	5.2	44.34	3.86	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
70	76	5.356426	GGCGCCCATGAAATTAAACTAAAT	58.644	37.500	18.11	0.00	0.00	1.40
158	171	1.396996	CTTTGATAACGCCAGAACCCG	59.603	52.381	0.00	0.00	0.00	5.28
165	178	3.081409	GCCAGAACCCGCCCTCTA	61.081	66.667	0.00	0.00	0.00	2.43
447	463	0.249398	ACAGTAATCTCGCCCGCTTT	59.751	50.000	0.00	0.00	0.00	3.51
459	475	4.193090	TCGCCCGCTTTGATTCTTAAATA	58.807	39.130	0.00	0.00	0.00	1.40
460	476	4.636648	TCGCCCGCTTTGATTCTTAAATAA	59.363	37.500	0.00	0.00	0.00	1.40
584	600	1.552337	ACTCCATTCATCTGCTGACGT	59.448	47.619	0.00	0.00	32.17	4.34
663	681	0.555769	CTCCCTCTGGCTCTACCTCT	59.444	60.000	0.00	0.00	40.22	3.69
664	682	1.777878	CTCCCTCTGGCTCTACCTCTA	59.222	57.143	0.00	0.00	40.22	2.43
665	683	1.777878	TCCCTCTGGCTCTACCTCTAG	59.222	57.143	0.00	0.00	40.22	2.43
666	684	1.616159	CCTCTGGCTCTACCTCTAGC	58.384	60.000	0.00	0.00	40.22	3.42
667	685	1.234821	CTCTGGCTCTACCTCTAGCG	58.765	60.000	0.00	0.00	39.71	4.26
752	770	1.078528	ACCCGGATGACTCACTGGA	59.921	57.895	0.73	0.00	34.76	3.86
985	1022	2.046892	CTTCAGCGAGGGTGGTGG	60.047	66.667	0.00	0.00	37.91	4.61
1060	1097	2.278792	CGATCATGTCGCCGCTGA	60.279	61.111	5.07	0.00	44.33	4.26
1128	1165	1.821258	GGTCGTGGGGATACTGACC	59.179	63.158	0.00	0.00	41.98	4.02
1611	1651	1.670406	CAAGAGCAAGGACGCAGCT	60.670	57.895	0.00	0.00	42.17	4.24
1719	1759	3.740397	CCTACGTCACGGCGGTCA	61.740	66.667	13.24	0.00	35.98	4.02
2343	2394	2.293122	GGCATCGCAGTAATTATTGCCA	59.707	45.455	22.72	13.80	45.75	4.92
2405	2462	4.821589	GAAGCCGCGACTGGAGGG	62.822	72.222	8.23	0.00	35.89	4.30
2423	2480	2.955609	GGGGGATGTTGCTTTCGAA	58.044	52.632	0.00	0.00	0.00	3.71
2509	2566	4.100084	TGCGGATGGGAGCCACAG	62.100	66.667	0.00	0.00	35.80	3.66
2511	2568	2.503061	CGGATGGGAGCCACAGAG	59.497	66.667	0.00	0.00	35.80	3.35
2513	2570	1.222936	GGATGGGAGCCACAGAGTG	59.777	63.158	0.00	0.00	35.80	3.51
2597	2662	0.875059	GAACCACGGAGAAAAGGCTG	59.125	55.000	0.00	0.00	0.00	4.85
2598	2663	0.182775	AACCACGGAGAAAAGGCTGT	59.817	50.000	0.00	0.00	0.00	4.40
2599	2664	0.182775	ACCACGGAGAAAAGGCTGTT	59.817	50.000	0.00	0.00	0.00	3.16
2600	2665	0.875059	CCACGGAGAAAAGGCTGTTC	59.125	55.000	9.51	9.51	0.00	3.18
2689	2756	6.672118	GCCTTTTCTTTTGTACAAGTTGTTGC	60.672	38.462	14.90	8.43	37.14	4.17
2720	2787	1.704641	CCTGGATCTACGGTGGATGA	58.295	55.000	11.99	0.00	0.00	2.92
2721	2788	2.251818	CCTGGATCTACGGTGGATGAT	58.748	52.381	11.99	0.10	0.00	2.45
2722	2789	2.028658	CCTGGATCTACGGTGGATGATG	60.029	54.545	11.99	1.74	0.00	3.07
2769	2836	5.995282	TCGCATCTTGTTTTCTTCTTCCTTA	59.005	36.000	0.00	0.00	0.00	2.69
2772	2839	6.072230	GCATCTTGTTTTCTTCTTCCTTAGCT	60.072	38.462	0.00	0.00	0.00	3.32
2789	2856	3.582714	AGCTGTTTGCCTTTGCTTATC	57.417	42.857	0.00	0.00	44.23	1.75
2812	2880	4.034510	CGCTAGGCTTTTCTAATCCTGTTG	59.965	45.833	0.00	0.00	32.33	3.33
2978	3047	1.760613	CCTAACGGCTAGGGATCACAA	59.239	52.381	0.00	0.00	43.39	3.33
3074	3160	1.024579	CCATCCTGTGTTACCCGTGC	61.025	60.000	0.00	0.00	0.00	5.34
3099	3185	0.109412	GTGCTGGACTTCATTGCTGC	60.109	55.000	0.00	0.00	33.22	5.25
3119	3205	2.508526	CTGCAAAGGGTGTTCTTAGCT	58.491	47.619	0.00	0.00	0.00	3.32
3148	3234	6.156429	GGTAAGAAGAGGTGGGATCTTAAGAA	59.844	42.308	9.71	0.00	37.14	2.52
3151	3237	4.828072	AGAGGTGGGATCTTAAGAACAC	57.172	45.455	20.99	20.99	0.00	3.32
3160	3246	3.396260	TCTTAAGAACACCTCCAACGG	57.604	47.619	1.68	0.00	0.00	4.44
3161	3247	2.038033	TCTTAAGAACACCTCCAACGGG	59.962	50.000	1.68	0.00	0.00	5.28
3163	3249	2.033602	GAACACCTCCAACGGGGG	59.966	66.667	0.00	0.00	37.22	5.40
3164	3250	4.280019	AACACCTCCAACGGGGGC	62.280	66.667	0.00	0.00	37.22	5.80
3186	3272	4.659874	CAAACGGACGCGCGCTTT	62.660	61.111	32.58	19.12	0.00	3.51
3187	3273	4.659874	AAACGGACGCGCGCTTTG	62.660	61.111	32.58	19.69	0.00	2.77
3199	3285	3.250220	CGCTTTGTCCGCTTTTTGT	57.750	47.368	0.00	0.00	0.00	2.83
3200	3286	1.120437	CGCTTTGTCCGCTTTTTGTC	58.880	50.000	0.00	0.00	0.00	3.18
3201	3287	1.487482	GCTTTGTCCGCTTTTTGTCC	58.513	50.000	0.00	0.00	0.00	4.02
3202	3288	1.753956	CTTTGTCCGCTTTTTGTCCG	58.246	50.000	0.00	0.00	0.00	4.79
3203	3289	1.064952	CTTTGTCCGCTTTTTGTCCGT	59.935	47.619	0.00	0.00	0.00	4.69
3204	3290	1.096416	TTGTCCGCTTTTTGTCCGTT	58.904	45.000	0.00	0.00	0.00	4.44
3205	3291	1.096416	TGTCCGCTTTTTGTCCGTTT	58.904	45.000	0.00	0.00	0.00	3.60

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
70	76	8.210265	AGATTTTGAATGTTTGCTAGGGAAAAA	58.790	29.630	0.00	0.00	0.00	1.94
158	171	2.631580	CGCGGGAGAGATAGAGGGC	61.632	68.421	0.00	0.00	0.00	5.19
187	200	2.358247	GTGCAACGATCGTGGGGT	60.358	61.111	23.51	2.27	0.00	4.95
247	260	2.048127	GCCTCGGTCACTGACACC	60.048	66.667	11.34	0.00	33.68	4.16
398	414	4.658451	CGCGATTTAAGAGCGTCTTAATCG	60.658	45.833	23.94	23.94	45.24	3.34
447	463	8.662781	AGCGAGTAATGCTTATTTAAGAATCA	57.337	30.769	1.52	0.00	40.48	2.57
459	475	2.668457	CTGTTTCGAGCGAGTAATGCTT	59.332	45.455	0.00	0.00	44.18	3.91
559	575	3.951680	TCAGCAGATGAATGGAGTACGTA	59.048	43.478	0.00	0.00	34.02	3.57
634	650	3.141488	AGAGGGAGTGGCGCTACG	61.141	66.667	18.69	0.00	40.28	3.51
735	753	1.257750	TGTCCAGTGAGTCATCCGGG	61.258	60.000	0.00	0.00	0.00	5.73
740	758	1.544825	CCGGGTGTCCAGTGAGTCAT	61.545	60.000	0.00	0.00	0.00	3.06
971	996	4.704833	CCACCACCACCCTCGCTG	62.705	72.222	0.00	0.00	0.00	5.18
985	1022	4.054825	CATTGCCGCCACCACCAC	62.055	66.667	0.00	0.00	0.00	4.16
1128	1165	0.534412	AGGTGATGGAGAAGACGCTG	59.466	55.000	0.00	0.00	0.00	5.18
1719	1759	2.765807	CCCACCTCCAGATCGGCT	60.766	66.667	0.00	0.00	33.14	5.52
2295	2335	0.108585	TGAACCCACTGGAGTGCTTC	59.891	55.000	0.91	5.20	44.34	3.86
2405	2462	0.526211	GTTCGAAAGCAACATCCCCC	59.474	55.000	0.00	0.00	0.00	5.40
2597	2662	1.190763	ACAACACGCATACGAACGAAC	59.809	47.619	0.14	0.00	43.93	3.95
2598	2663	1.489574	ACAACACGCATACGAACGAA	58.510	45.000	0.14	0.00	43.93	3.85
2599	2664	2.328655	TACAACACGCATACGAACGA	57.671	45.000	0.14	0.00	43.93	3.85
2600	2665	3.628053	ATTACAACACGCATACGAACG	57.372	42.857	0.00	0.00	43.93	3.95
2720	2787	3.508840	GGCACGCCGCTTTAGCAT	61.509	61.111	2.29	0.00	42.21	3.79
2769	2836	2.095059	CGATAAGCAAAGGCAAACAGCT	60.095	45.455	0.00	0.00	44.61	4.24
2812	2880	3.753797	CCTCCACTAGAAAGCAAAAGACC	59.246	47.826	0.00	0.00	0.00	3.85
2978	3047	9.626045	CAACAGAACAAAAGAAGTTAAGAAAGT	57.374	29.630	0.00	0.00	0.00	2.66
3023	3092	0.743701	TAGCGAGGACCAGACGAGTC	60.744	60.000	9.32	0.00	0.00	3.36
3074	3160	3.495193	CAATGAAGTCCAGCACAATTCG	58.505	45.455	0.00	0.00	0.00	3.34
3099	3185	2.508526	AGCTAAGAACACCCTTTGCAG	58.491	47.619	11.28	0.00	43.77	4.41
3106	3192	2.180432	ACCGAAAGCTAAGAACACCC	57.820	50.000	0.00	0.00	0.00	4.61
3119	3205	2.612000	TCCCACCTCTTCTTACCGAAA	58.388	47.619	0.00	0.00	0.00	3.46
3169	3255	4.659874	AAAGCGCGCGTCCGTTTG	62.660	61.111	32.35	0.04	36.67	2.93
3178	3264	4.683334	AAAGCGGACAAAGCGCGC	62.683	61.111	26.66	26.66	40.04	6.86
3179	3265	1.657181	AAAAAGCGGACAAAGCGCG	60.657	52.632	0.00	0.00	40.04	6.86
3180	3266	0.869880	ACAAAAAGCGGACAAAGCGC	60.870	50.000	0.00	0.00	40.04	5.92
3181	3267	1.120437	GACAAAAAGCGGACAAAGCG	58.880	50.000	0.00	0.00	40.04	4.68
3182	3268	1.487482	GGACAAAAAGCGGACAAAGC	58.513	50.000	0.00	0.00	0.00	3.51
3183	3269	1.064952	ACGGACAAAAAGCGGACAAAG	59.935	47.619	0.00	0.00	0.00	2.77
3184	3270	1.096416	ACGGACAAAAAGCGGACAAA	58.904	45.000	0.00	0.00	0.00	2.83
3185	3271	1.096416	AACGGACAAAAAGCGGACAA	58.904	45.000	0.00	0.00	0.00	3.18
3186	3272	1.096416	AAACGGACAAAAAGCGGACA	58.904	45.000	0.00	0.00	0.00	4.02
3187	3273	3.930400	AAACGGACAAAAAGCGGAC	57.070	47.368	0.00	0.00	0.00	4.79

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.