AutoCloner

Multiple sequence alignment - TraesCS7D01G489400

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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	TraesCS7D01G489400	chr7D	100.000	3875	0	0	1	3875	599187129	599183255	0.000000e+00	7156.0
1	TraesCS7D01G489400	chr7D	94.554	404	22	0	3364	3767	599183698	599183295	3.290000e-175	625.0
2	TraesCS7D01G489400	chr7D	94.554	404	22	0	3432	3835	599183766	599183363	3.290000e-175	625.0
3	TraesCS7D01G489400	chr7D	97.917	336	7	0	3364	3699	599183630	599183295	2.010000e-162	582.0
4	TraesCS7D01G489400	chr7D	97.917	336	7	0	3500	3835	599183766	599183431	2.010000e-162	582.0
5	TraesCS7D01G489400	chr7D	95.149	268	13	0	3364	3631	599183562	599183295	1.290000e-114	424.0
6	TraesCS7D01G489400	chr7D	96.500	200	7	0	3364	3563	599183494	599183295	8.020000e-87	331.0
7	TraesCS7D01G489400	chr7D	76.652	454	77	14	18	447	614483708	614483260	1.400000e-54	224.0
8	TraesCS7D01G489400	chr7D	96.212	132	5	0	3364	3495	599183426	599183295	2.340000e-52	217.0
9	TraesCS7D01G489400	chr7D	80.444	225	37	5	168	387	166482947	166483169	8.610000e-37	165.0
10	TraesCS7D01G489400	chr5D	95.243	3700	125	11	1	3671	445804446	445808123	0.000000e+00	5810.0
11	TraesCS7D01G489400	chr5D	95.970	397	16	0	3479	3875	445808392	445808788	0.000000e+00	645.0
12	TraesCS7D01G489400	chr5D	96.919	357	11	0	3411	3767	445808392	445808748	1.990000e-167	599.0
13	TraesCS7D01G489400	chr5D	95.536	336	15	0	3364	3699	445808413	445808748	4.410000e-149	538.0
14	TraesCS7D01G489400	chr5D	97.403	308	8	0	3500	3807	445807816	445808123	3.430000e-145	525.0
15	TraesCS7D01G489400	chr5D	96.886	289	9	0	3547	3835	445808392	445808680	5.820000e-133	484.0
16	TraesCS7D01G489400	chr5D	94.030	268	16	0	3568	3835	445807816	445808083	1.300000e-109	407.0
17	TraesCS7D01G489400	chr7A	93.174	3589	143	32	1	3570	691440760	691437255	0.000000e+00	5177.0
18	TraesCS7D01G489400	chr7A	78.346	254	41	12	165	409	85335165	85335413	6.710000e-33	152.0
19	TraesCS7D01G489400	chr7A	82.313	147	14	6	2311	2457	691438315	691438181	2.450000e-22	117.0
20	TraesCS7D01G489400	chr7A	97.872	47	1	0	2116	2162	691438582	691438536	8.920000e-12	82.4
21	TraesCS7D01G489400	chr7B	93.307	3003	154	14	1	2964	678639568	678636574	0.000000e+00	4388.0
22	TraesCS7D01G489400	chr7B	90.323	558	40	4	3013	3570	678636581	678636038	0.000000e+00	719.0
23	TraesCS7D01G489400	chr7B	95.745	47	2	0	2116	2162	678637326	678637280	4.150000e-10	76.8
24	TraesCS7D01G489400	chr4B	91.159	656	46	6	1265	1909	12867536	12868190	0.000000e+00	880.0
25	TraesCS7D01G489400	chr4B	83.277	592	81	10	8	583	12852074	12852663	2.650000e-146	529.0
26	TraesCS7D01G489400	chr4B	82.939	592	83	10	8	583	12873976	12874565	5.740000e-143	518.0
27	TraesCS7D01G489400	chr4B	86.580	231	15	7	1003	1227	12867318	12867538	1.390000e-59	241.0
28	TraesCS7D01G489400	chr3D	75.691	543	103	15	16	533	598343199	598342661	1.080000e-60	244.0
29	TraesCS7D01G489400	chr3D	77.143	455	74	16	18	447	2938166	2938615	1.800000e-58	237.0
30	TraesCS7D01G489400	chr1A	77.934	426	64	18	12	414	30337073	30337491	5.000000e-59	239.0
31	TraesCS7D01G489400	chr2D	74.330	522	108	18	5	505	646440482	646440998	8.490000e-47	198.0
32	TraesCS7D01G489400	chr3A	74.460	509	104	17	8	499	474207063	474206564	3.050000e-46	196.0
33	TraesCS7D01G489400	chr6B	75.111	450	77	19	5	424	101557913	101557469	1.110000e-40	178.0
34	TraesCS7D01G489400	chr3B	84.564	149	19	4	18	164	488316038	488315892	1.120000e-30	145.0
35	TraesCS7D01G489400	chr3B	82.692	156	24	3	12	164	820946098	820945943	6.750000e-28	135.0

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	TraesCS7D01G489400	chr7D	599183255	599187129	3874	True	1317.750000	7156	96.600375	1	3875	8	chr7D.!!$R2	3874
1	TraesCS7D01G489400	chr5D	445804446	445808788	4342	False	1286.857143	5810	95.998143	1	3875	7	chr5D.!!$F1	3874
2	TraesCS7D01G489400	chr7A	691437255	691440760	3505	True	1792.133333	5177	91.119667	1	3570	3	chr7A.!!$R1	3569
3	TraesCS7D01G489400	chr7B	678636038	678639568	3530	True	1727.933333	4388	93.125000	1	3570	3	chr7B.!!$R1	3569
4	TraesCS7D01G489400	chr4B	12867318	12868190	872	False	560.500000	880	88.869500	1003	1909	2	chr4B.!!$F3	906
5	TraesCS7D01G489400	chr4B	12852074	12852663	589	False	529.000000	529	83.277000	8	583	1	chr4B.!!$F1	575
6	TraesCS7D01G489400	chr4B	12873976	12874565	589	False	518.000000	518	82.939000	8	583	1	chr4B.!!$F2	575
7	TraesCS7D01G489400	chr3D	598342661	598343199	538	True	244.000000	244	75.691000	16	533	1	chr3D.!!$R1	517

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
269	291	0.028902	GTGTTGTCGCCACCACTTTC	59.971	55.0	0.00	0.00	0.00	2.62	F
325	351	0.690762	GTTGCACAACCCTCCCTCTA	59.309	55.0	1.97	0.00	35.36	2.43	F
2114	2207	0.333652	TCCATACCGGTGGAGTCTGA	59.666	55.0	19.93	0.83	43.20	3.27	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2114	2207	0.037877	AACTGCTGCAGCTTCATCCT	59.962	50.000	36.61	13.26	42.66	3.24	R
2213	2306	1.265365	GAAGAACTGCCACAGCTTCAC	59.735	52.381	8.96	2.97	40.80	3.18	R
3326	3434	5.289675	TGCAACACAAAAGTAAATTTGGACG	59.710	36.000	0.00	0.00	43.10	4.79	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
25	26	4.756642	TCGATGATGAAGCTTTTCAACAGT	59.243	37.500	14.66	1.79	37.20	3.55
243	265	1.907739	CATCACCACCATCGAGGGT	59.092	57.895	17.65	17.65	43.89	4.34
269	291	0.028902	GTGTTGTCGCCACCACTTTC	59.971	55.000	0.00	0.00	0.00	2.62
325	351	0.690762	GTTGCACAACCCTCCCTCTA	59.309	55.000	1.97	0.00	35.36	2.43
377	404	2.561037	GCCAAAGTCAACCACCGGG	61.561	63.158	6.32	0.00	41.29	5.73
510	540	1.525995	CACCACCGCCAAGTTGTCT	60.526	57.895	1.45	0.00	0.00	3.41
550	581	0.768221	ATACTGGGTCGGCCATGGAT	60.768	55.000	18.40	0.00	36.17	3.41
795	828	1.850377	TTTGCATGAAACGTTGCTGG	58.150	45.000	8.00	0.49	39.60	4.85
956	991	6.983906	AAAATGGAAGATTGGTGAAAGAGT	57.016	33.333	0.00	0.00	0.00	3.24
957	992	6.581171	AAATGGAAGATTGGTGAAAGAGTC	57.419	37.500	0.00	0.00	0.00	3.36
958	993	4.982241	TGGAAGATTGGTGAAAGAGTCT	57.018	40.909	0.00	0.00	0.00	3.24
959	994	4.899502	TGGAAGATTGGTGAAAGAGTCTC	58.100	43.478	0.00	0.00	0.00	3.36
1392	1477	1.834378	CCAGCCGCCATCCTCTCTA	60.834	63.158	0.00	0.00	0.00	2.43
1752	1837	1.302431	CAGGGACATGTTGCCGTCA	60.302	57.895	0.00	0.00	41.84	4.35
1842	1935	5.144159	TCTGGGACCTAGTACAGAATGAT	57.856	43.478	4.57	0.00	39.69	2.45
2099	2192	2.306847	GGTGGTCAACAACTTGTCCAT	58.693	47.619	4.57	0.00	44.30	3.41
2114	2207	0.333652	TCCATACCGGTGGAGTCTGA	59.666	55.000	19.93	0.83	43.20	3.27
2206	2299	4.143543	TCAAGTTCAACAGCAATCCATGA	58.856	39.130	0.00	0.00	0.00	3.07
2236	2329	2.057137	AGCTGTGGCAGTTCTTCAAA	57.943	45.000	0.00	0.00	41.70	2.69
2421	2514	1.881973	GGCAATCAACAGAAGCAGACA	59.118	47.619	0.00	0.00	0.00	3.41
2430	2523	3.668447	ACAGAAGCAGACATGTAACAGG	58.332	45.455	0.00	0.00	0.00	4.00
2478	2571	3.818773	CCATAGTGCTGAATGATGATGCA	59.181	43.478	0.00	0.00	0.00	3.96
2479	2572	4.277423	CCATAGTGCTGAATGATGATGCAA	59.723	41.667	0.00	0.00	35.34	4.08
2480	2573	5.452777	CATAGTGCTGAATGATGATGCAAG	58.547	41.667	0.00	0.00	35.34	4.01
2481	2574	2.099263	AGTGCTGAATGATGATGCAAGC	59.901	45.455	0.00	0.00	35.34	4.01
2482	2575	1.064952	TGCTGAATGATGATGCAAGCG	59.935	47.619	0.00	0.00	0.00	4.68
2483	2576	1.065102	GCTGAATGATGATGCAAGCGT	59.935	47.619	0.00	0.00	0.00	5.07
2484	2577	2.716398	CTGAATGATGATGCAAGCGTG	58.284	47.619	0.00	0.00	0.00	5.34
2485	2578	1.402613	TGAATGATGATGCAAGCGTGG	59.597	47.619	0.79	0.00	0.00	4.94
2486	2579	0.742505	AATGATGATGCAAGCGTGGG	59.257	50.000	0.79	0.00	0.00	4.61
2487	2580	1.731433	ATGATGATGCAAGCGTGGGC	61.731	55.000	0.79	0.00	40.37	5.36
2488	2581	2.361483	ATGATGCAAGCGTGGGCA	60.361	55.556	0.79	0.00	45.23	5.36
2489	2582	1.936436	GATGATGCAAGCGTGGGCAA	61.936	55.000	0.79	0.00	44.20	4.52
2496	2601	2.606587	AAGCGTGGGCAAGAGGGAT	61.607	57.895	0.00	0.00	43.41	3.85
2529	2634	4.641645	CTGGTGGAGCGTGGGCAA	62.642	66.667	0.00	0.00	43.41	4.52
2535	2640	3.123620	GAGCGTGGGCAAGCTGAG	61.124	66.667	0.00	0.00	45.76	3.35
2650	2755	4.566278	CCAGTGGATCAACAATCTCTTCCA	60.566	45.833	1.68	0.00	34.56	3.53
2794	2899	0.861837	GACACTGTCTGCAGAAACCG	59.138	55.000	20.19	10.33	45.28	4.44
2814	2919	3.043586	CGTCGTACATATCTTGCAGGAC	58.956	50.000	0.00	0.00	34.54	3.85
2815	2920	3.243101	CGTCGTACATATCTTGCAGGACT	60.243	47.826	0.00	0.00	35.34	3.85
2910	3017	1.406069	GCTCGAATGTGATCCTGGTGT	60.406	52.381	0.00	0.00	0.00	4.16
3326	3434	3.350219	TTTCTACTGATTGTCCCTGCC	57.650	47.619	0.00	0.00	0.00	4.85
3490	3598	8.770438	TTGGTTTGTTAGAAATATGGCATTTC	57.230	30.769	4.78	5.29	38.07	2.17
3613	3721	6.312918	GCGATAGTCAATCTTGGTTTGTTAGA	59.687	38.462	0.00	0.00	39.35	2.10
3623	3731	7.716799	TCTTGGTTTGTTAGAAATATGGCAT	57.283	32.000	4.88	4.88	0.00	4.40
3730	4231	6.775939	ATGACAGTGTTTATGATGCGATAG	57.224	37.500	0.00	0.00	0.00	2.08
3742	4243	4.371786	TGATGCGATAGTCAATCTTGGTC	58.628	43.478	0.00	0.00	39.35	4.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
9	10	3.242936	GGCGTTACTGTTGAAAAGCTTCA	60.243	43.478	0.00	0.00	39.87	3.02
14	15	4.527564	CTGAAGGCGTTACTGTTGAAAAG	58.472	43.478	0.00	0.00	0.00	2.27
178	198	2.370849	GTGAAAACCTAGGTCTGACCCA	59.629	50.000	22.81	9.13	39.75	4.51
243	265	1.821332	TGGCGACAACACATGTGCA	60.821	52.632	25.68	10.64	44.12	4.57
269	291	1.373497	GTAGATGCAGGGATCGCGG	60.373	63.158	6.13	5.53	0.00	6.46
325	351	5.407407	AACTATGGATGAAGACTTGACGT	57.593	39.130	0.00	0.00	0.00	4.34
377	404	5.398603	TTGGAGAGAGTTCATCTTCAGAC	57.601	43.478	0.00	0.00	38.84	3.51
510	540	7.013220	AGTATAGTTGCCCTGATTCAGATCTA	58.987	38.462	15.36	9.52	32.44	1.98
795	828	6.817765	TCCCAGTCATATTTCAAACACTTC	57.182	37.500	0.00	0.00	0.00	3.01
943	978	4.763793	CACCAATGAGACTCTTTCACCAAT	59.236	41.667	3.68	0.00	0.00	3.16
944	979	4.136796	CACCAATGAGACTCTTTCACCAA	58.863	43.478	3.68	0.00	0.00	3.67
945	980	3.390967	TCACCAATGAGACTCTTTCACCA	59.609	43.478	3.68	0.00	0.00	4.17
946	981	4.008074	TCACCAATGAGACTCTTTCACC	57.992	45.455	3.68	0.00	0.00	4.02
947	982	6.566197	ATTTCACCAATGAGACTCTTTCAC	57.434	37.500	3.68	0.00	35.83	3.18
948	983	7.391554	CCTTATTTCACCAATGAGACTCTTTCA	59.608	37.037	3.68	0.00	35.83	2.69
949	984	7.148171	CCCTTATTTCACCAATGAGACTCTTTC	60.148	40.741	3.68	0.00	35.83	2.62
950	985	6.660949	CCCTTATTTCACCAATGAGACTCTTT	59.339	38.462	3.68	0.57	35.83	2.52
951	986	6.012508	TCCCTTATTTCACCAATGAGACTCTT	60.013	38.462	3.68	0.00	35.83	2.85
952	987	5.488919	TCCCTTATTTCACCAATGAGACTCT	59.511	40.000	3.68	0.00	35.83	3.24
953	988	5.745227	TCCCTTATTTCACCAATGAGACTC	58.255	41.667	0.00	0.00	35.83	3.36
954	989	5.488919	TCTCCCTTATTTCACCAATGAGACT	59.511	40.000	0.00	0.00	35.83	3.24
955	990	5.586643	GTCTCCCTTATTTCACCAATGAGAC	59.413	44.000	0.00	0.00	35.58	3.36
956	991	5.626809	CGTCTCCCTTATTTCACCAATGAGA	60.627	44.000	0.00	0.00	35.83	3.27
957	992	4.572389	CGTCTCCCTTATTTCACCAATGAG	59.428	45.833	0.00	0.00	35.83	2.90
958	993	4.019681	ACGTCTCCCTTATTTCACCAATGA	60.020	41.667	0.00	0.00	0.00	2.57
959	994	4.094887	CACGTCTCCCTTATTTCACCAATG	59.905	45.833	0.00	0.00	0.00	2.82
1240	1307	2.941720	GCACTGCCTCTAGGATTCTTTG	59.058	50.000	0.00	0.00	37.39	2.77
1506	1591	2.363795	TGGTAGGAGGCGACCAGG	60.364	66.667	6.55	0.00	40.87	4.45
1842	1935	4.080582	TCCCTCTTTGGCAATTCGAGAATA	60.081	41.667	17.81	5.49	0.00	1.75
2092	2185	0.899720	GACTCCACCGGTATGGACAA	59.100	55.000	6.87	0.00	44.14	3.18
2099	2192	0.629596	ATCCTCAGACTCCACCGGTA	59.370	55.000	6.87	0.00	0.00	4.02
2114	2207	0.037877	AACTGCTGCAGCTTCATCCT	59.962	50.000	36.61	13.26	42.66	3.24
2213	2306	1.265365	GAAGAACTGCCACAGCTTCAC	59.735	52.381	8.96	2.97	40.80	3.18
2236	2329	1.754803	CACCATGGATTGCTGCTGAAT	59.245	47.619	21.47	0.00	0.00	2.57
2421	2514	5.925509	ACACTACACTTGTTCCTGTTACAT	58.074	37.500	0.00	0.00	0.00	2.29
2430	2523	4.056050	CACTGGGTACACTACACTTGTTC	58.944	47.826	0.00	0.00	31.94	3.18
2478	2571	1.271840	TATCCCTCTTGCCCACGCTT	61.272	55.000	0.00	0.00	35.36	4.68
2479	2572	1.689233	TATCCCTCTTGCCCACGCT	60.689	57.895	0.00	0.00	35.36	5.07
2480	2573	1.227674	CTATCCCTCTTGCCCACGC	60.228	63.158	0.00	0.00	0.00	5.34
2481	2574	1.227674	GCTATCCCTCTTGCCCACG	60.228	63.158	0.00	0.00	0.00	4.94
2482	2575	0.475906	ATGCTATCCCTCTTGCCCAC	59.524	55.000	0.00	0.00	0.00	4.61
2483	2576	0.475475	CATGCTATCCCTCTTGCCCA	59.525	55.000	0.00	0.00	0.00	5.36
2484	2577	0.251077	CCATGCTATCCCTCTTGCCC	60.251	60.000	0.00	0.00	0.00	5.36
2485	2578	0.767375	TCCATGCTATCCCTCTTGCC	59.233	55.000	0.00	0.00	0.00	4.52
2486	2579	2.502295	CTTCCATGCTATCCCTCTTGC	58.498	52.381	0.00	0.00	0.00	4.01
2487	2580	2.106166	AGCTTCCATGCTATCCCTCTTG	59.894	50.000	0.00	0.00	42.10	3.02
2488	2581	2.106166	CAGCTTCCATGCTATCCCTCTT	59.894	50.000	0.00	0.00	41.98	2.85
2489	2582	1.698532	CAGCTTCCATGCTATCCCTCT	59.301	52.381	0.00	0.00	41.98	3.69
2496	2601	1.225426	CAGGGCAGCTTCCATGCTA	59.775	57.895	3.64	0.00	41.98	3.49
2522	2627	3.368571	GTGCCTCAGCTTGCCCAC	61.369	66.667	0.00	0.00	40.80	4.61
2529	2634	1.074423	ATGCTTGTGTGCCTCAGCT	59.926	52.632	0.00	0.00	40.80	4.24
2535	2640	0.890542	TCACTCCATGCTTGTGTGCC	60.891	55.000	14.11	0.00	33.82	5.01
2650	2755	8.692710	TCCTATAATGTCACGAGAACTATTTGT	58.307	33.333	0.00	0.00	0.00	2.83
2689	2794	0.668096	TCCAGTCGCGCACGTTTAAT	60.668	50.000	8.75	0.00	41.18	1.40
2794	2899	4.036971	AGAGTCCTGCAAGATATGTACGAC	59.963	45.833	0.00	0.00	34.07	4.34
2889	2996	0.904649	ACCAGGATCACATTCGAGCA	59.095	50.000	0.00	0.00	0.00	4.26
2910	3017	6.763135	GCAAATCTACATCCTGTTACTGATCA	59.237	38.462	0.00	0.00	0.00	2.92
3326	3434	5.289675	TGCAACACAAAAGTAAATTTGGACG	59.710	36.000	0.00	0.00	43.10	4.79
3490	3598	5.490139	ACACTGTCATTCTTCAACAACAG	57.510	39.130	0.00	0.00	39.90	3.16
3613	3721	8.674263	TCTTCAACAACAAAAATGCCATATTT	57.326	26.923	0.00	0.00	0.00	1.40
3623	3731	7.151308	ACACTGTCATTCTTCAACAACAAAAA	58.849	30.769	0.00	0.00	0.00	1.94
3730	4231	8.616076	CCATATTTCTAACAGACCAAGATTGAC	58.384	37.037	0.00	0.00	0.00	3.18
3742	4243	9.206870	ACAACAAAAATGCCATATTTCTAACAG	57.793	29.630	0.00	0.00	0.00	3.16

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.