AutoCloner

Multiple sequence alignment - TraesCS7D01G201600

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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	TraesCS7D01G201600	chr7D	100.000	3329	0	0	1	3329	160627998	160631326	0.000000e+00	6148.0
1	TraesCS7D01G201600	chr7D	85.714	994	97	24	1605	2598	32370777	32371725	0.000000e+00	1007.0
2	TraesCS7D01G201600	chr7B	92.066	2861	142	31	1	2817	121882759	121885578	0.000000e+00	3947.0
3	TraesCS7D01G201600	chr7B	90.335	538	30	14	2801	3329	121885887	121886411	0.000000e+00	686.0
4	TraesCS7D01G201600	chr7A	90.053	2815	149	57	3	2773	161731227	161733954	0.000000e+00	3526.0
5	TraesCS7D01G201600	chr7A	83.681	527	48	25	2073	2598	180639723	180639234	2.340000e-126	462.0
6	TraesCS7D01G201600	chr7A	83.176	529	54	24	2070	2598	63575181	63575674	5.060000e-123	451.0
7	TraesCS7D01G201600	chr7A	84.127	504	29	27	2843	3328	161734247	161734717	1.100000e-119	440.0
8	TraesCS7D01G201600	chr7A	88.889	45	1	4	2911	2951	494132049	494132005	6.000000e-03	52.8
9	TraesCS7D01G201600	chr6B	88.145	1240	114	14	1102	2333	197247799	197246585	0.000000e+00	1445.0
10	TraesCS7D01G201600	chr6B	74.471	1277	264	43	1081	2329	603771651	603772893	2.310000e-136	496.0
11	TraesCS7D01G201600	chr6B	84.532	278	26	11	2324	2598	197246259	197245996	3.290000e-65	259.0
12	TraesCS7D01G201600	chr3A	82.787	1557	158	41	1060	2598	745812801	745811337	0.000000e+00	1290.0
13	TraesCS7D01G201600	chr5A	82.274	1557	164	48	1060	2598	119028973	119027511	0.000000e+00	1243.0
14	TraesCS7D01G201600	chr5A	81.824	1557	163	40	1060	2598	27733249	27734703	0.000000e+00	1197.0
15	TraesCS7D01G201600	chr5A	83.517	1086	100	43	1514	2598	592641135	592642142	0.000000e+00	941.0
16	TraesCS7D01G201600	chr4B	80.735	1552	221	40	1062	2598	423403811	423402323	0.000000e+00	1138.0
17	TraesCS7D01G201600	chr4B	85.345	232	27	7	1084	1310	479398126	479398355	2.000000e-57	233.0
18	TraesCS7D01G201600	chr1B	83.413	1248	147	32	1349	2595	41746952	41748140	0.000000e+00	1103.0
19	TraesCS7D01G201600	chr2B	84.560	978	116	12	1206	2181	773462368	773463312	0.000000e+00	937.0
20	TraesCS7D01G201600	chr5B	83.241	1086	103	43	1514	2598	75684748	75683741	0.000000e+00	924.0
21	TraesCS7D01G201600	chr3B	83.231	978	134	17	1206	2181	543582066	543583015	0.000000e+00	870.0
22	TraesCS7D01G201600	chr3B	82.470	502	43	26	2098	2598	110277182	110276725	6.690000e-107	398.0
23	TraesCS7D01G201600	chr6A	75.196	1278	253	47	1081	2329	549322005	549323247	2.260000e-151	545.0
24	TraesCS7D01G201600	chr2D	84.015	269	24	4	1060	1327	1671713	1671963	1.190000e-59	241.0
25	TraesCS7D01G201600	chr4D	84.483	232	29	7	1084	1310	389494994	389495223	4.320000e-54	222.0
26	TraesCS7D01G201600	chr4A	84.483	232	29	7	1084	1310	71166223	71166452	4.320000e-54	222.0

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	TraesCS7D01G201600	chr7D	160627998	160631326	3328	False	6148.0	6148	100.0000	1	3329	1	chr7D.!!$F2	3328
1	TraesCS7D01G201600	chr7D	32370777	32371725	948	False	1007.0	1007	85.7140	1605	2598	1	chr7D.!!$F1	993
2	TraesCS7D01G201600	chr7B	121882759	121886411	3652	False	2316.5	3947	91.2005	1	3329	2	chr7B.!!$F1	3328
3	TraesCS7D01G201600	chr7A	161731227	161734717	3490	False	1983.0	3526	87.0900	3	3328	2	chr7A.!!$F2	3325
4	TraesCS7D01G201600	chr6B	197245996	197247799	1803	True	852.0	1445	86.3385	1102	2598	2	chr6B.!!$R1	1496
5	TraesCS7D01G201600	chr6B	603771651	603772893	1242	False	496.0	496	74.4710	1081	2329	1	chr6B.!!$F1	1248
6	TraesCS7D01G201600	chr3A	745811337	745812801	1464	True	1290.0	1290	82.7870	1060	2598	1	chr3A.!!$R1	1538
7	TraesCS7D01G201600	chr5A	119027511	119028973	1462	True	1243.0	1243	82.2740	1060	2598	1	chr5A.!!$R1	1538
8	TraesCS7D01G201600	chr5A	27733249	27734703	1454	False	1197.0	1197	81.8240	1060	2598	1	chr5A.!!$F1	1538
9	TraesCS7D01G201600	chr5A	592641135	592642142	1007	False	941.0	941	83.5170	1514	2598	1	chr5A.!!$F2	1084
10	TraesCS7D01G201600	chr4B	423402323	423403811	1488	True	1138.0	1138	80.7350	1062	2598	1	chr4B.!!$R1	1536
11	TraesCS7D01G201600	chr1B	41746952	41748140	1188	False	1103.0	1103	83.4130	1349	2595	1	chr1B.!!$F1	1246
12	TraesCS7D01G201600	chr2B	773462368	773463312	944	False	937.0	937	84.5600	1206	2181	1	chr2B.!!$F1	975
13	TraesCS7D01G201600	chr5B	75683741	75684748	1007	True	924.0	924	83.2410	1514	2598	1	chr5B.!!$R1	1084
14	TraesCS7D01G201600	chr3B	543582066	543583015	949	False	870.0	870	83.2310	1206	2181	1	chr3B.!!$F1	975
15	TraesCS7D01G201600	chr6A	549322005	549323247	1242	False	545.0	545	75.1960	1081	2329	1	chr6A.!!$F1	1248

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
986	1027	0.039074	ACGCCTCTTCTCGTTCACAG	60.039	55.0	0.0	0.0	35.09	3.66	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2895	3722	1.176527	CGACATTTGAGGTGCCCAAT	58.823	50.0	0.0	0.0	0.0	3.16	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
42	43	8.519799	TTATTTCCCCATCTAAAGCTAAACAG	57.480	34.615	0.00	0.00	0.00	3.16
101	104	2.116366	GCTTTGCAGTTTAACACACGG	58.884	47.619	0.00	0.00	0.00	4.94
166	171	2.816083	CCGGCCGTAATCGTGCAA	60.816	61.111	26.12	0.00	35.88	4.08
167	172	2.392181	CCGGCCGTAATCGTGCAAA	61.392	57.895	26.12	0.00	35.88	3.68
168	173	1.498166	CGGCCGTAATCGTGCAAAA	59.502	52.632	19.50	0.00	35.88	2.44
169	174	0.110147	CGGCCGTAATCGTGCAAAAA	60.110	50.000	19.50	0.00	35.88	1.94
202	207	0.667993	TGCAAAACAAGCCGAAGAGG	59.332	50.000	0.00	0.00	44.97	3.69
336	346	3.320826	AGAAACCATTTTGTACAGTGGCC	59.679	43.478	18.51	0.00	35.11	5.36
375	385	4.070552	GGAGGAGCCGAACAGCGT	62.071	66.667	0.00	0.00	38.67	5.07
520	543	1.142748	GTCCAGCGGAGATGTCCAG	59.857	63.158	9.94	3.19	45.74	3.86
773	809	2.100991	CCGCCTACGTACGTCACC	59.899	66.667	26.53	12.66	37.70	4.02
838	874	2.363795	CGCACTACCTCCCCCAGA	60.364	66.667	0.00	0.00	0.00	3.86
845	881	2.220786	TACCTCCCCCAGACCTCGAC	62.221	65.000	0.00	0.00	0.00	4.20
848	884	2.760385	CCCCCAGACCTCGACCTC	60.760	72.222	0.00	0.00	0.00	3.85
894	935	0.935196	GACGCCAACGACTTCAACTT	59.065	50.000	0.00	0.00	43.93	2.66
895	936	0.935196	ACGCCAACGACTTCAACTTC	59.065	50.000	0.00	0.00	43.93	3.01
896	937	0.934496	CGCCAACGACTTCAACTTCA	59.066	50.000	0.00	0.00	43.93	3.02
897	938	1.332904	CGCCAACGACTTCAACTTCAC	60.333	52.381	0.00	0.00	43.93	3.18
898	939	1.940613	GCCAACGACTTCAACTTCACT	59.059	47.619	0.00	0.00	0.00	3.41
901	942	2.135664	ACGACTTCAACTTCACTCCG	57.864	50.000	0.00	0.00	0.00	4.63
912	953	2.206750	CTTCACTCCGTTCCGTTCAAA	58.793	47.619	0.00	0.00	0.00	2.69
913	954	1.574134	TCACTCCGTTCCGTTCAAAC	58.426	50.000	0.00	0.00	0.00	2.93
925	966	2.899044	TTCAAACTTTCCGGCCGCG	61.899	57.895	22.85	13.93	0.00	6.46
942	983	3.712881	GGCAACGTGCGACTGACC	61.713	66.667	0.00	0.00	46.21	4.02
979	1020	2.578178	CTCGCACGCCTCTTCTCG	60.578	66.667	0.00	0.00	0.00	4.04
983	1024	1.372997	GCACGCCTCTTCTCGTTCA	60.373	57.895	0.00	0.00	36.73	3.18
986	1027	0.039074	ACGCCTCTTCTCGTTCACAG	60.039	55.000	0.00	0.00	35.09	3.66
1779	1888	2.024871	GTCATCTCGAGGACGCCG	59.975	66.667	13.56	0.00	39.58	6.46
1977	2092	3.596066	GAGCGAGAAGGCACTGGCA	62.596	63.158	17.07	0.00	42.48	4.92
2473	2946	9.891828	TTTCTTTACACTGTAATTGCATACTTG	57.108	29.630	2.41	0.00	0.00	3.16
2630	3113	3.773418	TTCCACGAGTTGGGAAACATA	57.227	42.857	0.00	0.00	46.92	2.29
2631	3114	3.992943	TCCACGAGTTGGGAAACATAT	57.007	42.857	0.00	0.00	46.92	1.78
2632	3115	5.423704	TTCCACGAGTTGGGAAACATATA	57.576	39.130	0.00	0.00	46.92	0.86
2634	3117	5.424757	TCCACGAGTTGGGAAACATATAAG	58.575	41.667	0.00	0.00	46.92	1.73
2635	3118	5.188163	TCCACGAGTTGGGAAACATATAAGA	59.812	40.000	0.00	0.00	46.92	2.10
2636	3119	6.055588	CCACGAGTTGGGAAACATATAAGAT	58.944	40.000	0.00	0.00	42.54	2.40
2637	3120	6.542370	CCACGAGTTGGGAAACATATAAGATT	59.458	38.462	0.00	0.00	42.54	2.40
2639	3122	8.548721	CACGAGTTGGGAAACATATAAGATTAC	58.451	37.037	0.00	0.00	0.00	1.89
2670	3163	4.439057	TCAAACTGAGCGGTAATCCATAC	58.561	43.478	0.00	0.00	0.00	2.39
2685	3178	2.872388	ATACATCGGCCCAGGCTCG	61.872	63.158	8.89	10.59	41.60	5.03
2701	3194	5.650266	CCAGGCTCGTCTACTATCTATGATT	59.350	44.000	0.00	0.00	0.00	2.57
2773	3276	2.275134	TTGGCACTGAAAGATGCTCA	57.725	45.000	0.00	0.00	39.71	4.26
2778	3281	2.667724	GCACTGAAAGATGCTCAAGTGC	60.668	50.000	9.54	9.54	38.98	4.40
2798	3301	0.039527	GTCCGGAGCGTGCAAAATTT	60.040	50.000	3.06	0.00	0.00	1.82
2830	3657	1.895131	GGCATTTGAAAGCTCAAGGGA	59.105	47.619	0.00	0.00	42.48	4.20
2833	3660	3.424703	CATTTGAAAGCTCAAGGGAGGA	58.575	45.455	0.00	0.00	42.48	3.71
2834	3661	3.593442	TTTGAAAGCTCAAGGGAGGAA	57.407	42.857	0.00	0.00	42.48	3.36
2875	3702	6.910995	TGTTTTTAAGTTTCTTCGACAACCA	58.089	32.000	0.00	0.00	0.00	3.67
2877	3704	7.866393	TGTTTTTAAGTTTCTTCGACAACCAAA	59.134	29.630	0.00	0.00	0.00	3.28
2879	3706	8.989653	TTTTAAGTTTCTTCGACAACCAAATT	57.010	26.923	0.00	0.00	0.00	1.82
2885	3712	9.594478	AGTTTCTTCGACAACCAAATTTTATTT	57.406	25.926	0.00	0.00	0.00	1.40
3041	3877	1.021390	ATTCACGCCGCTCTCCAAAG	61.021	55.000	0.00	0.00	0.00	2.77
3116	3952	1.375908	TTCAGACTGCCGATGTGCC	60.376	57.895	0.00	0.00	0.00	5.01
3129	3965	1.035932	ATGTGCCTGCCTTCATCTGC	61.036	55.000	0.00	0.00	0.00	4.26
3268	4111	4.240096	CAACAGCTCCCTTTGCTTTATTG	58.760	43.478	0.00	0.00	38.92	1.90
3269	4112	3.766545	ACAGCTCCCTTTGCTTTATTGA	58.233	40.909	0.00	0.00	38.92	2.57
3298	4141	1.644786	AAAGGCGCGAATTTCTCCCG	61.645	55.000	12.10	0.00	0.00	5.14

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
8	9	9.467796	CTTTAGATGGGGAAATAAAGACTTCTT	57.532	33.333	0.00	0.00	37.40	2.52
16	17	8.887264	TGTTTAGCTTTAGATGGGGAAATAAA	57.113	30.769	0.00	0.00	0.00	1.40
42	43	5.462398	CAGTCGTAGGCAATACATAAAGGAC	59.538	44.000	0.00	0.00	33.65	3.85
168	173	2.500509	TTGCACGATTTCGGCTTTTT	57.499	40.000	4.84	0.00	44.95	1.94
169	174	2.500509	TTTGCACGATTTCGGCTTTT	57.499	40.000	4.84	0.00	44.95	2.27
170	175	2.124122	GTTTTGCACGATTTCGGCTTT	58.876	42.857	4.84	0.00	44.95	3.51
171	176	1.066303	TGTTTTGCACGATTTCGGCTT	59.934	42.857	4.84	0.00	44.95	4.35
172	177	0.665835	TGTTTTGCACGATTTCGGCT	59.334	45.000	4.84	0.00	44.95	5.52
173	178	1.451651	CTTGTTTTGCACGATTTCGGC	59.548	47.619	4.84	5.81	44.95	5.54
174	179	1.451651	GCTTGTTTTGCACGATTTCGG	59.548	47.619	4.84	0.00	44.95	4.30
175	180	1.451651	GGCTTGTTTTGCACGATTTCG	59.548	47.619	0.00	0.00	46.33	3.46
176	181	1.451651	CGGCTTGTTTTGCACGATTTC	59.548	47.619	0.00	0.00	0.00	2.17
177	182	1.066303	TCGGCTTGTTTTGCACGATTT	59.934	42.857	0.00	0.00	31.84	2.17
284	292	1.534163	GACTTTTTGGACCTGGTACGC	59.466	52.381	4.24	0.00	0.00	4.42
292	302	3.107642	TCTGTCGAGACTTTTTGGACC	57.892	47.619	4.78	0.00	0.00	4.46
362	372	2.387125	TTTGCAACGCTGTTCGGCTC	62.387	55.000	0.00	0.00	43.86	4.70
375	385	2.712539	CACGGACAGCGTTTGCAA	59.287	55.556	0.00	0.00	46.23	4.08
438	448	0.526954	CCCACGGTTAATCGACCTCG	60.527	60.000	16.45	0.00	37.56	4.63
483	494	4.008933	GAGTGGTCCGCACTGGCT	62.009	66.667	4.97	0.00	38.10	4.75
537	560	2.335011	GTGCCAGTTGCCCGAAAC	59.665	61.111	0.00	0.00	40.16	2.78
760	796	1.926511	AAGCGGGGTGACGTACGTAG	61.927	60.000	22.87	9.64	35.98	3.51
838	874	1.928714	GAGGGAGGAGAGGTCGAGGT	61.929	65.000	0.00	0.00	0.00	3.85
845	881	1.758906	GGAACGGAGGGAGGAGAGG	60.759	68.421	0.00	0.00	0.00	3.69
848	884	0.905337	AGTTGGAACGGAGGGAGGAG	60.905	60.000	0.00	0.00	0.00	3.69
925	966	3.712881	GGTCAGTCGCACGTTGCC	61.713	66.667	4.73	0.00	41.12	4.52
942	983	2.182030	GGAGCTTCCAGTCGGTCG	59.818	66.667	0.00	0.00	36.28	4.79
979	1020	1.168714	GGCAGAACCATCCTGTGAAC	58.831	55.000	0.00	0.00	38.86	3.18
983	1024	3.920817	TGGGCAGAACCATCCTGT	58.079	55.556	0.00	0.00	42.05	4.00
1074	1140	1.984570	CAGCTCCTCCTCGTTCCCA	60.985	63.158	0.00	0.00	0.00	4.37
1249	1315	2.993264	GTTGGGGACGAGGTCGGA	60.993	66.667	4.13	0.00	44.95	4.55
1641	1740	1.770518	CTTAAGGGAGGCCGGGGAT	60.771	63.158	2.18	0.00	0.00	3.85
1977	2092	2.986413	AGGACGCTGTCGAGCACT	60.986	61.111	0.00	0.00	46.62	4.40
2447	2915	9.891828	CAAGTATGCAATTACAGTGTAAAGAAA	57.108	29.630	19.19	6.99	0.00	2.52
2448	2916	8.511321	CCAAGTATGCAATTACAGTGTAAAGAA	58.489	33.333	19.19	10.34	0.00	2.52
2449	2917	7.663905	ACCAAGTATGCAATTACAGTGTAAAGA	59.336	33.333	19.19	4.76	0.00	2.52
2473	2946	6.312399	TCTGTGTTGATCATTTTGTGTACC	57.688	37.500	0.00	0.00	0.00	3.34
2642	3135	5.335661	GGATTACCGCTCAGTTTGATGTTTT	60.336	40.000	0.00	0.00	0.00	2.43
2659	3152	1.349688	TGGGCCGATGTATGGATTACC	59.650	52.381	0.00	0.00	0.00	2.85
2670	3163	4.899239	GACGAGCCTGGGCCGATG	62.899	72.222	22.16	8.39	43.17	3.84
2742	3239	5.843673	TTCAGTGCCAAAACATTTCAGTA	57.156	34.783	0.00	0.00	0.00	2.74
2743	3240	4.734398	TTCAGTGCCAAAACATTTCAGT	57.266	36.364	0.00	0.00	0.00	3.41
2778	3281	2.182614	AATTTTGCACGCTCCGGACG	62.183	55.000	20.16	20.16	0.00	4.79
2798	3301	4.564782	TTCAAATGCCATTTGCCCATTA	57.435	36.364	22.42	4.34	46.96	1.90
2825	3652	3.657727	TGAAGACCTGATTTTCCTCCCTT	59.342	43.478	0.00	0.00	0.00	3.95
2830	3657	6.983906	ACATTTTGAAGACCTGATTTTCCT	57.016	33.333	0.00	0.00	0.00	3.36
2895	3722	1.176527	CGACATTTGAGGTGCCCAAT	58.823	50.000	0.00	0.00	0.00	3.16
2896	3723	1.523154	GCGACATTTGAGGTGCCCAA	61.523	55.000	0.00	0.00	0.00	4.12
3006	3833	8.113675	GCGGCGTGAATTTAAATAAAATGAAAT	58.886	29.630	9.37	0.00	37.85	2.17
3007	3834	7.329717	AGCGGCGTGAATTTAAATAAAATGAAA	59.670	29.630	9.37	0.00	37.85	2.69
3010	3837	6.472163	AGAGCGGCGTGAATTTAAATAAAATG	59.528	34.615	9.37	0.00	37.85	2.32
3020	3851	0.605319	TTGGAGAGCGGCGTGAATTT	60.605	50.000	9.37	0.00	0.00	1.82
3025	3856	2.357517	ACTTTGGAGAGCGGCGTG	60.358	61.111	9.37	0.00	0.00	5.34
3116	3952	1.088340	CCACGAGCAGATGAAGGCAG	61.088	60.000	0.00	0.00	0.00	4.85
3129	3965	1.129326	GTGAAACACGACTCCACGAG	58.871	55.000	0.00	0.00	36.32	4.18
3175	4014	1.873591	ACGTACGTACCTGAAACTCGT	59.126	47.619	21.41	8.09	38.30	4.18
3181	4020	3.181492	TGTGAAACACGTACGTACCTGAA	60.181	43.478	25.17	2.64	45.67	3.02
3182	4021	2.357323	TGTGAAACACGTACGTACCTGA	59.643	45.455	25.17	2.42	45.67	3.86
3183	4022	2.730069	TGTGAAACACGTACGTACCTG	58.270	47.619	22.34	19.38	45.67	4.00
3268	4111	1.349973	GCGCCTTTCGATCTGCTTC	59.650	57.895	0.00	0.00	41.67	3.86
3269	4112	2.456119	CGCGCCTTTCGATCTGCTT	61.456	57.895	0.00	0.00	41.67	3.91
3298	4141	4.539509	TGTGAACGTGTGTGGAATAAAC	57.460	40.909	0.00	0.00	0.00	2.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.