AutoCloner

Multiple sequence alignment - TraesCS3D01G063300

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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	TraesCS3D01G063300	chr3D	100.000	3146	0	0	1	3146	27941594	27938449	0.000000e+00	5810.0
1	TraesCS3D01G063300	chr3D	82.289	2202	311	35	544	2729	27559616	27561754	0.000000e+00	1832.0
2	TraesCS3D01G063300	chr3D	78.074	675	118	22	1516	2181	27913422	27914075	1.760000e-107	399.0
3	TraesCS3D01G063300	chr3D	73.092	1048	225	43	1175	2194	28233660	28234678	1.410000e-83	320.0
4	TraesCS3D01G063300	chr3D	87.500	224	25	2	2916	3139	27561754	27561974	4.030000e-64	255.0
5	TraesCS3D01G063300	chr3A	94.951	2258	84	10	116	2348	37831152	37833404	0.000000e+00	3511.0
6	TraesCS3D01G063300	chr3A	97.211	502	12	2	2346	2845	37817050	37816549	0.000000e+00	848.0
7	TraesCS3D01G063300	chr3A	95.364	302	10	1	2845	3146	37816513	37816216	7.890000e-131	477.0
8	TraesCS3D01G063300	chr3A	73.982	1007	209	38	1175	2156	38198017	38198995	2.980000e-95	359.0
9	TraesCS3D01G063300	chr3A	82.063	223	37	2	685	904	37831603	37831825	1.490000e-43	187.0
10	TraesCS3D01G063300	chr3A	74.939	411	85	10	1830	2239	10926889	10927282	4.170000e-39	172.0
11	TraesCS3D01G063300	chr3A	98.039	51	1	0	1	51	37830892	37830942	4.320000e-14	89.8
12	TraesCS3D01G063300	chr3B	89.922	2570	218	18	252	2815	46789191	46786657	0.000000e+00	3273.0
13	TraesCS3D01G063300	chr3B	82.766	2466	304	68	725	3146	46592989	46590601	0.000000e+00	2087.0
14	TraesCS3D01G063300	chr3B	83.911	2250	286	44	616	2845	46059322	46061515	0.000000e+00	2080.0
15	TraesCS3D01G063300	chr3B	75.178	983	155	48	1317	2266	46038193	46039119	6.370000e-102	381.0
16	TraesCS3D01G063300	chr3B	91.154	260	20	1	2887	3146	46786624	46786368	1.800000e-92	350.0
17	TraesCS3D01G063300	chr3B	87.762	286	29	3	2854	3139	46061566	46061845	2.340000e-86	329.0
18	TraesCS3D01G063300	chr3B	88.889	207	13	6	69	272	46793821	46793622	2.420000e-61	246.0
19	TraesCS3D01G063300	chr3B	89.840	187	11	3	69	255	46790202	46790024	1.890000e-57	233.0
20	TraesCS3D01G063300	chr3B	73.384	789	133	50	2282	3040	46041252	46041993	4.080000e-54	222.0
21	TraesCS3D01G063300	chr3B	81.923	260	34	8	385	634	46593081	46592825	1.140000e-49	207.0
22	TraesCS3D01G063300	chr3B	74.143	642	101	39	2562	3146	46102820	46102187	4.110000e-49	206.0
23	TraesCS3D01G063300	chr3B	79.592	245	43	6	685	924	46788896	46788654	5.400000e-38	169.0
24	TraesCS3D01G063300	chr3B	90.909	66	5	1	2448	2513	47257675	47257739	1.550000e-13	87.9
25	TraesCS3D01G063300	chr3B	96.078	51	2	0	1	51	46794182	46794132	2.010000e-12	84.2
26	TraesCS3D01G063300	chr5B	90.323	186	14	1	69	254	159920527	159920346	1.130000e-59	241.0
27	TraesCS3D01G063300	chr5B	94.118	51	3	0	1	51	159920887	159920837	9.360000e-11	78.7
28	TraesCS3D01G063300	chrUn	76.889	225	50	2	1008	1231	197241947	197241724	3.290000e-25	126.0
29	TraesCS3D01G063300	chr7A	98.039	51	1	0	1	51	197299684	197299734	4.320000e-14	89.8

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	TraesCS3D01G063300	chr3D	27938449	27941594	3145	True	5810.000000	5810	100.000000	1	3146	1	chr3D.!!$R1	3145
1	TraesCS3D01G063300	chr3D	27559616	27561974	2358	False	1043.500000	1832	84.894500	544	3139	2	chr3D.!!$F3	2595
2	TraesCS3D01G063300	chr3D	27913422	27914075	653	False	399.000000	399	78.074000	1516	2181	1	chr3D.!!$F1	665
3	TraesCS3D01G063300	chr3D	28233660	28234678	1018	False	320.000000	320	73.092000	1175	2194	1	chr3D.!!$F2	1019
4	TraesCS3D01G063300	chr3A	37830892	37833404	2512	False	1262.600000	3511	91.684333	1	2348	3	chr3A.!!$F3	2347
5	TraesCS3D01G063300	chr3A	37816216	37817050	834	True	662.500000	848	96.287500	2346	3146	2	chr3A.!!$R1	800
6	TraesCS3D01G063300	chr3A	38198017	38198995	978	False	359.000000	359	73.982000	1175	2156	1	chr3A.!!$F2	981
7	TraesCS3D01G063300	chr3B	46059322	46061845	2523	False	1204.500000	2080	85.836500	616	3139	2	chr3B.!!$F3	2523
8	TraesCS3D01G063300	chr3B	46590601	46593081	2480	True	1147.000000	2087	82.344500	385	3146	2	chr3B.!!$R2	2761
9	TraesCS3D01G063300	chr3B	46786368	46794182	7814	True	725.866667	3273	89.245833	1	3146	6	chr3B.!!$R3	3145
10	TraesCS3D01G063300	chr3B	46038193	46041993	3800	False	301.500000	381	74.281000	1317	3040	2	chr3B.!!$F2	1723
11	TraesCS3D01G063300	chr3B	46102187	46102820	633	True	206.000000	206	74.143000	2562	3146	1	chr3B.!!$R1	584

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
89	429	0.458025	GGAGACGACGGTTAGGCAAG	60.458	60.0	0.00	0.0	0.00	4.01	F
100	440	0.819259	TTAGGCAAGGCGCATGGATC	60.819	55.0	10.83	0.0	45.17	3.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1443	6328	1.485294	TAAAGGGGCTCGAGTGGCAA	61.485	55.000	15.13	0.0	0.0	4.52	R
2362	9421	2.354259	ACCCGACAAACAAACGTAACA	58.646	42.857	0.00	0.0	0.0	2.41	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
51	52	1.284982	CGGCTGGTGTTTCTCGTCAG	61.285	60.000	0.00	0.00	0.00	3.51
52	53	0.951040	GGCTGGTGTTTCTCGTCAGG	60.951	60.000	0.00	0.00	0.00	3.86
68	408	3.679389	GTCAGGTCTCCATTGATTGTGT	58.321	45.455	0.00	0.00	0.00	3.72
71	411	3.192001	CAGGTCTCCATTGATTGTGTTGG	59.808	47.826	0.00	0.00	0.00	3.77
72	412	3.074390	AGGTCTCCATTGATTGTGTTGGA	59.926	43.478	0.00	0.00	36.81	3.53
76	416	3.073678	TCCATTGATTGTGTTGGAGACG	58.926	45.455	0.00	0.00	33.40	4.18
77	417	3.073678	CCATTGATTGTGTTGGAGACGA	58.926	45.455	0.00	0.00	0.00	4.20
78	418	3.120199	CCATTGATTGTGTTGGAGACGAC	60.120	47.826	0.00	0.00	45.61	4.34
85	425	3.413522	GTTGGAGACGACGGTTAGG	57.586	57.895	0.00	0.00	34.37	2.69
86	426	0.735287	GTTGGAGACGACGGTTAGGC	60.735	60.000	0.00	0.00	34.37	3.93
87	427	1.180456	TTGGAGACGACGGTTAGGCA	61.180	55.000	0.00	0.00	0.00	4.75
88	428	1.180456	TGGAGACGACGGTTAGGCAA	61.180	55.000	0.00	0.00	0.00	4.52
89	429	0.458025	GGAGACGACGGTTAGGCAAG	60.458	60.000	0.00	0.00	0.00	4.01
90	430	0.458025	GAGACGACGGTTAGGCAAGG	60.458	60.000	0.00	0.00	0.00	3.61
91	431	2.047560	ACGACGGTTAGGCAAGGC	60.048	61.111	0.00	0.00	0.00	4.35
92	432	3.186047	CGACGGTTAGGCAAGGCG	61.186	66.667	0.00	0.00	0.00	5.52
93	433	3.497031	GACGGTTAGGCAAGGCGC	61.497	66.667	0.00	0.00	41.28	6.53
94	434	4.323477	ACGGTTAGGCAAGGCGCA	62.323	61.111	10.83	0.00	45.17	6.09
95	435	2.824041	CGGTTAGGCAAGGCGCAT	60.824	61.111	10.83	0.00	45.17	4.73
96	436	2.800736	GGTTAGGCAAGGCGCATG	59.199	61.111	10.83	9.14	45.17	4.06
97	437	2.774799	GGTTAGGCAAGGCGCATGG	61.775	63.158	10.83	0.00	45.17	3.66
98	438	1.748879	GTTAGGCAAGGCGCATGGA	60.749	57.895	10.83	0.00	45.17	3.41
99	439	1.103398	GTTAGGCAAGGCGCATGGAT	61.103	55.000	10.83	0.00	45.17	3.41
100	440	0.819259	TTAGGCAAGGCGCATGGATC	60.819	55.000	10.83	0.00	45.17	3.36
101	441	1.699054	TAGGCAAGGCGCATGGATCT	61.699	55.000	10.83	3.68	45.17	2.75
102	442	2.550101	GGCAAGGCGCATGGATCTC	61.550	63.158	10.83	0.00	45.17	2.75
103	443	2.550101	GCAAGGCGCATGGATCTCC	61.550	63.158	10.83	0.00	41.79	3.71
120	460	5.220931	GGATCTCCATTGATTGTGCTGTTAC	60.221	44.000	0.00	0.00	35.64	2.50
167	507	5.412594	GTGCAAATCTTCAGGTCTTATGTCA	59.587	40.000	0.00	0.00	0.00	3.58
171	511	5.606348	ATCTTCAGGTCTTATGTCACTCC	57.394	43.478	0.00	0.00	0.00	3.85
203	543	5.945784	TGTAAGGGTGTCTACGTATGTACTT	59.054	40.000	0.00	0.00	0.00	2.24
210	550	7.253422	GGTGTCTACGTATGTACTTTGTGTAT	58.747	38.462	0.00	0.00	33.23	2.29
211	551	7.756722	GGTGTCTACGTATGTACTTTGTGTATT	59.243	37.037	0.00	0.00	33.23	1.89
248	590	6.103330	TGAATGAATACGTAGTGCTGCTTAA	58.897	36.000	0.00	0.00	45.73	1.85
307	5103	9.887862	AATTAATCATCATGAGGTAAATCCCTT	57.112	29.630	7.33	0.00	34.03	3.95
369	5168	2.039418	AGCATAATCGAGCCCTGTGTA	58.961	47.619	0.00	0.00	0.00	2.90
380	5180	3.034635	AGCCCTGTGTATTCTAGGTCAG	58.965	50.000	0.00	0.00	0.00	3.51
535	5340	4.560492	TCCACCCCCAAACCCCCT	62.560	66.667	0.00	0.00	0.00	4.79
660	5530	2.507102	CAACTCCACGCGAGCGAT	60.507	61.111	24.72	5.63	43.01	4.58
912	5782	0.838987	TCCACCCCCAAGTACACTCC	60.839	60.000	0.00	0.00	0.00	3.85
1005	5875	1.443872	GGACGACGACGACATGCTT	60.444	57.895	15.32	0.00	42.66	3.91
1121	5991	1.001860	GTTCCTCTGCAGCTTCTCTGT	59.998	52.381	9.47	0.00	44.66	3.41
1235	6105	1.956170	CGGAGCGCTTCAACACACT	60.956	57.895	17.68	0.00	0.00	3.55
1712	6626	8.547894	CGACATAATTGAGTTCGATTTGGATAA	58.452	33.333	0.18	0.00	32.50	1.75
2362	9421	4.164843	TGTGTTTGGGTTCTCTAAGCTT	57.835	40.909	3.48	3.48	33.51	3.74
3042	10217	9.334947	CAACATCTTCAGGATATAGTTTGTGAT	57.665	33.333	0.00	0.00	32.64	3.06
3043	10218	9.911788	AACATCTTCAGGATATAGTTTGTGATT	57.088	29.630	0.00	0.00	32.64	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
14	15	2.073816	CCGACACAACCTAAAATCGCT	58.926	47.619	0.00	0.00	0.00	4.93
51	52	3.420893	TCCAACACAATCAATGGAGACC	58.579	45.455	0.00	0.00	37.05	3.85
68	408	1.180456	TGCCTAACCGTCGTCTCCAA	61.180	55.000	0.00	0.00	0.00	3.53
71	411	0.458025	CCTTGCCTAACCGTCGTCTC	60.458	60.000	0.00	0.00	0.00	3.36
72	412	1.590147	CCTTGCCTAACCGTCGTCT	59.410	57.895	0.00	0.00	0.00	4.18
73	413	2.098831	GCCTTGCCTAACCGTCGTC	61.099	63.158	0.00	0.00	0.00	4.20
74	414	2.047560	GCCTTGCCTAACCGTCGT	60.048	61.111	0.00	0.00	0.00	4.34
75	415	3.186047	CGCCTTGCCTAACCGTCG	61.186	66.667	0.00	0.00	0.00	5.12
76	416	3.497031	GCGCCTTGCCTAACCGTC	61.497	66.667	0.00	0.00	37.76	4.79
77	417	3.622060	ATGCGCCTTGCCTAACCGT	62.622	57.895	4.18	0.00	45.60	4.83
78	418	2.824041	ATGCGCCTTGCCTAACCG	60.824	61.111	4.18	0.00	45.60	4.44
79	419	2.774799	CCATGCGCCTTGCCTAACC	61.775	63.158	4.18	0.00	45.60	2.85
80	420	1.103398	ATCCATGCGCCTTGCCTAAC	61.103	55.000	4.18	0.00	45.60	2.34
81	421	0.819259	GATCCATGCGCCTTGCCTAA	60.819	55.000	4.18	0.00	45.60	2.69
82	422	1.227943	GATCCATGCGCCTTGCCTA	60.228	57.895	4.18	0.00	45.60	3.93
83	423	2.517875	GATCCATGCGCCTTGCCT	60.518	61.111	4.18	0.00	45.60	4.75
84	424	2.517875	AGATCCATGCGCCTTGCC	60.518	61.111	4.18	0.00	45.60	4.52
85	425	2.550101	GGAGATCCATGCGCCTTGC	61.550	63.158	4.18	0.00	39.17	4.01
86	426	1.153107	TGGAGATCCATGCGCCTTG	60.153	57.895	4.18	2.08	42.01	3.61
87	427	3.323622	TGGAGATCCATGCGCCTT	58.676	55.556	4.18	0.00	42.01	4.35
96	436	3.285484	ACAGCACAATCAATGGAGATCC	58.715	45.455	0.00	0.00	0.00	3.36
97	437	4.978083	AACAGCACAATCAATGGAGATC	57.022	40.909	0.00	0.00	0.00	2.75
98	438	5.255687	TGTAACAGCACAATCAATGGAGAT	58.744	37.500	0.00	0.00	0.00	2.75
99	439	4.650734	TGTAACAGCACAATCAATGGAGA	58.349	39.130	0.00	0.00	0.00	3.71
100	440	5.571784	ATGTAACAGCACAATCAATGGAG	57.428	39.130	0.00	0.00	30.84	3.86
101	441	5.981088	AATGTAACAGCACAATCAATGGA	57.019	34.783	0.00	0.00	30.84	3.41
102	442	6.392354	AGAAATGTAACAGCACAATCAATGG	58.608	36.000	0.00	0.00	30.84	3.16
103	443	7.595875	TCAAGAAATGTAACAGCACAATCAATG	59.404	33.333	0.00	0.00	30.84	2.82
104	444	7.660112	TCAAGAAATGTAACAGCACAATCAAT	58.340	30.769	0.00	0.00	30.84	2.57
105	445	7.036996	TCAAGAAATGTAACAGCACAATCAA	57.963	32.000	0.00	0.00	30.84	2.57
106	446	6.631971	TCAAGAAATGTAACAGCACAATCA	57.368	33.333	0.00	0.00	30.84	2.57
107	447	8.430063	CAAATCAAGAAATGTAACAGCACAATC	58.570	33.333	0.00	0.00	30.84	2.67
108	448	7.385752	CCAAATCAAGAAATGTAACAGCACAAT	59.614	33.333	0.00	0.00	30.84	2.71
109	449	6.700960	CCAAATCAAGAAATGTAACAGCACAA	59.299	34.615	0.00	0.00	30.84	3.33
110	450	6.040278	TCCAAATCAAGAAATGTAACAGCACA	59.960	34.615	0.00	0.00	0.00	4.57
111	451	6.446318	TCCAAATCAAGAAATGTAACAGCAC	58.554	36.000	0.00	0.00	0.00	4.40
112	452	6.647334	TCCAAATCAAGAAATGTAACAGCA	57.353	33.333	0.00	0.00	0.00	4.41
113	453	7.276438	GGATTCCAAATCAAGAAATGTAACAGC	59.724	37.037	0.00	0.00	0.00	4.40
114	454	8.526147	AGGATTCCAAATCAAGAAATGTAACAG	58.474	33.333	5.29	0.00	0.00	3.16
120	460	7.360607	GCACAAAGGATTCCAAATCAAGAAATG	60.361	37.037	5.29	0.00	0.00	2.32
171	511	4.149396	CGTAGACACCCTTACAGAAAAACG	59.851	45.833	0.00	0.00	0.00	3.60
222	562	5.118990	AGCAGCACTACGTATTCATTCATT	58.881	37.500	0.00	0.00	0.00	2.57
223	563	4.697514	AGCAGCACTACGTATTCATTCAT	58.302	39.130	0.00	0.00	0.00	2.57
224	564	4.123497	AGCAGCACTACGTATTCATTCA	57.877	40.909	0.00	0.00	0.00	2.57
225	565	6.583912	TTAAGCAGCACTACGTATTCATTC	57.416	37.500	0.00	0.00	0.00	2.67
317	5113	8.990163	TTTTCAGTTTTTACTCCTACCTCATT	57.010	30.769	0.00	0.00	0.00	2.57
326	5122	9.361315	TGCTTTTACTTTTTCAGTTTTTACTCC	57.639	29.630	0.00	0.00	36.88	3.85
369	5168	2.444256	GCCGCCCCTGACCTAGAAT	61.444	63.158	0.00	0.00	0.00	2.40
535	5340	4.373116	GGTCGCTCCGGTGCTCAA	62.373	66.667	24.75	8.73	0.00	3.02
646	5516	2.653448	CTCATCGCTCGCGTGGAG	60.653	66.667	5.77	14.09	46.06	3.86
660	5530	2.023414	CTATTACGGCGCCACCCTCA	62.023	60.000	28.98	5.29	33.26	3.86
999	5869	0.755079	TGAGGATCTCCCGAAGCATG	59.245	55.000	0.00	0.00	40.87	4.06
1005	5875	2.861101	GCGCATGAGGATCTCCCGA	61.861	63.158	0.30	0.00	40.87	5.14
1235	6105	2.034179	CGGAAGCCACGTATCTGATGTA	59.966	50.000	0.00	0.00	0.00	2.29
1443	6328	1.485294	TAAAGGGGCTCGAGTGGCAA	61.485	55.000	15.13	0.00	0.00	4.52
2362	9421	2.354259	ACCCGACAAACAAACGTAACA	58.646	42.857	0.00	0.00	0.00	2.41
2470	9533	3.274288	CAGCAGGGACCTTCAATAAGTC	58.726	50.000	0.00	0.00	0.00	3.01
2475	9538	0.112995	TTGCAGCAGGGACCTTCAAT	59.887	50.000	0.00	0.00	0.00	2.57
2712	9791	3.969287	TGTGAAGACCATTCCTGAGAG	57.031	47.619	0.00	0.00	0.00	3.20
2826	9933	7.250569	CGAAGGCACAAACATAACTTCATAAT	58.749	34.615	0.00	0.00	35.33	1.28
2828	9935	5.391523	GCGAAGGCACAAACATAACTTCATA	60.392	40.000	0.00	0.00	39.62	2.15
2829	9936	4.615912	GCGAAGGCACAAACATAACTTCAT	60.616	41.667	0.00	0.00	39.62	2.57
2830	9937	3.304391	GCGAAGGCACAAACATAACTTCA	60.304	43.478	0.00	0.00	39.62	3.02
2831	9938	3.234386	GCGAAGGCACAAACATAACTTC	58.766	45.455	0.00	0.00	39.62	3.01
2833	9940	2.989422	GCGAAGGCACAAACATAACT	57.011	45.000	0.00	0.00	39.62	2.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.