AutoCloner

Multiple sequence alignment - TraesCS3B01G275000

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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	TraesCS3B01G275000	chr3B	100.000	4972	0	0	644	5615	443803307	443808278	0.000000e+00	9182.0
1	TraesCS3B01G275000	chr3B	100.000	165	0	0	1	165	443802664	443802828	7.070000e-79	305.0
2	TraesCS3B01G275000	chr3B	74.344	686	157	17	3653	4330	82625646	82626320	1.990000e-69	274.0
3	TraesCS3B01G275000	chr3D	96.546	5038	82	29	644	5615	344337883	344342894	0.000000e+00	8255.0
4	TraesCS3B01G275000	chr3D	89.697	165	10	2	1	165	344337563	344337720	2.650000e-48	204.0
5	TraesCS3B01G275000	chr3A	94.149	5059	122	69	644	5615	458683103	458678132	0.000000e+00	7542.0
6	TraesCS3B01G275000	chr3A	74.355	620	149	10	3653	4267	64281568	64282182	7.220000e-64	255.0
7	TraesCS3B01G275000	chr3A	80.488	328	39	13	1386	1713	12525890	12525588	1.570000e-55	228.0
8	TraesCS3B01G275000	chr3A	84.831	178	6	9	2	165	458683425	458683255	5.820000e-35	159.0
9	TraesCS3B01G275000	chr1B	84.217	849	91	25	1217	2050	534298215	534299035	0.000000e+00	785.0
10	TraesCS3B01G275000	chr7A	85.417	528	62	5	1248	1769	33657522	33658040	8.280000e-148	534.0
11	TraesCS3B01G275000	chr7A	91.416	233	19	1	1815	2046	33658041	33658273	9.080000e-83	318.0
12	TraesCS3B01G275000	chr7B	84.888	536	60	12	1241	1769	622301295	622300774	6.450000e-144	521.0
13	TraesCS3B01G275000	chr7B	94.059	202	11	1	1815	2015	622300773	622300572	7.070000e-79	305.0
14	TraesCS3B01G275000	chr5A	78.582	691	139	8	3593	4277	374646543	374645856	1.110000e-121	448.0
15	TraesCS3B01G275000	chr5D	78.520	689	140	8	3593	4277	282152986	282152302	3.990000e-121	446.0
16	TraesCS3B01G275000	chr5B	77.971	690	145	6	3593	4277	320153339	320152652	5.200000e-115	425.0
17	TraesCS3B01G275000	chr4A	81.111	540	62	17	1241	1769	716835122	716834612	4.080000e-106	396.0
18	TraesCS3B01G275000	chr4A	89.431	246	17	3	1815	2051	716834611	716834366	9.140000e-78	302.0
19	TraesCS3B01G275000	chr6B	80.741	540	63	18	1241	1769	244561784	244562293	3.170000e-102	383.0
20	TraesCS3B01G275000	chr6B	92.437	238	17	1	1815	2051	244562294	244562531	6.970000e-89	339.0
21	TraesCS3B01G275000	chr6B	89.623	106	10	1	1815	1919	693888104	693887999	3.530000e-27	134.0
22	TraesCS3B01G275000	chr6B	88.608	79	7	1	1972	2050	693888012	693887936	1.670000e-15	95.3
23	TraesCS3B01G275000	chr4B	92.083	240	17	2	1815	2052	613388609	613388848	2.510000e-88	337.0

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	TraesCS3B01G275000	chr3B	443802664	443808278	5614	False	4743.5	9182	100.0000	1	5615	2	chr3B.!!$F2	5614
1	TraesCS3B01G275000	chr3B	82625646	82626320	674	False	274.0	274	74.3440	3653	4330	1	chr3B.!!$F1	677
2	TraesCS3B01G275000	chr3D	344337563	344342894	5331	False	4229.5	8255	93.1215	1	5615	2	chr3D.!!$F1	5614
3	TraesCS3B01G275000	chr3A	458678132	458683425	5293	True	3850.5	7542	89.4900	2	5615	2	chr3A.!!$R2	5613
4	TraesCS3B01G275000	chr3A	64281568	64282182	614	False	255.0	255	74.3550	3653	4267	1	chr3A.!!$F1	614
5	TraesCS3B01G275000	chr1B	534298215	534299035	820	False	785.0	785	84.2170	1217	2050	1	chr1B.!!$F1	833
6	TraesCS3B01G275000	chr7A	33657522	33658273	751	False	426.0	534	88.4165	1248	2046	2	chr7A.!!$F1	798
7	TraesCS3B01G275000	chr7B	622300572	622301295	723	True	413.0	521	89.4735	1241	2015	2	chr7B.!!$R1	774
8	TraesCS3B01G275000	chr5A	374645856	374646543	687	True	448.0	448	78.5820	3593	4277	1	chr5A.!!$R1	684
9	TraesCS3B01G275000	chr5D	282152302	282152986	684	True	446.0	446	78.5200	3593	4277	1	chr5D.!!$R1	684
10	TraesCS3B01G275000	chr5B	320152652	320153339	687	True	425.0	425	77.9710	3593	4277	1	chr5B.!!$R1	684
11	TraesCS3B01G275000	chr4A	716834366	716835122	756	True	349.0	396	85.2710	1241	2051	2	chr4A.!!$R1	810
12	TraesCS3B01G275000	chr6B	244561784	244562531	747	False	361.0	383	86.5890	1241	2051	2	chr6B.!!$F1	810

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
86	96	1.009675	CCGAACCGTATCCGTACCG	60.010	63.158	0.0	0.00	0.00	4.02	F
938	1002	1.130561	CCGTGCTTAGCTTTGGTTAGC	59.869	52.381	5.6	1.56	41.53	3.09	F
1701	1817	0.173708	AGACGTTGAATCTCTCCGGC	59.826	55.000	0.0	0.00	0.00	6.13	F
3114	3241	0.824109	TTCTGTCTGGTGCTATCCCG	59.176	55.000	0.0	0.00	0.00	5.14	F
3123	3250	0.249238	GTGCTATCCCGACAGAGCTG	60.249	60.000	0.0	0.00	35.89	4.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1181	1265	1.477558	GGGAGCAGAGAGAGAGAGAGG	60.478	61.905	0.00	0.0	0.00	3.69	R
2628	2755	0.538057	CCAAGTTGCTGAGCTTCCCA	60.538	55.000	5.83	0.0	0.00	4.37	R
3123	3250	1.583477	GAGCTTCTTTGCACCAGCC	59.417	57.895	0.00	0.0	41.13	4.85	R
4314	4444	0.034186	TGTGCATCTTCACCCATCCC	60.034	55.000	0.00	0.0	36.17	3.85	R
5068	5211	0.369931	TTTCGATCAACTGATGCGCG	59.630	50.000	0.00	0.0	34.37	6.86	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
69	79	1.208358	GAAACTAAACCACGGCGCC	59.792	57.895	19.07	19.07	0.00	6.53
82	92	4.860261	GCGCCGAACCGTATCCGT	62.860	66.667	0.00	0.00	0.00	4.69
83	93	2.715005	CGCCGAACCGTATCCGTA	59.285	61.111	0.00	0.00	0.00	4.02
84	94	1.655350	CGCCGAACCGTATCCGTAC	60.655	63.158	0.00	0.00	0.00	3.67
85	95	1.299392	GCCGAACCGTATCCGTACC	60.299	63.158	0.00	0.00	0.00	3.34
86	96	1.009675	CCGAACCGTATCCGTACCG	60.010	63.158	0.00	0.00	0.00	4.02
743	765	2.776913	CGACCTCGCTCCTCCTTCC	61.777	68.421	0.00	0.00	0.00	3.46
785	817	1.470098	CCAAAGCAGTCATTTCCTCCG	59.530	52.381	0.00	0.00	0.00	4.63
938	1002	1.130561	CCGTGCTTAGCTTTGGTTAGC	59.869	52.381	5.60	1.56	41.53	3.09
969	1033	1.763634	GCACCGCGGATTACTACTAC	58.236	55.000	35.90	0.00	0.00	2.73
970	1034	1.601412	GCACCGCGGATTACTACTACC	60.601	57.143	35.90	0.00	0.00	3.18
971	1035	1.677576	CACCGCGGATTACTACTACCA	59.322	52.381	35.90	0.00	0.00	3.25
977	1041	4.614946	GCGGATTACTACTACCACGATTT	58.385	43.478	0.00	0.00	0.00	2.17
1085	1149	2.036475	CCTCTCTCCTCTCTCTCTCTCG	59.964	59.091	0.00	0.00	0.00	4.04
1088	1152	1.837439	TCTCCTCTCTCTCTCTCGCTT	59.163	52.381	0.00	0.00	0.00	4.68
1089	1153	2.158957	TCTCCTCTCTCTCTCTCGCTTC	60.159	54.545	0.00	0.00	0.00	3.86
1090	1154	1.837439	TCCTCTCTCTCTCTCGCTTCT	59.163	52.381	0.00	0.00	0.00	2.85
1092	1156	2.614057	CCTCTCTCTCTCTCGCTTCTTC	59.386	54.545	0.00	0.00	0.00	2.87
1093	1157	3.535561	CTCTCTCTCTCTCGCTTCTTCT	58.464	50.000	0.00	0.00	0.00	2.85
1133	1217	2.941025	CCCCCACCACCACCATCT	60.941	66.667	0.00	0.00	0.00	2.90
1134	1218	2.677228	CCCCACCACCACCATCTC	59.323	66.667	0.00	0.00	0.00	2.75
1178	1262	1.133792	CCACTCTCTCCCTCCTCTCTC	60.134	61.905	0.00	0.00	0.00	3.20
1179	1263	1.133792	CACTCTCTCCCTCCTCTCTCC	60.134	61.905	0.00	0.00	0.00	3.71
1180	1264	1.275002	ACTCTCTCCCTCCTCTCTCCT	60.275	57.143	0.00	0.00	0.00	3.69
1181	1265	1.421646	CTCTCTCCCTCCTCTCTCCTC	59.578	61.905	0.00	0.00	0.00	3.71
1243	1327	0.461961	ATGGTCTCAAGGTAGAGCGC	59.538	55.000	0.00	0.00	45.03	5.92
1701	1817	0.173708	AGACGTTGAATCTCTCCGGC	59.826	55.000	0.00	0.00	0.00	6.13
2179	2306	2.759783	CACTTCAGTGGCTCCATCG	58.240	57.895	0.00	0.00	42.10	3.84
2592	2719	2.421952	GCTCAACTGGATATCCTTGGCA	60.422	50.000	22.35	0.84	36.82	4.92
2772	2899	1.401905	GGATCAATTCCACCGCAACTC	59.598	52.381	0.00	0.00	44.74	3.01
3114	3241	0.824109	TTCTGTCTGGTGCTATCCCG	59.176	55.000	0.00	0.00	0.00	5.14
3123	3250	0.249238	GTGCTATCCCGACAGAGCTG	60.249	60.000	0.00	0.00	35.89	4.24
4038	4168	3.575256	ACAACTGCATTCCACACATCATT	59.425	39.130	0.00	0.00	0.00	2.57
4098	4228	1.943730	ATCTGGAGGCGAGGGTCTCT	61.944	60.000	0.00	0.00	44.49	3.10
4314	4444	2.213499	GGCGAGGACCATAATCTTGTG	58.787	52.381	0.00	0.00	0.00	3.33
4350	4480	3.242706	TGCACACAAAGTTGAAGATCACG	60.243	43.478	0.00	0.00	0.00	4.35
4760	4899	4.927782	TCCCACGCAACGCAAGCT	62.928	61.111	0.00	0.00	45.62	3.74
4978	5121	1.541588	GTGGATTCTCTTGGGTGCAAC	59.458	52.381	0.00	0.00	0.00	4.17
5068	5211	2.412770	GCTGGCATTTTGTACAATGTGC	59.587	45.455	25.72	25.72	36.63	4.57
5102	5246	1.735018	TCGAAACATGGTACCATTGCG	59.265	47.619	25.25	21.61	33.90	4.85
5119	5263	1.995991	CGGATGCACGGTAGAAACG	59.004	57.895	0.00	0.00	37.36	3.60
5120	5264	0.457166	CGGATGCACGGTAGAAACGA	60.457	55.000	0.00	0.00	34.93	3.85
5121	5265	1.717194	GGATGCACGGTAGAAACGAA	58.283	50.000	0.00	0.00	34.93	3.85
5127	5271	2.610232	GCACGGTAGAAACGAAACCCTA	60.610	50.000	0.00	0.00	34.93	3.53
5128	5272	2.989166	CACGGTAGAAACGAAACCCTAC	59.011	50.000	0.00	0.00	34.93	3.18
5129	5273	2.029020	ACGGTAGAAACGAAACCCTACC	60.029	50.000	0.00	0.00	44.64	3.18
5131	5275	2.568956	GGTAGAAACGAAACCCTACCCT	59.431	50.000	0.00	0.00	43.17	4.34
5132	5276	2.853235	AGAAACGAAACCCTACCCTG	57.147	50.000	0.00	0.00	0.00	4.45
5133	5277	2.332117	AGAAACGAAACCCTACCCTGA	58.668	47.619	0.00	0.00	0.00	3.86
5134	5278	2.302157	AGAAACGAAACCCTACCCTGAG	59.698	50.000	0.00	0.00	0.00	3.35
5135	5279	0.323957	AACGAAACCCTACCCTGAGC	59.676	55.000	0.00	0.00	0.00	4.26
5136	5280	0.544595	ACGAAACCCTACCCTGAGCT	60.545	55.000	0.00	0.00	0.00	4.09
5137	5281	1.272872	ACGAAACCCTACCCTGAGCTA	60.273	52.381	0.00	0.00	0.00	3.32
5138	5282	1.409427	CGAAACCCTACCCTGAGCTAG	59.591	57.143	0.00	0.00	0.00	3.42
5319	5471	2.766925	ATGGCCTGTGTGTGGGTGT	61.767	57.895	3.32	0.00	0.00	4.16
5546	5715	2.607187	CTCGCCTTATTATACTGCCCG	58.393	52.381	0.00	0.00	0.00	6.13
5579	5754	1.250328	CATGGTGCTGTGTCCAATGT	58.750	50.000	0.00	0.00	37.27	2.71

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
35	45	1.732809	GTTTCTTCCAGCCTTCGCTAC	59.267	52.381	0.00	0.00	46.25	3.58
51	61	1.208358	GGCGCCGTGGTTTAGTTTC	59.792	57.895	12.58	0.00	0.00	2.78
80	90	6.910878	GAGATTTGCTTTTCTCTCCGGTACG	61.911	48.000	0.00	0.00	42.70	3.67
82	92	4.504858	GAGATTTGCTTTTCTCTCCGGTA	58.495	43.478	0.00	0.00	36.32	4.02
83	93	3.339141	GAGATTTGCTTTTCTCTCCGGT	58.661	45.455	0.00	0.00	36.32	5.28
84	94	2.680339	GGAGATTTGCTTTTCTCTCCGG	59.320	50.000	0.00	0.00	43.10	5.14
86	96	2.680339	CCGGAGATTTGCTTTTCTCTCC	59.320	50.000	0.00	7.27	46.81	3.71
87	97	2.096657	GCCGGAGATTTGCTTTTCTCTC	59.903	50.000	5.05	0.00	38.71	3.20
88	98	2.087646	GCCGGAGATTTGCTTTTCTCT	58.912	47.619	5.05	0.00	38.71	3.10
89	99	1.133216	GGCCGGAGATTTGCTTTTCTC	59.867	52.381	5.05	2.84	38.10	2.87
90	100	1.177401	GGCCGGAGATTTGCTTTTCT	58.823	50.000	5.05	0.00	0.00	2.52
91	101	0.887933	TGGCCGGAGATTTGCTTTTC	59.112	50.000	5.05	0.00	0.00	2.29
92	102	0.890683	CTGGCCGGAGATTTGCTTTT	59.109	50.000	5.28	0.00	0.00	2.27
735	757	0.107456	CATCATCGTGGGGAAGGAGG	59.893	60.000	0.00	0.00	0.00	4.30
736	758	1.123077	TCATCATCGTGGGGAAGGAG	58.877	55.000	0.00	0.00	0.00	3.69
737	759	1.417517	CATCATCATCGTGGGGAAGGA	59.582	52.381	0.00	0.00	0.00	3.36
739	761	2.916702	TCATCATCATCGTGGGGAAG	57.083	50.000	0.00	0.00	0.00	3.46
740	762	2.705127	TCATCATCATCATCGTGGGGAA	59.295	45.455	0.00	0.00	0.00	3.97
741	763	2.301009	CTCATCATCATCATCGTGGGGA	59.699	50.000	0.00	0.00	0.00	4.81
743	765	3.324117	GTCTCATCATCATCATCGTGGG	58.676	50.000	0.00	0.00	0.00	4.61
977	1041	4.973055	CCCGTCCGCCAACGAACA	62.973	66.667	7.07	0.00	45.37	3.18
1085	1149	3.712016	AAGAAAGAGGGGAGAAGAAGC	57.288	47.619	0.00	0.00	0.00	3.86
1088	1152	5.608860	AGAAAGAAAGAAAGAGGGGAGAAGA	59.391	40.000	0.00	0.00	0.00	2.87
1089	1153	5.875224	AGAAAGAAAGAAAGAGGGGAGAAG	58.125	41.667	0.00	0.00	0.00	2.85
1090	1154	5.608860	AGAGAAAGAAAGAAAGAGGGGAGAA	59.391	40.000	0.00	0.00	0.00	2.87
1092	1156	5.487433	GAGAGAAAGAAAGAAAGAGGGGAG	58.513	45.833	0.00	0.00	0.00	4.30
1093	1157	4.287326	GGAGAGAAAGAAAGAAAGAGGGGA	59.713	45.833	0.00	0.00	0.00	4.81
1133	1217	2.284405	GGGGGAGGTCCAACTCGA	60.284	66.667	0.00	0.00	38.39	4.04
1134	1218	2.284699	AGGGGGAGGTCCAACTCG	60.285	66.667	0.00	0.00	38.39	4.18
1178	1262	1.492176	AGCAGAGAGAGAGAGAGGAGG	59.508	57.143	0.00	0.00	0.00	4.30
1179	1263	2.486191	GGAGCAGAGAGAGAGAGAGGAG	60.486	59.091	0.00	0.00	0.00	3.69
1180	1264	1.490490	GGAGCAGAGAGAGAGAGAGGA	59.510	57.143	0.00	0.00	0.00	3.71
1181	1265	1.477558	GGGAGCAGAGAGAGAGAGAGG	60.478	61.905	0.00	0.00	0.00	3.69
2179	2306	3.918220	CGCAGCGACGGAATCAGC	61.918	66.667	9.98	0.00	0.00	4.26
2628	2755	0.538057	CCAAGTTGCTGAGCTTCCCA	60.538	55.000	5.83	0.00	0.00	4.37
2772	2899	3.997064	CTTCCCCGACTGCTCTGCG	62.997	68.421	0.00	0.00	0.00	5.18
3114	3241	2.745492	GCACCAGCCAGCTCTGTC	60.745	66.667	2.09	0.00	32.32	3.51
3123	3250	1.583477	GAGCTTCTTTGCACCAGCC	59.417	57.895	0.00	0.00	41.13	4.85
4038	4168	1.468914	CTCGACTTCATGTCTCGGTGA	59.531	52.381	8.76	0.00	43.25	4.02
4098	4228	1.819208	CCTCGCCATGCCGAAATCA	60.819	57.895	0.00	0.00	36.72	2.57
4314	4444	0.034186	TGTGCATCTTCACCCATCCC	60.034	55.000	0.00	0.00	36.17	3.85
4350	4480	1.305930	GCTCCGGGTCAAACACATCC	61.306	60.000	0.00	0.00	0.00	3.51
4760	4899	8.717821	CGTGTACCATCAGAAGAAAATTCTAAA	58.282	33.333	0.00	0.00	36.28	1.85
4970	5113	1.603739	GTGGAGGGAAGTTGCACCC	60.604	63.158	1.76	1.76	45.88	4.61
4978	5121	1.298014	GCAGTGGAGTGGAGGGAAG	59.702	63.158	0.00	0.00	0.00	3.46
5057	5200	1.294659	TGATGCGCGCACATTGTACA	61.295	50.000	39.05	22.45	0.00	2.90
5068	5211	0.369931	TTTCGATCAACTGATGCGCG	59.630	50.000	0.00	0.00	34.37	6.86
5102	5246	1.717194	TTCGTTTCTACCGTGCATCC	58.283	50.000	0.00	0.00	0.00	3.51
5119	5263	2.468915	ACTAGCTCAGGGTAGGGTTTC	58.531	52.381	0.00	0.00	44.93	2.78
5120	5264	2.644060	ACTAGCTCAGGGTAGGGTTT	57.356	50.000	0.00	0.00	44.93	3.27
5121	5265	3.206866	TCATACTAGCTCAGGGTAGGGTT	59.793	47.826	0.00	0.00	44.93	4.11
5127	5271	5.132043	ACTACTTCATACTAGCTCAGGGT	57.868	43.478	0.00	0.00	0.00	4.34
5128	5272	6.300703	ACTACTACTTCATACTAGCTCAGGG	58.699	44.000	0.00	0.00	0.00	4.45
5129	5273	8.905660	TTACTACTACTTCATACTAGCTCAGG	57.094	38.462	0.00	0.00	0.00	3.86
5579	5754	5.493809	ACGATTAGTTTAGCAAGGCCTAAA	58.506	37.500	5.16	0.00	35.53	1.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.