AutoCloner

Multiple sequence alignment - TraesCS3B01G181700

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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	TraesCS3B01G181700	chr3B	100.000	2744	0	0	1	2744	190646614	190649357	0	5068
1	TraesCS3B01G181700	chr1B	93.149	2744	171	8	2	2743	299682105	299679377	0	4010
2	TraesCS3B01G181700	chr1B	92.860	2745	190	6	2	2744	426371895	426369155	0	3978
3	TraesCS3B01G181700	chr2B	93.008	2746	186	4	2	2744	473760364	473763106	0	4002
4	TraesCS3B01G181700	chr7B	92.935	2746	187	5	2	2744	299352317	299349576	0	3989
5	TraesCS3B01G181700	chr7B	92.787	2745	192	4	2	2744	202524074	202521334	0	3967
6	TraesCS3B01G181700	chr5B	92.896	2745	191	4	2	2744	297102969	297100227	0	3986
7	TraesCS3B01G181700	chr5B	92.495	2745	200	6	2	2744	241273093	241275833	0	3923
8	TraesCS3B01G181700	chr1D	92.834	2749	188	8	2	2744	206811905	206814650	0	3976
9	TraesCS3B01G181700	chr6B	92.782	2743	188	7	2	2741	128209331	128206596	0	3960

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	TraesCS3B01G181700	chr3B	190646614	190649357	2743	False	5068	5068	100.000	1	2744	1	chr3B.!!$F1	2743
1	TraesCS3B01G181700	chr1B	299679377	299682105	2728	True	4010	4010	93.149	2	2743	1	chr1B.!!$R1	2741
2	TraesCS3B01G181700	chr1B	426369155	426371895	2740	True	3978	3978	92.860	2	2744	1	chr1B.!!$R2	2742
3	TraesCS3B01G181700	chr2B	473760364	473763106	2742	False	4002	4002	93.008	2	2744	1	chr2B.!!$F1	2742
4	TraesCS3B01G181700	chr7B	299349576	299352317	2741	True	3989	3989	92.935	2	2744	1	chr7B.!!$R2	2742
5	TraesCS3B01G181700	chr7B	202521334	202524074	2740	True	3967	3967	92.787	2	2744	1	chr7B.!!$R1	2742
6	TraesCS3B01G181700	chr5B	297100227	297102969	2742	True	3986	3986	92.896	2	2744	1	chr5B.!!$R1	2742
7	TraesCS3B01G181700	chr5B	241273093	241275833	2740	False	3923	3923	92.495	2	2744	1	chr5B.!!$F1	2742
8	TraesCS3B01G181700	chr1D	206811905	206814650	2745	False	3976	3976	92.834	2	2744	1	chr1D.!!$F1	2742
9	TraesCS3B01G181700	chr6B	128206596	128209331	2735	True	3960	3960	92.782	2	2741	1	chr6B.!!$R1	2739

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
633	635	0.396435	TGCACTGTCCGGTGAAAGAT	59.604	50.0	10.39	0.0	39.34	2.4	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2627	2645	0.107654	GCACATAGCTTCCTCCCGTT	60.108	55.0	0.0	0.0	41.15	4.44	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	70	3.001168	GTGCAATATTTTAACTTGCGCCG	60.001	43.478	4.18	0.00	46.35	6.46
84	85	2.258013	GCCGTACTTTGTGCAGCCA	61.258	57.895	0.00	0.00	0.00	4.75
116	117	0.446616	CGTCGAACTGTCCTCATCGA	59.553	55.000	0.00	0.00	41.53	3.59
193	194	1.891919	GAAGCTTGGGCGTGACACA	60.892	57.895	2.10	0.00	44.37	3.72
268	269	3.239253	ACGGGAGCAACGGTTCCT	61.239	61.111	0.00	0.00	43.44	3.36
301	302	1.955495	GCGGGGGCGATTTTGGATTT	61.955	55.000	0.00	0.00	0.00	2.17
372	374	3.706373	GCAGCCCCTCTTGACGGA	61.706	66.667	0.00	0.00	0.00	4.69
533	535	2.762887	TGAGAGCGGACTGAATGAATCT	59.237	45.455	0.00	0.00	0.00	2.40
601	603	9.082313	ACCTTTGAAGATTTTCACAGTATGAAT	57.918	29.630	10.31	0.00	46.80	2.57
633	635	0.396435	TGCACTGTCCGGTGAAAGAT	59.604	50.000	10.39	0.00	39.34	2.40
645	647	3.068307	CGGTGAAAGATAGAGAACCGGAT	59.932	47.826	9.46	0.00	45.15	4.18
659	661	3.790089	ACCGGATAGGGGATCAAATTC	57.210	47.619	9.46	0.00	46.96	2.17
696	698	7.601886	GGAGACTTGGTTGATGACATATATCTG	59.398	40.741	0.00	0.00	0.00	2.90
781	785	1.993653	CAGAGTCTGGAATGGGCCA	59.006	57.895	9.61	9.61	36.30	5.36
798	802	0.598065	CCAAAGAAGAACTTGGCCGG	59.402	55.000	0.00	0.00	38.98	6.13
808	812	1.374947	CTTGGCCGGGTGAAGAAGA	59.625	57.895	2.18	0.00	0.00	2.87
865	869	8.519492	TTTTGATAAGTTAAGCACAAATGAGC	57.481	30.769	0.00	0.00	0.00	4.26
940	945	1.644509	TGAGGCACTGAAGAAGGCTA	58.355	50.000	0.00	0.00	41.55	3.93
985	990	2.359107	CGGAGCAGGCTCTTTGCA	60.359	61.111	19.67	0.00	43.92	4.08
1001	1006	2.501492	GCAAGAAGCATGAGGCCAT	58.499	52.632	5.01	0.00	46.50	4.40
1011	1016	1.954382	CATGAGGCCATGGTCATTGAG	59.046	52.381	20.74	3.20	44.88	3.02
1015	1020	0.183492	GGCCATGGTCATTGAGGCTA	59.817	55.000	12.68	0.00	44.60	3.93
1046	1051	1.604604	CAGGAGGCCGTGAAGAAAAA	58.395	50.000	0.00	0.00	0.00	1.94
1059	1064	5.049954	CGTGAAGAAAAACGATACCTTGGAA	60.050	40.000	0.00	0.00	42.32	3.53
1060	1065	6.371389	GTGAAGAAAAACGATACCTTGGAAG	58.629	40.000	0.00	0.00	0.00	3.46
1081	1086	4.612401	AGAGGGTCTAGTAGGGAAAGAAC	58.388	47.826	0.00	0.00	0.00	3.01
1089	1094	6.008960	TCTAGTAGGGAAAGAACTCGAACTT	58.991	40.000	0.00	0.00	0.00	2.66
1093	1098	2.218603	GGAAAGAACTCGAACTTGCCA	58.781	47.619	14.87	0.00	40.51	4.92
1117	1122	2.564771	CTCTCCAAGCCGCAAATGATA	58.435	47.619	0.00	0.00	0.00	2.15
1637	1642	2.751166	AAGTTGATGACTGAGGGACG	57.249	50.000	0.00	0.00	39.00	4.79
1678	1684	6.093495	GCACCGCAAGCCTGAATTATATTATA	59.907	38.462	0.00	0.00	0.00	0.98
1794	1800	5.179368	CGGGATACTGGCACTGTTATTATTG	59.821	44.000	0.00	0.00	41.74	1.90
1907	1916	1.426751	AGAAAGTACGGGGGTGTTCA	58.573	50.000	0.00	0.00	0.00	3.18
1933	1942	6.127026	GGACATACCTGAACACTCTTTATCCT	60.127	42.308	0.00	0.00	35.41	3.24
2028	2037	5.128827	TCACTTAGCCATAGGAATTCGAGTT	59.871	40.000	0.00	0.00	0.00	3.01
2068	2077	2.163010	GTGTTCGGAAGACCATACGAGA	59.837	50.000	6.75	0.00	41.84	4.04
2078	2087	2.293955	GACCATACGAGAGGCTCTAACC	59.706	54.545	18.75	4.15	0.00	2.85
2134	2143	4.202090	TGCATTTGTTATGGCATTATGCGA	60.202	37.500	4.78	7.82	46.21	5.10
2483	2497	2.046411	CACTATGTGCGGGTGCCA	60.046	61.111	0.00	0.00	41.78	4.92
2517	2535	1.144969	GCGTCAATGAGGAACAACGA	58.855	50.000	7.17	0.00	33.71	3.85
2570	2588	1.067846	GTGGAGTGACACGTCTATGCA	60.068	52.381	0.00	0.00	0.00	3.96
2624	2642	3.998672	GGCGGAACCTGTCACGGA	61.999	66.667	0.00	0.00	34.51	4.69
2627	2645	2.911484	CGGAACCTGTCACGGACGA	61.911	63.158	0.00	0.00	34.95	4.20
2666	2684	0.317479	GGATCCGAAGTGTATCCGGG	59.683	60.000	0.00	0.00	43.16	5.73
2729	2747	0.529337	CGAGCTGATTCCATGTCGCT	60.529	55.000	0.00	0.00	0.00	4.93

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	5.006358	GCGTATTCGGATTTTGTGTACTCAT	59.994	40.000	0.00	0.00	37.56	2.90
69	70	1.581447	GCCTGGCTGCACAAAGTAC	59.419	57.895	12.43	0.00	0.00	2.73
99	100	1.472878	CCTTCGATGAGGACAGTTCGA	59.527	52.381	0.00	0.00	39.25	3.71
116	117	3.803021	GCATCTGAGCTCATCGAATCCTT	60.803	47.826	18.63	0.00	0.00	3.36
125	126	0.693430	TCCAGGGCATCTGAGCTCAT	60.693	55.000	18.63	0.00	46.18	2.90
193	194	1.247419	CCTGCTGAGACGACACCTCT	61.247	60.000	0.00	0.00	0.00	3.69
234	235	3.161450	TGTATCCGGCCCCAGAGC	61.161	66.667	0.00	0.00	0.00	4.09
268	269	2.100797	CCGCCGTCGACGTTCATA	59.899	61.111	33.49	0.00	38.10	2.15
325	326	4.647564	TCCTGGAGCTTCAAAATTCTCT	57.352	40.909	0.00	0.00	0.00	3.10
330	331	3.629087	CCTGATCCTGGAGCTTCAAAAT	58.371	45.455	13.80	0.00	0.00	1.82
363	364	0.762418	TTGCCTCCTTTCCGTCAAGA	59.238	50.000	0.00	0.00	0.00	3.02
372	374	3.927481	GAGCGGGCTTGCCTCCTTT	62.927	63.158	11.71	0.00	34.65	3.11
392	394	2.397413	CTTGGACAGAGGTTGCCGGT	62.397	60.000	1.90	0.00	0.00	5.28
417	419	1.766059	TCGATAGGCCACCCTGCAT	60.766	57.895	5.01	0.00	42.90	3.96
509	511	0.175302	CATTCAGTCCGCTCTCAGCT	59.825	55.000	0.00	0.00	39.60	4.24
588	590	5.374500	AGGGGCTACCATTCATACTGTGAA	61.374	45.833	0.97	0.00	43.47	3.18
592	594	2.705658	TCAGGGGCTACCATTCATACTG	59.294	50.000	0.97	0.00	43.89	2.74
601	603	1.616327	AGTGCATCAGGGGCTACCA	60.616	57.895	0.00	0.00	43.89	3.25
633	635	2.720254	TGATCCCCTATCCGGTTCTCTA	59.280	50.000	0.00	0.00	33.22	2.43
730	734	1.478510	CACTTCCGCAGTATGAGAGGT	59.521	52.381	0.00	0.00	38.60	3.85
781	785	0.185175	ACCCGGCCAAGTTCTTCTTT	59.815	50.000	2.24	0.00	33.63	2.52
798	802	3.181454	TGTCCTCCAACTTCTTCTTCACC	60.181	47.826	0.00	0.00	0.00	4.02
808	812	1.215423	ACCTTGCTTGTCCTCCAACTT	59.785	47.619	0.00	0.00	0.00	2.66
865	869	6.869913	ACAAATATTTTCATCAGCCACAACTG	59.130	34.615	0.00	0.00	39.12	3.16
873	877	7.549649	CGCACAATACAAATATTTTCATCAGC	58.450	34.615	0.00	0.00	0.00	4.26
915	920	3.822735	CCTTCTTCAGTGCCTCAATTTCA	59.177	43.478	0.00	0.00	0.00	2.69
985	990	0.333993	ACCATGGCCTCATGCTTCTT	59.666	50.000	13.04	0.00	47.00	2.52
993	998	0.256752	CCTCAATGACCATGGCCTCA	59.743	55.000	13.04	9.83	0.00	3.86
1001	1006	2.565391	TCTCGTTTAGCCTCAATGACCA	59.435	45.455	0.00	0.00	0.00	4.02
1011	1016	0.179097	CCTGGAGCTCTCGTTTAGCC	60.179	60.000	14.64	0.00	41.02	3.93
1015	1020	1.893919	GCCTCCTGGAGCTCTCGTTT	61.894	60.000	18.51	0.00	34.57	3.60
1046	1051	2.108970	GACCCTCTTCCAAGGTATCGT	58.891	52.381	0.00	0.00	34.34	3.73
1059	1064	4.295506	AGTTCTTTCCCTACTAGACCCTCT	59.704	45.833	0.00	0.00	0.00	3.69
1060	1065	4.612401	AGTTCTTTCCCTACTAGACCCTC	58.388	47.826	0.00	0.00	0.00	4.30
1081	1086	1.462670	GAGAGCTTTGGCAAGTTCGAG	59.537	52.381	0.00	0.00	43.30	4.04
1213	1218	7.463515	GCTTGTCGCTTAGAGTTTCTTCTATTC	60.464	40.741	0.00	0.00	35.14	1.75
1530	1535	5.168569	CAGACTGACCGCTTAATTACTTCA	58.831	41.667	0.00	0.00	0.00	3.02
1536	1541	6.710597	TCTATACAGACTGACCGCTTAATT	57.289	37.500	10.08	0.00	0.00	1.40
1621	1626	0.895530	GGTCGTCCCTCAGTCATCAA	59.104	55.000	0.00	0.00	0.00	2.57
1637	1642	1.684734	TGCTCCTTACCCTCCGGTC	60.685	63.158	0.00	0.00	43.29	4.79
1678	1684	1.272147	GGCTCCTTTCAGGACACCATT	60.272	52.381	3.20	0.00	40.06	3.16
1794	1800	9.860898	AGAAAAACTTTCATATAACAGGCAATC	57.139	29.630	2.25	0.00	0.00	2.67
1933	1942	4.107311	ACCTCCTTCAAGGACCCAAAAATA	59.893	41.667	0.34	0.00	40.06	1.40
2028	2037	3.253838	AGGGGTTGCGCCTACCAA	61.254	61.111	24.72	2.15	45.12	3.67
2078	2087	2.399611	GTTTTCCGATCAGGCGCG	59.600	61.111	0.00	0.00	40.77	6.86
2282	2295	0.174845	CCTTACGTTCCGCTCCATCA	59.825	55.000	0.00	0.00	0.00	3.07
2304	2317	2.573340	CCGGCTCCCATGTTTTGC	59.427	61.111	0.00	0.00	0.00	3.68
2517	2535	5.479124	AGAACTAAATGACACTTACCGGT	57.521	39.130	13.98	13.98	0.00	5.28
2570	2588	9.772973	TTTTCATAGCATAAACCGTACTCATAT	57.227	29.630	0.00	0.00	0.00	1.78
2624	2642	0.460311	CATAGCTTCCTCCCGTTCGT	59.540	55.000	0.00	0.00	0.00	3.85
2627	2645	0.107654	GCACATAGCTTCCTCCCGTT	60.108	55.000	0.00	0.00	41.15	4.44
2666	2684	3.636153	AGTATTCCCCAAGAAGACAGC	57.364	47.619	3.37	0.00	46.96	4.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.