AutoCloner

Multiple sequence alignment - TraesCS2A01G284800

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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	TraesCS2A01G284800	chr2A	100.000	2192	0	0	1	2192	478763775	478761584	0.000000e+00	4048
1	TraesCS2A01G284800	chr2A	86.010	1208	154	10	973	2177	38309367	38310562	0.000000e+00	1280
2	TraesCS2A01G284800	chr2A	85.096	1201	162	15	968	2167	719541238	719540054	0.000000e+00	1210
3	TraesCS2A01G284800	chr2D	95.921	1618	50	10	587	2192	357702200	357700587	0.000000e+00	2608
4	TraesCS2A01G284800	chr2D	85.468	1218	161	12	964	2177	34988082	34989287	0.000000e+00	1254
5	TraesCS2A01G284800	chr2D	84.578	1219	166	18	966	2177	585477114	585475911	0.000000e+00	1190
6	TraesCS2A01G284800	chr2D	85.119	1176	159	14	964	2134	585517380	585516216	0.000000e+00	1188
7	TraesCS2A01G284800	chr2D	84.163	1206	177	10	964	2166	34994837	34996031	0.000000e+00	1157
8	TraesCS2A01G284800	chr2D	90.359	446	13	8	1	431	357702973	357702543	1.900000e-155	558
9	TraesCS2A01G284800	chr2B	95.272	1565	39	9	651	2192	425353784	425352232	0.000000e+00	2447
10	TraesCS2A01G284800	chr2B	85.808	1219	155	13	964	2177	57664587	57665792	0.000000e+00	1277
11	TraesCS2A01G284800	chr2B	91.727	411	16	7	1	406	425354455	425354058	2.460000e-154	555
12	TraesCS2A01G284800	chr2B	90.909	132	6	3	427	554	425353976	425353847	2.890000e-39	172

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	TraesCS2A01G284800	chr2A	478761584	478763775	2191	True	4048	4048	100.000	1	2192	1	chr2A.!!$R1	2191
1	TraesCS2A01G284800	chr2A	38309367	38310562	1195	False	1280	1280	86.010	973	2177	1	chr2A.!!$F1	1204
2	TraesCS2A01G284800	chr2A	719540054	719541238	1184	True	1210	1210	85.096	968	2167	1	chr2A.!!$R2	1199
3	TraesCS2A01G284800	chr2D	357700587	357702973	2386	True	1583	2608	93.140	1	2192	2	chr2D.!!$R3	2191
4	TraesCS2A01G284800	chr2D	34988082	34989287	1205	False	1254	1254	85.468	964	2177	1	chr2D.!!$F1	1213
5	TraesCS2A01G284800	chr2D	585475911	585477114	1203	True	1190	1190	84.578	966	2177	1	chr2D.!!$R1	1211
6	TraesCS2A01G284800	chr2D	585516216	585517380	1164	True	1188	1188	85.119	964	2134	1	chr2D.!!$R2	1170
7	TraesCS2A01G284800	chr2D	34994837	34996031	1194	False	1157	1157	84.163	964	2166	1	chr2D.!!$F2	1202
8	TraesCS2A01G284800	chr2B	57664587	57665792	1205	False	1277	1277	85.808	964	2177	1	chr2B.!!$F1	1213
9	TraesCS2A01G284800	chr2B	425352232	425354455	2223	True	1058	2447	92.636	1	2192	3	chr2B.!!$R1	2191

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
569	683	0.456142	TTGAGATTCGTCGGCGTCAG	60.456	55.0	10.18	0.0	39.49	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1506	1867	0.818296	CTGGTTACCTGACCCTCTCG	59.182	60.0	2.07	0.0	39.01	4.04	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
241	254	3.853475	CAAGGGTTTGGATTTCAGCATC	58.147	45.455	0.00	0.00	0.00	3.91
242	255	2.094675	AGGGTTTGGATTTCAGCATCG	58.905	47.619	0.00	0.00	0.00	3.84
243	256	1.134946	GGGTTTGGATTTCAGCATCGG	59.865	52.381	0.00	0.00	0.00	4.18
244	257	2.091541	GGTTTGGATTTCAGCATCGGA	58.908	47.619	0.00	0.00	0.00	4.55
245	258	2.689983	GGTTTGGATTTCAGCATCGGAT	59.310	45.455	0.00	0.00	0.00	4.18
246	259	3.131046	GGTTTGGATTTCAGCATCGGATT	59.869	43.478	0.00	0.00	0.00	3.01
250	263	2.483876	GATTTCAGCATCGGATTCGGA	58.516	47.619	0.00	0.00	36.95	4.55
257	270	1.605457	GCATCGGATTCGGATGCTGTA	60.605	52.381	34.25	1.54	41.74	2.74
274	287	3.126858	GCTGTACGCATTCTCATTTGGAA	59.873	43.478	5.07	0.00	38.92	3.53
298	312	8.567285	AATTTTGGAACTACTTCTCATGTAGG	57.433	34.615	0.00	0.00	41.03	3.18
373	392	5.053025	GCAAATCGTTACAAGAAATCATCGC	60.053	40.000	0.00	0.00	0.00	4.58
375	394	4.840401	TCGTTACAAGAAATCATCGCAG	57.160	40.909	0.00	0.00	0.00	5.18
378	397	2.119801	ACAAGAAATCATCGCAGCCT	57.880	45.000	0.00	0.00	0.00	4.58
380	399	1.004185	CAAGAAATCATCGCAGCCTCG	60.004	52.381	0.00	0.00	0.00	4.63
407	484	4.956085	TGGCATCAGCAATTACGTATACT	58.044	39.130	0.00	0.00	44.61	2.12
408	485	5.364778	TGGCATCAGCAATTACGTATACTT	58.635	37.500	0.00	0.00	44.61	2.24
409	486	5.820423	TGGCATCAGCAATTACGTATACTTT	59.180	36.000	0.00	0.00	44.61	2.66
410	487	6.987404	TGGCATCAGCAATTACGTATACTTTA	59.013	34.615	0.00	0.00	44.61	1.85
447	531	4.290711	TCACATCTCTTGGAAGATTGCA	57.709	40.909	0.00	0.00	33.68	4.08
449	533	4.008330	CACATCTCTTGGAAGATTGCAGT	58.992	43.478	0.00	0.00	33.68	4.40
450	534	4.094590	CACATCTCTTGGAAGATTGCAGTC	59.905	45.833	0.00	0.00	33.68	3.51
460	548	5.218139	GGAAGATTGCAGTCTTGTTCAAAG	58.782	41.667	27.02	0.00	38.51	2.77
472	560	2.215196	TGTTCAAAGGACGGTGTTAGC	58.785	47.619	0.00	0.00	0.00	3.09
522	610	6.038603	CCACAATTCGAACCATCACAAGATAT	59.961	38.462	0.00	0.00	31.88	1.63
523	611	7.128331	CACAATTCGAACCATCACAAGATATC	58.872	38.462	0.00	0.00	31.88	1.63
524	612	7.011763	CACAATTCGAACCATCACAAGATATCT	59.988	37.037	0.00	0.00	31.88	1.98
569	683	0.456142	TTGAGATTCGTCGGCGTCAG	60.456	55.000	10.18	0.00	39.49	3.51
619	953	6.320672	AGGATAATCAAGCAAGTTCTGGAATG	59.679	38.462	0.00	0.00	0.00	2.67
629	963	5.279156	GCAAGTTCTGGAATGGTTTTCAGAT	60.279	40.000	0.00	0.00	45.05	2.90
660	994	7.667557	CCATCGAATAGTGGATTTCCTACTTA	58.332	38.462	0.00	0.00	37.72	2.24
731	1070	1.774639	CGCCCAAGCATATGCAATTC	58.225	50.000	28.62	12.52	45.16	2.17
760	1116	0.730155	CGTACCGCGCAAACACTAGA	60.730	55.000	8.75	0.00	0.00	2.43
847	1207	5.174035	GGTCGAGATATCAACAGAATGAACG	59.826	44.000	5.32	0.00	39.69	3.95
875	1235	3.365832	CTGCTATTTTTGCCGCAGTATG	58.634	45.455	0.00	0.00	43.53	2.39
876	1236	3.013219	TGCTATTTTTGCCGCAGTATGA	58.987	40.909	0.00	0.00	39.69	2.15
877	1237	3.631686	TGCTATTTTTGCCGCAGTATGAT	59.368	39.130	0.00	0.00	39.69	2.45
880	1240	6.183360	TGCTATTTTTGCCGCAGTATGATTTA	60.183	34.615	0.00	0.00	39.69	1.40
881	1241	6.142320	GCTATTTTTGCCGCAGTATGATTTAC	59.858	38.462	0.00	0.00	39.69	2.01
882	1242	5.378292	TTTTTGCCGCAGTATGATTTACA	57.622	34.783	0.00	0.00	39.69	2.41
883	1243	4.349663	TTTGCCGCAGTATGATTTACAC	57.650	40.909	0.00	0.00	39.69	2.90
884	1244	1.930503	TGCCGCAGTATGATTTACACG	59.069	47.619	0.00	0.00	39.69	4.49
885	1245	1.931172	GCCGCAGTATGATTTACACGT	59.069	47.619	0.00	0.00	39.69	4.49
915	1275	7.222999	TGTGAAATAAATATGTACACGATGCGA	59.777	33.333	0.00	0.00	0.00	5.10
1097	1458	2.664851	CGAAGCAACCGCACCTGA	60.665	61.111	0.00	0.00	42.27	3.86
1149	1510	2.304180	CTCCCAGACAAACAGGATGACT	59.696	50.000	0.00	0.00	39.69	3.41
1269	1630	0.176680	CGTCCCTCAGGAGGTTGATG	59.823	60.000	14.00	6.94	45.21	3.07
1428	1789	1.315690	TATCGAAGGCCGTCCAGTAG	58.684	55.000	13.43	0.00	39.75	2.57
1506	1867	2.034558	CACAAACATGGACCTTGGTGAC	59.965	50.000	15.89	0.00	0.00	3.67
1560	1921	0.248565	TGAGATCAGCAGCTGTGGAC	59.751	55.000	22.10	12.56	32.61	4.02
1986	2347	1.814394	TGGTAGGTGTACAGCGTACAG	59.186	52.381	23.59	0.00	0.00	2.74
2017	2383	1.299648	CATCCTGAGCCCGGACAAA	59.700	57.895	0.73	0.00	32.41	2.83
2138	2504	7.824779	ACAGATACAGAGATAAAAACCTGGAAC	59.175	37.037	0.00	0.00	0.00	3.62

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
241	254	2.506544	CGTACAGCATCCGAATCCG	58.493	57.895	0.00	0.00	0.00	4.18
257	270	4.931002	CCAAAATTCCAAATGAGAATGCGT	59.069	37.500	0.00	0.00	34.23	5.24
274	287	7.918076	TCCTACATGAGAAGTAGTTCCAAAAT	58.082	34.615	6.68	0.00	37.78	1.82
298	312	3.093717	TCACGAGTCCACTTTGACTTC	57.906	47.619	0.00	0.00	45.41	3.01
378	397	0.608856	ATTGCTGATGCCAACCACGA	60.609	50.000	0.00	0.00	38.71	4.35
380	399	2.731968	CGTAATTGCTGATGCCAACCAC	60.732	50.000	0.00	0.00	38.71	4.16
447	531	2.093128	ACACCGTCCTTTGAACAAGACT	60.093	45.455	0.00	0.00	0.00	3.24
449	533	2.702592	ACACCGTCCTTTGAACAAGA	57.297	45.000	0.00	0.00	0.00	3.02
450	534	3.303791	GCTAACACCGTCCTTTGAACAAG	60.304	47.826	0.00	0.00	0.00	3.16
472	560	7.179410	GGCACATTTGAAAACAAACTTTAGTG	58.821	34.615	0.00	0.00	0.00	2.74
522	610	7.468631	GCTCCACACATTTGAAGAAGTTTAAGA	60.469	37.037	0.00	0.00	0.00	2.10
523	611	6.638468	GCTCCACACATTTGAAGAAGTTTAAG	59.362	38.462	0.00	0.00	0.00	1.85
524	612	6.321181	AGCTCCACACATTTGAAGAAGTTTAA	59.679	34.615	0.00	0.00	0.00	1.52
569	683	5.444218	CGAACTAAATCTCACACGCCTAAAC	60.444	44.000	0.00	0.00	0.00	2.01
619	953	2.611292	CGATGGCTCTGATCTGAAAACC	59.389	50.000	3.72	6.43	0.00	3.27
629	963	2.666317	TCCACTATTCGATGGCTCTGA	58.334	47.619	0.00	0.00	35.81	3.27
709	1048	1.727511	TTGCATATGCTTGGGCGCTC	61.728	55.000	27.13	2.47	42.66	5.03
760	1116	5.818857	AGTTTTCACATTTTGCTTGCTTGAT	59.181	32.000	0.00	0.00	0.00	2.57
882	1242	8.225107	GTGTACATATTTATTTCACACACACGT	58.775	33.333	0.00	0.00	35.90	4.49
883	1243	7.421331	CGTGTACATATTTATTTCACACACACG	59.579	37.037	0.00	0.00	45.24	4.49
884	1244	8.436970	TCGTGTACATATTTATTTCACACACAC	58.563	33.333	0.00	0.00	35.65	3.82
885	1245	8.535690	TCGTGTACATATTTATTTCACACACA	57.464	30.769	0.00	0.00	35.65	3.72
915	1275	4.166725	TGGGATGCCACAATAGAAGAGAAT	59.833	41.667	0.00	0.00	0.00	2.40
1269	1630	1.755179	TCTTCTTTGCAGCCATAGCC	58.245	50.000	0.00	0.00	41.25	3.93
1428	1789	1.948144	GCTCCTCTCACCTTTTGGCTC	60.948	57.143	0.00	0.00	45.59	4.70
1482	1843	1.266718	CCAAGGTCCATGTTTGTGTCG	59.733	52.381	0.00	0.00	0.00	4.35
1506	1867	0.818296	CTGGTTACCTGACCCTCTCG	59.182	60.000	2.07	0.00	39.01	4.04
1560	1921	3.873361	GTGGTGTCATGATGTCCATAGTG	59.127	47.826	15.77	0.00	33.31	2.74
1986	2347	3.065925	GCTCAGGATGGTAATGTTCTTGC	59.934	47.826	0.00	0.00	36.16	4.01
2138	2504	5.688807	ACTAAATTGTCTCTCCATCCCATG	58.311	41.667	0.00	0.00	0.00	3.66

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.