AutoCloner

Multiple sequence alignment - TraesCS2D01G093400

Loading Multiple Alignment...

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	TraesCS2D01G093400	chr2D	100.000	2465	0	0	1	2465	44601067	44598603	0.000000e+00	4553
1	TraesCS2D01G093400	chr2D	89.496	238	24	1	540	776	626932662	626932899	1.430000e-77	300
2	TraesCS2D01G093400	chr2D	88.285	239	27	1	540	777	444861054	444860816	4.010000e-73	285
3	TraesCS2D01G093400	chr2A	94.407	2092	108	6	378	2465	48457362	48455276	0.000000e+00	3206
4	TraesCS2D01G093400	chr2A	86.438	730	72	9	779	1497	48406068	48405355	0.000000e+00	774
5	TraesCS2D01G093400	chr2A	95.374	281	10	3	1	280	48458606	48458328	6.260000e-121	444
6	TraesCS2D01G093400	chr2A	89.121	239	25	1	540	777	468294048	468294286	1.850000e-76	296
7	TraesCS2D01G093400	chr2A	87.097	248	17	7	307	541	48406315	48406070	1.450000e-67	267
8	TraesCS2D01G093400	chr2B	88.473	1709	144	15	772	2465	71367800	71366130	0.000000e+00	2015
9	TraesCS2D01G093400	chr2B	86.059	746	73	11	776	1504	71316222	71315491	0.000000e+00	773
10	TraesCS2D01G093400	chr2B	87.049	471	42	9	307	775	71368688	71368235	4.700000e-142	514
11	TraesCS2D01G093400	chr2B	85.603	257	13	12	307	543	71316471	71316219	5.260000e-62	248
12	TraesCS2D01G093400	chr2B	95.833	72	2	1	222	293	71370768	71370698	5.570000e-22	115
13	TraesCS2D01G093400	chr5A	80.176	454	71	9	1643	2082	622409913	622410361	3.060000e-84	322
14	TraesCS2D01G093400	chr7D	88.797	241	26	1	540	779	176959307	176959067	6.670000e-76	294
15	TraesCS2D01G093400	chr7A	88.655	238	26	1	540	777	379688047	379688283	3.100000e-74	289
16	TraesCS2D01G093400	chr5D	88.285	239	27	1	540	777	344791308	344791070	4.010000e-73	285
17	TraesCS2D01G093400	chr3D	88.285	239	27	1	540	777	282684368	282684130	4.010000e-73	285
18	TraesCS2D01G093400	chr3B	87.600	250	26	5	533	780	112951563	112951809	4.010000e-73	285

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	TraesCS2D01G093400	chr2D	44598603	44601067	2464	True	4553.000000	4553	100.000000	1	2465	1	chr2D.!!$R1	2464
1	TraesCS2D01G093400	chr2A	48455276	48458606	3330	True	1825.000000	3206	94.890500	1	2465	2	chr2A.!!$R2	2464
2	TraesCS2D01G093400	chr2A	48405355	48406315	960	True	520.500000	774	86.767500	307	1497	2	chr2A.!!$R1	1190
3	TraesCS2D01G093400	chr2B	71366130	71370768	4638	True	881.333333	2015	90.451667	222	2465	3	chr2B.!!$R2	2243
4	TraesCS2D01G093400	chr2B	71315491	71316471	980	True	510.500000	773	85.831000	307	1504	2	chr2B.!!$R1	1197

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
768	3468	1.075536	GGGACCAAGAAACCAGGACAT	59.924	52.381	0.0	0.0	0.0	3.06	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2071	5240	0.252479	ATCTGCAGCTGGTGAGGAAG	59.748	55.0	17.12	2.36	0.0	3.46	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
27	28	9.291664	CTTGCATTTGTGAACAATTTTTCAAAT	57.708	25.926	8.56	3.97	37.24	2.32
53	54	6.371271	TCATGCGAAGAGATGTGAACAAAATA	59.629	34.615	0.00	0.00	0.00	1.40
116	118	1.680651	CACCCGGGCCATTTTGCTA	60.681	57.895	24.08	0.00	0.00	3.49
293	295	5.189928	TCCCAACTATGCGACAAAACATAT	58.810	37.500	0.00	0.00	0.00	1.78
294	296	6.350103	TCCCAACTATGCGACAAAACATATA	58.650	36.000	0.00	0.00	0.00	0.86
295	297	6.995686	TCCCAACTATGCGACAAAACATATAT	59.004	34.615	0.00	0.00	0.00	0.86
296	298	8.151596	TCCCAACTATGCGACAAAACATATATA	58.848	33.333	0.00	0.00	0.00	0.86
297	299	8.946085	CCCAACTATGCGACAAAACATATATAT	58.054	33.333	0.00	0.00	0.00	0.86
298	300	9.759259	CCAACTATGCGACAAAACATATATATG	57.241	33.333	19.21	19.21	39.55	1.78
331	3012	3.906998	AGGAAATGCTCGAGATACATCG	58.093	45.455	18.75	0.00	44.07	3.84
360	3042	2.238521	AGTTCGACCATGCCAAACATT	58.761	42.857	0.00	0.00	36.64	2.71
363	3045	1.742831	TCGACCATGCCAAACATTAGC	59.257	47.619	0.00	0.00	36.64	3.09
552	3252	5.356470	ACCTAGACACTTACTACATCCGTTC	59.644	44.000	0.00	0.00	0.00	3.95
564	3264	2.752903	ACATCCGTTCTGGTTTATTGGC	59.247	45.455	0.00	0.00	39.52	4.52
572	3272	1.762370	CTGGTTTATTGGCCCCCATTC	59.238	52.381	0.00	0.00	31.53	2.67
580	3280	6.987403	TTATTGGCCCCCATTCTATTTTAC	57.013	37.500	0.00	0.00	31.53	2.01
768	3468	1.075536	GGGACCAAGAAACCAGGACAT	59.924	52.381	0.00	0.00	0.00	3.06
809	3952	7.331026	AGTCTCTTCGATCCATTTAATTGACA	58.669	34.615	0.00	0.00	0.00	3.58
919	4062	6.183360	GGAGTAATGCATTCCACAAACGATAA	60.183	38.462	16.86	0.00	33.22	1.75
965	4111	4.471747	GGATAGGGAATATTGGGAGGAGAC	59.528	50.000	0.00	0.00	0.00	3.36
1004	4151	2.352960	GAGTTTGATCTTCGACCATGGC	59.647	50.000	13.04	3.65	0.00	4.40
1073	4220	5.720371	TTGCTAATATTGTTTGTGTGCCT	57.280	34.783	0.00	0.00	0.00	4.75
1077	4224	5.163663	GCTAATATTGTTTGTGTGCCTGCTA	60.164	40.000	0.00	0.00	0.00	3.49
1103	4250	0.588252	ACTGTGACTGATTGCGCAAC	59.412	50.000	27.64	19.15	0.00	4.17
1117	4264	2.190578	CAACGGAGATCCCTGCCC	59.809	66.667	0.00	0.00	0.00	5.36
1313	4467	1.827789	GCAATAAGCCATGCCGGGA	60.828	57.895	2.18	0.00	36.56	5.14
1503	4664	6.676950	TGTACTTGGCATCAAACACAATAAG	58.323	36.000	0.00	0.00	31.77	1.73
1559	4720	3.807622	CGTGTCCTTGTTACTGTGTTGAT	59.192	43.478	0.00	0.00	0.00	2.57
1802	4965	2.642171	TCCCATCCTCCTGTAGTTGT	57.358	50.000	0.00	0.00	0.00	3.32
1827	4990	3.684413	GCATCCGTTTTCCCAATCTAGGA	60.684	47.826	0.00	0.00	0.00	2.94
1835	4998	3.838244	TCCCAATCTAGGATTTCGGTG	57.162	47.619	0.00	0.00	0.00	4.94
1836	4999	2.438021	TCCCAATCTAGGATTTCGGTGG	59.562	50.000	0.00	0.00	0.00	4.61
1837	5000	2.172717	CCCAATCTAGGATTTCGGTGGT	59.827	50.000	0.00	0.00	0.00	4.16
1872	5035	2.434884	CGTTGGCGATGCTCCAGT	60.435	61.111	0.00	0.00	41.33	4.00
1899	5062	2.701780	CCGGTCCGTCTCCTGTCAG	61.702	68.421	11.06	0.00	0.00	3.51
1982	5145	3.626924	GGGGACGGCACAGTGAGT	61.627	66.667	4.15	3.00	0.00	3.41
2007	5176	3.378399	GAGGAGAGGCGGTGGCTTC	62.378	68.421	0.00	0.00	44.99	3.86
2056	5225	0.665835	GACAGAGCGATCCAGACGAT	59.334	55.000	0.00	0.00	0.00	3.73
2069	5238	1.146041	GACGATATGCCTGGTGCCA	59.854	57.895	0.00	0.00	40.16	4.92
2071	5240	2.256591	CGATATGCCTGGTGCCAGC	61.257	63.158	12.54	8.79	42.35	4.85
2089	5258	1.675801	CTTCCTCACCAGCTGCAGA	59.324	57.895	20.43	7.19	0.00	4.26
2099	5268	1.069823	CCAGCTGCAGATCCGTATCTT	59.930	52.381	20.43	0.00	40.65	2.40
2114	5283	1.002069	ATCTTGGTTCCTGCCCATCA	58.998	50.000	0.00	0.00	0.00	3.07
2211	5380	5.063204	TGAATTGTTCCGTTGTTCTCTCAT	58.937	37.500	0.00	0.00	0.00	2.90
2212	5381	5.530915	TGAATTGTTCCGTTGTTCTCTCATT	59.469	36.000	0.00	0.00	0.00	2.57
2273	5442	8.969260	TGTGTGCATCTATCTTTGATTCTTAT	57.031	30.769	0.00	0.00	0.00	1.73

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
4	5	9.286946	TGAATTTGAAAAATTGTTCACAAATGC	57.713	25.926	10.70	8.35	39.55	3.56
18	19	7.115236	CACATCTCTTCGCATGAATTTGAAAAA	59.885	33.333	0.00	0.00	32.61	1.94
27	28	3.663025	TGTTCACATCTCTTCGCATGAA	58.337	40.909	0.00	0.00	0.00	2.57
88	90	3.381136	CCCGGGTGTTGCAATGGG	61.381	66.667	14.18	5.86	0.00	4.00
161	163	8.340757	CCCTATCTCTAAATCTACCTGTATCCT	58.659	40.741	0.00	0.00	0.00	3.24
162	164	8.337739	TCCCTATCTCTAAATCTACCTGTATCC	58.662	40.741	0.00	0.00	0.00	2.59
293	295	6.872020	GCATTTCCTCTTACCGCTAACATATA	59.128	38.462	0.00	0.00	0.00	0.86
294	296	5.701290	GCATTTCCTCTTACCGCTAACATAT	59.299	40.000	0.00	0.00	0.00	1.78
295	297	5.054477	GCATTTCCTCTTACCGCTAACATA	58.946	41.667	0.00	0.00	0.00	2.29
296	298	3.877508	GCATTTCCTCTTACCGCTAACAT	59.122	43.478	0.00	0.00	0.00	2.71
297	299	3.055385	AGCATTTCCTCTTACCGCTAACA	60.055	43.478	0.00	0.00	0.00	2.41
298	300	3.532542	AGCATTTCCTCTTACCGCTAAC	58.467	45.455	0.00	0.00	0.00	2.34
299	301	3.737047	CGAGCATTTCCTCTTACCGCTAA	60.737	47.826	0.00	0.00	0.00	3.09
300	302	2.223735	CGAGCATTTCCTCTTACCGCTA	60.224	50.000	0.00	0.00	0.00	4.26
301	303	1.471676	CGAGCATTTCCTCTTACCGCT	60.472	52.381	0.00	0.00	0.00	5.52
302	304	0.931005	CGAGCATTTCCTCTTACCGC	59.069	55.000	0.00	0.00	0.00	5.68
303	305	2.099263	TCTCGAGCATTTCCTCTTACCG	59.901	50.000	7.81	0.00	0.00	4.02
304	306	3.802948	TCTCGAGCATTTCCTCTTACC	57.197	47.619	7.81	0.00	0.00	2.85
305	307	5.833082	TGTATCTCGAGCATTTCCTCTTAC	58.167	41.667	7.81	0.00	0.00	2.34
331	3012	3.548818	GGCATGGTCGAACTTTATGCATC	60.549	47.826	21.51	5.86	44.33	3.91
332	3013	2.358898	GGCATGGTCGAACTTTATGCAT	59.641	45.455	21.51	3.79	44.33	3.96
333	3014	1.742831	GGCATGGTCGAACTTTATGCA	59.257	47.619	21.51	0.00	44.33	3.96
337	3018	3.215151	TGTTTGGCATGGTCGAACTTTA	58.785	40.909	0.33	0.00	0.00	1.85
360	3042	9.459640	GAATATCTCTACGTACATTGTTTGCTA	57.540	33.333	0.00	0.00	0.00	3.49
363	3045	9.516314	TCAGAATATCTCTACGTACATTGTTTG	57.484	33.333	0.00	0.00	31.12	2.93
552	3252	1.762370	GAATGGGGGCCAATAAACCAG	59.238	52.381	4.39	0.00	36.95	4.00
564	3264	6.709018	ATTTGACGTAAAATAGAATGGGGG	57.291	37.500	9.24	0.00	0.00	5.40
736	3436	6.268158	GGTTTCTTGGTCCCCTTTGTAATTTA	59.732	38.462	0.00	0.00	0.00	1.40
768	3468	8.918116	TCGAAGAGACTATAACAGTACTACCTA	58.082	37.037	0.00	0.00	37.72	3.08
965	4111	0.401738	TCTTCTGGCTCTGTTTGGGG	59.598	55.000	0.00	0.00	0.00	4.96
1073	4220	2.632512	TCAGTCACAGTGATGGTTAGCA	59.367	45.455	6.51	0.00	0.00	3.49
1077	4224	2.816087	GCAATCAGTCACAGTGATGGTT	59.184	45.455	6.51	6.15	38.23	3.67
1103	4250	3.554342	CAGGGGCAGGGATCTCCG	61.554	72.222	0.00	0.00	41.52	4.63
1174	4327	9.313118	GCGATTAACCCAAAAATTATTCAATCT	57.687	29.630	0.00	0.00	0.00	2.40
1199	4353	0.250901	ATCCCATGGCCAATAGTCGC	60.251	55.000	10.96	0.00	0.00	5.19
1313	4467	3.821886	CCCCCTCGAACCCTTCTT	58.178	61.111	0.00	0.00	0.00	2.52
1559	4720	4.219507	ACTCGCTTCATTTTCTCTCTCTCA	59.780	41.667	0.00	0.00	0.00	3.27
1720	4883	1.419387	GGAGAGATTGGTAGCCAGCAT	59.581	52.381	0.00	0.00	33.81	3.79
1802	4965	2.091541	GATTGGGAAAACGGATGCAGA	58.908	47.619	0.00	0.00	0.00	4.26
1827	4990	2.740826	CGACCGCACCACCGAAAT	60.741	61.111	0.00	0.00	0.00	2.17
1836	4999	3.665675	ATGAAGAGGCCGACCGCAC	62.666	63.158	0.00	0.00	42.76	5.34
1837	5000	3.371097	GATGAAGAGGCCGACCGCA	62.371	63.158	0.00	0.00	42.76	5.69
1899	5062	1.344458	CACATCAGCACGAGACAGTC	58.656	55.000	0.00	0.00	0.00	3.51
2007	5176	7.068716	TCCCATGTGGACATAGATAATAGATCG	59.931	40.741	0.00	0.00	38.61	3.69
2034	5203	2.046285	TCTGGATCGCTCTGTCGCA	61.046	57.895	0.00	0.00	0.00	5.10
2071	5240	0.252479	ATCTGCAGCTGGTGAGGAAG	59.748	55.000	17.12	2.36	0.00	3.46
2089	5258	1.141053	GGCAGGAACCAAGATACGGAT	59.859	52.381	0.00	0.00	0.00	4.18
2099	5268	0.256752	CAGATGATGGGCAGGAACCA	59.743	55.000	0.00	0.00	43.22	3.67
2133	5302	3.117888	CCTTAGCCTTCTCCCAAAGCATA	60.118	47.826	0.00	0.00	0.00	3.14
2134	5303	2.357569	CCTTAGCCTTCTCCCAAAGCAT	60.358	50.000	0.00	0.00	0.00	3.79
2211	5380	6.071108	TGGACAACAAAGAAAATCCAGTCAAA	60.071	34.615	0.00	0.00	32.50	2.69
2212	5381	5.420421	TGGACAACAAAGAAAATCCAGTCAA	59.580	36.000	0.00	0.00	32.50	3.18
2273	5442	1.683365	GTGGGGCTAGGGACGTACA	60.683	63.158	0.00	0.00	0.00	2.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.