AutoCloner

Multiple sequence alignment - TraesCS4B01G038300

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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	TraesCS4B01G038300	chr4B	100.000	6683	0	0	1	6683	27781406	27774724	0.000000e+00	12342
1	TraesCS4B01G038300	chr4B	93.322	6724	350	42	2	6681	335936738	335930070	0.000000e+00	9838
2	TraesCS4B01G038300	chr4B	94.790	3378	129	21	3347	6683	139088561	139085190	0.000000e+00	5219
3	TraesCS4B01G038300	chr2B	96.149	6700	227	15	1	6683	24650825	24657510	0.000000e+00	10914
4	TraesCS4B01G038300	chr7B	95.278	6734	254	31	1	6683	412115067	412108347	0.000000e+00	10615
5	TraesCS4B01G038300	chr5B	94.738	6728	278	40	1	6683	180710569	180703873	0.000000e+00	10394
6	TraesCS4B01G038300	chr5B	92.469	6732	398	68	2	6683	180047117	180053789	0.000000e+00	9522
7	TraesCS4B01G038300	chr5B	92.896	6222	363	43	506	6683	680706244	680700058	0.000000e+00	8968
8	TraesCS4B01G038300	chr5B	92.842	5951	319	48	2	5899	105177529	105183425	0.000000e+00	8530
9	TraesCS4B01G038300	chr5B	93.983	5152	247	37	2	5109	529120776	529125908	0.000000e+00	7738
10	TraesCS4B01G038300	chr5B	95.533	4544	172	17	2160	6683	291230786	291235318	0.000000e+00	7238
11	TraesCS4B01G038300	chr3B	94.060	6717	316	39	2	6683	306800083	306806751	0.000000e+00	10117
12	TraesCS4B01G038300	chr3B	91.369	6569	445	68	176	6683	816571322	816577829	0.000000e+00	8877
13	TraesCS4B01G038300	chr3B	90.352	767	58	12	5	769	816570571	816571323	0.000000e+00	992
14	TraesCS4B01G038300	chr3B	94.872	156	5	2	1	156	306800138	306800290	2.410000e-59	241
15	TraesCS4B01G038300	chr1B	93.655	6730	349	47	2	6683	67113709	67107010	0.000000e+00	9991
16	TraesCS4B01G038300	chr1B	91.859	5331	339	54	2	5289	171621479	171626757	0.000000e+00	7352

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	TraesCS4B01G038300	chr4B	27774724	27781406	6682	True	12342.0	12342	100.0000	1	6683	1	chr4B.!!$R1	6682
1	TraesCS4B01G038300	chr4B	335930070	335936738	6668	True	9838.0	9838	93.3220	2	6681	1	chr4B.!!$R3	6679
2	TraesCS4B01G038300	chr4B	139085190	139088561	3371	True	5219.0	5219	94.7900	3347	6683	1	chr4B.!!$R2	3336
3	TraesCS4B01G038300	chr2B	24650825	24657510	6685	False	10914.0	10914	96.1490	1	6683	1	chr2B.!!$F1	6682
4	TraesCS4B01G038300	chr7B	412108347	412115067	6720	True	10615.0	10615	95.2780	1	6683	1	chr7B.!!$R1	6682
5	TraesCS4B01G038300	chr5B	180703873	180710569	6696	True	10394.0	10394	94.7380	1	6683	1	chr5B.!!$R1	6682
6	TraesCS4B01G038300	chr5B	180047117	180053789	6672	False	9522.0	9522	92.4690	2	6683	1	chr5B.!!$F2	6681
7	TraesCS4B01G038300	chr5B	680700058	680706244	6186	True	8968.0	8968	92.8960	506	6683	1	chr5B.!!$R2	6177
8	TraesCS4B01G038300	chr5B	105177529	105183425	5896	False	8530.0	8530	92.8420	2	5899	1	chr5B.!!$F1	5897
9	TraesCS4B01G038300	chr5B	529120776	529125908	5132	False	7738.0	7738	93.9830	2	5109	1	chr5B.!!$F4	5107
10	TraesCS4B01G038300	chr5B	291230786	291235318	4532	False	7238.0	7238	95.5330	2160	6683	1	chr5B.!!$F3	4523
11	TraesCS4B01G038300	chr3B	306800083	306806751	6668	False	10117.0	10117	94.0600	2	6683	1	chr3B.!!$F1	6681
12	TraesCS4B01G038300	chr3B	816570571	816577829	7258	False	4934.5	8877	90.8605	5	6683	2	chr3B.!!$F3	6678
13	TraesCS4B01G038300	chr1B	67107010	67113709	6699	True	9991.0	9991	93.6550	2	6683	1	chr1B.!!$R1	6681
14	TraesCS4B01G038300	chr1B	171621479	171626757	5278	False	7352.0	7352	91.8590	2	5289	1	chr1B.!!$F1	5287

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	Hairpin	End Stability	Orientation
631	695	1.676014	GCGACAACTTCACCCTAGCAT	60.676	52.381	0.00	0.00	3.79	F
1553	2223	1.910580	GAGGAAGCGATGTTCCCCCA	61.911	60.000	7.75	46.49	4.96	F
2823	3555	0.671781	GATGGACGTGCACTCAGCTT	60.672	55.000	13.47	45.94	3.74	F
3763	4509	0.398318	GTTGCCAGACCTGAGGAAGT	59.602	55.000	4.99	0.00	3.01	F
5048	5881	0.038744	CTGCAGTGGAAATCCCCAGT	59.961	55.000	5.25	40.37	4.00	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1924	2601	0.390340	GCATCGTGCAGGAAGTCAGA	60.390	55.000	13.87	44.26	3.27	R
3113	3849	1.066716	GTTGTAGTCATACCGGCCACA	60.067	52.381	0.00	0.00	4.17	R
4532	5346	0.248498	CAGCAGCATCCTTCATTGCG	60.248	55.000	0.00	43.61	4.85	R
5232	6065	1.368850	GACCACGAACAACTTGCGC	60.369	57.895	0.00	0.00	6.09	R
6205	7067	0.613777	AACTACCCTTTCCTGCCTCG	59.386	55.000	0.00	0.00	4.63	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
261	319	3.077484	ACATCAAGTGTGCCTATTGCT	57.923	42.857	0.00	0.00	40.28	3.91
310	373	4.681074	TGGAATGTGAACACACTGTCTA	57.319	40.909	9.83	3.97	45.05	2.59
328	391	7.336176	CACTGTCTATTGCCATAATGCAGATAT	59.664	37.037	0.00	0.00	43.21	1.63
407	471	4.988540	GTCAGATGCCATACATACGCTTTA	59.011	41.667	0.00	0.00	39.84	1.85
611	675	6.164408	TGTAGTATGTGTTTCATTTCAGCG	57.836	37.500	0.00	0.00	37.91	5.18
618	682	1.708680	GTTTCATTTCAGCGCGACAAC	59.291	47.619	12.10	0.00	0.00	3.32
631	695	1.676014	GCGACAACTTCACCCTAGCAT	60.676	52.381	0.00	0.00	0.00	3.79
714	1370	5.534278	TGCCACATCTTAGTTTTTGTGATGA	59.466	36.000	8.05	0.00	41.50	2.92
983	1643	4.649267	TCCACCATGACAATTTGGTCTA	57.351	40.909	0.00	0.00	44.38	2.59
1144	1807	4.042311	TCCTGCTTTATGTTACTGGTTGGA	59.958	41.667	0.00	0.00	0.00	3.53
1303	1972	3.186702	TGACTGACAAATTCACCGACA	57.813	42.857	0.00	0.00	0.00	4.35
1315	1984	1.974957	TCACCGACAATCAGAAGGGAA	59.025	47.619	0.00	0.00	0.00	3.97
1386	2056	2.632377	CTTGTCAACCCTGTATGCGAT	58.368	47.619	0.00	0.00	0.00	4.58
1543	2213	6.294787	GGTCAATAATGAGATAGAGGAAGCGA	60.295	42.308	0.00	0.00	35.88	4.93
1553	2223	1.910580	GAGGAAGCGATGTTCCCCCA	61.911	60.000	7.75	0.00	46.49	4.96
1987	2664	3.350219	AGGGTTGTCGACTGCATTTAT	57.650	42.857	17.92	0.00	0.00	1.40
2152	2853	7.065085	CCATCATATTAGTATGGCAACTGCTAC	59.935	40.741	5.50	0.00	38.57	3.58
2157	2858	2.239654	AGTATGGCAACTGCTACCACAT	59.760	45.455	1.06	0.00	41.70	3.21
2474	3180	4.337555	GCTGTTTCTGCATGGACTATCAAT	59.662	41.667	0.00	0.00	0.00	2.57
2480	3204	4.877823	TCTGCATGGACTATCAATGTTGTC	59.122	41.667	0.00	0.00	0.00	3.18
2481	3205	4.587891	TGCATGGACTATCAATGTTGTCA	58.412	39.130	0.00	0.00	0.00	3.58
2482	3206	5.008980	TGCATGGACTATCAATGTTGTCAA	58.991	37.500	0.00	0.00	0.00	3.18
2483	3207	5.124297	TGCATGGACTATCAATGTTGTCAAG	59.876	40.000	0.00	0.00	0.00	3.02
2484	3208	5.449588	GCATGGACTATCAATGTTGTCAAGG	60.450	44.000	0.00	0.00	0.00	3.61
2485	3209	4.009675	TGGACTATCAATGTTGTCAAGGC	58.990	43.478	0.00	0.00	0.00	4.35
2486	3210	4.263462	TGGACTATCAATGTTGTCAAGGCT	60.263	41.667	0.00	0.00	0.00	4.58
2487	3211	4.095483	GGACTATCAATGTTGTCAAGGCTG	59.905	45.833	0.00	0.00	0.00	4.85
2488	3212	4.655963	ACTATCAATGTTGTCAAGGCTGT	58.344	39.130	0.00	0.00	0.00	4.40
2489	3213	5.804639	ACTATCAATGTTGTCAAGGCTGTA	58.195	37.500	0.00	0.00	0.00	2.74
2655	3383	4.556233	GCTGTCTGCGTATTGTATCCATA	58.444	43.478	0.00	0.00	0.00	2.74
2768	3499	3.584406	TGGCCAAGCATGCTATAGACTAT	59.416	43.478	23.00	0.00	0.00	2.12
2823	3555	0.671781	GATGGACGTGCACTCAGCTT	60.672	55.000	13.47	0.00	45.94	3.74
3016	3752	1.578206	GCTTGCTCGGGAAGTTGGTC	61.578	60.000	0.00	0.00	0.00	4.02
3080	3816	2.742053	GCGAGGCAGTTCACTTCATTTA	59.258	45.455	0.00	0.00	0.00	1.40
3100	3836	5.862678	TTATCCCAGAACATACACATCGA	57.137	39.130	0.00	0.00	0.00	3.59
3148	3884	0.550914	ACAACAGTTCCCAAGAGCCA	59.449	50.000	0.00	0.00	0.00	4.75
3429	4167	2.125961	GGACCGATCCCGTAGCTGT	61.126	63.158	0.00	0.00	39.39	4.40
3456	4194	7.389607	CAGGAGGAGGTTCGACTTTAATTTTAA	59.610	37.037	0.00	0.00	0.00	1.52
3679	4425	3.481163	AAAGGTGCCCCCATTGCCA	62.481	57.895	0.00	0.00	34.66	4.92
3763	4509	0.398318	GTTGCCAGACCTGAGGAAGT	59.602	55.000	4.99	0.00	0.00	3.01
3840	4591	5.291178	TCTTGATTTTCCAATGCAACTGTG	58.709	37.500	0.00	0.00	0.00	3.66
3879	4631	1.119684	CTGTCATCGTCCCCCACATA	58.880	55.000	0.00	0.00	0.00	2.29
4002	4755	6.561519	ACTCTTACTGTACCTAATGGCAAT	57.438	37.500	0.00	0.00	36.63	3.56
4174	4956	2.863809	ACTACCAGCTTTTCCACTTGG	58.136	47.619	0.00	0.00	0.00	3.61
4410	5224	5.046591	CCATCAACTGTTCCCACTAACTCTA	60.047	44.000	0.00	0.00	0.00	2.43
4532	5346	5.356470	AGCTGAAATATTGCCAACTCTTCTC	59.644	40.000	0.00	0.00	0.00	2.87
4720	5534	6.150641	GCAGTTCACAATGATATGCCATCTAT	59.849	38.462	0.00	0.00	34.23	1.98
5048	5881	0.038744	CTGCAGTGGAAATCCCCAGT	59.961	55.000	5.25	0.00	40.37	4.00
5232	6065	1.533625	TTCACCTTTGGATTCTGCCG	58.466	50.000	0.00	0.00	0.00	5.69
5308	6142	0.318441	CCACCGAGCTTCAGTCTTGA	59.682	55.000	0.00	0.00	0.00	3.02
5726	6569	2.512705	TGCATTACACATGGCAACTGA	58.487	42.857	0.00	0.00	32.54	3.41
5844	6692	1.270305	ACTGTAGTTGCTGCGACATGT	60.270	47.619	21.37	0.00	0.00	3.21
5872	6720	2.624838	CAGTCAAACCAGATGGCAACTT	59.375	45.455	0.00	0.00	39.32	2.66
5944	6794	0.612732	CACACATGGCAACTCCCCAT	60.613	55.000	0.00	0.00	43.70	4.00
6205	7067	4.284550	TGCCACCCCTGGTTCTGC	62.285	66.667	0.00	0.00	40.17	4.26
6303	7165	4.433615	CCAGCTGTACGATATTGTCAAGT	58.566	43.478	13.81	0.00	0.00	3.16
6445	7323	9.692749	CTTTCTATACATGATCCGCTTAGTTTA	57.307	33.333	0.00	0.00	0.00	2.01
6446	7324	9.472361	TTTCTATACATGATCCGCTTAGTTTAC	57.528	33.333	0.00	0.00	0.00	2.01
6524	7407	3.759581	ACAGCTCATGTTTGGACAGAAT	58.240	40.909	0.00	0.00	39.96	2.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
261	319	8.201242	TGCCACATGAATATACTATCCAAGTA	57.799	34.615	0.00	0.00	44.76	2.24
310	373	6.008331	ACTGTCATATCTGCATTATGGCAAT	58.992	36.000	18.95	10.86	44.40	3.56
328	391	0.388659	GCCAATTTGCCACACTGTCA	59.611	50.000	0.00	0.00	0.00	3.58
407	471	1.485895	AGCCAAAAACTTGCCACATGT	59.514	42.857	0.00	0.00	0.00	3.21
532	596	4.183101	CTGAAAATTGCCACAGTGTGTTT	58.817	39.130	21.48	14.34	0.00	2.83
601	665	1.194547	GAAGTTGTCGCGCTGAAATGA	59.805	47.619	5.56	0.00	0.00	2.57
611	675	0.320421	TGCTAGGGTGAAGTTGTCGC	60.320	55.000	0.00	0.00	35.89	5.19
618	682	3.817647	GGCAGAAATATGCTAGGGTGAAG	59.182	47.826	0.00	0.00	45.75	3.02
631	695	1.003118	ACCTGTTCAGCGGCAGAAATA	59.997	47.619	9.49	1.83	34.87	1.40
714	1370	6.109359	CGATAGAAAGTCACAAAATCCTCCT	58.891	40.000	0.00	0.00	39.76	3.69
983	1643	3.651904	AGCCATTCTGCTGAGATAGGAAT	59.348	43.478	0.00	0.00	40.90	3.01
1144	1807	1.373497	CGACTGCAAGCTCGAGGTT	60.373	57.895	23.57	23.57	38.94	3.50
1190	1855	4.930963	TCAGTTGTTGCCATGTTTTACAG	58.069	39.130	0.00	0.00	0.00	2.74
1193	1858	5.301551	AGTGATCAGTTGTTGCCATGTTTTA	59.698	36.000	0.00	0.00	0.00	1.52
1303	1972	1.353694	AGCAGCAGTTCCCTTCTGATT	59.646	47.619	0.00	0.00	34.30	2.57
1315	1984	1.140452	CATACCCATCTCAGCAGCAGT	59.860	52.381	0.00	0.00	0.00	4.40
1386	2056	2.265367	TGGTAGATCTCACCAAGCCAA	58.735	47.619	16.89	0.00	43.08	4.52
1511	2181	7.175119	CCTCTATCTCATTATTGACCTCGTACA	59.825	40.741	0.00	0.00	0.00	2.90
1543	2213	2.905736	CAGGAAACAAATGGGGGAACAT	59.094	45.455	0.00	0.00	0.00	2.71
1825	2501	6.947733	AGGTTACCACATCAGAAATCAAATGA	59.052	34.615	3.51	0.00	0.00	2.57
1842	2518	2.757894	TCAGGGCAAAAAGGTTACCA	57.242	45.000	3.51	0.00	0.00	3.25
1924	2601	0.390340	GCATCGTGCAGGAAGTCAGA	60.390	55.000	13.87	0.00	44.26	3.27
1926	2603	4.284123	GCATCGTGCAGGAAGTCA	57.716	55.556	13.87	0.00	44.26	3.41
2029	2707	4.327898	GCCATGCATGAATAAAAGTGTGTG	59.672	41.667	28.31	6.84	0.00	3.82
2125	2826	5.939883	GCAGTTGCCATACTAATATGATGGA	59.060	40.000	4.32	0.00	42.41	3.41
2152	2853	3.088194	GCAGTTGCCATCATAATGTGG	57.912	47.619	0.00	0.00	38.55	4.17
2372	3078	4.700213	TCAAGACAGTCGACATACATGAGA	59.300	41.667	19.50	3.06	0.00	3.27
2474	3180	1.946768	GCAAGTACAGCCTTGACAACA	59.053	47.619	5.17	0.00	43.65	3.33
2484	3208	3.488090	GTCCGCGGCAAGTACAGC	61.488	66.667	23.51	0.00	0.00	4.40
2485	3209	2.048597	TGTCCGCGGCAAGTACAG	60.049	61.111	23.51	0.00	0.00	2.74
2486	3210	2.048597	CTGTCCGCGGCAAGTACA	60.049	61.111	23.51	18.45	0.00	2.90
2487	3211	2.813908	CCTGTCCGCGGCAAGTAC	60.814	66.667	23.51	14.18	0.00	2.73
2488	3212	4.077184	CCCTGTCCGCGGCAAGTA	62.077	66.667	23.51	0.00	0.00	2.24
2498	3222	7.607991	CCATATTTGATATCAGTTACCCTGTCC	59.392	40.741	5.39	0.00	42.19	4.02
2515	3239	6.719370	ACTAACCTGCAGTTTTCCATATTTGA	59.281	34.615	13.81	0.00	40.05	2.69
2655	3383	3.331889	AGAGTTCCCATGTGGAGTGAAAT	59.668	43.478	0.00	0.00	46.24	2.17
2823	3555	2.579878	CCTCAGTAGGGCAAGACGA	58.420	57.895	0.00	0.00	39.48	4.20
3080	3816	3.181465	GGTCGATGTGTATGTTCTGGGAT	60.181	47.826	0.00	0.00	0.00	3.85
3113	3849	1.066716	GTTGTAGTCATACCGGCCACA	60.067	52.381	0.00	0.00	0.00	4.17
3148	3884	5.019470	TCTAGATCATCTTGTGTGTCACCT	58.981	41.667	0.00	0.00	32.73	4.00
3429	4167	2.011122	AAAGTCGAACCTCCTCCTGA	57.989	50.000	0.00	0.00	0.00	3.86
3477	4216	5.492524	AGGAAAGGGATGAGTCTATTCCAAA	59.507	40.000	0.00	0.00	35.08	3.28
3524	4265	3.947196	TGTCAGACAACAAACTCATTGCT	59.053	39.130	0.00	0.00	43.13	3.91
3565	4311	0.752658	CTGCACGTATGAGATGGGGA	59.247	55.000	0.00	0.00	0.00	4.81
3602	4348	3.450578	TGTTTCTTCGTAACTGCTCGTT	58.549	40.909	0.00	0.00	39.64	3.85
3641	4387	2.571212	TGTTCAACCGAGCAGAAACAT	58.429	42.857	0.00	0.00	0.00	2.71
3679	4425	1.385347	TGGTGGAAGGGGTGTCACT	60.385	57.895	2.35	0.00	0.00	3.41
3763	4509	4.899457	TGGAGAAACCTACTTCTTGACTGA	59.101	41.667	0.00	0.00	35.76	3.41
3840	4591	1.198637	GAAGACCATGTGACAAGCTGC	59.801	52.381	0.00	0.00	0.00	5.25
3879	4631	5.916318	TCATTTGGAAAAACATCAGTTGCT	58.084	33.333	0.00	0.00	38.17	3.91
4410	5224	2.115052	TGGTCGGCCACTTGCATT	59.885	55.556	3.51	0.00	43.89	3.56
4532	5346	0.248498	CAGCAGCATCCTTCATTGCG	60.248	55.000	0.00	0.00	43.61	4.85
4622	5436	2.159184	GGAATCAGTGTCAGATGAGCGA	60.159	50.000	0.00	0.00	0.00	4.93
4720	5534	2.009681	TGTGCCAAGACTCTCACCTA	57.990	50.000	0.00	0.00	0.00	3.08
5048	5881	3.611530	GCTTGGAAGTGCGCAGATTTAAA	60.612	43.478	12.22	6.85	0.00	1.52
5232	6065	1.368850	GACCACGAACAACTTGCGC	60.369	57.895	0.00	0.00	0.00	6.09
5308	6142	4.321718	CACTGGTTCATCTTGACTGATGT	58.678	43.478	0.00	0.00	43.03	3.06
5844	6692	4.641396	CCATCTGGTTTGACTGTAGTTGA	58.359	43.478	0.00	0.00	0.00	3.18
5872	6720	1.879380	GTTGCCATGTAGTTGCACTGA	59.121	47.619	0.00	0.00	34.16	3.41
6174	7036	1.212935	GGTGGCACTCCTGATGGTATT	59.787	52.381	18.45	0.00	39.21	1.89
6205	7067	0.613777	AACTACCCTTTCCTGCCTCG	59.386	55.000	0.00	0.00	0.00	4.63
6303	7165	1.611491	GGACCTCGCATTTCCAAAACA	59.389	47.619	0.00	0.00	0.00	2.83
6524	7407	2.162208	GCTTCGCATTGAATGACCTTGA	59.838	45.455	9.76	0.00	35.63	3.02
6560	7443	1.617947	GGACTCGGCAAGATCACCCT	61.618	60.000	0.00	0.00	0.00	4.34

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.