AutoCloner

Multiple sequence alignment - TraesCS2A01G507100

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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	TraesCS2A01G507100	chr2A	100.000	4028	0	0	1	4028	734620298	734624325	0.000000e+00	7439.0
1	TraesCS2A01G507100	chr2A	95.288	2101	83	4	1934	4028	734525582	734523492	0.000000e+00	3317.0
2	TraesCS2A01G507100	chr2A	96.942	883	17	5	139	1013	734527620	734526740	0.000000e+00	1472.0
3	TraesCS2A01G507100	chr2A	92.075	795	41	8	1162	1938	734526451	734525661	0.000000e+00	1099.0
4	TraesCS2A01G507100	chr2A	100.000	98	0	0	1	98	734527718	734527621	8.890000e-42	182.0
5	TraesCS2A01G507100	chr2D	94.458	3609	152	15	1	3590	601181533	601185112	0.000000e+00	5513.0
6	TraesCS2A01G507100	chr2D	88.263	213	20	3	3817	4028	601188905	601189113	2.400000e-62	250.0
7	TraesCS2A01G507100	chr2B	95.215	1463	60	4	1615	3072	731311244	731312701	0.000000e+00	2305.0
8	TraesCS2A01G507100	chr2B	90.602	1096	93	7	2872	3960	731312694	731313786	0.000000e+00	1445.0
9	TraesCS2A01G507100	chr2B	94.253	522	26	4	570	1088	731309928	731310448	0.000000e+00	795.0
10	TraesCS2A01G507100	chr2B	93.319	479	29	3	1113	1590	731310771	731311247	0.000000e+00	704.0
11	TraesCS2A01G507100	chr2B	91.317	357	26	3	153	507	731309577	731309930	2.180000e-132	483.0
12	TraesCS2A01G507100	chr4B	75.589	807	142	32	655	1443	1991128	1990359	8.290000e-92	348.0
13	TraesCS2A01G507100	chr5B	72.039	608	127	26	3341	3914	629936475	629937073	1.510000e-29	141.0
14	TraesCS2A01G507100	chr3A	96.203	79	3	0	59	137	308688589	308688511	3.270000e-26	130.0
15	TraesCS2A01G507100	chr6A	96.203	79	2	1	59	137	318892224	318892301	1.180000e-25	128.0
16	TraesCS2A01G507100	chr6A	96.154	78	1	2	59	136	496582086	496582011	4.230000e-25	126.0
17	TraesCS2A01G507100	chr1B	95.122	82	0	2	59	136	26635601	26635520	4.230000e-25	126.0
18	TraesCS2A01G507100	chr1B	94.595	37	2	0	3853	3889	32557445	32557481	1.560000e-04	58.4
19	TraesCS2A01G507100	chr6B	100.000	66	0	0	59	124	606303205	606303270	5.470000e-24	122.0
20	TraesCS2A01G507100	chr4A	96.053	76	1	1	59	134	205657636	205657563	5.470000e-24	122.0
21	TraesCS2A01G507100	chr7A	92.857	84	3	3	59	140	94787541	94787459	7.070000e-23	119.0
22	TraesCS2A01G507100	chr1A	94.444	36	2	0	3853	3888	21614234	21614269	5.620000e-04	56.5

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	TraesCS2A01G507100	chr2A	734620298	734624325	4027	False	7439.0	7439	100.00000	1	4028	1	chr2A.!!$F1	4027
1	TraesCS2A01G507100	chr2A	734523492	734527718	4226	True	1517.5	3317	96.07625	1	4028	4	chr2A.!!$R1	4027
2	TraesCS2A01G507100	chr2D	601181533	601189113	7580	False	2881.5	5513	91.36050	1	4028	2	chr2D.!!$F1	4027
3	TraesCS2A01G507100	chr2B	731309577	731313786	4209	False	1146.4	2305	92.94120	153	3960	5	chr2B.!!$F1	3807
4	TraesCS2A01G507100	chr4B	1990359	1991128	769	True	348.0	348	75.58900	655	1443	1	chr4B.!!$R1	788

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
882	891	2.510613	TGGTGACATCTACTGTGACGA	58.489	47.619	0.0	0.0	42.28	4.20	F
1486	1811	0.580104	GTGGTTTCGACGTGAGGTTG	59.420	55.000	0.0	0.0	0.00	3.77	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1741	2066	1.273327	CATGCTGAAAAACCCTCCACC	59.727	52.381	0.00	0.0	0.00	4.61	R
3405	4030	0.609406	CTCCACCAGAGGTCTGTCGA	60.609	60.000	6.25	0.0	42.27	4.20	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
105	106	4.001618	AGGCTTTGTTGTTGTTGTTGTT	57.998	36.364	0.00	0.00	0.00	2.83
106	107	3.745458	AGGCTTTGTTGTTGTTGTTGTTG	59.255	39.130	0.00	0.00	0.00	3.33
107	108	3.496507	GGCTTTGTTGTTGTTGTTGTTGT	59.503	39.130	0.00	0.00	0.00	3.32
108	109	4.024472	GGCTTTGTTGTTGTTGTTGTTGTT	60.024	37.500	0.00	0.00	0.00	2.83
109	110	4.903016	GCTTTGTTGTTGTTGTTGTTGTTG	59.097	37.500	0.00	0.00	0.00	3.33
110	111	5.503194	GCTTTGTTGTTGTTGTTGTTGTTGT	60.503	36.000	0.00	0.00	0.00	3.32
111	112	6.422776	TTTGTTGTTGTTGTTGTTGTTGTT	57.577	29.167	0.00	0.00	0.00	2.83
112	113	5.395325	TGTTGTTGTTGTTGTTGTTGTTG	57.605	34.783	0.00	0.00	0.00	3.33
113	114	4.870426	TGTTGTTGTTGTTGTTGTTGTTGT	59.130	33.333	0.00	0.00	0.00	3.32
114	115	5.351465	TGTTGTTGTTGTTGTTGTTGTTGTT	59.649	32.000	0.00	0.00	0.00	2.83
115	116	5.395325	TGTTGTTGTTGTTGTTGTTGTTG	57.605	34.783	0.00	0.00	0.00	3.33
116	117	4.870426	TGTTGTTGTTGTTGTTGTTGTTGT	59.130	33.333	0.00	0.00	0.00	3.32
117	118	5.351465	TGTTGTTGTTGTTGTTGTTGTTGTT	59.649	32.000	0.00	0.00	0.00	2.83
118	119	5.395325	TGTTGTTGTTGTTGTTGTTGTTG	57.605	34.783	0.00	0.00	0.00	3.33
119	120	4.870426	TGTTGTTGTTGTTGTTGTTGTTGT	59.130	33.333	0.00	0.00	0.00	3.32
120	121	5.351465	TGTTGTTGTTGTTGTTGTTGTTGTT	59.649	32.000	0.00	0.00	0.00	2.83
121	122	5.395325	TGTTGTTGTTGTTGTTGTTGTTG	57.605	34.783	0.00	0.00	0.00	3.33
122	123	4.870426	TGTTGTTGTTGTTGTTGTTGTTGT	59.130	33.333	0.00	0.00	0.00	3.32
577	582	9.321562	TGTCTCTACCGATAACCAAAATTATTC	57.678	33.333	0.00	0.00	0.00	1.75
882	891	2.510613	TGGTGACATCTACTGTGACGA	58.489	47.619	0.00	0.00	42.28	4.20
1020	1046	1.910276	GCTGAAAGGGGGCTTTGCT	60.910	57.895	0.00	0.00	0.00	3.91
1203	1527	4.439563	GCCGGTTTGTTATTAATCAGTGGG	60.440	45.833	1.90	0.00	0.00	4.61
1267	1591	9.404848	CTCATCCTTAATTATACATGGCATGAT	57.595	33.333	32.74	21.88	0.00	2.45
1455	1779	4.790878	AGCGAAAATTCCCGTTCTTTAAC	58.209	39.130	0.00	0.00	0.00	2.01
1486	1811	0.580104	GTGGTTTCGACGTGAGGTTG	59.420	55.000	0.00	0.00	0.00	3.77
1488	1813	0.878961	GGTTTCGACGTGAGGTTGCT	60.879	55.000	0.00	0.00	0.00	3.91
1705	2030	5.548406	ACTTCTAGTTTGCGAATAAGTGGT	58.452	37.500	0.00	0.00	0.00	4.16
1741	2066	4.526970	AGTTACAAGCAGGGTATTGGATG	58.473	43.478	0.00	0.00	0.00	3.51
1790	2132	3.072211	GTTACAAGCAGGTAGGGAACAC	58.928	50.000	0.00	0.00	0.00	3.32
1795	2137	2.903926	AGCAGGTAGGGAACACTTAGT	58.096	47.619	0.00	0.00	0.00	2.24
2241	2666	0.612174	AGGCTGAGGAACGTGCTAGA	60.612	55.000	0.00	0.00	0.00	2.43
2324	2749	9.741647	GCTCCAGGAATCTGAAATTAATAAAAG	57.258	33.333	0.00	0.00	43.49	2.27
2352	2777	3.057315	CCGAGGACCGAGTTTTACAGTTA	60.057	47.826	0.00	0.00	41.76	2.24
2437	2862	8.877864	TTTAGAGAATGAGAATAAAAAGGCCA	57.122	30.769	5.01	0.00	0.00	5.36
2443	2868	4.735369	TGAGAATAAAAAGGCCAAGGACA	58.265	39.130	5.01	0.00	0.00	4.02
2621	3046	5.551977	AGGGGTCAGAGGAGAAGAATAAAAA	59.448	40.000	0.00	0.00	0.00	1.94
2645	3070	0.326264	GAGGAGCAAGCCAAGGAGAA	59.674	55.000	0.00	0.00	0.00	2.87
2681	3106	6.855836	TGAAAACTATTCTGGATGACAATGC	58.144	36.000	0.00	0.00	0.00	3.56
2693	3118	4.391830	GGATGACAATGCGAAACTAAGTGA	59.608	41.667	0.00	0.00	0.00	3.41
2780	3205	0.591170	TTGCAAAGTGTTCTAGCCGC	59.409	50.000	0.00	0.00	0.00	6.53
2801	3226	5.291614	CCGCAAACATGGATTTGGATAAAAG	59.708	40.000	9.95	0.00	39.52	2.27
2946	3565	1.421646	ACTCCAACCAAAGACTCTGGG	59.578	52.381	0.00	0.00	38.36	4.45
2978	3597	3.848272	CACTGTGTGGCGGATAAAAAT	57.152	42.857	0.00	0.00	0.00	1.82
3078	3697	9.325198	CTATTGCCTACATATACAAGTTCAACA	57.675	33.333	0.00	0.00	0.00	3.33
3079	3698	8.752005	ATTGCCTACATATACAAGTTCAACAT	57.248	30.769	0.00	0.00	0.00	2.71
3225	3844	5.265290	TCTATCGTATTGATCCACCCCTA	57.735	43.478	0.00	0.00	38.57	3.53
3270	3889	1.221414	GCCTTGATCCGTCAGTATGC	58.779	55.000	0.00	0.00	35.39	3.14
3382	4002	1.333619	GCGTTCCTTTTCTGAAGTGCA	59.666	47.619	0.00	0.00	0.00	4.57
3405	4030	3.353836	GTGGTCGTGCAATGGCGT	61.354	61.111	0.00	0.00	45.35	5.68
3451	4076	0.546122	TGGTCTGCTTGTTGTGTCCT	59.454	50.000	0.00	0.00	0.00	3.85
3603	4228	0.609131	CTTGGGCCGTCACCTTTCAT	60.609	55.000	0.00	0.00	0.00	2.57
3784	6909	3.392947	TCTGAGGTTGTTTGACCATGGTA	59.607	43.478	19.80	0.00	42.35	3.25
3785	6910	3.750371	TGAGGTTGTTTGACCATGGTAG	58.250	45.455	19.80	0.00	42.35	3.18
3786	6911	3.137544	TGAGGTTGTTTGACCATGGTAGT	59.862	43.478	19.80	0.00	42.35	2.73
3830	8021	3.825585	TGCTTGCAAGTGGTTGATCATTA	59.174	39.130	26.55	0.00	35.46	1.90
3849	8040	7.880160	TCATTATAATTCTGTCTGGGGTTTG	57.120	36.000	0.00	0.00	0.00	2.93
3914	8106	5.159209	TCGGACGATGTCTTCTTCTAAAAC	58.841	41.667	0.00	0.00	32.47	2.43
3931	8123	9.442047	CTTCTAAAACAAGGACTCTGACAATAT	57.558	33.333	0.00	0.00	0.00	1.28
3938	8130	7.495901	ACAAGGACTCTGACAATATACATCTG	58.504	38.462	0.00	0.00	0.00	2.90
3960	8152	5.632959	TGAACGTGAAAAACAACCAACTAG	58.367	37.500	0.00	0.00	0.00	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
105	106	8.516234	AGAAATAGTACAACAACAACAACAACA	58.484	29.630	0.00	0.00	0.00	3.33
106	107	8.905103	AGAAATAGTACAACAACAACAACAAC	57.095	30.769	0.00	0.00	0.00	3.32
107	108	9.991388	GTAGAAATAGTACAACAACAACAACAA	57.009	29.630	0.00	0.00	0.00	2.83
108	109	9.163899	TGTAGAAATAGTACAACAACAACAACA	57.836	29.630	0.00	0.00	0.00	3.33
109	110	9.991388	TTGTAGAAATAGTACAACAACAACAAC	57.009	29.630	0.00	0.00	35.84	3.32
269	272	9.435688	GAACAAATATGAGTTATTTTGGCCTTT	57.564	29.630	3.32	0.00	38.23	3.11
577	582	0.597637	ACGAGTTGTGACTTGAGCCG	60.598	55.000	0.00	0.00	39.29	5.52
612	618	9.760660	ACGTAGTAGTTACTATAAACTTTGACG	57.239	33.333	0.00	1.03	41.94	4.35
882	891	5.855045	ACTTTCTCACTTGGATAAAGACGT	58.145	37.500	8.56	0.00	40.37	4.34
1203	1527	1.701704	CATTCGCCTTGGAGTTTTGC	58.298	50.000	0.00	0.00	0.00	3.68
1267	1591	7.991084	ATTGATCAAAATGTGAGAGAGAACA	57.009	32.000	13.09	0.00	40.43	3.18
1455	1779	0.721718	GAAACCACGCTCTTGGATCG	59.278	55.000	3.08	0.00	39.24	3.69
1467	1792	0.580104	CAACCTCACGTCGAAACCAC	59.420	55.000	0.00	0.00	0.00	4.16
1705	2030	5.652891	TGCTTGTAACTAACTGAAAAACCCA	59.347	36.000	0.00	0.00	0.00	4.51
1741	2066	1.273327	CATGCTGAAAAACCCTCCACC	59.727	52.381	0.00	0.00	0.00	4.61
1790	2132	4.497006	GCATGTCATTGGCTAGCAACTAAG	60.497	45.833	18.24	0.88	0.00	2.18
1795	2137	2.133281	AGCATGTCATTGGCTAGCAA	57.867	45.000	18.24	0.85	35.82	3.91
2241	2666	6.539826	CACTTTCCATTTCTTTTTCTGCCTTT	59.460	34.615	0.00	0.00	0.00	3.11
2437	2862	2.381445	CCTCCTTGGCTCTGTCCTT	58.619	57.895	0.00	0.00	0.00	3.36
2645	3070	8.046107	CCAGAATAGTTTTCATCTCCTTCTCTT	58.954	37.037	0.00	0.00	0.00	2.85
2681	3106	9.831737	ATTTTTGAATCTGATCACTTAGTTTCG	57.168	29.630	0.00	0.00	0.00	3.46
2780	3205	6.114767	CCCCTTTTATCCAAATCCATGTTTG	58.885	40.000	2.55	2.55	38.50	2.93
2867	3292	7.665559	TCTTGTGACTTATGCCTTGTAATTTCT	59.334	33.333	0.00	0.00	0.00	2.52
2978	3597	1.006825	CGAAGATGTCGTTGCGGTCA	61.007	55.000	0.00	0.00	45.09	4.02
3243	3862	2.167693	TGACGGATCAAGGCGAAATAGT	59.832	45.455	0.00	0.00	0.00	2.12
3382	4002	1.070786	ATTGCACGACCACGAACCT	59.929	52.632	0.00	0.00	42.66	3.50
3405	4030	0.609406	CTCCACCAGAGGTCTGTCGA	60.609	60.000	6.25	0.00	42.27	4.20
3451	4076	3.727258	CCGGGAGCACCATGGGAA	61.727	66.667	18.09	0.00	40.22	3.97
3756	6881	2.933906	GTCAAACAACCTCAGACGACAA	59.066	45.455	0.00	0.00	0.00	3.18
3830	8021	3.336694	ACCCAAACCCCAGACAGAATTAT	59.663	43.478	0.00	0.00	0.00	1.28
3849	8040	2.704464	AGCCCGACTTACAATTACCC	57.296	50.000	0.00	0.00	0.00	3.69
3886	8077	0.526524	GAAGACATCGTCCGAGCCTG	60.527	60.000	0.00	0.00	32.18	4.85
3914	8106	7.720442	TCAGATGTATATTGTCAGAGTCCTTG	58.280	38.462	0.00	0.00	0.00	3.61
3931	8123	5.354513	TGGTTGTTTTTCACGTTCAGATGTA	59.645	36.000	0.00	0.00	0.00	2.29
3938	8130	5.633927	ACTAGTTGGTTGTTTTTCACGTTC	58.366	37.500	0.00	0.00	0.00	3.95

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.