AutoCloner

Multiple sequence alignment - TraesCS1A01G308200

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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	TraesCS1A01G308200	chr1A	100.000	3230	0	0	1	3230	499618673	499615444	0.000000e+00	5965.0
1	TraesCS1A01G308200	chr1A	95.221	544	21	3	2687	3230	517823425	517822887	0.000000e+00	856.0
2	TraesCS1A01G308200	chr1A	94.853	544	24	2	2687	3230	517856035	517855496	0.000000e+00	846.0
3	TraesCS1A01G308200	chr1A	97.505	481	11	1	1	481	570224808	570224329	0.000000e+00	821.0
4	TraesCS1A01G308200	chr1D	96.088	1508	48	5	887	2394	403940957	403939461	0.000000e+00	2447.0
5	TraesCS1A01G308200	chr1D	89.474	247	19	5	2383	2628	403939428	403939188	4.050000e-79	305.0
6	TraesCS1A01G308200	chr1B	94.004	1601	67	10	658	2234	543429904	543428309	0.000000e+00	2398.0
7	TraesCS1A01G308200	chr1B	97.619	42	1	0	2228	2269	543428203	543428162	4.470000e-09	73.1
8	TraesCS1A01G308200	chr4A	95.588	544	21	2	2688	3230	637247880	637248421	0.000000e+00	869.0
9	TraesCS1A01G308200	chr4A	95.212	543	23	1	2688	3230	29922330	29921791	0.000000e+00	856.0
10	TraesCS1A01G308200	chr4A	97.490	478	11	1	1	477	5408107	5407630	0.000000e+00	815.0
11	TraesCS1A01G308200	chrUn	95.580	543	21	1	2688	3230	190393196	190392657	0.000000e+00	867.0
12	TraesCS1A01G308200	chrUn	95.185	540	22	2	2688	3227	292034770	292035305	0.000000e+00	850.0
13	TraesCS1A01G308200	chrUn	95.028	543	24	1	2688	3230	467818671	467818132	0.000000e+00	850.0
14	TraesCS1A01G308200	chrUn	94.843	543	24	2	2688	3230	183464804	183465342	0.000000e+00	845.0
15	TraesCS1A01G308200	chr2A	95.028	543	23	2	2688	3230	22754601	22754063	0.000000e+00	850.0
16	TraesCS1A01G308200	chr2A	97.458	472	12	0	1	472	753482441	753481970	0.000000e+00	806.0
17	TraesCS1A01G308200	chr6A	97.505	481	11	1	1	481	67029919	67029440	0.000000e+00	821.0
18	TraesCS1A01G308200	chr2B	97.083	480	14	0	1	480	479850137	479849658	0.000000e+00	809.0
19	TraesCS1A01G308200	chr6B	97.263	475	12	1	1	474	626212908	626213382	0.000000e+00	804.0
20	TraesCS1A01G308200	chr5A	97.065	477	14	0	1	477	668187655	668187179	0.000000e+00	804.0
21	TraesCS1A01G308200	chr5A	79.350	523	82	12	1043	1548	485388322	485387809	8.580000e-91	344.0
22	TraesCS1A01G308200	chr5A	78.854	506	74	22	1038	1530	485469725	485469240	8.700000e-81	311.0
23	TraesCS1A01G308200	chr7A	96.875	480	14	1	1	479	129870379	129869900	0.000000e+00	802.0
24	TraesCS1A01G308200	chr5B	96.875	480	13	2	1	479	567583170	567582692	0.000000e+00	802.0
25	TraesCS1A01G308200	chr5B	79.730	518	85	14	1043	1544	461305495	461304982	1.100000e-94	357.0
26	TraesCS1A01G308200	chr5B	79.457	516	86	17	1041	1543	461545929	461545421	6.630000e-92	348.0
27	TraesCS1A01G308200	chr5B	76.731	520	98	19	1043	1548	461491875	461491365	5.310000e-68	268.0
28	TraesCS1A01G308200	chr5D	79.693	522	85	15	1043	1548	384480365	384479849	1.100000e-94	357.0

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	TraesCS1A01G308200	chr1A	499615444	499618673	3229	True	5965.00	5965	100.0000	1	3230	1	chr1A.!!$R1	3229
1	TraesCS1A01G308200	chr1A	517822887	517823425	538	True	856.00	856	95.2210	2687	3230	1	chr1A.!!$R2	543
2	TraesCS1A01G308200	chr1A	517855496	517856035	539	True	846.00	846	94.8530	2687	3230	1	chr1A.!!$R3	543
3	TraesCS1A01G308200	chr1D	403939188	403940957	1769	True	1376.00	2447	92.7810	887	2628	2	chr1D.!!$R1	1741
4	TraesCS1A01G308200	chr1B	543428162	543429904	1742	True	1235.55	2398	95.8115	658	2269	2	chr1B.!!$R1	1611
5	TraesCS1A01G308200	chr4A	637247880	637248421	541	False	869.00	869	95.5880	2688	3230	1	chr4A.!!$F1	542
6	TraesCS1A01G308200	chr4A	29921791	29922330	539	True	856.00	856	95.2120	2688	3230	1	chr4A.!!$R2	542
7	TraesCS1A01G308200	chrUn	190392657	190393196	539	True	867.00	867	95.5800	2688	3230	1	chrUn.!!$R1	542
8	TraesCS1A01G308200	chrUn	292034770	292035305	535	False	850.00	850	95.1850	2688	3227	1	chrUn.!!$F2	539
9	TraesCS1A01G308200	chrUn	467818132	467818671	539	True	850.00	850	95.0280	2688	3230	1	chrUn.!!$R2	542
10	TraesCS1A01G308200	chrUn	183464804	183465342	538	False	845.00	845	94.8430	2688	3230	1	chrUn.!!$F1	542
11	TraesCS1A01G308200	chr2A	22754063	22754601	538	True	850.00	850	95.0280	2688	3230	1	chr2A.!!$R1	542
12	TraesCS1A01G308200	chr5A	485387809	485388322	513	True	344.00	344	79.3500	1043	1548	1	chr5A.!!$R1	505
13	TraesCS1A01G308200	chr5B	461304982	461305495	513	True	357.00	357	79.7300	1043	1544	1	chr5B.!!$R1	501
14	TraesCS1A01G308200	chr5B	461545421	461545929	508	True	348.00	348	79.4570	1041	1543	1	chr5B.!!$R3	502
15	TraesCS1A01G308200	chr5B	461491365	461491875	510	True	268.00	268	76.7310	1043	1548	1	chr5B.!!$R2	505
16	TraesCS1A01G308200	chr5D	384479849	384480365	516	True	357.00	357	79.6930	1043	1548	1	chr5D.!!$R1	505

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
285	286	0.030369	GGTACGAGGCCTGACATACG	59.970	60.0	12.00	9.27	0.0	3.06	F
286	287	0.030369	GTACGAGGCCTGACATACGG	59.970	60.0	12.00	0.00	0.0	4.02	F
474	475	0.031917	TGGCAGTTATCGGGACCCTA	60.032	55.0	9.41	0.00	0.0	3.53	F
641	642	0.109086	TGTTGTTGTTGTTGCGGGTG	60.109	50.0	0.00	0.00	0.0	4.61	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1629	1682	1.078848	GACCAGCTTGCTCGTCCAT	60.079	57.895	8.79	0.0	0.0	3.41	R
2163	2216	2.264005	TTTTAAAGTGCCGGAGCTCA	57.736	45.000	17.19	0.0	40.8	4.26	R
2207	2260	3.737559	AATCATCCTTGCTGTTACCCA	57.262	42.857	0.00	0.0	0.0	4.51	R
2431	2640	4.200874	TCTTAACCAGAAAAGTTCCGCAA	58.799	39.130	0.00	0.0	0.0	4.85	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
31	32	3.238232	GCACATGGCAACTCTCTCA	57.762	52.632	0.00	0.00	43.97	3.27
32	33	1.527034	GCACATGGCAACTCTCTCAA	58.473	50.000	0.00	0.00	43.97	3.02
33	34	1.198637	GCACATGGCAACTCTCTCAAC	59.801	52.381	0.00	0.00	43.97	3.18
34	35	2.775890	CACATGGCAACTCTCTCAACT	58.224	47.619	0.00	0.00	37.61	3.16
35	36	2.483106	CACATGGCAACTCTCTCAACTG	59.517	50.000	0.00	0.00	37.61	3.16
36	37	1.467734	CATGGCAACTCTCTCAACTGC	59.532	52.381	0.00	0.00	37.61	4.40
37	38	2.549332	GGCAACTCTCTCAACTGCC	58.451	57.895	0.00	0.00	45.27	4.85
38	39	3.621953	GCAACTCTCTCAACTGCCT	57.378	52.632	0.00	0.00	0.00	4.75
39	40	2.751166	GCAACTCTCTCAACTGCCTA	57.249	50.000	0.00	0.00	0.00	3.93
40	41	2.615869	GCAACTCTCTCAACTGCCTAG	58.384	52.381	0.00	0.00	0.00	3.02
41	42	2.028567	GCAACTCTCTCAACTGCCTAGT	60.029	50.000	0.00	0.00	39.32	2.57
42	43	3.583806	CAACTCTCTCAACTGCCTAGTG	58.416	50.000	0.00	0.00	37.19	2.74
43	44	2.883026	ACTCTCTCAACTGCCTAGTGT	58.117	47.619	0.00	0.00	37.19	3.55
44	45	3.235200	ACTCTCTCAACTGCCTAGTGTT	58.765	45.455	0.00	0.00	37.19	3.32
45	46	4.408276	ACTCTCTCAACTGCCTAGTGTTA	58.592	43.478	0.00	0.00	37.19	2.41
46	47	4.461081	ACTCTCTCAACTGCCTAGTGTTAG	59.539	45.833	0.00	0.00	37.19	2.34
47	48	4.408276	TCTCTCAACTGCCTAGTGTTAGT	58.592	43.478	0.00	0.00	37.19	2.24
48	49	5.567430	TCTCTCAACTGCCTAGTGTTAGTA	58.433	41.667	0.00	0.00	37.19	1.82
49	50	6.188407	TCTCTCAACTGCCTAGTGTTAGTAT	58.812	40.000	0.00	0.00	37.19	2.12
50	51	6.095580	TCTCTCAACTGCCTAGTGTTAGTATG	59.904	42.308	0.00	0.00	37.19	2.39
51	52	5.715279	TCTCAACTGCCTAGTGTTAGTATGT	59.285	40.000	0.00	0.00	37.19	2.29
52	53	5.720202	TCAACTGCCTAGTGTTAGTATGTG	58.280	41.667	0.00	0.00	37.19	3.21
53	54	4.737855	ACTGCCTAGTGTTAGTATGTGG	57.262	45.455	0.00	0.00	35.34	4.17
54	55	3.118738	ACTGCCTAGTGTTAGTATGTGGC	60.119	47.826	0.00	0.00	35.34	5.01
55	56	2.835156	TGCCTAGTGTTAGTATGTGGCA	59.165	45.455	0.00	0.00	45.51	4.92

Showing 1 to 25 of 467 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
6	7	0.956633	AGTTGCCATGTGCTCACAAG	59.043	50.000	6.81	2.57	45.41	3.16
7	8	0.953727	GAGTTGCCATGTGCTCACAA	59.046	50.000	6.81	0.00	45.41	3.33
8	9	0.109153	AGAGTTGCCATGTGCTCACA	59.891	50.000	5.08	5.08	46.44	3.58
9	10	0.801251	GAGAGTTGCCATGTGCTCAC	59.199	55.000	7.54	0.00	42.00	3.51
10	11	0.689055	AGAGAGTTGCCATGTGCTCA	59.311	50.000	7.54	0.00	42.00	4.26
11	12	1.338484	TGAGAGAGTTGCCATGTGCTC	60.338	52.381	7.54	0.00	42.00	4.26
12	13	0.689055	TGAGAGAGTTGCCATGTGCT	59.311	50.000	7.54	0.00	42.00	4.40
13	14	1.198637	GTTGAGAGAGTTGCCATGTGC	59.801	52.381	0.00	0.00	41.77	4.57
14	15	2.483106	CAGTTGAGAGAGTTGCCATGTG	59.517	50.000	0.00	0.00	0.00	3.21
15	16	2.775890	CAGTTGAGAGAGTTGCCATGT	58.224	47.619	0.00	0.00	0.00	3.21
16	17	1.467734	GCAGTTGAGAGAGTTGCCATG	59.532	52.381	0.00	0.00	0.00	3.66
17	18	1.818642	GCAGTTGAGAGAGTTGCCAT	58.181	50.000	0.00	0.00	0.00	4.40
18	19	3.312404	GCAGTTGAGAGAGTTGCCA	57.688	52.632	0.00	0.00	0.00	4.92
19	20	2.549332	GGCAGTTGAGAGAGTTGCC	58.451	57.895	0.00	0.00	46.39	4.52
20	21	2.028567	ACTAGGCAGTTGAGAGAGTTGC	60.029	50.000	0.00	0.00	0.00	4.17
21	22	3.006323	ACACTAGGCAGTTGAGAGAGTTG	59.994	47.826	0.00	0.00	30.46	3.16
22	23	3.235200	ACACTAGGCAGTTGAGAGAGTT	58.765	45.455	0.00	0.00	30.46	3.01
23	24	2.883026	ACACTAGGCAGTTGAGAGAGT	58.117	47.619	0.00	0.00	30.46	3.24
24	25	3.951775	AACACTAGGCAGTTGAGAGAG	57.048	47.619	0.00	0.00	30.46	3.20
25	26	4.408276	ACTAACACTAGGCAGTTGAGAGA	58.592	43.478	7.49	0.00	30.46	3.10
26	27	4.792521	ACTAACACTAGGCAGTTGAGAG	57.207	45.455	7.49	1.59	30.46	3.20
27	28	5.715279	ACATACTAACACTAGGCAGTTGAGA	59.285	40.000	7.49	0.00	30.46	3.27
28	29	5.807520	CACATACTAACACTAGGCAGTTGAG	59.192	44.000	7.49	4.79	30.46	3.02
29	30	5.337250	CCACATACTAACACTAGGCAGTTGA	60.337	44.000	7.49	0.00	30.46	3.18
30	31	4.870426	CCACATACTAACACTAGGCAGTTG	59.130	45.833	7.49	0.00	30.46	3.16

Showing 1 to 25 of 513 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.