AutoCloner

Multiple sequence alignment - TraesCS6A01G128400

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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	TraesCS6A01G128400	chr6A	100.000	4136	0	0	1	4136	100754407	100758542	0.000000e+00	7638.0
1	TraesCS6A01G128400	chr6A	93.047	4142	254	9	1	4136	100796511	100800624	0.000000e+00	6023.0
2	TraesCS6A01G128400	chr6A	84.306	2364	349	14	1034	3394	100228869	100226525	0.000000e+00	2290.0
3	TraesCS6A01G128400	chr6A	82.491	2553	396	27	971	3506	100738200	100740718	0.000000e+00	2191.0
4	TraesCS6A01G128400	chr6A	91.791	134	11	0	3949	4082	100225973	100225840	1.960000e-43	187.0
5	TraesCS6A01G128400	chr6D	95.451	2814	103	5	2	2793	83524246	83527056	0.000000e+00	4464.0
6	TraesCS6A01G128400	chr6D	85.036	2506	343	13	1034	3537	83160399	83157924	0.000000e+00	2521.0
7	TraesCS6A01G128400	chr6D	82.224	2374	378	30	1035	3395	83057922	83055580	0.000000e+00	2006.0
8	TraesCS6A01G128400	chr6B	91.182	2801	205	28	753	3537	159395701	159398475	0.000000e+00	3766.0
9	TraesCS6A01G128400	chr6B	83.677	2426	355	20	971	3390	158163072	158160682	0.000000e+00	2248.0
10	TraesCS6A01G128400	chr6B	82.698	2543	396	24	971	3506	159377932	159380437	0.000000e+00	2218.0
11	TraesCS6A01G128400	chr6B	82.891	2186	328	25	847	3003	156376152	156373984	0.000000e+00	1923.0
12	TraesCS6A01G128400	chr6B	93.279	863	34	6	47	892	159394845	159395700	0.000000e+00	1251.0
13	TraesCS6A01G128400	chr6B	87.202	461	38	12	3549	3993	159398576	159399031	4.770000e-139	505.0
14	TraesCS6A01G128400	chr6B	92.000	100	5	1	3379	3478	158153210	158153114	2.010000e-28	137.0
15	TraesCS6A01G128400	chr6B	81.818	154	22	5	603	750	158190099	158189946	1.560000e-24	124.0
16	TraesCS6A01G128400	chr6B	82.836	134	6	3	4019	4136	158152761	158152629	2.030000e-18	104.0
17	TraesCS6A01G128400	chr6B	88.732	71	4	1	1	67	159394422	159394492	2.650000e-12	84.2
18	TraesCS6A01G128400	chr3B	86.382	492	47	7	3045	3536	680860899	680860428	1.700000e-143	520.0
19	TraesCS6A01G128400	chrUn	96.512	172	6	0	287	458	273235949	273236120	6.770000e-73	285.0
20	TraesCS6A01G128400	chrUn	96.512	172	6	0	287	458	432306038	432306209	6.770000e-73	285.0
21	TraesCS6A01G128400	chr7D	96.512	172	6	0	287	458	382015518	382015347	6.770000e-73	285.0
22	TraesCS6A01G128400	chr7B	96.512	172	6	0	287	458	743063456	743063627	6.770000e-73	285.0
23	TraesCS6A01G128400	chr7B	96.512	172	6	0	287	458	743116172	743116001	6.770000e-73	285.0
24	TraesCS6A01G128400	chr4D	96.512	172	6	0	287	458	123575739	123575910	6.770000e-73	285.0
25	TraesCS6A01G128400	chr4A	94.915	59	3	0	3479	3537	624286076	624286018	4.400000e-15	93.5

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	TraesCS6A01G128400	chr6A	100754407	100758542	4135	False	7638.00	7638	100.00000	1	4136	1	chr6A.!!$F2	4135
1	TraesCS6A01G128400	chr6A	100796511	100800624	4113	False	6023.00	6023	93.04700	1	4136	1	chr6A.!!$F3	4135
2	TraesCS6A01G128400	chr6A	100738200	100740718	2518	False	2191.00	2191	82.49100	971	3506	1	chr6A.!!$F1	2535
3	TraesCS6A01G128400	chr6A	100225840	100228869	3029	True	1238.50	2290	88.04850	1034	4082	2	chr6A.!!$R1	3048
4	TraesCS6A01G128400	chr6D	83524246	83527056	2810	False	4464.00	4464	95.45100	2	2793	1	chr6D.!!$F1	2791
5	TraesCS6A01G128400	chr6D	83157924	83160399	2475	True	2521.00	2521	85.03600	1034	3537	1	chr6D.!!$R2	2503
6	TraesCS6A01G128400	chr6D	83055580	83057922	2342	True	2006.00	2006	82.22400	1035	3395	1	chr6D.!!$R1	2360
7	TraesCS6A01G128400	chr6B	158160682	158163072	2390	True	2248.00	2248	83.67700	971	3390	1	chr6B.!!$R2	2419
8	TraesCS6A01G128400	chr6B	159377932	159380437	2505	False	2218.00	2218	82.69800	971	3506	1	chr6B.!!$F1	2535
9	TraesCS6A01G128400	chr6B	156373984	156376152	2168	True	1923.00	1923	82.89100	847	3003	1	chr6B.!!$R1	2156
10	TraesCS6A01G128400	chr6B	159394422	159399031	4609	False	1401.55	3766	90.09875	1	3993	4	chr6B.!!$F2	3992

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
333	723	0.995024	AGGGTAGTGGCAATGCTCTT	59.005	50.0	4.82	0.00	0.00	2.85	F
1953	2531	0.255033	TGCCATCAGCTCTGAGCAAT	59.745	50.0	29.49	19.48	45.56	3.56	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2109	2687	0.609406	AGAGCCGTAGTGCAGTCAGA	60.609	55.000	0.00	0.0	0.0	3.27	R
3213	3795	1.001641	GGGTCTGCAGCCACTGAAT	60.002	57.895	23.05	0.0	40.3	2.57	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
84	468	9.155975	GATAATACTAGGCAATAATGACACAGG	57.844	37.037	0.00	0.00	36.86	4.00
218	608	4.274950	CCGAAAAGAACTAGGTTTGAGCAA	59.725	41.667	0.00	0.00	0.00	3.91
263	653	6.159293	CCATATGACGATAGCTACAACACAT	58.841	40.000	3.65	1.87	42.67	3.21
333	723	0.995024	AGGGTAGTGGCAATGCTCTT	59.005	50.000	4.82	0.00	0.00	2.85
340	730	2.097825	GTGGCAATGCTCTTCCTTGAT	58.902	47.619	4.82	0.00	0.00	2.57
390	781	3.532641	AAGTTTCAATCTCCTGGCCTT	57.467	42.857	3.32	0.00	0.00	4.35
478	882	8.089625	TGGGACATCTTCTCTAAATCATGTAA	57.910	34.615	0.00	0.00	0.00	2.41
607	1011	9.546909	CGTGAATAAATTAGTGGATATGCAATC	57.453	33.333	0.00	0.00	0.00	2.67
641	1051	5.611796	TTGACCAGATTTTCTTGTCATCG	57.388	39.130	10.98	0.00	44.99	3.84
737	1147	6.215495	AGAGAAACTAGTACTTCATCCTGC	57.785	41.667	0.00	0.00	0.00	4.85
834	1384	1.825090	TTGGGCTGACTATTGTGCTG	58.175	50.000	0.00	0.00	0.00	4.41
894	1445	6.703165	CCATTTCTTTTCCTTTTCTTGAGTGG	59.297	38.462	0.00	0.00	0.00	4.00
1288	1865	0.984230	GGGGTCCATCTCACAGTTCA	59.016	55.000	0.00	0.00	0.00	3.18
1610	2187	0.877071	CTCAGCGCACCATCTTTTGT	59.123	50.000	11.47	0.00	0.00	2.83
1794	2371	4.729868	ACAATTGGTTAGAAGGAGCACTT	58.270	39.130	10.83	0.00	43.65	3.16
1795	2372	4.520492	ACAATTGGTTAGAAGGAGCACTTG	59.480	41.667	10.83	5.30	40.21	3.16
1879	2457	4.636206	GCAATATTCCGGATTCCATAGGTC	59.364	45.833	4.15	0.00	0.00	3.85
1953	2531	0.255033	TGCCATCAGCTCTGAGCAAT	59.745	50.000	29.49	19.48	45.56	3.56
2109	2687	3.185246	AGCTTATACTCGTGCAGCAAT	57.815	42.857	0.00	0.00	32.58	3.56
2130	2708	1.226435	GACTGCACTACGGCTCTCG	60.226	63.158	0.00	0.00	45.88	4.04
2220	2798	2.494870	TGCTAACCTCTCCCTTACGAAC	59.505	50.000	0.00	0.00	0.00	3.95
2283	2861	4.810345	TGACCAACCTTTTTATTGGGTCT	58.190	39.130	7.84	0.00	42.84	3.85
2304	2882	1.216064	ACTTCCTGCATGAGGCCATA	58.784	50.000	5.01	0.00	42.47	2.74
2334	2912	4.933505	TGACAGCATTGATGGTTTTGAA	57.066	36.364	6.88	0.00	36.17	2.69
2343	2921	7.881232	AGCATTGATGGTTTTGAAAATCTTCAT	59.119	29.630	16.86	8.63	36.98	2.57
2516	3094	8.565896	TTAGACATATCAAACAACAGCTTCAT	57.434	30.769	0.00	0.00	0.00	2.57
2860	3439	2.291465	GCTGCACTGAACAATCTGAACA	59.709	45.455	0.00	0.00	0.00	3.18
2881	3460	6.037786	ACATCCTTTCTGAGTTCGACATTA	57.962	37.500	0.00	0.00	0.00	1.90
3019	3598	1.300542	GCCGTAGCAGATCCAGAGC	60.301	63.158	0.00	0.00	39.53	4.09
3051	3630	4.713814	TCCAGAGAACAGATCAGCACTAAT	59.286	41.667	0.00	0.00	0.00	1.73
3115	3694	5.362430	GGAGTCCTATATGATCAGATGGTCC	59.638	48.000	13.11	9.15	0.00	4.46
3118	3697	7.713518	AGTCCTATATGATCAGATGGTCCTAA	58.286	38.462	13.11	0.00	0.00	2.69
3143	3723	5.221126	CCAGATATTTTGGCTAGAACCTTGC	60.221	44.000	0.00	0.00	0.00	4.01
3205	3787	3.070159	TCTCAAGTGGTTCTCAGTTCAGG	59.930	47.826	0.00	0.00	36.93	3.86
3213	3795	3.181454	GGTTCTCAGTTCAGGAAGACCAA	60.181	47.826	0.00	0.00	38.94	3.67
3214	3796	4.505742	GGTTCTCAGTTCAGGAAGACCAAT	60.506	45.833	0.00	0.00	38.94	3.16
3224	3806	1.815003	GGAAGACCAATTCAGTGGCTG	59.185	52.381	0.00	0.00	43.00	4.85
3243	3825	1.251251	GCAGACCCAGCAAGAACAAT	58.749	50.000	0.00	0.00	0.00	2.71
3277	3866	6.552445	AACCTGCTATCTTGAGTTAGTGAT	57.448	37.500	0.00	0.00	0.00	3.06
3323	3914	7.490962	AACAGAAACATGATTAACGAGTGAA	57.509	32.000	0.00	0.00	0.00	3.18
3341	3956	4.094887	AGTGAACAACATCAACAGTGTGTC	59.905	41.667	0.00	0.00	0.00	3.67
3346	3961	1.942657	ACATCAACAGTGTGTCAGCAC	59.057	47.619	0.00	0.00	45.44	4.40
3362	3981	6.747280	GTGTCAGCACATTATTATTGTGGAAC	59.253	38.462	16.41	4.63	43.69	3.62
3365	3985	5.965334	CAGCACATTATTATTGTGGAACGTC	59.035	40.000	16.41	3.57	43.69	4.34
4036	4865	2.765807	CATCCCCCTCGCCAGAGT	60.766	66.667	0.00	0.00	42.86	3.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
84	468	4.978083	TCCTAATTCCGTGTAGTCAGTC	57.022	45.455	0.00	0.00	0.00	3.51
218	608	7.961326	ATGGCCTTTCTTAGATTGTTAATGT	57.039	32.000	3.32	0.00	0.00	2.71
263	653	5.970317	AGTGCTGTTGATTGATTGAATGA	57.030	34.783	0.00	0.00	0.00	2.57
333	723	3.243839	GCAGTTTGCCAAAGAATCAAGGA	60.244	43.478	0.00	0.00	37.42	3.36
340	730	1.824230	AGTGTGCAGTTTGCCAAAGAA	59.176	42.857	0.00	0.00	44.23	2.52
607	1011	2.621338	TCTGGTCAAAGATTAGCTGCG	58.379	47.619	0.00	0.00	0.00	5.18
641	1051	0.465705	TCATCCCTTCTGGTCATCGC	59.534	55.000	0.00	0.00	34.77	4.58
732	1142	1.064003	TAAGCTTTGGTCTGGCAGGA	58.936	50.000	15.73	0.00	0.00	3.86
762	1172	5.189659	AGCGACTAGAAATTAGCCTGTAG	57.810	43.478	0.00	0.00	0.00	2.74
834	1384	1.731720	CTGTTGCCAAGGAGACTAGC	58.268	55.000	0.00	0.00	42.68	3.42
894	1445	4.021102	TGTTTGATCCTCTTTCAGGTCC	57.979	45.455	0.00	0.00	43.95	4.46
1193	1767	0.620556	GATCCCTTCCCAAGTGCAGA	59.379	55.000	0.00	0.00	0.00	4.26
1288	1865	2.094675	CAAGCCGGTGAGATTTCCAAT	58.905	47.619	1.90	0.00	0.00	3.16
1315	1892	1.202639	TGAGTTGCACGACAGGTTGAT	60.203	47.619	0.00	0.00	0.00	2.57
1439	2016	3.712907	GAGGCCGTGCAGGGGTTA	61.713	66.667	25.93	0.00	41.48	2.85
1610	2187	5.122554	TCGTTAAAACTGAGTTCAAGCACAA	59.877	36.000	0.00	0.00	0.00	3.33
1879	2457	2.697654	CTCCTCCAAACTCTTCAGCTG	58.302	52.381	7.63	7.63	0.00	4.24
1923	2501	1.695239	TGATGGCAGCTCCCCTGAT	60.695	57.895	3.69	0.00	44.64	2.90
1953	2531	4.652421	AATTGTTGTGAGATGTGTGCAA	57.348	36.364	0.00	0.00	0.00	4.08
2109	2687	0.609406	AGAGCCGTAGTGCAGTCAGA	60.609	55.000	0.00	0.00	0.00	3.27
2130	2708	1.761784	TGGCCATGTAAATGATTGCCC	59.238	47.619	0.00	0.00	36.58	5.36
2220	2798	5.243981	AGGATCTGAAGTGTTCTTGTGATG	58.756	41.667	0.00	0.00	33.64	3.07
2304	2882	1.911357	TCAATGCTGTCATCCTCTGGT	59.089	47.619	0.00	0.00	31.27	4.00
2334	2912	9.730705	TCACTCATAGAAAGAACATGAAGATTT	57.269	29.630	0.00	0.00	0.00	2.17
2343	2921	8.853077	ATGAACAATCACTCATAGAAAGAACA	57.147	30.769	0.00	0.00	38.69	3.18
2407	2985	7.906527	GCTTTGCAAAAATAGCATCCTTAAATG	59.093	33.333	13.84	0.00	42.33	2.32
2516	3094	7.309744	CCATTAAGGCAGTTGAAATTTCACCTA	60.310	37.037	21.88	12.15	36.83	3.08
2860	3439	6.287589	AGTAATGTCGAACTCAGAAAGGAT	57.712	37.500	0.00	0.00	0.00	3.24
2881	3460	3.200165	GGGCCTTCTAGGTCATTGTTAGT	59.800	47.826	0.84	0.00	43.30	2.24
3003	3582	1.028130	TGAGCTCTGGATCTGCTACG	58.972	55.000	16.19	0.00	37.16	3.51
3019	3598	2.630098	TCTGTTCTCTGGAGTTGGTGAG	59.370	50.000	0.00	0.00	0.00	3.51
3115	3694	7.283329	AGGTTCTAGCCAAAATATCTGGTTAG	58.717	38.462	15.93	15.93	44.74	2.34
3118	3697	5.717119	AGGTTCTAGCCAAAATATCTGGT	57.283	39.130	5.85	0.00	36.24	4.00
3156	3738	3.380004	GTCATGGTTTGGGCGATGATAAA	59.620	43.478	0.00	0.00	36.33	1.40
3157	3739	2.948979	GTCATGGTTTGGGCGATGATAA	59.051	45.455	0.00	0.00	36.33	1.75
3158	3740	2.571212	GTCATGGTTTGGGCGATGATA	58.429	47.619	0.00	0.00	36.33	2.15
3159	3741	1.392589	GTCATGGTTTGGGCGATGAT	58.607	50.000	0.00	0.00	36.33	2.45
3160	3742	1.024046	CGTCATGGTTTGGGCGATGA	61.024	55.000	0.00	0.00	32.53	2.92
3161	3743	1.305219	ACGTCATGGTTTGGGCGATG	61.305	55.000	0.00	0.00	0.00	3.84
3162	3744	1.002624	ACGTCATGGTTTGGGCGAT	60.003	52.632	0.00	0.00	0.00	4.58
3163	3745	1.963855	CACGTCATGGTTTGGGCGA	60.964	57.895	0.00	0.00	0.00	5.54
3205	3787	1.200948	GCAGCCACTGAATTGGTCTTC	59.799	52.381	0.00	0.00	39.09	2.87
3213	3795	1.001641	GGGTCTGCAGCCACTGAAT	60.002	57.895	23.05	0.00	40.30	2.57
3214	3796	2.401699	CTGGGTCTGCAGCCACTGAA	62.402	60.000	23.05	0.00	45.73	3.02
3224	3806	1.251251	ATTGTTCTTGCTGGGTCTGC	58.749	50.000	0.00	0.00	0.00	4.26
3243	3825	6.385759	TCAAGATAGCAGGTTTACAAGGGATA	59.614	38.462	0.00	0.00	0.00	2.59
3277	3866	4.265904	ACATGGAGTACAACGATGAACA	57.734	40.909	16.87	0.00	0.00	3.18
3323	3914	2.355756	GCTGACACACTGTTGATGTTGT	59.644	45.455	0.00	0.00	0.00	3.32
3341	3956	5.879237	ACGTTCCACAATAATAATGTGCTG	58.121	37.500	3.04	0.00	45.32	4.41
3362	3981	9.798994	AGTAAATACTGACCAAATAGTTAGACG	57.201	33.333	0.00	0.00	34.72	4.18
3498	4221	8.840833	TGCAAATAGTTACAGATTTGAGTGTA	57.159	30.769	19.84	4.64	42.95	2.90
3747	4560	4.704103	TCCCGCCTCAGCTGGTCT	62.704	66.667	15.13	0.00	43.49	3.85
4086	4915	2.743928	GCCGCACTCCCACTTCTG	60.744	66.667	0.00	0.00	0.00	3.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.