AutoCloner

Multiple sequence alignment - TraesCS6B01G420800

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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	TraesCS6B01G420800	chr6B	100.000	2582	0	0	1	2582	691975201	691977782	0.000000e+00	4769.0
1	TraesCS6B01G420800	chr6B	97.124	2156	42	7	434	2580	692045267	692043123	0.000000e+00	3620.0
2	TraesCS6B01G420800	chr6B	81.093	1116	148	37	844	1930	691944768	691945849	0.000000e+00	833.0
3	TraesCS6B01G420800	chr6B	82.851	898	109	26	875	1741	692574338	692575221	0.000000e+00	763.0
4	TraesCS6B01G420800	chr6B	94.100	339	18	1	1	337	692046530	692046192	5.230000e-142	514.0
5	TraesCS6B01G420800	chr6B	100.000	81	0	0	2660	2740	691977860	691977940	1.700000e-32	150.0
6	TraesCS6B01G420800	chr6B	93.827	81	5	0	2660	2740	692043061	692042981	3.710000e-24	122.0
7	TraesCS6B01G420800	chr6B	87.500	80	9	1	2257	2336	692074561	692074483	1.040000e-14	91.6
8	TraesCS6B01G420800	chr6B	87.500	48	4	2	2685	2731	174664514	174664560	1.000000e-03	54.7
9	TraesCS6B01G420800	chr6D	87.787	2178	176	36	451	2582	454968566	454966433	0.000000e+00	2466.0
10	TraesCS6B01G420800	chr6D	90.412	1700	134	8	893	2580	454962837	454961155	0.000000e+00	2209.0
11	TraesCS6B01G420800	chr6D	82.711	1151	149	31	844	1971	454996670	454995547	0.000000e+00	977.0
12	TraesCS6B01G420800	chr6D	87.500	80	6	2	2257	2336	454995135	454995060	3.760000e-14	89.8
13	TraesCS6B01G420800	chr6D	82.418	91	9	2	2253	2336	454960419	454960329	3.780000e-09	73.1
14	TraesCS6B01G420800	chr6D	90.476	42	2	2	2691	2731	24407562	24407602	1.000000e-03	54.7
15	TraesCS6B01G420800	chr6A	89.356	1879	121	35	670	2524	601241996	601240173	0.000000e+00	2289.0
16	TraesCS6B01G420800	chr6A	86.139	1616	159	37	396	1971	601257626	601256036	0.000000e+00	1683.0
17	TraesCS6B01G420800	chr6A	81.406	1124	146	41	877	1971	601264782	601263693	0.000000e+00	859.0
18	TraesCS6B01G420800	chr6A	79.710	1242	182	48	776	1972	602075402	602076618	0.000000e+00	833.0
19	TraesCS6B01G420800	chr6A	81.718	1001	141	30	954	1927	602131438	602132423	0.000000e+00	797.0
20	TraesCS6B01G420800	chr6A	81.707	246	26	12	404	640	601242308	601242073	1.300000e-43	187.0
21	TraesCS6B01G420800	chr6A	97.531	81	2	0	2660	2740	601240102	601240022	3.680000e-29	139.0
22	TraesCS6B01G420800	chrUn	87.326	647	40	20	660	1281	79445060	79444431	0.000000e+00	702.0
23	TraesCS6B01G420800	chrUn	83.665	251	16	12	401	640	79445379	79445143	2.140000e-51	213.0
24	TraesCS6B01G420800	chrUn	90.000	80	7	1	2257	2336	79448989	79448911	4.830000e-18	102.0
25	TraesCS6B01G420800	chrUn	90.476	42	2	2	2691	2731	278296825	278296865	1.000000e-03	54.7
26	TraesCS6B01G420800	chr1B	81.308	107	15	4	1997	2098	656662044	656661938	6.290000e-12	82.4
27	TraesCS6B01G420800	chr7A	82.353	85	12	3	1997	2078	589115007	589114923	1.360000e-08	71.3
28	TraesCS6B01G420800	chr2D	92.857	42	1	2	2698	2737	338661547	338661588	2.950000e-05	60.2
29	TraesCS6B01G420800	chr2D	97.059	34	0	1	2699	2731	42555809	42555842	3.810000e-04	56.5
30	TraesCS6B01G420800	chr4B	87.037	54	4	3	2690	2740	1115896	1115843	1.060000e-04	58.4
31	TraesCS6B01G420800	chr3B	92.683	41	0	3	2698	2736	420040421	420040460	3.810000e-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	TraesCS6B01G420800	chr6B	691975201	691977940	2739	False	2459.500000	4769	100.000000	1	2740	2	chr6B.!!$F4	2739
1	TraesCS6B01G420800	chr6B	692042981	692046530	3549	True	1418.666667	3620	95.017000	1	2740	3	chr6B.!!$R2	2739
2	TraesCS6B01G420800	chr6B	691944768	691945849	1081	False	833.000000	833	81.093000	844	1930	1	chr6B.!!$F2	1086
3	TraesCS6B01G420800	chr6B	692574338	692575221	883	False	763.000000	763	82.851000	875	1741	1	chr6B.!!$F3	866
4	TraesCS6B01G420800	chr6D	454960329	454968566	8237	True	1582.700000	2466	86.872333	451	2582	3	chr6D.!!$R1	2131
5	TraesCS6B01G420800	chr6D	454995060	454996670	1610	True	533.400000	977	85.105500	844	2336	2	chr6D.!!$R2	1492
6	TraesCS6B01G420800	chr6A	601256036	601257626	1590	True	1683.000000	1683	86.139000	396	1971	1	chr6A.!!$R1	1575
7	TraesCS6B01G420800	chr6A	601240022	601242308	2286	True	871.666667	2289	89.531333	404	2740	3	chr6A.!!$R3	2336
8	TraesCS6B01G420800	chr6A	601263693	601264782	1089	True	859.000000	859	81.406000	877	1971	1	chr6A.!!$R2	1094
9	TraesCS6B01G420800	chr6A	602075402	602076618	1216	False	833.000000	833	79.710000	776	1972	1	chr6A.!!$F1	1196
10	TraesCS6B01G420800	chr6A	602131438	602132423	985	False	797.000000	797	81.718000	954	1927	1	chr6A.!!$F2	973
11	TraesCS6B01G420800	chrUn	79444431	79448989	4558	True	339.000000	702	86.997000	401	2336	3	chrUn.!!$R1	1935

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
39	40	0.969894	AGTCAGTGACCGAAGAAGGG	59.03	55.0	19.71	0.0	32.18	3.95	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1994	10770	4.174305	CCACAGGTTGGTTCACCC	57.826	61.111	0.0	0.0	41.1	4.61	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
39	40	0.969894	AGTCAGTGACCGAAGAAGGG	59.030	55.000	19.71	0.00	32.18	3.95
43	44	2.436542	TCAGTGACCGAAGAAGGGAAAA	59.563	45.455	0.00	0.00	35.02	2.29
45	46	2.704065	AGTGACCGAAGAAGGGAAAAGA	59.296	45.455	0.00	0.00	35.02	2.52
53	54	6.049790	CCGAAGAAGGGAAAAGATAACCTAG	58.950	44.000	0.00	0.00	31.88	3.02
77	78	6.898521	AGCTAGACCCTTTATATCATCCCTAC	59.101	42.308	0.00	0.00	0.00	3.18
79	80	6.936968	AGACCCTTTATATCATCCCTACAC	57.063	41.667	0.00	0.00	0.00	2.90
128	129	9.381033	CATATTGAGATCAAATATGGAGAGGAC	57.619	37.037	22.00	0.00	39.55	3.85
135	136	4.349048	TCAAATATGGAGAGGACATGAGGG	59.651	45.833	0.00	0.00	0.00	4.30
237	240	9.844257	TCTTTTCTTTCTCTCTTCATTTTCTCT	57.156	29.630	0.00	0.00	0.00	3.10
285	288	2.770164	AGAGAAAATGAGGACCGTGG	57.230	50.000	0.00	0.00	0.00	4.94
309	312	1.405105	CATGCACGAACAAATAGGGGG	59.595	52.381	0.00	0.00	0.00	5.40
317	320	3.570550	CGAACAAATAGGGGGTCAAAACA	59.429	43.478	0.00	0.00	0.00	2.83
337	340	2.436646	CATGCCCGGACAGTGGTC	60.437	66.667	0.73	0.00	43.55	4.02
338	341	4.082523	ATGCCCGGACAGTGGTCG	62.083	66.667	0.73	0.00	45.28	4.79
341	344	4.065281	CCCGGACAGTGGTCGGAC	62.065	72.222	22.51	0.00	45.28	4.79
343	346	2.049433	CGGACAGTGGTCGGACAC	60.049	66.667	10.76	6.55	45.28	3.67
345	348	2.726274	GACAGTGGTCGGACACGT	59.274	61.111	10.76	8.57	45.80	4.49
346	349	1.371389	GACAGTGGTCGGACACGTC	60.371	63.158	10.76	12.61	45.80	4.34
347	350	2.049433	CAGTGGTCGGACACGTCC	60.049	66.667	10.76	6.12	45.80	4.79
356	359	4.546637	GACACGTCCACGAACGAT	57.453	55.556	6.03	4.54	45.37	3.73
357	360	2.805277	GACACGTCCACGAACGATT	58.195	52.632	6.03	3.24	45.37	3.34
358	361	1.134226	GACACGTCCACGAACGATTT	58.866	50.000	6.03	1.25	45.37	2.17
359	362	2.318578	GACACGTCCACGAACGATTTA	58.681	47.619	6.03	0.00	45.37	1.40
360	363	2.725723	GACACGTCCACGAACGATTTAA	59.274	45.455	6.03	0.00	45.37	1.52
361	364	3.319755	ACACGTCCACGAACGATTTAAT	58.680	40.909	6.03	0.00	45.37	1.40
362	365	3.122278	ACACGTCCACGAACGATTTAATG	59.878	43.478	6.03	5.80	45.37	1.90
364	367	3.122278	ACGTCCACGAACGATTTAATGTG	59.878	43.478	6.03	0.00	45.37	3.21
365	368	3.413558	GTCCACGAACGATTTAATGTGC	58.586	45.455	0.14	0.00	0.00	4.57
366	369	2.092995	TCCACGAACGATTTAATGTGCG	59.907	45.455	0.14	6.43	42.86	5.34
367	370	2.427169	CACGAACGATTTAATGTGCGG	58.573	47.619	10.79	0.55	41.49	5.69
369	372	1.661617	CGAACGATTTAATGTGCGGGA	59.338	47.619	0.00	0.00	33.45	5.14
372	979	4.668289	GAACGATTTAATGTGCGGGATTT	58.332	39.130	0.00	0.00	0.00	2.17
373	980	4.027572	ACGATTTAATGTGCGGGATTTG	57.972	40.909	0.00	0.00	0.00	2.32
378	985	6.528423	CGATTTAATGTGCGGGATTTGTTAAA	59.472	34.615	0.00	0.00	0.00	1.52
397	1004	7.168219	TGTTAAATCCAGCTGTAGATGTTCTT	58.832	34.615	13.81	3.37	0.00	2.52
399	1006	9.162764	GTTAAATCCAGCTGTAGATGTTCTTAA	57.837	33.333	13.81	7.90	0.00	1.85
400	1007	9.905713	TTAAATCCAGCTGTAGATGTTCTTAAT	57.094	29.630	13.81	0.00	0.00	1.40
403	1010	7.187824	TCCAGCTGTAGATGTTCTTAATCTT	57.812	36.000	13.81	0.00	35.92	2.40
405	1012	8.103305	TCCAGCTGTAGATGTTCTTAATCTTTT	58.897	33.333	13.81	0.00	35.92	2.27
429	3640	3.421844	TCTTGACAAGAGATCTCCGTCA	58.578	45.455	28.85	28.85	39.35	4.35
430	3641	4.019858	TCTTGACAAGAGATCTCCGTCAT	58.980	43.478	31.13	12.44	40.17	3.06
432	3643	5.652452	TCTTGACAAGAGATCTCCGTCATAA	59.348	40.000	31.13	23.27	40.17	1.90
539	3759	3.248602	CGTAAGCAGCAAAAGTCAGAAGT	59.751	43.478	0.00	0.00	0.00	3.01
557	3783	9.660180	GTCAGAAGTAAAATCAGGATAGTTTCT	57.340	33.333	0.00	0.00	0.00	2.52
578	3804	8.306761	GTTTCTTGGAGTAATTGACCAAATGAT	58.693	33.333	11.75	0.00	42.02	2.45
579	3805	7.395190	TCTTGGAGTAATTGACCAAATGATG	57.605	36.000	11.75	3.67	42.02	3.07
580	3806	7.174413	TCTTGGAGTAATTGACCAAATGATGA	58.826	34.615	11.75	5.31	42.02	2.92
1994	10770	8.760103	TTACATTTCAAACATTCCATGACATG	57.240	30.769	8.56	8.56	37.31	3.21
2051	10827	1.004277	GTGGTATTCTCAGCCCACCAA	59.996	52.381	0.00	0.00	40.78	3.67
2182	10988	2.703798	CCCCTGCATGTCCAAAGCG	61.704	63.158	0.00	0.00	0.00	4.68
2186	10992	1.135689	CCTGCATGTCCAAAGCGTAAC	60.136	52.381	0.00	0.00	0.00	2.50
2199	11005	3.313012	AGCGTAACAGCATCTACAACA	57.687	42.857	0.00	0.00	40.15	3.33
2426	11330	1.529438	GGCGACTCATTTCACGTTTCA	59.471	47.619	0.00	0.00	0.00	2.69
2467	11371	3.708631	TCCAGCCCAAATTTGACTTTTGA	59.291	39.130	19.86	9.36	36.40	2.69
2495	11399	2.241430	TCCTCGTGGATAGGAGACAGAA	59.759	50.000	1.10	0.00	40.41	3.02
2524	11428	0.815615	GTCCGCTTGATGTCCATCCC	60.816	60.000	4.90	0.00	37.02	3.85
2574	11478	5.880887	ACCAGCTCCTAGTACTTTTAAATGC	59.119	40.000	0.00	0.00	0.00	3.56
2580	11484	6.535540	TCCTAGTACTTTTAAATGCCACACA	58.464	36.000	0.00	0.00	0.00	3.72

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
39	40	6.734502	AGGGTCTAGCTAGGTTATCTTTTC	57.265	41.667	20.58	0.27	0.00	2.29
43	44	9.703677	GATATAAAGGGTCTAGCTAGGTTATCT	57.296	37.037	20.58	8.64	0.00	1.98
53	54	6.668283	TGTAGGGATGATATAAAGGGTCTAGC	59.332	42.308	0.00	0.00	0.00	3.42
103	104	9.109246	TGTCCTCTCCATATTTGATCTCAATAT	57.891	33.333	0.00	0.00	35.55	1.28
121	122	1.142748	CGTGCCCTCATGTCCTCTC	59.857	63.158	0.00	0.00	0.00	3.20
148	149	1.597797	TACGTGGCGGACTAACCTGG	61.598	60.000	0.00	0.00	36.31	4.45
149	150	0.179145	CTACGTGGCGGACTAACCTG	60.179	60.000	0.00	0.00	36.31	4.00
230	233	6.072508	GGTCACTTGCATGTGATTAGAGAAAA	60.073	38.462	30.91	8.59	46.77	2.29
237	240	2.355197	CCGGTCACTTGCATGTGATTA	58.645	47.619	30.91	12.44	46.77	1.75
285	288	2.223340	CCTATTTGTTCGTGCATGGAGC	60.223	50.000	5.98	1.85	45.96	4.70
309	312	1.067821	TCCGGGCATGTTTGTTTTGAC	59.932	47.619	0.00	0.00	0.00	3.18
317	320	1.603455	CCACTGTCCGGGCATGTTT	60.603	57.895	10.40	0.00	0.00	2.83
339	342	1.134226	AAATCGTTCGTGGACGTGTC	58.866	50.000	0.00	0.00	43.23	3.67
341	344	3.122278	ACATTAAATCGTTCGTGGACGTG	59.878	43.478	0.00	0.00	43.23	4.49
343	346	3.655581	CACATTAAATCGTTCGTGGACG	58.344	45.455	0.00	0.00	44.06	4.79
345	348	2.092995	CGCACATTAAATCGTTCGTGGA	59.907	45.455	0.00	0.00	0.00	4.02
346	349	2.427169	CGCACATTAAATCGTTCGTGG	58.573	47.619	0.00	0.00	0.00	4.94
347	350	2.427169	CCGCACATTAAATCGTTCGTG	58.573	47.619	0.00	0.00	0.00	4.35
348	351	1.395608	CCCGCACATTAAATCGTTCGT	59.604	47.619	0.00	0.00	0.00	3.85
349	352	1.661617	TCCCGCACATTAAATCGTTCG	59.338	47.619	0.00	0.00	0.00	3.95
351	354	4.082463	ACAAATCCCGCACATTAAATCGTT	60.082	37.500	0.00	0.00	0.00	3.85
352	355	3.442273	ACAAATCCCGCACATTAAATCGT	59.558	39.130	0.00	0.00	0.00	3.73
353	356	4.027572	ACAAATCCCGCACATTAAATCG	57.972	40.909	0.00	0.00	0.00	3.34
355	358	8.419076	GATTTAACAAATCCCGCACATTAAAT	57.581	30.769	0.00	0.00	41.08	1.40
356	359	7.820044	GATTTAACAAATCCCGCACATTAAA	57.180	32.000	1.00	0.00	41.08	1.52
369	372	7.944729	ACATCTACAGCTGGATTTAACAAAT	57.055	32.000	19.93	0.00	0.00	2.32
372	979	6.711277	AGAACATCTACAGCTGGATTTAACA	58.289	36.000	19.93	0.00	0.00	2.41
373	980	7.617041	AAGAACATCTACAGCTGGATTTAAC	57.383	36.000	19.93	3.24	0.00	2.01
378	985	7.372260	AGATTAAGAACATCTACAGCTGGAT	57.628	36.000	19.93	9.20	0.00	3.41
405	1012	5.215252	ACGGAGATCTCTTGTCAAGAAAA	57.785	39.130	21.81	8.05	37.02	2.29
407	1014	3.826729	TGACGGAGATCTCTTGTCAAGAA	59.173	43.478	31.30	18.29	39.79	2.52
408	1015	3.421844	TGACGGAGATCTCTTGTCAAGA	58.578	45.455	31.30	14.54	39.79	3.02
409	1016	3.857549	TGACGGAGATCTCTTGTCAAG	57.142	47.619	31.30	6.21	39.79	3.02
418	3629	3.244009	CCTGCATGTTATGACGGAGATCT	60.244	47.826	0.00	0.00	0.00	2.75
420	3631	2.700371	TCCTGCATGTTATGACGGAGAT	59.300	45.455	0.00	0.00	0.00	2.75
425	3636	2.159043	AGTCCTCCTGCATGTTATGACG	60.159	50.000	0.00	0.00	0.00	4.35
429	3640	3.643792	GACCTAGTCCTCCTGCATGTTAT	59.356	47.826	0.00	0.00	0.00	1.89
430	3641	3.031736	GACCTAGTCCTCCTGCATGTTA	58.968	50.000	0.00	0.00	0.00	2.41
432	3643	1.273267	TGACCTAGTCCTCCTGCATGT	60.273	52.381	0.00	0.00	0.00	3.21
557	3783	6.947733	AGTCATCATTTGGTCAATTACTCCAA	59.052	34.615	4.68	4.68	39.12	3.53
578	3804	4.356436	TCATTTGGATCAGAGAGGAGTCA	58.644	43.478	0.00	0.00	0.00	3.41
579	3805	5.115480	GTTCATTTGGATCAGAGAGGAGTC	58.885	45.833	0.00	0.00	0.00	3.36
580	3806	4.533707	TGTTCATTTGGATCAGAGAGGAGT	59.466	41.667	0.00	0.00	0.00	3.85
1994	10770	4.174305	CCACAGGTTGGTTCACCC	57.826	61.111	0.00	0.00	41.10	4.61
2051	10827	0.320160	GCGAACACCGGGACTTAACT	60.320	55.000	6.32	0.00	39.04	2.24
2182	10988	6.961554	GCTAATGTTGTTGTAGATGCTGTTAC	59.038	38.462	0.00	0.00	0.00	2.50
2186	10992	4.395854	TGGCTAATGTTGTTGTAGATGCTG	59.604	41.667	0.00	0.00	0.00	4.41
2199	11005	4.956075	CAGGGGTAAGATTTGGCTAATGTT	59.044	41.667	8.84	8.84	34.43	2.71
2426	11330	0.036388	AAATGAGACCACGCGGACAT	60.036	50.000	12.47	3.67	35.59	3.06
2495	11399	4.742201	AAGCGGACGTGCGATGCT	62.742	61.111	33.99	17.80	40.67	3.79

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.