AutoCloner

Multiple sequence alignment - TraesCS6B01G407900

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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	TraesCS6B01G407900	chr6B	100.000	3240	0	0	1	3240	682417373	682420612	0.000000e+00	5984.0
1	TraesCS6B01G407900	chr6B	92.410	1054	77	2	425	1475	681930869	681929816	0.000000e+00	1500.0
2	TraesCS6B01G407900	chr6B	91.383	940	72	5	1383	2317	681929816	681928881	0.000000e+00	1279.0
3	TraesCS6B01G407900	chr6B	73.944	1942	375	81	393	2273	682662256	682660385	0.000000e+00	662.0
4	TraesCS6B01G407900	chr6B	90.421	261	13	6	2351	2611	681928877	681928629	1.860000e-87	333.0
5	TraesCS6B01G407900	chr6B	78.044	542	101	9	1693	2230	682707636	682707109	3.120000e-85	326.0
6	TraesCS6B01G407900	chr6D	95.005	3243	135	11	4	3240	449845071	449841850	0.000000e+00	5066.0
7	TraesCS6B01G407900	chr6D	89.440	2178	194	17	392	2564	449818500	449816354	0.000000e+00	2715.0
8	TraesCS6B01G407900	chr6D	78.293	1078	181	30	577	1638	452082762	452081722	0.000000e+00	645.0
9	TraesCS6B01G407900	chr6D	75.424	944	164	44	1387	2310	450168337	450167442	2.340000e-106	396.0
10	TraesCS6B01G407900	chr6D	82.013	467	66	12	1175	1638	462409647	462409196	6.560000e-102	381.0
11	TraesCS6B01G407900	chr6D	72.582	1313	283	54	961	2230	450212096	450210818	3.070000e-95	359.0
12	TraesCS6B01G407900	chr6D	92.593	54	4	0	2558	2611	449815550	449815497	9.640000e-11	78.7
13	TraesCS6B01G407900	chr6A	92.832	1158	78	4	338	1490	595490133	595488976	0.000000e+00	1674.0
14	TraesCS6B01G407900	chr6A	85.881	1629	107	47	1642	3183	595488471	595486879	0.000000e+00	1620.0
15	TraesCS6B01G407900	chr6A	73.829	1750	337	77	582	2273	595664810	595663124	1.680000e-162	582.0
16	TraesCS6B01G407900	chr6A	77.135	1089	176	30	574	1647	609163407	609162377	6.070000e-157	564.0
17	TraesCS6B01G407900	chr6A	92.283	311	17	3	3	310	595490436	595490130	4.960000e-118	435.0
18	TraesCS6B01G407900	chr6A	77.218	496	52	31	2480	2932	595484976	595484499	1.940000e-57	233.0
19	TraesCS6B01G407900	chr6A	94.815	135	5	2	1527	1659	595488786	595488652	3.280000e-50	209.0
20	TraesCS6B01G407900	chr3B	84.264	394	32	19	3	394	653622889	653622524	1.110000e-94	357.0
21	TraesCS6B01G407900	chr3B	86.096	187	18	6	210	394	766180773	766180593	9.170000e-46	195.0
22	TraesCS6B01G407900	chr1B	86.096	187	19	5	210	394	26265274	26265093	9.170000e-46	195.0
23	TraesCS6B01G407900	chr5D	86.905	168	22	0	4	171	510148877	510149044	4.270000e-44	189.0
24	TraesCS6B01G407900	chr2D	84.293	191	26	1	4	194	35705404	35705590	1.990000e-42	183.0
25	TraesCS6B01G407900	chr2B	84.293	191	26	1	4	194	406883685	406883871	1.990000e-42	183.0
26	TraesCS6B01G407900	chr2B	81.675	191	22	6	210	394	76017707	76017524	2.600000e-31	147.0
27	TraesCS6B01G407900	chr5B	76.154	390	55	22	8	393	706344086	706344441	1.550000e-38	171.0
28	TraesCS6B01G407900	chr5B	82.266	203	24	7	195	394	485661511	485661704	7.190000e-37	165.0
29	TraesCS6B01G407900	chr5A	81.771	192	27	3	4	194	126762936	126763120	1.560000e-33	154.0

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	TraesCS6B01G407900	chr6B	682417373	682420612	3239	False	5984.000000	5984	100.000000	1	3240	1	chr6B.!!$F1	3239
1	TraesCS6B01G407900	chr6B	681928629	681930869	2240	True	1037.333333	1500	91.404667	425	2611	3	chr6B.!!$R3	2186
2	TraesCS6B01G407900	chr6B	682660385	682662256	1871	True	662.000000	662	73.944000	393	2273	1	chr6B.!!$R1	1880
3	TraesCS6B01G407900	chr6B	682707109	682707636	527	True	326.000000	326	78.044000	1693	2230	1	chr6B.!!$R2	537
4	TraesCS6B01G407900	chr6D	449841850	449845071	3221	True	5066.000000	5066	95.005000	4	3240	1	chr6D.!!$R1	3236
5	TraesCS6B01G407900	chr6D	449815497	449818500	3003	True	1396.850000	2715	91.016500	392	2611	2	chr6D.!!$R6	2219
6	TraesCS6B01G407900	chr6D	452081722	452082762	1040	True	645.000000	645	78.293000	577	1638	1	chr6D.!!$R4	1061
7	TraesCS6B01G407900	chr6D	450167442	450168337	895	True	396.000000	396	75.424000	1387	2310	1	chr6D.!!$R2	923
8	TraesCS6B01G407900	chr6D	450210818	450212096	1278	True	359.000000	359	72.582000	961	2230	1	chr6D.!!$R3	1269
9	TraesCS6B01G407900	chr6A	595484499	595490436	5937	True	834.200000	1674	88.605800	3	3183	5	chr6A.!!$R3	3180
10	TraesCS6B01G407900	chr6A	595663124	595664810	1686	True	582.000000	582	73.829000	582	2273	1	chr6A.!!$R1	1691
11	TraesCS6B01G407900	chr6A	609162377	609163407	1030	True	564.000000	564	77.135000	574	1647	1	chr6A.!!$R2	1073

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
951	982	0.689623	CTGCTCCTGTCTTCCCAACT	59.31	55.000	0.0	0.0	0.0	3.16	F
1423	1578	1.810151	GCTGATTCCTGTTGCCGTTTA	59.19	47.619	0.0	0.0	0.0	2.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1867	2450	0.106268	AATCACCAGCCACACACCAA	60.106	50.0	0.0	0.0	0.0	3.67	R
2422	3024	0.896923	GTGCCAGGGATTGAAATGCA	59.103	50.0	0.0	0.0	0.0	3.96	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
28	29	8.726870	ACAAAACTAAGTTAGCTTGAACACTA	57.273	30.769	22.79	0.00	36.22	2.74
37	38	4.513198	AGCTTGAACACTAGTCTGTCTC	57.487	45.455	0.00	0.00	0.00	3.36
73	74	9.778741	AGTGAAATTAGAACTCATTTGTAGTCA	57.221	29.630	0.00	0.00	0.00	3.41
133	137	9.638239	TTTCCATCTAAATTTGCAATGTAAGAC	57.362	29.630	0.00	0.00	0.00	3.01
172	176	6.038161	TGAATTTCTTACAGTGGGCATTATCG	59.962	38.462	0.00	0.00	0.00	2.92
174	178	4.955811	TCTTACAGTGGGCATTATCGAT	57.044	40.909	2.16	2.16	0.00	3.59
175	179	4.883083	TCTTACAGTGGGCATTATCGATC	58.117	43.478	0.00	0.00	0.00	3.69
208	215	3.754850	AGTACTCCACAATTTTTACGCCC	59.245	43.478	0.00	0.00	0.00	6.13
219	226	6.811170	ACAATTTTTACGCCCATATGTTGAAG	59.189	34.615	1.24	0.00	0.00	3.02
230	237	6.096846	GCCCATATGTTGAAGAATACCAAGTT	59.903	38.462	1.24	0.00	0.00	2.66
362	369	6.096846	GCTAGGCTTCCAATAAAAAGGATTCA	59.903	38.462	0.00	0.00	33.10	2.57
458	465	2.562296	TGGTTTCTCTGCCTATTCCCT	58.438	47.619	0.00	0.00	0.00	4.20
512	519	1.152963	AACAACTCGGCAGCCTTGT	60.153	52.632	10.54	10.81	0.00	3.16
551	558	1.002544	CACAAGGTCCAGGAGTCTTCC	59.997	57.143	0.00	0.00	44.39	3.46
625	635	2.045242	CCGACGACCTCCTCCAGA	60.045	66.667	0.00	0.00	0.00	3.86
951	982	0.689623	CTGCTCCTGTCTTCCCAACT	59.310	55.000	0.00	0.00	0.00	3.16
1423	1578	1.810151	GCTGATTCCTGTTGCCGTTTA	59.190	47.619	0.00	0.00	0.00	2.01
1720	2301	6.942532	AGTTTTCAAAGCATGTACTTCTGA	57.057	33.333	0.00	0.00	0.00	3.27
1792	2375	8.073467	TCTTGTTTAACCCTCTTCATTTTGTT	57.927	30.769	0.00	0.00	0.00	2.83
1844	2427	1.886542	GGTCCCCTGTGTTTAGCAAAG	59.113	52.381	0.00	0.00	32.13	2.77
1851	2434	6.325286	TCCCCTGTGTTTAGCAAAGTAAAAAT	59.675	34.615	0.00	0.00	30.30	1.82
2037	2625	1.002430	AGCTTCTGCCGACTTCATCAA	59.998	47.619	0.00	0.00	40.80	2.57
2250	2845	4.141937	TGACATCCAATAGAACCCTCTTCG	60.142	45.833	0.00	0.00	32.70	3.79
2317	2919	5.523552	TCTTCAATAGTCGGCATTGTACATG	59.476	40.000	0.00	0.00	35.36	3.21
2363	2965	1.661341	AGATCGAAGCAGCATTCCAC	58.339	50.000	0.00	0.00	0.00	4.02
2379	2981	2.325484	TCCACACTAGACCTTCTTGCA	58.675	47.619	0.00	0.00	0.00	4.08
2510	3115	6.040391	GCTTGATTAGTCAGAGTAGGAGATGT	59.960	42.308	0.00	0.00	35.39	3.06
2511	3116	7.229707	GCTTGATTAGTCAGAGTAGGAGATGTA	59.770	40.741	0.00	0.00	35.39	2.29
2557	3162	1.657804	AGGAAGACTTGTGTAGGGGG	58.342	55.000	0.00	0.00	0.00	5.40
2598	4013	3.673052	CGTAATGTGATTGGGGCAGTTTG	60.673	47.826	0.00	0.00	0.00	2.93
2618	4063	4.937201	TGAGTGAGTTGCTAGTCAAAGA	57.063	40.909	7.27	0.00	35.55	2.52
2647	4092	7.416890	CCACCTGTCAATTAACAAGTTAAACCA	60.417	37.037	9.22	4.06	38.38	3.67
2756	4218	2.834549	TCCAACTGAATCTCCTCCTGTC	59.165	50.000	0.00	0.00	0.00	3.51
2764	4226	1.223501	TCTCCTCCTGTCGTATCCCT	58.776	55.000	0.00	0.00	0.00	4.20
2964	4461	5.466819	TGACAGAACTCGTATGTAAACTGG	58.533	41.667	0.00	0.00	0.00	4.00
2995	4492	0.963856	CTTGGATGCAGCTGGAGCAA	60.964	55.000	25.07	11.78	46.27	3.91
3111	4608	2.262423	AGCTTTATTCCAGGATCGCC	57.738	50.000	0.00	0.00	0.00	5.54
3119	4616	1.048724	TCCAGGATCGCCCTAGGTTG	61.049	60.000	8.29	0.00	45.60	3.77
3168	4665	4.041198	TCCGTCTCCTGTTACCAGAAAATT	59.959	41.667	0.00	0.00	41.50	1.82

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	9.338622	AGTGTTCAAGCTAACTTAGTTTTGTAT	57.661	29.630	1.94	0.00	33.74	2.29
154	158	4.887748	AGATCGATAATGCCCACTGTAAG	58.112	43.478	0.00	0.00	42.29	2.34
377	384	1.697432	TCGTCCCAGGAATTGAACACT	59.303	47.619	0.00	0.00	0.00	3.55
458	465	3.196469	CAGTGAGAGGAAGCAACCAGATA	59.804	47.826	2.26	0.00	0.00	1.98
512	519	0.605319	GTTGACCATGTCGCCTCCAA	60.605	55.000	0.00	0.00	34.95	3.53
551	558	2.919228	CCCCTTCCATTTCCTCGTTAG	58.081	52.381	0.00	0.00	0.00	2.34
560	567	2.362889	CCAGCGCCCCTTCCATTT	60.363	61.111	2.29	0.00	0.00	2.32
625	635	2.550830	AGCAAGAAGGACATCACGTT	57.449	45.000	0.00	0.00	0.00	3.99
951	982	1.887198	GAAGAGACGAGAACCAGGTCA	59.113	52.381	0.00	0.00	33.18	4.02
1792	2375	8.868522	AATCCATTCTGAAAACAGATAACTGA	57.131	30.769	7.05	0.00	46.03	3.41
1844	2427	9.810231	CCAATTATTCAGCAACAACATTTTTAC	57.190	29.630	0.00	0.00	0.00	2.01
1851	2434	5.163468	ACACACCAATTATTCAGCAACAACA	60.163	36.000	0.00	0.00	0.00	3.33
1867	2450	0.106268	AATCACCAGCCACACACCAA	60.106	50.000	0.00	0.00	0.00	3.67
1998	2584	4.662278	AGCTACATGGCAACTTAAAAGGA	58.338	39.130	0.00	0.00	37.61	3.36
2018	2606	1.442769	TTGATGAAGTCGGCAGAAGC	58.557	50.000	0.00	0.00	41.10	3.86
2057	2652	4.876679	TGTTCCATTCACACGTTGTTTCTA	59.123	37.500	0.00	0.00	0.00	2.10
2250	2845	4.370917	TGGTTACTTACAGTCGAACAACC	58.629	43.478	0.00	0.00	34.18	3.77
2317	2919	8.410912	AGGTTGAAGTTTTTAATGGAGTACAAC	58.589	33.333	0.00	0.00	34.19	3.32
2363	2965	1.000955	ACGGTGCAAGAAGGTCTAGTG	59.999	52.381	0.00	0.00	0.00	2.74
2379	2981	1.816572	GCCAAAGGGTGTAGAAACGGT	60.817	52.381	0.00	0.00	36.17	4.83
2418	3020	2.234300	CAGGGATTGAAATGCATGGC	57.766	50.000	0.00	0.00	35.35	4.40
2422	3024	0.896923	GTGCCAGGGATTGAAATGCA	59.103	50.000	0.00	0.00	0.00	3.96
2524	3129	3.659089	TTCCTACCTTCGGCGCTGC	62.659	63.158	12.58	0.00	0.00	5.25
2557	3162	1.867233	CGATGATGAAATGGACGGACC	59.133	52.381	0.00	0.00	39.54	4.46
2558	3163	2.550978	ACGATGATGAAATGGACGGAC	58.449	47.619	0.00	0.00	0.00	4.79
2598	4013	3.670991	CGTCTTTGACTAGCAACTCACTC	59.329	47.826	0.00	0.00	35.91	3.51
2618	4063	2.264005	TGTTAATTGACAGGTGGCGT	57.736	45.000	0.00	0.00	0.00	5.68
2647	4092	6.757947	CCTTTTTGACATGAAACTGAACACAT	59.242	34.615	0.00	0.00	0.00	3.21
2740	4202	3.254657	GGATACGACAGGAGGAGATTCAG	59.745	52.174	0.00	0.00	0.00	3.02
2756	4218	3.278574	TGGAAGAAATGCAAGGGATACG	58.721	45.455	0.00	0.00	37.60	3.06
2764	4226	4.321452	GCTGAGAACATGGAAGAAATGCAA	60.321	41.667	0.00	0.00	30.96	4.08
2831	4301	1.555533	AGCTGTAAGTAAGCCTCCACC	59.444	52.381	0.00	0.00	41.82	4.61
2832	4302	2.028020	ACAGCTGTAAGTAAGCCTCCAC	60.028	50.000	20.16	0.00	41.82	4.02
2940	4420	5.573282	CCAGTTTACATACGAGTTCTGTCAG	59.427	44.000	0.00	0.00	0.00	3.51
2964	4461	2.749076	TGCATCCAAGCAAGACATACAC	59.251	45.455	0.00	0.00	42.46	2.90
2995	4492	1.865865	ACGATGAAACTGCAACGACT	58.134	45.000	0.00	0.00	37.47	4.18
3111	4608	4.021102	ACACATCTGGAAACAACCTAGG	57.979	45.455	7.41	7.41	42.06	3.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.