AutoCloner

Multiple sequence alignment - TraesCS3B01G489600

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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	TraesCS3B01G489600	chr3B	100.000	3175	0	0	1	3175	736168910	736165736	0.000000e+00	5864
1	TraesCS3B01G489600	chr3B	92.655	3186	209	21	1	3175	675591595	675594766	0.000000e+00	4564
2	TraesCS3B01G489600	chr3B	93.837	2888	162	12	1	2884	46768779	46771654	0.000000e+00	4333
3	TraesCS3B01G489600	chr2B	94.840	3178	149	11	1	3175	687304455	687301290	0.000000e+00	4946
4	TraesCS3B01G489600	chr2B	97.315	298	8	0	2877	3174	107105613	107105316	1.020000e-139	507
5	TraesCS3B01G489600	chr7B	93.243	3182	191	18	1	3173	26274275	26271109	0.000000e+00	4663
6	TraesCS3B01G489600	chr1B	94.003	2885	153	15	6	2884	547570685	547567815	0.000000e+00	4351
7	TraesCS3B01G489600	chr1B	97.333	300	8	0	2876	3175	306220478	306220777	7.860000e-141	510
8	TraesCS3B01G489600	chr6B	93.322	2890	172	17	1	2884	571753919	571751045	0.000000e+00	4248
9	TraesCS3B01G489600	chr6B	97.000	300	9	0	2876	3175	133976785	133976486	3.650000e-139	505
10	TraesCS3B01G489600	chr4A	92.835	2889	187	16	1	2884	744458465	744455592	0.000000e+00	4170
11	TraesCS3B01G489600	chr4A	97.000	300	9	0	2876	3175	647863382	647863681	3.650000e-139	505
12	TraesCS3B01G489600	chr5B	92.751	2883	191	12	7	2884	541107018	541109887	0.000000e+00	4150
13	TraesCS3B01G489600	chr5B	92.499	2893	194	19	1	2884	638657172	638660050	0.000000e+00	4119
14	TraesCS3B01G489600	chr5B	97.659	299	7	0	2876	3174	194198843	194198545	6.070000e-142	514
15	TraesCS3B01G489600	chr5B	96.990	299	9	0	2876	3174	532512147	532511849	1.310000e-138	503

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	TraesCS3B01G489600	chr3B	736165736	736168910	3174	True	5864	5864	100.000	1	3175	1	chr3B.!!$R1	3174
1	TraesCS3B01G489600	chr3B	675591595	675594766	3171	False	4564	4564	92.655	1	3175	1	chr3B.!!$F2	3174
2	TraesCS3B01G489600	chr3B	46768779	46771654	2875	False	4333	4333	93.837	1	2884	1	chr3B.!!$F1	2883
3	TraesCS3B01G489600	chr2B	687301290	687304455	3165	True	4946	4946	94.840	1	3175	1	chr2B.!!$R2	3174
4	TraesCS3B01G489600	chr7B	26271109	26274275	3166	True	4663	4663	93.243	1	3173	1	chr7B.!!$R1	3172
5	TraesCS3B01G489600	chr1B	547567815	547570685	2870	True	4351	4351	94.003	6	2884	1	chr1B.!!$R1	2878
6	TraesCS3B01G489600	chr6B	571751045	571753919	2874	True	4248	4248	93.322	1	2884	1	chr6B.!!$R2	2883
7	TraesCS3B01G489600	chr4A	744455592	744458465	2873	True	4170	4170	92.835	1	2884	1	chr4A.!!$R1	2883
8	TraesCS3B01G489600	chr5B	541107018	541109887	2869	False	4150	4150	92.751	7	2884	1	chr5B.!!$F1	2877
9	TraesCS3B01G489600	chr5B	638657172	638660050	2878	False	4119	4119	92.499	1	2884	1	chr5B.!!$F2	2883

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
503	507	0.037697	ACACTGATTCCAAGCGCGTA	60.038	50.0	8.43	0.0	0.00	4.42	F
523	527	0.320334	CGTGGTGCCACTGATGTGTA	60.320	55.0	17.96	0.0	44.16	2.90	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2092	2111	0.835971	TACCCTCTGCTGCCTCACAA	60.836	55.0	0.00	0.0	0.0	3.33	R
2469	2490	2.054232	TTTTACCGTTTGGCCTCACA	57.946	45.0	3.32	0.0	39.7	3.58	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
181	183	4.059511	TCGAACGCCTTCATTCAAAGTTA	58.940	39.130	0.00	0.00	0.00	2.24
185	187	5.296813	ACGCCTTCATTCAAAGTTATCAC	57.703	39.130	0.00	0.00	0.00	3.06
248	250	0.182537	TGCTACTGCACCACCAACTT	59.817	50.000	0.00	0.00	45.31	2.66
353	357	0.450583	GTGACGAGTCGGTATCTGCA	59.549	55.000	18.30	0.45	0.00	4.41
461	465	0.616679	CCCCCGAGACCAACCTAAGA	60.617	60.000	0.00	0.00	0.00	2.10
503	507	0.037697	ACACTGATTCCAAGCGCGTA	60.038	50.000	8.43	0.00	0.00	4.42
516	520	3.411351	GCGTACGTGGTGCCACTG	61.411	66.667	17.90	13.66	44.16	3.66
523	527	0.320334	CGTGGTGCCACTGATGTGTA	60.320	55.000	17.96	0.00	44.16	2.90
524	528	1.675714	CGTGGTGCCACTGATGTGTAT	60.676	52.381	17.96	0.00	44.16	2.29
572	576	5.353400	AGTTCATAATGATATGCCATCTGCG	59.647	40.000	0.00	0.00	45.60	5.18
733	739	2.450867	AGGAGCAGCAGAGATGAGTA	57.549	50.000	0.00	0.00	0.00	2.59
741	747	4.442052	GCAGCAGAGATGAGTATGGTTACA	60.442	45.833	0.00	0.00	0.00	2.41
868	874	2.194859	AGGTGAACATCCAGAGCAGAT	58.805	47.619	0.00	0.00	0.00	2.90
897	903	1.750399	CCCGCAGTGGAAATCCCTG	60.750	63.158	0.00	11.42	42.00	4.45
984	990	1.816074	TGTCAACAAATCTACGCCCC	58.184	50.000	0.00	0.00	0.00	5.80
993	999	4.789075	CTACGCCCCGTCACCACG	62.789	72.222	0.00	0.00	46.29	4.94
1020	1026	1.379309	GCCCCGCCCTATTGACAAA	60.379	57.895	0.00	0.00	0.00	2.83
1028	1034	3.356290	GCCCTATTGACAAACCTGATGT	58.644	45.455	0.00	0.00	0.00	3.06
1034	1040	6.430925	CCTATTGACAAACCTGATGTTTCTGA	59.569	38.462	0.00	0.00	45.35	3.27
1093	1099	0.393808	GGATTCTGCCCCGCAAGTTA	60.394	55.000	0.00	0.00	38.41	2.24
1145	1151	1.077265	CAATGGCCTTCACCCCACT	59.923	57.895	3.32	0.00	33.17	4.00
1199	1205	2.104451	CAGTGGCTCAAGATCCTATGCT	59.896	50.000	0.00	0.00	0.00	3.79
1222	1228	0.757188	TGCCTTTGCTTTTCCGGGAA	60.757	50.000	5.09	5.09	38.71	3.97
1229	1235	1.598701	GCTTTTCCGGGAAGCATGCT	61.599	55.000	27.68	16.30	46.67	3.79
1352	1358	3.543680	ATACACCTGTGCAGTATGACC	57.456	47.619	0.00	0.00	39.69	4.02
1409	1417	5.101648	TCTCATATGTGATGGCAACTGAA	57.898	39.130	1.90	0.00	32.98	3.02
2047	2066	2.363306	TCAAGTTCCAATGTGCCTGT	57.637	45.000	0.00	0.00	0.00	4.00
2054	2073	4.225042	AGTTCCAATGTGCCTGTAGATACA	59.775	41.667	0.00	0.00	34.56	2.29
2092	2111	2.520968	GAGTGCCACCCCTGGTTT	59.479	61.111	0.00	0.00	40.17	3.27
2172	2191	0.178990	GGCCACAAAGGAACAGACCT	60.179	55.000	0.00	0.00	41.22	3.85
2207	2226	2.816672	TGTCAAGCGATTTGGTAATGCA	59.183	40.909	0.00	0.00	37.39	3.96
2443	2464	2.265647	TCAATGCGAATCGACGTACA	57.734	45.000	6.91	0.00	35.59	2.90
2469	2490	4.421131	ACCTAGGTGATCTTGTTGAGTCT	58.579	43.478	15.42	0.00	0.00	3.24
2496	2517	2.031857	GCCAAACGGTAAAATGTCGACA	60.032	45.455	22.48	22.48	0.00	4.35
2511	2532	2.220133	GTCGACAAATGTAGTTGCGTGT	59.780	45.455	11.55	0.00	33.08	4.49
2549	2570	7.071069	TCAACAAGCATATGGATATGTCTCT	57.929	36.000	4.56	0.00	41.63	3.10
2740	2770	6.294731	GGTTTTCTGCCATCATCTACACTTTT	60.295	38.462	0.00	0.00	0.00	2.27
2789	2819	2.249309	CTGCCGTGCAAACTGACG	59.751	61.111	0.00	0.00	38.41	4.35
2796	2826	2.540769	CCGTGCAAACTGACGTTTTGAT	60.541	45.455	13.91	0.00	41.23	2.57
2797	2827	3.105203	CGTGCAAACTGACGTTTTGATT	58.895	40.909	13.91	0.00	41.23	2.57
2854	2885	9.659830	ACTTCAAAGTAAAATACACGACAAATC	57.340	29.630	0.00	0.00	37.52	2.17
3095	3126	0.647410	CAGACCTTACTTCGCATGCG	59.353	55.000	33.61	33.61	41.35	4.73

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
35	37	3.825143	ATTGGCCATGGTAGAAAATGC	57.175	42.857	14.67	0.00	0.00	3.56
181	183	1.380302	GGAGTTGCCACCTGGTGAT	59.620	57.895	27.94	8.15	35.23	3.06
248	250	4.202040	CCACTTGCATCAGAGTTTGTGAAA	60.202	41.667	0.00	0.00	0.00	2.69
284	288	0.251354	CCTACACATCTGCAGCAGGT	59.749	55.000	22.62	13.35	31.51	4.00
353	357	3.026694	GGGCAATATTTCAGCTGTCCTT	58.973	45.455	14.67	0.09	30.61	3.36
461	465	4.103153	TCATATGAGCGGGAATCTTCCTTT	59.897	41.667	0.00	0.00	46.72	3.11
481	485	1.089920	GCGCTTGGAATCAGTGTCAT	58.910	50.000	0.00	0.00	0.00	3.06
516	520	5.859114	CAGCCACTTCTATCGTATACACATC	59.141	44.000	3.32	0.00	0.00	3.06
523	527	3.319405	CACCTCAGCCACTTCTATCGTAT	59.681	47.826	0.00	0.00	0.00	3.06
524	528	2.688446	CACCTCAGCCACTTCTATCGTA	59.312	50.000	0.00	0.00	0.00	3.43
572	576	0.108585	TTGTGCCAAGACTCTCACCC	59.891	55.000	0.00	0.00	0.00	4.61
672	676	1.308047	ACGACTGTTGATTGCTTGCA	58.692	45.000	1.15	0.00	0.00	4.08
733	739	0.180406	GGACGCAGGGATGTAACCAT	59.820	55.000	0.00	0.00	0.00	3.55
741	747	1.768684	AACAGTGTGGACGCAGGGAT	61.769	55.000	0.00	0.00	0.00	3.85
804	810	3.368427	GCACCTGCATCAGTTGTACTCTA	60.368	47.826	0.00	0.00	41.59	2.43
868	874	3.053291	CTGCGGGTAAAGGCGCAA	61.053	61.111	10.83	0.00	36.91	4.85
897	903	1.202188	GGAAGTGCGCAGATTTAAGCC	60.202	52.381	12.22	2.54	0.00	4.35
953	959	8.999431	GTAGATTTGTTGACAATCCTCTTGTTA	58.001	33.333	0.00	0.00	35.55	2.41
984	990	2.048222	ATGCTGTCCGTGGTGACG	60.048	61.111	0.00	0.00	45.67	4.35
1020	1026	2.107204	AGCCACTTCAGAAACATCAGGT	59.893	45.455	0.00	0.00	0.00	4.00
1034	1040	5.948162	ACAAACATATCTGAATCAGCCACTT	59.052	36.000	5.18	0.00	0.00	3.16
1145	1151	2.359107	CGCCAAGGCTGAAGCTCA	60.359	61.111	9.73	0.00	41.70	4.26
1222	1228	2.030551	CCATCATTGCGAGCATGCT	58.969	52.632	22.92	22.92	35.36	3.79
1327	1333	6.542370	GGTCATACTGCACAGGTGTATAAAAT	59.458	38.462	2.21	0.00	0.00	1.82
1409	1417	3.281158	TCGATTGCCATGTCATCACATT	58.719	40.909	0.00	0.00	40.66	2.71
1698	1713	2.499289	TCCAGTTGCCATGTGTTTTTGT	59.501	40.909	0.00	0.00	0.00	2.83
1902	1921	7.410174	AGGATCAAAATGTGGTTTAGGATACA	58.590	34.615	0.00	0.00	41.41	2.29
2092	2111	0.835971	TACCCTCTGCTGCCTCACAA	60.836	55.000	0.00	0.00	0.00	3.33
2172	2191	5.656480	TCGCTTGACAATATTGTACAGCTA	58.344	37.500	30.48	23.79	42.43	3.32
2181	2200	6.697019	GCATTACCAAATCGCTTGACAATATT	59.303	34.615	0.00	0.00	37.17	1.28
2207	2226	4.608774	TGCTTGCTGCTGGCCCTT	62.609	61.111	0.00	0.00	43.37	3.95
2443	2464	4.023980	TCAACAAGATCACCTAGGTCGAT	58.976	43.478	12.84	17.70	0.00	3.59
2469	2490	2.054232	TTTTACCGTTTGGCCTCACA	57.946	45.000	3.32	0.00	39.70	3.58
2496	2517	2.264005	TCCCACACGCAACTACATTT	57.736	45.000	0.00	0.00	0.00	2.32
2549	2570	6.006759	TGTAATGCATGATTGTTTTGTCGA	57.993	33.333	0.00	0.00	0.00	4.20
2617	2638	5.563475	CGTGTTGAGCAAAATTCTTCCTCAT	60.563	40.000	0.00	0.00	33.10	2.90
2740	2770	6.157904	CACATGAAACATCTGCCACATAAAA	58.842	36.000	0.00	0.00	0.00	1.52
2854	2885	2.355197	TGCCGTCCATGTATGAACAAG	58.645	47.619	0.00	0.00	39.58	3.16
2889	2920	2.551459	AGTTCACATGAAGAACAGCAGC	59.449	45.455	25.92	8.58	45.93	5.25
2893	2924	4.063689	AGCAGAGTTCACATGAAGAACAG	58.936	43.478	25.92	19.13	45.93	3.16
2949	2980	1.225704	GCTCCTGGAACATGGGGAG	59.774	63.158	0.00	13.05	46.97	4.30
3095	3126	6.820470	TTGACGTTGTTGATGAAAAATTCC	57.180	33.333	0.00	0.00	0.00	3.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.