AutoCloner

Multiple sequence alignment - TraesCS3D01G128600

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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	TraesCS3D01G128600	chr3D	100.000	6291	0	0	1	6291	86351792	86358082	0.000000e+00	11618.0
1	TraesCS3D01G128600	chr3D	88.646	229	21	4	5993	6217	85896550	85896777	2.230000e-69	274.0
2	TraesCS3D01G128600	chr3D	86.179	246	13	5	5993	6217	86237047	86237292	4.870000e-61	246.0
3	TraesCS3D01G128600	chr3B	96.624	5657	123	15	1	5620	136479227	136484852	0.000000e+00	9326.0
4	TraesCS3D01G128600	chr3B	93.072	664	30	7	5054	5701	130308065	130307402	0.000000e+00	957.0
5	TraesCS3D01G128600	chr3B	95.775	568	17	2	5725	6291	136491740	136492301	0.000000e+00	909.0
6	TraesCS3D01G128600	chr3B	86.066	244	16	5	5993	6218	136091476	136091719	4.870000e-61	246.0
7	TraesCS3D01G128600	chr3A	94.898	5959	173	68	418	6291	102680825	102686737	0.000000e+00	9199.0
8	TraesCS3D01G128600	chr3A	97.642	424	9	1	1	423	102680364	102680787	0.000000e+00	726.0
9	TraesCS3D01G128600	chr3A	87.815	238	15	6	5993	6217	102554779	102555015	3.740000e-67	267.0
10	TraesCS3D01G128600	chr1D	83.333	216	23	11	5992	6202	114313562	114313355	2.990000e-43	187.0
11	TraesCS3D01G128600	chr1D	94.000	50	3	0	372	421	189655468	189655517	6.760000e-10	76.8
12	TraesCS3D01G128600	chr1D	89.286	56	6	0	365	420	20971946	20971891	3.150000e-08	71.3
13	TraesCS3D01G128600	chr1B	82.710	214	22	12	5992	6202	174763359	174763158	6.480000e-40	176.0
14	TraesCS3D01G128600	chr1B	81.938	227	24	13	5992	6202	174784125	174783900	6.480000e-40	176.0
15	TraesCS3D01G128600	chr7B	92.308	52	4	0	372	423	3177878	3177929	2.430000e-09	75.0
16	TraesCS3D01G128600	chr6D	92.308	52	4	0	372	423	7414519	7414570	2.430000e-09	75.0
17	TraesCS3D01G128600	chr6B	92.308	52	4	0	372	423	14312580	14312529	2.430000e-09	75.0
18	TraesCS3D01G128600	chr4D	89.286	56	6	0	365	420	73385892	73385837	3.150000e-08	71.3
19	TraesCS3D01G128600	chr4A	83.333	72	8	3	345	412	55957283	55957354	5.270000e-06	63.9

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	TraesCS3D01G128600	chr3D	86351792	86358082	6290	False	11618.0	11618	100.000	1	6291	1	chr3D.!!$F3	6290
1	TraesCS3D01G128600	chr3B	136479227	136484852	5625	False	9326.0	9326	96.624	1	5620	1	chr3B.!!$F2	5619
2	TraesCS3D01G128600	chr3B	130307402	130308065	663	True	957.0	957	93.072	5054	5701	1	chr3B.!!$R1	647
3	TraesCS3D01G128600	chr3B	136491740	136492301	561	False	909.0	909	95.775	5725	6291	1	chr3B.!!$F3	566
4	TraesCS3D01G128600	chr3A	102680364	102686737	6373	False	4962.5	9199	96.270	1	6291	2	chr3A.!!$F2	6290

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
256	257	3.896888	TCATGTTTTGAGCCTTGAATGGT	59.103	39.130	0.00	0.00	0.00	3.55	F
447	492	4.034742	CCCGAATAAACAAATACTGGGTCG	59.965	45.833	0.00	0.00	0.00	4.79	F
1251	1297	1.006043	TCCAACTTTGTTGACCACCCA	59.994	47.619	11.47	0.00	0.00	4.51	F
2558	2604	2.325484	TGCAGGTCTCAAGGTCAGTTA	58.675	47.619	0.00	0.00	0.00	2.24	F
4307	4368	0.375454	TGCAACCAGACGTTCGTTTG	59.625	50.000	8.54	8.54	29.93	2.93	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1230	1276	2.104170	GGGTGGTCAACAAAGTTGGAA	58.896	47.619	9.72	0.00	0.00	3.53	R
2286	2332	0.525761	CACGCATTTTGGACCGGAAT	59.474	50.000	9.46	0.00	0.00	3.01	R
2930	2978	4.081198	GGTGATAATGGACCATGGCAAAAA	60.081	41.667	13.04	0.00	31.97	1.94	R
4497	4559	1.321016	CATGAGCGCTCAAAAACACG	58.679	50.000	40.83	19.93	43.58	4.49	R
5686	5786	0.036294	CCCCTCCTCCGTTTTGTCTC	60.036	60.000	0.00	0.00	0.00	3.36	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
256	257	3.896888	TCATGTTTTGAGCCTTGAATGGT	59.103	39.130	0.00	0.00	0.00	3.55
447	492	4.034742	CCCGAATAAACAAATACTGGGTCG	59.965	45.833	0.00	0.00	0.00	4.79
655	700	6.153170	TCTGGATTGTTATTGGTACACGTAGA	59.847	38.462	0.00	0.00	39.29	2.59
955	1001	9.319223	GACTTCAAGATCGTTCTTTTGTATTTC	57.681	33.333	6.00	0.00	40.28	2.17
1251	1297	1.006043	TCCAACTTTGTTGACCACCCA	59.994	47.619	11.47	0.00	0.00	4.51
1513	1559	3.118531	AGCCATCCTACTGGAACTTCAT	58.881	45.455	0.00	0.00	46.80	2.57
1514	1560	3.118112	AGCCATCCTACTGGAACTTCATG	60.118	47.826	0.00	0.00	46.80	3.07
2395	2441	6.602410	AGTGTGTATGAGCATAGCTATCAT	57.398	37.500	2.34	8.33	39.88	2.45
2396	2442	7.002250	AGTGTGTATGAGCATAGCTATCATT	57.998	36.000	12.37	0.00	39.88	2.57
2513	2559	6.757897	TGTAAGTGATAAGCCCATTGAAAG	57.242	37.500	0.00	0.00	0.00	2.62
2558	2604	2.325484	TGCAGGTCTCAAGGTCAGTTA	58.675	47.619	0.00	0.00	0.00	2.24
2740	2787	2.469274	AGTGCTCTGACATCCACTTG	57.531	50.000	0.00	0.00	35.14	3.16
2930	2978	6.091169	CAGTTTCAAGCCGCATAAAATGATTT	59.909	34.615	6.68	0.00	30.70	2.17
3903	3956	3.122948	CACTAAGGAACAATGTCCGTTCG	59.877	47.826	0.00	0.00	43.00	3.95
4077	4138	3.444742	TGAAGATTGGTTGCTTAGCATGG	59.555	43.478	8.05	0.00	38.76	3.66
4157	4218	2.125512	GCCGTGGAGCCTACACTG	60.126	66.667	5.36	0.00	36.71	3.66
4218	4279	5.388944	CAGCAGCTTCTGTAATTTTCTGAC	58.611	41.667	5.07	0.00	33.43	3.51
4299	4360	3.691049	TTTTCTTCTTGCAACCAGACG	57.309	42.857	0.00	0.00	0.00	4.18
4307	4368	0.375454	TGCAACCAGACGTTCGTTTG	59.625	50.000	8.54	8.54	29.93	2.93
4313	4374	2.727798	ACCAGACGTTCGTTTGTATTCG	59.272	45.455	13.17	2.58	0.00	3.34
4387	4448	6.496338	AGATTTGTTCGGGAAGTTACAATC	57.504	37.500	0.00	0.00	31.30	2.67
4497	4559	5.064452	CCATTTCTGTGTCATAGCAGTTCTC	59.936	44.000	0.00	0.00	34.57	2.87
4795	4857	6.389830	TGTTGACTTTCACTTGCATGTTAT	57.610	33.333	1.83	0.00	0.00	1.89
4894	4956	3.243301	CGCTCCATTGGATCAAATTCCAG	60.243	47.826	5.70	0.00	46.22	3.86
5042	5104	1.489649	CCTGAGGTTGCCATGAGATCT	59.510	52.381	0.00	0.00	0.00	2.75
5209	5273	1.208293	GACAATCTGGAGTGGGAGGAC	59.792	57.143	3.21	0.00	0.00	3.85
5393	5463	3.829044	CCACCGTGCCATGCCATG	61.829	66.667	0.00	0.00	0.00	3.66
5412	5482	7.144661	TGCCATGTTGTTTGTGTATAAAAGAG	58.855	34.615	0.00	0.00	0.00	2.85
5435	5505	3.684305	GGAAAAGAGAAGAGAAGCTCAGC	59.316	47.826	0.00	0.00	33.62	4.26
5552	5636	5.049267	GGCAAAACCGGATTATTATTCGCTA	60.049	40.000	9.46	0.00	31.06	4.26
5572	5656	6.073058	TCGCTAATTATTGAATGCTGGATGTC	60.073	38.462	0.00	0.00	0.00	3.06
5651	5740	7.255381	CCTCCCTTTGTTCATAATGATGATGAC	60.255	40.741	0.00	0.00	41.77	3.06
5662	5751	8.431222	TCATAATGATGATGACATGTGGACTTA	58.569	33.333	1.15	0.00	37.15	2.24
5677	5777	5.654650	TGTGGACTTAACTTGAATGTTTGGT	59.345	36.000	0.00	0.00	0.00	3.67
5688	5788	9.965824	AACTTGAATGTTTGGTTATTTACAGAG	57.034	29.630	0.00	0.00	0.00	3.35
5689	5789	9.349713	ACTTGAATGTTTGGTTATTTACAGAGA	57.650	29.630	0.00	0.00	0.00	3.10
5690	5790	9.612620	CTTGAATGTTTGGTTATTTACAGAGAC	57.387	33.333	0.00	0.00	0.00	3.36
5693	5793	9.959749	GAATGTTTGGTTATTTACAGAGACAAA	57.040	29.630	0.00	0.00	0.00	2.83
5697	5797	6.548441	TGGTTATTTACAGAGACAAAACGG	57.452	37.500	0.00	0.00	0.00	4.44
5699	5799	6.425721	TGGTTATTTACAGAGACAAAACGGAG	59.574	38.462	0.00	0.00	0.00	4.63
5700	5800	6.128363	GGTTATTTACAGAGACAAAACGGAGG	60.128	42.308	0.00	0.00	0.00	4.30
5701	5801	4.675976	TTTACAGAGACAAAACGGAGGA	57.324	40.909	0.00	0.00	0.00	3.71
5703	5803	1.344763	ACAGAGACAAAACGGAGGAGG	59.655	52.381	0.00	0.00	0.00	4.30
5707	5807	1.462627	ACAAAACGGAGGAGGGGGA	60.463	57.895	0.00	0.00	0.00	4.81
5714	5814	2.710826	GGAGGAGGGGGAGAGAGCT	61.711	68.421	0.00	0.00	0.00	4.09
5721	5821	3.071206	GGGAGAGAGCTGCCGTCA	61.071	66.667	0.00	0.00	43.07	4.35
5722	5822	2.493973	GGAGAGAGCTGCCGTCAG	59.506	66.667	0.00	0.00	43.16	3.51
5804	5917	5.301979	TCTCCCCTCCTTTTTATAATCCCA	58.698	41.667	0.00	0.00	0.00	4.37
5861	5976	0.035820	ATTCTTAAACTCGCCCCGCA	60.036	50.000	0.00	0.00	0.00	5.69
5863	5978	2.744709	TTAAACTCGCCCCGCAGC	60.745	61.111	0.00	0.00	0.00	5.25
5880	5995	2.193248	CCCCTTCCATTCCTCGCC	59.807	66.667	0.00	0.00	0.00	5.54
6282	6445	2.967397	CTCCCTTGGCGTACGTGA	59.033	61.111	17.90	0.18	0.00	4.35

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
415	442	4.789012	TTGTTTATTCGGGAGTACTCGT	57.211	40.909	16.56	3.20	41.23	4.18
416	443	6.976925	AGTATTTGTTTATTCGGGAGTACTCG	59.023	38.462	16.56	7.21	41.91	4.18
922	968	2.852748	ACGATCTTGAAGTCTTCGACG	58.147	47.619	16.91	8.54	37.67	5.12
943	989	7.175990	AGCCAAGAATAACGGAAATACAAAAGA	59.824	33.333	0.00	0.00	0.00	2.52
955	1001	3.689161	TCAATGTGAGCCAAGAATAACGG	59.311	43.478	0.00	0.00	0.00	4.44
1005	1051	0.881118	GCGATCTTTTTGGAGCACCA	59.119	50.000	0.00	0.00	45.34	4.17
1230	1276	2.104170	GGGTGGTCAACAAAGTTGGAA	58.896	47.619	9.72	0.00	0.00	3.53
1513	1559	7.445402	GTCTTTATTATCTTTCCAGGCTATGCA	59.555	37.037	0.00	0.00	0.00	3.96
1514	1560	7.094592	GGTCTTTATTATCTTTCCAGGCTATGC	60.095	40.741	0.00	0.00	0.00	3.14
1556	1602	4.510711	CAGTATCATCTGGCTGATCAACAC	59.489	45.833	3.65	1.30	37.13	3.32
1992	2038	3.701205	TTAACAGCTCCATCAGAAGCA	57.299	42.857	0.00	0.00	0.00	3.91
2286	2332	0.525761	CACGCATTTTGGACCGGAAT	59.474	50.000	9.46	0.00	0.00	3.01
2396	2442	9.656040	CAAATTTCCAGAAATGGAATGTGATTA	57.344	29.630	10.35	0.00	46.18	1.75
2513	2559	9.535270	CAAGAAGAAATAAAAGAACGTGAGATC	57.465	33.333	0.00	0.00	0.00	2.75
2740	2787	7.095102	CCAAATGTGAAGGGATTTTGAACATTC	60.095	37.037	0.00	0.00	36.14	2.67
2930	2978	4.081198	GGTGATAATGGACCATGGCAAAAA	60.081	41.667	13.04	0.00	31.97	1.94
3470	3523	5.220491	GCTAATGGAAGAAGTTCGCTACAAG	60.220	44.000	0.00	0.00	32.92	3.16
3647	3700	4.345859	AGAAACGGTCATTAGAACACCA	57.654	40.909	0.00	0.00	0.00	4.17
4077	4138	3.042887	CACCTTTCTGCAAAGCGTAAAC	58.957	45.455	0.00	0.00	38.19	2.01
4157	4218	1.673665	CTCCACTGCAACTGGAGCC	60.674	63.158	21.59	0.00	46.53	4.70
4218	4279	4.766891	AGAGAGAGAGAGGAACAAAGAGTG	59.233	45.833	0.00	0.00	0.00	3.51
4290	4351	4.451557	GAATACAAACGAACGTCTGGTTG	58.548	43.478	14.21	14.21	39.50	3.77
4299	4360	5.574443	ACCTTAGTAGCGAATACAAACGAAC	59.426	40.000	0.00	0.00	36.79	3.95
4387	4448	2.926200	CTCGTTGCAGAGATTGTACTGG	59.074	50.000	0.00	0.00	40.57	4.00
4471	4533	2.009051	TGCTATGACACAGAAATGGCG	58.991	47.619	0.00	0.00	31.06	5.69
4497	4559	1.321016	CATGAGCGCTCAAAAACACG	58.679	50.000	40.83	19.93	43.58	4.49
4597	4659	7.750947	ATACTGTACTTTAACCTGAAGGGAT	57.249	36.000	0.56	0.00	40.27	3.85
4599	4661	7.494952	GCTTATACTGTACTTTAACCTGAAGGG	59.505	40.741	0.56	0.00	40.27	3.95
4682	4744	5.116882	GTTTCCAAGTATATGACTTCGCCT	58.883	41.667	0.00	0.00	45.81	5.52
4795	4857	7.121168	ACAAGACAAGATTTGAAAGACAGTGAA	59.879	33.333	0.00	0.00	0.00	3.18
4894	4956	1.133025	CCGGTTCCAAATCAGATGCAC	59.867	52.381	0.00	0.00	0.00	4.57
4969	5031	0.323629	GTCCCGGAGTTCATGTTCCA	59.676	55.000	0.73	0.00	32.87	3.53
5209	5273	3.406361	GTCTGCGACCACTGCACG	61.406	66.667	0.00	0.00	37.44	5.34
5393	5463	9.244799	CTTTTCCCTCTTTTATACACAAACAAC	57.755	33.333	0.00	0.00	0.00	3.32
5412	5482	4.252878	CTGAGCTTCTCTTCTCTTTTCCC	58.747	47.826	0.00	0.00	0.00	3.97
5435	5505	0.586319	CACAACACGGCCTACAACAG	59.414	55.000	0.00	0.00	0.00	3.16
5552	5636	7.262772	CAACTGACATCCAGCATTCAATAATT	58.737	34.615	0.00	0.00	46.81	1.40
5572	5656	8.830580	ACATTCGATGATAAATAGTTCCAACTG	58.169	33.333	2.01	0.00	40.07	3.16
5604	5688	1.382240	CCACCCATGGGCTACAACA	59.618	57.895	31.73	0.00	43.04	3.33
5651	5740	6.642131	CCAAACATTCAAGTTAAGTCCACATG	59.358	38.462	0.00	0.00	0.00	3.21
5662	5751	9.965824	CTCTGTAAATAACCAAACATTCAAGTT	57.034	29.630	0.00	0.00	0.00	2.66
5677	5777	6.761312	TCCTCCGTTTTGTCTCTGTAAATAA	58.239	36.000	0.00	0.00	0.00	1.40
5683	5783	1.344763	CCTCCTCCGTTTTGTCTCTGT	59.655	52.381	0.00	0.00	0.00	3.41
5684	5784	1.338200	CCCTCCTCCGTTTTGTCTCTG	60.338	57.143	0.00	0.00	0.00	3.35
5686	5786	0.036294	CCCCTCCTCCGTTTTGTCTC	60.036	60.000	0.00	0.00	0.00	3.36
5688	5788	1.002502	CCCCCTCCTCCGTTTTGTC	60.003	63.158	0.00	0.00	0.00	3.18
5689	5789	1.462627	TCCCCCTCCTCCGTTTTGT	60.463	57.895	0.00	0.00	0.00	2.83
5690	5790	1.198759	TCTCCCCCTCCTCCGTTTTG	61.199	60.000	0.00	0.00	0.00	2.44
5693	5793	2.231540	CTCTCTCCCCCTCCTCCGTT	62.232	65.000	0.00	0.00	0.00	4.44
5697	5797	1.457455	CAGCTCTCTCCCCCTCCTC	60.457	68.421	0.00	0.00	0.00	3.71
5699	5799	3.160748	GCAGCTCTCTCCCCCTCC	61.161	72.222	0.00	0.00	0.00	4.30
5700	5800	3.160748	GGCAGCTCTCTCCCCCTC	61.161	72.222	0.00	0.00	0.00	4.30
5703	5803	3.844090	GACGGCAGCTCTCTCCCC	61.844	72.222	0.00	0.00	0.00	4.81
5804	5917	0.601841	CGTCCGTTGCTAAAGGTGGT	60.602	55.000	0.00	0.00	0.00	4.16
5861	5976	3.049080	GCGAGGAATGGAAGGGGCT	62.049	63.158	0.00	0.00	0.00	5.19
5863	5978	2.193248	GGCGAGGAATGGAAGGGG	59.807	66.667	0.00	0.00	0.00	4.79

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.