AutoCloner

Multiple sequence alignment - TraesCS5D01G053000

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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	TraesCS5D01G053000	chr5D	100.000	6277	0	0	432	6708	50777385	50783661	0.000000e+00	11592.0
1	TraesCS5D01G053000	chr5D	100.000	72	0	0	1	72	50776954	50777025	4.220000e-27	134.0
2	TraesCS5D01G053000	chr5D	92.683	82	6	0	5218	5299	50782249	50782168	1.180000e-22	119.0
3	TraesCS5D01G053000	chr5D	88.235	85	10	0	3483	3567	297499910	297499826	1.190000e-17	102.0
4	TraesCS5D01G053000	chr5A	97.703	5138	92	14	432	5562	40097219	40102337	0.000000e+00	8811.0
5	TraesCS5D01G053000	chr5A	91.866	627	44	4	6088	6708	40110106	40110731	0.000000e+00	869.0
6	TraesCS5D01G053000	chr5A	92.607	514	27	8	5561	6073	40102578	40103081	0.000000e+00	728.0
7	TraesCS5D01G053000	chr5A	79.316	585	105	6	6121	6704	517858455	517859024	4.880000e-106	396.0
8	TraesCS5D01G053000	chr5A	97.222	72	2	0	1	72	40096865	40096936	9.140000e-24	122.0
9	TraesCS5D01G053000	chr5B	98.382	4080	56	6	874	4947	53657172	53661247	0.000000e+00	7160.0
10	TraesCS5D01G053000	chr5B	93.768	1059	22	17	4968	6026	53661941	53662955	0.000000e+00	1550.0
11	TraesCS5D01G053000	chr5B	91.493	623	46	5	6088	6708	53669884	53670501	0.000000e+00	850.0
12	TraesCS5D01G053000	chr5B	98.639	441	5	1	433	873	53656590	53657029	0.000000e+00	780.0
13	TraesCS5D01G053000	chr5B	98.611	72	1	0	1	72	53656107	53656178	1.960000e-25	128.0
14	TraesCS5D01G053000	chr6B	83.000	600	101	1	6086	6684	163800699	163801298	5.920000e-150	542.0
15	TraesCS5D01G053000	chr7A	92.391	92	7	0	3479	3570	232745457	232745366	1.520000e-26	132.0
16	TraesCS5D01G053000	chr2B	93.023	86	4	2	3482	3567	799282585	799282668	2.540000e-24	124.0
17	TraesCS5D01G053000	chr3B	90.000	90	8	1	3477	3565	405228863	405228774	1.530000e-21	115.0
18	TraesCS5D01G053000	chr3B	87.640	89	11	0	3479	3567	113517569	113517657	3.310000e-18	104.0
19	TraesCS5D01G053000	chr2A	88.506	87	10	0	3484	3570	102688124	102688038	9.200000e-19	106.0
20	TraesCS5D01G053000	chr2A	89.286	84	9	0	3483	3566	102688041	102688124	9.200000e-19	106.0
21	TraesCS5D01G053000	chr1D	85.897	78	11	0	5217	5294	69266638	69266561	4.310000e-12	84.2
22	TraesCS5D01G053000	chr1A	84.091	88	11	3	5215	5300	2945586	2945672	1.550000e-11	82.4

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	TraesCS5D01G053000	chr5D	50776954	50783661	6707	False	5863.000000	11592	100.000	1	6708	2	chr5D.!!$F1	6707
1	TraesCS5D01G053000	chr5A	40096865	40103081	6216	False	3220.333333	8811	95.844	1	6073	3	chr5A.!!$F3	6072
2	TraesCS5D01G053000	chr5A	40110106	40110731	625	False	869.000000	869	91.866	6088	6708	1	chr5A.!!$F1	620
3	TraesCS5D01G053000	chr5A	517858455	517859024	569	False	396.000000	396	79.316	6121	6704	1	chr5A.!!$F2	583
4	TraesCS5D01G053000	chr5B	53656107	53662955	6848	False	2404.500000	7160	97.350	1	6026	4	chr5B.!!$F2	6025
5	TraesCS5D01G053000	chr5B	53669884	53670501	617	False	850.000000	850	91.493	6088	6708	1	chr5B.!!$F1	620
6	TraesCS5D01G053000	chr6B	163800699	163801298	599	False	542.000000	542	83.000	6086	6684	1	chr6B.!!$F1	598

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
1044	1239	5.189736	TGATGCAGAAATGGAAGGTACTAGT	59.810	40.000	0.00	0.00	38.49	2.57	F
1617	1812	4.356436	TGAGATCAGTGAGGATCCTTTCA	58.644	43.478	17.42	7.75	43.79	2.69	F
2029	2224	5.523552	TGTGCATTTATGTTAGATGAGTCGG	59.476	40.000	0.00	0.00	0.00	4.79	F
3258	3453	6.737254	TTTGTTTAGTCCTTAGTAGCATGC	57.263	37.500	10.51	10.51	0.00	4.06	F
3491	3686	7.468496	TGAGTACCTTATTATCTACTCCCTCC	58.532	42.308	0.00	0.00	35.99	4.30	F
4326	4521	3.118629	TGATGCTCGTTTCTAGGCTTGAT	60.119	43.478	0.00	0.00	0.00	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2029	2224	6.582636	TCAGTAACCATTCATAGGATGTCAC	58.417	40.000	0.00	0.00	0.00	3.67	R
3589	3784	5.008019	CCTGGAATAGATGTAATGTGCACAC	59.992	44.000	24.37	10.59	0.00	3.82	R
3623	3818	3.202906	TGACTTGCTGAAACACCAGTAC	58.797	45.455	0.00	0.00	36.57	2.73	R
4066	4261	1.098869	GACAGATCGCTCAGACTCCA	58.901	55.000	0.00	0.00	0.00	3.86	R
4542	4740	2.880268	GGCTGTGCTGACATATTATGCA	59.120	45.455	3.52	0.00	0.00	3.96	R
6074	7193	0.110509	GCATCGATCATTCGCGCAAT	60.111	50.000	8.75	3.54	45.10	3.56	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
1044	1239	5.189736	TGATGCAGAAATGGAAGGTACTAGT	59.810	40.000	0.00	0.00	38.49	2.57
1449	1644	4.500499	AAAGGATGATGAGCAGCTTACT	57.500	40.909	0.00	0.00	32.29	2.24
1617	1812	4.356436	TGAGATCAGTGAGGATCCTTTCA	58.644	43.478	17.42	7.75	43.79	2.69
2029	2224	5.523552	TGTGCATTTATGTTAGATGAGTCGG	59.476	40.000	0.00	0.00	0.00	4.79
3258	3453	6.737254	TTTGTTTAGTCCTTAGTAGCATGC	57.263	37.500	10.51	10.51	0.00	4.06
3491	3686	7.468496	TGAGTACCTTATTATCTACTCCCTCC	58.532	42.308	0.00	0.00	35.99	4.30
4290	4485	4.397417	GGAAATCTCACTCAGTCCATTTGG	59.603	45.833	0.00	0.00	0.00	3.28
4326	4521	3.118629	TGATGCTCGTTTCTAGGCTTGAT	60.119	43.478	0.00	0.00	0.00	2.57
4328	4523	3.674997	TGCTCGTTTCTAGGCTTGATTT	58.325	40.909	0.00	0.00	0.00	2.17
4438	4636	3.624861	GGTTTCAATGCGATCTGACATCT	59.375	43.478	0.00	0.00	0.00	2.90
4439	4637	4.095483	GGTTTCAATGCGATCTGACATCTT	59.905	41.667	0.00	0.00	0.00	2.40
4444	4642	3.525268	TGCGATCTGACATCTTGCTTA	57.475	42.857	0.00	0.00	0.00	3.09
4542	4740	1.056700	AGTGTGGTCAGTGCTCCCTT	61.057	55.000	2.57	0.00	0.00	3.95
4755	4953	5.123820	TCGAGCCATTTAATTTGAGGACTTG	59.876	40.000	0.00	0.00	0.00	3.16
5231	6107	5.104360	TCACCAGTACTACCTCCGTAACTAT	60.104	44.000	0.00	0.00	0.00	2.12
5708	6827	3.751175	TGGTGGCGAAAGTAATTTCTGAG	59.249	43.478	13.26	0.12	0.00	3.35
5712	6831	5.123979	GTGGCGAAAGTAATTTCTGAGGAAT	59.876	40.000	13.26	0.00	0.00	3.01
5713	6832	5.123820	TGGCGAAAGTAATTTCTGAGGAATG	59.876	40.000	13.26	0.00	0.00	2.67
5714	6833	5.030936	GCGAAAGTAATTTCTGAGGAATGC	58.969	41.667	13.26	3.63	0.00	3.56
5715	6834	5.391950	GCGAAAGTAATTTCTGAGGAATGCA	60.392	40.000	13.26	0.00	0.00	3.96
5716	6835	6.253746	CGAAAGTAATTTCTGAGGAATGCAG	58.746	40.000	13.26	0.00	34.71	4.41
5717	6836	6.128172	CGAAAGTAATTTCTGAGGAATGCAGT	60.128	38.462	13.26	0.00	34.98	4.40
5747	6866	8.928448	AGTAGTACCATTGATGTGTGAATATCT	58.072	33.333	0.00	0.00	0.00	1.98
5790	6909	2.300956	TTGTTGTATGGGCATGGTGT	57.699	45.000	0.00	0.00	0.00	4.16
5822	6941	5.390087	TCCTAAGCTGTATGTAGGTCTCT	57.610	43.478	8.04	0.00	36.54	3.10
5899	7018	3.181445	TGGAGTGGAAGTATTGTGCAGTT	60.181	43.478	0.00	0.00	0.00	3.16
5939	7058	6.867662	GAGCATCTTAAATAGCAGCCTTAA	57.132	37.500	0.00	0.00	0.00	1.85
5955	7074	2.442413	CTTAATTTTGGGCACGAGGGA	58.558	47.619	0.00	0.00	0.00	4.20
5985	7104	1.228367	CTCCAACAGCTGCCCAACT	60.228	57.895	15.27	0.00	0.00	3.16
5986	7105	1.228245	TCCAACAGCTGCCCAACTC	60.228	57.895	15.27	0.00	0.00	3.01
5989	7108	1.545428	CCAACAGCTGCCCAACTCTAA	60.545	52.381	15.27	0.00	0.00	2.10
6029	7148	2.435372	TGGGCAGCCCTAAAATACAG	57.565	50.000	31.51	0.00	45.70	2.74
6042	7161	5.240623	CCTAAAATACAGCACCAAGTGTTGA	59.759	40.000	16.90	3.16	45.27	3.18
6056	7175	8.677300	CACCAAGTGTTGAAAATATATAGCACT	58.323	33.333	0.00	0.00	37.52	4.40
6073	7192	0.178992	ACTTGGGCTGTTGCTGCTAA	60.179	50.000	0.00	0.00	39.59	3.09
6074	7193	0.961019	CTTGGGCTGTTGCTGCTAAA	59.039	50.000	0.00	0.00	39.59	1.85
6075	7194	1.547372	CTTGGGCTGTTGCTGCTAAAT	59.453	47.619	0.00	0.00	39.59	1.40
6076	7195	1.631405	TGGGCTGTTGCTGCTAAATT	58.369	45.000	0.00	0.00	39.59	1.82
6077	7196	1.273048	TGGGCTGTTGCTGCTAAATTG	59.727	47.619	0.00	0.00	39.59	2.32
6078	7197	1.353076	GGCTGTTGCTGCTAAATTGC	58.647	50.000	0.00	0.00	39.59	3.56
6079	7198	0.986992	GCTGTTGCTGCTAAATTGCG	59.013	50.000	0.00	0.00	36.03	4.85
6080	7199	0.986992	CTGTTGCTGCTAAATTGCGC	59.013	50.000	0.00	0.00	35.36	6.09
6081	7200	0.728803	TGTTGCTGCTAAATTGCGCG	60.729	50.000	0.00	0.00	36.08	6.86
6082	7201	0.454285	GTTGCTGCTAAATTGCGCGA	60.454	50.000	12.10	0.00	36.08	5.87
6083	7202	0.239613	TTGCTGCTAAATTGCGCGAA	59.760	45.000	12.10	0.00	36.08	4.70
6084	7203	0.451383	TGCTGCTAAATTGCGCGAAT	59.549	45.000	12.10	3.86	36.08	3.34
6111	7230	4.751600	CGATGCAAGGAATGAATAGTAGCA	59.248	41.667	0.00	0.00	0.00	3.49
6297	7418	1.268352	AGAGACGCTATCGAATGCCTC	59.732	52.381	7.30	8.57	39.41	4.70
6325	7446	1.151668	CCAACTTCAGAAGGAGTGCG	58.848	55.000	14.90	1.41	0.00	5.34
6354	7475	0.743688	CGGCAGTGTAGAGCTCTGAT	59.256	55.000	26.78	6.25	40.17	2.90
6451	7577	1.865970	GTGCTGATGACTGATGCTAGC	59.134	52.381	8.10	8.10	0.00	3.42
6501	7627	3.044235	TGCTATGGAATGTATGAGGCG	57.956	47.619	0.00	0.00	0.00	5.52
6506	7632	2.046292	TGGAATGTATGAGGCGGATCA	58.954	47.619	0.00	0.00	0.00	2.92
6550	7676	2.970639	CCGTCCTTCTTCGGCAGA	59.029	61.111	0.00	0.00	40.28	4.26
6593	7719	2.376518	AGGTCAGAGAAATTGCCTCCAA	59.623	45.455	4.92	0.00	35.01	3.53
6629	7755	1.078759	CTCGAAGACCGCCATGACAC	61.079	60.000	0.00	0.00	38.37	3.67
6690	7816	4.104183	GAAACCATCCGGCCCCGA	62.104	66.667	8.54	0.00	42.83	5.14

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
16	17	6.152589	AACCAGGGTTTTCAAAATGGCACA	62.153	41.667	0.00	0.00	37.77	4.57
1044	1239	5.070981	GTCTCCATCAATCTCAATAGGGACA	59.929	44.000	0.00	0.00	0.00	4.02
1449	1644	5.321102	TCTGGCTTATTAAAGTTTGCCTCA	58.679	37.500	13.33	0.24	40.82	3.86
1617	1812	2.888414	CAGTGTACCGGGTTTTGGAATT	59.112	45.455	4.31	0.00	0.00	2.17
2029	2224	6.582636	TCAGTAACCATTCATAGGATGTCAC	58.417	40.000	0.00	0.00	0.00	3.67
3258	3453	9.445786	AAAACAACATAGTGATTTTGTTAGACG	57.554	29.630	3.39	0.00	42.44	4.18
3549	3744	7.184067	ACCTAAATACTCCCTCTGTAACTTG	57.816	40.000	0.00	0.00	0.00	3.16
3589	3784	5.008019	CCTGGAATAGATGTAATGTGCACAC	59.992	44.000	24.37	10.59	0.00	3.82
3623	3818	3.202906	TGACTTGCTGAAACACCAGTAC	58.797	45.455	0.00	0.00	36.57	2.73
4066	4261	1.098869	GACAGATCGCTCAGACTCCA	58.901	55.000	0.00	0.00	0.00	3.86
4290	4485	2.458592	GCATCAGGCGACATGTTTAC	57.541	50.000	0.00	0.00	0.00	2.01
4326	4521	3.550820	TCAAGCTGCTTACTTGACCAAA	58.449	40.909	15.51	0.00	46.46	3.28
4328	4523	2.928801	TCAAGCTGCTTACTTGACCA	57.071	45.000	15.51	0.00	46.46	4.02
4438	4636	4.757657	TGCCTTGAACTTTATCGTAAGCAA	59.242	37.500	0.00	0.00	37.18	3.91
4439	4637	4.320023	TGCCTTGAACTTTATCGTAAGCA	58.680	39.130	0.00	0.00	37.18	3.91
4444	4642	4.485163	GCAATTGCCTTGAACTTTATCGT	58.515	39.130	20.06	0.00	36.97	3.73
4542	4740	2.880268	GGCTGTGCTGACATATTATGCA	59.120	45.455	3.52	0.00	0.00	3.96
4755	4953	4.534168	GCCCTAAACTCAAAACTCGTTTC	58.466	43.478	0.00	0.00	33.40	2.78
5251	6127	6.397272	AGACATTTTTGCAGTTCAGTTTGAA	58.603	32.000	0.00	0.00	33.32	2.69
5252	6128	5.964758	AGACATTTTTGCAGTTCAGTTTGA	58.035	33.333	0.00	0.00	0.00	2.69
5253	6129	6.651755	AAGACATTTTTGCAGTTCAGTTTG	57.348	33.333	0.00	0.00	0.00	2.93
5713	6832	3.334691	TCAATGGTACTACTGCAACTGC	58.665	45.455	0.00	0.00	42.50	4.40
5714	6833	4.937620	ACATCAATGGTACTACTGCAACTG	59.062	41.667	0.00	0.00	0.00	3.16
5715	6834	4.937620	CACATCAATGGTACTACTGCAACT	59.062	41.667	0.00	0.00	0.00	3.16
5716	6835	4.695455	ACACATCAATGGTACTACTGCAAC	59.305	41.667	0.00	0.00	0.00	4.17
5717	6836	4.694982	CACACATCAATGGTACTACTGCAA	59.305	41.667	0.00	0.00	0.00	4.08
5790	6909	5.130975	ACATACAGCTTAGGATCATCCAACA	59.869	40.000	6.42	0.00	39.61	3.33
5822	6941	7.648142	ACATCAATTAGCGAAGTCAAAGAAAA	58.352	30.769	0.00	0.00	0.00	2.29
5899	7018	5.837979	AGATGCTCTTAGCTCCTAATTCTCA	59.162	40.000	0.00	0.00	42.97	3.27
5939	7058	1.710816	TTTTCCCTCGTGCCCAAAAT	58.289	45.000	0.00	0.00	0.00	1.82
5999	7118	1.905894	GGGCTGCCCAAAAGGAAATTA	59.094	47.619	32.46	0.00	44.65	1.40
6029	7148	7.432252	GTGCTATATATTTTCAACACTTGGTGC	59.568	37.037	0.00	0.00	36.98	5.01
6042	7161	6.461509	GCAACAGCCCAAGTGCTATATATTTT	60.462	38.462	0.00	0.00	40.32	1.82
6056	7175	1.631405	ATTTAGCAGCAACAGCCCAA	58.369	45.000	0.00	0.00	0.00	4.12
6073	7192	1.661178	GCATCGATCATTCGCGCAATT	60.661	47.619	8.75	0.00	45.10	2.32
6074	7193	0.110509	GCATCGATCATTCGCGCAAT	60.111	50.000	8.75	3.54	45.10	3.56
6075	7194	1.276547	GCATCGATCATTCGCGCAA	59.723	52.632	8.75	0.78	45.10	4.85
6076	7195	1.427592	TTGCATCGATCATTCGCGCA	61.428	50.000	8.75	0.00	45.50	6.09
6077	7196	0.720500	CTTGCATCGATCATTCGCGC	60.720	55.000	0.00	0.00	45.10	6.86
6078	7197	0.110956	CCTTGCATCGATCATTCGCG	60.111	55.000	0.00	0.00	45.10	5.87
6079	7198	1.220529	TCCTTGCATCGATCATTCGC	58.779	50.000	0.00	0.00	45.10	4.70
6080	7199	3.495753	TCATTCCTTGCATCGATCATTCG	59.504	43.478	0.00	0.00	46.87	3.34
6081	7200	5.428496	TTCATTCCTTGCATCGATCATTC	57.572	39.130	0.00	0.00	0.00	2.67
6082	7201	6.713903	ACTATTCATTCCTTGCATCGATCATT	59.286	34.615	0.00	0.00	0.00	2.57
6083	7202	6.236409	ACTATTCATTCCTTGCATCGATCAT	58.764	36.000	0.00	0.00	0.00	2.45
6084	7203	5.614308	ACTATTCATTCCTTGCATCGATCA	58.386	37.500	0.00	0.00	0.00	2.92
6095	7214	6.183361	CCCTTTCTCTGCTACTATTCATTCCT	60.183	42.308	0.00	0.00	0.00	3.36
6171	7290	1.176619	TCGTCCTGCCTTCTGAACGA	61.177	55.000	0.00	0.00	0.00	3.85
6297	7418	5.188434	TCCTTCTGAAGTTGGATATTGCTG	58.812	41.667	15.72	0.00	0.00	4.41
6343	7464	2.947652	GCAAAATGCCATCAGAGCTCTA	59.052	45.455	17.75	5.63	37.42	2.43
6354	7475	2.177394	TCTCTACGTGCAAAATGCCA	57.823	45.000	0.00	0.00	44.23	4.92
6451	7577	2.173356	TGCCAAGGTTCTATCCATGAGG	59.827	50.000	0.00	0.00	0.00	3.86
6501	7627	1.153349	GGTGACTTCCGGCTGATCC	60.153	63.158	0.00	0.00	0.00	3.36
6506	7632	2.671070	CATGGGTGACTTCCGGCT	59.329	61.111	0.00	0.00	0.00	5.52
6550	7676	0.620556	ACTCCACCATGATCGCCTTT	59.379	50.000	0.00	0.00	0.00	3.11
6593	7719	3.537580	TCGAGCACTTTTACAACTTGGT	58.462	40.909	0.00	0.00	0.00	3.67
6690	7816	2.436646	CTCCCGCGAACAAGGCAT	60.437	61.111	8.23	0.00	0.00	4.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.