AutoCloner

Multiple sequence alignment - TraesCS4A01G211300

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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	TraesCS4A01G211300	chr4A	100.000	2399	0	0	1	2399	504874850	504877248	0.000000e+00	4431
1	TraesCS4A01G211300	chr4A	90.674	2434	184	24	1	2399	23986701	23984276	0.000000e+00	3197
2	TraesCS4A01G211300	chr4A	90.357	2437	191	28	1	2399	325352084	325349654	0.000000e+00	3158
3	TraesCS4A01G211300	chr4A	95.918	245	10	0	1	245	504897656	504897900	4.810000e-107	398
4	TraesCS4A01G211300	chr4A	95.816	239	10	0	1	239	95770597	95770835	1.040000e-103	387
5	TraesCS4A01G211300	chr5A	92.184	2431	143	27	1	2399	379164997	379162582	0.000000e+00	3393
6	TraesCS4A01G211300	chr5A	91.233	2441	169	30	1	2399	115435385	115437822	0.000000e+00	3280
7	TraesCS4A01G211300	chr5A	90.741	2441	174	32	1	2399	358530010	358527580	0.000000e+00	3208
8	TraesCS4A01G211300	chr5A	95.102	245	12	0	1	245	626014016	626014260	1.040000e-103	387
9	TraesCS4A01G211300	chr2A	91.715	2438	157	28	1	2399	737482587	737485018	0.000000e+00	3341
10	TraesCS4A01G211300	chr2A	91.707	1459	87	18	1	1427	318389616	318388160	0.000000e+00	1993
11	TraesCS4A01G211300	chr2A	95.510	245	11	0	1	245	318384064	318383820	2.240000e-105	392
12	TraesCS4A01G211300	chr6A	91.571	2432	162	20	1	2399	496427101	496424680	0.000000e+00	3315
13	TraesCS4A01G211300	chr6A	89.349	2441	201	41	1	2399	41920784	41923207	0.000000e+00	3013
14	TraesCS4A01G211300	chr3A	87.838	2442	234	42	1	2399	625787216	625784795	0.000000e+00	2806
15	TraesCS4A01G211300	chr1A	95.510	245	11	0	1	245	191075104	191074860	2.240000e-105	392
16	TraesCS4A01G211300	chr1A	95.102	245	12	0	1	245	190883477	190883233	1.040000e-103	387
17	TraesCS4A01G211300	chr1A	95.102	245	12	0	1	245	445291966	445291722	1.040000e-103	387
18	TraesCS4A01G211300	chr7A	95.102	245	12	0	1	245	214881669	214881425	1.040000e-103	387
19	TraesCS4A01G211300	chrUn	92.653	245	17	1	1	245	180384497	180384740	3.790000e-93	351
20	TraesCS4A01G211300	chrUn	92.653	245	16	2	1	245	480774923	480775165	3.790000e-93	351

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	TraesCS4A01G211300	chr4A	504874850	504877248	2398	False	4431	4431	100.000	1	2399	1	chr4A.!!$F2	2398
1	TraesCS4A01G211300	chr4A	23984276	23986701	2425	True	3197	3197	90.674	1	2399	1	chr4A.!!$R1	2398
2	TraesCS4A01G211300	chr4A	325349654	325352084	2430	True	3158	3158	90.357	1	2399	1	chr4A.!!$R2	2398
3	TraesCS4A01G211300	chr5A	379162582	379164997	2415	True	3393	3393	92.184	1	2399	1	chr5A.!!$R2	2398
4	TraesCS4A01G211300	chr5A	115435385	115437822	2437	False	3280	3280	91.233	1	2399	1	chr5A.!!$F1	2398
5	TraesCS4A01G211300	chr5A	358527580	358530010	2430	True	3208	3208	90.741	1	2399	1	chr5A.!!$R1	2398
6	TraesCS4A01G211300	chr2A	737482587	737485018	2431	False	3341	3341	91.715	1	2399	1	chr2A.!!$F1	2398
7	TraesCS4A01G211300	chr2A	318388160	318389616	1456	True	1993	1993	91.707	1	1427	1	chr2A.!!$R2	1426
8	TraesCS4A01G211300	chr6A	496424680	496427101	2421	True	3315	3315	91.571	1	2399	1	chr6A.!!$R1	2398
9	TraesCS4A01G211300	chr6A	41920784	41923207	2423	False	3013	3013	89.349	1	2399	1	chr6A.!!$F1	2398
10	TraesCS4A01G211300	chr3A	625784795	625787216	2421	True	2806	2806	87.838	1	2399	1	chr3A.!!$R1	2398

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
690	734	0.179067	AGAAGTTCACGCAACCGGAA	60.179	50.0	9.46	0.0	39.22	4.3	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1688	1752	0.106619	GTGGTGGTGGTGGGTTGTTA	60.107	55.0	0.0	0.0	0.0	2.41	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
98	99	9.912634	CAACCATTCTCAATGTTTAACAACTAT	57.087	29.630	0.66	0.00	37.18	2.12
254	290	7.851963	GTGTTACTTTGTCAGCAAACGTTAATA	59.148	33.333	0.00	0.00	39.43	0.98
349	387	5.485353	TGATGGACTCACTTATCTTCCAAGT	59.515	40.000	0.00	0.00	39.77	3.16
448	488	8.745590	TGTAATAAGTGTGTGATTGCTACTCTA	58.254	33.333	0.00	0.00	0.00	2.43
503	543	4.506271	GCATTACTGATCCAGGGATGACAT	60.506	45.833	5.35	0.00	35.51	3.06
557	597	4.207955	AGTCGCTACAGAGATGGTATCAA	58.792	43.478	0.00	0.00	0.00	2.57
581	621	3.780902	CACACGCTGATTGTAGGACATA	58.219	45.455	0.00	0.00	0.00	2.29
611	652	9.073475	ACTAAGCTAAAGACCTAGATCACTATG	57.927	37.037	3.13	0.00	0.00	2.23
614	655	6.496565	AGCTAAAGACCTAGATCACTATGCAT	59.503	38.462	3.79	3.79	0.00	3.96
624	667	7.814107	CCTAGATCACTATGCATTCTCTTCTTC	59.186	40.741	3.54	0.00	0.00	2.87
672	716	1.450531	GGATGGCGGATGCAAGGAAG	61.451	60.000	0.00	0.00	45.35	3.46
690	734	0.179067	AGAAGTTCACGCAACCGGAA	60.179	50.000	9.46	0.00	39.22	4.30
714	758	2.838202	AGATACACCCTTTGGACGTCAT	59.162	45.455	18.91	0.00	34.81	3.06
717	761	2.253610	ACACCCTTTGGACGTCATCTA	58.746	47.619	18.91	0.00	34.81	1.98
760	804	3.802948	ACATAGGAGTACCAAGCTTCG	57.197	47.619	0.00	0.00	38.94	3.79
780	824	2.030958	CGGAACCTACAACGCCACC	61.031	63.158	0.00	0.00	0.00	4.61
798	842	2.231478	CACCTTACCTGAAGAAGAGCGA	59.769	50.000	0.00	0.00	37.33	4.93
856	900	1.912731	TGCCAGTCACTAAGCCCATAA	59.087	47.619	0.00	0.00	0.00	1.90
919	963	1.816679	GCAGCTCACATCGCCATGA	60.817	57.895	0.00	0.00	33.72	3.07
942	986	1.135083	CGCATTGGAGAAGTCTACCGT	60.135	52.381	0.00	0.00	0.00	4.83
1030	1079	6.994496	CAGCACCAGAAAGGATAGATCAATTA	59.006	38.462	0.00	0.00	41.22	1.40
1078	1127	1.260206	CATTCGACGTCAGGAGAACG	58.740	55.000	17.16	0.00	0.00	3.95
1080	1129	1.162698	TTCGACGTCAGGAGAACGAT	58.837	50.000	17.16	0.00	0.00	3.73
1111	1160	4.339530	CCGACATGATAGACCTGAAGAAGA	59.660	45.833	0.00	0.00	0.00	2.87
1119	1168	2.635427	AGACCTGAAGAAGACAAGGACC	59.365	50.000	0.00	0.00	0.00	4.46
1209	1258	4.647424	AGTGGAGAAGAATGACGATCTC	57.353	45.455	0.00	0.00	36.41	2.75
1272	1321	7.052873	CAGTAGATGAAGATGAAGAACCCAAT	58.947	38.462	0.00	0.00	0.00	3.16
1387	1436	1.071542	TCATGGAGTCTGCAACCGAAA	59.928	47.619	0.00	0.00	0.00	3.46
1579	1642	6.790319	TCTTTTCTAAACCCTTAGATGCCTT	58.210	36.000	0.00	0.00	42.46	4.35
1605	1669	1.206371	CGTGACCCGGATTTACCTTCT	59.794	52.381	0.73	0.00	36.31	2.85
1688	1752	6.723052	AGAATCAGAATCAAGGGAACAACAAT	59.277	34.615	0.00	0.00	0.00	2.71
1716	1792	2.150719	CCACCACCACCACCACCTA	61.151	63.158	0.00	0.00	0.00	3.08
1774	1850	0.872388	GTGTTTTCCAGTAGCACCGG	59.128	55.000	0.00	0.00	0.00	5.28
1801	1877	2.406559	AGTAGCAGATGATTGGCTCCT	58.593	47.619	0.00	0.00	39.01	3.69
1832	1908	1.302832	GGAGTTGACCACAGCAGGG	60.303	63.158	0.00	0.00	0.00	4.45
1964	2040	1.603802	CAGTTTCAGCAGGCTTTTCGA	59.396	47.619	0.00	0.00	0.00	3.71
2228	2304	4.641989	GCTCTTATGATTGAAGGGAAGCAA	59.358	41.667	0.00	0.00	0.00	3.91
2240	2316	2.699846	AGGGAAGCAACAGCAAATTGAA	59.300	40.909	0.00	0.00	0.00	2.69
2255	2331	7.225145	CAGCAAATTGAAAATCACAAGAGGAAA	59.775	33.333	0.00	0.00	0.00	3.13
2260	2336	8.937634	ATTGAAAATCACAAGAGGAAATATGC	57.062	30.769	0.00	0.00	0.00	3.14
2300	2376	2.047844	GCTCAGCAGAAGCCACGA	60.048	61.111	0.00	0.00	43.56	4.35
2305	2381	3.201290	CTCAGCAGAAGCCACGATTTAT	58.799	45.455	0.00	0.00	43.56	1.40
2313	2389	4.841246	AGAAGCCACGATTTATCCCTAGAT	59.159	41.667	0.00	0.00	36.44	1.98
2350	2426	3.006323	CAGCATACTCATGGAGGAGGTAC	59.994	52.174	0.00	0.00	39.27	3.34

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
142	146	7.461182	TGGTTACAGTTTTGCATAAAGCTAT	57.539	32.000	0.00	0.00	45.94	2.97
222	227	7.414436	GTTTGCTGACAAAGTAACACATAGAA	58.586	34.615	0.00	0.00	46.17	2.10
239	244	5.411361	AGTCTGCAATATTAACGTTTGCTGA	59.589	36.000	20.63	20.63	45.73	4.26
254	290	2.476619	CGTCGTCTGAAAAGTCTGCAAT	59.523	45.455	0.00	0.00	0.00	3.56
349	387	8.141909	CCATCTAATAACGATAACAGTGGAAGA	58.858	37.037	0.00	0.00	0.00	2.87
419	459	8.040727	AGTAGCAATCACACACTTATTACATCA	58.959	33.333	0.00	0.00	0.00	3.07
503	543	2.754002	CAGTCTGATCTCTGTGCTCAGA	59.246	50.000	17.04	17.04	46.85	3.27
570	610	7.484993	TTAGCTTAGTGGTTATGTCCTACAA	57.515	36.000	0.00	0.00	0.00	2.41
581	621	6.668283	TGATCTAGGTCTTTAGCTTAGTGGTT	59.332	38.462	4.28	0.00	34.60	3.67
611	652	4.160252	AGAGGTCAGAGAAGAAGAGAATGC	59.840	45.833	0.00	0.00	0.00	3.56
614	655	4.991776	TGAGAGGTCAGAGAAGAAGAGAA	58.008	43.478	0.00	0.00	0.00	2.87
624	667	6.603201	AGAGTAGAAAAGATGAGAGGTCAGAG	59.397	42.308	0.00	0.00	35.66	3.35
672	716	0.234884	CTTCCGGTTGCGTGAACTTC	59.765	55.000	0.00	0.00	34.66	3.01
690	734	2.904434	ACGTCCAAAGGGTGTATCTTCT	59.096	45.455	0.00	0.00	34.93	2.85
714	758	7.640313	TCAGGTATCTAGTGACTTCCTTTAGA	58.360	38.462	0.00	0.00	0.00	2.10
717	761	6.497259	TGTTCAGGTATCTAGTGACTTCCTTT	59.503	38.462	0.00	0.00	0.00	3.11
760	804	3.122971	GGCGTTGTAGGTTCCGGC	61.123	66.667	0.00	0.00	38.68	6.13
780	824	3.131223	TCCATCGCTCTTCTTCAGGTAAG	59.869	47.826	0.00	0.00	36.45	2.34
798	842	6.012113	TGGAACTTGAACTTGAATCATCCAT	58.988	36.000	0.00	0.00	31.70	3.41
856	900	5.733676	AGTTGGTGCATCAAAAGAAAACTT	58.266	33.333	15.37	0.00	0.00	2.66
919	963	2.166664	GGTAGACTTCTCCAATGCGTCT	59.833	50.000	0.00	0.00	38.40	4.18
967	1011	1.153449	CTCGGCGCCCACAAATCTA	60.153	57.895	23.46	0.00	0.00	1.98
1030	1079	6.723977	TGGTTTAATTCCTGGATAAAAGCTGT	59.276	34.615	19.68	0.00	0.00	4.40
1078	1127	1.432514	ATCATGTCGGCGCACATATC	58.567	50.000	19.35	0.00	35.10	1.63
1080	1129	1.611491	TCTATCATGTCGGCGCACATA	59.389	47.619	19.35	11.88	35.10	2.29
1111	1160	3.395941	AGTTCCTTGATTCTGGTCCTTGT	59.604	43.478	0.00	0.00	0.00	3.16
1119	1168	3.988976	TCCTCCAGTTCCTTGATTCTG	57.011	47.619	0.00	0.00	0.00	3.02
1209	1258	8.671921	CCCATAAATATTCCGATCTTCTTGATG	58.328	37.037	0.00	0.00	35.14	3.07
1272	1321	0.970937	AGTCTTCCGGGCGAATCTCA	60.971	55.000	0.00	0.00	0.00	3.27
1387	1436	9.213777	TGATGAGGTGGTCTACTAGAAATATTT	57.786	33.333	0.00	0.00	0.00	1.40
1579	1642	1.246056	AAATCCGGGTCACGTCTCGA	61.246	55.000	0.00	0.00	42.24	4.04
1605	1669	0.827925	AACTGAGTGAGCTCCGGTGA	60.828	55.000	12.15	0.00	40.95	4.02
1688	1752	0.106619	GTGGTGGTGGTGGGTTGTTA	60.107	55.000	0.00	0.00	0.00	2.41
1716	1792	4.589908	AGAAAACGGGCTAAGTGATCAAT	58.410	39.130	0.00	0.00	0.00	2.57
1743	1819	0.109919	GAAAACACCGGCGGATTCAC	60.110	55.000	35.78	17.83	0.00	3.18
1774	1850	3.257393	CAATCATCTGCTACTATCGGCC	58.743	50.000	0.00	0.00	0.00	6.13
1801	1877	2.563179	GTCAACTCCCTAGCTGTCTTGA	59.437	50.000	0.00	0.00	0.00	3.02
1964	2040	0.963962	CTGCTGAAACATGGGCAGTT	59.036	50.000	14.26	0.00	44.69	3.16
1995	2071	3.792401	TGTGAAACTCTCGCTTCTTCAA	58.208	40.909	0.00	0.00	38.04	2.69
2118	2194	8.980481	TCATTCAGTCCTTCTAGAAACTTTTT	57.020	30.769	6.63	0.00	0.00	1.94
2120	2196	8.378565	TCATCATTCAGTCCTTCTAGAAACTTT	58.621	33.333	6.63	0.00	0.00	2.66
2228	2304	5.987347	CCTCTTGTGATTTTCAATTTGCTGT	59.013	36.000	0.00	0.00	0.00	4.40
2240	2316	6.839124	TGTGCATATTTCCTCTTGTGATTT	57.161	33.333	0.00	0.00	0.00	2.17
2255	2331	7.148018	CCTGAATTGTACTTTCCTTGTGCATAT	60.148	37.037	0.00	0.00	30.79	1.78
2260	2336	5.335191	GCTCCTGAATTGTACTTTCCTTGTG	60.335	44.000	0.00	0.00	0.00	3.33
2313	2389	0.690192	TGCTGAAAATGTCCTCCCGA	59.310	50.000	0.00	0.00	0.00	5.14
2350	2426	0.179156	GCCATTGTGATTGTGCGAGG	60.179	55.000	0.00	0.00	0.00	4.63

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.