AutoCloner

Multiple sequence alignment - TraesCS3D01G209900

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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	TraesCS3D01G209900	chr3D	100.000	4806	0	0	1	4806	277542086	277537281	0.000000e+00	8876.0
1	TraesCS3D01G209900	chr3D	92.727	55	4	0	4622	4676	567708588	567708642	3.990000e-11	80.5
2	TraesCS3D01G209900	chr3A	96.765	3524	64	17	1	3487	361991567	361995077	0.000000e+00	5830.0
3	TraesCS3D01G209900	chr3A	96.095	1050	34	3	3578	4622	361995074	361996121	0.000000e+00	1705.0
4	TraesCS3D01G209900	chr3A	92.857	154	9	1	4655	4806	361996115	361996268	6.260000e-54	222.0
5	TraesCS3D01G209900	chr3B	95.871	3439	80	29	1	3408	372838900	372842307	0.000000e+00	5507.0
6	TraesCS3D01G209900	chr3B	92.724	1072	28	13	3580	4622	372842306	372843356	0.000000e+00	1502.0
7	TraesCS3D01G209900	chr3B	87.662	154	15	3	4656	4806	372843351	372843503	4.940000e-40	176.0
8	TraesCS3D01G209900	chr3B	96.000	50	2	0	4618	4667	628478802	628478851	1.110000e-11	82.4
9	TraesCS3D01G209900	chr3B	92.593	54	4	0	4617	4670	26648172	26648225	1.430000e-10	78.7
10	TraesCS3D01G209900	chr4D	93.636	110	6	1	3472	3580	26253940	26254049	3.850000e-36	163.0
11	TraesCS3D01G209900	chr7B	94.286	105	4	2	3483	3586	589348318	589348421	4.980000e-35	159.0
12	TraesCS3D01G209900	chr1A	93.519	108	6	1	3484	3590	351606858	351606751	4.980000e-35	159.0
13	TraesCS3D01G209900	chr7A	94.175	103	5	1	3481	3582	511927312	511927414	6.440000e-34	156.0
14	TraesCS3D01G209900	chr7A	93.333	105	5	2	3483	3586	628008575	628008472	2.320000e-33	154.0
15	TraesCS3D01G209900	chr7A	94.231	52	3	0	4620	4671	639594990	639594939	3.990000e-11	80.5
16	TraesCS3D01G209900	chr7D	93.333	105	5	2	3483	3586	545397537	545397640	2.320000e-33	154.0
17	TraesCS3D01G209900	chr7D	91.379	58	3	2	4608	4665	199127653	199127708	1.430000e-10	78.7
18	TraesCS3D01G209900	chr1B	91.892	111	7	2	3484	3592	56752488	56752378	2.320000e-33	154.0
19	TraesCS3D01G209900	chr1B	91.228	57	3	2	4618	4673	423585133	423585078	5.160000e-10	76.8
20	TraesCS3D01G209900	chr6D	90.351	114	8	3	3477	3589	368755201	368755090	3.880000e-31	147.0
21	TraesCS3D01G209900	chr4B	89.655	116	11	1	3480	3594	595278781	595278896	3.880000e-31	147.0
22	TraesCS3D01G209900	chr6B	94.545	55	1	2	4618	4672	277158983	277159035	3.080000e-12	84.2
23	TraesCS3D01G209900	chrUn	96.000	50	2	0	4618	4667	100223781	100223830	1.110000e-11	82.4
24	TraesCS3D01G209900	chr6A	92.727	55	2	2	4617	4670	613997767	613997714	1.430000e-10	78.7

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	TraesCS3D01G209900	chr3D	277537281	277542086	4805	True	8876.000000	8876	100.000000	1	4806	1	chr3D.!!$R1	4805
1	TraesCS3D01G209900	chr3A	361991567	361996268	4701	False	2585.666667	5830	95.239000	1	4806	3	chr3A.!!$F1	4805
2	TraesCS3D01G209900	chr3B	372838900	372843503	4603	False	2395.000000	5507	92.085667	1	4806	3	chr3B.!!$F3	4805

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
391	397	0.321034	ACATGATCCCATCGCCGATG	60.321	55.000	19.87	19.87	39.52	3.84	F
868	883	1.235281	ACAGCACGCGTGTAGAGAGA	61.235	55.000	36.80	0.00	0.00	3.10	F
969	1014	2.126734	CGTAAACCGACCGCTCGT	60.127	61.111	0.00	0.00	38.32	4.18	F
2057	2105	2.279517	CAGACGAGTATGCGGGCC	60.280	66.667	0.00	0.00	35.12	5.80	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1386	1431	0.654160	AGCGATCGTCGTCGTTGATA	59.346	50.000	17.81	42.81	2.15	R
2333	2384	2.489329	CAAAAAGTGCATCGGGTCTGAT	59.511	45.455	0.00	0.00	2.90	R
2341	2392	3.607422	TGAGTGACAAAAAGTGCATCG	57.393	42.857	0.00	0.00	3.84	R
3836	3888	1.004918	GTGAACTGCACGGCTAGGT	60.005	57.895	0.00	37.83	3.08	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
199	205	5.638234	AGAAGGTCGGTTATTCTTTCTTTCG	59.362	40.000	0.00	0.00	28.99	3.46
253	259	0.548510	AAGATGCTAACCCTCCCTGC	59.451	55.000	0.00	0.00	0.00	4.85
391	397	0.321034	ACATGATCCCATCGCCGATG	60.321	55.000	19.87	19.87	39.52	3.84
464	470	4.571984	TCTCCGCACAATCATATGACAAAG	59.428	41.667	7.78	0.96	0.00	2.77
475	481	8.767085	CAATCATATGACAAAGTGTTGCTTTTT	58.233	29.630	7.78	0.00	44.41	1.94
500	506	8.427902	TTCCAGATAGTATATGTGCTCTCATT	57.572	34.615	4.17	0.00	0.00	2.57
862	877	1.660264	CTCACACAGCACGCGTGTA	60.660	57.895	36.80	14.84	45.63	2.90
868	883	1.235281	ACAGCACGCGTGTAGAGAGA	61.235	55.000	36.80	0.00	0.00	3.10
969	1014	2.126734	CGTAAACCGACCGCTCGT	60.127	61.111	0.00	0.00	38.32	4.18
1386	1431	2.545810	CTCAGGGAGGAAGAGGACTTT	58.454	52.381	0.00	0.00	36.39	2.66
2057	2105	2.279517	CAGACGAGTATGCGGGCC	60.280	66.667	0.00	0.00	35.12	5.80
2317	2365	4.831674	TCATGCCTCATGAATATCCGAT	57.168	40.909	7.00	0.00	46.17	4.18
2318	2366	5.937975	TCATGCCTCATGAATATCCGATA	57.062	39.130	7.00	0.00	46.17	2.92
2319	2367	6.490241	TCATGCCTCATGAATATCCGATAT	57.510	37.500	7.00	0.00	46.17	1.63
2320	2368	6.519382	TCATGCCTCATGAATATCCGATATC	58.481	40.000	7.00	0.00	46.17	1.63
2333	2384	3.893521	TCCGATATCCTGTGTGTGTCTA	58.106	45.455	0.00	0.00	0.00	2.59
2341	2392	2.093973	CCTGTGTGTGTCTATCAGACCC	60.094	54.545	3.97	0.00	44.44	4.46
2512	2563	6.984474	CACCACCTCATCGTATTACAATAGTT	59.016	38.462	0.00	0.00	0.00	2.24
2527	2578	5.805728	ACAATAGTTACCCTGTGAAGAAGG	58.194	41.667	0.00	0.00	34.31	3.46
2603	2654	7.338449	TGTTTTGCTAGGTCAAAAGACTAAAGT	59.662	33.333	8.10	0.00	43.88	2.66
2627	2678	5.876357	ACCTATTGAATGGGCATACGTATT	58.124	37.500	7.55	0.00	33.57	1.89
2630	2681	7.040686	ACCTATTGAATGGGCATACGTATTTTC	60.041	37.037	7.55	5.41	33.57	2.29
2667	2719	6.209192	TGGAATGCTGTGAATTTTGTATCACT	59.791	34.615	7.35	0.00	44.86	3.41
2910	2962	1.794116	CAATTGCAAAGGAGCGGTTTG	59.206	47.619	1.71	0.00	37.85	2.93
2947	2999	4.997395	AGATAATGACGGGTACATGATTGC	59.003	41.667	0.00	0.00	0.00	3.56

Showing 1 to 25 of 121 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
199	205	9.494271	TTCAAGGATGTGATTATTGAGCTATAC	57.506	33.333	0.00	0.00	32.00	1.47
253	259	0.950836	TCCAAGTTGTTGCACATCCG	59.049	50.000	1.45	0.00	31.64	4.18
391	397	1.153549	CCGGCTCAGCTAGTTCCAC	60.154	63.158	0.00	0.00	0.00	4.02
475	481	8.427902	AATGAGAGCACATATACTATCTGGAA	57.572	34.615	0.00	0.00	0.00	3.53
500	506	3.581101	AGCCTGCCTCATCTTATACAGA	58.419	45.455	0.00	0.00	35.33	3.41
751	760	7.441458	AGCTGTAGAATCCATTAATTAACGGAC	59.559	37.037	14.89	4.23	0.00	4.79
862	877	1.736586	CCGCGCCAATAGTCTCTCT	59.263	57.895	0.00	0.00	0.00	3.10
1335	1380	1.273606	CACTCCTTCATGTGGTCGTCT	59.726	52.381	7.23	0.00	0.00	4.18
1386	1431	0.654160	AGCGATCGTCGTCGTTGATA	59.346	50.000	17.81	0.00	42.81	2.15
2045	2093	2.552231	AAACCCAGGCCCGCATACTC	62.552	60.000	0.00	0.00	0.00	2.59
2055	2103	2.963101	AGGTTCAAGTTTAAACCCAGGC	59.037	45.455	14.72	3.43	44.98	4.85
2057	2105	5.278315	GCAGTAGGTTCAAGTTTAAACCCAG	60.278	44.000	14.72	5.45	44.98	4.45
2177	2225	9.297586	TGAACGATGTAAAATCATGTACTCTAC	57.702	33.333	0.00	0.00	0.00	2.59
2270	2318	4.479156	TGGTAGAAAATTTTGGGGAGGT	57.521	40.909	8.47	0.00	0.00	3.85
2315	2363	6.442952	GTCTGATAGACACACACAGGATATC	58.557	44.000	4.20	0.00	44.45	1.63
2316	2364	5.303078	GGTCTGATAGACACACACAGGATAT	59.697	44.000	10.75	0.00	46.79	1.63
2317	2365	4.645136	GGTCTGATAGACACACACAGGATA	59.355	45.833	10.75	0.00	46.79	2.59
2318	2366	3.449018	GGTCTGATAGACACACACAGGAT	59.551	47.826	10.75	0.00	46.79	3.24
2319	2367	2.826128	GGTCTGATAGACACACACAGGA	59.174	50.000	10.75	0.00	46.79	3.86
2320	2368	3.238108	GGTCTGATAGACACACACAGG	57.762	52.381	10.75	0.00	46.79	4.00
2333	2384	2.489329	CAAAAAGTGCATCGGGTCTGAT	59.511	45.455	0.00	0.00	0.00	2.90
2341	2392	3.607422	TGAGTGACAAAAAGTGCATCG	57.393	42.857	0.00	0.00	0.00	3.84
2512	2563	4.412858	TGGTTTTACCTTCTTCACAGGGTA	59.587	41.667	0.00	0.00	39.58	3.69
2527	2578	5.587289	TGCTCAAACTTGATGTGGTTTTAC	58.413	37.500	0.00	0.00	36.46	2.01
2603	2654	4.967084	ACGTATGCCCATTCAATAGGTA	57.033	40.909	0.00	0.00	0.00	3.08

Showing 1 to 25 of 136 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.