AutoCloner

Multiple sequence alignment - TraesCS6D01G023400

Loading Multiple Alignment...

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	TraesCS6D01G023400	chr6D	100.000	3155	0	0	1	3155	8893058	8896212	0.000000e+00	5827.0
1	TraesCS6D01G023400	chr6D	99.152	1769	14	1	1387	3155	8402268	8400501	0.000000e+00	3182.0
2	TraesCS6D01G023400	chr6D	98.404	752	9	3	1	751	8404828	8404079	0.000000e+00	1319.0
3	TraesCS6D01G023400	chr6D	86.266	1165	156	4	993	2156	8397159	8395998	0.000000e+00	1262.0
4	TraesCS6D01G023400	chr6D	90.519	770	36	13	2	752	34006036	34006787	0.000000e+00	983.0
5	TraesCS6D01G023400	chr6D	78.768	1380	239	35	822	2173	33894860	33896213	0.000000e+00	876.0
6	TraesCS6D01G023400	chr6D	98.526	407	1	1	745	1151	8402667	8402266	0.000000e+00	713.0
7	TraesCS6D01G023400	chr6D	79.570	186	20	14	737	906	34006802	34006985	1.990000e-22	117.0
8	TraesCS6D01G023400	chr1B	91.587	2199	162	14	974	3155	630644723	630646915	0.000000e+00	3014.0
9	TraesCS6D01G023400	chr1B	85.105	1571	180	22	1003	2552	630649557	630651094	0.000000e+00	1555.0
10	TraesCS6D01G023400	chr1B	86.799	553	39	14	2616	3137	630651112	630651661	1.260000e-163	586.0
11	TraesCS6D01G023400	chr1B	92.553	94	7	0	12	105	99603427	99603520	5.490000e-28	135.0
12	TraesCS6D01G023400	chr6B	91.430	2077	146	14	1095	3155	15225632	15223572	0.000000e+00	2820.0
13	TraesCS6D01G023400	chr6B	86.798	2189	248	19	986	3155	65175128	65172962	0.000000e+00	2403.0
14	TraesCS6D01G023400	chr6B	94.383	1175	49	8	1396	2554	52573786	52572613	0.000000e+00	1788.0
15	TraesCS6D01G023400	chr6B	83.235	1181	194	3	978	2156	52568264	52567086	0.000000e+00	1081.0
16	TraesCS6D01G023400	chr6B	93.058	605	26	3	2548	3150	52572437	52571847	0.000000e+00	870.0
17	TraesCS6D01G023400	chr6B	84.437	604	60	15	238	818	52981804	52981212	5.910000e-157	564.0
18	TraesCS6D01G023400	chr6B	81.138	334	58	5	953	1284	55724058	55723728	2.410000e-66	263.0
19	TraesCS6D01G023400	chr6A	87.215	2190	256	8	988	3155	35581608	35579421	0.000000e+00	2471.0
20	TraesCS6D01G023400	chr6A	76.623	231	42	10	2677	2902	8394436	8394213	1.990000e-22	117.0
21	TraesCS6D01G023400	chr3A	82.909	1217	198	7	979	2189	45937993	45936781	0.000000e+00	1086.0
22	TraesCS6D01G023400	chr3D	81.558	1258	211	15	941	2189	33330545	33329300	0.000000e+00	1018.0
23	TraesCS6D01G023400	chr3D	92.500	40	3	0	117	156	81695013	81695052	1.220000e-04	58.4
24	TraesCS6D01G023400	chr3B	78.369	1202	230	25	990	2173	778342913	778341724	0.000000e+00	752.0
25	TraesCS6D01G023400	chr3B	87.069	116	12	2	13	126	406873521	406873407	9.190000e-26	128.0
26	TraesCS6D01G023400	chr4A	79.365	252	40	10	2652	2895	667381884	667382131	1.950000e-37	167.0
27	TraesCS6D01G023400	chr1A	88.889	108	11	1	2	109	495716116	495716222	7.100000e-27	132.0
28	TraesCS6D01G023400	chr1A	85.185	54	8	0	109	162	556171627	556171680	4.400000e-04	56.5
29	TraesCS6D01G023400	chr1D	87.963	108	12	1	2	109	398987454	398987560	3.300000e-25	126.0
30	TraesCS6D01G023400	chr5D	86.726	113	13	2	15	126	528814288	528814177	1.190000e-24	124.0
31	TraesCS6D01G023400	chr5D	92.453	53	4	0	822	874	499865208	499865156	3.370000e-10	76.8
32	TraesCS6D01G023400	chr7A	84.677	124	15	3	6	126	139417157	139417035	1.540000e-23	121.0
33	TraesCS6D01G023400	chr7A	85.345	116	15	1	13	126	150122236	150122121	5.530000e-23	119.0
34	TraesCS6D01G023400	chr7A	90.476	42	4	0	115	156	24857452	24857493	4.400000e-04	56.5
35	TraesCS6D01G023400	chr7A	92.308	39	3	0	118	156	675337653	675337615	4.400000e-04	56.5
36	TraesCS6D01G023400	chr5B	96.226	53	2	0	822	874	621238412	621238360	1.560000e-13	87.9
37	TraesCS6D01G023400	chr5B	84.375	64	3	4	117	175	586819365	586819304	4.400000e-04	56.5
38	TraesCS6D01G023400	chr5A	96.226	53	2	0	822	874	624205402	624205350	1.560000e-13	87.9
39	TraesCS6D01G023400	chr5A	92.308	39	3	0	118	156	552307901	552307863	4.400000e-04	56.5
40	TraesCS6D01G023400	chr4D	92.308	39	3	0	118	156	460563161	460563123	4.400000e-04	56.5

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	TraesCS6D01G023400	chr6D	8893058	8896212	3154	False	5827.000000	5827	100.000000	1	3155	1	chr6D.!!$F1	3154
1	TraesCS6D01G023400	chr6D	8395998	8404828	8830	True	1619.000000	3182	95.587000	1	3155	4	chr6D.!!$R1	3154
2	TraesCS6D01G023400	chr6D	33894860	33896213	1353	False	876.000000	876	78.768000	822	2173	1	chr6D.!!$F2	1351
3	TraesCS6D01G023400	chr6D	34006036	34006985	949	False	550.000000	983	85.044500	2	906	2	chr6D.!!$F3	904
4	TraesCS6D01G023400	chr1B	630644723	630651661	6938	False	1718.333333	3014	87.830333	974	3155	3	chr1B.!!$F2	2181
5	TraesCS6D01G023400	chr6B	15223572	15225632	2060	True	2820.000000	2820	91.430000	1095	3155	1	chr6B.!!$R1	2060
6	TraesCS6D01G023400	chr6B	65172962	65175128	2166	True	2403.000000	2403	86.798000	986	3155	1	chr6B.!!$R4	2169
7	TraesCS6D01G023400	chr6B	52567086	52573786	6700	True	1246.333333	1788	90.225333	978	3150	3	chr6B.!!$R5	2172
8	TraesCS6D01G023400	chr6B	52981212	52981804	592	True	564.000000	564	84.437000	238	818	1	chr6B.!!$R2	580
9	TraesCS6D01G023400	chr6A	35579421	35581608	2187	True	2471.000000	2471	87.215000	988	3155	1	chr6A.!!$R2	2167
10	TraesCS6D01G023400	chr3A	45936781	45937993	1212	True	1086.000000	1086	82.909000	979	2189	1	chr3A.!!$R1	1210
11	TraesCS6D01G023400	chr3D	33329300	33330545	1245	True	1018.000000	1018	81.558000	941	2189	1	chr3D.!!$R1	1248
12	TraesCS6D01G023400	chr3B	778341724	778342913	1189	True	752.000000	752	78.369000	990	2173	1	chr3B.!!$R2	1183

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
800	2269	3.005791	ACCAAAAACTATTCACTGCAGCC	59.994	43.478	15.27	0.0	0.0	4.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2609	17254	3.007831	ACAATTGTTTCCGCCATCCAAAT	59.992	39.13	4.92	0.0	0.0	2.32	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
679	701	9.133627	GCAAAGAACTCTTAAAATCTTGATTCC	57.866	33.333	0.00	0.00	34.61	3.01
799	2268	4.243007	ACCAAAAACTATTCACTGCAGC	57.757	40.909	15.27	0.00	0.00	5.25
800	2269	3.005791	ACCAAAAACTATTCACTGCAGCC	59.994	43.478	15.27	0.00	0.00	4.85
1326	11165	0.668535	GCGCCAAAGTGGAGAAAACT	59.331	50.000	0.00	0.00	39.92	2.66
1342	11181	3.083349	CTCTGGCCCCCATCGTCA	61.083	66.667	0.00	0.00	30.82	4.35
1370	11209	4.103103	CGCTCTCGGTCTGTCGCA	62.103	66.667	0.00	0.00	0.00	5.10
1383	11222	0.528466	TGTCGCATTCTGAGATCGCC	60.528	55.000	0.00	0.00	0.00	5.54
1389	11228	0.827925	ATTCTGAGATCGCCCGCCTA	60.828	55.000	0.00	0.00	0.00	3.93
1429	11268	1.606737	GCTTCCGCAGTAGATCCATCC	60.607	57.143	0.00	0.00	35.78	3.51
1443	11282	0.747283	CCATCCTCTCCAAGCTGCAC	60.747	60.000	1.02	0.00	0.00	4.57
1455	11294	0.616111	AGCTGCACTACTACCTGCCT	60.616	55.000	1.02	0.00	31.97	4.75
1463	11302	2.239150	ACTACTACCTGCCTCTCTTCGA	59.761	50.000	0.00	0.00	0.00	3.71
1747	16372	0.107993	CAGCAAGGAGAAGATCGCCA	60.108	55.000	3.00	0.00	38.94	5.69
1748	16373	0.615331	AGCAAGGAGAAGATCGCCAA	59.385	50.000	3.00	0.00	38.94	4.52
1750	16375	1.373570	CAAGGAGAAGATCGCCAACC	58.626	55.000	3.00	0.00	38.94	3.77
2045	16670	4.222366	AGCAGTCATGATCAGTGAGAAAGA	59.778	41.667	0.00	0.00	0.00	2.52
2200	16825	3.495377	GGTAACTGTGTATGACGCAACAA	59.505	43.478	0.00	0.00	38.24	2.83
2245	16870	5.995897	AGCTAGTAATTTCTGTTTCGGTGTT	59.004	36.000	0.00	0.00	0.00	3.32
2246	16871	7.156673	AGCTAGTAATTTCTGTTTCGGTGTTA	58.843	34.615	0.00	0.00	0.00	2.41
2247	16872	7.822822	AGCTAGTAATTTCTGTTTCGGTGTTAT	59.177	33.333	0.00	0.00	0.00	1.89
2543	17188	2.977405	GCAGTTTTCAGTGCGAATCT	57.023	45.000	0.00	0.00	39.59	2.40
2545	17190	3.229552	GCAGTTTTCAGTGCGAATCTTC	58.770	45.455	0.00	0.00	39.59	2.87
2571	17216	6.993079	ACTACCTTTCCATGAAAAATGTTCC	58.007	36.000	0.00	0.00	30.84	3.62
2661	17306	3.966979	TGATGGCCACAATGTGTAGATT	58.033	40.909	8.16	0.00	0.00	2.40
2884	17561	5.521906	TTTTCTAGGGACATCTGATCTCG	57.478	43.478	0.00	0.00	0.00	4.04
2904	17581	9.773328	GATCTCGAAATTGAATAATGTTGTTCA	57.227	29.630	1.45	1.45	36.67	3.18
2915	17592	9.681692	TGAATAATGTTGTTCATGTTCTGAAAG	57.318	29.630	1.45	0.00	45.27	2.62
2921	17598	7.471721	TGTTGTTCATGTTCTGAAAGTACTTG	58.528	34.615	9.34	0.00	45.27	3.16
3087	17769	4.395625	TGTTAGGACTGAAGTTCGAGAGA	58.604	43.478	8.67	0.00	39.20	3.10
3119	17801	6.364976	GTCCATTTTATGCCACACAAGTAAAC	59.635	38.462	0.00	0.00	0.00	2.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
129	132	7.981142	TCAAAGCACCCTTATATTTCTTTACG	58.019	34.615	0.00	0.00	0.00	3.18
679	701	1.012086	CTGATGCACTTCCATCCGTG	58.988	55.000	0.00	0.00	40.66	4.94
1326	11165	2.366837	ATGACGATGGGGGCCAGA	60.367	61.111	4.39	0.00	36.75	3.86
1355	11194	0.453793	AGAATGCGACAGACCGAGAG	59.546	55.000	0.00	0.00	0.00	3.20
1356	11195	0.171231	CAGAATGCGACAGACCGAGA	59.829	55.000	0.00	0.00	0.00	4.04
1362	11201	1.534805	GCGATCTCAGAATGCGACAGA	60.535	52.381	0.00	0.00	29.65	3.41
1370	11209	0.827925	TAGGCGGGCGATCTCAGAAT	60.828	55.000	0.00	0.00	0.00	2.40
1383	11222	2.054140	GACTGAGCGAGACTAGGCGG	62.054	65.000	0.00	0.00	0.00	6.13
1429	11268	2.159170	GGTAGTAGTGCAGCTTGGAGAG	60.159	54.545	0.00	0.00	0.00	3.20
1443	11282	2.614983	GTCGAAGAGAGGCAGGTAGTAG	59.385	54.545	0.00	0.00	36.95	2.57
1455	11294	0.107606	CCTCGGAGGAGTCGAAGAGA	60.108	60.000	19.57	0.00	37.67	3.10
1463	11302	0.033894	GAAGAGGTCCTCGGAGGAGT	60.034	60.000	26.70	16.94	46.90	3.85
1507	11346	2.482333	CGAGGTCGGCCGAGAGAAT	61.482	63.158	31.97	12.92	40.50	2.40
2045	16670	5.127682	GGGCATATGAACTTCTCCACAAATT	59.872	40.000	6.97	0.00	0.00	1.82
2245	16870	7.675062	ACAACAAACATCCAATTAGGCAAATA	58.325	30.769	0.00	0.00	37.29	1.40
2246	16871	6.532826	ACAACAAACATCCAATTAGGCAAAT	58.467	32.000	0.00	0.00	37.29	2.32
2247	16872	5.923204	ACAACAAACATCCAATTAGGCAAA	58.077	33.333	0.00	0.00	37.29	3.68
2350	16978	6.166984	ACTGGAATGGTGTGATAGACATAG	57.833	41.667	0.00	0.00	36.78	2.23
2538	17183	7.687941	TTCATGGAAAGGTAGTTGAAGATTC	57.312	36.000	0.00	0.00	0.00	2.52
2543	17188	8.017418	ACATTTTTCATGGAAAGGTAGTTGAA	57.983	30.769	9.83	0.00	32.93	2.69
2545	17190	7.384932	GGAACATTTTTCATGGAAAGGTAGTTG	59.615	37.037	11.30	3.13	32.93	3.16
2609	17254	3.007831	ACAATTGTTTCCGCCATCCAAAT	59.992	39.130	4.92	0.00	0.00	2.32
2661	17306	3.512329	TCAAAACTACATCCTCGGCAGTA	59.488	43.478	0.00	0.00	0.00	2.74
2688	17333	3.778954	AAGAGGAAGGAACCAACAGAG	57.221	47.619	0.00	0.00	0.00	3.35
2690	17335	4.625607	ACTAAGAGGAAGGAACCAACAG	57.374	45.455	0.00	0.00	0.00	3.16
2859	17535	6.989169	CGAGATCAGATGTCCCTAGAAAAATT	59.011	38.462	1.98	0.00	0.00	1.82
2904	17581	4.718961	ACTGCCAAGTACTTTCAGAACAT	58.281	39.130	28.12	12.53	33.79	2.71
2905	17582	4.150897	ACTGCCAAGTACTTTCAGAACA	57.849	40.909	28.12	12.43	33.79	3.18
2915	17592	2.148768	AGCCGTAAAACTGCCAAGTAC	58.851	47.619	0.00	0.00	34.77	2.73
2921	17598	2.419667	TGAAGTAGCCGTAAAACTGCC	58.580	47.619	0.00	0.00	0.00	4.85
3087	17769	2.225242	TGGCATAAAATGGACCCAGTGT	60.225	45.455	0.00	0.00	0.00	3.55

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.