AutoCloner

Multiple sequence alignment - TraesCS1B01G239600

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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	TraesCS1B01G239600	chr1B	100.000	2233	0	0	1	2233	427652323	427650091	0.000000e+00	4124.0
1	TraesCS1B01G239600	chr1B	93.313	2243	90	27	35	2230	633715654	633717883	0.000000e+00	3256.0
2	TraesCS1B01G239600	chr3A	93.458	2247	85	25	35	2230	105558280	105556045	0.000000e+00	3278.0
3	TraesCS1B01G239600	chr3A	94.000	50	3	0	1	50	609650120	609650169	2.380000e-10	76.8
4	TraesCS1B01G239600	chr3A	87.719	57	4	2	1	57	669929035	669929088	1.850000e-06	63.9
5	TraesCS1B01G239600	chr5D	93.324	2247	92	26	35	2230	6254603	6252364	0.000000e+00	3265.0
6	TraesCS1B01G239600	chr5D	93.182	2244	93	27	35	2230	503338120	503340351	0.000000e+00	3241.0
7	TraesCS1B01G239600	chr5D	92.816	2241	102	25	35	2230	503312185	503314411	0.000000e+00	3192.0
8	TraesCS1B01G239600	chr5D	93.333	2190	84	27	78	2218	299973782	299971606	0.000000e+00	3179.0
9	TraesCS1B01G239600	chr5D	92.655	1593	74	17	35	1585	329127231	329125640	0.000000e+00	2254.0
10	TraesCS1B01G239600	chr5D	96.903	226	7	0	35	260	481593643	481593868	1.620000e-101	379.0
11	TraesCS1B01G239600	chr5D	96.903	226	7	0	35	260	503335321	503335546	1.620000e-101	379.0
12	TraesCS1B01G239600	chr5D	93.878	49	2	1	1	48	481612285	481612237	3.080000e-09	73.1
13	TraesCS1B01G239600	chr5B	93.280	2247	89	23	35	2230	57516446	57514211	0.000000e+00	3256.0
14	TraesCS1B01G239600	chr7B	93.229	2245	90	24	35	2230	662756352	662754121	0.000000e+00	3247.0
15	TraesCS1B01G239600	chr1D	93.256	2239	94	27	35	2230	254458098	254460322	0.000000e+00	3245.0
16	TraesCS1B01G239600	chr1D	92.627	2238	110	25	35	2230	51833278	51831054	0.000000e+00	3168.0
17	TraesCS1B01G239600	chr1D	96.903	226	7	0	35	260	254455317	254455542	1.620000e-101	379.0
18	TraesCS1B01G239600	chr1D	90.909	55	2	3	1	52	236577828	236577882	1.110000e-08	71.3
19	TraesCS1B01G239600	chr4A	91.514	2239	124	29	35	2225	309447727	309445507	0.000000e+00	3022.0
20	TraesCS1B01G239600	chr3B	93.174	2007	79	24	35	1994	101923556	101925551	0.000000e+00	2894.0
21	TraesCS1B01G239600	chrUn	92.934	835	35	8	35	853	423338648	423337822	0.000000e+00	1194.0
22	TraesCS1B01G239600	chrUn	97.674	43	1	0	1	43	460236824	460236782	8.550000e-10	75.0
23	TraesCS1B01G239600	chr7A	92.092	822	36	10	226	1027	706286307	706285495	0.000000e+00	1131.0
24	TraesCS1B01G239600	chr3D	100.000	41	0	0	1	41	169547870	169547830	2.380000e-10	76.8
25	TraesCS1B01G239600	chr2A	97.674	43	1	0	1	43	310921679	310921721	8.550000e-10	75.0
26	TraesCS1B01G239600	chr6B	90.741	54	3	2	1	52	339954473	339954420	1.110000e-08	71.3
27	TraesCS1B01G239600	chr5A	85.714	63	8	1	1	62	355013569	355013507	5.150000e-07	65.8

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	TraesCS1B01G239600	chr1B	427650091	427652323	2232	True	4124	4124	100.0000	1	2233	1	chr1B.!!$R1	2232
1	TraesCS1B01G239600	chr1B	633715654	633717883	2229	False	3256	3256	93.3130	35	2230	1	chr1B.!!$F1	2195
2	TraesCS1B01G239600	chr3A	105556045	105558280	2235	True	3278	3278	93.4580	35	2230	1	chr3A.!!$R1	2195
3	TraesCS1B01G239600	chr5D	6252364	6254603	2239	True	3265	3265	93.3240	35	2230	1	chr5D.!!$R1	2195
4	TraesCS1B01G239600	chr5D	503312185	503314411	2226	False	3192	3192	92.8160	35	2230	1	chr5D.!!$F2	2195
5	TraesCS1B01G239600	chr5D	299971606	299973782	2176	True	3179	3179	93.3330	78	2218	1	chr5D.!!$R2	2140
6	TraesCS1B01G239600	chr5D	329125640	329127231	1591	True	2254	2254	92.6550	35	1585	1	chr5D.!!$R3	1550
7	TraesCS1B01G239600	chr5D	503335321	503340351	5030	False	1810	3241	95.0425	35	2230	2	chr5D.!!$F3	2195
8	TraesCS1B01G239600	chr5B	57514211	57516446	2235	True	3256	3256	93.2800	35	2230	1	chr5B.!!$R1	2195
9	TraesCS1B01G239600	chr7B	662754121	662756352	2231	True	3247	3247	93.2290	35	2230	1	chr7B.!!$R1	2195
10	TraesCS1B01G239600	chr1D	51831054	51833278	2224	True	3168	3168	92.6270	35	2230	1	chr1D.!!$R1	2195
11	TraesCS1B01G239600	chr1D	254455317	254460322	5005	False	1812	3245	95.0795	35	2230	2	chr1D.!!$F2	2195
12	TraesCS1B01G239600	chr4A	309445507	309447727	2220	True	3022	3022	91.5140	35	2225	1	chr4A.!!$R1	2190
13	TraesCS1B01G239600	chr3B	101923556	101925551	1995	False	2894	2894	93.1740	35	1994	1	chr3B.!!$F1	1959
14	TraesCS1B01G239600	chrUn	423337822	423338648	826	True	1194	1194	92.9340	35	853	1	chrUn.!!$R1	818
15	TraesCS1B01G239600	chr7A	706285495	706286307	812	True	1131	1131	92.0920	226	1027	1	chr7A.!!$R1	801

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
622	6233	1.473434	GCATTAAGGAGGGTGGAGTCG	60.473	57.143	0.0	0.0	0.0	4.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1967	7643	0.676466	ACCAATGAGCCGCGAAATGA	60.676	50.0	8.23	0.0	0.0	2.57	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
100	101	1.949525	GCAGTGCCCACGAATGATATT	59.050	47.619	2.85	0.00	36.20	1.28
260	3060	4.697828	TCACAAAACCATTATCGCTTAGCA	59.302	37.500	4.70	0.00	0.00	3.49
279	5872	3.009473	AGCAGGAATATATTGGCGGATGT	59.991	43.478	1.78	0.00	0.00	3.06
286	5879	8.548877	AGGAATATATTGGCGGATGTATTAGTT	58.451	33.333	1.78	0.00	0.00	2.24
287	5880	9.174166	GGAATATATTGGCGGATGTATTAGTTT	57.826	33.333	1.78	0.00	0.00	2.66
330	5923	6.817119	AGTCCCCTTAGTAATCCCTATACT	57.183	41.667	0.00	0.00	37.39	2.12
331	5924	7.918579	AGTCCCCTTAGTAATCCCTATACTA	57.081	40.000	0.00	0.00	35.34	1.82
381	5974	8.115490	AGCAGTATTCAAGCTCTTATTTTTGT	57.885	30.769	0.00	0.00	32.05	2.83
439	6032	5.762218	GGAGGGTCATCATTGAATTGACTAG	59.238	44.000	16.17	0.00	39.70	2.57
483	6084	2.295885	GCAGCCTAGCTCAATTCATGT	58.704	47.619	0.00	0.00	36.40	3.21
566	6170	6.946009	GCCTAGAGTTGTAGGAGAGAGAATAT	59.054	42.308	6.53	0.00	42.18	1.28
622	6233	1.473434	GCATTAAGGAGGGTGGAGTCG	60.473	57.143	0.00	0.00	0.00	4.18
699	6310	3.191791	GCGGGTTTCCACTTTAAGCAATA	59.808	43.478	0.00	0.00	0.00	1.90
700	6311	4.674362	GCGGGTTTCCACTTTAAGCAATAG	60.674	45.833	0.00	0.00	0.00	1.73
713	6324	9.227777	ACTTTAAGCAATAGTTTTAGAATCCGT	57.772	29.630	0.00	0.00	0.00	4.69
756	6368	9.995003	AAAATATGCAAACAAAATAGAGGAACA	57.005	25.926	0.00	0.00	0.00	3.18
760	6372	7.712264	TGCAAACAAAATAGAGGAACAAATG	57.288	32.000	0.00	0.00	0.00	2.32
761	6373	7.271511	TGCAAACAAAATAGAGGAACAAATGT	58.728	30.769	0.00	0.00	0.00	2.71
762	6374	8.417106	TGCAAACAAAATAGAGGAACAAATGTA	58.583	29.630	0.00	0.00	0.00	2.29
763	6375	9.423061	GCAAACAAAATAGAGGAACAAATGTAT	57.577	29.630	0.00	0.00	0.00	2.29
941	6569	7.114866	ACCCAATAGAGCTTAGAAGTAAGAC	57.885	40.000	0.00	0.00	38.39	3.01
1011	6643	5.491982	GAACTACTCACCATGAATCCACTT	58.508	41.667	0.00	0.00	0.00	3.16
1018	6662	7.050377	ACTCACCATGAATCCACTTACTATTG	58.950	38.462	0.00	0.00	0.00	1.90
1019	6663	5.822519	TCACCATGAATCCACTTACTATTGC	59.177	40.000	0.00	0.00	0.00	3.56
1024	6668	5.500234	TGAATCCACTTACTATTGCTGCTT	58.500	37.500	0.00	0.00	0.00	3.91
1034	6678	5.365021	ACTATTGCTGCTTCTAGATTGGT	57.635	39.130	0.00	0.00	0.00	3.67
1040	6684	3.181485	GCTGCTTCTAGATTGGTCGTAGT	60.181	47.826	0.00	0.00	0.00	2.73
1099	6744	1.168407	TGCAGGACAAGCTGTGAAGC	61.168	55.000	0.00	0.00	0.00	3.86
1109	6754	1.205655	AGCTGTGAAGCTATTGCGAGA	59.794	47.619	0.00	0.00	44.28	4.04
1110	6755	1.325943	GCTGTGAAGCTATTGCGAGAC	59.674	52.381	0.00	0.00	45.42	3.36
1111	6756	2.610433	CTGTGAAGCTATTGCGAGACA	58.390	47.619	0.00	0.00	45.42	3.41
1112	6757	2.995939	CTGTGAAGCTATTGCGAGACAA	59.004	45.455	0.00	0.00	45.42	3.18
1116	6761	2.472695	AGCTATTGCGAGACAACCAA	57.527	45.000	0.00	0.00	42.27	3.67
1126	6775	2.872245	CGAGACAACCAAAAGCAGAAGA	59.128	45.455	0.00	0.00	0.00	2.87
1290	6957	9.750125	CTTTTCTTTAGTAAATTGGTTGCTTCT	57.250	29.630	0.00	0.00	33.71	2.85
1441	7108	8.045720	AGATATGCTTACCTTCTTATTTCCCA	57.954	34.615	0.00	0.00	0.00	4.37
1465	7132	7.615757	CCATCCTTAGTTTAGGAAAGTGGAAAT	59.384	37.037	5.29	0.00	46.94	2.17
1518	7185	8.147704	GGGAATAGAACATTTCAACAAAGGAAA	58.852	33.333	0.00	0.00	38.49	3.13
1527	7194	8.260114	ACATTTCAACAAAGGAAATCTTTCACT	58.740	29.630	5.14	0.00	43.32	3.41
1648	7320	7.810282	TGATCGAAAAACTTTGTTCTTTGTTCA	59.190	29.630	0.00	0.00	0.00	3.18
1721	7394	1.264749	TTAGCTCACTGGCCATCCGT	61.265	55.000	5.51	0.00	34.14	4.69
1821	7497	4.703379	TTTTTGGAAAGGGATTGTGCAT	57.297	36.364	0.00	0.00	0.00	3.96
1839	7515	5.764686	TGTGCATGAGTTGTCTATTTCAAGT	59.235	36.000	0.00	0.00	0.00	3.16
1867	7543	2.103771	TGGATCTATCTGGCTGCACTTC	59.896	50.000	0.50	0.00	0.00	3.01
1876	7552	6.814506	ATCTGGCTGCACTTCATAATATTC	57.185	37.500	0.50	0.00	0.00	1.75
1932	7608	5.685954	GTGCACGATCTCGATGAATTACTTA	59.314	40.000	0.00	0.00	43.02	2.24
1977	7653	3.058914	GGAAGAACCATATCATTTCGCGG	60.059	47.826	6.13	0.00	38.79	6.46
1990	7666	1.524848	TTCGCGGCTCATTGGTAAAA	58.475	45.000	6.13	0.00	0.00	1.52
2028	7704	7.103641	TCTATAAACCAAGAATGTGAGACCAC	58.896	38.462	0.00	0.00	43.46	4.16
2050	7726	6.016276	CCACTAACATGGTTGAAGCTAAACTT	60.016	38.462	0.00	2.35	36.74	2.66
2230	7911	3.366985	CCCTTTCTTAACCAATGCCGAAC	60.367	47.826	0.00	0.00	0.00	3.95
2231	7912	3.254657	CCTTTCTTAACCAATGCCGAACA	59.745	43.478	0.00	0.00	0.00	3.18
2232	7913	4.475944	CTTTCTTAACCAATGCCGAACAG	58.524	43.478	0.00	0.00	0.00	3.16

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
19	20	3.444703	AGAGCATGATACGTCTCCAAC	57.555	47.619	0.00	0.00	0.00	3.77
20	21	4.471904	AAAGAGCATGATACGTCTCCAA	57.528	40.909	0.00	0.00	0.00	3.53
21	22	4.471904	AAAAGAGCATGATACGTCTCCA	57.528	40.909	0.00	0.00	0.00	3.86
22	23	4.745620	GGTAAAAGAGCATGATACGTCTCC	59.254	45.833	0.00	0.00	0.00	3.71
23	24	5.593010	AGGTAAAAGAGCATGATACGTCTC	58.407	41.667	0.00	0.00	0.00	3.36
24	25	5.599999	AGGTAAAAGAGCATGATACGTCT	57.400	39.130	0.00	0.00	0.00	4.18
25	26	5.006746	CCAAGGTAAAAGAGCATGATACGTC	59.993	44.000	0.00	0.00	0.00	4.34
26	27	4.876107	CCAAGGTAAAAGAGCATGATACGT	59.124	41.667	0.00	0.00	0.00	3.57
27	28	5.116180	TCCAAGGTAAAAGAGCATGATACG	58.884	41.667	0.00	0.00	0.00	3.06
28	29	7.391148	TTTCCAAGGTAAAAGAGCATGATAC	57.609	36.000	0.00	0.00	0.00	2.24
29	30	8.593945	ATTTTCCAAGGTAAAAGAGCATGATA	57.406	30.769	0.00	0.00	29.93	2.15
30	31	6.916360	TTTTCCAAGGTAAAAGAGCATGAT	57.084	33.333	0.00	0.00	0.00	2.45
31	32	6.916360	ATTTTCCAAGGTAAAAGAGCATGA	57.084	33.333	0.00	0.00	29.93	3.07
260	3060	8.090788	ACTAATACATCCGCCAATATATTCCT	57.909	34.615	0.00	0.00	0.00	3.36
286	5879	7.815549	GGGACTAAAGAAACAAGAACAACAAAA	59.184	33.333	0.00	0.00	0.00	2.44
287	5880	7.317390	GGGACTAAAGAAACAAGAACAACAAA	58.683	34.615	0.00	0.00	0.00	2.83
411	6004	4.801521	ATTCAATGATGACCCTCCATGA	57.198	40.909	0.00	0.00	34.61	3.07
468	6069	9.926158	ATCTAGAACATACATGAATTGAGCTAG	57.074	33.333	0.00	9.69	0.00	3.42
483	6084	7.442364	GCAACCAAGCAGATTATCTAGAACATA	59.558	37.037	0.00	0.00	0.00	2.29
834	6462	8.258850	TGTCCGAACTATATAGAAGGGAATTT	57.741	34.615	16.79	0.00	0.00	1.82
848	6476	8.908786	ATGATAATGTGAATTGTCCGAACTAT	57.091	30.769	0.00	0.00	0.00	2.12
897	6525	8.700439	TTGGGTAGAAGCAAAGTAACTAAAAT	57.300	30.769	0.00	0.00	0.00	1.82
911	6539	5.793030	TCTAAGCTCTATTGGGTAGAAGC	57.207	43.478	0.00	0.00	38.91	3.86
917	6545	6.898521	AGTCTTACTTCTAAGCTCTATTGGGT	59.101	38.462	0.00	0.00	30.85	4.51
1011	6643	6.485830	ACCAATCTAGAAGCAGCAATAGTA	57.514	37.500	0.00	0.00	0.00	1.82
1018	6662	2.301577	ACGACCAATCTAGAAGCAGC	57.698	50.000	0.00	0.00	0.00	5.25
1019	6663	4.355437	CACTACGACCAATCTAGAAGCAG	58.645	47.826	0.00	0.00	0.00	4.24
1024	6668	3.428999	GCAAGCACTACGACCAATCTAGA	60.429	47.826	0.00	0.00	0.00	2.43
1034	6678	3.194755	TCCAATAGAAGCAAGCACTACGA	59.805	43.478	0.00	0.00	0.00	3.43
1040	6684	2.618816	CCAGGTCCAATAGAAGCAAGCA	60.619	50.000	0.00	0.00	0.00	3.91
1099	6744	3.058293	TGCTTTTGGTTGTCTCGCAATAG	60.058	43.478	0.00	0.00	39.55	1.73
1109	6754	7.807907	CGTATTTTATCTTCTGCTTTTGGTTGT	59.192	33.333	0.00	0.00	0.00	3.32
1110	6755	8.020819	TCGTATTTTATCTTCTGCTTTTGGTTG	58.979	33.333	0.00	0.00	0.00	3.77
1111	6756	8.106247	TCGTATTTTATCTTCTGCTTTTGGTT	57.894	30.769	0.00	0.00	0.00	3.67
1112	6757	7.148239	CCTCGTATTTTATCTTCTGCTTTTGGT	60.148	37.037	0.00	0.00	0.00	3.67
1116	6761	8.258708	AGTACCTCGTATTTTATCTTCTGCTTT	58.741	33.333	0.00	0.00	0.00	3.51
1269	6924	6.934561	GCAGAAGCAACCAATTTACTAAAG	57.065	37.500	0.00	0.00	41.58	1.85
1381	7048	2.839228	ACTCAACTCAGCCCTTCCTAT	58.161	47.619	0.00	0.00	0.00	2.57
1425	7092	8.401955	AACTAAGGATGGGAAATAAGAAGGTA	57.598	34.615	0.00	0.00	0.00	3.08
1441	7108	9.601810	AAATTTCCACTTTCCTAAACTAAGGAT	57.398	29.630	0.00	0.00	45.14	3.24
1518	7185	6.281405	ACGTCTTGTTTGACTAGTGAAAGAT	58.719	36.000	7.82	0.00	35.00	2.40
1527	7194	9.403110	GATTAAGTCTTACGTCTTGTTTGACTA	57.597	33.333	0.00	0.00	39.42	2.59
1721	7394	1.917872	ATTAAGCCCGAAACTGCCAA	58.082	45.000	0.00	0.00	0.00	4.52
1804	7480	2.225091	ACTCATGCACAATCCCTTTCCA	60.225	45.455	0.00	0.00	0.00	3.53
1814	7490	6.262944	ACTTGAAATAGACAACTCATGCACAA	59.737	34.615	0.00	0.00	0.00	3.33
1905	7581	1.037579	TCATCGAGATCGTGCACCCT	61.038	55.000	12.15	5.99	40.80	4.34
1967	7643	0.676466	ACCAATGAGCCGCGAAATGA	60.676	50.000	8.23	0.00	0.00	2.57
1977	7653	7.653311	AGAATCAAAGTTGTTTTACCAATGAGC	59.347	33.333	0.00	0.00	0.00	4.26
1990	7666	9.793259	TCTTGGTTTATAGAGAATCAAAGTTGT	57.207	29.630	0.00	0.00	37.82	3.32
2050	7726	3.885297	CTCTTTTTGCCTGGACTTCAAGA	59.115	43.478	0.00	0.00	0.00	3.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.