AutoCloner

Multiple sequence alignment - TraesCS3B01G191200

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	TraesCS3B01G191200	chr3B	100.000	4074	0	0	1	4074	204278285	204282358	0.000000e+00	7524
1	TraesCS3B01G191200	chr3B	76.835	695	139	18	39	723	595668492	595667810	4.970000e-99	372
2	TraesCS3B01G191200	chr3D	94.970	3340	110	21	761	4074	142473669	142476976	0.000000e+00	5184
3	TraesCS3B01G191200	chr3D	93.260	727	45	3	1	725	253616111	253616835	0.000000e+00	1068
4	TraesCS3B01G191200	chr3D	79.535	215	32	10	1044	1252	402494127	402493919	4.240000e-30	143
5	TraesCS3B01G191200	chr3A	90.893	2328	120	40	1771	4074	161444504	161446763	0.000000e+00	3040
6	TraesCS3B01G191200	chr3A	93.097	1014	35	8	747	1746	161443512	161444504	0.000000e+00	1452
7	TraesCS3B01G191200	chr3A	94.083	338	17	3	1807	2144	375017931	375018265	1.010000e-140	510
8	TraesCS3B01G191200	chr3A	92.264	349	21	6	1797	2144	487860865	487860522	1.320000e-134	490
9	TraesCS3B01G191200	chr3A	87.778	90	11	0	1044	1133	523334098	523334009	5.570000e-19	106
10	TraesCS3B01G191200	chr6B	96.974	694	20	1	1	694	199937100	199936408	0.000000e+00	1164
11	TraesCS3B01G191200	chr7A	86.749	732	81	14	1	725	156136723	156136001	0.000000e+00	800
12	TraesCS3B01G191200	chr4A	85.597	729	90	10	1	722	741081406	741080686	0.000000e+00	750
13	TraesCS3B01G191200	chr4A	95.342	322	14	1	1807	2128	115566916	115567236	1.010000e-140	510
14	TraesCS3B01G191200	chr2B	94.048	336	17	3	1810	2143	136170537	136170203	1.310000e-139	507
15	TraesCS3B01G191200	chr5B	93.787	338	17	3	1807	2142	464890573	464890238	4.700000e-139	505
16	TraesCS3B01G191200	chr5D	94.012	334	17	2	1807	2138	386862040	386861708	1.690000e-138	503
17	TraesCS3B01G191200	chr5D	76.902	723	152	14	9	725	305722905	305722192	2.950000e-106	396
18	TraesCS3B01G191200	chr5A	93.215	339	20	3	1807	2145	366235148	366234813	2.830000e-136	496
19	TraesCS3B01G191200	chrUn	78.005	732	152	9	1	726	264103927	264104655	6.210000e-123	451
20	TraesCS3B01G191200	chr2D	77.715	709	130	22	30	725	65517155	65516462	3.790000e-110	409
21	TraesCS3B01G191200	chr1D	77.166	727	143	18	1	720	39276414	39277124	6.340000e-108	401
22	TraesCS3B01G191200	chr2A	75.650	731	155	19	3	722	103347699	103348417	3.900000e-90	342

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	TraesCS3B01G191200	chr3B	204278285	204282358	4073	False	7524	7524	100.000	1	4074	1	chr3B.!!$F1	4073
1	TraesCS3B01G191200	chr3B	595667810	595668492	682	True	372	372	76.835	39	723	1	chr3B.!!$R1	684
2	TraesCS3B01G191200	chr3D	142473669	142476976	3307	False	5184	5184	94.970	761	4074	1	chr3D.!!$F1	3313
3	TraesCS3B01G191200	chr3D	253616111	253616835	724	False	1068	1068	93.260	1	725	1	chr3D.!!$F2	724
4	TraesCS3B01G191200	chr3A	161443512	161446763	3251	False	2246	3040	91.995	747	4074	2	chr3A.!!$F2	3327
5	TraesCS3B01G191200	chr6B	199936408	199937100	692	True	1164	1164	96.974	1	694	1	chr6B.!!$R1	693
6	TraesCS3B01G191200	chr7A	156136001	156136723	722	True	800	800	86.749	1	725	1	chr7A.!!$R1	724
7	TraesCS3B01G191200	chr4A	741080686	741081406	720	True	750	750	85.597	1	722	1	chr4A.!!$R1	721
8	TraesCS3B01G191200	chr5D	305722192	305722905	713	True	396	396	76.902	9	725	1	chr5D.!!$R1	716
9	TraesCS3B01G191200	chrUn	264103927	264104655	728	False	451	451	78.005	1	726	1	chrUn.!!$F1	725
10	TraesCS3B01G191200	chr2D	65516462	65517155	693	True	409	409	77.715	30	725	1	chr2D.!!$R1	695
11	TraesCS3B01G191200	chr1D	39276414	39277124	710	False	401	401	77.166	1	720	1	chr1D.!!$F1	719
12	TraesCS3B01G191200	chr2A	103347699	103348417	718	False	342	342	75.650	3	722	1	chr2A.!!$F1	719

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
121	123	1.272769	ACTACTTCAGTCGGCTTGGTC	59.727	52.381	0.00	0.00	28.33	4.02	F
1256	1279	0.110238	CGCAACGACCAAGGTGATTG	60.110	55.000	0.00	2.17	38.74	2.67	F
1284	1307	0.257039	ACTCCTTGGCCTTGGCATAG	59.743	55.000	14.04	9.23	38.08	2.23	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1312	1335	0.109226	GACTAGCGCAAGAAGACCGT	60.109	55.000	11.47	0.0	43.02	4.83	R
2295	2334	0.249120	TCCAACTGTGTAGATGGCCG	59.751	55.000	0.00	0.0	44.24	6.13	R
3247	3318	1.672881	GCCAAGAGGAATCACAATCCG	59.327	52.381	0.00	0.0	42.03	4.18	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
121	123	1.272769	ACTACTTCAGTCGGCTTGGTC	59.727	52.381	0.00	0.00	28.33	4.02
182	184	1.841556	TTCCACGGTCCCTCTTGCT	60.842	57.895	0.00	0.00	0.00	3.91
699	717	2.107141	GATCGCCACCGGGAGAAG	59.893	66.667	6.32	0.00	46.54	2.85
805	825	4.144297	TGAAACTATGCAGCCCATTATCC	58.856	43.478	0.00	0.00	35.34	2.59
1233	1256	3.135530	AGACTGGCTCCATCATCTTTACC	59.864	47.826	0.00	0.00	0.00	2.85
1256	1279	0.110238	CGCAACGACCAAGGTGATTG	60.110	55.000	0.00	2.17	38.74	2.67
1284	1307	0.257039	ACTCCTTGGCCTTGGCATAG	59.743	55.000	14.04	9.23	38.08	2.23
1304	1327	4.170468	AGGGTGCCTTATGGTAGATTTG	57.830	45.455	0.00	0.00	35.27	2.32
1312	1335	6.069905	TGCCTTATGGTAGATTTGTTAGGACA	60.070	38.462	0.00	0.00	35.27	4.02
1322	1345	4.411256	TTTGTTAGGACACGGTCTTCTT	57.589	40.909	4.41	0.00	34.98	2.52
1385	1408	5.161358	GGTTAGGTGCTTCTAAATTTGTGC	58.839	41.667	0.00	0.72	31.85	4.57
1405	1428	1.593006	CAGCTTTAATAGTGGCGACGG	59.407	52.381	0.00	0.00	0.00	4.79
1513	1536	5.699458	GGTTATCTGGATGGTTGGTATTACG	59.301	44.000	0.00	0.00	0.00	3.18
1603	1628	1.527433	AAGGGAAAGCGCCTTTCTGC	61.527	55.000	22.65	12.66	46.20	4.26
1640	1678	5.480422	ACAATTTCCCAGATTACAAGTTCCC	59.520	40.000	0.00	0.00	0.00	3.97
1681	1719	4.021925	GAGACAACCGCCAGGCCT	62.022	66.667	5.63	0.00	42.76	5.19
1684	1722	4.643387	ACAACCGCCAGGCCTGTC	62.643	66.667	30.63	18.82	42.76	3.51
1696	1734	2.113139	CCTGTCGCCACAAAGGGT	59.887	61.111	0.00	0.00	38.09	4.34
1853	1891	1.361668	CGTCTGAGATGGTTTGGGCG	61.362	60.000	0.00	0.00	0.00	6.13
1938	1976	0.790993	AGAGAGGTTGGGGTAGACCA	59.209	55.000	0.21	0.00	42.91	4.02
1956	1994	2.162681	CCAAACTTGACATGGGAGGAC	58.837	52.381	0.00	0.00	0.00	3.85
2151	2189	3.791973	TGTTTGTTTGTTGGCCTGTAG	57.208	42.857	3.32	0.00	0.00	2.74
2180	2218	5.705609	TTGATTAGGTTTTGTCCTGAAGC	57.294	39.130	0.00	0.00	38.41	3.86
2363	2402	1.686355	TTTCCGAAACAGCACACCAT	58.314	45.000	0.00	0.00	0.00	3.55
2384	2423	7.063780	CACCATTCTTTTCCAATCTTGTATTGC	59.936	37.037	0.00	0.00	0.00	3.56
2407	2446	7.093354	TGCGCTATTGTTTATTTGAATCCAAA	58.907	30.769	9.73	0.00	45.28	3.28
2488	2528	7.041167	TGAGCTATTATTTCACCATACATGCAC	60.041	37.037	0.00	0.00	0.00	4.57
2503	2543	2.363788	TGCACGAAGTACATCTGACC	57.636	50.000	0.00	0.00	41.61	4.02
2506	2546	2.604914	GCACGAAGTACATCTGACCATG	59.395	50.000	0.00	0.00	41.61	3.66
2612	2652	7.381766	TCTTTGTCCTTTGATGTCATACATG	57.618	36.000	0.00	0.00	39.27	3.21
2660	2700	5.069251	GCACTACTACCTTCTGACATACCAT	59.931	44.000	0.00	0.00	0.00	3.55
2754	2804	4.221262	AGCACCTTTTGATGTTATGCATGT	59.779	37.500	10.16	0.00	38.06	3.21
2774	2824	6.586344	CATGTTAGGAATCCTGTACTCATGT	58.414	40.000	12.96	0.00	34.61	3.21
2790	2840	8.724229	TGTACTCATGTCATTTTTCAGATCTTG	58.276	33.333	0.00	0.00	0.00	3.02
2873	2943	6.295292	GCATGTACTATGGACTGATGGTATGA	60.295	42.308	0.00	0.00	0.00	2.15
2899	2970	4.460263	ACTATGCAGTTGACCTGTTGAAA	58.540	39.130	0.00	0.00	43.55	2.69
3031	3102	7.446625	AGCTTTACTGTGAATGAAGAGAACAAT	59.553	33.333	0.00	0.00	0.00	2.71
3247	3318	3.282021	TGAGCTTTCCATGCATCTTACC	58.718	45.455	0.00	0.00	0.00	2.85
3308	3379	1.891919	TGGAACAAGGTCAGCGTGC	60.892	57.895	0.00	0.00	31.92	5.34
3378	3449	7.254185	CCATTACATATTGTGTTGAATTGCTGC	60.254	37.037	0.00	0.00	42.29	5.25
3402	3474	9.171877	TGCTACATTGTGTTGATGTTATATTGA	57.828	29.630	0.00	0.00	38.58	2.57
3442	3514	2.963432	TCGTTGAGATCCGGTAAAACC	58.037	47.619	0.00	0.00	34.05	3.27
3444	3516	3.055675	TCGTTGAGATCCGGTAAAACCAT	60.056	43.478	0.00	0.00	38.47	3.55
3468	3540	1.400846	CATCTGCTGTTCCAGACATGC	59.599	52.381	0.00	0.00	44.00	4.06
3644	3719	1.045911	GTCGGAGGAGGAGGCAGAAT	61.046	60.000	0.00	0.00	0.00	2.40
3766	3841	3.991051	CGGTCGGTGGCTGTGAGT	61.991	66.667	0.00	0.00	0.00	3.41
3959	4034	3.062466	TCGTCCTCCAGACCTGCG	61.062	66.667	0.00	0.00	43.08	5.18
4047	4122	2.035626	CGGCCATTTCCACCAGGT	59.964	61.111	2.24	0.00	35.89	4.00

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
75	77	6.014669	GCTGGATAGTCTAGACATCTGGATTT	60.015	42.308	24.44	3.32	35.90	2.17
121	123	2.549064	TCACGCCCTATGATGGAATG	57.451	50.000	0.00	0.00	0.00	2.67
182	184	0.605319	GGTGATTGGGAGCGTGTGAA	60.605	55.000	0.00	0.00	0.00	3.18
699	717	2.333688	CCTCTAGCTAGGGTTTTGCC	57.666	55.000	19.37	0.00	32.55	4.52
734	753	9.819267	ATAATTTTGAACGTTTCCCTACAAAAA	57.181	25.926	20.27	10.49	39.44	1.94
735	754	9.819267	AATAATTTTGAACGTTTCCCTACAAAA	57.181	25.926	19.28	19.28	39.98	2.44
736	755	9.250624	CAATAATTTTGAACGTTTCCCTACAAA	57.749	29.630	0.46	4.32	0.00	2.83
737	756	7.868415	CCAATAATTTTGAACGTTTCCCTACAA	59.132	33.333	0.46	0.00	0.00	2.41
738	757	7.230913	TCCAATAATTTTGAACGTTTCCCTACA	59.769	33.333	0.46	0.00	0.00	2.74
739	758	7.595604	TCCAATAATTTTGAACGTTTCCCTAC	58.404	34.615	0.46	0.00	0.00	3.18
740	759	7.762588	TCCAATAATTTTGAACGTTTCCCTA	57.237	32.000	0.46	0.00	0.00	3.53
741	760	6.658188	TCCAATAATTTTGAACGTTTCCCT	57.342	33.333	0.46	0.00	0.00	4.20
742	761	7.093992	TGATCCAATAATTTTGAACGTTTCCC	58.906	34.615	0.46	0.00	0.00	3.97
743	762	8.702163	ATGATCCAATAATTTTGAACGTTTCC	57.298	30.769	0.46	0.00	0.00	3.13
805	825	2.289569	GGCTGAGCCTGATCCATTAGAG	60.290	54.545	17.96	0.00	46.69	2.43
1256	1279	2.283173	CCAAGGAGTGGCAACCCC	60.283	66.667	8.11	0.00	41.72	4.95
1284	1307	3.898482	ACAAATCTACCATAAGGCACCC	58.102	45.455	0.00	0.00	39.06	4.61
1293	1316	4.224370	ACCGTGTCCTAACAAATCTACCAT	59.776	41.667	0.00	0.00	37.08	3.55
1304	1327	2.067013	GCAAGAAGACCGTGTCCTAAC	58.933	52.381	1.06	0.00	32.18	2.34
1312	1335	0.109226	GACTAGCGCAAGAAGACCGT	60.109	55.000	11.47	0.00	43.02	4.83
1322	1345	2.346803	GAATCCAAACAGACTAGCGCA	58.653	47.619	11.47	0.00	0.00	6.09
1385	1408	1.593006	CCGTCGCCACTATTAAAGCTG	59.407	52.381	0.00	0.00	0.00	4.24
1405	1428	7.711339	CCACAAGATTTACACCTCTTATCCTAC	59.289	40.741	0.00	0.00	30.70	3.18
1550	1574	3.539604	GCATCTGAAATGTACTGCCTCT	58.460	45.455	0.00	0.00	0.00	3.69
1603	1628	3.365969	GGGAAATTGTAGTGCCTTGAACG	60.366	47.826	0.00	0.00	0.00	3.95
1606	1631	3.073798	TCTGGGAAATTGTAGTGCCTTGA	59.926	43.478	0.00	0.00	0.00	3.02
1693	1731	1.890979	CAGATGCAGATCGCCACCC	60.891	63.158	0.00	0.00	41.33	4.61
1694	1732	2.541120	GCAGATGCAGATCGCCACC	61.541	63.158	0.00	0.00	41.33	4.61
1696	1734	2.203112	GGCAGATGCAGATCGCCA	60.203	61.111	12.81	0.00	42.77	5.69
1762	1800	2.195741	TTTCAGCAGAGATGCTTGCT	57.804	45.000	0.00	0.00	43.52	3.91
1853	1891	1.889573	GGAGGCCTGCGCTGAATAC	60.890	63.158	12.00	4.64	34.44	1.89
1938	1976	2.040412	GGAGTCCTCCCATGTCAAGTTT	59.960	50.000	0.41	0.00	43.94	2.66
1956	1994	5.967088	TCCTTCAAATCTCTCTTTACGGAG	58.033	41.667	0.00	0.00	34.88	4.63
2151	2189	8.576442	TCAGGACAAAACCTAATCAATTTTCTC	58.424	33.333	0.00	0.00	38.32	2.87
2256	2295	2.706190	AGGATGGCAGGTAATGGTAGTC	59.294	50.000	0.00	0.00	0.00	2.59
2295	2334	0.249120	TCCAACTGTGTAGATGGCCG	59.751	55.000	0.00	0.00	44.24	6.13
2304	2343	3.214328	GTCCAAGTCAATCCAACTGTGT	58.786	45.455	0.00	0.00	0.00	3.72
2363	2402	5.048083	AGCGCAATACAAGATTGGAAAAGAA	60.048	36.000	11.47	0.00	0.00	2.52
2488	2528	5.862924	AAAACATGGTCAGATGTACTTCG	57.137	39.130	0.00	0.00	35.43	3.79
2503	2543	9.829507	AGAGGAAGATCTAGTATCAAAAACATG	57.170	33.333	0.00	0.00	0.00	3.21
2506	2546	9.744468	GAGAGAGGAAGATCTAGTATCAAAAAC	57.256	37.037	0.00	0.00	0.00	2.43
2530	2570	3.969287	TCCAGTTGAAGACATGGAGAG	57.031	47.619	0.00	0.00	36.92	3.20
2612	2652	7.875041	TGCTATATTAGGATGCTTTTCTCTGTC	59.125	37.037	0.00	0.00	0.00	3.51
2754	2804	7.437713	AATGACATGAGTACAGGATTCCTAA	57.562	36.000	4.51	0.00	29.64	2.69
2790	2840	7.094805	TGACCATGAGCAACTAAAAAGATGTAC	60.095	37.037	0.00	0.00	0.00	2.90
3031	3102	3.818387	CTCGTACTCTACTTGCGACAAA	58.182	45.455	0.00	0.00	0.00	2.83
3247	3318	1.672881	GCCAAGAGGAATCACAATCCG	59.327	52.381	0.00	0.00	42.03	4.18
3378	3449	9.636965	CGTCAATATAACATCAACACAATGTAG	57.363	33.333	0.00	0.00	36.35	2.74
3402	3474	3.247648	CGAAAATTCTGTTCTGGACACGT	59.752	43.478	0.00	0.00	33.82	4.49
3468	3540	3.308866	AGCGTTGCTTTTTATAGCCGTAG	59.691	43.478	0.00	0.00	40.49	3.51
3628	3703	2.021208	GCAAATTCTGCCTCCTCCTCC	61.021	57.143	2.35	0.00	46.13	4.30
3629	3704	1.387539	GCAAATTCTGCCTCCTCCTC	58.612	55.000	2.35	0.00	46.13	3.71
3630	3705	3.584947	GCAAATTCTGCCTCCTCCT	57.415	52.632	2.35	0.00	46.13	3.69
3760	3835	4.624364	CCCAGCACCGCACTCACA	62.624	66.667	0.00	0.00	0.00	3.58
3959	4034	0.980231	AGGGTGGAGCAGGAGATGAC	60.980	60.000	0.00	0.00	0.00	3.06
4023	4098	3.361977	GGAAATGGCCGTGTGCGT	61.362	61.111	0.00	0.00	42.61	5.24
4025	4100	2.258286	GTGGAAATGGCCGTGTGC	59.742	61.111	0.00	0.00	40.16	4.57
4027	4102	1.603455	CTGGTGGAAATGGCCGTGT	60.603	57.895	0.00	0.00	0.00	4.49

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.